diff --git a/_bibliography/citations-eu.bib b/_bibliography/citations-eu.bib index 5c45aa9d7..c4bfea40d 100644 --- a/_bibliography/citations-eu.bib +++ b/_bibliography/citations-eu.bib @@ -25,6 +25,77 @@ @phdthesis{___2019 year = {2019} } +@patent{_dna_2024, + assignee = {Zhejiang University ZJU}, + author = {鲍泽华 and 邓磊 and 蔡震坤}, + keywords = {{\textgreater}UseGalaxy.eu, cas9, editing, gene, library, seq}, + language = {zh}, + month = {August}, + nationality = {CN}, + number = {CN118460591A}, + title = {一种大规模并行dna序列编辑方法及应用}, + url = {https://patents.google.com/patent/CN118460591A/en?q=(%22usegalaxy.eu%22+OR+%22European+Galaxy%22)&oq=%22usegalaxy.eu%22+OR+%22European+Galaxy%22}, + urldate = {2025-04-14}, + year = {2024} +} + +@article{abdulhak_genomic_2025, + abstract = {Pseudomonas aeruginosa, recognized by the World Health Organization as a critical priority pathogen, exhibits significant genomic plasticity and a high potential for developing resistance to multiple antimicrobials. This study provides comprehensive genomic insights into colistin-resistant P. aeruginosa isolates obtained from cancer patients. Phenotypic assays were conducted to evaluate antibiotic susceptibility, biofilm formation, efflux pump activity, swarming motility, and pigment production. Whole genome sequencing of the collected isolates was performed using Oxford-Nanopore technology to examine sequence types, resistome profiles, virulence-associated genes, and mobile genetic elements. Our findings reveled that out of 52 isolates, 10 (19.2\%) were resistant to colistin. Ceftolozane/tazobactam demonstrated full efficacy against 60\% of colistin resistant P. aeruginosa isolates. Within this colistin resistant subset, high-risk clones ST308 and ST773 emerged as dominant, both harboring blaNDM-1 and exhibiting extensive resistance profiles, including resistance to colistin and, in some cases, ceftolozane/tazobactam. The first detection of ST1143 and ST1693 in Egypt carrying blaOXA-1028 and blaOXA-904, respectively was documented, neither of which had been previously reported in the country. The accessory genome, accounting for up to 34.6\% of the total genome, highlights the remarkable genomic plasticity of P. aeruginosa, and its capacity for horizontal acquisition of resistance and virulence genes via mobile genetic elements, such as integrative and conjugative elements (ICEs). Virulome analysis revealed the presence of the exoU gene in high-risk clones, a marker closely linked to hypervirulence in infection models, whereas other sequence types were associated with less virulent factors, such as exoS. Despite phenotypic variability in biofilm formation, pigment production, and motility, the underlying genetic determinants of these traits were highly conserved. Mutational analysis revealed mutations in the regulatory system PhoPQ as the primary mechanism of colistin resistance, with no mcr genes detected. In conclusion, the substantial genomic plasticity of P. aeruginosa, reflected by an extensive accessory genome facilitates horizontal gene transfer (HGT), and significantly influences antimicrobial resistance and virulence. Colistin resistance was predominantly mediated by chromosomal mutations. Virulome and resistome analyses underscores the high pathogenicity and resistance potential of high-risk clones ST773 and ST308. The detection of horizontally acquired elements, such as integrative and conjugative elements (ICEs) carrying resistance genes such as blaNDM-1, underscores their role in disseminating resistance determinants. These findings emphasize the need urgent for targeted antimicrobial stewardship and surveillance strategies within Egyptian healthcare settings.}, + author = {AbdulHak, Asmaa and Zedan, Hamdallah H and El-Mahallawy, Hadir A and Sayed, Ahmed A and Mohamed, Hend O and Zafer, Mai M}, + doi = {10.1371/journal.pgph.0004976}, + issn = {2767-3375}, + journal = {PLOS global public health}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + number = {8}, + pages = {e0004976}, + title = {The genomic configurations driving antimicrobial resistance and virulence in colistin resistant {Pseudomonas} aeruginosa from an {Egyptian} {Tertiary} {Oncology} {Hospital}}, + url = {http://europepmc.org/abstract/MED/40763289}, + volume = {5}, + year = {2025} +} + +@article{abedin_cladistic_2025, + abstract = {The endangered Peacock Softshell Turtle Nilssonia hurum (Gray, 1830) has undergone a steep population decline in recent decades because of habitat loss and anthropogenic pressures, highlighting the urgent need for scientific intervention to ensure its protection in the wild. Thus, the present study integrates mitogenomic and ecological data to guide proactive conservation strategies for this species. The study reports the first mitogenome (16,788 bp) of N. hurum from the upper Ganges region, which exhibits a typical gene composition and strong A + T bias. The mitogenome-based phylogenetic analyses reveal the monophyly of the genus Nilssonia Gray, 1872 and a close evolutionary relationship between N. hurum and N. nigricans (Anderson, 1875). The genetic distance and haplotype network analyses on the basis of the CYTB gene reveal substantial intraspecific diversity and spatial genetic structuring among populations across river basins within the easternmost range. Using species distribution modeling, the study identified 123,699 km2 (6.81\% of IUCN range) as presently suitable for N. hurum. However, future climate projections indicate drastic reductions in suitable habitat, with losses of up to 85\% due to climate change. The landscape genetic analyses revealed that the Meghna basin exhibits the highest mean functional connectivity (0.603), whereas the Brahmaputra basin shows the lowest connectivity (0.198) despite containing suitable habitat patches, consistent with its high genetic diversity. Moreover, projections under future climate scenarios, driven by anticipated losses in habitat suitability, indicate widespread declines in functional connectivity across all basins and sub-basins. The landscape geometry assessments further reveal increasing habitat fragmentation due to climate change. Therefore, populations persisting within suitable habitat patches across different river basins in the eastern range should be prioritized as distinct conservation units for future management. Overall, this study provides a critical foundation for site-specific conservation planning through landscape genetics to address habitat loss, fragmentation, and mitigating inbreeding depression for ensuring the long-term endurance of this threatened freshwater turtle in South Asia.}, + author = {Abedin, Imon and Putra, Angkasa and Kang, Hye-Eun and Singh, Arunima and Singh, Shailendra and Singha, Hilloljyoti and Kim, Hyun-Woo and Kundu, Shantanu}, + copyright = {© 2025 The Author(s). Ecology and Evolution published by British Ecological Society and John Wiley \& Sons Ltd.}, + doi = {10.1002/ece3.72751}, + issn = {2045-7758}, + journal = {Ecology and Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, climate change, ecology, mitogenome, phylogeny, species distribution model, testudines}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.72751}, + number = {12}, + pages = {e72751}, + shorttitle = {Cladistic {Relationships} and {Landscape} {Genetics} of the {Endangered} {Indian} {Peacock} {Softshell} {Turtle} {Nilssonia} hurum ({Gray}, 1830)}, + title = {Cladistic {Relationships} and {Landscape} {Genetics} of the {Endangered} {Indian} {Peacock} {Softshell} {Turtle} {Nilssonia} hurum ({Gray}, 1830): {Implications} for {Strategic} {Conservation} {Planning}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.72751}, + urldate = {2025-12-26}, + volume = {15}, + year = {2025} +} + +@article{abedin_lineages_2025, + abstract = {The Tricarinate Hill Turtle (Melanochelys tricarinata), endemic to the Indian subcontinent, faces significant threats from intensifying anthropogenic pressures and severe habitat degradation. Thus, to facilitate conservation efforts for this endangered species, a comprehensive assessment of its genomics and ecology is imperative. The present study adopts two independent approaches by characterizing the complete mitogenome and evaluating current and future habitat suitability. The mitogenome (16,745 bp) comprises 37 genes, with most protein-coding genes beginning with the canonical ATG start codon. The codon usage analysis revealed that arginine, leucine, and serine are the most frequently used amino acids. The control region contains a termination-associated sequence, four conserved sequence blocks, and two distinct tandem repeat motifs. The phylogenetic assessment using both Bayesian inference and Maximum-likelihood methods consistently placed M. tricarinata in a distinct clade, separate from other geoemydids. The mitogenome-based TimeTree analysis revealed that M. tricarinata diverged from its closest relatives during the Oligocene. The comparative analyses of partial mitochondrial genes revealed substantial divergence between Melanochelys congeners (3.71–5.20\% in cox1, 7.99–9.29\% in cytb), with low haplotypic diversity in M. tricarinata and high in M. trijuga. The ensemble model identified suitable habitats under both current and future climate scenarios. Under present scenario, approximately 374,657 km2 of ideal habitat was delineated within the training extent with a mean corridor connectivity of 0.377, which was reduced to 238,039 km2 and mean connectivity of 0.518 when restricted to existing forest cover. Moreover, only 31,450 km2 of the suitable habitat for this species falls within Protected Areas, representing just 11.912\% of the total identified favorable area. The future projections suggest a potential reduction of up to 40\% in suitable habitat area due to climatic changes, accompanied by increased fragmentation, smaller patch sizes, and over 80\% decline in connectivity across future scenarios. Thus, this study provides comprehensive insights into the systematic position, evolutionary history and ecological requirements of M. tricarinata, offering a critical scientific foundation to guide effective conservation and management strategies for this imperiled species across its native range.}, + author = {Abedin, Imon and Putra, Angkasa and Kang, Hye-Eun and Singh, Arunima and Singh, Shailendra and Jung, Won-Kyo and Kim, Hyun-Woo and Kundu, Shantanu}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-26890-5}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Ecology, Evolution, Genetics}, + language = {en}, + month = {November}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {42751}, + shorttitle = {Lineages to landscapes}, + title = {Lineages to landscapes: mitogenomic insights and climate refugia informing proactive conservation of the endangered {Tricarinate} {Hill} {Turtle} ({Melanochelys} tricarinata) in the {Indian} subcontinent}, + url = {https://www.nature.com/articles/s41598-025-26890-5}, + urldate = {2025-12-26}, + volume = {15}, + year = {2025} +} + @article{abusaleh_genetic_2024, abstract = {As a key enzyme of the renin-angiotensin system (RAS), angiotensin-converting enzyme 2 (ACE2) is a validated receptor for SARS-CoV-2, linking RAS to COVID-19. Functional ACE1/ACE2 gene polymorphisms likely cause an imbalance in the ACE1/ACE2 ratio, triggering RAS imbalance and may contribute to COVID-19 complications. This study aimed to investigate four single nucleotide polymorphisms (SNPs) of ACE1 and ACE2 genes, three for ACE1 (rs4343, rs4342, rs4341) and one for ACE2 (rs2285666), in patients with COVID-19 among the Palestinian population. A total of 130 blood samples were collected, including 50 negative controls without COVID-19 infection, 50 cases with COVID-19 infection but not hospitalized, and 30 patients with severe COVID-19 infection hospitalized in the intensive care unit. Fragments of the ACE1 and ACE2 genes, including the targeted SNPs, were amplified using multiplex PCR and subsequently genotyped by next-generation sequencing with specific virtual probes. Our results revealed that ACE2 rs2285666 GG genotype carriers were more prevalent in COVID-19 patients compared to the control group (P=0.049), while no statistical differences were observed in the distribution of ACE1 (rs4343, rs4342, rs4341) variants between COVID-19 patients and the control group. GA carriers of ACE2, rs2285666, among cases and ICU groups were at lower risk of getting COVID-19 infection (P=0.002 and P=0.013, respectively), and they were unlikely to develop fatigue (P=0.043), headache (P=0.007), loss of smell (P=0.028), and dyspnea (P=0.005). Age and comorbidities such as hypertension and coronary artery disease (CAD) were independent risk factors for COVID-19 disease. Symptoms of COVID-19 patients such as fatigue, headaches, runny noses, and loss of smell were significantly higher in non-hospitalized cases of COVID-19, while dyspnea was more frequent in the ICU patients. In conclusion, these findings indicate that the ACE2 rs2285666 GG genotype is associated with an increased risk of COVID-19 infection. This association suggests a potential genetic predisposition linked to the ACE2 gene, which may influence the susceptibility and severity of the disease.}, author = {AbuSaleh, Lama and Ereqat, Suheir and Al-Jawabreh, Amer and Nasereddin, Abedelmajeed and AbuSaleh, Lama and Ereqat, Suheir and Al-Jawabreh, Amer and Nasereddin, Abedelmajeed}, @@ -36,6 +107,7 @@ @article{abusaleh_genetic_2024 month = {August}, note = {Publisher: Cureus}, number = {8}, + pages = {e67670}, title = {Genetic {Polymorphisms} of {Angiotensin}-{Converting} {Enzyme} 1 ({ACE1}) and {ACE2} {Associated} {With} {Severe} {Acute} {Respiratory} {Syndrome} {COVID}-19 in the {Palestinian} {Population}}, url = {https://www.cureus.com/articles/276157-genetic-polymorphisms-of-angiotensin-converting-enzyme-1-ace1-and-ace2-associated-with-severe-acute-respiratory-syndrome-covid-19-in-the-palestinian-population}, urldate = {2024-09-02}, @@ -65,7 +137,8 @@ @article{achom_plant_2022 doi = {10.1093/jxb/erab526}, issn = {0022-0957}, journal = {Journal of Experimental Botany}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Circadian Clocks, Medicago truncatula, Sinorhizobium meliloti}, + language = {eng}, month = {April}, number = {7}, pages = {2142--2156}, @@ -76,6 +149,38 @@ @article{achom_plant_2022 year = {2022} } +@article{aciole_barbosa_novo_2025, + abstract = {Astyanax lacustris is a model of laboratory native fish species. Reproductive studies of this species have already been performed. Nevertheless, there is a relative shortcoming of gene sequence information available in public databases, which hinder their use in more comprehensive investigations that employ sensitivity molecular biology techniques to assess gene expression profile for biomarker identification. In this data article, we report the first de novo transcriptome assembly of A. lacustris testicles, ovaries and male / female pituitary gland improving gene sequence data available for this fish species and transcriptome of male liver. Illumina sequencing generated 808,023,356 raw reads, filtered in 752,739,866 high-quality reads. Initially, a de novo assembly was filtered to include protein coding elements only in each tissue sample, which were merged in a final pantranscriptome (PAN) containing 109,232 contigs. The PAN was functionally annotated against a custom Actinopterygii proteins dataset and EggNOG terms with the aid of EnTAP, retrieving homology queries for about 90 \% of all transcripts. Therefore, in this study we provide a PAN and a custom blast tool that can help discovery genomic information on metabolism pathways and their related genes in A. lacustris, enabling future research and molecular studies using this fish species as a model.}, + author = {Aciole Barbosa, David and Branco, Giovana Souza and Dal'Olio Gomes, Aline and Tolussi, Carlos Eduardo and Muñoz-Peñuela, Marcela and Araújo, Bruno C. and da Silva, Iuri Batista and Moreira, Renata Guimarães and Nunes, Luiz R. and Menegidio, Fabiano B.}, + doi = {10.1016/j.margen.2025.101190}, + issn = {1874-7787}, + journal = {Marine Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Hepatic, Ovaries, Pituitary, RNAseq, Reproduction, Testis}, + month = {June}, + pages = {101190}, + title = {\textit{{De} novo} assembly and annotation of the pantranscriptome of \textit{{Astyanax} lacustris} on the liver and pituitary-gonadal axis}, + url = {https://www.sciencedirect.com/science/article/pii/S1874778725000261}, + urldate = {2025-04-21}, + volume = {81}, + year = {2025} +} + +@misc{aciole_barbosa_novo_2025, + abstract = {Astyanax lacustris is a model of laboratory native fish species. Reproductive studies of this species have already been performed. Nevertheless, there is a relative shortcoming of gene sequence information available in public databases, which hinder their use in more comprehensive investigations that employ sensitivity molecular biology techniques to assess gene expression profile for biomarker identification. In this data article, we report the first de novo transcriptome assembly of A. lacustris testicles, ovaries and male / female pituitary gland improving gene sequence data available for this fish species and transcriptome of male liver. Illumina sequencing generated 808,023,356 raw reads, filtered in 752,739,866 high-quality reads. Initially, a de novo assembly was filtered to include protein coding elements only in each tissue sample, which were merged in a final pantranscriptome (PAN) containing 109,232 contigs. The PAN was functionally annotated against a custom Actinopterygii proteins dataset and EggNOG terms with the aid of EnTAP, retrieving homology queries for about 90\% of all transcripts. Therefore, in this study we provide a PAN and a custom blast tool that can help discovery genomic information on metabolism pathways and their related genes in A. lacustris, enabling future research and molecular studies using this fish species as a model.}, + address = {Rochester, NY}, + author = {Aciole Barbosa, David and Branco, Giovana Souza and Gomes, Aline Dal Olio and Tolussi, Carlos Eduardo and Muñoz-Peñuela, Marcela and Araujo, Bruno and Silva, Iuri Batista and Moreira, Renata Guimarães and Nunes, Luiz and Menegidio, Fabiano Bezerra}, + doi = {10.2139/ssrn.5129548}, + keywords = {{\textgreater}UseGalaxy.eu, RNAseq, hepatic, ovaries, pituitary, reproduction, testis}, + language = {en}, + month = {February}, + publisher = {Social Science Research Network}, + title = {De {Novo} {Assembly} and {Annotation} of the {Pantranscriptome} of {Astyanax} {Lacustris} on the {Liver} and {Pituitary}-{Gonadal} {Axis}}, + type = {{SSRN} {Scholarly} {Paper}}, + url = {https://papers.ssrn.com/abstract=5129548}, + urldate = {2025-02-16}, + year = {2025} +} + @article{aciole_barbosa_transcriptomic_2022, abstract = {Cobia (Rachycentron canadum) is a marine teleost species with great productive potential worldwide. However, the genomic information currently available for this species in public databases is limited. Such lack of information hinders gene expression assessments that might bring forward novel insights into the physiology, ecology, evolution, and genetics of this potential aquaculture species. In this study, we report the first de novo transcriptome assembly of R. canadum liver, improving the availability of novel gene sequences for this species. Illumina sequencing of liver transcripts generated 1,761,965,794 raw reads, which were filtered into 1,652,319,304 high-quality reads. De novo assembly resulted in 101,789 unigenes and 163,096 isoforms, with an average length of 950.61 and 1,617.34 nt, respectively. Moreover, we found that 126,013 of these transcripts bear potentially coding sequences, and 125,993 of these elements (77.3\%) correspond to functionally annotated genes found in six different databases. We also identified 701 putative ncRNA and 35,414 putative lncRNA. Interestingly, homologues for 410 of these putative lncRNAs have already been observed in previous analyses with Danio rerio, Lates calcarifer, Seriola lalandi dorsalis, Seriola dumerili, or Echeneis naucrates. Finally, we identified 7894 microsatellites related to cobia’s putative lncRNAs. Thus, the information derived from the transcriptome assembly described herein will likely assist future nutrigenomics and breeding programs involving this important fish farming species.}, author = {Aciole Barbosa, David and Araújo, Bruno C. and Branco, Giovana Souza and Simeone, Alexandre S. and Hilsdorf, Alexandre W. S. and Jabes, Daniela L. and Nunes, Luiz R. and Moreira, Renata G. and Menegidio, Fabiano B.}, @@ -98,8 +203,10 @@ @article{aerts_altered_2024 abstract = {Autism spectrum disorder (ASD) is a group of neurodevelopmental conditions associated with deficits in social interaction and communication, together with repetitive behaviours. The cell adhesion molecule protocadherin10 (PCDH10) is linked to ASD in humans. Pcdh10 is expressed in the nervous system during embryonic and early postnatal development and is important for neural circuit formation. In mice, strong expression of Pcdh10 in the ganglionic eminences and in the basolateral complex (BLC) of the amygdala was observed at mid and late embryonic stages, respectively. Both inhibitory and excitatory neurons expressed Pcdh10 in the BLC at perinatal stages and vocalization-related genes were enriched in Pcdh10-expressing neurons in adult mice. An epitope-tagged Pcdh10-HAV5 mouse line revealed endogenous interactions of PCDH10 with synaptic proteins in the young postnatal telencephalon. Nuanced socio-affective communication changes in call emission rates, acoustic features and call subtype clustering were primarily observed in heterozygous pups of a conditional knockout (cKO) with selective deletion of Pcdh10 in Gsh2-lineage interneurons. These changes were less prominent in heterozygous ubiquitous Pcdh10 KO pups, suggesting that altered anxiety levels associated with Gsh2-lineage interneuron functioning might drive the behavioural effects. Together, loss of Pcdh10 specifically in interneurons contributes to behavioural alterations in socio-affective communication with relevance to ASD.}, author = {Aerts, Tania and Boonen, Anneleen and Geenen, Lieve and Stulens, Anne and Masin, Luca and Pancho, Anna and Francis, Annick and Pepermans, Elise and Baggerman, Geert and Van Roy, Frans and Wöhr, Markus and Seuntjens, Eve}, doi = {10.1098/rsob.240113}, + issn = {2046-2441}, journal = {Open Biology}, - keywords = {{\textgreater}UseGalaxy.eu, amygdala development, autism spectrum disorder, conditional knockout, non-clustered protocadherin, proteomics, ultrasonic vocalization}, + keywords = {{\textgreater}UseGalaxy.eu, Amygdala, Cadherins, Interneurons, Mice, Knockout, Protocadherins, amygdala development, autism spectrum disorder, conditional knockout, non-clustered protocadherin, proteomics, ultrasonic vocalization}, + language = {eng}, month = {June}, note = {Publisher: Royal Society}, number = {6}, @@ -116,6 +223,7 @@ @article{afouda_culturing_2020 author = {Afouda, Pamela and Dubourg, Grégory and Levasseur, Anthony and Fournier, Pierre-Edouard and Delerce, Jeremy and Mediannikov, Oleg and Diene, Seydina M. and Nahon, Daniel and Bourlès, Didier and Rolain, Jean-Marc and Raoult, Didier}, copyright = {http://creativecommons.org/licenses/by/3.0/}, doi = {10.3390/microorganisms8101522}, + issn = {2076-2607}, journal = {Microorganisms}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Siberian permafrost, culturomics, genomic evolution, resistance genes}, language = {en}, @@ -131,6 +239,23 @@ @article{afouda_culturing_2020 year = {2020} } +@article{agaronyan_tissue_2022, + abstract = {Different effector arms of the immune system are optimized to protect from different classes of pathogens. In some cases, pathogens manipulate the host immune system to promote the wrong type of effector response-a phenomenon known as immune deviation. Typically, immune deviation helps pathogens to avoid destructive immune responses. Here, we report on a type of immune deviation whereby an opportunistic pathogen, Pseudomonas aeruginosa (P. aeruginosa), induces the type 2 immune response resulting in mucin production that is used as an energy source by the pathogen. Specifically, P. aeruginosa-secreted toxin, LasB, processed and activated epithelial amphiregulin to induce type 2 inflammation and mucin production. This "niche remodeling" by P. aeruginosa promoted colonization and, as a by-product, allergic sensitization. Our study thus reveals a type of bacterial immune deviation by increasing nutrient supply. It also uncovers a mechanism of allergic sensitization by a bacterial virulence factor.}, + author = {Agaronyan, Karen and Sharma, Lokesh and Vaidyanathan, Bharat and Glenn, Keith and Yu, Shuang and Annicelli, Charles and Wiggen, Talia D and Penningroth, Mitchell R and Hunter, Ryan C and Dela Cruz, Charles S and Medzhitov, Ruslan}, + doi = {10.1016/j.immuni.2022.04.001}, + issn = {1074-7613}, + journal = {Immunity}, + keywords = {{\textgreater}UseGalaxy.eu, Pseudomonas Infections, Pseudomonas aeruginosa}, + language = {eng}, + month = {May}, + number = {5}, + pages = {895--911.e10}, + title = {Tissue remodeling by an opportunistic pathogen triggers allergic inflammation}, + url = {http://europepmc.org/abstract/MED/35483356}, + volume = {55}, + year = {2022} +} + @article{agboli_interaction_2023, abstract = {Mosquito-specific viruses (MSVs) comprise a variety of different virus families, some of which are known to interfere with infections of medically important arboviruses. Viruses belonging to the family Mesoniviridae or taxon Negevirus harbor several insect-specific viruses, including MSVs, which are known for their wide geographical distribution and extensive host ranges. Although these viruses are regularly identified in mosquitoes all over the world, their presence in mosquitoes in Germany had not yet been reported.}, author = {Agboli, Eric and Schulze, Jonny and Jansen, Stephanie and Cadar, Daniel and Sreenu, Vattipally B. and Leggewie, Mayke and Altinli, Mine and Badusche, Marlis and Jöst, Hanna and Börstler, Jessica and Schmidt-Chanasit, Jonas and Schnettler, Esther}, @@ -165,6 +290,40 @@ @article{aggarwal_role_2021 year = {2021} } +@article{aguado-ramsay_erga-bge_2025, + abstract = {The reference genome of +Lewinskya acuminata +(H. Philib.) F. Lara, Garilleti \& Goffinet will enable phylogenomic, biogeographic, and evolutionary studies within the +Orthotrichaceae +and related bryophyte lineages at a depth previously inaccessible. This species of moss is among the most representative of the Mediterranean epiphytic communities and can be readily identified by its long-acuminate leaves, fusiform capsules with a vestigial exostome, a well-developed endostome of six broad segments, and a dark, puckered peristome mouth when dry. The entirety of the genome sequence was assembled into 6 contiguous chromosomal pseudomolecules, 1 mitochondrial genome, and 2 plastid genomes. This chromosome-level assembly encompasses 0.25 Gb, composed of 51 contigs and 13 scaffolds, with contig and scaffold N50 values of 11.5 Mb and 40.8 Mb, respectively.}, + author = {Aguado-Ramsay, Pablo and Lara, Francisco and Draper, Isabel and Conejero, Maria and Böhne, Astrid and Monteiro, Rita and Marcussen, Thomas and H. Struck, Torsten and A. Oomen, Rebekah and {Genomescope Sequencing Team} and Moussy, Alice and Cruaud, Corinne and Labadie, Karine and Demirdjian, Lola and Téodori, Emilie and Wincker, Patrick and H. Oliveira, Pedro and Aury, Jean-Marc and Bortoluzzi, Chiara}, + doi = {10.12688/openreseurope.21670.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {November}, + pages = {357}, + title = {{ERGA}-{BGE} reference genome of {Lewinskya} acuminata, a common epiphytic {Mediterranean} moss with disjunct populations in {California} and {Ethiopia}}, + url = {https://open-research-europe.ec.europa.eu/articles/5-357/v1}, + urldate = {2025-11-28}, + volume = {5}, + year = {2025} +} + +@article{agudelo-romero_advancing_2025, + author = {Agudelo-Romero, Patricia and Conradie, Talya and Caparros-Martin, Jose Antonio and Martino, David Jimmy and Kicic, Anthony and Stick, Stephen Michael and Hakkaart, Christopher and Sharma, Abhinav}, + issn = {2673-7647}, + journal = {Front Bioinform}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {January}, + title = {Advancing bioinformatics capacity through {Nextflow} and nf-core: lessons from an early-to mid-career researchers–focused program at {The} {Kids} {Research} {Institute} {Australia}}, + url = {http://europepmc.org/abstract/PMC/PMC12425987}, + volume = {5}, + year = {2025} +} + @article{aguirre_pranzoni_biofoams_2024, abstract = {White rot fungi are promising organisms for the production of mycelial-based biofoams, providing a sustainable means of valorizing lignocellulosic wastes. This study explores the utilization of two indigenous fungal species, isolated from Argentina and belonging to the genera Trametes, for producing biofoams from brewery waste. The resulting biofoams exhibited an average density of 0.30 g cm−3, a Young’s modulus of approximately 1 MPa, and a compressive stress of around 19 MPa. Additionally, the variation of laccase activity throughout the biofoam production process was evaluated. Surprisingly, residual laccase activity was detected in the biofoams following oven drying at temperatures of 60, 80, and 100 °C. This detection highlights the untapped enzymatic potential of the biofoams and positions them as promising green catalysts for various biotechnological applications.}, author = {Aguirre Pranzoni, Celeste and Bonilla, José and Carrillo, Ángeles and López-Vidal, Martín and Aguilera, Leonardo J. and Ariel Ochoa, Nelio and Kurina-Sanz, Marcela}, @@ -181,21 +340,6 @@ @article{aguirre_pranzoni_biofoams_2024 year = {2024} } -@misc{aguirre_pranzoni_biofoams_2024, - abstract = {White rot fungi are promising organisms for the production of mycelial-based biofoams, providing a sustainable means to of valorizing lignocellulosic wastes. This study focuses on the use of Trametes sanguinea LSR01 and Trametes villosa LSR02, two indigenous fungal species isolated from Argentina, for the production of biofoams from brewery waste. These biofoams were obtained with an average density of 0.30 g cm-3, Young's modulus around 1 MPa and a compressive stress around 19 MPa.  This study also evaluated the variation of laccase activity during each stage of the biofoam production process. Unexpectedly, residual laccase activity was detected in the biofoams after oven drying (60, 80 and 100 °C). This residual laccase ability to oxidize benzyl alcohol to benzaldehyde indicated that biofoams are not enzymatically inert.  This unexpected finding highlights the enzymatic potential of these mycelium-based materials and positions them as promising green catalysts for biotechnological endeavors.}, - address = {Rochester, NY}, - author = {Aguirre Pranzoni, Celeste and Bonilla, José and Carrillo, Ángeles and López-Vidal, Martín and Aguilera, Leonardo J. and Ochoa, Nelio Ariel and Kurina-Sanz, Marcela}, - doi = {10.2139/ssrn.4792539}, - keywords = {{\textgreater}UseGalaxy.eu, Beer Bagasse, Laccase activity, Trametes, White rot fungi, biooxidation}, - language = {en}, - month = {April}, - title = {Biofoams with {Untapped} {Enzymatic} {Potential} {Produced} from {Beer} {Bagasse} by {Indigenous} {Fungal} {Strains}}, - type = {{SSRN} {Scholarly} {Paper}}, - url = {https://papers.ssrn.com/abstract=4792539}, - urldate = {2024-04-28}, - year = {2024} -} - @phdthesis{ahmad_biosynthetic_2023, abstract = {This study delves into lichen symbioses' biosynthetic potential. It analyzed 460 biosynthetic gene clusters in Hypogymnia lichens, with mycobionts carrying 73-114 clusters. Predominant genes include T1PKS, NRPS, and terpene synthases. Furthermore, three prevalent lichen mycobionts shared nine conserved gene clusters. This research identifies unexplored biosynthetic potential in lichens and lays the foundation for biotechnological applications and natural product investigations unique to lichens.}, author = {Ahmad, Syed Nadim Marc}, @@ -246,6 +390,41 @@ @article{ahmad_development_2019 year = {2019} } +@article{ahmad_discovery_2025, + abstract = {Antimicrobial resistance is escalating among Staphylococcus species, which are major pathogens affecting both humans and animals. As therapeutic options continue to narrow, phage therapy is re-emerging as a promising strategy to combat resistant strains. In this study, we isolated from pig farm effluents a bacteriophage named CSF, infecting a Staphylococcus xylosus strain. The CSF phage demonstrated a broad host range, lysing mecA-positive, multidrug-resistant strains across nine species of the genera Staphylococcus and Mammaliicoccus. Notably, it also inhibited biofilm formation in strains that it could not infect directly, and this activity persisted at low virus concentrations and in combination with antibiotics. The phage maintained its lytic activity under extreme conditions of temperature, pH, and UV exposure, underscoring its resilience for practical use. Sequencing of the viral genome revealed that it is 140 kb in length and has a genetic composition consistent with a lytic lifestyle. Phylogenetic analysis showed that phage CSF is related to members of the family Herelleviridae that are found globally, suggesting a widespread distribution of related viral lineages. Importantly, the phage genome was found to lack bacterial virulence or antimicrobial resistance genes, suggesting its safety for biotechnological applications. Intergenomic comparisons indicated that CSF should be classified as a member of a new genus, expanding the known diversity of bacteriophages. These findings demonstrate potential of CSF for phage therapy and other biotechnological applications.}, + author = {Ahmad, Faizan and Viana, Vitor Emanuel Lanes and de Rezende, Rafael Reis and Martuchelle, Samuel Sathler and Cabral, Anderson Souza and Andrade-Oliveira, Ana Luisa and Carvalho, Isabella Monteiro and de Almada Estanislau, Sandy and Rasheed, Nohman and Zerbini, Poliane Alfenas and Pereira, Monalessa Fábia and Giambiagi-deMarval, Marcia and Rossi, Ciro César}, + doi = {10.1007/s00705-025-06370-x}, + issn = {1432-8798}, + journal = {Archives of Virology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {July}, + number = {8}, + pages = {188}, + title = {Discovery of phage {CSF}, a novel generalist bacteriophage targeting multidrug-resistant and potentially pathogenic {Staphylococcus} spp. and {Mammaliicoccus} spp.}, + url = {https://doi.org/10.1007/s00705-025-06370-x}, + urldate = {2025-09-03}, + volume = {170}, + year = {2025} +} + +@article{ahmad_effects_2022, + abstract = {Ventricular arrhythmias associated with myocardial infarction (MI) have a significant impact on mortality in patients following heart attack. Therefore, targeted reduction of arrhythmia represents a therapeutic approach for the prevention and treatment of severe events after infarction. Recent research transplanting mesenchymal stem cells (MSC) showed their potential in MI therapy. Our study aimed to investigate the effects of MSC injection on post-infarction arrhythmia. We used our murine double infarction model, which we previously established, to more closely mimic the clinical situation and intramyocardially injected hypoxic pre-conditioned murine MSC to the infarction border. Thereafter, various types of arrhythmias were recorded and analyzed. We observed a homogenous distribution of all types of arrhythmias after the first infarction, without any significant differences between the groups. Yet, MSC therapy after double infarction led to a highly significant reduction in simple and complex arrhythmias. Moreover, RNA-sequencing of samples from stem cell treated mice after re-infarction demonstrated a significant decline in most arrhythmias with reduced inflammatory pathways. Additionally, following stem-cell therapy we found numerous highly expressed genes to be either linked to lowering the risk of heart failure, cardiomyopathy or sudden cardiac death. Moreover, genes known to be associated with arrhythmogenesis and key mutations underlying arrhythmias were downregulated. In summary, our stem-cell therapy led to a reduction in cardiac arrhythmias after MI and showed a downregulation of already established inflammatory pathways. Furthermore, our study reveals gene regulation pathways that have a potentially direct influence on arrhythmogenesis after myocardial infarction.}, + author = {Ahmad, Beschan and Skorska, Anna and Wolfien, Markus and Sadraddin, Haval and Lemcke, Heiko and Vasudevan, Praveen and Wolkenhauer, Olaf and Steinhoff, Gustav and David, Robert and Gaebel, Ralf}, + doi = {10.3390/ijms23168843}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Mesenchymal Stem Cell Transplantation, Mesenchymal Stem Cells, Myocardial Infarction}, + language = {eng}, + month = {August}, + number = {16}, + pages = {8843}, + title = {The {Effects} of {Hypoxic} {Preconditioned} {Murine} {Mesenchymal} {Stem} {Cells} on {Post}-{Infarct} {Arrhythmias} in the {Mouse} {Model}}, + url = {http://europepmc.org/abstract/MED/36012110}, + volume = {23}, + year = {2022} +} + @article{ahmed_high_2020, abstract = {Colistin is a last-resort antimicrobial used for the treatment of human infections caused by multidrug-resistant Gram-negative bacteria. However, colistin is still widely used in intensive poultry production in Bangladesh. We aimed to investigate the dynamics and genetic diversity of colistin-resistant commensal Escherichia coli from broiler chickens. A total of 1200 E. coli strains were characterized from 20 broiler farms at three-time points along the production period. All strains were screened for mcr-1 to mcr-5 genes by a multiplex PCR, and their genetic diversity was measured by repetitive extragenic palindromic (REP)-PCR fingerprinting. Genomic diversity and characterization were performed by whole genome sequencing (WGS). Twenty-five percent of the commensal E. coli strains harbored mcr-1 genes. Frequency of mcr-1 gene detection correlated positively (odds ratio 1.71; 95\% CI 0.96–3.06; p = 0.068) with the use of colistin in poultry flocks. REP-PCR profiles and WGS analysis showed diverse E. coli population carrying multiple antimicrobial resistance genes. Phylogenetic comparison of mcr-1-bearing strains recovered from this study with a global strain collection revealed wide phylogenetic relationship. This study identified a high prevalence of mcr-1 gene among genetically diverse E. coli populations from broiler chickens in Bangladesh suggesting a massive horizontal spread of mcr-1 rather than by clonal expansion.}, author = {Ahmed, Shahana and Das, Tridip and Islam, Md Zohorul and Herrero-Fresno, Ana and Biswas, Paritosh Kumar and Olsen, John Elmerdahl}, @@ -289,8 +468,10 @@ @article{akol_multimodal_2023 abstract = {Forkhead box G1 (FOXG1) has important functions in neuronal differentiation and balances excitatory/inhibitory network activity. Thus far, molecular processes underlying FOXG1 function are largely unexplored. Here, we present a multiomics data set exploring how FOXG1 impacts neuronal maturation at the chromatin level in the mouse hippocampus. At a genome-wide level, FOXG1 i) both represses and activates transcription, ii) binds mainly to enhancer regions, iii) reconfigures the epigenetic landscape through bidirectional alteration of H3K27ac, H3K4me3, and chromatin accessibility, and iv) operates synergistically with NEUROD1. Interestingly, we could not detect a clear hierarchy of FOXG1 and NEUROD1, but instead, provide the evidence that they act in a highly cooperative manner to control neuronal maturation. Genes affected by the chromatin alterations impact synaptogenesis and axonogenesis. Inhibition of histone deacetylases partially rescues transcriptional alterations upon FOXG1 reduction. This integrated multiomics view of changes upon FOXG1 reduction reveals an unprecedented multimodality of FOXG1 functions converging on neuronal maturation. It fuels therapeutic options based on epigenetic drugs to alleviate, at least in part, neuronal dysfunction.}, author = {Akol, Ipek and Izzo, Annalisa and Gather, Fabian and Strack, Stefanie and Heidrich, Stefanie and Ó hAilín, Darren and Villarreal, Alejandro and Hacker, Christine and Rauleac, Tudor and Bella, Chiara and Fischer, Andre and Manke, Thomas and Vogel, Tanja}, doi = {10.1073/pnas.2122467120}, + issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Forkhead Transcription Factors, Rett Syndrome}, + language = {eng}, month = {January}, note = {Publisher: Proceedings of the National Academy of Sciences}, number = {2}, @@ -318,6 +499,43 @@ @article{akpinar_characterization_2024 year = {2024} } +@article{al-jawabreh_complete_2021, + abstract = {{\textless}h4{\textgreater}Objectives{\textless}/h4{\textgreater}SARS-CoV-2, severe respiratory syndrome coronavirus-2, is an RNA virus that emerged from China sweeping the globe in the form of a pandemic that became an international public health concern. This pilot study aimed to describe the genetic variation and molecular epidemiology of SARS-CoV-2 in Palestine in fall 2020.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}To achieve these aims, whole genome sequencing of SARS-CoV-2, phylogenetic analysis, haplotype networking and genetic diversity analysis were performed. These analyses revealed a unique spike mutation H245N that has never been reported before. The phylogenetic analysis depicted that three clusters existed in Palestinian SARS-CoV-2 genome sequences, in which cluster-I comprised the majority of clusters by 90\%. Congruently, the haplotype network analysis depicted the same three clusters with a total of 39 haplotypes. The genetic diversity analysis showed that Cluster-I is highly diverse as confirmed by statistically significant mutation rate indices, Tajima's D and Fu-Li's-F tests (- 2.11 and 2.74, respectively), highest number of mutations (Eta = 120), highest number of haplotypes (h = 17), and highest average number of nucleotide differences between any two sequences (S = 118). The study confirmed the high genetic diversity among the Palestinian of SARS-CoV-2 which possessed high number of mutations including one which was reported for the first time.}, + author = {Al-Jawabreh, Amer and Ereqat, Suheir and Dumaidi, Kamal and Al-Jawabreh, Hanan and Nasereddin, Abedelmajeed}, + doi = {10.1186/s13104-021-05874-4}, + issn = {1756-0500}, + journal = {BMC research notes}, + keywords = {{\textgreater}UseGalaxy.eu, Genome, Viral, SARS-CoV-2}, + language = {eng}, + month = {December}, + number = {1}, + pages = {466}, + title = {Complete genome sequencing of {SARS}-{CoV}-2 strains: {A} pilot survey in {Palestine} reveals spike mutation {H245N}}, + url = {http://europepmc.org/abstract/MED/34949225}, + volume = {14}, + year = {2021} +} + +@phdthesis{al-jawabreh_molecular_2025, + abstract = {Molecular Epidemiology: Prevalence of Human Cutaneous Leishmaniasis in Palestine in the Period between 2016 and 2024 Using Next Generation Sequencing + +Hanan Al-Jawabreh + +Abstract +Background: Leishmaniasis is a vector-borne disease caused by protozoan parasite of the genus Leishmania. The infection is transmitted by bite of infected female sandflies of the genus Phlebotomus in the old world or Lutzomyia in the new world. The diagnosis is made by stained smear microscopy, in-vitro culture, and DNA-based detection methods. +Materials and Methods: In this study that spanned from 2016 to 2024 included patients from eleven districts in the West Bank of Palestine. The diagnostic methods used in the study included microscopy of Giemsa-stained touch smears, in-vitro culture using NNN medium, and ITS1-PCR. The amplicon-based next-generation sequencing of ITS1-219 was included in the comparison part of the study. The comparison arm of the study compared two groups, CL-confirmed group in w were positive by any of the tests used in the epidemiologic part of the study and a non-CL group which were negative by all diagnostic methods. The NGS1-219-PCR was compared to ITS1-PCR, which is considered as a gold standard owing to its superiority over microscopy and in-vitro culture. +Results: The positivity rate during the study period was 17\% (213/1262) with a prevalence of 7.0 per 100,000. The annual incidence rate 0.84 per 100,000 (25 cases per year) with approximately equal distribution between males (52\%) and females (48\%). The age range between 0 to 14 yrs was the most affected by CL. The CL lesions primarily affected the head (45\%), followed by the upper extremities (38\%) and the lower extremities (17\%). +The choropleth mapping showed that Jericho is still the district with highest annual incidence rate (21 per 100,000). The study revealed that Leishmania tropica is the predominating species with L. major restricted mainly to Jericho. The year 2017 was the last year to witness a CL peak in Palestine with Jericho contributing to 40\% of peak cases. More than half (52\%) of the cases appeared in the months of January to March. As for the comparison arm of the study, ITS1-219-NGS was shown to have a higher sensitivity of 94\% compared to the imperfect gold standard (ITS1-PCR) of 86\%. The agreement between the two tests was fair (Kappa-0.24) only agreed on 56\% of the cases only. Furthermore, the standard ITS1-PCR was unable to genotype 29 CL cases but were genotyped by ITS1-219-NGS and confirmed by BLAST search. Unlike the ITS1-PCR, imperfect gold standard, ITS1-219-NGS genotypes all its positive results correctly as confirmed by BLAST search. Moreover, 13 ITS1-PCR weak positive CL cases were found to be negative by ITS1-219-NGS and upon BLAST search shown to be contamination of human and bacterial origin. +Conclusion: Jericho area remains the main focus of CL in Palestine with L. tropica as the main species in the country and L. major restricted to Jericho area. Incidence rate has dropped compared to the two decades preceding this study as result of control measures implemented. Amplicon-based NGS is a feasible, highly sensitive, and high throughput diagnostic method with accurate species identification that can be used in clinical practice and epidemiologic survey.}, + author = {Al-Jawabreh, Hanan and Thesis, M}, + doi = {10.13140/RG.2.2.29025.62569}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {February}, + shorttitle = {Molecular {Epidemiology}}, + title = {Molecular {Epidemiology}: {Prevalence} of {Human} {Cutaneous} {Leishmaniasis} in {Palestine} in the {Period} between 2016 and 2024 {Using} {Next} {Generation} {Sequencing}}, + year = {2025} +} + @inproceedings{alam_reusability_2023, abstract = {Scientific workflow has become essential in software engineering because it provides a structured approach to designing, executing, and analyzing scientific experiments. Software developers and researchers have developed hundreds of scientific workflow management systems so scientists in various domains can benefit from them by automating repetitive tasks, enhancing collaboration, and ensuring the reproducibility of their results. However, even for expert users, workflow creation is a complex task due to the dramatic growth of tools and data heterogeneity. Thus, scientists attempt to reuse existing workflows shared in workflow repositories. Unfortunately, several challenges prevent scientists from reusing those workflows. Thus, we first attempted to identify those reusability challenges in this study. We also offered an action list and evidence-based guidelines to promote the reusability of scientific workflows. Our intensive manual investigation examined the reusability of existing workflows and exposed several challenges. The challenges preventing reusability include tool upgrading, tool support unavailability, design flaws, incomplete workflows, failure to load a workflow, etc. Such challenges and our action list offered guidelines to future workflow composers to create better workflows with enhanced reusability. In the future, we plan to develop a recommender system using reusable workflows that can assist scientists in creating effective and error-free workflows.}, author = {Alam, Khairul and Roy, Banani and Serebrenik, Alexander}, @@ -390,6 +608,23 @@ @article{alcaraz_development_2021 year = {2021} } +@article{alessandri_credo_2024, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}The analysis of large and complex biological datasets in bioinformatics poses a significant challenge to achieving reproducible research outcomes due to inconsistencies and the lack of standardization in the analysis process. These issues can lead to discrepancies in results, undermining the credibility and impact of bioinformatics research and creating mistrust in the scientific process. To address these challenges, open science practices such as sharing data, code, and methods have been encouraged.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}CREDO, a Customizable, REproducible, DOcker file generator for bioinformatics applications, has been developed as a tool to moderate reproducibility issues by building and distributing docker containers with embedded bioinformatics tools. CREDO simplifies the process of generating Docker images, facilitating reproducibility and efficient research in bioinformatics. The crucial step in generating a Docker image is creating the Dockerfile, which requires incorporating heterogeneous packages and environments such as Bioconductor and Conda. CREDO stores all required package information and dependencies in a Github-compatible format to enhance Docker image reproducibility, allowing easy image creation from scratch. The user-friendly GUI and CREDO's ability to generate modular Docker images make it an ideal tool for life scientists to efficiently create Docker images. Overall, CREDO is a valuable tool for addressing reproducibility issues in bioinformatics research and promoting open science practices.}, + author = {Alessandri, Simone and Ratto, Maria L and Rabellino, Sergio and Piacenti, Gabriele and Contaldo, Sandro Gepiro and Pernice, Simone and Beccuti, Marco and Calogero, Raffaele A and Alessandri, Luca}, + doi = {10.1186/s12859-024-05695-9}, + issn = {1471-2105}, + journal = {BMC bioinformatics}, + keywords = {{\textgreater}UseGalaxy.eu, Computational Biology, Software}, + language = {eng}, + month = {March}, + number = {1}, + pages = {110}, + title = {{CREDO}: a friendly {Customizable}, {REproducible}, {DOcker} file generator for bioinformatics applications}, + url = {http://europepmc.org/abstract/MED/38475691}, + volume = {25}, + year = {2024} +} + @incollection{ali_bioinformatics_2024, abstract = {Bioinformatics and computational biology integrate computer science, molecular biology, statistics, mathematics, and engineering to collect, manage, and analyze biological data. This interdisciplinary synergy has led to innovative advances in our understanding of plant diseases and the development of effective strategies for disease management. Bioinformatics plays a diverse and influential role in addressing the fundamental challenges faced by plant pathologists. Bioinformatics in plant pathology is vital for analyzing pathogen genomes, achieved through DNA sequencing and annotation. Comparative genomics involves comparing different pathogen genomes to identify commonalities and differences, shedding light on the genetic basis of pathogenicity, virulence, drug resistance, and evolutionary relationships. Bioinformatics also aids in studying pathogen evolution, reconstructing their history, and tracking new variants, essential for predicting disease outbreaks and developing mitigation strategies. Additionally, bioinformatics contributes to advanced diagnostic tools, detecting specific genetic markers for rapid and accurate disease identification, crucial for minimizing crop losses and ensuring food security. This chapter introduces and uses different bioinformatics tools and resources used to study plant pathogens. Moreover, applications and methods of the tools involved in BLAST, multiple sequence alignment, phylogenetics, gene structure analysis, protein domain and motif, gene localization on the chromosome, protein expression analysis, and molecular docking and interaction networks are also discussed.}, address = {Singapore}, @@ -408,6 +643,23 @@ @incollection{ali_bioinformatics_2024 year = {2024} } +@article{ali_characterization_2021, + abstract = {Currently, there are increasing concerns about the possibility of a new epidemic due to emerging reports of Mayaro virus (MAYV) fever outbreaks in areas of South and Central America. Haemagogus mosquitoes, the primary sylvan vectors of MAYV are poorly characterized and a better understanding of the mosquito's viral transmission dynamics and interactions with MAYV and other microorganisms would be important in devising effective control strategies. In this study, a metatranscriptomic based approach was utilized to determine the prevalence of RNA viruses in field-caught mosquitoes morphologically identified as Haemagogus janthinomys from twelve (12) forest locations in Trinidad, West Indies. Known insect specific viruses including the Phasi Charoen-like and Humaiata-Tubiacanga virus dominated the virome of the mosquitoes throughout sampling locations while other viruses such as the avian leukosis virus, MAYV and several unclassified viruses had a narrower distribution. Additionally, assembled contigs from the Ecclesville location suggests the presence of a unique uncharacterized picorna-like virus. Mapping of RNA sequencing reads to reference mitochondrial sequences of potential feeding host animals showed hits against avian and rodent sequences, which putatively adds to the growing body of evidence of a potentially wide feeding host-range for the Haemagogus mosquito vector.}, + author = {Ali, Renee and Jayaraj, Jayaraman and Mohammed, Azad and Chinnaraja, Chinnadurai and Carrington, Christine V F and Severson, David W and Ramsubhag, Adesh}, + doi = {10.1038/s41598-021-95842-6}, + issn = {2045-2322}, + journal = {Scientific reports}, + keywords = {{\textgreater}UseGalaxy.eu, Virome}, + language = {eng}, + month = {August}, + number = {1}, + pages = {16584}, + title = {Characterization of the virome associated with {Haemagogus} mosquitoes in {Trinidad}, {West} {Indies}}, + url = {http://europepmc.org/abstract/MED/34400676}, + volume = {11}, + year = {2021} +} + @article{ali_characterization_2021, author = {Ali, Renee and Jayaraman, Jayaraj and Mohammed, Azad and Chinnaraja, Chinnadurai and Carrington, Christine V. F. and Severson, David W. and Ramsubhag, Adesh}, doi = {10.21203/rs.3.rs-380784/v1}, @@ -474,6 +726,73 @@ @article{aljindan_phenomics_2024 year = {2024} } +@article{almeida_giant_2025, + abstract = {The mitochondrial genomes of plants are large, with the majority ranging between 500 and 800 kb. However, the mitochondrial genomes of Cyperaceae (sedges) species were found to be much larger, exceeding 1 Mb in size. Here, we aimed to investigate the gigantism of the mitochondrial genomes of three Rhynchospora (beak-sedges) species and one related species of the sister family Juncaceae, the common rush (Juncus effusus).Long PacBio HiFi reads were sequenced and assembled using Hifiasm software. The mitochondrial genomes were annotated using Geneious and Mitofy software. Transposable elements were annotated using DANTE and RepeatModeler pipelines, and gene prediction in intergenic regions was conducted using Augustus. The predicted genes were annotated using BLAST and gene ontology terms.The mitogenome of R. breviuscula was 2,222,920 bp, that of R. pubera was 2,064,773 bp, that of R. tenuis was 1,678,054 bp, and that of the species of J. effusus was 553,985 bp. The results revealed giant intergenic spaces in all Rhynchospora, containing predicted nuclear genes and LTR retrotransposons. BLASTn revealed a high migration of DNA from the nucleus to the mitogenome.Our findings show that the Rhynchospora mitogenome is the largest among the monocotyledons. These mitogenomes feature giant intergenic spaces, incorporation of chloroplast DNA and numerous rearrangements. Gigantism of the intergenic spaces is associated with the movement of nuclear DNA segments, suggesting a mechanism of DNA transfer from the nuclear genome to the mitochondrial genome.}, + author = {Almeida, Cicero and Marques, André}, + doi = {10.1093/aob/mcaf098}, + issn = {0305-7364}, + journal = {Annals of Botany}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {May}, + pages = {mcaf098}, + title = {Giant mitogenomes in {Rhynchospora} are a result of nuclear gene and retrotransposon insertions in intergenic spaces}, + url = {https://doi.org/10.1093/aob/mcaf098}, + urldate = {2025-05-28}, + year = {2025} +} + +@article{alminana_brines_p-346_2025, + abstract = {Does endometriosis-associated infertility (E) change the microRNA (miRNA) profile of cumulus cells (CCs) with a differential footprint between fertilized oocytes and oocytes that failed fertilization?The CCs miRNA profile is altered in E versus control (C) patients (male/non-hormonal causes), with a differential signature between oocytes with successful or failed fertilization.For E patients, ART are often considered as an option to achieve successful pregnancy. But the impact of E on oocyte quality and its potential to be fertilized are still under debate with very few molecular clues supporting clinical data. Endometriosis causes alterations in gene expression in oocytes and CCs, but little is known about the changes at miRNA level. MicroRNAs are small non-coding RNAs with an important role in gene regulation. They are active players in oocyte maturation and fertilization, have been pointed as diagnostic biomarkers of E and thus, making them promising biomarkers of oocyte quality in E.Thirty-six CCs from metaphase II oocytes from 33 patients, i.e., 15 E patients and 18 C patients (11 male, 7 non-hormonal factors) undergoing ART between 2019-2023 at the University Hospital Zurich were analyzed. CCs samples were retrospectively classified into: 1) E patients with fertilized oocytes (2PN) (n = 11; E2); 2) E patients with oocytes that failed fertilization (0PN) (n = 4; E0); 3) C patients with 2PN oocytes (n = 12; C2); 4) C patients with 0PN oocytes (n = 7; C0).Small RNA-sequencing was performed for 36 single CCs samples. RNA-seq data was analyzed using the Galaxy Europe server (usegalaxy.eu) and differential expression analysis was performed with the Bioconductor R package EdgeR. The differential abundance of two miRNAs, miR-143-3p and miR-10b-5p, was further validated in 24 remaining samples by qPCR. MIENTURNET was used to identify miRNA target genes and DAVID and KEGG pathway databases to examine biological functions and pathways associated to the predicted target genes.Ninety-nine differential abundant (DA) miRNAs were identified between E and C patients (false discovery rate, FDR \<5\%). Regardless the disease/health status, 31 miRNAs were DA between 2PN and 0PN oocytes (FDR \<20\%). In E patients, 27 DA miRNAs were found between E2 and E0 oocytes (FDR \<5\%). In C patients, 15 DA miRNAs were found between C2 and C0 oocytes (FDR \<5\%). Around 60\% of the DA miRNAs in CCs from E versus C comparison have been found in endometrium or plasma samples from E patients. Comparisons among identified DA miRNAs revealed three sets of miRNAs: 1) affected only by E, 2) affected by both E and the potential to be fertilized; and 3) reporting a E2 miRNA signature in CCs of E patients but still with the potential to be fertilized. Target genes of DA miRNAs were involved in known biological functions and pathways affected by E, e.g.: oxidative stress, calcium signaling, mitochondria and spindle alterations, embryo development, estrogen signaling, and TGF-beta pathway. Interestingly, 11 DA miRNAs identified in set 1 - unique to E, and 3 DA miRNAs in set 3 - reflecting E2 oocyte signature, target 39 and 32 genes involved in progesterone-mediated oocyte maturation pathway, respectively.The sample size of the study cannot be considered as large, with a particular small group of E patients with 0PN oocytes compared to the other experimental groups. We cannot rule out that other unknown individual genetic or clinical factors may have influenced the reported results.Our findings can inspire new diagnosis approaches and personalized treatments with therapeutic miRNAs for underexpressed miRNAs or with miRNA inhibitors for miRNAs overexpressed in CCs of oocytes from E patients. The potential applications can be of value to E patients with low number and poor quality of oocytes retrieved.No}, + author = {Almiñana Brines, C and Makieva, S and Bauersachs, S and Saenz-de-Juano, M D and Xie, M and Velasco, A and Cervantes, N and Ulbrich, S E and Leeners, B}, + doi = {10.1093/humrep/deaf097.653}, + issn = {1460-2350}, + journal = {Human Reproduction}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {June}, + number = {Supplement\_1}, + pages = {deaf097.653}, + title = {P-346 {Endometriosis}-associated infertility changes the {microRNA} profile of cumulus cells with a notably pronounced effect on oocytes that failed fertilisation}, + url = {https://doi.org/10.1093/humrep/deaf097.653}, + urldate = {2025-07-12}, + volume = {40}, + year = {2025} +} + +@article{alminana_endometriosis-associated_2025, + abstract = {\<h4\>Background\</h4\>Endometriosis (E) is multifactorial disease affecting around 10\% of women worldwide. The association between E and infertility is clinically well recognized. For E patients to achieve a successful pregnancy, assisted reproductive technologies (ART) are considered as a treatment option. However, the impact of E on oocyte quality, its potential to be fertilized as well as pregnancy rates, is still under debate and with very few molecular clues explaining the clinical data. Alterations in protein-coding RNAs in cumulus cells (CCs), cells surrounding the oocytes and contributing to oocyte maturation, have been reported in E patients. But there is a lack of information regarding microRNAs (miRNAs), which control protein translation. Thus, we aimed: (1) to identify altered miRNA expression in CCs of E patients versus patients without the disease (control, C); and (2) to unveil if in E patients, CCs from fertilized oocytes display a different miRNA profile versus oocytes that failed fertilization. Small RNA-sequencing was performed on CCs from patients undergoing ART.\<h4\>Results\</h4\>A total of 85 differentially expressed (DE) miRNAs were identified in E versus C patients (FDR \< 0.05). In E patients, 25 DE miRNAs were found between fertilized oocytes and oocytes that failed fertilization, while 13 DE miRNAs in C patients (FDR \< 0.05). Comparisons among DE miRNAs highlighted three notable miRNA sets: Set (1) 35 DE miRNAs specific to E; Set (2) 27 DE miRNAs affected by both E and the potential to be fertilized; and Set (3) 6 DE miRNAs characteristic of a competent oocyte successfully fertilized despite the disease. Target gene analysis of DE miRNAs unveiled genes involved in oocyte meiosis, progesterone-mediated oocyte maturation pathway, embryo development, mitochondria and spindle alterations, calcium signaling, and oxidative stress.\<h4\>Conclusion\</h4\>This study identified for the first time an altered miRNA signature in CCs of E patients, pointing towards compromised oocyte competence. Besides, in E patients, a characteristic CCs miRNA footprint for oocytes that can be successfully fertilized despite the disease has been revealed. The study charts new territory for non-invasive diagnosis and personalized treatments based on miRNAs to improve oocyte competence in E patients under ART treatments.}, + author = {Almiñana, Carmen and Makieva, Sofia and Bauersachs, Stefan and Saenz-de-Juano, Mara D and Xie, Min and Velasco, Ana and Cervantes, Natalia and Spalinger, Marianne R and Ulbrich, Susanne E and Leeners, Brigitte}, + doi = {10.1186/s40659-025-00641-2}, + issn = {0716-9760}, + journal = {Biological research}, + keywords = {{\textgreater}UseGalaxy.eu, Cumulus Cells, Endometriosis-associated Infertility, Fertilized Oocyte, Mirnas., Oocyte Quality}, + month = {September}, + number = {1}, + pages = {62}, + title = {Endometriosis-associated infertility alters the {microRNA} signatures of cumulus cells with a particularly pronounced effect in oocytes that failed fertilization}, + url = {https://europepmc.org/articles/PMC12465895}, + volume = {58}, + year = {2025} +} + +@article{altaf_unveiling_2025, + abstract = {Micronutrient deficiencies, such as manganese (Mn), pose significant global health risks, affecting millions of people worldwide and leading to serious health conditions. Biofortifying crops, notably common beans, offer a sustainable solution to combat these deficiencies. This study aimed to uncover the genetic basis associated with Mn content in Turkish common bean (Phaseolus vulgaris) germplasm through a genome-wide association study (GWAS), which is crucial for developing nutrient-rich bean varieties. Here, we examined variation among 183 common bean accessions, collected from 19 provinces of Turkey and identified the genetic basis linked to seed Mn content. Genotype by environment interaction significantly influenced Mn content (p {\textless} 0.05). The mean Mn content was observed 31.69 mg kg−1 across the germplasm. Bingol-16 had the lowest, while Malatya-59 had the highest Mn contents. Stability analysis was performed using the ‘STABILITYSOFT’ method and found 10 stable accessions. The cluster constellation plot was generated using JMP statistical software. A total of 7900 DArTseq markers were used for association analysis, identifying 16 markers across four chromosomes (Pv2, Pv5, Pv7 and Pv11). Notably, markers DArT-3374915 and DArT-3375187 exhibited consistent associations across different environments, making them promising candidates for Mn-focused breeding programmes. Gene annotation and interactome analysis, including BLAST searches and protein–protein interaction analysis, revealed associations of candidate genes with Mn concentration regulation, shedding light on potential mechanisms underlying Mn accumulation in common beans. Our findings lay a foundation for marker-assisted breeding efforts in common bean improvement.}, + author = {Altaf, Muhammad Tanveer and Nadeem, Muhammad Azhar and Ayten, Sefa and Aksoy, Emre and Sönmez, Ferit and Çiftçi, Vahdettin and Baloch, Faheem Shehzad}, + copyright = {© 2024 Wiley-VCH GmbH. Published by John Wiley \& Sons Ltd}, + doi = {10.1111/pbr.13251}, + issn = {1439-0523}, + journal = {Plant Breeding}, + keywords = {{\textgreater}UseGalaxy.eu, DArTseq, GWAS, Phaseolus vulgaris, biofortification, manganese, micronutrient deficiency}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbr.13251}, + number = {3}, + pages = {285--309}, + title = {Unveiling {Genetic} {Basis} {Associated} {With} {Manganese} {Content} in {Turkish} {Common} {Bean} ({Phaseolus} vulgaris {L}.) {Germplasm} {Through} a {Genome}-{Wide} {Association} {Study}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbr.13251}, + urldate = {2025-07-12}, + volume = {144}, + year = {2025} +} + @article{alvandi_pathovar-specific_2023, abstract = {Bacterial leaf streak disease caused by Xanthomonas translucens pv. undulosa is an economically important disease threatening wheat and barley crops around the globe. So far, specific PCR-based detection and identification tests for X. translucens pathovars are not available. In this study, we used comparative genomics approach to design a pathovar-specific primer pair for detection of X. translucens pv. undulosa in naturally infected seeds and its differentiation from other pathovars of the species. For this aim, complete genome sequences of strains of different X. translucens pathovars were compared and the specific PCR primer pair XtuF/XtuR was designed. These primers were strictly specific to X. translucens pv. undulosa as the expected 229 bp DNA fragment was not amplified in the closely-related pathovars nor in other xanthomonads, wheat pathogenic bacteria, and other plant pathogenic bacteria. High sensitivity of the primer pair XtuF/XtuR allowed detection of pure DNA of the pathogen in a concentration as low as 4.5 pg/µl. The pathogen was also detected in water suspension at a concentration of 8.6 × 102 cfu/ml. The PCR test was capable of detecting the pathogen in extracts of naturally infected wheat seeds at a concentration of 3.5 × 104 cfu/g while culture plate method was able to detect the pathogen at a concentration of 50 × 105 cfu/g of the same seeds. The PCR test developed in this study is a step forward for precise detection and identification of X. translucens pv. undulosa to prevent outbreaks of the bacterial leaf streak disease.}, author = {Alvandi, Hosna and Taghavi, Seied Mohsen and Khojasteh, Moein and Rahimi, Touraj and Dutrieux, Cecile and Taghouti, Geraldine and Jacques, Marie-Agnès and Portier, Perrine and Osdaghi, Ebrahim}, @@ -489,6 +808,23 @@ @article{alvandi_pathovar-specific_2023 year = {2023} } +@article{alves_genome-wide_2022, + abstract = {Epigenetic regulators are proteins involved in controlling gene expression. Information about the epigenetic regulators within the Fagaceae, a relevant family of trees and shrubs of the northern hemisphere ecosystems, is scarce. With the intent to characterize these proteins in Fagaceae, we searched for orthologs of DNA methyltransferases (DNMTs) and demethylases (DDMEs) and Histone modifiers involved in acetylation (HATs), deacetylation (HDACs), methylation (HMTs), and demethylation (HDMTs) in Fagus, Quercus, and Castanea genera. Blast searches were performed in the available genomes, and freely available RNA-seq data were used to de novo assemble transcriptomes. We identified homologs of seven DNMTs, three DDMEs, six HATs, 11 HDACs, 32 HMTs, and 21 HDMTs proteins. Protein analysis showed that most of them have the putative characteristic domains found in these protein families, which suggests their conserved function. Additionally, to elucidate the evolutionary history of these genes within Fagaceae, paralogs were identified, and phylogenetic analyses were performed with DNA and histone modifiers. We detected duplication events in all species analyzed with higher frequency in Quercus and Castanea and discuss the evidence of transposable elements adjacent to paralogs and their involvement in gene duplication. The knowledge gathered from this work is a steppingstone to upcoming studies concerning epigenetic regulation in this economically important family of Fagaceae.}, + author = {Alves, Sofia and Braga, Ângelo and Parreira, Denise and Alhinho, Ana Teresa and Silva, Helena and Ramos, Miguel Jesus Nunes and Costa, Maria Manuela Ribeiro and Morais-Cecílio, Leonor}, + doi = {10.1111/ppl.13788}, + issn = {1399-3054}, + journal = {Physiol Plant}, + keywords = {{\textgreater}UseGalaxy.eu, Histones, Quercus}, + language = {eng}, + month = {September}, + number = {5}, + pages = {e13788}, + title = {Genome-wide identification, phylogeny, and gene duplication of the epigenetic regulators in {Fagaceae}}, + url = {http://europepmc.org/abstract/MED/36169620}, + volume = {174}, + year = {2022} +} + @article{amaral_tcti_2022, author = {Amaral, Milena do and Freitas, Ana Camila Oliveira and Santos, Ariana Silva and Santos, Everton Cruz dos and Ferreira, Monaliza Macêdo and Gesteira, Abelmon da Silva and Gramacho, Karina Peres and Marinho-Prado, Jeanne Scardini and Pirovani, Carlos Priminho}, doi = {10.1038/s41598-021-04700-y}, @@ -503,6 +839,23 @@ @article{amaral_tcti_2022 year = {2022} } +@article{ambros_distribution_2022, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Lactic acid bacteria (LAB) are used as starters in a wide variety of food fermentations. While the number of reports of phages infecting other LAB steadily increased over the years, information about phage associated with Latilactobacillus sakei, a frequently used meat starter, remains scarce.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}In this study, a predictive genomic analysis of 43 Latilactobacillus sakei genomes revealed the presence of 26 intact, eleven questionable and 52 incomplete prophage sequences across all analysed genomes with a range of one to five predicted prophage sequences per strain. Screening 24 sakei strains for inducible prophages by utilising UV light or mitomycin C, we identified seven lysogenic strains showing lysis after induction during subsequent growth monitoring. Electron microscopic analysis revealed fully assembled virions in the purified lysates of four samples, thus confirming successful prophage induction. All virions featured icosahedral, isomeric heads and long, most likely non-contractile tails indicating siphoviruses. By performing phylogenetic analyses with various marker genes as well as full prophage sequences, we displayed a remarkably high diversity of prophages, that share a similar gene module organisation and six different chromosomal integration sites were identified. By sequencing viral DNA purified from lysates of Latilactobacillus sakei TMW 1.46, we demonstrate that simultaneous induction of multiple prophages is possible.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}With this work, we not only provide data about the incidence of prophages harboured by the meat starter Latilactobacillus sakei, we also demonstrated their potential to impact growth of their host after induction, as well as forming seemingly fully assembled virions.}, + author = {Ambros, Conrad L and Ehrmann, Matthias A}, + doi = {10.1186/s12866-022-02675-y}, + issn = {1471-2180}, + journal = {BMC microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Bacteriophages, Prophages}, + language = {eng}, + month = {November}, + number = {1}, + pages = {267}, + title = {Distribution, inducibility, and characterisation of prophages in {Latilactobacillus} sakei}, + url = {http://europepmc.org/abstract/MED/36348293}, + volume = {22}, + year = {2022} +} + @article{ambros_distribution_2023, abstract = {Aim: Temperate phages are known to heavily impact the growth of their host, be it in a positive way, e.g., when beneficial genes are provided by the phage, or negatively when lysis occurs after prophage induction. This study provides an in-depth look into the distribution and variety of prophages in Latilactobacillus curvatus (L. curvatus). This species is found in a wide variety of ecological niches and is routinely used as a meat starter culture., Methods: Fourty five L. curvatus genomes were screened for prophages. The intact predicted prophages and their chromosomal integration loci were described. Six L. curvatus lysogens were analysed for phage-mediated lysis post induction via UV light and/or mitomycin C. Their lysates were analysed for phage particles via viral DNA sequencing and transmission electron microscopy., @@ -577,6 +930,7 @@ @article{andriyanov_genomic_2024 language = {English}, month = {January}, note = {Publisher: Frontiers}, + pages = {1321122}, title = {Genomic analysis of multidrug-resistant {Delftia} tsuruhatensis isolated from raw bovine milk}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1321122/full}, urldate = {2024-05-17}, @@ -605,6 +959,51 @@ @article{annor_melibiosex-galmacconkey_2023 year = {2023} } +@misc{anwar_complete_2025, + abstract = {Bali cattle, domesticated from wild banteng (Bos javanicus), represent Indonesia’s valuable indigenous genetic resource. A detailed mitochondrial genome (mitogenome) sequence of Bali cattle is essential for population genetic studies and supporting sustainable breeding. This study aimed to assemble the complete mitogenome sequence of Bali cattle, characterize its genetic features, and investigate its phylogenetic position within the Bos genus. High-molecular-weight genomic DNA was extracted from a male Bali cattle blood, and mitogenome sequencing was conducted using long-read Oxford nanopore sequencing by combining adaptive sampling (NAS) and amplicon-based approaches. Both NAS and amplicon-based approaches can assemble a complete mitogenome sequence of Bali cattle. However, amplicon-based gives better accuracy and completeness. The complete mitogenome of Bali cattle spans 16,387 bp, comprising 13 PCGs, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region (CR), which showed similar structure observed in other Bos species. Phylogenetic analysis revealed that Bali cattle are grouped within the same clade as the B. javanicus species, with the closest relationship to Javan banteng (B. j. javanicus). Interestingly, a unique tandem repeat motif was exclusively identified in the CR of B. j. javanicus, including Bali cattle. This study offers novel insights into the comprehensive mitogenomic architecture of Bali cattle. Furthermore, discovering a unique tandem repeat motif offers potential as a marker for Bali cattle identification and its applications in forensic and product authentication.}, + address = {Rochester, NY}, + author = {Anwar, Saiful and Shidiq, Fajrin and Noor, Ronny Rachman and Semiadi, Gono and Dharmayanthi, Anik Budhi and Furqon, Ahmad and Khaerunnisa, Isyana and Sutikno, Sutikno and Margawati, Endang Tri and Jakaria, Jakaria}, + doi = {10.2139/ssrn.5202444}, + keywords = {{\textgreater}UseGalaxy.eu, Bovidae, Domestication, Long-read sequencing, mitochondrial DNA, repetitive DNA}, + language = {en}, + month = {April}, + publisher = {Social Science Research Network}, + title = {The {Complete} {Mitochondrial} {Genome} {Assembly} of {Bali} {Cattle} ({Bos} {Javanicus}) {Using} {Oxford} {Nanopore} {Long}-{Read} {Sequencing} {Technology}}, + type = {{SSRN} {Scholarly} {Paper}}, + url = {https://papers.ssrn.com/abstract=5202444}, + urldate = {2025-05-28}, + year = {2025} +} + +@article{apiwatsiri_metagenomic_2022, + abstract = {This study used metagenomic analysis to investigate the gut microbiota and resistome in piglets that were or were not challenged with enterotoxigenic Escherichia coli (ETEC) and had or had not received dietary supplementation with microencapsulated probiotics. The 72 piglets belonged to six groups that were either non-ETEC challenged (groups 1-3) or ETEC challenged (receiving 5ml of 109 CFU/ml pathogenic ETEC strain L3.2 one week following weaning at three weeks of age: groups 4-6). On five occasions at 2, 5, 8, 11, and 14 days of piglet age, groups 2 and 5 were supplemented with 109 CFU/ml of multi-strain probiotics (Lactiplantibacillus plantarum strains 22F and 25F, and Pediococcus acidilactici 72N) while group 4 received 109 CFU/ml of P. acidilactici 72N. Group 3 received 300mg/kg chlortetracycline in the weaner diet to mimic commercial conditions. Rectal faecal samples were obtained for metagenomic and resistome analysis at 2 days of age, and at 12 hours and 14 days after the timing of post-weaning challenge with ETEC. The piglets were all euthanized at 42 days of age. The piglets in groups 2 and 5 were enriched with several desirable microbial families, including Lactobacillaceae, Lachnospiraceae and Ruminococcaceae, while piglets in group 3 had increases in members of the Bacteroidaceae family and exhibited an increase in tetW and tetQ genes. Group 5 had less copper and multi-biocide resistance. Mobile genetic elements IncQ1 and IncX4 were the most prevalent replicons in antibiotic-fed piglets. Only groups 6 and 3 had the integrase gene (intl) class 2 and 3 detected, respectively. The insertion sequence (IS) 1380 was prevalent in group 3. IS3 and IS30, which are connected to dietary intake, were overrepresented in group 5. Furthermore, only group 5 showed genes associated with detoxification, with enrichment of genes associated with oxidative stress, glucose metabolism, and amino acid metabolism compared to the other groups. Overall, metagenomic analysis showed that employing a multi-strain probiotic could transform the gut microbiota, reduce the resistome, and boost genes associated with food metabolism.}, + author = {Apiwatsiri, Prasert and Pupa, Pawiya and Sirichokchatchawan, Wandee and Sawaswong, Vorthon and Nimsamer, Pattaraporn and Payungporn, Sunchai and Hampson, David J and Prapasarakul, Nuvee}, + doi = {10.1371/journal.pone.0269959}, + issn = {1932-6203}, + journal = {PloS one}, + keywords = {{\textgreater}UseGalaxy.eu, Enterotoxigenic Escherichia coli, Escherichia coli Infections, Gastrointestinal Microbiome, Microbiota, Probiotics, Swine Diseases}, + language = {eng}, + number = {6}, + pages = {e0269959}, + title = {Metagenomic analysis of the gut microbiota in piglets either challenged or not with enterotoxigenic {Escherichia} coli reveals beneficial effects of probiotics on microbiome composition, resistome, digestive function and oxidative stress responses}, + url = {http://europepmc.org/abstract/MED/35749527}, + volume = {17}, + year = {2022} +} + +@article{apletsch_type_2025, + author = {A. Pletsch, Elizabeth and D. Dawson, Harry and Cheung, Lumei and S. Ragonese, Jack and T. Chen, Celine and D. Smith, Allen}, + doi = {10.1039/D4FO04697H}, + journal = {Food \& Function}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + note = {Publisher: Royal Society of Chemistry}, + title = {A type 4 resistant potato starch alters the cecal microbiome, gene expression and resistance to colitis in mice fed a {Western} diet based on {NHANES} data}, + url = {https://pubs.rsc.org/en/content/articlelanding/2025/fo/d4fo04697h}, + urldate = {2025-04-15}, + year = {2025} +} + @article{apostolakos_functional_2022, abstract = {Strains belonging to the Weissella genus are frequently recovered from spontaneously fermented foods. Their functional, microbial-modulating, and probiotic traits enhance not only the sensorial properties but also the nutritional value, beneficial effects, and safety of fermented products. Sporadic cases of opportunistic pathogenicity and antibiotic resistance have deprived safety status from all Weissella species, which thus remain understudied. Our study increased the number of available high-quality and taxonomically accurate W. paramesenteroides genomes by 25\% (9 genomes reported, leading to a total of 36 genomes). We conducted a phylogenetic and comparative genomic analysis of the most dominant Weissella species (W. cibaria, W. paramesenteroides, W. viridescens, W. soli, W. koreensis, W. hellenica and W. thailadensis). The phylogenetic tree corroborated species assignment but also revealed phylogenetic diversity within the Weissella species, which is likely related to the adaptation of Weissella in different niches. Using robust alignment criteria, we showed the overall absence of resistance and virulence genes in Weissella spp., except for one W. cibaria isolate carrying blaTEM-181. Enrichment analysis showed the association of Weissella species several CAZymes, which are essential for biotechnological applications. Additionally, the combination of CAZyme metabolites with probiotics can potentially lead to beneficial effects for hosts, such as the inhibition of inflammatory processes and the reduction of cholesterol levels. Bacteriocins and mobile genetic elements MGEs (Inc11 plasmid and ISS1N insertion sequence) were less abundant, however W. thailadensis and W. viridescens showed significant association with specific bacteriocin-encoding genes. Lastly, an analysis of phenotypic traits underlined the need to carefully evaluate W. cibaria strains before use as food additives and suggested the possibility of employing W. paramesenteroides and W. hellenica in the fermentation process of vegetable products. More studies providing high-resolution characterization of Weissella strains from various sources are necessary to elucidate the safety of Weissella spp. and exploit their beneficial characteristics.}, author = {Apostolakos, Ilias and Paramithiotis, Spiros and Mataragas, Marios}, @@ -633,7 +1032,7 @@ @article{apostolakos_genomic_2023 doi = {10.3390/ijms241813883}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {{\textgreater}UseGalaxy.eu, dairy products, lactic acid bacteria, mastitis, probiotics, sheep’s milk, staphylococci, whole-genome sequencing}, + keywords = {{\textgreater}UseGalaxy.eu, Mastitis, Milk, Probiotics, Staphylococcus, dairy products, lactic acid bacteria, mastitis, probiotics, sheep’s milk, staphylococci, whole-genome sequencing}, language = {en}, month = {January}, note = {Number: 18 @@ -648,11 +1047,16 @@ @article{apostolakos_genomic_2023 } @article{apostolakos_occurrence_2021, + abstract = {Avian pathogenic \textit{Escherichia coli} (APEC) causes colibacillosis, the disease with the highest economic loss for the broiler industry. However, studies focusing on the prevalence and population structure of APEC in the broiler production pyramid are scarce. Here, we used genotyping and serotyping data to elucidate the APEC population structure and its changes in different broiler production stages along with whole-genome sequencing (WGS) in a subset of APEC isolates to determine transmission patterns amongst dominant APEC sequence types (STs) and characterize them in detail. Comparison of genotypes encountered in both APEC and avian fecal \textit{E. coli} (AFEC) provided further insights. Overall, APEC-related mortality, as the proportion of the total sampled mortality in the broiler production, was high (35\%), while phylogroup C and serogroup O78 were predominant amongst APEC isolates. We found a low (34.0\%) and high (53.3\%) incidence of colibacillosis in chicks and end-cycle broilers, respectively, which may be related to a shift in APEC genotypes, suggesting a trend from commensalism to pathogenicity across different broiler production stages. Despite considerable APEC genotypic diversity, there was substantial genotype overlap (40.9\%, overall) over the production stages and convergence of STs to the four clusters. Within these clusters, WGS data provided evidence of clonal transmission events and revealed an enriched virulence and resistance APEC repertoire. More specifically, sequenced APEC were assigned to defined pathotypes based on their virulence gene content while the majority (86\%) was genotypically multi-drug resistant. Interestingly, WGS-based phylogeny showed that a subset of APEC, which are cephalosporin-resistant, may originate directly from cephalosporin-resistant AFEC. Finally, exploration of the APEC plasmidome indicated that the small fraction of the APEC virulome carried by IncF plasmids is pivotal for the manifestation of the APEC pathotype; thus, plasmid exchange can promote pathogenicity in strains that are at the edge of the commensal and pathogenic states.}, author = {Apostolakos, Ilias and Laconi, Andrea and Mughini-Gras, Lapo and Yapicier, Özlem Şahan and Piccirillo, Alessandra}, doi = {10.3389/fvets.2021.737720}, + issn = {2297-1769}, + journal = {Frontiers in veterinary science}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {September}, note = {Publisher: Frontiers Media SA}, + pages = {737720}, title = {Occurrence of {Colibacillosis} in {Broilers} and {Its} {Relationship} {With} {Avian} {Pathogenic} {Escherichia} coli ({APEC}) {Population} {Structure} and {Molecular} {Characteristics}}, url = {https://doi.org/10.3389/fvets.2021.737720}, volume = {8}, @@ -682,7 +1086,8 @@ @article{arcari_ceftazidimeavibactam_2023 doi = {10.1099/mgen.0.000931}, issn = {2057-5858}, journal = {Microbial Genomics}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Klebsiella pneumoniae}, + language = {eng}, note = {Publisher: Microbiology Society,}, number = {2}, pages = {000931}, @@ -699,7 +1104,7 @@ @article{arcari_genotypic_2023 author = {Arcari, Gabriele and Cecilia, Federico and Oliva, Alessandra and Polani, Riccardo and Raponi, Giammarco and Sacco, Federica and Francesco, Alice De and Pugliese, Francesco and Carattoli, Alessandra}, doi = {10.3201/eid2911.230921}, journal = {Emerging Infectious Diseases}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Ceftazidime, Klebsiella Infections}, language = {en}, month = {November}, note = {Publisher: Centers for Disease Control and Prevention}, @@ -714,10 +1119,13 @@ @article{arcari_genotypic_2023 } @article{arcari_interplay_2022, + abstract = {The objective was to study ceftazidime-avibactam resistant and susceptible Klebsiella pneumoniae isolated from a patient admitted to the Policlinico Umberto I of Rome for SARS-CoV2. Data on the evolution of patient's conditions, antimicrobial therapies, and microbiological data were collected. Whole-genome sequencing performed by Illumina and Nanopore sequencing methods were used to type the strains. During the hospitalization, a SARS-CoV2-infected patient was colonized by a KPC-producing K. pneumoniae strain and empirically treated with ceftazidime-avibactam (CZA) when presenting spiking fever symptoms. Successively, ST2502 CZA-resistant strain producing the KPC-31 variant gave a pulmonary infection to the patient. The infection was treated with high doses of meropenem. The KPC-31-producing strain disappeared but the patient remained colonized by a KPC-3-producing K. pneumoniae strain. An interplay between highly conserved KPC-31- and KPC-3-producing ST2502 strains occurred in the SARS-CoV2 patient during the hospitalization, selected by CZA and carbapenem treatments, respectively.}, author = {Arcari, Gabriele and Oliva, Alessandra and Sacco, Federica and Lella, Federica Maria Di and Raponi, Giammarco and Tomolillo, Dario and Curtolo, Ambrogio and Venditti, Mario and Carattoli, Alessandra}, doi = {10.1007/s10096-021-04388-y}, + issn = {0934-9723}, journal = {European Journal of Clinical Microbiology \& Infectious Diseases}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Ceftazidime-avibactam, KPC, Klebsiella pneumoniae}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, COVID-19, Ceftazidime-avibactam, KPC, Klebsiella Infections, Klebsiella pneumoniae, Meropenem}, + language = {eng}, month = {January}, note = {Publisher: Springer Science and Business Media LLC}, number = {3}, @@ -732,8 +1140,10 @@ @article{arcari_multiplicity_2023 abstract = {In 2021, Klebsiella pneumoniae sequence type 307 (ST307) strains causing pulmonary and bloodstream infections identified in a hospital in Rome, Italy, reached high levels of resistance to ceftazidime-avibactam (CZA). One of these strains reached high levels of resistance to both CZA and carbapenems and carried two copies of blaKPC-3 and one copy of blaKPC-31 located on plasmid pKpQIL. The genomes and plasmids of CZA-resistant ST307 strains were analyzed to identify the molecular mechanisms leading to the evolution of resistance and compared with ST307 genomes at local and global levels. A complex pattern of multiple plasmids in rearranged configurations, coresident within the CZA-carbapenem–resistant K. pneumoniae strain, was observed. Characterization of these plasmids revealed recombination and segregation events explaining why K. pneumoniae isolates from the same patient had different antibiotic resistance profiles. This study illustrates the intense genetic plasticity occurring in ST307, one of the most worldwide-diffused K. pneumoniae high-risk clones.}, author = {Arcari, Gabriele and Polani, Riccardo and Santilli, Stefania and Capitani, Valerio and Sacco, Federica and Bruno, Francesco and Garcia-Fernandez, Aurora and Raponi, Giammarco and Villa, Laura and Gentile, Giuseppe and Carattoli, Alessandra}, doi = {10.1128/aac.00368-23}, + issn = {0066-4804}, journal = {Antimicrobial Agents and Chemotherapy}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Klebsiella Infections}, + language = {eng}, month = {July}, note = {Publisher: American Society for Microbiology}, number = {0}, @@ -752,7 +1162,7 @@ @article{ardisasmita_comprehensive_2022 doi = {10.1038/s42003-022-04046-9}, issn = {2399-3642}, journal = {Communications Biology}, - keywords = {{\textgreater}UseGalaxy.eu, Data integration, Hepatocytes, RNA sequencing, Stem-cell differentiation}, + keywords = {{\textgreater}UseGalaxy.eu, Data integration, Hepatocytes, Induced Pluripotent Stem Cells, Pluripotent Stem Cells, RNA sequencing, Stem-cell differentiation}, language = {en}, month = {October}, note = {Number: 1 @@ -766,6 +1176,17 @@ @article{ardisasmita_comprehensive_2022 year = {2022} } +@article{ardisasmita_novel_2024, + abstract = {Accurate liver disease modeling and drug toxicity testing still remain challenging as liver cells in vitro poorly resemble adult hepatocytes, as we previously demonstrated using whole transcriptome and cell identity analysis. To address this, we used our insights into hepatic modeling to develop hepatocyte-like liver organoids (HeLLOs), a novel human organoid model with mature hepatocyte functions superior to existing models. HeLLOs are easily established from (small) healthy or diseased liver tissues and rapidly expanded for an extended period in optimized culture conditions. Transcriptomic and functional analyses revealed that differentiated HeLLOs closely resemble fresh primary human hepatocytes (PHHs) and perform key hepatic functions such as gluconeogenesis, drug metabolism, and bile acid synthesis. We developed a HeLLO-based toxicity assay with higher sensitivity in predicting liver toxicity of known liver-toxic drugs compared to the gold-standard PHHs. By modeling disease-related mechanisms, such as bile acid transport, HeLLOs uncover transport-inhibition toxicity mechanisms of known liver toxic drugs. Single cell sequencing analysis of HeLLOs identified a heterogeneous cluster of cells with cholangiocyte-like and hepatocyte-like cells, overall resembling liver regenerative cells. As such, HeLLOs hold great promise for advancing liver disease modeling and drug testing. To our knowledge, HeLLOs are the best expandable liver model for predicting adverse drug reactions as well as modeling various liver disease mechanisms.}, + author = {Ardisasmita, AI and Joore, IP and Levy, N and Myszczyszyn, A and Marsee, A and Sinnige, T and Ruiter, J and Ferdinandusse, S and Dudaryeva, O and Gruber, E and Daive, V and Levato, R and Spee, B and Verstegen, M.M.A. and van der Laan, L.J.W. and Nieuwenhuis, EES and Schene, IF and Fuchs, SA}, + doi = {10.1101/2024.10.29.620824}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Novel hepatocyte-like liver organoids recapitulate crucial mature hepatic functions}, + url = {http://europepmc.org/abstract/PPR/PPR932234}, + year = {2024} +} + @article{argenta_american_2024, abstract = {American lobsters (Homarus americanus) stored in open tidal pounds can develop impoundment shell disease (ISD), resulting in decreased marketability of the lobsters on the live market. Little is known about ISD or the immunological responses of lobsters exhibiting this disease. The objective of this project was to identify genes from H. americanus hepatopancreas that are differentially expressed in response to ISD. Lobsters were separated into asymptomatic, moderately symptomatic, and severely symptomatic groups, which represent animals with 0\%, 5\%–20\%, and {\textgreater}20\% lesion coverage of the carapace, respectively. RNA-seq analysis found that 134 genes were differentially expressed between groups (false discovery rate (FDR) {\textless} 0.05). Most, 80, of these genes were found exclusively in the comparison between moderately symptomatic and asymptomatic groups. All animals clustered in their proposed groups based on the expression of the differently expressed genes (DEGs), and the asymptomatic group clustered as an out-group. The expression of most DEGs was higher in the asymptomatic group than the others, which could be related to a stronger response against the disease or differences in individual resistance against ISD development. Among these genes, we highlight eight chitin-related genes, one α-2-macroglobulin-like gene, one acute phase serum amyloid A gene, one pseudohaemocyanin gene, and one trypsin-1-like gene.}, author = {Argenta, Nicolas and Rampaul, Marianna and Clark, K. Fraser}, @@ -782,6 +1203,40 @@ @article{argenta_american_2024 year = {2024} } +@article{aribisala_cheminformatics_2022, + abstract = {The spike protein (SP) of SARS-CoV-2 (SC-2) is susceptible to high mutation and has contributed to the multiple waves of COVID-19 being experienced. Hence, targeting the SP remains a logical approach in the development of potent therapeutics against SARS-CoV-2. Here, a computational technique was adopted to identify broad-spectrum plant secondary metabolites with indigenous relevance in the management of respiratory infections against the SPs of the SC-2 wild- type (SC-2WT) and omicron variants. Following 100 ns molecular dynamic (MD) simulation and binding free energy calculation of the top five compounds identified through molecular docking, maysin (SC-2WT (-34.85 kcal/mol), omicron (-38.88 kcal/mol)) and geraniin (SC-2WT (-36.90 kcal/mol) omicron (-31.28 kcal/mol)) had better broad-spectrum activities for the investigated SPs than zafirlukast (SC-2WT (-33.73 kcal/mol) omicron (-22.38 kcal/mol)). Furthermore, 6-hydroxycyanidin-3-rutinoside (-42.97 kcal/mol) and kaempferol-7-glucoside (-37.11 kcal/mol) had the best affinity for the SPs of omicron and SC-2WT, respectively. Interestingly, except for Kaempferol-7-glucoside against omicron SP, all the top-ranked compounds were thermodynamically stable with the SP of both variants, and this observation was linked to the number, nature, and bond length in the resulting complexes in each case. Also, except for geraniin, all the top-ranked compounds had lower toxicity profiles compared to zafirlukast and this could be attributed to their phenolic moieties. Nevertheless, the in vitro and in vivo confirmation of the activities observed in this study is recommended, especially for maysin and geraniin with the best broad-spectrum activity, towards development of COVID-19 drug candidates.}, + author = {Aribisala, Jamiu Olaseni and Aruwa, Christiana Eleojo and Uthman, Taofik Olatunde and Nurain, Ismaila Olanrewaju and Idowu, Kehinde and Sabiu, Saheed}, + doi = {10.3390/metabo12100982}, + issn = {2218-1989}, + journal = {Metabolites}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {October}, + number = {10}, + pages = {982}, + title = {Cheminformatics {Bioprospection} of {Broad} {Spectrum} {Plant} {Secondary} {Metabolites} {Targeting} the {Spike} {Proteins} of {Omicron} {Variant} and {Wild}-{Type} {SARS}-{CoV}-2}, + url = {http://europepmc.org/abstract/MED/36295884}, + volume = {12}, + year = {2022} +} + +@article{aribisala_cheminformatics_2022-1, + abstract = {The acquisition of penicillin-binding protein (PBP) 2a in resistant strains of \textit{Staphylococcus aureus} allows for the continuous production of cell walls even after the inactivation of intrinsic PBPs. Thus, the discovery of novel therapeutics with enhanced modulatory activity on PBP2a is crucial, and plant secondary metabolites, such as phenolics, have found relevance in this regard. In this study, using computational techniques, phenolics were screened against the active site of PBP2a, and the ability of the lead phenolics to modulate PBP2a's active and allosteric sites was studied. The top-five phenolics (leads) identified through structure-activity-based screening, pharmacokinetics and synthetic feasibility evaluations were subjected to molecular dynamics simulations. Except for propan-2-one at the active site, the leads had a higher binding free energy at both the active and allosteric sites of PBP2a than amoxicillin. The leads, while promoting the thermodynamic stability of PBP2a, showed a more promising affinity at the allosteric site than the active site, with silicristin (-25.61 kcal/mol) and epicatechin gallate (-47.65 kcal/mol) having the best affinity at the active and allosteric sites, respectively. Interestingly, the modulation of Tyr446, the active site gatekeeper residue in PBP2a, was noted to correlate with the affinity of the leads at the allosteric site. Overall, these observations point to the leads' ability to inhibit PBP2a, either directly or through allosteric modulation with conventional drugs. Further confirmatory in vitro studies on the leads are underway.}, + author = {Aribisala, Jamiu Olaseni and Sabiu, Saheed}, + doi = {10.3390/pharmaceutics14091818}, + issn = {1999-4923}, + journal = {Pharmaceutics}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {August}, + number = {9}, + pages = {1818}, + title = {Cheminformatics {Identification} of {Phenolics} as {Modulators} of {Penicillin}-{Binding} {Protein} 2a of {Staphylococcus} aureus: {A} {Structure}-{Activity}-{Relationship}-{Based} {Study}}, + url = {http://europepmc.org/abstract/MED/36145565}, + volume = {14}, + year = {2022} +} + @article{aribisala_cheminformatics_2023, abstract = {Data implicating the mutation in penicillin-binding protein (PBP) 3 and occasionally PBP5 in the resistance of Escherichia coli to beta−lactams is intriguing. Thus, the identification of an improved class of inhibitors of PBP3 and PBP5 is imperative, and in this study, phenolics due to their promising antibacterial activities were screened using structure−based pharmacophore and molecular docking approaches against PBP3, and the ability of the lead phenolics to modulate PBP3 and PBP5 was studied using molecular dynamics simulation. The results demonstrated various inhibitory capacities of the lead phenolics, with lysidicichin (−41.66 kcal/mol) and silicristin (−31.11 kcal/mol) being the most potent against PBP3, while epicatechin 3-O-(3-O-methylgallate) (−38.97 kcal/mol) and epigallocatechin-4-benzyl thioether (−37.01 kcal/mol) had higher affinities towards PBP5. Overall, epicatechin gallate had the best broad-spectrum of activity, as the compound was able to bind favourably to both targets. Additionally, the thermodynamic information confirmed the stability of the lead phenolics with both targets. Conclusively, while these observations are suggestive of the modulatory role of the lead phenolics on the growth of E. coli, further in vitro and in vivo validation of the activity elicited by the phenolics in this study is imperative, and efforts are underway in this direction.}, author = {Aribisala, Jamiu Olaseni and Idowu, Kehinde and Makhanya, Talent Raymond and Sabiu, Saheed}, @@ -808,7 +1263,7 @@ @article{aribisala_silico_2024 doi = {10.1038/s41598-024-59489-3}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, Computational biology and bioinformatics, Drug discovery}, + keywords = {{\textgreater}UseGalaxy.eu, Amoxicillin, Computational biology and bioinformatics, Drug discovery, Streptococcus pneumoniae}, language = {en}, month = {April}, note = {Publisher: Nature Publishing Group}, @@ -821,16 +1276,35 @@ @article{aribisala_silico_2024 year = {2024} } +@misc{arif_transcriptome_2025, + abstract = {Frontotemporal dementia (FTD) is a neurodegenerative disorder characterised by impaired behaviour and language. It affects individuals between 45 and 65 years of age. The present study aims to identify potential phytochemicals against target receptor of FTD. Transcriptome data analysis guided computer-aided drug design (CADD) was conducted to investigate molecular interactions between active phytochemicals present in Indian spices and differentially expressed genes. In present study, samples for patients with FTD were obtained from GEO dataset [GSE92340]. The samples were pre-processed followed by differential gene expression analysis using DESeq2. The patient sample was analyzed for 1882 upregulated genes. Hub gene out of DEGs was identified using CytoHubba Plugin of Cytoscape based on eleven parameters (Degree, Edge Percolated Component (EPC), Maximum Neighbourhood Component (MNC), Density of Maximum Neighbourhood Component (DMNC), Maximal Clique Centrality (MCC), Bottleneck, EcCentricity, Closeness, Radiality, Betweenness, and Stress). HDAC1 gene was identified as hub gene and key target in case of FTD. CADD pipeline was used to identify phytochemicals against HDAC1 gene. A list of eighty-one phytochemicals found in Indian spices was analyzed for their drug likeness abilities using molinspiration and toxicity prediction using ProTox-II, which identified twenty-three phytochemicals as safe drug-like compounds. PatchDock was employed to examine interactions between phytochemical compounds and HDAC1. Molecular interactions revealed rosmarinic acid derived from rosemary (Salvia rosmarinus) as the most effective drug for FTD having lowest ACE value of −395 kcal/mol. In conclusion, this study demonstrates essential role of HDAC1 in pathogenesis of FTD and demonstrates the neuroprotective potential of rosmarinic acid against FTD.}, + author = {Arif, Amaan and Garg, Prekshi and Srivastava, Prachi}, + copyright = {© 2025, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/}, + doi = {10.1101/2025.09.05.674389}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {September}, + note = {ISSN: 2692-8205 +Pages: 2025.09.05.674389 +Section: New Results}, + publisher = {bioRxiv}, + title = {Transcriptome {Network} {Biology} {Reveals} the {Neuroprotective} {Potential} of {Rosmarinic} {Acid} {Against} {Frontotemporal} {Dementia}}, + url = {https://www.biorxiv.org/content/10.1101/2025.09.05.674389v2}, + urldate = {2025-10-02}, + year = {2025} +} + @article{arlat_generation_2024, abstract = {{\textless}sec{\textgreater}{\textless}title{\textgreater}Introduction{\textless}/title{\textgreater}{\textless}p{\textgreater}Within adipose tissue (AT), different macrophage subsets have been described, which played pivotal and specific roles in upholding tissue homeostasis under both physiological and pathological conditions. Nonetheless, studying resident macrophages {\textless}italic{\textgreater}in-vitro{\textless}/italic{\textgreater} poses challenges, as the isolation process and the culture for extended periods can alter their inherent properties.{\textless}/p{\textgreater}{\textless}/sec{\textgreater}{\textless}sec{\textgreater}{\textless}title{\textgreater}Methods{\textless}/title{\textgreater}{\textless}p{\textgreater}Stroma-vascular cells isolated from murine subcutaneous AT were seeded on ultra-low adherent plates in the presence of macrophage colony-stimulating factor. After 4 days of culture, the cells spontaneously aggregate to form spheroids. A week later, macrophages begin to spread out of the spheroid and adhere to the culture plate.{\textless}/p{\textgreater}{\textless}/sec{\textgreater}{\textless}sec{\textgreater}{\textless}title{\textgreater}Results{\textless}/title{\textgreater}{\textless}p{\textgreater}This innovative three-dimensional (3D) culture method enables the generation of functional mature macrophages that present distinct genic and phenotypic characteristics compared to bone marrow–derived macrophages. They also show specific metabolic activity and polarization in response to stimulation, but similar phagocytic capacity. Additionally, based on single-cell analysis, AT-macrophages generated in 3D culture mirror the phenotypic and functional traits of {\textless}italic{\textgreater}in-vivo{\textless}/italic{\textgreater} AT resident macrophages.{\textless}/p{\textgreater}{\textless}/sec{\textgreater}{\textless}sec{\textgreater}{\textless}title{\textgreater}Discussion{\textless}/title{\textgreater}{\textless}p{\textgreater}Our study describes a 3D {\textless}italic{\textgreater}in-vitro{\textless}/italic{\textgreater} system for generating and culturing functional AT-resident macrophages, without the need for cell sorting. This system thus stands as a valuable resource for exploring the differentiation and function of AT-macrophages {\textless}italic{\textgreater}in vitro{\textless}/italic{\textgreater} in diverse physiological and pathological contexts.{\textless}/p{\textgreater}{\textless}/sec{\textgreater}}, author = {Arlat, Adèle and Renoud, Marie-Laure and Nakhle, Jean and Thomas, Miguel and Fontaine, Jessica and Arnaud, Emmanuelle and Dray, Cédric and Authier, Hélène and Monsarrat, Paul and Coste, Agnès and Casteilla, Louis and Ousset, Marielle and Cousin, Béatrice}, doi = {10.3389/fimmu.2024.1356397}, issn = {1664-3224}, journal = {Frontiers in Immunology}, - keywords = {3D culture, {\textgreater}UseGalaxy.eu, Adipose Tissue, Bone Marrow, Metabolism, Phagocytosis, Resident macrophage, macrophage subpopulation}, + keywords = {3D culture, {\textgreater}UseGalaxy.eu, Adipose Tissue, Bone Marrow, Cell Culture Techniques, Three Dimensional, Cell Differentiation, Macrophages, Metabolism, Phagocytosis, Resident macrophage, macrophage subpopulation}, language = {English}, month = {June}, note = {Publisher: Frontiers}, + pages = {1356397}, title = {Generation of functionally active resident macrophages from adipose tissue by {3D} cultures}, url = {https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1356397/full}, urldate = {2024-10-20}, @@ -872,6 +1346,7 @@ @article{arshad_comparative_2024 abstract = {Abstract. Arshad A, Aditama R, Rahayu MS, Natawijaya A, Matra DD, Sudarsono S. 2024. Comparative study of chloroplast genomes across seven Salacca species. Biodiversitas 25: 4043-4058. Chloroplast (Cp) genomes play a vital role in comprehending plant evolution, biodiversity, and phylogenetics. Snake fruit is a tropical fruit in the Indo-Malayan region. This work compares seven Salacca species Cp genomes to clarify their genetics and evolutionary connections. Cp genomes were constructed using sequencing data from the BGISeq-500 platform and the GetOrganelle assemblers. The assembled Cp genomes have a standard four-part structure and vary in length from 157,047 to 158,182 kilobase pairs (kbp). Comparative genomics analysis found the ycf1 gene to have the highest number of single nucleotide polymorphisms (SNPs), revealing missing amino acids in Salacca affinis. The Cp genomes showed a high prevalence of mononucleotide SSR motifs. With a few exceptions, especially Salacca wallichiana, most Cp genomes showed stable borders between the large single copy (LSC), inverted repeat (IR), and short single copy (SSC) sections. This research underscores the importance of Cp genome information for identifying species, a crucial tool for evolutionary studies and breeding purposes. Furthermore, it emphasizes the intimate genetic connection between Salacca and Cocos nucifera, which contrasts with Phoenix dactylifera. This thorough research provides vital insights into the genetics of Salacca species and highlights the usefulness of Cp genome data in subsequent analyses.}, author = {Arshad, Arslan and Aditama, Redi and Rahayu, Megayani Sri and Natawijaya, Azis and Matra, Deden Deradjat and Sudarsono, Sudarsono}, copyright = {Copyright (c) 2024 Biodiversitas Journal of Biological Diversity}, + doi = {10.13057/biodiv/d251104}, issn = {2085-4722}, journal = {Biodiversitas Journal of Biological Diversity}, keywords = {{\textgreater}UseGalaxy.eu}, @@ -886,11 +1361,55 @@ @article{arshad_comparative_2024 year = {2024} } +@article{aruwa_staphylococcus_2025, + abstract = {South African plants are an underutilized metabolites source for novel antimicrobials targeting key quorum sensing (QS) systems like the Staphylococcus aureus AgrA. AgrA modulating metabolites constitute a new approach to reducing resistance development. This study created a library of 1211 metabolites from 266 South African plants with antimicrobial action. Metabolites’ anti-QS activities were assessed using advanced computational methods. Molecular docking showed 5 top metabolites (hinokiflavone, asphodelin, elliptinone, mamegakinone, robustaflavone). Most leads conformed to the Lipinski’s rule of 5. Dynamics simulation revealed closest ∆Gbind for robustaflavone (-25.50 kcal/mol), and hinokiflavone (-20.94 kcal/mol) compared to the standard (-26.59 kcal/mol). Leads interacted with key residues (Asn62/201, Asp75/214, Arg94/233, Asn95/234) and high number of interactions that ensured thermodynamic stability and compactness. The identified leads could be key mechanistic contributors to the antimicrobial activity of their inherent plants. Both the plants and metabolites (robustaflavone, hinokiflavone) could be further explored following structural modification as QS inhibitors.}, + author = {Aruwa, Christiana Eleojo and Sabiu, Saheed}, + copyright = {© 2025 Wiley-VCH GmbH}, + doi = {10.1002/cbdv.202403220}, + issn = {1612-1880}, + journal = {Chemistry \& Biodiversity}, + keywords = {{\textgreater}UseGalaxy.eu, AgrA, Antisense, Dynamics simulation, Fingerprinting, Virtual screening}, + language = {en}, + month = {April}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cbdv.202403220}, + number = {n/a}, + pages = {e202403220}, + title = {Staphylococcus {Aureus} {AgrA} {Modulators} from {South} {African} {Antimicrobial} {Plants}.}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cbdv.202403220}, + urldate = {2025-04-21}, + volume = {n/a}, + year = {2025} +} + +@article{asadi_exploring_2025, + abstract = {Rhynchosporium commune is a fungal pathogen responsible for causing scald disease in barley, leading to significant yield losses and reduced grain quality in susceptible cultivars. Effector proteins secreted by R. commune play crucial roles in manipulating host defenses and facilitating infection. Hence, this study aimed to identify and characterize effector candidates (ECs) in R. commune using a comprehensive bioinformatics approach combined with experimental validation. Initially, a dataset of 12,211 genes from the R. commune strain UK7 genome was analyzed to identify potential ECs, resulting in the selection of 48 candidate proteins. These candidates were further validated using RNA-Seq analysis, which confirmed significant expression of 27 ECs during infection. Our analysis re-identified key effectors, including CZT06923 and CZT13833, with 100\% identity to NIP3 and NIP2, respectively, in R. commune. Novel ECs, such as CZT07600, CZT13755, and CZT13375, were identified with lower identity to NIP2, suggesting potential variants. Additionally, structural analysis revealed that CZT07873 EC indicates significant structural similarity to known fungal effector. qRT-PCR validation confirmed the differential expression of CZS93219 and CZT13755, with peak expression at 9 and 12 dpi, respectively. This comprehensive approach enhances our understanding of R. commune’s pathogenic mechanisms and provides insights into potential targets for developing disease management strategies in barley cultivation.}, + author = {Asadi, Samin and Soorni, Aboozar and Mehrabi, Rahim and Talebi, Majid}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-02572-0}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Ascomycota, Fungal Proteins, Fungal genetics, Fungal pathogenesis, Gene Expression Regulation, Fungal, Hordeum, Plant Diseases, Plant molecular biology}, + language = {en}, + month = {May}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {17667}, + shorttitle = {Exploring effector candidates in {Rhynchosporium} commune}, + title = {Exploring effector candidates in {Rhynchosporium} commune: insights into their expression dynamics during barley infection}, + url = {https://www.nature.com/articles/s41598-025-02572-0}, + urldate = {2025-05-28}, + volume = {15}, + year = {2025} +} + @article{ashrafi_two_2022, + abstract = {Root nodules of legume plants are primarily inhabited by rhizobial nitrogen-fixing bacteria. Here, we propose two new \textit{Rhizobiales} species isolated from root nodules of common sainfoin (Onobrychis viciifolia), as shown by core-gene phylogeny, overall genome relatedness indices, and pan-genome analysis. Mesorhizobium onobrychidis sp. nov. actively induces nodules and achieves atmospheric nitrogen and carbon dioxide fixation. This species appears to be depleted in motility genes and is enriched in genes for direct effects on plant growth performance. Its genome reveals functional and plant growth-promoting signatures, like a large unique chromosomal genomic island with high density of symbiotic genetic traits. Onobrychidicola muellerharveyae gen. nov. sp. nov. is described as a type species of the new genus \textit{Onobrychidicola} in \textit{Rhizobiaceae}. This species comprises unique genetic features and plant growth-promoting traits (PGPTs), which strongly indicate its function in biotic stress reduction and motility. We applied a newly developed bioinformatics approach for \textit{in silico} prediction of PGPTs (PGPT-Pred), which supports the different lifestyles of the two new species and the plant growth-promoting performance of M. onobrychidis in the greenhouse trial. \textbf{IMPORTANCE} The intensive use of chemical fertilizers has a variety of negative effects on the environment. Increased utilization of biological nitrogen fixation (BNF) is one way to mitigate those negative impacts. In order to optimize BNF, suitable candidates for different legume species are required. Despite intensive search for new rhizobial bacteria associated with legumes, no new rhizobia have recently been identified from sainfoin (Onobrychis viciifolia). Here, we report on the discovery of two new rhizobial species associated with sainfoin, which are of high importance for the host and may help to increase sustainability in agricultural practices. We employed the combination of \textit{in silico} prediction and \textit{in planta} experiments, which is an effective way to detect promising plant growth-promoting bacteria.}, author = {Ashrafi, Samad and Kuzmanović, Nemanja and Patz, Sascha and Lohwasser, Ulrike and Bunk, Boyke and Spröer, Cathrin and Lorenz, Maria and Elhady, Ahmed and Frühling, Anja and Neumann-Schaal, Meina and Verbarg, Susanne and Becker, Matthias and Thünen, Torsten}, doi = {10.1128/spectrum.01099-22}, + issn = {2165-0497}, journal = {Microbiology Spectrum}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Fabaceae, Mesorhizobium, Rhizobium}, + language = {eng}, month = {August}, note = {Publisher: American Society for Microbiology}, number = {0}, @@ -902,12 +1421,28 @@ @article{ashrafi_two_2022 year = {2022} } -@article{asiri_-silico_2024, - abstract = {Background: Lung carcinoma has become one of the most noteworthy and dangerous health problems discovered today. The disease is mainly caused by smoking and becomes among the leading causes of death spread by growing the cancerous cells into the lining of the lungs and nearby lobes. The FDA has given clearance to numerous drugs and chemotherapy agents; nevertheless, they can be exceedingly costly as well as frequently fall short of entirely addressing the ailment. In the medical management of lung cancer, new medicines or active leads with high efficacy and minimal toxicity are required in this era.Methods: The study has been conducted with the intent to uncover a prospective approach to treating lung cancer through structural modification of Hesperetin by creating its analogs to enhance its efficacy compared to its parent compound with the computational drug design. The analysis has been conducted with various approaches followed by PASS prediction, ADME, toxicity profile, molecular docking, data filtration, and anticancer activity.Results: All the compounds showed satisfactory criteria in each parameter that was assessed. The data mining was done carefully by pointing out the compounds that had the greatest value among all the compounds in each investigation, which resulted in a total of 3 compounds out of 50. Conclusions: Finally, the selected compounds were further analyzed for MD simulation studies. Afterward, PCA analysis was also conducted in order to get the lead compound with this additional investigation.Keywords: Lung cancer; Anti-cancer lead; Hesperetin; Drug designing; Molecular docking; MD simulation; PCA}, - author = {Asiri, Abdulaziz}, - copyright = {Copyright (c) 2024 Advancements in Life Sciences}, - doi = {10.62940/als.v11i4.3308}, - issn = {2310-5380}, +@article{asif_whole-genome_2021, + abstract = {Fowlpox (FP) is an economically important viral disease of commercial poultry. The fowlpox virus (FPV) is primarily characterised by immunoblotting, restriction enzyme analysis in combination with PCR, and/or nucleotide sequencing of amplicons. Whole-genome sequencing (WGS) of FPV directly from clinical specimens prevents the risk of potential genome modifications associated with in vitro culturing of the virus. Only one study has sequenced FPV genomes directly from clinical samples using Nanopore sequencing, however, the study didn't compare the sequences against Illumina sequencing or laboratory propagated sequences. Here, the suitability of WGS for strain identification of FPV directly from cutaneous tissue was evaluated, using a combination of Illumina and Nanopore sequencing technologies. Sequencing results were compared with the sequence obtained from FPV grown in chorioallantoic membranes (CAMs) of chicken embryos. Complete genome sequence of FPV was obtained directly from affected comb tissue using a map to reference approach. FPV sequence from cutaneous tissue was highly similar to that of the virus grown in CAMs with a nucleotide identity of 99.8\%. Detailed polymorphism analysis revealed the presence of a highly comparable number of single nucleotide polymorphisms (SNPs) in the two sequences when compared to the reference genome, providing essentially the same strain identification information. Comparative genome analysis of the map to reference consensus sequences from the two genomes revealed that this field isolate had the highest nucleotide identity of 99.5\% with an FPV strain from the USA (Fowlpox virus isolate, FWPV-MN00.2, MH709124) and 98.8\% identity with the Australian FPV vaccine strain (FWPV-S, MW142017). Sequencing results showed that WGS directly from cutaneous tissues is not only rapid and cost-effective but also provides essentially the same strain identification information as in-vitro grown virus, thus circumventing in vitro culturing.}, + author = {Asif, Kinza and O'Rourke, Denise and Legione, Alistair R and Shil, Pollob and Marenda, Marc S and Noormohammadi, Amir H}, + doi = {10.1371/journal.pone.0261122}, + issn = {1932-6203}, + journal = {PloS one}, + keywords = {{\textgreater}UseGalaxy.eu, Genome, Viral}, + language = {eng}, + number = {12}, + pages = {e0261122}, + title = {Whole-genome based strain identification of fowlpox virus directly from cutaneous tissue and propagated virus}, + url = {http://europepmc.org/abstract/MED/34914770}, + volume = {16}, + year = {2021} +} + +@article{asiri_-silico_2024, + abstract = {Background: Lung carcinoma has become one of the most noteworthy and dangerous health problems discovered today. The disease is mainly caused by smoking and becomes among the leading causes of death spread by growing the cancerous cells into the lining of the lungs and nearby lobes. The FDA has given clearance to numerous drugs and chemotherapy agents; nevertheless, they can be exceedingly costly as well as frequently fall short of entirely addressing the ailment. In the medical management of lung cancer, new medicines or active leads with high efficacy and minimal toxicity are required in this era.Methods: The study has been conducted with the intent to uncover a prospective approach to treating lung cancer through structural modification of Hesperetin by creating its analogs to enhance its efficacy compared to its parent compound with the computational drug design. The analysis has been conducted with various approaches followed by PASS prediction, ADME, toxicity profile, molecular docking, data filtration, and anticancer activity.Results: All the compounds showed satisfactory criteria in each parameter that was assessed. The data mining was done carefully by pointing out the compounds that had the greatest value among all the compounds in each investigation, which resulted in a total of 3 compounds out of 50. Conclusions: Finally, the selected compounds were further analyzed for MD simulation studies. Afterward, PCA analysis was also conducted in order to get the lead compound with this additional investigation.Keywords: Lung cancer; Anti-cancer lead; Hesperetin; Drug designing; Molecular docking; MD simulation; PCA}, + author = {Asiri, Abdulaziz}, + copyright = {Copyright (c) 2024 Advancements in Life Sciences}, + doi = {10.62940/als.v11i4.3308}, + issn = {2310-5380}, journal = {Advancements in Life Sciences}, keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, @@ -922,6 +1457,22 @@ @article{asiri_-silico_2024 year = {2024} } +@article{askari_new_2022, + abstract = {SARS-CoV-2 is the RNA virus responsible for COVID-19, the prognosis of which has been found to be slightly worse in men. The present study aimed to analyze the expression of different mRNAs and their regulatory molecules (miRNAs and lncRNAs) to consider the potential existence of sex-specific expression patterns and COVID-19 susceptibility using bioinformatics analysis. The binding sites of all human mature miRNA sequences on the SARS-CoV-2 genome nucleotide sequence were predicted by the miRanda tool. Sequencing data was excavated using the Galaxy web server from GSE157103, and the output of feature counts was analyzed using DEseq2 packages to obtain differentially expressed genes (DEGs). Gene set enrichment analysis (GSEA) and DEG annotation analyses were performed using the ToppGene and Metascape tools. Using the RNA Interactome Database, we predicted interactions between differentially expressed lncRNAs and differentially expressed mRNAs. Finally, their networks were constructed with top miRNAs. We identified 11 miRNAs with three to five binding sites on the SARS-COVID-2 genome reference. MiR-29c-3p, miR-21-3p, and miR-6838-5p occupied four binding sites, and miR-29a-3p had five binding sites on the SARS-CoV-2 genome. Moreover, miR-29a-3p, and miR-29c-3p were the top miRNAs targeting DEGs. The expression levels of miRNAs (125, 181b, 130a, 29a, b, c, 212, 181a, 133a) changed in males with COVID-19, in whom they regulated ACE2 expression and affected the immune response by affecting phagosomes, complement activation, and cell-matrix adhesion. Our results indicated that XIST lncRNA was up-regulated, and TTTY14, TTTY10, and ZFY-AS1 lncRN as were down-regulated in both ICU and non-ICU men with COVID-19. Dysregulation of noncoding-RNAs has critical effects on the pathophysiology of men with COVID-19, which is why they may be used as biomarkers and therapeutic agents. Overall, our results indicated that the miR-29 family target regulation patterns and might become promising biomarkers for severity and survival outcome in men with COVID-19.}, + author = {Askari, Nahid and Hadizadeh, Morteza and Rashidifar, Maryam}, + doi = {10.1016/j.meegid.2021.105195}, + issn = {1567-1348}, + journal = {Infect Genet Evol}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {January}, + pages = {105195}, + title = {A new insight into sex-specific non-coding {RNAs} and networks in response to {SARS}-{CoV}-2}, + url = {http://europepmc.org/abstract/MED/34954105}, + volume = {97}, + year = {2022} +} + @article{atac_identification_2024, abstract = {The proneural transcription factor atonal basic helix–loop–helix transcription factor 7 (ATOH7) is expressed in early progenitors in the developing neuroretina. In vertebrates, this is crucial for the development of retinal ganglion cells (RGCs), as mutant animals show an almost complete absence of RGCs, underdeveloped optic nerves, and aberrations in retinal vessel development. Human mutations are rare and result in autosomal recessive optic nerve hypoplasia (ONH) or severe vascular changes, diagnosed as autosomal recessive persistent hyperplasia of the primary vitreous (PHPVAR). To better understand the role of ATOH7 in neuroretinal development, we created ATOH7 knockout and eGFP-expressing ATOH7 reporter human induced pluripotent stem cells (hiPSCs), which were differentiated into early-stage retinal organoids. Target loci regulated by ATOH7 were identified by Cleavage Under Targets and Release Using Nuclease with sequencing (CUT\&RUN-seq) and differential expression by RNA sequencing (RNA-seq) of wildtype and mutant organoid-derived reporter cells. Additionally, single-cell RNA sequencing (scRNA-seq) was performed on whole organoids to identify cell type-specific genes. Mutant organoids displayed substantial deficiency in axon sprouting, reduction in RGCs, and an increase in other cell types. We identified 469 differentially expressed target genes, with an overrepresentation of genes belonging to axon development/guidance and Notch signaling. Taken together, we consolidate the function of human ATOH7 in guiding progenitor competence by inducing RGC-specific genes while inhibiting other cell fates. Furthermore, we highlight candidate genes responsible for ATOH7-associated optic nerve and retinovascular anomalies, which sheds light to potential future therapy targets for related disorders.}, author = {Atac, David and Maggi, Kevin and Feil, Silke and Maggi, Jordi and Cuevas, Elisa and Sowden, Jane C. and Koller, Samuel and Berger, Wolfgang}, @@ -929,7 +1480,7 @@ @article{atac_identification_2024 doi = {10.3390/cells13131142}, issn = {2073-4409}, journal = {Cells}, - keywords = {{\textgreater}UseGalaxy.eu, ATOH7, CUT\&RUN sequencing, RNA sequencing, retinal development, retinal ganglion cells, retinal organoids, retinal progenitor cells, scRNA sequencing}, + keywords = {{\textgreater}UseGalaxy.eu, ATOH7, Basic Helix-Loop-Helix Transcription Factors, CUT\&RUN sequencing, Induced Pluripotent Stem Cells, RNA sequencing, Retina, retinal development, retinal ganglion cells, retinal organoids, retinal progenitor cells, scRNA sequencing}, language = {en}, month = {January}, note = {Number: 13 @@ -964,13 +1515,88 @@ @article{atxaerandio-landa_practical_2022 year = {2022} } +@article{aurelle_erga-bge_2025, + abstract = {The +Eunicella cavolini +reference genome provides an important resource to study the adaptation of this species to different environments and anthropic pressures. This species is impacted by human activities, including climate change, and this reference genome will be useful to study the genomic evolution of this species. The entirety of the genome sequence was assembled into 17 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 0.49 Gb, composed of 159 contigs and 46 scaffolds, with contig and scaffold N50 values of 7.7 Mb and 51.1 Mb, respectively.}, + author = {Aurelle, Didier and Guillemain, Dorian and Zuberer, Frédéric and Malengros, Denys and Böhne, Astrid and Monteiro, Rita and Marcussen, Thomas and Struck, Torsten H. and A. Oomen, Rebekah and {Genoscope Sequencing Team} and Moussy, Alice and Cruaud, Corinne and Labadie, Karine and Demirdjian, Lola and Belser, Caroline and Wincker, Patrick and H. Oliveira, Pedro and Aury, Jean-Marc and Bortoluzzi, Chiara}, + doi = {10.12688/openreseurope.21514.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {October}, + pages = {323}, + title = {{ERGA}-{BGE} reference genome of {Eunicella} cavolini, an {IUCN} {Near} {Threatened} {Gorgonian} of the {Mediterranean} {Sea}}, + url = {https://open-research-europe.ec.europa.eu/articles/5-323/v1}, + urldate = {2025-10-25}, + volume = {5}, + year = {2025} +} + +@article{bacchetti_investigating_2025, + abstract = {Cryptosporidium parvum is a zoonotic protozoan parasite of human and veterinary public health concern that causes gastrointestinal disease. Animal contact is a major risk factor for C. parvum outbreaks which require thorough investigation through the use of molecular subtyping. Recently, a multi-locus variable-number tandem repeat analysis (MLVA) scheme was established for C. parvum, offering improved subtyping resolution compared to the commonly used single-locus 60 kDa glycoprotein gene (gp60) subtyping approach. Using the C. parvum MLVA scheme, the genetic diversity of known gp60 subtyped faecal DNA extracts collected between April 1st 2023 and March 31st 2024 was explored. A representative group of a common Scottish gp60 subtype (IIaA15G2R1, n = 28) was analysed by MLVA and found to consist of 8 distinct complete MLVA profiles, with 4-12-5-7-27-36-16 (n = 12) being the most common. Genetic diversity within samples involved in three historic animal contact outbreaks (Outbreaks A, B and C) was investigated. Outbreak A, involving a single gp60 subtype (IIaA19G1R1), consisted of only one MLVA profile (4-12-5-8-27-15-17). Outbreak B was caused by two gp60 subtypes (IIaA17G1R1 and IIaA15G2R1), which were further subdivided into four MLVA profiles, two per gp60 subtype (4-14-4-7-27-37-15 and 4-14-5-7-27-27-15, and 4-13-4-8-27-31-17 and 4-12-5-7-27-42-16, respectively). Lastly, Outbreak C, thought to have two-point sources of infection, involved one gp60 subtype (IIaA15G2R1), which was subdivided into four distinct MLVA profiles (4-12-5-7-27-36-16, 4-12-5-7-27-32-15, 4-12-5-7-27-30-15, and 4-14-5-7-36-33-15). Improved MLVA resolution allowed outbreak specimens with insufficient epidemiological data to be linked to a source through sharing a common MLVA profile.}, + author = {Bacchetti, Ross and McCormack, Paula and Connelly, Lisa and Brown, Derek J and Chaput, Dominique L and Alexander, Claire L}, + copyright = {cc by}, + doi = {10.1016/j.crpvbd.2025.100332}, + issn = {2667-114X}, + journal = {Current research in parasitology \& vector-borne diseases}, + keywords = {{\textgreater}UseGalaxy.eu, Gp60, Mlva, Outbreak Investigation, Subtyping, cryptosporidium parvum}, + language = {eng}, + month = {January}, + pages = {100332}, + pmcid = {PMC12639845}, + pmid = {41282434}, + title = {Investigating genetic diversity within \<i\>{Cryptosporidium} parvum\</i\> outbreaks using multi-locus variable number tandem repeat analysis}, + url = {https://europepmc.org/articles/PMC12639845}, + urldate = {2025-12-26}, + volume = {8}, + year = {2025} +} + +@article{bader_phylogenetic_2021, + abstract = {In Aspergillus fumigatus, the repetitive region of the \textit{csp1} gene is one of the most frequently used loci for intraspecies typing of this human pathogenic mold. Using PCR amplification and Sanger sequencing of only a single marker, \textit{csp1} typing is readily available to most laboratories and highly reproducible. Here, I evaluate the usefulness of the \textit{csp1} marker for resistance detection and epidemiologic stratification among A. fumigatus isolates. After resolving nomenclature conflicts from published studies and adding novel \textit{csp1} types, the number of known types now adds up to 38. Their distribution mostly correlates with A. fumigatus population structure, and they are also meaningful for narrowly defined cases of azole resistance phenotypes. Isolates carrying the pandemic resistance allele TR$_{\textrm{34}}$/L98H show signs of interclade crossing of strains with t02 or t04A, into the t11 clade. Furthermore, absolute differences in voriconazole MIC values between t02/t04B versus t11 TR$_{\textrm{34}}$/L98H isolates indicate that the genetic background of resistance mutations may have a pivotal role in cross-resistance phenotypes and, thus, clinical outcome and environmental selection. Despite the general genetic similarity of isolates with identical \textit{csp1} types, outcrossing into other clades is also observed. The \textit{csp1} type alone, therefore, does not sufficiently discriminate genetic clades to be used as the sole marker in epidemiologic studies. \textbf{IMPORTANCE} Aspergillus fumigatus is a ubiquitously distributed saprophytic mold and a leading cause of invasive aspergillosis in human hosts. Pandemic azole-resistant strains have emerged on a global scale, which are thought to be propagated through use of azole-based fungicides in agriculture. To perform epidemiologic studies, genetic typing of large cohorts is key. Here, I evaluate the usefulness of the frequently used \textit{csp1} marker for resistance detection and epidemiologic stratification among A. fumigatus isolates. The phylogenetic distribution of \textit{csp1} types mostly correlates with A. fumigatus population structure and is also meaningful for narrowly defined cases of azole resistance phenotypes. Nevertheless, outcrossing of \textit{csp1} into other clades is also observed. The \textit{csp1} type alone, therefore, does not sufficiently discriminate genetic clades and should not be used as the sole marker in epidemiologic studies.}, + author = {Bader, Oliver}, + doi = {10.1128/spectrum.01214-21}, + issn = {2165-0497}, + journal = {Microbiol Spectr}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {December}, + number = {3}, + pages = {e0121421}, + title = {Phylogenetic {Distribution} of csp1 {Types} in {Aspergillus} fumigatus and {Their} {Correlates} to {Azole} {Antifungal} {Drug} {Resistance}}, + url = {http://europepmc.org/abstract/MED/34787484}, + volume = {9}, + year = {2021} +} + +@article{baei_pharmacophore_2025, + abstract = {Due to its global burden, Targeting Hepatitis B virus (HBV) infection in humans is crucial. Herbal medicine has long been significant, with flavonoids demonstrating promising results. Hence, the present study aimed to establish a way of identifying flavonoids with anti-HBV activities. Flavonoid structures with anti-HBV activities were retrieved. A flavonol-based pharmacophore model was established using LigandScout v4.4. Screening was performed using the PharmIt server. A QSAR equation was developed and validated with independent sets of compounds. The applicability domain (AD) was defined using Euclidean distance calculations for model validation. The best model, consisting of 57 features, was generated. High-throughput screening (HTS) using the flavonol-based model resulted in 509 unique hits. The model’s accuracy was further validated using a set of FDA-approved chemicals, demonstrating a sensitivity of 71\% and a specificity of 100\%. Additionally, the QSAR model with two predictors, x4a and qed, exhibited predictive solid performance with an adjusted-R2 value of 0.85 and 0.90 of Q2. PCA showed essential patterns and relationships within the dataset, with the first two components explaining nearly 98\% of the total variance. Current HBV therapies tend to fail to provide a complete cure, emphasizing the need for new therapies. This study’s importance was to highlight flavonols as potential anti-HBV medicines, presenting a supplementary option for existing therapy. The QSAR model has been validated with two separate chemical sets, guaranteeing its reproducibility and usefulness for other flavonols by utilizing the predictive characteristics of X4A and qed. These results provide new possibilities for discovering future anti-HBV drugs by integrating modeling and experimental research.}, + author = {Baei, Basireh and Askari, Parnia and Askari, Fatemeh Sana and Kiani, Seyed Jalal and Mohebbi, Alireza}, + doi = {10.1371/journal.pone.0316765}, + issn = {1932-6203}, + journal = {PLOS ONE}, + keywords = {{\textgreater}ChemicalToolbox, {\textgreater}UseGalaxy.eu, Antiviral Agents, Antiviral therapy, Drug discovery, Drug research and development, Drug screening, Flavonols, Hepatitis B virus, High throughput screening, Library screening, Principal component analysis, Quantitative Structure-Activity Relationship}, + language = {en}, + month = {January}, + note = {Publisher: Public Library of Science}, + number = {1}, + pages = {e0316765}, + title = {Pharmacophore modeling and {QSAR} analysis of anti-{HBV} flavonols}, + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0316765}, + urldate = {2025-01-19}, + volume = {20}, + year = {2025} +} + @article{bafna_dynamic_2023, abstract = {The mammalian suprachiasmatic nucleus (SCN), located in the ventral hypothalamus, synchronizes and maintains daily cellular and physiological rhythms across the body, in accordance with environmental and visceral cues. Consequently, the systematic regulation of spatiotemporal gene transcription in the SCN is vital for daily timekeeping. So far, the regulatory elements assisting circadian gene transcription have only been studied in peripheral tissues, lacking the critical neuronal dimension intrinsic to the role of the SCN as central brain pacemaker. By using histone-ChIP-seq, we identified SCN-enriched gene regulatory elements that associated with temporal gene expression. Based on tissue-specific H3K27ac and H3K4me3 marks, we successfully produced the first-ever SCN gene-regulatory map. We found that a large majority of SCN enhancers not only show robust 24-h rhythmic modulation in H3K27ac occupancy, peaking at distinct times of day, but also possess canonical E-box (CACGTG) motifs potentially influencing downstream cycling gene expression. To establish enhancer–gene relationships in the SCN, we conducted directional RNA-seq at six distinct times across the day and night, and studied the association between dynamically changing histone acetylation and gene transcript levels. About 35\% of the cycling H3K27ac sites were found adjacent to rhythmic gene transcripts, often preceding the rise in mRNA levels. We also noted that enhancers encompass noncoding, actively transcribing enhancer RNAs (eRNAs) in the SCN, which in turn oscillate, along with cyclic histone acetylation, and correlate with rhythmic gene transcription. Taken together, these findings shed light on genome-wide pretranscriptional regulation operative in the central clock that confers its precise and robust oscillation necessary to orchestrate daily timekeeping in mammals.}, author = {Bafna, Akanksha and Banks, Gareth and Hastings, Michael H. and Nolan, Patrick M.}, doi = {10.1101/gr.277581.122}, issn = {1088-9051, 1549-5469}, journal = {Genome Research}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Circadian Clocks}, language = {en}, month = {May}, pages = {genome;gr.277581.122v2}, @@ -986,7 +1612,7 @@ @article{bafna_harvesting_2023 doi = {10.1016/j.xpro.2023.102618}, issn = {2666-1667}, journal = {STAR Protocols}, - keywords = {{\textgreater}UseGalaxy.eu, Genetics, Model Organisms, Molecular Biology, Neuroscience}, + keywords = {{\textgreater}UseGalaxy.eu, Circadian Clocks, Circadian Rhythm, Genetics, Model Organisms, Molecular Biology, Neuroscience}, month = {December}, number = {4}, pages = {102618}, @@ -1040,7 +1666,7 @@ @article{baig_genome-wide_2023 doi = {10.1371/journal.pone.0286428}, issn = {1932-6203}, journal = {PLOS ONE}, - keywords = {{\textgreater}UseGalaxy.eu, Aspergillus, Aspergillus fumigatus, Fungal genetics, Fungal structure, Fusarium, Genome analysis, Protein structure, Protein structure prediction}, + keywords = {{\textgreater}UseGalaxy.eu, Ascomycota, Aspergillus, Aspergillus fumigatus, Aspergillus oryzae, Fungal genetics, Fungal structure, Fusarium, Genome analysis, Protein structure, Protein structure prediction}, language = {en}, month = {June}, note = {Publisher: Public Library of Science}, @@ -1059,7 +1685,7 @@ @article{baker_no_2020 doi = {10.1371/journal.ppat.1008643}, issn = {1553-7374}, journal = {PLOS Pathogens}, - keywords = {+Galactic, +IsGalaxy, +Methods, +Project, +Reproducibility, +Shared, +UseMain, +UsePublic, {\textgreater}UseGalaxy.be, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org.au, COVID 19, Genome analysis, Genomics, Open source software, Preprocessing, SARS, SARS CoV 2, Transmissible gastroenteritis coronavirus}, + keywords = {+Galactic, +IsGalaxy, +Methods, +Project, +Reproducibility, +Shared, +UseMain, +UsePublic, {\textgreater}UseGalaxy.be, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org.au, COVID 19, Genome analysis, Genomics, Open source software, Preprocessing, Public Health, SARS, SARS CoV 2, Transmissible gastroenteritis coronavirus}, language = {en}, month = {August}, note = {Publisher: Public Library of Science}, @@ -1073,6 +1699,23 @@ @article{baker_no_2020 year = {2020} } +@article{bakkali_novo_2021, + abstract = {We sequenced the sporophyte transcriptome of Killarney fern (\textit{Vandenboschia speciosa} (Willd.) G. Kunkel). In addition to being a rare endangered Macaronesian-European endemism, this species has a huge genome (10.52 Gb) as well as particular biological features and extreme ecological requirements. These characteristics, together with the systematic position of ferns among vascular plants, make it of high interest for evolutionary, conservation and functional genomics studies. The transcriptome was constructed de novo and contained 36,430 transcripts, of which 17,706 had valid BLAST hits. A total of 19,539 transcripts showed at least one of the 7362 GO terms assigned to the transcriptome, whereas 6547 transcripts showed at least one of the 1359 KEGG assigned terms. A prospective analysis of functional annotation results provided relevant insights on genes involved in important functions such as growth and development as well as physiological adaptations. In this context, a catalogue of genes involved in the genetic control of plant development, during the vegetative to reproductive transition, in stress response as well as genes coding for transcription factors is given. Altogether, this study provides a first step towards understanding the gene expression of a significant fern species and the in silico functional and comparative analyses reported here provide important data and insights for further comparative evolutionary studies in ferns and land plants in general.}, + author = {Bakkali, Mohammed and Martín-Blázquez, Rubén and Ruiz-Estévez, Mercedes and Garrido-Ramos, Manuel A}, + doi = {10.3390/genes12071017}, + issn = {2073-4425}, + journal = {Genes}, + keywords = {{\textgreater}UseGalaxy.eu, Endangered Species, Gene Expression Regulation, Plant, Genome, Plant, Transcriptome}, + language = {eng}, + month = {June}, + number = {7}, + pages = {1017}, + title = {De {Novo} {Sporophyte} {Transcriptome} {Assembly} and {Functional} {Annotation} in the {Endangered} {Fern} {Species} {Vandenboschia} speciosa ({Willd}.) {G}. {Kunkel}}, + url = {http://europepmc.org/abstract/MED/34208974}, + volume = {12}, + year = {2021} +} + @article{balcke_coordinated_2024, abstract = {In plants, exposure to high light irradiation induces various stress responses, which entail complex metabolic rearrangements. To explore these dynamics, we conducted time-course experiments spanning 2 min to 72 h with Arabidopsis thaliana under high and control light. Comparative metabolomics, transcriptomics, redox proteomics, and stable isotope labeling on leaf rosettes identified a series of synchronous and successive responses that provide a deeper insight into well-orchestrated mechanisms contributing to high-light acclimation. We observed transient transcriptome downregulation related to light harvesting and electron flow before the profound remodeling of the photosynthetic apparatus. Throughout the entire time course, redox homeostasis is tightly balanced between downregulation of production and enhanced transformation of NADPH accompanied by redistribution of reducing equivalents across several subcellular compartments. In both light conditions, C4 acids such as malate and fumarate are produced via anaplerosis. In carbon units, their accumulation in vacuoles surpasses plastidic levels of starch and intensifies notably under high light. In parallel, citrate synthesis from pyruvate is significantly hindered diurnally. Isotopic labeling in 2-oxoglutarate and glutamate suggests a moderate de novo synthesis of C5 acids from a vacuolar citrate reservoir during the light phase while they are largely renewed during the night. In the absence of a diurnal clockwise flow through the tricarboxylic acid (TCA) cycle, increased oxidation of photorespiratory glycine takes over as a source of reductants to fuel mitochondrial ATP production. These findings, along with previous research, contribute to a model integrating redox balance and linking increased carbon assimilation and nitrogen metabolism, especially in the context of an incomplete TCA cycle.}, author = {Balcke, Gerd Ulrich and Vahabi, Khabat and Giese, Jonas and Finkemeier, Iris and Tissier, Alain}, @@ -1109,9 +1752,45 @@ @phdthesis{baldwin_evaluating_2019 year = {2019} } +@article{ballesteros-gonzalez_repressor_2025, + abstract = {KRAS mutations are responsible for a quarter of all lung adenocarcinomas. However, the molecular mechanisms linking these mutations and their frequent secondary dosage amplification to tumor formation are still not fully understood. While ample evidence supports a crucial role for the MAPK pathway in tumor development, the primary effectors targeted by this pathway remain largely unexplored. Here we identify the transcriptional repressor Capicua (CIC) as a key target inactivated by KRAS/MAPK signaling in lung adenocarcinoma. We show that genetic loss of CIC recapitulates the phenotypic consequences of amplified KRAS signaling. Genetic disruption of CIC suppressed the requirement for Kras allelic imbalances and accelerated the transformation of bronchiolar Club cells. We also demonstrate that restoring CIC repressor activity impaired proliferation of CIC-deficient tumor cells and reverted resistance to MAPK pathway inhibitors. These results highlight the key role of CIC during lung tumor formation and suggest that selective pressure for effective CIC inactivation favors secondary amplification of KRAS/MAPK signaling in tumor cells.}, + author = {Ballesteros-González, Irene and Hernández-Navas, Iván and Brehey, Oksana and Lechuga, Carmen G. and Salmón, Marina and Scotece, Morena and Velasco-Vicente, Ricardo and Flores-Gómez, Alejandra A. and Cebriá, Antonio and Simón-Carrasco, Lucía and Jiménez, Gerardo and Musteanu, Monica and Guerra, Carmen and Domínguez, Orlando and Caleiras, Eduardo and Blanco-Aparicio, Carmen and Pons, Tirso and Ferrer, Irene and Paz-Ares, Luis and Torres-Ruiz, Raul and Rodríguez-Perales, Sandra and Barbacid, Mariano and Drosten, Matthias}, + doi = {10.1038/s44321-025-00326-z}, + issn = {1757-4684}, + journal = {EMBO Molecular Medicine}, + keywords = {{\textgreater}UseGalaxy.eu, Allelic Imbalance, Drug Resistance, KRAS, Lung Cancer, Repression}, + language = {en}, + month = {December}, + number = {12}, + pages = {3377--3406}, + title = {The repressor {Capicua} is a barrier to lung tumor development driven by {Kras}/{Trp53} mutations}, + url = {https://doi.org/10.1038/s44321-025-00326-z}, + urldate = {2025-12-26}, + volume = {17}, + year = {2025} +} + +@article{balobaid_arabidopsis_2025, + abstract = {DNA repair is crucial for genome stability, in particular for plants which are exposed to high levels of damage arising from UV irradiation, soil pollutants and reactive oxygen species. Damage that affects both strands of the DNA duplex is harder to repair due to both the lack of a template strand and the potential for physical separation of fragmented chromosomes. As such, DNA double-strand breaks (DSBs) and interstrand DNA crosslinks (ICL) are particularly cytotoxic forms of damage. Here we report the functions of FANCONI ANAEMIA I (FANCI), an Arabidopsis thaliana homologue of the mammalian ICL repair protein. We show that in plant cells, as in mammals, FANCI forms a nuclear localised complex with FANCD2. Genetic analysis of plants lacking FANCI displays significant hypersensitivity to the DNA crosslinking reagent mitomycin C. Furthermore, mutation of FANCI in combination with mutations in a second ICL repair factor, METHYL METHANESULFONATE AND UV-SENSITIVE PROTEIN 81 (MUS81), results in increased levels of programmed cell death compared to the corresponding single mutants, revealing roles in maintaining plant genome stability. Sequence analysis of mutational repair of CRISPR-Cas9-induced DSBs revealed that FANCI promotes single nucleotide insertions and reduces longer deletions. This pattern of mutations may reflect roles for FA proteins in replication-coupled repair of a subset of DSBs. Taken together, this analysis finds evidence for multiple roles for FANCI in the maintenance of plant genome stability.}, + author = {Balobaid, Atheer and Waterworth, Wanda M and Vila Nova, Sophya F and Causier, Barry and Sharma, Vinay and Park, Madeline R and Pandey, Manish K and West, Christopher E}, + doi = {10.1111/tpj.70533}, + issn = {0960-7412}, + journal = {The Plant journal : for cell and molecular biology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + number = {2}, + pages = {e70533}, + title = {Arabidopsis thaliana {FANCONI} {ANAEMIA} {I} ({FANCI}) has roles in the repair of interstrand crosslinks and {CRISPR}-{Cas9} induced {DNA} double strand breaks}, + url = {https://europepmc.org/articles/PMC12541362}, + volume = {124}, + year = {2025} +} + @article{bamford_collaboration_2021, + abstract = {SARS-CoV-2 continues to evolve, resulting in several ‘variants of concern’ with novel properties. The factors driving SARS-CoV-2 fitness and evolution in the human respiratory tract remain poorly defined. Here, we provide evidence that both viral and host factors co-operate to shape SARS-CoV-2 genotypic and phenotypic change. Through viral whole-genome sequencing, we explored the evolution of two clinical isolates of SARS-CoV-2 during passage in unmodified Vero-derived cell lines and in parallel, in well-differentiated primary nasal epithelial cell (WD-PNEC) cultures. We identify a consistent, rich genetic diversity arising in vitro, variants of which could rapidly rise to near-fixation with 2 passages. Within isolates, SARS-CoV-2 evolution was dependent on host cells, with Vero-derived cells facilitating more profound genetic changes. However, most mutations were not shared between strains. Furthermore, comparison of both Vero-grown isolates on WD-PNECs disclosed marked growth attenuation mapping to the loss of the polybasic cleavage site (PBCS) in Spike while the strain with mutations in NSP12 (T293I), Spike (P812R) and a truncation of ORF7a remained viable in WD-PNECs. Our work highlights the significant genetic plasticity of SARS-CoV-2 while uncovering an influential role for collaboration between viral and host cell factors in shaping viral evolution and fitness in human respiratory epithelium.}, author = {Bamford, Connor G. G. and Broadbent, Lindsay and Aranday-Cortes, Elihu and McCabe, Mary and McKenna, James and Courtney, David and Touzelet, Olivier and Ali, Ahlam and Roberts, Grace and Campos, Guillermo Lopez and Simpson, David and McCaughey, Conall and Fairley, Derek and Mills, Ken and and, Ultan F. Power}, doi = {10.1101/2021.07.16.452629}, + journal = {bioRxiv}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {July}, note = {Publisher: Cold Spring Harbor Laboratory}, @@ -1121,10 +1800,13 @@ @article{bamford_collaboration_2021 } @article{bamford_comparison_2022, + abstract = {SARS-CoV-2 can efficiently infect both children and adults, albeit with morbidity and mortality positively associated with increasing host age and presence of co-morbidities. SARS-CoV-2 continues to adapt to the human population, resulting in several variants of concern (VOC) with novel properties, such as Alpha and Delta. However, factors driving SARS-CoV-2 fitness and evolution in paediatric cohorts remain poorly explored. Here, we provide evidence that both viral and host factors co-operate to shape SARS-CoV-2 genotypic and phenotypic change in primary airway cell cultures derived from children. Through viral whole-genome sequencing, we explored changes in genetic diversity over time of two pre-VOC clinical isolates of SARS-CoV-2 during passage in paediatric well-differentiated primary nasal epithelial cell (WD-PNEC) cultures and in parallel, in unmodified Vero-derived cell lines. We identified a consistent, rich genetic diversity arising in vitro, variants of which could rapidly rise to near fixation within two passages. Within isolates, SARS-CoV-2 evolution was dependent on host cells, with paediatric WD-PNECs showing a reduced diversity compared to Vero (E6) cells. However, mutations were not shared between strains. Furthermore, comparison of both Vero-grown isolates on WD-PNECs disclosed marked growth attenuation mapping to the loss of the polybasic cleavage site (PBCS) in Spike, while the strain with mutations in Nsp12 (T293I), Spike (P812R) and a truncation of Orf7a remained viable in WD-PNECs. Altogether, our work demonstrates that pre-VOC SARS-CoV-2 efficiently infects paediatric respiratory epithelial cells, and its evolution is restrained compared to Vero (E6) cells, similar to the case of adult cells. We highlight the significant genetic plasticity of SARS-CoV-2 while uncovering an influential role for collaboration between viral and host cell factors in shaping viral evolution and ultimately fitness in human respiratory epithelium.}, author = {Bamford, Connor G. G. and Broadbent, Lindsay and Aranday-Cortes, Elihu and McCabe, Mary and McKenna, James and Courtney, David G. and Touzelet, Olivier and Ali, Ahlam and Roberts, Grace and Campos, Guillermo Lopez and Simpson, David and McCaughey, Conall and Fairley, Derek and Mills, Ken and and, Ultan F. Power}, doi = {10.3390/v14020325}, + issn = {1999-4915}, journal = {Viruses}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Evolution, Molecular}, + language = {eng}, month = {February}, note = {Publisher: MDPI AG}, number = {2}, @@ -1135,6 +1817,37 @@ @article{bamford_comparison_2022 year = {2022} } +@article{banar_novel_2025, + abstract = {Bovine mastitis is a considerable challenge within the dairy industry, causing significant financial losses and threatening public health. The increased occurrence of methicillin-resistant Staphylococcus aureus (MRSA) has provoked difficulties in managing bovine mastitis. Bacteriophage therapy presents a novel treatment strategy to combat MRSA infections, emerging as a possible substitute for antibiotics. This study evaluated the therapeutic potency of a novel bacteriophage cocktail against MRSA mastitis. Two new bacteriophages (vB\_SauR\_SW21 and vB\_SauR\_SW25) with potent lytic activity against MRSA were isolated and characterized. The one-step growth curve displayed a rapid latent period (20–35 min) and substantial burst size (418 and 316 PFU/ cell). In silico analyses have confirmed the absence of antimicrobial resistance or virulence factor-encoding genes within their genomes. According to the results, combining these phages augmented their host range and virulence. The phage cocktail significantly reduced bacterial burden in a BALB/c mastitis model, demonstrating efficacy comparable to antibiotic treatment. Moreover, its administration led to decreased concentrations of IL-1β and TNF-α compared to the negative control group. The bacteriophage cocktail (SW21-SW25) exhibits a promising profile for therapeutic applications and may represent a novel substitute to antibiotics for managing MRSA bovine mastitis.}, + author = {Banar, Maryam and Kamyab, Haniyeh and Torkashvand, Narges and Salehi, Taghi Zahraei and Sepehrizadeh, Zargham and Shahverdi, Ahmad Reza and Pourmand, Mohammad Reza and Yazdi, Mohammad Hossein}, + doi = {10.1371/journal.pone.0316157}, + issn = {1932-6203}, + journal = {PLOS ONE}, + keywords = {{\textgreater}UseGalaxy.eu, Antibiotic resistance, Antibiotics, Bacteriophages, Bovine mastitis, Mastitis, Methicillin-Resistant Staphylococcus aureus, Methicillin-resistant Staphylococcus aureus, Phage Therapy, Staphylococcal Infections, Staphylococcus, Staphylococcus Phages, Viral genomics}, + language = {en}, + month = {January}, + note = {Publisher: Public Library of Science}, + number = {1}, + pages = {e0316157}, + shorttitle = {A novel broad-spectrum bacteriophage cocktail against methicillin-resistant {Staphylococcus} aureus}, + title = {A novel broad-spectrum bacteriophage cocktail against methicillin-resistant {Staphylococcus} aureus: {Isolation}, characterization, and therapeutic potential in a mastitis mouse model}, + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0316157}, + urldate = {2025-05-29}, + volume = {20}, + year = {2025} +} + +@article{bandyopadhyay_polypharmacology_2020, + abstract = {{\textless}h4{\textgreater}Background: {\textless}/h4{\textgreater} Medicinal plants, as rich sources of bioactive compounds with antiviral properties, are now being explored for the development of drugs against SARS-CoV-2. {\textless}h4{\textgreater}Aims: {\textless}/h4{\textgreater}: Identification of promising compounds for the treatment of COVID-19 from natural products via molecular modelling against NSP9, including some other viral and host targets and evaluation of polypharmacological indications. Main methods: A manually curated library of 521 phytochemicals (from 19 medicinal plants) was virtually screened using Mcule server and binding interactions were studied using DS Visualiser. Docking thresholds were set based on the scores of standard controls and rigorous ADMET properties were used to finally get the potential inhibitors. Free binding energies of the docked complexes were calculated employing MM-GBSA method. MM-GBSA informed our choice for MD simulation studies performed against NSP9 to study the stability of the drug-receptor interaction. NSP9 structure comparison was also performed. Key findings: Extensive screening of the molecules identified 5 leads for NSP9, 23 for Furin, 18 for ORF3a, and 19 for interleukin-6. Ochnaflavone and Licoflavone B, obtained from Lonicera japonica (Japanese Honeysuckle) and Glycyrrhiza glabra (Licorice), respectively, were identified to have the highest potential multi-target inhibition properties for NSP9, furin, ORF3a, and IL-6. Additionally, molecular dynamics simulation supports the robust stability of Ochnaflavone and Licoflavone B against NSP9 at the active sites via hydrophobic interactions, H-bonding, and H-bonding facilitated by water. Significance: These compounds with the highest drug-like ranking against multiple viral and host targets have the potential to be drug candidates for the treatment of SARS-CoV-2 infection that may possibly act on multiple pathways simultaneously to inhibit viral entry and replication as well as disease progression.}, + author = {Bandyopadhyay, Suritra and Abiodun, Omobolanle Abimbola and Ogboo, Blessing Chinweotito and Kola-Mustapha, Adeola Tawakalitu and Attah, Emmanuel Ifeanyi and Edemhanria, Lawrence and Kumari, Ankita and Jaganathan, Ravindran and Adelakun, Niyi Samuel}, + doi = {10.26434/chemrxiv.12945833.v1}, + journal = {ChemRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Polypharmacology of {Some} {Medicinal} {Plant} {Metabolites} {Against} {SARS}-{CoV}-2 and {Host} {Targets}: {Molecular} {Dynamics} {Evaluation} of {NSP9} {RNA} {Binding} {Protein}}, + url = {http://europepmc.org/abstract/PPR/PPR213792}, + year = {2020} +} + @article{bandyopadhyay_polypharmacology_2021, author = {Bandyopadhyay, Suritra and Abiodun, Omobolanle Abimbola and Ogboo, Blessing Chinweotito and Kola-Mustapha, Adeola Tawakalitu and Attah, Emmanuel Ifeanyi and Edemhanria, Lawrence and Kumari, Ankita and Jaganathan, Ravindran and Adelakun, Niyi S.}, doi = {10.1080/07391102.2021.1959401}, @@ -1158,13 +1871,34 @@ @article{barbosa_new_2021 year = {2021} } +@article{barker_mutations_2025, + author = {Barker, Katherine S. and Santana, Darian J. and Zhang, Qing and Peters, Tracy L. and Rybak, Jeffrey M. and Morschhäuser, Joachim and Cuomo, Christina A. and Rogers, P. David}, + doi = {10.1128/aac.00300-25}, + journal = {Antimicrobial Agents and Chemotherapy}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e00300--25}, + title = {Mutations in {TAC1B} drive increased {CDR1} and {MDR1} expression and azole resistance in {Candida} auris}, + url = {https://journals.asm.org/doi/10.1128/aac.00300-25}, + urldate = {2025-09-03}, + volume = {0}, + year = {2025} +} + @article{baron_multidrug-resistant_2021, + abstract = {Antibiotic resistance genes exist naturally in various environments far from human usage. Here, we investigated multidrug-resistant Klebsiella pneumoniae, a common pathogen of chimpanzees and humans. We screened antibiotic-resistant K. pneumoniae from 48 chimpanzee stools and 38 termite mounds (\textit{n} = 415 samples) collected in protected areas in Senegal. The microsatellite method was used to identify chimpanzee individuals (\textit{n} = 13). Whole-genome sequencing was performed on K. pneumoniae complex isolates to identify antibiotic-resistant genes and characterize clones. We found a high prevalence of carbapenem-resistant K. pneumoniae among chimpanzee isolates (18/48 samples from 7/13 individuals) and ceftriaxone resistance among both chimpanzee individuals (19/48) and termite mounds (7/415 termites and 3/38 termite mounds). The \textit{bla}$_{\textrm{OXA-48}}$ and the \textit{bla}$_{\textrm{KPC-2}}$ genes were carried by international pOXA-48 and pKPC-2 plasmids, respectively. The ESBL plasmid carried \textit{bla}$_{\textrm{CTX-M-15}}$, \textit{bla}$_{\textrm{TEM-1B}}$, and \textit{bla}$_{\textrm{OXA-1}}$ genes. Genome sequencing of 56 isolates identified two major clones associated with hospital-acquired infections of K. pneumoniae (ST307 and ST147) in chimpanzees and termites, suggesting circulation of strains between the two species, as chimpanzees feed on termites. The source and selection pressure of these clones in this environment need to be explored.}, author = {Baron, Sophie Alexandra and Mediannikov, Oleg and Abdallah, Rim and Yimagou, Edmond Kuete and Medkour, Hacène and Dubourg, Gregory and Elamire, Youssouf and Afouda, Pamela and Ngom, Issa Isaac and Angelakis, Emmanouil and Davoust, Bernard and Diatta, Georges and Barciela, Amanda and Hernandez-Aguilar, R. Adriana and Sokhna, Cheikh and Caputo, Aurelia and Levasseur, Anthony and Rolain, Jean-Marc and Raoult, Didier}, doi = {10.1128/aac.02557-20}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {0066-4804}, + journal = {Antimicrob Agents Chemother}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Isoptera, Klebsiella Infections}, + language = {eng}, month = {August}, note = {Publisher: American Society for Microbiology}, number = {9}, + pages = {e0255720}, title = {Multidrug-{Resistant} {Klebsiella} pneumoniae {Clones} from {Wild} {Chimpanzees} and {Termites} in {Senegal}}, url = {https://doi.org/10.1128/aac.02557-20}, volume = {65}, @@ -1172,9 +1906,13 @@ @article{baron_multidrug-resistant_2021 } @article{barragan-rosillo_genome_2021, + abstract = {As phosphorus is one of the most limiting nutrients in many natural and agricultural ecosystems, plants have evolved strategies that cope with its scarcity. Genetic approaches have facilitated the identification of several molecular elements that regulate the phosphate (Pi) starvation response (PSR) of plants, including the master regulator of the transcriptional response to phosphate starvation PHOSPHATE STARVATION RESPONSE1 (PHR1). However, the chromatin modifications underlying the plant transcriptional response to phosphate scarcity remain largely unknown. Here, we present a detailed analysis of changes in chromatin accessibility during phosphate starvation in \textit{Arabidopsis thaliana} root cells. Root cells undergo a genome-wide remodeling of chromatin accessibility in response to Pi starvation that is often associated with changes in the transcription of neighboring genes. Analysis of chromatin accessibility in the \textit{phr1 phl2} double mutant revealed that the transcription factors PHR1 and PHL2 play a key role in remodeling chromatin accessibility in response to Pi limitation. We also discovered that PHR1 and PHL2 play an important role in determining chromatin accessibility and the associated transcription of many genes under optimal Pi conditions, including genes involved in the PSR. We propose that a set of transcription factors directly activated by PHR1 in Pi-starved root cells trigger a second wave of epigenetic changes required for the transcriptional activation of the complete set of low-Pi-responsive genes.}, author = {Barragán-Rosillo, Alfonso Carlos and Peralta-Alvarez, Carlos Alberto and Ojeda-Rivera, Jonathan Odilón and Arzate-Mejía, Rodrigo G. and Recillas-Targa, Félix and Herrera-Estrella, Luis}, doi = {10.1073/pnas.2107558118}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {0027-8424}, + journal = {Proc Natl Acad Sci U S A}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Genome, Plant}, + language = {eng}, month = {August}, note = {Publisher: Proceedings of the National Academy of Sciences}, number = {33}, @@ -1185,6 +1923,25 @@ @article{barragan-rosillo_genome_2021 year = {2021} } +@article{barragan-rosillo_role_2025, + abstract = {Whole-genome duplication is an evolutionary force that drives speciation in all living kingdoms and is notably prevalent in plants. The evolutionary history of plants involved at least two genomic duplications that significantly expanded the plant morphology and physiology spectrum. Many important crops are polyploids, showing valuable features relative to morphological and stress response traits. After genome duplication, diploidization processes facilitate genomic adjustments to restore disomic inheritance. However, little is known about the chromatin changes triggered by nuclear DNA content alterations. Here, we report that synthetically induced genome duplication leads to chromatinization and significant changes in gene expression, resulting in a transcriptional landscape resembling a natural tetraploid. Interestingly, synthetic diploidization elicits only minor alterations in transcriptional activity and chromatin accessibility compared to the more pronounced effects of tetraploidization. We identified epigenetic factors, including specific histone variants, that showed increased expression following genome duplication and decreased expression after genome reduction. These changes may play a key role in the epigenetic mechanisms underlying the phenotypic complexity after tetraploidization in plants. Our findings shed light on the mechanisms that modulate chromatin accessibility remodeling and gene transcription regulation underlying plant genome adaptation in response to changes in genome size.}, + author = {Barragán-Rosillo, Alfonso Carlos and Chávez Montes, Ricardo A. and Herrera-Estrella, Luis}, + copyright = {© 2025 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.}, + doi = {10.1111/tpj.70116}, + issn = {1365-313X}, + journal = {The Plant Journal}, + keywords = {{\textgreater}UseGalaxy.eu, ATAC-seq, Arabidopsis thaliana, Chromatin, DNA, Plant, Gene Expression Regulation, Plant, RNA-seq, chromatin accessibility, gene transcription regulation, whole genome duplication, whole genome reduction}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.70116}, + number = {6}, + pages = {e70116}, + title = {The role of {DNA} content in shaping chromatin architecture and gene expression}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.70116}, + urldate = {2025-03-29}, + volume = {121}, + year = {2025} +} + @mastersthesis{barreira_predictability_2024, abstract = {Predicting genomic evolution, which is influenced by selection, genetic drift, and population history, is a central question in evolutionary biology. This study investigates the genetic basis of @@ -1222,10 +1979,54 @@ @mastersthesis{barreira_predictability_2024 year = {2024} } +@article{barrera_natural_2021, + abstract = {\textit{Spodoptera ornithogalli} (Guenée) (Lepidoptera: Noctuidae) is an important pest in different crops of economic relevance in America. For its control, strategies that include chemicals are usually used; so, the description of entomopathogens would be very useful for the formulation of biopesticides. In this regard, two different baculoviruses affecting \textit{S. ornithogalli} were isolated in Colombia, with one of them being an NPV and the other a GV. Ultrastructural, molecular, and biological characterization showed that both isolates possess the 38 core genes and are novel species in \textit{Baculoviridae}, named as \textit{Spodoptera ornithogalli nucleopolyhedrovirus} (SporNPV) and \textit{Spodoptera ornithogalli granulovirus} (SporGV). The bioassays carried out in larvae of \textit{S. ornithogalli} and \textit{S. frugiperda} showed infectivity in both hosts but being higher in the first. In addition, it was observed that SporGV potentiates the insecticidal action of SporNPV (maximum value in ratio 2.5:97.5). Both viruses are individually infective but coexist in nature, producing mixed infections with a synergistic effect that improves the performance of the NPV and enables the transmission of the GV, which presents a slowly killing phenotype.}, + author = {Barrera, Gloria Patricia and Villamizar, Laura Fernanda and Araque, Gustavo Adolfo and Gómez, Juliana Andrea and Guevara, Elsa Judith and Cerrudo, Carolina Susana and Belaich, Mariano Nicolás}, + doi = {10.3390/v13122520}, + issn = {1999-4915}, + journal = {Viruses}, + keywords = {{\textgreater}UseGalaxy.eu, Baculoviridae}, + language = {eng}, + month = {December}, + number = {12}, + pages = {2520}, + title = {Natural {Coinfection} between {Novel} {Species} of {Baculoviruses} in {Spodoptera} ornithogalli {Larvae}}, + url = {http://europepmc.org/abstract/MED/34960789}, + volume = {13}, + year = {2021} +} + +@article{barroso_genomic_2025, + abstract = {Objectives +This study aimed to elucidate the genomic background of a carbapenemase-producing Klebsiella quasipneumoniae subsp. similipneumoniae that colonized and infected a patient during hospitalization. +Methods +The isolates recovered from a surveillance swab (isolate CV39) and a subsequent surgical site infection (isolate 415/18) in the same patient were identified, and antimicrobial susceptibility was tested. Biofilm production and genome restriction typing (XbaI-PFGE) were subsequently performed. Last, the first isolate obtained was whole-genome sequenced (WGS) using the MiSeq platform, and online tools were applied for bioinformatic analysis of the relevant information. +Results +Both CV39 and 415/18 were categorized as multidrug-resistant, they exhibited low biofilm production ability, and presented a high genetic similarity (92.9\%) by XbaI-PFGE typing. In view of this, the first isolate was submitted to WGS, which demonstrated that CV39 belonged to the sequence type ST138, expressing the K1 and O5 serotypes. Moreover, it presented genes codifying resistance to all beta-lactams, fosfomycin, fluoroquinolones, and quaternary ammonium compounds, as well as virulence systems comprising fimbriae, iron uptake, and immune bypass. Despite four plasmid incompatibility groups being detected, the IncM1 was identified as responsible for the blaKPC-2 mobilization. Finally, the CV39 genome is closely related to other ST138-K1-K. quasipneumoniae strains isolated around the world. +Conclusions +These results revealed the potential of a colonization scenario by a KPC-2-producing K1 K. quasipneumoniae in progressing to an infectious process in an impaired patient, which may help programs intended to combat antimicrobial resistance.}, + author = {Barroso, Marlon do Valle and Oshiro, Beatriz dos Santos and Nogueira, Mara Corrêa Lelles and Casella, Tiago}, + doi = {10.1016/j.jgar.2025.05.018}, + issn = {2213-7165}, + journal = {Journal of Global Antimicrobial Resistance}, + keywords = {{\textgreater}UseGalaxy.eu, Epidemiological surveillance, Genomics, Hypervirulence, Multidrug-resistance}, + month = {September}, + pages = {12--14}, + title = {Genomic insights into a colonization-infection progression by a carbapenemase-producing \textit{{Klebsiella} quasipneumoniae} {K1} serotype}, + url = {https://www.sciencedirect.com/science/article/pii/S2213716525001213}, + urldate = {2025-07-12}, + volume = {44}, + year = {2025} +} + @article{bartas_changes_2021, + abstract = {Recently, the quest for the mythical fountain of youth has produced extensive research programs that aim to extend the healthy lifespan of humans. Despite advances in our understanding of the aging process, the surprisingly extended lifespan and cancer resistance of some animal species remain unexplained. The p53 protein plays a crucial role in tumor suppression, tissue homeostasis, and aging. Long-lived, cancer-free African elephants have 20 copies of the \textit{TP}53 gene, including 19 retrogenes (38 alleles), which are partially active, whereas humans possess only one copy of \textit{TP}53 and have an estimated cancer mortality rate of 11-25\%. The mechanism through which p53 contributes to the resolution of the Peto's paradox in Animalia remains vague. Thus, in this work, we took advantage of the available datasets and inspected the p53 amino acid sequence of phylogenetically related organisms that show variations in their lifespans. We discovered new correlations between specific amino acid deviations in p53 and the lifespans across different animal species. We found that species with extended lifespans have certain characteristic amino acid substitutions in the p53 DNA-binding domain that alter its function, as depicted from the Phenotypic Annotation of p53 Mutations, using the PROVEAN tool or SWISS-MODEL workflow. In addition, the loop 2 region of the human p53 DNA-binding domain was identified as the longest region that was associated with longevity. The 3D model revealed variations in the loop 2 structure in long-lived species when compared with human p53. Our findings show a direct association between specific amino acid residues in p53 protein, changes in p53 functionality, and the extended animal lifespan, and further highlight the importance of p53 protein in aging.}, author = {Bartas, Martin and Brázda, Václav and Volná, Adriana and Červeň, Jiří and Pečinka, Petr and Zawacka-Pankau, Joanna E.}, doi = {10.3390/ijms22168512}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Databases, Genetic, Gene Dosage, Longevity, Models, Molecular}, + language = {eng}, month = {August}, note = {Publisher: MDPI AG}, number = {16}, @@ -1236,6 +2037,26 @@ @article{bartas_changes_2021 year = {2021} } +@article{bassu_positive_2025, + abstract = {Growing crops in controlled-environment indoor farming systems offers new ways of producing high-yield, pesticide-free, environmental-friendly food. However, it replaces soil with hydroponics and the sun with LED lights. Compared with the field, wheat grown indoors showed a much higher yield potential and bread-making quality parameters. Many mineral concentrations were higher due to the unrestricted water supply and nutrients in hydroponics. However, concentrations declined with increasing yields. The microbiome richness inside the grains of wheat grown without soil indoors was still within the range of wheat grown in the field. However, taxa were different among cultivars and treatments. There were differences in the presence of undefined secondary metabolites between indoor and outdoor wheat and across the indoor experiments. Regardless of the growing environment, immunoreactive proteins were present. Indoor-grown wheat had a higher share of ω5-gliadins but lower shares of γ-gliadins and low‐molecular‐weight glutenin subunits, which may affect the gluten protein immunoreactive potential for individuals with wheat-related disorders (allergy and celiac disease). Growing wheat without soil and sunlight indoors can produce high-yielding, high-quality grains. However, the food quality and health aspects associated with gluten proteins might deteriorate with a further, theoretically possible, yield increase in a controlled growing environment.}, + author = {Bassu, Simona and Eichelsbacher, Sebastian and Giunta, Francesco and Motzo, Rosella and Dawid, Corinna and Gastl, Martina and Schloter, Michael and Scherf, Katharina A. and Hör, Stefan and De Souza, Yuri Pinheiro Alves and Schulz, Stefanie and Stark, Timo D. and Mohler, Volker and Asseng, Senthold}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-16204-0}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Hydroponics, Light, Physiology, Plant sciences, Triticum}, + language = {en}, + month = {August}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {30768}, + title = {Positive impact of hydroponics and artificial light on yield and quality of wheat}, + url = {https://www.nature.com/articles/s41598-025-16204-0}, + urldate = {2025-09-03}, + volume = {15}, + year = {2025} +} + @article{bastide_genome_2024, abstract = {Social insects’ nests harbor intruders known as inquilines,1 which are usually related to their hosts.2,3 However, distant non-social inquilines may also show convergences with their hosts,4,5 although the underlying genomic changes remain unclear. We analyzed the genome of the wingless and blind bee louse fly Braula coeca, an inquiline kleptoparasite of the western honey bee, Apis mellifera.6,7 Using large phylogenomic data, we confirmed recent accounts that the bee louse fly is a drosophilid8,9 and showed that it had likely evolved from a sap-breeder ancestor associated with honeydew and scale insects’ wax. Unlike many parasites, the bee louse fly genome did not show significant erosion or strict reliance on an endosymbiont, likely due to a relatively recent age of inquilinism. However, we observed a horizontal transfer of a transposon and a striking parallel evolution in a set of gene families between the honey bee and the bee louse fly. Convergences included genes potentially involved in metabolism and immunity and the loss of nearly all bitter-tasting gustatory receptors, in agreement with life in a protective nest and a diet of honey, pollen, and beeswax. Vision and odorant receptor genes also exhibited rapid losses. Only genes whose orthologs in the closely related Drosophila melanogaster respond to honey bee pheromone components or floral aroma were retained, whereas the losses included orthologous receptors responsive to the anti-ovarian honey bee queen pheromones. Hence, deep genomic convergences can underlie major phenotypic transitions during the evolution of inquilinism between non-social parasites and their social hosts.}, author = {Bastide, Héloïse and Legout, Hélène and Dogbo, Noé and Ogereau, David and Prediger, Carolina and Carcaud, Julie and Filée, Jonathan and Garnery, Lionel and Gilbert, Clément and Marion-Poll, Frédéric and Requier, Fabrice and Sandoz, Jean-Christophe and Yassin, Amir}, @@ -1250,6 +2071,22 @@ @article{bastide_genome_2024 year = {2024} } +@article{batiha_gene_2025, + abstract = {Spermatogenesis is a complex biological process encompasses several stages of cellular divisions, ultimately resulting in producing mature spermatozoa capable of fertilization. Numerous factors involved in the precise regulation of the spermatogenesis, and any disruptions or alterations in these regulatory mechanisms can lead to spermatogenesis arrest, which may result in male infertility. Among these factors, genetic influences play essential role in regulating the process. This study aimed to identify genes that are differentially expressed in relation to spermatogenesis arrest. Testicular biopsy samples were collected from 22 non-obstructive azoospermic patients diagnosed with spermatogenesis arrest (cases) and nine obstructive azoospermic patients (controls). RNA sequencing (RNA-seq) was performed on five samples from the 22 non-obstructive azoospermic patients and compared to previously published transcriptomic data from obstructive azoospermic patients, which served as the control group. Differential expression analysis of the RNA-seq data identified 1,915 differentially expressed genes, comprising 337 upregulated and 1,578 downregulated genes. Among these, several key candidate genes were identified for further analysis, including the upregulation of FOS, FOSB, RGS1, and CXCL8, as well as the downregulation of TNP2, SPRR2C, LINC02314, and C16orf78. RT-qPCR validation confirmed the RNA-seq findings for these genes in the tested samples. Subsequently, RT-qPCR was performed on the remaining 17 non-obstructive (n = 17) and obstructive azoospermic samples (n = 9) collected in this study. The results from these additional samples were consistent with the RNA-seq data, further supporting the findings. Using gene ontology (GO) analysis and published literature, we linked these genes with spermatogenesis arrest, identifying promising targets that could serve as potential biomarkers for this condition in the future.}, + author = {Batiha, Osamah and Al-Zoubi, Esra'a and Almomani, Rowida and Al Smadi, Mohammad A and Alrawabdeh, Sura and Alshokaibi, Omar and Abu-Farsakh, Hussam and Alkhateeb, Abedalrhman and Abu-Halima, Masood}, + doi = {10.1371/journal.pone.0332025}, + issn = {1932-6203}, + journal = {PloS one}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + number = {9}, + pages = {e0332025}, + title = {Gene expression alterations in testicular biopsies from males with spermatogenesis arrest identified by transcriptome analysis}, + url = {http://europepmc.org/abstract/MED/40938846}, + volume = {20}, + year = {2025} +} + @article{batista_da_silva_discovery_2023, abstract = {Astyanax mexicanus is a well-known model species, that has two morphotypes, cavefish, from subterranean rivers and surface fish, from surface rivers. They are morphologically distinct due to many troglomorphic traits in the cavefish, such as the absence of eyes. Most studies on A. mexicanus are focused on eye development and protein-coding genes involved in the process. However, lncRNAs did not get the same attention and very little is known about them. This study aimed to fill this knowledge gap, identifying, describing, classifying, and annotating lncRNAs expressed in the embryo’s eye tissue of cavefish and surface fish. To do so, we constructed a concise workflow to assemble and evaluate transcriptomes, annotate protein-coding genes, ncRNAs families, predict the coding potential, identify putative lncRNAs, map them and predict interactions. This approach resulted in the identification of 33,069 and 19,493 putative lncRNAs respectively mapped in cavefish and surface fish. Thousands of these lncRNAs were annotated and identified as conserved in human and several species of fish. Hundreds of them were validated in silico, through ESTs. We identified lncRNAs associated with genes related to eye development. This is the case of a few lncRNAs associated with sox2, which we suggest being isomorphs of the SOX2-OT, a lncRNA that can regulate the expression of sox2. This work is one of the first studies to focus on the description of lncRNAs in A. mexicanus, highlighting several lncRNA targets and opening an important precedent for future studies focusing on lncRNAs expressed in A. mexicanus.}, author = {Batista da Silva, Iuri and Aciole Barbosa, David and Kavalco, Karine Frehner and Nunes, Luiz R. and Pasa, Rubens and Menegidio, Fabiano B.}, @@ -1257,7 +2094,7 @@ @article{batista_da_silva_discovery_2023 doi = {10.1038/s41598-023-34198-5}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, Long non-coding RNAs, Transcriptomics}, + keywords = {{\textgreater}UseGalaxy.eu, Characidae, Long non-coding RNAs, RNA, Long Noncoding, Transcriptomics}, language = {en}, month = {July}, note = {Number: 1 @@ -1328,9 +2165,13 @@ @incollection{batut_rna-seq_2021 } @article{bauer_functional_2021, + abstract = {Epithelial ovarian cancer (EOC) is the most lethal disease of the female reproductive tract, and although most patients respond to the initial treatment with platinum (cPt)-based compounds, relapse is very common. We investigated the role of epigenetic changes in cPt-sensitive and -resistant EOC cell lines and found distinct differences in their enhancer landscape. Clinical data revealed that two genes (JAK1 and FGF10), which gained large enhancer clusters in resistant EOC cell lines, could provide novel biomarkers for early patient stratification with statistical independence for JAK1. To modulate the enhancer remodeling process and prevent the acquisition of cPt resistance in EOC cells, we performed a chromatin-focused RNAi screen in the presence of cPt. We identified subunits of the Nucleosome Remodeling and Deacetylase (NuRD) complex as critical factors sensitizing the EOC cell line A2780 to platinum treatment. Suppression of the Methyl-CpG Binding Domain Protein 3 (MBD3) sensitized cells and prevented the establishment of resistance under prolonged cPt exposure through alterations of H3K27ac at enhancer regions, which are differentially regulated in cPt-resistant cells, leading to a less aggressive phenotype. Our work establishes JAK1 as an independent prognostic marker and the NuRD complex as a potential target for combinational therapy.}, author = {Bauer, Tabea L. and Collmar, Katrin and Kaltofen, Till and Loeffler, Ann-Katrin and Decker, Lorena and Mueller, Jan and Pinter, Sabine and Eisler, Stephan A. and Mahner, Sven and Fraungruber, Patricia and Kommoss, Stefan and Staebler, Annette and Francis, Lewis and Conlan, R. Steven and Zuber, Johannes and Jeschke, Udo and Trillsch, Fabian and Rathert, Philipp}, doi = {10.3390/cancers13153801}, + issn = {2072-6694}, + journal = {Cancers}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {July}, note = {Publisher: MDPI AG}, number = {15}, @@ -1347,7 +2188,7 @@ @article{bawin_cuscuta_2024 doi = {10.1093/plphys/kiad505}, issn = {0032-0889}, journal = {Plant Physiology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Cuscuta, Parasites, Solanum, Solanum lycopersicum}, month = {January}, number = {1}, pages = {258--273}, @@ -1453,6 +2294,34 @@ @article{becker_correlation_2024 year = {2024} } +@article{beer_impaired_2022, + abstract = {Severity of COVID-19 shows an extraordinary correlation with increasing age. We generated a mouse model for severe COVID-19 and show that the age-dependent disease severity is caused by the disruption of a timely and well-coordinated innate and adaptive immune response due to impaired interferon (IFN) immunity. Aggravated disease in aged mice was characterized by a diminished IFN-γ response and excessive virus replication. Accordingly, adult IFN-γ receptor-deficient mice phenocopied the age-related disease severity, and supplementation of IFN-γ reversed the increased disease susceptibility of aged mice. Further, we show that therapeutic treatment with IFN-λ in adults and a combinatorial treatment with IFN-γ and IFN-λ in aged Ifnar1-/- mice was highly efficient in protecting against severe disease. Our findings provide an explanation for the age-dependent disease severity and clarify the nonredundant antiviral functions of type I, II, and III IFNs during SARS-CoV-2 infection in an age-dependent manner. Our data suggest that highly vulnerable individuals could benefit from immunotherapy combining IFN-γ and IFN-λ.}, + author = {Beer, Julius and Crotta, Stefania and Breithaupt, Angele and Ohnemus, Annette and Becker, Jan and Sachs, Benedikt and Kern, Lisa and Llorian, Miriam and Ebert, Nadine and Labroussaa, Fabien and Nhu Thao, Tran Thi and Trueeb, Bettina Salome and Jores, Joerg and Thiel, Volker and Beer, Martin and Fuchs, Jonas and Kochs, Georg and Wack, Andreas and Schwemmle, Martin and Schnepf, Daniel}, + doi = {10.1084/jem.20220621}, + issn = {0022-1007}, + journal = {J Exp Med}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19}, + language = {eng}, + month = {December}, + number = {12}, + pages = {e20220621}, + title = {Impaired immune response drives age-dependent severity of {COVID}-19}, + url = {http://europepmc.org/abstract/MED/36129445}, + volume = {219}, + year = {2022} +} + +@article{beer_impaired_2022, + abstract = {SARS-CoV-2 is a highly contagious respiratory virus and the causative agent for COVID-19. The severity of disease varies from mildly symptomatic to lethal and shows an extraordinary correlation with increasing age, which represents the major risk factor for severe COVID-19 1 . However, the precise pathomechanisms leading to aggravated disease in the elderly are currently unknown. Delayed and insufficient antiviral immune responses early after infection as well as dysregulated and overshooting immunopathological processes late during disease were suggested as possible mechanisms. Here we show that the age-dependent increase of COVID-19 severity is caused by the disruption of a timely and well-coordinated innate and adaptive immune response due to impaired interferon (IFN) responses. To overcome the limitations of mechanistic studies in humans, we generated a mouse model for severe COVID-19 and compared the kinetics of the immune responses in adult and aged mice at different time points after infection. Aggravated disease in aged mice was characterized by a diminished IFN-γ response and excessive virus replication. Accordingly, adult IFN-γ receptor-deficient mice phenocopied the age-related disease severity and supplementation of IFN-γ reversed the increased disease susceptibility of aged mice. Mimicking impaired type I IFN immunity in adult and aged mice, a second major risk factor for severe COVID-19 2–4 , we found that therapeutic treatment with IFN-λ in adult and a combinatorial treatment with IFN-γ and IFN-λ in aged Ifnar1 -/- mice was highly efficient in protecting against severe disease. Our findings provide an explanation for the age-dependent disease severity of COVID-19 and clarify the nonredundant antiviral functions of type I, II and III IFNs during SARS-CoV-2 infection in an age-dependent manner. Based on our data, we suggest that highly vulnerable individuals combining both risk factors, advanced age and an impaired type I IFN immunity, may greatly benefit from immunotherapy combining IFN-γ and IFN-λ.}, + author = {Beer, Julius and Crotta, Stefania and Breithaupt, Angele and Ohnemus, Annette and Becker, Jan and Sachs, Benedikt and Kern, Lisa and Llorian, Miriam and Ebert, Nadine and Labroussaa, Fabien and Thao, Tran Thi Nhu and Trueeb, Bettina Salome and Jores, Joerg and Thiel, Volker and Beer, Martin and Fuchs, Jonas and Kochs, Georg and Wack, Andreas and Schwemmle, Martin and Schnepf, Daniel}, + doi = {10.1101/2022.04.21.489072}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Impaired immune response drives age-dependent severity of {COVID}-19}, + url = {http://europepmc.org/abstract/PPR/PPR493531}, + year = {2022} +} + @inproceedings{beerling_enhanced_2023, abstract = {Enhanced weathering (EW) with crushed basalt on farmlands is a promising scalable atmospheric carbon dioxide removal strategy that urgently requires performance assessment with commercial farming practices. Our large-scale replicated EW field trial in the heart of the U.S. Corn Belt shows cumulative time-integrated carbon sequestration of 15.4 +/- 4.1 t CO2 ha-1 over four years, with additional emissions mitigation of {\textasciitilde}0.1 - 0.4 t CO2,e ha-1 yr-1 for soil nitrous oxide, a potent long-lived greenhouse gas. Maize and soybean yields increased 12-16\% with EW following improved soil fertility, decreased soil acidification, and upregulation of root nutrient transport genes. Our findings suggest that widespread adoption of EW across farming sectors has the potential to contribute significantly to net-zero greenhouse gas emissions goals and global food and soil security.}, author = {Beerling, D. and Epihov, D. and Kantola, I. and Masters, M. and Reershemius, Tom and Planavsky, N. and Reinhard, Chris and Jordan, J. and Thorne, Sarah J. and Weber, James and Martin, Maria Val and Freckleton, R. and Hartley, S. and James, R. and Pearce, C. and DeLucia, E. and Banwart, S.}, @@ -1468,8 +2337,10 @@ @article{beerling_enhanced_2024 abstract = {Terrestrial enhanced weathering (EW) of silicate rocks, such as crushed basalt, on farmlands is a promising scalable atmospheric carbon dioxide removal (CDR) strategy that urgently requires performance assessment with commercial farming practices. We report findings from a large-scale replicated EW field trial across a typical maize-soybean rotation on an experimental farm in the heart of the United Sates Corn Belt over 4 y (2016 to 2020). We show an average combined loss of major cations (Ca2+ and Mg2+) from crushed basalt applied each fall over 4 y (50 t ha−1 y−1) gave a conservative time-integrated cumulative CDR potential of 10.5 ± 3.8 t CO2 ha−1. Maize and soybean yields increased significantly (P {\textless} 0.05) by 12 to 16\% with EW following improved soil fertility, decreased soil acidification, and upregulation of root nutrient transport genes. Yield enhancements with EW were achieved with significantly (P {\textless} 0.05) increased key micro- and macronutrient concentrations (including potassium, magnesium, manganese, phosphorus, and zinc), thus improving or maintaining crop nutritional status. We observed no significant increase in the content of trace metals in grains of maize or soybean or soil exchangeable pools relative to controls. Our findings suggest that widespread adoption of EW across farming sectors has the potential to contribute significantly to net-zero greenhouse gas emissions goals while simultaneously improving food and soil security.}, author = {Beerling, David J. and Epihov, Dimitar Z. and Kantola, Ilsa B. and Masters, Michael D. and Reershemius, Tom and Planavsky, Noah J. and Reinhard, Christopher T. and Jordan, Jacob S. and Thorne, Sarah J. and Weber, James and Val Martin, Maria and Freckleton, Robert P. and Hartley, Sue E. and James, Rachael H. and Pearce, Christopher R. and DeLucia, Evan H. and Banwart, Steven A.}, doi = {10.1073/pnas.2319436121}, + issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Silicates, Trace Elements, Zea mays}, + language = {eng}, month = {February}, note = {Publisher: Proceedings of the National Academy of Sciences}, number = {9}, @@ -1506,7 +2377,7 @@ @article{ben-oz_dual_2023 doi = {10.1038/s41467-023-43495-6}, issn = {2041-1723}, journal = {Nature Communications}, - keywords = {{\textgreater}UseGalaxy.eu, DNA damage and repair, DNA damage response}, + keywords = {{\textgreater}UseGalaxy.eu, DNA damage and repair, DNA damage response, Genes, cdc, Tumor Suppressor Protein p53}, language = {en}, month = {November}, note = {Number: 1 @@ -1520,12 +2391,32 @@ @article{ben-oz_dual_2023 year = {2023} } +@article{benatto_perino_suberin_2025, + abstract = {Suberin is a hydrophobic biopolymer that acts as an internal and external diffusion and transpiration barrier in plants. It is involved in two phases of wound healing, i.e. initial closing layer formation and subsequent wound periderm development. Transcriptomic and metabolomic analyses of wounded potato leaf tissue revealed preferential induction of cell wall modifying processes during closing layer formation, accompanied by a highly active defense response. To address the importance of suberin in this process, we generated loss of function mutants by CRISPR-Cas9 editing the suberin transporter gene StABCG1. Both wound-induced StABCG1 transcript levels and suberin formation around wounded leaf tissue were reduced in CRISPR-lines. Moreover, wound-induced tissue damage was characterized by browning of wound-adjacent areas. Transcriptome analyses of these areas revealed up-regulation of genes encoding defense proteins and enzymes of the phenylpropanoid pathway. Levels of hydroxycinnamic acid amides, acting in defense and in cell wall reinforcement, were drastically enhanced in CRISPR compared to control plants. These results suggest that the reduction in suberin formation around wounded tissue leads to a loss of barrier function, resulting in tissue browning due to enhanced exposure to oxygen.}, + author = {Benatto Perino, Elvio Henrique and Smolka, Ulrike and Gorzolka, Karin and Grützner, Ramona and Marillonnet, Sylvestre and Vahabi, Khabat and Rosahl, Sabine}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-89032-x}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Secondary metabolism, Wounding}, + language = {en}, + month = {March}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {7930}, + title = {The suberin transporter {StABCG1} is required for barrier formation in potato leaves}, + url = {https://www.nature.com/articles/s41598-025-89032-x}, + urldate = {2025-03-09}, + volume = {15}, + year = {2025} +} + @article{bennett-keki_sex-biased_2023, abstract = {Differences in lifespan between males and females are found across many taxa and may be determined, at least in part, by differential responses to diet. Here we tested the hypothesis that the higher dietary sensitivity of female lifespan is mediated by higher and more dynamic expression in nutrient-sensing pathways in females. We first reanalysed existing RNA-seq data, focusing on 17 nutrient-sensing genes with reported lifespan effects. This revealed, consistent with the hypothesis, a dominant pattern of female-biased gene expression, and among sex-biased genes there tended to be a loss of female-bias after mating. We then tested directly the expression of these 17 nutrient-sensing genes in wild-type third instar larvae, once-mated 5- and 16-day-old adults. This confirmed sex-biased gene expression and showed that it was generally absent in larvae, but frequent and stable in adults. Overall, the findings suggest a proximate explanation for the sensitivity of female lifespan to dietary manipulations. We suggest that the contrasting selective pressures to which males and females are subject create differing nutritional demands and requirements, resulting in sex differences in lifespan. This underscores the potential importance of the health impacts of sex-specific dietary responses.}, author = {Bennett-Keki, Suzanne and Fowler, Emily K. and Folkes, Leighton and Moxon, Simon and Chapman, Tracey}, doi = {10.1098/rspb.2022.2086}, journal = {Proceedings of the Royal Society B: Biological Sciences}, - keywords = {{\textgreater}UseGalaxy.eu, diet, fruitfly, lifespan, nutrient-sensing}, + keywords = {{\textgreater}UseGalaxy.eu, Cell Communication, Longevity, diet, fruitfly, lifespan, nutrient-sensing}, month = {March}, note = {Publisher: Royal Society}, number = {1994}, @@ -1553,6 +2444,100 @@ @article{berlanga_biodiversity_2024 year = {2024} } +@article{berlanga_changes_2025, + abstract = {\<h4\>Introduction\</h4\>The gut microbiome plays a crucial role in host health through complex host-microbe interactions. Beta-glucans, structural polysaccharides found in yeast cell walls, have emerged as promising modulators of immune function and microbial ecology. Cava lees, a by-product of sparkling wine production composed of \<i\>Saccharomyces cerevisiae\</i\> cell walls, represent a rich source of beta-glucans that could be upcycled for nutritional and therapeutic applications.\<h4\>Methods\</h4\>Twenty-four Wistar rats (12 males, 12 females) were randomly divided into control and treatment groups. The treatment group received daily doses of 2,000 mg lees/kg body weight for 14 days. Shotgun metagenomic analysis was performed to assess microbial composition and functional changes.\<h4\>Results\</h4\>A 14-day cava lees supplementation study revealed significant shifts in gut microbiota composition and function. Baseline microbiota was dominated by Bacillota (64-72\%) and Bacteroidota (23-32\%) with sex-specific differences at the family level. Post-supplementation analysis showed increased Shannon diversity across both sexes, with beneficial enrichment of \<i\>Bifidobacteriaceae\</i\> and \<i\>Rikenellaceae\</i\> families and reduction of \<i\>Eubacteriaceae\</i\>. While global metabolic profiles remained stable, targeted functional pathways were significantly changed, including butyrate production genes. Females exhibited particularly elevated secondary bile acid modification genes (Mann-Whitney-Wilcoxon test \<i\>p\</i\> = 0.032), and male oxidative stress response pathways (Mann-Whitney-Wilcoxon test \<i\>p\</i\> = 0.016) showing both a potentially sex-dependent responses to dietary intervention.\<h4\>Conclusion\</h4\>Working with healthy individuals provides a clear understanding of the normal, baseline microbiota composition and function before any intervention. These findings suggest a degree of plasticity of the gut microbiome and its responsiveness to dietary modifications. Beta-glucans from cava lees appear to create a favorable environment for beneficial bacteria, with sex-specific changes of certain bacterial families and functions. These findings provide a foundation for future translational research in humans. Nonetheless, to establish their true impact on human health, these observations in rodent models must be validated through appropriately designed human clinical studies.}, + author = {Berlanga, Mercedes and Martín-García, Alba and Guerrero, Ricardo and Riu-Aumatell, Montserrat and López-Tamames, Elvira}, + doi = {10.3389/fnut.2025.1641612}, + issn = {2296-861X}, + journal = {Frontiers in nutrition}, + keywords = {{\textgreater}UseGalaxy.eu, Beta-glucans Cava Lees, Gut Functionality, Gut Microbiota Diversity, Healthy Wistar Rat, Metagenomics Analysis}, + pages = {1641612}, + title = {Changes in healthy {Wistar} rat gut microbiome by short-term dietary cava lees intervention}, + url = {https://europepmc.org/articles/PMC12484048}, + volume = {12}, + year = {2025} +} + +@article{berlanga_disentangling_2025, + abstract = {Gut microbiota enable wood-feeding insects to digest recalcitrant diets. Two DNA-based analyses were performed. Amplicon sequencing of gut microbiota samples from Cryptocercus punctulatus showed inter-individual heterogeneity with visually distinct ordination patterns; however, no statistically significant differences were detected. Shotgun metagenomics was used to compare the taxonomic and functional profiles of C. punctulatus gut microbiota with those of other xylophagous Dictyoptera. Despite taxonomic differences, C. punctulatus microbiota revealed functional convergence with termites (Mastotermes darwiniensis and Nasutitermes sp.). Carbohydrate metabolism was performed by different bacterial phyla across all insects. All insect species possessed metabolic potential for cellulose, hemicellulose, pectin, and starch digestion, but lignin degradation capabilities were not detected. Termites showed higher abundance of chitin and xylan degradation pathways and nitrogen fixation genes, though nitrogen fixation was also present in Cryptocercus cockroaches. Genes for oxidative stress tolerance were present across all species but were most abundant in cockroaches, particularly, Cryptocercus. All insects harbored antibiotic resistance genes, with highest levels found in cockroaches. These findings indicate that metabolic requirements for wood digestion shape gut microbial community assembly across xylophagous insects, with distinct microbial taxa contributing to cellulose and hemicellulose breakdown. Moreover, the widespread presence of antibiotic resistance genes raises concerns about the potential transmission of antibiotic resistance within insect-associated microbiomes.}, + author = {Berlanga, Mercedes and Miñana-Galbis, David and Guerrero, Ricardo}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/insects16111128}, + issn = {2075-4450}, + journal = {Insects}, + keywords = {\textit{Cryptocercus}, {\textgreater}UseGalaxy.eu, functional microbiome, gut microbiota, xylophagous dyctioptera insects}, + language = {en}, + month = {November}, + note = {Publisher: Multidisciplinary Digital Publishing Institute}, + number = {11}, + pages = {1128}, + title = {Disentangling {Gut} {Bacterial} {Community} {Patterns} in {Cryptocercus} punctulatus and {Comparing} {Their} {Metagenomes} with {Other} {Xylophagous} {Dyctioptera} {Insects}}, + url = {https://www.mdpi.com/2075-4450/16/11/1128}, + urldate = {2025-12-26}, + volume = {16}, + year = {2025} +} + +@article{berns_homozygous_2024, + abstract = {Wnt signaling plays important roles during vertebrate development, including left-right axis specification as well as heart and kidney organogenesis. We identified a homozygous human WNT11 variant in an infant with Situs inversus totalis , complex heart defects and renal hypodysplasia, and we used Xenopus embryos to functionally characterize this variant. WNT11 c.814delG encodes a loss-of-function protein with reduced stability that lost signaling activity in vivo . This is remarkable, because the variant encodes a truncated ligand with nearly identical length and predicted structure to dominant-negative Wnts. Furthermore, we demonstrate that alteration of the truncated C-terminal end can restore stability and dominant-negative signaling activity. Our study also suggests similar functions for WNT11 in human development as described in model organisms. Therefore, biallelic WNT11 dysfunction should be considered as novel genetic cause in syndromal human phenotypes presenting with congenital heart defects and renal hypoplasia, with or without laterality defects. The work presented here enhances our understanding of human development and structure-function relationships in Wnt ligands.}, + author = {Berns, Henrike and Haas, Maximilian and Bakey, Zeineb and Brislinger-Engelhardt, Magdalena Maria and Schmidts, Miriam and Walentek, Peter}, + doi = {10.1101/2024.11.14.623711}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {A homozygous {humanWNT11loss}-of-function variant associated with laterality, heart and renal defects}, + url = {http://europepmc.org/abstract/PPR/PPR939784}, + year = {2024} +} + +@article{berns_homozygous_2025, + abstract = {Wnt signaling plays important roles during vertebrate development, including left-right axis specification as well as heart and kidney organogenesis. We identified a homozygous human WNT11 variant in an infant with Situs inversus totalis, complex heart defects and renal hypodysplasia, and we used Xenopus embryos to functionally characterize this variant. WNT11c.814delG encodes a protein with reduced stability that lost signaling activity in vivo. This is remarkable, because the variant encodes a truncated ligand with nearly identical length and predicted structure to dominant-negative Wnts. Furthermore, we demonstrate that alteration of the truncated C-terminal end can restore stability and signaling activity similar to Xenopus dominant-negative Wnt11b. Our study also suggests similar functions for WNT11 in human development as described in model organisms. Therefore, biallelic WNT11 dysfunction should be considered as novel genetic cause in syndromal human phenotypes presenting with congenital heart defects and renal hypoplasia, with or without laterality defects. The work presented here enhances our understanding of human development and structure-function relationships in Wnt ligands.}, + author = {Berns, Henrike and Weber, Damian and Haas, Maximilian and Bakey, Zeineb and Brislinger-Engelhardt, Magdalena Maria and Schmidts, Miriam and Walentek, Peter}, + doi = {10.1242/dmm.052211}, + issn = {1754-8403}, + journal = {Disease Models \& Mechanisms}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {April}, + pages = {dmm.052211}, + title = {A homozygous human {WNT11} variant is associated with laterality, heart and renal defects}, + url = {https://doi.org/10.1242/dmm.052211}, + urldate = {2025-04-11}, + year = {2025} +} + +@article{bertucci_molecular_2025, + abstract = {Climate change and pollution represent critical stressors for marine ecosystems, particularly for calcifying organisms such as the sea urchin Paracentrotus lividus. This study examines the combined effects of ocean acidification (OA), ocean warming (OW), and microplastics (MP) loaded with chlorpyrifos (CPF), a broad-spectrum organophosphate insecticide, on sea urchin larvae, evaluating growth and molecular endpoints. Experimental treatments simulated future ocean conditions predicted for 2100, exposing larvae to varying temperature and pH levels, alongside CPF-contaminated MP. RNA sequencing (RNA-seq) was utilized to assess gene expression changes, revealing significant transcriptional shifts in metabolic, cellular, and developmental pathways. Morphological responses showed reduced larval growth, exacerbated under OA and OW conditions. Molecular analyses identified key upregulated pathways associated with stress response, including nitrogen metabolism and extracellular matrix remodelling, while downregulated genes involved DNA stability, cell cycle regulation, and enzymatic activities. These findings suggest a dual compensatory and deleterious response to combined stressors. Notably, temperature acted as a modulator of stressor effects, amplifying oxidative stress and metabolic costs at higher temperatures. Potential biomarkers, such as genes involved in actin regulation and embryonic development, were identified, offering possible tools for early detection of environmental stress. This study highlights the compounded impacts of anthropogenic and climate-induced stressors on marine invertebrates, emphasizing the need for integrative molecular approaches in ecotoxicology. Our findings contribute to the understanding of organismal adaptation and vulnerability in the face of global climate change and pollution, informing conservation strategies for marine ecosystems.}, + author = {Bertucci, Juan Ignacio and Blanco Osorio, Angie and Vidal-Liñán, Leticia and Bellas, Juan}, + doi = {10.1016/j.cbpc.2025.110320}, + issn = {1532-0456}, + journal = {Comparative Biochemistry and Physiology Part C: Toxicology \& Pharmacology}, + keywords = {{\textgreater}UseGalaxy.eu, Chlorpyrifos, Ecotoxicology, Microplastics, Ocean acidification, Ocean warming, RNA sequencing, Sea urchin larvae}, + month = {December}, + pages = {110320}, + shorttitle = {Molecular markers of stress in the sea urchin embryo test}, + title = {Molecular markers of stress in the sea urchin embryo test: {Analysing} the effect of climate change and pollutant mixtures on \textit{{Paracentrotus} lividus} larvae}, + url = {https://www.sciencedirect.com/science/article/pii/S1532045625002017}, + urldate = {2025-09-03}, + volume = {298}, + year = {2025} +} + +@misc{bessette_integrated_2025, + abstract = {This study addresses the potential species complex of gregarine parasites infecting cricket hosts by investigating Leidyana gryllorum (Cuenot, 1897) Watson, 1916 and L. erratica (Crawley, 1907) Watson, 1916, described from Acheta domesticus and Gryllus pennsylvanicus, respectively, and later synonymised. Although molecular data exist for L. erratica, none were available for L. gryllorum. To address this gap, gregarine specimens were isolated from an A. domesticus colony and examined using integrated morphological and molecular approaches. Hybrid genome sequencing with Illumina and Nanopore platforms yielded a high-quality L. gryllorum assembly, which enabled the design of specific 18S primers and subsequent phylogenetic analyses that revealed 91.6–92.6\% similarity to the L. erratica reference. Genome annotation revealed a partial ubiquinol-cytochrome c reductase, consistent with previous observations of reduced mitochondrial function in eugregarines. Functional annotation using eggNOG, InterProScan, and KEGG mapping uncovered genes involved in amino acid, carbohydrate, and nucleotide metabolism, while GO analysis highlighted a diverse functional repertoire. Data mining of NCBI cricket sequencing datasets further identified additional putative Leidyana 18S sequences in various Gryllidae hosts, confirming a broader host range. Eventually, phylogenomic analyses placed L. gryllorum within the Gregarinoidea clade near the root of terrestrial gregarines, supporting its status as an early-diverging lineage.}, + address = {Rochester, NY}, + author = {Bessette, Edouard and Vitt Meyling, Nicolai and Williams, Bryony A. P.}, + doi = {10.2139/ssrn.5218124}, + keywords = {{\textgreater}UseGalaxy.eu, Data mining, Eugregarine, Genomic, Orthoptera, Phylogeny}, + language = {en}, + month = {April}, + publisher = {Social Science Research Network}, + shorttitle = {Integrated {Morphological} and {Genome} {Redescription} of {Leidyana} {Gryllorum} in {Acheta} {Domesticus}}, + title = {Integrated {Morphological} and {Genome} {Redescription} of {Leidyana} {Gryllorum} in {Acheta} {Domesticus}: {Uncovering} {Gregarine} {Diversity} in {Gryllidae}}, + type = {{SSRN} {Scholarly} {Paper}}, + url = {https://papers.ssrn.com/abstract=5218124}, + urldate = {2025-05-28}, + year = {2025} +} + @article{besson_pan-flavivirus_2024, author = {Besson, Benoit and Overheul, Gijs J. and Wolfinger, Michael T. and Junglen, Sandra and van Rij, Ronald P.}, doi = {10.1128/jvi.01215-24}, @@ -1569,6 +2554,41 @@ @article{besson_pan-flavivirus_2024 year = {2024} } +@article{bessonov_ectyper_2021, + abstract = {\textit{Escherichia coli} is a priority foodborne pathogen of public health concern and phenotypic serotyping provides critical information for surveillance and outbreak detection activities. Public health and food safety laboratories are increasingly adopting whole-genome sequencing (WGS) for characterizing pathogens, but it is imperative to maintain serotype designations in order to minimize disruptions to existing public health workflows. Multiple \textit{in silico} tools have been developed for predicting serotypes from WGS data, including SRST2, SerotypeFinder and EToKi EBEis, but these tools were not designed with the specific requirements of diagnostic laboratories, which include: speciation, input data flexibility (fasta/fastq), quality control information and easily interpretable results. To address these specific requirements, we developed ECTyper (https://github.com/phac-nml/ecoli\_serotyping) for performing both speciation within \textit{Escherichia} and \textit{Shigella}, and \textit{in silico} serotype prediction. We compared the serotype prediction performance of each tool on a newly sequenced panel of 185 isolates with confirmed phenotypic serotype information. We found that all tools were highly concordant, with 92-97 \% for O-antigens and 98-100 \% for H-antigens, and ECTyper having the highest rate of concordance. We extended the benchmarking to a large panel of 6954 publicly available \textit{E. coli} genomes to assess the performance of the tools on a more diverse dataset. On the public data, there was a considerable drop in concordance, with 75-91 \% for O-antigens and 62-90 \% for H-antigens, and ECTyper and SerotypeFinder being the most concordant. This study highlights that \textit{in silico} predictions show high concordance with phenotypic serotyping results, but there are notable differences in tool performance. ECTyper provides highly accurate and sensitive \textit{in silico} serotype predictions, in addition to speciation, and is designed to be easily incorporated into bioinformatic workflows.}, + author = {Bessonov, Kyrylo and Laing, Chad and Robertson, James and Yong, Irene and Ziebell, Kim and Gannon, Victor P J and Nichani, Anil and Arya, Gitanjali and Nash, John H E and Christianson, Sara}, + doi = {10.1099/mgen.0.000728}, + issn = {2057-5858}, + journal = {Microb Genom}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {December}, + number = {12}, + title = {{ECTyper}: in silico {Escherichia} coli serotype and species prediction from raw and assembled whole-genome sequence data}, + url = {http://europepmc.org/abstract/MED/34860150}, + volume = {7}, + year = {2021} +} + +@article{bhuiyan_taf2_2025, + abstract = {{\textless}h2{\textgreater}Summary{\textless}/h2{\textgreater}{\textless}p{\textgreater}TFIID is an essential basal transcription factor, crucial for RNA polymerase II (pol II) promoter recognition and transcription initiation. The TFIID complex consists of the TATA binding protein (TBP) and 13 TBP-associated factors (TAFs) that contain intrinsically disordered regions (IDRs) with currently unknown functions. Here, we show that a conserved IDR drives TAF2 to nuclear speckle condensates independently of other TFIID subunits. Quantitative mass spectrometry analyses reveal TAF2 proximity to RNA splicing factors including specific interactions of the TAF2 IDR with SRRM2 in nuclear speckles. Deleting the IDR from TAF2 does not majorly impact global gene expression but results in changes of alternative splicing events. Further, genome-wide binding analyses suggest that the TAF2 IDR impedes TAF2 promoter association by guiding TAF2 to nuclear speckles. This study demonstrates that an IDR within the large multiprotein complex TFIID controls nuclear compartmentalization and thus links distinct molecular processes, namely transcription initiation and RNA splicing.{\textless}/p{\textgreater}}, + author = {Bhuiyan, Tanja and Arecco, Niccolò and Sanchez, Paulina Karen Mendoza and Kim, Juhyeong and Schwan, Carsten and Weyrauch, Sophie and Nizamuddin, Sheikh and Prunotto, Andrea and Tekman, Mehmet and Biniossek, Martin L. and Knapp, Bettina and Koidl, Stefanie and Drepper, Friedel and Huesgen, Pitter F. and Grosse, Robert and Hugel, Thorsten and Arnold, Sebastian J.}, + doi = {10.1016/j.celrep.2025.115616}, + issn = {2211-1247}, + journal = {Cell Reports}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {English}, + month = {May}, + note = {Publisher: Elsevier}, + number = {5}, + pmid = {40287942}, + title = {{TAF2} condensation in nuclear speckles links basal transcription factor {TFIID} to {RNA} splicing factors}, + url = {https://www.cell.com/cell-reports/abstract/S2211-1247(25)00387-0}, + urldate = {2025-05-29}, + volume = {44}, + year = {2025} +} + @article{bianconi_characterization_2024, abstract = {Multidrug-resistant Escherichia coli, particularly carbapenemase producers, are a major source of concern. This study aims to investigate the long-term epidemiology of Verona integron-encoded metallo-β-lactamase (VIM)-producing E. coli in the health district of Bolzano, Northern Italy, by examining the phenotypic and genotypic characteristics of 26 isolates obtained during 2005–2020. Isolates were identified with matrix-assisted laser desorption/ionization time-of-flight, susceptibility testing was by Vitek 2, Sensititre, and Etest; carbapenemase activity was confirmed by Etest and Carbapenemase Inactivation Method (CIM) test; and the VIM-antigen was identified by the NG-Test CARBA 5. Genome sequencing was performed on an Illumina MiSeq platform. Carbapenem minimum inhibitory concentrations varied across methodologies, and overall category agreement between phenotypic methods was low. All 23 sequenced isolates contained blaVIM-1. Eleven (47.8\%) isolates belonged to the clonal lineage ST131, with fimH30 being the most common subclone. In Bolzano ST131-fimH30 was present as early as 2005. While the ST131 clonal lineage predominated for the first 10 years, various clonal lineages were present, especially in subsequent years, indicating the concurrent circulation of multiple clonal lineages. Future efforts should focus on the implementation of surveillance methods, including genomic analysis, as well as the use of updated infection control strategies and antibiotic stewardship programs to prevent the spread of these carbapenem-resistant strains.}, author = {Bianconi, Irene and Spath, Manuela and Aschbacher, Richard and Pedron, Renato and Wieser, Stefanie and Pagani, Elisabetta}, @@ -1593,15 +2613,29 @@ @article{bianconi_disseminated_2024 doi = {10.1007/s15010-024-02315-9}, issn = {1439-0973}, journal = {Infection}, - keywords = {{\textgreater}UseGalaxy.eu, Echovirus 11, Illumina, Nanopore, Newborn, Non-polio Enteroviruses, Phylogeny, WGS}, + keywords = {{\textgreater}UseGalaxy.eu, Echovirus 11, Echovirus Infections, Enterovirus B, Human, Illumina, Nanopore, Newborn, Non-polio Enteroviruses, Phylogeny, WGS}, language = {en}, month = {August}, + number = {6}, + pages = {2501--2506}, title = {Disseminated {Echovirus} 11 infection in a newborn in the {Province} of {Bolzano}, {Italy}}, url = {https://doi.org/10.1007/s15010-024-02315-9}, urldate = {2024-10-20}, + volume = {52}, year = {2024} } +@article{bihani_metaproteomic_2023, + abstract = {Respiratory infections disrupt the microbiota in the upper respiratory tract (URT), putting patients at a risk for subsequent infections. During the pandemic, cases of COVID-19 were aggravated by secondary infections because of impaired immunity and medical interventions, which was clearly evident in the second wave of COVID-19 in India. The potential dangers and clinical difficulties of bacterial and fungal secondary infections in COVID-19 patients necessitate microbial exploration of the URT. In this regard, mass spectrometry (MS)-based proteome data of nasopharyngeal swab samples from COVID-19 patients was used to investigate the metaproteome. The MS datasets were searched against a comprehensive protein sequence database of common URT pathogens using multiple search platforms (MaxQuant, MSFragger, and Search GUI/PeptideShaker). The detected microbial peptides were verified using PepQuery, which analyses peptide-spectrum pairs to give statistical output for determining confident microbial peptides. Finally, a protein sequence database was generated using the list of verified microbial peptides for identification and quantitation of microbial peptides and proteins, respectively. The taxonomic analysis of the detected peptides revealed several opportunistic pathogens like Streptococcus pneumoniae, Rhizopus microsporus, Clavispora lusitaniae , and Syncephalastrum racemosum among others. Using parallel reaction monitoring (PRM), we validated a few identified microbial peptides in clinical samples. The analysis also revealed proteins belonging to species like Pseudomonas fluorescens, Enterobacter , and Clostridium to be up-regulated in severe COVID-19 samples. Thus, MS can serve as a powerful tool for untargeted detection of a wide range of microorganisms. Metaproteomic analysis in COVID-19 patients for early identification and characterisation of co-infecting microorganisms can significantly impact the diagnosis and treatment of patients.}, + author = {Bihani, Surbhi and Gupta, Aryan and Mehta, Subina and Rajczewski, Andrew and Johnson, James and Borishetty, Dhanush and Griffin, Timothy and Srivastava, Sanjeeva and Jagtap, Pratik}, + doi = {10.1101/2023.01.31.525328}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Metaproteomic analysis of nasopharyngeal swab samples to identify microbial peptides and potential co-infection status in {COVID}-19 patients}, + url = {http://europepmc.org/abstract/PPR/PPR610725}, + year = {2023} +} + @article{bihani_metaproteomic_2023, abstract = {During the COVID-19 pandemic, impaired immunity and medical interventions resulted in cases of secondary infections. The clinical difficulties and dangers associated with secondary infections in patients necessitate the exploration of their microbiome. Metaproteomics is a powerful approach to study the taxonomic composition and functional status of the microbiome under study. In this study, the mass spectrometry (MS)-based data of nasopharyngeal swab samples from COVID-19 patients was used to investigate the metaproteome. We have established a robust bioinformatics workflow within the Galaxy platform, which includes (a) generation of a tailored database of the common respiratory tract pathogens, (b) database search using multiple search algorithms, and (c) verification of the detected microbial peptides. The microbial peptides detected in this study, belong to several opportunistic pathogens such as Streptococcus pneumoniae, Klebsiella pneumoniae, Rhizopus microsporus, and Syncephalastrum racemosum. Microbial proteins with a role in stress response, gene expression, and DNA repair were found to be upregulated in severe patients compared to negative patients. Using parallel reaction monitoring (PRM), we confirmed some of the microbial peptides in fresh clinical samples. MS-based clinical metaproteomics can serve as a powerful tool for detection and characterization of potential pathogens, which can significantly impact the diagnosis and treatment of patients.}, author = {Bihani, Surbhi and Gupta, Aryan and Mehta, Subina and Rajczewski, Andrew T. and Johnson, James and Borishetty, Dhanush and Griffin, Timothy J. and Srivastava, Sanjeeva and Jagtap, Pratik D.}, @@ -1660,8 +2694,34 @@ @article{biswas_integrated_2023 year = {2023} } -@article{blacklock_examination_2022, - author = {Blacklock, Emily}, +@article{black_genome-wide_2024, + abstract = {When exposed single-stranded DNA accumulates at stalled or collapsed replication forks, the replication stress response is triggered to prevent genome instability. Leishmania are parasitic eukaryotes where gene expression is universally polycistronic and whose plastic genomes facilitate rapid adaptations in response to stress, with evidence implicating intrinsic replication stress as a source. Little is known about the Leishmania replication stress response. In this study, we reveal the global dynamics of the replication stress response in L. major promastigotes by performing ChIP-seq on three key replication stress response proteins, γH2A, RPA1 and RAD9, in the absence and presence of replication stress. We show that common ‘hotspots’ of replication stress correlate with DNA replication initiation and transcription termination in Leishmania . When DNA replication is stalled, replication stress response factors accumulate at early S-phase origins, with a signal pattern reminiscent of bidirectional replication fork progression. Under conditions of chronic replication stress, increased accumulation of replication stress response factors emerges at wider sites of transcription initiation, suggesting Leishmania may possess compensatory strategies to limit the effects of replication stress and ensure DNA replication can complete under these conditions. In contrast, chronic replication stress enhances RSR factor accumulation at transcription termination sites, highlighting these regions as key replication stress ‘hotspots’ in Leishmania . Lastly, variations in RPA dynamics in ATR-deficient cells uncover crucial roles of this protein kinase in managing polycistronic transcription and DNA replication, particularly under replication stress, in Leishmania . {\textless}h4{\textgreater}Summary{\textless}/h4{\textgreater} Strict controls operate to precisely copy an organism’s DNA. However, cells need ways to rapidly adapt and respond to stimuli. In some cases, these beneficial adaptations come from problems during replication. Leishmania parasites cause serious neglected infections in humans and animals across the world’s tropics and sub-tropics. Remarkably, recent evidence suggests that Leishmania DNA experiences enhanced stress during replication that can drive its ability to rapidly adapt in response to stress. How L eishmania respond to DNA replication stress is still poorly understood. Here, using a genome-wide approach to map the locations of key proteins that manage DNA replication stress and maintain genome integrity, we show ‘hotspots’ of DNA replication stress coincide with start sites of DNA replication and regions of transcription termination.}, + author = {Black, J.A. and Virgilio, S and Bastos, M.S. and Silva, G.L.A. and Damasceno, J.D. and Lapsley, C and McCulloch, R and Tosi, L.R.O.}, + doi = {10.1101/2024.11.04.621868}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Genome-wide mapping of {RPA1} and {RAD9} reveals the management of polycistronic transcription, replication initiation, and responses to replication stress {inLeishmania}}, + url = {http://europepmc.org/abstract/PPR/PPR935225}, + year = {2024} +} + +@article{black_resolution_2025, + abstract = {Bacteriophage contaminations pose substantial risks to biomolecular production pipelines, and their resolution is especially difficult when the identity of the offending agent is unknown. We recently experienced an outbreak of Escherichia coli culture lysis in our Melbourne-based structural biology labs that halted protein production despite our use of T1-resistant (TonA/FhuA-disrupted) strains. Genetic analysis of the isolated phage yielded a 45,053 bp genome showing 80–90\% identity with multiple Rtp-like siphophages, and transmission electron microscopy images were consistent with this classification. Further analysis revealed that our isolate was nearly identical to a highly virulent lytic coliphage MSK, recently isolated in Hangzhou, China, whose host receptor has not been determined. Sequence and structural modelling analysis of its putative receptor-binding protein suggested that its terminal receptor was likely to be LptD, an essential outer membrane protein involved in lipopolysaccharide transport. Based on a recent report of spontaneously arising mutations that blocked infection by other LptD-dependent bacteriophages, we designed a targeted genomic LptD loop deletion that successfully generated resistance to vB\_EcoS\_OzMSK in E. coli BL21(DE3) without apparent detriment to fitness. Here, we report a CRISPR-based, single-plasmid solution that will benefit other labs or facilities experiencing challenges due to LptD-dependent lytic phage outbreaks.}, + author = {Black, Katrina A. and Nguyen, Julie V. and Ramsey, Jolene R. and Tovey, Jack C. and Cameron, Daniel L. and Alexandrovics, Jack and Glukhova, Alisa and Papenfuss, Anthony T. and Call, Melissa J. and Young, Ryland and Call, Matthew E.}, + doi = {10.1007/s12033-025-01453-1}, + issn = {1559-0305}, + journal = {Molecular Biotechnology}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial Genes, Bacteriophage receptor, Bacteriophage resistance, Bacteriophages, CRISPR/Cas9, Escherichia Coli, LptD, Pattern Recognition Receptors in Plants, Receptor engineering, Siphophage, T-cell receptor, Toll-like receptors}, + language = {en}, + month = {June}, + title = {Resolution of a {T1}-{Like} {Bacteriophage} {Outbreak} by {Receptor} {Engineering}}, + url = {https://doi.org/10.1007/s12033-025-01453-1}, + urldate = {2025-07-12}, + year = {2025} +} + +@article{blacklock_examination_2022, + author = {Blacklock, Emily}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, title = {Examination of crustacean immune responses through {dsRNA}-nanoparticle injection and phylogenetic analysis}, year = {2022} @@ -1692,15 +2752,17 @@ @article{blomberg_connecting_2020 doi = {10.1038/s41431-020-0637-5}, issn = {1476-5438}, journal = {European Journal of Human Genetics}, - keywords = {+RefPublic, +Stellar, {\textgreater}UseGalaxy.eu}, + keywords = {+RefPublic, +Stellar, {\textgreater}UseGalaxy.eu, Pandemics}, language = {en}, month = {May}, note = {Publisher: Nature Publishing Group}, + number = {6}, pages = {1--5}, shorttitle = {Connecting data, tools and people across {Europe}}, title = {Connecting data, tools and people across {Europe}: {ELIXIR}’s response to the {COVID}-19 pandemic}, url = {https://www.nature.com/articles/s41431-020-0637-5}, urldate = {2020-05-22}, + volume = {28}, year = {2020} } @@ -1710,7 +2772,7 @@ @article{bloor_rna_2024 doi = {10.1093/nar/gkae1165}, issn = {0305-1048}, journal = {Nucleic Acids Research}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Gene Silencing, RNA, RNA-Binding Proteins}, month = {December}, pages = {gkae1165}, title = {{RNA} binding by {Periphilin} plays an essential role in initiating silencing by the {HUSH} complex}, @@ -1719,6 +2781,20 @@ @article{bloor_rna_2024 year = {2024} } +@article{blows_genome_2025, + abstract = {We present a genome assembly from a male specimen of \<i\>Buteo buteo\</i\> (Common Buzzard; Chordata; Aves; Accipitriformes; Accipitridae). The assembly contains two haplotypes with total lengths of 1,303.68 megabases and 1,330.55 megabases. Most of haplotype 1 (94.6\%) is scaffolded into 34 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 is a scaffold-level assembly. The mitochondrial genome has also been assembled, with a length of 18.36 kilobases.}, + author = {Blows, Elizabeth and {Natural History Museum Genome Acquisition Lab} and {Darwin Tree of Life Barcoding collective} and {Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team} and {Wellcome Sanger Institute Scientific Operations: Sequencing Operations} and {Wellcome Sanger Institute Tree of Life Core Informatics team} and {Tree of Life Core Informatics collective} and {Darwin Tree of Life Consortium}}, + doi = {10.12688/wellcomeopenres.23873.2}, + issn = {2398-502X}, + journal = {Wellcome open research}, + keywords = {{\textgreater}UseGalaxy.eu}, + pages = {130}, + title = {The genome sequence of the {Common} {Buzzard}, \&lt;i\&gt;{Buteo} buteo\&lt;/i\&gt; ({Linnaeus}, 1758)}, + url = {https://europepmc.org/articles/PMC12481152}, + volume = {10}, + year = {2025} +} + @article{bode_catecholamine_2024, abstract = {Catecholamines are commonly used as therapeutic drugs in intensive care medicine to maintain sufficient organ perfusion during shock. However, excessive or sustained adrenergic activation drives detrimental cardiac remodeling and may lead to heart failure. Whether catecholamine treatment in absence of heart failure causes persistent cardiac injury, is uncertain. In this experimental study, we assessed the course of cardiac remodeling and recovery during and after prolonged catecholamine treatment and investigated the molecular mechanisms involved.}, author = {Bode, Christine and Preissl, Sebastian and Hein, Lutz and Lother, Achim}, @@ -1812,14 +2888,76 @@ @article{bokharaie_analysis_2022 doi = {10.3390/biom12070993}, issn = {2218-273X}, journal = {Biomolecules}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Antineoplastic Agents, Melanoma}, + language = {eng}, number = {7}, + pages = {993}, title = {Analysis of {Alternative} {mRNA} {Splicing} in {Vemurafenib}-{Resistant} {Melanoma} {Cells}}, url = {https://www.mdpi.com/2218-273X/12/7/993}, volume = {12}, year = {2022} } +@article{bolanakis_erga-bge_2025, + abstract = {Dendarus foraminosus +Mulsant and Rey, 1855 is a darkling beetle in the family Tenebrionidae and one of the many +Dendarus +species endemic to the island of Crete. +Dendarus foraminosus +is a commonly found species and is widespread in the lowland and montane phrygana and maquis of central Crete. The species is classified as Least Concern (LC) by the IUCN Red List. The reference genome of +Dendarus foraminosus +will enable phylogenetic, population, and evolutionary research regarding this endemic species and its close relatives. A total of 11 contiguous chromosomal pseudomolecules (sex chromosomes included) were assembled from the genome sequence. This chromosome-level assembly encompasses 0.59 Gb, composed of 430 contigs and 415 scaffolds, with contig and scaffold N50 values of 24.4 Mb and 51.9 Mb, respectively.}, + author = {Bolanakis, Giannis and Karakasi, Danae and Trichas, Apostolos and Böhne, Astrid and Monteiro, Rita and Fernández, Rosa and Escudero, Nuria and Bitzilekis, Eleftherios and Stratakis, Manos and Lymberakis, Petros and Poulakakis, Nikolaos and {Genoscope Sequencing Team} and Moussy, Alice and Cruaud, Corinne and Labadie, Karine and Demirdjian, Lola and Duprat, Simone and Téodori, Emilie and Wincker, Patrick and H. Oliveira, Pedro and Aury, Jean-Marc and Haggerty, Leanne and Sinha, Swati and Martin, Fergal and Bortoluzzi, Chiara}, + doi = {10.12688/openreseurope.20489.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {June}, + pages = {173}, + shorttitle = {{ERGA}-{BGE} genome of {Dendarus} foraminosus}, + title = {{ERGA}-{BGE} genome of {Dendarus} foraminosus: an {IUCN} {Least} {Concern} darkling beetle endemic to {Crete} ({Greece})}, + url = {https://open-research-europe.ec.europa.eu/articles/5-173/v1}, + urldate = {2025-10-19}, + volume = {5}, + year = {2025} +} + +@article{bolanakis_erga-bge_2025, + abstract = {Dailognatha quadricollis +(Coleoptera: Tenebrionidae) is a darkling beetle native to the Balkans and Eastern Mediterranean, with a range extending from Croatia to Lebanon. It is a morphologically diverse species, comprising numerous subspecies, particularly concentrated in the Aegean region. The reference genome of +Dailognatha quadricollis +will enable phylogenetic, population and evolutionary research. The entirety of the genome sequence was assembled into 11 contiguous chromosomal pseudomolecules (sex chromosome included). This chromosome-level assembly encompasses 0.52 Gb, composed of 393 contigs and 322 scaffolds, with contig and scaffold N50 values of 4.3 Mb and 23.6 Mb, respectively.}, + author = {Bolanakis, Giannis and Karakasi, Danae and Bitzilekis, Eleftherios and Stratakis, Manos and Trichas, Apostolos and Lymberakis, Petros and Poulakakis, Nikos and Böhne, Astrid and Monteiro, Rita and Fernández, Rosa and Escudero, Nuria and {Genoscope Sequencing Team} and Moussy, Alice and Cruaud, Corinne and Labadie, Karine and Demirdjian, Lola and Téodori, Emilie and Wincker, Patrick and H. Oliveira, Pedro and Aury, Jean-Marc and Bortoluzzi, Chiara}, + doi = {10.12688/openreseurope.20840.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {August}, + pages = {225}, + title = {{ERGA}-{BGE} genome of {Dailognatha} quadricollis, an {East} {Mediterranean} darkling beetle}, + url = {https://open-research-europe.ec.europa.eu/articles/5-225/v1}, + urldate = {2025-10-19}, + volume = {5}, + year = {2025} +} + +@article{boneva_-depth_2021, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Retinal neovascularization (RNV) membranes can lead to a tractional retinal detachment, the primary reason for severe vision loss in end-stage disease proliferative diabetic retinopathy (PDR). The aim of this study was to characterize the molecular, cellular and immunological features of RNV in order to unravel potential novel drug treatments for PDR.{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}A total of 43 patients undergoing vitrectomy for PDR, macular pucker or macular hole (control patients) were included in this study. The surgically removed RNV and epiretinal membranes were analyzed by RNA sequencing, single-cell based Imaging Mass Cytometry and conventional immunohistochemistry. Immune cells of the vitreous body, also known as hyalocytes, were isolated from patients with PDR by flow cytometry, cultivated and characterized by immunohistochemistry. A bioinformatical drug repurposing approach was applied in order to identify novel potential drug options for end-stage diabetic retinopathy disease.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}The in-depth transcriptional and single-cell protein analysis of diabetic RNV tissue samples revealed an accumulation of endothelial cells, macrophages and myofibroblasts as well as an abundance of secreted ECM proteins such as SPARC, FN1 and several types of collagen in RNV tissue. The immunohistochemical staining of cultivated vitreal hyalocytes from patients with PDR showed that hyalocytes express α-SMA (alpha-smooth muscle actin), a classic myofibroblast marker. According to our drug repurposing analysis, imatinib emerged as a potential immunomodulatory drug option for future treatment of PDR.{\textless}h4{\textgreater}Conclusion{\textless}/h4{\textgreater}This study delivers the first in-depth transcriptional and single-cell proteomic characterization of RNV tissue samples. Our data suggest an important role of hyalocyte-to-myofibroblast transdifferentiation in the pathogenesis of diabetic vitreoretinal disease and their modulation as a novel possible clinical approach.}, + author = {Boneva, Stefaniya Konstantinova and Wolf, Julian and Hajdú, Rozina Ida and Prinz, Gabriele and Salié, Henrike and Schlecht, Anja and Killmer, Saskia and Laich, Yannik and Faatz, Henrik and Lommatzsch, Albrecht and Busch, Martin and Bucher, Felicitas and Stahl, Andreas and Böhringer, Daniel and Bengsch, Bertram and Schlunck, Günther and Agostini, Hansjürgen and Lange, Clemens A K}, + doi = {10.3389/fimmu.2021.757607}, + issn = {1664-3224}, + journal = {Frontiers in immunology}, + keywords = {{\textgreater}UseGalaxy.eu, Cell Transdifferentiation}, + language = {eng}, + pages = {757607}, + title = {In-{Depth} {Molecular} {Characterization} of {Neovascular} {Membranes} {Suggests} a {Role} for {Hyalocyte}-to-{Myofibroblast} {Transdifferentiation} in {Proliferative} {Diabetic} {Retinopathy}}, + url = {http://europepmc.org/abstract/MED/34795670}, + volume = {12}, + year = {2021} +} + @article{boneva_3_2020, abstract = {This study aims to compare the potential of standard RNA-sequencing (RNA-Seq) and 3′ massive analysis of c-DNA ends (MACE) RNA-sequencing for the analysis of fresh tissue and describes transcriptome profiling of formalin-fixed paraffin-embedded (FFPE) archival human samples by MACE. To compare MACE to standard RNA-Seq on fresh tissue, four healthy conjunctiva from four subjects were collected during vitreoretinal surgery, halved and immediately transferred to RNA lysis buffer without prior fixation and then processed for either standard RNA-Seq or MACE RNA-Seq analysis. To assess the impact of FFPE preparation on MACE, a third part was fixed in formalin and processed for paraffin embedding, and its transcriptional profile was compared with the unfixed specimens analyzed by MACE. To investigate the impact of FFPE storage time on MACE results, 24 FFPE-treated conjunctival samples from 24 patients were analyzed as well. Nineteen thousand six hundred fifty-nine transcribed genes were detected by both MACE and standard RNA-Seq on fresh tissue, while 3251 and 2213 transcripts were identified explicitly by MACE or RNA-Seq, respectively. Standard RNA-Seq tended to yield longer detected transcripts more often than MACE technology despite normalization, indicating that the MACE technology is less susceptible to a length bias. FFPE processing revealed negligible effects on MACE sequencing results. Several quality-control measurements showed that long-term storage in paraffin did not decrease the diversity of MACE libraries. We noted a nonlinear relation between storage time and the number of raw reads with an accelerated decrease within the first 1000 days in paraffin, while the numbers remained relatively stable in older samples. Interestingly, the number of transcribed genes detected was independent on FFPE storage time. RNA of sufficient quality and quantity can be extracted from FFPE samples to obtain comprehensive transcriptome profiling using MACE technology. We thus present MACE as a novel opportunity for utilizing FFPE samples stored in histological archives.}, author = {Boneva, Stefaniya and Schlecht, Anja and Böhringer, Daniel and Mittelviefhaus, Hans and Reinhard, Thomas and Agostini, Hansjürgen and Auw-Haedrich, Claudia and Schlunck, Günther and Wolf, Julian and Lange, Clemens}, @@ -1827,14 +2965,16 @@ @article{boneva_3_2020 doi = {10.1038/s41374-020-0446-z}, issn = {1530-0307}, journal = {Laboratory Investigation}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Gene Expression Profiling, Tissue Preservation}, language = {en}, month = {May}, note = {Publisher: Nature Publishing Group}, + number = {10}, pages = {1--11}, title = {3′ {MACE} {RNA}-sequencing allows for transcriptome profiling in human tissue samples after long-term storage}, url = {https://www.nature.com/articles/s41374-020-0446-z}, urldate = {2020-08-12}, + volume = {100}, year = {2020} } @@ -1845,7 +2985,7 @@ @article{boneva_mace_2020 doi = {10.1038/s41598-020-78339-6}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Transcriptome}, language = {en}, month = {December}, note = {Number: 1 @@ -1865,7 +3005,7 @@ @article{boneva_multifaceted_2024 doi = {10.1186/s12974-024-03291-5}, issn = {1742-2094}, journal = {Journal of Neuroinflammation}, - keywords = {{\textgreater}UseGalaxy.eu, Angiomodulation, Erythrophagocytosis, Hyalocytes, Inflammation, Proliferative diabetic retinopathy, RNA-Sequencing, Vitreous macrophages}, + keywords = {{\textgreater}UseGalaxy.eu, Angiomodulation, Diabetic Retinopathy, Erythrophagocytosis, Hyalocytes, Inflammation, Proliferative diabetic retinopathy, RNA-Sequencing, Vitreous Body, Vitreous macrophages}, month = {November}, number = {1}, pages = {297}, @@ -1883,9 +3023,10 @@ @article{boneva_transcriptional_2020 doi = {10.3389/fimmu.2020.567274}, issn = {1664-3224}, journal = {Frontiers in Immunology}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Hyalocytes, Immune Privilege, Myeloid Cells, Viterous Body, Vitreous Macrophages, innate immunity}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Gene Expression Profiling, Hyalocytes, Immune Privilege, Immunity, Innate, Myeloid Cells, Transcriptome, Viterous Body, Vitreous Macrophages, innate immunity}, language = {English}, note = {Publisher: Frontiers}, + pages = {567274}, title = {Transcriptional {Profiling} {Uncovers} {Human} {Hyalocytes} as a {Unique} {Innate} {Immune} {Cell} {Population}}, url = {https://www.frontiersin.org/articles/10.3389/fimmu.2020.567274/full}, urldate = {2021-05-15}, @@ -1893,13 +3034,30 @@ @article{boneva_transcriptional_2020 year = {2020} } +@article{boondech_complete_2025, + abstract = {Rice (Oryza sativa L.) is a vital global crop with a predominant presence in Asia, including Thailand. However, it faces a significant threat from bacterial blight disease, primarily caused by Xanthomonas oryzae pv. oryzae (Xoo). This research aims to provide valuable insights into the genetic virulence factors and genomic variations of Xoo strains isolated in Thailand. Furthermore, we present the first complete genomic database of Thai Xoo, offering a comprehensive resource for studying pathogen diversity, tracking virulence evolution and supporting disease management strategies in rice production. Our phylogenetic analysis unveils that the 20 Thai strains align with the Asian strains, setting them apart from African and US strains. Remarkably, the average nt identity values, in comparison with Xanthomonas oryzae type strain 35933 (XO35933), consistently exceed 99\%. These strains can be classified into three assigned ribosomal sequence types. Our investigation into the pangenome and the phylogenetic relationships of these 20 Xoo genomes reveals a diverse genetic landscape, with the pangenome comprising 11,872 orthologous gene clusters, of which roughly 30\% form the core genome. Notably, all of these genomes exhibit a clustered regularly interspaced short palindromic repeats-Cas I-C array, indicative of their adaptive immune mechanisms. All strains belonged to BXO1 type LPS cassette with high identity. Furthermore, our analysis identifies two distinct types of plasmids, namely, Xanthomonas oryzae pv. oryzicola strain GX01 plasmid pXOCgx01 (A46, A57, A83, A112, D and E) and the X. oryzae strain AH28 plasmid pAH28 (A97). This genomic resource will be valuable for advancing research on surveillance, prevention, management and comparative studies of this critical pathogen in the future.}, + author = {Boondech, Atirada and Ainmani, Phatthira and Khieokhajonkhet, Anurak and Boonsrangsom, Thanita and Pongcharoen, Pongsanat and Rungrat, Tepsuda and Sujipuli, Kawee and Ratanasut, Kumrop and Aeksiri, Niran}, + doi = {10.1099/acmi.0.000986.v4}, + issn = {2516-8290}, + journal = {Access Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + note = {Publisher: Microbiology Society,}, + number = {6}, + pages = {000986.v4}, + title = {Complete genome and comparative analysis of {Xanthomonas} oryzae pv. oryzae isolated from northern {Thailand}}, + url = {https://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000986.v4}, + urldate = {2025-07-12}, + volume = {7}, + year = {2025} +} + @article{borchel_sex_2022, abstract = {Salmon lice are ectoparasites on salmonids and feed on blood, mucus, and skin from their hosts. This causes high annual costs for treatment and control for the aquaculture industry. Salmon lice have a life cycle consisting of eight life stages. Sex determination by eye is only possible from the sixth stage onwards. A molecular sex determination has not been carried out so far, even though few individual sex-linked SNPs have been reported. In the present study, we used known sex-specific SNPs as a basis to sequence the complete sex-specific gene variants and used the sequence information to develop a sex determination assay. This assay could be used to determine the developmental speed of the two sexes already in the earliest life stages. Additionally, we sampled salmon lice in the nauplius II stage, determined the sex of each individual, pooled their RNA according to their sex, and used RNA sequencing to search for differences in gene expression and further sex-specific SNPs. We succeeded in developing a sex-determination assay that works on DNA or RNA from even the earliest larval stages of the salmon louse after hatching. At these early developmental stages, male salmon lice develop slightly quicker than females. We detected several previously unknown, sex-specific SNPs in our RNA-data seq, but only very few genes showed a differential expression between the sexes. Potential connections between SNPs, gene expression, and development are discussed.}, author = {Borchel, Andreas and Komisarczuk, Anna Zofia and Nilsen, Frank}, doi = {10.1371/journal.pone.0266022}, issn = {1932-6203}, journal = {PLOS ONE}, - keywords = {{\textgreater}UseGalaxy.eu, Eggs, Gene expression, Heterozygosity, Lice, Molting, Polymerase chain reaction, Sex ratio, Single nucleotide polymorphisms}, + keywords = {{\textgreater}UseGalaxy.eu, Copepoda, Eggs, Fish Diseases, Gene expression, Heterozygosity, Lice, Molting, Polymerase chain reaction, Sex ratio, Single nucleotide polymorphisms}, language = {en}, month = {March}, note = {Publisher: Public Library of Science}, @@ -1968,6 +3126,41 @@ @article{bossche_critical_2021 year = {2021} } +@article{boualam_millennial_2023, + abstract = {{\textless}h4{\textgreater}Introduction{\textless}/h4{\textgreater}The lack of well-preserved material upon which to base the paleo-microbiological detection of \textit{Plasmodium} parasites has prevented extensive documentation of past outbreaks of malaria in Europe. By trapping intact erythrocytes at the time of death, dental pulp has been shown to be a suitable tissue for documenting ancient intraerythrocytic pathogens such as \textit{Plasmodium} parasites.{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}Total DNA and proteins extracted from 23 dental pulp specimens collected from individuals exhumed from the 9th to 13th century archaeological site in Mariana, Corsica, were analyzed using open-mind paleo-auto-immunohistochemistry and direct metagenomics, \textit{Plasmodium}-targeting immunochromatography assays. All experiments incorporated appropriate negative controls.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}Paleo-auto-immunohistochemistry revealed the presence of parasites \textit{Plasmodium} spp. in the dental pulp of nine teeth. A further immunochromatography assay identified the presence of at least one \textit{Plasmodium} antigen in nine individuals. The nine teeth, for which the PfHRP-2 antigen specific of \textit{P. falciparum} was detected, were also positive using paleo-autoimmunohistochemistry and metagenomics.{\textless}h4{\textgreater}Conclusion{\textless}/h4{\textgreater}Dental pulp erythrocytes proved to be suitable for the direct paleomicrobiology documentation of malaria in nine individuals buried in medieval Corsica, in agreement with historical data. This provides additional information on the millennial dynamics of \textit{Plasmodium} spp. in the Mediterranean basin.}, + author = {Boualam, Mahmoud Abdelwadoud and Corbara, Anne-Gaëlle and Aboudharam, Gérard and Istria, Daniel and Signoli, Michel and Costedoat, Caroline and Drancourt, Michel and Pradines, Bruno}, + doi = {10.3389/fmed.2023.1265964}, + issn = {2296-858X}, + journal = {Frontiers in medicine}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {1265964}, + title = {The millennial dynamics of malaria in the mediterranean basin: documenting {Plasmodium} spp. on the medieval island of {Corsica}}, + url = {http://europepmc.org/abstract/MED/38143446}, + volume = {10}, + year = {2023} +} + +@article{boulogne_meta-analysis_2025, + abstract = {The marine diatom Phaeodactylum tricornutum is currently used for various industrial applications, including the pharmaceutical industry as a cost-effective cell biofactory to produce Biologics. Recent studies demonstrated that P. tricornutum can produce functional monoclonal antibodies, such application is currently limited by the production yield that hinders industrialization. Therefore, it is necessary to understand and control the cell biology of P. tricornutum to improve the Biologics production yield. Transcriptomic analyses have recently been used by the pharmaceutical industry to improve the production of Biologics in mammalian cells, especially Biologics titer and cell productivity. Hence, in the present work, we performed a meta-analysis of seven publicly available RNA-Seq datasets from different strains of P. tricornutum, for which the culture conditions were chosen as similar as possible. We analyzed the differential expression of genes that are involved in biological processes that are well known to potentially impact the bioproduction and critical quality attributes of Biologics. Therefore, the expression of genes involved in the N-glycan biosynthesis, protein export and secretion, protein quality control and proteasome, as well as those encoding proteases were analyzed and compared. The results pave the way towards optimizing Biologics production in P. tricornutum and highlight that the Pt4, Pt3 Ov and Pt8 strains seem to be the most promising P. tricornutum strains.}, + author = {Boulogne, Isabelle and Toustou, Charlotte and Bardor, Muriel}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-87620-5}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}Plant Galaxy, {\textgreater}UseGalaxy.eu, Bioinformatics, Glycobiology, Marine biology, RNA}, + language = {en}, + month = {January}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {3603}, + title = {Meta-analysis of {RNA}-{Seq} datasets allows a better understanding of {P}. tricornutum cellular biology, a requirement to improve the production of {Biologics}}, + url = {https://www.nature.com/articles/s41598-025-87620-5}, + urldate = {2025-02-01}, + volume = {15}, + year = {2025} +} + @article{boutigny_direct_2023, abstract = {A targeted enrichment method was developed to sequence Xylella fastidiosa genomic DNA directly from plant samples. The method was evaluated on various plant species infected with different strains at different levels of contamination. After enrichment, X. fastidiosa genome coverage was above 99.9\% for all tested samples.}, author = {Boutigny, Anne-Laure and Remenant, Benoit and Legendre, Bruno and Beven, Véronique and Rolland, Mathieu and Blanchard, Yannick and Cunty, Amandine}, @@ -2000,13 +3193,39 @@ @article{bovio_differential_2018 year = {2018} } +@article{bovio_isolation_2018, + abstract = {Brain development is a complex process, which is controlled in a temporo-spatial manner by gradients of morphogens and different transcriptional programs. Additionally, epigenetic chromatin modifications, like histone methylation, have an important role for establishing and maintaining specific cell fates within this process. The vast majority of histone methylation occurs on the flexible histone tail, which is accessible to histone modifiers, erasers, and histone reader proteins. In contrast, H3K79 methylation is located in the globular domain of histone 3 and is implicated in different developmental functions. H3K79 methylation is evolutionarily conserved and can be found in a wide range of species from Homo sapiens to Saccharomyces cerevisiae. The modification occurs in different cell populations within organisms, including neural progenitors. The location of H3K79 methylation in the globular domain of histone 3 makes it difficult to assess. Here, we present methods to isolate and culture cortical progenitor cells (CPCs) from embryonic cortical brain tissue (E11.5-E14.5) or cerebellar granular neuron progenitors (CGNPs) from postnatal tissue (P5-P7), and to efficiently immunoprecipitate H3K79me2 for quantitative PCR (qPCR) and genome-wide sequencing.}, + author = {Bovio, Patrick and Roidl, Deborah and Heidrich, Stefanie and Vogel, Tanja and Franz, Henriette}, + doi = {10.3791/56631}, + issn = {1940-087X}, + journal = {Journal of visualized experiments : JoVE}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {January}, + number = {131}, + title = {Isolation and {Cultivation} of {Neural} {Progenitors} {Followed} by {Chromatin}-{Immunoprecipitation} of {Histone} 3 {Lysine} 79 {Dimethylation} {Mark}}, + url = {http://europepmc.org/abstract/MED/29443015}, + year = {2018} +} + +@article{bowran_novel_2023, + abstract = {{\textless}h4{\textgreater}ABSTRACT{\textless}/h4{\textgreater} The Type VIIb protein secretion system (T7SSb) is found in Bacillota (firmicute) bacteria and has been shown to mediate interbacterial competition. EssC is a membrane-bound ATPase that is a critical component of the T7SSb and plays a key role in substrate recognition. Prior analysis of available genome sequences of the foodborne bacterial pathogen Listeria monocytogenes has shown that although the T7SSb was encoded as part of the core genome, EssC could be found as one of seven different sequence variants. While each sequence variant was associated with a specific suite of candidate substrate proteins encoded immediately downstream of essC , many LXG-domain proteins were encoded across multiple essC sequence variants. Here we have extended this analysis using a diverse collection of 37,930 L. monocytogenes genomes. We have identified a rare eighth variant of EssC present in ten L. monocytogenes Lineage III genomes. These genomes also encode a large toxin of the rearrangement hotspot (Rhs) repeat family adjacent to essC8 , along with a probable immunity protein and three small accessory proteins. We have further identified nine novel LXG-domain proteins, and four additional chromosomal hotspots across L. monocytogenes genomes where LXG proteins can be encoded. The eight L. monocytogenes EssC variants were also found in other Listeria species, with additional novel EssC types also identified. Across the genus, species frequently encoded multiple EssC types, indicating that T7SSb diversity is a primary feature of the genus Listeria . {\textless}h4{\textgreater}DATA SUMMARY{\textless}/h4{\textgreater} All genome sequences used in this study are available via Genbank, and the assembly accession numbers are provided in Table S1. This file also lists relevant metadata (name, source category, country, year and clonal complex). {\textless}h4{\textgreater}IMPACT STATEMENT{\textless}/h4{\textgreater} Listeria monocytogenes is a soil-borne saprophytic bacterium and a food-borne pathogen of humans. Decomposing plant matter and the human GI tract are rich in diverse microbial species and to colonise these niches L. monocytogenes must be able to compete with other bacteria. The type VII secretion system (T7SS) of Bacillota has been shown to secrete protein toxins that target other bacteria. In this study we have analysed a diverse collection of L. monocytogenes genome sequences to study the diversity of the Listeria T7SS and its putative effector proteins. We show that the EssC component of the L. monocytogenes T7SS is highly diverse, clustering into one of eight sequence variants. Each EssC variant is associated with a specific toxin candidate, and the EssC8 variant T7SS likely secretes a novel rearrangement hotspot (Rhs) repeat toxin. We also identify multiple new LXG-families of T7SS toxins and describe genomic hotspots where they are encoded. We find no link between EssC variants and clinical outcome. In agreement with this, analysis of EssC variability in available genomes of other Listeria species showed that all eight L. monocytogenes EssC variants are present in non-monocytogenes Listeria species.}, + author = {Bowran, Kieran and Garrett, Stephen and Vliet, Arnoud van and Palmer, Tracy}, + doi = {10.1101/2023.02.17.528482}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {A novel variant of {theListeria} monocytogenestype {VII} secretion system {EssC} component is associated with an {Rhs} toxin}, + url = {http://europepmc.org/abstract/PPR/PPR618080}, + year = {2023} +} + @article{bowran_novel_2023, abstract = {The type VIIb protein secretion system (T7SSb) is found in Bacillota (firmicute) bacteria and has been shown to mediate interbacterial competition. EssC is a membrane-bound ATPase that is a critical component of the T7SSb and plays a key role in substrate recognition. Prior analysis of available genome sequences of the foodborne bacterial pathogen Listeria monocytogenes has shown that although the T7SSb was encoded as part of the core genome, EssC could be found as one of seven different sequence variants. While each sequence variant was associated with a specific suite of candidate substrate proteins encoded immediately downstream of essC, many LXG-domain proteins were encoded across multiple essC sequence variants. Here, we have extended this analysis using a diverse collection of 37 930 L . monocytogenes genomes. We have identified a rare eighth variant of EssC present in ten L. monocytogenes lineage III genomes. These genomes also encode a large toxin of the rearrangement hotspot (Rhs) repeat family adjacent to essC8, along with a probable immunity protein and three small accessory proteins. We have further identified nine novel LXG-domain proteins, and four additional chromosomal hotspots across L. monocytogenes genomes where LXG proteins can be encoded. The eight L. monocytogenes EssC variants were also found in other Listeria species, with additional novel EssC types also identified. Across the genus, species frequently encoded multiple EssC types, indicating that T7SSb diversity is a primary feature of the genus Listeria .}, author = {Bowran, Kieran and Garrett, Stephen R. and van Vliet, Arnoud H. M. and Palmer, Tracy}, doi = {10.1099/mgen.0.001036}, issn = {2057-5858}, journal = {Microbial Genomics}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Listeria monocytogenes, Type VII Secretion Systems}, note = {Publisher: Microbiology Society,}, number = {6}, pages = {001036}, @@ -2074,6 +3293,7 @@ @article{bray_chemicaltoolbox_2020 issn = {1758-2946}, journal = {Journal of Cheminformatics}, keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}ChemicalToolbox}, + language = {eng}, month = {June}, number = {1}, pages = {40}, @@ -2111,6 +3331,7 @@ @article{bray_intuitive_2020 issn = {1758-2946}, journal = {Journal of Cheminformatics}, keywords = {+Galactic, +HowTo, +IsGalaxy, +Shared, {\textgreater}BRIDGE, {\textgreater}ChemicalToolbox, Galaxy, Molecular Dynamics, Reproducible}, + language = {eng}, month = {September}, number = {1}, pages = {54}, @@ -2150,6 +3371,83 @@ @article{breidenbach_microcystin-lr_2022 year = {2022} } +@misc{breidenbach_microcystin-lr_2025, + abstract = {Microcystin-LR (MC-LR) is one of a large family of cyanotoxins which are naturally produced by cyanobacteria within harmful algal blooms occurring in bodies of water globally. Early findings of the toxicity of such blooms stemmed from fatalities of livestock drinking from affected water. Since then, various toxins have been identified such as the microcystins. Microcystin-LR has been studied as a representative congener due to its abundance and toxicity. While there have been extensive studies of microcystin-LR by oral route exposure, we have turned our attention to inhalation route exposure due to the recent findings of microcystin-containing lake and sea-spray aerosol. We have shown inflammatory outcomes in the airways of mice and in human cell culture models after microcystin aerosol exposure, and have found a consistent molecular patterns similar to those of Type 1/Type 17 driven neutrophilic asthma. Here we address the hypothesis that MC-LR will increase the inflammatory mediators of neutrophilic asthma leading to worsening symptoms. This is tested and characterized in both in vitro and in vivo models. We found that asthma symptoms and molecular signatures of inflammation are both worsened by MC-LR exposure in a mouse model of neutrophilic asthma. We found that 3D human airway cell culture models reconstructed from asthmatic donor cells are similarly affected, however healthy donor cells are nearly unaltered by comparison. Aggregating these findings with RNA sequencing data from all models, we developed a hypothetical molecular mechanism which relies on MC-LR mediated amplification of existing inflammatory signaling. We test this in a human reporter cell line of NF-κB activity and further demonstrate the mechanism by inhibitor testing. This study sheds light on the risk to asthmatic patients living near or recreating on affected bodies of water. Beyond asthma, we believe this study provides crucial insight into the findings over the last 40 years concerning disparate outcomes of MC-LR exposure as the result of exposure will be dependent on the signaling state of the tissue upon exposure.}, + author = {Breidenbach, Joshua D. and Timalsina, Bivek and French, Benjamin W. and Stanoszek, Lauren and Lavik, John-Paul and Breidenbach, Irum S. and Shrestha, Upasana and Kleinhenz, Andrew and Lad, Apurva and Dube, Prabhatchandra and Zhang, Shungang and Faleel, Dhilhani and Wooten, R. Mark and Willey, James C. and Hammersley, Jeffrey R. and Modyanov, Nikolai N. and Malhotra, Deepak and Dworkin, Lance D. and Haller, Steven T. and Kennedy, David J.}, + copyright = {© 2025, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}, + doi = {10.1101/2025.09.13.676033}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {September}, + note = {ISSN: 2692-8205 +Pages: 2025.09.13.676033 +Section: New Results}, + publisher = {bioRxiv}, + title = {Microcystin-{LR} aerosol exposure increases inflammatory drivers of asthma, {Evidence} of an {NF}-κ{B} amplification mechanism}, + url = {https://www.biorxiv.org/content/10.1101/2025.09.13.676033v2}, + urldate = {2025-10-03}, + year = {2025} +} + +@article{breunis_patient-derived_2025, + abstract = {High-risk sarcomas, such as metastatic and relapsed Ewing and CIC-rearranged sarcoma, still have a poor prognosis despite intensive therapeutic regimens. Precision medicine approaches offer hope, and ex vivo drug response profiling of patient-derived tumor cells emerges as a promising tool to identify effective therapies for individual patients. Here, we establish ex vivo culture conditions to propagate Ewing sarcoma and CIC::DUX4 sarcoma as tumoroids. These models retain their original molecular and functional characteristics, including recurrent ARID1A mutations in CIC::DUX4 sarcoma, and serve as tumor avatars for large-scale drug testing. Screening a large drug library on a small living biobank of such tumors not only reveals distinct differences in drug response between the two entities, but also identifies a dependency of CIC::DUX4 sarcoma cells on MCL1. Mechanistically, MCL1 is identified as a direct transcriptional target of the CIC::DUX4 fusion oncogene. Genetic and pharmacological inhibition of MCL1 induces rapid apoptosis in CIC::DUX4 sarcoma cells and inhibits tumor growth in a xenograft model. Thus, MCL1 represents a potential therapeutic target for CIC::DUX4 sarcoma. Overall, our study highlights the feasibility of drug response profiling for individual sarcoma cases and suggests that further clinical assessments of its benefit are warranted.}, + author = {Breunis, Willemijn and Brack, Eva and Ehlers, Anna C. and Bechtold, Ingrid and Kisele, Samanta and Wurth, Jakob and Mous, Lieke and Zabele, Dorita and Steffen, Fabio and Zahnow, Felina and Britschgi, Christian and Bankel, Lorenz and Rothermundt, Christian and Vetter, Cornelia and Müller, Daniel and Botter, Sander and Pauli, Chantal and Bode, Peter and Rinner, Beate and Bourquin, Jean-Pierre and Roessler, Jochen and Grünewald, Thomas G. P. and Schäfer, Beat W. and Surdez, Didier and Wachtel, Marco}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41467-025-62629-6}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Myeloid Cell Leukemia Sequence 1 Protein, Sarcoma, Sarcoma, Ewing, Targeted therapies}, + language = {en}, + month = {August}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {7688}, + shorttitle = {Patient-derived tumoroids from {CIC}}, + title = {Patient-derived tumoroids from {CIC}::{DUX4} rearranged sarcoma identify {MCL1} as a therapeutic target}, + url = {https://www.nature.com/articles/s41467-025-62629-6}, + urldate = {2025-09-03}, + volume = {16}, + year = {2025} +} + +@article{bright_temporal_2025, + abstract = {Diverse types of GABAergic projection neuron and interneurons of the telencephalon derive from progenitors in a ventral germinal zone called the ganglionic eminence. Using single-cell transcriptomics, chromatin accessibility profiling, lineage tracing, birthdating, transplantation across developmental stages and perturbation sequencing in mouse embryos, we investigated how progenitor competence influences the maturation and differentiation of these neurons. We found that the temporal progression of neurogenesis shapes maturation competence in ganglionic eminence progenitors, influencing how their progeny progress toward mature states. By contrast, differentiation competence—defined as the ability of progenitors to produce diverse transcriptomic identities—was maintained throughout neurogenesis. Chromatin remodeling, together with a regulatory module composed of the transcription factor NFIB and its target genes, influenced maturation competence in late-born neurons. These findings reveal how transcriptional programs and chromatin accessibility govern neuronal maturation and the diversification of GABAergic neuron subtypes during neurodevelopment.}, + author = {Bright, Ann Rose and Kotlyarenko, Yana and Neuhaus, Florian and Rodrigues, Diana and Feng, Chao and Peters, Christian and Vitali, Ilaria and Dönmez, Elif and Myoga, Michael H. and Dvoretskova, Elena and Mayer, Christian}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41593-025-01999-y}, + issn = {1546-1726}, + journal = {Nature Neuroscience}, + keywords = {{\textgreater}UseGalaxy.eu, Cell fate and cell lineage, GABAergic Neurons, Genetics of the nervous system, Neural Stem Cells, Neurogenesis, Telencephalon}, + language = {en}, + month = {July}, + note = {Publisher: Nature Publishing Group}, + pages = {1--13}, + title = {Temporal control of progenitor competence shapes maturation in {GABAergic} neuron development in mice}, + url = {https://www.nature.com/articles/s41593-025-01999-y}, + urldate = {2025-07-12}, + year = {2025} +} + +@article{brimson_collective_2025, + abstract = {{\textless}h2{\textgreater}Summary{\textless}/h2{\textgreater}{\textless}p{\textgreater}Oscillatory phenomena play widespread roles in the control of biological systems. In \textit{D. discoideum}, oscillatory cyclic adenosine monophosphate (cAMP) signaling drives collective behavior and induces a temporal developmental gene expression program. How collective cAMP oscillations emerge or how they encode temporal transcriptional information is still poorly understood. To address this, we identified a transcription factor required for the initiation of collective behavior. Hbx5 activity is cAMP dependent and provides a sensitive single-cell readout for cAMP signaling. Extensive stochastic pulsatile cAMP signaling is found to precede collective oscillations. Stochastic signaling induces Hbx5-dependent transcriptional feedback, which enhances signal sensitivity and cell-cell coupling. This results in the emergence of synchronized collective oscillations, which subsequently activates the GtaC transcription factor and triggers shifts in developmental gene expression. Our results suggest this temporal coordination is encoded by changes in the amplitude of cAMP oscillations and differential sensitivity of these transcription factors to the cAMP-regulated kinase ErkB.{\textless}/p{\textgreater}}, + author = {Brimson, Christopher A. and Baines, Robert and Sams-Dodd, Elisabeth and Stefanescu, Ioanina and Evans, Bethany and Kuwana, Satoshi and Hashimura, Hidenori and Sawai, Satoshi and Thompson, Christopher R. L.}, + doi = {10.1016/j.devcel.2024.11.016}, + issn = {1534-5807}, + journal = {Developmental Cell}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {English}, + month = {March}, + note = {Publisher: Elsevier}, + number = {6}, + pages = {918--933.e4}, + pmid = {39672161}, + title = {Collective oscillatory signaling in {Dictyostelium} discoideum acts as a developmental timer initiated by weak coupling of a noisy pulsatile signal}, + url = {https://www.cell.com/developmental-cell/abstract/S1534-5807(24)00698-1}, + urldate = {2025-05-29}, + volume = {60}, + year = {2025} +} + @mastersthesis{brink_identification_2024, abstract = {Cardiomyopathy is one of the major causes of heart failure that affects approximately 26 million patients worldwide. In a healthy situation, the heart depends on fatty acid oxidation (FAO) to maintain its energy demand. In failing hearts, the heart reverts to a fetal-like metabolic state in which FAO is downregulated and the heart switches to glucose metabolism. Peroxisome proliferator-activated receptor alpha (PPARA), a regulator of FAO, has recently been found to be hypoacetylated and its downstream effectors downregulated in dilated cardiomyopathy. However, the exact mechanisms remain largely unknown. The main purpose of this internship was to identify the specific FAO expression patterns in a large heterogenic patient cohort and investigate the involvement of PPARA regulation. The secondary goal was to set up a transcriptomic pipeline within Galaxy, a user-friendly bioinformatics platform, and test whether this platform can be used in diagnostics in the future. Differential expression analysis and gene enrichment of RNA-sequencing data show a type-specific FAO expression pattern of DCM and LVH versus HCM and confirm a downregulation of FAO related processes. Public RNA-sequencing data after the use of a bezafibrate, a PPARA agonist, which has been integrated, shows the upregulation of genes that are downregulated in our data. Combined, the results confirm the downregulation of FAO, but indicate a disease-type-specific FAO expression pattern. The results from the Galaxy pipeline show that this pipeline is suitable for transcriptomic analyses. Furthermore, we highlight the potential therapeutic role of bezafibrate in cardiomyopathy.}, author = {Brink, Alyssa van den}, @@ -2201,6 +3499,24 @@ @article{broche_genome-wide_2023 year = {2023} } +@article{bronnec_speckseq_2026, + abstract = {Variants of uncertain significance (VUS) are a major obstacle in genetic diagnosis, particularly when involving gain-of-function (GoF) mutations that are poorly predicted in silico. MEFV, which encodes the inflammasome sensor pyrin, is mutated in two autoinflammatory diseases, familial Mediterranean fever (FMF) and pyrin-associated autoinflammation with neutrophilic dermatosis (PAAND). Here, we developed SpeckSeq, a method that combines DNA bar-coding, ASC speck–based single-cell sorting and next-generation sequencing to systematically identify hypermorphic MEFV variants in response to different stimuli. SpeckSeq identified 49 GoF mutations separated into two distinct groups containing either PAAND variants or FMF variants. SpeckSeq was validated using patients’ cells and supported a reclassification of MEFV variant pathogenicity, leading to novel diagnoses. As a large-scale mutagenesis approach, using human genetics as a guide, SpeckSeq revealed structural and functional pyrin features, including a putative ligand-accommodating cavity in the B30.2 domain. Altogether, SpeckSeq classifies VUS to refine molecular diagnostics and improve our knowledge on the pyrin inflammasome.}, + author = {Bronnec, Pauline and Dalmon, Sarah and Briand, Chloe and Allatif, Omran and Broly, Martin and Marcotte, Melissa and Lombardi, Gianluca and Barthes, Kevin and Martel, Nora and Hughes, Sandrine and Gillet, Benjamin and Milhavet, Florian and Atilgan, Aysima and Bachelez, Hervé and Palmeri, Serena and Prigione, Ignazia and Madrange, Marine and Savey, Léa and Moutschen, Michel and Jeru, Isabelle and El Moussaoui, Majdouline and Belot, Alexandre and Sbidian, Emilie and Carbone, Alessandra and Jamilloux, Yvan and Gattorno, Marco and Smahi, Asma and Georgin-Lavialle, Sophie and Boursier, Guilaine and Magnotti, Flora and Henry, Thomas}, + doi = {10.1084/jem.20251065}, + issn = {0022-1007, 1540-9538}, + journal = {Journal of Experimental Medicine}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {February}, + number = {2}, + pages = {e20251065}, + title = {{SpeckSeq} enables high-throughput functional stratification of \textit{{MEFV}} variants in autoinflammatory diseases}, + url = {https://rupress.org/jem/article/223/2/e20251065/278546/SpeckSeq-enables-high-throughput-functional}, + urldate = {2025-12-05}, + volume = {223}, + year = {2026} +} + @article{bruck_ploidy_2023, abstract = {Vibrio natriegens is the fastest-growing bacterium, with a doubling time of approximately 12–14 min. It has a high potential for basic research and biotechnological applications, e.g., it can be used for the cell-free production of (labeled) heterologous proteins, for synthetic biological applications, and for the production of various compounds. However, the ploidy level in V. natriegens remains unknown. At nine time points throughout the growth curve, we analyzed the numbers of origins and termini of both chromosomes with qPCR and the relative abundances of all genomic sites with marker frequency analyses. During the lag phase until early exponential growth, the origin copy number and origin/terminus ratio of chromosome 1 increased severalfold, but the increase was lower for chromosome 2. This increase was paralleled by an increase in cell volume. During the exponential phase, the origin/terminus ratio and cell volume decreased again. This highly dynamic and fast regulation has not yet been described for any other species. In this study, the gene dosage increase in origin-adjacent genes during the lag phase is discussed together with the nonrandom distribution of genes on the chromosomes of V. natriegens. Taken together, the results of this study provide the first comprehensive overview of the chromosome dynamics in V. natriegens and will guide the optimization of molecular biological characterization and biotechnological applications.}, author = {Brück, Patrik and Wasser, Daniel and Soppa, Jörg}, @@ -2208,7 +3524,7 @@ @article{bruck_ploidy_2023 doi = {10.3390/genes14071437}, issn = {2073-4425}, journal = {Genes}, - keywords = {\textit{Vibrio natriegens}, {\textgreater}UseGalaxy.eu, cell size, cell volume, chromosome copy number, dynamic regulation, growth curve, origin of replication, ploidy, polyploidy, terminus of replication}, + keywords = {\textit{Vibrio natriegens}, {\textgreater}UseGalaxy.eu, DNA Copy Number Variations, Vibrio, cell size, cell volume, chromosome copy number, dynamic regulation, growth curve, origin of replication, ploidy, polyploidy, terminus of replication}, language = {en}, month = {July}, note = {Number: 7 @@ -2223,6 +3539,22 @@ @article{bruck_ploidy_2023 year = {2023} } +@article{brunet_ftz-f1_2021, + abstract = {The salmon louse, Lepeophtheirus salmonis, is an ectoparasitic crustacean that annually inflicts substantial losses to the aquaculture industry in the northern hemisphere and poses a threat to the wild populations of salmonids. The salmon louse life cycle consists of eight developmental stages each separated by a molt. Fushi Tarazu Factor-1 (FTZ-F1) is an ecdysteroid-regulated gene that encodes a member of the NR5A family of nuclear receptors that is shown to play a crucial regulatory role in molting in insects and nematodes. Characterization of an FTZ-F1 orthologue in the salmon louse gave two isoforms named αFTZ-F1 and βFTZ-F1, which are identical except for the presence of a unique N-terminal domain (A/B domain). A comparison suggest conservation of the FTZ-F1 gene structure among ecdysozoans, with the exception of nematodes, to produce isoforms with unique N-terminal domains through alternative transcription start and splicing. The two isoforms of the salmon louse FTZ-F1 were expressed in different amounts in the same tissues and showed a distinct cyclical expression pattern through the molting cycle with βFTZ-F1 being the highest expressed isoform. While RNA interference knockdown of βFTZ-F1 in nauplius larvae and in pre-adult males lead to molting arrest, knockdown of βFTZ-F1 in pre-adult II female lice caused disruption of oocyte maturation at the vitellogenic stage. No apparent phenotype could be observed in αFTZ-F1 knockdown larvae, or in their development to adults, and no genes were found to be differentially expressed in the nauplii larvae following αFTZ-F1 knockdown. βFTZ-F1 knockdown in nauplii larvae caused both down and upregulation of genes associated with proteolysis and chitin binding and affected a large number of genes which are in normal salmon louse development expressed in a cyclical pattern. This is the first description of FTZ-F1 gene function in copepod crustaceans and provides a foundation to expand the understanding of the molecular mechanisms of molting in the salmon louse and other copepods.}, + author = {Brunet, Joakim and Eichner, Christiane and Male, Rune}, + doi = {10.1371/journal.pone.0251575}, + issn = {1932-6203}, + journal = {PloS one}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + number = {5}, + pages = {e0251575}, + title = {The {FTZ}-{F1} gene encodes two functionally distinct nuclear receptor isoforms in the ectoparasitic copepod salmon louse ({Lepeophtheirus} salmonis)}, + url = {http://europepmc.org/abstract/MED/34014986}, + volume = {16}, + year = {2021} +} + @article{brunet_mass_2019, abstract = {Genome annotation is central to today's proteomic research as it draws the outlines of the proteomic landscape. Traditional models of open reading frame (ORF) annotation impose two arbitrary criteria: a minimum length of 100 codons and a single ORF per transcript. However, a growing number of studies report expression of proteins from allegedly non-coding regions, challenging the accuracy of current genome annotations. These novel proteins were found encoded either within non-coding RNAs, 5' or 3' untranslated regions (UTRs) of mRNAs, or overlapping a known coding sequence (CDS) in an alternative ORF. OpenProt is the first database that enforces a polycistronic model for eukaryotic genomes, allowing annotation of multiple ORFs per transcript. OpenProt is freely accessible and offers custom downloads of protein sequences across 10 species. Using OpenProt database for proteomic experiments enables novel proteins discovery and highlights the polycistronic nature of eukaryotic genes. The size of OpenProt database (all predicted proteins) is substantial and need be taken in account for the analysis. However, with appropriate false discovery rate (FDR) settings or the use of a restricted OpenProt database, users will gain a more realistic view of the proteomic landscape. Overall, OpenProt is a freely available tool that will foster proteomic discoveries.}, author = {Brunet, Marie A. and Roucou, Xavier}, @@ -2239,6 +3571,40 @@ @article{brunet_mass_2019 year = {2019} } +@article{brunetti_longitudinal_2025, + abstract = {\textbf{Background}: SARS-CoV-2 was the causing agent of the COVID-19 pandemic, which resulted in millions of deaths worldwide and massive economic losses. Although there are already several vaccines licensed, as novel variants develop, understanding the immune response induced by vaccination and natural infection is key for the development of future vaccines. \textbf{Methods}: In this study, we have used flow cytometry and next-generation sequencing to assess the longitudinal CD8$^{\textrm{+}}$ T-cell response against natural infection and vaccination in convalescent and vaccinated individuals, from early activation to immune memory establishment. Moreover, we have characterized the T-cell receptor clonality and diversity at different stages post-infection and post-vaccination. \textbf{Results}: We have found no significant differences in CD8$^{\textrm{+}}$ T-cell activation during the first three weeks post-infection compared to the first three weeks after first vaccination. Conversely, natural infection resulted in sustained high levels of T-cell activation at four weeks post-infection, a point in which we observed a decline in T-cell activation post-vaccination despite boosting with a second vaccination shot. Moreover, additional vaccination did not result in enhanced T-cell activation. Of note, we have observed variations in the memory subset structure at every stage of disease and vaccination. Overall, both infection and immunization induced a highly diverse T-cell receptor repertoire, which was observed both between study groups and between patients inside a given group. \textbf{Conclusions}: These data contribute to expand our knowledge about the immune response to SARS-CoV-2 infection and vaccination and call for additional strategies to enhance T-cell responses by booster immunization.}, + author = {Brunetti, Jesús Emanuel and Escudero-Pérez, Beatriz and Lasala, Fátima and Rivas, Gonzalo and Mancheño-Losa, Mikel and Rial-Crestelo, David and Lora-Tamayo, Jaime and Cadar, Dániel and Carroll, Miles and Delgado, Rafael and Muñoz-Fontela, César and Rodríguez, Estefanía}, + doi = {10.3390/vaccines13060551}, + issn = {2076-393X}, + journal = {Vaccines}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {May}, + number = {6}, + pages = {551}, + title = {Longitudinal {Immunoprofiling} of the {CD8}$^{\textrm{+}}$ {T}-{Cell} {Response} in {SARS}-{CoV}-2 {mRNA} {Vaccinees} and {COVID}-19 {Patients}}, + url = {http://europepmc.org/abstract/MED/40573882}, + volume = {13}, + year = {2025} +} + +@article{brunner_fbxl12_2023, + abstract = {Fanconi anemia (FA) signaling, a key genomic maintenance pathway, is activated in response to replication stress. Here, we report that phosphorylation of the pivotal pathway protein FANCD2 by CHK1 triggers its FBXL12-dependent proteasomal degradation, facilitating FANCD2 clearance at stalled replication forks. This promotes efficient DNA replication under conditions of CYCLIN E- and drug-induced replication stress. Reconstituting FANCD2-deficient fibroblasts with phosphodegron mutants failed to re-establish fork progression. In the absence of FBXL12, FANCD2 becomes trapped on chromatin, leading to replication stress and excessive DNA damage. In human cancers, FBXL12, CYCLIN E, and FA signaling are positively correlated, and FBXL12 upregulation is linked to reduced survival in patients with high CYCLIN E-expressing breast tumors. Finally, depletion of FBXL12 exacerbated oncogene-induced replication stress and sensitized cancer cells to drug-induced replication stress by WEE1 inhibition. Collectively, our results indicate that FBXL12 constitutes a vulnerability and a potential therapeutic target in CYCLIN E-overexpressing cancers.}, + author = {Brunner, Andrä and Li, Qiuzhen and Fisicaro, Samuele and Kourtesakis, Alexandros and Viiliäinen, Johanna and Johansson, Henrik J and Pandey, Vijaya and Mayank, Adarsh K and Lehtiö, Janne and Wohlschlegel, James A and Spruck, Charles and Rantala, Juha K and Orre, Lukas M and Sangfelt, Olle}, + doi = {10.1016/j.molcel.2023.07.026}, + issn = {1097-2765}, + journal = {Mol Cell}, + keywords = {{\textgreater}UseGalaxy.eu, Fanconi Anemia, Neoplasms}, + language = {eng}, + month = {October}, + number = {20}, + pages = {3720--3739.e8}, + title = {{FBXL12} degrades {FANCD2} to regulate replication recovery and promote cancer cell survival under conditions of replication stress}, + url = {http://europepmc.org/abstract/MED/37591242}, + volume = {83}, + year = {2023} +} + @article{bruno_collisions_2023, abstract = {DNA replication produces a global disorganization of chromatin structure that takes hours to be restored. However, how these chromatin rearrangements affect the regulation of gene expression and the maintenance of cell identity is not clear. Here, we use ChOR-seq and ChrRNA-seq experiments to analyze RNA polymerase II (RNAPII) activity and nascent RNA synthesis during the first hours after chromatin replication in human cells. We observe that transcription elongation is rapidly reactivated in nascent chromatin but that RNAPII abundance and distribution are altered, producing heterogeneous changes in RNA synthesis. Moreover, this first wave of transcription results in RNAPII blockages behind the replication fork, leading to changes in alternative splicing. Altogether, our results deepen our understanding of how transcriptional programs are regulated during cell division and uncover molecular mechanisms that explain why chromatin replication is an important source of gene expression variability.}, author = {Bruno, Federica and Coronel-Guisado, Cristóbal and González-Aguilera, Cristina}, @@ -2286,6 +3652,27 @@ @article{buhl_prevotella_2020 year = {2020} } +@article{burel_trichosporon_2025, + abstract = {During 2022-2024, six cases of invasive fungal infection occurred among immunocompromised patients at Marseille University Hospital, Marseille, France. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry initially identified Trichosporon inkin fungi. However, phylogenetic analysis of intergenic spacer region 1 and whole-genome sequences revealed the genetically distinct species T. austroamericanum. Analysis of core genome and mitogenome from 6 patient isolates and 1 environmental isolate revealed substantial genetic diversity among T. austroamericanum strains, indicating a polyclonal outbreak. Furthermore, the mitochondrial genome emerged as a potential marker for intraspecies differentiation, which potentially could aid in epidemiologic investigations. Identified in 2024 but potentially underestimated, T. austroamericanum has since been reported in case clusters from hospital settings in France, highlighting the need for accurate fungal identification and suggesting previously identified T. inkin cases should be re-evaluated for T. austroamericanum. Clinical T. austroamericanum is emerging in hospital settings and should be included in the differential diagnosis of fungal infections.}, + author = {Burel, Emilie and Sartor, Catherine and Moal, Valérie and Bossi, Vincent and Sevestre, Jacques and Solignac, Justine and Charrel, Rémi and Desnos-Ollivier, Marie and Ranque, Stéphane and Menu, Estelle}, + copyright = {cc by}, + doi = {10.3201/eid3111.250503}, + issn = {1080-6059}, + journal = {Emerging infectious diseases}, + keywords = {{\textgreater}UseGalaxy.eu, Emerging Disease, France, Fungi, Opportunistic Agents, Trichosporon Austroamericanum, Trichosporonosis, Yeast, outbreak}, + language = {eng}, + month = {November}, + number = {11}, + pages = {2080--2090}, + pmcid = {PMC12704532}, + pmid = {41379602}, + title = {Trichosporon austroamericanum {Infections} among {Hospitalized} {Patients}, {France}, 2022-2024}, + url = {https://europepmc.org/articles/PMC12704532}, + urldate = {2025-12-26}, + volume = {31}, + year = {2025} +} + @article{busch_iclip_2019, abstract = {Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understanding the complex post-transcriptional regulation of gene expression. This information can be obtained from individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) experiments. Here, we present a complete data analysis workflow to reliably detect RBP binding sites from iCLIP data. The workflow covers all steps from the initial quality control of the sequencing reads up to peak calling and quantification of RBP binding. For each tool, we explain the specific requirements for iCLIP data analysis and suggest optimised parameter settings.}, author = {Busch, Anke and Brüggemann, Mirko and Ebersberger, Stefanie and Zarnack, Kathi}, @@ -2307,6 +3694,7 @@ @article{buttimer_isolation_2020 author = {Buttimer, Colin and Lynch, Caoimhe and Hendrix, Hanne and Neve, Horst and Noben, Jean-Paul and Lavigne, Rob and Coffey, Aidan}, copyright = {http://creativecommons.org/licenses/by/3.0/}, doi = {10.3390/antibiotics9060352}, + issn = {2079-6382}, journal = {Antibiotics}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Certrevirus, Pectobacterium atrosepticum, Vequintavirinae, homing endonuclease, phage, phytopathogen, potato blackleg, sigma70 promoter, soft rot disease}, language = {en}, @@ -2323,6 +3711,23 @@ @article{buttimer_isolation_2020 year = {2020} } +@article{camacho-beltran_complete_2024, + abstract = {We purified a lytic bacteriophage from soil collected in Guasave, Sinaloa: phiExGM16. This bacteriophage was isolated using the host, \textit{Exiguobacterium acetilycum}. Its 17.6 kb genome contains 33 putative genes and shows a cover of 64\% with 76.37\% of nucleotide identity to \textit{Microbacterium phage} Noelani.}, + author = {Camacho-Beltrán, Erika and Morales-Aguilar, Juan José and López-Meyer, Melina and Rincón-Enríquez, Gabriel and Quiñones-Aguilar, Evangelina Esmeralda}, + doi = {10.1128/mra.00342-24}, + issn = {2576-098X}, + journal = {Microbiol Resour Announc}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {July}, + number = {7}, + pages = {e0034224}, + title = {Complete genome sequence of the {Exiguobacterium} bacteriophage}, + url = {http://europepmc.org/abstract/MED/38860812}, + volume = {13}, + year = {2024} +} + @article{camacho-beltran_complete_2024, author = {Camacho-Beltrán, Erika and Morales-Aguilar, Juan José and López-Meyer, Melina and Rincón-Enríquez, Gabriel and Quiñones-Aguilar, Evangelina Esmeralda}, doi = {10.1128/mra.00302-24}, @@ -2392,6 +3797,21 @@ @misc{camargo_romera_isoform_2021 year = {2021} } +@article{candeliere_-glucuronidase_2022, + abstract = {β-glucuronidases (GUS) of intestinal bacteria remove glucuronic acid from glucoronides, reversing phase II metabolism of the liver and affecting the level of active deconjugated metabolites deriving from drugs or xenobiotics. Two hundred seventy-nine non-redundant GUS sequences are known in the gut microbiota, classified in seven structural categories (NL, L1, L2, mL1, mL2, mL1,2, and NC) with different biocatalytic properties. In the present study, the intestinal metagenome of 60 healthy subjects from five geographically different cohorts was assembled, binned, and mined to determine qualitative and quantitative differences in GUS profile, potentially affecting response to drugs and xenobiotics. Each metagenome harbored 4-70 different GUS, altogether accounting for 218. The amount of intestinal bacteria with at least one GUS gene was highly variable, from 0.7 to 82.2\%, 25.7\% on average. No significant difference among cohorts could be identified, except for the Ethiopia (ETH) cohort where GUS-encoding bacteria were significantly less abundant. The structural categories were differently distributed among the metagenomes, but without any statistical significance related to the cohorts. GUS profiles were generally dominated by the category NL, followed by mL1, L2, and L1. The GUS categories most involved in the hydrolysis of small molecules, including drugs, are L1 and mL1. Bacteria contributing to these categories belonged to \textit{Bacteroides ovatus}, \textit{Bacteroides dorei}, \textit{Bacteroides fragilis}, \textit{Escherichia coli}, \textit{Eubacterium eligens}, \textit{Faecalibacterium prausnitzii}, \textit{Parabacteroides merdae}, and \textit{Ruminococcus gnavus}. Bacteria harboring L1 GUS were generally scarcely abundant ({\textless}1.3\%), except in three metagenomes, where they reached up to 24.3\% for the contribution of \textit{E. coli} and \textit{F. prausnitzii.} Bacteria harboring mL1 GUS were significantly more abundant (mean = 4.6\%), with \textit{Bacteroides} representing a major contributor. Albeit mL1 enzymes are less active than L1 ones, \textit{Bacteroides} likely plays a pivotal role in the deglucuronidation, due to its remarkable abundance in the microbiomes. The observed broad interindividual heterogeneity of GUS profiles, particularly of the L1 and mL1 categories, likely represent a major driver of pharmacomicrobiomics variability, affecting drug response and toxicity. Different geographical origins, genetic, nutritional, and lifestyle features of the hosts seemed not to be relevant in the definition of glucuronidase activity, albeit they influenced the richness of the GUS profile.}, + author = {Candeliere, Francesco and Raimondi, Stefano and Ranieri, Raffaella and Musmeci, Eliana and Zambon, Alfonso and Amaretti, Alberto and Rossi, Maddalena}, + doi = {10.3389/fmicb.2022.826994}, + issn = {1664-302X}, + journal = {Frontiers in microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {826994}, + title = {β-{Glucuronidase} {Pattern} {Predicted} {From} {Gut} {Metagenomes} {Indicates} {Potentially} {Diversified} {Pharmacomicrobiomics}}, + url = {http://europepmc.org/abstract/MED/35308380}, + volume = {13}, + year = {2022} +} + @article{candeliere_draft_2020, abstract = {Leuconostoc carnosum is a lactic acid bacterium that preferentially colonizes meat. In this work, we present the draft genome sequences of 12 Leuconostoc carnosum strains isolated from modified-atmosphere-packaged cooked ham and fresh sausages. Three strains harbor bacteriocin genes.}, author = {Candeliere, Francesco and Raimondi, Stefano and Spampinato, Gloria and Tay, Moon Yue Feng and Amaretti, Alberto and Schlundt, Joergen and Rossi, Maddalena}, @@ -2403,6 +3823,7 @@ @article{candeliere_draft_2020 language = {en}, month = {January}, number = {2}, + pages = {e01247--19}, pmid = {31919169}, title = {Draft {Genome} {Sequences} of 12 {Leuconostoc} carnosum {Strains} {Isolated} from {Cooked} {Ham} {Packaged} in a {Modified} {Atmosphere} and from {Fresh} {Sausages}}, url = {https://mra.asm.org/content/9/2/e01247-19}, @@ -2421,6 +3842,7 @@ @article{candeliere_genomic_2024 language = {English}, month = {March}, note = {Publisher: Frontiers}, + pages = {1359726}, title = {Genomic and functional analysis of the mucinolytic species {Clostridium} celatum, {Clostridium} tertium, and {Paraclostridium} bifermentans}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1359726/full}, urldate = {2024-05-17}, @@ -2428,6 +3850,40 @@ @article{candeliere_genomic_2024 year = {2024} } +@article{cannazza_characterization_2021, + abstract = {\textit{Komagataeibacter} spp. has been used for the bioconversion of industrial wastes and lignocellulosic hydrolysates to bacterial cellulose (BC). Recently, studies have demonstrated the capacity of \textit{Komagataeibacter} spp. in the biotransformation of inhibitors found in lignocellulosic hydrolysates, aromatic lignin-derived monomers (LDMs) and acetate. In general, detoxification and BC synthesis from lignocellulosic inhibitors requires a carbon flow from acetyl-coA towards tricarboxylic acid and gluconeogenesis, respectively. However, the related molecular aspects have not yet been identified in \textit{Komagataeibacter} spp. In this study, we isolated a cellulose-producing bacterium capable of synthesizing BC in a minimal medium containing crude glycerol, a by-product from the biodiesel production process. The isolate, affiliated to \textit{Komagataeibacter} genus, synthesized cellulose in a minimal medium containing glucose (3.3 ± 0.3 g/L), pure glycerol (2.2 ± 0.1 g/L) and crude glycerol (2.1 ± 0.1 g/L). Genome assembly and annotation identified four copies of bacterial cellulose synthase operon and genes for redirecting the carbon from the central metabolic pathway to gluconeogenesis. According to the genome annotations, a BC production route from acetyl-CoA, a central metabolic intermediate, was hypothesized and was validated using acetate. We identified that when \textit{K. rhaeticus} ENS9b was grown in a minimal medium supplemented with acetate, BC production was not observed. However, in the presence of readily utilizable substrates, such as spent yeast hydrolysate, acetate supplementation improved BC synthesis.}, + author = {Cannazza, Pietro and Rissanen, Antti J and Guizelini, Dieval and Losoi, Pauli and Sarlin, Essi and Romano, Diego and Santala, Ville and Mangayil, Rahul}, + doi = {10.3390/microorganisms9112230}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {October}, + number = {11}, + pages = {2230}, + title = {Characterization of {Komagataeibacter} {Isolate} {Reveals} {New} {Prospects} in {Waste} {Stream} {Valorization} for {Bacterial} {Cellulose} {Production}}, + url = {http://europepmc.org/abstract/MED/34835356}, + volume = {9}, + year = {2021} +} + +@article{cantarella_alu_2019, + abstract = {\textit{Alu} retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate \textit{Alu} RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. \textit{Alu} transcription is generally kept to extremely low levels by tight epigenetic silencing, but it has been reported to increase under different types of cell perturbation, such as viral infection and cancer. \textit{Alu} RNAs, being able to act as gene expression modulators, may be directly involved in the mechanisms determining cellular behavior in such perturbed states. To directly address the regulatory potential of \textit{Alu} RNAs, we generated IMR90 fibroblasts and HeLa cell lines stably overexpressing two slightly different \textit{Alu} RNAs, and analyzed genome-wide the expression changes of protein-coding genes through RNA-sequencing. Among the genes that were upregulated or downregulated in response to \textit{Alu} overexpression in IMR90, but not in HeLa cells, we found a highly significant enrichment of pathways involved in cell cycle progression and mitotic entry. Accordingly, \textit{Alu} overexpression was found to promote transition from G1 to S phase, as revealed by flow cytometry. Therefore, increased \textit{Alu} RNA may contribute to sustained cell proliferation, which is an important factor of cancer development and progression.}, + author = {Cantarella, Simona and Carnevali, Davide and Morselli, Marco and Conti, Anastasia and Pellegrini, Matteo and Montanini, Barbara and Dieci, Giorgio}, + doi = {10.3390/ijms20133315}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Gene Expression Regulation}, + language = {eng}, + month = {July}, + number = {13}, + pages = {E3315}, + title = {Alu {RNA} {Modulates} the {Expression} of {Cell} {Cycle} {Genes} in {Human} {Fibroblasts}}, + url = {http://europepmc.org/abstract/MED/31284509}, + volume = {20}, + year = {2019} +} + @phdthesis{cantarella_insights_2020, abstract = {A large portion of the human genome is composed of repeated sequences, with Alu retrotransposons representing the most abundant repetitive elements. Alu sequences belong to the class of the Short Interspersed Nuclear Elements (SINEs) and depend on the Long Interspersed Nuclear Elements (LINEs) for their mobilization into the genome. The efficiency of Alu amplification during primate evolution suggests a positive driving force for their accumulation, bringing up to 1 million copies in the human genome. For unclear reasons, the majority of Alu sequences is repressed by tight epigenetic silencing, which is released in response to cell stresses such as virus infection and cancer progression. Adenovirus 5 (Ad5) is known to cause an increase of Alu transcription in HeLa, myelogenous leukemia and embryonic kidney cell lines, even though the virus factors that are responsible for this transcriptional enhancement have not been identified yet. Potential candidates could be represented by oncovirus proteins that induce a global remodeling of the host epigenetic landscape. For example, the Adenovirus early E1A protein interacts with the host tumor suppressor Rb, the lysine acetylase p300 and the p400 ATP-dependent chromatin remodeling complex, resulting in the induction of quiescent fibroblasts to enter the S-phase of the cell cycle. The exceptional success of Alu expansion and their retention even at the cost of a strong epigenetic silencing, which is released by virus infection, led us to investigate the molecular mechanism of Alus activation and their potential involvement in various cell processes. @@ -2475,7 +3931,7 @@ @article{capitani_vivo_2024 author = {Capitani, Valerio and Arcari, Gabriele and Ambrosi, Cecilia and Scribano, Daniela and Ceparano, Mariateresa and Polani, Riccardo and De Francesco, Alice and Raponi, Giammarco and Ceccarelli, Giancarlo and Villari, Paolo and Palamara, Anna Teresa and Marzuillo, Carolina and Carattoli, Alessandra}, doi = {10.1128/msphere.00423-24}, journal = {mSphere}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Azabicyclo Compounds, Ceftazidime, Drug Combinations, Klebsiella Infections, Klebsiella pneumoniae, Liver Abscess, Microbial Sensitivity Tests}, month = {August}, note = {Publisher: American Society for Microbiology}, number = {9}, @@ -2487,6 +3943,23 @@ @article{capitani_vivo_2024 year = {2024} } +@article{cappelletti_robertsonian_2022, + abstract = {Centromeres are epigenetically specified by the histone H3 variant CENP-A and typically associated with highly repetitive satellite DNA. We previously discovered natural satellite-free neocentromeres in Equus caballus and Equus asinus. Here, through ChIP-seq with an anti-CENP-A antibody, we found an extraordinarily high number of centromeres lacking satellite DNA in the zebras Equus burchelli (15 of 22) and Equus grevyi (13 of 23), demonstrating that the absence of satellite DNA at the majority of centromeres is compatible with genome stability and species survival and challenging the role of satellite DNA in centromere function. Nine satellite-free centromeres are shared between the two species in agreement with their recent separation. We assembled all centromeric regions and improved the reference genome of E. burchelli. Sequence analysis of the CENP-A binding domains revealed that they are LINE-1 and AT-rich with four of them showing DNA amplification. In the two zebras, satellite-free centromeres emerged from centromere repositioning or following Robertsonian fusion. In five chromosomes, the centromeric function arose near the fusion points, which are located within regions marked by traces of ancestral pericentromeric sequences. Therefore, besides centromere repositioning, Robertsonian fusions are an important source of satellite-free centromeres during evolution. Finally, in one case, a satellite-free centromere was seeded on an inversion breakpoint. At 11 chromosomes, whose primary constrictions seemed to be associated with satellite repeats by cytogenetic analysis, satellite-free neocentromeres were instead located near the ancestral inactivated satellite-based centromeres; therefore, the centromeric function has shifted away from a satellite repeat containing locus to a satellite-free new position.}, + author = {Cappelletti, Eleonora and Piras, Francesca M and Sola, Lorenzo and Santagostino, Marco and Abdelgadir, Wasma A and Raimondi, Elena and Lescai, Francesco and Nergadze, Solomon G and Giulotto, Elena}, + doi = {10.1093/molbev/msac162}, + issn = {0737-4038}, + journal = {Mol Biol Evol}, + keywords = {{\textgreater}UseGalaxy.eu, Centromere, DNA, Satellite}, + language = {eng}, + month = {August}, + number = {8}, + pages = {msac162}, + title = {Robertsonian {Fusion} and {Centromere} {Repositioning} {Contributed} to the {Formation} of {Satellite}-free {Centromeres} {During} the {Evolution} of {Zebras}}, + url = {http://europepmc.org/abstract/MED/35881460}, + volume = {39}, + year = {2022} +} + @article{capra_cpg_2023, abstract = {During epididymal transit spermatozoa acquire specific morphological features which enhance their ability to swim in a progressive manner and interact with the oocytes. At the same time, sperm cells undergo specific molecular rearrangements essential for the fertilizing sperm to drive a correct embryo development. To assess epigenetic sperm changes during epididymal maturation, the caput, corpus and cauda epididymis sperm tracts were isolated from eight bulls and characterized for different sperm quality parameters and for CpG DNA methylation using Reduced Representation Bisulfite Sequencing (RRBS) able to identify differentially methylated regions (DMRs) in higher CpG density regions.}, author = {Capra, Emanuele and Turri, F. and Lazzari, B. and Biffani, S. and Lange Consiglio, A. and Ajmone Marsan, P. and Stella, A. and Pizzi, F.}, @@ -2505,18 +3978,45 @@ @article{capra_cpg_2023 } @article{carattoli_evolutionary_2021, + abstract = {From January 2019 to April 2020, 32 KPC-producing, ceftazidime-avibactam (CZA)-resistant Klebsiella pneumoniae strains were isolated in a university hospital in Rome, Italy. These strains belonged to the sequence type 512 (ST512), ST101, and ST307 high-risk clones. Nine different CZA-resistant KPC-3 protein variants were identified, five of them never previously reported (KPC-66 to KPC-70). Among the nine, KPC-31, KPC-39, KPC-49, KPC-66, KP-68, KPC-69, and KPC-70 showed amino acid substitutions, insertions, and deletions in the Ω loop of the protein. KPC-29 has a duplication, while the novel KPC-67 has a triplication, of the KDD triplet in the 270-loop, a secondary loop of the KPC-3 protein. Genomics performed on contemporary resistant and susceptible clones underlined that these novel mutations emerged in \textit{bla}$_{\textrm{KPC-3}}$ genes located on conserved plasmids: in ST512, all \textit{bla}$_{\textrm{KPC-3}}$ mutant genes were located in pKpQIL plasmids, while the three novel \textit{bla}$_{\textrm{KPC-3}}$ mutants identified in ST101 were on FIIk-FIA(HI1)-R plasmids. Selection also promoted multiplication of the carbapenemase gene copy number by transposition, recombination, and fusion of resident plasmids. When expressed in Escherichia coli recipient cells cloned in the high-copy-number pTOPO vector, the Ω loop mutated variants showed the CZA-resistant phenotype associated with susceptibility to carbapenems, while KPC variants with insertions in the 270-loop showed residual activity on carbapenems. The investigation of CZA resistance mechanisms offered the unique opportunity to study vertical, horizontal, and oblique evolutionary trajectories of K. pneumoniae high-risk clones.}, author = {Carattoli, Alessandra and Arcari, Gabriele and Bibbolino, Giulia and Sacco, Federica and Tomolillo, Dario and Lella, Federica Maria Di and Trancassini, Maria and Faino, Luigi and Venditti, Mario and Antonelli, Guido and Raponi, Giammarco}, doi = {10.1128/aac.00574-21}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {0066-4804}, + journal = {Antimicrob Agents Chemother}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Klebsiella Infections, Klebsiella pneumoniae}, + language = {eng}, month = {September}, note = {Publisher: American Society for Microbiology}, number = {10}, + pages = {e0057421}, title = {Evolutionary {Trajectories} toward {Ceftazidime}-{Avibactam} {Resistance} in {Klebsiella} pneumoniae {Clinical} {Isolates}}, url = {https://doi.org/10.1128/aac.00574-21}, volume = {65}, year = {2021} } +@article{carranza_erga-bge_2025, + abstract = {The reference genome of the freshwater snake, +Natrix maura, +offers a crucial resource for uncovering the genetic basis of adaptability to freshwater environments, while providing insights into hybridization and gene flow within the genus +Natrix +. A total of 18 contiguous chromosomal pseudomolecules were assembled from the genome sequence, corresponding to the 16 autosomes and 2 sex chromosomes. This chromosome-level assembly encompasses 1.7 Gb, composed of 284 contigs and 209 scaffolds, with contig and scaffold N50 values of 36.5 Mb and 174.4 Mb, respectively.}, + author = {Carranza, Salvador and Fernández-Guiberteau, Daniel and Blasón, Laura and Tulloch, Sergi and Monteiro, Rita and Böhne, Astrid and Fernández, Rosa and Escudero, Nuria and Aguilera, Laura and Gut, Marta and Alioto, Tyler S and Câmara Ferreira, Francisco and Gómez-Garrido, Jèssica and Cruz, Fernando and Sinha, Swati and Haggerty, Leanne and Martin, Fergal and Brown, Tom}, + doi = {10.12688/openreseurope.20863.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {August}, + pages = {215}, + shorttitle = {{ERGA}-{BGE} {Genome} of the viperine water snake ({Natrix} maura)}, + title = {{ERGA}-{BGE} {Genome} of the viperine water snake ({Natrix} maura): a key species for evolutionary insights of freshwater snakes}, + url = {https://open-research-europe.ec.europa.eu/articles/5-215/v1}, + urldate = {2025-10-19}, + volume = {5}, + year = {2025} +} + @techreport{carval_pangeo_2024, author = {Carval, Thierry and Jossé, Marie and Detoc, Jérôme}, doi = {10.5194/egusphere-egu24-6216}, @@ -2533,10 +4033,13 @@ @techreport{carval_pangeo_2024 } @article{carvalho_genomics_2024, + abstract = {Chloroviruses exhibit a close relationship with their hosts with the phenotypic aspect of their ability to form lytic plaques having primarily guided the taxonomy. However, with the isolation of viruses that are only able to complete their replication cycle in one strain of \textit{Chlorella variabilis}, systematic challenges emerged. In this study, we described the genomic features of 53 new chlorovirus isolates and used them to elucidate part of the evolutionary history and taxonomy of this clade. Our analysis revealed new chloroviruses with the largest genomes to date ({\textgreater}400 kbp) and indicated that four genomic features are statistically different in the viruses that only infect the Syngen 2-3 strain of \textit{C. variabilis} (OSy viruses). We found large regions of dissimilarity in the genomes of viruses PBCV-1 and OSy-NE5 when compared with the other genomes. These regions contained genes related to the interaction with the host cell machinery and viral capsid proteins, which provided insights into the evolution of the replicative and structural modules in these giant viruses. Phylogenetic analysis using hallmark genes of \textit{Nucleocytoviricota} revealed that OSy-viruses evolved from the NC64A-viruses, possibly emerging as a result of the strict relationship with their hosts. Merging phylogenetics and nucleotide identity analyses, we propose strategies to demarcate viral species, resulting in seven new species of chloroviruses. Collectively, our results show how genomic data can be used as lines of evidence to demarcate viral species. Using the chloroviruses as a case study, we expect that similar initiatives will emerge using the basis exhibited here.IMPORTANCEChloroviruses are a group of giant viruses with long dsDNA genomes that infect different species of \textit{Chlorella-}like green algae. They are host-specific, and some isolates can only replicate within a single strain of \textit{Chlorella variabilis}. The genomics of these viruses is still poorly explored, and the characterization of new isolates provides important data on their genetic diversity and evolution. In this work, we describe 53 new chlorovirus genomes, including many isolated from alkaline lakes for the first time. Through comparative genomics and molecular phylogeny, we provide evidence of genomic gigantism in chloroviruses and show that a subset of viruses became highly specific for their hosts at a particular point in evolutionary history. We propose criteria to demarcate species of chloroviruses, paving the way for an update in the taxonomy of other groups of viruses. This study is a new and important piece in the complex puzzle of giant algal viruses.}, author = {Carvalho, João Victor R. P. and Carlson, Roger M. and Ghosh, Jayadri and Queiroz, Victória F. and de Oliveira, Ellen G. and Botelho, Bruna B. and Filho, Clécio A. C. and Agarkova, Irina V. and McClung, O. William and Van Etten, James L. and Dunigan, David D. and Rodrigues, Rodrigo A. L.}, doi = {10.1128/jvi.00361-24}, + issn = {0022-538X}, journal = {Journal of Virology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Chlorella, Evolution, Molecular, Genome, Viral, Genomics, Giant Viruses, Phycodnaviridae, Phylogeny}, + language = {eng}, month = {October}, note = {Publisher: American Society for Microbiology}, number = {0}, @@ -2562,6 +4065,28 @@ @article{casal_plant_2024 year = {2024} } +@article{casella_novel_2025, + abstract = {With rising concerns about antimicrobial resistance, the identification of new lead compounds to target multidrug-resistant bacteria is essential. This study employed a fast miniaturized screening to simultaneously cultivate and evaluate about 300 marine strains for biosurfactant and antibacterial activities, leading to the selection of the deep-sea Bacillus halotolerans BCP32. The integration of tandem mass spectrometry molecular networking and bioassay-guided fractionation unveiled this strain as a prolific factory of surfactins and nobilamides. Particularly, 84 nobilamide congeners were identified in the bacterial exometabolome, 71 of them being novel metabolites. Among these, four major compounds were isolated, including the known TL-119 and nobilamide I, as well as the two new nobilamides T1 and S1. TL-119 and nobilamide S1 exhibited potent antibiotic activity against various multidrug-resistant Staphylococcus strains and other Gram-positive pathogens, including the foodborne pathogen Listeria monocytogenes. Finally, in silico analysis of Bacillus halotolerans BCP32 genome revealed nobilamide biosynthesis to be directed by a previously unknown heptamodular nonribosomal peptide synthetase.}, + author = {Casella, Vincenza and Della Sala, Gerardo and Scarpato, Silvia and Buonocore, Carmine and Ragozzino, Costanza and Tedesco, Pietro and Coppola, Daniela and Vitale, Giovanni Andrea and de Pascale, Donatella and Palma Esposito, Fortunato}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/md23010041}, + issn = {1660-3397}, + journal = {Marine Drugs}, + keywords = {\textit{Bacillus}, \textit{Listeria monocytogenes}, {\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Bacillus, Depsipeptides, MDR \textit{Staphyloccus aureus}, NRPS, Peptides, Cyclic, antimicrobials, biosurfactant, genome mining, molecular networking, nobilamides, surfactins}, + language = {en}, + month = {January}, + note = {Number: 1 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {1}, + pages = {41}, + shorttitle = {Novel {Insights} into the {Nobilamide} {Family} from a {Deep}-{Sea} {Bacillus}}, + title = {Novel {Insights} into the {Nobilamide} {Family} from a {Deep}-{Sea} {Bacillus}: {Chemical} {Diversity}, {Biosynthesis} and {Antimicrobial} {Activity} {Towards} {Multidrug}-{Resistant} {Bacteria}}, + url = {https://www.mdpi.com/1660-3397/23/1/41}, + urldate = {2025-05-29}, + volume = {23}, + year = {2025} +} + @article{castellana_pannonibacter_2024, abstract = {This study describes two cases of bacteraemia sustained by a new putative Pannonibacter species isolated at the U.O.C. of Microbiology and Virology of the Policlinico of Bari (Bari, Italy) from the blood cultures of two patients admitted to the Paediatric Oncohaematology Unit. Pannonibacter spp. is an environmental Gram-negative bacterium not commonly associated with nosocomial infections. Species identification was performed using Sanger sequencing of the 16S rRNA gene and Whole-Genome Sequencing (WGS) for both strains. Genomic analyses for the two isolates, BLAST similarity search, and phylogeny for the 16S rDNA sequences lead to an assignment to the species Pannonibacter phragmitetus. However, by performing ANIb, ANIm, tetranucleotide correlation, and DNA-DNA digital hybridization, analyses of the two draft genomes showed that they were very different from those of the species P. phragmitetus. MALDI-TOF analysis, assessment of antimicrobial susceptibility by E-test method, and Analytical Profile Index (API) tests were also performed. This result highlights how environmental bacterial species can easily adapt to the human host and, especially in nosocomial environments, also gain pathogenic potential through antimicrobial resistance.}, author = {Castellana, Stefano and De Laurentiis, Vittoriana and Bianco, Angelica and Del Sambro, Laura and Grassi, Massimo and De Leonardis, Francesco and Derobertis, Anna Maria and De Carlo, Carmen and Sparapano, Eleonora and Mosca, Adriana and Stolfa, Stefania and Ronga, Luigi and Santacroce, Luigi and Chironna, Maria and Parisi, Michela and Capozzi, Loredana and Parisi, Antonio}, @@ -2583,28 +4108,98 @@ @article{castellana_pannonibacter_2024 year = {2024} } -@article{cermak_unexpected_2020, - abstract = {In plants, posttranscriptional gene silencing (PTGS) is induced by small RNAs (sRNAs) generated from various dsRNA precursors. To assess the impact of dsRNA origin, we compared downregulation of GFP expression triggered by inverted repeat (IR), antisense (AS) and unterminated sense (UT) transcripts transiently expressed from the estradiol-inducible promoter. The use of homogeneously responding tobacco BY-2 cell lines allowed monitoring the onset of silencing and its reversibility. In this system, IR induced the strongest and fastest silencing accompanied by dense DNA methylation. At low induction, silencing in individual cells was binary (either strong or missing), suggesting that a certain threshold sRNA level had to be exceeded. The AS variant specifically showed a deviated sRNA-strand ratio shifted in favor of antisense orientation. In AS lines and weakly induced IR lines, only the silencer DNA was methylated, but the same target GFP sequence was not, showing that DNA methylation accompanying PTGS was influenced both by the level and origin of sRNAs, and possibly also by the epigenetic state of the locus. UT silencing appeared to be the least effective and resembled classical sense PTGS. The best responding UT lines behaved relatively heterogeneously possibly due to complexly arranged T-DNA insertions. Unlike IR and AS variants that fully restored GFP expression upon removal of the inducer, only partial reactivation was observed in some UT lines. Our results pointed out several not yet described phenomena and differences between the long-known silencer variants that may direct further research and affect selection of proper silencer variants for specific applications.}, - author = {Čermák, Vojtěch and Tyč, Dimitrij and Přibylová, Adéla and Fischer, Lukáš}, - doi = {10.1016/j.bbagrm.2020.194647}, - issn = {1874-9399}, - journal = {Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, DNA methylation, PTGS, RNAi, Tobacco BY-2 cell line, dsRNA, siRNA}, - language = {en}, - month = {November}, - number = {11}, - pages = {194647}, - title = {Unexpected variations in posttranscriptional gene silencing induced by differentially produced {dsRNAs} in tobacco cells}, - url = {https://www.sciencedirect.com/science/article/pii/S1874939920302303}, - urldate = {2021-05-15}, - volume = {1863}, - year = {2020} +@article{castellano_ribonuclease_2025, + abstract = {Cell membranes are thought of as barriers to extracellular RNA (exRNA) uptake. While naked exRNAs can be spontaneously internalized by certain cells, functional cytosolic delivery has been rarely observed. Here, we show that extracellular ribonucleases (RNases)-primarily from cell culture supplements-have obscured the study of exRNA functionality. When ribonuclease inhibitor (RI) is added to cell cultures, naked exRNAs can trigger pro-inflammatory responses in dendritic cells and macrophages, largely via endosomal Toll-like receptors (TLRs). Moreover, naked exRNAs can escape endosomes, engaging cytosolic RNA sensors. In addition, naked extracellular mRNAs can be spontaneously internalized and translated by various cell types in an RI-dependent manner. In vivo, RI co-injection amplifies naked-RNA-induced activation of splenic lymphocytes and myeloid leukocytes. Furthermore, naked RNA is inherently pro-inflammatory in RNase-poor compartments like the peritoneal cavity. These findings demonstrate that naked RNA is bioactive without requiring vesicular encapsulation, making a case for nonvesicular-exRNA-mediated intercellular communication.}, + author = {Castellano, Mauricio and Blanco, Valentina and Li Calzi, Marco and Costa, Bruno and Witwer, Kenneth and Hill, Marcelo and Cayota, Alfonso and Segovia, Mercedes and Tosar, Juan Pablo}, + doi = {10.1016/j.xgen.2025.100874}, + issn = {2666-979X}, + journal = {Cell Genom}, + keywords = {{\textgreater}UseGalaxy.eu, RNA, Ribonucleases}, + language = {eng}, + month = {May}, + number = {5}, + pages = {100874}, + title = {Ribonuclease activity undermines immune sensing of naked extracellular {RNA}}, + url = {http://europepmc.org/abstract/MED/40334662}, + volume = {5}, + year = {2025} } -@article{ceylan_whole-genome_2024, - abstract = {Common sage (Salvia officinalis L.), the type species of the genus Salvia, is a historically acknowledged medicinal and aromatic plant that is utilized in several different industries for manufacturing diverse end products, including food, pharmaceuticals, cosmetics, personal hygiene products and insect repellants. The medical uses of sage essential oil terpenoids have made these secondary metabolites a focus of medical/pharmaceutical chemistry research. In the present work, the common sage genome was resequenced and assembled, and the protein-encoding gene content was annotated. The terpenoid biosynthesis gene repertoire, which includes 75 terpene synthase and 67 terpenoid backbone biosynthesis pathway genes, was predicted and located on assembly scaffolds, revealing tandem duplication blocks on the chromosomes. Variant analysis identified 188 variable single-nucleotide loci in the coding sequences of sage terpenoid biosynthesis genes. A total of 24,570 single-nucleotide polymorphisms were identified in the common sage total exome, representing a database of potential variable loci for targeted genotyping research. Given that terpene synthase activity is highly prone to modulation by point mutations and that the genotype plays an important role in the complex traits of terpenoid composition, single-nucleotide polymorphisms located in coding sequences constitute candidate functional markers that can be associated with terpenoid compositional traits in future research.}, - author = {Ceylan, Fatima and Uncu, Ayse Ozgur and Soyturk Patat, Aysenur and Uncu, Ali Tevfik}, - doi = {10.1007/s10722-024-01900-z}, +@article{castillo-villamizar_unveiling_2024, + abstract = {{\textless}p{\textgreater}Citrus cultivation is vital to global agriculture, necessitating a comprehensive understanding of the soil microbiome’s diversity for sustainable practices. This study provides initial insights into the bacteriome in citrus crops in Santander, Colombia, employing a holistic approach combining culture-based techniques, sequencing methods, and bioinformatics analyses. The study explores organic and non-organic cultivation systems, revealing statistically significant differences in bacterial community composition between both practices. In general, the communities are dominated by members of the Actinobacteria and Proteobacteria, along with bacterial orders Gaiellales and Burkholderiales, all contributing to intricate ecological processes. Culture-based methods aided in the isolation of potential biotechnologically relevant strains. Among them, strain CP102 showed a pronounced carboxymethylcellulose (CMC) degradation capacity. Genetic analysis of the isolate resulted in the generation of the first closed genome of a member of the species {\textless}italic{\textgreater}Enterobacter soli{\textless}/italic{\textgreater} and identified an unreported 109 kb plasmid. Further genomic examination revealed genes potentially associated with cellulose degradation in this species, which provides the isolate with biotechnological potential. This research significantly advances the global understanding of citrus-associated bacteriomes, shaping future agricultural practices and promoting the development of sustainable bioproducts.{\textless}/p{\textgreater}}, + author = {Castillo-Villamizar, Genis Andrés and Tapia-Perdomo, Valentina and Maldonado-Pava, Julieth and Santamaría-Gálvis, Pedro and Sayavedra, Lizbeth and Hernandez-Torres, Jorge and Puentes-Cala, Edinson}, + doi = {10.3389/fevo.2024.1372284}, + issn = {2296-701X}, + journal = {Frontiers in Ecology and Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, Agricultural practices, Biocatalysts, Biodiversity, Bioprospection, citrus cultivation, microbiome, soil-associated bacteria}, + language = {English}, + month = {May}, + note = {Publisher: Frontiers}, + title = {Unveiling soil bacterial ecosystems in andean citrus orchards of {Santander}, {Colombia}}, + url = {https://www.frontiersin.org/journals/ecology-and-evolution/articles/10.3389/fevo.2024.1372284/full}, + urldate = {2025-02-28}, + volume = {12}, + year = {2024} +} + +@patent{cathomen_truly_2021, + assignee = {Albert-Ludwigs-Universität Freiburg}, + author = {CATHOMEN, Toni and HAAS, Simone Alexandra and HILDENBEUTEL, Markus and MUSSOLINO, Claudio and BOERRIES, Melanie and ANDRIEUX, Geoffroy}, + keywords = {{\textgreater}UseGalaxy.eu, adapter, coverage, dsdna, sequence, target}, + language = {en}, + month = {April}, + nationality = {WO}, + number = {WO2021078645A1}, + title = {A truly unbiased in vitro assay to profile off-target activity of one or more target-specific programmable nucleases in cells (abnoba-seq)}, + url = {https://patents.google.com/patent/WO2021078645A1/en?q=(%22usegalaxy.eu%22+OR+%22European+Galaxy%22)&oq=%22usegalaxy.eu%22+OR+%22European+Galaxy%22}, + urldate = {2025-04-14}, + year = {2021} +} + +@article{cen_morpho-molecular_2025, + abstract = {Archaeognatha (bristletails) represent an evolutionarily significant but understudied insect group. Notably, the morphological identification method proposed by Mendes for Archaeognatha has certain limitations, which may lead to the underestimation or misidentification of some cryptic species. To address this issue, we employed an integrated strategy that combines morphological and molecular identification methods. Therefore, this study aimed to (1) identify cryptic diversity within Pedetontus silvestrii using mitogenomic data; (2) clarify phylogenetic relationships among Archaeognatha lineages; and (3) estimate divergence times for key taxonomic splits. We analyzed mitochondrial genomes from six P. silvestrii populations (Liaoning, Jilin, and Hebei Provinces) alongside 14 published Archaeognatha genomes. Key findings include the following: (1) Integrative analyses of genetic distances, phylogenetic reconstruction, bPTP-based molecular species delimitation, and divergence time estimation collectively revealed four evolutionarily distinct lineages within P. silvestrii. (2) Machilidae and Machilinae were non-monophyletic, whereas Petrobiellinae showed close affinity to Meinertellidae. (3) Archaeognatha originated {\textasciitilde}301.19 Mya (Late Carboniferous); the Machilinae–Petrobiinae split occurred approximately 153.99 Mya (Jurassic). This study underscores the critical importance of mitogenomic analysis in elucidating cryptic biodiversity, while emphasizing the necessity of integrating morphological identification with molecular characterization for comprehensive species delineation in future taxonomic investigations.}, + author = {Cen, Wei and Li, Jia-Wen and He, Jia-Tao and Chen, Xin-Yu and Li, Luo-Ying and Storey, Kenneth B. and Yu, Dan-Na and Zhang, Jia-Yong}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/insects16050452}, + issn = {2075-4450}, + journal = {Insects}, + keywords = {{\textgreater}UseGalaxy.eu, Archaeognatha, cryptic species, divergence time, mitochondrial genome, phylogenetic relationship}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {452}, + shorttitle = {Morpho-{Molecular} {Discordance} and {Cryptic} {Diversity} in {Jumping} {Bristletails}}, + title = {Morpho-{Molecular} {Discordance} and {Cryptic} {Diversity} in {Jumping} {Bristletails}: {A} {Mitogenomic} {Analysis} of {Pedetontus} silvestrii ({Insecta}: {Archaeognatha}: {Machilidae})}, + url = {https://www.mdpi.com/2075-4450/16/5/452}, + urldate = {2025-05-29}, + volume = {16}, + year = {2025} +} + +@article{cermak_unexpected_2020, + abstract = {In plants, posttranscriptional gene silencing (PTGS) is induced by small RNAs (sRNAs) generated from various dsRNA precursors. To assess the impact of dsRNA origin, we compared downregulation of GFP expression triggered by inverted repeat (IR), antisense (AS) and unterminated sense (UT) transcripts transiently expressed from the estradiol-inducible promoter. The use of homogeneously responding tobacco BY-2 cell lines allowed monitoring the onset of silencing and its reversibility. In this system, IR induced the strongest and fastest silencing accompanied by dense DNA methylation. At low induction, silencing in individual cells was binary (either strong or missing), suggesting that a certain threshold sRNA level had to be exceeded. The AS variant specifically showed a deviated sRNA-strand ratio shifted in favor of antisense orientation. In AS lines and weakly induced IR lines, only the silencer DNA was methylated, but the same target GFP sequence was not, showing that DNA methylation accompanying PTGS was influenced both by the level and origin of sRNAs, and possibly also by the epigenetic state of the locus. UT silencing appeared to be the least effective and resembled classical sense PTGS. The best responding UT lines behaved relatively heterogeneously possibly due to complexly arranged T-DNA insertions. Unlike IR and AS variants that fully restored GFP expression upon removal of the inducer, only partial reactivation was observed in some UT lines. Our results pointed out several not yet described phenomena and differences between the long-known silencer variants that may direct further research and affect selection of proper silencer variants for specific applications.}, + author = {Čermák, Vojtěch and Tyč, Dimitrij and Přibylová, Adéla and Fischer, Lukáš}, + doi = {10.1016/j.bbagrm.2020.194647}, + issn = {1874-9399}, + journal = {Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, DNA methylation, PTGS, RNAi, Tobacco BY-2 cell line, dsRNA, siRNA}, + language = {en}, + month = {November}, + number = {11}, + pages = {194647}, + title = {Unexpected variations in posttranscriptional gene silencing induced by differentially produced {dsRNAs} in tobacco cells}, + url = {https://www.sciencedirect.com/science/article/pii/S1874939920302303}, + urldate = {2021-05-15}, + volume = {1863}, + year = {2020} +} + +@article{ceylan_whole-genome_2024, + abstract = {Common sage (Salvia officinalis L.), the type species of the genus Salvia, is a historically acknowledged medicinal and aromatic plant that is utilized in several different industries for manufacturing diverse end products, including food, pharmaceuticals, cosmetics, personal hygiene products and insect repellants. The medical uses of sage essential oil terpenoids have made these secondary metabolites a focus of medical/pharmaceutical chemistry research. In the present work, the common sage genome was resequenced and assembled, and the protein-encoding gene content was annotated. The terpenoid biosynthesis gene repertoire, which includes 75 terpene synthase and 67 terpenoid backbone biosynthesis pathway genes, was predicted and located on assembly scaffolds, revealing tandem duplication blocks on the chromosomes. Variant analysis identified 188 variable single-nucleotide loci in the coding sequences of sage terpenoid biosynthesis genes. A total of 24,570 single-nucleotide polymorphisms were identified in the common sage total exome, representing a database of potential variable loci for targeted genotyping research. Given that terpene synthase activity is highly prone to modulation by point mutations and that the genotype plays an important role in the complex traits of terpenoid composition, single-nucleotide polymorphisms located in coding sequences constitute candidate functional markers that can be associated with terpenoid compositional traits in future research.}, + author = {Ceylan, Fatima and Uncu, Ayse Ozgur and Soyturk Patat, Aysenur and Uncu, Ali Tevfik}, + doi = {10.1007/s10722-024-01900-z}, issn = {1573-5109}, journal = {Genetic Resources and Crop Evolution}, keywords = {{\textgreater}UseGalaxy.eu, Genome assembly, Lamiaceae, Mint, Secondary metabolite, Variant calling}, @@ -2616,6 +4211,23 @@ @article{ceylan_whole-genome_2024 year = {2024} } +@article{chaity_genomic_2025, + abstract = {Klebsiella pneumoniae is an opportunistic pathogen associated with nosocomial infections, known for its multidrug resistance (MDR) and biofilm-forming abilities. ST48 is a particularly concerning sequence type and an emerging international clone linked to global spread and MDR infections. This study examines the comprehensive genomic epidemiology of the local and global populations of K. pneumoniae ST48 strains using whole genomes sequence data. We performed phenotypic and genotypic characterization of a K. pneumoniae strain S3C and conducted molecular epidemiological analyses of local ST48 isolates in Bangladesh, followed by pan-genome and phylogenetic analyses of 397 global ST48 strains. The S3C strain was resistant to 17 out of 19 tested antibiotics and was a moderate biofilm former. Whole genome sequencing identified it as ST48 clonal type, with 13 acquired antibiotic resistance genes, 76 virulence-associated genes, and multiple mobile genetic elements. Comparative analysis of Bangladeshi ST48 strains indicated a high prevalence of MDR genes, particularly bla$_{\textrm{CTX-M-15}}$, and a diverse array of virulence factors associated with biofilm formation, siderophore production, capsular biosynthesis and others. Pan-genome analysis of Bangladeshi ST48 strains revealed 8,030 genes, with 56.26\% classified as core genes. In contrast, global ST48 strains had 16,307 genes, with 75.3\% as accessory genes, highlighting extensive genomic plasticity. The phylogenetic analysis revealed that isolates from different regions clustered within the major clade, indicating the global dissemination of this sequence type. Our findings underscore the substantial genomic diversity and high resistance levels of K. pneumoniae ST48, emphasizing the need for targeted infection control measures and continuous surveillance.}, + author = {Chaity, Sudipta Chowdhury and Hosen, Md Arman and Rahman, Sabita Rezwana and Khan, Md Abu Sayem}, + doi = {10.1016/j.jgeb.2025.100557}, + issn = {1687-157X}, + journal = {J Genet Eng Biotechnol}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {September}, + number = {3}, + pages = {100557}, + title = {Genomic characterization and comparative analysis of antibiotic resistance and virulence in {Bangladeshi} and global {Klebsiella} pneumoniae {ST48} strains}, + url = {http://europepmc.org/abstract/MED/40854671}, + volume = {23}, + year = {2025} +} + @article{chanama_comparative_2023, abstract = {Actinobacteria are well known as a rich source of diversity of bioactive secondary metabolites. Kutzneria, a rare actinobacteria belonging to the family Pseudonocardiaceae has abundance of secondary metabolite biosynthetic gene clusters (BGCs) and is one of important source of natural products and worthy of priority investigation. Currently, Kutzneria chonburiensis SMC256T has been the latest type-strain of the genus and its genome sequence has not been reported yet. Therefore, we present the first report of new complete genome sequence of SMC256T (genome size of 10.4 Mbp) with genome annotation and feature comparison between SMC256T and other publicly available Kutzneria species. The results from comparative and functional genomic analyses regarding the phylogenomic and the clusters of orthologous groups of proteins (COGs) analyses indicated that SMC256T is most closely related to Kutzneria sp. 744, Kutzneria kofuensis, Kutzneria sp. CA-103260 and Kutzneria buriramensis. Furthermore, a total of 322 BGCs were also detected and showed diversity among the Kutzneria genomes. Out of which, 38 clusters showing the best hit to the most known BGCs were predicted in the SMC256Tgenome. We observed that six clusters responsible for biosynthesis of antimicrobials/antitumor metabolites were strain-specific in Kutzneria chonburiensis. These putative metabolites include virginiamycin S1, lysolipin I, esmeraldin, rakicidin, aclacinomycin and streptoseomycin. Based on these findings, the genome of Kutzneria chonburiensis contains distinct and unidentified BGCs different from other members of the genus, and the use of integrative genomic-based approach would be a useful alternative effort to target, isolate and identify putative and undiscovered secondary metabolites suspected to have new and/or specific bioactivity in the Kutzneria.}, author = {Chanama, Manee and Prombutara, Pinidphon and Chanama, Suchart}, @@ -2623,7 +4235,7 @@ @article{chanama_comparative_2023 doi = {10.1038/s41598-023-36039-x}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, Bacteria, Comparative genomics, Phylogenomics}, + keywords = {{\textgreater}UseGalaxy.eu, Actinomycetales, Bacteria, Comparative genomics, Phylogenomics}, language = {en}, month = {May}, note = {Number: 1 @@ -2637,6 +4249,23 @@ @article{chanama_comparative_2023 year = {2023} } +@article{charlton_fork_2024, + abstract = {The inheritance of parental histones across the replication fork is thought to mediate epigenetic memory. Here, we reveal that fission yeast Mrc1 (CLASPIN in humans) binds H3-H4 tetramers and operates as a central coordinator of symmetric parental histone inheritance. Mrc1 mutants in a key connector domain disrupted segregation of parental histones to the lagging strand comparable to Mcm2 histone-binding mutants. Both mutants showed clonal and asymmetric loss of H3K9me-mediated gene silencing. AlphaFold predicted co-chaperoning of H3-H4 tetramers by Mrc1 and Mcm2, with the Mrc1 connector domain bridging histone and Mcm2 binding. Biochemical and functional analysis validated this model and revealed a duality in Mrc1 function: disabling histone binding in the connector domain disrupted lagging-strand recycling while another histone-binding mutation impaired leading strand recycling. We propose that Mrc1 toggles histones between the lagging and leading strand recycling pathways, in part by intra-replisome co-chaperoning, to ensure epigenetic transmission to both daughter cells.}, + author = {Charlton, Sebastian Jespersen and Flury, Valentin and Kanoh, Yutaka and Genzor, Aitana Victoria and Kollenstart, Leonie and Ao, Wantong and Brøgger, Peter and Weisser, Melanie Bianca and Adamus, Marek and Alcaraz, Nicolas and Delvaux de Fenffe, Charlotte M and Mattiroli, Francesca and Montoya, Guillermo and Masai, Hisao and Groth, Anja and Thon, Geneviève}, + doi = {10.1016/j.cell.2024.07.017}, + issn = {0092-8674}, + journal = {Cell}, + keywords = {{\textgreater}UseGalaxy.eu, DNA Replication, Epigenesis, Genetic, Histones, Schizosaccharomyces, Schizosaccharomyces pombe Proteins}, + language = {eng}, + month = {September}, + number = {18}, + pages = {5029--5047.e21}, + title = {The fork protection complex promotes parental histone recycling and epigenetic memory}, + url = {http://europepmc.org/abstract/MED/39094569}, + volume = {187}, + year = {2024} +} + @article{chatti_genome-wide_2024, abstract = {The R2R3-MYB transcription factor (TF) family is crucial for regulating plant growth, stress response, and fruit ripening. Although this TF family has been examined in a multitude of plants, the R2R3-MYB TFs in Ficus carica, a Mediterranean fruit species, have yet to be characterized. This study identified and classified 63 R2R3-MYB genes (FcMYB1 to FcMYB63) in the F. carica genome. We analyzed these genes for physicochemical properties, conserved motifs, phylogenetic relationships, gene architecture, selection pressure, and gene expression profiles and networks. The genes were classified into 29 clades, with members of the same clade showing similar exon–intron structures and motif compositions. Of the 54 orthologous gene pairs shared with mulberry (Morus notabilis), 52 evolved under negative selection, while two pairs (FcMYB55/MnMYB20 and FcMYB59/MnMYB31) experienced diversifying selection. RNA-Seq analysis showed that FcMYB26, FcMYB33, and FcMYB34 were significantly overexpressed in fig fruit peel during maturation phase III. Weighted gene co-expression network analysis (WGCNA) indicated that these genes are part of an expression module associated with the anthocyanin pathway. RT-qPCR validation confirmed these findings and revealed that the Tunisian cultivars 'Zidi' and 'Soltani' have cultivar-specific R2R3-FcMYB genes highly overexpressed during the final stage of fruit maturation and color acquisition. These genes likely influence cultivar-specific pigment synthesis. This study provides a comprehensive overview of the R2R3-MYB TF family in fig, offering a framework for selecting genes related to fruit peel color in breeding programs.}, author = {Chatti, Khaled and Kmeli, Narjes and Bettaieb, Inchirah and Hamdi, Jihen and Gaaied, Sonia and Mlouka, Rania and Mars, Messaoud and Bouktila, Dhia}, @@ -2652,6 +4281,44 @@ @article{chatti_genome-wide_2024 year = {2024} } +@article{cheffer_dot1l_2023, + abstract = {The cortical plate (CP) is composed of excitatory and inhibitory neurons, the latter of which originate in the ganglionic eminences. From their origin in the ventral telencephalon, maturing postmitotic interneurons migrate during embryonic development over some distance to reach their final destination in the CP. The histone methyltransferase Disruptor of Telomeric Silencing 1-like (DOT1L) is necessary for proper CP development and layer distribution of glutamatergic neurons. However, its specific role on cortical interneuron development has not yet been explored. Here, we demonstrate that DOT1L affects interneuron development in a cell autonomous manner. Deletion of Dot1l in Nkx2.1-expressing interneuron precursor cells results in an overall reduction and altered distribution of GABAergic interneurons in the CP from postnatal day 0 onwards. We observed an altered proportion of GABAergic interneurons in the cortex, with a significant decrease in parvalbumin-expressing interneurons. Moreover, a decreased number of mitotic cells at the embryonic day E14.5 was observed upon Dot1l deletion. Altogether, our results indicate that reduced numbers of cortical interneurons upon DOT1L deletion result from premature cell cycle exit, but effects on postmitotic differentiation, maturation, and migration are likely at play as well.}, + author = {Cheffer, Arquimedes and Garcia-Miralles, Marta and Maier, Esther and Akol, Ipek and Franz, Henriette and Srinivasan, Vandana Shree Vedartham and Vogel, Tanja}, + doi = {10.1093/cercor/bhad281}, + issn = {1047-3211}, + journal = {Cereb Cortex}, + keywords = {{\textgreater}UseGalaxy.eu, Histone-Lysine N-Methyltransferase, Interneurons, Parvalbumins, Telencephalon}, + language = {eng}, + month = {September}, + number = {19}, + pages = {10272--10285}, + title = {{DOT1L} deletion impairs the development of cortical parvalbumin-expressing interneurons}, + url = {http://europepmc.org/abstract/MED/37566909}, + volume = {33}, + year = {2023} +} + +@article{chen_bacillus_2025, + abstract = {BackgroundPyridine-2,6-dicarboxylic acid (DPA) is a valuable dicarboxylic acid that has the potential to serve as a precursor for bio-sustainable and bio-degradable materials and self-healing polymers. It also plays a crucial role in the heat resistance of Bacillus subtilis spores. However, extracting DPA from spores is resource-intensive and technically complex, limiting its industrial application. To overcome these challenges, this study aims to engineer B. subtilis as a microbial cell factory for the direct production of free and soluble DPA.ResultsThis study first demonstrated that blocking sporulation reduced DPA production due to the repression of dipicolinate synthase expression. To enhance extracellular DPA production, dipicolinate synthase expression was fine-tuned, increasing the extracellular DPA titer to 330 ± 10 mg/l in strain BSDYvyDVF. Transcriptomic analysis revealed that spore coat assembly genes modulate DPA production. By disrupting a spore coat assembly activator in strain BSDYvyDVF-gerE, sporulation was successfully inhibited, significantly boosting the DPA yield to 944 ± 3 mg/l. Further optimization of fermentation conditions was performed using an orthogonal design. The highest DPA titer of 1250 mg/l was achieved and validated through fed-batch fermentation in a 1.5-l bioreactor.ConclusionThis study demonstrates the potential of engineered B. subtilis BSDYvyDVF-gerE as an efficient cell factory for sustainable DPA biosynthesis. In addition, it identifies key challenges in DPA production, including synthesis efficiency (regulation of key enzyme expression) and transport (intracellular-to-extracellular export), and proposes corresponding solutions.}, + author = {Chen, Taichi and Uzunovic, Haris and Brul, Stanley and Hugenholtz, Jeroen}, + copyright = {cc by-nc-nd}, + doi = {10.1186/s12934-025-02859-x}, + issn = {1475-2859}, + journal = {Microbial cell factories}, + keywords = {{\textgreater}UseGalaxy.eu, Biopolymer, Dicarboxylic acid, Dipicolinic Acid, Fermentation optimization, Spore Coat Assembly}, + language = {eng}, + month = {November}, + number = {1}, + pages = {233}, + pmcid = {PMC12613536}, + pmid = {41225485}, + title = {Bacillus subtilis as cell factory for enhanced production of the biopolymer precursor pyridine-2,6-dicarboxylic acid}, + url = {https://europepmc.org/articles/PMC12613536}, + urldate = {2025-12-26}, + volume = {24}, + year = {2025} +} + @article{chen_canonical_2024, abstract = {The androgen receptor (AR) is central in prostate tissue identity and differentiation, and controls normal growth-suppressive, prostate-specific gene expression. It also drives prostate tumorigenesis when hijacked for oncogenic transcription. The execution of growth-suppressive AR transcriptional programs in prostate cancer (PCa) and the potential for reactivation remain unclear. Here, we use a genome-wide approach to modulate canonical androgen response element (ARE) motifs—the classic DNA binding elements for AR—to delineate distinct AR transcriptional programs. We find that activating these AREs promotes differentiation and growth-suppressive transcription, potentially leading to AR+ PCa cell death, while ARE repression is tolerated by PCa cells but deleterious to normal prostate cells. Gene signatures driven by ARE activity correlate with improved prognosis and luminal phenotypes in PCa patients. Canonical AREs maintain a normal, lineage-specific transcriptional program that can be reengaged in PCa cells, offering therapeutic potential and clinical relevance.}, author = {Chen, Xuanrong and Augello, Michael A. and Liu, Deli and Lin, Kevin and Hakansson, Alex and Sjöström, Martin and Khani, Francesca and Deonarine, Lesa D. and Liu, Yang and Travascio-Green, Jaida and Wu, Jiansheng and Chan, Un In and Owiredu, Jude and Loda, Massimo and Feng, Felix Y. and Robinson, Brian D. and Davicioni, Elai and Sboner, Andrea and Barbieri, Christopher E.}, @@ -2659,7 +4326,7 @@ @article{chen_canonical_2024 doi = {10.1038/s41467-024-53734-z}, issn = {2041-1723}, journal = {Nature Communications}, - keywords = {{\textgreater}UseGalaxy.eu, Cancer genomics, Cell growth, Prostate cancer}, + keywords = {{\textgreater}UseGalaxy.eu, Cancer genomics, Cell growth, Gene Expression Regulation, Neoplastic, Prostate, Prostate cancer, Prostatic Neoplasms, Receptors, Androgen, Response Elements}, language = {en}, month = {December}, note = {Publisher: Nature Publishing Group}, @@ -2672,6 +4339,40 @@ @article{chen_canonical_2024 year = {2024} } +@article{chen_comparative_2025, + abstract = {Hibernation is an elaborate response strategy employed by numerous mammals to survive in cold conditions that involves active suppression of metabolism. Despite the role of mitochondria as energy metabolism centers during hibernation, the adaptive and evolutionary mechanisms of mitochondrial genes in hibernating animals, like hedgehogs in eulipotyphlan species, are not yet fully understood. In this study, we sequenced and assembled mitochondrial genomes of the hibernating four-toed hedgehog (Atelerix albiventris) and the non-hibernating Asian house shrew (Suncus murinus). While no significant positive selection was detected, we identified unique amino acid substitutions and accelerated evolutionary rates of mitochondrial proteins and the encoding genes in hibernating hedgehogs. Moreover, the distinctive evolutionary patterns indicated a potential link among the adaptive evolution of mitochondrial genes (such as ATP6, CYTB, and ND6), the phenotypes of hibernation and longevity in eulipotyphlan species. These three genes evolved rapidly in hibernating Erinaceidae species and exhibited significant correlations with the two distinct phenotypes, indicating their pivotal roles in the evolution of hibernation and longevity. These findings provide insights into the genetic mechanisms responsible for metabolic plasticity and longevity in eulipotyphlan hibernators, with implications for other mammalian taxa.}, + author = {Chen, Lijia and Yang, Guang and Chai, Simin}, + doi = {10.1080/24701394.2025.2558619}, + issn = {2470-1394}, + journal = {Mitochondrial DNA Part A}, + keywords = {{\textgreater}UseGalaxy.eu, Eulipotyphla, hibernation, lifespan, mitogenomics}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/24701394.2025.2558619}, + number = {0}, + pages = {1--13}, + pmid = {40931882}, + title = {Comparative mitogenomics of the eulipotyphlan species ({Mammalia}, {Eulipotyphla}) provides novel insights into the molecular evolution of hibernation}, + url = {https://doi.org/10.1080/24701394.2025.2558619}, + urldate = {2025-09-15}, + volume = {0}, + year = {2025} +} + +@article{chen_developing_2025, + abstract = {Pulcherrimin, a natural metabolite produced by Bacillus subtilis, demonstrates a range of biological activities, including its potential use as a natural antimicrobial, antioxidant, or coloring agent. PS832 was selected as the host cell from four B. subtilis strains. Transcriptome data revealed that the leucine pathway has minimal impact on pulcherrimin titer, whereas the enzymes encoded by the yvmC-cypX operon are essential for achieving high pulcherrimin production. Alleviating transcriptional repression of the yvmC-cypX operon led to an increase in pulcherrimin titer representing a 9.5-fold enhancement to 487 mg/l. The mutant BSP17 showed 65 \% inhibition rate on a phytopathogen, revealing its potential as a biocontrol agent. Furthermore, optimizing iron concentration in the medium resulted in pulcherrimin titers of 610 mg/l in shake flasks and 811 mg/l in a 1.5-l bioreactor. It is the highest reported titer and sets the stage for further metabolic engineering to achieve industrial-scale production of pulcherrimin.}, + author = {Chen, Taichi and Uzunovic, Haris and Brul, Stanley and Hugenholtz, Jeroen}, + doi = {10.1016/j.biortech.2025.132433}, + issn = {0960-8524}, + journal = {Bioresource Technology}, + keywords = {{\textgreater}UseGalaxy.eu, Biocontrol, Diketopiperazines, Fermentation optimization, Non-ribosomal peptide}, + month = {March}, + pages = {132433}, + title = {Developing \textit{{Bacillus} subtilis} as cell factory for the production of the natural biocontrol compound pulcherrimin}, + url = {https://www.sciencedirect.com/science/article/pii/S0960852425003992}, + urldate = {2025-03-29}, + year = {2025} +} + @article{chen_first_2021, author = {Chen, Dong-Bin and Zhang, Ru-Song and Jin, Xiang-Dong and Yang, Jian and Li, Peng and Liu, Yan-Qun}, doi = {10.1017/s0007485321000808}, @@ -2684,6 +4385,38 @@ @article{chen_first_2021 year = {2021} } +@article{chen_high-light_2025, + abstract = {Photosynthetic organisms have evolved mechanisms to manage excess light, crucial for maximizing photosynthetic efficiency. High-light (HL) tolerant Synechocystis sp. PCC6803 strains were developed through laboratory evolution, with tolerance attributed to specific point mutations. Key mutations affected the NDH-1L complex F1-subunit (NdhF1 F124L ) and translation elongation factor G2 (EF-G2 R461C ). Reintroducing these mutations into laboratory strains conferred HL tolerance. Comparisons with knockout and overexpressor lines showed NdhF1 F124L and EF-G2 R461C result in gain of function. Transcriptomic and proteomic analysis unveiled a network of responses contributing to HL tolerance, including maintenance of phosphate metabolism and decreased antenna size by depleting a specific linker protein in EF-G2 R461C cells. Consequently, overexpression of Pho regulon genes increased HL tolerance. NdhF1 F124L enhances cyclic electron flow (CEF) by increasing NDH-1 complex subunit accumulation. Other HL-adapted strains demonstrated that increased CEF and decreased antenna size are recurring outcomes, achievable through various mutations. This study demonstrates how limited mutations can reconfigure cells for enhanced HL tolerance, offering insights for improving photosynthetic efficiency.}, + author = {Chen, Weiyang and Abdel-Salam, Eslam and Dann, Marcel and Ott, Caroline and Schwenkert, Serena and Leister, Dario}, + doi = {10.1101/2025.07.21.665844}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {High-light adaptation in {Synechocystis} by accumulating {NDH} proteins and depleting specific phycobilisome linker proteins}, + url = {http://europepmc.org/abstract/PPR/PPR1055333}, + year = {2025} +} + +@article{chen_terrestrial_2025, + abstract = {Background/Objectives: Mitochondrial genomes are widely used in phylogenetics and evolutionary and ecological research. Methods: In this study, the newest mitochondrial genome of Chelonoidis vicina was assembled and annotated. The comparative mitochondrial genome and selection pressure analyses were used to examine the terrestrial adaptive evolution characteristics of C. vicina and other terrestrial reptiles. Results: The results reveal that the mitochondrial genome of the tortoise C. vicina is consistent with that of other tortoise species, comprising 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs, and 1 noncoding control region (CR). The analysis of selection pressure reveals the presence of positive selection sites in the COX2, COX3, Cytb, ND3, ND4, ND4L, ND5, and ND6 genes of terrestrial reptiles. Of these, the COX2 and ND3 genes exhibited faster evolutionary rates. The mitochondrial genome structure of C. vicina is consistent with that of different terrestrial reptiles. The positive selection sites of COX2 and ND3 in terrestrial reptiles are closely related to a change in mitochondrial energy metabolism, which is possibly related to terrestrial adaptability. Conclusions: The results of this study provide new insights into the adaptive evolution of C. vicina to terrestrial niches from a mitogenomic perspective, as well as genetic resources for the protection of C. vicina.}, + author = {Chen, Yao and Wang, Xibao and Wu, Xiaoyang and Shang, Yongquan and Wei, Qinguo and Cai, Haotian and Sha, Weilai and Qi, Yan and Liu, Shuli and Zhang, Honghai}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/genes16020173}, + issn = {2073-4425}, + journal = {Genes}, + keywords = {\textit{Chelonoidis vicina}, {\textgreater}UseGalaxy.eu, Adaptation, Physiological, Genome, Mitochondrial, Turtles, adaptation, evolution, mitochondrial genomes, positive selection}, + language = {en}, + month = {February}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {2}, + pages = {173}, + title = {Terrestrial {Adaptation} in {Chelonoidis} vicina as {Revealed} {Based} on {Analysis} of the {Complete} {Mitochondrial} {Genome}}, + url = {https://www.mdpi.com/2073-4425/16/2/173}, + urldate = {2025-05-29}, + volume = {16}, + year = {2025} +} + @article{chen_versatile_2018, abstract = {Abstract. Advances in RNA sequencing technologies and computational methodologies have provided a huge impetus to noncoding RNA (ncRNA) study. Once regarded as}, author = {Chen, Qi and Meng, Xianwen and Liao, Qi and Chen, Ming}, @@ -2705,7 +4438,7 @@ @article{cheron_usp7maged1-mediated_2023 doi = {10.1038/s41467-023-44120-2}, issn = {2041-1723}, journal = {Nature Communications}, - keywords = {{\textgreater}UseGalaxy.eu, Addiction, Epigenetics in the nervous system}, + keywords = {{\textgreater}UseGalaxy.eu, Addiction, Cocaine, Cocaine-Related Disorders, Epigenetics in the nervous system, Substance-Related Disorders}, language = {en}, month = {December}, note = {Number: 1 @@ -2726,7 +4459,7 @@ @article{cherrad_new_2023 doi = {10.1371/journal.pone.0268385}, issn = {1932-6203}, journal = {PLOS ONE}, - keywords = {{\textgreater}UseGalaxy.eu, DNA extraction, DNA isolation, Downy mildew, Fungicides, Gene sequencing, Leaves, Next-generation sequencing, Polymerase chain reaction}, + keywords = {{\textgreater}UseGalaxy.eu, DNA extraction, DNA isolation, Downy mildew, Fungicides, Fungicides, Industrial, Gene sequencing, Leaves, Next-generation sequencing, Oomycetes, Polymerase chain reaction, Vitis}, language = {en}, month = {January}, note = {Publisher: Public Library of Science}, @@ -2760,6 +4493,20 @@ @article{chetverikov_molecular_2024 year = {2024} } +@article{chiappa_evolutionary_2025, + abstract = {open}, + author = {Chiappa, Giacomo}, + keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, + language = {eng}, + month = {January}, + note = {Accepted: 2025-02-10T15:01:17Z +Publisher: Università degli Studi di Roma "La Sapienza"}, + title = {Evolutionary biology of {Raphitoma} {Bellardi}, 1847 ({Neogastropoda}, {Conoidea})}, + url = {https://iris.uniroma1.it/handle/11573/1733327}, + urldate = {2025-05-29}, + year = {2025} +} + @article{chiappa_potential_2024, abstract = {Venomous marine gastropods of the superfamily Conoidea possess a rich arsenal of toxins, including neuroactive toxins. Venom adaptations might have played a fundamental role in the radiation of conoideans; nevertheless, there is still no knowledge about the venom of the most diversified family of the group: Raphitomidae Bellardi, 1875. In this study, transcriptomes were produced from the carcase, salivary glands, and proximal and distal venom ducts of the northeastern Atlantic species Raphitoma purpurea (Montagu, 1803). Using a gut barcoding approach, we were also able to report, for the first time, molecular evidence of a vermivorous diet for the genus. Transcriptomic analyses revealed over a hundred putative venom components (PVC), including 69 neurotoxins. Twenty novel toxin families, including some with high levels of expansion, were discovered. No significant difference was observed between the distal and proximal venom duct secretions. Peptides related to cone snail toxins (Cerm06, Pgam02, and turritoxin) and other venom-related proteins (disulfide isomerase and elevenin) were retrieved from the salivary glands. These salivary venom components may constitute ancestral adaptations for venom production in conoideans. Although often neglected, salivary gland secretions are of extreme importance for understanding the evolutionary history of conoidean venom.}, author = {Chiappa, Giacomo and Fassio, Giulia and Modica, Maria Vittoria and Oliverio, Marco}, @@ -2767,7 +4514,7 @@ @article{chiappa_potential_2024 doi = {10.3390/toxins16080348}, issn = {2072-6651}, journal = {Toxins}, - keywords = {{\textgreater}UseGalaxy.eu, Raphitomidae, conotoxin, salivary glands, transcriptome, trophic ecology, venom duct, venom evolution}, + keywords = {{\textgreater}UseGalaxy.eu, Mollusk Venoms, Raphitomidae, Snails, conotoxin, salivary glands, transcriptome, trophic ecology, venom duct, venom evolution}, language = {en}, month = {August}, note = {Number: 8 @@ -2800,6 +4547,42 @@ @article{chiara_next_2021 year = {2021} } +@article{chisembe_nationwide_2024, + abstract = {AbstractBackground. Antimicrobial resistance is a global health challenge with profound implications across sectors. Livestock, a significant field at the}, + author = {Chisembe, Pilirani and Suzuki, Masato and Dao, Duc Trung and Njunga, Gilson and Nkhoma, Joseph and Mthilakuwili, Lecollins and Kinoshita-Daitoku, Ryo and Kuroda, Eisuke and Kimura, Kouji and Shibayama, Keigo}, + doi = {10.1093/jacamr/dlae200}, + issn = {2632-1823}, + journal = {JAC-Antimicrobial Resistance}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {October}, + note = {Publisher: Oxford Academic}, + number = {6}, + pages = {dlae200}, + title = {A nationwide survey of antimicrobial resistance of {Escherichia} coli isolated from broiler chickens in {Malawi}}, + url = {https://dx.doi.org/10.1093/jacamr/dlae200}, + urldate = {2025-09-03}, + volume = {6}, + year = {2024} +} + +@article{chondrou_lrf_2022, + abstract = {The hemoglobin switch from fetal (HbF) to adult (HbA) has been studied intensively as an essential model for gene expression regulation, but also as a beneficial therapeutic approach for β-hemoglobinopathies, towards the objective of reactivating HbF. The transcription factor LRF (Leukemia/lymphoma-related), encoded from the \textit{ZBTB7A} gene has been implicated in fetal hemoglobin silencing, though has a wide range of functions that have not been fully clarified. We thus established the LRF/\textit{ZBTB7A}-overexpressing and \textit{ZBTB7A}-knockdown K562 (human erythroleukemia cell line) clones to assess fetal vs. adult hemoglobin production pre- and post-induction. Transgenic K562 clones were further developed and studied under the influence of epigenetic chromatin regulators, such as DNA methyl transferase 3 (DNMT3) and Histone Deacetylase 1 (HDAC1), to evaluate LRF's potential disturbance upon the aberrant epigenetic background and provide valuable information of the preferable epigenetic frame, in which LRF unfolds its action on the β-type globin's expression. The ChIP-seq analysis demonstrated that LRF binds to γ-globin genes (\textit{HBG2/1}) and apparently associates BCL11A for their silencing, but also during erythropoiesis induction, LRF binds the \textit{BGLT3} gene, promoting \textit{BGLT3}-lncRNA production through the γ-δ intergenic region of β-type globin's locus, triggering the transcriptional events from γ- to β-globin switch. Our findings are supported by an up-to-date looping model, which highlights chromatin alterations during erythropoiesis at late stages of gestation, to establish an "open" chromatin conformation across the γ-δ intergenic region and accomplish β-globin expression and hemoglobin switch.}, + author = {Chondrou, Vasiliki and Shaukat, Athanasios-Nasir and Psarias, Georgios and Athanasopoulou, Katerina and Iliopoulou, Evanthia and Damanaki, Ariadne and Stathopoulos, Constantinos and Sgourou, Argyro}, + doi = {10.3390/ijms23137025}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {{\textgreater}UseGalaxy.eu, RNA, Long Noncoding, Transcription Factors}, + language = {eng}, + month = {June}, + number = {13}, + pages = {7025}, + title = {{LRF} {Promotes} {Indirectly} {Advantageous} {Chromatin} {Conformation} via {BGLT3}-{lncRNA} {Expression} and {Switch} from {Fetal} to {Adult} {Hemoglobin}}, + url = {http://europepmc.org/abstract/MED/35806029}, + volume = {23}, + year = {2022} +} + @article{choudalakis_repentools_2024, abstract = {Repeat elements (REs) play important roles for cell function in health and disease. However, RE enrichment analysis in short-read high-throughput sequencing (HTS) data, such as ChIP-seq, is a challenging task.}, author = {Choudalakis, Michel and Bashtrykov, Pavel and Jeltsch, Albert}, @@ -2818,6 +4601,37 @@ @article{choudalakis_repentools_2024 year = {2024} } +@patent{christoph_biotechnological_2022, + address = {WO}, + author = {Christoph, Schwarz and Christian, Preuss and Amira, Antelmann}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {April}, + number = {WO 2022/229378 A1}, + title = {Biotechnological {Production} {Of} {Terpenes}}, + url = {https://lens.org/145-167-699-352-803}, + year = {2022} +} + +@article{chuchaona_metagenomic_2025, + abstract = {Acute gastroenteritis (AGE) remains a significant global health concern, with noroviruses among the most prevalent viral pathogens. However, other enteric viruses also contribute substantially to the public health burden. This study provides the first molecular characterization of a co-infection involving a rarely reported enterovirus A76 (EV-A76) and a norovirus GI.6[P11] in a patient from Thailand. Metagenomic sequencing successfully identified complete viral genomes, revealing unique genetic variations. Phylogenetic analysis demonstrated that the EV-A76 strain shares high nucleotide similarity with a recently reported strain from Nepal, distinguishing it from previously identified recombinant strains. The amino acid sequence alignment of the complete EV-A76 genome revealed several distinctive amino acid substitutions compared to the most closely related strains. Notably, variations in the VP1 C-terminus and VP2 EF loop, known for high variability, were observed. These regions, crucial for epitope formation, are particularly susceptible to high-frequency mutations. This study reports the first documented co-infection of EV-A76 and norovirus GI.6[P11] in a single sample, identified through metagenomic sequencing in an AGE case in Thailand in 2023. The observed genetic variations highlight the necessity for ongoing monitoring of viral diversity to strengthen genomic surveillance and inform prevention strategies, especially for emerging pathogens with significant public health implications.}, + author = {Chuchaona, Watchaporn and Izquierdo-Lara, Ray W. and Schapendonk, Claudia M. E. and Khongwichit, Sarawut and Koopmans, Marion P. G. and de Graaf, Miranda and Poovorawan, Yong}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-16816-6}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Diseases, Microbiology, Molecular biology, Viral infection, Virology}, + language = {en}, + month = {August}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {30672}, + title = {Metagenomic analysis and genomic characterization of enterovirus {A76} and {Norovirus} {GI}.6[{P11}] co-infection in a patient with acute gastroenteritis in {Thailand}}, + url = {https://www.nature.com/articles/s41598-025-16816-6}, + urldate = {2025-09-03}, + volume = {15}, + year = {2025} +} + @article{cigana_monitoraggio_2023, abstract = {La tesi ha come oggetto di analisi lo studio delle comunità microbiche associate ai bioreattori, individuando quelli che sono i parametri biotici e abiotici che possono influenzare la loro struttura e composizione. Per monitorare la comunità in questione, sono stati utilizzati approcci a coltura indipendente che richiedono il prelievo regolare di campioni dal bioreattore, l'estrazione del DNA dai campioni e sequenziamento avvenuto presso una ditta esterna. Successivamente sono stati analizzati i dati prodotti mediante l'utilizzo di software bioinformatici al fine di stimare la diversità microbica presente nel bioreattore e determinare i vari fattori ambientali che possano influenzarla.}, author = {Cigana, Kevin {\textless}1994{\textgreater}}, @@ -2845,18 +4659,70 @@ @misc{cisternas_ramos_mapeo_2023 year = {2023} } +@article{colin_complete_2021, + abstract = {We present the first mitochondrial genomes from Chagos Archipelago, Indian Ocean, of three putative species of reef forming Acropora (Acropora aff. tenuis, Acropora aff.cytherea and Acropora aff. orbicularis). The circular genome consists respectively of 18,334 bp, 18,353 bp and 18,584 bp. All mitochondrial genomes recovered comprise 13 protein-coding genes, two transfer RNA genes and two ribosomal RNA genes, with an overall GC content ranging from 37.9\% to 38.0\%. These new genomic data contribute to our increased understanding of genus \textit{Acropora} and its species boundaries, ultimately aiding species monitoring and conservation efforts.}, + author = {Colin, Luigi and Yesson, Chris and Head, Catherine E I}, + doi = {10.3897/bdj.9.e72762}, + issn = {1314-2828}, + journal = {Biodiversity data journal}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {e72762}, + title = {Complete mitochondrial genomes of three reef forming {Acropora} corals ({Acroporidae}, {Scleractinia}) from {Chagos} {Archipelago}, {Indian} {Ocean}}, + url = {http://europepmc.org/abstract/MED/34707458}, + volume = {9}, + year = {2021} +} + @article{colin_whats_2022, + abstract = {The unprecedented threats to coral reef ecosystems from global climate change require an urgent response from the aquarium community, which is becoming an increasingly vital coral conservation resource. Unfortunately, many hermatypic corals in aquaria are not identified to species level, which hinders assessment of their conservation significance. Traditional methods of species identification using morphology can be challenging, especially to non-taxonomists. DNA barcoding is an option for species identification of Scleractinian corals, especially when used in concert with morphology-based assessment. This study uses DNA barcodes to try to identify aquarium specimens of the diverse reef-forming genus \textit{Acropora} from 127 samples. We identified to our best current knowledge, to species name 44\% of the analysed samples and provided provisional identification for 80\% of them (101/127, in the form of a list of species names with associate confidence values). We highlighted a sampling bias in public nucleotide sequences repertories (e.g. GenBank) towards more charismatic and more studied species, even inside a well-studied genus like \textit{Acropora}. In addition, we showed a potential "single observer" effect with over a quarter of the reference sequences used for these identifications coming from the same study. We propose the use of barcoding and query matching as an additional tool for taxonomic experts and general aquarists, as an additional tool to increase their chances of making high confidence species-level identifications. We produce a standardised and easily repeatable methodology to increase the capacity of aquariums and other facilities to assess non-ascribed species, emphasising the value of integrating this approach with morphological identification optimising usage of authoritative identification guides and expert opinion.{\textless}h4{\textgreater}Supplementary information{\textless}/h4{\textgreater}The online version contains supplementary material available at 10.1007/s12686-021-01250-3.}, author = {Colin, Luigi and Abed-Navandi, Daniel and Conde, Dalia A. and Craggs, Jamie and Silva, Rita da and Janse, Max and Källström, Björn and Pearce-Kelly, Alexander and Yesson, Chris}, doi = {10.1007/s12686-021-01250-3}, + issn = {1877-7252}, journal = {Conservation Genetics Resources}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {January}, note = {Publisher: Springer Science and Business Media LLC}, + number = {2}, + pages = {167--182}, title = {What's left in the tank? {Identification} of non-ascribed aquarium's coral collections with {DNA} barcodes as part of an integrated diagnostic approach}, url = {https://doi.org/10.1007/s12686-021-01250-3}, + volume = {14}, + year = {2022} +} + +@article{conte_effects_2022, + abstract = {\textit{Candida} spp. represent the third most frequent worldwide cause of infection in Intensive Care Units with a mortality rate of almost 40\%. The classes of antifungals currently available include azoles, polyenes, echinocandins, pyrimidine derivatives, and allylamines. However, the therapeutical options for the treatment of candidiasis are drastically reduced by the increasing antifungal resistance. The growing need for a more targeted antifungal therapy is limited by the concern of finding molecules that specifically recognize the microbial cell without damaging the host. Epigenetic writers and erasers have emerged as promising targets in different contexts, including the treatment of fungal infections. In \textit{C. albicans}, Hst3p, a sirtuin that deacetylates H3K56ac, represents an attractive antifungal target as it is essential for the fungus viability and virulence. Although the relevance of such epigenetic regulator is documented for the development of new antifungal therapies, the molecular mechanism behind Hst3p-mediated epigenetic regulation remains unrevealed. Here, we provide the first genome-wide profiling of H3K56ac in \textit{C. albicans} resulting in H3K56ac enriched regions associated with \textit{Candida} sp. pathogenicity. Upon Hst3p inhibition, 447 regions gain H3K56ac. Importantly, these genomic areas contain genes encoding for adhesin proteins, degradative enzymes, and white-opaque switching. Moreover, our RNA-seq analysis revealed 1330 upregulated and 1081 downregulated transcripts upon Hst3p inhibition, and among them, we identified 87 genes whose transcriptional increase well correlates with the enrichment of H3K56 acetylation on their promoters, including some well-known regulators of phenotypic switching and virulence. Based on our evidence, Hst3p is an appealing target for the development of new potential antifungal drugs.}, + author = {Conte, Marisa and Eletto, Daniela and Pannetta, Martina and Petrone, Anna M and Monti, Maria C and Cassiano, Chiara and Giurato, Giorgio and Rizzo, Francesca and Tessarz, Peter and Petrella, Antonello and Tosco, Alessandra and Porta, Amalia}, + doi = {10.3389/fcimb.2022.1031814}, + issn = {2235-2988}, + journal = {Frontiers in cellular and infection microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Candida albicans, Candidiasis}, + language = {eng}, + pages = {1031814}, + title = {Effects of {Hst3p} inhibition in {Candida} albicans: a genome-wide {H3K56} acetylation analysis}, + url = {http://europepmc.org/abstract/MED/36389164}, + volume = {12}, year = {2022} } +@article{contreras_novo_2025, + abstract = {Thraustochytrids are heterotrophic marine protists known for their ability to produce valuable lipids such as docosahexaenoic acid (DHA). However, like many non-model organisms, they present challenges for transcriptomic studies due to the limited reliable reference genomes and compatibility with curated protein databases, complicating the respective assembly and annotation. This study presents a de novo transcriptome assembly and functional annotation for the recently isolated thraustochytrid strain Ulkenia visurgensis Lng2 using solely free access software and code available in public domain repositories. The assembled transcriptome presented 45,867 unique gene models, with a total of 66,623 transcripts and a contig N50 of 3162. Functional annotations highlighted high amounts of transcripts related to the biosynthesis of relevant lipidic molecules, as well as stress-adaptive features including catalytic and xenobiotic degrading activity. Likewise, 2381 transcripts were linked to enzymes with potential biotechnological applications. Notably, several transcripts corresponding to uncommon enzymatic activities in thraustochytrids, including laccases, cellulases, and chitinases, were identified. Additionally, evidence for a potential lactamase activity was found, marking the first report of such activity in thraustochytrids. Overall, this study offers a simple free-access procedural strategy for a de novo transcriptome assembly and functional annotation in non-model organisms. These results provide valuable insights into the biotechnological potential of thraustochytrids, while also expanding the limited transcriptomic data available for these protists. Notably, it represents the first transcriptomic analysis of the Ulkenia genus.}, + author = {Contreras, Pedro and Fica-León, Víctor and Navarrete, José and Oviedo, Claudia}, + doi = {10.1016/j.gene.2025.149492}, + issn = {0378-1119}, + journal = {Gene}, + keywords = {{\textgreater}UseGalaxy.eu, Annotation, Assembly, Non-model, Thraustochytrids, Transcriptome}, + month = {July}, + pages = {149492}, + title = {\textit{{De} novo} transcriptome assembly and functional annotation supports potential biotechnological applications for the non-model thraustochytrid \textit{{Ulkenia} visurgensis} {Lng2}}, + url = {https://www.sciencedirect.com/science/article/pii/S037811192500280X}, + urldate = {2025-04-21}, + volume = {958}, + year = {2025} +} + @article{cordellier_next-generation_2021, author = {Cordellier, Mathilde and Wojewodzic, Marcin W. and Wessels, Martin and Kuster, Christian and Elert, Eric von}, doi = {10.1016/j.zool.2021.125895}, @@ -2870,6 +4736,37 @@ @article{cordellier_next-generation_2021 year = {2021} } +@mastersthesis{cordova_bastidas_comparacion_2025, + abstract = {This study analyzed genomes from various species of the genus, obtained from +isolates reported in Ecuador between 2020 and 2023, with the aim of exploring their +genetic diversity and antimicrobial resistance mechanisms. Both local and online +bioinformatics tools were used for functional annotation with Prokka, genomic +alignments using Mauve and MAFFT, and the construction of a comparative +pangenome via Panaroo. Based on metadata associated with each isolate, a +molecular clock analysis was performed to observe mutation patterns over time. By +cross-referencing with specialized databases, resistance genes against betalactams, aminoglycosides, quinolones, tetracyclines, and others, were identified +across multiple species. The results revealed phylogenetic groupings primarily +driven by taxonomic differences among the strains, although in some cases, clusters +corresponding to geographic or temporal origin were also observed, suggesting +potential clonal transmission events. Both conserved and fragmented regions were +detected in the genomes, attributable to biological differences or variability in +assembly quality. The integration of automatic annotation, phylogenetic and +pangenomic analysis, and temporal approaches enabled a comprehensive +evaluation of the evolution and dissemination of Klebsiella in the country. +Collectively, these findings represent a valuable contribution to genomic +surveillance and the control of multidrug-resistant bacterial infections in Ecuador.}, + author = {Córdova Bastidas, Daniel Alejandro}, + copyright = {openAccess}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {spa}, + note = {Accepted: 2025-06-24T21:28:03Z}, + shorttitle = {Comparación genómica de especies de klebsiella secuenciadas en {Ecuador}}, + title = {Comparación genómica de especies de klebsiella secuenciadas en {Ecuador}: resistencia y diversidad}, + url = {http://dspace.ups.edu.ec/handle/123456789/30567}, + urldate = {2025-07-12}, + year = {2025} +} + @article{corneo_proceedings_2023, abstract = {Ciborinia camelliae Kohn is the causal agent of camellia flower blight. The fungus infects only the flowers of camellias causing serious damage to the plant, particularly from an aesthetic point of view. The disease has been reported in almost all countries where camellia is grown for ornamental purposes, but there are not many studies on the variability of the population of this phytopathogen. The main objective of this study was to contribute to study the level of variability within the Italian population. More than 130 C. camelliae strains were collected from six localities distributed in five Italian regions and identified also based on molecular characterization of the ITS nucleotide sequences. The population variability was assessed by comparing the morphological characters. From a phenological point of view, 11 different colony morphotypes were identified, whose presence/absence and frequency are different in the various locations considered. The study of the taxonomically valid nucleotide sequences to differentiate fungi at the species level confirmed that the strains under study belong to a single species. To further investigate Italian population of C. camelliae we sequenced by a combination of long and short reads technologies the genome of a representative strain. This genome represents a worldwide reference for future C. cameliae diversity and pathogenicity studies.}, author = {Corneo, Andrea}, @@ -2885,7 +4782,8 @@ @article{cosenza-contreras_proteometabolomics_2024 doi = {10.1093/neuonc/noad208}, issn = {1522-8517}, journal = {Neuro-Oncology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Brain Neoplasms, Glioblastoma}, + language = {eng}, month = {March}, number = {3}, pages = {488--502}, @@ -2896,6 +4794,43 @@ @article{cosenza-contreras_proteometabolomics_2024 year = {2024} } +@article{costa-ribeiro_application_2025, + abstract = {Millions of foodborne infections are reported yearly worldwide due to a variety of pathogens. A promising approach to tackle this issue relies on Next Generation Sequencing (NGS). In this work a novel multi-foodborne pathogen detection was developed. The method combines a selective enrichment step in a novel broth, multiplex PCR with interlaboratory-validated primers, long-read Flongle MinION sequencing, and data analysis in three cloud-based pipelines to overcome complex, command line-based bioinformatic data analyses. The method, was evaluated in salmon samples spiked with fresh, heat and cold stressed, bacterial cultures of Salmonella spp., E. coli O157:H7 and L. monocytogenes, as well as with in-house, and commercial mock communities, doped with Y. enterocolitica and thermotolerant Campylobacter spp. No major deviations from the expected results were obtained, reaching a limit of detection  90\% regardless the bioinformatic pipeline selected and concordance values between 0.9 to 1.0. Taken together, the proposed method allows for simple and reliable implementation of NGS as testing tool to streamline foodborne pathogen detection, and overcoming the typical limitations associated with this technology.}, + author = {Costa-Ribeiro, Ana and Lamas, Alexandre and Prado, Marta and Garrido-Maestu, Alejandro}, + copyright = {cc by-nc-nd}, + doi = {10.1038/s41538-025-00452-5}, + issn = {2396-8370}, + journal = {NPJ science of food}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {October}, + number = {1}, + pages = {211}, + pmcid = {PMC12569004}, + pmid = {41152310}, + title = {Application of {MSB} selective enrichment followed by amplicon {MinION} sequencing for multipathogen detection in smoked salmon}, + url = {https://europepmc.org/articles/PMC12569004}, + urldate = {2025-12-26}, + volume = {9}, + year = {2025} +} + +@article{costa_olfactory_2025, + abstract = {Increased carbon dioxide (CO2) in the ocean is changing seawater chemistry. Behavioural alterations in CO2 exposed fish have been linked to changes in the central nervous system (CNS). However, we hypothesise that receptor cells in direct contact with the environment are more susceptible to changes in water chemistry than the CNS. Electrophysiology, histology, and transcriptomics were used to explore the effect of exposure to CO2 acidified water on the olfactory epithelium (OE) of the Senegalese sole (Solea senegalensis). The upper and lower OE of this flatfish detect different odorants and are in contact with different environments. Acute exposure to acidified water decreased olfactory sensitivity more in the upper than in the lower OE. After chronic exposure to high CO2 there was no histological changes in the upper OE, however, in the lower OE, there was a massive infiltration of melanomacrophage (MMC) and tissue disorganization. In addition, in the upper OE, differential expressed gene transcripts (DETs) were related to inflammation and innate immune processes whereas in the lower OE, DETs were related to the adaptative immune response. Differential regulation of genes related to neurogenesis and plasticity occurred in both epithelia. The effects of ocean acidification in sole OE depends on the nostril, however the occurrence of an exacerbated immune response, OE remodelling and reduced sensitivity indicate that ocean acidification is likely to have significant and unpredictable consequences for behaviour.}, + author = {Costa, Rita A. and Hubbard, Peter and Manchado, Manuel and Power, Deborah M. and Velez, Zélia}, + doi = {10.1016/j.cbpa.2025.111820}, + issn = {1095-6433}, + journal = {Comparative Biochemistry and Physiology Part A: Molecular \& Integrative Physiology}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, CO, Differential gene expression, Immunity, Ocean acidification, Olfaction}, + month = {February}, + pages = {111820}, + shorttitle = {Olfactory specialization in the {Senegalese} sole (\textit{{Solea} senegalensis})}, + title = {Olfactory specialization in the {Senegalese} sole (\textit{{Solea} senegalensis}): {CO2} acidified water triggers nostril-specific immune processes}, + url = {https://www.sciencedirect.com/science/article/pii/S1095643325000182}, + urldate = {2025-02-08}, + year = {2025} +} + @misc{costa_unique_2024, abstract = {Increased carbon dioxide (CO2) in the ocean is changing seawater chemistry and impacting the marine biosphere. Behavioural alterations in CO2 exposed fish have previously been linked to changes at the level of the central nervous system (CNS). However, we hypothesise that sensory receptor cells that are in direct contact with the environment will be more susceptible to changes in water chemistry than the CNS. In the current study electrophysiology, histology, and transcriptomics were used to explore the impact of exposure to CO2 acidified water on the olfactory epithelium (OE) of the Senegalese sole (Solea senegalensis). The upper and lower OE in this asymmetric species detect different odorants and are in contact with different ecological environments making it an excellent experimental model. Exposure of the nostrils to acidified water decreased olfactory sensitivity with a more pronounced effect in the upper nostril. There were no apparent histological PCO2 driven changes in the upper OE, however in the lower there was a massive infiltration of melanomacrophage (MMC) with disorganization of the OE. Differential regulation of genes related to neurogenesis, plasticity, and immune processes occurred in both OE. In the upper OE differential expressed genes (DEGs) were related to inflammation and innate immune processes while in the lower OE DEGs were related to the adaptative immune response. We suggest that exposure to acidified water decreases olfactory sensitivity, and as a consequence, mechanisms of neuromodulation and plasticity are activated. In the lower OE, exposure to acidified seawater triggered an exacerbated immune response and compromised olfactory detection. The OE remodelling, associated immune response and modified electrophysiology indicate ocean acidification is likely to have significant and unpredictable consequences for behaviour.}, address = {Rochester, NY}, @@ -2913,12 +4848,17 @@ @misc{costa_unique_2024 } @article{cova_helios_2021, + abstract = {Our understanding of cell fate decisions in hematopoietic stem cells is incomplete. Here, we show that the transcription factor Helios is highly expressed in murine hematopoietic stem and progenitor cells (HSPCs), where it is required to suppress the separation of the platelet/megakaryocyte lineage from the HSPC pool. Helios acts mainly in quiescent cells, where it directly represses the megakaryocyte gene expression program in cells as early as the stem cell stage. Helios binding promotes chromatin compaction, notably at the regulatory regions of platelet-specific genes recognized by the Gata2 and Runx1 transcriptional activators, implicated in megakaryocyte priming. Helios null HSPCs are biased toward the megakaryocyte lineage at the expense of the lymphoid and partially resemble cells of aging animals. We propose that Helios acts as a guardian of HSPC pluripotency by continuously repressing the megakaryocyte fate, which in turn allows downstream lymphoid priming to take place. These results highlight the importance of negative and positive priming events in lineage commitment.}, author = {Cova, Giovanni and Taroni, Chiara and Deau, Marie-Céline and Cai, Qi and Mittelheisser, Vincent and Philipps, Muriel and Jung, Matthieu and Cerciat, Marie and Gras, Stéphanie Le and Thibault-Carpentier, Christelle and Jost, Bernard and Carlsson, Leif and Thornton, Angela M. and Shevach, Ethan M. and Kirstetter, Peggy and Kastner, Philippe and Chan, Susan}, doi = {10.1084/jem.20202317}, + issn = {0022-1007}, + journal = {J Exp Med}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {August}, note = {Publisher: Rockefeller University Press}, number = {10}, + pages = {e20202317}, title = {Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells}, url = {https://doi.org/10.1084/jem.20202317}, volume = {218}, @@ -2939,6 +4879,7 @@ @article{crespo_pcid2_2024 pmcid = {PMC10879814}, pmid = {38384833}, title = {{PCID2} dysregulates transcription and viral {RNA} processing to promote {HIV}-1 latency}, + url = {http://europepmc.org/abstract/MED/38384833}, volume = {27}, year = {2024} } @@ -2970,13 +4911,54 @@ @article{cruz-ojeda_silico_2025 year = {2025} } +@misc{cruz-tapias_automethylation_2025, + abstract = {Histone H3 lysine 9 trimethylation is essential for heterochromatin formation and maintenance, genome stability, and silencing of transposable elements (TEs) in embryonic stem cells (ESCs). The H3K9-specific lysine methyltransferase SETDB1 is crucial for mammalian development, as it controls ESC pluripotency and viability by regulating gene expression and TE silencing. Here, we demonstrate that SETDB1 undergoes automethylation on two lysine residues located within H3K9-like motifs in its catalytic domain. Notably, these automethylated lysines are necessary for the normal growth and viability of ESCs. While SETDB1 automethylation does not affect its catalytic activity, it is crucial for its interaction with chromodomain-containing partners, including SUV39H1, CDYL, and Heterochromatin Protein 1 gamma (HP1gamma). The integrity of the two automethylated lysines is required for SETDB1 localization to its target sites and for effective silencing of both coding genes and TEs. Expression of an automethylation-deficient SETDB1 fails to properly establish H3K9me3 and disrupts HP1gamma recruitment at target loci. Collectively, our findings uncover a previously unknown mechanism regulating SETDB1 function, essential for maintaining the fitness of mouse ESCs. +Highlights– SETDB1 undergoes automethylation on two lysines within its catalytic domain– The automethylation-deficient form of SETDB1 is enzymatically active, yet it compromises mESCs fitness– SETDB1 automethylation-deficient mutant impairs chromatin association and pan-genomic H3K9me3 landscape– SETDB1 automethylation regulates its interactions with many chromodomain-containing partners}, + author = {Cruz-Tapias, Paola and Velasco, Guillaume and Rapone, Roberta and Maestro, Laurence Del and Cochard, Victor and Chevreux, Guillaume and Joliot, Véronique and Boyarchuk, Ekaterina and Ait-Si-Ali, Slimane}, + copyright = {© 2025, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}, + doi = {10.1101/2025.10.22.683908}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {October}, + note = {ISSN: 2692-8205 +Pages: 2025.10.22.683908 +Section: New Results}, + publisher = {bioRxiv}, + title = {Automethylation of lysine methyltransferase {SETDB1} on {H3K9}-like motifs regulates interactions with chromodomain proteins and controls its functions}, + url = {https://www.biorxiv.org/content/10.1101/2025.10.22.683908v1}, + urldate = {2025-12-22}, + year = {2025} +} + +@article{cunha_characterization_2025, + abstract = {Staphylococcus aureus is a globally significant pathogen associated with severe infections, foodborne illnesses, and animal diseases. Its control has become increasingly challenging due to the spread of antibiotic-resistant strains, highlighting the urgent need for effective alternatives. In this context, bacteriophages have emerged as promising biocontrol agents. This study aimed to characterize the newly isolated Staphylococcus phage CapO46 and evaluate its efficacy in reducing S. aureus in milk. Identified as a new species within the Rosenblumvirus genus, CapO46 exhibited a podovirus-like structure and a small linear dsDNA genome (17,107 bp), with no lysogeny-related, antimicrobial resistance, or virulence genes. Host range assays demonstrated its ability to infect all 31 S. aureus isolates from two different countries and in diverse environmental contexts, achieving high efficiency of plating (EOP {\textgreater} 0.5) in 64.5\% of cases. Kinetic analyses revealed rapid adsorption and a short latent period, with a burst size of approximately 30 PFU/cell. In UHT whole-fat milk, CapO46 achieved a maximum reduction of 7.2 log10 CFU/mL in bacterial load after 12 h, maintaining significant suppression (1.6 log10 CFU/mL) after 48 h. Due to its genetic safety, high infectivity across multiple isolates, and antimicrobial activity in milk, CapO46 can be considered a promising candidate for S. aureus biocontrol applications.}, + author = {Cunha, Paloma Cavalcante and de Souza, Pedro Samuel and Rosseto, Ana Julia Dill and Rodrigues, Isabella Ribeiro and Dias, Roberto Sousa and da Silva Duarte, Vinícius and Porcellato, Davide and da Silva, Cynthia Canêdo and de Paula, Sérgio Oliveira}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/microorganisms13030664}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {\textit{Rosenblumvirus}, \textit{Staphylococcus} phage, {\textgreater}UseGalaxy.eu, biocontrol, host range}, + language = {en}, + month = {March}, + note = {Number: 3 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {3}, + pages = {664}, + title = {Characterization of {Newly} {Isolated} {Rosenblumvirus} {Phage} {Infecting} {Staphylococcus} aureus from {Different} {Sources}}, + url = {https://www.mdpi.com/2076-2607/13/3/664}, + urldate = {2025-05-29}, + volume = {13}, + year = {2025} +} + @article{cupic_first_2023, abstract = {Cave animals are an excellent model system for studying adaptive evolution. At present, however, little is known about the mechanisms that enable surface colonizers to survive in the challenging environment of caves. One possibility is that these species have the necessary genetic background to respond with plastic changes to the pressures of underground habitats. To gain insight into this process, we conducted a comparative study with the fish species Telestes karsticus, which occurs in a hydrological system consisting of an interconnected stream and a cave. Results showed that T. karsticus resided year-round and spawned in Sušik cave, making it the first known cavefish in the Dinaric Karst. Cave and surface populations differed in morphological and physiological characteristics, as well as in patterns of gene expression without any evidence of genetic divergence. To test whether observed trait differences were plastic or genetic, we placed adult fish from both populations under light/dark or constant dark conditions. Common laboratory conditions erased all morphometric differences between the two morphs, suggesting phenotypic plasticity is driving the divergence of shape and size in wild fish. Lighter pigmentation and increased fat deposition exhibited by cave individuals were also observed in surface fish kept in the dark in the laboratory. Our study also revealed that specialized cave traits were not solely attributed to developmental plasticity, but also arose from adult responses, including acclimatization. Thus, we conclude that T. karsticus can adapt to cave conditions, with phenotypic plasticity playing an important role in the process of cave colonization.}, author = {Čupić, Mateo and Marčić, Zoran and Lukić, Marko and Gračan, Romana and Bilandžija, Helena}, doi = {10.24272/j.issn.2095-8137.2022.528}, issn = {2095-8137}, journal = {Zoological Research}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Caves, Cypriniformes}, + language = {eng}, month = {July}, number = {4}, pages = {821--833}, @@ -3007,6 +4989,100 @@ @article{dad_molecular_2020 year = {2020} } +@article{dahdouh_revisiting_2025, + abstract = {Over 60 years ago, researchers started the genetic analysis of bacterial cell division by isolating conditional, temperature-sensitive mutants of essential Escherichia coli cell division genes. These early mutants were obtained by mutagenesis with chemical agents that introduced dozens to hundreds of mutations in the bacterial genomes. In this work, we present the complete genome sequences of six of these original mutants on ftsA, ftsZ and ftsQ genes, along with two of the strains used to generate them. The genomes of mutants obtained by exposure to nitrosoguanidine had 100 to 400 mutations. Transducing target alleles into a new strain effectively reduced the number of mutations, but those near the target gene were co-transduced with it. In contrast, a mutant generated by site-directed mutagenesis maintained the genomic background intact. The genomic analysis improves our understanding of these foundational strains, offering insights into the effects of historical mutagenesis techniques. These findings underscore the importance of genomic characterization in ensuring accurate interpretations of experimental results in microbiological research.}, + author = {Dahdouh, Elias and García-Pérez, Isabel and Reyes-Zuñagua, Diana Soledad and Mingorance, Jesús and Vicente, Miguel}, + copyright = {cc by}, + doi = {10.1099/mgen.0.001558}, + issn = {2057-5858}, + journal = {Microbial genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Cell division, Escherichia Coli, Genomic analysis, Mutagenesis}, + language = {eng}, + month = {November}, + number = {11}, + pmcid = {PMC12584984}, + pmid = {41186981}, + title = {Revisiting classical \<i\>{Escherichia} coli\</i\> cell division mutants by whole-genome sequencing}, + url = {https://europepmc.org/articles/PMC12584984}, + urldate = {2025-12-26}, + volume = {11}, + year = {2025} +} + +@article{daly_dual-transcriptomic_2021, + abstract = {Biological control is a promising approach to suppress diseases caused by \textit{Pythium} spp. such as Pythium soft rot of ginger caused by \textit{P. myriotylum}. Unusually for a single genus, it also includes species that can antagonize \textit{Pythium} plant pathogens, such as \textit{Pythium oligandrum}. We investigated if a new isolate of \textit{P. oligandrum} could antagonize \textit{P. myriotylum}, what changes occurred in gene expression when \textit{P. oligandrum} (antagonist) and \textit{P. myriotylum} (host) interacted, and whether \textit{P. oligandrum} could control soft-rot of ginger caused by \textit{P. myriotylum}. An isolate of \textit{P. oligandrum}, GAQ1, recovered from soil could antagonize \textit{P. myriotylum} in a plate-based confrontation assay whereby \textit{P. myriotylum} became non-viable. The loss of viability of \textit{P. myriotylum} coupled with how \textit{P. oligandrum} hyphae could coil around and penetrate the hyphae of \textit{P. myriotylum}, indicated a predatory interaction. We investigated the transcriptional responses of \textit{P. myriotylum} and \textit{P. oligandrum} using dual-RNAseq at a stage in the confrontation where similar levels of total transcripts were measured from each species. As part of the transcriptional response of \textit{P. myriotylum} to the presence of \textit{P. oligandrum}, genes including a subset of putative Kazal-type protease inhibitors were strongly upregulated along with cellulases, elicitin-like proteins and genes involved in the repair of DNA double-strand breaks. In \textit{P. oligandrum}, proteases, cellulases, and peroxidases featured prominently in the upregulated genes. The upregulation along with constitutive expression of \textit{P. oligandrum} proteases appeared to be responded to by the upregulation of putative protease inhibitors from \textit{P. myriotylum}, suggesting a \textit{P. myriotylum} defensive strategy. Notwithstanding this \textit{P. myriotylum} defensive strategy, \textit{P. oligandrum} had a strong disease control effect on soft-rot of ginger caused by \textit{P. myriotylum}. The newly isolated strain of \textit{P. oligandrum} is a promising biocontrol agent for suppressing the soft-rot of ginger. The dual-RNAseq approach highlights responses of \textit{P. myriotylum} that suggests features of a defensive strategy, and are perhaps another factor that may contribute to the variable success and durability of biological attempts to control diseases caused by \textit{Pythium} spp.}, + author = {Daly, Paul and Chen, Siqiao and Xue, Taiqiang and Li, Jingjing and Sheikh, Taha Majid Mahmood and Zhang, Qimeng and Wang, Xuehai and Zhang, Jinfeng and Fitzpatrick, David A and McGowan, Jamie and Shi, Xiujuan and Deng, Sheng and Jiu, Min and Zhou, Dongmei and Druzhinina, Irina S and Wei, Lihui}, + doi = {10.3389/fmicb.2021.765872}, + issn = {1664-302X}, + journal = {Frontiers in microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {765872}, + title = {Dual-{Transcriptomic}, {Microscopic}, and {Biocontrol} {Analyses} of the {Interaction} {Between} the {Bioeffector} {Pythium} oligandrum and the {Pythium} {Soft}-{Rot} of {Ginger} {Pathogen} {Pythium} myriotylum}, + url = {http://europepmc.org/abstract/MED/34867897}, + volume = {12}, + year = {2021} +} + +@article{daly_genome_2022, + abstract = {The \textit{Pythium} (Peronosporales, Oomycota) genus includes devastating plant pathogens that cause widespread diseases and severe crop losses. Here, we have uncovered a far greater arsenal of virulence factor-related genes in the necrotrophic Pythium myriotylum than in other \textit{Pythium} plant pathogens. The genome of a plant-virulent \textit{P. myriotylum} strain ({\textasciitilde}70 Mb and 19,878 genes) isolated from a diseased rhizome of ginger (Zingiber officinale) encodes the largest repertoire of putative effectors, proteases, and plant cell wall-degrading enzymes (PCWDEs) among the studied species. \textit{P. myriotylum} has twice as many predicted secreted proteins than any other \textit{Pythium} plant pathogen. Arrays of tandem duplications appear to be a key factor of the enrichment of the virulence factor-related genes in \textit{P. myriotylum}. The transcriptomic analysis performed on two \textit{P. myriotylum} isolates infecting ginger leaves showed that proteases were a major part of the upregulated genes along with PCWDEs, Nep1-like proteins (NLPs), and elicitin-like proteins. A subset of \textit{P. myriotylum} NLPs were analyzed and found to have necrosis-inducing ability from agroinfiltration of tobacco (Nicotiana benthamiana) leaves. One of the heterologously produced infection-upregulated putative cutinases found in a tandem array showed esterase activity with preferences for longer-chain-length substrates and neutral to alkaline pH levels. Our results allow the development of science-based targets for the management of \textit{P. myriotylum}-caused disease, as insights from the genome and transcriptome show that gene expansion of virulence factor-related genes play a bigger role in the plant parasitism of \textit{Pythium} spp. than previously thought. \textbf{IMPORTANCE} \textit{Pythium} species are oomycetes, an evolutionarily distinct group of filamentous fungus-like stramenopiles. The \textit{Pythium} genus includes several pathogens of important crop species, e.g., the spice ginger. Analysis of our genome from the plant pathogen Pythium myriotylum uncovered a far larger arsenal of virulence factor-related genes than found in other \textit{Pythium} plant pathogens, and these genes contribute to the infection of the plant host. The increase in the number of virulence factor-related genes appears to have occurred through the mechanism of tandem gene duplication events. Genes from particular virulence factor-related categories that were increased in number and switched on during infection of ginger leaves had their activities tested. These genes have toxic activities toward plant cells or activities to hydrolyze polymeric components of the plant. The research suggests targets to better manage diseases caused by \textit{P. myriotylum} and prompts renewed attention to the genomics of \textit{Pythium} plant pathogens.}, + author = {Daly, Paul and Zhou, Dongmei and Shen, Danyu and Chen, Yifan and Xue, Taiqiang and Chen, Siqiao and Zhang, Qimeng and Zhang, Jinfeng and McGowan, Jamie and Cai, Feng and Pang, Guan and Wang, Nan and Sheikh, Taha Majid Mahmood and Deng, Sheng and Li, Jingjing and Soykam, Hüseyin Okan and Kara, Irem and Fitzpatrick, David A and Druzhinina, Irina S and Bayram Akcapinar, Günseli and Wei, Lihui}, + doi = {10.1128/spectrum.02268-21}, + issn = {2165-0497}, + journal = {Microbiol Spectr}, + keywords = {{\textgreater}UseGalaxy.eu, Pythium, Zingiber officinale}, + language = {eng}, + month = {August}, + number = {4}, + pages = {e0226821}, + title = {Genome of {Pythium} myriotylum {Uncovers} an {Extensive} {Arsenal} of {Virulence}-{Related} {Genes} among the {Broad}-{Host}-{Range} {Necrotrophic} {Pythium} {Plant} {Pathogens}}, + url = {http://europepmc.org/abstract/MED/35946960}, + volume = {10}, + year = {2022} +} + +@article{dantanarayana_understanding_2025, + abstract = {Efficient extracellular electron transfer (EET) is critical to harnessing bacteria like Shewanella oneidensis MR-1 in microbial electrochemical systems (MESs) aimed at sustainable energy production, environmental remediation, and resource recovery. This study investigates how palladium ions (Pd2+), which are of significant interest for catalysis and resource recovery, impact the bioelectrocatalysis of S. oneidensis MR-1 using electrochemical, transcriptomic, and microscopic methods. Pd2+ exposure significantly increased the observed current via EET, which correlated with substantially increased viable biofilm formation on the electrode. Transcriptomics revealed a coordinated cellular response, including upregulation of genes facilitating EET (the Mtr pathway), metabolism, motility, and biofilm processes, alongside downregulation of competing pathways. Cellular reduction of Pd2+ to palladium nanoparticles, mainly near the outer membrane, was confirmed via microscopy. Pd2+ boosts S. oneidensis MR-1 bioelectrocatalysis through the combined effects of promoting biofilm development and upregulating essential cellular pathways, informing fundamental strategies for enhanced MESs targeted for sustainable engineering, bioremediation, and resource and material recovery applications.}, + author = {Dantanarayana, Ashwini and Beaver, Kevin and Van Devener, Brian and Chandler, Nancy B. and Minteer, Shelley D.}, + doi = {10.1021/acselectrochem.5c00244}, + journal = {ACS Electrochemistry}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: American Chemical Society}, + title = {Understanding {Palladium} {Ion} {Induced} {Bioelectrocatalysis} in {Shewanella} oneidensis {MR}-1 through {Electrochemical} and {Genetic} {Interrogations}}, + url = {https://doi.org/10.1021/acselectrochem.5c00244}, + urldate = {2025-09-03}, + year = {2025} +} + +@article{darilag_uncovering_2025, + abstract = {Skin cancer, particularly melanoma, remains a major public health concern due to its high mortality rate. Current treatment options, including chemotherapy with dacarbazine and doxorubicin, have shown limited efficacy, achieving only a 20\% objective response rate over six months, along with severe side effects such as cardiotoxicity. Given these limitations, there is a growing interest in herbal medicine as a source of novel anticancer compounds. \textit{Bambusa stenostachya}, a bamboo species native to Taiwan, was investigated for its potential anti-melanoma properties using network pharmacology and molecular docking. LC-MS analysis identified seven bioactive compounds, including quinic acid and isovitexin, which satisfied Lipinski's drug-likeness criteria. Among the seven bioactive compounds identified, five belong to the flavonoid family, while two are classified as phenolic compounds that modulate signaling pathways related to cancer and exhibit antioxidant activity, respectively. Through pathway enrichment analysis, four key melanoma-associated genes (PIM1, MEK1, CDK2, and PDK1) were identified as potential therapeutic targets. Ensemble docking results demonstrated that naringin-7-rhamnoglucoside exhibited the highest binding affinity (-6.30 kcal/mol) with phosphoinositide-dependent kinase-1, surpassing the affinities of standard chemotherapeutic agents. Additionally, the average docking scores for naringin-7-rhamnoglucoside and the remaining three proteins were as follows: PIM1 (-5.92), MEK1 (-6.07), and CDK2 (-5.26). These findings suggest that the bioactive compounds in \textit{B. stenostachya} may play a crucial role in inhibiting melanoma progression by modulating metabolic and signaling pathways. Further in vitro and in vivo studies are necessary to validate these computational findings and explore the potential of \textit{B. stenostachya} as a complementary therapeutic agent for melanoma.}, + author = {Darilag, Gen Maxxine C and Liu, Hsuan-Chieh and Hsieh, Cheng-Yang and Tayo, Lemmuel L and Talubo, Nicholas Dale D and Yang, Shu-Ching and Chang, Ching-Hui and Huang, Ying-Pin and Lee, Shih-Chi and Liu, Yung-Chuan and Tsai, Po-Wei}, + doi = {10.3390/ijms26136120}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Antineoplastic Agents, Phytogenic, Melanoma, Network Pharmacology, Plant Extracts, Plant Leaves}, + language = {eng}, + month = {June}, + number = {13}, + pages = {6120}, + title = {Uncovering {Anti}-{Melanoma} {Mechanisms} of \textit{{Bambusa} stenostachya} {Leaf} {Compounds} via {Network} {Pharmacology} and {Molecular} {Docking}}, + url = {http://europepmc.org/abstract/MED/40649898}, + volume = {26}, + year = {2025} +} + +@article{darino_identification_2023, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater} Fusarium Head Blight is a destructive floral disease of different cereal crops. The Ascomycete fungus Fusarium graminearum ( Fg ) is one of the main causal agents of FHB in wheat and barley. The role(s) in virulence of Fg genes include genetic studies that involve the transformation of the fungus with different expression cassettes. We have observed in several studies where Fg genes functions were characterised that integration of expression cassettes occurred randomly. Random insertion of a cassette may disrupt gene expression and/or protein functions and hence the overall conclusion of the study. Target site integration (TSI) is an approach that consists in identifying a chromosomal region where the cassette can be inserted. The identification of a suitable locus for TSI in Fg would avert the potential risks of ectopic integration. {\textless}h4{\textgreater}Results{\textless}/h4{\textgreater} Here, we identified a highly conserved intergenic region on chromosome 1 suitable for TSI. We named this intergenic region the TSI locus 1. We developed an efficient cloning vector system based on the Golden Gate method to clone different expression cassettes for use in combination with TSI locus 1. We present evidence that integrations in the TSI locus 1 affects neither fungal virulence nor fungal growth under different stress conditions. Integrations at the TSI locus 1 resulted in the expression of different gene fusions. In addition, the activities of Fg native promoters were not altered by integration into the TSI locus 1. We have developed a bespoke bioinformatic pipeline to analyse the existence of ectopic integrations and tandem insertions of the cassette that may occurred during the transformation process. Finally, we established a protocol to study protein secretion in wheat coleoptiles using confocal microscopy and the TSI locus 1. {\textless}h4{\textgreater}Conclusion{\textless}/h4{\textgreater} The TSI locus 1 can be used in Fg and potentially other cereal infecting Fusarium species for diverse studies including promoter activity analysis, secretion, protein localisation studies and gene complementation. The bespoke bioinformatic pipeline developed in this work can be an alternative to southern blotting, the gold standard technique to identify ectopic integration and tandem insertions in fungal transformation.}, + author = {Darino, Martin and Urban, Martin and Kaur, Navneet and Machado-Wood, Ana and Grimwade-Mann, Michael and Smith, Dan and Beacham, Andrew and Hammond-Kosack, Kim}, + doi = {10.1101/2023.08.20.553861}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Identification and functional characterisation of a locus for target site integration {inFusarium} graminearum}, + url = {http://europepmc.org/abstract/PPR/PPR705187}, + year = {2023} +} + @article{darino_identification_2024, abstract = {Fusarium Head Blight (FHB) is a destructive floral disease of different cereal crops. The Ascomycete fungus Fusarium graminearum (Fg) is one of the main causal agents of FHB in wheat and barley. The role(s) in virulence of Fg genes include genetic studies that involve the transformation of the fungus with different expression cassettes. We have observed in several studies where Fg genes functions were characterised that integration of expression cassettes occurred randomly. Random insertion of a cassette may disrupt gene expression and/or protein functions and hence the overall conclusion of the study. Target site integration (TSI) is an approach that consists of identifying a chromosomal region where the cassette can be inserted. The identification of a suitable locus for TSI in Fg would avert the potential risks of ectopic integration.}, author = {Darino, Martin and Urban, Martin and Kaur, Navneet and Machado Wood, Ana and Grimwade-Mann, Mike and Smith, Dan and Beacham, Andrew and Hammond-Kosack, Kim}, @@ -3028,9 +5104,12 @@ @article{darino_identification_2024 @article{darkow_small_2021, abstract = {In search of more efficacious and safe pharmacological treatments for atrial fibrillation (AF), atria-selective antiarrhythmic agents have been promoted that target ion channels principally expressed in the atria. This concept allows one to engage antiarrhythmic effects in atria, but spares the ventricles from potentially proarrhythmic side effects. It has been suggested that cardiac small conductance Ca2+-activated K+ (SK) channels may represent an atria-selective target in mammals including humans. However, there are conflicting data concerning the expression of SK channels in different stages of AF, and recent findings suggest that SK channels are upregulated in ventricular myocardium when patients develop heart failure. To address this issue, RNA-sequencing was performed to compare expression levels of three SK channels (KCNN1, KCNN2, and KCNN3) in human atrial and ventricular tissue samples from transplant donor hearts (no cardiac disease), and patients with cardiac disease in sinus rhythm or with AF. In addition, for control purposes expression levels of several genes known to be either chamber-selective or differentially expressed in AF and heart failure were determined. In atria, as compared to ventricle from transplant donor hearts, we confirmed higher expression of KCNN1 and KCNA5, and lower expression of KCNJ2, whereas KCNN2 and KCNN3 were statistically not differentially expressed. Overall expression of KCNN1 was low compared to KCNN2 and KCNN3. Comparing atrial tissue from patients with AF to sinus rhythm samples we saw downregulation of KCNN2 in AF, as previously reported. When comparing ventricular tissue from heart failure patients to non-diseased samples, we found significantly increased ventricular expression of KCNN3 in heart failure, as previously published. The other channels showed no significant difference in expression in either disease. Our results add weight to the view that SK channels are not likely to be an atria-selective target, especially in failing human hearts, and modulators of these channels may prove to have less utility in treating AF than hoped. Whether targeting SK1 holds potential remains to be elucidated.}, author = {Darkow, Elisa and Nguyen, Thong T. and Stolina, Marina and Kari, Fabian A. and Schmidt, Constanze and Wiedmann, Felix and Baczkó, István and Kohl, Peter and Rajamani, Sridharan and Ravens, Ursula and Peyronnet, Rémi}, + doi = {10.3389/fphys.2021.650964}, issn = {1664-042X}, journal = {Frontiers in Physiology}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {650964}, shorttitle = {Small {Conductance} {Ca2} +-{Activated} {K}+ ({SK}) {Channel} {mRNA} {Expression} in {Human} {Atrial} and {Ventricular} {Tissue}}, title = {Small {Conductance} {Ca2} +-{Activated} {K}+ ({SK}) {Channel} {mRNA} {Expression} in {Human} {Atrial} and {Ventricular} {Tissue}: {Comparison} {Between} {Donor}, {Atrial} {Fibrillation} and {Heart} {Failure} {Tissue}}, url = {https://www.frontiersin.org/article/10.3389/fphys.2021.650964}, @@ -3074,6 +5153,51 @@ @article{davey_intrinsically_2019 year = {2019} } +@article{david_mitigating_2024, + abstract = {Biofilm-associated candidiasis poses a significant challenge in clinical settings due to the limited effectiveness of existing antifungal treatments. The challenges include increased pathogen virulence, multi-drug resistance, and inadequate penetration of antimicrobials into biofilm structures. One potential solution to this problem involves the development of novel drugs that can modulate fungal virulence and biofilm formation, which is essential for pathogenesis. Resistance in Candida albicans is initiated by morphological changes from yeast to hyphal form. This transition triggers a series of events such as cell wall elongation, increased adhesion, invasion of host tissues, pathogenicity, biofilm formation, and the initiation of an immune response. The cell wall is a critical interface for interactions with host cells, primarily through various cell wall proteins, particularly mannoproteins. Thus, cell wall proteins and enzymes are considered potential antifungal targets. In this regard, we explored α-glucosidase as our potential target which plays a crucial role in processing mannoproteins. Previous studies have shown that inhibition of α-glucosidase leads to defects in cell wall integrity, reduced adhesion, diminished secretion of hydrolytic enzymes, alterations in immune recognition, and reduced pathogenicity. Since α-glucosidase, primarily converts carbohydrates, our study focuses on FDA-approved carbohydrate mimic drugs (Glycomimetics) with well-documented applications in various biological contexts. Through virtual screening of 114 FDA-approved carbohydrate-based drugs, a pseudo-sugar Acarbose, emerged as a top hit. Acarbose is known for its pharmacological potential in managing type 2 diabetes mellitus by targeting α-glucosidase. Our preliminary investigations indicate that Acarbose effectively inhibits C. albicans biofilm formation, reduces virulence, impairs morphological switching, and hinders the adhesion and invasion of host cells, all at very low concentrations in the nanomolar range. Furthermore, transcriptomic analysis reveals the mechanism of action of Acarbose, highlighting its role in targeting α-glucosidase.}, + author = {David, Helma and Vasudevan, Sahana and Solomon, Adline Princy}, + doi = {10.1038/s41598-024-62684-x}, + issn = {2045-2322}, + journal = {Scientific reports}, + keywords = {{\textgreater}UseGalaxy.eu, Acarbose, Antifungal Agents, Candida albicans, Candidiasis, alpha-Glucosidases}, + language = {eng}, + month = {May}, + number = {1}, + pages = {11890}, + title = {Mitigating candidiasis with acarbose by targeting {Candida} albicans α-glucosidase: in-silico, in-vitro and transcriptomic approaches}, + url = {http://europepmc.org/abstract/MED/38789465}, + volume = {14}, + year = {2024} +} + +@article{dawson_carbon_2025, + abstract = {Carbon monoxide (CO) oxidising microorganisms are present in volcanic deposits throughout succession, with levels of vegetation and soil influencing the communities present. Carboxydovores are a subset of CO oxidisers that use CO as an energy source, which raises questions about the physiological and metabolic features that make them more competitive in harsh volcanic ecosystems. To address these questions, samples were taken from volcanic strata formed by eruptions from Calbuco Volcano (Chile) in 2015 (tephra) and 1917 (soil). Two carboxydovore members of the Burkholderiaceae family were isolated for further study to elucidate the benefits of carboxydovory for the survival of these strains in extreme volcanic ecosystems. The isolates were identified as Paraburkholderia terrae COX (isolated from the 2015 tephra) and Cupriavidus str. CV2 (isolated from the 1917 soil). 16S rRNA gene sequencing showed that within the family Burkholderiacea, the genus Paraburkholderia dominated the 2015 volcanic deposit with an average relative abundance of 73.81\%, whereas in the 1917 volcanic deposit, Cupriavidus accounted for 33.64\% (average relative abundance). Both strains oxidise CO across a broad range of concentrations ({\textless} 100 ppmv - 10,000 ppmv), and genome sequence analysis revealed a candidate form-I carbon monoxide dehydrogenase (CODH), which is likely to catalyse this process. Each strain oxidised CO specifically at stationary phase but the conditions for induction of CODH expression were distinct. Cupriavidus strain CV2 expressed CODH only when CO was added to cultures (100 ppm), while Pb. terrae COX expressed CODH regardless of supplementary CO addition. Based on comparative metabolic and phylogenetic analyses, Cupriavidus strain CV2 is proposed as a novel species within the genus Cupriavidus with the name Cupriavidus ulmosensis sp. nov. for the type strain CV2$^{\textrm{T}}$ (= NCIMB 15506$^{\textrm{ T}}$, = CECT 30956$^{\textrm{ T}}$). This study provides valuable insights into the physiology and metabolism of carboxydovores which colonise volcanic ecosystems.}, + author = {Dawson, Robin A and Fantom, Nicola and Martin-Pozas, Tamara and Aguila, Patricia and King, Gary M and Hernández, Marcela}, + doi = {10.1186/s40793-025-00672-y}, + issn = {2524-6372}, + journal = {Environmental microbiome}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {January}, + number = {1}, + pages = {12}, + title = {Carbon monoxide-oxidising {Pseudomonadota} on volcanic deposits}, + url = {http://europepmc.org/abstract/MED/39865271}, + volume = {20}, + year = {2025} +} + +@article{de_allende_characterisation_2025, + abstract = {Ornithobacterium hominis is a recently described Gram-negative bacterium that colonises the human nasopharynx and may be associated with poor upper respiratory tract health. Here, we describe the isolation of O. hominis from samples collected from a South African birth cohort, creating the first archive of cultured strains of the species from Africa. Sequenced genomes from this archive reveal that South African O. hominis is more similar to Australian strains than those from Southeast Asia, and that it may share genes with other members of the microbiome that are relevant for virulence, colonisation, and antibiotic resistance. Leveraging existing microbiome data from the cohort, O. hominis was found to be closely associated with bacterial co-colonisers that are rare in non-carrier individuals, including Suttonella , Helcococcus , Moraxella spp., and Gracilibacteria. Their collective acquisition has a significant impact on the diversity of nasopharyngeal communities that contain O. hominis . Individuals who have not yet acquired O. hominis have a higher abundance of Moraxella (particularly M. lincolnii ) than individuals who never acquire O. hominis , suggesting that this could be a precursor state for successful colonisation. Finally, a novel co-coloniser species, Helcococcus ekapensis , was successfully isolated and sequenced. {\textless}h4{\textgreater}Data Summary{\textless}/h4{\textgreater} Ornithobacterium hominis data have been deposited under project accession ERP149886. This comprises genome sequences for isolates SA-OH-C1 (ERR13967269), SA-OH-C2 (ERR13967270), SA-OH-C3 (ERR13967271), SA-OH-C4 (ERR13967272, ERR13967275), SA-OH-C5 (ERR13967273), SA-OH-C6 (ERR13967274, ERR13967276). Previously published 16S rRNA gene data are deposited under project accessions PRJNA790843 and PRJNA548658. Helcococcus ekapensis genome data are deposited under project accession PRJEB85661. {\textless}h4{\textgreater}Software used{\textless}/h4{\textgreater} AMRFinderPlus v3.12.8: https://github.com/ncbi/amr AssembleBAC-ONT v1.1.1: https://github.com/avantonder/assembleBAC-ONT BAKTA v1.8.1: https://bakta.computational.bio/ BLAST v2.16.0: https://blast.ncbi.nlm.nih.gov/Blast.cgi Comprehensive Antibiotic Resistance Database (CARD) Resistance Gene Identifier (RGI) tool v1.2.1: https://card.mcmaster.ca/analyze/rgi Decontam v1.12 (R package): https://github.com/benjjneb/decontam Eggnog-mapper v2.0.1: http://eggnog-mapper.embl.de/ FastANI v1.1.0: https://github.com/ParBLiSS/FastANI Flye v2.9.2: https://github.com/fenderglass/Flye Guppy v6.5.7: https://community.nanoporetech.com/downloads/guppy/release\_notes ISEScan v1.7.2.3: https://usegalaxy.eu/root?tool\_id=toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1 Medaka v1.9.1: https://github.com/nanoporetech/medaka MEGA11: https://www.megasoftware.net/ MMseqs2 v17: https://github.com/soedinglab/MMseqs2 Mothur v1.44.3: https://github.com/mothur/mothur NetCoMi v1.2.0 (R package): https://github.com/stefpeschel/NetCoMi Panaroo v1.4.3: https://github.com/gtonkinhill/panaroo PHASTEST: https://phastest.ca/submissions/new Prowler (commit ID c3041ba): https://github.com/ProwlerForNanopore/ProwlerTrimmer R v4.4.3: https://www.r-project.org/ {\textless}h4{\textgreater}Databases used{\textless}/h4{\textgreater} Comprehensive Antibiotic Resistance Database (CARD): https://card.mcmaster.ca/ European Nucleotide Archive: https://www.ebi.ac.uk/ena/ Genome Taxonomy Database (GTDB) release 09-RS220: https://gtdb.ecogenomic.org/ RefSeq release 228: https://www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/ SILVA v132: https://www.arb-silva.de/ {\textless}h4{\textgreater}Impact statement{\textless}/h4{\textgreater} First described in 2019, Ornithobacterium hominis is an understudied bacterium that may be associated with poor respiratory health in children. The study builds upon existing knowledge of O. hominis by describing the first African isolates of the species, its potential as a reservoir of virulence and antibiotic resistance genes in the upper respiratory tract, and the unique microbiome profile of O. hominis carriers.}, + author = {De Allende, Celine and Salter, Susannah and Brigg, Siobhan and Claassen-Weitz, Shantelle and Mwaikono, Kilaza and Workman, Lesley and Zar, Heather and Nicol, Mark and Parkhill, Julian and Dube, Felix}, + doi = {10.1101/2025.05.24.655922}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Characterisation of {Ornithobacterium} hominis colonisation dynamics and interaction with the nasopharyngeal microbiome in a {South} {African} birth cohort}, + url = {http://europepmc.org/abstract/PPR/PPR1025646}, + year = {2025} +} + @article{de_andrade_whole_2023, abstract = {Bacillus anthracis causes anthrax disease and can affect humans and other animals. This zoonotic disease has an impact on the economic and health aspects. B. anthracis population is divided into three major clades: A (with worldwide distribution), B, and C (restricted to specific regions). Anthrax is most common in agricultural regions of central and southwestern Asia, sub-Saharan Africa, Southern and Eastern Europe, the Caribbean, and Central and South America. Here, we sequenced by short and long reads technologies to generate a hybrid assembly of a lineage of B. anthracis recovered from animal source in the 1960s in Brazil. Isolate identification was confirmed by phenotypic/biochemical tests and MALDI-TOF MS. Antimicrobial susceptibility was performed by in-house broth microdilution. B. anthracis IAL52 was susceptible to penicillin, amoxicillin, doxycycline, levofloxacin, and tetracycline but non-susceptible to ciprofloxacin. IAL52 was classified as sequence type ST2, clade A.Br.069 (V770 group). Sequencing lineages of B. anthracis, especially from underrepresented regions, can help determine the evolution of this critical zoonotic and virulent pathogen.}, author = {de Andrade, Tânia Sueli and Camargo, Carlos Henrique and Campos, Karoline Rodrigues and Reis, Alex Domingos and Santos, Marlon Benedito do Nascimento and Zanelatto, Vanessa Nieri and Takagi, Elizabeth Harummyy and Sacchi, Claudio Tavares}, @@ -3092,10 +5216,13 @@ @article{de_andrade_whole_2023 } @article{de_azevedo_genomic_2024, + abstract = {Marseilleviruses (MsV) are a group of viruses that compose the Marseilleviridae family within the Nucleocytoviricota phylum. They have been found in different samples, mainly in freshwater. MsV are classically organized into five phylogenetic lineages (A/B/C/D/E), but the current taxonomy does not fully represent all the diversity of the MsV lineages. Here, we describe a novel strain isolated from a Brazilian saltwater sample named Marseillevirus cajuinensis. Based on genomics and phylogenetic analyses, M. cajuinensis exhibits a 380,653-bp genome that encodes 515 open reading frames. Additionally, M. cajuinensis encodes a transfer RNA, a feature that is rarely described for Marseilleviridae. Phylogeny suggests that \textit{M. cajuinensis} forms a divergent branch within the MsV lineage A. Furthermore, our analysis suggests that the common ancestor for the five classical lineages of MsV diversified into three major groups. The organization of MsV into three main groups is reinforced by a comprehensive analysis of clusters of orthologous groups, sequence identities, and evolutionary distances considering several MsV isolates. Taken together, our results highlight the importance of discovering new viruses to expand the knowledge about known viruses that belong to the same lineages or families. This work proposes a new perspective on the \textit{Marseilleviridae} lineages organization that could be helpful to a future update in the taxonomy of the Marseilleviridae family.{\textless}h4{\textgreater}Importance{\textless}/h4{\textgreater}Marseilleviridae is a family of viruses whose members were mostly isolated from freshwater samples. In this work, we describe the first \textit{Marseillevirus} isolated from saltwater samples, which we called \textit{Marseillevirus cajuinensis}. Most of \textit{M. cajuinensis} genomic features are comparable to other Marseilleviridae members, such as its high number of unknown proteins. On the other hand, \textit{M. cajuinensis} encodes a transfer RNA, which is a gene category involved in protein translation that is rarely described in this viral family. Additionally, our phylogenetic analyses suggested the existence of, at least, three major Marseilleviridae groups. These observations provide a new perspective on Marseilleviridae lineages organization, which will be valuable in future updates to the taxonomy of the family since the current official classification does not capture all the Marseilleviridae known diversity.}, author = {de Azevedo, Bruna Luiza and Queiroz, Victória Fulgêncio and de Aquino, Isabella Luiza Martins and Machado, Talita Bastos and de Assis, Felipe Lopes and Reis, Erik and Araújo Júnior, João Pessoa and Ullmann, Leila Sabrina and Colson, Philippe and Greub, Gilbert and Aylward, Frank and Rodrigues, Rodrigo Araújo Lima and Abrahão, Jônatas Santos}, doi = {10.1128/jvi.00513-24}, + issn = {0022-538X}, journal = {Journal of Virology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Genome, Viral, Viruses}, + language = {eng}, month = {May}, note = {Publisher: American Society for Microbiology}, number = {0}, @@ -3107,6 +5234,24 @@ @article{de_azevedo_genomic_2024 year = {2024} } +@article{de_carvalho_first_2025, + abstract = {Infectious Bovine Keratoconjunctivitis (IBK) is a widespread ocular disease that affects dairy and beef cattle worldwide, caused by Gram-negative bacteria from the genus Moraxella. It is the most common eye disease in cattle, with symptoms including tearing, ocular pain, corneal opacity, photophobia, ulceration, and, in severe cases, permanent blindness. This study focused on characterizing Moraxella species in a 2022 IBK outbreak in Minas Gerais, Brazil. Ocular swabs from 18 symptomatic Holstein cattle were analyzed through colony isolation, physiological tests, and molecular techniques, including PCR-RFLP and sequencing. Results revealed one isolate of Moraxella bovoculi genotype 1 and five isolates of Moraxella oculi, marking the first report of the latter species in Brazil. This study represents the second report of Moraxella oculi isolation and the first in a country different from the initial report. Notably, Moraxella bovis was not isolated in this outbreak. All isolates exhibited susceptibility to the tested antibiotics. Comparative genomic analysis between the Brazilian Moraxella oculi isolate and the American strain (Tifton 1) revealed 99.5\% similarity in the 16–23 S rRNA locus and 99.0\% average nucleotide identity.}, + author = {de Carvalho, Clarissa Vidal and Domingues, Robert and de Carvalho Coutinho, Cinthia and de Brito Silva Honório, Nicole Tafnes and Ribeiro de Lima Reis Faza, Daniele and Barbosa Ferreira-Machado, Alessandra and Carvalho, Wanessa Araújo and Gaspar, Emanuelle Baldo and Martins, Marta Fonseca}, + doi = {10.1007/s11259-025-10713-z}, + issn = {1573-7446}, + journal = {Veterinary Research Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Conjunctival diseases, Corneal diseases, Hepatitis B virus, Hereditary eye disease, IBK, Lyme disease, Moraxella oculi, Ocular motility disorders, PCR-RFLP, Sequencing}, + language = {en}, + month = {March}, + number = {3}, + pages = {143}, + title = {First report of {Moraxella} oculi in {Brazil} in an infectious bovine keratoconjunctivitis outbreak}, + url = {https://doi.org/10.1007/s11259-025-10713-z}, + urldate = {2025-03-29}, + volume = {49}, + year = {2025} +} + @article{de_jesus_bertani_whole_2023, abstract = {This study analyzes the genomic findings of the first report of Salmonella isolate carrying the blaCTX-M-55 gene, recovered from a bacteremic patient from Brazil. A bacterial isolate positive for the blaCTX-M-55 gene was submitted to antimicrobial susceptibility testing by disk diffusion and epsilometric test. Whole genome sequencing was performed using Illumina technology. Conjugation assay was performed; plasmid sizes determined by S1-PFGE and plasmid content were investigated by hybrid assembly after MinION long reads sequencing. Isolate 288\_18 was identified as sequence type ST13, resistant to ampicillin, cefotaxime, ceftazidime, cefepime, ceftriaxone, and aztreonam. A transferable IncFII plasmid sized approximately 67 kb was found to carry the blaTEM-1 and blaCTX-M-55 in a module consisting of IS26-blaTEM-1B-WbuC-blaCTX-M-55-IS26. In addition, an 117 kb IncI1plasmid was also identified in the 288\_18 isolate, but without additional resistance genes. To the best of our knowledge, this is the first report of blaCTX-M-55 in Salmonella isolated from human infection in Brazil. The occurrence of blaCTX-M-55 in the IncFII epidemic plasmid in a relevant clinical human isolate of Salmonella Agona underscores the urgent need for enhanced and effective continuous surveillance for controlling its dissemination.}, author = {de Jesus Bertani, Amanda Maria and Vieira, Thais and Reis, Alex Domingos and dos Santos, Carla Adriana and de Almeida, Elisabete Aparecida and Camargo, Carlos Henrique and Casas, Monique Ribeiro Tiba}, @@ -3114,7 +5259,7 @@ @article{de_jesus_bertani_whole_2023 doi = {10.1038/s41598-023-29599-5}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, Antimicrobials, Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Antimicrobials, Escherichia coli, Microbiology}, language = {en}, month = {February}, note = {Number: 1 @@ -3128,6 +5273,23 @@ @article{de_jesus_bertani_whole_2023 year = {2023} } +@article{de_melo-ximenes_first_2025, + abstract = {Genomic resources, such as draft genomes, are vital for biodiversity monitoring and conservation. For endangered species, they enable the development of tools like organellar genomes and molecular markers, which are crucial for population genetics. Advances in sequencing technologies now allow high-throughput genotyping with detailed amplicon sequences, enhancing genetic variation studies. The northern muriqui (\textit{Brachyteles hypoxanthus}), a critically endangered primate endemic to Brazil's Atlantic Forest, currently lacks both nuclear and mitochondrial genome data and species-specific microsatellite markers for population genetic studies. We assembled a 2.52 Gb draft genome for \textit{B. hypoxanthus} with 202,243 contigs (N50 = 29,134 bp), and BUSCO analyses indicated 52\% completeness and 15.5\% fragmented genes. The complete 16,635 bp mitochondrial genome retains the conserved mammalian structure with 22 tRNAs, 2 rRNAs, 13 CDS, and an origin of replication. Additionally, we designed 31 SSR primer pairs suitable for non-invasive sampling and genotyping, alongside two mtDNA and two sex-determination primers, configured into three multiplex PCR sets. These genomic resources, including the draft genome, complete mitochondrial genome, and microsatellite markers, provide essential tools for evolutionary analyses and the genetic monitoring of \textit{B. hypoxanthus} populations, supporting its conservation.}, + author = {de Melo-Ximenes, Amanda Alves and Batista, Romina and Corvalán, Leonardo Carlos Jeronimo and Marques-Bonet, Tomas and Kuderna, Lukas and Farh, Kyle and Rogers, Jeffrey and Kaizer, Mariane da Cruz and Boubli, Jean Philippe and de Melo, Fabiano Rodrigues and Nunes, Rhewter and Telles, Mariana Pires de Campos}, + doi = {10.1002/ece3.71356}, + issn = {2045-7758}, + journal = {Ecology and evolution}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {August}, + number = {8}, + pages = {e71356}, + title = {First {Assembly} of a {Draft} {Genome} of the {Critically} {Endangered} {Northern} {Muriqui} (\textit{{Brachyteles} hypoxanthus}, {Primates}, {Atelidae}) {Including} {Non}-{Invasive} {Genotyping} {Strategies} for the {Species}}, + url = {http://europepmc.org/abstract/MED/40843033}, + volume = {15}, + year = {2025} +} + @article{de_melo_mitochondrial_2024, abstract = {Syagrus coronata (Mart.) Becc. belongs to the Arecaceae family. It is a species native to Brazil of ecological, social, and economic importance. To date, there are few mitochondrial genomes in Arecaceae (Cocos nucifera and Phoenix dactylifera L.), and studies of the mitochondrial genome are essential to understand the evolution of the Arecaceae family. This study reports and compares the newly sequenced genome of S. coronata. Single-end and paired-end reads were used to obtain de novo contigs. The mitochondrial contigs were selected using C. nucifera as a reference and were merged using mate paired-end reads. The mitochondrial genome showed 642,817 bp, circular structure, containing 73 predicted functional genes, including four ribosomal RNA (rRNA) genes, 27 transfer RNA (tRNA) genes, and 42 coding protein genes. Large chloroplast genomic fragments were identified in the mitochondrial genome, and large DNA repetitive fragments were into intergenic space regions. Arecaceae mitochondrial genomes showed partial similarities in size, genome structure, and gene content. However, they exhibited numerous rearrangements. In summary, (1) we sequenced the mitochondrial genome of S. coronata and compared with other mitogenomes of Arecaceae. (2) Genomic rearrangements and gene transfer have been identified from the chloroplast genome to the mitochondrial genome. (3) The mitochondrial genome of Arecareae showed similarities in size, structure, and gene content. (4) The expansion of intergenic space size occurs due to the insertion of genes originating from the nucleus.}, author = {de Melo, Suzyanne Morais Firmino and Marques, André and Almeida, Cícero}, @@ -3163,6 +5325,23 @@ @article{de_oliveira_apoplastomes_2024 year = {2024} } +@article{de_oliveira_whole-genome_2022, + abstract = {Antimicrobial peptides (AMPs) can efficiently control different microbial pathogens and show the potential to be applied in clinical practice and livestock production. In this work, the aim was to isolate AMP-producing ruminal streptococci and to characterize their genetic features through whole-genome sequencing. We cultured 463 bacterial isolates from the rumen of Nelore bulls, 81 of which were phenotypically classified as being \textit{Streptococcaceae}. Five isolates with broad-range activity were genome sequenced and confirmed as being \textit{Streptococcus lutetiensis}. The genetic features linked to their antimicrobial activity or adaptation to the rumen environment were characterized through comparative genomics. The genome of \textit{S. lutetiensis} UFV80 harbored a putative CRISPR-Cas9 system (Type IIA). Computational tools were used to discover novel biosynthetic clusters linked to the production of bacteriocins. All bacterial genomes harbored genetic clusters related to the biosynthesis of class I and class II bacteriocins. SDS-PAGE confirmed the results obtained in silico and demonstrated that the class II bacteriocins predicted in the genomes of three \textit{S. lutetiensis} strains had identical molecular mass (5197 Da). These results demonstrate that ruminal bacteria of the \textit{Streptococcus bovis}/\textit{equinus} complex represent a promising source of novel antimicrobial peptides.}, + author = {de Oliveira, Isabela Maria Fernandes and Godoy-Santos, Fernanda and Oyama, Linda Boniface and Moreira, Sofia Magalhães and Dias, Rodrigo Gonçalves and Huws, Sharon Ann and Creevey, Christopher J and Mantovani, Hilário Cuquetto}, + doi = {10.3390/microorganisms10030551}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {March}, + number = {3}, + pages = {551}, + title = {Whole-{Genome} {Sequencing} and {Comparative} {Genomic} {Analysis} of {Antimicrobial} {Producing} {Streptococcus} lutetiensis from the {Rumen}}, + url = {http://europepmc.org/abstract/MED/35336126}, + volume = {10}, + year = {2022} +} + @article{de_souza_mitochondrial_2024, abstract = {Plant mitochondrial genomes are characterized by high homologous recombination, extensive intergenic spacers, conservation in DNA sequences, and gene content. The Hancornia genus belongs to the Apocynaceae family, with H. speciosa Gomes being the sole species in the genus. It is an siganificant commercial fruit crop; however, only a number of studies have been conducted. In this study, we present the mitochondrial genome of H. speciosa and compare it with other mitochondrial genomes within the Apocynaceae family.}, author = {de Souza, Fernanda Danielle and Marques, André and Almeida, Cícero}, @@ -3200,6 +5379,23 @@ @article{de_souza_seeds_2024 year = {2024} } +@article{debat_south_2022, + abstract = {Morbilliviruses are negative-sense single-stranded monosegmented RNA viruses in the family \textit{Paramyxoviridae} (order \textit{Mononegavirales}). Morbilliviruses infect diverse mammals including humans, dogs, cats, small ruminants, seals, and cetaceans, which serve as natural hosts. Here, I report the identification and characterization of novel viruses detected in public RNAseq datasets of South American long-haired and olive field mice. The divergent viruses dubbed Ratón oliváceo morbillivirus (RoMV) detected in renal samples from mice collected from Chile and Argentina are characterized by an unusually large genome including long intergenic regions and the presence of an accessory protein between the F and H genes redounding in a genome architecture consisting in 3'-N-P/V/C-M-F-hp-H-L-5'. Structural and functional annotation, genetic distance, and evolutionary insights suggest that RoMV is a member of a novel species within genus \textit{Morbillivirus} tentatively named as South American mouse morbillivirus. Phylogenetic analysis suggests that this mouse morbillivirus is closely related to and clusters into a monophyletic group of novel rodent-borne morbilliviruses. This subclade of divergent viruses expands the host range, redefines the genomic organization and provides insights on the evolutionary history of genus \textit{Morbillivirus}.}, + author = {Debat, Humberto J}, + doi = {10.3390/v14112403}, + issn = {1999-4915}, + journal = {Viruses}, + keywords = {{\textgreater}UseGalaxy.eu, Morbillivirus, Morbillivirus Infections}, + language = {eng}, + month = {October}, + number = {11}, + pages = {2403}, + title = {A {South} {American} {Mouse} {Morbillivirus} {Provides} {Insight} into a {Clade} of {Rodent}-{Borne} {Morbilliviruses}}, + url = {http://europepmc.org/abstract/MED/36366501}, + volume = {14}, + year = {2022} +} + @article{dederichs_nonpreferential_2024, abstract = {BACKGROUND: Clonal hematopoiesis of indeterminate potential (CHIP) is an acquired genetic risk factor for both leukemia and cardiovascular disease. It results in proinflammatory myeloid cells in the bone marrow and blood; however, how these cells behave in the cardiovascular tissue remains unclear. Our study aimed at investigating whether CHIP-mutated macrophages accumulate preferentially in cardiovascular tissues and examining the transcriptome of tissue macrophages from DNMT3A (DNA methyltransferase 3 alpha) or TET2 (Tet methylcytosine dioxygenase 2) mutation carriers. @@ -3248,6 +5444,23 @@ @article{dehghanian_zfp982_2024 year = {2024} } +@article{delaleau_comprehensive_2025, + abstract = {Recent evidence indicates that the bacterial Rho helicase regulates Bacillus subtilis gene expression in a growth-dependent manner. This regulation, along with extensive in vivo trimming of Rho-dependent transcript 3′-ends, complicates the identification of Rho-dependent transcription terminators using standard transcriptomic approaches. To overcome this challenge, we applied Helicase-SELEX to precisely map Rho utilization (Rut) sites genome-wide. Using B. subtilis Rho (BsRho), we identified 600 putative Rut sites, while the more permissive Escherichia coli Rho (EcRho) revealed 4189 sites, including specimens known to regulate B. subtilis genes. Comparative analysis showed that both enzymes recognize similar pyrimidine-rich sequences, though BsRho favors short unstructured Rut motifs whereas EcRho can act on presumably more structured RNAs without requiring accessory factors. In vivo validation of selected Rut sites confirmed Rho-dependent regulation and extensive PNPase-mediated processing of Rho-terminated transcripts. Collectively, our results reveal a rich and complex Rho-dependent regulatory network in B. subtilis, encompassing the widespread control of antisense transcription and genes/operons of both primary and secondary metabolism. Although nonessential under standard laboratory conditions, Rho thus likely contributes to B. subtilis fitness and survival in more demanding environments. Our comprehensive compendium of Rut sites offers a valuable resource for exploring this adaptive regulatory landscape.}, + author = {Delaleau, Mildred and Bidnenko, Vladimir and Eveno, Eric and Kostova, Gergana and Black, Johnathan C and McGovern, Stephen and Pellegrini, Olivier and Dérozier, Sandra and Jules, Matthieu and Condon, Ciaran and Durand, Sylvain and Bidnenko, Elena and Boudvillain, Marc}, + doi = {10.1093/nar/gkaf765}, + issn = {1362-4962}, + journal = {Nucleic Acids Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + number = {15}, + pages = {gkaf765}, + title = {Comprehensive mapping of transcription terminator {Rho} utilization ({Rut}) sites across the {Bacillus} subtilis genome}, + url = {https://doi.org/10.1093/nar/gkaf765}, + urldate = {2025-09-03}, + volume = {53}, + year = {2025} +} + @article{delandre_long-read_2024, abstract = {Antimalarial drug resistance has become a real public health problem despite WHO measures. New sequencing technologies make it possible to investigate genomic variations associated with resistant phenotypes at the genome-wide scale. Based on the use of hemisynthetic nanopores, the PromethION technology from Oxford Nanopore Technologies can produce long-read sequences, in contrast to previous short-read technologies used as the gold standard to sequence Plasmodium. Two clones of P. falciparum (Pf3D7 and PfW2) were sequenced in long-read using the PromethION sequencer from Oxford Nanopore Technologies without genomic amplification. This made it possible to create a processing analysis pipeline for human Plasmodium with ONT Fastq only. De novo assembly revealed N50 lengths of 18,488 kb and 17,502 kb for the Pf3D7 and PfW2, respectively. The genome size was estimated at 23,235,407 base pairs for the Pf3D7 clone and 21,712,038 base pairs for the PfW2 clone. The average genome coverage depth was estimated at 787X and 653X for the Pf3D7 and PfW2 clones, respectively. This study proposes an assembly processing pipeline for the human Plasmodium genome using software adapted to large ONT data and the high AT percentage of Plasmodium. This search provides all the parameters which were optimized for use with the software selected in the pipeline.}, author = {Delandre, Océane and Lamer, Ombeline and Loreau, Jean-Marie and Papa Mze, Nasserdine and Fonta, Isabelle and Mosnier, Joel and Gomez, Nicolas and Javelle, Emilie and Pradines, Bruno}, @@ -3281,6 +5494,27 @@ @article{delroisse_photophore_2021 year = {2021} } +@article{demeter_flow_2025, + abstract = {Plasmacytoid dendritic cells (pDCs) are a unique subset of dendritic cells specialized in rapid and robust type I interferon (IFN) production, playing critical roles in the pathogenesis and pathomechanisms of many human diseases. Accurate identification of pDCs in peripheral blood mononuclear cells (PBMCs) is challenging due to dynamic and non-exclusive specific expression of surface markers such as blood dendritic cell antigen (BDCA)-2 and BDCA-4. Although BDCA-4 is generally more stably expressed than BDCA-2, prolonged stimulation or inflammatory conditions can induce its expression on multiple non-pDC cell types, reducing the accuracy of pDC identification. Here, we thoroughly investigated BDCA-4 expression dynamics on pDCs and other PBMC subsets following prolonged activation with Toll-like receptor (TLR) 7 and TLR9 agonists. Our flow cytometry analysis revealed a significant increase in BDCA-4-positive non-pDC populations after extended stimulation, primarily corresponding to CD14+ monocytes. To overcome this limitation, we performed a gating strategy combining BDCA-4 positivity with a cocktail of non-pDC markers, enabling the exclusion of non-pDCs and accurate identification of pDCs. This approach enables the reliable identification of pDCs within heterogeneous cell populations using only two fluorescent channels in healthy conditions and even during strong activation or pathological states characterized by chronic inflammation.}, + author = {Demeter, Sarolta and Fekete, Tünde and Scholtz, Beáta and Veréb, Zoltán and Kemény, Lajos and Bácsi, Attila and Pázmándi, Kitti}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms262210979}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, BDCA-4, flow cytometry, gating strategy, monocyte, plasmacytoid dendritic cell}, + language = {en}, + month = {January}, + note = {Publisher: Multidisciplinary Digital Publishing Institute}, + number = {22}, + pages = {10979}, + shorttitle = {Flow {Cytometric} {Challenges} in {Plasmacytoid} {Dendritic} {Cell} ({pDC}) {Identification}}, + title = {Flow {Cytometric} {Challenges} in {Plasmacytoid} {Dendritic} {Cell} ({pDC}) {Identification}: {Limitation} of {BDCA}-4 ({CD304})-{Based} {Gating}}, + url = {https://www.mdpi.com/1422-0067/26/22/10979}, + urldate = {2025-12-26}, + volume = {26}, + year = {2025} +} + @article{deng_atlas_2024, abstract = {Endothelial cells play crucial roles in physiology and are increasingly recognized as therapeutic targets in cardiovascular disease. Here, we analyzed the regulatory landscape of cardiac endothelial cells by assessing chromatin accessibility, histone modifications, and 3D chromatin organization and confirmed the functional relevance of enhancer-promoter interactions by CRISPRi-mediated enhancer silencing. We used this dataset to explore mechanisms of transcriptional regulation in cardiovascular disease and compared six different experimental models of heart failure, hypertension, or diabetes. Enhancers that regulate gene expression in diseased endothelial cells were enriched with binding sites for a distinct set of transcription factors, including the mineralocorticoid receptor (MR), a known drug target in heart failure and hypertension. For proof of concept, we applied endothelial cell-specific MR deletion in mice to confirm MR-dependent gene expression and predicted direct MR target genes. Overall, we have compiled here a comprehensive atlas of cardiac endothelial cell enhancer elements that provides insight into the role of transcription factors in cardiovascular disease.}, author = {Deng, Lisa and Pollmeier, Luisa and Bednarz, Rebecca and Cao, Can and Laurette, Patrick and Wirth, Luisa and Mamazhakypov, Argen and Bode, Christine and Hein, Lutz and Gilsbach, Ralf and Lother, Achim}, @@ -3299,6 +5533,21 @@ @article{deng_atlas_2024 year = {2024} } +@article{deng_eco_2022, + abstract = {Endothelial cell (EC) plays critical roles in vascular physiological and pathological processes. With the development of high-throughput technologies, transcriptomics analysis of EC has increased dramatically and a large amount of informative data have been generated. The dynamic patterns of gene expression in ECs under various conditions were revealed. Unfortunately, due to the lack of bioinformatics infrastructures, reuse of these large-scale datasets is challenging for many scientists. Here, by systematic re-analyzing, integrating, and standardizing of 203 RNA sequencing samples from freshly isolated mouse ECs under 71 conditions, we constructed an integrated mouse EC gene expression omnibus (ECO). The ECO database enables one-click retrieval of endothelial expression profiles from different organs under different conditions including disease models, genetic modifications, and clinically relevant treatments \textit{in vivo}. The EC expression profiles are visualized with user-friendly bar-plots. It also provides a convenient search tool for co-expressed genes. ECO facilitates endothelial research with an integrated tool and resource for transcriptome analysis. The ECO database is freely available at https://heomics.shinyapps.io/ecodb/.}, + author = {Deng, Xiangyi and Yang, Fan and Zhang, Lei and Wang, Jianhao and Liu, Boxuan and Liang, Wei and Tang, Jiefu and Xie, Yuan and He, Liqun}, + doi = {10.3389/fgene.2022.844544}, + issn = {1664-8021}, + journal = {Frontiers in genetics}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {844544}, + title = {{ECO}: {An} {Integrated} {Gene} {Expression} {Omnibus} for {Mouse} {Endothelial} {Cells} {In} {Vivo}}, + url = {http://europepmc.org/abstract/MED/35309132}, + volume = {13}, + year = {2022} +} + @article{deng_gene_2020, abstract = {Endothelial cells take pivotal roles in the heart and the vascular system and their differentiation, subspecification and function is determined by gene expression. A stable, in vitro cardiac endothelial cell line could provide high cell numbers as needed for many epigenetic analyses and facilitate the understanding of molecular mechanisms involved in endothelial cell biology. To test their suitability for transcriptomic or epigenetic studies, we compared the transcriptome of cultured immortalized mouse cardiac endothelial cells (MCEC) to primary cardiac endothelial cells (pEC). Whole transcriptome comparison of MCEC and pEC showed a correlation of 0.75–0.77. Interestingly, correlation of gene expression declined in endothelial cell-typical genes. In MCEC, we found a broad downregulation of genes that are highly expressed in pEC, including well-described markers of endothelial cell differentiation. Accordingly, systematic analysis revealed a downregulation of genes associated with typical endothelial cell functions in MCEC, while genes related to mitotic cell cycle were upregulated when compared to pEC. In conclusion, the findings from this study suggest that primary cardiac endothelial cells should preferably be used for genome-wide transcriptome or epigenome studies. The suitability of in vitro cell lines for experiments investigating single genes or signaling pathways should be carefully validated before use.}, author = {Deng, Lisa and Pollmeier, Luisa and Zhou, Qian and Bergemann, Stella and Bode, Christoph and Hein, Lutz and Lother, Achim}, @@ -3339,8 +5588,10 @@ @article{deng_massively_2024 abstract = {Performing saturation editing of chromosomal genes will enable the study of genetic variants in situ and facilitate protein and cell engineering. However, current in vivo editing of endogenous genes either lacks flexibility or is limited to discrete codons and short gene fragments, preventing a comprehensive exploration of genotype-phenotype relationships. To enable facile saturation editing of full-length genes, we used a protospacer adjacent motif–relaxed Cas9 variant and homology-directed repair to achieve above 60\% user-defined codon replacement efficiencies in Saccharomyces cerevisiae genome. Coupled with massively parallel DNA design and synthesis, we developed a saturation gene editing method termed CRISPR-Cas9– and homology-directed repair–assisted saturation editing (CHASE) and achieved highly saturated codon swapping of long genomic regions. By applying CHASE to massively edit a well-studied global transcription factor gene, we found known and unreported genetic variants affecting an industrially relevant microbial trait. The user-defined codon editing capability and wide targeting windows of CHASE substantially expand the scope of saturation gene editing.}, author = {Deng, Lei and Zhou, Yi-Lian and Cai, Zhenkun and Zhu, Jie and Li, Zenan and Bao, Zehua}, doi = {10.1126/sciadv.adj9382}, + issn = {2375-2548}, journal = {Science Advances}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, CRISPR-Cas Systems, Gene Editing, Homologous Recombination, Saccharomyces cerevisiae}, + language = {eng}, month = {May}, note = {Publisher: American Association for the Advancement of Science}, number = {20}, @@ -3352,6 +5603,22 @@ @article{deng_massively_2024 year = {2024} } +@article{denis_identification_2025, + author = {Denis, J. and Gommenginger, C. and Beal, L. and Cimon, B. and Deleplancque, A. S. and Fricker Hidalgo, H. and L'Ollivier, C. and Paris, L. and Pelloux, H. and Pomares, C. and Houze, S. and Pfaff, A. W. and Villena, I. and Villard, O.}, + doi = {10.1128/spectrum.02040-24}, + journal = {Microbiology Spectrum}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {March}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e02040--24}, + title = {Identification of {Toxoplasma} gondii antigenic proteins using an in vivo approach and in silico investigation of their polymorphism}, + url = {https://journals.asm.org/doi/10.1128/spectrum.02040-24}, + urldate = {2025-03-29}, + volume = {0}, + year = {2025} +} + @misc{depari_long-read_2024, abstract = {Abstract* Azadirachta excelsa (Jack) Jacobs, Kayu bawang (Meliaceae) is economically valuable and widely used by the local community in Bengkulu (Sumatra) as carpentry and construction wood because of its good durability class. However, it still has ambiguous scientific multiple names, such as Azadirachta excelsa , Protium javanicum , and Dysoxylum mollissimum. Additional tools such as molecular approaches can be used to verify whether it is true or not that Kayu bawang is scientifically named as Azadirachta excelsa based on previous morphological identification. This study aimed to construct draft chloroplast genome and verify the scientific name based on molecular identification using a single rbc L gene marker. Genomic DNA was extracted from bark cambium originated from three different provenances in Bengkulu, Indonesia, namely TBT-A, TBT-K, and TBT-S. MinION from Oxford Nanopore Technologies was used to sequence the samples following manufacture protocols SQK-LSK109 yielding 481.6 Mb for TBT-A, 597.4 Mb for TBT-K, and 853.1 Mb for TBT-S, respectively. Generated data were assembled and constructed, namely 58,780 bp (14 tRNAs and 47 encoding genes) for TBT-A, 142,139 bp (4 rRNAs, 24 tRNAs, and 78 encoding genes) for TBT-K, and 84,906 bp (24 tRNAs and 53 encoding genes) for TBT-S. Based on the phylogenetic tree, Azadirachta excelsa from three identified tree stands were placed in the same group with other Azadirachta excelsa accessions.}, author = {Depari, Efratenta Katherina and Wijayanto, Nurheni and Karlinasari, Lina and Rafi, Mohamad and Siregar, Iskandar Zulkarnaen}, @@ -3373,7 +5640,7 @@ @article{desouza_effect_2024 doi = {10.1093/femsec/fiae096}, issn = {0168-6496}, journal = {FEMS Microbiology Ecology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Bacteria, Biodiversity, Droughts, Plants, Seasons, Soil Microbiology}, month = {August}, number = {8}, pages = {fiae096}, @@ -3384,6 +5651,49 @@ @article{desouza_effect_2024 year = {2024} } +@article{devasahayam_microbial_2025, + abstract = {Microbial Biological Control Agents (MBCAs) offer sustainable crop protection alternatives. Competition for ecological niches is mediated by secondary metabolites (SMs), which can be altered by other microbes into toxic cocktails, affecting various taxa, including humans. This study analyzed confrontations between the maize pathogen C. graminicola, biocontrol B. amyloliquefaciens, and the saprophyte A. nidulans. Transcriptomics revealed 69\% and 86\% SMBGC deregulation in C. graminicola under confrontations with B. amyloliquefaciens and A. nidulans. LC-MS/MS identified 1,738 and 1,466 novel features, including compounds putatively toxic to humans. Further, confrontations between A. nidulans and various biocontrol species showed 31\%, 59\%, and 74\% SMBGC deregulation. Metabolomics revealed confrontation specific SMs, and cytotoxicity studies showed reduced human cell viability from confrontation-derived SMs. These findings highlight the need for safer, more effective biocontrol strategies.}, + author = {Devasahayam, Bennet}, + copyright = {https://creativecommons.org/licenses/by/4.0/}, + doi = {10.25673/118336}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + note = {Accepted: 2025-02-25T13:50:32Z +ISBN: 9781918520897}, + title = {Microbial confrontations trigger broad array synthesis of human-toxic secondary metabolites}, + url = {https://opendata.uni-halle.de//handle/1981185920/120295}, + urldate = {2025-03-07}, + year = {2025} +} + +@article{dhalluin_conditional_2022, + abstract = {{\textless}h4{\textgreater}SUMMARY{\textless}/h4{\textgreater} Little is known about the decisions behind transcription elongation versus termination in the human pathogen Mycobacterium tuberculosis . By applying Term-seq to M. tuberculosis we found that the majority of transcription termination is premature and associated with translated regions, i.e. within previously annotated or newly identified open reading frames. Computational predictions and Term-seq analysis upon depletion of termination factor Rho suggests that Rho-dependent transcription termination dominates all TTS including those associated with regulatory 5’ leaders. Moreover, our results suggest that tightly coupled translation, in the form of overlapping stop and start codons, may suppress Rho-dependent termination. This study provides detailed insights into novel M. tuberculosis cis -regulatory elements, where Rho-dependent, conditional termination of transcription and translational coupling together play major roles in gene expression control. Our findings contribute to a deeper understanding of the fundamental regulatory mechanisms that enable M. tuberculosis adaptation to the host environment offering novel potential points of intervention.}, + author = {D’Halluin, Alexandre and Polgar, Peter and Kipkorir, Terry and Patel, Zaynah and Cortes, Teresa and Arnvig, Kristine}, + doi = {10.1101/2022.06.01.494293}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Conditional termination of transcription is shaped by {Rho} and translated {uORFS} {inMycobacterium} tuberculosis}, + url = {http://europepmc.org/abstract/PPR/PPR501841}, + year = {2022} +} + +@article{dhalluin_premature_2023, + abstract = {Little is known about the decisions behind transcription elongation versus termination in the human pathogen \textit{Mycobacterium tuberculosis} \textit{(M.TB)}. By applying Term-seq to \textit{M.TB} we found that the majority of transcription termination is premature and associated with translated regions, i.e., within previously annotated or newly identified open reading frames. Computational predictions and Term-seq analysis, upon depletion of termination factor Rho, suggests that Rho-dependent transcription termination dominates all transcription termination sites (TTS), including those associated with regulatory 5' leaders. Moreover, our results suggest that tightly coupled translation, in the form of overlapping stop and start codons, may suppress Rho-dependent termination. This study provides detailed insights into novel \textit{M}.\textit{TB cis}-regulatory elements, where Rho-dependent, conditional termination of transcription and translational coupling together play major roles in gene expression control. Our findings contribute to a deeper understanding of the fundamental regulatory mechanisms that enable \textit{M}.\textit{TB} adaptation to the host environment offering novel potential points of intervention.}, + author = {D'Halluin, Alexandre and Polgar, Peter and Kipkorir, Terry and Patel, Zaynah and Cortes, Teresa and Arnvig, Kristine B}, + doi = {10.1016/j.isci.2023.106465}, + issn = {2589-0042}, + journal = {iScience}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {April}, + number = {4}, + pages = {106465}, + title = {Premature termination of transcription is shaped by {Rho} and translated {uORFS} in \textit{{Mycobacterium} tuberculosis}}, + url = {http://europepmc.org/abstract/MED/37096044}, + volume = {26}, + year = {2023} +} + @article{dhamija_pan-cancer_2020, abstract = {Nonstop or stop-loss mutations convert a stop into a sense codon, resulting in translation into the 3′ untranslated region as a nonstop extension mutation to the next in-frame stop codon or as a readthrough mutation into the poly-A tail. Nonstop mutations have been characterized in hereditary diseases, but not in cancer genetics. In a pan-cancer analysis, we curated and analysed 3,412 nonstop mutations from 62 tumour entities, generating a comprehensive database at http://NonStopDB.dkfz.de. Six different nonstop extension mutations affected the tumour suppressor SMAD4, extending its carboxy terminus by 40 amino acids. These caused rapid degradation of the SMAD4 mutants via the ubiquitin–proteasome system. A hydrophobic degron signal sequence of ten amino acids within the carboxy-terminal extension was required to induce complete loss of the SMAD4 protein. Thus, we discovered that nonstop mutations can be functionally important in cancer and characterize their loss-of-function impact on the tumour suppressor SMAD4.}, author = {Dhamija, Sonam and Yang, Chul Min and Seiler, Jeanette and Myacheva, Ksenia and Caudron-Herger, Maiwen and Wieland, Angela and Abdelkarim, Mahmoud and Sharma, Yogita and Riester, Marisa and Groß, Matthias and Maurer, Jochen and Diederichs, Sven}, @@ -3451,6 +5761,27 @@ @article{dias_pathogenicity_2022 year = {2022} } +@article{diz-kucukkaya_jak2v617f_2024, + abstract = {OBJECTIVE: It has been shown that clonal mutations occur in hematopoietic stem cells with advancing age and increase the risk of death due to atherosclerotic vascular diseases, similarly to myeloproliferative neoplasms. Endothelial cells (ECs) and hematopoietic stem cells develop from common stem cells called hemangioblasts in the early embryonic period. However, the presence of hemangioblasts in the postnatal period is controversial. In this study, JAK2 gene variants were examined in patients with atherosclerotic carotid disease and without any hematological malignancies. +MATERIALS AND METHODS: Ten consecutive patients (8 men and 2 women) with symptomatic atherosclerotic carotid stenosis were included in this study. ECs (CD31+CD45-) were separated from tissue samples taken by carotid endarterectomy. JAK2 variants were examined in ECs, peripheral blood mononuclear cells, and oral epithelial cells of the patients with next-generation sequencing. +RESULTS: The median age of the patients was 74 (range: 58-80) years and the median body mass index value was 24.44 (range: 18.42-30.85) kg/m2. Smoking history was present in 50\%, hypertension in 80\%, diabetes in 70\%, and ischemic heart disease in 70\% of the cases. The JAK2V617F mutation was detected in the peripheral blood mononuclear cells of 3 of the 10 patients, and 2 patients also had the JAK2V617F mutation in their ECs. The JAK2V617F mutation was not found in the oral epithelial cells of any of the patients. +CONCLUSION: In this study, for the first time in the literature, we showed that the JAK2V617F mutation was found somatically in both peripheral blood cells and ECs in patients with atherosclerosis. This finding may support that ECs and hematopoietic cells originate from a common clone or that somatic mutations can be transmitted to ECs by other mechanisms. Examining the molecular and functional changes caused by the JAK2V617F mutation in ECs may help open a new avenue for treating atherosclerosis.}, + author = {Diz-Küçükkaya, Reyhan and İyigün, Taner and Albayrak, Özgür and Eker, Candan and Günel, Tuba}, + doi = {10.4274/tjh.galenos.2024.2024.0161}, + issn = {1308-5263}, + journal = {Turkish Journal of Haematology: Official Journal of Turkish Society of Haematology}, + keywords = {{\textgreater}UseGalaxy.eu, Aged, Aged, 80 and over, Atherosclerosis, Carotid Artery Diseases, Clonal hematopoiesis, Endothelial Cells, Female, Humans, JAK2V617F mutation, Janus Kinase 2, Leukocytes, Mononuclear, Male, Middle Aged, Mutation, Myeloproliferative neoplasms}, + language = {eng}, + month = {August}, + number = {3}, + pages = {167--174}, + pmcid = {PMC11589362}, + pmid = {38801025}, + title = {{JAK2V617F} {Mutation} in {Endothelial} {Cells} of {Patients} with {Atherosclerotic} {Carotid} {Disease}}, + volume = {41}, + year = {2024} +} + @article{do_carmo_santos_proteomics_2023, abstract = {Necrosis- and ethylene-inducing proteins are effector molecules of microorganisms able to induce cell death in plant tissues and/or ethylene biosynthesis. The fungus Moniliophthora perniciosa, which causes the witches' broom disease in Theobroma cacao, contains five genes that encode these proteins (MpNep1-5) in its genome. Among these, MpNep2 is the most expressed Nep during disease's development, especially in the necrotic phase. Although widely studied, little is known about the mechanisms by which these proteins induce cell death. In this perspective, the present study aimed to identify potential MpNEP2 target proteins in protein extracts of Theobroma cacao (genotype Catongo) and propose, from the results achieved, mechanisms by which MpNEP2 can induce the process of cell death. Molecular targets captured in vitro by rMpNEP2 immobilized on CNBr-Sepharose were identified by ms/ms. Candidate targets were identified as an Auxin Response Factor, Sphingosine Kinase and a Formin like protein. These proteins are known to participate in important processes in primary metabolism, molecular function and regulation of the plant's response. The targets:MpNEP2 interactions were validated in silico. We discussed the different signaling pathways, membrane modulation and cell cytoskeleton, by which MpNEP2 can act and induce responses in the plant that leads to necrosis.}, author = {do Carmo Santos, Maria Luíza and dos Santos Lopes, Natasha and Ferreira, Monaliza Macedo and Amaral, Geiseane Velozo and Santos, Ariana Silva and Dias, Cristiano Villela and Pirovani, Carlos Priminho and Alvim, Fátima Cerqueira}, @@ -3468,6 +5799,23 @@ @article{do_carmo_santos_proteomics_2023 year = {2023} } +@article{do_clinical_2025, + abstract = {Clinical metaproteomics reveals host-microbiome interactions underlying diseases. However, challenges to this approach exist. In particular, the characterization of microbial proteins present in low abundance relative to host proteins is difficult. Other significant challenges are attributed to using very large protein sequence databases, which impedes sensitivity and accuracy during peptide and protein identification from mass spectrometry data in addition to retrieving taxonomy and functional annotations and performing statistical analysis. To address these problems, we present an integrated bioinformatics workflow for mass spectrometry-based metaproteomics that combines custom protein sequence database generation, peptide-spectrum match generation and verification, quantification, taxonomic and functional annotations, and statistical analysis. This workflow also offers characterization of human proteins (while prioritizing microbial proteins), thus offering insights into host-microbe dynamics in disease. The tools and workflow are deployed in the Galaxy ecosystem, enabling the development, optimization, and dissemination of these computational resources. We have applied this workflow for metaproteomic analysis of numerous clinical sample types, such as nasopharyngeal swabs and bronchoalveolar lavage fluid. Here, we demonstrate its utility via the analysis of residual fluid from cervical swabs. The complete workflow and accompanying training resources are accessible on the Galaxy Training Network to equip non-experts and experienced researchers with the necessary knowledge and tools to analyze their data.}, + author = {Do, Katherine and Mehta, Subina and Wagner, Reid and Griffin, Timothy J. and Jagtap, Pratik D.}, + doi = {10.3791/67581}, + issn = {1940-087X}, + journal = {Journal of Visualized Experiments (JoVE)}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {January}, + number = {215}, + pages = {e67581}, + title = {A {Clinical} {Metaproteomics} {Workflow} {Implemented} within {Galaxy} {Bioinformatics} {Platform} to {Analyze} {Host}-{Microbiome} {Interactions} {Underlying} {Human} {Disease}}, + url = {https://app.jove.com/t/67581/a-clinical-metaproteomics-workflow-implemented-within-galaxy}, + urldate = {2025-02-16}, + year = {2025} +} + @article{donatova_changes_2024, abstract = {Influenza type A virus (IAV) infection is a major cause of morbidity and mortality during influenza epidemics. Recently, a specific link between IAV infection and neurodegenerative disease progression has been established. The non-structural NS1 protein of IAV regulates viral replication during infection and antagonizes host antiviral responses, contributing to influenza virulence. In the present study, we have prepared a mouse lung-to-lung adapted to the NS1-truncated virus (NS80ad). Transcriptome analysis of the gene expression in the lungs revealed that infection with wild-type A/WSN/33 (WSN), NS80, and NS80ad viruses resulted in different regulation of genes involved in signaling pathways associated with the cell proliferation, inflammatory response, and development of neurodegenerative diseases. NS1 protein did not influence the genes involved in the RIG-I-like receptor signaling pathway in the brains. Lethal infection with IAVs dysregulated expression of proteins associated with the development of neurodegenerative diseases (CX3CL1/Fractalkine, Coagulation factor III, and CD105/Endoglin, CD54/ICAM-1, insulin-like growth factor-binding protein (IGFBP)-2, IGFBP-5, IGFBP-6, chitinase 3-like 1 (CHI3L1), Myeloperoxidase (MPO), Osteopontin (OPN), cystatin C, and LDL R). Transcription of GATA3 mRNA was decreased, and expression of MPO was inhibited in the brain infected with NS80 and NS80ad viruses. In addition, the truncation of NS1 protein led to reduced expression of IGFBP-2, CHI3L1, MPO, and LDL-R proteins in the brains. Our results indicate that the influenza virus influences the expression of proteins involved in brain function, and this might occur mostly through the NS1 protein. These findings suggest that the abovementioned proteins represent a promising target for the development of potentially effective immunotherapy against neurodegeneration.}, author = {Donátová, Karin and Mladá, Miriam and Lopušná, Katarína and Baran, Filip and Betáková, Tatiana}, @@ -3475,7 +5823,7 @@ @article{donatova_changes_2024 doi = {10.3390/ijms25052460}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {{\textgreater}UseGalaxy.eu, NS1 protein, adaptation, brain, immune response, inflammation, influenza virus, neurodegeneration}, + keywords = {{\textgreater}UseGalaxy.eu, Influenza A virus, Influenza, Human, NS1 protein, Neurodegenerative Diseases, adaptation, brain, immune response, inflammation, influenza virus, neurodegeneration}, language = {en}, month = {January}, note = {Number: 5 @@ -3494,6 +5842,7 @@ @article{dorn_linc00261_2020 author = {Dorn, Agnes and Glaß, Markus and Neu, Carolin T. and Heydel, Beate and Hüttelmaier, Stefan and Gutschner, Tony and Haemmerle, Monika}, copyright = {http://creativecommons.org/licenses/by/3.0/}, doi = {10.3390/cancers12051227}, + issn = {2072-6694}, journal = {Cancers}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, CDH1, EMT, FOXA2, LINC00261, PDAC, TGFβ, lncRNA}, language = {en}, @@ -3509,19 +5858,6 @@ @article{dorn_linc00261_2020 year = {2020} } -@patent{dorone_floe1-mediated_2023, - assignee = {Carnegie Institution of Washington, Leland Stanford Junior University}, - author = {Dorone, Yanniv and Boeynaems, Steven and Gitler, Aaron D. and Rhee, Seung Yon}, - keywords = {{\textgreater}UseGalaxy.eu, domain, floe1, germination, plant, seeds}, - month = {December}, - nationality = {US}, - number = {US20230416772A1}, - title = {Floe1-mediated modulation of seed longevity and germination rates}, - url = {https://patents.google.com/patent/US20230416772A1/en}, - urldate = {2024-11-17}, - year = {2023} -} - @article{dorone_prion-like_2021, abstract = {Many organisms evolved strategies to survive desiccation. Plant seeds protect dehydrated embryos from various stressors and can lay dormant for millennia. Hydration is the key trigger to initiate germination, but the mechanism by which seeds sense water remains unresolved. We identified an uncharacterized Arabidopsis thaliana prion-like protein we named FLOE1, which phase separates upon hydration and allows the embryo to sense water stress. We demonstrate that biophysical states of FLOE1 condensates modulate its biological function in vivo in suppressing seed germination under unfavorable environments. We find intragenic, intraspecific, and interspecific natural variation in FLOE1 expression and phase separation and show that intragenic variation is associated with adaptive germination strategies in natural populations. This combination of molecular, organismal, and ecological studies uncovers FLOE1 as a tunable environmental sensor with direct implications for the design of drought-resistant crops, in the face of climate change.}, author = {Dorone, Yanniv and Boeynaems, Steven and Flores, Eduardo and Jin, Benjamin and Hateley, Shannon and Bossi, Flavia and Lazarus, Elena and Pennington, Janice G. and Michiels, Emiel and De Decker, Mathias and Vints, Katlijn and Baatsen, Pieter and Bassel, George W. and Otegui, Marisa S. and Holehouse, Alex S. and Exposito-Alonso, Moises and Sukenik, Shahar and Gitler, Aaron D. and Rhee, Seung Y.}, @@ -3560,6 +5896,52 @@ @article{dossmann_specific_2024 year = {2024} } +@article{doyle_multiple_2025, + abstract = {Migration is a widely observed phenomenon supported by morphological, physiological and behavioural traits that vary with season and sex in many species. Recently, the genetic components underpinning migration in the marmalade hoverfly (Diptera: Syrphidae) have been unpacked through detection of differentially expressed genes between migrant and non-migrant females. Males also migrate, but changing sex ratios during autumn migration, from around 50\% female in northern Europe to around 90\% in southern Europe, suggests males are poor long-distance fliers. To elucidate the mechanisms underpinning this sex difference, we performed morphological, physiological and transcriptomic characterization of actively migrating females and males. Both sexes show similar physiological adaptations including hyperphagia and starvation resistance, but females display higher tolerance to cold, have lower wing loading values and display a greater flight capacity. In addition, females modulate the expression of genes involved in immunity, hypoxia and longevity while suppressing hormonal pathways involved in maintaining reproductive diapause. These traits contribute to the success of female migrants and underlie the diminishing pool of males, influencing population dynamics across huge geographic areas and through the whole migratory and overwintering period.}, + author = {Doyle, Toby D. and Poole, Oliver M. and Barnes, Jaimie Christopher and Hawkes, Will Leo S. and Jimenez Guri, Eva and Wotton, Karl R.}, + doi = {10.1098/rsob.240235}, + journal = {Open Biology}, + keywords = {{\textgreater}UseGalaxy.eu, Episyrphus balteatus, Syrphidae, genetics of migration, insect migration, migratory hoverflies, sex bias}, + month = {February}, + note = {Publisher: Royal Society}, + number = {2}, + pages = {240235}, + title = {Multiple factors contribute to female dominance in migratory bioflows}, + url = {https://royalsocietypublishing.org/doi/10.1098/rsob.240235}, + urldate = {2025-02-16}, + volume = {15}, + year = {2025} +} + +@article{dubey_characterization_2022, + abstract = {\textit{Aeromonas media} is a Gram-negative bacterium ubiquitously found in aquatic environments. It is a foodborne pathogen associated with diarrhea in humans and skin ulceration in fish. In this study, we used whole genome sequencing to profile all antimicrobial resistance (AMR) and virulence genes found in \textit{A}. \textit{media} strain SD/21-15 isolated from marine sediments in Denmark. To gain a better understanding of virulence and AMR genes found in several \textit{A}. \textit{media} strains, we included 24 whole genomes retrieved from the public databanks whose isolates originate from different host species and environmental samples from Asia, Europe, and North America. We also compared the virulence genes of strain SD/21-15 with \textit{A}. \textit{hydrophila}, \textit{A}. \textit{veronii}, and \textit{A}. \textit{salmonicida} reference strains. We detected \textit{Msh} pili, tap IV pili, and lateral flagella genes responsible for expression of motility and adherence proteins in all isolates. We also found \textit{hylA}, \textit{hylIII}, and \textit{TSH} hemolysin genes in all isolates responsible for virulence in all isolates while the \textit{aerA} gene was not detected in all \textit{A}. \textit{media} isolates but was present in \textit{A}. \textit{hydrophila, A}. \textit{veronii}, and \textit{A}. \textit{salmonicida} reference strains. In addition, we detected \textit{LuxS} and \textit{mshA-Q} responsible for quorum sensing and biofilm formation as well as the ferric uptake regulator (\textit{Fur}), heme and siderophore genes responsible for iron acquisition in all \textit{A}. \textit{media} isolates. As for the secretory systems, we found all genes that form the T2SS in all isolates while only the \textit{vgrG1}, \textit{vrgG3}, \textit{hcp}, and \textit{ats} genes that form parts of the T6SS were detected in some isolates. Presence of \textit{bla} $_{\textrm{MOX-9}}$ and \textit{bla} $_{\textrm{OXA-427}}$ β-lactamases as well as \textit{crp} and \textit{mcr} genes in all isolates is suggestive that these genes were intrinsically encoded in the genomes of all \textit{A}. \textit{media} isolates. Finally, the presence of various transposases, integrases, recombinases, virulence, and AMR genes in the plasmids examined in this study is suggestive that \textit{A}. \textit{media} has the potential to transfer virulence and AMR genes to other bacteria. Overall, we anticipate these data will pave way for further studies on virulence mechanisms and the role of \textit{A}. \textit{media} in the spread of AMR genes.}, + author = {Dubey, Saurabh and Ager-Wick, Eirill and Peng, Bo and Evensen, Øystein and Sørum, Henning and Munang'andu, Hetron Mweemba}, + doi = {10.3389/fmicb.2022.1022639}, + issn = {1664-302X}, + journal = {Frontiers in microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {1022639}, + title = {Characterization of virulence and antimicrobial resistance genes of {Aeromonas} media strain {SD}/21-15 from marine sediments in comparison with other {Aeromonas} spp}, + url = {http://europepmc.org/abstract/MED/36532448}, + volume = {13}, + year = {2022} +} + +@misc{duffy_rapid_2025, + abstract = {Biodiversity and its associated genetic diversity are being lost at an unprecedented rate. Simultaneously, the distributions of flora, fauna, fungi, microbes and pathogens are rapidly changing. Novel ways to capture and record genetic diversity before it is lost, and to measure population shifts and pathogen distributions are urgently required. Here we report the rapid application of shotgun long-read environmental DNA (eDNA) analysis for non-invasive biodiversity, genetic diversity and pathogen assessments from air. We also compared air eDNA with water and soil eDNA. Coupling long-read sequencing with established cloud-based biodiversity pipelines enabled a two-day turnaround from airborne sample collection to completed analysis, by a single investigator. To determine the full utility of airborne eDNA, we also conducted a local bioinformatic analysis and deep short-read shotgun sequencing. From outdoor air eDNA alone, comprehensive genetic analysis was performed including population genetics (phylogenetic placement) of a charismatic mammal (bobcat, Lynx rufus), and a venomous spider (golden silk orb weaver, Trichonephila clavipes), and haplotyping humans (Homo sapiens), from natural complex community settings, such as sub-tropical forests and temperate locations. The rich datasets also enabled deeper analysis of specific species and genomic regions of interest, including viral variant calling, human variant analysis, and antimicrobial resistance gene surveillance from airborne DNA. Our results highlight the speed, versatility, and specificity of pan-biodiversity monitoring via non-invasive eDNA sampling using current benchtop/portable and cloud-based approaches. Furthermore, they reveal the future feasibility of scaling down (equipment and temporally) these approaches for near real-time analysis. Together these approaches can enable rapid lifeform and genetic diversity detection from air, water, and sediment samples for unbiased non-targeted information-rich genomics-empowered i) biodiversity monitoring, ii) population genetics, iii) pathogen and disease vector genomic surveillance, iv) allergen and narcotic surveillance, v) antimicrobial resistance surveillance and vi) bioprospecting.}, + author = {Duffy, David J. and McCauley, Mark and Nousias, Orestis and Stammnitz, Maximilian R. and Farrell, Jessica A. and Koda, Samantha A. and Summers, Victoria and Eastman, Catherine B. and Duffy, Fiona G. and Duffy, Isabelle J. and Whilde, Jenny}, + doi = {10.21203/rs.3.rs-5953812/v1}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {February}, + note = {ISSN: 2693-5015}, + publisher = {Research Square}, + title = {Rapid pan-biodiversity lifeform and genomic diversity detection from shotgun sequencing of air {eDNA}}, + url = {https://www.researchsquare.com/article/rs-5953812/v1}, + urldate = {2025-02-09}, + year = {2025} +} + @article{dugar_chromosomal_2022, author = {Dugar, Gaurav and Hofmann, Andreas and Heermann, Dieter W and Hamoen, Leendert W}, journal = {Nature Genetics}, @@ -3570,6 +5952,36 @@ @article{dugar_chromosomal_2022 year = {2022} } +@article{dumaidi_sero-molecular_2025, + abstract = {\<b\>Background:\</b\> Hepatitis B virus (HBV) infection remains a major global health challenge, especially among high-risk groups such as hemodialysis (HD) patients. \<b\>Aim:\</b\> This study investigated the prevalence of sero-molecular markers and the genetic diversity of HBV in 160 Palestinian HD patients. Blood samples were tested for HBV serological markers (HBsAg, anti-HBc, and anti-HBs) and screened using nested PCR. Whole genome sequencing was conducted on PCR-positive samples to identify HBV genotypes and subgenotypes. \<b\>Results:\</b\> The overall HBV prevalence among HD patients was 3.75\%, comprising 1.9\% with overt infection (HBsAg +ve) and 1.9\% with occult HBV infection (OBI). HCV was detected in 1.9\% of patients. Evidence of past exposure (anti-HBc positive) was observed in 20\% of patients, and 45\% showed serological immunity with anti-HBs levels ≥ 10 IU/mL. Although the values of the genetic diversity estimators such as K, S, \<i\>η\</i\>, and \<i\>π\</i\> were approximately as twice as those for the S-region, the S-region produced a more reasonable phylogenetic tree and haplotype networking but under the condition of accurate sequencing and adequate number of investigated sequences. Phylogenetic trees and haplotype networking of the WGS and S-region revealed a clustering pattern based on genotypes and subgenotypes with two Palestinian WGS clustering in Subgenotype D1, while the other two in Subgenotype D3. Genetic diversity analysis revealed high haplotype diversity (Hd) (0.98-1.00) with high h:n ratio (0.9-1.00) and low nucleotide diversity (\<i\>π\</i\>) (0.007-0.027) indicating slight variation between any two given sequences. This is explained by purifying selection, recent population expansion, or constrained evolution as neutrality test values such as Tajima's D were negative (-0.5 to -1.86). \<b\>Conclusion:\</b\> HBV infection remains prevalent among HD patients, including both overt and occult forms. Genotype \<i\>D\</i\>, specifically Subgenotypes D1 and D3, predominates in the study population. The HBV S-region is a sufficient surrogate for population genetics investigations.}, + author = {Dumaidi, Kamal and Al-Jawabreh, Amer and Zraiqi, Areej and Zaid, Jana and Ereqat, Suhair and Salami, Nabeel and Nasereddin, Abedelmajeed}, + doi = {10.1155/cjid/6981644}, + issn = {1712-9532}, + journal = {The Canadian journal of infectious diseases \& medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, + keywords = {{\textgreater}UseGalaxy.eu, Haplotype Networking, Occult Hepatitis B Virus Infection (Obi), Phylogenetic analysis, Whole Genome Sequence (Wgs), hepatitis B virus (HBV)}, + pages = {6981644}, + title = {Sero-{Molecular} {Markers} and {Genetic} {Diversity} of {Hepatitis} {B} {Virus} {Isolated} {From} {Hemodialysis} {Patients} {From} {Jenin} {District}, {West} {Bank}, {Palestine}}, + url = {https://europepmc.org/articles/PMC12473736}, + volume = {2025}, + year = {2025} +} + +@article{duong_ima_2021, + author = {Duong, Tuan Anh and Aylward, Janneke and Ametrano, Claudio Gennaro and Poudel, Barsha and Santana, Quentin Carlo and Wilken, Pieter Markus and Martin, Anke and Arun-Chinnappa, Kiruba Shankari and de Vos, Lieschen and DiStefano, Isabel and Grewe, Felix and Huhndorf, Sabine and Lumbsch, Helge Thorsten and Rakoma, Jostina Raesetsa and Poudel, Barsha and Steenkamp, Emma Theodora and Sun, Yukun and van der Nest, Magriet A and Wingfield, Michael John and Yilmaz, Neriman and Wingfield, Brenda Diana}, + doi = {10.1186/s43008-021-00077-9}, + issn = {2210-6340}, + journal = {IMA fungus}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {October}, + number = {1}, + pages = {30}, + title = {{IMA} {Genome} - {F15} : {Draft} genome assembly of {Fusarium} pilosicola, {Meredithiella} fracta, {Niebla} homalea, {Pyrenophora} teres hybrid {WAC10721}, and {Teratosphaeria} viscida}, + url = {http://europepmc.org/abstract/MED/34645521}, + volume = {12}, + year = {2021} +} + @article{duque-afonso_identification_2024, abstract = {Aberrant gene expression patterns in acute myeloid leukemia (AML) with balanced chromosomal translocations are often associated with dysregulation of epigenetic modifiers. The AML1/ETO (RUNX1/MTG8) fusion protein, caused by the translocation (8;21)(q22;q22), leads to the epigenetic repression of its target genes. We aimed in this work to identify critical epigenetic modifiers, on which AML1/ETO-positive AML cells depend on for proliferation and survival using shRNA library screens and global transcriptomics approaches. Using shRNA library screens, we identified 41 commonly depleted genes in two AML1/ETO-positive cell lines Kasumi-1 and SKNO-1. We validated, genetically and pharmacologically, DNMT1 and ATR using several AML1/ETO-positive and negative cell lines. We also demonstrated in vivo differentiation of myeloblasts after treatment with the DNMT1 inhibitor decitabine in a patient with an AML1/ETO-positive AML. Bioinformatic analysis of global transcriptomics after AML1/ETO induction in 9/14/18-U937 cells identified 973 differentially expressed genes (DEGs). Three genes (PARP2, PRKCD, and SMARCA4) were both downregulated after AML1/ETO induction, and identified in shRNA screens. In conclusion, using unbiased shRNA library screens and global transcriptomics, we have identified several driver epigenetic regulators for proliferation in AML1/ETO-positive AML. DNMT1 and ATR were validated and are susceptible to pharmacological inhibition by small molecules showing promising preclinical and clinical efficacy.}, author = {Duque-Afonso, Jesús and Veratti, Pia and Rehman, Usama-Ur and Herzog, Heike and Mitschke, Jan and Greve, Gabriele and Eble, Julian and Berberich, Bettina and Thomas, Johanna and Pantic, Milena and Waterhouse, Miguel and Gentile, Gaia and Heidenreich, Olaf and Miething, Cornelius and Lübbert, Michael}, @@ -3589,6 +6001,24 @@ @article{duque-afonso_identification_2024 year = {2024} } +@article{durrani_silico_2025, + abstract = {Plants contain a ubiquitous group of proteins called germin-like proteins that belong to the cupin superfamily. These proteins are known to be expressed in response to biotic and abiotic stress.}, + author = {Durrani, Irfan Safdar and Asim, Noreen and Jan, Asad and Nissa, Iffat U. and Shah, Syed Tanveer and Shah, Syed Jehangir and Basit, Abdul and Mohamed, Heba I.}, + doi = {10.1007/s11033-025-10936-y}, + issn = {1573-4978}, + journal = {Molecular Biology Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Abscisic acid stress, Drought stress, Expression analysis, Germin-like proteins}, + language = {en}, + month = {August}, + number = {1}, + pages = {840}, + title = {In silico expression analysis of germin-like protein genes from rice cultivar {Nipponbare}}, + url = {https://doi.org/10.1007/s11033-025-10936-y}, + urldate = {2025-09-03}, + volume = {52}, + year = {2025} +} + @article{dvir_uncovering_2021, author = {Dvir, Shlomi and Argoetti, Amir and Lesnik, Chen and Roytblat, Mark and Shriki, Kohava and Amit, Michal and Hashimshony, Tamar and Mandel-Gutfreund, Yael}, doi = {10.1016/j.celrep.2021.109198}, @@ -3603,6 +6033,35 @@ @article{dvir_uncovering_2021 year = {2021} } +@article{dwiyanti_whole_2025, + abstract = {The Neolamarckia cadamba (Roxb.) Bosser, commonly known as white jabon, and Neolamarckia macrophylla (Roxb.) Bosser, referred to as red jabon, are fast-growing tree species native to Indonesia, belonging to the Rubiaceae family. In recent years, these trees have drawn significant attention for their versatile applications in industrial plantations, community forests, and projects focused on forest and land rehabilitation (Kallio et al., 2011;Irawan and Purwanto, 2014;Sarjono et al., 2017). Both N. cadamba and N. macrophylla are used for various purposes, including the production of wood for the pulp industry, plywood manufacturing, and construction and carpentry materials (Soerianegara and Lemmens, 1993;Kartawinata, 1994;Lempang, 2014). Additionally, N. cadamba is recognized for its potential medicinal benefits, including pain relief, anti-inflammatory properties, antipyretic effects (Mondal et al., 2009), as well as antimicrobial (Acharyya et al., 2011), and antibacterial (Mishra and Siddique, 2011) activities.The cultivation of N. cadamba and N. macrophylla is still hindered by the lack of access to superior seeds from breeding programs. Most seeds used for various planting initiatives are sourced from natural forests or plantation forests that are classified as Identified Seed Stands (TBT), where no tree breeding activities have been conducted (UPT Perbenihan Tanaman Hutan Jawa Timur, 2022). As a result, these stands often exhibit high growth variability, along with low productivity and poor wood quality. To address these issues, prioritizing the development of fast-growing native species should be a focus for tree breeding and silviculture research. This approach can help create superior native forest plant species that could potentially reduce the dominance of exotic species in virtually all industrial plantation forests across Indonesia. However, there is still limited genetic information available for N. cadamba and N. macrophylla from Indonesia, particularly concerning genome sequencing and microsatellite markers, also known as Simple Sequence Repeats (SSRs). This lack of data poses challenges for developing effective cultivation strategies, as these data are needed for genetic research and breeding.Chloroplast genomes are valuable for phylogenetic analysis because they are predominantly maternally inherited, possess a conserved gene structure and content, and exhibit a low mutation frequency (Palmer et al., 1988). Moreover, chloroplast genomes provide essential data for population genetics, molecular identification, and genetic engineering (Powell et al., 1995;Daniell et al., 2016;Cao et al., 2022). On the other hand, microsatellite markers play crucial role in cultivar identification, assessing genetic diversity, genome mapping, quantitative trait loci (QTL) analysis, paternity analysis, crossspecies transferability, segregation analysis, phylogenetic relationships, and identification of wild cross hybrids in plant species (Miah et al., 2013;Ahmad et al., 2018).To date, several studies have focused on whole-genome sequencing of two species. One study characterized the complete genome of Neolamarckia macrophylla from South Sulawesi, Indonesia, using the Illumina HiSeq Nova platform and examined its phylogenetic relationship with N. cadamba and other species (Shi et al., 2020). Another study characterized the complete chloroplast genome of Neolamarckia cadamba from Guangdong province of China using Illumina pair-end sequencing (Li et al., 2018). However, both studies lack the development of microsatellite markers. This gap highlights the critical need to investigate the genomes and microsatellites of N. cadamba and N. macrophylla from Indonesia, as these populations may harbor unique genetic characteristics. In this study, whole genome sequencing data from N. cadamba and N. macrophylla were used to complete the chloroplast genome and screen microsatellite (or Simple Sequence Repeats, SSRs) markers for future molecular studies.The plant material used in this study consisted of silica-gel dried leaf samples collected from the adult tree of Neolamarckia cadamba (white jabon) planted in Kediri Forest Management Unit (KPH), Kediri Regency, East Java Province, Indonesia (-7\&\#176;55\&\#39;38,61163\" S, 112\&\#176;11\&\#39;46,13546 E) and the adult tree of Neolamarckia macrophylla (red jabon) planted in Special Purpose Forest Area (KHDTK) Parung Panjang, Bogor Regency, West Java Province, Indonesia (-6\&\#176;23\&\#39;9,54262\" S, 106\&\#176;31\&\#39;23,97738\" E). The Neolamarckia cadamba tree used in this study originated from Nusakambangan Island, Indonesia (Sample code: AI NJ18), while the Neolamarckia macrophylla tree was sourced from Laeya District, South Konawe Regency, Southeast Sulawesi Province, Indonesia (Sample code: S016-1 Prov1 Blok3).The silica-gel dried leaf samples from the two species underwent genomic DNA extraction using the Cetyltrimethylammonium bromide (CTAB) method (Doyle and Doyle, 1990). Initial quantification and purity of the genomic DNA were observed using Nanodrop 2000 (Thermo Scientific) and visualized through agarose gel electrophoresis. Qubit dsDNA BR Assay Kits (Thermo Scientific) were used for accurate DNA quantification. The genomic DNA of N. cadamba (concentration of 120 ng/μL and amount of 2,23 μg) and N. macrophylla (concentration of 7,96 ng/μL and amount of 0,398 μg) that passed the quality check were then subjected to library preparation and whole genome sequencing utilizing the Illumina NextSeq 500 System, producing a data output of 6 GB per sample.Sequencing data were uploaded to the Galaxy web platform, specifically the public server at usegalaxy.org version 23.1.2.dev0 (https://usegalaxy.eu/) for analysis (Afgan et al., 2016). The quality of raw reads was assessed using FASTQC version 0.12.1 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) (Andrews, 2010), and clean reads were filtered with Fastp version 0.23.2 (https://github.com/OpenGene/fastp) (Chen et al., 2018) using the default parameters. Clean reads were assembled using SPAdes version 3.15.3 (Bankevich et al., 2012) and NOVOPlasty version 4.3.1 (Dierckxsens et al., 2017), both with default parameters. The assembly results were then annotated using GeSeq (https://chlorobox.mpimp-golm.mpg.de/geseq.html) (Tillich et al., 2017). The fully annotated genome was illustrated using OrganellarGenomeDRAW v1.3.1 (Greiner et al., 2019).Microsatellite (SSR) markers were extracted using Krait: Microsatellites Investigation and Primer Design version v1.5.1 (Du et al., 2018) from the scaffolds of N. cadamba and N. macrophylla. The minimum repetition rates were set as follows: six for motifs with two bases and five for motifs with three, four, five, and six bases. A minimum gap of 100 bases was maintained between different microsatellite motifs. Sequences containing these microsatellite motifs were selected based on two criteria: (i) the flanking regions must be at least 150 base pairs (bp) in length on both sides and (ii) the microsatellite repeats should have the longest repeat motif. The microsatellite markers were then designed using Krait: Microsatellites Investigation and Primer Design, version 1.5.1 (Du et al., 2018), with default parameters.The chloroplast genome of N. cadamba exhibited a typical quadripartite structure (Figure 1) with a total length of 154,973 bp. This genome comprises small single copy (SSC: 17,845 bp) and large single copy (LSC: 85,861 bp) regions, separated by a pair of inverted repeat regions: inverted repeat A (IRA: 25.633 bp) and inverted repeat B (IRB: 25,634 bp) (Figure 1). The N. cadamba chloroplast genome contained 126 genes in total, including 84 protein-coding genes (78 of which are unique), 36 transfer RNA (tRNA) genes (29 unique), and 8 ribosomal RNA (rRNA) genes, comprising 4 unique rRNA sequences (Supplementary Table 1). The GC content of the N. cadamba sequence is 37.6\% (LSC: 35.4\%; SSC: 31.6\%; IR: 43.2\%). These findings are consistent with previous results reported by Li et al. (2018), that the size of the chloroplast genome of N. cadamba was 154,999 bp, harbouring an SSC of 17,851 bp, LSC of 85,880 bp, and a pair of inverted repeats (IRs) of 25,634 bp. Li et al. (2018) also reported the presence of 130 genes, where 96 were unique and 17 were duplicated in the IRs. The coding regions comprised 79 protein genes, 30 tRNA genes, and 4 rRNA genes, and the overall GC content of the chloroplast genome was 37.6\%.Similarly, the chloroplast genome of N. macrophylla also displays a quadripartite structure (Figure 1) with a length of 155,498 bp. This genome includes small single copy (SSC: 18,100 bp) and large single copy (LSC: 88,847 bp) regions, similarly separated by inverted repeat regions: IRA (24,275 bp) and IRB (24,276 bp) (Figure 2). The N. macrophylla chloroplast genome consisted of 126 genes, encompassing 84 protein-coding sequences with 29 unique sequences, 36 transfer RNA (tRNA) genes (29 unique), and 8 ribosomal RNA (rRNA) genes comprising 4 unique rRNA sequences (Supplementary Table 1). The GC content of the N. macrophylla sequence is 37.5\% (LSC: 35.6\%; SSC: 31.6\%; IR: 43.4\%). These findings align with the study by Shi et al. (2020), which revealed that the complete chloroplast genome of N. macrophylla is 155,406 bp and includes an SSC of 18,063 bp, an LSC of 86,013 bp, and a pair of IR regions of 25,665 bp each. Shi et al. (2020) also identified 128 genes, including 8 rRNA, 36 tRNA, and 84 protein-coding genes, and reported that the overall GC content of the chloroplast genome was 37.56\%.The analysis of microsatellites (SSRs) in N. macrophylla and N. cadamba (Table 1) revealed that N. macrophylla contained a greater number of SSRs, totaling 157,972, compared to 112,439 for N. cadamba. Additionally, the number of sequences containing SSRs was also greater in N. macrophylla, with 50,133 sequences compared to 34,884 in N. cadamba. Furthermore, candidate microsatellite markers were selected based on the richness of T/C content, consisting of 20 markers for N. cadamba (Supplementary Table 2) and 20 markers for N. macrophylla (Supplementary Table 3). The selected microsatellite marker candidates for each species will play a crucial role in future comprehensive analyses aimed at unraveling the genetic diversity of each species. This investigation will enhance the understanding of their unique genetic structures and evolutionary relationships, thereby providing invaluable support for advanced breeding programs.}, + author = {Dwiyanti, Fifi Gus and Kamal, Irsyad and Pratama, Rahadian and Syaputra, Dhika and Rustam, Evayusvita and Damayanti, Ratna Uli and Siregar, Iskandar Z. and Sudrajat, Dede J.}, + doi = {10.3389/fpls.2025.1608577}, + issn = {1664-462X}, + journal = {Frontiers in Plant Science}, + keywords = {{\textgreater}UseGalaxy.eu, Genome, Illumina, Neolamarckia, chloroplast, microsatellite, plant breeding}, + language = {English}, + month = {May}, + note = {Publisher: Frontiers}, + shorttitle = {Whole {Genome} {Sequencing} of {Neolamarckia} macrophylla ({Roxb}.) {Bosser} and {Neolamarckia} cadamba ({Roxb}.) {Bosser} from {Indonesia}}, + title = {Whole {Genome} {Sequencing} of {Neolamarckia} macrophylla ({Roxb}.) {Bosser} and {Neolamarckia} cadamba ({Roxb}.) {Bosser} from {Indonesia}: {A} vital resource for completing chloroplast genomes and mining microsatellite markers}, + url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2025.1608577/full}, + urldate = {2025-05-30}, + volume = {16}, + year = {2025} +} + +@article{dziuba_hidden_2022, + abstract = {Magnetosomes are unique organelles synthesized by magnetotactic bacteria (MTB) for magnetic navigation. Their complex biosynthesis is controlled by large magnetosome gene clusters (MGC). Here, we report the discovery and comprehensive analysis of silent but functional MGCs in the non-magnetotactic phototrophic bacterium Rhodovastum atsumiense . Our findings suggest that these MGCs were acquired by horizontal gene transfer and inactivated through transcriptional silencing and antisense RNA regulation. At least several magnetosome genes from G2-11 retained functionality, as their products restore magnetosome biosynthesis in isogenic deletion mutants of the model MTB Magnetospirillum gryphiswaldense . Although G2-11 was found to form magnetosomes upon the laboratory transfer of the MGCs from M. gryphiswaldense , strong negative selection led to rapid loss of this trait upon subcultivation. Our results provide the first insight into the horizontal dissemination of gene clusters encoding bacterial magnetic organelles outside MTB and illuminate the potential mechanisms of their genomic preservation in a latent state.}, + author = {Dziuba, M.V. and Paulus, A and Schramm, L and Awal, R.P. and Pósfai, M and Monteil, C.L. and Fouteau, S and Uebe, R and Schüler, D}, + doi = {10.1101/2022.04.19.488322}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Hidden {Talents}: {Silent} {Gene} {Clusters} {Encoding} {Magnetic} {Organelle} {Biosynthesis} in a {Non}-{Magnetotactic} {Phototrophic} {Bacterium}}, + url = {http://europepmc.org/abstract/PPR/PPR483515}, + year = {2022} +} + @article{dziuba_silent_2023, abstract = {Horizontal gene transfer is a powerful source of innovations in prokaryotes that can affect almost any cellular system, including microbial organelles. The formation of magnetosomes, one of the most sophisticated microbial mineral-containing organelles synthesized by magnetotactic bacteria for magnetic navigation in the environment, was also shown to be a horizontally transferrable trait. However, the mechanisms determining the fate of such genes in new hosts are not well understood, since non-adaptive gene acquisitions are typically rapidly lost and become unavailable for observation. This likely explains why gene clusters encoding magnetosome biosynthesis have never been observed in non-magnetotactic bacteria. Here, we report the first discovery of a horizontally inherited dormant gene clusters encoding biosynthesis of magnetosomes in a non-magnetotactic phototrophic bacterium Rhodovastum atsumiense. We show that these clusters were inactivated through transcriptional silencing and antisense RNA regulation, but retain functionality, as several genes were able to complement the orthologous deletions in a remotely related magnetotactic bacterium. The laboratory transfer of foreign magnetosome genes to R. atsumiense was found to endow the strain with magnetosome biosynthesis, but strong negative selection led to rapid loss of this trait upon subcultivation, highlighting the trait instability in this organism. Our results provide insight into the horizontal dissemination of gene clusters encoding complex prokaryotic organelles and illuminate the potential mechanisms of their genomic preservation in a dormant state.}, author = {Dziuba, M. V. and Paulus, A. and Schramm, L. and Awal, R. P. and Pósfai, M. and Monteil, C. L. and Fouteau, S. and Uebe, R. and Schüler, D.}, @@ -3610,7 +6069,7 @@ @article{dziuba_silent_2023 doi = {10.1038/s41396-022-01348-y}, issn = {1751-7370}, journal = {The ISME Journal}, - keywords = {{\textgreater}UseGalaxy.eu, Bacterial evolution, Bacterial genetics, Microbial ecology}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial evolution, Bacterial genetics, Magnetosomes, Magnetospirillum, Microbial ecology}, language = {en}, month = {March}, note = {Number: 3 @@ -3631,7 +6090,7 @@ @article{edet_genomic_2024 doi = {10.1038/s41598-024-61062-x}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Computational biology and bioinformatics, Genetics, Molecular biology, Plant sciences}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Computational biology and bioinformatics, Gene Expression Regulation, Plant, Genetics, Molecular biology, Mutation, Plant Leaves, Plant sciences, Vigna}, language = {en}, month = {May}, note = {Publisher: Nature Publishing Group}, @@ -3696,6 +6155,21 @@ @article{ehle_downregulation_2024 year = {2024} } +@article{eiber_lack_2020, + abstract = {Desmin, the major intermediate filament (IF) protein in muscle cells, interlinks neighboring myofibrils and connects the whole myofibrillar apparatus to myonuclei, mitochondria, and the sarcolemma. However, desmin is also known to be enriched at postsynaptic membranes of neuromuscular junctions (NMJs). The pivotal role of the desmin IF cytoskeletal network is underscored by the fact that over 120 mutations of the human \textit{DES} gene cause hereditary and sporadic myopathies and cardiomyopathies. A subgroup of human desminopathies comprises autosomal recessive cases resulting in the complete abolition of desmin protein. In these patients, who display a more severe phenotype than the autosomal dominant cases, it has been reported that some individuals also suffer from a myasthenic syndrome in addition to the classical occurrence of myopathy and cardiomyopathy. Since further studies on the NMJ pathology are hampered by the lack of available human striated muscle biopsy specimens, we exploited homozygous desmin knock-out mice which closely mirror the striated muscle pathology of human patients lacking desmin protein. Here, we report on the impact of the lack of desmin on the structure and function of NMJs and the transcription of genes coding for postsynaptic proteins. Desmin knock-out mice display a fragmentation of NMJs in soleus, but not in the extensor digitorum longus muscle. Moreover, soleus muscle fibers show larger NMJs. Further, transcription levels of acetylcholine receptor (AChR) genes are increased in muscles from desmin knock-out mice, especially of the AChRγ subunit, which is known as a marker of muscle fiber regeneration. Electrophysiological recordings depicted a pathological decrement of nerve-dependent endplate potentials and an increased rise time of the nerve-independent miniature endplate potentials. The latter appears related to the fragmentation of NMJs in desmin knockout mice. Our study highlights the essential role of desmin for the structural and functional integrity of mammalian NMJs.}, + author = {Eiber, Nane and Fröb, Franziska and Schowalter, Mirjam and Thiel, Christian and Clemen, Christoph S and Schröder, Rolf and Hashemolhosseini, Said}, + doi = {10.3389/fnmol.2020.567084}, + issn = {1662-5099}, + journal = {Frontiers in molecular neuroscience}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {567084}, + title = {Lack of {Desmin} in {Mice} {Causes} {Structural} and {Functional} {Disorders} of {Neuromuscular} {Junctions}}, + url = {http://europepmc.org/abstract/MED/33192292}, + volume = {13}, + year = {2020} +} + @article{eisenhardt_genotyping_2022, abstract = {Background: Synovial sarcoma (SS) is a malignant soft tissue tumor of mesenchymal origin that frequently occurs in young adults. Translocation of the SYT gene on chromosome 18 to the SSX genes on chromosome X leads to the formation of oncogenic fusion genes, which lead to initiation and proliferation of tumor cells. The detection and quantification of circulating tumor DNA (ctDNA) can serve as a non-invasive method for diagnostics of local or distant tumor recurrence, which could improve survival rates due to early detection. Methods: We developed a subtype-specific targeted next-generation sequencing (NGS) approach specifically targeting SS t(X;18)(p11;q11), which fuses SS18 (SYT) in chromosome 18 to SSX1 or SSX2 in chromosome x, and recurrent point mutations. In addition, patient-specific panels were designed from tumor exome sequencing. Both approaches were used to quantify ctDNA in patients’ plasma. Results: The subtype-specific assay allowed detection of somatic mutations from 25/25 tumors with a mean of 1.68 targetable mutations. The minimal limit of detection was determined at a variant allele frequency of 0.05\%. Analysis of 29 plasma samples from 15 tumor patients identified breakpoint ctDNA in 6 patients (sensitivity: 40\%, specificity 100\%). The addition of more mutations further increased assay sensitivity. Quantification of ctDNA in plasma samples (n = 11) from one patient collected over 3 years, with a patient-specific panel based on tumor exome sequencing, correlated with the clinical course, response to treatment and tumor volume. Conclusions: Targeted NGS allows for highly sensitive tumor profiling and non-invasive detection of ctDNA in SS patients, enabling non-invasive monitoring of tumor dynamics.}, author = {Eisenhardt, Anja E. and Brugger, Zacharias and Lausch, Ute and Kiefer, Jurij and Zeller, Johannes and Runkel, Alexander and Schmid, Adrian and Bronsert, Peter and Wehrle, Julius and Leithner, Andreas and Liegl-Atzwanger, Bernadette and Giunta, Riccardo E. and Eisenhardt, Steffen U. and Braig, David}, @@ -3733,12 +6207,28 @@ @article{el-sawalhi_epidemiological_2023 year = {2023} } +@article{elnouty_assessing_2025, + abstract = {Natural Killer (NK) cells are vital components of the innate immune system, playing a crucial role in defending the body against tumors and virally infected cells. While various methods exist for their isolation, the profound impact of these techniques on NK cell biology remains poorly characterized.This study presents a comprehensive analysis of the transcriptomic profiles of NK cells isolated using different positive selection methods; anti-CD56, anti-CD7 (with two distinct lineage depletion protocols), and a combination of anti-CD16 and anti-CD56 antibodies, compared to negative selection using immunomagnetic beads. Our integrated analysis of RNA-Seq datasets revealed that the isolation method is a dominant source of transcriptomic variation, accounting for 68.6 \% of the total dataset variance, with technical factors being inextricably confounded with this biological signal. We identified extensive method-specific transcriptional signatures, with minimal overlap ({\textless}0.1 \%) in differentially expressed genes (DEGs) across techniques. Functional enrichment analysis demonstrated that these signatures correspond to starkly different functional states: anti-CD16/anti-CD56 selection enriched for a highly activated, cytotoxically competent NK cell population with upregulated pathways in cytotoxicity and immune surveillance, while one anti-CD7-based method captured NK cells in a suppressed state, showing significant downregulation of lymphocyte activation and cytotoxicity pathways. Marker expression analysis further revealed extreme inter-study heterogeneity, with fold-changes in key cytotoxic genes exceeding 70,000-fold between methods. These findings highlight that the choice of isolation technique is not neutral but fundamentally determines the transcriptional and functional identity of the studied NK cell population. Our results highlight the critical importance of methodological standardization in NK cell research and provide essential guidance for selecting isolation strategies tailored to specific research or therapeutic applications.}, + author = {ElNouty, Rana and Moustafa, Ahmed and Mostafa, Maha and Ouf, Amged and Abou-Aisha, Khaled and Rady, Mona}, + doi = {10.1016/j.trim.2025.102298}, + issn = {0966-3274}, + journal = {Transplant Immunology}, + keywords = {{\textgreater}UseGalaxy.eu, Batch effects, Cellular activation, Gene expression, NK cell isolation, Natural killer cells, Negative selection, Positive selection, RNA-Seq analysis, Transcriptomic profiling}, + month = {December}, + pages = {102298}, + title = {Assessing the influence of isolation techniques on {NK} cell transcriptomic profiles}, + url = {https://www.sciencedirect.com/science/article/pii/S0966327425001261}, + urldate = {2025-10-03}, + volume = {93}, + year = {2025} +} + @article{emperle_mutations_2019, abstract = {Abstract. Somatic DNMT3A mutations at R882 are frequently observed in AML patients including the very abundant R882H, but also R882C, R882P and R882S. Using de}, author = {Emperle, Max and Adam, Sabrina and Kunert, Stefan and Dukatz, Michael and Baude, Annika and Plass, Christoph and Rathert, Philipp and Bashtrykov, Pavel and Jeltsch, Albert}, doi = {10.1093/nar/gkz911}, journal = {Nucleic Acids Research}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Missense, Mutation}, language = {en}, month = {October}, title = {Mutations of {R882} change flanking sequence preferences of the {DNA} methyltransferase {DNMT3A} and cellular methylation patterns}, @@ -3747,29 +6237,12 @@ @article{emperle_mutations_2019 year = {2019} } -@article{emser_mitochondrial_2023, - abstract = {{\textless}p{\textgreater}Heterothermic thermoregulation requires intricate regulation of metabolic rate and activation of pro-survival factors. Eliciting these responses and coordinating the necessary energy shifts likely involves retrograde signalling by mitochondrial-derived peptides (MDPs). Members of the group were suggested before to play a role in heterothermic physiology, a key component of hibernation and daily torpor. Here we studied the mitochondrial single-nucleotide polymorphism (SNP) m.3017C\>T that resides in the evolutionarily conserved gene {\textless}italic{\textgreater}MT-SHLP6.{\textless}/italic{\textgreater} The substitution occurring in several mammalian orders causes truncation of SHLP6 peptide size from twenty to nine amino acids. Public mass spectrometric (MS) data of human SHLP6 indicated a canonical size of 20 amino acids, but not the use of alternative translation initiation codons that would expand the peptide. The shorter isoform of SHLP6 was found in heterothermic rodents at higher frequency compared to homeothermic rodents ({\textless}italic{\textgreater}p{\textless}/italic{\textgreater} \< 0.001). In heterothermic mammals it was associated with lower minimal body temperature ({\textless}italic{\textgreater}T{\textless}/italic{\textgreater}$_{\textrm{{\textless}italic{\textgreater}b{\textless}/italic{\textgreater}}}$, {\textless}italic{\textgreater}p{\textless}/italic{\textgreater} \< 0.001). In the thirteen-lined ground squirrel, brown adipose tissue—a key organ required for hibernation, showed dynamic changes of the steady-state transcript level of {\textless}italic{\textgreater}mt-Shlp6{\textless}/italic{\textgreater}. The level was significantly higher before hibernation and during interbout arousal and lower during torpor and after hibernation. Our finding argues to further explore the mode of action of SHLP6 size isoforms with respect to mammalian thermoregulation and possibly mitochondrial retrograde signalling.{\textless}/p{\textgreater}}, - author = {Emser, Sarah V. and Spielvogel, Clemens P. and Millesi, Eva and Steinborn, Ralf}, - doi = {10.3389/fphys.2023.1207620}, - issn = {1664-042X}, - journal = {Frontiers in Physiology}, - keywords = {{\textgreater}UseGalaxy.eu, Hibernation, MicroProteins, Mitochondrial-derived peptides, SORF, genetics mitogenomics}, - language = {English}, - month = {August}, - note = {Publisher: Frontiers}, - title = {Mitochondrial polymorphism m.{3017C}\>{T} of {SHLP6} relates to heterothermy}, - url = {https://www.frontiersin.org/journals/physiology/articles/10.3389/fphys.2023.1207620/full}, - urldate = {2024-11-17}, - volume = {14}, - year = {2023} -} - @article{emser_mitochondrial_2023, abstract = {Heterothermic thermoregulation requires intricate regulation of metabolic rate and activation of pro-survival factors. Eliciting these responses and coordinating the necessary energy shifts likely involves retrograde signalling by mitochondrial-derived peptides (MDPs). Members of the group were suggested before to play a role in heterothermic physiology, a key component of hibernation and daily torpor. Here we studied the mitochondrial single-nucleotide polymorphism (SNP) m.3017C{\textgreater}T that resides in the evolutionarily conserved gene MT-SHLP6. The substitution occurring in several mammalian orders causes truncation of SHLP6 peptide size from twenty to nine amino acids. Public mass spectrometric (MS) data of human SHLP6 indicated a canonical size of 20 amino acids, but not the use of alternative translation initiation codons that would expand the peptide. The shorter isoform of SHLP6 was found in heterothermic rodents at higher frequency compared to homeothermic rodents (p {\textless} 0.001). In heterothermic mammals it was associated with lower minimal body temperature (Tb, p {\textless} 0.001). In the thirteen-lined ground squirrel, brown adipose tissue—a key organ required for hibernation, showed dynamic changes of the steady-state transcript level of mt-Shlp6. The level was significantly higher before hibernation and during interbout arousal and lower during torpor and after hibernation. Our finding argues to further explore the mode of action of SHLP6 size isoforms with respect to mammalian thermoregulation and possibly mitochondrial retrograde signalling.}, author = {Emser, Sarah V. and Spielvogel, Clemens P. and Millesi, Eva and Steinborn, Ralf}, issn = {1664-042X}, journal = {Frontiers in Physiology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Hibernation, MicroProteins, Mitochondrial-derived peptides, SORF, genetics mitogenomics}, title = {Mitochondrial polymorphism m.{3017C}{\textgreater}{T} of {SHLP6} relates to heterothermy}, url = {https://www.frontiersin.org/articles/10.3389/fphys.2023.1207620}, urldate = {2023-08-30}, @@ -3777,13 +6250,24 @@ @article{emser_mitochondrial_2023 year = {2023} } +@article{epihov_contrasting_2024, + abstract = {{\textless}title{\textgreater}Abstract{\textless}/title{\textgreater} {\textless}p{\textgreater}The global iron (Fe) cycle governs important aspects of biosphere function by defining Fe availability thus supporting productivity of terrestrial and ocean ecosystems. However, the link between soil microbiome function to global patterns in terrestrial iron cycling remains poorly investigated. Here, we developed a novel database termed {\textless}italic{\textgreater}IR{\textless}/italic{\textgreater}on {\textless}italic{\textgreater}cyc{\textless}/italic{\textgreater}le {\textless}italic{\textgreater}A{\textless}/italic{\textgreater}nnotation (IRcyc-A) targeted at discovering and annotating Fe cycle genes within omics data that we validated against known localized patterns of iron cycling. We leveraged this new tool to analyse the Fe cycle of over 220 publicly available soil metagenomes and metatranscriptomes encompassing a wide range of biomes on Earth. We show that the greatest abundance of Fe(III)-reduction and Fe(II)-oxidation genes were attributed to Acidobacteriota and were most abundant in the microbiomes of peatlands and iron sulfide soils, respectively. This is consistent with the high levels of dissolved Fe recorded in rivers draining such areas. In contrast, genes encoding the biosynthesis of siderophores deployed in iron sequestration in response to Fe deficiency peaked in agroecosystems with the majority assigned to Actinomycetota. Siderophore synthesis genes were negatively correlated with Fe(III)-reduction and Fe(II)-oxidation genes, supporting the view of divergent communities under low and high iron availability. Our findings highlight how iron availability shapes terrestrial microbial communities and how microbial processes can in turn contribute to global patterns in terrestrial Fe and C cycling.{\textless}/p{\textgreater}}, + author = {Epihov, Dimitar and Bryce, Casey}, + doi = {10.21203/rs.3.rs-4248419/v1}, + journal = {Research Square}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Contrasting microbial communities drive iron cycling across global biomes}, + url = {http://europepmc.org/abstract/PPR/PPR843566}, + year = {2024} +} + @article{epihov_iron_2024, abstract = {Enhanced rock weathering (EW) is an emerging atmospheric carbon dioxide removal (CDR) strategy being scaled up by the commercial sector. Here, we combine multiomics analyses of belowground microbiomes, laboratory-based dissolution studies, and incubation investigations of soils from field EW trials to build the case for manipulating iron chelators in soil to increase EW efficiency and lower costs. Microbial siderophores are high-affinity, highly selective iron (Fe) chelators that enhance the uptake of Fe from soil minerals into cells. Applying RNA-seq metatranscriptomics and shotgun metagenomics to soils and basalt grains from EW field trials revealed that microbial communities on basalt grains significantly upregulate siderophore biosynthesis gene expression relative to microbiomes of the surrounding soil. Separate in vitro laboratory incubation studies showed that micromolar solutions of siderophores and high-affinity synthetic chelator (ethylenediamine-N,N′-bis-2-hydroxyphenylacetic acid, EDDHA) accelerate EW to increase CDR rates. Building on these findings, we develop a potential biotechnology pathway for accelerating EW using the synthetic Fe-chelator EDDHA that is commonly used in agronomy to alleviate the Fe deficiency in high pH soils. Incubation of EW field trial soils with potassium-EDDHA solutions increased potential CDR rates by up to 2.5-fold by promoting the abiotic dissolution of basalt and upregulating microbial siderophore production to further accelerate weathering reactions. Moreover, EDDHA may alleviate potential Fe limitation of crops due to rising soil pH with EW over time. Initial cost-benefit analysis suggests potassium-EDDHA could lower EW-CDR costs by up to U.S. \$77 t CO2 ha–1 to improve EW’s competitiveness relative to other CDR strategies.}, author = {Epihov, Dimitar Z. and Banwart, Steven A. and McGrath, Steve P. and Martin, David P. and Steeley, Isabella L. and Cobbold, Vicky and Kantola, Ilsa B. and Masters, Michael D. and DeLucia, Evan H. and Beerling, David J.}, doi = {10.1021/acs.est.3c10146}, issn = {0013-936X}, journal = {Environmental Science \& Technology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Carbon Dioxide, Soil}, month = {July}, note = {Publisher: American Chemical Society}, number = {27}, @@ -3822,6 +6306,7 @@ @article{ereqat_association_2022 issn = {2049-9434}, journal = {Biomedical Reports}, keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org}, + language = {eng}, month = {July}, note = {Publisher: Spandidos Publications}, number = {1}, @@ -3853,6 +6338,25 @@ @article{erkelenz_rbm3_2024 year = {2024} } +@article{erturkmen_microbiota_2025, + abstract = {Colostrum microbiota is diverse and rich in beneficial bacteria with potential probiotic properties. The current study investigates the buffalo colostrum from Turkey, assessing its cultivable microbial diversity and conducting a metagenomic analysis. The metagenomic analysis of Day 2 colostrum shows a diverse bacterial composition, dominated by Bacteroidota (49.75\%) and Firmicutes (44.934\%), followed by Proteobacteria (5.11\%) and Actinobacteriota (1.50\%). Bifidobacterium spp., Lactobacillus acidophilus, and Lactococcus spp. were counted above 7.00 log CFU/mL in culturable microbiota. Thirty-six lactic acid bacteria (LAB) strains were selected, with 14 strains showing positive bile salt hydrolase (BSH) activity with glycocholic acid (GCA) and taurocholic acid (TCA) and resistance to bile salts and acidic conditions (survival in pH 2 medium and 0.3\% (w/v) bile salt). These strains were identified with high scores ({\textgreater} 1.80 genus levels) by MALDI-TOF MS and exhibited cholesterol assimilation ranging from 49.21\% to 68.22\% and exopolysaccharide (EPS) production from 7.9 to 12.4 mg/L. L. acidophilus PB4, grouped as high cholesterol assimilation and EPS production capacity, was well-characterized for safety through whole-genome sequencing (WGS) analysis using the Illumina NovaSeq platform and assigned an average nucleotide identity (ANI) value of 99.1\%. The findings from this study could advance research on the potential of probiotic microorganisms and probiotic food products derived from them in lowering cholesterol risk.}, + author = {Ertürkmen, P.}, + copyright = {Copyright © 2025 P. Ertürkmen. Journal of Food Quality published by John Wiley \& Sons Ltd.}, + doi = {10.1155/jfq/4406517}, + issn = {1745-4557}, + journal = {Journal of Food Quality}, + keywords = {{\textgreater}UseGalaxy.eu, MALDI-TOF MS, cholesterol, colostrum microbiota, probiotic, whole-genome sequencing}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1155/jfq/4406517}, + number = {1}, + pages = {4406517}, + title = {Microbiota {Composition} of {Buffalo} {Colostrum} and {Characterization} of {Potential} {Probiotic} {Bacteria} {With} {High} {Exopolysaccharide} {Production} and {Cholesterol} {Assimilation} {Capacity}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1155/jfq/4406517}, + urldate = {2025-07-12}, + volume = {2025}, + year = {2025} +} + @article{esha_exploring_2023, abstract = {The present investigation utilized in silico methodologies to explore the diverse pharmacological activities, toxicity profiles, and chemical reactivity of a series of fluoro-flavonoid compounds (1–14), which are secondary metabolites of plants known for their broad range of biological effects. A comprehensive strategy is utilized, incorporating methods such as prediction of activity spectra for substances (PASS) prediction, absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessments, and density functional theory (B3LYP) calculations using three basis sets: 6-31G(d,p), 6-311G(d,p), and 6-311++G(d,p). Furthermore, the study employed molecular docking technique to identify target proteins, including HER2 (7JXH), EGFR (4UV7), FPPS (1YQ7), HPGDS (1V40), DCK (1P60), and KEAP1 on Nrf2 (1X2J), for the investigated compounds, with cianidanol and genistein serving as reference drugs for the docking process. The investigated fluoro-flavonoid compounds exhibited significantly greater binding affinities (ranging from −8.3 to −10.6 kcal mol−1) toward HER2, HPGDS, and KEAP1 compared to the reference drugs, cianidanol and genistein, which displayed binding affinities ranging from −8.4 to −9.4 kcal mol−1. Furthermore, molecular dynamics simulations were conducted to assess the stability of the protein-ligand interaction, using the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), Radius of gyration (Rg) parameters and principle component analysis (PCA). Among the tested fluoro-flavonoid analogs, analog 11 showed a RMSD value of .15 nm with the HER2 protein target, indicating a stable interaction. Based on in silico results, it appears that the fluoro-flavonoid compound 11 has the potential to serve as a targeted anti-lung cancer drug. However, additional in vivo and in vitro studies are necessary to confirm this hypothesis.}, author = {Esha, Nusrat Jahan Ikbal and Quayum, Syeda Tasnim and Saif, Minhaz Zabin and Almatarneh, Mansour H. and Rahman, Shofiur and Alodhayb, Abdullah and Poirier, Raymond A. and Uddin, Kabir M.}, @@ -3874,6 +6378,25 @@ @article{esha_exploring_2023 year = {2023} } +@article{espadinha_casecontrol_2025, + abstract = {Shiga toxin–producing Escherichia coli (STEC) infection can cause potentially fatal hemolytic uremic syndrome (HUS). To determine epidemiologic and bacterial genomic factors associated with HUS, we conducted a retrospective case–control study with 108 HUS cases and 416 unmatched controls (non-HUS) selected among STEC notifications in Ireland during 2017–2020. We combined routinely collected epidemiologic data on STEC notifications with genomewide association study findings and used logistic regression to estimate adjusted odds ratios. Our findings reaffirmed known risk factors, such as young age (0–9 years) and presence of specific stx genes or gene combinations (stx2a; stx1a + stx2a; stx1a + stx2c), and additionally suggest that having outbreak-associated infection, residence within the East region of Ireland, and the combined presence of both ygiW and group\_5720 or both pfkA and fieF genes are potentially associated with developing HUS. Our findings could improve early identification of high-risk STEC infections and help guide enhanced surveillance and public health management.}, + author = {Espadinha, Diana and Brady, Melissa and Brehony, Carina and Hamilton, Douglas and O’Connor, Lois and Cunney, Robert and Cotter, Suzanne and Carroll, Anne and Garvey, Patricia and McNamara, Eleanor}, + doi = {10.3201/eid3104.240060}, + issn = {1080-6040}, + journal = {Emerging Infectious Diseases}, + keywords = {{\textgreater}UseGalaxy.eu, Escherichia coli Infections, Hemolytic-Uremic Syndrome, Shiga-Toxigenic Escherichia coli}, + month = {April}, + number = {4}, + pages = {728--740}, + pmcid = {PMC11950266}, + pmid = {40133048}, + title = {Case–{Control} {Study} of {Factors} {Associated} with {Hemolytic} {Uremic} {Syndrome} among {Shiga} {Toxin}–{Producing} {Escherichia} coli {Patients}, {Ireland}, 2017–2020}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11950266/}, + urldate = {2025-04-13}, + volume = {31}, + year = {2025} +} + @article{espenshade_influence_2019, abstract = {The aerial surfaces of plants harbour diverse communities of microorganisms. The rising awareness concerning the potential roles of these phyllosphere microbiota for airborne pollutant remediation and plant growth promotion, advocates for a better understanding of their community structure and dynamics in urban ecosystems. Here, we characterised the epiphytic microbial communities on leaves of Platanus x hispanica trees in the city centre of Hasselt (Belgium), and the nearby forest area of Bokrijk, Genk (Belgium). We compared the influences of season, site, and air pollutants concentration variations on the tree’s phyllosphere microbiome by determining the intra- and inter-individual variation in leaf bacterial communities. High-throughput amplicon sequencing of the 16S rRNA gene revealed large variation in the bacterial community structure and diversity throughout the years but also allowed to discriminate an environment effect on community assembly. Partial drivers for this environment effect on composition can be correlated with the huge differences in ultrafine particulate matter (UFP) and black carbon on the leaves. A change in bacterial community composition was noted for trees growing in the city centre compared to the natural site, and also more human-associated genera were found colonising the leaves from the city centre. These integrated results offer an original and first insight in the Platanus phyllomicrobiota, which can offer new opportunities to use phyllosphere microorganisms to enhance air pollution degradation.}, author = {Espenshade, Jordan and Thijs, Sofie and Gawronski, Stanislaw and Bové, Hannelore and Weyens, Nele and Vangronsveld, Jaco}, @@ -3896,7 +6419,7 @@ @article{espindola-hernandez_genomic_2020 editor = {Mank, Judith}, issn = {1759-6653}, journal = {Genome Biology and Evolution}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Biological Evolution, Predatory Behavior, Selection, Genetic}, language = {en}, month = {October}, number = {10}, @@ -3909,11 +6432,16 @@ @article{espindola-hernandez_genomic_2020 } @article{estell_zc3h4_2021, + abstract = {The human genome encodes thousands of non-coding RNAs. Many of these terminate early and are then rapidly degraded, but how their transcription is restricted is poorly understood. In a screen for protein-coding gene transcriptional termination factors, we identified ZC3H4. Its depletion causes upregulation and extension of hundreds of unstable transcripts, particularly antisense RNAs and those transcribed from so-called super-enhancers. These loci are occupied by ZC3H4, suggesting that it directly functions in their transcription. Consistently, engineered tethering of ZC3H4 to reporter RNA promotes its degradation by the exosome. ZC3H4 is predominantly metazoan -interesting when considering its impact on enhancer RNAs that are less prominent in single-celled organisms. Finally, ZC3H4 loss causes a substantial reduction in cell proliferation, highlighting its overall importance. In summary, we identify ZC3H4 as playing an important role in restricting non-coding transcription in multicellular organisms.}, author = {Estell, Chris and Davidson, Lee and Steketee, Pieter C. and Monier, Adam and West, Steven}, doi = {10.7554/elife.67305}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {2050-084X}, + journal = {eLife}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Genetic, Transcription}, + language = {eng}, month = {April}, note = {Publisher: eLife Sciences Publications, Ltd}, + pages = {e67305}, title = {{ZC3H4} restricts non-coding transcription in human cells}, url = {https://doi.org/10.7554/elife.67305}, volume = {10}, @@ -3945,11 +6473,13 @@ @article{etherington_galaxy-based_2019 abstract = {AbstractBackground. It is not a trivial step to move from single-cell RNA-sequencing (scRNA-seq) data production to data analysis. There is a lack of intuitive}, author = {Etherington, Graham J. and Soranzo, Nicola and Mohammed, Suhaib and Haerty, Wilfried and Davey, Robert P. and Palma, Federica Di}, doi = {10.1093/gigascience/giz144}, + issn = {2047-217X}, journal = {GigaScience}, keywords = {+Education, +Galactic, +RefPublic, +Tools, {\textgreater}SingleCell, {\textgreater}UseGalaxy.eu}, language = {en}, month = {December}, number = {12}, + pages = {giz144}, title = {A {Galaxy}-based training resource for single-cell {RNA}-sequencing quality control and analyses}, url = {https://academic.oup.com/gigascience/article/8/12/giz144/5673460}, urldate = {2019-12-21}, @@ -3964,7 +6494,7 @@ @article{fabian-morales_identification_2024 doi = {10.1002/mgg3.70019}, issn = {2324-9269}, journal = {Molecular Genetics \& Genomic Medicine}, - keywords = {{\textgreater}UseGalaxy.eu, copy number variation, deletion, exome sequencing, retinal dystrophy}, + keywords = {{\textgreater}UseGalaxy.eu, DNA Copy Number Variations, Exome Sequencing, Retinal Dystrophies, copy number variation, deletion, exome sequencing, retinal dystrophy}, language = {en}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/mgg3.70019}, number = {10}, @@ -3977,12 +6507,17 @@ @article{fabian-morales_identification_2024 } @article{faddetta_endophytic_2021, + abstract = {Citrus limon (L.) Burm. F. is an important evergreen fruit crop whose rhizosphere and phyllosphere microbiota  have been characterized, while seed microbiota is still unknown. Bacterial and fungal endophytes were isolated from C. limon surface-sterilized seeds. The isolated fungi-belonging to Aspergillus, Quambalaria and Bjerkandera genera-and bacteria-belonging to Staphylococcus genus-were characterized for indoleacetic acid production and phosphate solubilization. Next Generation Sequencing based approaches were then used to characterize the endophytic bacterial and fungal microbiota structures of surface-sterilized C. limon seeds and of shoots obtained under aseptic conditions from in vitro growing seedlings regenerated from surface-sterilized seeds. This analysis highlighted that Cutibacterium and Acinetobacter were the most abundant bacterial genera in both seeds and shoots, while Cladosporium and Debaryomyces were the most abundant fungal genera in seeds and shoots, respectively. The localization of bacterial endophytes in seed and shoot tissues was revealed by Fluorescence In Situ Hybridization coupled with Confocal Laser Scanning Microscopy revealing vascular bundle colonization. Thus, these results highlighted for the first time the structures of endophytic microbiota of C. limon seeds and the transmission to shoots, corroborating the idea of a vertical transmission of plant microbiota and suggesting its crucial role in seed germination and plant development.}, author = {Faddetta, Teresa and Abbate, Loredana and Alibrandi, Pasquale and Arancio, Walter and Siino, Davide and Strati, Francesco and Filippo, Carlotta De and Bosco, Sergio Fatta Del and Carimi, Francesco and Puglia, Anna Maria and Cardinale, Massimiliano and Gallo, Giuseppe and Mercati, Francesco}, doi = {10.1038/s41598-021-86399-5}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {2045-2322}, + journal = {Scientific reports}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Microbiota}, + language = {eng}, month = {March}, note = {Publisher: Springer Science and Business Media LLC}, number = {1}, + pages = {7078}, title = {The endophytic microbiota of {Citrus} limon is transmitted from seed to shoot highlighting differences of bacterial and fungal community structures}, url = {https://doi.org/10.1038/s41598-021-86399-5}, volume = {11}, @@ -3990,11 +6525,15 @@ @article{faddetta_endophytic_2021 } @article{fahrner_democratizing_2022, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Data-independent acquisition (DIA) has become an important approach in global, mass spectrometric proteomic studies because it provides in-depth insights into the molecular variety of biological systems. However, DIA data analysis remains challenging owing to the high complexity and large data and sample size, which require specialized software and vast computing infrastructures. Most available open-source DIA software necessitates basic programming skills and covers only a fraction of a complete DIA data analysis. In consequence, DIA data analysis often requires usage of multiple software tools and compatibility thereof, severely limiting the usability and reproducibility.{\textless}h4{\textgreater}Findings{\textless}/h4{\textgreater}To overcome this hurdle, we have integrated a suite of open-source DIA tools in the Galaxy framework for reproducible and version-controlled data processing. The DIA suite includes OpenSwath, PyProphet, diapysef, and swath2stats. We have compiled functional Galaxy pipelines for DIA processing, which provide a web-based graphical user interface to these pre-installed and pre-configured tools for their use on freely accessible, powerful computational resources of the Galaxy framework. This approach also enables seamless sharing workflows with full configuration in addition to sharing raw data and results. We demonstrate the usability of an all-in-one DIA pipeline in Galaxy by the analysis of a spike-in case study dataset. Additionally, extensive training material is provided to further increase access for the proteomics community.{\textless}h4{\textgreater}Conclusion{\textless}/h4{\textgreater}The integration of an open-source DIA analysis suite in the web-based and user-friendly Galaxy framework in combination with extensive training material empowers a broad community of researches to perform reproducible and transparent DIA data analysis.}, author = {Fahrner, Matthias and Föll, Melanie Christine and Grüning, Björn Andreas and Bernt, Matthias and Röst, Hannes and Schilling, Oliver}, doi = {10.1093/gigascience/giac005}, + issn = {2047-217X}, journal = {GigaScience}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+IsGalaxy, +UsePublic, {\textgreater}UseGalaxy.eu, Computational Biology, Proteomics}, + language = {eng}, note = {Publisher: Oxford University Press (OUP)}, + pages = {giac005}, title = {Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the {Galaxy} framework}, url = {https://doi.org/10.1093/gigascience/giac005}, volume = {11}, @@ -4006,6 +6545,7 @@ @article{fahrner_systematic_2021 author = {Fahrner, Matthias and Kook, Lucas and Fröhlich, Klemens and Biniossek, Martin L. and Schilling, Oliver}, copyright = {http://creativecommons.org/licenses/by/3.0/}, doi = {10.3390/proteomes9020026}, + issn = {2227-7382}, journal = {Proteomes}, keywords = {+Methods, +Shared, +Stellar, +UsePublic, {\textgreater}UseGalaxy.eu, NCI-60 reanalysis, endogenous proteolysis, fragment mass tolerance, mass spectrometry, semispecific peptide search}, language = {en}, @@ -4021,12 +6561,49 @@ @article{fahrner_systematic_2021 year = {2021} } +@article{falcone_spread_2022, + abstract = {{\textless}h4{\textgreater}Objectives{\textless}/h4{\textgreater}To report an outbreak of hypervirulent Klebsiella pneumoniae (hvKp) in COVID-19 patients.{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}Prospective, observational study including consecutive COVID-19 patients with hvKp infections admitted to the University Hospital of Pisa (Italy). Clinical data and outcome of patients were collected. All patients were followed-up to 30 days from the diagnosis of infection. Mortality within 30 days of the diagnosis of hvKp infection was reported. The hypermucoviscous phenotype was determined by the 'string test'. Molecular typing was performed on three strains collected during different periods of the outbreak. The strains underwent whole genome sequencing using the Illumina MiSeq instrument. The complete circular assemblies were also obtained for the chromosome and a large plasmid using the Unicycler tool.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}From November 2020 to March 2021, hvKp has been isolated from 36 COVID-19 patients: 29/36 (80.6\%) had infections (15 bloodstream infections, 8 ventilator-associated pneumonias and 6 complicated urinary tract infections), while 7/36 (19.4\%) had colonization (3 urine, 2 rectal and 2 skin). The isolates belonged to ST147 and their plasmid carried three replicons of the IncFIB (Mar), IncR and IncHI1B types and several resistance genes, including the rmpADC genes encoding enhancers of capsular synthesis. The hvKp isolates displayed an ESBL phenotype, with resistance to piperacillin/tazobactam and ceftolozane/tazobactam and susceptibility only to meropenem and ceftazidime/avibactam. The majority of patients were treated with meropenem alone or in combination with fosfomycin. Thirty-day mortality was 48.3\% (14/29).{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}ST147 ESBL-producing hvKp is associated with high mortality in COVID-19 patients. Strict microbiological surveillance and infection control measures are needed in this population.}, + author = {Falcone, Marco and Tiseo, Giusy and Arcari, Gabriele and Leonildi, Alessandro and Giordano, Cesira and Tempini, Sara and Bibbolino, Giulia and Mozzo, Roberto and Barnini, Simona and Carattoli, Alessandra and Menichetti, Francesco}, + doi = {10.1093/jac/dkab495}, + issn = {0305-7453}, + journal = {J Antimicrob Chemother}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19, Klebsiella Infections}, + language = {eng}, + month = {March}, + number = {4}, + pages = {1140--1145}, + title = {Spread of hypervirulent multidrug-resistant {ST147} {Klebsiella} pneumoniae in patients with severe {COVID}-19: an observational study from {Italy}, 2020-21}, + url = {http://europepmc.org/abstract/MED/35040981}, + volume = {77}, + year = {2022} +} + +@article{falconieri_extremely_2025, + abstract = {Mechanical force plays a pivotal role in all aspects of axon development. In this paper, the use of nano-pulling, a technology that enables the intracellular generation of extremely low mechanical forces is explored. It is demonstrated that force-mediated axon growth also exerts global effects that extend to the nuclear level. The mechanistic studies support a model in which exogenous forces induce microtubule stabilization, and significant remodeling of perinuclear microtubules, which preferentially align perpendicularly to the nuclear envelope. An increase in the lateral tension of the nucleus is observed, leading to substantial remodeling of nuclear morphology, characterized by an increase in nuclear grooves and a higher sphericity index (indicating less flattened nuclei). Notably, these changes in nuclear shape are linked to chromatin remodeling, resulting in global transcriptional activation.}, + author = {Falconieri, Alessandro and Da Palmata, Lorenzo and Cappello, Valentina and Schmidt, Tiziana Julia Nadjeschda and Folino, Pietro and Storti, Barbara and Bizzarri, Ranieri and Raffa, Vittoria}, + copyright = {© 2025 The Author(s). Small published by Wiley-VCH GmbH}, + doi = {10.1002/smll.202503011}, + issn = {1613-6829}, + journal = {Small}, + keywords = {{\textgreater}UseGalaxy.eu, chromatin, mechanical force, microtubule, neuron, nucleus, remodelling, transcription}, + language = {en}, + month = {December}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/smll.202503011}, + number = {n/a}, + pages = {2503011}, + title = {The {Extremely} {Low} {Mechanical} {Force} {Generated} by {Nano}-{Pulling} {Induces} {Global} {Changes} in the {Microtubule} {Network}, {Nuclear} {Morphology}, and {Chromatin} {Transcription} in {Neurons}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.202503011}, + urldate = {2025-07-12}, + volume = {n/a}, + year = {2025} +} + @article{fallmann_rna_2019, abstract = {Abstract. RNA has become one of the major research topics in molecular biology. As a central player in key processes regulating gene expression, RNA is in the}, author = {Fallmann, Jörg and Videm, Pavankumar and Bagnacani, Andrea and Batut, Bérénice and Doyle, Maria A. and Klingstrom, Tomas and Eggenhofer, Florian and Stadler, Peter F. and Backofen, Rolf and Grüning, Björn}, doi = {10.1093/nar/gkz353}, journal = {Nucleic Acids Research}, - keywords = {+Education, +Galactic, +IsGalaxy, {\textgreater}RNA Workbench}, + keywords = {+Education, +Galactic, +IsGalaxy, {\textgreater}RNA Workbench, Software}, language = {en}, month = {May}, shorttitle = {The {RNA} workbench 2.0}, @@ -4036,6 +6613,23 @@ @article{fallmann_rna_2019 year = {2019} } +@article{fancello_analysis_2022, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Proteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom protein databases. However, empirical observations reveal that these large proteogenomic databases produce lower-sensitivity peptide identifications. Various strategies have been proposed to avoid this, including the generation of reduced transcriptome-informed protein databases, which only contain proteins whose transcripts are detected in the sample-matched transcriptome. These were found to increase peptide identification sensitivity. Here, we present a detailed evaluation of this approach.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}We establish that the increased sensitivity in peptide identification is in fact a statistical artifact, directly resulting from the limited capability of target-decoy competition to accurately model incorrect target matches when using excessively small databases. As anti-conservative false discovery rates (FDRs) are likely to hamper the robustness of the resulting biological conclusions, we advocate for alternative FDR control methods that are less sensitive to database size. Nevertheless, reduced transcriptome-informed databases are useful, as they reduce the ambiguity of protein identifications, yielding fewer shared peptides. Furthermore, searching the reference database and subsequently filtering proteins whose transcripts are not expressed reduces protein identification ambiguity to a similar extent, but is more transparent and reproducible.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}In summary, using transcriptome information is an interesting strategy that has not been promoted for the right reasons. While the increase in peptide identifications from searching reduced transcriptome-informed databases is an artifact caused by the use of an FDR control method unsuitable to excessively small databases, transcriptome information can reduce the ambiguity of protein identifications.}, + author = {Fancello, Laura and Burger, Thomas}, + doi = {10.1186/s13059-022-02701-2}, + issn = {1474-7596}, + journal = {Genome biology}, + keywords = {{\textgreater}UseGalaxy.eu, Proteogenomics, Proteomics}, + language = {eng}, + month = {June}, + number = {1}, + pages = {132}, + title = {An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics}, + url = {http://europepmc.org/abstract/MED/35725496}, + volume = {23}, + year = {2022} +} + @article{farias_basidin_2023, abstract = {The fungus Moniliophthora perniciosa secretes protein effectors that manipulate the physiology of the host plant, but few effectors of this fungus have had their functions confirmed. We performed functional characterization of a promising candidate effector of M. perniciosa. The inoculation of rBASIDIN at 4 µmol L−1 in the mesophyll of leaflets of Solanum lycopersicum caused symptoms of shriveling within 6 h without the presence of necrosis. However, when sprayed on the plant at a concentration of 11 µmol L−1, it caused wilting symptoms only 2 h after application, followed by necrosis and cell death at 48 h. rBASIDIN applied to Theobroma cacao leaves at the same concentration caused milder symptoms. rBASIDIN caused hydrogen peroxide production in leaf tissue, damaging the leaf membrane and negatively affecting the photosynthetic rate of Solanum lycopersicum plants. Phylogenetic analysis indicated that BASIDIN has orthologs in other phytopathogenic basidiomycetes. Analysis of the transcripts revealed that BASIDIN and its orthologs are expressed in different fungal species, suggesting that this protein is differentially regulated in these basidiomycetes. Therefore, the results of applying BASIDIN allow the inference that it is an effector of the fungus M. perniciosa, with a strong potential to interfere in the defense system of the host plant.}, author = {Farias, Keilane Silva and Ferreira, Monaliza Macêdo and Amaral, Geiseane Veloso and Zugaib, Maria and Santos, Ariana Silva and Gomes, Fábio Pinto and Rezende, Rachel Passos and Gramacho, Karina Peres and Aguiar, Eric Roberto Guimarães Rocha and Pirovani, Carlos Priminho}, @@ -4063,7 +6657,7 @@ @article{farmiloe_structural_2023 doi = {10.1093/gbe/evad184}, issn = {1759-6653}, journal = {Genome Biology and Evolution}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Primates, Zinc Fingers}, month = {November}, number = {11}, pages = {evad184}, @@ -4074,6 +6668,24 @@ @article{farmiloe_structural_2023 year = {2023} } +@article{farmiloe_transcriptomic_2025, + abstract = {Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by the expansion of a CGG repeat in the 5’UTR of the FMR1 (fragile X messenger ribonucleoprotein 1) gene. Healthy individuals possess a repeat 30–55 CGG units in length. Once the CGG repeat exceeds 200 copies it triggers methylation at the locus. This methylation covers the FMR1 promoter region and silences expression of the gene and the production of FMRP (fragile X messenger ribonucleoprotein). The loss of FMRP is responsible for a number of pathologies including neurodevelopmental delay and autism spectrum disorder. Methylation of the expanded repeat in the FMR1 locus is the causal factor for FXS, however it is not known why the expanded repeat triggers this epigenetic change or how exactly DNA methylation is established. Intriguingly, genetic engineering of expanded CGG repeats of over 300 copies in the FMR1 locus in mice remains unmethylated. Also in humans, in very rare cases, individuals can have an FMR1 CGG expansion {\textgreater} 200 copies but the locus remains unmethylated. These unmethylated full mutation (UFM) individuals give us a rare opportunity to investigate the mechanism of FMR1 promoter methylation.}, + author = {Farmiloe, Grace and Bejczy, Veronika and Tabolacci, Elisabetta and Willemsen, Rob and Jacobs, Frank}, + doi = {10.1186/s11689-025-09609-5}, + issn = {1866-1955}, + journal = {Journal of Neurodevelopmental Disorders}, + keywords = {{\textgreater}UseGalaxy.eu, DNA Methylation, DNA methylation, Epigenetic memory, Epigenetics, Fragile X Mental Retardation Protein, Fragile X Syndrome, Gene Mutation, Methylation, Methylation analysis, Trinucleotide Repeat Expansion}, + language = {en}, + month = {April}, + number = {1}, + pages = {22}, + title = {Transcriptomic profiling of unmethylated full mutation carriers implicates {TET3} in {FMR1} {CGG} repeat expansion methylation dynamics in fragile {X} syndrome}, + url = {https://doi.org/10.1186/s11689-025-09609-5}, + urldate = {2025-05-28}, + volume = {17}, + year = {2025} +} + @article{farmiloe_widespread_2020, abstract = {The large family of KRAB zinc finger (KZNF) genes are transcription factors implicated in recognizing and repressing repetitive sequences such as transposable elements (TEs) in our genome. Through successive waves of retrotransposition-mediated insertions, various classes of TEs have invaded mammalian genomes at multiple timepoints throughout evolution. Even though most of the TE classes in our genome lost the capability to retrotranspose millions of years ago, it remains elusive why the KZNFs that evolved to repress them are still retained in our genome. One hypothesis is that KZNFs become repurposed for other regulatory roles. Here, we find evidence that evolutionary changes in KZNFs provide them not only with the ability to repress TEs, but also to bind to gene promoters independent of TEs. Using KZNF binding site data in conjunction with gene expression values from the Allen Brain Atlas, we show that KZNFs have the ability to regulate gene expression in the human brain in a region-specific manner. Our analysis shows that the expression of KZNFs shows correlation with the expression of their target genes, suggesting that KZNFs have a direct influence on gene expression in the developing human brain. The extent of this regulation and the impact it has on primate brain evolution are still to be determined, but our results imply that KZNFs have become widely integrated into neuronal gene regulatory networks. Our analysis predicts that gene expression networks have been repeatedly innovated throughout primate evolution, continuously gaining new layers of gene regulation mediated by both TEs and KZNFs in our genome.This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.}, author = {Farmiloe, Grace and Lodewijk, Gerrald A. and Robben, Stijn F. and van Bree, Elisabeth J. and Jacobs, Frank M. J.}, @@ -4108,6 +6720,23 @@ @article{farrell_detection_2022 year = {2022} } +@article{fathi_microencapsulation_2021, + abstract = {Alginate is a common agent used for microencapsulation; however, the formed capsule is easily damaged. Therefore, alginate requires blending with other biopolymers to reduce capsule vulnerability. Whey protein is one polymer that can be incorporated with alginate to improve microcapsule structure. In this study, three different encapsulation methods (extrusion, emulsification, and spray drying) were tested for their ability to stabilize microencapsulated \textit{Pseudomonas} strain VUPF506. Extrusion and emulsification methods enhanced encapsulation efficiency by up to 80\% and gave the best release patterns over two months. A greenhouse experiment using potato plants treated with alginate-whey protein microcapsules showed a decrease in \textit{Rhizoctonia} disease intensity of up to 70\%. This is because whey protein is rich in amino acids and can serve as a resistance induction agent for the plant. In this study, the use of CNT in the ALG-WP system increased the rooting and proliferation and reduced physiological complication. The results of this study showed that the technique used in encapsulation could have a significant effect on the efficiency and persistence of probiotic bacteria. Whole genome sequence analysis of strain VUPF506 identified it as \textit{Pseudomonas chlororaphis} and revealed some genes that control pathogens.}, + author = {Fathi, Fariba and Saberi Riseh, Roohallah and Khodaygan, Pejman and Hosseini, Samin and Skorik, Yury A}, + doi = {10.3390/polym13234269}, + issn = {2073-4360}, + journal = {Polymers}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {December}, + number = {23}, + pages = {4269}, + title = {Microencapsulation of a {Pseudomonas} {Strain} ({VUPF506}) in {Alginate}-{Whey} {Protein}-{Carbon} {Nanotubes} and {Next}-{Generation} {Sequencing} {Identification} of {This} {Strain}}, + url = {http://europepmc.org/abstract/MED/34883770}, + volume = {13}, + year = {2021} +} + @article{fatima_book_2023, abstract = {The publication contains abstracts submitted to the\ 1st Colloquium on Bioinformatics Learning, Education and Training in the categories of oral presentations, poster presentations, keynote speeches and training workshops.}, author = {Fatima, Ayesha and Khan, Mohammad Asif}, @@ -4145,13 +6774,15 @@ @article{faulstich_evidence_2024 editor = {McFall-Ngai, Margaret J. and Weis, Virginia}, issn = {2150-7511}, journal = {mBio}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Cell Division, Phosphates, Sea Anemones, Symbiosis}, language = {en}, month = {August}, + number = {9}, pages = {e01059--24}, title = {Evidence for phosphate-dependent control of symbiont cell division in the model anemone \textit{{Exaiptasia} diaphana}}, url = {https://journals.asm.org/doi/10.1128/mbio.01059-24}, urldate = {2024-08-09}, + volume = {15}, year = {2024} } @@ -4161,7 +6792,8 @@ @article{feldker_genome-wide_2020 doi = {10.15252/embj.2019103209}, issn = {0261-4189}, journal = {The EMBO Journal}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, AP-1, ZEB1, breast cancer, epithelial to mesenchymal transition}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, AP-1, Epithelial-Mesenchymal Transition, Genome, Human, ZEB1, breast cancer, epithelial to mesenchymal transition}, + language = {eng}, month = {July}, note = {Publisher: John Wiley \& Sons, Ltd}, number = {n/a}, @@ -4173,6 +6805,22 @@ @article{feldker_genome-wide_2020 year = {2020} } +@misc{feliciano_microbial_2025, + abstract = {Lentils are promoted as an alternative protein source given their agricultural and nutritional benefits. However, the information on microbial risks associated with the lentil supply chain in France and Hungary is limited. Bacillus cereus was identified as the pathogen of concern in both hot and cold dishes while Listeria monocytogenes was identified only in cold dishes. A probabilistic model accounting for uncertainty and variability was constructed. This estimates the microbial concentration, foodborne illness cases, and DALYs at subsequent stages of domestic handling: cooking, cooling, and 24 to 96 hours of chilled storage.First, the results were analysed at each stage, for example, at 96 h for B. cereus with mean values of 2.52 [1.75; 4.12] log CFU/g in France and 2.03 [1.24; 3.56] log CFU/g in Hungary. Meanwhile, for Listeria monocytogenes, the mean estimates were lower at 0.48 [-0.20; 1.16] log CFU/g for France and 0.69 [0.07; 1.36] log CFU/g in Hungary. Second, the overall foodborne illness cases from both pathogens were computed based on consumption frequency. They were estimated to be 0 [0-44] cases per 100,000 in France and [0-5.8] in Hungary.The confidence intervals are relatively large, reflecting the uncertainty in the estimates, meaning the risk is not an absolute zero. Moreover, it's likely that the protein shifts towards plant-based diets promoted by different institutions (e.g., EAT Lancet) and extended batch cooking practices will lead to a higher risk in the future.}, + address = {Rochester, NY}, + author = {Feliciano, Rodney and Membré, Jeanne-marie and Delaunay, Louis}, + doi = {10.2139/ssrn.5371268}, + keywords = {{\textgreater}UseGalaxy.eu, Bacillus cereus, DALY, Listeria monocytogenes, Monte Carlo, domestic practices, food safety, leguminous}, + language = {en}, + month = {July}, + publisher = {Social Science Research Network}, + title = {Microbial {Risk} and {Health} {Burden} {Associated} with the {Domestic} {Preparation} of {Lentils} in {France} and {Hungary}}, + type = {{SSRN} {Scholarly} {Paper}}, + url = {https://papers.ssrn.com/abstract=5371268}, + urldate = {2025-09-03}, + year = {2025} +} + @article{fell_fibcd1_2021, author = {Fell, Christopher W. and Hagelkruys, Astrid and Cicvaric, Ana and Horrer, Marion and Liu, Lucy and Li, Joshua Shing Shun and Stadlmann, Johannes and Polyansky, Anton A. and Mereiter, Stefan and Tejada, Miguel Angel and Kokotović, Tomislav and Scaramuzza, Angelica and Twyman, Kimberly A. and Morrow, Michelle M. and Juusola, Jane and Yan, Huifang and Wang, Jingmin and Burmeister, Margit and Andersen, Thomas Levin and Wirnsberger, Gerald and Holmskov, Uffe and Perrimon, Norbert and Zagrović, Bojan and Monje, Francisco J. and Moeller, Jesper Bonnet and Penninger, Josef M. and Nagy, Vanja}, doi = {10.1101/2021.09.09.459581}, @@ -4185,19 +6833,41 @@ @article{fell_fibcd1_2021 } @article{feng_scarless_2021, + abstract = {We describe a simple and efficient technique that allows scarless engineering of Drosophila genomic sequences near any landing site containing an inverted attP cassette, such as a MiMIC insertion. This two-step method combines phiC31 integrase-mediated site-specific integration and homing nuclease-mediated resolution of local duplications, efficiently converting the original landing site allele to modified alleles that only have the desired change(s). Dominant markers incorporated into this method allow correct individual flies to be efficiently identified at each step. In principle, single attP sites and FRT sites are also valid landing sites. Given the large and increasing number of landing site lines available in the fly community, this method provides an easy and fast way to efficiently edit the majority of the Drosophila genome in a scarless manner. This technique should also be applicable to other species.}, author = {Feng, Siqian and Lu, Shan and Grueber, Wesley B. and Mann, Richard S.}, doi = {10.1093/genetics/iyab012}, editor = {Rong, Y. S.}, + issn = {0016-6731}, + journal = {Genetics}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {January}, note = {Publisher: Oxford University Press (OUP)}, number = {3}, + pages = {iyab012}, title = {Scarless engineering of the {Drosophila} genome near any site-specific integration site}, url = {https://doi.org/10.1093/genetics/iyab012}, volume = {217}, year = {2021} } +@article{feng_spychip_2022, + abstract = {Chromatin immunoprecipitation (ChIP) is an important technique for characterizing protein-DNA binding in vivo. One drawback of ChIP-based techniques is the lack of cell type-specificity when profiling complex tissues. To overcome this limitation, we developed SpyChIP to identify cell type-specific transcription factor (TF) binding sites in native physiological contexts without tissue dissociation or nuclei sorting. SpyChIP takes advantage of a specific covalent isopeptide bond that rapidly forms between the 15-amino acid SpyTag and the 17-kDa protein SpyCatcher. In SpyChIP, the target TF is fused with SpyTag by genome engineering, and an epitope tagged SpyCatcher is expressed in cell populations of interest, where it covalently binds to SpyTag-TF. Cell type-specific ChIP is obtained by immunoprecipitating chromatin prepared from whole tissues using antibodies directed against the epitope-tagged SpyCatcher. Using SpyChIP, we identified the genome-wide binding profiles of the Hox protein Ultrabithorax (Ubx) in two distinct cell types of the \textit{Drosophila} haltere imaginal disc. Our results revealed extensive region-specific Ubx-DNA binding events, highlighting the significance of cell type-specific ChIP and the limitations of whole-tissue ChIP approaches. Analysis of Ubx::SpyChIP results provided insights into the relationship between chromatin accessibility and Ubx-DNA binding, as well as different mechanisms Ubx employs to regulate its downstream \textit{cis}-regulatory modules. In addition to SpyChIP, we suggest that SpyTag-SpyCatcher technology, as well as other protein pairs that form covalent isopeptide bonds, will facilitate many additional in vivo applications that were previously impractical.}, + author = {Feng, Siqian and Mann, Richard S}, + doi = {10.1073/pnas.2122900119}, + issn = {0027-8424}, + journal = {Proc Natl Acad Sci U S A}, + keywords = {{\textgreater}UseGalaxy.eu, Chromatin Immunoprecipitation Sequencing, Drosophila Proteins, Drosophila melanogaster, Homeodomain Proteins, Transcription Factors}, + language = {eng}, + month = {June}, + number = {25}, + pages = {e2122900119}, + title = {{SpyChIP} identifies cell type-specific transcription factor occupancy from complex tissues}, + url = {http://europepmc.org/abstract/MED/35696584}, + volume = {119}, + year = {2022} +} + @article{feng_transcription_2022, abstract = {In eukaryotes, members of transcription factor families often exhibit similar DNA binding properties in vitro, yet orchestrate paralog-specific gene regulatory networks in vivo. The serially homologous first (T1) and third (T3) thoracic legs of Drosophila, which are specified by the Hox proteins Scr and Ubx, respectively, offer a unique opportunity to address this paradox in vivo. Genome-wide analyses using epitope-tagged alleles of both Hox loci in the T1 and T3 leg imaginal discs, the precursors to the adult legs and ventral body regions, show that {\textasciitilde}8\% of Hox binding is paralog-specific. Binding specificity is mediated by interactions with distinct cofactors in different domains: the Hox cofactor Exd acts in the proximal domain and is necessary for Scr to bind many of its paralog-specific targets, while in the distal leg domain, the homeodomain protein Distal-less (Dll) enhances Scr binding to a different subset of loci. These findings reveal how Hox paralogs, and perhaps paralogs of other transcription factor families, orchestrate alternative downstream gene regulatory networks with the help of multiple, context-specific cofactors.}, author = {Feng, Siqian and Rastogi, Chaitanya and Loker, Ryan and Glassford, William J. and Tomas Rube, H. and Bussemaker, Harmen J. and Mann, Richard S.}, @@ -4205,7 +6875,7 @@ @article{feng_transcription_2022 doi = {10.1038/s41467-022-31501-2}, issn = {2041-1723}, journal = {Nature Communications}, - keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Experimental organisms, Molecular biology}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Drosophila Proteins, Experimental organisms, Molecular biology, Transcription Factors}, language = {en}, month = {July}, note = {Number: 1 @@ -4222,7 +6892,7 @@ @article{feng_transcription_2022 @article{fernandes_alise_2023, abstract = {Alternative Splicing (AS) is a co-transcriptional mechanism that enables the eukaryote to extend its proteome even with a limited number of genes. The cellular machinery performs AS by combining alternative regions of the isoforms in both productive and non-productive transcripts. AS events can be predicted using RNASeq data. In plants, the most frequent event is the retention of introns (IR) that can have a regulatory effect, for example, inserting a premature stop codon (PTC) that leads to degradation of the transcript through the nonsense-mediated decay (NMD) pathway. To study potential AS events in the biological process of coffee bean and tomato ripening, we conducted a DAS study using RNASeq data obtained for differential expression experiment and the referential coffee genome to identify differential AS (DAS). For this, we developed pipelines in Python to perform an automated curation of the 202 target genes that were identified with 241 DAS events by rMATS in the comparisons of early green fruits, intermediate yellow and final red ripening stage. We then carried out a manual curation of the 241 events enriched with the Interproscan5 annotation with further experimentally validating of Potassium channel AKT1 and Apyrase 7 genes under differential alternative expression during coffee grain ripening using conventional PCR and qPCR. Due to challenges identified during this analysis associated with the relationship of AS events and RNASeq data processing, we built an application of user- friendly APP to predict AS in RNASeq data. The application development is composed of three modules named GeneAPPScript, GeneAPPServer, GeneAPPExplorer. The GeneAPPScript module is a powerful wrapper that enables to perform a complete DAS analysis from obtaining network data to functional annotation of genes under DAS. This module can run on Debian distros, such as the Google Collaboratory (Colab) environment where it was developed. The GeneAPPServer module is a Flask backend that allows you to integrate outputs from different DAS analysis software that generate data in tabular outputs. Using GeneAPPExplorer, the user can generate dozens of graphs to graphically visualize important results implicit in technical tables exported by DAS analysis software. In addition, through the webapp, the researcher has access to tables enriched with functional and structural annotation data and event attributes. GeneAPP will contribute to the analysis of AS in several other works deposited in public databases where only differential expression at the gene level was analyzed, allowing further explanation when exploring the transcriptome at the isoform level.}, author = {Fernandes, Miquéias}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, language = {en}, month = {August}, note = {Accepted: 2024-04-17T00:37:44Z @@ -4277,12 +6947,34 @@ @mastersthesis{fernandes_lama2-cmd_2024 year = {2024} } +@article{fernandez-alvarez_erga-bge_2025, + abstract = {The +Stigmatoteuthis arcturi +reference genome offers a valuable resource for understanding the evolutionary patterns of oceanic squids, who perform important ecological roles as both predators and prey in mesopelagic and deep-sea environments, while their genomes remain understudied. The entirety of the genome sequence was assembled into 46 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 3.25 Gb, composed of 1,268 contigs and 497 scaffolds, with contig and scaffold N50 values of 11.0 Mb and 74.6 Mb, respectively.}, + author = {Fernández-Álvarez, Fernando Ángel and Bernal-Bajo, Ainhoa and Escudero, Nuria and Conejero, María and Riesgo, Ana and Fernández, Rosa and Monteiro, Rita and Böhne, Astrid and Aguilera, Laura and Gut, Marta and Alioto, Tyler S and Câmara Ferreira, Francisco and Cruz, Fernando and Gómez-Garrido, Jèssica and Haggerty, Leanne and Martin, Fergal and Brown, Tom}, + doi = {10.12688/openreseurope.20439.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {September}, + pages = {270}, + shorttitle = {{ERGA}-{BGE} genome of {Stigmatoteuthis} arcturi {Robson}, 1948}, + title = {{ERGA}-{BGE} genome of {Stigmatoteuthis} arcturi {Robson}, 1948: the jewelled squid}, + url = {https://open-research-europe.ec.europa.eu/articles/5-270/v1}, + urldate = {2025-10-19}, + volume = {5}, + year = {2025} +} + @article{fernandez-diaz_draft_2023, abstract = {This study presents a draft genome sequence of a Newcastle disease virus (NDV) strain (VFAR-136) isolated from a fighting cock (Gallus gallus) in the south of Peru. Strain VFAR-136 is a new report of NDV genotype VII circulating in Peru.}, author = {Fernández-Díaz, Manolo and Montalván-Avalos, Angela and Isasi-Rivas, Gisela and Villanueva-Pérez, Doris and Quiñones-Garcia, Stefany and Tataje-Lavanda, Luis and Rios-Matos, Dora and Lulo-Vargas, Milagros and Fernández-Sánchez, Manolo and Guevara-Sarmiento, Luis A. and Zimic, Mirko and Rojas-Neyra, Aldo and Calderón, Katherine}, doi = {10.1128/mra.01293-22}, + issn = {2576-098X}, journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, month = {January}, note = {Publisher: American Society for Microbiology}, number = {2}, @@ -4294,6 +6986,23 @@ @article{fernandez-diaz_draft_2023 year = {2023} } +@article{fernando_devasahayam_confrontations_2025, + abstract = {Microbial biological control agents are increasingly used as an alternative to synthetic pesticides. The application of these microorganisms massively affects all members of plant-colonising microbial communities, including pathogenic fungi. In the majority of cases, the resulting competition for ecological niches is decided by the toxicity of microbial secondary metabolites (SMs) formed. In this study, we devised confrontation experiments employing the fungal maize pathogen Colletotrichum graminicola and antagonistic partners, that is the biocontrol bacterium Bacillus amyloliquefaciens and the ubiquitous ascomycete Aspergillus nidulans. Transcriptome studies uncovered strong de-regulation of the vast majority of the C. graminicola secondary metabolite biosynthetic gene clusters (SMBGCs), with 69\% and 86\% of these clusters de-regulated at confrontation sites with B. amyloliquefaciens or A. nidulans, respectively. In the biocontrol bacterium and in A. nidulans confronting the maize pathogen, 100\% and 74\% of the SMBGCs were transcriptionally de-regulated, respectively. Correspondingly, non-targeted high-resolution LC-MS/MS revealed a large repertoire of 1738 and 1466 novel features formed in the fungus-bacterium and fungus-fungus confrontation, respectively. Surprisingly, several of these belong to chemical classes with lead structures of synthetic fungicides.}, + author = {Fernando Devasahayam, Bennet Rohan and Uthe, Henriette and Poeschl, Yvonne and Deising, Holger B}, + doi = {10.1111/1462-2920.70145}, + issn = {1462-2912}, + journal = {Environ Microbiol}, + keywords = {{\textgreater}UseGalaxy.eu, Aspergillus nidulans, Bacillus amyloliquefaciens, Colletotrichum, Fungicides, Industrial}, + language = {eng}, + month = {July}, + number = {7}, + pages = {e70145}, + title = {Confrontations of the {Pathogenic} {Fungus} {Colletotrichum} graminicola {With} a {Biocontrol} {Bacterium} or a {Ubiquitous} {Fungus} {Trigger} {Synthesis} of {Secondary} {Metabolites} {With} {Lead} {Structures} of {Synthetic} {Fungicides}}, + url = {http://europepmc.org/abstract/MED/40660705}, + volume = {27}, + year = {2025} +} + @article{ferreira_avaliacao_2023, abstract = {Infertility is linked to different functions of male gametes, one of which is caused by impaired motility due to anomalies in sperm flagella. Several genetic @@ -4359,9 +7068,13 @@ @article{ferreira_tcserpin_2024 } @article{fiedler_taxonomic_2021, + abstract = {The genetic heterogeneity of \textit{Heyndrickxia sporothermodurans} (formerly \textit{Bacillus}\textit{sporothermodurans)} was evaluated using whole genome sequencing. The genomes of 29 previously identified \textit{Heyndrickxia}\textit{sporothermodurans} and two \textit{Heyndrickxia vini} strains isolated from ultra-high-temperature (UHT)-treated milk were sequenced by short-read (Illumina) sequencing. After sequence analysis, the two \textit{H. vini} strains could be reclassified as \textit{H. sporothermodurans}. In addition, the genomes of the \textit{H.}\textit{sporothermodurans} type strain (DSM 10599$^{\textrm{T}}$) and the closest phylogenetic neighbors \textit{Heyndrickxia}\textit{oleronia} (DSM 9356$^{\textrm{T}}$) and \textit{Heyndrickxia vini} (JCM 19841$^{\textrm{T}}$) were also sequenced using both long (MinION) and short-read (Illumina) sequencing. By hybrid sequence assembly, the genome of the \textit{H. sporothermodurans} type strain was enlarged by 15\% relative to the short-read assembly. This noticeable increase was probably due to numerous mobile elements in the genome that are presumptively related to spore heat tolerance. Phylogenetic studies based on 16S rDNA gene sequence, core genome, single-nucleotide polymorphisms and ANI/dDDH, showed that \textit{H. vini} is highly related to \textit{H. sporothermodurans}. When examining the genome sequences of all \textit{H.}\textit{sporothermodurans} strains from this study, together with 4 \textit{H. sporothermodurans} genomes available in the GenBank database, the majority of the 36 strains examined occurred in a clonal lineage with less than 100 SNPs. These data substantiate previous reports on the existence and spread of a genetically highly homogenous and heat resistant spore clone, i.e., the HRS-clone.}, author = {Fiedler, Gregor and Herbstmann, Anna-Delia and Doll, Etienne and Wenning, Mareike and Brinks, Erik and Kabisch, Jan and Breitenwieser, Franziska and Lappann, Martin and Böhnlein, Christina and Franz, Charles M. A. P.}, doi = {10.3390/microorganisms9020246}, + issn = {2076-2607}, + journal = {Microorganisms}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {January}, note = {Publisher: MDPI AG}, number = {2}, @@ -4397,7 +7110,7 @@ @article{fischer_expanding_2024 doi = {10.3390/v16050658}, issn = {1999-4915}, journal = {Viruses}, - keywords = {{\textgreater}UseGalaxy.eu, human adenoviruses, mutagenesis of viral genomes, replication-competent vectors, transgene insertion sites, viral bacmids}, + keywords = {{\textgreater}UseGalaxy.eu, Genetic Vectors, Recombination, Genetic, human adenoviruses, mutagenesis of viral genomes, replication-competent vectors, transgene insertion sites, viral bacmids}, language = {en}, month = {May}, note = {Number: 5 @@ -4429,6 +7142,40 @@ @article{fischer_peptide-mediated_2023 year = {2023} } +@article{fischer_two_2025, + abstract = {The emergence of infectious diseases, particularly those caused by fungal pathogens, poses serious threats to public health, wildlife and ecosystem stability$^{\textrm{1}}$. Host-fungus interactions and environmental factors have been extensively examined$^{\textrm{2-4}}$. However, the role of genetic variability in pathogens is often less well-studied, even for diseases such as white-nose in bats, which has caused one of the highest disease-driven death tolls documented in nonhuman mammals$^{\textrm{5}}$. Previous research on white-nose disease has primarily focused on variations in disease outcomes attributed to host traits or environmental conditions$^{\textrm{6-8}}$, but has neglected pathogen variability. Here we leverage an extensive reference collection of 5,479 fungal isolates from 27 countries to reveal that the widespread causative agent is not a single species but two sympatric cryptic species, each exhibiting host specialization. Our findings provide evidence of recombination in each species, but significant genetic differentiation across their genomes, including differences in genome organization. Both species contain geographically differentiated populations, which enabled us to identify the species introduced to North America and trace its source population to a region in Ukraine. In light of our discovery of the existence of two cryptic species of the causative agent of white-nose disease, our research underscores the need to integrate the study of pathogen variability into comprehensive disease surveillance, management and prevention strategies. This holistic approach is crucial for enhancing our understanding of diseases and implementing effective measures to prevent their spread.}, + author = {Fischer, Nicola M and Dumville, Imogen and Nabholz, Benoit and Zhelyazkova, Violeta and Stecker, Ruth-Marie and Blomberg, Anna S and Dool, Serena E and Fritze, Marcus and Tilak, Marie-Ka and Bashta, Andriy-Taras and Chenal, Clothilde and Fiston-Lavier, Anna-Sophie and Puechmaille, Sebastien J}, + doi = {10.1038/s41586-025-09060-5}, + issn = {0028-0836}, + journal = {Nature}, + keywords = {{\textgreater}UseGalaxy.eu, Ascomycota, Chiroptera, Mycoses}, + language = {eng}, + month = {June}, + number = {8069}, + pages = {1034--1040}, + title = {Two distinct host-specialized fungal species cause white-nose disease in bats}, + url = {http://europepmc.org/abstract/MED/40437097}, + volume = {642}, + year = {2025} +} + +@article{fleming_proser1_2024, + abstract = {The link between DNA methylation and neurodevelopmental disorders is well established. However, how DNA methylation is fine-tuned-ensuring precise gene expression and developmental fidelity-remains poorly understood. PROSER1, a known TET2 interactor, was recently linked to a severe neurodevelopmental disorder. Here, we demonstrate that PROSER1 interacts with all TET enzymes and stabilizes chromatin-bound TET-OGT-PROSER1-DBHS (TOPD) complexes, which regulate DNA demethylation and developmental gene expression. Surprisingly, we found that PROSER1 also sequesters TET enzymes, preventing widespread demethylation and transposable element derepression. Our findings identify PROSER1 as a key factor that both positively and negatively regulates DNA demethylation essential for mammalian neurodevelopment.}, + author = {Fleming, Anna and Knatko, Elena V and Li, Xiang and Zoch, Ansgar and Heckhausen, Zoe and Stransky, Stephanie and Brenes, Alejandro J and Sidoli, Simone and Hajkova, Petra and O'Carroll, Dónal and Rasmussen, Kasper D}, + doi = {10.1101/gad.352176.124}, + issn = {0890-9369}, + journal = {Genes \& development}, + keywords = {{\textgreater}UseGalaxy.eu, DNA Demethylation, Gene Expression Regulation, Developmental}, + language = {eng}, + month = {November}, + number = {21-24}, + pages = {952--964}, + title = {{PROSER1} modulates {DNA} demethylation through dual mechanisms to prevent syndromic developmental malformations}, + url = {http://europepmc.org/abstract/MED/39562138}, + volume = {38}, + year = {2024} +} + @article{flores_orozco_evaluation_2024, abstract = {Anaerobic digestion (AD) has shown the potential to reduce the abundance of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in animal manures. It stands as a promising option to reduce the risk of the spread of antimicrobial resistance (AMR) due to livestock production and manure applications. However, the underlying mechanisms driving these changes still need to be fully understood. This multidisciplinary study aimed to utilize metagenomics to investigate the molecular and microbial mechanisms associated with the evolution of ARGs and MGEs during the anaerobic digestion (AD) of bovine dairy manure. The research focused on three main aspects: 1) examining the long-term effects of mesophilic (MAD) and thermophilic (TAD) anaerobic digestion on the entire set of ARGs (resistome) and MGEs (mobilome) in manure; 2) comparing the impact of alternative manure treatments, such as storage and solid-liquid separation, on resistomes and mobilomes; 3) identifying microbial groups potentially associated with ARGs and MGEs and microbial shifts potentially driving changes in resistomes and mobilomes. A meta-analysis conducted early in this research informed the primary focus of this research. Two anaerobic digesters operating at mesophilic (36 °C) and the other at thermophilic (55 °C) temperatures were set up, operated, monitored, and studied for 4 and 2 years, respectively. Metagenomics analyses were used to evaluate resistomes, mobilomes, and microbiomes in the mesophilic and thermophilic digesters operating under steady state and in the bovine manure used as substrate. The results indicated that MAD and TAD lowered ARG levels in fresh cattle manure by over 50\% and MGEs by over 65\%. Surprisingly, TAD did not outperform MAD at reducing ARGs and MGEs. Co-occurrence analysis indicated a strong association between microbial groups from the phyla Bacillota (e.g., Jeotgalicoccus, Streptococcus, Enterococcus), Actinomycetota (e.g., Brevibacterium, Rhodococcus), and Pseudomonadota (e.g., Acinetobacter, Comamonas) with these AMR elements. The decline in the abundance of aerobic and facultative anaerobes likely linked to hydrolytic functions was suggested as one of the main drivers of the changes in resistomes and mobilomes. The proximity of toxin-antitoxin systems and transposon structures to specific ARGs (e.g., Erm, tet, Ant(6)-la) was discovered, which could explain the persistence of such ARGs in digestates. The study of the effects of other manure treatments, such as aerobic storage in an open tank and solid-liquid separation, revealed that they are less efficient in reducing ARGs and MGEs from manures than AD. In this study, the high levels of ARGs and genes conferring resistance to heavy metals in a farm operating in an antibiotic-free environment suggested that other antimicrobials, such as foot bathing solutions, may be causing the indirect selection of ARGs. Overall, this research made several contributions to understanding AMR in the context of anaerobic digestion of animal manure that could be extrapolated to other manure treatments. These contributions not only bridge existing gaps in the literature but also pave the way for future research, providing valuable insights that can be used to inform the development of more effective strategies to mitigate the dissemination of AMR associated with manure management, application, and disposal.}, author = {Flores Orozco, Daniel}, @@ -4445,11 +7192,13 @@ @article{foll_accessible_2019 abstract = {AbstractBackground. Mass spectrometry imaging is increasingly used in biological and translational research because it has the ability to determine the spatial}, author = {Föll, Melanie Christine and Moritz, Lennart and Wollmann, Thomas and Stillger, Maren Nicole and Vockert, Niklas and Werner, Martin and Bronsert, Peter and Rohr, Karl and Grüning, Björn Andreas and Schilling, Oliver}, doi = {10.1093/gigascience/giz143}, + issn = {2047-217X}, journal = {GigaScience}, keywords = {+Education, +Galactic, +IsGalaxy, +RefPublic, +Shared, +Tools, {\textgreater}Galaxy-P, {\textgreater}MSI, {\textgreater}PhenoMeNal, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, {\textgreater}Workflow4Metabolomics}, language = {en}, month = {December}, number = {12}, + pages = {giz143}, title = {Accessible and reproducible mass spectrometry imaging data analysis in {Galaxy}}, url = {https://academic.oup.com/gigascience/article/8/12/giz143/5670614}, urldate = {2020-01-06}, @@ -4472,8 +7221,7 @@ @article{foll_moving_2021 note = {Company: Cold Spring Harbor Laboratory Distributor: Cold Spring Harbor Laboratory Label: Cold Spring Harbor Laboratory -Section: New Results -Type: article}, +Section: New Results}, pages = {2021.08.09.455649}, shorttitle = {Moving translational mass spectrometry imaging towards transparent and reproducible data analyses}, title = {Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: {A} case study of an urothelial cancer cohort analyzed in the {Galaxy} framework}, @@ -4482,6 +7230,40 @@ @article{foll_moving_2021 year = {2021} } +@article{foll_moving_2022, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Mass spectrometry imaging (MSI) derives spatial molecular distribution maps directly from clinical tissue specimens and thus bears great potential for assisting pathologists with diagnostic decisions or personalized treatments. Unfortunately, progress in translational MSI is often hindered by insufficient quality control and lack of reproducible data analysis. Raw data and analysis scripts are rarely publicly shared. Here, we demonstrate the application of the Galaxy MSI tool set for the reproducible analysis of a urothelial carcinoma dataset.{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}Tryptic peptides were imaged in a cohort of 39 formalin-fixed, paraffin-embedded human urothelial cancer tissue cores with a MALDI-TOF/TOF device. The complete data analysis was performed in a fully transparent and reproducible manner on the European Galaxy Server. Annotations of tumor and stroma were performed by a pathologist and transferred to the MSI data to allow for supervised classifications of tumor vs. stroma tissue areas as well as for muscle-infiltrating and non-muscle infiltrating urothelial carcinomas. For putative peptide identifications, m/z features were matched to the MSiMass list.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}Rigorous quality control in combination with careful pre-processing enabled reduction of m/z shifts and intensity batch effects. High classification accuracy was found for both, tumor vs. stroma and muscle-infiltrating vs. non-muscle infiltrating urothelial tumors. Some of the most discriminative m/z features for each condition could be assigned a putative identity: stromal tissue was characterized by collagen peptides and tumor tissue by histone peptides. Immunohistochemistry confirmed an increased histone H2A abundance in the tumor compared to the stroma tissues. The muscle-infiltration status was distinguished via MSI by peptides from intermediate filaments such as cytokeratin 7 in non-muscle infiltrating carcinomas and vimentin in muscle-infiltrating urothelial carcinomas, which was confirmed by immunohistochemistry. To make the study fully reproducible and to advocate the criteria of FAIR (findability, accessibility, interoperability, and reusability) research data, we share the raw data, spectra annotations as well as all Galaxy histories and workflows. Data are available via ProteomeXchange with identifier PXD026459 and Galaxy results via https://github.com/foellmelanie/Bladder\_MSI\_Manuscript\_Galaxy\_links .{\textless}h4{\textgreater}Conclusion{\textless}/h4{\textgreater}Here, we show that translational MSI data analysis in a fully transparent and reproducible manner is possible and we would like to encourage the community to join our efforts.}, + author = {Föll, Melanie Christine and Volkmann, Veronika and Enderle-Ammour, Kathrin and Timme, Sylvia and Wilhelm, Konrad and Guo, Dan and Vitek, Olga and Bronsert, Peter and Schilling, Oliver}, + doi = {10.1186/s12014-022-09347-z}, + issn = {1542-6416}, + journal = {Clinical proteomics}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {April}, + number = {1}, + pages = {8}, + title = {Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: a case study of an urothelial cancer cohort analyzed in the {Galaxy} framework}, + url = {http://europepmc.org/abstract/MED/35439943}, + volume = {19}, + year = {2022} +} + +@article{fonseca_amazonian_2024, + abstract = {Bacterial wilt, caused by \textit{Ralstonia solanacearum}, is one of the main challenges for sustainable tomato production in the Amazon region. This study evaluated the potential of bacteria isolated from sediments of the Solimões and Negro rivers for the biocontrol of this disease. From 36 bacteria selected through in vitro antibiosis, three promising isolates were identified: \textit{Priestia aryabhattai} RN 11, \textit{Streptomyces} sp. RN 24, and \textit{Kitasatospora} sp. SOL 195, which inhibited the growth of the phytopathogen by 100\%, 87.62\%, and 100\%, respectively. These isolates also demonstrated the ability to produce extracellular enzymes and plant growth-promoting compounds, such as indole-3-acetic acid (IAA), siderophore, and ammonia. In plant assays, during both dry and rainy seasons, \textit{P. aryabhattai} RN 11 reduced disease incidence by 40\% and 90\%, respectively, while promoting the growth of infected plants. \textit{Streptomyces} sp. RN 24 and \textit{Kitasatospora} sp. SOL 195 exhibited high survival rates (85-90\%) and pathogen suppression in the soil ({\textgreater}90\%), demonstrating their potential as biocontrol agents. This study highlights the potential of Amazonian bacteria as biocontrol agents against bacterial wilt, contributing to the development of sustainable management strategies for this important disease.}, + author = {Fonseca, Jennifer Salgado da and Sousa, Thiago Fernandes and Almeida, Suene Vanessa Reis de and Silva, Carina Nascimento and Castro, Gleucinei Dos Santos and Yamagishi, Michel Eduardo Beleza and Koolen, Hector Henrique Ferreira and Hanada, Rogério Eiji and Silva, Gilvan Ferreira da}, + doi = {10.3390/microorganisms12071364}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {July}, + number = {7}, + pages = {1364}, + title = {Amazonian {Bacteria} from {River} {Sediments} as a {Biocontrol} {Solution} against {Ralstonia} solanacearum}, + url = {http://europepmc.org/abstract/MED/39065132}, + volume = {12}, + year = {2024} +} + @article{fonseca_mineracao_2024, abstract = {The Amazon, with its vast biodiversity, harbors a complex network of ecosystems interconnected by rivers such as the Negro and Solimões. This unique dynamic favors the emergence and diversification of microbial lineages, rendering the region a hotspot for the discovery of innovative biological solutions. Within this context, this thesis investigated the biotechnological potential of 36 bacteria isolated from Amazonian river sediments, focusing on applications in phytopathogen biocontrol and plant growth promotion. The bacterial isolates were evaluated in vitro against agriculturally significant phytopathogens, including Corynespora cassiicola, Colletotrichum siamense, Rhizoctonia solani, and Ralstonia solanacearum. This initial screening gave rise to two main chapters: the first investigates the biocontrol of R. solanacearum, while the second examines the genomic potential and agricultural applications of Alcaligenes nematophilus SOL 109. In Chapter 1, three isolates - Priestia aryabhattai RN 11, Streptomyces sp. RN 24, and Kitasatospora sp. SOL 195 - demonstrated remarkable efficacy against R. solanacearum, with in vitro inhibition of 87-100\%, reduction of disease incidence by 40-90\% in tomato seedlings, and promotion of plant growth. Phylogenomic analyses based on ANI and dDDH revealed that RN 11 belongs to the species Priestia aryabhattai (ANI: 98.61\%, dDDH: 88.3\%), while RN 24 and SOL 195 presented values below the cut-off points for new species, potentially representing novel species within the genera Streptomyces and Kitasatospora, respectively. Chapter 2 elucidates the multifaceted potential of A. nematophilus SOL 109, demonstrating in vitro inhibition ranging from 74 to 93\% against phytopathogenic fungi. Under greenhouse conditions, evaluations indicate that the SOL 109 effectively controlled the pathogen R. solani and promoted growth in tomato plants. Genomic and chemical analyses of SOL 109 identified unique and shared biosynthetic gene clusters (BGCs) within the genus Alcaligenes, genes conferring resistance to antibiotics and heavy metals, and metabolites with antimicrobial properties. The results of this thesis highlight the unexplored potential of Amazonian aquatic microorganisms, revealing new actinobacterial species (RN 24 and SOL 195) and reporting for the first time the occurrence of A. nematophilus in Brazil. This study significantly contributes to the development of sustainable plant disease management strategies, offers valuable insights into the secondary metabolism of the genus Alcaligenes, and opens new perspectives for biotechnological applications in agriculture, reinforcing the importance of conservation and study of Amazonian microbial biodiversity.}, author = {Fonseca, Jennifer Salgado da}, @@ -4563,13 +7345,97 @@ @article{fouilloux_building_2023 year = {2023} } +@article{fraccalvieri_isolamento_2025, + abstract = {open}, + author = {FRACCALVIERI, ROSA}, + keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, + language = {ita}, + month = {March}, + note = {Accepted: 2025-05-23T11:24:15Z +Publisher: Università degli studi di Bari}, + shorttitle = {Isolamento di batteri appartenenti alla famiglia delle {Enterobatteriacee} resistenti agli antibiotici in alimenti di origine animale e vegetale}, + title = {Isolamento di batteri appartenenti alla famiglia delle {Enterobatteriacee} resistenti agli antibiotici in alimenti di origine animale e vegetale: analisi genomica e implicazioni per la sicurezza alimentare}, + url = {https://ricerca.uniba.it/handle/11586/539587}, + urldate = {2025-05-29}, + year = {2025} +} + +@article{fraccalvieri_isolation_2025, + author = {Fraccalvieri, Rosa and Castellana, Stefano and Bianco, Angelica and Difato, Laura Maria and Capozzi, Loredana and Del Sambro, Laura and Donatiello, Adelia and Pugliese, Domenico and Tempesta, Maria and Parisi, Antonio and Caruso, Marta}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {July}, + number = {8}, + title = {Isolation of {ESBL}-{Producing} {Enterobacteriaceae} in {Food} of {Animal} and {Plant} {Origin}: {Genomic} {Analysis} and {Implications} for {Food} {Safety}}, + url = {http://europepmc.org/abstract/PMC/PMC12388533}, + volume = {13}, + year = {2025} +} + +@article{fraccalvieri_isolation_2025, + abstract = {The emergence of colistin-resistant Enterobacteriaceae in food products is a growing concern due to the potential transfer of resistance to human pathogens. This study aimed to assess the prevalence of colistin-resistant Enterobacteriaceae in raw and ready-to-eat food samples collected from two regions of Italy (Apulia and Basilicata) and to evaluate their resistance phenotypes and genetic characteristics. A total of 1000 food samples were screened, with a prevalence of 4.4\% of colistin-resistant Enterobacteriaceae. The majority of the isolates belonged to Enterobacter spp. (60\%), followed by Moellerella wisconsensis, Atlantibacter hermannii, Klebsiella pneumoniae, and Escherichia coli, among others. Genomic sequencing and antimicrobial susceptibility testing revealed high levels of resistance to β-lactams, with most isolates exhibiting multidrug resistance (MDR). Notably, seven isolates harbored mcr genes (mcr-1, mcr-9, and mcr-10). Additionally, in four of them were predicted the IncHI2 plasmids, known to facilitate the spread of colistin resistance. Furthermore, 56 antimicrobial resistance genes were identified, suggesting the genetic mechanisms underlying resistance to several antibiotic classes. Virulence gene analysis showed that E. coli and other isolates carried genes linked to pathogenicity, increasing the potential risk to public health. This study emphasizes the role of food as a potential reservoir for colistin-resistant bacteria and the importance of monitoring the spread of AMR genes in foodborne pathogens.}, + author = {Fraccalvieri, Rosa and Bianco, Angelica and Difato, Laura Maria and Capozzi, Loredana and Del Sambro, Laura and Castellana, Stefano and Donatiello, Adelia and Serrecchia, Luigina and Pace, Lorenzo and Farina, Donatella and Galante, Domenico and Caruso, Marta and Tempesta, Maria and Parisi, Antonio}, + doi = {10.3390/microorganisms13010163}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + number = {1}, + pages = {163}, + pmcid = {PMC11767609}, + pmid = {39858930}, + title = {Isolation and {Characterization} of {Colistin}-{Resistant} {Enterobacteriaceae} from {Foods} in {Two} {Italian} {Regions} in the {South} of {Italy}}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11767609/}, + urldate = {2025-02-16}, + volume = {13}, + year = {2025} +} + +@article{frank_complex-type_2021, + abstract = {Roots supply plants with nutrients and water, besides anchoring them in the soil. The primary root with its lateral roots constitutes the central skeleton of the root system. In particular, root hairs increase the root surface, which is critical for optimizing uptake efficiency. During root-cell growth and development, many proteins that are components of, e.g., the cell wall and plasma membrane are constitutively transported through the secretory system and become posttranslationally modified. Here, the best-studied posttranslational modification is protein N-glycosylation. While alterations in the attachment/modification of N-glycans within the ER lumen results in severe developmental defects, the impact of Golgi-localized complex N-glycan modification, particularly on root development, has not been studied in detail. We report that impairment of complex-type N-glycosylation results in a differential response to synthetic phytohormones with earlier and increased root-hair elongation. Application of either the cytokinin BAP, the auxin NAA, or the ethylene precursor ACC revealed an interaction of auxin with complex N-glycosylation during root-hair development. Especially in \textit{gntI} mutant seedlings, the early block of complex N-glycan formation resulted in an increased auxin sensitivity. RNA-seq experiments suggest that \textit{gntI} roots have permanently elevated nutrient-, hypoxia-, and defense-stress responses, which might be a consequence of the altered auxin responsiveness.}, + author = {Frank, Manuel and Kaulfürst-Soboll, Heidi and Fischer, Kerstin and von Schaewen, Antje}, + doi = {10.3389/fpls.2021.635714}, + issn = {1664-462X}, + journal = {Frontiers in plant science}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {635714}, + title = {Complex-{Type} {N}-{Glycans} {Influence} the {Root} {Hair} {Landscape} of {Arabidopsis} {Seedlings} by {Altering} the {Auxin} {Output}}, + url = {http://europepmc.org/abstract/MED/33679849}, + volume = {12}, + year = {2021} +} + +@article{freedman_plasmid_2025, + author = {Freedman, Ashley and Malmstrom, Kendall and Gruber, Paige and Borlee, Bradley R. and Mehaffy, Carolina}, + doi = {10.1128/mra.00341-25}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org}, + month = {June}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e00341--25}, + title = {Plasmid and chromosomal sequences of {Pantoea} agglomerans isolated from air in {Fort} {Collins}, {Colorado}}, + url = {https://journals.asm.org/doi/full/10.1128/mra.00341-25}, + urldate = {2025-06-12}, + volume = {0}, + year = {2025} +} + @article{friedrich_identification_2021, + abstract = {Autosomal dominant polycystic kidney disease (ADPKD) affects more than 12 million people worldwide. Mutations in PKD1 and PKD2 cause cyst formation through unknown mechanisms. To unravel the pathogenic mechanisms in ADPKD, multiple studies have investigated transcriptional mis-regulation in cystic kidneys from patients and mouse models, and numerous dysregulated genes and pathways have been described. Yet, the concordance between studies has been rather limited. Furthermore, the cellular and genetic diversity in cystic kidneys has hampered the identification of mis-expressed genes in kidney epithelial cells with homozygous PKD mutations, which are critical to identify polycystin-dependent pathways. Here we performed transcriptomic analyses of Pkd1- and Pkd2-deficient mIMCD3 kidney epithelial cells followed by a meta-analysis to integrate all published ADPKD transcriptomic data sets. Based on the hypothesis that Pkd1 and Pkd2 operate in a common pathway, we first determined transcripts that are differentially regulated by both genes. RNA sequencing of genome-edited ADPKD kidney epithelial cells identified 178 genes that are concordantly regulated by Pkd1 and Pkd2. Subsequent integration of existing transcriptomic studies confirmed 31 previously described genes and identified 61 novel genes regulated by Pkd1 and Pkd2. Cluster analyses then linked Pkd1 and Pkd2 to mRNA splicing, specific factors of epithelial mesenchymal transition, post-translational protein modification and epithelial cell differentiation, including CD34, CDH2, CSF2RA, DLX5, HOXC9, PIK3R1, PLCB1 and TLR6. Taken together, this model-based integrative analysis of transcriptomic alterations in ADPKD annotated a conserved core transcriptomic profile and identified novel candidate genes for further experimental studies.}, author = {Friedrich, Sebastian and Müller, Hannah and Riesterer, Caroline and Schüller, Hannah and Friedrich, Katja and Wörner, Carlotta Leonie and Busch, Tilman and Viau, Amandine and Kuehn, E. Wolfgang and Köttgen, Michael and Hofherr, Alexis}, doi = {10.1038/s41598-021-94442-8}, + issn = {2045-2322}, + journal = {Scientific reports}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {July}, note = {Publisher: Springer Science and Business Media LLC}, number = {1}, + pages = {15139}, title = {Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia}, url = {https://doi.org/10.1038/s41598-021-94442-8}, volume = {11}, @@ -4615,6 +7481,75 @@ @article{frohlich_benchmarking_2022 year = {2022} } +@article{fuchs_sars-cov-2_2025, + abstract = {A 48-year-old patient underwent lung transplantation because of severe COVID-19, which aggravated his underlying interstitial lung disease, despite the presence of detectable SARS-CoV-2. Subsequently, the graft is re-infected early in the post-procedural phase, leading to viral persistence for more than five months. By analyzing viral evolution and effector immune response within the transplanted organ, we observe three main findings. First, virus evolution differs in the transplanted organ compared to that in the upper respiratory tract and is affected by monoclonal SARS-CoV-2-specific antibodies and molnupiravir. Second, we show the potential clinical relevance of T cell HLA restriction that may facilitate viral clearance in the upper respiratory tract compared to the ongoing viral replication in the HLA mismatch organ. Third, close monitoring and modulation of immunosuppressive and antiviral therapy enables viral clearance in a lung transplantation setting despite incomplete SARS-CoV-2 clearance prior to transplantation.}, + author = {Fuchs, Jonas and Karl, Vivien and Hettich, Ina and Alvarado, Jaime and Eckert, Daniel and Jaki, Lena and Kohl, Ann-Kathrin and Kremser, Anastasia and Maks, Anastasija and Terschluse, Charlott and Agarwal, Prerana and Emmerich, Florian and Fähndrich, Sebastian and Flügler, Annabelle and Hornuss, Daniel and Kalbhenn, Johannes and Kneidinger, Nikolaus and Lau, Inga and Lother, Achim and Moneke, Isabelle and Schibilsky, David and Schygulla, Elisabeth and Venhoff, Nils and Zissel, Gernot and Czerny, Martin and Huzly, Daniela and Kochs, Georg and Neumann-Haefelin, Christoph and Passlick, Bernward and Stolz, Daiana and Thimme, Robert and Panning, Marcus and Hofmann, Maike and Frye, Björn C}, + doi = {10.1038/s41467-025-63681-y}, + issn = {2041-1723}, + journal = {Nature communications}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {September}, + number = {1}, + pages = {8292}, + title = {{SARS}-{CoV}-2 infection dynamics in a {MHCI}-mismatched lung transplant recipient}, + url = {https://europepmc.org/articles/PMC12441153}, + volume = {16}, + year = {2025} +} + +@article{fuchs_varvamp_2025, + abstract = {Time- and cost-saving surveillance of viral pathogens is achieved by tiled sequencing in which a viral genome is amplified in overlapping PCR amplicons and qPCR. However, designing pan-specific primers for viral pathogens with high genomic variability represents a significant challenge. Here, we present a bioinformatics command-line tool, called varVAMP (variable virus amplicons), which addresses this issue. It relies on multiple sequence alignments of highly variable virus sequences and enables degenerate primer design for qPCR or tiled amplicon whole genome sequencing. We demonstrate the utility of varVAMP by designing and evaluating novel pan-specific primer schemes suitable for sequencing the genomes of SARS-CoV-2, Hepatitis E virus, rat Hepatitis E virus, Hepatitis A virus, Borna-disease-virus-1, and Poliovirus using clinical samples. Importantly, we also designed primers on the same input data using the software packages PrimalScheme and Olivar and showed that varVAMP minimizes primer mismatches most efficiently. Finally, we established highly sensitive and specific Poliovirus qPCR assays that could potentially simplify current Poliovirus surveillance. varVAMP is open-source and available through PyPI, UseGalaxy, Bioconda, and https://github.com/jonas-fuchs/varVAMP .}, + author = {Fuchs, Jonas and Kleine, Johanna and Schemmerer, Mathias and Kreibich, Julian and Maier, Wolfgang and Battur, Namuun and Krannich, Thomas and Sedaghatjoo, Somayyeh and Jaki, Lena and Maks, Anastasija and Boehm, Christina and Wilhelm, Carina and Schulze, Jessica and Mache, Christin and Berger, Elischa and Panajotov, Jessica and Arnold, Lisa and Grüning, Björn and Bauswein, Markus and Böttcher, Sindy and Johne, Reimar and Wenzel, Jürgen and Hölzer, Martin and Panning, Marcus}, + doi = {10.1038/s41467-025-60175-9}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Infectious-disease diagnostics, Software, Virology}, + language = {eng}, + month = {May}, + number = {1}, + pages = {5067}, + pmid = {40449995}, + shorttitle = {{varVAMP}}, + title = {{varVAMP}: degenerate primer design for tiled full genome sequencing and {qPCR}}, + volume = {16}, + year = {2025} +} + +@article{fullstone_epigenomic_2025, + abstract = {Long-duration spaceflight imposes significant physiological stress on astronauts, including profound alterations in immune function. This study investigated epigenetic changes in immune cells following prolonged orbital spaceflight by analysing histone modifications in CD4+ and CD8+ T-cells from astronauts before, immediately after, and during recovery from spaceflight. Using Cleavage Under Targets and Tagmentation (Cut\&Tag) to assess H3K27ac modifications, we identified significant alterations in chromatin accessibility, predominantly involving immune response pathways, gene regulation, and cellular adaptation mechanisms. While some epigenetic changes were transient, others persisted beyond 50 days post-return, suggesting long-term effects. These findings enhance our understanding of immune adaptation to spaceflight and have implications for mitigating spaceflight-associated health risks. Furthermore, they provide valuable insights into immune system regulation under high-stress conditions, potentially informing research on immunodeficiency disorders, cancer epigenetics, and aging-related immune decline on Earth. This study underscores the critical role of epigenetics in long-term space missions and terrestrial health applications.}, + author = {Fullstone, Tabea L and Fischer, Lukas F J and Bohmeier, Maria and Frings-Meuthen, Petra and Crucian, Brian E and Rathert, Philipp}, + doi = {10.1038/s41598-025-17930-1}, + issn = {2045-2322}, + journal = {Scientific reports}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {September}, + number = {1}, + pages = {32445}, + title = {Epigenomic profiling of immune cell subtypes reveals {H3K27ac}-marked stress signatures after long-duration spaceflight}, + url = {https://europepmc.org/articles/PMC12432228}, + volume = {15}, + year = {2025} +} + +@article{fullstone_identification_2025, + abstract = {Platinum-based combination chemotherapy remains the backbone of first-line treatment for patients with advanced epithelial ovarian cancer (EOC). While most patients initially respond well to the treatment, patients with relapse ultimately develop platinum resistance. This study identified FLYWCH-type zinc finger-containing protein 1 (FLYWCH1) as an important regulator in the resistance development process. We showed that the loss of FLYWCH1 promotes platinum resistance in EOC cells, and the low FLYWCH1 expression is correlated with poor prognosis of EOC patients. In platinum-sensitive cells, FLYWCH1 colocalizes with H3K9me3, but this association is significantly reduced when cells acquire resistance. The suppression of FLYWCH1 induces gene expression changes resulting in the deregulation of pathways associated with resistance. In line with its connection to H3K9me3, FLYWCH1 induces gene silencing in a synthetic reporter assay and the suppression of FLYWCH1 alters H3K9me3 at promoter regions and repeat elements. The loss of FLYWCH1 leads to the derepression of LTR and Alu repeats, thereby increasing transcriptional plasticity and driving the resistance development process. Our data highlight the importance of FLYWCH1 in chromatin biology and acquisition of platinum resistance through transcriptional plasticity and propose FLYWCH1 as a potential biomarker for predicting treatment responses in EOC patients.}, + author = {Fullstone, Tabea L and Rohm, Helene and Kaltofen, Till and Hierlmayer, Sophia and Reichenbach, Juliane and Schweikert, Simon and Knodel, Franziska and Loeffler, Ann-Kathrin and Mayr, Doris and Jeschke, Udo and Mahner, Sven and Kessler, Mirjana and Trillsch, Fabian and Rathert, Philipp}, + copyright = {https://creativecommons.org/licenses/by/4.0/}, + doi = {10.1093/narcan/zcaf012}, + issn = {2632-8674}, + journal = {NAR Cancer}, + keywords = {{\textgreater}UseGalaxy.eu, Carcinoma, Ovarian Epithelial, Drosophila Proteins, Drug Resistance, Neoplasm, Neoplasms, Glandular and Epithelial, Ovarian Neoplasms}, + language = {en}, + month = {April}, + number = {2}, + pages = {zcaf012}, + title = {Identification of {FLYWCH1} as a regulator of platinum-resistance in epithelial ovarian cancer}, + url = {https://academic.oup.com/narcancer/article/doi/10.1093/narcan/zcaf012/8106440}, + urldate = {2025-04-15}, + volume = {7}, + year = {2025} +} + @article{gaafar_novel_2020, abstract = {Background Physostegia chlorotic mottle virus (PhCMoV; genus: Alphanucleorhabdovirus, family: Rhabdoviridae) and tomato brown rugose fruit virus (ToBRFV; genus: Tobamovirus, family: Virgaviridae) are newly emerging plant viruses that have a dramatic effect on tomato production. Among various known virus-control strategies, RNAi-mediated defence has shown the potential to protect plants against various pathogens including viral infections. Micro(mi)RNAs play a major role in RNAi-mediated defence. Methods Using in silico analyses, we investigated the possibility of tomato-encoded miRNAs (TomiRNA) to target PhCMoV and ToBRFV genomes using five different algorithms, i.e., miRanda, RNAhybrid, RNA22, Tapirhybrid and psRNATarget. Results The results revealed that 14 loci on PhCMoV and 10 loci on ToBRFV can be targeted by the TomiRNAs based on the prediction of at least three algorithms. Interestingly, one TomiRNA, miR6026, can target open reading frames from both viruses, i.e., the phosphoprotein encoding gene of PhCMoV, and the two replicase components of ToBRFV. There are currently no commercially available PhCMoV- or ToBRFV-resistant tomato varieties, therefore the predicted data provide useful information for the development of PhCMoV- and ToBFRV-resistant tomato plants.}, author = {Gaafar, Yahya Zakaria Abdou and Ziebell, Heiko}, @@ -4634,6 +7569,25 @@ @article{gaafar_novel_2020 year = {2020} } +@article{gadkar_rlb-malbac_2025, + abstract = {Successful sequencing of genomes on Oxford Nanopore Technologies (ONT) sequencing platforms is dependant on obtaining sufficient amounts of high-quality genomic DNA. ONT’s Rapid PCR kit (SQK-RPB114.24) kit is specifically designed to address input template limitations, whereby low amounts of target DNA (1–5 ng) is pre-amplified to {\textgreater} 100–200 ng using PCR. The success of this workflow is however dependent on the quality of input DNA, which as per the SQK-RPB114.24 kit’s instructions, should be of length {\textgreater} 4 kb for an efficient tagmentation—a step pre-cursor to PCR amplification. Obtaining high quality, intact genomic DNA from clinical samples or viral genomes, can sometimes be challenging and this method seeks to address this limitation.}, + author = {Gadkar, Vijay J. and Goldfarb, David M. and Dhaliwal, Sukh and Gubbay, Jonathan B. and Tilley, Peter A. G.}, + doi = {10.1186/s44330-025-00024-9}, + issn = {3004-8729}, + journal = {BMC Methods}, + keywords = {{\textgreater}UseGalaxy.eu, Antimicrobial resistance (AMR), Comprehensive Antibiotic Resistance Database (CARD), Low-input DNA, Multiple Annealing and Looping Based Amplification Cycles chemistry (MALBAC), Oxford Nanopore’s Technologies (ONT), RLB- MALBAC, Rapid Adapter (RA), Rapid PCR Barcoding (SQK-RPB114.24), Whole Genome Amplification (WGA)}, + language = {en}, + month = {March}, + number = {1}, + pages = {4}, + shorttitle = {{RLB}-{MALBAC}}, + title = {{RLB}-{MALBAC}: a rapid, non-transposase method for synthesizing unbiased sequencing libraries from low amount of genomic {DNA} for {Nanopore} sequencing}, + url = {https://doi.org/10.1186/s44330-025-00024-9}, + urldate = {2025-03-09}, + volume = {2}, + year = {2025} +} + @article{gains_identification_2023, abstract = {Objective The study aimed to investigate the role of the PGN2012 gene of the periodontitis contributing pathobiont Porphyromonas gingivalis. PGN2012 is a homolgue of TolC and is a gene our group previously showed was overexpressed in hyperinvasive cells. @@ -4658,6 +7612,34 @@ @article{gains_identification_2023 year = {2023} } +@article{galaxy_and_hyphy_developments_teams_no_2020, + abstract = {The current state of much of the Wuhan pneumonia virus (COVID-19) research shows a regrettable lack of data sharing and considerable analytical obfuscation. This impedes global research cooperation, which is essential for tackling public health emergencies, and requires unimpeded access to data, analysis tools, and computational infrastructure. Here we show that community efforts in developing open analytical software tools over the past ten years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an open and transparent manner. Specifically, we use all COVID-19 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and to (2) demonstrate that existing community efforts in curation and deployment of biomedical software can reliably support rapid, reproducible research during global health crises. All our analyses are fully documented at https://github.com/galaxyproject/SARS-CoV-2 .}, + author = {{=Galaxy and HyPhy developments teams} and Nekrutenko, Anton and Kosakovsky Pond, Sergei}, + doi = {10.1101/2020.02.21.959973}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics}, + url = {http://europepmc.org/abstract/PPR/PPR114129}, + year = {2020} +} + +@article{galaxy_community_galaxy_2024, + abstract = {Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO2 emissions generated by each Galaxy job.}, + author = {{=Galaxy Community}}, + doi = {10.1093/nar/gkae410}, + issn = {0305-1048}, + journal = {Nucleic Acids Res}, + keywords = {{\textgreater}UseGalaxy.eu, Software}, + language = {eng}, + month = {July}, + number = {W1}, + pages = {W83--W94}, + title = {The {Galaxy} platform for accessible, reproducible, and collaborative data analyses: 2024 update}, + url = {http://europepmc.org/abstract/MED/38769056}, + volume = {52}, + year = {2024} +} + @article{galgano_pilot_2023, abstract = {The indiscriminate use of antimicrobials in poultry farms is linked to the increase in multi-resistant bacteria. Accordingly, based on the antimicrobial properties of Thyme Essential Oil (TEO), the present study evaluated the effects of TEO on the reduction of common microbial contaminants and Salmonella on poultry litter. A litter bulk sample was collected in a broiler farm and qualitative/quantitative investigations identified Escherichia coli and Mammaliicoccus lentus. The experimental contamination with Salmonella Derby wild strain was also performed. All pathogens showed phenotypic and genotypic resistance to different classes of antibiotics. The litter, split in different units, was treated with aqueous solutions of TEO at different concentrations (5\% to 1.25\%), demonstrating its effectiveness in reducing the total number of bacteria. The strongest antibacterial action was observed at the lowest concentration against Enterobacteriaceae, with a growth reduction compared to the positive control of 73.3\% and 77.8\% against E. coli and Salmonella Derby, respectively, while towards M. lentus the reduction was 50\%. Our data confirm the antimicrobial activity of TEO and suggest its possible application for the treatment of poultry litter as an effective and natural approach for the prevention of diseases caused by the most common bacteria that colonize poultry farms, counteracting the onset of antibiotic resistance.}, author = {Galgano, Michela and Pellegrini, Francesco and Fracchiolla, Giuseppe and Mrenoshki, Daniela and Zarea, Aya Attia Koraney and Bianco, Angelica and Del Sambro, Laura and Capozzi, Loredana and Schiavone, Antonella and Saleh, Medhat S. and Camero, Michele and Tempesta, Maria and Cirone, Francesco and Buonavoglia, Domenico and Pratelli, Annamaria and Buonavoglia, Alessio}, @@ -4696,6 +7678,23 @@ @article{galia-camps_jumping_2024 year = {2024} } +@article{galindo-moreno_aurora_2025, + abstract = {Aurora B kinase, as part of the chromosomal passenger complex (CPC), controls key processes during the cell cycle such as DNA compaction, genome partitioning, or cytokinesis. Nonetheless, increased Aurora B levels are a potential threat for the cells and have been linked to different tumor types. We have carried out an exhaustive characterization of the global consequences of the overexpression of Aurora B and INCENP, the scaffold of the CPC and an activator of Aurora B kinase activity, in non-transformed human cells. Our data demonstrate not only that an individual increase in the levels of Aurora B or INCENP have a different impact on the cells, but more importantly that their simultaneous overexpression stabilizes both CPC components, exacerbates Aurora B activity, severely impairs mitotic progression and chromosome dynamics, and has a distinctive and more dramatic effect on the transcriptional landscape of the cells.}, + author = {Galindo-Moreno, María and Muñoz-Barrera, Marta and Marcozzi, Chiara and Bruno, Federica and Maya-Álvarez, Cristina and Cortés-Ledesma, Felipe and Ríos, Rosa María and González-Aguilera, Cristina and Monje-Casas, Fernando}, + doi = {10.1016/j.isci.2025.112731}, + issn = {2589-0042}, + journal = {iScience}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {June}, + number = {6}, + pages = {112731}, + title = {Aurora {B} and {INCENP} co-overexpression severely disrupts mitosis and distinctly modifies the global transcriptional landscape}, + url = {http://europepmc.org/abstract/MED/40530423}, + volume = {28}, + year = {2025} +} + @article{gallus_fructobacillus_2022, abstract = {A Fructobacillus strain was isolated from the flower of a nodding thistle (Carduus nutans) collected in Bavaria, Germany. The strain is Gram-positive, rod-shaped, non-motile, non-sporulating, catalase- and oxidase-negative, and facultatively anaerobic. Growth can be detected at 10–37 °C and pH 4 to 9. The genome size is about 1.56 Mbp and the G+C content is 43.76 mol\%. Assignment to the genus Fructobacillus was done by average nucleotide identity (ANI), 16S rRNA gene sequence and multilocus sequence analyses. Calculations of ANI and digital DNA–DNA hybridization values indicate a novel species with Fructobacillus tropaeoli DSM 23246T (93.58\% ANI and 57.9 \% dDDH) being its closest relative. Therefore, a new species named Fructobacillus cardui sp. nov. with TMW 2.2452T (=DSM 113480T=CECT 30515T) as type strain is proposed.,}, author = {Gallus, Marion K. and Beer, Irina and Ivleva, Natalia P. and Ehrmann, Matthias A.YR 2022}, @@ -4723,7 +7722,7 @@ @article{galvis_dimet_2024 doi = {10.1093/bioinformatics/btae282}, issn = {1367-4811}, journal = {Bioinformatics (Oxford, England)}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Isotope Labeling, Metabolomics, Software}, language = {eng}, month = {April}, pages = {btae282}, @@ -4733,6 +7732,45 @@ @article{galvis_dimet_2024 year = {2024} } +@article{galvis_using_2025, + abstract = {Stable-isotope resolved metabolomics (SIRM) is a powerful approach for characterizing metabolic states in cells and organisms. By incorporating isotopes, such as 13C, into substrates, researchers can trace reaction rates across specific metabolic pathways. Integrating metabolomics data with gene expression profiles further enriches the analysis, as we demonstrated in our prior study on glioblastoma metabolic symbiosis. However, the bioinformatics tools for analyzing tracer metabolomics data have been limited. In this protocol, we encourage the researchers to use SIRM and transcriptomics data and to perform the downstream analysis using our software tool DIMet. Indeed, DIMet is the first comprehensive tool designed for the differential analysis of tracer metabolomics data, alongside its integration with transcriptomics data. DIMet facilitates the analysis of stable-isotope labeling and metabolic abundances, offering a streamlined approach to infer metabolic changes without requiring complex flux analysis. Its pathway-based "metabologram" visualizations effectively integrate metabolomics and transcriptomics data, offering a versatile platform capable of analyzing corrected tracer datasets across diverse systems, organisms, and isotopes. We provide detailed steps for sample preparation and data analysis using DIMet through its intuitive, web-based Galaxy interface. To showcase DIMet's capabilities, we analyzed LDHA/B knockout glioblastoma cell lines compared to controls. Accessible to all researchers through Galaxy, DIMet is free, user-friendly, and open source, making it a valuable resource for advancing metabolic research., +Key features +, • Glioblastoma tumor spheroids in vitro replicate tumors’ three-dimensional structure and natural nutrient, metabolite, and gas gradients, providing a more realistic model of tumor biology., • Joint analysis of tracer metabolomics and transcriptomics datasets provides deeper insights into the metabolic states of cells., • DIMet is a web-based tool for differential analysis and seamless integration of metabolomics and transcriptomics data, making it accessible and user-friendly., • DIMet enables researchers to infer metabolic changes, offering intuitive and visually appealing "metabologram" outputs, surpassing conventional visual representations commonly used in the field.}, + author = {Galvis, Johanna and Guyon, Joris and Daubon, Thomas and Nikolski, Macha}, + doi = {10.21769/BioProtoc.5168}, + issn = {2331-8325}, + journal = {Bio-protocol}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + number = {2}, + pages = {e5168}, + pmcid = {PMC11769753}, + pmid = {39872723}, + shorttitle = {Using {DIMet} for {Differential} {Analysis} of {Labeled} {Metabolomics} {Data}}, + title = {Using {DIMet} for {Differential} {Analysis} of {Labeled} {Metabolomics} {Data}: {A} {Step}-by-step {Guide} {Showcasing} the {Glioblastoma} {Metabolism}}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11769753/}, + urldate = {2025-02-16}, + volume = {15}, + year = {2025} +} + +@article{gao_comprehensive_2020, + abstract = {Mammalian DNA methylation patterns are established by two de novo DNA methyltransferases, DNMT3A and DNMT3B, which exhibit both redundant and distinctive methylation activities. However, the related molecular basis remains undetermined. Through comprehensive structural, enzymology and cellular characterization of DNMT3A and DNMT3B, we here report a multi-layered substrate-recognition mechanism underpinning their divergent genomic methylation activities. A hydrogen bond in the catalytic loop of DNMT3B causes a lower CpG specificity than DNMT3A, while the interplay of target recognition domain and homodimeric interface fine-tunes the distinct target selection between the two enzymes, with Lysine 777 of DNMT3B acting as a unique sensor of the +1 flanking base. The divergent substrate preference between DNMT3A and DNMT3B provides an explanation for site-specific epigenomic alterations seen in ICF syndrome with DNMT3B mutations. Together, this study reveals distinctive substrate-readout mechanisms of the two DNMT3 enzymes, implicative of their differential roles during development and pathogenesis.}, + author = {Gao, Linfeng and Emperle, Max and Guo, Yiran and Grimm, Sara A and Ren, Wendan and Adam, Sabrina and Uryu, Hidetaka and Zhang, Zhi-Min and Chen, Dongliang and Yin, Jiekai and Dukatz, Michael and Anteneh, Hiwot and Jurkowska, Renata Z and Lu, Jiuwei and Wang, Yinsheng and Bashtrykov, Pavel and Wade, Paul A and Wang, Gang Greg and Jeltsch, Albert and Song, Jikui}, + doi = {10.1038/s41467-020-17109-4}, + issn = {2041-1723}, + journal = {Nature communications}, + keywords = {{\textgreater}UseGalaxy.eu, DNA Methylation}, + language = {eng}, + month = {July}, + number = {1}, + pages = {3355}, + title = {Comprehensive structure-function characterization of {DNMT3B} and {DNMT3A} reveals distinctive de novo {DNA} methylation mechanisms}, + url = {http://europepmc.org/abstract/MED/32620778}, + volume = {11}, + year = {2020} +} + @article{gao_comprehensive_2020, abstract = {{\textless}p{\textgreater}Mammalian DNA methylation patterns are established by two \textit{de novo} DNA methyltransferases DNMT3A and DNMT3B, which exhibit both redundant and distinctive methylation activities. However, the related molecular basis remains undetermined. Through comprehensive structural, enzymology and cellular characterization of DNMT3A and DNMT3B, we here report a multi-layered substrate-recognition mechanism underpinning their divergent genomic methylation activities. A hydrogen bond in the catalytic loop of DNMT3B causes a lower CpG specificity than DNMT3A, while the interplay of target recognition domain and homodimeric interface fine-tunes the distinct target selection between the two enzymes, with Lysine 777 of DNMT3B acting as a unique sensor of the +1 flanking base. The divergent substrate preference between DNMT3A and DNMT3B provides an explanation for site-specific epigenomic alterations seen in ICF syndrome with DNMT3B mutations. Together, this study reveals crucial and distinctive substrate-readout mechanisms of the two DNMT3 enzymes, implicative of their differential roles during development and pathogenesis.{\textless}/p{\textgreater}}, author = {Gao, Linfeng and Emperle, Max and Guo, Yiran and Grimm, Sara A. and Ren, Wendan and Adam, Sabrina and Uryu, Hidetaka and Zhang, Zhi-Min and Chen, Dongliang and Yin, Jiekai and Dukatz, Michael and Anteneh, Hiwot and Jurkowska, Renata Z. and Lu, Jiuwei and Wang, Yinsheng and Bashtrykov, Pavel and Wade, Paul A. and Wang, Gang Greg and Jeltsch, Albert and Song, Jikui}, @@ -4786,13 +7824,17 @@ @article{gao_pluripotency_2020 } @article{gao_pluripotency_2022, + abstract = {Awakening of zygotic transcription in animal embryos relies on maternal pioneer transcription factors. The interplay of global and specific functions of these proteins remains poorly understood. Here, we analyze chromatin accessibility and time-resolved transcription in single and double mutant zebrafish embryos lacking pluripotency factors Pou5f3 and Sox19b. We show that two factors modify chromatin in a largely independent manner. We distinguish four types of direct enhancers by differential requirements for Pou5f3 or Sox19b. We demonstrate that changes in chromatin accessibility of enhancers underlie the changes in zygotic expression repertoire in the double mutants. Pou5f3 or Sox19b promote chromatin accessibility of enhancers linked to the genes involved in gastrulation and ventral fate specification. The genes regulating mesendodermal and dorsal fates are primed for activation independently of Pou5f3 and Sox19b. Strikingly, simultaneous loss of Pou5f3 and Sox19b leads to premature expression of genes, involved in regulation of organogenesis and differentiation.}, author = {Gao, Meijiang and Veil, Marina and Rosenblatt, Marcus and Riesle, Aileen Julia and Gebhard, Anna and Hass, Helge and Buryanova, Lenka and Yampolsky, Lev Y. and Grüning, Björn and Ulianov, Sergey V. and Timmer, Jens and Onichtchouk, Daria}, doi = {10.1038/s41467-022-28434-1}, + issn = {2041-1723}, journal = {Nature Communications}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Gene Expression Regulation, Developmental, Genome}, + language = {eng}, month = {February}, note = {Publisher: Springer Science and Business Media LLC}, number = {1}, + pages = {788}, title = {Pluripotency factors determine gene expression repertoire at zygotic genome activation}, url = {https://doi.org/10.1038/s41467-022-28434-1}, volume = {13}, @@ -4809,6 +7851,7 @@ @article{garcia-fernandez_antibiotic_2024 language = {English}, month = {January}, note = {Publisher: Frontiers}, + pages = {1293666}, title = {Antibiotic resistance, plasmids, and virulence-associated markers in human strains of {Campylobacter} jejuni and {Campylobacter} coli isolated in {Italy}}, url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1293666/full}, urldate = {2024-05-17}, @@ -4816,6 +7859,59 @@ @article{garcia-fernandez_antibiotic_2024 year = {2024} } +@article{garcia-jimenez_exploring_2025, + abstract = {IntroductionThe discovery of transposable elements (TEs), or transposons, by Barbara McClintock in 1950 revolutionized our understanding of genome dynamics. TEs are recognized for their critical role in genetic variability and evolution. They are categorized into two main classes: class I (retrotransposons), which transpose via an RNA intermediate, and class II, which transpose directly via DNA. TEs significantly influence gene expression through insertions that can disrupt gene function. Consequently, organisms have evolved mechanisms to regulate TE activity, particularly under stress conditions, where TE activation can lead to mutations. In marine macroalgae, TEs are known to shape genome architecture, yet little is known about their dynamics.MethodsIn this study, 17 publicly available but non-annotated algal genomes were analyzed to identify and characterize transposable elements. The Earlgrey pipeline, a powerful tool for TE annotation, was used to quantify their diversity and historical activity. A local script was further employed to investigate the genomic co-localization of TEs with annotated protein-coding sequences.ResultsThe analysis revealed significant diversity in TE composition among red, brown, and green algae. Retrotransposons with long terminal repeats (LTRs) were found to be particularly abundant in red algae. Many of these LTRs were located near or within regions encoding proteins, as identified through three protein databases. Notably, these included LTR-specific enzymes such as ribonuclease H, as well as nucleic acid–binding proteins and cation-binding proteins like CCHC-type zinc-finger proteins and haem peroxidase superfamily members, which are involved in stress response pathways.DiscussionThe co-localization of LTRs with stress-responsive protein-coding genes raises intriguing questions about the potential regulatory interplay between TEs and stress adaptation. It remains to be determined whether LTR activity is modulated by the activation of these proteins under stress, or if LTRs have been assimilated into the cellular network to promote protein expression as part of an adaptive response. These findings suggest a promising avenue for exploring the functional integration of TEs into stress resilience mechanisms and highlight their potential role in the evolutionary dynamics of marine algae.}, + author = {Garcia-Jimenez, Pilar and Robaina, Rafael R.}, + doi = {10.3389/fmars.2025.1592442}, + issn = {2296-7745}, + journal = {Frontiers in Marine Science}, + keywords = {{\textgreater}UseGalaxy.eu, LTR type, evolutionary dynamics, gene products, seaweed, stress response, transposons}, + language = {English}, + month = {June}, + note = {Publisher: Frontiers}, + shorttitle = {Exploring transposons in macroalgae}, + title = {Exploring transposons in macroalgae: {LTR} elements and neighboring genes in red seaweeds}, + url = {https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2025.1592442/full}, + urldate = {2025-07-12}, + volume = {12}, + year = {2025} +} + +@incollection{garcia_exploring_2025, + abstract = {Overexpressing a gene in a mammalian cell line can be an extremely powerful technique to investigate and explore a gene’s biological functions and associated pathways. Here we describe how combining wet-lab methodology and in-silico transcriptomic approaches can aid in the discovery of unknown gene functions, perturbation of molecular processes or the elucidation of mechanism of action.}, + address = {New York, NY}, + author = {Garcia, Isabella R. and Larcombe, Lee D.}, + booktitle = {Target {Identification} and {Validation} in {Drug} {Discovery}: {Methods} and {Protocols}}, + doi = {10.1007/978-1-0716-4418-8_7}, + editor = {Moll, Jürgen and Carotta, Sebastian}, + isbn = {978-1-0716-4418-8}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + pages = {121--136}, + publisher = {Springer US}, + title = {Exploring the {Perturbation} of {Biological} {Processes} {Caused} by {Gene} {Upregulation} {Using} {Knock}-{In} {Transfection}, {Transcriptomics}, and {Bioinformatics} {Analysis}}, + url = {https://doi.org/10.1007/978-1-0716-4418-8_7}, + urldate = {2025-04-21}, + year = {2025} +} + +@article{garrido-gala_comprehensive_2022, + abstract = {WRKY transcription factors play critical roles in plant growth and development or stress responses. Using up-to-date genomic data, a total of 64 and 257 WRKY genes have been identified in the diploid woodland strawberry, \textit{Fragaria vesca}, and the more complex allo-octoploid commercial strawberry, \textit{Fragaria} × \textit{ananassa} cv. Camarosa, respectively. The completeness of the new genomes and annotations has enabled us to perform a more detailed evolutionary and functional study of the strawberry WRKY family members, particularly in the case of the cultivated hybrid, in which homoeologous and paralogous \textit{FaWRKY} genes have been characterized. Analysis of the available expression profiles has revealed that many strawberry \textit{WRKY} genes show preferential or tissue-specific expression. Furthermore, significant differential expression of several \textit{FaWRKY} genes has been clearly detected in fruit receptacles and achenes during the ripening process and pathogen challenged, supporting a precise functional role of these strawberry genes in such processes. Further, an extensive analysis of predicted development, stress and hormone-responsive cis-acting elements in the strawberry WRKY family is shown. Our results provide a deeper and more comprehensive knowledge of the \textit{WRKY} gene family in strawberry.}, + author = {Garrido-Gala, José and Higuera, José-Javier and Rodríguez-Franco, Antonio and Muñoz-Blanco, Juan and Amil-Ruiz, Francisco and Caballero, José L}, + doi = {10.3390/plants11121585}, + issn = {2223-7747}, + journal = {Plants (Basel, Switzerland)}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {June}, + number = {12}, + pages = {1585}, + title = {A {Comprehensive} {Study} of the {WRKY} {Transcription} {Factor} {Family} in {Strawberry}}, + url = {http://europepmc.org/abstract/MED/35736736}, + volume = {11}, + year = {2022} +} + @article{garrido_identification_2020, abstract = {Meiosis is a specialized type of cell division occurring in sexually reproducing organisms to generate haploid cells known as gametes. In flowering plants, male gametes are produced in anthers, being encased in pollen grains. Understanding the genetic regulation of meiosis key events such as chromosome recognition and pairing, synapsis and recombination, is needed to manipulate chromosome associations for breeding purposes, particularly in important cereal crops like wheat. Reverse transcription-quantitative PCR (RT-qPCR) is widely used to analyse gene expression and to validate the results obtained by other transcriptomic analyses, like RNA-seq. Selection and validation of appropriate reference genes for RT-qPCR normalization is essential to obtain reproducible and accurate expression data. In this work, twelve candidate reference genes were evaluated using the mainstream algorithms geNorm, Normfinder, BestKeeper and ΔCt, then ranked from most to least suitable for normalization with RefFinder. Different sets of reference genes were recommended to normalize gene expression data in anther meiosis of bread and durum wheat, their corresponding genotypes in the absence of the Ph1 locus and for comparative studies among wheat genotypes. Comparisons between meiotic (anthers) and somatic (leaves and roots) wheat tissues were also carried out. To the best of our knowledge, our study provides the first comprehensive list of reference genes for robust RT-qPCR normalization to study differentially expressed genes during male meiosis in wheat in a breeding framework.}, author = {Garrido, José and Aguilar, Miguel and Prieto, Pilar}, @@ -4823,7 +7919,7 @@ @article{garrido_identification_2020 doi = {10.1038/s41598-020-59580-5}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Gene Expression Regulation, Plant, Genes, Essential, Meiosis, Transcriptome}, language = {en}, month = {February}, note = {Number: 1 @@ -4837,6 +7933,40 @@ @article{garrido_identification_2020 year = {2020} } +@article{gather_lincrna_2025, + abstract = {Derailed gene expression programs within the developing nervous system, encompassing both transcriptional and post-transcriptional processes, can cause diverse neurodevelopmental diseases (NDD). The NDD FOXG1-syndrome lacks full understanding of the mechanistic role of its eponymous gene product. While it is known that FOXG1 acts in part at the chromatin by binding to regulative regions, it is unclear what factors control its presence at specific sites. Long non-coding RNAs (lncRNAs) can mediate site-directed transcription factor binding, but their potential role in FOXG1-syndrome has not been described. Here, we show that FOXG1 localisation is regulated at selected loci through the lncRNA Pantr1. We identified FOXG1 as an upstream transcriptional activator of Pantr1 in human and mice. Further, we discovered that FOXG1 has the ability to associate with RNAs. Both transcriptional regulation of Pantr1 by FOXG1 and binding of both partners build up a regulative network that impacts the localisation of FOXG1 at selected genomic loci. Specifically, Pantr1 facilitates cooperative presence of FOXG1/NEUROD1 at specific sites, and Pantr1 reduction leads to redistribution of FOXG1 to comparably more generic binding sites. The rescue of impaired dendritic outgrowth upon FOXG1 reduction by simultaneous overexpression of Pantr1 underlines the importance of the FOXG1/Pantr1 regulative network.}, + author = {Gather, Fabian and Rauleac, Tudor and Akol, Ipek and Arumugam, Ganeshkumar and Fullio, Camila L and Müller, Teresa and Kleidonas, Dimitrios and Geiss-Friedlander, Ruth and Fischer, Andre and Vlachos, Andreas and Backofen, Rolf and Vogel, Tanja}, + doi = {10.1093/nar/gkaf539}, + issn = {1362-4962}, + journal = {Nucleic Acids Research}, + keywords = {{\textgreater}UseGalaxy.eu, Chromatin, Forkhead Transcription Factors, Nerve Tissue Proteins, RNA, Long Noncoding}, + month = {July}, + number = {12}, + pages = {gkaf539}, + title = {The {lincRNA} {Pantr1} is a {FOXG1} target gene conferring site-specific chromatin binding of {FOXG1}}, + url = {https://doi.org/10.1093/nar/gkaf539}, + urldate = {2025-07-12}, + volume = {53}, + year = {2025} +} + +@article{gavalda-garcia_bio2byte_2024, + abstract = {{\textless}h4{\textgreater}Summary{\textless}/h4{\textgreater}We introduce a unified Python package for the prediction of protein biophysical properties, streamlining previous tools developed by the Bio2Byte research group. This suite facilitates comprehensive assessments of protein characteristics, incorporating predictors for backbone and sidechain dynamics, local secondary structure propensities, early folding, long disorder, beta-sheet aggregation, and fused in sarcoma (FUS)-like phase separation. Our package significantly eases the integration and execution of these tools, enhancing accessibility for both computational and experimental researchers.{\textless}h4{\textgreater}Availability and implementation{\textless}/h4{\textgreater}The suite is available on the Python Package Index (PyPI): https://pypi.org/project/b2bTools/ and Bioconda: https://bioconda.github.io/recipes/b2btools/README.html for Linux and macOS systems, with Docker images hosted on Biocontainers: https://quay.io/repository/biocontainers/b2btools?tab=tags\&tag=latest and Docker Hub: https://hub.docker.com/u/bio2byte. Online deployments are available on Galaxy Europe: https://usegalaxy.eu/root?tool\_id=b2btools\_single\_sequence and our online server: https://bio2byte.be/b2btools/. The source code can be found at https://bitbucket.org/bio2byte/b2btools\_releases.}, + author = {Gavalda-Garcia, Jose and Díaz, Adrián and Vranken, Wim}, + doi = {10.1093/bioinformatics/btae543}, + issn = {1367-4803}, + journal = {Bioinformatics}, + keywords = {{\textgreater}UseGalaxy.eu, Proteins, Software}, + language = {eng}, + month = {September}, + number = {9}, + pages = {btae543}, + title = {{bio2Byte} {Tools} deployment as a {Python} package and {Galaxy} tool to predict protein biophysical properties}, + url = {http://europepmc.org/abstract/MED/39240327}, + volume = {40}, + year = {2024} +} + @misc{gavalda-garcia_bio2byte_2024, abstract = {We introduce a unified Python package for the prediction of protein biophysical properties, streamlining previous tools developed by the Bio2Byte research group. This suite facilitates comprehensive assessments of protein characteristics, incorporating predictors for backbone and sidechain dynamics, local secondary structure propensities, early folding, long disorder, beta-sheet aggregation and FUS-like phase separation. Our package significantly eases the integration and execution of these tools, enhancing accessibility for both computational and experimental researchers.}, author = {Gavalda-Garcia, Jose and Diaz, Adrian and Vranken, Wim}, @@ -4851,6 +7981,22 @@ @misc{gavalda-garcia_bio2byte_2024 year = {2024} } +@article{geiszelhardt_glia_2025, + abstract = {Nanosized titanium dioxide is widely used by the industry, e.g., in pigments, suncreams, and food colors. Its environmental and biological effects have been investigated in the past; however, few studiesd have focused on its crystal structure-specific effects. In our experiments, the toxicity of two types of synthetic nanoparticles was examined on primary neural cultures with different cell compositions using MTT and LDH assays. Primary murine cell cultures containing only astroglia cells originated from two brain regions, as well as mixed neurons and glia cells or microglia cells exclusively, were treated with anatase (15.8 ± 1.7 nm average diameter) and rutile (46.7 ± 2.2 nm average length and 13.7 ± 0.7 nm average diameter) TiO\<sub\>2\</sub\> nanoparticles at varying concentrations for 24 or 48 h. Our results show that neither anatase nor rutile nanoparticles reduced viability in cell cultures containing a mixture of neurons and glial cells, independently of the applied concentration and treatment time. Rutile but not anatase form induced cell death in cortical astroglia cultures already at 24 h of treatment above 10 µg/mL, while hippocampus-derived glial cultures were much less sensitive to rutile. The rutile form also damaged microglia. These findings suggest that products containing rutile-form nano-titanium particles may pose a targeted risk to astroglia and microglial cells in the central nervous system.}, + author = {Geiszelhardt, Eszter and Tóth, Erika and Bóka, Károly and Bencsik, Norbert and Schlett, Katalin and Tárnok, Krisztián}, + doi = {10.3390/ijms26199684}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Cell-type Dependent Sensitivity, Crystal structure, In Vitro Cell Viability, Nanoparticles, Neural cells, Titanium dioxide}, + month = {October}, + number = {19}, + pages = {9684}, + title = {Glia {Cells} {Are} {Selectively} {Sensitive} to {Nanosized} {Titanium} {Dioxide} {Mineral} {Forms}}, + url = {https://europepmc.org/articles/PMC12524891}, + volume = {26}, + year = {2025} +} + @article{gener_full-coverage_2019, abstract = {Objective: To evaluate native RNA sequencing for sequencing HIV-1 viral genomes. Methods: Fifteen HIV-1 strains were processed with Direct RNA Sequencing (SQK-RNA002) library kits and sequenced on MinION Mk1B devices with RevD flow cells (Oxford Nanopore Technologies (ONT), Oxford, UK). Raw reads were converted to FASTQ, aligned to reference sequences, and assembled into contigs. Multi-sequence alignments of the contigs were generated and used for cladistics analysis. Results: We sequenced full-length HIV-1 from the transcriptional start site to 39 LTR (100\% virion genome) in 3 out of 15 isolates (89.6, NLAD8, AD17), achieving majority coverage (defined as \> 50\%) in another 7 out of 15 isolates. Inspection of NLAD8 sequence alignments revealed splicing or deletion signatures. Despite the strong 3′ bias, read coverage was sufficient to evaluate single-nucleotide variants (SNVs), insertions and deletions in 9 isolates, and to assemble HIV-1 genomes directly from viral RNA, achieving a maximum of 94\% assembly coverage for NLAD8. Phylogenetic relationships were maintained at the level of contigs, as well as individual reads. Conclusions: ONT native RNA sequencing performed as expected, covering full-length HIV-1 RNA without PCR or cDNA sequencing. Native single-molecule RNA sequencing supported previous models of HIV-1 replication, and samples exhibited strain-specific transcriptional signals. We propose Context Dependency Variant Classification to describe variants occurring in information-dense regions of HIV. These data provide a rich resource for emerging RNA modification detection schemes. Future work will expand HIV-1 transcript profiling to infection models and clinical samples.}, author = {Gener, Alejandro R. and Kimata, Jason T.}, @@ -4886,22 +8032,69 @@ @article{genolet_identification_2020 } @article{genolet_identification_2021, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}X-chromosomal genes contribute to sex differences, in particular during early development, when both X chromosomes are active in females. Double X-dosage shifts female pluripotent cells towards the naive stem cell state by increasing pluripotency factor expression, inhibiting the differentiation-promoting MAP kinase (MAPK) signaling pathway, and delaying differentiation.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}To identify the genetic basis of these sex differences, we use a two-step CRISPR screening approach to comprehensively identify X-linked genes that cause the female pluripotency phenotype in murine embryonic stem cells. A primary chromosome-wide CRISPR knockout screen and three secondary screens assaying for different aspects of the female pluripotency phenotype allow us to uncover multiple genes that act in concert and to disentangle their relative roles. Among them, we identify Dusp9 and Klhl13 as two central players. While Dusp9 mainly affects MAPK pathway intermediates, Klhl13 promotes pluripotency factor expression and delays differentiation, with both factors jointly repressing MAPK target gene expression.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}Here, we elucidate the mechanisms that drive sex-induced differences in pluripotent cells and our approach serves as a blueprint to discover the genetic basis of the phenotypic consequences of other chromosomal effects.}, author = {Genolet, Oriana and Monaco, Anna A. and Dunkel, Ilona and Boettcher, Michael and Schulz, Edda G.}, doi = {10.1186/s13059-021-02321-2}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {1474-7596}, + journal = {Genome biology}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Clustered Regularly Interspaced Short Palindromic Repeats, Genes, X-Linked, Sex Characteristics}, + language = {eng}, month = {April}, note = {Publisher: Springer Science and Business Media LLC}, number = {1}, + pages = {110}, title = {Identification of {X}-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical {CRISPR} screening approach}, url = {https://doi.org/10.1186/s13059-021-02321-2}, volume = {22}, year = {2021} } +@article{georgakakis_erga-bge_2025, + abstract = {Hanak's bat ( +Pipistrellus hanaki +Hulva and Benda 2004) is one of the most range restricted mammals in Europe, since it occurs only in Cyrenaica, Libya, and Crete (Greece). It is currently classified as 'Vulnerable' on the IUCN Red List, with its foraging habitat threatened by a number of human activities. The reference genome of Hanak's bat ( +Pipistrellus hanaki +) will provide a crucial resource for uncovering the species phylogenetic history and will help assess the degree of genetic isolation among its populations. A total of 23 contiguous chromosomal pseudomolecules (sex chromosomes included) were assembled from the genome sequence. This chromosome-level assembly encompasses 1.9 Gb, composed of 447 contigs and 141 scaffolds, with contig and scaffold N50 values of 48.7 Mb and 89.1 Mb, respectively.}, + author = {Georgakakis, Panagiotis and Karakasi, Danae and Lymberakis, Petros and Papadimitrakis, Manolis and Stratakis, Manos and Bitzilekis, Eleftherios and Poulakakis, Nikolaos and Böhne, Astrid and Monteiro, Rita and Fernández, Rosa and Escudero, Nuria and {Genoscope Sequencing Team} and Moussy, Alice and Cruaud, Corinne and Labadie, Karine and Demirdjian, Lola and Mangenot, Sophie and Belser, Caroline and Wincker, Patrick and Oliveira, Pedro H. and Aury, Jean-Marc and Haggerty, Leanne and Sinha, Swati and Martin, Fergal and Bortoluzzi, Chiara}, + doi = {10.12688/openreseurope.20937.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {September}, + pages = {298}, + title = {{ERGA}-{BGE} reference genome of {Hanak}'s bat ({Pipistrellus} hanaki), an {IUCN} {Vulnerable} species restricted to forest-like biotopes}, + url = {https://open-research-europe.ec.europa.eu/articles/5-298/v1}, + urldate = {2025-10-19}, + volume = {5}, + year = {2025} +} + +@article{germain_srna-mediated_2025, + abstract = {Staphylococcus aureus is an opportunistic pathogen responsible for a wide range of diseases in humans. During infections, this bacterium is exposed to various stresses that target its cell wall, such as oxidative or acid environments as well as various cell wall-acting antimicrobials. Staphylococcus aureus has effective regulatory systems for responding to environmental stresses, enabling the expression of factors necessary for its survival. Bacterial small RNAs (sRNAs) play a crucial role in this adaptation process. In this study, we show that RsaOI, an S. aureus sRNA, accumulates under acid stress conditions. This response is mediated via the two-component system VraSR, which is associated with the cell wall damage response. As a component of the VraSR regulon, RsaOI contributes to the survival of S. aureus under acid stress and affects its susceptibility to glycopeptide antibiotics. Our findings reveal that RsaOI targets the lacABCDFEG operon, which encodes components of tagatose pathway, a unique mechanism responsible for galactose metabolism in S. aureus. By antisense base pairing near the ribosome binding site of lacD, RsaOI inhibits the expression of this gene, encoding tagatose-6-phosphate aldolase. This regulation disrupts the tagatose pathway, impairing galactose utilization in S. aureus. These findings highlight the role of RsaOI in the mediation between cell wall stress responses and a specific metabolic pathway.}, + author = {Germain, Maëliss and Robin, Hugo and Le Huyen, Kim Boi and Massier, Sébastien and Nalpas, Nicolas and Hardouin, Julie and Bouloc, Philippe and Rouillon, Astrid and Chabelskaya, Svetlana}, + doi = {10.1093/nar/gkaf616}, + issn = {0305-1048}, + journal = {Nucleic Acids Res}, + keywords = {{\textgreater}UseGalaxy.eu, Cell Wall, Galactose, RNA, Bacterial, RNA, Small Untranslated, Staphylococcus aureus, Stress, Physiological}, + language = {eng}, + month = {July}, + number = {13}, + pages = {gkaf616}, + title = {{sRNA}-mediated crosstalk between cell wall stress and galactose metabolism in {Staphylococcus} aureus}, + url = {http://europepmc.org/abstract/MED/40671522}, + volume = {53}, + year = {2025} +} + @article{gessara_highly_2021, + abstract = {The ability to genetically manipulate organisms has led to significant insights into functional genomics in many species. In birds, manipulation of the genome is hindered by the inaccessibility of the one-cell embryo. During embryonic development, avian primordial germ cells (PGCs) migrate through the bloodstream and reach the gonadal anlage, where they develop into mature germ cells. Here, we explored the use of PGCs to produce transgenic offspring in the zebra finch, which is a major animal model for sexual brain differentiation, vocal learning, and vocal communication. Zebra finch PGCs (zfPGCs) obtained from embryonic blood significantly proliferated when cultured in an optimized culture medium and conserved the expression of germ and stem cell markers. Transduction of cultured zfPGCs with lentiviral vectors was highly efficient, leading to strong expression of the enhanced green fluorescent protein. Transduced zfPGCs were injected into the host embryo and transgenic songbirds were successfully generated.}, author = {Gessara, Ivana and Dittrich, Falk and Hertel, Moritz and Hildebrand, Staffan and Pfeifer, Alexander and Frankl-Vilches, Carolina and McGrew, Mike and Gahr, Manfred}, doi = {10.1016/j.stemcr.2021.02.015}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {2213-6711}, + journal = {Stem Cell Reports}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Genome}, + language = {eng}, month = {April}, note = {Publisher: Elsevier BV}, number = {4}, @@ -4912,6 +8105,42 @@ @article{gessara_highly_2021 year = {2021} } +@article{ghiglione_outbreak_2025, + abstract = {\textbf{Background:} During the COVID-19 pandemic, the emergence of multidrug-resistant (MDR) pathogens, driven by heightened antibiotic usage and device-associated infections, has posed significant challenges to healthcare. This study reports an outbreak of \textit{Proteus mirabilis} producing NDM-5 and CTX-M-15 β-lactamases in a hospital in Buenos Aires, Argentina, from October 2020 to April 2021. To our knowledge, this represents the first documented outbreak of NDM-5-producing \textit{P. mirabilis} in the country. \textbf{Methods:} A total of 82 isolates were recovered from 40 patients, with 41.5\% from blood cultures and 18.3\% from respiratory and urinary samples, among others. Antimicrobial susceptibility testing, PCR-based methods, and MALDI-TOF MS cluster analysis were conducted. Whole genome sequencing (WGS) was performed to characterize the MLST, resistome and plasmid content. Biofilm formation assays and in vitro rifampicin susceptibility tests were also conducted. \textbf{Result:} Most isolates exhibited resistance to carbapenems, cephalosporins, aminoglycosides, and fluoroquinolones, while retaining susceptibility to aztreonam. Genetic analysis confirmed the co-presence of the \textit{bla}$_{\textrm{NDM-5}}$ and \textit{bla}$_{\textrm{CTX-M-15}}$ genes. Clonal relationships was supported by PCR-based typing and MALDI-TOF MS cluster analysis. WGS revealed a resistome comprising 25 resistance genes, including \textit{rmtB} and both β-lactamases, as well as the presence of an incomplete IncQ1 replicon associated with multiple resistance determinants. MLST classified this clone as belonging to ST135. Despite the biofilm-forming capacity observed across strains, rifampicin demonstrated potential for disrupting established biofilms at concentrations ≥32 µg/mL in vitro. The MDR profile of the outbreak strain significantly limited therapeutic options. \textbf{Conclusions:} This study highlights the growing threat of NDM-producing \textit{P. mirabilis} in Argentina. The absence of surveillance cultures from the index case limits insights into the outbreak's origin. These findings underscore the importance of integrating genomic surveillance into infection control protocols to mitigate the spread of MDR pathogens.}, + author = {Ghiglione, Barbara and Rodriguez, Ana Paula and Haim, María Sol and Friedman, Laura Esther and Lincopan, Nilton and Ochiuzzi, María Eugenia and Di Conza, José Alejandro}, + doi = {10.3390/antibiotics14060557}, + issn = {2079-6382}, + journal = {Antibiotics (Basel, Switzerland)}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {May}, + number = {6}, + pages = {557}, + title = {Outbreak of {NDM}-5-{Producing} \textit{{Proteus} mirabilis} {During} the {COVID}-19 {Pandemic} in an {Argentine} {Hospital}}, + url = {http://europepmc.org/abstract/MED/40558147}, + volume = {14}, + year = {2025} +} + +@article{ghosh_mitogenomics_2024, + abstract = {Complete mitochondrial genome of two species of subfamily Panchaetothripinae, Astrothrips tumiceps (16,467 bp) and Monilothrips kempi (14,773 bp) are generated by Next-Generation Sequencing Method. In this study, the detailed annotation of these mitogenomes as well as comparative analyses are carried out to explore the codon usage, gene composition, and phylogenetic relationship of subfamilies of family Thripidae. Moreover, the gene rearrangement of subfamily Panchaetothripinae of family Thripidae is also studied. Both the mitogenomes featured by 37 genes including 13 PCGs, 22 tRNAs, 2 rRNAs and with single putative control region with a positive AT-skew and negative GC-skew. trnS1 without DHU arm in both species, trnV without DHU arm in M. kempi, and trnE without TΨC loop in As. tumiceps. Further, codon based comparative analysis depicted the existence of natural selection pressure on all the PCGs in all the subfamilies of family Thripidae. The phylogenetic analyses, using the Bayesian inference (BI) and Maximum likelihood (ML) supported the monophyly of two suborders and family Phlaeothripidae. The family Thripidae is recovered as paraphyletic and subfamily Panchaetothripinae is in sister relationship with family Aeolothripidae and Stenurothripidae rather than the other subfamilies of family Thripidae. The gene order of the order Thysanoptera is highly rearranged, while few members of the subfamily Panchaetothripinae showed similar gene order to family Stenurothripidae. Therefore, this study suggests that the phylogenetic relationship between the subfamily Panchaetothripinae and other families is uncertain, necessitating a whole genome-based study to clarify the position of Panchaetothripinae within the suborder Terebrantia.}, + author = {Ghosh, Abhishek and Tyagi, Kaomud and Banerjee, Dhriti and Kumar, Vikas}, + doi = {10.1007/s10709-024-00218-z}, + issn = {1573-6857}, + journal = {Genetica}, + keywords = {{\textgreater}UseGalaxy.eu, Astrothrips tumiceps, Comparative analysis, Drosophila, Genome Evolution, Mitochondrial genome, Monilothrips kempi, Panchaetothripinae, Phylogenetics, Phylogeny, Sequence Annotation, Thrips}, + language = {en}, + month = {November}, + number = {1}, + pages = {3}, + shorttitle = {Mitogenomics providing new insights into the phylogenetic structure of subfamily {Panchaetothripinae} ({Thripidae}}, + title = {Mitogenomics providing new insights into the phylogenetic structure of subfamily {Panchaetothripinae} ({Thripidae}: {Terebrantia})}, + url = {https://doi.org/10.1007/s10709-024-00218-z}, + urldate = {2025-02-28}, + volume = {153}, + year = {2024} +} + @article{ghosh_suppressive_2024, abstract = {Nonstop extension mutations, a.k.a. stop-lost or stop-loss mutations, convert a stop codon into a sense codon resulting in translation into the 3’ untranslated region until the next in-frame stop codon, thereby extending the C-terminus of a protein. In cancer, only nonstop mutations in SMAD4 have been functionally characterized, while the impact of other nonstop mutations remain unknown. Here, we exploit our pan-cancer NonStopDB dataset and test all 2335 C-terminal extensions arising from somatic nonstop mutations in cancer for their impact on protein expression. In a high-throughput screen, 56.1\% of the extensions effectively reduce protein abundance. Extensions of multiple tumor suppressor genes like PTEN, APC, B2M, CASP8, CDKN1B and MLH1 are effective and validated for their suppressive impact. Importantly, the effective extensions possess a higher hydrophobicity than the neutral extensions linking C-terminal hydrophobicity with protein destabilization. Analyzing the proteomes of eleven different species reveals conserved patterns of amino acid distribution in the C-terminal regions of all proteins compared to the proteomes like an enrichment of lysine and arginine and a depletion of glycine, leucine, valine and isoleucine across species and kingdoms. These evolutionary selection patterns are disrupted in the cancer-derived effective nonstop extensions.}, author = {Ghosh, Avantika and Riester, Marisa and Pal, Jagriti and Lainde, Kadri-Ann and Tangermann, Carla and Wanninger, Angela and Dueren, Ursula K. and Dhamija, Sonam and Diederichs, Sven}, @@ -4933,10 +8162,13 @@ @article{ghosh_suppressive_2024 } @article{gilbertson_conservation_2021, + abstract = {Model organisms such as mice are important for basic research and serve as valuable tools in preclinical translational studies. A challenge with translating findings from mice to humans is identifying and separating evolutionarily conserved mechanisms in the immune system from those diverging between species. A significant emphasis has been placed on defining conserved gene regulation principles, with divergent mechanisms often overlooked. We put forward the perspective that both conserved and divergent mechanisms that regulate gene expression programs are of equal importance. With recent advances and availability of datasets, immunologists should take a closer look at the role for genetic diversity in altering gene expression programs between mouse and human immune cells.}, author = {Gilbertson, Sarah E. and Weinmann, Amy S.}, doi = {10.1016/j.it.2021.10.007}, + issn = {1471-4906}, journal = {Trends in Immunology}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Gene Expression Regulation, Immune System}, + language = {eng}, month = {December}, note = {Publisher: Elsevier BV}, number = {12}, @@ -5001,6 +8233,23 @@ @article{giufre_detection_2024 year = {2024} } +@article{giyahchi_sustainable_2025, + abstract = {Polyethylene terephthalate (PET) is a widely used plastic polymer, and its microplastics pose significant threats to ecosystems. One promising approach to addressing this issue is biodegradation using microbial consortia. This study implemented a two-stage biodegradation strategy using microbial consortia to degrade PET microplastics and detoxify their by-products. In the first stage, a bacterial/fungal consortium dominated by Ralstonia, Bradyrhizobium, Exophiala, and Vanrija achieved a 28 ± 2 \% degradation efficiency over 60 days, converting PET into medium-chain alkanes (as confirmed by GC-MS analysis), with a maximum CO2 evolution rate of 722 ppm. Physical and chemical analyses, including Scanning electron microscopy (SEM), Brunauer-Emmett-Teller (BET) analysis, and Fourier transform infrared (FTIR) spectroscopy, revealed structural destruction, mesopore formation, and ester bond breakage of the microplastics. Toxicity assessment of by-products showed a 40 \% reduction in human endothelial cell viability, necessitating further detoxification. The second stage utilized a bacterial consortium dominated by Ochrobacterium and Achromobacter, which effectively reduced toxic by-products to 20 \%. This study emphasizes the dual focus on efficient PET degradation and the safe decomposition of harmful by-products, showcasing the potential of sequential biodegradation strategies as sustainable solutions for microplastic pollution.}, + author = {Giyahchi, Minoo and Moghimi, Hamid}, + doi = {10.1016/j.ecoenv.2025.118738}, + issn = {0147-6513}, + journal = {Ecotoxicology and Environmental Safety}, + keywords = {{\textgreater}UseGalaxy.eu, Bioremediation, Cell viability, Microbial consortium, Microplastics, Toxicity}, + month = {September}, + pages = {118738}, + shorttitle = {Sustainable solution for microplastic removal}, + title = {Sustainable solution for microplastic removal: {Sequential} biodegradation and detoxification of polyethylene terephthalate microplastics by two natural microbial consortia}, + url = {https://www.sciencedirect.com/science/article/pii/S0147651325010838}, + urldate = {2025-09-03}, + volume = {302}, + year = {2025} +} + @article{gjaltema_distal_2021, author = {Gjaltema, Rutger A. F. and Schwämmle, Till and Kautz, Pauline and Robson, Michael and Schöpflin, Robert and Lustig, Liat Ravid and Brandenburg, Lennart and Dunkel, Ilona and Vechiatto, Carolina and Ntini, Evgenia and Mutzel, Verena and Schmiedel, Vera and Marsico, Annalisa and Mundlos, Stefan and Schulz, Edda G.}, doi = {10.1101/2021.03.29.437476}, @@ -5036,7 +8285,8 @@ @article{glaerum_postnatal_2024 doi = {10.1242/dev.202236}, issn = {0950-1991}, journal = {Development}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Hippocampus, Proteomics}, + language = {eng}, month = {January}, number = {1}, pages = {dev202236}, @@ -5048,9 +8298,13 @@ @article{glaerum_postnatal_2024 } @article{glaros_limited_2021, + abstract = {Cell fate decisions during early B cell activation determine the outcome of responses to pathogens and vaccines. We examined the early B cell response to T-dependent antigen in mice by single-cell RNA sequencing. Early after immunization, a homogeneous population of activated precursors (APs) gave rise to a transient wave of plasmablasts (PBs), followed a day later by the emergence of germinal center B cells (GCBCs). Most APs rapidly exited the cell cycle, giving rise to non-GC-derived early memory B cells (eMBCs) that retained an AP-like transcriptional profile. Rapid decline of antigen availability controlled these events; provision of excess antigen precluded cell cycle exit and induced a new wave of PBs. Fate mapping revealed a prominent contribution of eMBCs to the MBC pool. Quiescent cells with an MBC phenotype dominated the early response to immunization in primates. A reservoir of APs/eMBCs may enable rapid readjustment of the immune response when failure to contain a threat is manifested by increased antigen availability.}, author = {Glaros, Vassilis and Rauschmeier, René and Artemov, Artem V. and Reinhardt, Annika and Ols, Sebastian and Emmanouilidi, Aikaterini and Gustafsson, Charlotte and You, Yuanyuan and Mirabello, Claudio and Björklund, Åsa K. and Perez, Laurent and King, Neil P. and Månsson, Robert and Angeletti, Davide and Loré, Karin and Adameyko, Igor and Busslinger, Meinrad and Kreslavsky, Taras}, doi = {10.1016/j.immuni.2021.08.017}, + issn = {1074-7613}, + journal = {Immunity}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {September}, note = {Publisher: Elsevier BV}, number = {9}, @@ -5061,13 +8315,27 @@ @article{glaros_limited_2021 year = {2021} } +@article{glykeria-myrto_comparative_2025, + author = {Glykeria-Myrto, Anagnostou and Theodora, Skarlatoudi and Vasileios, Theodorakis and Loulouda, Bosnea and Marios, Mataragas}, + issn = {2306-7381}, + journal = {Vet Sci}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {July}, + number = {8}, + title = {Comparative {Genomic} {Analysis} and {Antimicrobial} {Resistance} {Profile} of {Enterococcus} {Strains} {Isolated} from {Raw} {Sheep} {Milk}}, + url = {http://europepmc.org/abstract/PMC/PMC12390221}, + volume = {12}, + year = {2025} +} + @article{gobel_myc_2023, abstract = {Group 3 medulloblastoma is one of the most aggressive types of childhood brain tumors. Roughly 30\% of cases carry genetic alterations in MYC, SMARCA4, or both genes combined. While overexpression of MYC has previously been shown to drive medulloblastoma formation in mice, the functional significance of SMARCA4 mutations and their suitability as a therapeutic target remain largely unclear. To address this issue, we combined overexpression of MYC with a loss of SMARCA4 in granule cell precursors. Both alterations did not increase proliferation of granule cell precursors in vitro. However, combined MYC overexpression and SMARCA4 loss successfully induced tumor formation in vivo after orthotopic transplantation in recipient mice. Resulting tumors displayed anaplastic histology and exclusively consisted of SMARCA4-negative cells although a mixture of recombined and non-recombined cells was injected. These observations provide first evidence for a tumor-promoting role of a SMARCA4 deficiency in the development of medulloblastoma. In comparing the transcriptome of tumors to the cells of origin and an established Sonic Hedgehog medulloblastoma model, we gathered first hints on deregulated gene expression that could be specifically involved in SMARCA4/MYC driven tumorigenesis. Finally, an integration of RNA sequencing and DNA methylation data of murine tumors with human samples revealed a high resemblance to human Group 3 medulloblastoma on the molecular level. Altogether, the development of SMARCA4-deficient medulloblastomas in mice paves the way to deciphering the role of frequently occurring SMARCA4 alterations in Group 3 medulloblastoma with the perspective to explore targeted therapeutic options.}, author = {Göbel, Carolin and Godbole, Shweta and Schoof, Melanie and Holdhof, Dörthe and Kresbach, Catena and Loose, Carolin and Neumann, Julia and Schüller, Ulrich}, doi = {10.1186/s40478-023-01654-2}, issn = {2051-5960}, journal = {Acta Neuropathologica Communications}, - keywords = {{\textgreater}UseGalaxy.eu, BAF complex, BRG1, Chromatin remodeling, Group 3 medulloblastoma, MYC}, + keywords = {{\textgreater}UseGalaxy.eu, BAF complex, BRG1, Brain Neoplasms, Cerebellar Neoplasms, Chromatin remodeling, Group 3 medulloblastoma, MYC, Medulloblastoma}, language = {en}, month = {November}, number = {1}, @@ -5131,6 +8399,87 @@ @article{goglio_performance_2024 year = {2024} } +@article{gomes_shigella_2023, + abstract = {Trained immunity is a long-term memory of innate immune cells, generating an improved response upon reinfection. \textit{Shigella} is an important human pathogen and inflammatory paradigm for which there is no effective vaccine. Using zebrafish larvae, we demonstrate that after \textit{Shigella} training, neutrophils are more efficient at bacterial clearance. We observe that \textit{Shigella}-induced protection is nonspecific and has differences with training by BCG and β-glucan. Analysis of histone ChIP-seq on trained neutrophils revealed that \textit{Shigella} training deposits the active H3K4me3 mark on promoter regions of 1612 genes, dramatically changing the epigenetic landscape of neutrophils toward enhanced microbial recognition and mitochondrial ROS production. Last, we demonstrate that mitochondrial ROS plays a key role in enhanced antimicrobial activity of trained neutrophils. It is envisioned that signals and mechanisms we discover here can be used in other vertebrates, including humans, to suggest new therapeutic strategies involving neutrophils to control bacterial infection.}, + author = {Gomes, Margarida C and Brokatzky, Dominik and Bielecka, Magdalena K and Wardle, Fiona C and Mostowy, Serge}, + doi = {10.1126/sciadv.adf9706}, + issn = {2375-2548}, + journal = {Sci Adv}, + keywords = {{\textgreater}UseGalaxy.eu, Enterobacteriaceae Infections, Epigenesis, Genetic, Mycobacterium bovis, Neutrophils, Trained Immunity, beta-Glucans}, + language = {eng}, + month = {September}, + number = {36}, + pages = {eadf9706}, + title = {\textit{{Shigella}} induces epigenetic reprogramming of zebrafish neutrophils}, + url = {http://europepmc.org/abstract/MED/37672585}, + volume = {9}, + year = {2023} +} + +@article{gomes_shigellainduces_2022, + abstract = {{\textless}h4{\textgreater}SUMMARY{\textless}/h4{\textgreater} Trained immunity is a long-term memory of innate immune cells, generating an improved response upon re-infection. Shigella is an important human pathogen and inflammatory paradigm for which there is no effective vaccine. Using zebrafish larvae we demonstrate that after Shigella priming neutrophils are more efficient at bacterial clearance. We observe that Shigella -induced protection is non-specific and long-lasting, and is unlike training by BCG and β-glucan. Analysis of histone ChIP-seq on primed neutrophils revealed that Shigella training deposits the active H3K4me3 mark on promoter regions of 1612 genes, significantly changing the epigenetic landscape of neutrophils towards enhanced microbial recognition and mitochondrial ROS production. Finally, we demonstrate that mitochondrial ROS plays a key role in enhanced antimicrobial activity of trained neutrophils. It is envisioned that signals and mechanisms we discover here can be used in other vertebrates, including humans, to suggest new therapeutic strategies involving neutrophils to control bacterial infection.}, + author = {Gomes, Margarida and Brokatzky, Dominik and Bielecka, Magdalena and Wardle, Fiona and Mostowy, Serge}, + doi = {10.1101/2022.11.03.515069}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Shigellainduces epigenetic reprogramming of zebrafish neutrophils}, + url = {http://europepmc.org/abstract/PPR/PPR567136}, + year = {2022} +} + +@article{gomes_unlocking_2025, + abstract = {Astaxanthin and Canthaxanthin are high-value ketocarotenoids with applications in various sectors, including food and feed industries. Growing demand for healthy diets and changing consumer eating habits have led to an increase in the market size of dietary supplements and functional foods. This increase has a direct impact on the supply of antioxidants and other valuable molecules known for their health benefits. Due to the increasing demand for these pigments, there is a need for new bioproducers. In this study, we present a novel production platform based on metabolically engineered plant-cultured cells. The carotenoid pigments, Astaxanthin and Canthaxanthin, were synthesized using non-photosynthetic Medicago cells in suspension culture. Agrobacterium-mediated transformation was used to introduce a single β-carotene ketolase gene from the marine bacterium Brevundimonas sp. into Medicago cells, generating several stable metabolically engineered lines. HPLC and transcriptomic analyses were performed, showing significant variability in carotenoid content and gene expression, suggesting that intracellular responses influence production levels. The highest-producing line yielded 178.3 μg g−1 DW of Astaxanthin and 37.7 μg g−1 DW of Canthaxanthin. This plant-based platform will contribute to a more sustainable food and feed industry, addressing the growing challenges of global food production and consumption.}, + author = {Gomes, Susana M. and Rebelo, Bárbara A. and Abranches, Rita}, + copyright = {© 2025 Wiley Periodicals LLC.}, + doi = {10.1002/bit.29009}, + issn = {1097-0290}, + journal = {Biotechnology and Bioengineering}, + keywords = {{\textgreater}UseGalaxy.eu, A17 Medicago truncatula, cell factories, ketocarotenoids, metabolic engineering, molecular farming, β-carotene ketolase}, + language = {en}, + month = {May}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/bit.29009}, + number = {n/a}, + title = {Unlocking the {Potential} of {Medicago} truncatula {A17} {Cell} {Suspension} {Cultures} for {Bioproduction} of {Astaxanthin} and {Canthaxanthin}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/bit.29009}, + urldate = {2025-05-28}, + volume = {n/a}, + year = {2025} +} + +@article{gonzalez-vinceiro_plamseq_2025, + abstract = {Chromatin immunoprecipitation and coimmunoprecipitation assays are common approaches to characterize the genomic localization and protein interactors, respectively, for a protein of interest. However, these approaches require the use of specific antibodies, which often face sensitivity and specificity issues. On the basis of TurboID, we developed proximity-labeled affinity-purified mass spectrometry and sequencing (PLAMseq), which enables, in the same workflow, identification of the genomic loci and the interacting proteome of a protein of interest. Moreover, PLAMseq can also be applied to specifically map protein interactions and ubiquitin(-like)–modified proteins. We validated PLAMseq with two well-characterized proteins, RNA polymerase II, and CTCF, with excellent robustness and reproducibility. Next, we applied PLAMseq to characterize histone H1 SUMOylation, in which study has remained elusive due to the lack of specific reagents, and found that SETDB1 binds to SUMOylated histones H1.2 and H1.4 that also colocalize with H3K9me3 at repetitive regions of the genome.}, + author = {González-Vinceiro, Lourdes and Espejo-Serrano, Carmen and Soler-Oliva, María Eugenia and Soto-Hidalgo, Emily and Mateos-Martín, María Luisa and Rico, Daniel and González-Aguilera, Cristina and González-Prieto, Román}, + doi = {10.1126/sciadv.ady4151}, + journal = {Science Advances}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {November}, + note = {Publisher: American Association for the Advancement of Science}, + number = {45}, + pages = {eady4151}, + title = {{PLAMseq} enables the proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single workflow}, + url = {https://www.science.org/doi/10.1126/sciadv.ady4151}, + urldate = {2025-12-26}, + volume = {11}, + year = {2025} +} + +@misc{gonzalez-vinceiro_plamseq_2025, + abstract = {Chromatin Immunoprecipitation (ChIP) and Co-Immunoprecipitation (CoIP) assays are the most common approaches to characterize the genomic localization and protein interactors, respectively, for a protein of interest. However, these approaches require the use of specific antibodies, which are costly reagents that often face sensitivity and specificity issues. Based on TurboID, we developed PLAMseq (Proximity Labelled Affinity-purified Mass spectrometry plus sequencing), which enables, in the same workflow, to identify the genomic loci and the interacting proteome of a protein of interest. Moreover, PLAMseq can also be applied to specifically map protein interactions across the genome or to specifically detect proteins which are ubiquitin(-like) modified. After a short biotin pulse, DNA-protein crosslinks are induced by formaldehyde and the interactors of a protein of interest, together with their associated DNA sequences, are purified simultaneously and identified by mass spectrometry-based proteomics and Next Generation Sequencing, respectively. To validate PLAMseq, we performed the proteo-genomic characterization of two proteins which genomic loci are very well characterized, namely, RNA polymerase II and CTCF, with excellent robustness and reproducibility. Next, we applied PLAMseq to characterize Histone H1 SUMOylation, a histone post-translational modification which study has remained elusive due to the lack of specific reagents. We found that SETDB1 binds to SUMOylated histone H1.2 and H1.4 and, accordingly, SUMOylated histone H1 colocalizes with H3K9me3 at repetitive regions of the genome.}, + author = {González-Vinceiro, Lourdes and Espejo-Serrano, Carmen and Soler-Oliva, María Eugenia and Mateos-Martín, María Luisa and Rico, Daniel and González-Aguilera, Cristina and Prieto, Román González}, + copyright = {© 2025, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}, + doi = {10.1101/2025.04.27.650851}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {April}, + note = {Pages: 2025.04.27.650851 +Section: New Results}, + publisher = {bioRxiv}, + title = {{PLAMseq} enables the proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single experimental workflow.}, + url = {https://www.biorxiv.org/content/10.1101/2025.04.27.650851v1}, + urldate = {2025-05-01}, + year = {2025} +} + @article{goossens_obligate_2023, abstract = {Hyaloperonospora arabidopsidis (Hpa) is an obligately biotrophic downy mildew that is routinely cultured on Arabidopsis thaliana hosts that harbour complex microbiomes. We hypothesized that the culturing procedure proliferates Hpa-associated microbiota (HAM) in addition to the pathogen and exploited this model system to investigate which microorganisms consistently associate with Hpa. Using amplicon sequencing, we found nine bacterial sequence variants that are shared between at least three out of four Hpa cultures in the Netherlands and Germany and comprise 34\% of the phyllosphere community of the infected plants. Whole-genome sequencing showed that representative HAM bacterial isolates from these distinct Hpa cultures are isogenic and that an additional seven published Hpa metagenomes contain numerous sequences of the HAM. Although we showed that HAM benefit from Hpa infection, HAM negatively affect Hpa spore formation. Moreover, we show that pathogen-infected plants can selectively recruit HAM to both their roots and shoots and form a soil-borne infection-associated microbiome that helps resist the pathogen. Understanding the mechanisms by which infection-associated microbiomes are formed might enable breeding of crop varieties that select for protective microbiomes.}, author = {Goossens, Pim and Spooren, Jelle and Baremans, Kim C. M. and Andel, Annemiek and Lapin, Dmitry and Echobardo, Nakisa and Pieterse, Corné M. J. and Van den Ackerveken, Guido and Berendsen, Roeland L.}, @@ -5158,7 +8507,7 @@ @article{gosch_spitting_2023 doi = {10.1007/s00414-023-03100-3}, issn = {1437-1596}, journal = {International Journal of Legal Medicine}, - keywords = {{\textgreater}UseGalaxy.eu, Forensic RNA analysis, Massive parallel sequencing, Saliva}, + keywords = {{\textgreater}UseGalaxy.eu, Body Fluids, DNA sequencing, Epigenomics, Forensic Anthropology, Forensic RNA analysis, Forensic Science, Massive parallel sequencing, RNA sequencing, Saliva, Transcriptomics}, language = {en}, month = {October}, shorttitle = {Spitting in the wind?}, @@ -5168,11 +8517,63 @@ @article{gosch_spitting_2023 year = {2023} } +@article{goshi_direct_2025, + abstract = {Cognitive impairment is one of the many symptoms reported by individuals suffering from long-COVID and other post-viral infection disorders such as myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). A common factor among these conditions is a sustained immune response and increased levels of inflammatory cytokines. Tumor necrosis factor alpha (TNF-α) and interleukin-6 (IL-6) are two such cytokines that are elevated in patients diagnosed with long-COVID and ME/CFS. In this study, we characterized the changes in neural functionality, secreted cytokine profiles, and gene expression in co-cultures of human iPSC-derived neurons and primary astrocytes in response to prolonged exposure to TNF-α and IL-6. We found that exposure to TNF-α produced both a concentration-independent and concentration-dependent response in neural activity. Burst duration was significantly reduced within a few days of exposure regardless of concentration (1 pg/mL – 100 ng/mL) but returned to baseline after 7 days. Treatment with low concentrations of TNF-α (e.g., 1 and 25 pg/mL) did not lead to changes in the secreted cytokine profile or gene expression but still resulted in significant changes to electrophysiological features such as interspike interval and burst duration. Conversely, treatment with high concentrations of TNF-α (e.g., 10 and 100 ng/mL) led to reduced spiking activity, which may be correlated to changes in neural health, gene expression, and increases in inflammatory cytokine secretion (e.g., IL-1β, IL-4, and CXCL-10) that were observed at higher TNF-α concentrations. Prolonged exposure to IL-6 led to changes in bursting features, with significant reduction in the number of spikes in bursts across a wide range of treatment concentrations (i.e., 1 pg/mL–10 ng/mL). In combination, the addition of IL-6 appears to counteract the changes to neural function induced by low concentrations of TNF-α, while at high concentrations of TNF-α the addition of IL-6 had little to no effect. Conversely, the changes to electrophysiological features induced by IL-6 were lost when the cultures were co-stimulated with TNF-α regardless of the concentration, suggesting that TNF-α may play a more pronounced role in altering neural function. These results indicate that increased concentrations of key inflammatory cytokines associated with long-COVID can directly impact neural function and may be a component of the cognitive impairment associated with long-COVID and other post-viral infection disorders.}, + author = {Goshi, Noah and Lam, Doris and Bogguri, Chandrakumar and George, Vivek Kurien and Sebastian, Aimy and Cadena, Jose and Leon, Nicole F. and Hum, Nicholas R. and Weilhammer, Dina R. and Fischer, Nicholas O. and Enright, Heather A.}, + copyright = {© 2025. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.}, + doi = {10.3389/fncel.2025.1512591}, + journal = {Frontiers in Cellular Neuroscience}, + keywords = {{\textgreater}UseGalaxy.eu, Astrocytes, Cell culture, Chemokines, Chronic fatigue syndrome, Chronic infection, Cognitive ability, Cytokines, Encephalomyelitis, Firing pattern, Gene expression, IL-6, Immune response, Infections, Interleukin 6, Neurons, Severe acute respiratory syndrome coronavirus 2, TNF-α, Tumor necrosis factor-TNF, Tumor necrosis factor-α, Viral infections, cytokine, human iPSC derived neurons, inflammation, long-COVID, multi-electrode array, neuron networks}, + language = {English}, + month = {February}, + note = {Place: Lausanne, Switzerland +Publisher: Frontiers Research Foundation}, + title = {Direct effects of prolonged {TNF}-α and {IL}-6 exposure on neural activity in human {iPSC}-derived neuron-astrocyte co-cultures}, + url = {https://www.proquest.com/docview/3165948049/abstract/9D6077E8D5E84209PQ/1}, + urldate = {2025-02-24}, + year = {2025} +} + +@article{grausa_integrative_2022, + abstract = {Genome-scale metabolic modeling is widely used to study the impact of metabolism on the phenotype of different organisms. While substrate modeling reflects the potential distribution of carbon and other chemical elements within the model, the additional use of omics data, e.g., transcriptome, has implications when researching the genotype-phenotype responses to environmental changes. Several algorithms for transcriptome analysis using genome-scale metabolic modeling have been proposed. Still, they are restricted to specific objectives and conditions and lack flexibility, have software compatibility issues, and require advanced user skills. We classified previously published algorithms, summarized transcriptome pre-processing, integration, and analysis methods, and implemented them in the newly developed transcriptome analysis tool \textit{IgemRNA}, which (1) has a user-friendly graphical interface, (2) tackles compatibility issues by combining previous data input and pre-processing algorithms in MATLAB, and (3) introduces novel algorithms for the automatic comparison of different transcriptome datasets with or without Cobra Toolbox 3.0 optimization algorithms. We used publicly available transcriptome datasets from Saccharomyces cerevisiae BY4741 and H4-S47D strains for validation. We found that \textit{IgemRNA} provides a means for transcriptome and environmental data validation on biochemical network topology since the biomass function varies for different phenotypes. Our tool can detect problematic reaction constraints.}, + author = {Grausa, Kristina and Mozga, Ivars and Pleiko, Karlis and Pentjuss, Agris}, + doi = {10.3390/biom12040586}, + issn = {2218-273X}, + journal = {Biomolecules}, + keywords = {{\textgreater}UseGalaxy.eu, Models, Biological, Software}, + language = {eng}, + month = {April}, + number = {4}, + pages = {586}, + title = {Integrative {Gene} {Expression} and {Metabolic} {Analysis} {Tool} {IgemRNA}}, + url = {http://europepmc.org/abstract/MED/35454176}, + volume = {12}, + year = {2022} +} + +@article{green_btr_2024, + abstract = {{\textless}h4{\textgreater}Motivation{\textless}/h4{\textgreater}The rapid expansion of Bioinformatics research has led to a proliferation of computational tools for scientific analysis pipelines. However, constructing these pipelines is a demanding task, requiring extensive domain knowledge and careful consideration. As the Bioinformatics landscape evolves, researchers, both novice and expert, may feel overwhelmed in unfamiliar fields, potentially leading to the selection of unsuitable tools during workflow development.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}In this article, we introduce the Bioinformatics Tool Recommendation system (BTR), a deep learning model designed to recommend suitable tools for a given workflow-in-progress. BTR leverages recent advances in graph neural network technology, representing the workflow as a graph to capture essential context. Natural language processing techniques enhance tool recommendations by analyzing associated tool descriptions. Experiments demonstrate that BTR outperforms the existing Galaxy tool recommendation system, showcasing its potential to streamline scientific workflow construction.{\textless}h4{\textgreater}Availability and implementation{\textless}/h4{\textgreater}The Python source code is available at https://github.com/ryangreenj/bioinformatics\_tool\_recommendation.}, + author = {Green, Ryan and Qu, Xufeng and Liu, Jinze and Yu, Tingting}, + doi = {10.1093/bioinformatics/btae275}, + issn = {1367-4803}, + journal = {Bioinformatics}, + keywords = {{\textgreater}UseGalaxy.eu, Computational Biology, Software, Workflow}, + language = {eng}, + month = {May}, + number = {5}, + pages = {btae275}, + title = {{BTR}: a bioinformatics tool recommendation system}, + url = {http://europepmc.org/abstract/MED/38662583}, + volume = {40}, + year = {2024} +} + @article{greenfield_modification_2020, abstract = {Dysregulation of epigenetic processes is increasingly understood to play a role in the pathogenesis of myeloproliferative neoplasms (MPNs). Ruxolitinib, a JAK/STAT inhibitor, has proved a useful addition to the therapeutic arsenal for these disorders, but has limited disease modifying activity. We determined the effect of JAK inhibition on the histone landscape of MPN cells in cell line models of MPNs and validated using samples from the MAJIC randomised clinical trial of ruxolitinib in polycythaemia vera and essential thrombocythaemia. We demonstrated an epigenetic modifying effect of ruxolitinib using a histone modification assay. The majority of 21 histone H3 modifications were upregulated, with H3K27me3 and H3K36me2 significant in the combined cell line results. Chromatin immunoprecipitation and sequencing (CHIP-seq) for three marks of interest, H3K4me1, H3K4me3 and H3K27ac, was consistent with the histone modification assay showing a significant increase in H3K4me3 and H3K27ac peaks at promoter regions, both marks of active transcription. In contrast, RNA sequencing demonstrates a coordinated reduction in gene expression in a number of cell pathways including PI3K-AKT signalling, transcriptional misregulation in cancer and JAK-STAT signalling in spite of these histone changes. This highlights the complex mechanisms of transcriptional control within the cells which was reflected in analysis of the histone landscape in patient samples following ruxolitinib treatment.}, author = {Greenfield, Graeme and McPherson, Suzanne and Smith, James and Mead, Adam and Harrison, Claire and Mills, Ken and McMullin, Mary Frances}, copyright = {http://creativecommons.org/licenses/by/3.0/}, doi = {10.3390/cancers12092669}, + issn = {2072-6694}, journal = {Cancers}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, JAK inhibition, epigenetics, histone modification, myeloproliferative neoplasms}, language = {en}, @@ -5206,13 +8607,38 @@ @article{greenfield_p989_2022 year = {2022} } +@article{gregoric_erga-bge_2025, + abstract = {The +Leviellus thorelli +reference genome provides the first high-quality genomic resource for +Zygiellidae +, a family of orb-weaving spiders with a dynamic systematic history and distinct for constructing webs with a characteristic spiral-free sector. As part of the European Reference Genome Atlas (ERGA), we generated a chromosome-level assembly for +L. thorelli +that is organized into 13 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 2.20 Gb and is composed of 939 contigs and 130 scaffolds, with contig and scaffold N50 values of 5.4 Mb and 167.1 Mb, respectively. This genome represents a valuable addition to the growing collection of spider genomes. With +Zygiellidae +now included among the available genomes of true orb-weavers, this is a key resource for comparative studies into the genomic basis of orb web and silk evolution.}, + author = {Gregorič, Matjaz and Bužan, Elena and Böhne, Astrid and Monteiro, Rita and Fernández, Rosa and Escudero, Nuria and Gut, Marta and Aguilera, Laura and Câmara Ferreira, Francisco and Cruz, Fernando and Gómez-Garrido, Jèssica and S. Alioto, Tyler and Bortoluzzi, Chiara}, + doi = {10.12688/openreseurope.21671.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {November}, + pages = {365}, + title = {{ERGA}-{BGE} reference genome of {Leviellus} thorelli, a common orb-weaving spider representing the {Zygiellidae} family}, + url = {https://open-research-europe.ec.europa.eu/articles/5-365/v1}, + urldate = {2025-11-30}, + volume = {5}, + year = {2025} +} + @article{gress_prostaglandin_2024, abstract = {Increased production of Prostaglandin D2 (PGD2) is linked to development and progression of asthma and allergy. PGD2 is rapidly degraded to its metabolites, which initiate type 2 innate lymphoid cells (ILC2) migration and IL-5/IL-13 cytokine secretion in a PGD2 receptor 2 (DP2)-dependent manner. Blockade of DP2 has shown therapeutic benefit in subsets of asthma patients. Cellular mechanisms of ILC2 activity in response to PGD2 and its metabolites are still unclear. We hypothesized that ILC2 respond non-uniformly to PGD2 metabolites. ILC2s were isolated from peripheral blood of patients with atopic asthma. ILC2s were stimulated with PGD2 and four PGD2 metabolites (Δ12-PGJ2, Δ12-PGD2, 15-deoxyΔ12,14-PGD2, 9α,11β-PGF2) with or without the selective DP2 antagonist fevipiprant. Total RNA was sequenced, and differentially expressed genes (DEG) were identified by DeSeq2. Differential gene expression analysis revealed an upregulation of pro-inflammatory DEGs in ILC2s stimulated with PGD2 (14 DEGs), Δ12-PGD2 (27 DEGs), 15-deoxyΔ12,14-PGD2 (56 DEGs) and Δ12-PGJ2 (136 DEGs), but not with 9α,11β-PGF2. Common upregulated DEGs were i.e. ARG2, SLC43A2, LAYN, IGFLR1, or EPHX2. Inhibition of DP2 via fevipiprant mainly resulted in downregulation of pro-inflammatory genes such as DUSP4, SPRED2, DUSP6, ETV1, ASB2, CD38, ADGRG1, DDIT4, TRPM2, or CD69. DEGs were related to migration and various immune response-relevant pathways such as “chemokine (C-C motif) ligand 4 production”, “cell migration”, “interleukin-13 production”, “regulation of receptor signaling pathway via JAK-STAT”, or “lymphocyte apoptotic process”, underlining the pro-inflammatory effects of PGD2 metabolite-induced immune responses in ILC2s as well as the anti-inflammatory effects of DP2 inhibition via fevipiprant. Furthermore, PGD2 and metabolites showed distinct profiles in ILC2 activation. Overall, these results expand our understanding of DP2 initiated ILC2 activity.}, author = {Gress, Christina and Fuchs, Maximilian and Carstensen-Aurèche, Saskia and Müller, Meike and Hohlfeld, Jens M.}, doi = {10.1371/journal.pone.0307750}, issn = {1932-6203}, journal = {PLOS ONE}, - keywords = {{\textgreater}UseGalaxy.eu, Asthma, Cell metabolism, Cytokines, Gene expression, Immune response, Metabolic pathways, Metabolites, RNA sequencing}, + keywords = {{\textgreater}UseGalaxy.eu, Asthma, Cell metabolism, Cytokines, Gene expression, Immune response, Immunity, Innate, Lymphocytes, Metabolic pathways, Metabolites, Prostaglandin D2, RNA sequencing, Receptors, Immunologic, Receptors, Prostaglandin, Signal Transduction}, language = {en}, month = {July}, note = {Publisher: Public Library of Science}, @@ -5232,7 +8658,7 @@ @article{gress_transcriptomic_2024 doi = {10.1038/s41598-024-51547-0}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, Biomarkers, Experimental models of disease, Gene regulation in immune cells, Inflammation, RNA sequencing}, + keywords = {{\textgreater}UseGalaxy.eu, Asthma, Biomarkers, Experimental models of disease, Gene regulation in immune cells, Inflammation, Pneumonia, Pulmonary Disease, Chronic Obstructive, RNA sequencing}, language = {en}, month = {January}, note = {Number: 1 @@ -5290,6 +8716,36 @@ @article{greve_three_2024 year = {2024} } +@patent{grey_african_2025, + assignee = {The University Court Of The University Of Edinburgh}, + author = {GREY, Finn and BAILLIE, Kenneth and PANNHORST, Katrin and Fuchs, Walter}, + keywords = {{\textgreater}UseGalaxy.eu, asfv, cells, compound, protein, sla}, + language = {en}, + month = {February}, + nationality = {WO}, + number = {WO2025040892A1}, + title = {African swine fever viral infections}, + url = {https://patents.google.com/patent/WO2025040892A1/en?q=(%22usegalaxy.eu%22+OR+%22European+Galaxy%22)&oq=%22usegalaxy.eu%22+OR+%22European+Galaxy%22}, + urldate = {2025-04-14}, + year = {2025} +} + +@article{gruber_complete_2025, + author = {Gruber, Paige and Freedman, Ashley and Malmstrom, Kendall and Borlee, Bradley R. and Mehaffy, Carolina}, + doi = {10.1128/mra.00193-25}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org}, + month = {April}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e00193--25}, + title = {Complete genome sequence of {Planococcus} koreensis isolated from soil in {Fort} {Collins}, {Colorado}}, + url = {https://journals.asm.org/doi/full/10.1128/mra.00193-25}, + urldate = {2025-04-21}, + volume = {0}, + year = {2025} +} + @article{gruning_rna_2017, author = {Grüning, Björn A. and Fallmann, Jörg and Yusuf, Dilmurat and Will, Sebastian and Erxleben, Anika and Eggenhofer, Florian and Houwaart, Torsten and Batut, Bérénice and Videm, Pavankumar and Bagnacani, Andrea and Wolfien, Markus and Lott, Steffen C. and Hoogstrate, Youri and Hess, Wolfgang R. and Wolkenhauer, Olaf and Hoffmann, Steve and Akalin, Altuna and Ohler, Uwe and Stadler, Peter F. and Backofen, Rolf}, doi = {10.1093/nar/gkx409}, @@ -5311,7 +8767,7 @@ @article{gu_galaxy-ml_2021 doi = {10.1371/journal.pcbi.1009014}, issn = {1553-7358}, journal = {PLOS Computational Biology}, - keywords = {+Galactic, +IsGalaxy, +Project, +Shared, +Tools, {\textgreater}ML Workbench, {\textgreater}UseGalaxy.eu, Cancers and neoplasms, Decision trees, Deep learning, Galaxies, Machine learning, Medicine and health sciences, Scientists, Supervised machine learning}, + keywords = {+Galactic, +IsGalaxy, +Project, +Shared, +Tools, {\textgreater}ML Workbench, {\textgreater}UseGalaxy.eu, Cancers and neoplasms, Decision trees, Deep learning, Galaxies, Machine Learning, Machine learning, Medicine and health sciences, Scientists, Supervised machine learning}, language = {en}, month = {June}, note = {Publisher: Public Library of Science}, @@ -5401,7 +8857,7 @@ @article{guerler_fast_2023 doi = {10.1186/s12859-023-05389-8}, issn = {1471-2105}, journal = {BMC Bioinformatics}, - keywords = {+Galactic, +IsGalaxy, +Project, +Shared, +Tools, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Galaxy workflow, Protein–protein interactions, Structural modeling}, + keywords = {+Galactic, +IsGalaxy, +Project, +Shared, +Tools, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, COVID-19, Galaxy workflow, Protein Interaction Mapping, Protein–protein interactions, Structural modeling}, language = {en}, month = {June}, number = {1}, @@ -5418,7 +8874,7 @@ @article{guesdon_combining_2023 author = {Guesdon, Gabrielle and Gourgues, Géraldine and Rideau, Fabien and Ipoutcha, Thomas and Manso-Silván, Lucía and Jules, Matthieu and Sirand-Pugnet, Pascal and Blanchard, Alain and Lartigue, Carole}, doi = {10.1021/acssynbio.3c00248}, journal = {ACS Synthetic Biology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, CRISPR-Cas Systems, Saccharomyces cerevisiae}, month = {November}, note = {Publisher: American Chemical Society}, number = {11}, @@ -5430,6 +8886,23 @@ @article{guesdon_combining_2023 year = {2023} } +@article{guillen_genomic_2024, + abstract = {Methicillin-resistant \textit{Staphylococcus aureus} (MRSA) is one of the major human pathogens. It could carry numerous resistance genes and virulence factors in its genome, some of which are related to the severity of the infection. An observational, descriptive, cross-sectional study was designed to molecularly analyze MRSA isolates that cause invasive infections in Paraguayan children from 2009 to 2013. Ten representative MRSA isolates of the main clonal complex identified were analyzed with short-read paired-end sequencing and assessed for the virulome, resistome, and phylogenetic relationships. All the genetically linked MRSA isolates were recovered from diverse clinical sources, patients, and hospitals at broad gap periods. The pan-genomic analysis of these clones revealed three major and different clonal complexes (CC30, CC5, and CC8), each composed of clones closely related to each other. The CC30 genomes prove to be a successful clone, strongly installed and disseminated throughout our country, and closely related to other CC30 public genomes from the region and the world. The CC5 shows the highest genetic variability, and the CC8 carried the complete arginine catabolic mobile element (ACME), closely related to the USA300-NAE-ACME+, identified as the major cause of CA-MRSA infections in North America. Multiple virulence and resistance genes were identified for the first time in this study, highlighting the complex virulence profiles of MRSA circulating in the country. This study opens a wide range of new possibilities for future projects and trials to improve the existing knowledge on the epidemiology of MRSA circulating in Paraguay.{\textless}h4{\textgreater}Importance{\textless}/h4{\textgreater}The increasing prevalence of methicillin-resistant \textit{Staphylococcus aureus} (MRSA) is a public health problem worldwide. The most frequent MRSA clones identified in Paraguay in previous studies (including community and hospital acquired) were the Pediatric (CC5-ST5-IV), the Cordobes-Chilean (CC5-ST5-I), the SouthWest Pacific (CC30-ST30-IV), and the Brazilian (CC8-ST239-III) clones. In this study, the pan-genomic analysis of the most representative MRSA clones circulating in invasive infection in Paraguayan children over the years 2009-2013, such as the CC30-ST30-IV, CC5-ST5-IV, and CC8-ST8-IV, was carried out to evaluate their genetic diversity, their repertoire of virulence factors, and antimicrobial resistance determinants. This revealed multiple virulence and resistance genes, highlighting the complex virulence profiles of MRSA circulating in Paraguay. Our work is the first genomic study of MRSA in Paraguay and will contribute to the development of genomic surveillance in the region and our understanding of the global epidemiology of this pathogen.}, + author = {Guillén, Rosa and Salinas, Claudia and Mendoza-Álvarez, Alejandro and Rubio Rodríguez, Luis A and Díaz-de Usera, Ana and Lorenzo-Salazar, José M and González-Montelongo, Rafaela and Flores, Carlos and Rodríguez, Fátima}, + doi = {10.1128/spectrum.03012-23}, + issn = {2165-0497}, + journal = {Microbiol Spectr}, + keywords = {{\textgreater}UseGalaxy.eu, Methicillin-Resistant Staphylococcus aureus, Staphylococcal Infections}, + language = {eng}, + month = {April}, + number = {4}, + pages = {e0301223}, + title = {Genomic epidemiology of the primary methicillin-resistant {Staphylococcus} aureus clones causing invasive infections in {Paraguayan} children}, + url = {http://europepmc.org/abstract/MED/38415665}, + volume = {12}, + year = {2024} +} + @article{guindo_tetragenococcus_2022, abstract = {Tetragenococcus halophilus (T. halophilus) is a facultative anaerobic, coccus-shaped halophilic lactic acid-producing bacterium previously detected and cultured in various salty foods and credited for beneficial effects on human health. In this study, we investigated the presence of T. halophilus in human samples using a polyphasic approach including scanning electron microscopy, molecular biology methods and microbial culture. This unique investigation yielded the unprecedented presence of T. halophilus in human feces samples, thus enriching the repertoire of halophilic microorganisms colonizing the human gastrointestinal tract with the isolation and culture of T. halophilus for the first time in humans. Using the E-test strips, the MIC was assessed for T. halophilus strain CSURQ6002: rifampicin (MIC at 0.002 μg/mL), benzylpenicillin (MIC at 0.094 μg/mL), amoxicillin (MIC at 0.5 μg/mL), erythromycin (MIC at 2 μg/mL), clindamycin (MIC at 4 μg/mL), and vancomycin (MIC at 8 μg/mL). However, this strain showed a MIC up to 256 μg/mL for ciprofloxacin, fosfomycin, doxycyclin, imipenem, and colistin. In-silico profiling derived from whole genome sequencing (NCBI accession number: PRJNA780809), was confirmed. This discovery suggested that T. halophilus was part of the human digestive microbiota and that its potential role on human health should be considered.}, author = {Guindo, Cheick Oumar and Morsli, Madjid and Bellali, Sara and Drancourt, Michel and Grine, Ghiles}, @@ -5447,6 +8920,40 @@ @article{guindo_tetragenococcus_2022 year = {2022} } +@article{guo_3d_2021, + abstract = {RNA-sequencing (RNA-seq) analysis of gene expression and alternative splicing should be routine and robust but is often a bottleneck for biologists because of different and complex analysis programs and reliance on specialized bioinformatics skills. We have developed the '3D RNA-seq' App, an R shiny App and web-based pipeline for the comprehensive analysis of RNA-seq data from any organism. It represents an easy-to-use, flexible and powerful tool for analysis of both gene and transcript-level gene expression to identify differential gene/transcript expression, differential alternative splicing and differential transcript usage (3D) as well as isoform switching from RNA-seq data. 3D RNA-seq integrates state-of-the-art differential expression analysis tools and adopts best practice for RNA-seq analysis. The program is designed to be run by biologists with minimal bioinformatics experience (or by bioinformaticians) allowing lab scientists to analyse their RNA-seq data. It achieves this by operating through a user-friendly graphical interface which automates the data flow through the programs in the pipeline. The comprehensive analysis performed by 3D RNA-seq is extremely rapid and accurate, can handle complex experimental designs, allows user setting of statistical parameters, visualizes the results through graphics and tables, and generates publication quality figures such as heat-maps, expression profiles and GO enrichment plots. The utility of 3D RNA-seq is illustrated by analysis of data from a time-series of cold-treated Arabidopsis plants and from dexamethasone-treated male and female mouse cortex and hypothalamus data identifying dexamethasone-induced sex- and brain region-specific differential gene expression and alternative splicing.}, + author = {Guo, Wenbin and Tzioutziou, Nikoleta A and Stephen, Gordon and Milne, Iain and Calixto, Cristiane Pg and Waugh, Robbie and Brown, John W S and Zhang, Runxuan}, + doi = {10.1080/15476286.2020.1858253}, + issn = {1547-6286}, + journal = {RNA Biol}, + keywords = {{\textgreater}UseGalaxy.eu, Alternative Splicing}, + language = {eng}, + month = {November}, + number = {11}, + pages = {1574--1587}, + title = {{3D} {RNA}-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of {RNA}-seq data for biologists}, + url = {http://europepmc.org/abstract/MED/33345702}, + volume = {18}, + year = {2021} +} + +@article{guo_deep_2020, + abstract = {{\textless}h4{\textgreater}Motivation{\textless}/h4{\textgreater}Mass spectrometry imaging (MSI) characterizes the molecular composition of tissues at spatial resolution, and has a strong potential for distinguishing tissue types, or disease states. This can be achieved by supervised classification, which takes as input MSI spectra, and assigns class labels to subtissue locations. Unfortunately, developing such classifiers is hindered by the limited availability of training sets with subtissue labels as the ground truth. Subtissue labeling is prohibitively expensive, and only rough annotations of the entire tissues are typically available. Classifiers trained on data with approximate labels have sub-optimal performance.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}To alleviate this challenge, we contribute a semi-supervised approach mi-CNN. mi-CNN implements multiple instance learning with a convolutional neural network (CNN). The multiple instance aspect enables weak supervision from tissue-level annotations when classifying subtissue locations. The convolutional architecture of the CNN captures contextual dependencies between the spectral features. Evaluations on simulated and experimental datasets demonstrated that mi-CNN improved the subtissue classification as compared to traditional classifiers. We propose mi-CNN as an important step toward accurate subtissue classification in MSI, enabling rapid distinction between tissue types and disease states.{\textless}h4{\textgreater}Availability and implementation{\textless}/h4{\textgreater}The data and code are available at https://github.com/Vitek-Lab/mi-CNN\_MSI.}, + author = {Guo, Dan and Föll, Melanie Christine and Volkmann, Veronika and Enderle-Ammour, Kathrin and Bronsert, Peter and Schilling, Oliver and Vitek, Olga}, + doi = {10.1093/bioinformatics/btaa436}, + issn = {1367-4803}, + journal = {Bioinformatics}, + keywords = {{\textgreater}UseGalaxy.eu, Computer, Neural Networks}, + language = {eng}, + month = {July}, + number = {Suppl\_1}, + pages = {i300--i308}, + title = {Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations}, + url = {http://europepmc.org/abstract/MED/32657378}, + volume = {36}, + year = {2020} +} + @article{guo_mitogenome-based_2024, abstract = {Heptageniidae are known for their flat heads and bodies and are divided into three subfamilies. Despite the extensive diversity within this group and considerable efforts made to understand their evolutionary history, the internal classifications and origin time of Heptageniidae remains controversial. In this study, we newly sequenced 17 complete mitogenomes of Heptageniidae to reconstruct their phylogenetic positions within this family. Because of the ambiguous time of origin, our study also estimated the divergence time within Heptageniidae based on five fossil calibration points. The results of BI and ML trees all highly supported the monophyly of Heptageniidae and three subfamilies. The phylogenetic relationship of Rhithrogeninae + (Ecdyonurinae + Heptageniinae) was also recovered. The divergence time showed that Heptageniidae originated from 164.38 Mya (95\% HPD, 150.23–181.53 Mya) in the mid-Jurassic, and Rhithrogeninae originated from 95.54 Mya (95\% HPD, 73.86–120.19 Mya) in the mid-Cretaceous. Ecdyonurinae and Heptageniinae began to diverge at 90.08 Mya (95\% HPD, 68.81–113.16 Mya) in the middle Cretaceous. After morphological identification, analysis of the mitogenome’s composition, genetic distance calculation, phylogenetic analysis, and divergence time calculation, we suggest that two different populations of Epeorus montanus collected from Aksu, Xinjiang Uygur Autonomous Region (40°16′ N, 80°26′ E) and Xinyuan, Xinjiang Uygur Autonomous Region (43°20′ N, 83°43′ E) in China are cryptic species of E. montanus, but further detailed information on their morphological characteristics is needed to fully identify them.}, author = {Guo, Zhi-Qiang and Shen, Chen-Yang and Cheng, Hong-Yi and Chen, Yu-Xin and Wu, Hui-Yuan and Storey, Kenneth B. and Yu, Dan-Na and Zhang, Jia-Yong}, @@ -5468,12 +8975,30 @@ @article{guo_mitogenome-based_2024 year = {2024} } +@article{gupta_targeted_2025, + abstract = {Base editors create precise genomic edits by directing nucleobase deamination or removal without inducing double-stranded DNA breaks. However, a vast chemical space of other DNA modifications remains to be explored for genome editing. Here we harness the bacterial antiphage toxin DarT2 to append ADP-ribosyl moieties to DNA, unlocking distinct editing outcomes in bacteria versus eukaryotes. Fusing an attenuated DarT2 to a Cas9 nickase, we program site-specific ADP-ribosylation of thymines within a target DNA sequence. In tested bacteria, targeting drives homologous recombination, offering flexible and scar-free genome editing without base replacement or counterselection. In tested yeast, plant and human cells, targeting drives substitution of the modified thymine to adenine or a mixture of adenine and cytosine with limited insertions or deletions, offering edits inaccessible to current base editors. Altogether, our approach, called append editing, leverages the addition of chemical moieties to DNA to expand current modalities for precision gene editing.}, + author = {Gupta, Darshana and Patinios, Constantinos and Bassett, Harris V. and Kibe, Anuja and Collins, Scott P. and Kamm, Charlotte and Wang, Yanyan and Zhao, Chengsong and Vollen, Katie and Toussaint, Christophe and Calvin, Irene and Cullot, Grégoire and Aird, Eric J. and Polkoff, Kathryn M. and Nguyen-Vo, Thuan Phu and Migur, Angela and Schut, Friso and Al’Abri, Ibrahim S. and Achmedov, Tatjana and Del Re, Alessandro and Corn, Jacob E. and Saliba, Antoine-Emmanuel and Crook, Nathan and Stepanova, Anna N. and Alonso, Jose M. and Beisel, Chase L.}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41587-025-02802-w}, + issn = {1546-1696}, + journal = {Nature Biotechnology}, + keywords = {{\textgreater}UseGalaxy.eu, Genetic engineering, Synthetic biology}, + language = {en}, + month = {September}, + note = {Publisher: Nature Publishing Group}, + pages = {1--12}, + title = {Targeted {DNA} {ADP}-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes}, + url = {https://www.nature.com/articles/s41587-025-02802-w}, + urldate = {2025-09-10}, + year = {2025} +} + @article{gussak_precision_2023, abstract = {Streptococcussuis is an important zoonotic pathogen that causes severe invasive disease in pigs and humans. Current methods for genome engineering of S. suis rely on the insertion of antibiotic resistance markers, which is time-consuming and labor-intensive and does not allow the precise introduction of small genomic mutations. Here we developed a system for CRISPR-based genome editing in S. suis, utilizing linear DNA fragments for homologous recombination (HR) and a plasmid-based negative selection system for bacteria not edited by HR. To enable the use of this system in other bacteria, we engineered a broad-host-range replicon in the CRISPR plasmid. We demonstrated the utility of this system to rapidly introduce multiple gene deletions in successive rounds of genome editing and to make precise nucleotide changes in essential genes. Furthermore, we characterized a mechanism by which S. suis can escape killing by a targeted Cas9-sgRNA complex in the absence of HR. A characteristic of this new mechanism is the presence of very slow-growing colonies in a persister-like state that may allow for DNA repair or the introduction of mutations, alleviating Cas9 pressure. This does not impact the utility of CRISPR-based genome editing because the escape colonies are easily distinguished from genetically edited clones due to their small colony size. Our CRISPR-based editing system is a valuable addition to the genetic toolbox for engineering of S. suis, as it accelerates the process of mutant construction and simplifies the removal of antibiotic markers between successive rounds of genome editing.}, author = {Gussak, Alex and Ferrando, Maria Laura and Schrama, Mels and van Baarlen, Peter and Wells, Jerry Mark}, doi = {10.1021/acssynbio.3c00110}, journal = {ACS Synthetic Biology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Streptococcus suis}, month = {August}, note = {Publisher: American Chemical Society}, title = {Precision {Genome} {Engineering} in {Streptococcus} suis {Based} on a {Broad}-{Host}-{Range} {Vector} and {CRISPR}-{Cas9} {Technology}}, @@ -5500,6 +9025,22 @@ @article{haas_n-tp63_2019 year = {2019} } +@article{habib_immunoinformatic_2025, + abstract = {Acquired Immunodeficiency Syndrome (AIDS) is caused by Human Immunodeficiency Virus (HIV), and continues to be responsible for a substantial number of deaths worldwide each year. Development of a robust and efficient HIV-1 vaccine remains a critical priority. Structural analysis of viral proteins provides a foundational approach to designing peptide-based immunogenic vaccines. In the current experiment, we used computational prediction approaches alongside molecular docking and molecular dynamics (MD) simulations to identify potential epitopes within gp120 and Nef proteins. The selected co-epitopes were fused with the HBsAg-binding protein (SBP), a 344-amino acid protein previously identified in our laboratory through screening of a human liver cDNA expression library against HBsAg, to facilitate efficient delivery to and uptake by dendritic cells (DCs), thereby enhancing antigen (Ag) presentation. Flexible linkers are used to connect B cells, Helper T Lymphocytes (HTLs), and Cytotoxic T Lymphocytes (CTLs) in a sequential manner. The assembled vaccine construct comprises 757 amino acids, corresponding to a recombinant protein of 83.64 kDa molecular weight. Structural analysis through docking studies, MD simulations, and 3D structure validation revealed that the designed protein exhibits high structural stability and potential for interaction with Toll-like receptors (TLRs). These findings support the vaccine's ability to enhance cellular and humoral feedback, including the stimulation of T and B cells and induction of antibody (Ab) production. The results underscore the promise of this in silico designed co-epitope vaccine as a viable candidate for HIV-1 prevention and suggest that such constructs may serve as effective immunogens in future HIV-1 vaccine strategies.}, + author = {Habib, Arslan and Xu, Xinyi and Xie, Jun and Zhu, Naishuo}, + doi = {10.3390/ijms26199828}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + number = {19}, + pages = {9828}, + title = {Immunoinformatic {Prediction} of {HIV}-1 {Glycoprotein} gp120 and {Nef} {Epitopes} {Conjugated} to {HBsAg}-{Binding} {Protein} ({SBP}) to {Induce} the {Humoral} and {Cellular} {Immune} {Response}}, + url = {https://europepmc.org/articles/PMC12524554}, + volume = {26}, + year = {2025} +} + @article{hahn_dna_2020, abstract = {Increased life expectancy in modern society comes at the cost of age-associated disabilities and diseases. Aged brains not only show reduced excitability and plasticity, but also a decline in inhibition. Age-associated defects in inhibitory circuits likely contribute to cognitive decline and age-related disorders. Molecular mechanisms that exert epigenetic control of gene expression contribute to age-associated neuronal impairments. Both DNA methylation, mediated by DNA methyltransferases (DNMTs), and histone modifications maintain neuronal function throughout lifespan. Here we provide evidence that DNMT1 function is implicated in the age-related loss of cortical inhibitory interneurons. Dnmt1 deletion in parvalbumin-positive interneurons attenuates their age-related decline in the cerebral cortex. Moreover, DNMT1-deficient mice show improved somatomotor performance and reduced aging-associated transcriptional changes. A decline in the proteostasis network, responsible for the proper degradation and removal of defective proteins, is implicated in age- and disease- related neurodegeneration. Our data suggest that DNMT1 acts indirectly on interneuron survival in aged mice by modulating the proteostasis network during life-time.}, author = {Hahn, Anne and Pensold, Daniel and Bayer, Cathrin and Tittelmeier, Jessica and González-Bermúdez, Lourdes and Marx-Blümel, Lisa and Linde, Jenice and Groß, Jonas and Salinas-Riester, Gabriela and Lingner, Thomas and von Maltzahn, Julia and Spehr, Marc and Pieler, Tomas and Urbach, Anja and Zimmer-Bensch, Geraldine}, @@ -5509,6 +9050,7 @@ @article{hahn_dna_2020 keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Aging, Cerebral Cortex, DNA Methylation, GABA, inhibitory interneurons, proteostasis, synapse, transcriptional control}, language = {English}, note = {Publisher: Frontiers}, + pages = {639}, title = {{DNA} {Methyltransferase} 1 ({DNMT1}) {Function} {Is} {Implicated} in the {Age}-{Related} {Loss} of {Cortical} {Interneurons}}, url = {https://www.frontiersin.org/articles/10.3389/fcell.2020.00639/full}, urldate = {2021-02-08}, @@ -5516,6 +9058,40 @@ @article{hahn_dna_2020 year = {2020} } +@article{haidar_neural_2025, + abstract = {The nervous system undergoes dynamic structural remodeling to infiltrate cancerous tumors, contributing to their growth and progression. Emerging evidence indicates that neuroplasticity initiates early, with nerve terminals detecting and responding to tissue changes even during precancerous stages. Notably, dense sympathetic axon sprouting has been observed around pancreatic intraepithelial neoplasia (PanIN), a common precursor lesion to pancreatic cancer. However, the molecular signals driving this early neuroplasticity and its functional consequences remain poorly understood. Here, we identify the axon guidance molecule Netrin-1 as a key factor secreted by pancreatic cells within precursor lesions of pancreatic cancer. Netrin-1 promotes sympathetic axon growth and branching through its receptor, Deleted in Colorectal Cancer (DCC). Inhibition of Netrin-1 disrupts sympathetic axon remodeling while accelerating PanIN formation and progression, driven by increased precancerous cell proliferation. Furthermore, human pancreatic tissue analysis corroborates Netrin-1 expression in precursor lesions. These findings suggest that Netrin-1-driven sympathetic neuroplasticity plays a protective role in the precancerous microenvironment by modulating local cellular dynamics, providing insights into early cancer progression.}, + author = {Haidar, Hiba and Bellon, Anaïs and Sleiman, Karen and Hocine, Mélanie and Rama, Nicolas and Gadot, Nicolas and Carpizo, Darren R. and Mehlen, Patrick and Mann, Fanny}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41467-025-62299-4}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Autonomic nervous system, Cancer microenvironment}, + language = {en}, + month = {August}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {7094}, + title = {Neural function of {Netrin}-1 in precancerous lesions of the pancreas}, + url = {https://www.nature.com/articles/s41467-025-62299-4}, + urldate = {2025-09-03}, + volume = {16}, + year = {2025} +} + +@article{haider_multi-level_2025, + abstract = {Schwann cells (SC) are crucial for physiological impulse conduction in peripheral nerves. They produce myelin, provide axonal metabolic support, and contribute to reparatory processes after nerve injury. During aging, peripheral nerves acquire myelin structural anomalies and are characterized by a lower fraction of SC and a higher fraction of senescent cells. All these changes correlate with impaired electrical conduction and consequently altered function of target tissues including skeletal muscle weakness and cardiac arrhythmia. To characterize and compare cardiac and sciatic nerve SC, as well as to explore age-related differences in SC abundance and their properties, we analyzed two TdTomato reporter mouse strains to isolate Sox10 or Plp1 expressing SC. We performed RNA-sequencing on sorted TdTomato-positive cells from the heart and sciatic nerve and validated transcriptomic findings at the protein level using immunofluorescence. Our data reveal a pro-angiogenic profile in cardiac SC when compared to sciatic SC. In addition, higher levels of neural-death associated genes and lower gene and protein expression levels of the fatty acid co-transporter Fabp4/FABP4 are detected in cardiac SC from old compared to young mice, suggesting an aging-related impairment of fatty acid transport. Finally, sciatic SC activate collagen remodeling and increased pro-inflammatory signaling including TNFα. Thus, cardiac and musculoskeletal SC have different expression profiles, and undergo different changes during aging, which may contribute to impaired nerve function in both organ systems.}, + author = {Haider, Severin and Stefanovska, Dragana and Sassu, Eliza and Domisch, Claudia and Hossfeld, Madelon and Iaconianni, Pia and Perez-Feliz, Stefanie and Schneider-Warme, Franziska and Kohl, Peter and Preissl, Sebastian and Hortells, Luis}, + doi = {10.1016/j.yjmcc.2025.10.001}, + issn = {0022-2828}, + journal = {Journal of Molecular and Cellular Cardiology}, + keywords = {{\textgreater}UseGalaxy.eu, Aging, Heart, Peripheral nervous system, Schwann cell}, + month = {October}, + title = {Multi-level expression profiling of cardiac and musculoskeletal {Schwann} cells in young and old mice}, + url = {https://www.sciencedirect.com/science/article/pii/S0022282825001798}, + urldate = {2025-10-06}, + year = {2025} +} + @article{hakkanen_molecular_2024, abstract = {The aims of the study were to characterise the distribution of Cryptosporidium spp. and subtypes causing infections in Finland during 2021. This was carried out with 60 clinical samples from the hospital districts of Helsinki and Uusimaa, Vaasa, Kymenlaakso, South Karelia, and Central Finland, as well as with Finnish Infectious Diseases Register (FIDR) data. Additionally, the study aimed to explore the potential exposures related to Cryptosporidium mortiferum (Cryptosporidium chipmunk genotype I) infections via interview. Species identification was carried out with quantitative real-time PCR (qPCR) and 18S sequencing. Further typing was performed with gp60 subtyping. Over 70\% of the samples were identified as Cryptosporidium parvum and 20\% as C. mortiferum, which had not been identified in Finland before. Two cases of Cryptosporidium hominis were identified from patients reported to have travelled outside Europe. The C. parvum subtype IIaA15G2R1 and the C. mortiferum subtype XIVaA20G2T1 were the most common subtypes identified. The interviewed C. mortiferum cases did not report shared exposures such as contact with wild rodents. In conclusion, C. parvum and C. mortiferum were the major causes of cryptosporidiosis in the five studied Finnish hospital districts.}, author = {Häkkänen, Tessa and Rimhanen-Finne, Ruska and Antikainen, Jenni and Ruotsalainen, Eeva and Vainio, Anni}, @@ -5534,6 +9110,23 @@ @article{hakkanen_molecular_2024 year = {2024} } +@article{hamar_zebrafish_2025, + abstract = {Small nucleolar RNAs (snoRNAs) are one of the most abundant and evolutionary ancient group of functional non-coding RNAs. They were originally described as guides of post-transcriptional rRNA modifications, but emerging evidence suggests that snoRNAs fulfil an impressive variety of cellular functions. To reveal the true complexity of snoRNA-dependent functions, we need to catalogue first the complete repertoire of snoRNAs in a given cellular context. While the systematic mapping and characterization of “snoRNAomes” for some species have been described recently, this has not been done hitherto for the zebrafish (Danio rerio). Using size-fractionated RNA sequencing data from adult zebrafish tissues, we created an interactive “snoRNAome” database for this species. Our custom-designed analysis pipeline allowed us to identify with high-confidence 67 previously unannotated snoRNAs in the zebrafish genome, resulting in the most complete set of snoRNAs to date in this species. Reanalyzing multiple previously published datasets, we also provide evidence for the dynamic expression of some snoRNAs during the early stages of zebrafish development and tissue-specific expression patterns for others in adults. To facilitate further investigations into the functions of snoRNAs in zebrafish, we created a novel interactive database, snoDanio, which can be used to explore small RNA expression from transcriptomic data.}, + author = {Hamar, Renáta and Varga, Máté}, + doi = {10.1093/nargab/lqaf013}, + issn = {2631-9268}, + journal = {NAR Genomics and Bioinformatics}, + keywords = {{\textgreater}UseGalaxy.eu, RNA, Small Nucleolar, Zebrafish}, + month = {March}, + number = {1}, + pages = {lqaf013}, + title = {The zebrafish ({Danio} rerio) {snoRNAome}}, + url = {https://doi.org/10.1093/nargab/lqaf013}, + urldate = {2025-07-12}, + volume = {7}, + year = {2025} +} + @article{hamdi_wall-associated_2024, abstract = {The wall-associated kinase (WAK) and WAK-associated kinase-like (WAKL) genes belong to the major receptor-like kinase (RLK) gene family in plants. They are well-known as important candidates for directly transmitting extracellular signals to the cytoplasm by connecting the extracellular matrix with intracellular compartments. As a result, they participate in developmental processes as well as stress responses. Although genome-wide investigations of the WAK/WAKL gene family have been carried out in a number of plant species, little is known about the WAK/WAKL genes in sugar beet, Beta vulgaris subsp. vulgaris L. (BvWAK/WAKLs). In this study, we performed a computational large-scale characterization of the members of this gene family in sugar beet. Fifty five (55) sugar beet WAK/WAKL proteins exhibited a wide range of physicochemical properties. A total of 10 conserved motifs were identified from all BvWAK/WAKL proteins, of which 3 motifs could be used as specific motif markers for distinguishing BvWAKs from BvWAKLs. Gene structure analysis showed that most BvWAK/WAKL genes contained 3 or 4 exons with no obvious phylogenetic organization. Among BvWAK/WAKL genes, 50 were assigned to their chromosomal locations and shown to have expanded primarily through tandem duplication. Comparative phylogeny revealed that sugar beet WAK/WAKL genes were divided into six clades, and orthologous gene pairs were identified between sugar beet and its wild-related species, the sea beet (Beta vulgaris subsp. maritima L.), while B. maritima lineage-specific genes provided clues for the introduction of wild genes in sugar beet cultivars. The gene expression data analysis revealed that the BvWAK/WAKL genes of susceptible and resistant cultivars were differentially expressed in response to beet cyst nematode (BCN) infection, and that 13 BvWAK/WAKL genes were up-regulated only in the resistant cultivar, suggesting that they are potentially involved in the resistance of sugar beet against this nematode. For the first time in sugar beet, our study presents an extensive computation-based knowledge platform on WAK/WAKL gene family and provides candidate genes for deeper molecular investigation of their potential role in sugar cyst nematode resistance.}, author = {Hamdi, Jihen and Kmeli, Narjes and Bettaieb, Inchirah and Bouktila, Dhia}, @@ -5572,7 +9165,7 @@ @article{han_dna-directed_2023 doi = {10.1016/j.molcel.2023.08.007}, issn = {1097-2765}, journal = {Molecular Cell}, - keywords = {{\textgreater}UseGalaxy.eu, CPSF73, DSIF, RNA polymerase II, Rat1, Spt5, TFIIS, XRN2, intrinsic termination site, termination, torpedo}, + keywords = {{\textgreater}UseGalaxy.eu, CPSF73, DSIF, RNA Polymerase II, RNA polymerase II, Rat1, Saccharomyces cerevisiae Proteins, Spt5, TFIIS, XRN2, intrinsic termination site, termination, torpedo}, language = {English}, month = {September}, note = {Publisher: Elsevier}, @@ -5601,6 +9194,24 @@ @phdthesis{haque_profiling_2023 year = {2023} } +@article{harahap-carrillo_chronic_2025, + abstract = {Methamphetamine (METH) use is frequent among people with HIV (PWH) and appears to increase the risk of neuronal injury and neurocognitive impairment (NCI). This study explored in vivo the effects of a 12 week (long-term), low-dose METH regimen in a transgenic animal model of neuroHIV with inducible expression of HIV-1 transactivator of transcription (Tat). Seven months after transient Tat induction and five months after METH exposure ended, we detected behavioral changes in the Barnes maze (BM) spatial memory task in the Tat and METH groups but not the combined Tat + METH group. The novel object recognition (NOR) task revealed that Tat extinguished discrimination in female animals with and without METH, although METH alone slightly improved NOR. In contrast, in males, Tat, METH, and Tat + METH all compromised NOR. Neuropathological examination detected sex-dependent and brain region-specific changes of pre-synaptic terminals, neurites, and activation of astrocytes and microglia. RNA-sequencing and quantitative reverse transcription polymerase chain reaction indicated that METH and Tat significantly altered gene expression, including factors linked to Alzheimer's disease-like NCI. In summary, chronic low-dose METH exerts long-term effects on behavioral function, neuropathology, and mRNA expression, and modulates the effects of Tat, suggesting sex-dependent and -independent mechanisms may converge in HIV brain injury and NCI.}, + author = {Harahap-Carrillo, Indira S. and Fok, Dominic and Wong, Frances and Malik, Gabriel and Maung, Ricky and Qiu, Xinru and Ojeda-Juárez, Daniel and Thaney, Victoria E. and Sanchez, Ana B. and Godzik, Adam and Roberts, Amanda J. and Kaul, Marcus}, + doi = {10.3390/v17030361}, + issn = {1999-4915}, + journal = {Viruses}, + keywords = {{\textgreater}UseGalaxy.eu, HIV-1, Memory, Methamphetamine, tat Gene Products, Human Immunodeficiency Virus}, + language = {en}, + month = {February}, + number = {3}, + pages = {361}, + title = {Chronic, {Low}-{Dose} {Methamphetamine} {Reveals} {Sexual} {Dimorphism} of {Memory} {Performance}, {Histopathology}, and {Gene} {Expression} {Affected} by {HIV}-1 {Tat} {Protein} in a {Transgenic} {Model} of {NeuroHIV}}, + url = {https://escholarship.org/uc/item/7924f58g}, + urldate = {2025-03-29}, + volume = {17}, + year = {2025} +} + @article{hardtner_comparative_2023, abstract = {Background and aims Atherosclerosis is a systemic and chronic inflammatory disease propagated by monocytes and macrophages. Yet, our knowledge on how transcriptome of these cells evolves in time and space is limited. We aimed at characterizing gene expression changes in site-specific macrophages and in circulating monocytes during the course of atherosclerosis. @@ -5631,7 +9242,7 @@ @article{hashempour_reverse_2024 doi = {10.1186/s12879-024-09775-2}, issn = {1471-2334}, journal = {BMC Infectious Diseases}, - keywords = {{\textgreater}UseGalaxy.eu, Bioinformatic, HIV, Main HIV subtypes and CRF, Molecular dynamic, TLR, Vaccine}, + keywords = {{\textgreater}UseGalaxy.eu, AIDS Vaccines, Bioinformatic, Computational Biology, HIV, HIV Infections, HIV-1, Main HIV subtypes and CRF, Molecular dynamic, TLR, Vaccine, Vaccinology}, language = {en}, month = {August}, number = {1}, @@ -5644,6 +9255,22 @@ @article{hashempour_reverse_2024 year = {2024} } +@article{hashimoto_oncoprotein_2025, + abstract = {The oncogenic protein DEK interacts with the DNA-binding domains of bZIP and bHLH-ZIP transcription factors (TFs). DEK assists and enhances the DNA binding of TFs to affect transcriptional regulation...}, + author = {Hashimoto, Takuma and Saito, Shoko and Ohata, Mike and Okuwaki, Mitsuru}, + doi = {10.1111/febs.70124}, + issn = {1742-4658}, + journal = {The FEBS Journal}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {May}, + note = {Publisher: John Wiley \& Sons, Ltd}, + title = {The oncoprotein {DEK} controls growth-regulated gene expression by enhancing the {DNA}-binding activity of basic leucine zipper transcription factors}, + url = {https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.70124}, + urldate = {2025-05-29}, + year = {2025} +} + @article{hassan_genome-wide_2023, author = {Hassan, Zarqa and Abbas, Amjad and Shafique, Ikhlas}, doi = {10.22194/pdc/3.1017}, @@ -5660,13 +9287,104 @@ @article{hassan_genome-wide_2023 year = {2023} } +@article{haufschild_novel_2025, + abstract = {Members of the phylum Planctomycetota possess a plethora of intriguing and hitherto underexplored features including an enlarged periplasmic space, asymmetric cell division (“budding”), and a mostly undiscovered small molecule portfolio. Due to the large phylogenetic distance to frequently used and easily genetically accessible model bacteria, most of the established genetic tools are not readily applicable for the here-investigated bacterial phylum. However, techniques for targeted gene inactivation and the introduction of heterologous genes are crucial to investigate the cell biology in the phylum in greater detail. In this study, the targeted genomic modification of model planctomycetes was achieved by enforcing two types of homologous recombination events: simultaneous double homologous recombination for the deletion of coding regions and insertion-duplication mutagenesis for the introduction of foreign DNA into the chromosome. Upon testing the expression of commonly used fluorescent protein-encoding genes, many of the tested native promoters could not be harnessed for variation of the expression strength. Since also four commonly used inducible gene expression systems did not work in the tested model strain Planctopirus limnophila, a native rhamnose-dependent transcriptional regulator/promoter pair was established as an inducible expression system. The expanded molecular toolbox will allow the future characterization of genome-encoded features in the understudied phylum.}, + author = {Haufschild, Tom and Hammer, Jonathan and Rabold, Nico and Plut, Veronika and Jogler, Christian and Kallscheuer, Nicolai}, + doi = {10.1007/s00253-025-13462-w}, + issn = {1432-0614}, + journal = {Applied Microbiology and Biotechnology}, + keywords = {{\textgreater}UseGalaxy.eu, Cell biology, Fluorescent proteins, Gene inactivation, Inducible gene expression, Planctomycetes, Planctopirus limnophila}, + language = {en}, + month = {March}, + number = {1}, + pages = {79}, + title = {Novel tools for genomic modification and heterologous gene expression in the phylum {Planctomycetota}}, + url = {https://doi.org/10.1007/s00253-025-13462-w}, + urldate = {2025-04-02}, + volume = {109}, + year = {2025} +} + +@article{hausdorf_erga-bge_2025, + abstract = {We have generated a high-quality reference genome for +Anisus vorticulus +to support monitoring of the genetic diversity of populations of this declining freshwater species. The chromosome-level genome assembly encompasses 1.04 Gb, composed of 835 contigs and 77 scaffolds, with contig and scaffold N50 values of 2.35 Mb and 59.2 Mb, respectively. The genome was assembled into 18 chromosomal pseudomolecules.}, + author = {Hausdorf, Bernhard and Tapia, Elicio and Monteiro, Rita and Böhne, Astrid and Marcussen, Thomas and Struck, Torsten and Oomen, Rebekah A and {Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team} and {Wellcome Sanger Institute Scientific Operations: Sequencing Operations} and {Wellcome Sanger Institute Tree of Life Core Informatics team} and Haggerty, Leanne and Martin, Fergal and Brown, Thomas}, + doi = {10.12688/openreseurope.20499.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {July}, + pages = {190}, + shorttitle = {{ERGA}-{BGE} genome of {Anisus} vorticulus ({Troschel}, 1834)}, + title = {{ERGA}-{BGE} genome of {Anisus} vorticulus ({Troschel}, 1834): the {Lesser} {Ramshorn} {Snail}, an endangered freshwater snail protected under the {EU}'s {Habitats} and {Species} {Directive}}, + url = {https://open-research-europe.ec.europa.eu/articles/5-190/v1}, + urldate = {2025-10-19}, + volume = {5}, + year = {2025} +} + +@article{he_complete_2024, + abstract = {In this study, we sequenced and analyzed the mitochondrial genome of the Satanas beetle, Dynastes satanas Moser, 1909, which was intercepted by Chinese Customs during an attempted smuggling operati...}, + author = {He, Xunuo and Wei, Shuang and Li, Panpan and Li, Xianfeng}, + copyright = {© 2024 The Author(s). Published by Informa UK Limited, trading as Taylor \& Francis Group.}, + doi = {10.1080/23802359.2024.2432373}, + issn = {2380-2359}, + journal = {Mitochondrial DNA Part B}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {EN}, + month = {December}, + note = {Publisher: Taylor \& Francis}, + number = {12}, + pages = {1627--1631}, + shorttitle = {Complete mitochondrial genome of the {Satanas} beetle, {Dynastes} satanas {Moser}, 1909 ({Coleoptera}}, + title = {Complete mitochondrial genome of the {Satanas} beetle, {Dynastes} satanas {Moser}, 1909 ({Coleoptera}: {Scarabaeidae})}, + url = {https://www.tandfonline.com/doi/abs/10.1080/23802359.2024.2432373}, + urldate = {2025-09-03}, + volume = {9}, + year = {2024} +} + +@article{he_depletion_2025, + abstract = {Prostate cancer (PCa) preferentially metastasizes to bone, which remains incurable and contributes significantly to mortality and morbidity. The P2X4 receptor (P2X4R) is a receptor for ATP that is highly expressed in many cancer types including PCa and is positively associated with tumorigenesis. To understand the role of P2X4R in PCa biology, particularly in PCa bone metastasis, P2X4R (P2RX4) was knocked out in human PCa cell line PC3 cells using the CRISPR/Cas9 system. Cell proliferation, apoptosis, migration, and invasion were examined using CyQUANT, Cell Meter Caspase 3/7, scratch and transwell assays. Results showed that depleting P2X4R significantly reduced cell proliferation and invasion and increased apoptosis compared to PC3 wildtype (WT) controls in vitro. To test their metastatic potential in vivo, PC3 WT and knock-out (KO) cells were intracardiacally injected into male BALB/c immunocompromised mice. Twenty-five days post-injection, there were no detectable tumours and associated bone destruction in the tibias of mice injected with KO cells, whereas tibias of over 50\% mice injected with WT cells were occupied by tumour cells, with significant bone destruction observed ex vivo using micro-CT. Furthermore, RNA-seq and bioinformatic analysis of P2X4R KO cells demonstrated links between P2X4R and PCa cell adhesion, and other key signalling such as Wnt signalling. These findings suggest that P2X4R is a potential therapeutic target for PCa metastasis, particularly bone metastasis.}, + author = {He, Jiepei and Zhou, Yuhan and Carrera, Hector M. Arredondo and Li, Nan and Gartland, Alison and Wang, Ning}, + doi = {10.1007/s11302-025-10096-5}, + issn = {1573-9546}, + journal = {Purinergic Signalling}, + keywords = {{\textgreater}UseGalaxy.eu, Apoptosis, Bone metastases, Bone metastasis, Cancer Stem Cells, Cell adhesion, Metastasis, P2X4 receptor, Phase IV trials, Prostate cancer, RNA-seq}, + language = {en}, + month = {June}, + title = {Depletion of {P2X4} receptor alleviates prostate cancer bone metastasis through reduced cancer cell invasiveness and enhanced cell adhesion activities}, + url = {https://doi.org/10.1007/s11302-025-10096-5}, + urldate = {2025-07-12}, + year = {2025} +} + +@article{he_navigating_2025, + abstract = {Mass spectrometry (MS)-based proteomics data, including Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA), are widely used in biological research. However, the application of these datasets in validation studies is still limited due to the lack of clear demonstrations on how to effectively search and analyze proteomic data. To fill this gap, we selected one DDA and one DIA dataset deposited in the PRoteomics IDEntifications Database (PRIDE) data repository to better illustrate the proteomic data analysis workflow and downstream post-processing of protein search results. For demonstration purposes, we used two free computational tools: FragPipe (v22.0) for DDA datasets and DIA-NN (2.1.0) for DIA datasets. Post-processing steps, such as generating volcano plots and lists of dysregulated proteins, were demonstrated using R code. This study provides basic protocols for searching and analyzing proteomic data, serving as an essential beginner's guide to effectively handle proteomic datasets. Through this work, we aim to empower researchers with the knowledge necessary to leverage proteomic data in their biological investigations.}, + author = {He, Shijie and Zhang, Fangfei}, + doi = {10.3791/68707}, + issn = {1940-087X}, + journal = {Journal of Visualized Experiments (JoVE)}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {August}, + number = {222}, + pages = {e68707}, + title = {Navigating the {Mass} {Spectrometry}-{Based} {Proteomic} {Data} {Using} {Free} {Computational} {Tools}}, + url = {https://app.jove.com/t/68707/navigating-mass-spectrometry-based-proteomic-data-using-free, https://app.jove.com/t/68707/navigating-mass-spectrometry-based-proteomic-data-using-free}, + urldate = {2025-09-03}, + year = {2025} +} + @article{he_novel_2024, abstract = {The holothurians, commonly known as sea cucumbers, are marine organisms that possess significant dietary, nutritional, and medicinal value. However, the National Center for Biotechnology Information (NCBI) currently possesses only approximately 70 complete mitochondrial genome datasets of Holothurioidea, which poses limitations on conducting comprehensive research on their genetic resources and evolutionary patterns. In this study, a novel species of sea cucumber belonging to the genus Benthodytes, was discovered in the western Pacific Ocean. The genomic DNA of the novel sea cucumber was extracted, sequenced, assembled and subjected to thorough analysis.}, author = {He, Yingying and Zhao, Hancheng and Wang, Yongxin and Qu, Changfeng and Gao, Xiangxing and Miao, Jinlai}, doi = {10.1186/s12864-024-10607-5}, issn = {1471-2164}, journal = {BMC Genomics}, - keywords = {{\textgreater}UseGalaxy.eu, Benthodytes sp. Gxx-2023, Bioinformatics analysis, Mitogenome, Phylogenetic evolution, Sea cucumber}, + keywords = {{\textgreater}UseGalaxy.eu, Benthodytes sp. Gxx-2023, Bioinformatics analysis, Evolution, Molecular, Genome, Mitochondrial, Mitogenome, Phylogenetic evolution, Phylogeny, Sea Cucumbers, Sea cucumber}, language = {en}, month = {July}, number = {1}, @@ -5699,7 +9417,7 @@ @article{hedhly_s-locus_2023 doi = {10.3390/ijms24043932}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {\textit{Prunus salicina}, \textit{S}-allele, \textit{S}-genotyping-by-sequencing, {\textgreater}UseGalaxy.eu, Japanese plum, self-incompatibility}, + keywords = {\textit{Prunus salicina}, \textit{S}-allele, \textit{S}-genotyping-by-sequencing, {\textgreater}UseGalaxy.eu, Japanese plum, Prunus, Prunus domestica, self-incompatibility}, language = {en}, month = {January}, note = {Number: 4 @@ -5731,6 +9449,62 @@ @article{heine_activation_2024 year = {2024} } +@article{heise_evidence_2025, + abstract = {Oxygenic photosynthesis in streptophytic algae, such as Charophyceae, is often impeded by low CO2 levels in aquatic habitats. Consequently, many algal groups evolved a CO2-concentrating mechanism (CCM). However, its presence in Charophyceae remains controversial. To explore this, we analyzed the acclimation of photosynthesis, carbon isotope composition, and gene expression in Chara braunii under varying inorganic carbon (Ci) conditions. The photosynthetic activity changed complementarily under low- or high-Ci levels. Notably, the Ci compensation point of photosynthesis was significantly lower in thalli grown at ambient Ci than in elevated Ci. Correspondingly, the delta 13C levels were lower in thalli from high than low Ci. These results indicate that C. braunii performs a CCM under low Ci, which is suppressed under high Ci. Transcriptomic analyses of algae from different Ci cultivations provided insight into Ci-regulated genes and pointed to the possible association between carbonic anhydrases and aquaporins with the CCM. Collectively, our results indicate that C. braunii expresses a CCM allowing efficient use of CO2 and bicarbonate under limiting Ci conditions. A tentative scenario is provided summarizing the role of potential players in the CCM.}, + author = {Heise, Carolin M. and Heß, Daniel A. and Walke, Peter and Voß, Maren and Schubert, Hendrik and Hess, Wolfgang R. and Hagemann, Martin}, + copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.}, + doi = {10.1111/nph.70283}, + issn = {1469-8137}, + journal = {New Phytologist}, + keywords = {{\textgreater}UseGalaxy.eu, CO2 limitation, Charophyceae, bicarbonate, carbonic anhydrase, gene expression, transport}, + language = {en}, + month = {June}, + note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.70283}, + number = {n/a}, + title = {Evidence for a {CO2}-concentrating mechanism in the model streptophyte green alga {Chara} braunii}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.70283}, + urldate = {2025-06-17}, + volume = {n/a}, + year = {2025} +} + +@article{hemm_interactors_2024, + abstract = {Throughout the tree of life RNA-binding proteins play important roles, but they are poorly characterized in cyanobacteria. Overexpression of the predicted RNA-binding protein Ssr1238 in the cyanobacterium \textit{Synechocystis} 6803 for 24 h led to higher levels of RNase P RNA, tRNAs, and stress-related mRNAs. Co-immunoprecipitation of proteins followed by MS analysis and sequencing of UV crosslinked, co-immunoprecipitated RNA samples identified potential interaction partners of Ssr1238. The most enriched transcript was RNase P RNA, and RnpA, the protein component of RNase P, was among the most highly enriched proteins. A second highly enriched transcript is derived from gene \textit{ssl3177}, which encodes a central enzyme in cell wall remodelling during cell division. The data also showed a strong connection to the RNA maturation and modification system indicated by co-precipitation of RNA modifying enzymes, riboendonuclease E and enolase. Surprisingly, cyanophycin synthetase and urease were highly enriched as well. In conclusion, Ssr1238 specifically binds to two different transcripts and could be involved in the coordination of RNA maturation, translation, cell division, and aspects of nitrogen metabolism. Our results are consistent with recent findings that the \textit{B. subtilis} YlxR protein functions as an RNase P modulator (RnpM), extending its proposed role to the phylum cyanobacteria, and suggesting additional functionalities.}, + author = {Hemm, Luisa and Miucci, Anna and Kraus, Alexander and Riediger, Matthias and Tholen, Stefan and Abdelaziz, Nouha and Georg, Jens and Schilling, Oliver and Hess, Wolfgang R}, + doi = {10.1080/15476286.2024.2429230}, + issn = {1547-6286}, + journal = {RNA Biol}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial Proteins, Gene Expression Regulation, Bacterial, RNA-Binding Proteins, Synechocystis}, + language = {eng}, + month = {January}, + number = {1}, + pages = {1--19}, + title = {Interactors and effects of overexpressing {YlxR}/{RnpM}, a conserved {RNA} binding protein in cyanobacteria}, + url = {http://europepmc.org/abstract/MED/39625117}, + volume = {21}, + year = {2024} +} + +@article{henriques_revealing_2025, + abstract = {A new level of viral complexity has emerged from the isolation of green algae-infecting chloroviruses from diverse aquatic environments around the world over the past few decades. This study focuses on describing and comparing the genomic features of gammachloroviruses, previously referred to as SAG-viruses. We present 24 novel isolates capable of forming plaques on lawns of Chlorella heliozoae SAG 3.83, including the first giant virus isolated from Greenland. Together with 13 previous isolates, these new viruses form a robust dataset that we used to investigate the genomic landscape and to test whether environmental conditions influence the species diversity of gammachloroviruses. Genome sizes range from 283 kbp to 385 kbp, with one new isolate having the smallest genome found in the genus Chlorovirus. Based on phylogenomics and global genome identity analysis, we defined 10 species of “Gammachlorovirus”, half of which are represented by a single isolate. We observed a high level of genome synteny, and the tRNA islets maintain a distinct interspecific pattern, although some notable variations are evident. Our analysis reveals an open pan-genome composed of 681 COGs, more than 30\% of which consist of uncharacterized genes, highlighting significant innovative genetic potential for these viruses. Our results suggest that the subgenus “Gammachlorovirus” exhibits the greatest genetic diversity among chloroviruses, with variability that is independent of geographic location. Overall, these findings underscore the considerable diversity within these ten newly defined species and the importance of isolating and characterizing chloroviruses from new locations worldwide to enhance our understanding of the ecology and evolution of this group of giant algal viruses.}, + author = {Henriques, Lethícia R. and Botelho, Bruna B. F. and Carlson, Roger M. and Carvalho, João Victor R. P. and Oliveira, Ellen G. and Agarkova, Irina V. and Van Etten, James L. and Dunigan, David D. and Rodrigues, Rodrigo A. L.}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s44298-025-00088-y}, + issn = {2948-1767}, + journal = {npj Viruses}, + keywords = {{\textgreater}UseGalaxy.eu, Microbiology, Viral evolution, Virology}, + language = {en}, + month = {February}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {1--11}, + title = {Revealing the hidden diversity of {Chlorella} heliozoae-infecting giant viruses}, + url = {https://www.nature.com/articles/s44298-025-00088-y}, + urldate = {2025-02-28}, + volume = {3}, + year = {2025} +} + @article{hering_eikenella_2021, author = {Hering, Silvio and Jansson, Moritz K. and Buhl, Michael E. J.}, doi = {10.1099/ijsem.0.004977}, @@ -5744,6 +9518,26 @@ @article{hering_eikenella_2021 year = {2021} } +@article{hermawaty_novo_2025, + abstract = {Agarwood is a highly prized resinous wood produced by select members of the Thymelaeaceae plant family. Its formation in Aquilaria species has been expedited using various induction techniques, revealing insights into factors affecting the chemical constituents of artificially induced agarwood. Building on this, our research delved into the potential of another Thymelaeaceae member, Gyrinops versteegii, as an alternate agarwood source. Inoculation of juvenile G. versteegii stems with local strain of Fusarium solani successfully induced the production of sesquiterpenes and chromone compounds. On a molecular level, a de novo transcriptome reconstruction and analysis highlighted biological processes related to the plant-type hypersensitive response and DNA damage 2 days post-fungal inoculation. Notably, terpenoid biosynthesis was observed only in the group exposed to the fungus for an extended duration (28 days), where DNA damage response also played a pivotal role. Despite the inherent limitations of de novo transcriptome reconstruction, capturing only a few of sesquiterpenes biosynthesis-related genes, our findings underscore the potential of G. verteegii in producing high-quality agarwood. Future high-resolution transcriptome data could further elucidate this promising avenue.}, + author = {Hermawaty, Dina and Setyobudi, Titis and Nugrahapraja, Husna and Turjaman, Maman and Faizal, Ahmad}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-87486-7}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Metabolomics, Plant biotechnology, Plant genetics, Plant physiology, Plant stress responses, Plant symbiosis, Seedlings, Sequencing, Thymelaeaceae, Transcriptome, Wood}, + language = {en}, + month = {January}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {2977}, + title = {De novo transcriptome assembly and analysis during agarwood induction in {Gyrinops} versteegii {Gilg}. seedling}, + url = {https://www.nature.com/articles/s41598-025-87486-7}, + urldate = {2025-01-27}, + volume = {15}, + year = {2025} +} + @article{hernandez_design_2020, abstract = {Biological control is emerging as a feasible alternative to chemical pesticides in agriculture. Measuring the microbial biocontrol agent (mBCA) populations in the environment is essential for an accurate risk assessment and to optimize the usage of an mBCA-based plant protection product. In this manuscript, a workflow to obtain a large number of qPCR markers suitable for robust strain-specific detection and quantification is presented. The workflow starts from whole genome sequencing data and consists on (i) identifying the strain-specific sequences, (ii) designing specific primer/probe sets for qPCR assays, and (iii) empirically verifying the performance of the assays. The first two stages involve exclusively computer work, but they are intended for researchers with little or no bioinformatic background: only knowledge of the BLAST suite tools and working with spreadsheets are required, and familiarity with the Galaxy environment and next-generation sequencing concepts are strongly advised. All bioinformatic work can be implemented using publically available resources and a regular desktop computer, no matter the operating system, connected to the Internet. The workflow was tested with 5 bacterial strains from different species under development as mBCAs, and yielded thousands of candidate markers and a triplex qPCR assay for each candidate mBCA. The qPCR assays were successfully tested in soils of different nature, water from different sources, and samples from different plant tissues. The mBCA detection limits and population dynamics in the different matrices are similar to those in qPCR assasys designed by other means. In summary a new accessible, amenable, cost-effective and robust, workflow to obtain a large number of strain-specific qPCR markers, is presented.}, author = {Hernández, Iker and Sant, Clara and Martínez, Raquel and Fernández, Carolina}, @@ -5753,6 +9547,7 @@ @article{hernandez_design_2020 keywords = {+HowTo, +RefPublic, +Stellar, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org.au, Bacterial strain-specific, NGS, biocontrol, marker, qPCR, risk assesment}, language = {English}, note = {Publisher: Frontiers}, + pages = {208}, title = {Design of {Bacterial} {Strain}-{Specific} {qPCR} {Assays} {Using} {NGS} {Data} and {Publicly} {Available} {Resources} and {Its} {Application} to {Track} {Biocontrol} {Strains}}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.00208/full}, urldate = {2020-03-23}, @@ -5767,7 +9562,7 @@ @article{herwibawa_association_2024 doi = {10.3390/ijms25021040}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {{\textgreater}UseGalaxy.eu, CRE, SNP, TFBS, cullin, indel, phylogenetic}, + keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, CRE, Oryza, SNP, TFBS, cullin, indel, phylogenetic}, language = {en}, month = {January}, note = {Number: 2 @@ -5836,11 +9631,16 @@ @article{hesse_proximity_2021 } @article{hetz_burkholderiaceae_2021, + abstract = {Cryoturbated peat circles (pH 4) in the Eastern European Tundra harbor up to 2 mM pore water nitrate and emit the greenhouse gas N$_{\textrm{2}}$O like heavily fertilized agricultural soils in temperate regions. The main process yielding N$_{\textrm{2}}$O under oxygen limited conditions is denitrification, which is the sequential reduction of nitrate/nitrite to N$_{\textrm{2}}$O and/or N$_{\textrm{2}}$. N$_{\textrm{2}}$O reduction to N$_{\textrm{2}}$ is impaired by pH {\textless} 6 in classical model denitrifiers and many environments. Key microbes of peat circles are important but largely unknown catalysts for \textit{C}- and \textit{N}-cycling associated N$_{\textrm{2}}$O fluxes. Thus, we hypothesized that the peat circle community includes hitherto unknown taxa and is essentially unable to efficiently perform complete denitrification, i.e., reduce N$_{\textrm{2}}$O, due to a low \textit{in situ} pH. 16S rRNA analysis indicated a diverse active community primarily composed of the bacterial class-level taxa Alphaproteobacteria, Acidimicrobiia, Acidobacteria, Verrucomicrobiae, and Bacteroidia, as well as archaeal Nitrososphaeria. Euryarchaeota were not detected. $^{\textrm{13}}$C$_{\textrm{2}}$- and $^{\textrm{12}}$C$_{\textrm{2}}$-acetate supplemented anoxic microcosms with endogenous nitrate and acetylene at an \textit{in situ} near pH of 4 were used to assess acetate dependent carbon flow, denitrification and N$_{\textrm{2}}$O production. Initial nitrate and acetate were consumed within 6 and 11 days, respectively, and primarily converted to CO$_{\textrm{2}}$ and N$_{\textrm{2}}$, suggesting complete acetate fueled denitrification at acidic pH. Stable isotope probing coupled to 16S rRNA analysis via Illumina MiSeq amplicon sequencing identified acetate consuming key players of the family \textit{Burkholderiaceae} during complete denitrification correlating with \textit{Rhodanobacter} spp. The archaeal community consisted primarily of ammonia-oxidizing Archaea of Nitrososphaeraceae, and was stable during the incubation. The collective data indicate that peat circles (i) host acid-tolerant denitrifiers capable of complete denitrification at pH 4-5.5, (ii) other parameters like carbon availability rather than pH are possible reasons for high N$_{\textrm{2}}$O emissions \textit{in situ}, and (iii) \textit{Burkholderiaceae} are responsive key acetate assimilators co-occurring with \textit{Rhodanobacter} sp. during denitrification, suggesting both organisms being associated with acid-tolerant denitrification in peat circles.}, author = {Hetz, Stefanie A. and Horn, Marcus A.}, doi = {10.3389/fmicb.2021.628269}, + issn = {1664-302X}, + journal = {Frontiers in microbiology}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {February}, note = {Publisher: Frontiers Media SA}, + pages = {628269}, title = {Burkholderiaceae {Are} {Key} {Acetate} {Assimilators} {During} {Complete} {Denitrification} in {Acidic} {Cryoturbated} {Peat} {Circles} of the {Arctic} {Tundra}}, url = {https://doi.org/10.3389/fmicb.2021.628269}, volume = {12}, @@ -5853,7 +9653,7 @@ @article{hildebrandt_activina_2021 doi = {10.1007/s12015-020-10103-9}, issn = {2629-3277}, journal = {Stem Cell Reviews and Reports}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Induced Pluripotent Stem Cells, Myositis Ossificans}, language = {en}, month = {June}, number = {3}, @@ -5883,6 +9683,56 @@ @article{hille_ultrastructural_2020 year = {2020} } +@article{hiltemann_galaxy_2022, + abstract = {There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis and stewardship are still rarely taught in life science educational programs [1], resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform ( https://training.galaxyproject.org ); an open access, community-driven framework for the collection of FAIR training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform [2]. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments.}, + author = {Hiltemann, Saskia and Rasche, Helena and Gladman, Simon and Hotz, Hans-Rudolf and Larivière, Delphine and Blankenberg, Daniel and Jagtap, Pratik and Wollmann, Thomas and Bretaudeau, Anthony and Goué, Nadia and Griffin, Timothy and Royaux, Coline and Le Bras, Yvan and Mehta, Subina and Syme, Anna and Coppens, Frederik and Droesbeke, Bert and Soranzo, Nicola and Bacon, Wendi and Psomopoulos, Fotis and Gallardo-Alba, Cristóbal and Davis, John and Föll, Melanie Christine and Fahrner, Matthias and Doyle, Maria and Serrano-Solano, Beatriz and Fouilloux, Anne and van Heusden, Peter and Maier, Wolfgang and Clements, Dave and Heyl, Florian and Grüning, Björn and Batut, Bérénice and {=the Galaxy Training Network}}, + doi = {10.1101/2022.06.02.494505}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Galaxy {Training}: {A} {Powerful} {Framework} for {Teaching}!}, + url = {http://europepmc.org/abstract/PPR/PPR502297}, + year = {2022} +} + +@article{hiltemann_galaxy_2023, + abstract = {There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org), an open access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics, and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments.}, + author = {Hiltemann, Saskia and Rasche, Helena and Gladman, Simon and Hotz, Hans-Rudolf and Larivière, Delphine and Blankenberg, Daniel and Jagtap, Pratik D and Wollmann, Thomas and Bretaudeau, Anthony and Goué, Nadia and Griffin, Timothy J and Royaux, Coline and Le Bras, Yvan and Mehta, Subina and Syme, Anna and Coppens, Frederik and Droesbeke, Bert and Soranzo, Nicola and Bacon, Wendi and Psomopoulos, Fotis and Gallardo-Alba, Cristóbal and Davis, John and Föll, Melanie Christine and Fahrner, Matthias and Doyle, Maria A and Serrano-Solano, Beatriz and Fouilloux, Anne Claire and van Heusden, Peter and Maier, Wolfgang and Clements, Dave and Heyl, Florian and {=Galaxy Training Network} and Grüning, Björn and Batut, Bérénice}, + doi = {10.1371/journal.pcbi.1010752}, + issn = {1553-734X}, + journal = {PLoS computational biology}, + keywords = {{\textgreater}UseGalaxy.eu, Computational Biology, Software}, + language = {eng}, + month = {January}, + number = {1}, + pages = {e1010752}, + title = {Galaxy {Training}: {A} powerful framework for teaching!}, + url = {http://europepmc.org/abstract/MED/36622853}, + volume = {19}, + year = {2023} +} + +@article{hoang_comprehensive_2025, + abstract = {Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), represents a major threat to poultry production, leading to significant mortality and economic losses. This study aimed to characterize an APEC strain, HPVN24, isolated from diarrheic chickens at a farm in Hai Phong, Vietnam. The strain was investigated through phenotypic assays, antibiotic susceptibility profiling, and whole-genome sequencing using the Illumina platform. HPVN24 exhibited β-hemolytic activity and resistance to trimethoprim, ampicillin, and ciprofloxacin. Whole-genome analysis identified the strain as serotype O78:H9 and sequence type ST23, with a genome size of 5.05 Mb and a GC content of 50.57\%. Genome annotation revealed a wide repertoire of genes involved in metabolism, secretion systems, virulence, and biofilm formation. Virulence-associated genes included those related to adhesion, iron acquisition, hemolysin production, and stress response. Analysis predicted multidrug resistance to 18 antibiotic classes, with particularly strong resistance to fluoroquinolones. Phylogenetic comparison demonstrated that HPVN24 clustered closely with O78:H9 strains isolated from poultry in other regions, suggesting potential transmission across populations. These findings indicate that HPVN24 is a multidrug-resistant and highly virulent APEC strain linked to colibacillosis outbreaks in Vietnam and highlight the need for ongoing surveillance, judicious antibiotic usage, and alternative strategies to ensure poultry health and food safety.}, + author = {Hoang, Minh Duc and Lanh, Pham Thi and Hien, Vu Thi and Kao, Cheng-Yen and Quyen, Dong Van}, + copyright = {cc by}, + doi = {10.3390/microorganisms13102265}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu, Antibiotic Resistance, Avian Pathogenic Escherichia Coli, Colibacillosis, Vietnam Poultry, Whole Genome Sequencing, virulence factors}, + language = {eng}, + month = {September}, + number = {10}, + pages = {2265}, + pmcid = {PMC12565876}, + pmid = {41156725}, + shorttitle = {Comprehensive {Genomic} and {Phenotypic} {Characterization} of \<i\>{Escherichia} coli\</i\> {O78}}, + title = {Comprehensive {Genomic} and {Phenotypic} {Characterization} of \<i\>{Escherichia} coli\</i\> {O78}:{H9} {Strain} {HPVN24} {Isolated} from {Diarrheic} {Poultry} in {Vietnam}}, + url = {https://europepmc.org/articles/PMC12565876}, + urldate = {2025-12-26}, + volume = {13}, + year = {2025} +} + @article{hodzhev_analysis_2023, abstract = {Pulmonary sarcoidosis is a complex inflammatory disease characterized by granulomas in the lung tissue, leading to breathing difficulties and chest pain. Its etiology remains not fully understood, with factors such as allergies, autoimmune responses and genetics playing a role. This study explores the potential of blood microbiome dysbiosis, defined as an imbalance in the microbial ecosystem, as a missing piece of the puzzle in understanding the etiology of the disease. Our objective was to apply a decision-tree supervised machine learning hierarchical model to distinguish potential patterns of microbiome dysbiosis in blood samples from patients with pulmonary sarcoidosis as compared to healthy age-matched controls. Blood microbiome analysis, being individually-specific and stable, offers a unique perspective. Utilizing 16S rRNA gene amplicon sequencing, we analyzed the blood microbiome composition characterized by non-normally distributed and sparse data. Because of the rarity of the disease in Bulgaria, we studied a relatively small patient group, n = 7. The findings were compared to 21 healthy age-matched controls. Bioinformatics and statistical analysis play a pivotal role in microbiome analysis, especially when discerning associations between taxonomic composition and disorders such as pulmonary sarcoidosis. By analyzing the microbial diversity, we identified alterations in the blood microbiome composition between healthy individuals and those with sarcoidosis, which potentially may trigger the disease. Advanced machine learning techniques provided additional power to the analysis, that might be overlooked by the usual group statistics, confirming the differentiation of the diversity within the studied microbiome.}, author = {Hodzhev, Yordan}, @@ -5907,8 +9757,9 @@ @article{hofacker_engineering_2020 author = {Hofacker, Daniel and Broche, Julian and Laistner, Laura and Adam, Sabrina and Bashtrykov, Pavel and Jeltsch, Albert}, copyright = {http://creativecommons.org/licenses/by/3.0/}, doi = {10.3390/ijms21020502}, + issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {+Methods, +UseLocal, +UsePublic, {\textgreater}UseGalaxy.eu, DNMT3A-DNMT3L, SunTag, dCas9, epigenome editing, targeted DNA methylation}, + keywords = {+Methods, +UseLocal, +UsePublic, {\textgreater}UseGalaxy.eu, Cellular Reprogramming Techniques, DNA (Cytosine-5-)-Methyltransferases, DNA Methylation, DNMT3A-DNMT3L, Gene Expression Regulation, Protein Engineering, SunTag, dCas9, epigenome editing, targeted DNA methylation}, language = {en}, month = {January}, number = {2}, @@ -5956,10 +9807,31 @@ @article{hoffmann_role_2024 year = {2024} } +@article{hoffmann_transcriptome-wide_2021, + abstract = {Ribonucleases are crucial enzymes in RNA metabolism and post-transcriptional regulatory processes in bacteria. Cyanobacteria encode the two essential ribonucleases RNase E and RNase J. Cyanobacterial RNase E is shorter than homologues in other groups of bacteria and lacks both the chloroplast-specific N-terminal extension as well as the C-terminal domain typical for RNase E of enterobacteria. In order to investigate the function of RNase E in the model cyanobacterium Synechocystis sp. PCC 6803, we engineered a temperature-sensitive RNase E mutant by introducing two site-specific mutations, I65F and the spontaneously occurred V94A. This enabled us to perform RNA-seq after the transient inactivation of RNase E by a temperature shift (TIER-seq) and to map 1472 RNase-E-dependent cleavage sites. We inferred a dominating cleavage signature consisting of an adenine at the -3 and a uridine at the +2 position within a single-stranded segment of the RNA. The data identified mRNAs likely regulated jointly by RNase E and an sRNA and potential 3' end-derived sRNAs. Our findings substantiate the pivotal role of RNase E in post-transcriptional regulation and suggest the redundant or concerted action of RNase E and RNase J in cyanobacteria.}, + author = {Hoffmann, Ute A and Heyl, Florian and Rogh, Said N and Wallner, Thomas and Backofen, Rolf and Hess, Wolfgang R and Steglich, Claudia and Wilde, Annegret}, + doi = {10.1093/nar/gkab1161}, + issn = {0305-1048}, + journal = {Nucleic Acids Res}, + keywords = {{\textgreater}UseGalaxy.eu, Transcriptome}, + language = {eng}, + month = {December}, + number = {22}, + pages = {13075--13091}, + title = {Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease {E} reveals insights into its function and substrate recognition}, + url = {http://europepmc.org/abstract/MED/34871439}, + volume = {49}, + year = {2021} +} + @article{holper_genome-wide_2021, + abstract = {Herpesviruses are large DNA viruses, which encode up to 300 different proteins including enzymes enabling efficient replication. Nevertheless, they depend on a multitude of host cell proteins for successful propagation. To uncover cellular host factors important for replication of pseudorabies virus (PrV), an alphaherpesvirus of swine, we performed an unbiased genome-wide CRISPR/Cas9 forward screen. To this end, a porcine CRISPR-knockout sgRNA library (SsCRISPRko.v1) targeting 20,598 genes was generated and used to transduce porcine kidney cells. Cells were then infected with either wildtype PrV (PrV-Ka) or a PrV mutant (PrV-gD$^{\textrm{-}}$Pass) lacking the receptor-binding protein gD, which regained infectivity after serial passaging in cell culture. While no cells survived infection with PrV-Ka, resistant cell colonies were observed after infection with PrV-gD$^{\textrm{-}}$Pass. In these cells, sphingomyelin synthase 1 (SMS1) was identified as the top hit candidate. Infection efficiency was reduced by up to 90\% for PrV-gD$^{\textrm{-}}$Pass in rabbit RK13-sgms1$_{\textrm{KO}}$ cells compared to wildtype cells accompanied by lower viral progeny titers. Exogenous expression of SMS1 partly reverted the entry defect of PrV-gD$^{\textrm{-}}$Pass. In contrast, infectivity of PrV-Ka was reduced by 50\% on the knockout cells, which could not be restored by exogenous expression of SMS1. These data suggest that SMS1 plays a pivotal role for PrV infection, when the gD-mediated entry pathway is blocked.}, author = {Hölper, Julia E. and Grey, Finn and Baillie, John Kenneth and Regan, Tim and Parkinson, Nicholas J. and Höper, Dirk and Thamamongood, Thiprampai and Schwemmle, Martin and Pannhorst, Katrin and Wendt, Lisa and Mettenleiter, Thomas C. and Klupp, Barbara G.}, doi = {10.3390/v13081574}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {1999-4915}, + journal = {Viruses}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Genome, Viral, Host Microbial Interactions, Mutation}, + language = {eng}, month = {August}, note = {Publisher: MDPI AG}, number = {8}, @@ -5970,6 +9842,23 @@ @article{holper_genome-wide_2021 year = {2021} } +@article{holtappels_preparing_2020, + abstract = {The prevalence of \textit{Pseudomonas syringae} pv. \textit{porri} (Pspo) in Belgium continues to increase and sustainable treatments for this pathogen remain unavailable. A potentially attractive biocontrol strategy would be the application of bacteriophages. The ideal application strategy of phages in an agricultural setting remains unclear, especially in a field-based production such as for leek plants in Flanders. Therefore, more insight in bacteria-phage interaction is required, along with the evaluation of different application strategies. In this study, we further characterized the infection strategy of two Pspo phages, KIL3b and KIL5. We found that both phages recognize lipopolysaccharide (LPS) moieties on the surface of the bacterium. LPS is an important pathogenicity factor of Pspo. Our data also suggest that KIL5 requires an additional protein in the bacterial cytoplasmatic membrane to efficiently infect its host. Virulence tests showed that this protein also contributes to Pspo virulence. Furthermore, a cocktail of both phages was applied in a seed bioassay. A combination of KIL3b and KIL5 reduced the bacterial concentration 100-fold. However, in vitro Pspo resistance against phage infection developed quite rapidly. However, the impact of this phage resistance might be mitigated as is suggested by the fact that those resistance mutations preferably occur in genes involved in LPS metabolism, and that the virulence of those mutants is possibly reduced. Our data suggest that the phage cocktail has promising potential to lower the prevalence of Pspo and to be integrated in a pest management strategy. Targeted research is needed to further explore the applicability of the phages in combination with other disease control strategies.}, + author = {Holtappels, Dominique and Kerremans, Alison and Busschots, Yoni and Van Vaerenbergh, Johan and Maes, Martine and Lavigne, Rob and Wagemans, Jeroen}, + doi = {10.3390/ijms21082930}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Host-Pathogen Interactions}, + language = {eng}, + month = {April}, + number = {8}, + pages = {E2930}, + title = {Preparing for the {KIL}: {Receptor} {Analysis} of {Pseudomonas} syringae pv. porri {Phages} and {Their} {Impact} on {Bacterial} {Virulence}}, + url = {http://europepmc.org/abstract/MED/32331264}, + volume = {21}, + year = {2020} +} + @phdthesis{holthausen_bermejo_workflow-based_2019, abstract = {La comparación de secuencias de textos es un área de notable relevancia dentro de las Ciencias de la Computación. Existen varios problemas clásicos representativos del área, como el problema de la Subsecuencia Común de mayor Longitud, consistente en encontrar información compartida por diferentes cadenas de texto. Sus aplicaciones van desde la Lingüística Computacional hasta la Bioinformática, entre otras. Al respecto de esta última, el área de la comparación de secuencias de genomas ha recibido mucha atención durante los últimos años, lo que ha llevado a un crecimiento destacado. Esto, junto a las mejoras técnicas en el rendimiento computacional, está contribuyendo a ampliar el conocimiento sobre quiénes somos. En particular, la evolución de las especies, a pesar de haber sido extensamente estudiada, sigue necesitando ser analizada, debido a su complejidad, tanto analítica como computacional. Nuevas herramientas para el estudio de Eventos Evolutivos pueden proveernos de información relevante sobre rasgos y enfermedades, además de una mayor comprensión de los mecanismos que subyacen a la evolución (que tienen un @@ -6007,6 +9896,25 @@ @article{homchan_reproducible_2024 year = {2024} } +@article{honecker_entamoeba_2025, + abstract = {The parasitic protozoan Entamoeba histolytica secretes extracellular vesicles (EVs), but so far little is known about their function in the interaction with the host immune system. Infection with E. histolytica trophozoites can lead to formation of amebic liver abscesses (ALAs), in which pro-inflammatory immune responses of Ly6Chi monocytes contribute to liver damage. Men exhibit a more severe pathology as the result of higher monocyte recruitment and a stronger immune response. To investigate the role of EVs and pathogenicity in the host immune response, we studied the effect of EVs secreted by low pathogenic EhA1 and highly pathogenic EhB2 amebae on monocytes. Size and quantity of isolated EVs from both clones were similar. However, they differed in their proteome and miRNA cargo, providing insight into factors potentially involved in amebic pathogenicity. In addition, EVs were enriched in proteins with signaling peptides compared with the total protein content of trophozoites. Exposure to EVs from both clones induced monocyte activation and a pro-inflammatory immune response as evidenced by increased surface presentation of the activation marker CD38 and upregulated gene expression of key signaling pathways (including NF-κB, IL-17 and TNF signaling). The release of pro-inflammatory cytokines was increased in EV-stimulated monocytes and more so in male- than in female-derived cells. While EhA1 EV stimulation caused elevated myeloperoxidase (MPO) release by both monocytes and neutrophils, EhB2 EV stimulation did not, indicating the protective role of MPO during amebiasis. Collectively, our results suggest that parasite-released EVs contribute to the male-biased immunopathology mediated by pro-inflammatory monocytes during ALA formation.}, + author = {Honecker, Barbara and Bärreiter, Valentin A. and Höhn, Katharina and Horváth, Balázs and Harant, Karel and Metwally, Nahla Galal and Marggraff, Claudia and Anders, Juliett and Leyk, Stephanie and Martínez-Tauler, Maria del Pilar and Bea, Annika and Hansen, Charlotte and Fehling, Helena and Lütkemeyer, Melanie and Lorenzen, Stephan and Franzenburg, Sören and Lotter, Hanna and Bruchhaus, Iris}, + doi = {10.1371/journal.pntd.0012997}, + issn = {1935-2735}, + journal = {PLOS Neglected Tropical Diseases}, + keywords = {{\textgreater}UseGalaxy.eu, Cloning, Cytokines, Entamoeba histolytica, MicroRNAs, Monocytes, Neutrophils, Proteomes, Trophozoites}, + language = {en}, + month = {October}, + note = {Publisher: Public Library of Science}, + number = {4}, + pages = {e0012997}, + title = {Entamoeba histolytica extracellular vesicles drive pro-inflammatory monocyte signaling}, + url = {https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0012997}, + urldate = {2025-05-29}, + volume = {19}, + year = {2025} +} + @phdthesis{honecker_extracellular_2023, abstract = {Infection with the protozoan parasite Entamoeba histolytica (E. histolytica) is the cause of amebiasis. While most intestinal infections remain asymptomatic, a minority result in invasive disease. Invasive amebiasis, particularly amebic liver abscess (ALA) formation, occurs predominantly in adult men. An underlying immunopathology, crucially mediated by pro-inflammatory Ly6Chi monocytes, is known to contribute to liver damage in the murine model for the disease and differs between males and females. The mechanisms behind the switch from asymptomatic colonization to parasite invasion are incompletely understood to date. In order to investigate the interaction of the parasite with the host immune system, extracellular vesicles (EVs) as communicators between host and parasite were the focus of this study. EVs are membranous vesicles released by cells into their environment that contain protein, lipids, micro RNAs (miRNAs), and other types of cargo. They are involved in intercellular communication and pathogen-derived EVs have been demonstrated to modulate the host immune response in the context of a variety of infectious diseases. E. histolytica EVs and their effects on primary murine monocytes in vitro were studied here. @@ -6067,6 +9975,7 @@ @article{hosseini_astrocytes_2024 @article{hosseinzadeh_gene_2023, abstract = {Heat stress in poultry houses, especially in warm areas, is one of the main environmental factors that restrict the growth of broilers or laying performance of layers, suppresses the immune system, and deteriorates egg quality and feed conversion ratio. The molecular mechanisms underlying the response of chicken to acute heat stress (AHS) have not been comprehensively elucidated. Therefore, the main object of the current work was to investigate the liver gene expression profile of chickens under AHS in comparison with their corresponding control groups, using four RNA-seq datasets. The meta-analysis, GO and KEGG pathway enrichment, WGCNA, machine-learning, and eGWAS analyses were performed. The results revealed 77 meta-genes that were mainly related to protein biosynthesis, protein folding, and protein transport between cellular organelles. In other words, under AHS, the expression of genes involving in the structure of rough reticulum membrane and in the process of protein folding was adversely influenced. In addition, genes related to biological processes such as “response to unfolded proteins,” “response to reticulum stress” and “ERAD pathway” were differentially regulated. We introduce here a couple of genes such as HSPA5, SSR1, SDF2L1, and SEC23B, as the most significantly differentiated under AHS, which could be used as bio-signatures of AHS. Besides the mentioned genes, the main findings of the current work may shed light to the identification of the effects of AHS on gene expression profiling of domestic chicken as well as the adaptive response of chicken to environmental stresses.}, author = {Hosseinzadeh, Sevda and Hasanpur, Karim}, + doi = {10.3389/fgene.2023.1102136}, issn = {1664-8021}, journal = {Frontiers in Genetics}, keywords = {{\textgreater}UseGalaxy.eu, EGWAS, Heat stress, WGCNA, chicken, machine learning}, @@ -6084,7 +9993,7 @@ @article{hosseinzadeh_whole_2024 doi = {10.1038/s41598-024-56757-0}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, Animal breeding, Genetics}, + keywords = {{\textgreater}UseGalaxy.eu, Animal breeding, Genetics, MicroRNAs, RNA, Long Noncoding}, language = {en}, month = {March}, note = {Publisher: Nature Publishing Group}, @@ -6113,6 +10022,45 @@ @article{howard_complete_2023 year = {2023} } +@article{howard_whole-genome_2022, + abstract = {The genomes of two human monkeypox virus strains from recently reported cases in our local region that were associated with the 2022 global outbreak were sequenced. Genomes from clinical isolates provide valuable information for epidemiological tracking and analysis of strain evolution and can be especially important during the early phases of outbreaks.}, + author = {Howard, Mondraya and Maki, Joel J and Connelly, Sara and Hardy, Dwight J and Cameron, Andrew}, + doi = {10.1128/mra.00846-22}, + issn = {2576-098X}, + journal = {Microbiol Resour Announc}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {December}, + number = {12}, + pages = {e0084622}, + title = {Whole-{Genome} {Sequences} of {Human} {Monkeypox} {Virus} {Strains} from {Two} 2022 {Global} {Outbreak} {Cases} in {Western} {New} {York} {State}}, + url = {http://europepmc.org/abstract/MED/36374079}, + volume = {11}, + year = {2022} +} + +@article{huang_rising_2025, + abstract = {Objectives +The emergence of metallo-beta-lactamases (MBLs) within the Klebsiella oxytoca complex (CRKO) poses a significant challenge in Taiwan, with so far incomplete characterization of species distribution and carbapenemase variants. This study aimed to elucidate the diversity, variants, and clinical presentations of CRKO isolates collected from 2013 to 2022. +Methods +We analyzed production of carbapenemases by the modified carbapenem inhibitory method (mCIM) and the NG testTM CARBA-5. Confirmation of five common carbapenemases and multilocus sequence typing were determined by polymerase chain reaction and sequencing. Nanopore whole-genome sequencing was used for the species differentiation and plasmids analysis. We also evaluated the clinical characteristics of the CRKO-infected patients. +Results +Three species were identified: K. michiganensis (n = 102), K. pasteurii (n = 13), and K. oxytoca (n = 3). A majority of isolates (91.5\%, n = 108) harbored at least one MBL gene, including blaVIM-1 (n = 56), blaIMP-8 (n = 26), and blaNDM-1 (n = 19), with six isolates carrying dual carbapenemase genes. The blaNDM-1 and blaIMP-8 genes were located on IncFII(Yp) and IncA/C2 plasmids, respectively. Notably, 34.7\% of isolates carried kleboxymycin gene clusters (KGC). Using CLSI and EUCAST criteria, 92.4\% and 82.4\% of isolates, respectively, were susceptible to cefiderocol. Among 92 infected patients, the 30-day mortality rate was 21.7\%, associated with female gender, higher Charlson Comorbidity Index, higher Pitt bacteremia scores, presence of bacteremia, and inversely associated with KGC. +Conclusion +The high prevalence of CRKO carrying MBLs and the recent surge of the ST27-blaNDM-1 genotype, poses significant treatment challenges and underscores the urgent need for enhanced surveillance in Taiwan.}, + author = {Huang, Yu-Tsung and Bregente, Carl Jay Ballena and Yu Hsu, Wei- and Liao, Chun-Hsing and Kuo, Yao-Wen and Lee, Jia-Arng and Lee, Tai-fen and Kao, Cheng-Yen and Hsueh, Po-Ren}, + doi = {10.1016/j.ijantimicag.2025.107515}, + issn = {0924-8579}, + journal = {International Journal of Antimicrobial Agents}, + keywords = {{\textgreater}UseGalaxy.eu, Carbapenem-resistant, Cefiderocol, Metallo-β-lactamase, complex}, + month = {April}, + pages = {107515}, + title = {Rising threat of metallo-β-lactamase-producing \textit{{Klebsiella} oxytoca} complex in {Taiwan}, 2013-2022}, + url = {https://www.sciencedirect.com/science/article/pii/S092485792500072X}, + urldate = {2025-04-21}, + year = {2025} +} + @article{huang_rs1347093_2024, abstract = {Background Single nucleotide polymorphism (SNP) rs1347093 shows statistically significant association with lung cancer risk, but there is no further rs1347093 expression quantitative trait loci (eQTL) effect information. SNP rs1347093 is located in microRNA-216/-217 (miR-216/-217) locus. In addition, miR-216/-217 have pancreas-enriched expressions. In this study, we examined a potential miR-216/-217 promoter region, and investigated the effect of rs1347093-A allele on the miR-216/-217 promoter activity. @@ -6141,7 +10089,7 @@ @article{huang_translational_2023 doi = {10.1038/s41467-023-40429-0}, issn = {2041-1723}, journal = {Nature Communications}, - keywords = {{\textgreater}UseGalaxy.eu, Plant hormones, Plant molecular biology, Translation}, + keywords = {{\textgreater}UseGalaxy.eu, Oryza, Plant hormones, Plant molecular biology, Translation}, language = {en}, month = {August}, note = {Number: 1 @@ -6155,13 +10103,58 @@ @article{huang_translational_2023 year = {2023} } +@article{hufsky_computational_2021, + abstract = {SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de.}, + author = {Hufsky, Franziska and Lamkiewicz, Kevin and Almeida, Alexandre and Aouacheria, Abdel and Arighi, Cecilia and Bateman, Alex and Baumbach, Jan and Beerenwinkel, Niko and Brandt, Christian and Cacciabue, Marco and Chuguransky, Sara and Drechsel, Oliver and Finn, Robert D and Fritz, Adrian and Fuchs, Stephan and Hattab, Georges and Hauschild, Anne-Christin and Heider, Dominik and Hoffmann, Marie and Hölzer, Martin and Hoops, Stefan and Kaderali, Lars and Kalvari, Ioanna and von Kleist, Max and Kmiecinski, Renó and Kühnert, Denise and Lasso, Gorka and Libin, Pieter and List, Markus and Löchel, Hannah F and Martin, Maria J and Martin, Roman and Matschinske, Julian and McHardy, Alice C and Mendes, Pedro and Mistry, Jaina and Navratil, Vincent and Nawrocki, Eric P and O'Toole, Áine Niamh and Ontiveros-Palacios, Nancy and Petrov, Anton I and Rangel-Pineros, Guillermo and Redaschi, Nicole and Reimering, Susanne and Reinert, Knut and Reyes, Alejandro and Richardson, Lorna and Robertson, David L and Sadegh, Sepideh and Singer, Joshua B and Theys, Kristof and Upton, Chris and Welzel, Marius and Williams, Lowri and Marz, Manja}, + doi = {10.1093/bib/bbaa232}, + issn = {1467-5463}, + journal = {Brief Bioinform}, + keywords = {{\textgreater}UseGalaxy.eu, Computational Biology}, + language = {eng}, + month = {March}, + number = {2}, + pages = {642--663}, + title = {Computational strategies to combat {COVID}-19: useful tools to accelerate {SARS}-{CoV}-2 and coronavirus research}, + url = {http://europepmc.org/abstract/MED/33147627}, + volume = {22}, + year = {2021} +} + +@article{hui_complete_2025, + abstract = {Hasora schoenherr is a Hesperiidae species belonging to the subfamily Coeliadinae. Here, we report the complete mitogenome dataset of Hasora schoenherr sampled from Endau-Rompin Johor National Park, Malaysia, sequenced using the Illumina NovaSeq 6000 technology. The mitogenome is 15,353 bp long, comprising a set of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. All PCGs were initiated by the typical ATN codon, except for COX1 which started with a CGA start codon. Out of the 13 PCGs, three PCGs (COX1, COX2 and NADH4) were terminated with an incomplete stop codon T. Phylogenetic analysis supported the placement of Hasora schonherr within Coeliadinae with a high support value and it is clustered with the Hasora vitta (NC027170) sample from China.}, + author = {Hui, Lam Boon and Miga, Marylin and Siang, Chan Vei and Rahman, Aqilah Awg Abdul and Parimannan, Sivachandran and Rajandas, Heera and Sitam, Frankie Thomas and Tokiman, Lili and Kemalok, Jai and Shamsir, Mohd Shahir and Salleh, Faezah Mohd}, + doi = {10.1016/j.dib.2025.112218}, + issn = {2352-3409}, + journal = {Data in Brief}, + keywords = {{\textgreater}UseGalaxy.eu, Assembly, Endau-rompin, Johor national park, Phylogeny}, + month = {December}, + pages = {112218}, + shorttitle = {The complete mitogenome dataset of \textit{{Hasora} {Schoenherr}} ({Latreille}, 1824) ({Lepidoptera}}, + title = {The complete mitogenome dataset of \textit{{Hasora} {Schoenherr}} ({Latreille}, 1824) ({Lepidoptera}: {Hesperiidae}: {Coeliadinae}) from {Malaysia}}, + url = {https://www.sciencedirect.com/science/article/pii/S2352340925009394}, + urldate = {2025-12-22}, + volume = {63}, + year = {2025} +} + +@article{humphrey_characterisation_2024, + abstract = {Genome sequencing of Clostridium clostridioforme strain LM41 revealed the presence of an atypically high proportion of mobile genetic elements for this species, with a particularly high abundance of prophages. Bioinformatic analysis of prophage sequences sought to characterise these elements and identify prophage-linked genes contributing to enhanced fitness of the host bacteria in the dysbiotic gut. This work has identified 15 prophages, of which 4 are predicted to be intact, 2 are predicted to be defective, and 9 are unclassified. qPCR analysis revealed spontaneous release of four of the LM41 prophages into the culture supernatant, the majority of which had morphology akin to podoviruses when visualised using Transmission Electron Microscopy. We observed diversity in the lysogeny mechanisms utilised by the prophages, with examples of the classical λ-like CI/Cro system, the ICE Bs 1 ImmR/ImmA-like system, and the Mu-like C/Ner system. Classical morons, such as toxins or immune evasion factors, were not observed. We did, however, identify a variety of genes with roles in mediating restriction modification and genetic diversity, as well as some candidate genes with potential roles in host adaptation. Despite being the most abundant entities in the intestine, there is a dearth of information about phages associated with members of the microbiome. This work begins to shed light on the contribution of these elements to the lifestyle of C. clostridioforme LM41.}, + author = {Humphrey, Suzanne and Marouli, Angeliki and Thümmler, Katja and Mullin, Margaret and Wall, Daniel}, + doi = {10.1101/2024.02.29.582698}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Characterisation of prophages {inClostridium} clostridioforme: an understudied component of the intestinal microbiome}, + url = {http://europepmc.org/abstract/PPR/PPR812490}, + year = {2024} +} + @article{humphrey_genomic_2024, abstract = {Genome sequencing of Clostridium clostridioforme strain LM41 revealed the presence of an atypically high proportion of mobile genetic elements for this species, with a particularly high abundance of prophages. Bioinformatic analysis of prophage sequences sought to characterize these elements and identify prophage-linked genes contributing to enhanced fitness of the host bacteria in the dysbiotic gut. Using PHASTER, PhageScope and manual curation, this work has identified 15 prophages: 4 predicted to be intact, 2 predicted to be defective and 9 which are unclassified. Quantitative PCR (qPCR) analysis revealed spontaneous release of four of the LM41 prophages (φ1, φ2, φ4 and φ10) into the culture supernatant, with virion-like particles visualized using transmission electron microscopy. The majority (12/14) of these particles had morphology akin to podoviruses, which is consistent with morphology predictions for φ1 and φ4. We observed diversity in the lysogeny mechanisms utilized by the prophages, with examples of the classical λ-like CI/Cro system, the ICEBs1 ImmR/ImmA-like system and the Mu-like C/Ner system. Classical morons, such as toxins or immune evasion factors, were not observed. We did, however, identify a variety of genes with roles in mediating restriction modification and genetic diversity, as well as some candidate genes with potential roles in host adaptation. Despite being the most abundant entities in the intestine, there is a dearth of information about phages associated with members of the microbiome. This work begins to shed light on the contribution of these elements to the lifestyle of C. clostridioforme LM41.}, author = {Humphrey, Suzanne and Marouli, Angeliki and Thümmler, Katja and Mullin, Margaret and Pritchard, Leighton and Wall, Daniel M.}, doi = {10.1099/mic.0.001486}, issn = {1465-2080}, journal = {Microbiology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Clostridium, Gastrointestinal Microbiome, Prophages}, note = {Publisher: Microbiology Society,}, number = {8}, pages = {001486}, @@ -6173,6 +10166,42 @@ @article{humphrey_genomic_2024 year = {2024} } +@article{hunold_dynatag_2025, + abstract = {Systematic discovery of transcription factor (TF) landscapes in low-input samples and at single cell level is a major challenge in the fields of molecular biology, genetics, and epigenetics. Here, we present cleavage under Dynamic targets and Tagmentation (DynaTag), enabling robust mapping of TF-DNA interactions using a physiological salt solution during sample preparation. DynaTag uncovers occupancy alterations for 15 TFs in stem cell and cancer tissue models. We highlight changes in TF-DNA binding for NANOG, MYC, and OCT4, during stem-cell differentiation, at both bulk and single-cell resolutions. DynaTag surpasses CUT\&RUN and ChIP-seq in signal-to-background ratio and resolution. Furthermore, using tumours of a small cell lung cancer model derived from a single female donor, DynaTag reveals increased chromatin occupancy of FOXA1, MYC, and the mutant p53 R248Q at enriched gene pathways (e.g. epithelial-mesenchymal transition), following chemotherapy treatment. Collectively, we believe that DynaTag represents a significant technological advancement, facilitating precise characterization of TF landscapes across diverse biological systems and complex models.}, + author = {Hunold, Pascal and Pizzolato, Giulia and Heramvand, Nadia and Kaiser, Laura and Barbiera, Giulia and van Ray, Olivia and Thomas, Roman and George, Julie and Peifer, Martin and Hänsel-Hertsch, Robert}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41467-025-61797-9}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Chromatin, Epigenetics analysis, Gene regulation, Stem-cell differentiation, Transcription factors}, + language = {en}, + month = {July}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {6585}, + title = {{DynaTag} for efficient mapping of transcription factors in low-input samples and at single-cell resolution}, + url = {https://www.nature.com/articles/s41467-025-61797-9}, + urldate = {2025-08-04}, + volume = {16}, + year = {2025} +} + +@article{hurtado_one_2025, + author = {Hurtado, Ana and Ocejo, Medelin and Oporto, Beatriz and Lavín, José Luis and Rodríguez, Ruth and Marcos, María Ángeles and Urrutikoetxea-Gutiérrez, Mikel and Alkorta, Miriam and Marimón, José María}, + doi = {10.3389/fmicb.2025.1540210}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Campylobacter coli, Campylobacter jejuni, Nanopore long-fragment sequencing, antimicrobial resistance, one health, pangenome, resistome, whole-genome sequencing}, + language = {English}, + month = {January}, + note = {Publisher: Frontiers}, + title = {A {One} {Health} approach for the genomic characterization of antibiotic-resistant {Campylobacter} isolates using {Nanopore} whole-genome sequencing}, + url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1540210/full}, + urldate = {2025-02-16}, + volume = {16}, + year = {2025} +} + @article{husaini_investigating_2023, abstract = {Cassine koordersii Kosterm. (Celastraceae) is a critically endangered species indigenous to Jember, East Java. Programs for genetic conservation and plant breeding have recently implemented next-generation sequencing (NGS) techniques based on genomic data. This research aims to explore and distinguish between perfect and imperfect SSR patterns in the assembled genome. The Abyss assembler produced 3,060,362 scaffolds with 35.63 \% GC content for the assembled genome. The investigation and identification of SSRs using the Krait tool found 139,236 and 582,360 sequences for including perfect and imperfect SSRs, respectively. There were six motif repeats of perfect and imperfect SSRs consisting of 73,175 and 202,438 sequences of mononucleotide (the most motif was A); 17,179 and 65,705 sequences of dinucleotide (the most motif was AT); 5,175 and 51,948 sequences of trinucleotide (the most motif was AAT); 3,824 and 14,010 sequences of tetranucleotide (the most motif was AAAT); 659 and 3,082 sequences of pentanucleotide (the most motif is AAAAT); 118 and 757 sequences of hexanucleotide (the most motif is AAAAAT). The depicted perfect and imperfect SSRs markers can be employed in future genetic studies of Cassine and related genera for either recommendation effort or improvement in conservation genetic concerns.}, author = {Husaini, I. P. A. and Rinandio, D. S. and Martiansyah, I. and Magandhi, M. and Suhatman, A. and Irsyam, A. S. D. and Irwanto, R. R. and Setiawan, E. and Hariri, M. R.}, @@ -6236,7 +10265,7 @@ @article{hwang_reduction_2024 doi = {10.1038/s41380-024-02586-6}, issn = {1476-5578}, journal = {Molecular Psychiatry}, - keywords = {{\textgreater}UseGalaxy.eu, Biomarkers, Diseases, Neuroscience}, + keywords = {{\textgreater}UseGalaxy.eu, Apolipoproteins E, Biomarkers, Brain, Diseases, Fetal Alcohol Spectrum Disorders, Genome-Wide Association Study, Neuroscience, Prenatal Exposure Delayed Effects}, language = {en}, month = {May}, note = {Publisher: Nature Publishing Group}, @@ -6264,6 +10293,27 @@ @article{iaffaldano_crispr_2023 year = {2023} } +@article{iliev_first_2025, + abstract = {The submerged petrified forest in Sozopol Bay, located along Bulgaria’s southeastern coast in the Black Sea, is an extraordinarily rare natural phenomenon that has remained unexplored in terms of microbial diversity until now. This study focuses on characterizing the microbial communities associated with this unique habitat. Ancient petrified tree remnants located at depths of 18–20 m were sampled in August–September 2024, targeting four tree trunks from different sites within the bay. The quantitative assessment of selected bacterial groups, essential for nutrient cycling, organic matter degradation, and marine ecosystem health, revealed distinct community profiles. 16S rDNA sequencing of cultivated isolates identified a diverse microbial community predominantly composed of γ-Proteobacteria, with key representatives such as Vibrio aestuarianus, Vibrio orientalis, Pseudoalteromonas, and Cobetia sp. The culture-independent approach confirmed the dominance of Proteobacteria, along with other prevalent phyla like Bacteroidetes, Planctomycetes, and Actinobacteria. The most abundant taxa included Woeseia oceani, Ilumatobacter coccineus, Halioglobus maricola, and Vibrio breoganii. Archaea made up about 3\% of classified reads. Fungal sequences accounted for less than 2\% of the total reads, indicating a low fungal prevalence. These results provide essential baseline data for future monitoring and the conservation of this unique habitat and its diverse microbial communities.}, + author = {Iliev, Mihail and Ilieva, Ralitsa and Peykov, Slavil and Terziyska, Viktoria and Pelkin, Anton and Kenderov, Lyubomir}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/d17080583}, + issn = {1424-2818}, + journal = {Diversity}, + keywords = {16S sequencing, {\textgreater}UseGalaxy.eu, Black Sea microbiology, culturable microbiota, shotgun metagenome sequencing, submerged petrified forest}, + language = {en}, + month = {August}, + note = {Publisher: Multidisciplinary Digital Publishing Institute}, + number = {8}, + pages = {583}, + shorttitle = {First {Microbial} {Survey} of a {Submerged} {Petrified} {Forest} in the {Black} {Sea}}, + title = {First {Microbial} {Survey} of a {Submerged} {Petrified} {Forest} in the {Black} {Sea}: {Culture}-{Based} and {Metagenomic} {Insights}}, + url = {https://www.mdpi.com/1424-2818/17/8/583}, + urldate = {2025-09-03}, + volume = {17}, + year = {2025} +} + @article{ilikkan_laktik_2023, abstract = {Laktik asit bakterileri, endüstride starter kültür veya probiyotik olarak kullanılmaktadırlar. European Food Safety Authority (EFSA) tarafından 2021 yılında yayımlanan raporda gıdalarda kullanılacak bakterilerin tüm genom dizileri üzerinden risk değerlendirmesi yapılması gerekliliği vurgulanmıştır. Bu nedenle, laktik asit bakterilerinde dirençlilik geni araştırmaları önem kazanmıştır. Çünkü antibiyotik direnç genlerinin bağırsak sisteminde bulunan patojen bakterilere aktarılma olasılığı vardır ya da laktik asit bakterilerini barındıran gıdalar aracılığıyla alınmaları olasıdır. Bu nedenle, çalışmada, farklı fermente gıdalardan izole edilen dört laktik asit bakterisi (Lentilactobacillus buchneri Egmn17, Levilactobacillus brevis Atlas17, Levilactobacillus namurensis Ozge01, Lactiplantibacillus plantarum Gmze16) ve probiyotik bir bakteri olan Lactiplantibacillus plantarum 299v suşu kullanılmıştır. Çalışmada, laktik asit bakterileri arasında en yaygın antibiyotik dirençliliği gözlenen tetrasiklin seçilmiştir. 3 bakterinin tetrasiklin antibiyotiğine orta derecede dirençli (zon çapı 15-18 mm) (299v, Gmze16 ve Egmn17) ve 2 bakterinin duyarlı (zon çapı {\textgreater}19 mm) (Atlas17 ve Ozge01) olduğu belirlenmiştir. Laktik asit bakterilerinin tüm genom sekanslarının incelenmesi sonucu, orta dirençli bakterilerin tetrasikline bağlı antimikrobiyal direnç (AMR) genlerinden tetA (MFS dışa atım pompası) ve tetO’ya (ribozomal koruma proteini) sahip oldukları görülmüştür. Levilactobacillus brevis Atlas17’de ise TetA proteini mevcutken 322. aminoasit sekansında M → T değişimi gözlenmiştir. Ayrıca probiyotik bakteri olan Lactiplantibacillus plantarum 299v’nin direnç genlerine sahip olması bu genlerin bağırsaktaki patojenlere aktarılma riskini de arttırmaktadır. tetA genine sahip olduğu gözlenen Levilactobacillus brevis Atlas17 gibi fenotipi duyarlı olan türler de sessiz dirençlilik genlerine sahip olduklarında bunu diğer bakterilere aktarabilmeleri olasıdır. Bu nedenle genotip ve fenotip birlikte incelenmesi önemlidir}, author = {Ilikkan, Özge}, @@ -6291,7 +10341,7 @@ @article{imre_epigenetic_2024 doi = {10.1038/s41467-024-53514-9}, issn = {2041-1723}, journal = {Nature Communications}, - keywords = {{\textgreater}UseGalaxy.eu, Epigenetics, Gene regulation, Nuclear organization}, + keywords = {{\textgreater}UseGalaxy.eu, Epigenesis, Genetic, Epigenetics, Gene regulation, Heterochromatin, Histones, Nuclear organization, Nucleosomes}, language = {en}, month = {October}, note = {Publisher: Nature Publishing Group}, @@ -6304,6 +10354,24 @@ @article{imre_epigenetic_2024 year = {2024} } +@article{inabnit_mitochondrial_2025, + abstract = {Melampus bidentatus was recently divided into three genetically divergent cryptic species: Melampus bidentatus, Melampus jaumei, and Melampus gundlachi. We have assembled and annotated a mitochondrial genome for each of these species. Comparisons with other taxa showed that these three species possess a gene order that is distinct from the conserved gene order found in the six (out of nine available) Ellobiid genera. Among the species with a derived gene order, mean nucleotide divergence over all genes was on average 1.57× higher than among mitogenomes with the conserved gene order. This suggests varying evolutionary rates of mitochondrial genes in this family.}, + author = {Inäbnit, Thomas and Tiedemann, Ralph and Dennis, Alice B.}, + doi = {10.1002/ece3.71282}, + issn = {2045-7758}, + journal = {Ecology and Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, Melampus, control region, gastropod, mitochondrial genomes}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.71282}, + number = {4}, + pages = {e71282}, + title = {Mitochondrial {Genomes} of {Three} {Melampus} {Species} ({Ellobiidae}; {Gastropoda})}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.71282}, + urldate = {2025-04-17}, + volume = {15}, + year = {2025} +} + @article{iniesta-pallares_changes_2023, abstract = {The Doñana wetlands comprise an emblematic Mediterranean landscape protected as a UNESCO World Heritage Site. Some parts of these wetlands have been transformed into intensive rice cultivation areas, which are currently the most productive rice-growing areas in Europe. We examined the bacterial communities in these domesticated soils as they are key for plant health and productivity and have a strong influence on biochemical cycles. To identify the bacteria, we used metabarcoding analysis coupled with metabolic predictions and co-occurrence networks. This analysis was performed in the bulk and rhizosphere soils during different stages in the growing season. These soil compartments had a greater effect on the bacterial communities than the plant phenological stages. The diversity and richness of the bacterial population inhabiting the rhizosphere was much lower than that in the bulk soil, comprising taxa that were significantly more represented in this soil compartment, such as bacteria from the genus Hydrogenophaga, three genera from the order Rhizobiales, and unclassified genera from the families Desulfocapsaceae and Actinobacteria. Rhizosphere co-occurrence networks revealed a high number of negative connections, indicating unstable bacterial communities that may be highly influenced by biotic and abiotic factors. Rhizosphere networks mostly rely on two taxa belonging to the phyla Proteobacteria and Cyanobacteria, which are the predicted network hubs in this soil compartment. The bulk soil conserved high bacterial diversity and richness that was stable throughout the growth period of rice. Anaerobic bacteria from genera Marmoricola, the uncultured Gemmatimonadota bacteria SDR1034 terrestrial group, Anaerolinea, and the sulphur oxidizer, Thiobacillus were highly represented. This analysis provides valuable information for understanding bacterial diversity in the rhizosphere of rice cultivated in this region, which is critical for enhancing plant growth and productivity.}, author = {Iniesta-Pallarés, Macarena and Brenes-Álvarez, Manuel and Lasa, Ana V. and Fernández-López, Manuel and Álvarez, Consolación and Molina-Heredia, Fernando P. and Mariscal, Vicente}, @@ -6339,11 +10407,30 @@ @article{ioos_harnessing_2023 year = {2023} } +@article{ipoutcha_evolution_2024, + abstract = {Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are bacterial defences that target bacteriophages and mobile genetic elements. How these defences evolve in novel host environments remains largely unknown. We studied the evolution of the CRISPR-Cas system in \textit{Mycoplasma gallisepticum} (also named \textit{Mycoplasmoides gallisepticum}), a bacterial pathogen of poultry that jumped into a passerine host {\textasciitilde}30 years ago. Over the decade following the host shift, all isolates displaying a functional CRISPR-Cas system were found not only to harbour completely new sets of spacers, but the DNA protospacer adjacent motif recognized by the main effector \textit{M. gallisepticum} Cas9 (MgCas9) was also different. These changes in CRISPR-Cas diversity and specificity are consistent with a change in the community of phages and mobile elements infecting \textit{M. gallisepticum} as it colonized the novel host. In the years following the host shift, we also detected a gradual rise in isolates displaying non-functional MgCas9. After 12 years, all circulating isolates harboured inactive forms only. This loss of CRISPR-Cas function comes at a time when the passerine host is known to have evolved widespread resistance, which in turn drove the evolution of increasing \textit{M. gallisepticum} virulence through antagonistic coevolution. Such striking concordance in the rise of inactivated forms of CRISPR-Cas and the evolution of host resistance suggests that the inactivation of the CRISPR-Cas system was necessary for enabling adaptive bacterial responses to host-driven selection. We highlight the need to consider both host and pathogen selection pressures on bacteria for understanding the evolution of CRISPR-Cas systems and the key factors driving the emergence of a pathogenic bacterium in a novel host.}, + author = {Ipoutcha, Thomas and Tsarmpopoulos, Iason and Gourgues, Géraldine and Baby, Vincent and Dubos, Paul and Hill, Geoffrey E and Arfi, Yonathan and Lartigue, Carole and Thébault, Patricia and Bonneaud, Camille and Sirand-Pugnet, Pascal}, + doi = {10.1099/mgen.0.001320}, + issn = {2057-5858}, + journal = {Microb Genom}, + keywords = {{\textgreater}UseGalaxy.eu, CRISPR-Cas Systems, Evolution, Molecular, Mycoplasma gallisepticum}, + language = {eng}, + month = {November}, + number = {11}, + title = {Evolution of the {CRISPR}-{Cas9} defence system in \textit{{Mycoplasma} gallisepticum} following colonization of a novel bird host}, + url = {http://europepmc.org/abstract/MED/39556419}, + volume = {10}, + year = {2024} +} + @article{ipoutcha_synthetic_2024, + abstract = {The rise in the frequency of antibiotic resistance has made bacterial infections, specifically \textit{Pseudomonas aeruginosa}, a cause for greater concern. Phage therapy is a promising solution that uses naturally isolated phages to treat bacterial infections. Ecological limitations, which stipulate a discrete host range and the inevitable evolution of resistance, may be overcome through a better understanding of phage biology and the utilization of engineered phages. In this study, we developed a synthetic biology approach to construct tailed phages that naturally target clinically relevant strains of \textit{Pseudomonas aeruginosa}. As proof of concept, we successfully cloned and assembled the JG024 and DMS3 phage genomes in yeast using transformation-associated recombination cloning and rebooted these two phage genomes in two different strains of \textit{P. aeruginosa}. We identified factors that affected phage reboot efficiency like the phage species or the presence of antiviral defense systems in the bacterial strain. We have successfully extended this method to two other phage species and observed that the method enables the reboot of phages that are naturally unable to infect the strain used for reboot. This research represents a critical step toward the construction of clinically relevant, engineered \textit{P. aeruginosa} phages.IMPORTANCE\textit{Pseudomonas aeruginosa} is a bacterium responsible for severe infections and a common major complication in cystic fibrosis. The use of antibiotics to treat bacterial infections has become increasingly difficult as antibiotic resistance has become more prevalent. Phage therapy is an alternative solution that is already being used in some European countries, but its use is limited by the narrow host range due to the phage receptor specificity, the presence of antiviral defense systems in the bacterial strain, and the possible emergence of phage resistance. In this study, we demonstrate the use of a synthetic biology approach to construct and reboot clinically relevant \textit{P. aeruginosa} tailed phages. This method enables a significant expansion of possibilities through the construction of engineered phages for therapy applications.}, author = {Ipoutcha, Thomas and Racharaks, Ratanachat and Huttelmaier, Stefanie and Wilson, Cole J. and Ozer, Egon A. and Hartmann, Erica M.}, doi = {10.1128/spectrum.02897-23}, + issn = {2165-0497}, journal = {Microbiology Spectrum}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial Infections, Bacteriophages, Pseudomonas Infections, Pseudomonas Phages}, + language = {eng}, month = {January}, note = {Publisher: American Society for Microbiology}, number = {3}, @@ -6376,6 +10463,36 @@ @article{ishola_comparative_2024 year = {2024} } +@article{ishtiaq_discovering_2025, + abstract = {Parkinson’s disease (PD) is a progressive neurological disorder with an increasing prevalence in aging populations. Identifying effective therapeutic targets and treatments remains a critical challenge. This study aimed to discover potential therapeutic targets and design novel compounds for PD treatment. Gene expression analysis was conducted using diverse datasets, including microarray, mRNA sequencing, and miRNA sequencing. While no common genes were identified across all datasets, the RNA-seq dataset GSE-135036 was prioritized. The investigation focused on downregulated miRNAs targeting upregulated mRNAs, revealing that hsa-mir-5585 regulates Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) within the Shigellosis pathway. Given RIPK1’s role in cell death and inflammation, it emerged as a promising therapeutic target for PD. To identify RIPK1 inhibitors, 67 compounds were screened via molecular docking, with CHEMBL-3109201 exhibiting the highest binding affinity. A structurally similar compound, CHEMBL-76328382, also demonstrated strong interactions. A fragment-based drug design approach generated two novel compounds, BI-1215 and BI-146, which, along with RIPK1-IN-4 and CHEMBL-70909876, were shortlisted based on docking scores and ADME profiles. Molecular dynamics simulations confirmed the stability of CHEMBL-70909876 and BI-1215, with RMSD fluctuations between 0.005 and 0.2 nm. MM-PBSA analysis further validated their superior thermodynamic stability and binding affinity compared to other candidates. This study offers novel insights into PD pathogenesis and potential therapeutic interventions, marking a significant step toward effective treatment strategies for this debilitating disorder.}, + author = {Ishtiaq, Bisma and Paracha, Rehan Zafar and Nisar, Maryum and Ejaz, Saima and Hussain, Zamir}, + doi = {10.1007/s10822-025-00586-4}, + issn = {1573-4951}, + journal = {Journal of Computer-Aided Molecular Design}, + keywords = {{\textgreater}UseGalaxy.eu, Docking, Fragment-based drug designing, MD simulations, Mi-RNA seq, Microarray analysis, Neuroinflammation, Parkinson’s disease, RIPK1, RNA-seq, Shigellosis pathway}, + language = {en}, + month = {February}, + number = {1}, + pages = {8}, + shorttitle = {Discovering promising drug candidates for {Parkinson}’s disease}, + title = {Discovering promising drug candidates for {Parkinson}’s disease: integrating {miRNA} and {DEG} analysis with molecular dynamics and {MMPBSA}}, + url = {https://doi.org/10.1007/s10822-025-00586-4}, + urldate = {2025-05-29}, + volume = {39}, + year = {2025} +} + +@article{izquierdo-lara_monitoring_2020, + abstract = {{\textless}h4{\textgreater}ABSTRACT{\textless}/h4{\textgreater} The current SARS-CoV-2 pandemic has rapidly become a major global health problem for which public health surveillance is crucial to monitor virus spread. Given the presence of viral RNA in feces in around 40\% of infected persons, wastewater-based epidemiology has been proposed as an addition to disease-based surveillance to assess the spread of the virus at the community level. Here we have explored the possibility of using next-generation sequencing (NGS) of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level from routine wastewater testing, and compared these results with the virus diversity in patients from the Netherlands and Belgium. Phylogenetic analysis revealed the presence of viruses belonging to the most prevalent clades (19A, 20A and 20B) in both countries. Clades 19B and 20C were not identified, while they were present in clinical samples during the same period. Low frequency variant (LFV) analysis showed that some known LFVs can be associated with particular clusters within a clade, different to those of their consensus sequences, suggesting the presence of at least 2 clades within a single sewage sample. Additionally, combining genome consensus and LFV analyses we found a total of 57 unique mutations in the SARS-CoV-2 genome which have not been described before. In conclusion, this work illustrates how NGS analysis of wastewater can be used to approximate the diversity of SARS-CoV-2 viruses circulating in a community.}, + author = {Izquierdo-Lara, Ray and Elsinga, Goffe and Heijnen, Leo and Oude Munnink, Bas and Schapendonk, Claudia and Nieuwenhuijse, David and Kon, Matthijs and Lu, Lu and Aarestrup, Frank and Lycett, Samantha and Medema, Gertjan and Koopmans, Marion P.G. and de Graaf, Miranda}, + doi = {10.1101/2020.09.21.20198838}, + journal = {medRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Monitoring {SARS}-{CoV}-2 circulation and diversity through community wastewater sequencing}, + url = {http://europepmc.org/abstract/PPR/PPR217109}, + year = {2020} +} + @article{izquierdo-lara_rise_2023, abstract = {Monitoring of SARS-CoV-2 in wastewater (WW) is a promising tool for epidemiological surveillance, correlating not only viral RNA levels with the infection dynamics within the population, but also to viral diversity. However, the complex mixture of viral lineages in WW samples makes tracking of specific variants or lineages circulating in the population a challenging task. We sequenced sewage samples of 9 WW-catchment areas within the city of Rotterdam, used specific signature mutations from individual SARS-CoV-2 lineages to estimate their relative abundances in WW and compared them against those observed in clinical genomic surveillance of infected individuals between September 2020 and December 2021. We showed that especially for dominant lineages, the median of the frequencies of signature mutations coincides with the occurrence of those lineages in Rotterdam's clinical genomic surveillance. This, along with digital droplet RT-PCR targeting signature mutations of specific variants of concern (VOCs), showed that several VOCs emerged, became dominant and were replaced by the next VOC in Rotterdam at different time points during the study. In addition, single nucleotide variant (SNV) analysis provided evidence that spatio-temporal clusters can also be discerned from WW samples. We were able to detect specific SNVs in sewage, including one resulting in the Q183H amino acid change in the Spike gene, that was not captured by clinical genomic surveillance. Our results highlight the potential use of WW samples for genomic surveillance, increasing the set of epidemiological tools to monitor SARS-CoV-2 diversity.}, author = {Izquierdo-Lara, Ray W. and Heijnen, Leo and Oude Munnink, Bas B. and Schapendonk, Claudia M. E. and Elsinga, Goffe and Langeveld, Jeroen and Post, Johan and Prasad, Divyae K. and Carrizosa, Christian and Been, Frederic and van Beek, Janko and Schilperoort, Remy and Vriend, Rianne and Fanoy, Ewout and de Schepper, Evelien I. T. and Sikkema, Reina S. and Molenkamp, Richard and Aarestrup, Frank M. and Medema, Gertjan and Koopmans, Marion P. G. and de Graaf, Miranda}, @@ -6410,6 +10527,23 @@ @techreport{izzo_nucleophosmin_2023 year = {2023} } +@article{jackson_substrate_2025, + abstract = {Sortases are critical cysteine transpeptidases that facilitate the attachment of proteins to the cell wall in Gram-positive bacteria. These enzymes are potential targets for novel antibiotic development, and versatile tools in protein engineering applications. There are six classes of sortases recognized, yet class A sortases (SrtA) are the most widely studied and utilized. SrtA enzymes endogenously recognize the amino acid sequence LPXTG, where X = any amino acid, with additional promiscuity now recognized in multiple positions for certain SrtA enzymes. Much less is known about Class B sortases (SrtB), which target a distinct sequence, typically with an N-terminal Asn, e.g., variations of NPXTG or NPQTN. Although understudied overall, two SrtB enzymes were previously shown to be specific for heme transporter proteins, and in vitro experiments with the catalytic domains of these enzymes reveal activities significantly worse than SrtA from the same organisms. Here, we use protein biochemistry, structural analyses, and computational simulations to better understand and characterize these enzymes, specifically investigating Bacillus anthracis SrtB (baSrtB) as a model SrtB protein. Structural modeling predicts a plausible enzyme-substrate complex, which is verified by mutagenesis of binding cleft residues. Furthermore, residues N- and C-terminal to the pentapeptide recognition motif are critical for observed activity. Finally, we use chimeric proteins to identify mutations that improve baSrtB activity by ∼4-fold, and demonstrate the feasibility of sortase-mediated ligation using a baSrtB enzyme variant. These studies provide insight into SrtB-target binding as well as evidence that SrtB enzymes can be modified to be of potential use in protein engineering.}, + author = {Jackson, Sophie N and Lee, Darren E and Blount, Jadon M and Croney, Kayla A and Ibershof, Justin W and Ceravolo, Caroline M and Brown, Kate M and Goodwin-Rice, Noah J and Whitham, Kyle M and McCarty, James and Antos, John M and Amacher, Jeanine F}, + doi = {10.1016/j.jbc.2025.108382}, + issn = {0021-9258}, + journal = {J Biol Chem}, + keywords = {{\textgreater}UseGalaxy.eu, Aminoacyltransferases, Bacillus anthracis, Bacterial Proteins, Cysteine Endopeptidases}, + language = {eng}, + month = {April}, + number = {4}, + pages = {108382}, + title = {Substrate recognition in {Bacillus} anthracis sortase {B} beyond its canonical pentapeptide binding motif and use in sortase-mediated ligation}, + url = {http://europepmc.org/abstract/MED/40049417}, + volume = {301}, + year = {2025} +} + @article{jain_human_2024, abstract = {Coronavirus disease (Covid-19) is an infectious disease which is caused by a virus named as SARS-COV. This virus belongs to the Coronavirus family that causes a variety of diseases including head and chest colds, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS). Metagenomics is the study of genetic material that is recuperated from the environmental samples directly. By examining and elucidating microbial genomes in healthy and infected samples, the metagenomics branch has allowed us to discover the significance of microbial genomes. The metagenomic approach used in the covid-19 infectious disease will serve as a prominent tool for explicating the relationship between host-associated microbial communities and host phenotype. European Nucleotide Archive (ENA) was used to retrieve the metagenome data of the Gut Microbiome of Covid-19 patients with the project id PRJDB12349. For metagenomics analyses, Galaxy server was used identification and classification of microbial communities furhter taxonomic analysis and functional analysis was also performed. Different tools from the galaxy like FastQC, MultiQC, Trim Galore, Megahit, Kraken 2, Convert Kraken, Krona Pie Chart and HUMANn2 were used for complete metagenomic analysis. Metagenomic Analysis shows that there is difference in the percentage and abundance of bacteria in all the covid-19 patients sample. The fungi that were commonly present in all the samples were identified as Eurotiales 78-93\% and Mycospaerellales 7-20\% and the other fungi that were not common but were observed are Dipodasceae 10\% and Sordariales 4-6\%. Further, the gene abundance and the families of the samples were also observed. This study highlights the metagenome of the Covid-19 infectious disease. The metagenomic analysis of the gut microbiome of the Covid-19 patients shows difference in the microbial community among all the samples}, author = {Jain, Kashish and Yadav, Ruchi}, @@ -6437,7 +10571,7 @@ @article{jaki_total_2023 doi = {10.1038/s41467-023-37591-w}, issn = {2041-1723}, journal = {Nature Communications}, - keywords = {{\textgreater}UseGalaxy.eu, Immune evasion, Outcomes research, SARS-CoV-2, Viral evolution, Viral infection}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19, Immune evasion, Outcomes research, SARS-CoV-2, Viral evolution, Viral infection}, language = {en}, month = {April}, note = {Number: 1 @@ -6457,7 +10591,7 @@ @article{jalili_galaxy_2020 doi = {10.1093/nar/gkaa434}, issn = {0305-1048}, journal = {Nucleic Acids Research}, - keywords = {+Education, +Galactic, +IsGalaxy, +Project, +RefPublic, +Tools, {\textgreater}Live EU, {\textgreater}Metabolomics EU, {\textgreater}Metagenomics EU, {\textgreater}Proteomics EU, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au}, + keywords = {+Education, +Galactic, +IsGalaxy, +Project, +RefPublic, +Tools, {\textgreater}Live EU, {\textgreater}Metabolomics EU, {\textgreater}Metagenomics EU, {\textgreater}Proteomics EU, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Software}, language = {en}, month = {July}, note = {Publisher: Oxford Academic}, @@ -6471,6 +10605,25 @@ @article{jalili_galaxy_2020 year = {2020} } +@article{janet-maitre_strain-specific_2025, + abstract = {Bloodstream infections caused by \textit{Pseudomonas aeruginosa} are associated with high mortality rates. The complement system, a key component of the innate immune response, plays a major role in eliminating \textit{P. aeruginosa} from human blood. However, the sensitivity of \textit{P. aeruginosa} strains to plasma varies widely, ranging from highly sensitive to persistent or fully resistant. Although most studies use model strains, the species genomic and phenotypic diversities suggest more complex interactions with complement than previously appreciated. In this study, we characterized the plasma resistome of \textit{P. aeruginosa} using Tn-seq in three strains with varying levels of plasma sensitivity. A gain-of-function screen in the plasma-sensitive strain PA14 revealed numerous bacterial factors influencing plasma resistance, including components of the RetS-LadS/Gac/Rsm regulatory pathway and outer membrane porins. In the plasma-resistant strains CHA and YIK, Tn-seq analysis indicated that each strain relies on a distinct, limited set of proteins to evade complement-mediated killing. Despite these differences, we identified common mechanisms across all three strains. These include the production of exopolysaccharides (EPSs), the presence of surface appendages, and modifications in the O-specific antigen. Notably, we identified Ssg and Crc as shared contributors to plasma resistance. Although deletion mutants lacking \textit{ssg} and/or \textit{crc} exhibited reduced survival in plasma, a subpopulation of these mutants was able to persist during prolonged exposure. Overall, this work provides new insights into the complex interplay between \textit{P. aeruginosa} and the human complement system in the context of bloodstream infections and raises concerns regarding the efficacy of therapies that target individual virulence factors.}, + author = {Janet-Maitre, Manon and Robert-Genthon, Mylène and Cretin, François and Elsen, Sylvie and Attrée, Ina}, + doi = {10.1128/iai.00055-25}, + issn = {0019-9567}, + journal = {Infection and Immunity}, + keywords = {{\textgreater}UseGalaxy.eu, Complement System Proteins, Pseudomonas Infections, Pseudomonas aeruginosa}, + language = {eng}, + month = {August}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e00055--25}, + title = {Strain-specific variation in the complement resistome of {Pseudomonas} aeruginosa}, + url = {https://journals.asm.org/doi/full/10.1128/iai.00055-25}, + urldate = {2025-09-03}, + volume = {0}, + year = {2025} +} + @article{jarvis_semi-automated_2022, abstract = {The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent–child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1\% of the length of CHM13. Nearly 48\% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.}, author = {Jarvis, Erich D. and Formenti, Giulio and Rhie, Arang and Guarracino, Andrea and Yang, Chentao and Wood, Jonathan and Tracey, Alan and Thibaud-Nissen, Francoise and Vollger, Mitchell R. and Porubsky, David and Cheng, Haoyu and Asri, Mobin and Logsdon, Glennis A. and Carnevali, Paolo and Chaisson, Mark J. P. and Chin, Chen-Shan and Cody, Sarah and Collins, Joanna and Ebert, Peter and Escalona, Merly and Fedrigo, Olivier and Fulton, Robert S. and Fulton, Lucinda L. and Garg, Shilpa and Gerton, Jennifer L. and Ghurye, Jay and Granat, Anastasiya and Green, Richard E. and Harvey, William and Hasenfeld, Patrick and Hastie, Alex and Haukness, Marina and Jaeger, Erich B. and Jain, Miten and Kirsche, Melanie and Kolmogorov, Mikhail and Korbel, Jan O. and Koren, Sergey and Korlach, Jonas and Lee, Joyce and Li, Daofeng and Lindsay, Tina and Lucas, Julian and Luo, Feng and Marschall, Tobias and Mitchell, Matthew W. and McDaniel, Jennifer and Nie, Fan and Olsen, Hugh E. and Olson, Nathan D. and Pesout, Trevor and Potapova, Tamara and Puiu, Daniela and Regier, Allison and Ruan, Jue and Salzberg, Steven L. and Sanders, Ashley D. and Schatz, Michael C. and Schmitt, Anthony and Schneider, Valerie A. and Selvaraj, Siddarth and Shafin, Kishwar and Shumate, Alaina and Stitziel, Nathan O. and Stober, Catherine and Torrance, James and Wagner, Justin and Wang, Jianxin and Wenger, Aaron and Xiao, Chuanle and Zimin, Aleksey V. and Zhang, Guojie and Wang, Ting and Li, Heng and Garrison, Erik and Haussler, David and Hall, Ira and Zook, Justin M. and Eichler, Evan E. and Phillippy, Adam M. and Paten, Benedict and Howe, Kerstin and Miga, Karen H.}, @@ -6515,7 +10668,7 @@ @article{jdeed_redistribution_2022 doi = {10.3390/cells11172633}, issn = {2073-4409}, journal = {Cells}, - keywords = {{\textgreater}UseGalaxy.eu, ARID1A, FoxQ1, SWI/SNF, TGF-β, bexarotene, epithelial–mesenchymal transition}, + keywords = {{\textgreater}UseGalaxy.eu, ARID1A, Epithelial-Mesenchymal Transition, FoxQ1, Neoplasms, SWI/SNF, TGF-β, bexarotene, epithelial–mesenchymal transition}, language = {en}, month = {January}, number = {17}, @@ -6548,6 +10701,20 @@ @article{jeon_tailored_2023 year = {2023} } +@misc{jepsen_linker_2025, + abstract = {The chromosomal translocation t(12;21)(p13;q22) gives rise to ETV6::RUNX1, the most common oncogenic fusion gene in pediatric B cell precursor acute lymphoblastic leukemia (BCP-ALL). ETV6::RUNX1 arises before birth at high frequency and induces a clinically silent state that can persist for over a decade. In \<1\% of carriers, these preleukemic cells acquire secondary mutations that induce transformation to overt leukemia. The mechanisms contributing to quiescence of ETV6::RUNX1+ preleukemic cells still remain elusive. In this thesis, factors involved in ETV6::RUNX1+ preleukemia are characterized by generating CRISPR/Cas9-edited human induced pluripotent stem cell (hiPSC) models. These preleukemic hiPSC models express ETV6::RUNX1 at physiological levels via the endogenous ETV6 promoter. Transcriptional analyses identified upregulation of linker histone H1-0 at the ETV6::RUNX1+ preleukemic state, both in hiPSCs and during early B lymphoid differentiation. Moreover, publicly available expression data of 3,026 leukemia patient samples showed significantly elevated H1-0 levels in ETV6::RUNX1+ BCP-ALL compared to other leukemia entities. Dual-luciferase promoter assays revealed that H1-0 promoter activity can be induced by ETV6::RUNX1, but not by RUNX1. While chromatin immunoprecipitation assays did not indicate direct binding of ETV6::RUNX1 to the H1-0 promoter, H1-0 expression might be indirectly regulated via DNA methylation of a CpG island shore element or histone acetylation. Depletion of H1-0 via RNA interference affected epigenetic processes and inhibited ETV6::RUNX1 signature genes, including RAG1 and EPOR, indicating a key role of H1-0 in regulating the ETV6::RUNX1 transcriptome. Analysis of single-cell sequencing data showed that H1-0 is highly expressed in quiescent hematopoietic cells. H1-0 expression can be induced in BCP-ALL cell lines by addition of histone deacetylase inhibitors (HDACis) and H1-0 protein levels correspond to susceptibility towards this drug class. Following up on these findings, combinatorial drug treatments using the H1-0-inducing HDACi Quisinostat were performed. These experiments showed promising synergism of Quisinostat with established chemotherapeutic drugs used for B-ALL treatment and the proteasome inhibitor Bortezomib in ETV6::RUNX1+ cells. Taken together, these data identify H1-0 as a key regulator of the ETV6::RUNX1+ transcriptome and indicate that induction of H1-0 via HDACis might be a potential novel approach to improve ETV6::RUNX1+ BCP-ALL treatment.}, + author = {Jepsen, Vera Helena}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {March}, + shorttitle = {Linker histone variant {H1}-0 dysregulation in {ETV6}}, + title = {Linker histone variant {H1}-0 dysregulation in {ETV6}::{RUNX1}+ preleukemia and {B} cell acute lymphoblastic leukemia}, + type = {Dissertation}, + url = {https://docserv.uni-duesseldorf.de/servlets/DocumentServlet?id=68891}, + urldate = {2025-03-29}, + year = {2025} +} + @article{jesudoss_chelladurai_comparative_2023, abstract = {Dipylidium caninum (Linnaeus, 1758) is a common zoonotic cestode of dogs and cats worldwide. Previous studies have demonstrated the existence of largely host-associated canine and feline genotypes based on infection studies, differences at the 28S rDNA gene, and complete mitochondrial genomes. There have been no comparative genome-wide studies. Here, we sequenced the genomes of a dog and cat isolate of Dipylidium caninum from the United States using the Illumina platform at mean coverage depths of 45× and 26× and conducted comparative analyses with the reference draft genome. Complete mitochondrial genomes were used to confirm the genotypes of the isolates. Genomes of D. caninum canine and feline genotypes generated in this study, had an average identity of 98\% and 89\%, respectively, when compared to the reference genome. SNPs were 20 times higher in the feline isolate. Comparison and species delimitation using universally conserved orthologs and protein-coding mitochondrial genes revealed that the canine and feline isolates are different species. Data from this study build a base for future integrative taxonomy. Further genomic studies from geographically diverse populations are necessary to understand implications for taxonomy, epidemiology, veterinary clinical medicine, and anthelmintic resistance.}, author = {Jesudoss Chelladurai, Jeba R. J. and Abraham, Aloysius and Quintana, Theresa A. and Ritchie, Deb and Smith, Vicki}, @@ -6589,6 +10756,28 @@ @article{jhinjharia_high-throughput_2023 year = {2023} } +@article{ji_unusual_2025, + abstract = {As one of the four primary evolutionary groups within myriapods, centipedes (Chilopoda) comprise approximately 3150 valid species. Recent molecular studies have begun to elucidate the phylogeny and time to divergence in Chilopoda; yet, identifying scutigeromorphs at the species level remains a notoriously challenging task. In this study, we obtained seven new complete mitogenomes of Thereuopoda clunifera (Wood, 1862) to investigate the phylogeny and divergence times of Chilopoda. Both maximum likelihood (ML) and Bayesian inference (BI) analyses recovered the relationship of (Scutigeromorpha + (Scolopendromorpha + (Lithobiomorpha + Geophilomorpha))). For Scutigeromorpha, seven newly sequenced mitogenomes of T. clunifera were divided into four distinct clades. Divergence time estimates suggest that the basal split of Chilopoda occurred during the Middle Ordovician period, with the origins of Scolopendromorpha, Lithobiomorpha, and Geophilomorpha dating to the Devonian period. Factors such as warm climates, coevolution between predator and prey, and the rifting of the Hainan Island may have driven the diversification of Scutigeromorpha. Based on genetic distance, the delimitation of molecular species, phylogenetic relationships, and divergence time analyses, we identified three cryptic species that existed within T. clunifera. This exceptionally high degree of hidden diversity can be ascribed to the morphological stasis that has occurred since the Paleozoic era and taxonomic impediment.}, + author = {Ji, Jie-Hong and Wu, Hui-Yuan and Gao, Yi-Xin and Shen, Chen-Yang and Yang, Zi-Wen and Storey, Kenneth B. and Yu, Dan-Na and Zhang, Jia-Yong}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/insects16050486}, + issn = {2075-4450}, + journal = {Insects}, + keywords = {{\textgreater}UseGalaxy.eu, Chilopoda, cryptic species, divergence time, mitogenomes, phylogeny}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {486}, + shorttitle = {Unusual {Genetic} {Diversity} {Within} {Thereuopoda} clunifera ({Wood}, 1862) ({Chilopoda}}, + title = {Unusual {Genetic} {Diversity} {Within} {Thereuopoda} clunifera ({Wood}, 1862) ({Chilopoda}: {Scutigeromorpha}) {Revealed} by {Phylogeny} and {Divergence} {Times} {Using} {Mitochondrial} {Genomes}}, + url = {https://www.mdpi.com/2075-4450/16/5/486}, + urldate = {2025-05-28}, + volume = {16}, + year = {2025} +} + @incollection{jia_salmonella_2024, abstract = {Salmonella is a widespread pathogen that can cause a variety of disease syndromes, thereby having a tremendous impact on human health and animal husbandry. Currently, whole genome sequencing technology has been widely used to study the phylogenetic relationships of Salmonella, primarily using the Illumina short-read platform. Complete genome sequence data of Salmonella are rarely systematically analyzed in similar studies considering the relatively high cost currently. Therefore, here we collected the complete genome sequence data of 1819 Salmonella in GenBank and classified these strains into different subspecies, serovars, and STs by SISTR, Seqsero2, multilocus sequence typing (MLST), and other sophisticated software. In addition, we constructed and demonstrated different phylogenetic trees by four methods with high discriminatory power: core single-nucleotide polymorphism typing, core genome MLST (cgMLST), clustered regularly interspaced short palindromic repeat typing, and pan-genome typing. The different typing methods are systematically presented, along with a comparison of the characteristics of the four distinct typing methods used in this chapter. In conclusion, we have made a new attempt to use complete genome sequence datasets to study the phylogenetic relationships of Salmonella. Additional considerations regarding the time required to be consumed, the clustering effect, and the cgMLST method are also discussed.}, author = {Jia, Chenghao and Zhou, Haiyang and Wang, Zining and Liu, Yuhao and Yue, Min}, @@ -6606,6 +10795,55 @@ @incollection{jia_salmonella_2024 year = {2024} } +@article{jiang_-depth_2022, + abstract = {The human oral microbiome correlates with numerous diseases, including lung cancer. Identifying the functional changes by metaproteomics helps understand the disease-related dysbiosis, yet characterizing low-abundant bacteria is challenging. Here, we developed a free-flow isoelectric focusing electrophoresis-mass spectrometry- (FFIEF-MS-) based metaproteomics strategy to reduce host interferences and enrich low-abundant bacteria for in-depth interpretation of the oral microbiome. With our method, the number of interfering peptides decreased by 52.87\%, whereas the bacterial peptides and species increased by 94.97\% and 44.90\%, respectively, compared to the conventional metaproteomics approach. We identified 3647 bacterial proteins, which is the most comprehensive oral metaproteomics study to date. Lung cancer-associated bacteria were validated among an independent cohort. The imbalanced \textit{Fusobacterium nucleatum} and \textit{Prevotella histicola} and their dysregulated functions in inhibiting immune response and maintaining cell redox homeostasis were revealed. The FFIEF-MS may serve as a valuable strategy to study the mechanisms between human diseases and microbiomes with broader applications.}, + author = {Jiang, Xiaoteng and Zhang, Yan and Wang, Huiyu and Wang, Zeyuan and Hu, Shen and Cao, Chengxi and Xiao, Hua}, + doi = {10.34133/2022/9781578}, + issn = {2639-5274}, + journal = {Research (Washington, D.C.)}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {9781578}, + title = {In-{Depth} {Metaproteomics} {Analysis} of {Oral} {Microbiome} for {Lung} {Cancer}}, + url = {http://europepmc.org/abstract/MED/36320634}, + volume = {2022}, + year = {2022} +} + +@article{jonsson_enhanced_2025, + author = {Jönsson, Alexander and Iatrou, Antonia and Wildfang, Louise and J. Neumann, Dana and Gürbüz, Hakan and A. Schoenmaker, Carina A. and Danner Dalgaard, Marlene and Rose Jensen, Pernille and Dufva, Martin}, + doi = {10.1039/D4MA01191K}, + journal = {Materials Advances}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + note = {Publisher: Royal Society of Chemistry}, + shorttitle = {Enhanced biocompatibility of {3D} printed resin parts via wet autoclave postprocessing}, + title = {Enhanced biocompatibility of {3D} printed resin parts via wet autoclave postprocessing: implications for stem cell organ-on-a-chip culture}, + url = {https://pubs.rsc.org/en/content/articlelanding/2025/ma/d4ma01191k}, + urldate = {2025-03-29}, + year = {2025} +} + +@article{joshi_insights_2025, + abstract = {Most hospital-acquired urinary tract infections are the result of implanted urinary catheter, with majority of studies focused on a single species colonisation, but recently polymicrobial colonisations are being reported. In this study, indwelling urinary catheters were collected from ICU patients and the colonising microbiome was isolated and identified by the traditional; culturing method and metagenomics. It was observed that majority of catheters were colonised by polymicrobial biofilms, containing both bacterial and fungal isolates making them diverse and complex. However, the metagenomics results were quite surprising showing the presence of multiple organisms of which only 1or 2 showed growth when cultured. Later, in vitro assays were performed by selecting 6 combinations, with each combination containing one Candida spp. – C. albicans or C. tropicalis with one bacteria K. pneumoniae, P. aeruginosa or E. coli. It was observed that polymicrobial biofilms were stronger than mono-microbial biofilms, suggesting their increased surface adhesion. Furthermore, to simulate the dynamic environment in which cells are exposed to a certain level of fluid movement, a flow system was established to imitate the flow generated in colonized urinary catheter. We have observed changes in biofilm architecture, adhesion and thickness under flow conditions compared with static conditions, with a uniformly adhered biofilm with increased thickness of polymicrobial biofilms as compared to mono-species biofilms. The biofilm formed under flow was more viable than the static biofilm with higher number of live cells in flow condition.}, + author = {Joshi, Purvi and Bhattacharjee, Rohit and Sahu, Muskan and Gajjar, Devarshi}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-00457-w}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Bacteria, Biofilms, Candida, Microbial communities, Urinary Catheters}, + language = {en}, + month = {May}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {15375}, + title = {Insights into urinary catheter colonisation and polymicrobial biofilms of {Candida}- bacteria under flow condition}, + url = {https://www.nature.com/articles/s41598-025-00457-w}, + urldate = {2025-05-28}, + volume = {15}, + year = {2025} +} + @article{joshi_physicochemical_2024, abstract = {Prostate cancer is the most common cancer among men which has major diagnosis in the United States in 2017. Among DYRK class II members, dual specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2) is the functional target for prostate cancer treatment. Studies show that subfamilies of DYRKs are also capable to phosphorylate (tyrosine, serine, and threonine) residues, yet little research has been carried out for its inhibitors. In this article, conceptual density theory is used to estimate the physicochemical properties of 30 experimentally synthesized inhibitors targeting DYRK2. The HOMO–LUMO gap showed low reactivity and high chemical activity for the inhibitors. The biological efficacy of these 30 inhibitors is predicted by bioavailability, mutagenicity, and cardiotoxicity measures. The inhibitors showed low toxicity and no blood brain barrier permeability. Results indicated that the physiological actions of these inhibitors involve multiple target interactions. Since the experimental results of the DYRK2 protein showed great water solubility, favorable safety properties, and potential anti-prostate cancer activities for ligand 24, docking and molecular dynamics simulations from the Galaxy webserver using Gromacs open-source tools are also performed for (DYRK2-24) complex (PDB: 7EJV). (DYRK2-24) showed strong binding affinity and noncovalent interactions.}, author = {Joshi, Sravani and Srivastava, Ruby}, @@ -6625,6 +10863,21 @@ @article{joshi_physicochemical_2024 year = {2024} } +@article{joshi_theoretical_2025, + abstract = {The neural melanocortin receptors, specifically MC3R and MC4R, play a crucial role in regulating energy homeostasis in rats. This study focuses on the theoretical evaluation of 16 orally bioavailable, small-molecule MC4R antagonists identified through experimental hit identification processes. Conceptual Density Functional Theory (CDFT) is applied to study the reactivity and stability of 16 antagonists. The physicochemical properties and metabolic activities are studied using various bioinformatics tools. Ramachandran plot analysis of MC4R protein is carried out for experimental MC4R protein structure. The active sites for MC4R protein is predicted with Active site prediction tool. MD simulations for (MC4R-antagonists) are carried out with HDOCK server. The (MC4R-16) complex showed strong binding interactions which validated the experimental results. MD simulations for Alphafold3 docked (MC4R-16) complex is carried out using Galaxy based GroMacs tools for 30 ns due to potential shortcomings of the single-trajectory approach. Further various tools are used to evaluate the physicochemical properties, metabolic properties and toxicity assessment of the studied 16 complexes. SwissTargetPrediction webserver is used to predict the multitarget activities of the antagonists. High ionization potentials (IP), low electron affinities (EA), and larger HOMO–LUMO (HL) gaps suggest the stability and reactivity of complexes. All 16 MC4R antagonists are found to be non-toxic (MUT, TUM), with its potential safety for arrhythmia and hypertension. High gastrointestinal (GI) absorption and blood–brain barrier (BBB) permeability is observed for the antagonists. (MC4R-16) complex demonstrated system adaptability and increased conformational flexibility in loop regions, with strong hydrophobic interactions, validating the experimental findings which showed that complex 16 is effective in an aged rat model of anorexia-cachexia syndrome and has progressed to clinical trials.}, + author = {Joshi, Sravani and Srivastava, Ruby}, + doi = {10.1007/s42485-025-00178-8}, + issn = {2524-4663}, + journal = {Journal of Proteins and Proteomics}, + keywords = {{\textgreater}UseGalaxy.eu, Antagonists, Computational Chemistry, Defects, Homeostasis, Melanocortin receptors, Obesity, Protein Complex, Protein-Ligand Interactions, Receptor Pharmacology, Small Molecules, Theoretical Chemistry}, + language = {en}, + month = {February}, + title = {Theoretical studies on safety and efficacy of 16 small-molecule {MC4R} antagonists as therapeutics for obesity}, + url = {https://doi.org/10.1007/s42485-025-00178-8}, + urldate = {2025-02-28}, + year = {2025} +} + @article{joshi_tracing_2024, abstract = {Pharmacological drugs targeting specific pathways involved in various diseases have seen recent advancement with newer and more efficient emerging drug targets but these drugs are limited in terms of their side effects and patient adherence. The potential of plant-based diets in the form of functional foods is increasingly being realized as an option to treat and/or prevent several diseases. In this work, we have selected flaxseed (Linum usitatissimum), also known as linseed to study its pharmacological efficacy and proposed mechanisms of action for medicinal purposes. The target genes of linseed with disease specificity index (DSI {\textgreater} 0.6) are compared to the associated genes of diabetes mellitus, decrease in appetite, addictive behavior, cardiovascular diseases, Inflammatory Bowel Diseases (IMD), Polycystic Ovary Syndrome (PCOS) and the selected genes are evaluation further using in silico methods. The binding affinity of flaxseed to three common target proteins family (CCDC28b, PDCD6IP and USP34) is assessed by docking and Molecular dynamics (MD) simulations. Results show that linseed is safe to use for mutagenic toxicity and other cardiotoxicity measures but linseed is unsafe for embryotoxicity, herG toxicity and cardiac failure. The protein-protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis indicates that flaxseed can be used as a medicinal herb for diabetes mellitus, cardiovascular diseases, Inflammatory Bowel Diseases (IMD) and Polycystic Ovary Syndrome (PCOS).}, author = {Joshi, Sravani and Srivastava, Ruby}, @@ -6718,6 +10971,26 @@ @article{junge_atp-gated_2024 year = {2024} } +@article{justen_genetics_2025, + abstract = {Extrinsic postzygotic isolation, where hybrids experience reductions in fitness due to a mismatch with their environment, is central to speciation. Knowledge of genetic variants that underlie extrinsic isolation is crucial for understanding the early stages of speciation. Differences in seasonal migration are strong candidates for extrinsic isolation (e.g., if hybrids take intermediate and inferior routes compared to pure forms). Here, we used a hybrid zone between two subspecies of the songbird Swainson’s thrush (Catharus ustulatus) with different migratory routes and tests for viability selection (locus-specific changes in interspecific heterozygosity and ancestry mismatch across age classes) to gain insight into the genetic basis of extrinsic isolation. Using data from over 900 individuals we find strong evidence for viability selection on both interspecific heterozygosity and ancestry mismatch at loci linked to migration. Much of this selection was dependent on genome-wide ancestry; as expected, a subset of hybrids exhibited reduced viability, but remarkably, another subset appears to fill an unoccupied fitness peak within the species, exhibiting higher viability than even parental forms. Many of the variants that influence hybrid viability appear to occur in structural variants, including a putative pericentric inversion. Our study emphasizes the importance of epistatic interactions and structural variants in speciation.}, + author = {Justen, Hannah C. and Blain, Stephanie A. and Delmore, Kira E.}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41467-025-63188-6}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Evolutionary genetics, Molecular evolution, Speciation}, + language = {en}, + month = {August}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {7897}, + title = {The genetics of extrinsic postzygotic selection in a migratory divide between subspecies of the {Swainson}’s thrush}, + url = {https://www.nature.com/articles/s41467-025-63188-6}, + urldate = {2025-09-03}, + volume = {16}, + year = {2025} +} + @article{kaari_integrated_2024, abstract = {Ralstonia solanacearum is one of the most destructive soil-borne pathogen, causing bacterial wilt to the solanaceae vegetables. Streptomyces sp. UP1A-1 isolated from healthy solanaceae rhizosphere soil, exhibited the lowest disease incidence and increased fruit yield of solanaceae vegetables. However, the genomic and functional properties of UP1A-1 are unclear. Therefore, we conducted the present study to elucidate the genomic characteristics of UP1A-1 by whole genome sequencing. The results indicate that the genome of Streptomyces sp. UP1A-1 consists of 8,252,902 bp and contains 72.42 \% G + C. We identified the genes that confer plant growth promoting (PGP) function, which include those involved in siderophore production, indole-3-acetic acid biosynthesis, phosphate solubilization, nitrogen metabolism, and potassium metabolism. We also identified several other genes, such as chitinase, peroxidase, superoxide dismutase, catalase, proline biosynthesis, and glucose dehydrogenase, which are believed to be involved in the control of wilt disease. These genes revealed that the strain UP1A-1 has physiologically adapted to varied environmental conditions and could potentially control both abiotic and biotic stresses.}, author = {Kaari, Manigundan and Manikkam, Radhakrishnan and Joseph, Jerrine and Krishnan, Sakthivel and Annamalai, Kishore Kumar and Khan, Abujunaid and Rajput, Vinay and Dastager, Syed Gulam and Dharne, Mahesh S. and Umar, Md and Venugopal, Gopikrishnan and Alexander, Balamurugan}, @@ -6734,13 +11007,42 @@ @article{kaari_integrated_2024 year = {2024} } +@article{kabir_genome_2025, + abstract = {Antibiotic resistance against human pathogenic bacteria is a global problem and the issue is becoming increasingly serious. Klebsiella aerogenes, a Gram-negative pathogen, is usually found in soil and water, but there are increasing number of reports in on isolation of antibiotic-resistant strains of it. Here, we report the draft genome of a food-borne Klebsiella aerogenes strain isolated from street food of Dhaka, Bangladesh. The WGS analysis revealed the presence of a number of virulence genes and antibiotic-resistance genes. Using the infection model of the larvae of the silk moth, Bombyx mori, we show that the K. aerogenes strain killed larvae within 72 h of injection into the hemolymph (blood) or midgut. Although the strain showed resistance to ampicillin in vitro among the antibiotics tested, it showed sensitivity to ampicillin in vivo in Bombyx larvae. Direct injection of aqueous extracts of hog plum or Indian gooseberry into the midgut of larvae infected with K. aerogenes increased larval survival rate to {\textasciitilde} 75\% after 72 h. These results indicate that Bombyx larvae could be used to carry out in vivo screening of plant extracts with potential therapeutic effects against pathogenic bacteria like K. aerogenes.}, + author = {Kabir, Tansha and Hossain, Md. Ismail and Jepu, Tangerul A. and Sarker, Mrinmoy and Saleh, Nusrat U. A. and Monir, Hafsa and Nawaar, Nafisa and Jene, Sadia A. and Hossain, Md Mahtab and Uddin, M. Aftab and Bari, M. Latiful and Hossain, Muktadir S.}, + doi = {10.1186/s12866-025-03942-4}, + issn = {1471-2180}, + journal = {BMC Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Antibiotic resistance, Bombyx, Bombyx infection model, Genome, Bacterial, Klebsiella, Klebsiella Infections, Pathogens, Plant extract, Therapeutic effect}, + language = {en}, + month = {April}, + number = {1}, + pages = {209}, + title = {Genome characterization, pathogenicity, and evaluation of therapeutics of {Klebsiella} aerogenes in {Bombyx} larvae infection model}, + url = {https://doi.org/10.1186/s12866-025-03942-4}, + urldate = {2025-04-21}, + volume = {25}, + year = {2025} +} + +@article{kaczmarczyk_genome-wide_2025, + abstract = {{\textless}h4{\textgreater}ABSTRACT{\textless}/h4{\textgreater} Pseudomonas aeruginosa is a metabolically versatile opportunistic human pathogen. It causes acute and chronic infections and is notorious for its multidrug resistance and tolerance. To systematically uncover genetic vulnerabilities that could be exploited as therapeutic targets, we present a portable high-density CRISPR interference (CRISPRi) library comprising {\textgreater}80’000 single-guide RNAs (sgRNAs) targeting virtually all annotated coding sequences and intergenic regions of P. aeruginosa PAO1. This library was used to assess the genome-wide fitness landscapes under different growth conditions, uncovering gain- and loss- of-function phenotypes for more than a thousand genes upon depletion. Many of the phenotypes are likely caused by hypomorphic (partial loss-of-function) alleles that would not be easily accessible by traditional transposon sequencing (Tn-Seq). Focusing on central carbon metabolism, we reveal two glyceraldehyde-3-phosphate dehydrogenases as central, non-redundant nodes in glycolytic and gluconeogenic growth conditions that might be promising targets to redirect carbon flux away from metabolically persistent states associated with chronic infections. More generally, our comprehensive sgRNA libraries are a valuable resource to access genome-wide quantitative phenotypes through CRISPRi beyond the binary phenotypes offered by Tn-Seq.}, + author = {Kaczmarczyk, Andreas and Klotz, Alexander and Manfredi, Pablo and Jenal, Urs}, + doi = {10.1101/2025.08.12.669819}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Genome-wide high-density {CRISPR} interference screens reveal condition-specific metabolic vulnerabilities in {Pseudomonas} aeruginosa {PAO1}}, + url = {http://europepmc.org/abstract/PPR/PPR1064713}, + year = {2025} +} + @article{kahraman-ilikkan_comparative_2024, abstract = {Lactic acid bacteria (LAB) can be used as a probiotic or starter culture in dairy, meat, and vegetable fermentation. Therefore, their isolation and identification are essential. Recent advances in omics technologies and high-throughput sequencing have made the identification and characterization of bacteria. This study firstly aimed to demonstrate the sensitivity of the Vitek MS (MALDI-TOF) system in the identification of lactic acid bacteria and, secondly, to characterize bacteria using various bioinformatics approaches. Probiotic potency-related genes and secondary metabolite biosynthesis gene clusters were examined. The Vitek MS (MALDI-TOF) system was able to identify all of the bacteria at the genus level. According to whole genome sequencing, the bacteria were confirmed to be Lentilactobacillus buchneri, Levilactobacillus brevis, Lactiplantibacillus plantarum, Levilactobacillus namurensis. Bacteria had most of the probiotic potency-related genes, and different toxin-antitoxin systems such as PemIK/MazEF, Hig A/B, YdcE/YdcD, YefM/YoeB. Also, some of the secondary metabolite biosynthesis gene clusters, some toxic metabolite-related genes, and antibiotic resistance-related genes were detected. In addition, Lentilactobacillus buchneri Egmn17 had a type II-A CRISPR/Cas system. Lactiplantibacillus plantarum Gmze16 had a bacteriocin, plantaricin E/F.}, author = {Kahraman-Ilıkkan, Özge}, doi = {10.1007/s00438-024-02129-2}, issn = {1617-4623}, journal = {Molecular Genetics and Genomics}, - keywords = {{\textgreater}UseGalaxy.eu, Identification, Lactic acid bacteria, Vitek MS (MALDI-TOF), Whole genome sequencing}, + keywords = {{\textgreater}UseGalaxy.eu, Identification, Lactic acid bacteria, Lactobacillales, Lactobacillus, Vitek MS (MALDI-TOF), Whole genome sequencing}, language = {en}, month = {March}, number = {1}, @@ -6780,6 +11082,34 @@ @article{kaiser_mutational_2021 year = {2021} } +@article{kaleta_antibody_2021, + abstract = {{\textless}title{\textgreater}Abstract{\textless}/title{\textgreater} {\textless}p{\textgreater}In spring 2021, an increasing number of infections was observed caused by the hitherto rarely described SARS-CoV-2 variant A.27 in south-west Germany. From December 2020 to June 2021 this lineage has been detected in 31 countries. Phylogeographic analyses of A.27 sequences obtained from national and international databases reveal a global spread of this lineage through multiple introductions from its inferred origin in Western Africa. Variant A.27 is characterized by a mutational pattern in the spike gene that includes the L18F, L452R and N501Y spike amino acid substitutions found in various variants of concern but lacks the globally dominant D614G. Neutralization assays demonstrated an escape of A.27 from convalescent and vaccine-elicited antibody-mediated immunity. Moreover, the therapeutic monoclonal antibody Bamlanivimab and partially the REGN-COV2 cocktail failed to block infection by A.27. Our data emphasize the need for continued global monitoring of novel lineages because of the independent evolution of new escape mutations.{\textless}/p{\textgreater}}, + author = {Kaleta, Tamara and Kern, Lisa and Hong, Samuel and Hölzer, Martin and Kochs, Georg and Beer, Julius and Schnepf, Daniel and Schwemmle, Martin and Bollen, Nena and Kolb, Philipp and Huber, Magdalena and Ulferts, Svenja and Weigang, Sebastian and Dudas, Gytis and Wittig, Alice and Jaki, Lena and Padane, Abdou and Lagare, Adamou and Salou, Mounerou and Ozer, Egon and Nnaemeka, Ndodo and Odoom, John and Rutayisire, Robert and Benkahla, Alia and Akoua-Koffi, Chantal and Ouedraogo, Abdoul-Salam and SIMON-LORIERE, Etienne and Enouf, Vincent and Kröger, Stefan and Calvignac-Spencer, Sébastien and Baele, Guy and Panning, Marcus and Fuchs, Jonas}, + doi = {10.21203/rs.3.rs-995033/v1}, + journal = {Research Square}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Antibody escape and global spread of {SARS}-{CoV}-2 lineage {A}.27}, + url = {http://europepmc.org/abstract/PPR/PPR414796}, + year = {2021} +} + +@article{kaleta_antibody_2022, + abstract = {In spring 2021, an increasing number of infections was observed caused by the hitherto rarely described SARS-CoV-2 variant A.27 in south-west Germany. From December 2020 to June 2021 this lineage has been detected in 31 countries. Phylogeographic analyses of A.27 sequences obtained from national and international databases reveal a global spread of this lineage through multiple introductions from its inferred origin in Western Africa. Variant A.27 is characterized by a mutational pattern in the spike gene that includes the L18F, L452R and N501Y spike amino acid substitutions found in various variants of concern but lacks the globally dominant D614G. Neutralization assays demonstrate an escape of A.27 from convalescent and vaccine-elicited antibody-mediated immunity. Moreover, the therapeutic monoclonal antibody Bamlanivimab and partially the REGN-COV2 cocktail fail to block infection by A.27. Our data emphasize the need for continued global monitoring of novel lineages because of the independent evolution of new escape mutations.}, + author = {Kaleta, Tamara and Kern, Lisa and Hong, Samuel Leandro and Hölzer, Martin and Kochs, Georg and Beer, Julius and Schnepf, Daniel and Schwemmle, Martin and Bollen, Nena and Kolb, Philipp and Huber, Magdalena and Ulferts, Svenja and Weigang, Sebastian and Dudas, Gytis and Wittig, Alice and Jaki, Lena and Padane, Abdou and Lagare, Adamou and Salou, Mounerou and Ozer, Egon Anderson and Nnaemeka, Ndodo and Odoom, John Kofi and Rutayisire, Robert and Benkahla, Alia and Akoua-Koffi, Chantal and Ouedraogo, Abdoul-Salam and Simon-Lorière, Etienne and Enouf, Vincent and Kröger, Stefan and Calvignac-Spencer, Sébastien and Baele, Guy and Panning, Marcus and Fuchs, Jonas}, + doi = {10.1038/s41467-022-28766-y}, + issn = {2041-1723}, + journal = {Nature communications}, + keywords = {{\textgreater}UseGalaxy.eu, Pandemics}, + language = {eng}, + month = {March}, + number = {1}, + pages = {1152}, + title = {Antibody escape and global spread of {SARS}-{CoV}-2 lineage {A}.27}, + url = {http://europepmc.org/abstract/MED/35241661}, + volume = {13}, + year = {2022} +} + @article{kalmbach_genome-wide_2019, abstract = {The switch/sucrose non-fermenting (SWI/SNF) complex is an ATP-dependent chromatin remodeller that regulates the spacing of nucleosomes and thereby controls gene expression. Heterozygous mutations in genes encoding subunits of the SWI/SNF complex have been reported in individuals with Coffin-Siris syndrome (CSS), with the majority of the mutations in \textit{ARID1B}. CSS is a rare congenital disorder characterized by facial dysmorphisms, digital anomalies, and variable intellectual disability. We hypothesized that mutations in genes encoding subunits of the ubiquitously expressed SWI/SNF complex may lead to alterations of the nucleosome profiles in different cell types. We performed the first study on CSS-patient samples and investigated the nucleosome landscapes of cell-free DNA (cfDNA) isolated from blood plasma by whole-genome sequencing. In addition, we studied the nucleosome landscapes of CD14$^{\textrm{+}}$ monocytes from CSS-affected individuals by nucleosome occupancy and methylome-sequencing (NOMe-seq) as well as their expression profiles. In cfDNA of CSS-affected individuals with heterozygous \textit{ARID1B} mutations, we did not observe major changes in the nucleosome profile around transcription start sites. In CD14$^{\textrm{+}}$ monocytes, we found few genomic regions with different nucleosome occupancy when compared to controls. RNA-seq analysis of CD14$^{\textrm{+}}$ monocytes of these individuals detected only few differentially expressed genes, which were not in proximity to any of the identified differential nucleosome-depleted regions. In conclusion, we show that heterozygous mutations in the human SWI/SNF subunit ARID1B do not have a major impact on the nucleosome landscape or gene expression in blood cells. This might be due to functional redundancy, cell-type specificity, or alternative functions of ARID1B.}, author = {Kalmbach, Alexander and Schröder, Christopher and Klein-Hitpass, Ludger and Nordström, Karl and Ulz, Peter and Heitzer, Ellen and Speicher, Michael R. and Rahmann, Sven and Wieczorek, Dagmar and Horsthemke, Bernhard and Bramswig, Nuria C.}, @@ -6805,6 +11135,7 @@ @article{kalnytska_sorcs2_2024 issn = {2589-0042}, journal = {iScience}, keywords = {{\textgreater}UseGalaxy.eu, Biological sciences, Endocrinology, Natural sciences, Physiology}, + language = {eng}, month = {January}, number = {1}, pages = {108725}, @@ -6880,7 +11211,7 @@ @article{kandinov_mini-multilocus_2024 doi = {10.3390/ijms25115781}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {\textit{Neisseria gonorrhoeae}, {\textgreater}UseGalaxy.eu, antimicrobial resistance, genogroups, informative polymorphisms, multilocus sequence typing, oligonucleotide microarray, phylogenetic analysis}, + keywords = {\textit{Neisseria gonorrhoeae}, {\textgreater}UseGalaxy.eu, Gonorrhea, Multilocus Sequence Typing, Neisseria gonorrhoeae, Phylogeny, antimicrobial resistance, genogroups, informative polymorphisms, multilocus sequence typing, oligonucleotide microarray, phylogenetic analysis}, language = {en}, month = {January}, note = {Number: 11 @@ -6894,6 +11225,57 @@ @article{kandinov_mini-multilocus_2024 year = {2024} } +@article{kandinov_molecular_2025, + author = {Kandinov, Ilya and Shaskolskiy, Boris and Kravtsov, Dmitry and Larkin, Anatoliy and Kubanov, Alexei and Shpilevaya, Marina and Shagabieva, Julia and Nosov, Nikita and Gryadunov, Dmitry}, + doi = {10.3389/fcimb.2025.1526859}, + issn = {2235-2988}, + journal = {Frontiers in Cellular and Infection Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Gonorrhea, Neisseria gonorrhoeae, antibiotic resistance, genetic determinants of drug resistance, genotyping, molecular epidemiology}, + language = {English}, + month = {February}, + note = {Publisher: Frontiers}, + shorttitle = {Molecular epidemiology of {Neisseria} gonorrhoeae isolates in {Russia}, 2015–2023}, + title = {Molecular epidemiology of {Neisseria} gonorrhoeae isolates in {Russia}, 2015–2023: current trends and forecasting}, + url = {https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2025.1526859/full}, + urldate = {2025-02-23}, + volume = {15}, + year = {2025} +} + +@article{kansou_human_2025, + abstract = {A link between idiopathic male infertility and viral infections exhibiting seminal carriage has emerged recently. In this respect, human papillomavirus (HPV) appears to be the most prevalent sexually transmitted agent worldwide. The viruses present in the genital environment comprise the genital virome. HPV infection reportedly disrupts homeostasis of the virome in women but this topic has not previously been studied in men.}, + author = {Kansou, Elissa and Aubry, Aurélien and Brochot, Etienne and Priam, Armin and Cabry-Goubet, Rosalie and Bosquet, Dorian and Demey, Baptiste}, + doi = {10.1186/s12958-025-01488-8}, + issn = {1477-7827}, + journal = {Reproductive Biology and Endocrinology}, + keywords = {{\textgreater}UseGalaxy.eu, High-throughput sequencing, Human papillomavirus, Male infertility, Metagenomic, Sperm, Virome}, + language = {en}, + month = {November}, + number = {1}, + pages = {154}, + shorttitle = {Human papillomavirus seminal carriage alters virome diversity and male fertility}, + title = {Human papillomavirus seminal carriage alters virome diversity and male fertility: a case-control study}, + url = {https://doi.org/10.1186/s12958-025-01488-8}, + urldate = {2025-12-26}, + volume = {23}, + year = {2025} +} + +@article{kao_influence_2025, + abstract = {Staphylococcus aureus is the leading cause of infectious-related deaths. Vaccine development has been hampered by the recall of nonprotective immune responses from prior exposure, suggesting an effective vaccine may need to be given early in life. The goal of this pilot study was to correlate the maternal serologic response against S. aureus to an infant’s risk for skin and soft tissue infection (SSTI) and colonization in the first year of life.Pregnant women were enrolled and maternal-infant dyads followed for 12 months. Maternal 3rd trimester and cord blood were obtained to determine the anti-S. aureus IgG and anti-α-toxin (Hla) neutralizing antibody (NAb) titers. Serial surveys and skin swabs were obtained from mothers at enrollment and from infants longitudinally to ascertain S. aureus colonization status and the incidence of SSTI.63 pregnant women were enrolled, 54\% with history of SSTI or asymptomatic S. aureus colonization at enrollment. Within 48-hours of delivery, 23\% of infants had S. aureus colonization and 43\% at 1-month. Maternal S. aureus colonization resulted in 7.4 increased odds of infant colonization at delivery. Higher cord blood anti-Hla Nab titer was associated with significantly lower risk for infant SSTI in the first year of life.S. aureus colonization occurs early in life, with over 40\% of infants colonized by 1-month. These results are the first to demonstrate an association between higher transplacental anti-Hla NAb and protection against infant SSTI in the first year of life. Overall, these findings support Hla as a promising vaccine target.}, + author = {Kao, Carol M and Wylie, Kristine M and Boyle, Mary G and Schneider, Alaina and Uhlir, Rachel and Crick, Scott L and Bubeck Wardenburg, Juliane and Fritz, Stephanie A}, + doi = {10.1093/jpids/piaf077}, + issn = {2048-7207}, + journal = {Journal of the Pediatric Infectious Diseases Society}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + pages = {piaf077}, + title = {The {Influence} of {Maternal} {S}. aureus anti-{Hla} neutralizing antibody on infant skin and soft tissue ({SSTI}) development in the first year of life}, + url = {https://doi.org/10.1093/jpids/piaf077}, + urldate = {2025-09-03}, + year = {2025} +} + @article{karim_silico_2024, abstract = {The rising antimicrobial resistance crisis has diminished the effectiveness of traditional antibiotics against pathogenic bacteria. This study addresses this urgent challenge by exploring the antibacterial potential of novel quinolone derivatives (1–33). Using computational in silico modeling to simulate biological interactions, we aimed to identify candidates with potent antibacterial activity. A total of 33 quinolone derivatives were assessed for their physicochemical properties and effectiveness against a range of clinically relevant pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), Klebsiella pneumoniae, Streptococcus pneumoniae, and Enterococcus faecalis. Molecular docking studies identified compounds 28, 29, 32, and 33 as having notable binding affinities, particularly against MRSA. Further molecular dynamics simulations of compound 29 confirmed its favorable stability and potential for disrupting MRSA, reinforcing the docking results and showing strong alignment with in vitro findings. These findings position compound 29 as a promising lead for developing alternative MRSA therapies and underscore the need for further in vivo studies to evaluate its therapeutic potential.}, author = {Karim, Tafsir and Almatarneh, Mansour H. and Rahman, Shofiur and Alodhayb, Abdullah N. and Albrithen, Hamad and Hossain, Md. Mainul and Kawsar, Sarkar M. A. and Poirier, Raymond A. and Uddin, Kabir M.}, @@ -6930,13 +11312,43 @@ @article{karthik_foremost_2023 year = {2023} } +@article{kashani_silico_2025, + abstract = {Introduction +Warts are dermal disorders resulting from HPV infection and can be transmitted by direct contact. Existing treatment approaches, such as topical treatment with salicylate, have low efficiency and demonstrate side effects. Thus, the discovery of potent drug treatments for skin warts is necessary. Here we propose the use of alternative medications for the possible treatment of skin warts with the help of comparative transcriptome analysis and drug repurposing approaches. +Methods +Gene expression datasets related to HPV-induced warts and cervical cancer were extracted from the GEO database. Differentially expressed genes (DEGs) were identified using DESeq2 in the Galaxy database. Upregulated DEGs were assessed for druggability using the DGIdb tool. Gene ontology and enrichment analysis were performed to investigate the characteristics of druggable DEGs. A molecular docking virtual screening was conducted using PyRx software to identify potential therapeutic targets for skin warts. The interactions between selected drug candidates and the target protein were analyzed using the BIOVIA Discovery Studio. The physicochemical characteristics of potential pharmaceuticals were evaluated using the SwissADME database. Finally, the molecular dynamics (MD) simulation was performed to validate the stability and dynamic behavior of drug-protein interactions. +Results +Based on the findings from gene expression profiling, Integrin Alpha-X (ITGAX, CD11c) has been identified as a candidate protein that is significantly upregulated in individuals afflicted with skin warts. Integrin Alpha-X plays a crucial role in mediating intercellular interactions during inflammatory processes and notably enhances the adhesion and chemotactic activity of monocytes. Through molecular docking, MD, and physicochemical analyses, it has been demonstrated that dihydroergotamine effectively inhibits the ITGAX protein, suggesting its potential as a therapeutic agent for the management of skin warts. +Conclusion +Dihydroergotamine can be repurposed as a potential drug in the treatment of skin warts by targeting Integrin Alpha-X protein.}, + author = {Kashani, Navid and Sabbaghian, Amir and Ahmadi, Khadijeh and Aalikhani, Mahdi}, + doi = {10.1016/j.jgeb.2025.100485}, + issn = {1687-157X}, + journal = {Journal of Genetic Engineering and Biotechnology}, + keywords = {{\textgreater}UseGalaxy.eu, Gene expression analysis, HPV, Molecular docking, RNA-sequencing, Skin wart}, + language = {eng}, + month = {June}, + number = {2}, + pages = {100485}, + title = {\textit{{In} silico} drug repurposing for potential {HPV}-induced skin wart treatment − {A} comparative transcriptome analysis}, + url = {https://www.sciencedirect.com/science/article/pii/S1687157X25000290}, + urldate = {2025-05-29}, + volume = {23}, + year = {2025} +} + @article{katsanos_gene_2021, + abstract = {The epidermis of Caenorhabditis elegans is an essential tissue for survival because it contributes to the formation of the cuticle barrier as well as facilitating developmental progression and animal growth. Most of the epidermis consists of the hyp7 hypodermal syncytium, the nuclei of which are largely generated by the seam cells, which exhibit stem cell-like behaviour during development. How seam cell progenitors differ transcriptionally from the differentiated hypodermis is poorly understood. Here, we introduce Targeted DamID (TaDa) in C. elegans as a method for identifying genes expressed within a tissue of interest without cell isolation. We show that TaDa signal enrichment profiles can be used to identify genes transcribed in the epidermis and use this method to resolve differences in gene expression between the seam cells and the hypodermis. Finally, we predict and functionally validate new transcription and chromatin factors acting in seam cell development. These findings provide insights into cell type-specific gene expression profiles likely associated with epidermal cell fate patterning.}, author = {Katsanos, Dimitris and Ferrando-Marco, Mar and Razzaq, Iqrah and Aughey, Gabriel and Southall, Tony D. and Barkoulas, Michalis}, doi = {10.1242/dev.199452}, + issn = {0950-1991}, + journal = {Development}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {September}, note = {Publisher: The Company of Biologists}, number = {17}, + pages = {dev199452}, title = {Gene expression profiling of epidermal cell types in {C}. elegans using {Targeted} {DamID}}, url = {https://doi.org/10.1242/dev.199452}, volume = {148}, @@ -6944,13 +11356,17 @@ @article{katsanos_gene_2021 } @article{katsanos_targeted_2022, + abstract = {Transcription factors are key players in gene networks controlling cell fate specification during development. In multicellular organisms, they display complex patterns of expression and binding to their targets, hence, tissue specificity is required in the characterization of transcription factor-target interactions. We introduce here targeted DamID (TaDa) as a method for tissue-specific transcription factor target identification in intact \textit{Caenorhabditis elegans} animals. We use TaDa to recover targets in the epidermis for two factors, the HES1 homolog LIN-22, and the NR5A1/2 nuclear hormone receptor NHR-25. We demonstrate a direct link between LIN-22 and the Wnt signaling pathway through repression of the Frizzled receptor \textit{lin-17}. We report a direct role for NHR-25 in promoting cell differentiation via repressing the expression of stem cell-promoting GATA factors. Our results expand our understanding of the epidermal gene network and highlight the potential of TaDa to dissect the architecture of tissue-specific gene regulatory networks.}, author = {Katsanos, Dimitris and Barkoulas, Michalis}, doi = {10.1126/sciadv.abk3141}, + issn = {2375-2548}, journal = {Science Advances}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Caenorhabditis elegans, Caenorhabditis elegans Proteins}, + language = {eng}, month = {February}, note = {Publisher: American Association for the Advancement of Science (AAAS)}, number = {5}, + pages = {eabk3141}, title = {Targeted {DamID} in {C}. elegans reveals a direct role for {LIN}-22 and {NHR}-25 in antagonizing the epidermal stem cell fate}, url = {https://doi.org/10.1126/sciadv.abk3141}, volume = {8}, @@ -6958,9 +11374,13 @@ @article{katsanos_targeted_2022 } @article{kavas_genome-wide_2021, + abstract = {Plant-specific BURP domain-containing proteins have an essential role in the plant's development and stress responses. Although BURP domain-containing proteins have been identified in several plant species, genome-wide analysis of the BURP gene family has not been investigated in the common bean. In the present study, we identified 11 BURP family members in the common bean (\textit{Phaseolus vulgaris}) genome with a comprehensive in silico analysis. Pairwise alignment and phylogenetic analyses grouped \textit{PvBURP} members into four subfamilies [RD-22 like (3), PG1β-like (4), BNM2-like (3), and USP-like (1)] according to their amino acid motifs, protein domains and intron-exon structure. The physical and biochemical characteristics of amino acids, motif and intron-exon structure, and \textit{cis}-regulatory elements of BURPs members were determined. Promoter regions of BURP members included stress, light, and hormone response-related cis-elements. Therefore, expression profiles of \textit{PvBURP} genes were identified with in silico tools and qRT-PCR analyses under stress (salt and drought) and hormone treatment (ABA, IAA) in the current study. While significant activity changes were not observed in BURP genes in RNA-seq data sets related to salt stress, it was determined that some BURP genes were expressed differently in those with drought stress. We identified 12 different miRNA, including miRNA395, miRNA156, miRNA169, miRNA171, miRNA319, and miRNA390, targeting the nine \textit{PvBURP} genes using two different in silico tools based on perfect or near-perfect complementarity to their targets. Here we present the first study to identify and characterize the \textit{BURP} genes in common bean using whole-genome analysis, and the findings may serve as a reference for future functional research in common bean.{\textless}h4{\textgreater}Supplementary information{\textless}/h4{\textgreater}The online version contains supplementary material available at 10.1007/s12298-021-01052-9.}, author = {Kavas, Musa and Yıldırım, Kubilay and Seçgin, Zafer and Abdulla, Mohamed Farah and Gökdemir, Gökhan}, doi = {10.1007/s12298-021-01052-9}, + issn = {0971-5894}, + journal = {Physiol Mol Biol Plants}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {September}, note = {Publisher: Springer Science and Business Media LLC}, number = {9}, @@ -7008,7 +11428,7 @@ @article{khan_comparative_2023 doi = {10.1038/s41598-023-28665-2}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, Molecular biology, Plant sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Brassica, Molecular biology, Plant sciences, Seeds}, language = {en}, month = {March}, note = {Number: 1 @@ -7022,6 +11442,23 @@ @article{khan_comparative_2023 year = {2023} } +@article{khan_sorafenib_2024, + abstract = {Chemotherapeutics used in cancer therapy are often linked to muscle wasting or cachexia. Insights into the molecular basis of chemotherapy-induced cachexia is essential to improve treatment strategies. Here, we demonstrated that Sorafenib-tyrosine kinase inhibitor (TKI) class of chemotherapeutic agents-induced cachexia. System-wide analyses revealed that Sorafenib alters the global transcriptional program and proteostasis in muscle cells. Mechanistically, Sorafenib treatment reduced active epigenetic mark H3K4 methylation on distinct muscle-specific genes by impeding chromatin association of SET1A-catalytic component of the SET1/MLL histone methyltransferase complex. This mechanism favored transcriptional disorientation that led to disrupted sarcomere assembly, calcium homeostasis and mitochondrial respiration. Consequently, the contractile ability of muscle cells was severely compromised. Interestingly, the other prominent TKIs Nilotinib and Imatinib did not exert similar effects on muscle cell physiology. Collectively, we identified an unanticipated transcriptional mechanism underlying Sorafenib-induced cachexia. Our findings hold the potential to strategize therapy regimens to minimize chemotherapy-induced cachexia.}, + author = {Khan, Bushra and Lanzuolo, Chiara and Rosti, Valentina and Santarelli, Philina and Pich, Andreas and Kraft, Theresia and Amrute-Nayak, Mamta and Nayak, Arnab}, + doi = {10.1016/j.isci.2024.110913}, + issn = {2589-0042}, + journal = {iScience}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {October}, + number = {10}, + pages = {110913}, + title = {Sorafenib induces cachexia by impeding transcriptional signaling of the {SET1}/{MLL} complex on muscle-specific genes}, + url = {http://europepmc.org/abstract/MED/39386761}, + volume = {27}, + year = {2024} +} + @article{khine_comparative_2023, abstract = {In this study, genomic and plasmid characteristics of Escherichia coli were determined with the aim of deducing how mcr genes may have spread on a colistin withdrawn pig farm. Whole genome hybrid sequencing was applied to six mcr-positive E. coli (MCRPE) strains isolated from pigs, a farmworker and wastewater collected between 2017 and 2019. Among these, mcr-1.1 genes were identified on IncI2 plasmids from a pig and wastewater, and on IncX4 from the human isolate, whereas mcr-3 genes were found on plasmids IncFII and IncHI2 in two porcine strains. The MCRPE isolates exhibited genotypic and phenotypic multidrug resistance (MDR) traits as well as heavy metal and antiseptic resistance genes. The mcr-1.1-IncI2 and IncX4 plasmids carried only colistin resistance genes. Whereas, the mcr-3.5-IncHI2 plasmid presented MDR region, with several mobile genetic elements. Despite the MCRPE strains belonged to different E. coli lineages, mcr-carrying plasmids with high similarities were found in isolates from pigs and wastewater recovered in different years. This study highlighted that several factors, including the resistomic profile of the host bacteria, co-selection via adjunct antibiotic resistance genes, antiseptics, and/or disinfectants, and plasmid-host fitness adaptation may encourage the maintenance of plasmids carrying mcr genes in E. coli.}, author = {Khine, Nwai Oo and Wongsurawat, Thidathip and Jenjaroenpun, Piroon and Hampson, David J. and Prapasarakul, Nuvee}, @@ -7029,7 +11466,7 @@ @article{khine_comparative_2023 doi = {10.1038/s41598-023-32406-w}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, Environmental sciences, Evolution, Genetics, Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Environmental sciences, Escherichia coli, Escherichia coli Proteins, Evolution, Genetics, Microbiology}, language = {en}, month = {March}, note = {Number: 1 @@ -7043,6 +11480,24 @@ @article{khine_comparative_2023 year = {2023} } +@article{khine_genetic_2024, + abstract = {IntroductionCarbapenem-resistant Enterobacterales (CRE), particularly carbapenemase-producing Escherichia coli and Klebsiella pneumoniae, pose a significant global health challenge due to their resistance to last-resort antibiotics. This study investigates the genetic characteristics and clonal relationships of CRE isolated from canine and human clinical samples in Bangkok to understand potential interspecies transmission.MethodsFifty-two CRE isolates were collected from 477 clinical samples from dogs and humans at Chulalongkorn University between 2017–2021. Bacterial species were identified using MALDI-TOF, and antimicrobial resistance was confirmed through broth microdilution testing. Genetic analyses included plasmid replicon typing, multilocus sequence typing (MLST), whole genome sequencing (WGS), and pulsed-field gel electrophoresis (PFGE) to assess resistance genes and clonal relatedness.ResultsCRE isolates from both species exhibited genetic variability with high ARG counts, particularly in human isolates. MLST identified ST410 in most E. coli isolates from both dogs and humans, and IncFIA/IncFIB plasmids were predominant among blaNDM-positive isolates. PFGE patterns and SNP analysis showed no clonal relationship between canine and human isolates, suggesting independent acquisition pathways for CRE in the two hosts.DiscussionThe study highlights the absence of direct clonal transmission between canine and human isolates but reveals overlapping sequence types and plasmid types. The findings underscore the potential for interspecies transmission under certain conditions, emphasizing the importance of a One Health approach for monitoring CRE in both human and animal populations.}, + author = {Khine, Nwai Oo and Shah, Asad Ali and Chatsuwan, Tanittha and Yindee, Jitrapa and Supimon, Natthapong and Saenkankam, Imporn and Hampson, David John and Prapasarakul, Nuvee}, + doi = {10.3389/fvets.2024.1464934}, + issn = {2297-1769}, + journal = {Frontiers in Veterinary Science}, + keywords = {{\textgreater}UseGalaxy.eu, Escherichia coli, Klebsiella pneumoniae, carbapenemase-producing Enterobacteriaceae, clonal relatedness, genetic characterization}, + language = {English}, + month = {November}, + note = {Publisher: Frontiers}, + pages = {1464934}, + title = {Genetic characterization and clonal analysis of carbapenemase-producing {Escherichia} coli and {Klebsiella} pneumoniae from canine and human origins}, + url = {https://www.frontiersin.org/journals/veterinary-science/articles/10.3389/fvets.2024.1464934/full}, + urldate = {2025-09-03}, + volume = {11}, + year = {2024} +} + @article{kifle_shotgun_2024, abstract = {Antibiotic resistance is a worldwide problem that imposes a devastating effect on developing countries and requires immediate interventions. Initially, most of the antibiotic drugs were identified by culturing soil microbes. However, this method is prone to discovering the same antibiotics repeatedly. The present study employed a shotgun metagenomics approach to investigate the taxonomic diversity, functional potential, and biosynthetic capacity of microbiomes from two natural agricultural farmlands located in Bekeka and Welmera Choke Kebelle in Ethiopia for the first time. Analysis of the small subunit rRNA revealed bacterial domain accounting for 83.33\% and 87.24\% in the two selected natural farmlands. Additionally, the analysis showed the dominance of Proteobacteria representing 27.27\% and 28.79\% followed by Actinobacteria making up 12.73\% and 13.64\% of the phyla composition. Furthermore, the analysis revealed the presence of unassigned bacteria in the studied samples. The metagenome functional analysis showed 176,961 and 104, 636 number of protein-coding sequences (pCDS) from the two samples found a match with 172,655 and 102, 275 numbers of InterPro entries, respectively. The Genome ontology annotation suggests the presence of 5517 and 3293 pCDS assigned to the “biosynthesis process”. Numerous Kyoto Encyclopedia of Genes and Genomes modules (KEGG modules) involved in the biosynthesis of terpenoids and polyketides were identified. Furthermore, both known and novel Biosynthetic gene clusters, responsible for the production of secondary metabolites, such as polyketide synthases, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides (Ripp), and Terpene, were discovered. Generally, from the results it can be concluded that the microbiomes in the selected sampling sites have a hidden functional potential for the biosynthesis of secondary metabolites. Overall, this study can serve as a strong preliminary step in the long journey of bringing new antibiotics to the market.}, author = {Kifle, Bezayit Amare and Sime, Amsale Melkamu and Gemeda, Mesfin Tafesse and Woldesemayat, Adugna Abdi}, @@ -7097,6 +11552,40 @@ @article{kim_complete_2022-1 year = {2022} } +@article{kim_dbc1_2022, + abstract = {Histone modification is a key epigenetic mechanism for regulation of chromatin dynamics and gene expression. Deleted in breast cancer 1 (DBC1) has been shown to act as a negative regulator of epigenetic modifiers and as a co-activator for nuclear receptors and other transcription factors. However, little is known about the role of DBC1 in the regulation of histone modifications and chromatin landscapes. Here, we analyzed genome-wide profiles of active enhancer and promoter marks in colorectal cancer cells and report DBC1 as a critical positive regulator of histone epigenetic writers KMT2D (H3K4 methyltransferase) and p300 (histone acetyltransferase). DBC1 is required for establishing the landscape of active enhancers, for genome-wide chromatin binding and enhancer recruitment of KMT2D and p300, and for gene activation involved in colorectal cancer progression. DBC1 interacts directly with KMT2D and p300, and enhances KMT2D-mediated histone H3K4 methylation (H3K4me1/2/3) and p300-mediated H3 acetylation. Importantly, DBC1 contributes to super-enhancer formation and function by facilitating the recruitment of KMT2D and p300 and by enhancing their functional interaction and cooperative cross-talk. Our results highlight the critical role of DBC1 as a key positive regulator of KMT2D and p300, and provide insights into regulatory mechanisms underlying the interplay between the enhancer epigenomic writers in enhancer activation.}, + author = {Kim, Hwa Jin and Moon, Sue Jin and Hong, Sanghoon and Won, Hong-Hee and Kim, Jeong Hoon}, + doi = {10.1093/nar/gkac585}, + issn = {0305-1048}, + journal = {Nucleic Acids Res}, + keywords = {{\textgreater}UseGalaxy.eu, Colorectal Neoplasms, Histones}, + language = {eng}, + month = {August}, + number = {14}, + pages = {7873--7888}, + title = {{DBC1} is a key positive regulator of enhancer epigenomic writers {KMT2D} and p300}, + url = {http://europepmc.org/abstract/MED/35801925}, + volume = {50}, + year = {2022} +} + +@article{kim_nucleotide-level_2025, + abstract = {The commonly used arabinose- and rhamnose-inducible Escherichia coli promoters, PBAD and PRha, exhibit tight regulation through activation via their respective transcription factors, AraC and RhaS, alongside the cyclic AMP receptor protein. The mechanisms of these promoters have been characterized on a parts level, but nucleotide-level analysis has yet to be elucidated. Therefore, we describe here a massively parallel reporter assay that maps regulatory sites at the nucleotide level. The relative importance of nucleotides in each binding site is revealed, including loci not included in previous annotations. For PBAD, we confirm known sites and reveal novel binding sites involved in modulating gene expression. In PRha, we refine the length and sequence specificity of rhaI half-sites, updating previous annotations and providing nucleotide level insights into RhaS-mediated regulation. Mutations that lead to increased promoter strength, wider dynamic range, and altered basal expression are identified for both promoters. Engineered versions of PBAD and PRha promoters based on this data show improvements in dynamic range alongside a seven- and three-fold increase in promoter strength, respectively, with a slight increase in basal expression for the PBAD promoters and no significant increase for PRha. This work expands the genetic parts “toolkit” and increases the understanding of these important commonly used promoters.}, + author = {Kim, Nancy M and Peng, Danqia and Sandoval, Nicholas R}, + doi = {10.1093/nar/gkaf224}, + issn = {1362-4962}, + journal = {Nucleic Acids Research}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Arabinose, Escherichia coli, Gene Expression Regulation, Bacterial, Promoter Regions, Genetic, Rhamnose}, + month = {April}, + number = {7}, + pages = {gkaf224}, + title = {Nucleotide-level characterization and improvement of l-arabinose- and l-rhamnose-inducible systems in {E}. coli using a high-throughput approach}, + url = {https://doi.org/10.1093/nar/gkaf224}, + urldate = {2025-04-13}, + volume = {53}, + year = {2025} +} + @article{kimura_overexpression_2021, abstract = {An amino acid exchange (P209L) in the HSPB8 binding site of the human co-chaperone BAG3 gives rise to severe childhood cardiomyopathy. To phenocopy the disease in mice and gain insight into its mechanisms, we generated humanized transgenic mouse models. Expression of human BAG3P209L-eGFP in mice caused Z-disc disintegration and formation of protein aggregates. This was accompanied by massive fibrosis resulting in early-onset restrictive cardiomyopathy with increased mortality as observed in patients. RNA-Seq and proteomics revealed changes in the protein quality control system and increased autophagy in hearts from hBAG3P209L-eGFP mice. The mutation renders hBAG3P209L less soluble in vivo and induces protein aggregation, but does not abrogate hBAG3 binding properties. In conclusion, we report a mouse model mimicking the human disease. Our data suggest that the disease mechanism is due to accumulation of hBAG3P209L and mouse Bag3, causing sequestering of components of the protein quality control system and autophagy machinery leading to sarcomere disruption.}, author = {Kimura, Kenichi and Ooms, Astrid and Graf-Riesen, Kathrin and Kuppusamy, Maithreyan and Unger, Andreas and Schuld, Julia and Daerr, Jan and Lother, Achim and Geisen, Caroline and Hein, Lutz and Takahashi, Satoru and Li, Guang and Röll, Wilhelm and Bloch, Wilhelm and van der Ven, Peter F. M. and Linke, Wolfgang A. and Wu, Sean M. and Huesgen, Pitter F. and Höhfeld, Jörg and Fürst, Dieter O. and Fleischmann, Bernd K. and Hesse, Michael}, @@ -7119,9 +11608,13 @@ @article{kimura_overexpression_2021 } @article{king_resistome_2021, + abstract = {{\textless}h4{\textgreater}Objectives{\textless}/h4{\textgreater}Klebsiella michiganensis is an emerging pathogen implicated in nosocomial infections. Here we report on the resistome, virulome and mobilome of a carbapenemase-producing K. michiganensis isolate from urban hospital effluent in Pietermaritzburg, KwaZulu-Natal, South Africa. Klebsiella sp. isolate KP124 was originally isolated from the final effluent of an urban tertiary hospital in Pietermaritzburg, KwaZulu-Natal.{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}Following phenotypic characterisation and antibiotic susceptibility testing, the genome of carbapenemase-producing isolate KP124 was sequenced using an Illumina MiSeq platform, de novo assembled and analysed using established bioinformatics tools.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}The draft genome of strain KP124 was 6 544 586 bp in length, comprising 203 contigs {\textgreater}200 bp. Following confirmation of isolate KP124 as K. michiganensis using reference genomes, the bla$_{\textrm{OXA-181}}$ carbapenemase gene as well as 11 additional genes encoding resistance against β-lactams, aminoglycosides, fluoroquinolones and sulfonamides were detected. Virulence factors enabling iron acquisition and cell adherence, capsule locus type and plasmid replicon types were identified.{\textless}h4{\textgreater}Conclusion{\textless}/h4{\textgreater}This study represents the first report of an OXA-181 carbapenemase-producing K. michiganensis isolate from hospital effluent in South Africa. The presence of such a strain in the environment owing to the absence of hospital effluent treatment presents a potential risk to informal communities that may use contaminated surface water domestically.}, author = {King, T. L. and Schmidt, S. and Thakur, S. and Fedorka-Cray, P. and Keelara, S. and Harden, L. and Essack, S. Y.}, doi = {10.1016/j.jgar.2021.01.004}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {2213-7165}, + journal = {J Glob Antimicrob Resist}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Klebsiella}, + language = {eng}, month = {March}, note = {Publisher: Elsevier BV}, pages = {321--324}, @@ -7131,6 +11624,23 @@ @article{king_resistome_2021 year = {2021} } +@article{kiser_comparative_2025, + abstract = {Mantis shrimp (order Stomatopoda) are known for their aggressive nature and powerful raptorial appendages. Among them, the Philippine mantis shrimp Gonodactylaceus falcatus is suspected to comprise a cryptic species complex with 6 primary synonyms. This study aims to explore this complex focusing on G. falcatus ‘sensu stricto’ and three of its primary synonyms: G. insularis, G. mutatus, and G. siamensis. Complete mitochondrial genomes were fully assembled using Illumina sequencing. The AT-rich studied mitogenomes ranged from 15,894 to 16,267 bp in length. Each contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and one control region. Mitochondrial synteny is identical to previously reported stomatopod mitogenomes, except Gonodactylus smithii. In all studied species, 21 of the 22 tRNA genes were predicted to have the typical ‘cloverleaf’ structure: trnS1 either lacked a D-arm or both a D-arm and D-loop. All mitochondrial protein-coding genes experience purifying selection, noting a Ka/Ks value for the G. insularis nad4l gene was not calculated due to the absence of non-synonymous substitutions. AT-rich di- and tri-nucleotide microsatellites were found in all studied control regions while short tandem repeats were detected in all except G. insularis. Phylomitogenomic analysis supports the monophyly of the order Stomatopoda but not the superfamilies Gonodactyloidea, Lysiosquilloidea, and Squilloidea. Furthermore, phylogenomic placement and genetic distances supported the species status of G. insularis and G. mutatus but not G. siamensis. Our study provides genomic resources to continue improving knowledge of cryptic species complexes in the order Stomatopoda.}, + author = {Kiser, Helen and Hwang, Hee-seung and Jung, Jongwoo and Baeza, J. Antonio}, + doi = {10.1016/j.genrep.2025.102248}, + issn = {2452-0144}, + journal = {Gene Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Cryptic species, Mitochondrial genome, Phylogenetics, Shrimp, Stomatopoda}, + month = {September}, + pages = {102248}, + shorttitle = {Comparative mitochondrial and phylomitogenomic analyses support the existence of a cryptic species complex in \textit{{Gonodactylaceus} falcatus} ({Stomatopoda}}, + title = {Comparative mitochondrial and phylomitogenomic analyses support the existence of a cryptic species complex in \textit{{Gonodactylaceus} falcatus} ({Stomatopoda}: {Gonodactyloidea})}, + url = {https://www.sciencedirect.com/science/article/pii/S2452014425001219}, + urldate = {2025-05-28}, + volume = {40}, + year = {2025} +} + @article{klaas_olfactomedin-4_2022, abstract = {Olfactomedin-4 (OLFM4) is an olfactomedin-domain-containing glycoprotein, which regulates cell adhesion, proliferation, gastrointestinal inflammation, innate immunity and cancer metastasis. In the present study we investigated its role in skin regeneration. We found that OLFM4 expression is transiently upregulated in the proliferative phase of cutaneous wound healing in humans as well as in mice. Moreover, a significant increase in OLFM4 expression was detected in the skin of lesional psoriasis, a chronic inflammatory disease characterized by keratinocyte hyperproliferation. In vitro experiments demonstrated that OLFM4 selectively stimulated keratinocyte proliferation and increased both keratinocyte and fibroblast migration. Using proteotranscriptomic pathway analysis we revealed that transcription factors POU5F1/OCT4 and ESR1 acted as hubs for OLFM4-induced signalling in keratinocytes. In vivo experiments utilizing mouse splinted full-thickness cutaneous wound healing model showed that application of recombinant OLFM4 protein can significantly improve wound healing efficacy. Taken together, our results suggest that OLFM4 acts as a transiently upregulated inflammatory signal that promotes wound healing by regulating both dermal and epidermal cell compartments of the skin.}, author = {Klaas, Mariliis and Mäemets-Allas, Kristina and Heinmäe, Elizabeth and Lagus, Heli and Arak, Terje and Eller, Mart and Kingo, Külli and Kankuri, Esko and Jaks, Viljar}, @@ -7149,12 +11659,32 @@ @article{klaas_olfactomedin-4_2022 year = {2022} } +@article{klaas_thrombospondin-4_2021, + abstract = {Thrombospondin-4 (THBS4) is a non-structural extracellular matrix molecule associated with tissue regeneration and a variety of pathological processes characterized by increased cell proliferation and migration. However, the mechanisms of how THBS4 regulates cell behavior as well as the pathways contributing to its effects have remained largely unexplored. In the present study we investigated the role of THBS4 in skin regeneration both \textit{in vitro} and \textit{in vivo}. We found that THBS4 expression was upregulated in the dermal compartment of healing skin wounds in humans as well as in mice. Application of recombinant THBS4 protein promoted cutaneous wound healing in mice and selectively stimulated migration of primary fibroblasts as well as proliferation of keratinocytes \textit{in vitro}. By using a combined proteotranscriptomic pathway analysis approach we discovered that β-catenin acted as a hub for THBS4-dependent cell signaling and likely plays a key role in promoting its downstream effects. Our results suggest that THBS4 is an important contributor to wound healing and its incorporation into novel wound healing therapies may be a promising strategy for treatment of cutaneous wounds.}, + author = {Klaas, Mariliis and Mäemets-Allas, Kristina and Heinmäe, Elizabeth and Lagus, Heli and Cárdenas-León, Claudia Griselda and Arak, Terje and Eller, Mart and Kingo, Külli and Kankuri, Esko and Jaks, Viljar}, + doi = {10.3389/fcell.2021.745637}, + issn = {2296-634X}, + journal = {Frontiers in cell and developmental biology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {745637}, + title = {Thrombospondin-4 {Is} a {Soluble} {Dermal} {Inflammatory} {Signal} {That} {Selectively} {Promotes} {Fibroblast} {Migration} and {Keratinocyte} {Proliferation} for {Skin} {Regeneration} and {Wound} {Healing}}, + url = {http://europepmc.org/abstract/MED/34631719}, + volume = {9}, + year = {2021} +} + @article{klein_pruriception_2021, + abstract = {In humans, intradermal administration of β-alanine (ALA) and bovine adrenal medulla peptide 8-22 (BAM8-22) evokes the sensation of itch. Currently, it is unknown which human dorsal root ganglion (DRG) neurons express the receptors of these pruritogens, MRGPRD and MRGPRX1, respectively, and which cutaneous afferents these pruritogens activate in primate. In situ hybridization studies revealed that MRGPRD and MRGPRX1 are co-expressed in a subpopulation of TRPV1+ human DRG neurons. In electrophysiological recordings in nonhuman primates (\textit{Macaca nemestrina}), subtypes of polymodal C-fiber nociceptors are preferentially activated by ALA and BAM8-22, with significant overlap. When pruritogens ALA, BAM8-22, and histamine, which activate different subclasses of C-fiber afferents, are administered in combination, human volunteers report itch and nociceptive sensations similar to those induced by a single pruritogen. Our results provide evidence for differences in pruriceptive processing between primates and rodents, and do not support the spatial contrast theory of coding of itch and pain.}, author = {Klein, Amanda and Solinski, Hans Jürgen and Malewicz, Nathalie M. and Ieong, Hada Fong-ha and Sypek, Elizabeth I. and Shimada, Steven G. and Hartke, Timothy V. and Wooten, Matthew and Wu, Gang and Dong, Xinzhong and Hoon, Mark A. and LaMotte, Robert H. and Ringkamp, Matthias}, doi = {10.7554/elife.64506}, + issn = {2050-084X}, + journal = {eLife}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {April}, note = {Publisher: eLife Sciences Publications, Ltd}, + pages = {e64506}, title = {Pruriception and neuronal coding in nociceptor subtypes in human and nonhuman primates}, url = {https://doi.org/10.7554/elife.64506}, volume = {10}, @@ -7196,7 +11726,7 @@ @article{kmeli_genome-level_2023 doi = {10.1007/s00344-023-11151-4}, issn = {1435-8107}, journal = {Journal of Plant Growth Regulation}, - keywords = {{\textgreater}UseGalaxy.eu, Comparative genomics, Expression analysis, Ficus carica, Fruit ripening, Gene family, Transcription factor}, + keywords = {{\textgreater}UseGalaxy.eu, Comparative genomics, Drosophila, Expression analysis, Ficus carica, Fruit ripening, Fungal Genes, Gene Transcription, Gene family, Saccharomyces cerevisiae, Transcription factor, Transcription factors}, language = {en}, month = {November}, title = {Genome-{Level} {Investigation} of {WRKY} {Transcription} {Factors} and {Their} {Potential} {Roles} in {Fruit} {Peel} {Ripening} and {Coloration} in the {Common} {Fig} ({Ficus} carica {L}.)}, @@ -7220,6 +11750,21 @@ @article{kmeli_genome-wide_2023 year = {2023} } +@article{knecht_novel_2022, + abstract = {According to the World Health Organization, carbapenem-resistant \textit{Enterobacteriaceae} (CRE) belong to the highest priority group for the development of new antibiotics. Argentina-WHONET data showed that Gram-negative resistance frequencies to imipenem have been increasing since 2010 mostly in two CRE bacteria: \textit{Klebsiella pneumoniae} and \textit{Enterobacter cloacae} Complex (ECC). This scenario is mirrored in our hospital. It is known that \textit{K. pneumoniae} and the ECC coexist in the human body, but little is known about the outcome of these species producing KPC, and colonizing or infecting a patient. We aimed to contribute to the understanding of the rise of the ECC in Argentina, taking as a biological model both a patient colonized with two KPC-producing strains (one \textit{Enterobacter hormaechei} and one \textit{K. pneumoniae}) and \textit{in vitro} competition assays with prevalent KPC-producing ECC (KPC-ECC) versus KPC-producing \textit{K. pneumoniae} (KPC-Kp) high-risk clones from our institution. A KPC-producing \textit{E. hormaechei} and later a KPC-Kp strain that colonized a patient shared an identical novel conjugative IncM1 plasmid harboring \textit{bla} $_{\textrm{KPC-2}}$. In addition, a total of 19 KPC-ECC and 58 KPC-Kp strains isolated from nosocomial infections revealed that high-risk clones KPC-ECC ST66 and ST78 as well as KPC-Kp ST11 and ST258 were prevalent and selected for competition assays. The competition assays with KCP-ECC ST45, ST66, and ST78 versus KPC-Kp ST11, ST18, and ST258 strains analyzed here showed no statistically significant difference. These assays evidenced that high-risk clones of KPC-ECC and KPC-Kp can coexist in the same hospital environment including the same patient, which explains from an ecological point of view that both species can exchange and share plasmids. These findings offer hints to explain the worldwide rise of KPC-ECC strains based on the ability of some pandemic clones to compete and occupy a certain niche. Taken together, the presence of the same new plasmid and the fitness results that showed that both strains can coexist within the same patient suggest that horizontal genetic transfer of \textit{bla} $_{\textrm{KPC-2}}$ within the patient cannot be ruled out. These findings highlight the constant interaction that these two species can keep in the hospital environment, which, in turn, can be related to the spread of KPC.}, + author = {Knecht, Camila A and García Allende, Natalia and Álvarez, Verónica E and Prack McCormick, Barbara and Massó, Mariana G and Piekar, María and Campos, Josefina and Fox, Bárbara and Camicia, Gabriela and Gambino, Anahí S and Leguina, Ana Carolina Del Valle and Donis, Nicolás and Fernández-Canigia, Liliana and Quiroga, María Paula and Centrón, Daniela}, + doi = {10.3389/fcimb.2022.951049}, + issn = {2235-2988}, + journal = {Frontiers in cellular and infection microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Carbapenem-Resistant Enterobacteriaceae, Cross Infection}, + language = {eng}, + pages = {951049}, + title = {Novel insights related to the rise of {KPC}-producing {Enterobacter} cloacae complex strains within the nosocomial niche}, + url = {http://europepmc.org/abstract/MED/36439236}, + volume = {12}, + year = {2022} +} + @article{koch_tigecycline_2023, abstract = {Despite recent advances in locoregional, systemic, and novel checkpoint inhibitor treatment, hepatocellular carcinoma (HCC) is still associated with poor prognosis. The feasibility of potentially curative liver resection (LR) and transplantation (LT) is limited by the underlying liver disease and a shortage of organ donors. Especially after LR, high recurrence rates present a problem and circulating tumor cells are a major cause of extrahepatic recurrence. Tigecycline, a commonly used glycylcycline antibiotic, has been shown to have antitumorigenic effects and could be used as a perioperative and adjuvant therapeutic strategy to target circulating tumor cells. We aimed to investigate the effect of tigecycline on HCC cell lines and its mechanisms of action.}, author = {Koch, Dominik T. and Yu, Haochen and Beirith, Iris and Schirren, Malte and Drefs, Moritz and Liu, Yunfei and Knoblauch, Mathilda and Koliogiannis, Dionysios and Sheng, Weiwei and De Toni, Enrico N. and Bazhin, Alexandr V. and Renz, Bernhard W. and Guba, Markus O. and Werner, Jens and Ilmer, Matthias}, @@ -7244,7 +11789,7 @@ @article{kocsmar_proteome_2023 doi = {10.1007/s00018-023-04754-3}, issn = {1420-9071}, journal = {Cellular and Molecular Life Sciences}, - keywords = {{\textgreater}UseGalaxy.eu, Autopsy, Degradation, Proteomics}, + keywords = {{\textgreater}UseGalaxy.eu, Autopsy, Degradation, Postmortem Changes, Proteome, Proteomics}, language = {en}, month = {April}, number = {5}, @@ -7256,11 +11801,30 @@ @article{kocsmar_proteome_2023 year = {2023} } +@article{koeberle_silybin_2025, + abstract = {\textbf{Rationale:} \textit{Silybum marianum} is used to protect against degenerative liver damage. The molecular mechanisms of its bioactive component, silybin, remained enigmatic, although membrane-stabilizing properties, modulation of membrane protein function, and metabolic regulation have been discussed for decades. \textbf{Methods}: Experiments were performed with hepatocyte cell lines and primary monocytes \textit{in vitro} under both basal and stressed conditions, and in mice \textit{in vivo}. Quantitative lipidomics was used to detect changes in phospholipids and triglycerides. Key findings were confirmed by Western blotting, quantitative PCR, microscopy, enzyme activity assays, metabolic flux studies, and functional relationships were investigated using selective inhibitors. \textbf{Results}: We show that specifically the stereoisomer silybin A decreases triglyceride levels and lipid droplet content, while enriching major phospholipid classes and maintaining a homeostatic phospholipid composition in human hepatocytes \textit{in vitro} and in mouse liver \textit{in vivo} under normal and pre-disease conditions. Conversely, in cell-based disease models of lipid overload and lipotoxic stress, silybin treatment primarily depletes triglycerides. Mechanistically, silymarin/silybin suppresses phospholipid-degrading enzymes, induces phospholipid biosynthesis to varying degrees depending on the conditions, and down-regulates triglyceride remodeling/biosynthesis, while inducing complex changes in sterol and fatty acid metabolism. Structure-activity relationship studies highlight the importance of the 1,4-benzodioxane ring configuration of silybin A in triglyceride reduction and the saturated 2,3-bond of the flavanonol moiety in phospholipid accumulation. Enrichment of hepatic phospholipids and intracellular membrane expansion are associated with a heightened biotransformation capacity. \textbf{Conclusion}: Our study deciphers the structural features of silybin contributing to hepatic lipid remodeling and suggests that silymarin/silybin protects the liver in individuals with mild metabolic dysregulation, involving a lipid class switch from triglycerides to phospholipids, whereas it may be less effective in disease states associated with severe metabolic dysregulation.}, + author = {Koeberle, Solveigh C and Thürmer, Maria and Su, Fengting and Werner, Markus and Grander, Julia and Hofer, Laura and Gollowitzer, André and Xuan, Loc Le and Benscheid, Felix J and Bonyadi Rad, Ehsan and Zarrelli, Armando and Di Fabio, Giovanni and Werz, Oliver and Romanucci, Valeria and Lupp, Amelie and Koeberle, Andreas}, + doi = {10.7150/thno.99562}, + issn = {1838-7640}, + journal = {Theranostics}, + keywords = {{\textgreater}UseGalaxy.eu, Lipid Metabolism, Phospholipids, Silybin, Silybum marianum, Triglycerides}, + language = {eng}, + number = {5}, + pages = {2006--2034}, + title = {Silybin {A} from \textit{{Silybum} marianum} reprograms lipid metabolism to induce a cell fate-dependent class switch from triglycerides to phospholipids}, + url = {http://europepmc.org/abstract/MED/39897559}, + volume = {15}, + year = {2025} +} + @article{koeppel_sars-cov-2_2022, + abstract = {Reverse-zoonotic infections of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) from humans to wildlife species internationally raise concern over the emergence of new variants in animals. A better understanding of the transmission dynamics and pathogenesis in susceptible species will mitigate the risk to humans and wildlife occurring in Africa. Here we report infection of an exotic puma (July 2020) and three African lions (July 2021) in the same private zoo in Johannesburg, South Africa. One Health genomic surveillance identified transmission of a Delta variant from a zookeeper to the three lions, similar to those circulating in humans in South Africa. One lion developed pneumonia while the other cases had mild infection. Both the puma and lions remained positive for SARS-CoV-2 RNA for up to 7 weeks.}, author = {Koeppel, Katja Natalie and Mendes, Adriano and Strydom, Amy and Rotherham, Lia and Mulumba, Misheck and Venter, Marietjie}, doi = {10.3390/v14010120}, + issn = {1999-4915}, journal = {Viruses}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, SARS-CoV-2, reverse zoonosis, wildlife}, + language = {eng}, month = {January}, note = {Publisher: MDPI AG}, number = {1}, @@ -7311,13 +11875,16 @@ @article{kojima_cytochrome_2024 doi = {10.1111/cas.16289}, issn = {1349-7006}, journal = {Cancer Science}, - keywords = {{\textgreater}UseGalaxy.eu, DNA damage, austocystin D, cytotoxicity, gene expression, knockout screening}, + keywords = {{\textgreater}UseGalaxy.eu, Cytochrome P-450 CYP2J2, Cytochrome P-450 Enzyme System, DNA Damage, DNA damage, austocystin D, cytotoxicity, gene expression, knockout screening}, language = {en}, month = {July}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/cas.16289}, + number = {9}, + pages = {3054--3066}, title = {Cytochrome {P450} {2J2} is required for the natural compound austocystin {D} to elicit cancer cell toxicity}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cas.16289}, urldate = {2024-07-19}, + volume = {115}, year = {2024} } @@ -7342,6 +11909,74 @@ @article{kolosov_malpighian_2019 year = {2019} } +@article{komine_draft_2022, + abstract = {Mycobacterium marinum is a ubiquitous nontuberculous mycobacterium that causes infections in various animals. Here, we report the annotated draft genome sequences of 25 strains isolated from vertebrates, invertebrates, and environmental components in aquaria and an aquaculture farm in Japan, sampled between 2015 and 2020.}, + author = {Komine, Takeshi and Fukano, Hanako and Inohana, Mari and Hoshino, Yoshihiko and Kurata, Osamu and Wada, Shinpei}, + doi = {10.1128/mra.00851-22}, + issn = {2576-098X}, + journal = {Microbiol Resour Announc}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {October}, + number = {10}, + pages = {e0085122}, + title = {Draft {Genome} {Sequences} of 25 {Mycobacterium} marinum {Strains} {Isolated} from {Animals} and {Environmental} {Components} in {Aquaria} and an {Aquaculture} {Farm}}, + url = {http://europepmc.org/abstract/MED/36154152}, + volume = {11}, + year = {2022} +} + +@article{kongsomboonchoke_rapid_2025, + abstract = {Urinary tract infections are commonly caused by uropathogenic Escherichia coli (UPEC). Due to the emergence of multidrug-resistant UPEC, rendering antibiotic treatment ineffective, phage combination-based therapy has been proposed as a potential alternative. Here, we present a formulation of a genetically diverse phage-derived cocktail that is rapidly customized for UPEC using E. coli UTI89 as a model strain. Through our rapid selection and combination of four phages against UPEC strain UTI89 (SR01, SR02, SR04, and Zappy) from our library, the combination of two lytic phages, SR02 and SR04, exhibits the strongest suppression of bacterial growth for at least 16 h, with no emergence of phage resistance observed in vitro. Phage SR02 undergoes subcellular activity for 25 min, producing approximately 106 progeny particles per cell, while SR04 completes its replication cycle in 20 min, generating around 564 progeny particles per cell. These two novel phages are genetically diverse, and their cocktail exhibited potent suppression of bacterial growth, independent of multiplicities of infection (MOIs), significantly reducing the viable bacterial counts after treatment in vitro. The phage cocktail has low immunogenicity and does not induce any proinflammatory gene responses in human bladder uroepithelial cells. Moreover, the cocktail effectively eradicates the invading UPEC strain UTI89 in the uroepithelial cells at a comparable level to that of phage SR04 alone, likely releasing some immunostimulatory agents that, in turn, trigger upregulation of MIP-3 and IL-8 genes. Altogether, this study offers an alternative pipeline for rapidly formulating genetically diverse phage-derived cocktails, which is specifically customized for targeted bacteria.}, + author = {Kongsomboonchoke, Pattida and Mongkolkarvin, Panupon and Khunti, Patiphan and Vijitphichiankul, Jarukit and Nonejuie, Poochit and Thiennimitr, Parameth and Chaikeeratisak, Vorrapon}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-96561-y}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Bacteriophages, Escherichia coli Infections, Phage Therapy, Phage biology, Urinary Tract Infections, Uropathogenic Escherichia coli}, + language = {en}, + month = {April}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {12832}, + title = {Rapid formulation of a genetically diverse phage cocktail targeting uropathogenic {Escherichia} coli infections using the {UTI89} model}, + url = {https://www.nature.com/articles/s41598-025-96561-y}, + urldate = {2025-05-29}, + volume = {15}, + year = {2025} +} + +@article{konkol_encouraging_2025, + abstract = {The growing demand for reproducible research is based on the expectation that publishing research in this form will enable its reuse and the generation of new knowledge. However, reproducibility alone does not guarantee these benefits. Users still need to make considerable efforts to understand the data and analysis code before they can reuse these components in other contexts. To address this challenge, we introduce the Data-to-Knowledge Package (D2K-Package), a collection of research materials including source code and open FAIR data, virtual labs, web API services, and computational workflows. The D2K-Package's core is the reproducible basis composed of the data and source code on which an analysis is based. This core is designed such that the other components can be derived from it. The main goal of the package is to help researchers generate new knowledge by facilitating the understanding and encouraging the reuse of reproducible research. We demonstrate the applicability of the D2K-Package with a hydrological use case which can be also used for testing, and discuss its seamless integration into the research cycle.}, + author = {Konkol, Markus and Labuce, Astra and Domisch, Sami and Buurman, Merret and Bremerich, Vanessa}, + doi = {10.12688/openreseurope.20221.3}, + issn = {2732-5121}, + journal = {Open research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + pages = {123}, + title = {Encouraging reusability of computational research through {Data}-to-{Knowledge} {Packages} - {A} hydrological use case}, + url = {https://europepmc.org/articles/PMC12334915}, + volume = {5}, + year = {2025} +} + +@article{konkol_encouraging_2025, + abstract = {The growing demand for reproducible research is based on the expectation that publishing research in this form will enable its reuse and the generation of new knowledge. However, reproducibility alone does not guarantee these benefits. Users still need to make considerable efforts to understand the data and analysis code before they can reuse these components in other contexts. To address this challenge, we introduce the Data-to-Knowledge Package (D2K-Package), a collection of research materials including source code and open FAIR data, virtual labs, web API services, and computational workflows. The D2K-Package’s core is the reproducible basis composed of the data and source code on which an analysis is based. This core is designed such that the other components can be derived from it. The main goal of the package is to help researchers generate new knowledge by facilitating the understanding and encouraging the reuse of reproducible research. We demonstrate the applicability of the D2K-Package with a hydrological use case which can be also used for testing, and discuss its seamless integration into the research cycle.}, + author = {Konkol, Markus and Labuce, Astra and Domisch, Sami and Buurman, Merret and Bremerich, Vanessa}, + doi = {10.12688/openreseurope.20221.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {May}, + pages = {123}, + title = {Encouraging reusability of computational research through {Data}-to-{Knowledge} {Packages} - {A} hydrological use case}, + url = {https://open-research-europe.ec.europa.eu/articles/5-123/v1}, + urldate = {2025-05-09}, + volume = {5}, + year = {2025} +} + @phdthesis{konovalovas_molecular_2018, author = {Konovalovas, Aleksandras}, keywords = {+Methods, +UseMain, +UsePublic, {\textgreater}UseGalaxy.eu}, @@ -7398,6 +12033,24 @@ @article{koutras_integrated_2023 year = {2023} } +@article{kouvela_coupling_2025, + abstract = {Redundancy in transfer RNA (tRNA) gene copies across species remains poorly understood and, in many cases, largely unexplored. In Staphylococcus aureus, multiple tRNAGly genes encode isoacceptors involved in protein synthesis and cell wall formation, aminoacylated by a sole glycyl-tRNA synthetase (GlyRS) which is under the transcription regulation of a species-specific glyS T-box riboswitch. The T-box can interact with all tRNAGly isoacceptors to adopt species-specific conformations and affect both pathways. Using CRISPR/Cas9 editing, we ablated a gene copy corresponding to the proteinogenic P1 tRNAGlyGCC. Surprisingly, the growth and the overall translational activity of the edited strain were found unaffected, suggesting functional compensation by the remaining tRNAGly genes. On the other hand, transcriptomics and proteomics analyses combined with functional assays revealed nutrient-dependent stress responses with surprisingly impaired cell wall integrity and increased susceptibility to cell wall-targeting antibiotics. Additionally, the edited strain displayed reduced biofilm formation but retained the ability to invade human cells in vitro. Overall, the present study underscores the critical role of tRNA gene redundancy in the physiology of S. aureus and highlights tRNAs as regulators of metabolic homeostasis in pathogenic bacteria.Staphylococcus aureus has multiple copies of tRNAGly genes involved in either protein production or cell wall formation. Removing one tRNAGly copy, used in translation, via CRISPR/Cas9 didn’t affect growth but weakened the cell wall, making it more susceptible to antibiotics, and reduced biofilm formation. This study reveals how S. aureus can adapt with fewer tRNA genes by sacrificing its ability to infect and resist to antibiotics.}, + author = {Kouvela, Adamantia and Jaramillo Ponce, Jose R and Giarimoglou, Nikoleta and Chicher, Johana and Marzi, Stefano and Stathopoulos, Constantinos and Stamatopoulou, Vassiliki}, + doi = {10.1093/nar/gkaf599}, + issn = {1362-4962}, + journal = {Nucleic Acids Research}, + keywords = {{\textgreater}UseGalaxy.eu, Cell Wall, Staphylococcus aureus}, + language = {eng}, + month = {July}, + number = {13}, + pages = {gkaf599}, + title = {Coupling {tRNAGly} gene redundancy with staphylococcal cell wall integrity, antibiotic susceptibility, and virulence potential}, + url = {https://doi.org/10.1093/nar/gkaf599}, + urldate = {2025-07-30}, + volume = {53}, + year = {2025} +} + @article{kowalski_eplerenone_2021, abstract = {Download figureDownload PowerPoint}, author = {Kowalski, Jessica and Deng, Lisa and Suennen, Chiara and Koca, Duygu and Meral, David and Bode, Christoph and Hein, Lutz and Lother, Achim}, @@ -7435,11 +12088,28 @@ @article{kramer_cyclic_2024 year = {2024} } +@patent{kristen_method_2024, + assignee = {Johannes Gutenberg Universitaet Mainz}, + author = {Kristen, Marco and Helm, Mark}, + keywords = {{\textgreater}UseGalaxy.eu, cell sample, complementary dna, oligonucleotides, trna, trnas}, + language = {en}, + month = {June}, + nationality = {EP}, + number = {EP4386088A1}, + title = {Method for the accurate quantification of non-coding rnas in minute quantities}, + url = {https://patents.google.com/patent/EP4386088A1/en?q=(%22usegalaxy.eu%22+OR+%22European+Galaxy%22)&oq=%22usegalaxy.eu%22+OR+%22European+Galaxy%22}, + urldate = {2025-04-14}, + year = {2024} +} + @article{kruk_integrated_2024, + abstract = {Airway microbiota are known to contribute to lung diseases, such as cystic fibrosis (CF), but their contributions to pathogenesis are still unclear. To improve our understanding of host-microbe interactions, we have developed an integrated analytical and bioinformatic mass spectrometry (MS)-based metaproteomics workflow to analyze clinical bronchoalveolar lavage (BAL) samples from people with airway disease. Proteins from BAL cellular pellets were processed and pooled together in groups categorized by disease status (CF vs. non-CF) and bacterial diversity, based on previously performed small subunit rRNA sequencing data. Proteins from each pooled sample group were digested and subjected to liquid chromatography tandem mass spectrometry (MS/MS). MS/MS spectra were matched to human and bacterial peptide sequences leveraging a bioinformatic workflow using a metagenomics-guided protein sequence database and rigorous evaluation. Label-free quantification revealed differentially abundant human peptides from proteins with known roles in CF, like neutrophil elastase and collagenase, and proteins with lesser-known roles in CF, including apolipoproteins. Differentially abundant bacterial peptides were identified from known CF pathogens (e.g., \textit{Pseudomonas}), as well as other taxa with potentially novel roles in CF. We used this host-microbe peptide panel for targeted parallel-reaction monitoring validation, demonstrating for the first time an MS-based assay effective for quantifying host-microbe protein dynamics within BAL cells from individual CF patients. Our integrated bioinformatic and analytical workflow combining discovery, verification, and validation should prove useful for diverse studies to characterize microbial contributors in airway diseases. Furthermore, we describe a promising preliminary panel of differentially abundant microbe and host peptide sequences for further study as potential markers of host-microbe relationships in CF disease pathogenesis.IMPORTANCEIdentifying microbial pathogenic contributors and dysregulated human responses in airway disease, such as CF, is critical to understanding disease progression and developing more effective treatments. To this end, characterizing the proteins expressed from bacterial microbes and human host cells during disease progression can provide valuable new insights. We describe here a new method to confidently detect and monitor abundance changes of both microbe and host proteins from challenging BAL samples commonly collected from CF patients. Our method uses both state-of-the art mass spectrometry-based instrumentation to detect proteins present in these samples and customized bioinformatic software tools to analyze the data and characterize detected proteins and their association with CF. We demonstrate the use of this method to characterize microbe and host proteins from individual BAL samples, paving the way for a new approach to understand molecular contributors to CF and other diseases of the airway.}, author = {Kruk, Monica E. and Mehta, Subina and Murray, Kevin and Higgins, LeeAnn and Do, Katherine and Johnson, James E. and Wagner, Reid and Wendt, Chris H. and O’Connor, John B. and Harris, J. Kirk and Laguna, Theresa A. and Jagtap, Pratik D. and Griffin, Timothy J.}, doi = {10.1128/msystems.00929-23}, + issn = {2379-5077}, journal = {mSystems}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Bronchoalveolar Lavage Fluid, Cystic Fibrosis, Proteomics, Tandem Mass Spectrometry, Workflow}, + language = {eng}, month = {June}, note = {Publisher: American Society for Microbiology}, number = {0}, @@ -7458,7 +12128,7 @@ @article{kruse_synaptopodin_2024 doi = {10.3390/cells13020114}, issn = {2073-4409}, journal = {Cells}, - keywords = {{\textgreater}UseGalaxy.eu, denervation, lesion-induced plasticity, local protein synthesis, synaptopodin}, + keywords = {{\textgreater}UseGalaxy.eu, Mossy Fibers, Hippocampal, Neuronal Plasticity, Synapses, denervation, lesion-induced plasticity, local protein synthesis, synaptopodin}, language = {en}, month = {January}, note = {Number: 2 @@ -7472,6 +12142,26 @@ @article{kruse_synaptopodin_2024 year = {2024} } +@article{kruszewski_sensitization_2025, + abstract = {The treatment of elderly, nonfit acute myeloid leukemia (AML)/MDS patients with relapsed/refractory (R/R) disease remains challenging. As histone demethylase LSD1 (KDM1A) is a rational therapeutic target in AML, we conducted a phase I trial (“rolling-six design”) with the LSD1 inhibitor tranylcypromine (TCP, dose levels [DL] 20, 40, 60, 80 mg p.o. d1-28) combined with fixed-dose ATRA (45 mg/m2 p.o. d10-28) and low-dose cytarabine (LDAC, 40 mg s.c. d1-10). The primary endpoint was dose-limiting toxicity (DLT) in the first 28 days of treatment. The aim was the determination of the maximum tolerated TCP dose (MTD). Twenty-three patients with AML and 2 with MDS were accrued. TCP was administered for a median of 39.5 days (range: 11–228). No DLTs were observed at any DL; MTD could not be established. No differentiation syndrome occurred. Two patients attained a PR; SD was achieved in 10 of 22 evaluable patients. Median OS was 62 days (range: 14–325). Accompanying studies included pharmacokinetics, serial determinations of fetal hemoglobin (HbF), detection of CD38 upregulation with treatment, as well as transcriptome changes in purified blood blasts over time. In conclusion, the combination of TCP with ATRA and LDAC was well feasible, even at the highest DL. Hence, studies with more potent LSD1 inhibitors appear warranted. Trial Registration: German Clinical Trials Register (DRKS): DRKS00006055. For further Information see https://drks.de/search/en/trial/DRKS00006055}, + author = {Kruszewski, Michael and Schmoor, Claudia and Berg, Tobias and Rehman, Usama-Ur and Schittenhelm, Marcus and Götze, Katharina and Kündgen, Andrea and Pabst, Caroline and Ma, Tobias and Frey, Anna and Stomper, Julia and Pfeifer, Dietmar and Metzger, Eric and Jung, Johannes and Moschallski, Kevin and Thomas, Johanna and Bug, Gesine and Duyster, Justus and Jung, Manfred and Schüle, Roland and Wäsch, Ralph and Grishina, Olga and Lübbert, Michael}, + copyright = {© 2025 The Author(s). European Journal of Haematology published by John Wiley \& Sons Ltd.}, + doi = {10.1111/ejh.14426}, + issn = {1600-0609}, + journal = {European Journal of Haematology}, + keywords = {{\textgreater}UseGalaxy.eu, CD38, LSD1, chromatin, differentiation, histone demethylase, myelodysplastic syndrome}, + language = {en}, + month = {December}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ejh.14426}, + number = {n/a}, + shorttitle = {Sensitization of {Non}-{M3} {Acute} {Myeloid} {Leukemia} {Blasts} to {All}-{Trans} {Retinoic} {Acid} by the {LSD1} {Inhibitor} {Tranylcypromine}}, + title = {Sensitization of {Non}-{M3} {Acute} {Myeloid} {Leukemia} {Blasts} to {All}-{Trans} {Retinoic} {Acid} by the {LSD1} {Inhibitor} {Tranylcypromine}: {TRANSATRA} {Phase} {I} {Study}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ejh.14426}, + urldate = {2025-07-12}, + volume = {n/a}, + year = {2025} +} + @article{kumar_accessible_2022, abstract = {BACKGROUND: Artificial intelligence (AI) programs that train on large datasets require powerful compute infrastructure consisting of several CPU cores and GPUs. JupyterLab provides an excellent framework for developing AI programs, but it needs to be hosted on such an infrastructure to enable faster training of AI programs using parallel computing. FINDINGS: An open-source, docker-based, and GPU-enabled JupyterLab infrastructure is developed that runs on the public compute infrastructure of Galaxy Europe consisting of thousands of CPU cores, many GPUs, and several petabytes of storage to rapidly prototype and develop end-to-end AI projects. Using a JupyterLab notebook, long-running AI model training programs can also be executed remotely to create trained models, represented in open neural network exchange (ONNX) format, and other output datasets in Galaxy. Other features include Git integration for version control, the option of creating and executing pipelines of notebooks, and multiple dashboards and packages for monitoring compute resources and visualization, respectively. @@ -7514,6 +12204,7 @@ @article{kumar_dataset_2024 issn = {2352-3409}, journal = {Data in Brief}, keywords = {{\textgreater}UseGalaxy.eu, Human fecal sample, Illumina, Next-generating sequencing, Oxford Nanopore Technologies}, + language = {eng}, month = {December}, pages = {110961}, title = {Dataset of metagenomic profiles of human gut microbiome from frozen fecal samples sequenced using {Illumina} and {ONT} chemistries}, @@ -7573,15 +12264,28 @@ @article{kumar_quantp:_2018 year = {2018} } +@article{kumar_tool_2019, + abstract = {Galaxy is a web-based and open-source scientific data-processing platform. Researchers compose pipelines in Galaxy to analyse scientific data. These pipelines, also known as workflows, can be complex and difficult to create from thousands of tools, especially for researchers new to Galaxy. To make creating workflows easier, faster and less error-prone, a predictive system is developed to recommend tools facilitating further analysis. A model is created to recommend tools by analysing workflows, composed by researchers on the European Galaxy server, using a deep learning approach. The higher-order dependencies in workflows, represented as directed acyclic graphs, are learned by training a gated recurrent units (GRU) neural network, a variant of a recurrent neural network (RNN). The weights of tools used in the neural network training are derived from their usage frequencies over a period of time. The hyper-parameters of the neural network are optimised using Bayesian optimisation. An accuracy of 97\% in predicting tools is achieved by the model for precision@1, precision@2 and precision@3 metrics. It is accessed by a Galaxy API to recommend tools in real-time. Multiple user interface (UI) integrations on the server communicate with this API to apprise researchers of these recommended tools interactively. {\textless}h4{\textgreater}Contact{\textless}/h4{\textgreater} kumara@informatik.uni-freiburg.de gruening@informatik.uni-freiburg.de backofen@informatik.uni-freiburg.de}, + author = {Kumar, Anup and Grüning, Björn and Backofen, Rolf}, + doi = {10.1101/838599}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Tool recommender system in {Galaxy} using deep learning}, + url = {http://europepmc.org/abstract/PPR/PPR101761}, + year = {2019} +} + @article{kumar_tool_2021, abstract = {Galaxy is a web-based and open-source scientific data-processing platform. Researchers compose pipelines in Galaxy to analyse scientific data. These pipelines, also known as workflows, can be complex and difficult to create from thousands of tools, especially for researchers new to Galaxy. To help researchers with creating workflows, a system is developed to recommend tools that can facilitate further data analysis.A model is developed to recommend tools using a deep learning approach by analysing workflows composed by researchers on the European Galaxy server. The higher-order dependencies in workflows, represented as directed acyclic graphs, are learned by training a gated recurrent units neural network, a variant of a recurrent neural network. In the neural network training, the weights of tools used are derived from their usage frequencies over time and the sequences of tools are uniformly sampled from training data. Hyperparameters of the neural network are optimized using Bayesian optimization. Mean accuracy of 98\% in recommending tools is achieved for the top-1 metric.The model is accessed by a Galaxy API to provide researchers with recommended tools in an interactive manner using multiple user interface integrations on the European Galaxy server. High-quality and highly used tools are shown at the top of the recommendations. The scripts and data to create the recommendation system are available under MIT license at https://github.com/anuprulez/galaxy\_tool\_recommendation.}, author = {Kumar, Anup and Rasche, Helena and Grüning, Björn and Backofen, Rolf}, doi = {10.1093/gigascience/giaa152}, issn = {2047-217X}, journal = {GigaScience}, - keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}UseGalaxy.eu}, + keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}UseGalaxy.eu, Deep Learning, Software}, + language = {eng}, month = {January}, number = {giaa152}, + pages = {giaa152}, title = {Tool recommender system in {Galaxy} using deep learning}, url = {https://doi.org/10.1093/gigascience/giaa152}, urldate = {2021-02-06}, @@ -7623,8 +12327,10 @@ @article{kumaran_vitro_2022 } @article{kumarhalder_oxa-376_2022, + abstract = {Antimicrobial resistance is a major global health crisis, resulting in thousands of deaths each year. Antibiotics' effectiveness against microorganisms deteriorates over time as multidrug resistance (MDR) develops, which is exacerbated by irregular antibiotic use, poor disease management, and the evasive nature of bacteria. The World Health Organization has recognized multidrug resistance as a critical public health concern, and \textit{Acinetobacter baumannii} has been at the center of attention due to its ability to develop multidrug resistance (MDR). It generally produces carbapenem-hydrolyzing oxacillinase, which has been identified as the primary source of beta-lactam resistance in MDR bacteria. Recently, point mutations in \textit{A. baumannii} have been identified as a key factor of multidrug resistance, making them a prime concern for researchers. The goal of the current work was to establish a unique way of finding multidrug-resistant variants and identify the most damaging mutations in the existing databases. We characterized the deleterious variants of oxacillinases using several computational tools. Following a thorough analysis, Oxa-376 and Oxa-530 were found to be more damaging when compared with the wild-type Oxa-51. The mutants' 3D structures were then prepared and refined with RaptorX, GalaxyRefine, and SAVES servers. Our research incorporates seven antimicrobial agents to illustrate the resistance capability of the variants of oxacillinase by evaluating binding affinity in Autodock-vina and Schrodinger software. RMSD, RMSF, Radius of gyration analysis, the solvent-accessible surface area (SASA), hydrogen bonding analysis and MM-GBSA from Molecular Dynamics Simulation revealed the dynamic nature and stability of wild-type and Oxa-376 and Oxa-530 variants. Our findings will benefit researchers looking for the deleterious mutations of \textit{Acinetobacter baumannii} and new therapeutics to combat those variants. However, further studies are necessary to evaluate the mechanism of hydrolyzing activity and antibiotic resistance of these variants.}, author = {Kumar Halder, Sajal and Mulla Mim, Maria and Hassan Alif, Md Meharab and Fardous Shathi, Jannatul and Alam, Nuhu and Shil, Aparna and Kabir Himel, Mahbubul}, doi = {10.1039/D2RA02939A}, + issn = {2046-2069}, journal = {RSC Advances}, keywords = {{\textgreater}UseGalaxy.eu}, language = {en}, @@ -7639,6 +12345,25 @@ @article{kumarhalder_oxa-376_2022 year = {2022} } +@article{kumari_rapid_2025, + abstract = {Antimicrobial resistance (AMR) is a major global challenge that disproportionately affects low- and middle-income countries (LMICs). Environmental contamination by resistant bacteria from animal production facilities is a major driver of the spread of AMR through the food chain, requiring a robust one-health control approach. Traditional culture-based AMR surveillance is time-consuming and less sensitive, and fails to fully capture the spectrum of AMR, evolutionary trends, and epidemiological patterns of AMR spread. Whole-genome sequencing (WGS) has revolutionized AMR surveillance capabilities. Rapid WGS captures the full AMR spectrum with minimum samples, aids source attribution, and provides insights into trends in AMR spread. The portable Oxford Nanopore® Technology (ONT) platform, coupled with open-source software such as Galaxy and Konstanz Information Miner (KNIME), enables the establishment of a potentially portable, transferable workflow for low-resource settings. This study aimed to assess the AMR burden on four dairy farms in Kandy, Sri Lanka, via a resource-limited LMIC using a low-cost high-throughput screening assay and rapid WGS via ONT with Galaxy and KNIME processing to obtain full antibiotic resistomes.}, + author = {Kumari, Lakmini S. and Siriwardhana, Dinushika M. and Liyanapathirana, Veranja and Jinadasa, Rasika and Wijesinghe, Priyanga}, + doi = {10.1186/s12917-025-04800-1}, + issn = {1746-6148}, + journal = {BMC Veterinary Research}, + keywords = {{\textgreater}UseGalaxy.eu, Antimicrobial Resistance, Archaeal Genomics, Drug Resistance, Multiple, Bacterial, Enterobacter cloacae, Enterobacter cloacae complex, Enterobacteriaceae Infections, Multidrug-resistant bacteria, Nanopores, Next-generation sequencing, Oxford Nanopore sequencing, Polysaccharide sequencing, Whole Genome Sequencing, Whole genome amplification}, + language = {en}, + month = {May}, + number = {1}, + pages = {351}, + shorttitle = {Rapid whole genome sequencing for {AMR} surveillance in low- and middle-income countries}, + title = {Rapid whole genome sequencing for {AMR} surveillance in low- and middle-income countries: {Oxford} {Nanopore} {Technology} reveals multidrug-resistant {Enterobacter} cloacae complex from dairy farms in {Sri} {Lanka}}, + url = {https://doi.org/10.1186/s12917-025-04800-1}, + urldate = {2025-05-28}, + volume = {21}, + year = {2025} +} + @article{kumawat_association_2024, abstract = {Knowledge of variability in phenological traits is of utmost importance in breeding new almond cultivars in the context of impending climate change. The Northwestern Himalayan region is characterized by extreme winters, and phenological studies of fruit crops in relation to environmental variables in this region are scant. Flowering time being an important trait governing agricultural productivity, the objectives of this study were the evaluation of local and exotic almond cultivars for blooming initiation and other associated parameters. This study also aimed at deciphering the association between bloom dates in almonds and prevailing temperatures. Field phenological observations were performed during seven growing seasons (2012–2018) in Kashmir. Phenological traits like endodormancy breaking were estimated using the correlation model. The heat requirements for blooming were estimated using the growing degree days (GDD) method. The association between average temperatures and days to flowering was studied using partial least squares (PLS) regression. Local cultivars ‘Makhdoom’ and ‘Shalimar’ were earliest to bloom within 80 days, while the exotic cultivars were late bloomers, requiring 87 days. Cultivars ‘Makhdoom’, ‘Shalimar’, ‘Drake’ and ‘Pranyaj’ broke their endodormancy on the same date, i.e. December 26, although another group including ‘Waris’, ‘California Paper Shell’ and ‘Merced’ exhibited endo- to ecodormancy transition on January 21. In general, Himalayan-origin almond cultivars revealed low heat requirements for flowering compared to the exotic ones. PLS regression analysis identified four major periods in which average temperatures successfully explained variation in days to blooming in almonds. In conclusion, a phenological prediction model is presented here that explains variation in blooming dates in almond cultivars as a function of average temperatures. This model addresses the almond cultivars growing in the Himalayan region and is expected to be of great practical utility to the farming community to efficiently plan their orchard management practices.}, author = {Kumawat, Kishan Lal and Raina, Susheel Kumar and Kumar, Dinesh and Verma, Mahendra Kumar and Singh, Deshbeer and Mir, Javid Iqbal and Sultan, Sheikh M. and Sharma, Om Chand}, @@ -7657,19 +12382,129 @@ @article{kumawat_association_2024 year = {2024} } +@article{kunz_avirulence_2025, + abstract = {Wheat production is threatened by multiple fungal pathogens, such as the wheat powdery mildew fungus (Blumeria graminis f. sp. tritici, Bgt). Wheat resistance breeding frequently relies on the use of resistance (R) genes that encode diverse immune receptors which detect specific avirulence (AVR) effectors and subsequently induce an immune response. While R gene cloning has accelerated recently, AVR identification in many pathogens including Bgt lags behind, preventing pathogen-informed deployment of resistance sources. Here we describe a new “avirulence depletion (AD) assay” for rapid identification of AVR genes in Bgt. This assay relies on the selection of a segregating, haploid F1 progeny population on a resistant host, followed by bulk sequencing, thereby allowing rapid avirulence candidate gene identification with high mapping resolution. In a proof-of-concept experiment we mapped the AVR component of the wheat immune receptor Pm3a to a 25 kb genomic interval in Bgt harboring a single effector, the previously described AvrPm3a2/f2. Subsequently, we applied the AD assay to map the unknown AVR effector recognized by the Pm60 immune receptor. We show that AvrPm60 is encoded by three tandemly arrayed, nearly identical effector genes that trigger an immune response upon co-expression with Pm60 and its alleles Pm60a and Pm60b. We furthermore provide evidence that Pm60 outperforms Pm60a and Pm60b through more efficient recognition of AvrPm60 effectors, suggesting it should be prioritized for wheat breeding. Finally, we show that virulence towards Pm60 is caused by simultaneous deletion of all AvrPm60 gene paralogs and that isolates lacking AvrPm60 are especially prevalent in the US thereby limiting the potential of Pm60 in this region. The AD assay is a powerful new tool for rapid and inexpensive AVR identification in Bgt with the potential to contribute to pathogen-informed breeding decisions for the use of novel R genes and regionally tailored gene deployment.}, + author = {Kunz, Lukas and Jigisha, Jigisha and Menardo, Fabrizio and Sotiropoulos, Alexandros G. and Zbinden, Helen and Zou, Shenghao and Tang, Dingzhong and Hückelhoven, Ralph and Keller, Beat and Müller, Marion C.}, + doi = {10.1371/journal.ppat.1012799}, + issn = {1553-7374}, + journal = {PLOS Pathogens}, + keywords = {{\textgreater}UseGalaxy.eu, Ascomycota, Disease Resistance, Gene sequencing, Genetic loci, Genetic mapping, Genomics, Plant Diseases, Plant pathogens, Powdery mildew, Single nucleotide polymorphisms, Triticum, Wheat}, + language = {en}, + month = {July}, + note = {Publisher: Public Library of Science}, + number = {1}, + pages = {e1012799}, + shorttitle = {Avirulence depletion assay}, + title = {Avirulence depletion assay: {Combining} {R} gene-mediated selection with bulk sequencing for rapid avirulence gene identification in wheat powdery mildew}, + url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1012799}, + urldate = {2025-05-29}, + volume = {21}, + year = {2025} +} + +@article{kuppannan_novel_2022, + abstract = {In the ciliate Tetrahymena thermophila, lysosome-related organelles called mucocysts accumulate at the cell periphery where they secrete their contents in response to extracellular events, a phenomenon called regulated exocytosis. The molecular bases underlying regulated exocytosis have been extensively described in animals but it is not clear whether similar mechanisms exist in ciliates or their sister lineage, the Apicomplexan parasites, which together belong to the ecologically and medically important superphylum Alveolata. Beginning with a T. thermophila mutant in mucocyst exocytosis, we used a forward genetic approach to uncover MDL1 (Mucocyst Discharge with a LamG domain), a novel gene that is essential for regulated exocytosis of mucocysts. Mdl1p is a 40 kDa membrane glycoprotein that localizes to mucocysts, and specifically to a tip domain that contacts the plasma membrane when the mucocyst is docked. This sub-localization of Mdl1p, which occurs prior to docking, underscores a functional asymmetry in mucocysts that is strikingly similar to that of highly polarized secretory organelles in other Alveolates. A mis-sense mutation in the LamG domain results in mucocysts that dock but only undergo inefficient exocytosis. In contrast, complete knockout of MDL1 largely prevents mucocyst docking itself. Mdl1p is physically associated with 9 other proteins, all of them novel and largely restricted to Alveolates, and sedimentation analysis supports the idea that they form a large complex. Analysis of three other members of this putative complex, called MDD (for Mucocyst Docking and Discharge), shows that they also localize to mucocysts. Negative staining of purified MDD complexes revealed distinct particles with a central channel. Our results uncover a novel macromolecular complex whose subunits are conserved within alveolates but not in other lineages, that is essential for regulated exocytosis in T. thermophila.}, + author = {Kuppannan, Aarthi and Jiang, Yu-Yang and Maier, Wolfgang and Liu, Chang and Lang, Charles F and Cheng, Chao-Yin and Field, Mark C and Zhao, Minglei and Zoltner, Martin and Turkewitz, Aaron P}, + doi = {10.1371/journal.pgen.1010194}, + issn = {1553-7390}, + journal = {PLoS genetics}, + keywords = {{\textgreater}UseGalaxy.eu, Tetrahymena, Tetrahymena thermophila}, + language = {eng}, + month = {May}, + number = {5}, + pages = {e1010194}, + title = {A novel membrane complex is required for docking and regulated exocytosis of lysosome-related organelles in {Tetrahymena} thermophila}, + url = {http://europepmc.org/abstract/MED/35587496}, + volume = {18}, + year = {2022} +} + +@article{kuzmanovska_comprehensive_2021, + abstract = {Influenza viruses know no boundaries, representing an example of rapid virus evolution combined with pressure exerted by the host's immune system. Seasonal influenza causes 4-50 million symptomatic cases in the EU/EEA each year, with a global death toll reaching 650,000 deaths. That being the case, in 2014 North Macedonia introduced the sentinel surveillance in addition to the existing influenza surveillance in order to obtain more precise data on the burden of disease, circulating viruses and to implement timely preventive measures. The aims of this study were to give a comprehensive virological and epidemiological overview of four influenza seasons (2016-2020), assess the frequency and distribution of influenza circulating in North Macedonia and to carry out molecular and phylogenetic analyses of the hemagglutinin (HA) and neuraminidase (NA) genes of influenza A(H1N1)pdm09, A(H3N2) from ILI and SARI patients. Our results showed that out of 1,632 tested samples, 46.4\% were influenza positive, with influenza A(H1N1)pdm09 accounting for the majority of cases (44\%), followed by influenza B (32\%) and A(H3N2) (17\%). By comparing the sentinel surveillance system to the routine surveillance system, we showed that the newly applied system works efficiently and gives great results in the selection of cases. Statistically significant differences (\textit{p} = {\textless} 0.0000001) were observed when comparing the number of reported ILI cases among patients aged 0-4, 5-14, 15-29, and 30-64 years to the reference age group. The phylogenetic analysis of the HA sequences unveiled the resemblance of mutations circulating seasonally worldwide, with a vast majority of circulating viruses belonging to subclade 6B.1A. The PROVEAN analysis showed that the D187A substitution in the receptor binding site (RBS) of the A(H1N1)pdm09 HA has a deleterious effect on the its function. The A(H3N2) viruses fell into the 3C.2a and 3C.3a throughout the analyzed seasons. Molecular characterization revealed that various substitutions in the A(H3N2) viruses gradually replaced the parental variant in subsequent seasons before becoming the dominant variant. With the introduction of sentinel surveillance, accompanied by the advances made in whole-genome sequencing and vaccine therapeutics, public health officials can now modify their approach in disease management and intervene effectively and in a timely manner to prevent major morbidity and mortality from influenza.}, + author = {Kuzmanovska, Maja and Boshevska, Golubinka and Janchevska, Elizabeta and Buzharova, Teodora and Simova, Milica and Peshnacka, Aneta and Nikolovska, Gordana and Kochinski, Dragan and Ilioska, Radica Stoleska and Stavridis, Kristina and Mikikj, Vladimir and Kuzmanovska, Gordana and Memeti, Shaban and Gjorgoski, Icko}, + doi = {10.3389/fmicb.2021.713408}, + issn = {1664-302X}, + journal = {Frontiers in microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {713408}, + title = {A {Comprehensive} {Molecular} and {Epidemiological} {Characterization} of {Influenza} {Viruses} {Circulating} 2016-2020 in {North} {Macedonia}}, + url = {http://europepmc.org/abstract/MED/34745027}, + volume = {12}, + year = {2021} +} + +@article{lacchini_engineering_2025, + abstract = {The limited cytosolic delivery of DNA and protein-based therapeutics due to endosomal entrapment reduces drug efficacy, increasing treatment costs and possible side effects in human and veterinary medicine as a consequence of higher administered dosages. Plant-derived triterpenoid saponins, specifically those with endosomal escape-enhancing (EEE) properties, have shown promise in overcoming this limitation by disrupting endosomal membranes. QS-21, a well-known EEE saponin, has been used as an adjuvant in vaccines, and recent studies have elucidated its biosynthetic pathway. However, EEE saponins are typically present as minor compounds in plants, posing challenges for their large-scale production and purification. Here we investigated the possibility of engineering SO1861 production, an EEE saponin from Saponaria officinalis, using heterologous gene expression in Gypsophila elegans hairy roots, a plant species known to synthesize structurally related saponins. Via S. officinalis transcriptomics, we identified jasmonate-responsive saponin biosynthetic genes, and three cytochrome P450s (CYP450s) involved in C23, C28 and C16 oxidations were characterised. Heterologous expression of these CYP450s in G. elegans hairy roots successfully altered the saponin profile, with notable increases in SO1861 precursors in lines expressing the C23-oxidases SoCYP72A984 and SoCYP72A1003. Interestingly, expression of only SoCYP72A1003, a non-canonical C23 oxidase, resulted in the accumulation of a compound matching the SO1861 standard, suggesting the activation of a potentially latent pathway and of silent enzymes in a novel combination. This work underscores the potential of engineering strategies in heterologous plant systems to steer triterpenoid saponin biosynthetic pathways and suggests new avenues for producing high-value EEE saponins.}, + author = {Lacchini, Elia and Qu, Tongtong and Moses, Tessa and Volkov, Alexander N. and Goossens, Alain}, + copyright = {© 2025 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley \& Sons Ltd.}, + doi = {10.1111/pbi.70122}, + issn = {1467-7652}, + journal = {Plant Biotechnology Journal}, + keywords = {{\textgreater}UseGalaxy.eu, CYP450, Caryophyllaceae, Endosomes, Plant Roots, Saponaria, Saponins, endosomal escape, hairy roots, oleanane, triterpenoid saponins, β-amyrin}, + language = {en}, + month = {May}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.70122}, + number = {n/a}, + pages = {3068--3082}, + title = {Engineering {Gypsophila} elegans hairy root cultures to produce endosomal escape-enhancing saponins}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.70122}, + urldate = {2025-05-28}, + volume = {n/a}, + year = {2025} +} + +@article{lacerda_effect_2025, + abstract = {Survival of brachyuran crabs is temperature-dependent and thermal stress promotes changes during molting. We aimed to decipher the impact of thermal stresses on the X-organ/sinus gland (XO/SG) complex, a temperature-sensitive neuroendocrine tissue involved in the molting regulation of Callinectes sapidus during the intermolt and premolt phases. We employed a proteogenomic approach using specimens subjected to control (24 °C), cold (19 °C), and heat (29 °C) temperatures. A total of 1463 protein groups with at least two unique peptides were identified and quantified. C. sapidus in the premolt stage exposed to the cold condition exhibited a proteome closely resembling that of the intermolt stage, as evidenced by measurements of circulating ecdysteroid levels. Compared to the intermolt at control temperature, the premolt stage exhibited increased energy metabolism, structural changes in the cuticle mediated by chitin metabolism and glycoproteins, biosynthesis of methyl farnesoate (MF), and elevated tissue levels of molt-inhibiting hormone (MIH) and crustacean hyperglycemic hormone (CHH), indicating lower secretion rates. Heat temperature (29 °C) seems to induce mitochondrial metabolism in the intermolt XO/SG, while cold temperature elicited a delayed molt cycle in the premolt phase, marked by reduced tissue levels of CHH, indicating increased secretion and Y-organ (YO) inhibition, and decreased MF production (reduced YO stimulation). +Significance statement +Temperature plays a pivotal role in regulating the metabolism, growth, molting, reproduction, and survival of crabs, such as the blue crab (Callinectes sapidus). Despite the blue crab's significance on both economic and ecological realms, there has been a notable lack of molecular information related to this species and therefore a gap in our knowledge of the blue crab's molecular makeup and genetic diversity. This research established a comprehensive proteome landscape to elucidate the molecular and functional changes in the XO/SG complex involved in the molting process of C. sapidus, and how thermal stresses significantly influence biotransformation processes. Utilizing a proteogenomics approach with multi-round homologous database analysis, we have generated a highly accurate protein repertoire with at least two unique peptide of XO/SG tissue proteome. This resource will be invaluable for future molecular analyses of this species. Our findings demonstrate that thermal stresses induced specific modifications in the XO/SG tissue, depending on the molt cycle phase. Temperature-mediated responses influences the biological processes, enhancing the functional morphogenesis and comprehensive metabolic adaptations on molting cycle supported by a relationship between the XO/SG tissue proteome and circulating ecdysteroid levels.}, + author = {Lacerda, José Thalles and David, Daniela Dantas and Castrucci, Ana Maria L.}, + doi = {10.1016/j.jprot.2025.105382}, + issn = {1874-3919}, + journal = {Journal of Proteomics}, + keywords = {{\textgreater}UseGalaxy.eu, Blue crab, Molt cycle, Proteogenomics, Temperature, XO/SG tissue}, + month = {March}, + pages = {105382}, + title = {The effect of thermal stress on the {X}-organ/sinus gland proteome of the estuarine blue crab \textit{{Callinectes} sapidus} during the intermolt and premolt stages}, + url = {https://www.sciencedirect.com/science/article/pii/S1874391925000090}, + urldate = {2025-02-16}, + volume = {313}, + year = {2025} +} + +@article{lagman_ancient_2022, + abstract = {Cyclic nucleotide-gated (CNG) cation channels are important heterotetrameric proteins in the retina, with different subunit composition in cone and rod photoreceptor cells: three CNGA3 and one CNGB3 in cones and three CNGA1 and one CNGB1 in rods. CNGA and CNGB subunits form separate subfamilies. We have analyzed the evolution of the CNG gene family in metazoans, with special focus on vertebrates by using sequence-based phylogeny and conservation of chromosomal synteny to deduce paralogons resulting from the early vertebrate whole genome duplications (WGDs). Our analyses show, unexpectedly, that the CNGA subfamily had four sister subfamilies in the ancestor of bilaterians and cnidarians that we named CNGC, CNGD, CNGE and CNGF. Of these, CNGC, CNGE and CNGF were lost in the ancestor of Olfactores while CNGD was lost in the vertebrate ancestor. The remaining CNGA and CNGB genes were expanded by a local duplication of CNGA and the subsequent chromosome duplications in the basal vertebrate WGD events. Upon some losses, this resulted in the gnathostome ancestor having three members in the visual CNGA subfamily (CNGA1-3), a single CNGA4 gene, and two members in the CNGB subfamily (CNGB1 and CNGB3). The nature of chromosomal rearrangements in the vertebrate CNGA paralogon was resolved by including the genomes of a non-teleost actinopterygian and an elasmobranch. After the teleost-specific WGD, additional duplicates were generated and retained for CNGA1, CNGA2, CNGA3 and CNGB1. Furthermore, teleosts retain a local duplicate of CNGB3. The retention of duplicated CNG genes is explained by their subfunctionalisation and photoreceptor-specific expression. In conclusion, this study provides evidence for four previously unknown CNG subfamilies in metazoans and further evidence that the early vertebrate WGD events were instrumental in the evolution of the vertebrate visual and central nervous systems.}, + author = {Lagman, David and Haines, Helen J and Abalo, Xesús M and Larhammar, Dan}, + doi = {10.1371/journal.pone.0279548}, + issn = {1932-6203}, + journal = {PloS one}, + keywords = {{\textgreater}UseGalaxy.eu, Cyclic Nucleotide-Gated Cation Channels, Gene Duplication}, + language = {eng}, + number = {12}, + pages = {e0279548}, + title = {Ancient multiplicity in cyclic nucleotide-gated ({CNG}) cation channel repertoire was reduced in the ancestor of {Olfactores} before re-expansion by whole genome duplications in vertebrates}, + url = {http://europepmc.org/abstract/MED/36584110}, + volume = {17}, + year = {2022} +} + @article{lahm_congenital_2020, + abstract = {Genetic factors undoubtedly affect the development of congenital heart disease (CHD) but still remain ill defined. We sought to identify genetic risk factors associated with CHD and to accomplish a functional analysis of SNP-carrying genes. We performed a genome-wide association study (GWAS) of 4034 White patients with CHD and 8486 healthy controls. One SNP on chromosome 5q22.2 reached genome-wide significance across all CHD phenotypes and was also indicative for septal defects. One region on chromosome 20p12.1 pointing to the MACROD2 locus identified 4 highly significant SNPs in patients with transposition of the great arteries (TGA). Three highly significant risk variants on chromosome 17q21.32 within the GOSR2 locus were detected in patients with anomalies of thoracic arteries and veins (ATAV). Genetic variants associated with ATAV are suggested to influence the expression of WNT3, and the variant rs870142 related to septal defects is proposed to influence the expression of MSX1. We analyzed the expression of all 4 genes during cardiac differentiation of human and murine induced pluripotent stem cells in vitro and by single-cell RNA-Seq analyses of developing murine and human hearts. Our data show that MACROD2, GOSR2, WNT3, and MSX1 play an essential functional role in heart development at the embryonic and newborn stages.}, author = {Lahm, Harald and Jia, Meiwen and Dreßen, Martina and Wirth, Felix F. M. and Puluca, Nazan and Gilsbach, Ralf and Keavney, Bernard and Cleuziou, Julie and Beck, Nicole and Bondareva, Olga and Dzilic, Elda and Burri, Melchior and König, Karl C. and Ziegelmüller, Johannes A. and Abou-Ajram, Claudia and Neb, Irina and Zhang, Zhong and Doppler, Stefanie A. and Mastantuono, Elisa and Lichtner, Peter and Eckstein, Gertrud and Hörer, Jürgen and Ewert, Peter and Priest, James R. and Hein, Lutz and Lange, Rüdiger and Meitinger, Thomas and Cordell, Heather J. and Müller-Myhsok, Bertram and Krane, Markus}, doi = {10.1172/JCI141837}, issn = {0021-9738}, journal = {The Journal of Clinical Investigation}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Genetic Loci, Polymorphism, Single Nucleotide}, language = {en}, month = {November}, note = {Publisher: American Society for Clinical Investigation}, + number = {2}, + pages = {141837}, pmid = {0}, title = {Congenital heart disease risk loci identified by genome-wide association study in {European} patients}, url = {https://www.jci.org/articles/view/141837}, urldate = {2021-01-12}, + volume = {131}, year = {2020} } @@ -7691,16 +12526,34 @@ @article{lahm_genome-wide_2020 year = {2020} } +@article{laich_single-cell_2022, + abstract = {{\textless}h4{\textgreater}Purpose{\textless}/h4{\textgreater}Proliferative vitreoretinopathy (PVR) remains an unresolved clinical challenge and can lead to frequent revision surgery and blindness vision loss. The aim of this study was to characterize the microenvironment of epiretinal PVR tissue, in order to shed more light on the complex pathophysiology and to unravel new treatment options.{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}A total of 44 tissue samples were analyzed in this study, including 19 epiretinal PVRs, 13 epiretinal membranes (ERMs) from patients with macular pucker, as well as 12 internal limiting membranes (ILMs). The cellular and molecular microenvironment was assessed by cell type deconvolution analysis (xCell), RNA sequencing data and single-cell imaging mass cytometry. Candidate drugs for PVR treatment were identified in silico via a transcriptome-based drug-repurposing approach.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}RNA sequencing of tissue samples demonstrated distinct transcriptional profiles of PVR, ERM, and ILM samples. Differential gene expression analysis revealed 3194 upregulated genes in PVR compared with ILM, including FN1 and SPARC, which contribute to biological processes, such as extracellular matrix (ECM) organization. The xCell and IMC analyses showed that PVR membranes were composed of macrophages, retinal pigment epithelium, and α-SMA-positive myofibroblasts, the latter predominantly characterized by the co-expression of immune cell signature markers. Finally, 13 drugs were identified as potential therapeutics for PVR, including aminocaproic acid and various topoisomerase-2A inhibitors.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}Epiretinal PVR membranes exhibit a unique and complex transcriptional and cellular profile dominated by immune cells and myofibroblasts, as well as a variety of ECM components. Our findings provide new insights into the pathophysiology of PVR and suggest potential targeted therapeutic options.}, + author = {Laich, Yannik and Wolf, Julian and Hajdu, Rozina Ida and Schlecht, Anja and Bucher, Felicitas and Pauleikhoff, Laurenz and Busch, Martin and Martin, Gottfried and Faatz, Henrik and Killmer, Saskia and Bengsch, Bertram and Stahl, Andreas and Lommatzsch, Albrecht and Schlunck, Günther and Agostini, Hansjürgen and Boneva, Stefaniya and Lange, Clemens}, + doi = {10.1167/iovs.63.5.17}, + issn = {0146-0404}, + journal = {Invest Ophthalmol Vis Sci}, + keywords = {{\textgreater}UseGalaxy.eu, Epiretinal Membrane, Vitreoretinopathy, Proliferative}, + language = {eng}, + month = {May}, + number = {5}, + pages = {17}, + title = {Single-{Cell} {Protein} and {Transcriptional} {Characterization} of {Epiretinal} {Membranes} {From} {Patients} {With} {Proliferative} {Vitreoretinopathy}}, + url = {http://europepmc.org/abstract/MED/35579905}, + volume = {63}, + year = {2022} +} + @article{lalli_reappraisal_2023, abstract = {{\textless}sec{\textgreater}{\textless}title{\textgreater}Background{\textless}/title{\textgreater}{\textless}p{\textgreater}Overexpression of the transcription factor NR5A1 and constitutive activation of canonical Wnt signalling leading to nuclear translocation of beta-catenin are hallmarks of malignancy in adrenocortical carcinoma (ACC). Based on the analysis of genomic profiles in H295R ACC cells, Mohan et al. ({\textless}italic{\textgreater}Cancer Res{\textless}/italic{\textgreater}. 2023; 83: 2123-2141) recently suggested that a major determinant driving proliferation and differentiation in malignant ACC is the interaction of NR5A1 and beta-catenin on chromatin to regulate gene expression.{\textless}/p{\textgreater}{\textless}/sec{\textgreater}{\textless}sec{\textgreater}{\textless}title{\textgreater}Methods{\textless}/title{\textgreater}{\textless}p{\textgreater}I reanalyzed the same set of data generated by Mohan et al. and other published data of knockdown-validated NR5A1 and beta-catenin target genes,{\textless}/p{\textgreater}{\textless}/sec{\textgreater}{\textless}sec{\textgreater}{\textless}title{\textgreater}Results{\textless}/title{\textgreater}{\textless}p{\textgreater}Beta-catenin is mainly found in association to canonical T cell factor/lymphoid enhancer factor (TCF/LEF) motifs in genomic DNA. NR5A1 and beta-catenin regulate distinct target gene sets in ACC cells.{\textless}/p{\textgreater}{\textless}/sec{\textgreater}{\textless}sec{\textgreater}{\textless}title{\textgreater}Conclusion{\textless}/title{\textgreater}{\textless}p{\textgreater}Overall, my analysis suggests a model where NR5A1 overexpression and beta-catenin activation principally act independently, rather than functionally interacting, to drive ACC malignancy.{\textless}/p{\textgreater}{\textless}/sec{\textgreater}}, author = {Lalli, Enzo}, doi = {10.3389/fendo.2023.1303332}, issn = {1664-2392}, journal = {Frontiers in Endocrinology}, - keywords = {{\textgreater}UseGalaxy.eu, Adrenocortical Carcinoma, Genomics, Nuclear Receptors, Transcriptional regulation, beta-Catenin}, + keywords = {{\textgreater}UseGalaxy.eu, Adrenal Cortex Neoplasms, Adrenocortical Carcinoma, Genomics, Nuclear Receptors, Transcriptional regulation, beta-Catenin}, language = {English}, month = {December}, note = {Publisher: Frontiers}, + pages = {1303332}, title = {A reappraisal of transcriptional regulation by {NR5A1} and beta-catenin in adrenocortical carcinoma}, url = {https://www.frontiersin.org/journals/endocrinology/articles/10.3389/fendo.2023.1303332/full}, urldate = {2024-10-27}, @@ -7708,6 +12561,38 @@ @article{lalli_reappraisal_2023 year = {2023} } +@article{lam_dose-dependent_2022, + abstract = {Fentanyl is one of the most common opioid analgesics administered to patients undergoing surgery or for chronic pain management. While the side effects of chronic fentanyl abuse are recognized (e.g., addiction, tolerance, impairment of cognitive functions, and inhibit nociception, arousal, and respiration), it remains poorly understood what and how changes in brain activity from chronic fentanyl use influences the respective behavioral outcome. Here, we examined the functional and molecular changes to cortical neural network activity following sub-chronic exposure to two fentanyl concentrations, a low (0.01 μM) and high (10 μM) dose. Primary rat co-cultures, containing cortical neurons, astrocytes, and oligodendrocyte precursor cells, were seeded in wells on either a 6-well multi-electrode array (MEA, for electrophysiology) or a 96-well tissue culture plate (for serial endpoint bulk RNA sequencing analysis). Once networks matured (at 28 days \textit{in vitro}), co-cultures were treated with 0.01 or 10 μM of fentanyl for 4 days and monitored daily. Only high dose exposure to fentanyl resulted in a decline in features of spiking and bursting activity as early as 30 min post-exposure and sustained for 4 days in cultures. Transcriptomic analysis of the complex cultures after 4 days of fentanyl exposure revealed that both the low and high dose induced gene expression changes involved in synaptic transmission, inflammation, and organization of the extracellular matrix. Collectively, the findings of this \textit{in vitro} study suggest that while neuroadaptive changes to neural network activity at a systems level was detected only at the high dose of fentanyl, transcriptomic changes were also detected at the low dose conditions, suggesting that fentanyl rapidly elicits changes in plasticity.}, + author = {Lam, Doris and Sebastian, Aimy and Bogguri, Chandrakumar and Hum, Nicholas R and Ladd, Alexander and Cadena, Jose and Valdez, Carlos A and Fischer, Nicholas O and Loots, Gabriela G and Enright, Heather A}, + doi = {10.3389/ftox.2022.983415}, + issn = {2673-3080}, + journal = {Frontiers in toxicology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {983415}, + title = {Dose-dependent consequences of sub-chronic fentanyl exposure on neuron and glial co-cultures}, + url = {http://europepmc.org/abstract/MED/36032789}, + volume = {4}, + year = {2022} +} + +@article{lamas_complete_2021, + abstract = {Non-\textit{enterica} subspecies of Salmonella enterica are associated with cold-blood animals. We report the complete genomes of six S. enterica strains (one S. enterica subsp. \textit{arizonae} strain, four S. enterica subsp. \textit{salamae} strains, and one S. enterica subsp. \textit{diarizonae} strain) isolated from Spanish poultry houses. This will increase our knowledge of these non-\textit{enterica} subspecies.}, + author = {Lamas, Alexandre and Regal, Patricia and Cepeda, Alberto and Franco, Carlos Manuel}, + doi = {10.1128/mra.00768-21}, + issn = {2576-098X}, + journal = {Microbiol Resour Announc}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {October}, + number = {41}, + pages = {e0076821}, + title = {Complete {Genome} {Sequences} of {Six} {Salmonella} enterica {Strains} ({S}. enterica subsp. arizonae, {S}. enterica subsp. diarizonae, and {S}. enterica subsp. salamae) {Isolated} from {Poultry} {Houses}}, + url = {http://europepmc.org/abstract/MED/34647803}, + volume = {10}, + year = {2021} +} + @article{lamas_whole_2023, abstract = {Whole Genome Sequencing (WGS) implementation in food safety laboratories is a significant advancement in food pathogen control and outbreak tracking. However, the initial investment for acquiring next-generation sequencing platforms and the need for bioinformatic ...}, author = {Lamas, Alexandre and Garrido-Maestu, Alejandro and Prieto, Alberto and Cepeda, Alberto and Franco, Carlos Manuel}, @@ -7732,7 +12617,7 @@ @article{lambrecht_interplay_2019 doi = {10.1038/s41598-019-49881-9}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Gene Expression Regulation, Bacterial, Gene Regulatory Networks}, language = {en}, month = {October}, number = {1}, @@ -7744,6 +12629,43 @@ @article{lambrecht_interplay_2019 year = {2019} } +@article{lanave_discovery_2025, + abstract = {Two feral cats (from the same colony) were presented to the veterinary clinic for weakness, weight loss, and anorexia. The cats were part of a study on feline hepatotropic viruses (collection A, 43 animals). On metaviromic investigation, parvoviral reads were identified in the sera of the two cats. The feline parvovirus genome was 5.3 kb long with an organization similar to other members of the Erythroparvovirus genus. In the ORF1 (nonstructural proteins) and ORF2 (VP1/VP2 precursor) the feline virus displayed 43.1\% and 49.1\% nucleotide identity to human parvovirus B19, and 48.9\% and 56.6\% to chipmunk parvovirus. Sequence identity to canine/feline protoparvovirus (Protoparvovirus carnivoran 1) was as low as 36.5\% \% and 29.2\% in the ORF1 and ORF2, respectively. Using a quantitative PCR assay, the virus was also identified in an additional ten cats (prevalence 27.6\%, 12/43) from collection A and in 15/1150 (1.3\%) of archival sera (collection B), revealing a higher infection rate in cats with altered hepatic markers, suggestive of hepatic distress. The findings of our study extend the list of known parvoviruses in the feline host.}, + author = {Lanave, Gianvito and Pellegrini, Francesco and Diakoudi, Georgia and Catella, Cristiana and Cavalli, Alessandra and Capozza, Paolo and Elia, Gabriella and Di Martino, Barbara and Zini, Eric and Pollicino, Giuseppe and Zatelli, Andrea and Bányai, Krisztián and Lavazza, Antonio and Decaro, Nicola and Camero, Michele and Martella, Vito}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-94123-w}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}NanoGalaxy, {\textgreater}UseGalaxy.eu, Pathogens, Virology}, + language = {en}, + month = {March}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {9650}, + title = {Discovery of a human parvovirus {B19} analog ({Erythroparvovirus}) in cats}, + url = {https://www.nature.com/articles/s41598-025-94123-w}, + urldate = {2025-03-29}, + volume = {15}, + year = {2025} +} + +@article{lang-meli_case_2022, + abstract = {Patients with primary antibody deficiency are at risk for severe and in many cases for prolonged COVID-19. Convalescent plasma treatment of immunocompromised individuals could be an option especially in countries with limited access to monoclonal antibody therapies. While studies in immunocompetent COVID19 patients have demonstrated only a limited benefit, evidence for the safety, timing, and effectiveness of this treatment in antibody-deficient patients is lacking. Here, we describe 16 cases with primary antibody deficiency treated with convalescent plasma in four medical centers. In our cohort, treatment was associated with a reduction in viral load and improvement of clinical symptoms, even when applied over a week after onset of infection. There were no relevant side effects besides a short-term fever reaction in one patient. Longitudinal full-genome sequencing revealed the emergence of mutations in the viral genome, potentially conferring an antibody escape in one patient with persistent viral RNA shedding upon plasma treatment. However, he resolved the infection after a second course of plasma treatment. Thus, our data suggest a therapeutic benefit of convalescent plasma treatment in patients with primary antibody deficiency even months after infection. While it appears to be safe, PCR follow-up for SARS-CoV-2 is advisable and early re-treatment might be considered in patients with persistent viral shedding.}, + author = {Lang-Meli, Julia and Fuchs, Jonas and Mathé, Philipp and Ho, Hsi-En and Kern, Lisa and Jaki, Lena and Rusignuolo, Giuseppe and Mertins, Susanne and Somogyi, Vivien and Neumann-Haefelin, Christoph and Trinkmann, Frederik and Müller, Michael and Thimme, Robert and Umhau, Markus and Quinti, Isabella and Wagner, Dirk and Panning, Marcus and Cunningham-Rundles, Charlotte and Laubner, Katharina and Warnatz, Klaus}, + doi = {10.1007/s10875-021-01193-2}, + issn = {0271-9142}, + journal = {J Clin Immunol}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {February}, + number = {2}, + pages = {253--265}, + title = {Case {Series}: {Convalescent} {Plasma} {Therapy} for {Patients} with {COVID}-19 and {Primary} {Antibody} {Deficiency}}, + url = {http://europepmc.org/abstract/MED/34893946}, + volume = {42}, + year = {2022} +} + @article{lange_expression_2020, abstract = {SARS-CoV-2 is assumed to use angiotensin-converting enzyme 2 (ACE2) and other auxiliary proteins for cell entry. Recent studies have described conjunctival congestion in 0.8\% of patients with laboratory-confirmed SARS-CoV-2, and there has been speculation that SARS-CoV-2 can be transmitted through the conjunctiva. However, it is currently unclear whether conjunctival epithelial cells express ACE2 and its cofactors. In this study, a total of 38 conjunctival samples from 38 patients, including 12 healthy conjunctiva, 12 melanoma, 7 squamous cell carcinoma and 7 papilloma samples, were analyzed using high-throughput RNA sequencing to assess mRNA expression of the SARS-CoV-2 receptor ACE2 and its cofactors including TMPRSS2, ANPEP, DPP4, and ENPEP. ACE2 protein expression was assessed in eight healthy conjunctival samples using immunohistochemistry. Our results show that the SARS-CoV-2 receptor ACE2 is not substantially expressed in conjunctival samples on the mRNA (median 0.0 transcripts per million (TPM), min 0.0 TPM, max 1.7 TPM) and protein levels. Similar results were obtained for the transcription of other auxiliary molecules. In conclusion, this study finds no evidence for a significant expression of ACE2 and its auxiliary mediators for cell entry in conjunctival samples, making conjunctival infection with SARS-CoV-2 via these mediators unlikely. This article is protected by copyright. All rights reserved.}, author = {Lange, Clemens and Wolf, Julian and Auw‐Haedrich, Claudia and Schlecht, Anja and Boneva, Stefaniya and Lapp, Thabo and Horres, Ralf and Agostini, Hansjürgen and Martin, Gottfried and Reinhard, Thomas and Schlunck, Günther}, @@ -7756,6 +12678,7 @@ @article{lange_expression_2020 month = {May}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/jmv.25981}, number = {n/a}, + pages = {2081--2086}, title = {Expression of the {COVID}-19 receptor {ACE2} in the human conjunctiva}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.25981}, urldate = {2020-05-22}, @@ -7763,6 +12686,22 @@ @article{lange_expression_2020 year = {2020} } +@article{lapadula_characterization_2025, + abstract = {Ribosome-inactivating proteins (RIPs) are rRNA N-glycosylases (EC 3.2.2.22) that depurinate an adenine residue from the conserved alpha-sarcin/ricin loop in rRNA, blocking protein synthesis. In previous research, we demonstrated that whiteflies from the Aleyrodidae family (e.g., Bemisia tabaci), mosquitoes from the Culicinae subfamily (e.g., Aedes aegypti), and flies of Sciaroidea superfamily (e.g., Contarinia nasturtii) acquired these genes via three independent horizontal gene transfer events. The temporal expression profiles analyzed in mosquitoes and flies are consistent with the expected for immune effector molecules of insects. Notably, in A. aegypti, we found that these genes contribute to immunity. In whiteflies, codon analysis suggests that RIP genes have evolved under the influence of natural selection. Public transcriptomic experiments have shown that these genes are expressed in the adult stage of B. tabaci. Despite computational findings supporting RIP genes functionality in whiteflies, no experimental studies have been conducted. Furthermore, there is currently no publicly available RNA-seq data evaluating gene expression throughout ontogeny in the Aleyrodidae family. In this work, we experimentally demonstrated the presence of these foreign genes in the genome of Trialeurodes vaporariorum. We quantified their expression across the life cycle stages of this species and analyzed their untranslated regions. The results obtained contribute to a deeper understanding of the biological roles that these ribotoxin encoding genes may play in whiteflies and other insects.}, + author = {Lapadula, Walter J. and Cañadas, María Guadalupe and Ayub, Maximiliano Juri}, + doi = {10.1016/j.gene.2025.149356}, + issn = {0378-1119}, + journal = {Gene}, + keywords = {{\textgreater}UseGalaxy.eu, Horizontal Gene Transfer, Ribosome inactivating proteins, Whiteflies}, + month = {May}, + pages = {149356}, + title = {Characterization of {Ribosome} inactivating protein genes and their transcripts in \textit{{Trialeurodes} vaporariorum}}, + url = {https://www.sciencedirect.com/science/article/pii/S0378111925001441}, + urldate = {2025-02-28}, + volume = {948}, + year = {2025} +} + @article{lapadula_ribosome_2023, abstract = {Ribosome-inactivating proteins (RIPs) are RNA N-glycosidases that depurinate an adenine residue in the conserved alpha-sarcin/ricin loop (SRL) of rRNA, inhibiting protein synthesis. Previously, we reported the existence of these toxins in insects, whose presence is restricted to mosquitoes from the Culicinae subfamily (e.g., Aedes aegypti) and whiteflies from the Aleyrodidae family (e.g., Bemisia tabaci). Both groups of genes are derived from two independent horizontal gene transfer (HGT) events and are evolving under purifying selection. Here, we report and characterize the occurrence of a third HGT event in the Sciaroidea superfamily, which supports the recurrent acquisition of RIP genes by insects. Transcriptomic experiments, available in databases, allowed us to describe the temporal and spatial expression profiles for these foreign genes in these organisms. Furthermore, we found that RIP expression is induced after infection with pathogens and provided, for the first time, transcriptomic evidence of parasite SRL depurination. This evidence suggests a possible role of these foreign genes as immune effectors in insects.}, author = {Lapadula, Walter J. and Juri Ayub, Maximiliano}, @@ -7787,10 +12726,11 @@ @article{lapp_transcriptional_2024 doi = {10.3389/fcimb.2023.1285676}, issn = {2235-2988}, journal = {Frontiers in Cellular and Infection Microbiology}, - keywords = {{\textgreater}UseGalaxy.eu, Bacterial keratitis, FFPE (formalin fixed paraffin embedded), Infectious keratitis, Keratoplasty, RNA sequencing, Viral keratitis, host response, human}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial keratitis, Corneal Ulcer, Eye Infections, Bacterial, Eye Infections, Fungal, FFPE (formalin fixed paraffin embedded), Infectious keratitis, Keratitis, Keratoplasty, RNA sequencing, Viral keratitis, host response, human}, language = {English}, month = {January}, note = {Publisher: Frontiers}, + pages = {1285676}, title = {Transcriptional profiling specifies the pathogen-specific human host response to infectious keratitis}, url = {https://www.frontiersin.org/articles/10.3389/fcimb.2023.1285676}, urldate = {2024-05-17}, @@ -7798,13 +12738,24 @@ @article{lapp_transcriptional_2024 year = {2024} } +@article{lariviere_scalable_2023, + abstract = {Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last ∼500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).}, + author = {Larivière, Delphine and Abueg, Linelle and Brajuka, Nadolina and Gallardo-Alba, Cristóbal and Grüning, Bjorn and Ko, Byung June and Ostrovsky, Alex and Palmada-Flores, Marc and Pickett, Brandon and Rabbani, Keon and Balacco, Jennifer and Chaisson, Mark and Cheng, Haoyu and Collins, Joanna and Denisova, Alexandra and Fedrigo, Olivier and Gallo, Guido Roberto and Giani, Alice Maria and Gooder, Grenville MacDonald and Jain, Nivesh and Johnson, Cassidy and Kim, Heebal and Lee, Chul and Marques-Bonet, Tomas and O’Toole, Brian and Rhie, Arang and Secomandi, Simona and Sozzoni, Marcella and Tilley, Tatiana and Uliano-Silva, Marcela and van den Beek, Marius and Waterhouse, Robert and Phillippy, Adam and Jarvis, Erich and Schatz, Michael and Nekrutenko, Anton and Formenti, Giulio}, + doi = {10.1101/2023.06.28.546576}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Scalable, accessible, and reproducible reference genome assembly and evaluation in {Galaxy}}, + url = {http://europepmc.org/abstract/PPR/PPR684412}, + year = {2023} +} + @article{lariviere_scalable_2024, author = {Larivière, Delphine and Abueg, Linelle and Brajuka, Nadolina and Gallardo-Alba, Cristóbal and Grüning, Bjorn and Ko, Byung June and Ostrovsky, Alex and Palmada-Flores, Marc and Pickett, Brandon D. and Rabbani, Keon and Antunes, Agostinho and Balacco, Jennifer R. and Chaisson, Mark J. P. and Cheng, Haoyu and Collins, Joanna and Couture, Melanie and Denisova, Alexandra and Fedrigo, Olivier and Gallo, Guido Roberto and Giani, Alice Maria and Gooder, Grenville MacDonald and Horan, Kathleen and Jain, Nivesh and Johnson, Cassidy and Kim, Heebal and Lee, Chul and Marques-Bonet, Tomas and O’Toole, Brian and Rhie, Arang and Secomandi, Simona and Sozzoni, Marcella and Tilley, Tatiana and Uliano-Silva, Marcela and van den Beek, Marius and Williams, Robert W. and Waterhouse, Robert M. and Phillippy, Adam M. and Jarvis, Erich D. and Schatz, Michael C. and Nekrutenko, Anton and Formenti, Giulio}, copyright = {2024 The Author(s), under exclusive licence to Springer Nature America, Inc.}, doi = {10.1038/s41587-023-02100-3}, issn = {1546-1696}, journal = {Nature Biotechnology}, - keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Computational platforms and environments, Genome assembly algorithms}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Computational Biology, Computational platforms and environments, Genome assembly algorithms, Software}, language = {en}, month = {January}, note = {Publisher: Nature Publishing Group}, @@ -7821,7 +12772,7 @@ @article{laroute_natural_2023 doi = {10.1186/s12934-023-02181-4}, issn = {1475-2859}, journal = {Microbial Cell Factories}, - keywords = {{\textgreater}UseGalaxy.eu, GAD system, Lactococcus cremoris, Lactococcus lactis, γ-aminobutyric acid}, + keywords = {{\textgreater}UseGalaxy.eu, Chlorides, GAD system, Lactococcus, Lactococcus cremoris, Lactococcus lactis, γ-aminobutyric acid}, language = {en}, month = {September}, number = {1}, @@ -7856,7 +12807,7 @@ @article{lasolle_dual_2024 doi = {10.1038/s41388-023-02889-y}, issn = {1476-5594}, journal = {Oncogene}, - keywords = {{\textgreater}UseGalaxy.eu, Cancer models, Phenotypic screening}, + keywords = {{\textgreater}UseGalaxy.eu, Cancer models, Phenotypic screening, Proto-Oncogene Proteins B-raf, Thyroid Neoplasms}, language = {en}, month = {January}, note = {Publisher: Nature Publishing Group}, @@ -7885,6 +12836,26 @@ @article{lastic_entropic_2020 year = {2020} } +@article{lata_surveillance_2025, + abstract = {Antimicrobial resistance (AMR) is a growing concern in human and veterinary medicine. Misuse and overuse of antimicrobials in human medicine, veterinary medicine, agriculture, and aquaculture are major drivers of AMR development, with resistant bacteria also being selected in livestock and transmitted through meat. Research on AMR in livestock and animal-derived foods is lacking in Fiji; thus, the associated risks remain unclear. Chicken is widely consumed in Fiji and is predominantly served frozen. This study is aimed at determining the prevalence and resistance profiles of Escherichia coli in frozen chicken meat from Fijian supermarkets. A total of 100 frozen chicken meat samples were purchased from supermarkets and retail outlets in Fiji for this study. E. coli was isolated from 72\% of the samples. The E. coli isolates showed relatively high levels of resistance to ampicillin (36\%), tetracycline (24\%), and streptomycin (17\%). Only one cefotaxime-resistant isolate was obtained, which was identified as an extended-spectrum β-lactamase (ESBL)–producing bacterium. This isolate harbored the ESBL-producing gene blaCTX-M-1 and was classified as ST2522. One colistin-resistant isolate was obtained, and its resistance was attributed to a chromosomal mutation in the pmrB gene. The high level of intestinal bacterial contamination in frozen chicken meat suggests that improved hygiene management is necessary throughout the production and distribution chains. Furthermore, because resistance to antimicrobials is important in both human and veterinary medicine (cefotaxime- and colistin-resistant E. coli), careful monitoring of AMR trends in Fiji is essential. These results suggest that AMR surveillance in meat and livestock is necessary to prevent its spread in Fiji.}, + author = {Lata, Deepika Darshani and Sabala, Rana Fahmi and Fukuda, Akira and Nakajima, Chie and Suzuki, Yasuhiko and Usui, Masaru}, + copyright = {Copyright © 2025 Deepika Darshani Lata et al. International Journal of Food Science published by John Wiley \& Sons Ltd.}, + doi = {10.1155/ijfo/5487064}, + issn = {2314-5765}, + journal = {International Journal of Food Science}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1155/ijfo/5487064}, + number = {1}, + pages = {5487064}, + shorttitle = {Surveillance of {Escherichia} coli {From} {Frozen} {Chicken} {Meat} in {Fiji}}, + title = {Surveillance of {Escherichia} coli {From} {Frozen} {Chicken} {Meat} in {Fiji}: {Resistance} {Characteristics} and {Public} {Health} {Concerns}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1155/ijfo/5487064}, + urldate = {2025-12-26}, + volume = {2025}, + year = {2025} +} + @article{latif_nfatc1_2022, abstract = {Objectives Non-alcoholic fatty liver disease (NAFLD) can persist in the stage of simple hepatic steatosis or progress to steatohepatitis (NASH) with an increased risk for cirrhosis and cancer. We examined the mechanisms controlling the progression to severe NASH in order to develop future treatment strategies for this disease. Design NFATc1 activation and regulation was examined in livers from patients with NAFLD, cultured and primary hepatocytes and in transgenic mice with differential hepatocyte-specific expression of the transcription factor (Alb-cre, NFATc1c.a. and NFATc1Δ/Δ). Animals were fed with high-fat western diet (WD) alone or in combination with tauroursodeoxycholic acid (TUDCA), a candidate drug for NAFLD treatment. NFATc1-dependent ER stress-responses, NLRP3 inflammasome activation and disease progression were assessed both in vitro and in vivo. @@ -7895,18 +12866,38 @@ @article{latif_nfatc1_2022 doi = {10.1136/gutjnl-2021-325013}, issn = {0017-5749, 1468-3288}, journal = {Gut}, - keywords = {{\textgreater}UseGalaxy.eu, fatty liver, hepatic fibrosis, inflammation, nonalcoholic steatohepatitis}, + keywords = {{\textgreater}UseGalaxy.eu, Non-alcoholic Fatty Liver Disease, fatty liver, hepatic fibrosis, inflammation, nonalcoholic steatohepatitis}, language = {en}, month = {March}, note = {Publisher: BMJ Publishing Group Section: Hepatology}, + number = {12}, + pages = {2561--2573}, pmid = {35365570}, title = {{NFATc1} signaling drives chronic {ER} stress responses to promote {NAFLD} progression}, url = {https://gut.bmj.com/content/early/2022/03/31/gutjnl-2021-325013}, urldate = {2022-09-24}, + volume = {71}, year = {2022} } +@article{laugero_lncrna_2025, + abstract = {Lymphedema is a lymphatic dysfunction leading to an accumulation of fluid and fat in the arm or leg. Here, we performed noncoding RNA profiling of human breast cancer–induced secondary lymphedema. We identified the long intergenic non–protein coding RNA, P53-induced transcript (LINC-PINT), as essential for the lymphedema development. LINC-PINT is the most expressed lncRNA in human lymphatic endothelial cells (LECs) under stress condition. Knocking down LINC-PINT in LECs promotes the expression of inflammation-related genes. Mechanistically, ATAC-seq revealed that LINC-PINT induces the transcription of genes involved in lymphangiogenesis and immune cell adhesion by increasing chromatin accessibility. Notably, LINC-PINT deficiency impairs LEC proliferation, migration, and sprouting. Conditional deletion of Lnc-Pint in mouse lymphatic endothelium (Lnc-Pintlecko) leads to a reduction in dermal lymphatic network density. Lnc-Pintlecko mice exhibit decreased lymphedema, reduced dermal backflow, fibrosis, and inflammation. Our findings unveil a crucial molecular role of LINC-PINT in lymphatic function and hold substantial clinical implications for lncRNA as biomarker of lymphedema.}, + author = {Laugero, Nathalie and Peghaire, Claire and Verdu, Léna and Balzan, Elisa and Draia-Nicolau, Tangra and Sylvestre, Roxane and Malloizel-Delaunay, Julie and Bura-Rivière, Alessandra and Morfoisse, Florent and Prats, Anne-Catherine and Lacazette, Eric and Garmy-Susini, Barbara}, + doi = {10.1126/sciadv.aea2960}, + journal = {Science Advances}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {December}, + note = {Publisher: American Association for the Advancement of Science}, + number = {51}, + pages = {eaea2960}, + title = {{lncRNA} {LINC}-{PINT} controls lymphatic function and inflammatory profile in lymphedema}, + url = {https://www.science.org/doi/10.1126/sciadv.aea2960}, + urldate = {2025-12-26}, + volume = {11}, + year = {2025} +} + @article{laurette_vivo_2024, author = {Laurette, P. and Cao, C. and Ramanujam, D. and Schwaderer, M. and Lueneburg, T. and Kuss, S. and Weiss, L. and Dilshat, R. and Furlong, E.E.M. and Rezende, F. and Engelhardt, S. and Gilsbach, R.}, doi = {10.1161/CIRCRESAHA.123.323854}, @@ -7973,7 +12964,7 @@ @article{lee_genomic_2022 doi = {10.1038/s41598-022-26803-w}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, Infectious diseases, SARS-CoV-2, Viral epidemiology, Virology}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19, Infectious diseases, SARS-CoV-2, Viral epidemiology, Virology}, language = {en}, month = {December}, note = {Number: 1 @@ -7993,7 +12984,8 @@ @article{lee_global_2023 doi = {10.1242/jcs.261256}, issn = {0021-9533}, journal = {Journal of Cell Science}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Tetrahymena, Tetrahymena thermophila}, + language = {eng}, month = {October}, number = {5}, pages = {jcs261256}, @@ -8020,6 +13012,22 @@ @article{lee_little_2025 year = {2025} } +@article{lee_recruitment_2020, + abstract = {RNA granules are protein/RNA condensates. How specific mRNAs are recruited to cytoplasmic RNA granules is not known. Here, we characterize the transcriptome and assembly of P granules, RNA granules in the \textit{C. elegans} germ plasm. We find that P granules recruit mRNAs by condensation with the disordered protein MEG-3. MEG-3 traps mRNAs into non-dynamic condensates in vitro and binds to {\textasciitilde}500 mRNAs in vivo in a sequence-independent manner that favors embryonic mRNAs with low ribosome coverage. Translational stress causes additional mRNAs to localize to P granules and translational activation correlates with P granule exit for two mRNAs coding for germ cell fate regulators. Localization to P granules is not required for translational repression but is required to enrich mRNAs in the germ lineage for robust germline development. Our observations reveal similarities between P granules and stress granules and identify intrinsically-disordered proteins as drivers of RNA condensation during P granule assembly.}, + author = {Lee, Chih-Yung S and Putnam, Andrea and Lu, Tu and He, ShuaiXin and Ouyang, John Paul T and Seydoux, Geraldine}, + doi = {10.7554/elife.52896}, + issn = {2050-084X}, + journal = {eLife}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {January}, + pages = {e52896}, + title = {Recruitment of {mRNAs} to {P} granules by condensation with intrinsically-disordered proteins}, + url = {http://europepmc.org/abstract/MED/31975687}, + volume = {9}, + year = {2020} +} + @phdthesis{lehmann_immunoregulatory_2023, abstract = {The protozoan parasite Trypanosoma cruzi (T. cruzi) is the causative agent of the potentially life-threatening Chagas disease and leads to lifelong infection. During the infection, T. cruzi-specific cytotoxic CD8+ T cells are necessary for long-term reduction of parasite burden and inflammation. However, in humans with Chagas disease, CD8+ T cells progressively lose function, characterised by decreased cytokine production, advanced differentiation, and increased expression of co-inhibitory receptors. Nevertheless, high levels of pro-inflammatory cytokines, such as IFN-γ and TNF-α, are present throughout the infection, which are mainly secreted by T cells and NK cells. One of the key features of T. cruzi is a chronic infection over the whole lifespan of the host. Especially skeletal muscle cells, were shown to be persistently infected in mice models. Here, strong evidence is presented that skeletal muscle cells provide a unique niche for T. cruzi by inhibiting clearance of the parasite by CD8+ T cells, thereby allowing the parasite to persist in the body. It could be shown that muscle cells actively shape the immune response. Infected primary human skeletal muscle cells produce immune-recruiting chemokines and cytokines, such as IL-6, IL-8, IL-15 and CCL-19. Furthermore, co-inhibitory receptor ligands, such as PD-L1, PD-L2, galectin-9, HVEM, CD155 and CD122 were expressed by the muscle cells upon stimulation with pro-inflammatory cytokines and infection with T. cruzi. While, the soluble forms of the ligands PD-L1, PD-L2 and galectin-9 are simultaneously found in the supernatant of muscle cell cultures. Proliferation-analysis of CD8+ and CD4+ T cells revealed suppressive capacity of T. cruzi-infected muscle cells in a PD-1 and TIM-3-dependent manner. In line, stimulation of the muscle cells with IFN-γ prior to the co-culture resulted in even higher suppression capacity. High levels of galectin-9 are present in the serum of Chagas patients, indicating a potential systemic inhibition of T cell function. Moreover, the secretion of the IL4-I1 enzyme by muscle cells could be demonstrated. This molecule can upregulate co-inhibitory receptor ligands on T cells, reduce T cell proliferation and induce apoptosis. Thus, IL4-I1 might represent a promising new candidate whose immunoregulatory role during T. cruzi infection needs to be further investigated. In conclusion, multiple mechanisms by which muscle cells can regulate the immune cell response are presented here and indicate that blocking only one of those mechanisms might not be sufficient to augment T cell activity. @@ -8054,6 +13062,41 @@ @article{lengfelder_complex_2019 year = {2019} } +@article{lengyel_zymogen_2025, + abstract = {High tissue density of the mammary gland is considered a pro-tumorigenic factor, hence suppressing the stimuli that induce matrix buildup carries the potential for cancer interception. We found that in non-malignant mammary epithelial cells the combination of the chemopreventive agents bexarotene (Bex) and carvedilol (Carv) suppresses the zymogen granule protein 16B (ZG16B, PAUF) through an interaction of ARID1A with a proximal enhancer. Bex + Carv also reduced ZG16B levels in vivo in normal breast tissue and MDA-MB231 tumor xenografts. The relevance of ZG16B is underscored by ongoing clinical trials targeting ZG16B in pancreatic cancers, but its role in breast cancer development is unclear. In immortalized mammary epithelial cells, secreted recombinant ZG16B stimulated mitogenic kinase phosphorylation, detachment and mesenchymal characteristics, and promoted proliferation, motility and clonogenic growth. Highly concerted induction of specific laminin, collagen and integrin isoforms indicated a shift in matrix properties toward increased density and cell-matrix interactions. Exogenous ZG16B alone blocked Bex + Carv-mediated control of cell growth and migration, and antagonized Bex + Carv-induced gene programs regulating cell adhesion and migration. In breast cancer cells ZG16B induced colony formation and anchorage-independent growth, and stimulated migration in a PI3K/Akt-dependent manner. In contrast, Bex + Carv inhibited colony formation, reduced Ki67 levels, ZG16B expression and glucose uptake in MDA-MB231 xenografts. These data establish ZG16B as a druggable pro-tumorigenic target in breast cell transformation and suggest a key role of the matrisome network in rexinoid-dependent antitumor activity.}, + author = {Lengyel, Máté and Molnár, Ádám and Nagy, Tamás and Jdeed, Sham and Garai, Ildikó and Horváth, Zsolt and Uray, Iván P.}, + copyright = {© 2024 The Author(s). Cancer Science published by John Wiley \& Sons Australia, Ltd on behalf of Japanese Cancer Association.}, + doi = {10.1111/cas.16382}, + issn = {1349-7006}, + journal = {Cancer Science}, + keywords = {{\textgreater}UseGalaxy.eu, ARID1A, Breast Neoplasms, ECM, Extracellular Matrix, ZG16B, rexinoid}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/cas.16382}, + number = {1}, + pages = {81--94}, + title = {Zymogen granule protein {16B} ({ZG16B}) is a druggable epigenetic target to modulate the mammary extracellular matrix}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cas.16382}, + urldate = {2025-02-16}, + volume = {116}, + year = {2025} +} + +@article{lenz_all-trans_2021, + abstract = {Previously we showed that the vitamin A metabolite all-trans retinoic acid (atRA) induces synaptic plasticity in acute brain slices prepared from the mouse and human neocortex (Lenz et al., 2021). Depending on the brain region studied, distinct effects of atRA on excitatory and inhibitory neurotransmission have been reported. Here, we used intraperitoneal injections of atRA (10 mg/kg) in adult C57BL/6J mice to study the effects of atRA on excitatory and inhibitory neurotransmission in the mouse fascia dentata-a brain region implicated in memory acquisition. No major changes in synaptic transmission were observed in the ventral hippocampus while a significant increase in both spontaneous excitatory postsynaptic current frequencies and synapse numbers were evident in the dorsal hippocampus 6 hr after atRA administration. The intrinsic properties of hippocampal dentate granule cells were not significantly different and hippocampal transcriptome analysis revealed no essential neuronal changes upon atRA treatment. In light of these findings, we tested for the metaplastic effects of atRA, that is, for its ability to modulate synaptic plasticity expression in the absence of major changes in baseline synaptic strength. Indeed, in vivo long-term potentiation (LTP) experiments demonstrated that systemic atRA treatment improves the ability of dentate granule cells to express LTP. The plasticity-promoting effects of atRA were not observed in synaptopodin-deficient mice, therefore, extending our previous results regarding the relevance of synaptopodin in atRA-mediated synaptic strengthening in the mouse prefrontal cortex. Taken together, our data show that atRA mediates synaptopodin-dependent metaplasticity in mouse dentate granule cells.}, + author = {Lenz, Maximilian and Eichler, Amelie and Kruse, Pia and Muellerleile, Julia and Deller, Thomas and Jedlicka, Peter and Vlachos, Andreas}, + doi = {10.7554/elife.71983}, + issn = {2050-084X}, + journal = {eLife}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {November}, + pages = {e71983}, + title = {All-trans retinoic acid induces synaptopodin-dependent metaplasticity in mouse dentate granule cells}, + url = {http://europepmc.org/abstract/MED/34723795}, + volume = {10}, + year = {2021} +} + @article{lenz_amyloid_2023, abstract = {The perforant path provides the primary cortical excitatory input to the hippocampus. Because of its important role in information processing and coding, entorhinal projections to the dentate gyrus have been studied in considerable detail. Nevertheless, synaptic transmission between individual connected pairs of entorhinal stellate cells and dentate granule cells remains to be characterized. Here, we have used mouse organotypic entorhino-hippocampal tissue cultures of either sex, in which the entorhinal cortex (EC) to dentate granule cell (GC; EC–GC) projection is present, and EC–GC pairs can be studied using whole-cell patch-clamp recordings. By using cultures of wild-type mice, the properties of EC–GC synapses formed by afferents from the lateral and medial entorhinal cortex were compared, and differences in short-term plasticity were identified. As the perforant path is severely affected in Alzheimer's disease, we used tissue cultures of amyloid precursor protein (APP)–deficient mice to examine the role of APP at this synapse. APP deficiency altered excitatory neurotransmission at medial perforant path synapses, which was accompanied by transcriptomic and ultrastructural changes. Moreover, presynaptic but not postsynaptic APP deletion through the local injection of Cre-expressing adeno-associated viruses in conditional APPflox/flox tissue cultures increased the neurotransmission efficacy at perforant path synapses. In summary, these data suggest a physiological role for presynaptic APP at medial perforant path synapses that may be adversely affected under altered APP processing conditions. SIGNIFICANCE STATEMENT The hippocampus receives input from the entorhinal cortex via the perforant path. These projections to hippocampal dentate granule cells are of utmost importance for learning and memory formation. Although there is detailed knowledge about perforant path projections, the functional synaptic properties at the level of individual connected pairs of neurons are not well understood. In this study, we investigated the role of APP in mediating functional properties and transmission rules in individually connected neurons using paired whole-cell patch-clamp recordings and genetic tools in organotypic tissue cultures. Our results show that presynaptic APP expression limits excitatory neurotransmission via the perforant path, which could be compromised in pathologic conditions such as Alzheimer's disease.}, @@ -8062,7 +13105,7 @@ @article{lenz_amyloid_2023 doi = {10.1523/JNEUROSCI.1824-22.2023}, issn = {0270-6474, 1529-2401}, journal = {Journal of Neuroscience}, - keywords = {{\textgreater}UseGalaxy.eu, amyloid precursor protein, dentate gyrus, entorhinal cortex, hilar mossy cell, perforant path, stellate cells}, + keywords = {{\textgreater}UseGalaxy.eu, Alzheimer Disease, Perforant Pathway, amyloid precursor protein, dentate gyrus, entorhinal cortex, hilar mossy cell, perforant path, stellate cells}, language = {en}, month = {July}, note = {Publisher: Society for Neuroscience @@ -8093,13 +13136,53 @@ @article{lenz_denervated_2023 year = {2023} } +@article{lenz_hangover_2025, + abstract = {The RNA-binding protein Hangover (Hang) is essential for several stress responses in Drosophila melanogaster. Here, we discover a novel function of Hang in the regulation of gene expression. Hang binds to {\textgreater}2000 genes in the Drosophila genome and modulates transcription. We identify a diverse set of chromatin regulators as Hang interactors, including NSL, dMec, Sin3A, dREAM, and Ino80. Among these, the non-specific lethal complex (NSL) is the most prominent one. We show that Hang attenuates NSL-mediated H4K16 acetylation at transcriptional start sites to downregulate gene expression. Our work uncovers novel roles for Hang in epigenetic gene regulation and suggests that it coordinates the function of multiple chromatin regulators.}, + author = {Lenz, Jonathan and Schmelzer, Laura and Forné, Ignasi and Nist, Andrea and Imhof, Axel and Stiewe, Thorsten and Brehm, Alexander}, + copyright = {cc by-nc}, + doi = {10.1093/nar/gkaf1349}, + issn = {1362-4962}, + journal = {Nucleic acids research}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {November}, + number = {22}, + pages = {gkaf1349}, + pmcid = {PMC12709178}, + pmid = {41404805}, + title = {Hangover regulates gene expression by limiting {NSL}-mediated {H4K16} acetylation}, + url = {https://europepmc.org/articles/PMC12709178}, + urldate = {2025-12-26}, + volume = {53}, + year = {2025} +} + +@misc{lenz_hangover_2025, + abstract = {The RNA-binding protein hangover is essential for several stress responses in Drosophila melanogaster. Here, we discover a novel function of hangover in the regulation of gene expression. Hangover binds to more than 2.000 genes in the Drosophila genome and modulates transcription. We identify a diverse set of chromatin regulators as hangover interactors, including NSL, dMec, Sin3A, dREAM and Ino80. Among these, the non-specific lethal complex (NSL) is the most prominent one. We show that hangover attenuates NSL-mediated H4K16 acetylation at transcriptional start sites to downregulate gene expression. +Our work uncovers novel roles for hangover in epigenetic gene regulation and suggests that it coordinates the function of multiple chromatin regulators. +{\textless}img class="highwire-fragment fragment-image" alt="Figure" src="https://www.biorxiv.org/content/biorxiv/early/2025/04/24/2025.04.22.649938/F1.medium.gif" width="440" height="183"/{\textgreater}Download figureOpen in new tab}, + author = {Lenz, Jonathan and Schmelzer, Laura and Forné, Ignasi and Nist, Andrea and Imhof, Axel and Stiewe, Thorsten and Brehm, Alexander}, + copyright = {© 2025, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}, + doi = {10.1101/2025.04.22.649938}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {April}, + note = {Pages: 2025.04.22.649938 +Section: New Results}, + publisher = {bioRxiv}, + title = {Hangover regulates gene expression by limiting {NSL}-mediated {H4K16} acetylation}, + url = {https://www.biorxiv.org/content/10.1101/2025.04.22.649938v1}, + urldate = {2025-05-01}, + year = {2025} +} + @article{lenz_transcriptomic_2024, abstract = {Understanding the mechanisms of synaptic plasticity is crucial for elucidating how the brain adapts to internal and external stimuli. A key objective of plasticity is maintaining physiological activity states during perturbations by adjusting synaptic transmission through negative feedback mechanisms. However, identifying and characterizing novel molecular targets orchestrating synaptic plasticity remains a significant challenge. This study investigated the effects of tetrodotoxin (TTX)-induced synaptic plasticity within organotypic entorhino-hippocampal tissue cultures, offering insights into the functional, transcriptomic, and proteomic changes associated with network inhibition via voltage-gated sodium channel blockade. Our experiments demonstrate that TTX treatment induces substantial functional plasticity of excitatory synapses, as evidenced by increased miniature excitatory postsynaptic current (mEPSC) amplitudes and frequencies in both dentate granule cells and CA1 pyramidal neurons. Correlating transcriptomic and proteomic data, we identified novel targets for future research into homeostatic plasticity, including cytoglobin, SLIT-ROBO Rho GTPase Activating Protein 3, Transferrin receptor, and 3-Hydroxy-3-Methylglutaryl-CoA Synthase 1. These data provide a valuable resource for future studies aiming to understand the orchestration of homeostatic plasticity by metabolic pathways in distinct cell types of the central nervous system.}, author = {Lenz, Maximilian and Turko, Paul and Kruse, Pia and Eichler, Amelie and Chen, Zhuo Angel and Rappsilber, Juri and Vida, Imre and Vlachos, Andreas}, doi = {10.1186/s13041-024-01153-y}, issn = {1756-6606}, journal = {Molecular Brain}, - keywords = {{\textgreater}UseGalaxy.eu, homeostatic synaptic plasticity, organotypic tissue culture, proteomics, transcriptome}, + keywords = {{\textgreater}UseGalaxy.eu, Hippocampus, Neuronal Plasticity, Proteomics, Signal Transduction, Tetrodotoxin, Transcriptome, homeostatic synaptic plasticity, organotypic tissue culture, proteomics, transcriptome}, month = {November}, number = {1}, pages = {78}, @@ -8129,6 +13212,36 @@ @phdthesis{leon_estudio_2023 year = {2023} } +@article{lestin_modulation_2025, + abstract = {\<h4\>Background\</h4\>Nitrate (NO\<sub\>3\</sub\> \<sup\>-\</sup\>) can accumulate in closed-circuit ecosystems to a toxic level. Adding heterotrophic denitrification process to the water treatment is a strategy to reduce this level. This type of process usually requires the addition of a carbon source. Carbon-to-nitrogen ratio (C/N) is a key parameter known to influence both the function and the activity of microbial communities in bioprocesses. Few studies have examined the influence of C/N on denitrification systems operated under methylotrophic and marine conditions. Here we assessed the influence of C/N (methanol and NO\<sub\>3\</sub\> \<sup\>-\</sup\>) on the performance of a laboratory-scale, recirculating denitrifying reactor operated under marine conditions. We monitored the evolution of the bacterial community in the biofilm to assess its stability during the operating conditions. Finally, the relative gene expression profiles of \<i\>Methylophaga nitratireducenticrescens\</i\> strain GP59, the main denitrifier in the denitrifying biofilm, were determined during the operating conditions and compared with those of GP59 planktonic pure cultures.\<h4\>Methodology\</h4\>A 500-mL methanol-fed recirculating denitrification reactor operated under marine conditions and colonized by a naturally occurring multispecies denitrifying biofilm was subjected to eight different C/N. We monitored several physico-chemical parameters (denitrifying activities, methanol consumption, CO\<sub\>2\</sub\> production) throughout the operating conditions. The evolution of the bacterial community in the biofilm during these conditions was determined by 16S rRNA gene amplicon sequencing. Metatranscriptomes were derived from the biofilm to determine (1) the relative gene expression profiles of strain GP59, and (2) the functional diversity of the active microorganisms in the biofilm.\<h4\>Results\</h4\>Changes in C/N did not correlate with the denitrification dynamics (NO\<sub\>3\</sub\> \<sup\>-\</sup\> and NO\<sub\>2\</sub\> \<sup\>-\</sup\> reduction rates, NO\<sub\>2\</sub\> \<sup\>-\</sup\> and N\<sub\>2\</sub\>O dynamics), but did correlate with the methanol consumption rates, and the CO\<sub\>2\</sub\> production rates. Throughout the operating conditions, nitrite and N\<sub\>2\</sub\>O appeared transiently, and ammonium was not observed. The bacterial community in the reactor increased in diversity with biofilm aging, especially among heterotrophic bacteria, at the expense of methylotrophic bacteria. The relative expression profiles of strain GP59 in the biofilm are distinct from those of planktonic pure cultures of strain GP59, and that the expression of several riboswitches and \<i\>xoxF\</i\> would be involved in these differences.\<h4\>Conclusions\</h4\>When the biofilm community is well established in the reactor, it can withstand changes in C/N with limited impact on the denitrification performance. The increase in the proportion of heterotrophs would allow the reactor to be more flexible regarding carbon sources. This knowledge can be useful for improving the efficiency of denitrification system treating close circuit systems such as marine recirculating aquaculture wastewater or seawater aquarium.}, + author = {Lestin, Livie and Villemur, Richard}, + doi = {10.7717/peerj.20129}, + issn = {2167-8359}, + journal = {PeerJ}, + keywords = {{\textgreater}UseGalaxy.eu, Biofilm, Carbon-to-nitrogen Ratio, Denitrification, Marine, Methanol, Methylophaga, Methylotrophs, Nitrate}, + pages = {e20129}, + title = {Modulation of carbon-to-nitrogen ratio shapes the microbial ecology in a methanol-fed recirculating marine denitrifying reactor}, + url = {https://europepmc.org/articles/PMC12530212}, + volume = {13}, + year = {2025} +} + +@article{levi_genome-wide_2025, + author = {Levi, Ofri and Zuchman, Rina and Sleman, Nour and Koren, Roni and Khamaisi, Hazem and Horwitz, Benjamin A.}, + doi = {10.1128/mbio.01909-25}, + journal = {mBio}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e01909--25}, + title = {Genome-wide {CRISPRi} screen and proteomic profiling identify key genes related to ferulic acid’s antifungal activity}, + url = {https://journals.asm.org/doi/full/10.1128/mbio.01909-25}, + urldate = {2025-09-12}, + volume = {0}, + year = {2025} +} + @article{lezameta_draft_2020, abstract = {Providencia stuartii is an opportunistic pathogen of the Enterobacteriales order. Here, we report the 4,594,658-bp draft genome sequence of a New Delhi metallo-β-lactamase (NDM-1)-producing Providencia stuartii strain that was isolated from an emergency patient in a private clinic in Lima, Peru.}, author = {Lezameta, Lizet and Cuicapuza, Diego and Dávila-Barclay, Alejandra and Torres, Susan and Salvatierra, Guillermo and Tsukayama, Pablo and Tamariz, Jesús}, @@ -8142,6 +13255,7 @@ @article{lezameta_draft_2020 note = {Publisher: American Society for Microbiology Section: Genome Sequences}, number = {39}, + pages = {e00788--20}, pmid = {32972938}, title = {Draft {Genome} {Sequence} of a {New} {Delhi} {Metallo}-β-{Lactamase} ({NDM}-1)-{Producing} {Providencia} stuartii {Strain} {Isolated} in {Lima}, {Peru}}, url = {https://mra.asm.org/content/9/39/e00788-20}, @@ -8150,6 +13264,39 @@ @article{lezameta_draft_2020 year = {2020} } +@article{lheraud_identification_2025, + abstract = {Sex-determining genes remain largely uncharacterized outside classical models in vertebrates and insects, leaving a gap in our understanding of their evolutionary emergence. The terrestrial isopod Armadillidium vulgare provides an excellent model for investigating this question, as it presents multiple genetic sex determinants. Some lineages possess a masculinizing dominant allele at a locus called the ‘M gene’, which is analogous to an XY system. This allele is hypothesized to have been selected due to the deficit of males caused by a non-Mendelian feminizing factor previously described. The existence of the M gene was inferred from crosses carried out in the 1990s, but its molecular nature remains unresolved. Here, we conducted a genome-wide single-nucleotide polymorphisms analysis combining pooled sequencing of male and female progenies with sequencing of individual parents across two families. Bayesian estimation of haplotype frequencies in progenies pinpointed a candidate genomic region of approximately two megabases. Notably, this region contains the gene encoding the androgenic gland hormone, a protein involved in male sexual differentiation. Our findings lay the groundwork for functional investigations of the M gene, offering novel insights into the dynamics of sex determination in terrestrial isopods and into the turnover of sex chromosomes in response to sex-ratio distortion.}, + author = {Lhéraud, Baptiste and Dussert, Yann and Chebbi, Mohamed Amine and Giraud, Isabelle and Cordaux, Richard and Peccoud, Jean}, + doi = {10.1098/rsbl.2025.0287}, + issn = {1744-9561}, + journal = {Biology Letters}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + number = {10}, + pages = {20250287}, + title = {Identification of a sex-determining region potentially involved in resolving genetic conflicts over sex ratio}, + url = {https://doi.org/10.1098/rsbl.2025.0287}, + urldate = {2025-12-22}, + volume = {21}, + year = {2025} +} + +@article{li_functional_2025, + abstract = {Camptothecin (CAM), a well-known plant-derived antitumor compound, is a structurally complex pentacyclic pyrroloquinoline monoterpene indole alkaloid (MIA) found in various plant species. As a specific MIA, CAM had been thought to share a common upstream biosynthetic pathway with other MIAs such as the antitumor vinblastine and vincristine from Catharanthus roseus. Nevertheless the key enzymes responsible for the consecutive three-step oxidation of the –CH3 of nepetalactol to form the –COOH of 7-deoxyloganetic acid and the subsequent glycosylation of 7-deoxyloganetic acid to yield 7-deoxyloganic acid have yet to be functionally characterized. Here we established an in vivo tandem catalysis assay for the enzymatic catalytic activity characterization of 7-deoxyloganetic acid synthase (7DLS) and 7-deoxyloganetic acid glucosyltransferase (7DLGT), two crucial catalytic enzymes in MIAs biosynthesis, thereby avoiding the difficulty in the detection of the unstable biosynthetic intermediates. The enzyme activity assay platform was conducted through the co-expression of functionally characterized Cr7DLS and Cr7DLGT in Saccharomyces cerevisiae WAT11, substrate feeding, and enzymatic product verification. Two cytochrome P450 enzymes (CYPs) from Camptotheca acuminata, the prestigious resource for CAM, CaCYP76A75 and CaCYP76A76, were identified and functionally characterized to be responsible for the consecutive three-step oxidation of nepetalactol to yield 7-deoxyloganetic acid through reciprocal replacement of Cr7DLS in the in vivo tandem enzyme activity assay platform. Two uridine 5′-diphosphate glycosyltransferases (UGTs), CaUGT709C10 and CaUGT709C11, were functionally characterized to be capable of glycosylating 7-deoxyloganetic acid to yield 7-deoxyloganic acid. This study provides two CYPs as 7DLSs and two UGTs as 7DLGTs, offering potential applications in MIAs biosynthesis.}, + author = {Li, Yi and Wang, Xuefei and Jiang, Honglan and Xu, Shuangyu and Xu, Ying and Liu, Zhan and Luo, Yinggang}, + doi = {10.1016/j.plaphy.2024.109305}, + issn = {0981-9428}, + journal = {Plant Physiology and Biochemistry}, + keywords = {7-Deoxyloganetic acid glucosyltransferase, 7-Deoxyloganetic acid synthase, {\textgreater}UseGalaxy.eu, Camptothecin, Cytochrome P450 enzyme, Glycosyltransferase}, + month = {January}, + pages = {109305}, + title = {Functional characterization of \textit{{Camptotheca} acuminata} 7-deoxyloganetic acid synthases and 7-deoxyloganetic acid glucosyltransferases involved in camptothecin biosynthesis}, + url = {https://www.sciencedirect.com/science/article/pii/S0981942824009732}, + urldate = {2025-02-23}, + volume = {218}, + year = {2025} +} + @article{li_mitochondrial_2021, author = {Li, X.-Y. and Liu, Y.-C. and Zhang, R.-S. and Chen, D.-B. and Chen, M.-M. and Li, Y.-P. and Liu, Y.-Q. and Qin, L.}, doi = {10.3920/jiff2020.0054}, @@ -8164,6 +13311,28 @@ @article{li_mitochondrial_2021 year = {2021} } +@article{li_new_2025, + abstract = {Macellicephaloides Uschakov, 1955 (Annelida: Polynoidae) is a genus of deep-sea polychaetes characterized by a specialized pharynx bearing two pairs of jaws (with the dorsal pair fused) and three pairs of lateral papillae, the middle pair of which is greatly elongated, and remarkable adaptability to diverse deep-sea habitats. Most species in this genus inhabit abyssal depths ({\textgreater}7200 m), with high diversity in western Pacific trenches, while a few occur in relatively shallow habitats such as deep-sea seamounts and hydrothermal vents. This paper presents a new species, Macellicephaloides lingshuiensis sp. nov., found in deep-sea cold seeps in the South China Sea, representing the shallowest distribution record for the genus to date and the first record from cold seep environments. The classification and phylogeny of Macellicephaloides and related genera have long been the subject of debate. A previous study suggested that Macellicephaloides is nested within the Macellicephala clade, but our analyses-based on 13 mitochondrial protein-coding genes, 12S, 16S, 18S, 28S rRNA, and ITS1-ITS2 sequences-tentatively indicate that these two genera form independent evolutionary clades. Additionally, our phylogeny indicates a close evolutionary relationship between deep-sea Macellicephaloides and cave-dwelling polynoids (e.g., Gesiella), highlighting ecological connections between deep-sea and cave habitats. These conclusions are supported by morphological comparisons and genetic distance analyses. Although the subfamily Macellicephalinae is recovered as a monophyletic group, intergeneric phylogenetic relationships within it remain unresolved, highlighting the need for additional data from more species and genera. We amend the generic diagnosis of Macellicephaloides and provide an identification key to all valid species in the genus. This study clarifies the taxonomy and phylogeny of Macellicephaloides and related taxa, emphasizing the importance of continued sampling in understudied deep-sea habitats to enhance our understanding of their biodiversity.}, + author = {Li, Jie and Zhang, Linlin and Wang, Mingxiao and Wu, Xuwen}, + copyright = {cc by}, + doi = {10.3390/cimb47110897}, + issn = {1467-3045}, + journal = {Current issues in molecular biology}, + keywords = {{\textgreater}UseGalaxy.eu, Chemosynthetic Environment, Deep-sea, Morphology, Polychaetes, Systematics}, + language = {eng}, + month = {October}, + number = {11}, + pages = {897}, + pmcid = {PMC12651276}, + pmid = {41296401}, + shorttitle = {A {New} {Species} of \<i\>{Macellicephaloides}\</i\> {Uschakov}, 1955 ({Annelida}, {Polynoidae}) from {Cold} {Seeps} in the {South} {China} {Sea}}, + title = {A {New} {Species} of \<i\>{Macellicephaloides}\</i\> {Uschakov}, 1955 ({Annelida}, {Polynoidae}) from {Cold} {Seeps} in the {South} {China} {Sea}: {Insights} into the {Taxonomy} and {Phylogeny} of \<i\>{Macellicephaloides}\</i\> and {Related} {Genera}}, + url = {https://europepmc.org/articles/PMC12651276}, + urldate = {2025-12-26}, + volume = {47}, + year = {2025} +} + @article{li_proteogenomic_2023, author = {Li, Yize and Dou, Yongchao and Leprevost, Felipe Da Veiga and Geffen, Yifat and Calinawan, Anna P. and Aguet, François and Akiyama, Yo and Anand, Shankara and Birger, Chet and Cao, Song and Chaudhary, Rekha and Chilappagari, Padmini and Cieslik, Marcin and Colaprico, Antonio and Zhou, Daniel Cui and Day, Corbin and Domagalski, Marcin J. and Selvan, Myvizhi Esai and Fenyö, David and Foltz, Steven M. and Francis, Alicia and Gonzalez-Robles, Tania and Gümüş, Zeynep H. and Heiman, David and Holck, Michael and Hong, Runyu and Hu, Yingwei and Jaehnig, Eric J. and Ji, Jiayi and Jiang, Wen and Katsnelson, Lizabeth and Ketchum, Karen A. and Klein, Robert J. and Lei, Jonathan T. and Liang, Wen-Wei and Liao, Yuxing and Lindgren, Caleb M. and Ma, Weiping and Ma, Lei and MacCoss, Michael J. and Rodrigues, Fernanda Martins and McKerrow, Wilson and Nguyen, Ngoc and Oldroyd, Robert and Pilozzi, Alexander and Pugliese, Pietro and Reva, Boris and Rudnick, Paul and Ruggles, Kelly V. and Rykunov, Dmitry and Savage, Sara R. and Schnaubelt, Michael and Schraink, Tobias and Shi, Zhiao and Singhal, Deepak and Song, Xiaoyu and Storrs, Erik and Terekhanova, Nadezhda V. and Thangudu, Ratna R. and Thiagarajan, Mathangi and Wang, Liang-Bo and Wang, Joshua M. and Wang, Ying and Wen, Bo and Wu, Yige and Wyczalkowski, Matthew A. and Xin, Yi and Yao, Lijun and Yi, Xinpei and Zhang, Hui and Zhang, Qing and Zuhl, Maya and Getz, Gad and Ding, Li and Nesvizhskii, Alexey I. and Wang, Pei and Robles, Ana I. and Zhang, Bing and Payne, Samuel H. and Lazar, Alexander J. and Paulovich, Amanda G. and Colaprico, Antonio and Iavarone, Antonio and Chinnaiyan, Arul M. and Druker, Brian J. and Kumar-Sinha, Chandan and Newton, Chelsea J. and Huang, Chen and Mani, D. R. and Smith, Richard D. and Huntsman, Emily and Schadt, Eric E. and An, Eunkyung and Petralia, Francesca and Hostetter, Galen and Omenn, Gilbert S. and Cho, Hanbyul and Rodriguez, Henry and Zhang, Hui and Kolodziejczak, Iga and Johnson, Jared L. and Bavarva, Jasmin and Tan, Jimin and Rodland, Karin D. and Clauser, Karl R. and Krug, Karsten and Cantley, Lewis C. and Wiznerowicz, Maciej and Ellis, Matthew J. and Anurag, Meenakshi and Mesri, Mehdi and Gillette, Michael A. and Birrer, Michael J. and Ceccarelli, Michele and Dhanasekaran, Saravana M. and Edwards, Nathan and Tignor, Nicole and Babur, Özgün and Pugliese, Pietro and Gosline, Sara J. C. and Jewell, Scott D. and Satpathy, Shankha and Chowdhury, Shrabanti and Schürer, Stephan and Carr, Steven A. and Liu, Tao and Hiltke, Tara and Yaron, Tomer M. and Stathias, Vasileios and Liu, Wenke and Zhang, Xu and Song, Yizhe and Zhang, Zhen and Chan, Daniel W.}, doi = {10.1016/j.ccell.2023.06.009}, @@ -8183,6 +13352,27 @@ @article{li_proteogenomic_2023 year = {2023} } +@article{li_stram_2025, + abstract = {Multiple assessment checks are required to handle the increasingly complex engineered-cell and cell-line provenance. To manage the biosafety and efficacy demands, we developed a bioinformatic pipeline for de novo profiling of short tandem repeats and mutations (STRaM) to identify and track homologous edited/engineered cells. The core technology of STRaM comprises an error-sensing bioinformatic pipeline with 3 analysis modules (STR analysis, STR flanking analysis and EMS analysis) for profiling, and an integrated assessment system with three indices for the respective reporting of identity, purity and genetic modifications of tested cells. STRaM maintains a transformed pathway for backward compatibility with traditional capillary gel electrophoresis (CE) based DNA databases. To introduce our integrative and cost-effective STRaM system to best practices in the management of modern cell products, we applied our enhanced DNA fingerprinting technique to several basic and translational cell research examples.}, + author = {Li, Binglin and Le, Chi and Lei, Wen and Zhou, Yingqi and Zhang, Ying and Wang, Yanwen and Wang, Yanyan and Li, Xian and Zheng, Weiyan and Sun, Jie and Tu, Yuanbiao and Yang, Wangren and Zhou, Kuncheng and Meena, Stephene S. and Li, Yufei and Zhu, Keying and Zhou, Shuqin and Liu, Liyan and Chen, Hao and Peng, Qing and Qian, Wenbin and Han, Ray P. S. and Guo, Wei}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s42003-025-08547-1}, + issn = {2399-3642}, + journal = {Communications Biology}, + keywords = {{\textgreater}UseGalaxy.eu, Cancer genomics, Personalized medicine}, + language = {en}, + month = {August}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {1232}, + shorttitle = {{STRaM}}, + title = {{STRaM}: {A} genetic framework for improved cell product provenance for research and clinical translations}, + url = {https://www.nature.com/articles/s42003-025-08547-1}, + urldate = {2025-09-03}, + volume = {8}, + year = {2025} +} + @article{li_trna_2024, abstract = {An adaptive feature of malaria-causing parasites is the digestion of host hemoglobin (HB) to acquire amino acids (AAs). Here we describe a link between nutrient availability and translation dependent regulation of gene expression as an adaptive strategy. We show that tRNA expression in Plasmodium falciparum does not match the decoding need expected for optimal translation. A subset of tRNAs decoding AAs that are insufficiently provided by HB are lowly expressed, wherein the abundance of a protein-coding transcript is negatively correlated with the decoding requirement of these tRNAs. Proliferation-related genes have evolved a high requirement of these tRNAs, thereby proliferation can be modulated by repressing protein synthesis of these genes during nutrient stress. We conclude that the parasite modulates translation elongation by maintaining a discordant tRNA profile to exploit variations in AA-composition among genes as an adaptation strategy. This study exemplifies metabolic adaptation as an important driving force for protein evolution.}, author = {Li, Qian and Vetter, Leonie and Veith, Ylva and Christ, Elena and Végvári, Ákos and Sahin, Cagla and Ribacke, Ulf and Wahlgren, Mats and Ankarklev, Johan and Larsson, Ola and Chun-Leung Chan, Sherwin}, @@ -8204,7 +13394,8 @@ @article{liang_characterization_2024 doi = {10.1186/s12974-024-03223-3}, issn = {1742-2094}, journal = {Journal of Neuroinflammation}, - keywords = {{\textgreater}UseGalaxy.eu, Angiogenesis, Diabetic retinopathy, Endothelial cell, IL-6 family cytokines, Interleukin 11, Müller cell, Oxygen in retinopathy, STAT3, Trans-signaling}, + keywords = {{\textgreater}UseGalaxy.eu, Angiogenesis, Diabetic retinopathy, Endothelial cell, IL-6 family cytokines, Interleukin 11, Interleukin-11, Müller cell, Oxygen in retinopathy, Retina, STAT3, Signal Transduction, Trans-signaling}, + language = {eng}, month = {September}, number = {1}, pages = {230}, @@ -8249,6 +13440,43 @@ @article{liang_reciprocal_2020 year = {2020} } +@article{liang_species_2025, + abstract = {Widespread species may exhibit considerable genetic variation among populations due to their extensive distribution ranges, and may even give rise to new species in remote areas. Integrative species delimitation via multiple types can provide a robust framework for accurate species identification and rapid discovery of cryptic diversity. The subgenus Tliponius (Hemiptera: Coreidae: Homoeocerus) has several species and three broadly distributed species across China. In this study, we selected as many geographical sample sites of widely distributed species as possible and conducted species identification based on integrated taxonomy of morphological, mitochondrial and SNP data for 28 individuals within Tliponius. Our results revealed a cryptic lineage previously subsumed under the polytypic H. unipunctatus in Yunnan Province and described as Homoeocerus (Tliponius) dianensis Liang, Li \& Bu sp. nov. The presence of seven distinct species within Tliponius was supported by species delimitation and divided into two clades: (H. dilatatus + (H. marginellus + (H. unipunctatus + H. dianensis sp. nov.))) and (H. yunnanensis + (H. laevilineus + H. marginiventris). Based on our findings, extensive sampling of widespread species is highly important for the accuracy of species delimitation and the discovery of cryptic species.}, + author = {Liang, Jingyu and Wang, Shujing and Zhang, Jingyao and Chen, Juhong and Fu, Siying and Ye, Zhen and Xue, Huai-Jun and Li, Yanfei and Bu, Wenjun}, + doi = {10.3390/insects16080797}, + issn = {2075-4450}, + journal = {Insects}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {August}, + number = {8}, + pages = {797}, + shorttitle = {Species {Delimitation} {Methods} {Facilitate} the {Identification} of {Cryptic} {Species} {Within} the {Broadly} {Distributed} {Species} in {Homoeocerus} ({Tliponius}) ({Insecta}}, + title = {Species {Delimitation} {Methods} {Facilitate} the {Identification} of {Cryptic} {Species} {Within} the {Broadly} {Distributed} {Species} in {Homoeocerus} ({Tliponius}) ({Insecta}: {Hemiptera}: {Coreidae})}, + url = {https://www.mdpi.com/2075-4450/16/8/797}, + urldate = {2025-10-27}, + volume = {16}, + year = {2025} +} + +@article{liao_-depth_2025, + abstract = {Mitochondrial genomes, with their maternal inheritance, rapid evolution, and compact organization, are ideal for phylogenetic analysis.}, + author = {Liao, Jian and Li, Jia-Yu and Li, Yi-Yang and Zhang, Shui-Yuan and Yang, Yuan-Feng and Guo, Yu-Song and Wang, Zhong-Duo}, + doi = {10.1007/s11033-025-10651-8}, + issn = {1573-4978}, + journal = {Molecular Biology Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Alpheus euphrosyne, Comparative Genomics, Conservation genomics, Genome, Genome Evolution, Marine biodiversity, Mitochondrial genome, Mitochondrial genomes, Next-generation sequencing, Phylogenetic, Protein-coding genes}, + language = {en}, + month = {June}, + number = {1}, + pages = {579}, + title = {In-depth analysis of the first complete mitochondrial genome of the rare shrimp {Alpheus} euphrosyne, with comparative phylogenetic genomics insights into the {Alpheus} species}, + url = {https://doi.org/10.1007/s11033-025-10651-8}, + urldate = {2025-07-12}, + volume = {52}, + year = {2025} +} + @article{lin_characteristics_2024, abstract = {This study sequenced and assembled the mitochondrial genome of the rare dragonfly species Libellula melli, and submitted the results to the NCBI GenBank database, obtaining the accession number PP588458. The mitochondrial genome spans a total length of 15,149 bp, encompassing 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a control region or D-loop. Of these, 25 genes and segments are located on the heavy strand (H-strand), while the remaining 13 reside on the light strand (L-strand). The nucleotide composition of the L. melli mitochondrial genome exhibits a prominent AT bias (AT = 73.3 \%), with T, C, A, and G bases comprising 34.5 \%, 15.6 \%, 38.8 \%, and 11.1 \% respectively, displaying a positive AT skew of 0.059. Among the 13 PCGs, the primary start codons are ATT, ATG, and TTG, while the primary stop codons are TAA, with instances of TA(C) and T(AT) also observed. RSCU analysis reveals that the most frequently used codon is UUA, with an RSCU value of 3.75, encoding leucine (Leu). The secondary structures of the proteins encoded by the 13 PCGs generally exhibit a trend of α-helix {\textgreater} random coil {\textgreater} extended strand {\textgreater} β-turn. Phylogenetic analysis uncovers the phylogenetic relationships of L. melli within the reported Libellulidae species, revealing (((((((L. melli + L. quadrimaculata) + L. angelina) + ((O. chrysis + O. glaucum) + O. albistylum)) + ((C. servilia servilia + T. virginia) + N. fulvia) + (L. albifrons + S. eroticum)) + (P. flavescens + T. aurora)) + (D. phaon + H. croceus)) + (B. contaminate + P. zonata)). This study provides insights into the mitochondrial genome and its characteristics of this rare dragonfly species, contributing to our understanding of the intricate evolutionary relationships within the Odonata order. The data obtained serve as a foundation for further exploration of the complex phylogenetic relationships among dragonfly insects.}, author = {Lin, Binquan and Chen, Hao and Li, Jiayu and Liao, Jian}, @@ -8265,6 +13493,25 @@ @article{lin_characteristics_2024 year = {2024} } +@article{lin_integrative_2025, + abstract = {Delectopecten is a small genus of the family Pectinidae (Bivalvia: Pectinida) that remains poorly studied in terms of both morphology and phylogeny. Here, we describe the first member of this genus from deep-sea hydrothermal vent ecosystems, D. thermus sp. nov., based on morphological investigations and molecular analyses of a specimen collected from the Higashi–Ensei vent field (962-m depth) in the northern Okinawa Trough. Morphologically, this new species resembles D. vancouverensis and D. gelatinosus in shell size, shape, auricle size and sculpture. However, D. thermus sp. nov. can be distinguished from its congeneric species (including 9 extant and 12 fossil species) by its unequal auricles (the anterior one being larger than the posterior), inwardly recurved anterior auricle of the left valve and a large byssal notch angle of {\textasciitilde}90°. Comparisons of genetic sequences from three mitochondrial and three nuclear gene fragments supported the placement of the new species in the genus Delectopecten. Further phylogenetic analyses using these gene markers support that Delectopecten is monophyletic and positioned as an early diverging clade of the family Pectinidae. Additionally, the mitogenome of D. thermus sp. nov. was assembled and annotated, a first for its genus – revealing significant divergences in gene order compared to other pectinids. The 16S rRNA amplicon analysis of the gill tissue indicated that this vent-dwelling scallop does not exhibit symbiosis with chemosynthetic bacteria. A key to all known species of Delectopecten is provided to aid the identification of species in this understudied genus. ZooBank: urn:lsid:zoobank.org:pub:D3D5D4AD-EE39-49F0-9782-12A5D6752A67}, + author = {Lin, Yi-Tao and Peng, Ying-Bei and Chen, Chong and Xu, Ting and Qiu, Jian-Wen}, + doi = {10.1071/IS24091}, + issn = {1447-2600}, + journal = {Invertebrate Systematics}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {February}, + note = {Publisher: CSIRO PUBLISHING}, + number = {2}, + pages = {NULL--NULL}, + title = {Integrative morphological, mitogenomic and phylogenetic analyses reveal new vent-dwelling scallop species}, + url = {https://www.publish.csiro.au/is/IS24091}, + urldate = {2025-02-16}, + volume = {39}, + year = {2025} +} + @phdthesis{link_characterization_2024, abstract = {{\textless}em{\textgreater}T. halophilus{\textless}/em{\textgreater} and {\textless}em{\textgreater}D. hansenii{\textless}/em{\textgreater} are key players in the fermentation of lupine moromi. Comparative genomic analyses and transcriptomic profiling of {\textless}em{\textgreater}T. halophilus{\textless}/em{\textgreater} strains isolated from lupine moromi led to the identification of genes beneficial in this environment. Further, the competitiveness of isolated {\textless}em{\textgreater}T. halophilus{\textless}/em{\textgreater} strains in a lupine moromi model fermentation was investigated. The {\textless}em{\textgreater}D. hansenii{\textless}/em{\textgreater} strain that dominated the lupine moromi fermentation was fully sequenced and genomically analyzed.}, author = {Link, Tobias}, @@ -8276,13 +13523,30 @@ @phdthesis{link_characterization_2024 year = {2024} } +@article{link_diversity_2021, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Tetragenococcus (T.) halophilus can be isolated from a variety of fermented foods, such as soy sauce, different soy pastes, salted fish sauce and from cheese brine or degraded sugar beet thick juice. This species contributes by the formation of short chain acids to the flavor of the product. Recently, T. halophilus has been identified as a dominant species in a seasoning sauce fermentation based on koji made with lupine seeds.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}In this study we characterized six strains of T. halophilus isolated from lupine moromi fermentations in terms of their adaptation towards this fermentation environment, salt tolerance and production of biogenic amines. Phylogenic and genomic analysis revealed three distinctive lineages within the species T. halophilus with no relation to their isolation source, besides the lineage of T. halophilus subsp. flandriensis. All isolated strains from lupine moromi belong to one lineage in that any of the type strains are absent. The strains form lupine moromi could not convincingly be assigned to one of the current subspecies. Taken together with strain specific differences in the carbohydrate metabolism (arabinose, mannitol, melibiose, gluconate, galactonate) and amino acid degradation pathways such as arginine deiminase pathway (ADI) and the agmatine deiminase pathway (AgDI) the biodiversity in the species of T. halophilus is greater than expected. Among the new strains, some strains have a favorable combination of traits wanted in a starter culture.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}Our study characterized T. halophilus strains that were isolated from lupine fermentation. The lupine moromi environment appears to select strains with specific traits as all of the strains are phylogenetically closely related, which potentially can be used as a starter culture for lupine moromi. We also found that the strains can be clearly distinguished phylogenetically and phenotypically from the type strains of both subspecies T. halophilus subsp. halophilus and T. halophilus subsp. flandriensis.}, + author = {Link, Tobias and Vogel, Rudi F and Ehrmann, Matthias A}, + doi = {10.1186/s12866-021-02381-1}, + issn = {1471-2180}, + journal = {BMC microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {November}, + number = {1}, + pages = {320}, + title = {The diversity among the species {Tetragenococcus} halophilus including new isolates from a lupine seed fermentation}, + url = {http://europepmc.org/abstract/MED/34798831}, + volume = {21}, + year = {2021} +} + @article{lipinska_rhodoexplorer_2023, abstract = {Macroalgal (seaweed) genomic resources are generally lacking as compared with other eukaryotic taxa, and this is particularly true in the red algae (Rhodophyta). Understanding red algal genomes is critical to understanding eukaryotic evolution given that red algal genes are spread across eukaryotic lineages from secondary endosymbiosis and red algae diverged early in the Archaeplastids. The Gracilariales is a highly diverse and widely distributed order including species that can serve as ecosystem engineers in intertidal habitats and several notorious introduced species. The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also emerging as a model for algal evolutionary ecology. Here, we report new whole-genome assemblies for two species (Gracilaria chilensis and Gracilaria gracilis), a draft genome assembly of Gracilaria caudata, and genome annotation of the previously published Gracilaria vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution.}, author = {Lipinska, Agnieszka P and Krueger-Hadfield, Stacy A and Godfroy, Olivier and Dittami, Simon M and Ayres-Ostrock, Lígia and Bonthond, Guido and Brillet-Guéguen, Loraine and Coelho, Susana and Corre, Erwan and Cossard, Guillaume and Destombe, Christophe and Epperlein, Paul and Faugeron, Sylvain and Ficko-Blean, Elizabeth and Beltrán, Jessica and Lavaut, Emma and Le Bars, Arthur and Marchi, Fabiana and Mauger, Stéphane and Michel, Gurvan and Potin, Philippe and Scornet, Delphine and Sotka, Erik E and Weinberger, Florian and Cabral de Oliveira, Mariana and Guillemin, Marie-Laure and Plastino, Estela M and Valero, Myriam}, doi = {10.1093/gbe/evad124}, issn = {1759-6653}, journal = {Genome Biology and Evolution}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Gracilaria, Rhodophyta}, month = {July}, number = {7}, pages = {evad124}, @@ -8312,6 +13576,43 @@ @article{liu_comparative_2022 year = {2022} } +@article{liu_complete_2020, + abstract = {Here, we report the complete mitochondrial (mt) genome of \textit{Antheraea pernyi} Qing\_6, an improved strain serving silk production and edible insect resource for 50 years in Northeast China. The circular mt genome spans 15,572 bp in length and contains 37 typical coding genes (13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes). Its A + T-rich region is 552 bp in size exhibiting identical sequence with the first modern improved strain Qinghuang\_1. Comparison analysis identified only 12 variable sites (5 substitutions and 7 indels) between Qing\_6 and Qinghuang\_1. The phylogenetic analysis also clustered Qing\_6 and Qinghuang\_1 together first, which was in line with the breeding history of the two strains.}, + author = {Liu, Yun-Can and Li, Xin-Yu and Chen, Dong-Bin and Liu, Yan-Qun and Li, Xi-Sheng}, + doi = {10.1080/23802359.2020.1823903}, + issn = {2380-2359}, + journal = {Mitochondrial DNA. Part B, Resources}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {September}, + number = {3}, + pages = {3379--3380}, + title = {The complete mitochondrial genome of antheraea pernyi strain qing\_6 (lepidoptera: {Saturniidae})}, + url = {http://europepmc.org/abstract/MED/33458176}, + volume = {5}, + year = {2020} +} + +@article{liu_complete_2025, + abstract = {This study aimed to examine the complete mitogenome sequence of Crocidura rapax Allen, 1923 using polymerase chain reaction. The mitochondrial genome of C. rapax is a circular double-stranded structure with a complete length of 17,517 bp. The mitochondrial genome of C. rapax included 13 protein-coding genes, one control region, 22 tRNA genes, two rRNA genes, and one origin of L-strand replication. This study confirmed the phylogenetic position of C. rapax in the Crocidura genus at the molecular level. The mitochondrial genome is of significant importance for elucidating the genetic background of C. rapax.}, + author = {Liu, Zhu and , Lu, Miao and , Qiu-Ying, Guo and and Han, Mei-Feng}, + doi = {10.1080/23802359.2025.2475839}, + issn = {null}, + journal = {Mitochondrial DNA Part B}, + keywords = {{\textgreater}UseGalaxy.eu, Crocidura rapax, mitogenome, phylogenetic trees}, + month = {April}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/23802359.2025.2475839}, + number = {4}, + pages = {288--291}, + pmid = {40084134}, + title = {The complete mitochondrial genome of {Crocidura} rapax {Allen}, 1923 and its phylogenetic analyses}, + url = {https://doi.org/10.1080/23802359.2025.2475839}, + urldate = {2025-03-29}, + volume = {10}, + year = {2025} +} + @article{liu_comprehensive_2023, abstract = {Precisely calling chromatin loops has profound implications for further analysis of gene regulation and disease mechanisms. Technological advances in chromatin conformation capture (3C) assays make it possible to identify chromatin loops in the genome. However, a variety of experimental protocols have resulted in different levels of biases, which require distinct methods to call true loops from the background. Although many bioinformatics tools have been developed to address this problem, there is still a lack of special introduction to loop-calling algorithms. This review provides an overview of the loop-calling tools for various 3C-based techniques. We first discuss the background biases produced by different experimental techniques and the denoising algorithms. Then, the completeness and priority of each tool are categorized and summarized according to the data source of application. The summary of these works can help researchers select the most appropriate method to call loops and further perform downstream analysis. In addition, this survey is also useful for bioinformatics scientists aiming to develop new loop-calling algorithms.}, author = {Liu, Li and Han, Kaiyuan and Sun, Huimin and Han, Lu and Gao, Dong and Xi, Qilemuge and Zhang, Lirong and Lin, Hao}, @@ -8342,6 +13643,23 @@ @article{liu_denovoprofiling_2021 year = {2021} } +@article{liu_pre-synaptic_2022, + abstract = {Hypersensitivity to mechanical stimuli is a cardinal symptom of neuropathic and inflammatory pain. A reduction in spinal inhibition is generally considered a causal factor in the development of mechanical hypersensitivity after injury. However, the extent to which presynaptic inhibition contributes to altered spinal inhibition is less well established. Here, we used conditional deletion of GABA$_{\textrm{A}}$ in NaV1.8-positive sensory neurons (\textit{Scn10a$^{\textrm{Cre}}$};\textit{Gabrb3$^{\textrm{fl/fl}}$}) to manipulate selectively presynaptic GABAergic inhibition. Behavioral testing showed that the development of inflammatory punctate allodynia was mitigated in mice lacking pre-synaptic GABA$_{\textrm{A}}$. Dorsal horn cellular circuits were visualized in single slices using stimulus-tractable dual-labelling of \textit{c-fos} mRNA for punctate and the cognate c-Fos protein for dynamic mechanical stimulation. This revealed a substantial reduction in the number of cells activated by punctate stimulation in mice lacking presynaptic GABA$_{\textrm{A}}$ and an approximate 50\% overlap of the punctate with the dynamic circuit, the relative percentage of which did not change following inflammation. The reduction in dorsal horn cells activated by punctate stimuli was equally prevalent in parvalbumin- and calretinin-positive cells and across all laminae I-V, indicating a generalized reduction in spinal input. In peripheral DRG neurons, inflammation following complete Freund's adjuvant (CFA) led to an increase in axonal excitability responses to GABA, suggesting that presynaptic GABA effects in NaV1.8$^{\textrm{+}}$ afferents switch from inhibition to excitation after CFA. In the days after inflammation, presynaptic GABA$_{\textrm{A}}$ in NaV1.8$^{\textrm{+}}$ nociceptors constitutes an "open gate" pathway allowing mechanoreceptors responding to punctate mechanical stimulation access to nociceptive dorsal horn circuits.}, + author = {Liu, Sheng and Bonalume, Veronica and Gao, Qi and Chen, Jeremy Tsung-Chieh and Rohr, Karl and Hu, Jing and Carr, Richard}, + doi = {10.3390/cells11152390}, + issn = {2073-4409}, + journal = {Cells}, + keywords = {{\textgreater}UseGalaxy.eu, Hyperalgesia, Nociceptors}, + language = {eng}, + month = {August}, + number = {15}, + pages = {2390}, + title = {Pre-{Synaptic} {GABAA} in {NaV1}.8+ {Primary} {Afferents} {Is} {Required} for the {Development} of {Punctate} but {Not} {Dynamic} {Mechanical} {Allodynia} following {CFA} {Inflammation}}, + url = {http://europepmc.org/abstract/MED/35954234}, + volume = {11}, + year = {2022} +} + @article{livingstone_novo_2023, abstract = {Here, we report the complete genome sequences of Pasteurella multocida strains P504190 and P504188/1, which were isolated from the diseased lungs of a sow and her piglet, respectively. Despite the unusual clinical presentation, whole-genome sequence typing revealed both strains to be capsular type D and lipopolysaccharide (LPS) group 6, commonly found in pigs.}, author = {Livingstone, Morag and Jorgensen, Pernille and McCall, Margaret and Thomson, Jill and Longbottom, David}, @@ -8360,6 +13678,25 @@ @article{livingstone_novo_2023 year = {2023} } +@article{loach_galaxy_2025, + author = {Loach, Marisa and Nilchi, Amirhossein Naghsh and Chiang, Diana and Howells, Morgan and Heyl, Florian and Rasche, Helena and Jakiela, Julia and Tekman, Mehmet and Gamal, Menna and Moreno, Pablo and Hiltemann, Saskia and Schlegel, Timon and Grüning, Björn and Backofen, Rolf and Videm, Pavankumar and Bacon, Wendi}, + doi = {10.1016/j.xgen.2025.101005}, + issn = {2666-979X}, + journal = {Cell Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Galaxy platform, RDM, data life cycle, global collaboration, multiomics, open-source software, reproducibility, research data management, single-cell, spatial, training resources}, + language = {English}, + month = {September}, + note = {Publisher: Elsevier}, + number = {0}, + pmid = {40997812}, + shorttitle = {Galaxy single-cell \& spatial omics community update}, + title = {Galaxy single-cell \& spatial omics community update: {Navigating} new frontiers in 2025}, + url = {https://www.cell.com/cell-genomics/abstract/S2666-979X(25)00261-7}, + urldate = {2025-09-28}, + volume = {0}, + year = {2025} +} + @article{lodewijk_evolution_2020, abstract = {Summary. Ever since the availability of genomes from Neanderthals, Denisovans and ancient humans, the field of evolutionary genomics has been searching for pro}, author = {Lodewijk, Gerrald A. and Fernandes, Diana P. and Vretzakis, Iraklis and Savage, Jeanne E. and Jacobs, Frank M. J.}, @@ -8374,18 +13711,41 @@ @article{lodewijk_evolution_2020 year = {2020} } +@article{lopes_erga-bge_2025, + abstract = {Pyrrhula murina +’s reference genome will substantially enhance the current monitoring of genetic diversity and population viability and will allow us to understand the effective population size trends throughout time and recent bottlenecks and population expansions. A total of 42 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 1.2 Gb, composed of 65 contigs and 60 scaffolds, with contig and scaffold N50 values of 64.8 Mb and 76 Mb, respectively.}, + author = {Lopes, Ricardo Jorge and Böhne, Astrid and Marcussen, Thomas and Oomen, Rebekah A. and Struck, Torsten Hugo and Aguilera, Laura and Gut, Marta and Câmara Ferreira, Francisco and Cruz, Fernando and Gómez-Garrido, Jèssica and Alioto, Tyler S. and Monteiro, Rita}, + doi = {10.12688/openreseurope.20666.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {August}, + pages = {210}, + shorttitle = {{ERGA}-{BGE} reference genome of the {Azores} {Bullfinch} - {Pyrrhula} murina {Godman}, 1866}, + title = {{ERGA}-{BGE} reference genome of the {Azores} {Bullfinch} - {Pyrrhula} murina {Godman}, 1866: an {IUCN} {Vulnerable} {Species} endemic to a single island in the {Azores} {Archipelago} ({Portugal})}, + url = {https://open-research-europe.ec.europa.eu/articles/5-210/v1}, + urldate = {2025-10-19}, + volume = {5}, + year = {2025} +} + @article{lopez-delisle_pygenometracks_2020, abstract = {AbstractMotivation. Generating publication ready plots to display multiple genomic tracks can pose a serious challenge. Making desirable and accurate figures r}, author = {Lopez-Delisle, Lucille and Rabbani, Leily and Wolff, Joachim and Bhardwaj, Vivek and Backofen, Rolf and Grüning, Björn and Ramírez, Fidel and Manke, Thomas}, doi = {10.1093/bioinformatics/btaa692}, + issn = {1367-4803}, journal = {Bioinformatics}, - keywords = {+Galactic, +Tools, +Visualization, {\textgreater}UseGalaxy.eu}, + keywords = {+Galactic, +Tools, +Visualization, {\textgreater}UseGalaxy.eu, Genome, Genomics}, language = {en}, month = {August}, + number = {3}, + pages = {422--423}, shorttitle = {{pyGenomeTracks}}, title = {{pyGenomeTracks}: reproducible plots for multivariate genomic data sets}, url = {https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa692/5879987}, urldate = {2020-08-20}, + volume = {37}, year = {2020} } @@ -8406,13 +13766,28 @@ @article{lopez-santamarina_evaluation_2022 year = {2022} } +@article{lopez-santamarina_nutritional_2022, + abstract = {In this study, an undervalued marine crustacean (\textit{Talitrus saltator}) was characterized in terms of nutritional and heavy metal composition and its potential to affect human gut microbiota. Nutritional analysis of this crustacean revealed that it complies with the criteria established in European legislation to include nutritional claims in their labeling, such as "source of fiber," "low in fat," "low in sugars" and "high in protein." The analysis of the heavy metal content did not reveal any risk derived from the presence of Cd, Hg, or Pb, whereas essential metals contained in 100 g exceeded the minimum daily requirements recommended in Europe for Zn (19.78 mg/kg), Cu (2.28 mg/kg), and Fe (32.96 mg/kg). Using an \textit{in vitro} system, the effect of \textit{T. saltator} on the human colonic microbiota shows some beneficial effects, such as fermentation-maintained populations of \textit{Bifidobacterium} or \textit{Lactobacillus}, did not increase Firmicutes \textit{phylum} counts, decreased the Firmicutes/Bacteroidetes ratio, and stimulated 11 metabolic pathways with respect to baseline. These results are unusual in a high protein content-food. However, negative effects were also found in gut microbiota relative proportions, such as an increase in the Proteobacteria \textit{phylum} and especially some opportunistic bacteria from this \textit{phylum}, probably due to the antimicrobial effect of chitin on other groups more sensitive to its effect. This work shows for the first time the effect of \textit{T. saltator} on human colonic microbiota using and \textit{in vitro} system. The presence of chitin in its composition could provide some beneficial effects by modulating the microbiota, but as \textit{T. saltator} is a high-protein food, more studies should be carried out showing these benefits.}, + author = {Lopez-Santamarina, Aroa and Cardelle-Cobas, Alejandra and Lamas, Alexandre and Mondragon-Portocarrero, Alicia and Cepeda, Alberto and Miranda, Jose Manuel}, + doi = {10.3389/fnut.2022.943133}, + issn = {2296-861X}, + journal = {Frontiers in nutrition}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {943133}, + title = {Nutritional composition, heavy metal content and in vitro effect on the human gut microbiota of {Talitrus} saltator, an underutilized crustacean from the {Atlantic} coast}, + url = {http://europepmc.org/abstract/MED/36313116}, + volume = {9}, + year = {2022} +} + @article{lopez_epigenomic_2024, abstract = {In plants, epigenetic stress memory has so far been found to be largely transient. Here, we wanted to assess the heritability of heat stress-induced epigenetic and transcriptomic changes following woodland strawberry (Fragaria vesca) reproduction. Strawberry is an ideal model to study epigenetic inheritance because it presents two modes of reproduction: sexual (self-pollinated plants) and asexual (clonally propagated plants named daughter plants). Taking advantage of this model, we investigated whether heat stress-induced DNA methylation changes can be transmitted via asexual reproduction.}, author = {López, María-Estefanía and Denoyes, Béatrice and Bucher, Etienne}, doi = {10.1186/s12870-024-05093-6}, issn = {1471-2229}, journal = {BMC Plant Biology}, - keywords = {{\textgreater}UseGalaxy.eu, Asexual, Epigenetic, Fragaria, Memory, Plant, Reproduction, Stress}, + keywords = {{\textgreater}UseGalaxy.eu, Asexual, DNA Methylation, Epigenesis, Genetic, Epigenetic, Fragaria, Heat-Shock Response, Memory, Plant, Reproduction, Stress, Transcriptome}, language = {en}, month = {May}, number = {1}, @@ -8424,6 +13799,23 @@ @article{lopez_epigenomic_2024 year = {2024} } +@article{lorentzen_genomic_2021, + abstract = {Chitin is an abundant natural polysaccharide that is hard to degrade because of its crystalline nature and because it is embedded in robust co-polymeric materials containing other polysaccharides, proteins, and minerals. Thus, it is of interest to study the enzymatic machineries of specialized microbes found in chitin-rich environments. We describe a genomic and proteomic analysis of \textit{Andreprevotia ripae}, a chitinolytic Gram-negative bacterium isolated from an anthill. The genome of \textit{A. ripae} encodes four secreted family GH19 chitinases of which two were detected and upregulated during growth on chitin. In addition, the genome encodes as many as 25 secreted GH18 chitinases, of which 17 were detected and 12 were upregulated during growth on chitin. Finally, the single lytic polysaccharide monooxygenase (LPMO) was strongly upregulated during growth on chitin. Whereas 66\% of the 29 secreted chitinases contained two carbohydrate-binding modules (CBMs), this fraction was 93\% (13 out of 14) for the upregulated chitinases, suggesting an important role for these CBMs. Next to an unprecedented multiplicity of upregulated chitinases, this study reveals several chitin-induced proteins that contain chitin-binding CBMs but lack a known catalytic function. These proteins are interesting targets for discovery of enzymes used by nature to convert chitin-rich biomass. The MS proteomic data have been deposited in the PRIDE database with accession number PXD025087.}, + author = {Lorentzen, Silje B and Arntzen, Magnus Ø and Hahn, Thomas and Tuveng, Tina R and Sørlie, Morten and Zibek, Susanne and Vaaje-Kolstad, Gustav and Eijsink, Vincent G H}, + doi = {10.1021/acs.jproteome.1c00358}, + issn = {1535-3893}, + journal = {J Proteome Res}, + keywords = {{\textgreater}UseGalaxy.eu, Chitinases, Proteomics}, + language = {eng}, + month = {August}, + number = {8}, + pages = {4041--4052}, + title = {Genomic and {Proteomic} {Study} of {Andreprevotia} ripae {Isolated} from an {Anthill} {Reveals} an {Extensive} {Repertoire} of {Chitinolytic} {Enzymes}}, + url = {http://europepmc.org/abstract/MED/34191517}, + volume = {20}, + year = {2021} +} + @article{lorenzo_camacho_incorporacion_2023, abstract = {En el estudio de mutaciones del genoma, las herramientas desarrolladas en el ámbito de la bioinformática han marcado un antes y después, facilitando la rápida detección de variaciones en el ADN y favoreciendo el ejercicio de la medicina personalizada dentro del ámbito de la oncología. En este trabajo se ha hecho un estudio experimental con la finalidad de aprender sobre las diferentes herramientas bioinformáticas para el análisis de genoma humano y la detección de variantes o mutaciones en el mismo. Para ello, se utilizaron muestras de ADN y ARN de pacientes anonimizados (identificados por códigos). Estas muestras fueron aportadas y secuenciadas por el servicio de Anatomía Patológica del Hospital Universitario de Canarias. En ellas, se detectaron mutaciones o variaciones concordantes con diferentes patologías. En la actualidad, la bioinformática a pesar de aportar una mejoría exponencial en la detección y entendimiento de las patologías, sigue siendo una subespecialidad de “nicho”, principalmente debido a su larga curva de aprendizaje. Sin embargo, es necesario dedicar esfuerzos a la formación y la divulgación de la bioinformática entre los profesionales de la salud, ya que esta subespecialidad tiene una previsión de desarrollo muy grande y podría ser indispensable a la hora de hacer más eficiente el diagnóstico y la terapéutica médica.}, author = {Lorenzo Camacho, Valentina}, @@ -8437,6 +13829,23 @@ @article{lorenzo_camacho_incorporacion_2023 year = {2023} } +@article{lorite_cytogenetic_2025, + abstract = {\textit{Sphaerophoria rueppellii} is a Palearctic hoverfly widely used as a native biocontrol agent against aphid pests in Mediterranean agroecosystems. In this study, we present a cytogenetic analysis and characterization of the mitochondrial genome of this species. Chromosomal preparations, obtained from third-instar larvae, were used for conventional staining, DAPI staining and C-banding techniques, and major ribosomal DNA (rDNA) location by fluorescence in situ hybridization (FISH). Karyotype analysis revealed a diploid number of 2n = 10, with heterochromatic blocks in the pericentromeric regions of all autosomes and rDNA clusters on both sex chromosomes. The complete mitochondrial genome (16,605 bp) was sequenced and annotated using next-generation sequencing and assembly pipelines. It contains the typical 37 mitochondrial genes and a highly A + T-rich control region with tandem repeats. Gene order and codon usage were conserved compared with other Syrphidae. Phylogenetic reconstruction based on mitochondrial protein-coding genes clarifies the species' placement within the Syrphini tribe. Our results contribute valuable genomic and cytogenetic information that supports comparative analyses and may aid in taxonomic clarification within the genus. These findings also offer key data that could guide the genetic optimization of \textit{S. rueppellii} as an efficient, environmentally safe biological control agent in sustainable agriculture.}, + author = {Lorite, Pedro and Rico-Porras, José M and Palomeque, Teresa and Marcos-García, Mª Ángeles and Cabral-de-Mello, Diogo C and Mora, Pablo}, + doi = {10.3390/insects16060604}, + issn = {2075-4450}, + journal = {Insects}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {June}, + number = {6}, + pages = {604}, + title = {Cytogenetic and {Molecular} {Characterization} of \textit{{Sphaerophoria} rueppellii} ({Diptera}, {Syrphidae})}, + url = {http://europepmc.org/abstract/MED/40559034}, + volume = {16}, + year = {2025} +} + @article{lother_diabetes_2020, abstract = {{\textless}h2{\textgreater}Abstract{\textless}/h2{\textgreater}{\textless}h3{\textgreater}Background{\textless}/h3{\textgreater}{\textless}p{\textgreater}Diabetes mellitus is a worldwide epidemic that causes high mortality due to cardiovascular complications, in particular heart failure. Diabetes is associated with profound pathophysiological changes in the heart. The aim of this study was to investigate the impact of diabetes on gene expression and DNA methylation in cardiac cells.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Methods and results{\textless}/h3{\textgreater}{\textless}p{\textgreater}Transcriptome analysis of heart tissue from mice with streptozotocin-induced diabetes revealed only 39 genes regulated, whereas cell type-specific analysis of the diabetic heart was more sensitive and more specific than heart tissue analysis and revealed a total of 3205 differentially regulated genes in five cell types. Whole genome DNA methylation analysis with basepair resolution of distinct cardiac cell types identified highly specific DNA methylation signatures of genic and regulatory regions. Interestingly, despite marked changes in gene expression, DNA methylation remained stable in streptozotocin-induced diabetes. Integrated analysis of cell type-specific gene expression enabled us to assign the particular contribution of single cell types to the pathophysiology of the diabetic heart. Finally, analysis of gene regulation revealed ligand-receptor pairs as potential mediators of heterocellular interaction in the diabetic heart, with fibroblasts and monocytes showing the highest degree of interaction.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Conclusion{\textless}/h3{\textgreater}{\textless}p{\textgreater}In summary, cell type-specific analysis reveals differentially regulated gene programs that are associated with distinct biological processes in diabetes. Interestingly, despite these changes in gene expression, cell type-specific DNA methylation signatures of genic and regulatory regions remain stable in diabetes. Analysis of heterocellular interactions in the diabetic heart suggest that the interplay between fibroblasts and monocytes is of pivotal importance.{\textless}/p{\textgreater}}, author = {Lother, Achim and Bondareva, Olga and Saadatmand, Ali R. and Pollmeier, Luisa and Härdtner, Carmen and Hilgendorf, Ingo and Weichenhan, Dieter and Eckstein, Volker and Plass, Christoph and Bode, Christoph and Backs, Johannes and Hein, Lutz and Gilsbach, Ralf}, @@ -8486,11 +13895,30 @@ @book{lu_engineering_2023 } @article{lucaci_rascl_2022, + abstract = {An important unmet need revealed by the COVID-19 pandemic is the near-real-time identification of potentially fitness-altering mutations within rapidly growing SARS-CoV-2 lineages. Although powerful molecular sequence analysis methods are available to detect and characterize patterns of natural selection within modestly sized gene-sequence datasets, the computational complexity of these methods and their sensitivity to sequencing errors render them effectively inapplicable in large-scale genomic surveillance contexts. Motivated by the need to analyze new lineage evolution in near-real time using large numbers of genomes, we developed the Rapid Assessment of Selection within CLades (RASCL) pipeline. RASCL applies state of the art phylogenetic comparative methods to evaluate selective processes acting at individual codon sites and across whole genes. RASCL is scalable and produces automatically updated regular lineage-specific selection analysis reports: even for lineages that include tens or hundreds of thousands of sampled genome sequences. Key to this performance is (i) generation of automatically subsampled high quality datasets of gene/ORF sequences drawn from a selected "query" viral lineage; (ii) contextualization of these query sequences in codon alignments that include high-quality "background" sequences representative of global SARS-CoV-2 diversity; and (iii) the extensive parallelization of a suite of computationally intensive selection analysis tests. Within hours of being deployed to analyze a novel rapidly growing lineage of interest, RASCL will begin yielding JavaScript Object Notation (JSON)-formatted reports that can be either imported into third-party analysis software or explored in standard web-browsers using the premade RASCL interactive data visualization dashboard. By enabling the rapid detection of genome sites evolving under different selective regimes, RASCL is well-suited for near-real-time monitoring of the population-level selective processes that will likely underlie the emergence of future variants of concern in measurably evolving pathogens with extensive genomic surveillance.}, + author = {Lucaci, Alexander G and Zehr, Jordan D and Shank, Stephen D and Bouvier, Dave and Ostrovsky, Alexander and Mei, Han and Nekrutenko, Anton and Martin, Darren P and Kosakovsky Pond, Sergei L}, + doi = {10.1371/journal.pone.0275623}, + issn = {1932-6203}, + journal = {PloS one}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19, SARS-CoV-2}, + language = {eng}, + number = {11}, + pages = {e0275623}, + title = {{RASCL}: {Rapid} {Assessment} of {Selection} in {CLades} through molecular sequence analysis}, + url = {http://europepmc.org/abstract/MED/36322581}, + volume = {17}, + year = {2022} +} + +@article{lucaci_rascl_2022, + abstract = {An important component of efforts to manage the ongoing COVID19 pandemic is the R apid A ssessment of how natural selection contributes to the emergence and proliferation of potentially dangerous S ARS-CoV-2 lineages and CL ades (RASCL). The RASCL pipeline enables continuous comparative phylogenetics-based selection analyses of rapidly growing clade-focused genome surveillance datasets, such as those produced following the initial detection of potentially dangerous variants. From such datasets RASCL automatically generates down-sampled codon alignments of individual genes/ORFs containing contextualizing background reference sequences, analyzes these with a battery of selection tests, and outputs results as both machine readable JSON files, and interactive notebook-based visualizations. {\textless}h4{\textgreater}Availability{\textless}/h4{\textgreater} RASCL is available from a dedicated repository at https://github.com/veg/RASCL and as a Galaxy workflow https://usegalaxy.eu/u/hyphy/w/rascl . Existing clade/variant analysis results are available here: https://observablehq.com/@aglucaci/rascl . {\textless}h4{\textgreater}Contact{\textless}/h4{\textgreater} Dr. Sergei L Kosakovsky Pond ( spond@temple.edu ). {\textless}h4{\textgreater}Supplementary information{\textless}/h4{\textgreater} N/A}, author = {Lucaci, Alexander G and Zehr, Jordan D and Shank, Stephen D and Bouvier, Dave and Mei, Han and Nekrutenko, Anton and Martin, Darren P and Pond, Sergei}, + doi = {10.1101/2022.01.15.476448}, journal = {bioRxiv}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, note = {Publisher: Cold Spring Harbor Laboratory}, title = {{RASCL}: {Rapid} {Assessment} {Of} {SARS}-{CoV}-2 {Clades} {Through} {Molecular} {Sequence} {Analysis}}, + url = {http://europepmc.org/abstract/PPR/PPR443709}, year = {2022} } @@ -8500,10 +13928,11 @@ @article{luenstedt_partial_2024 doi = {10.3389/fimmu.2024.1388272}, issn = {1664-3224}, journal = {Frontiers in Immunology}, - keywords = {{\textgreater}UseGalaxy.eu, Partial hepatectomy, Tight Junctions, colorectal cancer, liver metastasis, premetastatic niche}, + keywords = {{\textgreater}UseGalaxy.eu, Colorectal Neoplasms, Hepatectomy, Liver Neoplasms, Partial hepatectomy, Tight Junctions, colorectal cancer, liver metastasis, premetastatic niche}, language = {English}, month = {June}, note = {Publisher: Frontiers}, + pages = {1388272}, title = {Partial hepatectomy accelerates colorectal metastasis by priming an inflammatory premetastatic niche in the liver}, url = {https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1388272/full}, urldate = {2024-06-17}, @@ -8529,6 +13958,69 @@ @article{luo_3d_2021 year = {2021} } +@article{luo_comparative_2025, + abstract = {Background: Lonchodidae is the largest family within the order Phasmatodea, and although many studies have been conducted on this family, the monophyly of the family has not been established. Methods: Eight mitogenomes from Lonchodidae, including the first complete mitogenomes of four genera, were sequenced and annotated to explore their features and phylogenetic relationships. Results: The total length ranged from 15,942–18,021 bp, and the mitogenome consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a control region (CR). atp8 had the highest A + T content in Lonchodidae, except for Neohirasea stephanus and Asceles clavatus, in which the highest A + T contents were detected in nad6. The phylogenetic trees were reconstructed via Bayesian inference (BI) and maximum likelihood (ML) based on the PCG123 and PCG12 datasets. As the phylogenetic trees show, Necrosciinae is recognized as monophyletic, but the monophyly of Lonchodinae has not been supported. Gene deletion and rearrangement have occurred mainly in Lonchodidae and Aschiphasmatidae. The most common reason for gene rearrangements was tandem duplication random loss (TDRL), but trnI of Stheneboea repudiosa inverted into the CR. In addition, genes within the same family or genus share related sequences and conserved gene blocks. Conclusions: we expanded the mitochondrial genomic data for this family, thereby establishing a foundational dataset for future studies.}, + author = {Luo, Ting and Zhang, Qianwen and Pang, Siyu and Qin, Yanting and Zhang, Bin and Bian, Xun}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/genes16050565}, + issn = {2073-4425}, + journal = {Genes}, + keywords = {{\textgreater}UseGalaxy.eu, Genome, Mitochondrial, Phylogeny, mitogenome, phylogenetic analysis, stick insects}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {565}, + shorttitle = {Comparative {Mitochondrial} {Genomic} and {Phylogenetic} {Study} of {Eight} {Species} of the {Family} {Lonchodidae} ({Phasmatodea}}, + title = {Comparative {Mitochondrial} {Genomic} and {Phylogenetic} {Study} of {Eight} {Species} of the {Family} {Lonchodidae} ({Phasmatodea}: {Euphasmatodea})}, + url = {https://www.mdpi.com/2073-4425/16/5/565}, + urldate = {2025-05-29}, + volume = {16}, + year = {2025} +} + +@article{lv_first_2025, + abstract = {Baetidae is a globally diverse mayfly family. While COI DNA barcode studies are abundant, its mitogenomic data remain scarce. In this study, we present the first mitochondrial genome of Cloeon viridulum Navás, 1931. The mitogenome of C. viridulum spans 14,431 bp and includes 13 protein-coding genes, 22 transfer RNA genes, and one 16S ribosomal RNA (rRNA) gene. However, it features an incomplete 12S rRNA gene and lacks a control region. This mitogenome has a GC content of 32.4\%. Phylogenetic analysis strongly supports a sister relationship between C. viridulum and C. dipterum. Our findings offer genomic insights into Baetidae evolution.}, + author = {Lv, Mengyu and Zhu, Tianzhe}, + doi = {10.1080/23802359.2025.2602240}, + issn = {null}, + journal = {Mitochondrial DNA Part B}, + keywords = {{\textgreater}UseGalaxy.eu, Baetidae, mitochondrial genome, phylogeny}, + month = {December}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/23802359.2025.2602240}, + number = {1}, + pages = {74--78}, + shorttitle = {First report of mitochondrial genome of {Cloeon} viridulum ({Ephemeroptera}}, + title = {First report of mitochondrial genome of {Cloeon} viridulum ({Ephemeroptera}: {Baetidae}) from {Hebei}, {China}}, + url = {https://doi.org/10.1080/23802359.2025.2602240}, + urldate = {2025-12-26}, + volume = {11}, + year = {2025} +} + +@article{lydon_comparative_2025, + abstract = {Vibrionaceae are a diverse family of bacteria that contain pathogenic species, including those within the Vulnificus clade: Vibrio vulnificus, Vibrio navarrensis, and Vibrio cidicii. While V. vulnificus is a generally well-characterized environmental pathogen, V. cidicii and V. navarrensis are relatively rare, recently identified species that our current understanding of virulence and environmental adaptation is limited. Here, we investigate genetic relatedness across these three species to identify shared and species-specific genes, including markers of virulence. Using publicly available genome assemblies (n = 76), we evaluated phylogenetic and genomic diversity across this clade. We sampled all available V. navarrensis and V. cidicii genomes and a biodiverse curated set of four V. vulnificus ecotypes to ensure representative coverage. Our results indicate that all three species share 2,313 core genes, many of which are core bacterial functions in addition to pathways important to environmental response, host immune evasion, and iron acquisition. Moreover, V. cidicii and V. navarrensis have extensive genetic similarity between them, including average nucleotide identities {\textgreater}95\% and 370 shared genes. Despite this similarity, they both remain more phylogenetically distant from V. vulnificus and lack key virulence genes, such as rtxA, indicating alternative pathogenic potential. Overall, these findings reveal distinct evolutionary strategies within the Vulnificus clade, with V. vulnificus specializing in enhanced pathogenesis, while V. navarrensis and V. cidicii have evolved enhanced environmental persistence capabilities.ImportanceVibrio species are important environmental aquatic bacteria that pose a threat to human and animal health across the globe. This study applied comparative genomics to investigate the genetic relatedness of Vibrio vulnificus, Vibrio navarrensis, and Vibrio cidicii, with special focus on genes associated with environmental adaptation and virulence between and within each species. Results indicate V. navarrensis and V. cidicii share many genes, are phylogenetically close, and exhibit genomic signatures of enhanced environmental persistence and stress tolerance in addition to survival in anthropogenically impacted marine systems. Furthermore, V. vulnificus possesses an overall different virulence potential with the presence of RTX systems. This adds to our understanding of genetic diversity and pathogenic mechanisms within an important group of marine pathogens.}, + author = {Lydon, Keri Ann and Lott, Megan E J}, + copyright = {cc by}, + doi = {10.1128/aem.01827-25}, + issn = {1098-5336}, + journal = {Applied and environmental microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Comparative genomics, One Health, Vibrio Cidicii, Vibrio Navarrensis, Vibrio vulnificus, Virulence Potential}, + language = {eng}, + month = {December}, + number = {12}, + pages = {e0182725}, + pmcid = {PMC12724252}, + pmid = {41251342}, + title = {Comparative genomics reveals specialization and divergent virulence potential in \<i\>{Vibrio} vulnificus\</i\>, \<i\>{Vibrio} navarrensis\</i\>, and \<i\>{Vibrio} cidicii\</i\>}, + url = {https://europepmc.org/articles/PMC12724252}, + urldate = {2025-12-26}, + volume = {91}, + year = {2025} +} + @article{ma_somatostatin_2020, abstract = {Somatostatin is a neuropeptide and a key regulator of the growth axis. Six Sst encoding genes (sst1 to sst6) have been identified in teleost fish genomes but little is known about their function. The present study aimed at replicating the context of the inflammatory bowel disease (IBD) and clarifying the involvement of sst3 in the intestine innate defence barrier in zebrafish larvae. We first established a CRISP/Cas9 sst3 deficient line (MT) and analysed the morphological and transcriptomic response to 0.4\% dextran sulfate sodium (DSS). Alcian blue staining of larval sections 6 days post fertilization showed an increased in acidic mucins in the intestinal bulb and mid-intestine, with a much stronger response in the MT compared to wild type (WT). The transcriptomic analysis revealed that WT and MT shared enriched gene ontology (GO) terms and pathways linked to catabolism, chondrocyte development, innate immune system, xenobiotic metabolism and oxidative stress. In contrast, the WT specific response to DSS was enriched in GO terms and pathways linked to transcription and translation, various developmental processes, regulation of biosynthetic processes, apelin signalling and apoptosis while the MT specific response included terms and pathways linked to protein metabolism and catabolic processes, extracellular matrix – receptor interaction and proteasome and chondrocyte development. Overall, this study demonstrated that Sst3 deficiency impairs insulin growth factor and adipocytokine signalling exacerbating the inflammatory response to DSS.}, author = {Ma, Jing and Chen, Jie and Louro, Bruno and Martins, Rute S. T. and Canario, Adelino V. M.}, @@ -8544,6 +14036,23 @@ @article{ma_somatostatin_2020 year = {2020} } +@article{machado_exploring_2025, + abstract = {Huanglongbing (HLB), caused mainly by \textit{Candidatus} Liberibacter \textit{asiaticus} (CLas), is a devastating disease threatening citrus production worldwide, leading to leaf mottling, fruit deformation, and significant yield losses. This study generated a comprehensive co-expression network analysis using RNA-seq data from 17 public datasets. Weighted gene co-expression network analysis (WGCNA) was applied to identify gene modules associated with citrus species, tissue types, and days post-infection (DPIs). These modules revealed significant enrichment in biological pathways related to stress responses, metabolic reprograming, ribosomal protein synthesis, chloroplast and plastid function, cellular architecture, and intracellular transport. The results offer a molecular framework for understanding HLB pathogenesis and host response. By elucidating module-specific functions and their correlation with species- and tissue-specific responses, this study provides a robust foundation for identifying key genetic targets. These insights facilitate breeding programs focused on developing HLB-tolerant citrus cultivars, contributing to the long-term sustainability and resilience of global citrus production.}, + author = {Machado, Rodrigo and Moschen, Sebastián and Conti, Gabriela and González, Sergio A and Rivarola, Máximo and Gómez, Claudio and Hopp, Horacio Esteban and Fernández, Paula}, + doi = {10.3390/plants14121792}, + issn = {2223-7747}, + journal = {Plants (Basel, Switzerland)}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {June}, + number = {12}, + pages = {1792}, + title = {Exploring the {Genetic} {Networks} of {HLB} {Tolerance} in {Citrus}: {Insights} {Across} {Species} and {Tissues}}, + url = {http://europepmc.org/abstract/MED/40573779}, + volume = {14}, + year = {2025} +} + @article{mack-bowles_mechanisms_2024, abstract = {Mycophenolate Mofetil (MMF) is a commonly prescribed immunosuppressant that demonstrates important clinical relevance. However, MMF therapy is linked to frequent gastrointestinal (GI) side effects that limit its use. Little is known about the mechanisms underlying MMF-induced GI injury. Using a primary mouse colon organoid model, we have found that mycophenolic acid (MPA), the pharmacologically active metabolite of MMF, significantly alters intestinal barrier function and permeability through modulation of tight junctions. RNA sequencing revealed that MPA significantly disrupted pathways related to cell cycle regulation, DNA replication, cytoskeleton dynamics, and suppression of senescence. MPA was observed to significantly reduce cellular proliferation, which was ameliorated through guanosine supplementation. Addition of exogenous guanosine was also observed to significantly restore barrier function back to control levels. The guanosine studies presented in this thesis suggest MPA’s inhibition of nucleotide metabolism is not selective for lymphocytes but is broader than originally described. This work represents one of the first investigations of MPA using a colon organoid model, providing critical insights into the intracellular mechanisms of MPA-induced GI toxicity.}, author = {Mack-Bowles, Brenan}, @@ -8556,14 +14065,35 @@ @article{mack-bowles_mechanisms_2024 year = {2024} } +@article{mack_further_2022, + abstract = {Reduction of insulin/insulin-like growth factor 1 (IGF1) signaling (IIS) promotes longevity across species. In the nematode \textit{Caenorhabditis elegans}, ablation of germline stem cells (GSCs) and activity changes of the conserved signaling mediators \textit{unc-43/CaMKII} (calcium/calmodulin-dependent kinase type II) and \textit{egl-8/PLCβ} (phospholipase Cβ) also increase lifespan. Like IIS, these pathways depend on the conserved transcription factor \textit{daf-16/FOXO} for lifespan extension, but how they functionally interact is unknown. Here, we show that altered \textit{unc-43/egl-8} activity further increases the lifespan of long-lived GSC-deficient worms, but not of worms that are long-lived due to a strong reduction-of-function mutation in the insulin/IGF1-like receptor \textit{daf-2}. Additionally, we provide evidence for \textit{unc-43} and, to a lesser extent, \textit{egl-8} modulating the expression of certain collagen genes, which were reported to be dispensable for longevity of these particular \textit{daf-2} mutant worms, but not for other forms of longevity. Together, these results provide new insights into the conditions and potential mechanisms by which CaMKII- and PLCβ-signals modulate \textit{C. elegans} lifespan.}, + author = {Mack, Hildegard I D and Buck, Laura G and Skalet, Sonja and Kremer, Jennifer and Li, Hao and Mack, Elisabeth K M}, + doi = {10.3390/cells11223527}, + issn = {2073-4409}, + journal = {Cells}, + keywords = {{\textgreater}UseGalaxy.eu, Caenorhabditis elegans Proteins, Insulins}, + language = {eng}, + month = {November}, + number = {22}, + pages = {3527}, + title = {Further {Extension} of {Lifespan} by {Unc}-43/{CaMKII} and {Egl}-8/{PLCβ} {Mutations} in {Germline}-{Deficient} {Caenorhabditis} elegans}, + url = {http://europepmc.org/abstract/MED/36428956}, + volume = {11}, + year = {2022} +} + @article{mack_regulation_2022, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}In the nematode Caenorhabditis elegans, longevity in response to germline ablation, but not in response to reduced insulin/IGF1-like signaling, is strongly dependent on the conserved protein kinase minibrain-related kinase 1 (MBK-1). In humans, the MBK-1 ortholog DYRK1A is associated with a variety of disorders, most prominently with neurological defects observed in Down syndrome. To better understand mbk-1's physiological roles and their dependence on genetic background, we analyzed the influence of mbk-1 loss on the transcriptomes of wildtype and long-lived, germline-deficient or insulin-receptor defective, C. elegans strains by RNA-sequencing.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}mbk-1 loss elicited global changes in transcription that were less pronounced in insulin-receptor mutant than in germline-deficient or wildtype C. elegans. Irrespective of genetic background, mbk-1 regulated genes were enriched for functions in biological processes related to organic acid metabolism and pathogen defense. qPCR-studies confirmed mbk-1 dependent induction of all three C. elegans Δ9-fatty acid desaturases, fat-5, fat-6 and fat-7, in wildtype, germline-deficient and insulin-receptor mutant strains. Conversely, mbk-1 dependent expression patterns of selected pathogen resistance genes, including asp-12, dod-24 and drd-50, differed across the genetic backgrounds examined. Finally, cth-1 and cysl-2, two genes which connect pathogen resistance to the metabolism of the gaseous messenger and lifespan regulator hydrogen sulfide (H$_{\textrm{2}}$S), were commonly suppressed by mbk-1 loss only in wildtype and germline-deficient, but not in insulin-receptor mutant C. elegans.{\textless}h4{\textgreater}Conclusion{\textless}/h4{\textgreater}Our work reveals previously unknown roles of C. elegans mbk-1 in the regulation of fatty acid desaturase- and H$_{\textrm{2}}$S metabolic-genes. These roles are only partially dependent on genetic background. Considering the particular importance of fatty acid desaturation and H$_{\textrm{2}}$S for longevity of germline-deficient C. elegans, we propose that these processes at least in part account for the previous observation that mbk-1 preferentially regulates lifespan in these worms.}, author = {Mack, Hildegard I. D. and Kremer, Jennifer and Albertini, Eva and Mack, Elisabeth K. M. and Jansen-Dürr, Pidder}, doi = {10.1186/s12864-021-08176-y}, + issn = {1471-2164}, journal = {BMC Genomics}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Longevity}, + language = {eng}, month = {January}, note = {Publisher: Springer Science and Business Media LLC}, number = {1}, + pages = {25}, title = {Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/{DYRK1A} in {Caenorhabditis} elegans}, url = {https://doi.org/10.1186/s12864-021-08176-y}, volume = {23}, @@ -8571,15 +14101,21 @@ @article{mack_regulation_2022 } @article{macnee_simtext_2021, + abstract = {{\textless}h4{\textgreater}Summary{\textless}/h4{\textgreater}Literature exploration in PubMed on a large number of biomedical entities (e.g. genes, diseases or experiments) can be time-consuming and challenging, especially when assessing associations between entities. Here, we describe SimText, a user-friendly toolset that provides customizable and systematic workflows for the analysis of similarities among a set of entities based on text. SimText can be used for (i) text collection from PubMed and extraction of words with different text mining approaches, and (ii) interactive analysis and visualization of data using unsupervised learning techniques in an interactive app.{\textless}h4{\textgreater}Availability and implementation{\textless}/h4{\textgreater}We developed SimText as an open-source R software and integrated it into Galaxy (https://usegalaxy.eu), an online data analysis platform with supporting self-learning training material available at https://training.galaxyproject.org. A command-line version of the toolset is available for download from GitHub (https://github.com/dlal-group/simtext) or as Docker image (https://hub.docker.com/r/dlalgroup/simtext/tags.).{\textless}h4{\textgreater}Supplementary information{\textless}/h4{\textgreater}Supplementary data are available at Bioinformatics online.}, author = {Macnee, Marie and Pérez-Palma, Eduardo and Schumacher-Bass, Sarah and Dalton, Jarrod and Leu, Costin and Blankenberg, Daniel and Lal, Dennis}, doi = {10.1093/bioinformatics/btab365}, editor = {Wren, Jonathan}, + issn = {1367-4803}, journal = {Bioinformatics}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Data Mining, Software}, + language = {eng}, month = {May}, note = {Publisher: Oxford University Press (OUP)}, + number = {22}, + pages = {4285--4287}, title = {{SimText}: a text mining framework for interactive analysis and visualization of similarities among biomedical entities}, url = {https://doi.org/10.1093/bioinformatics/btab365}, + volume = {37}, year = {2021} } @@ -8599,11 +14135,56 @@ @article{maffei_complete_2024 year = {2024} } +@incollection{mahanandia_bioinformatics_2025, + abstract = {Bioinformatics is a critical interdisciplinary domain that combines computational techniques with the analysis of biological data. Structural bioinformatics primarily examines the biomolecular structures, such as proteins and nucleic acids as well as their interactions. The rice of high-throughput sequencing and big data analytics has rendered bioinformatics tools increasingly vital in structural biology, facilitating the comprehension of molecular functions, drug development and evolutionary relationships. This chapter examines various computational tools that enable structural analysis, including homology modeling, molecular docking, molecular dynamics (MD) simulations and protein-protein interaction. Furthermore, it highlights recent progress in artificial intelligence (AI), machine learning (ML), and deep learning (DL), which are revolutionizing conventional operations through enhanced feature extraction and predictive modeling. Additionally, the chapter emphasizes the significance of quantum computing and high-performance computing (HPC) in improving simulation accuracy and scalability. Collectively, these advancements are transforming the bioinformatics domain, offering robust solutions for the analysis of complex biological systems and expediting biomedical research.}, + address = {Singapore}, + author = {Mahanandia, Nimai Charan and Biswal, Satyaranjan and Nayak, Chirasmita and Farooqi, Mohammad Samir and Srivastava, Sudhir and Mishra, Dwijesh Chandra and Chaturvedi, Krishna Kumar and Sharma, Anu}, + booktitle = {Advances in {Omics} {Technologies}: {Exploring} {Genomics}, {Proteomics}, and {Metabolomics}}, + doi = {10.1007/978-981-95-0285-1_9}, + editor = {Rout, Ajaya Kumar and Singh, Ram Kewal and Shukla, Arvind Kumar and Behera, Bijay Kumar}, + isbn = {9789819502851}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + pages = {177--191}, + publisher = {Springer Nature}, + shorttitle = {Bioinformatics {Tools}}, + title = {Bioinformatics {Tools}: {Insights} from {Structural} {Approaches}}, + url = {https://doi.org/10.1007/978-981-95-0285-1_9}, + urldate = {2025-09-03}, + year = {2025} +} + +@article{mahilkar_experimental_2021, + abstract = {Environmental cues in an ecological niche are often temporal in nature. For instance, in temperate climates, temperature is higher in daytime compared to during night. In response to these temporal cues, bacteria have been known to exhibit anticipatory regulation, whereby triggering response to a yet to appear cue. Such an anticipatory response in known to enhance Darwinian fitness, and hence, is likely an important feature of regulatory networks in microorganisms. However, the conditions under which an anticipatory response evolves as an adaptive response are not known. In this work, we develop a quantitative model to study response of a population to two temporal environmental cues, and predict variables which are likely important for evolution of anticipatory regulatory response. We follow this with experimental evolution of \textit{Escherichia coli} in alternating environments of rhamnose and paraquat for ∼850 generations. We demonstrate that growth in this cyclical environment leads to evolution of anticipatory regulation. As a result, pre-exposure to rhamnose leads to a greater fitness in paraquat environment. Genome sequencing reveals that this anticipatory regulation is encoded \textit{via} mutations in global regulators. Overall, our study contributes to understanding of how environment shapes the topology of regulatory networks in an organism.}, + author = {Mahilkar, Anjali and Venkataraman, Pavithra and Mall, Akshat and Saini, Supreet}, + doi = {10.3389/fmicb.2021.796228}, + issn = {1664-302X}, + journal = {Frontiers in microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {796228}, + title = {Experimental {Evolution} of {Anticipatory} {Regulation} in {Escherichia} coli}, + url = {http://europepmc.org/abstract/MED/35087497}, + volume = {12}, + year = {2021} +} + +@article{mahilkar_rapid_2023, + abstract = {Adaptive divergence leading to speciation is the major evolutionary process generating diversity in life forms. The most commonly observed form of speciation is allopatric speciation which requires that gene flow be prevented between populations by physical or temporal barriers, as they adapt to their respective environments. Eventually, these adaptive responses drive the populations far apart in the genotypic space such that individuals from the two populations become reproductively isolated. A widely accepted theory is that speciation simply occurs as a by-product of adaptive response of the populations 1,2 . Several ecological and laboratory examples of allopatric speciation exist 3–6 . However, we know little about the nature (pre- or post-zygotic) of barriers that arise first in this process. Understanding the first barriers that arise between populations is key, as populations diverge towards becoming distinct species. In recent years, fungi been used as model organisms to answer questions related to evolution of reproductive isolation 3,7–9 . Here we show rapid evolution of pre-zygotic barriers between allopatric yeast populations. We further demonstrate that these pre-zygotic barriers arise due to altered mating kinetics of the evolved population. Moreover, our non-adaptive evolution experiments with yeast under limited selection pressure also show rapid emergence of reproductive isolation. Overall, our results show that evolution of pre-zygotic reproductive barriers can occur as result of natural selection or drift. These barriers result because of altered mating kinetics or mate preference. {\textless}h4{\textgreater}One sentence summary{\textless}/h4{\textgreater} Pre-zygotic barriers to gene flow can arise due to adaptation or drift.}, + author = {Mahilkar, Anjali and Nagendra, Prachitha and Venkataraman, Pavithra and Deshmukh, Saniya and Saini, Supreet}, + doi = {10.1101/2023.03.18.533249}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Rapid evolution of pre-zygotic reproductive barriers in allopatric populations}, + url = {http://europepmc.org/abstract/PPR/PPR632875}, + year = {2023} +} + @article{mahilkar_rapid_2023, author = {Mahilkar, Anjali and Nagendra, Prachitha and Venkataraman, Pavithra and Deshmukh, Saniya and Saini, Supreet}, doi = {10.1128/spectrum.01950-23}, journal = {Microbiology Spectrum}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Reproduction, Saccharomyces cerevisiae}, month = {October}, note = {Publisher: American Society for Microbiology}, number = {6}, @@ -8615,6 +14196,27 @@ @article{mahilkar_rapid_2023 year = {2023} } +@article{mahtab_complete_2025, + abstract = {Here, we report the complete genome sequence of bacteriophage PaFZ4, a lytic bacteriophage infecting Pseudomonas aeruginosa strains. The PaFZ4 was isolated from hospital wastewater in Dhaka, Bangladesh, and predicted to be under the genus Phikmvvirus (family Autographiviridae). The genome of PaFZ4 has a 43,335-bp linear genome with 65 coding sequences.}, + author = {Mahtab, Zuhayr and Tamanna, Fahmida Haque and Jabeen, Ishrat and Islam, Sohidul and Rahman, Sezanur and Rahman, Mustafizur and Shuvo, Sabbir R}, + copyright = {cc by}, + doi = {10.1128/mra.00993-25}, + issn = {2576-098X}, + journal = {Microbiology resource announcements}, + keywords = {{\textgreater}UseGalaxy.eu, Bacteriophages, Bangladesh, Phage Genomics, Phikmvvirus, Pseudomonas aeruginosa, Whole-genome Sequencing}, + language = {eng}, + month = {December}, + number = {12}, + pages = {e0099325}, + pmcid = {PMC12697138}, + pmid = {41170983}, + title = {Complete genome sequence of \<i\>{Pseudomonas} aeruginosa\</i\> bacteriophage {PaFZ4} isolated from {Dhaka}, {Bangladesh}}, + url = {https://europepmc.org/articles/PMC12697138}, + urldate = {2025-12-26}, + volume = {14}, + year = {2025} +} + @article{maier_freely_2021, abstract = {{\textless}p{\textgreater}The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data. Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available at https://covid19.galaxyproject.org.{\textless}/p{\textgreater}}, author = {Maier, Wolfgang and Bray, Simon and Beek, Marius van den and Bouvier, Dave and Coraor, Nathaniel and Miladi, Milad and Singh, Babita and Argila, Jordi Rambla De and Baker, Dannon and Roach, Nathan and Gladman, Simon and Coppens, Frederik and Martin, Darren and Lonie, Andrew and Gruning, Bjorn and Pond, Sergei Kosakovsky and Nekrutenko, Anton}, @@ -8639,7 +14241,7 @@ @article{maier_ready--use_2021 doi = {10.1038/s41587-021-01069-1}, issn = {1546-1696}, journal = {Nature Biotechnology}, - keywords = {+Galactic, +IsGalaxy, +Project, +UsePublic, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au}, + keywords = {+Galactic, +IsGalaxy, +Project, +UsePublic, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Databases, Factual, Pandemics}, language = {en}, month = {September}, note = {Bandiera\_abtest: a @@ -8648,10 +14250,12 @@ @article{maier_ready--use_2021 Publisher: Nature Publishing Group Subject\_term: Genomic analysis;SARS-CoV-2 Subject\_term\_id: genomic-analysis;sars-cov-2}, + number = {10}, pages = {1--2}, title = {Ready-to-use public infrastructure for global {SARS}-{CoV}-2 monitoring}, url = {https://www.nature.com/articles/s41587-021-01069-1}, urldate = {2021-10-01}, + volume = {39}, year = {2021} } @@ -8660,7 +14264,7 @@ @article{maki_species_2023 author = {Maki, Joel J. and Howard, Mondraya and Connelly, Sara and Pettengill, Matthew A. and Hardy, Dwight J. and Cameron, Andrew}, doi = {10.1128/jcm.00046-23}, journal = {Journal of Clinical Microbiology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Campylobacter, Campylobacter Infections, Campylobacter jejuni, Gastroenteritis}, month = {April}, note = {Publisher: American Society for Microbiology}, number = {5}, @@ -8672,6 +14276,57 @@ @article{maki_species_2023 year = {2023} } +@article{maldonado-pava_exploring_2024, + abstract = {{\textless}p{\textgreater}Phosphorus (P) is essential for biological systems, playing a pivotal role in energy metabolism and forming crucial structural components of DNA and RNA. Yet its bioavailable forms are scarce. Phytate, a major form of stored phosphorus in cereals and soils, is poorly bioavailable due to its complex structure. Phytases, enzymes that hydrolyze phytate to release useable phosphorus, are vital in overcoming this limitation and have significant biotechnological applications. This study employed novel method to isolate and characterize bacterial strains capable of metabolizing phytate as the sole carbon and phosphorus source from the Andes mountains soils. Ten strains from the genera {\textless}italic{\textgreater}Klebsiella{\textless}/italic{\textgreater} and Chryseobacterium were isolated, with {\textless}italic{\textgreater}Chryseobacterium{\textless}/italic{\textgreater} sp. CP-77 and {\textless}italic{\textgreater}Klebsiella pneumoniae{\textless}/italic{\textgreater} CP-84 showing specific activities of 3.5 ± 0.4 nkat/mg and 40.8 ± 5 nkat/mg, respectively. Genomic sequencing revealed significant genetic diversity, suggesting CP-77 may represent a novel {\textless}italic{\textgreater}Chryseobacterium{\textless}/italic{\textgreater} species. A fosmid library screening identified several phytase genes, including a 3-phytase in CP-77 and a glucose 1-phosphatase and 3-phytase in CP-84. Phylogenetic analysis confirmed the novelty of these enzymes. These findings highlight the potential of phytase-producing bacteria in sustainable agriculture by enhancing phosphorus bioavailability, reducing reliance on synthetic fertilizers, and contributing to environmental management. This study expands our biotechnological toolkit for microbial phosphorus management and underscores the importance of exploring poorly characterized environments for novel microbial functions. The integration of direct cultivation with metagenomic screening offers robust approaches for discovering microbial biocatalysts, promoting sustainable agricultural practices, and advancing environmental conservation.{\textless}/p{\textgreater}}, + author = {Maldonado-Pava, Julieth and Tapia-Perdomo, Valentina and Estupinan-Cardenas, Liliana and Puentes-Cala, Edinson and Castillo-Villamizar, Genis Andrés}, + doi = {10.3389/fbioe.2024.1426208}, + issn = {2296-4185}, + journal = {Frontiers in Bioengineering and Biotechnology}, + keywords = {{\textgreater}UseGalaxy.eu, Biocatalyst, Metagenomics, Microbial Diversity, Phosphorus metabolism, Phytate hydrolysis, agricultural sustainability, phytase}, + language = {English}, + month = {June}, + note = {Publisher: Frontiers}, + pages = {1426208}, + title = {Exploring the biotechnological potential of novel soil-derived {Klebsiella} sp. and {Chryseobacterium} sp. strains using phytate as sole carbon source}, + url = {https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2024.1426208/full}, + urldate = {2024-07-01}, + volume = {12}, + year = {2024} +} + +@article{mamut_comparative_2025, + abstract = {The genus Peltigera includes terricolous and muscicolous foliose macrolichens that are common and widespread across the majority of continents. The genus is well-defined by the absence of a lower cortex and the presence of a dense arachnoid-tomentose pilema that usually bears anastomosing pale or dark veins with numerous solitary or confluent rhizines. However, the high morphological similarity among its species poses significant taxonomic challenges for accurate identification, often necessitating the use of molecular data. This study presents a comprehensive mitogenomic analysis of 11 Peltigera species, with the aim of elucidating their genetic structure and taxonomic status. We sequenced and performed de novo assembly of the complete mitochondrial genomes, followed by comprehensive genomic analysis. This analysis revealed that the circular genome length ranged in length from 52,107 bp to 76,353 bp with guanine and cytosine (GC) contents between 26.4 and 27.4\%. The mitogenomes encoded 15 protein-coding genes (PCGs), 26–27 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs). Our analysis revealed a variety of scattered repeats, simple repeats, and tandem repeats, predominantly in intergenic and intron regions. Additionally, we examined codon usage and conducted a synteny analysis within the mitogenomes of Peltigera species. These findings enhance our understanding of the genetic evolution and phylogenetic relationships within Peltigera, providing a scientific foundation for future research on the diversity and evolution of lichenized fungi.}, + author = {Mamut, Reyim and Yisilam, Gulbar and Adil, Guldiyar and Anwar, Gulmira}, + doi = {10.3389/fmicb.2025.1599036}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Peltigera, genomics, mitochondrial genome, phylogeny, repeat sequences}, + language = {English}, + month = {July}, + note = {Publisher: Frontiers}, + pages = {1599036}, + title = {Comparative mitogenomics analysis of {Peltigera} species and new insights into the lichen phylogenetics}, + url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1599036/full}, + urldate = {2025-09-03}, + volume = {16}, + year = {2025} +} + +@article{mandal_dataset_2025, + abstract = {Sundarbans, the world's largest contiguous mangrove wetland, a UNESCO World Heritage Site and a RAMSAR site formed on the delta of Ganga-Brahmaputra-Meghna (GBM) and influenced by coastal Bay of Bengal contribute immensely to biodiversity and blue economy. To track the changes driven by natural and anthropogenic stressors, sediment based environmental DNA (eDNA) biomonitoring of benthic foraminifera communities, an important biological group sensitive to changes, has been initiated along with estimation of dissolved nutrients from estuarine surface water. In pre-monsoon of 2022 (June), sediment cores and surface water were collected as well as in situ environmental parameters were measured from two pre-designated sampling points of Sundarbans to elucidate the benthic foraminifera community based on sediment eDNA approach. Based on Oxford Nanopore Technologies (ONT) sequencing in MinION platform, high abundance of Sorites sp., Elphidium excavatum, Textularia gramen, Quinqueloculina sp. and Trochammina hadai were detected. The increasing nutrient concentrations and elucidated benthic foraminiferal signals can contribute towards tracking the state of ecological health of Sundarbans. This study is aimed at generating baseline information on mangrove benthic foraminifera communities using sediment eDNA based high-throughput sequencing.}, + author = {Mandal, Arkaprava and Ghosh, Anwesha and Kumar, Gauraw and Bhadury, Punyasloke}, + doi = {10.1016/j.dib.2025.111554}, + issn = {2352-3409}, + journal = {Data in Brief}, + keywords = {{\textgreater}UseGalaxy.eu, Benthic Foraminifera, Sediment-eDNA, Mangrove, Nanopore}, + month = {April}, + pages = {111554}, + title = {Dataset of benthic foraminiferal community structure from sediment {eDNA} of {Sundarbans} mangrove ecosystem}, + url = {https://www.sciencedirect.com/science/article/pii/S2352340925002860}, + urldate = {2025-04-21}, + year = {2025} +} + @article{manna_endosomal_2023, abstract = {Contractile vacuoles (CVs), enigmatic osmoregulatory organelles, share common characteristics, such as a requirement for RAB11 and high levels of V-ATPase. These commonalities suggest a conserved evolutionary origin for the CVs with implications for understanding of the last common ancestor of eukaryotes and eukaryotic diversification more broadly. A taxonomically broader sampling of CV-associated machinery is required to address this question further. We used a transcriptomics-based approach to identify CV-associated gene products in Dictyostelium discoideum. This approach was first validated by assessing a set of known CV-associated gene products, which were significantly upregulated following hypo-osmotic exposure. Moreover, endosomal and vacuolar gene products were enriched in the upregulated gene set. An upregulated SNARE protein (NPSNB) was predominantly plasma membrane localised and enriched in the vicinity of CVs, supporting the association with this organelle found in the transcriptomic analysis. We therefore confirm that transcriptomic approaches can identify known and novel players in CV function, in our case emphasizing the role of endosomal vesicle fusion machinery in the D. discoideum CV and facilitating future work to address questions regarding the deep evolution of eukaryotic organelles.}, author = {Manna, Paul T. and Barlow, Lael D. and Ramirez-Macias, Inmaculada and Herman, Emily K. and Dacks, Joel B.}, @@ -8689,22 +14344,96 @@ @article{manna_endosomal_2023 year = {2023} } +@misc{mapunda_coxsackievirus_2025, + abstract = {Background On 15 January 2024, the Ministry of Health (MOH) reported a notable outbreak of acute viral conjunctivitis in the city of Dar es Salaam. In this study we investigated the causative agent of acute conjunctivitis outbreak which occurred in Dar es Salaam between Jan 2024 and Feb 2024. +Methodology We conveniently collected a pair of eye swab samples from twenty-five patients presenting with symptoms of acute conjunctivitis at clinics in Dar es Salaam during the outbreak. One for bacterial culture and another for molecular detection. MacConkey and Blood agar were used to culture patient samples to identify possible bacterial causes. A Multiplex Real-time RT-PCR targeting Adenovirus, Metapneumovirus, Human Enterovirus and Parainfluenza. Positive samples with Ct value less than 30 for enterovirus were subjected to genomic sequencing by Illumina Miseq after library preparation and enrichment by Illumina’s Respiratory Pathogen ID/AMR enrichment panel kit as per manufacturer’s instructions (RPIP kit), followed by bioinformatics and phylogenetic analysis. +Results Out of 25 samples, nine samples were positive for human enterovirus by Real-time PCR. Of the nine positive samples four were sequenced and Coxsackievirus A24 variant, was identified as the most probable cause of the outbreak. Phylogenetic analysis showed that samples collected during the outbreak (28AO and 26HB) belong to a clade with Coxsackievirus A24 sequences from France Mayotte from a 2024 outbreak, also close to sequences from neighbouring East African countries (Uganda, Kenya) as well as South American countries (Brazil, Mexico, and French Guiana). +Conclusion This study demonstrated the utility of genomic epidemiology in identifying Coxsackievirus A24 as the pathogen responsible for the outbreak and its circulation within the East African region. +Background On 15 January 2024, the Ministry of Health (MOH) reported a notable outbreak of acute viral conjunctivitis in the city of Dar es Salaam. In this study we investigated the causative agent of acute conjunctivitis outbreak which occurred in Dar es Salaam between Jan 2024 and Feb 2024. +Methodology We conveniently collected a pair of eye swab samples from twenty-five patients presenting with symptoms of acute conjunctivitis at clinics in Dar es Salaam during the outbreak. One for bacterial culture and another for molecular detection. MacConkey and Blood agar were used to culture patient samples to identify possible bacterial causes. A Multiplex Real-time RT-PCR targeting Adenovirus, Metapneumovirus, Human Enterovirus and Parainfluenza. Positive samples with Ct value less than 30 for enterovirus were subjected to genomic sequencing by Illumina Miseq after library preparation and enrichment by Illumina’s Respiratory Pathogen ID/AMR enrichment panel kit as per manufacturer’s instructions (RPIP kit), followed by bioinformatics and phylogenetic analysis. +Results Out of 25 samples, nine samples were positive for human enterovirus by Real-time PCR. Of the nine positive samples four were sequenced and Coxsackievirus A24 variant, was identified as the most probable cause of the outbreak. Phylogenetic analysis showed that samples collected during the outbreak (28AO and 26HB) belong to a clade with Coxsackievirus A24 sequences from France Mayotte from a 2024 outbreak, also close to sequences from neighbouring East African countries (Uganda, Kenya) as well as South American countries (Brazil, Mexico, and French Guiana). +Conclusion This study demonstrated the utility of genomic epidemiology in identifying Coxsackievirus A24 as the pathogen responsible for the outbreak and its circulation within the East African region.}, + author = {Mapunda, Lawrence A. and Heusden, Peter van and Baluhya, Robert and Machange, Olympia G. and Mwafulango, Ambele and Francis, Monica Fredrick and Ituka, Aziz and Machange, Omega and Kisanga, Adela and Mgimba, Edna E. and Matimba, Hamza H. and Kado, Dennis M. and Kimaro, Elson E. and Libenanga, Ramadhani A. and Mushumbusi, Jackson Peter and Swalehe, Hamisi M. and Mauki, Ibrahim and Hellar, James and Henerico, Shimba and Kelly, Maria E. and Moremi, Nyambura}, + copyright = {© 2025, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), CC BY-NC 4.0, as described at http://creativecommons.org/licenses/by-nc/4.0/}, + doi = {10.1101/2025.04.28.24315795}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {April}, + note = {Pages: 2025.04.28.24315795}, + publisher = {medRxiv}, + shorttitle = {Coxsackievirus {A24}}, + title = {Coxsackievirus {A24}: {A} {Causative} {Agent} of {Acute} {Haemorrhagic} {Conjunctivitis} {Outbreak} in {Dar} es {Salaam}, {Tanzania}, between {January} and {February} 2024}, + url = {https://www.medrxiv.org/content/10.1101/2025.04.28.24315795v1}, + urldate = {2025-05-06}, + year = {2025} +} + @article{marco_dorq-seq_2024, abstract = {Due to its high modification content tRNAs are notoriously hard to quantify by reverse transcription and RNAseq. Bypassing numerous biases resulting from concatenation of enzymatic treatments, we here report a hybrid approach that harnesses the advantages of hybridization-based and deep sequencing–based approaches. The method renders obsolete any RNAseq related workarounds and correction factors that affect accuracy, sensitivity, and turnaround time. Rather than by reverse transcription, quantitative information on the isoacceptor composition of a tRNA pool is transferred to a cDNA mixture in a single step procedure, thereby omitting all enzymatic conversations except for the subsequent barcoding PCR. As a result, a detailed tRNA composition matrix can be obtained from femtomolar amounts of total tRNA. The method is fast, low in cost, and its bioinformatic data workup surprisingly simple. These properties make the approach amenable to high-throughput investigations including clinical samples, as we have demonstrated by application to a collection of variegated biological questions, each answered with novel findings. These include tRNA pool quantification of polysome-bound tRNA, of tRNA modification knockout strains under stress conditions, and of Alzheimer patients’ brain tissues.}, author = {Marco, Kristen and Marc, Lander and Lea-Marie, Kilz and Lukas, Gleue and Marko, Jörg and Damien, Bregeon and Djemel, Hamdane and Virginie, Marchand and Yuri, Motorin and Kristina, Friedland and Mark, Helm}, doi = {10.1093/nar/gkae765}, issn = {0305-1048}, journal = {Nucleic Acids Research}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, DNA, Complementary, High-Throughput Nucleotide Sequencing, Nucleic Acid Hybridization, RNA, Transfer}, + language = {eng}, month = {September}, + number = {18}, pages = {gkae765}, shorttitle = {{DORQ}-seq}, title = {{DORQ}-seq: high-throughput quantification of femtomol {tRNA} pools by combination of {cDNA} hybridization and {Deep} sequencing}, url = {https://doi.org/10.1093/nar/gkae765}, urldate = {2024-09-14}, + volume = {52}, year = {2024} } +@patent{marco_method_2022, + address = {EP}, + author = {Marco, Kristen and Mark, Helm}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {December}, + number = {EP 4386088 A1}, + title = {Method {For} {The} {Accurate} {Quantification} {Of} {Non}-coding {Rnas} {In} {Minute} {Quantities}}, + url = {https://lens.org/137-121-698-687-093}, + year = {2022} +} + +@article{maree_trypanosoma_2022, + abstract = {Trypanosomes diverged from the main eukaryotic lineage about 600 million years ago, and display some unusual genomic and epigenetic properties that provide valuable insight into the early processes employed by eukaryotic ancestors to regulate chromatin-mediated functions. We analysed Trypanosoma brucei core histones by high mass accuracy middle-down mass spectrometry to map core histone post-translational modifications (PTMs) and elucidate cis-histone combinatorial PTMs (cPTMs). T. brucei histones are heavily modified and display intricate cPTMs patterns, with numerous hypermodified cPTMs that could contribute to the formation of non-repressive euchromatic states. The Trypanosoma brucei H2A C-terminal tail is hyperacetylated, containing up to five acetylated lysine residues. MNase-ChIP-seq revealed a striking enrichment of hyperacetylated H2A at Pol II transcription start regions, and showed that H2A histones that are hyperacetylated in different combinations localised to different genomic regions, suggesting distinct epigenetic functions. Our genomics and proteomics data provide insight into the complex epigenetic mechanisms used by this parasite to regulate a genome that lacks the transcriptional control mechanisms found in later-branched eukaryotes. The findings further demonstrate the complexity of epigenetic mechanisms that were probably shared with the last eukaryotic common ancestor.}, + author = {Maree, Johannes P and Tvardovskiy, Andrey and Ravnsborg, Tina and Jensen, Ole N and Rudenko, Gloria and Patterton, Hugh-G}, + doi = {10.1093/nar/gkac759}, + issn = {0305-1048}, + journal = {Nucleic Acids Res}, + keywords = {{\textgreater}UseGalaxy.eu, Trypanosoma brucei brucei}, + language = {eng}, + month = {September}, + number = {17}, + pages = {9705--9723}, + title = {Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark {Pol} {II} transcription start regions with hyperacetylated {H2A}}, + url = {http://europepmc.org/abstract/MED/36095123}, + volume = {50}, + year = {2022} +} + +@article{mariduena-zavala_babaco_2025, + abstract = {The recent emergence of Babacco Mosaic Virus (BabMV), a potexvirus known to infect Vasconcellea heilbornii (babaco), has raised concerns about its potential to infect papaya cultivars. To assess the impact of BabMV on papaya plants, we conducted a comprehensive genome-wide transcriptome analysis to evaluate the effect of the virus on gene expression and defense responses in Papaya (Carica papaya). Leaves from papaya plants of 3–4-month-old plants were examined at 2, 10, 15, and 30 days post-infection (dpi) with BabMV and compared to uninfected controls. In mock and virus-infected plants at 2 and 10 dpi, more than 90\% of the RNAseq reads were mapped with the papaya genome. In contrast, at 15 and 30 dpi, only 31\% mapped to the papaya genome in BabMV-infected leaves, while the remaining 69\% of the reads aligned to the virus genome, demonstrating a high viral load. Overall, 1585 papaya genes were differentially expressed between mock and BabMV-inoculated leaves. At 2–10 dpi, early responses included increased expression of genes related to sugar metabolism and cell wall modification, including lignin synthesis. At 30 dpi, late responses included the induction of genes involved in reactive oxygen species (ROS) production and antioxidants, potentially via cytochrome P450 enzyme activation. This explained the upregulation of Mitogen-Activated Protein Kinases (MAPK3,18) and transcription factors including WRKY40,60,70 and Ethylene Response Factor 1 (ERF1), known to induce the expression of genes encoding pathogenesis-related proteins (PR1) and activating the plant defense mechanisms. This research enhances our understanding of BabMV infections, enabling the development of effective strategies for disease control.}, + author = {Maridueña-Zavala, Maria Gabriela and AbdElgawad, Hamada and Okla, Mohammad K. and Cevallos, Juan Manuel and Beemster, Gerrit T. S. and Noceda, Carlos}, + copyright = {© 2025 Scandinavian Plant Physiology Society.}, + doi = {10.1111/ppl.70270}, + issn = {1399-3054}, + journal = {Physiologia Plantarum}, + keywords = {{\textgreater}UseGalaxy.eu, BabMV, Carica papaya, WRKY gene family, cell wall, oxidative stress}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70270}, + number = {3}, + pages = {e70270}, + title = {Babaco {Mosaic} {Virus} ({BabMV}) {Induces} {Genome}-{Wide} {Transcriptomic} {Reprogramming} in {Carica} papaya}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70270}, + urldate = {2025-06-03}, + volume = {177}, + year = {2025} +} + @article{marimon_pertussis_2024, abstract = {Background: Pertussis has re-emerged in many countries despite the wide use of vaccines for over 60 years. During 2023, we observed an increase in the incidence of pertussis in Gipuzkoa, north of Spain (with a population of 657,140 inhabitants), mainly affecting children between 11 and 15 years of age. Methods: This study included all confirmed cases diagnosed by PCR in nasopharyngeal swab samples. The genome of seven isolates collected in 2023 was sequenced. Results: Between 2018 and 2023, 884 cases of whooping cough were diagnosed. Pertussis incidence (in cases per 100,000 inhabitants) decreased from 36.7 in 2018 to no cases in 2021, increasing again to 56.8 in 2023. In 2023, the age group of 11–15 years old had the highest incidence rate of 409.3. Only 2 of the 56 children {\textless} 6 years old required hospitalization, and there were no deaths. The seven isolates collected in 2023 showed the same BPagST-4 (ptxA1/ptxP3/prn2/fim2-1/fim3-1 allelic combination), with all of them expressing the pertactin antigen. Conclusions: Immunity waning after the last dose of vaccination at 6 years old, together with the lack of circulation of Bordetella pertussis during the COVID-19 pandemic, were probably the main reasons for the high increase in the incidence of pertussis in Gipuzkoa in 2023.}, author = {Marimón, José María and Montes, Milagrosa and Vizuete, Nahikari and Alvarez Guerrico, Lorea and Aginagalde, Adrian Hugo and Mir-Cros, Alba and González-López, Juan José and Vicente, Diego}, @@ -8726,6 +14455,23 @@ @article{marimon_pertussis_2024 year = {2024} } +@article{marimon_two_2025, + abstract = {\textbf{Background}: The aging of the population has increased the number of frail people living in long-term care facilities, underscoring the need for continuous updates in infectious diseases prevention strategies. The aim of this study was to analyze two pneumococcal disease outbreaks in elderly residences in Gipuzkoa, northern Spain, their impact on residents, and the containment measures implemented. \textbf{Material and methods}: The outbreaks took place in 2023 and in 2024 in two residences of 111 and of 155 residents, respectively. Diagnosis was based on clinical criteria, radiological findings, and microbiological techniques. Pneumococcal isolates were characterized by whole-genome sequencing. \textbf{Results}: The outbreaks involved five and six residents, respectively. Most residents in both facilities had been vaccinated with the pneumococcal polysaccharide 23-valent vaccine (PPV23) more than five years prior. The median attack rates were 4.5\% and 3.9\%, lower than those reported in similar outbreaks. The adopted infection transmission prevention measures successfully limited the spread of the outbreaks. \textbf{Conclusions}: PPV23 vaccination did not prevent invasive pneumococcal infection in the affected residents. The vaccination of elderly people living in long-term care facilities with 20-valent and 21-valent pneumococcal conjugated vaccines should be evaluated as a new preventive measure.}, + author = {Marimón, José María and Manzanal, Ayla and Mokoroa, Olatz and Alvarez, Lorea and Rekalde, Maite and Vicente, Diego}, + doi = {10.3390/vaccines13060570}, + issn = {2076-393X}, + journal = {Vaccines}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {May}, + number = {6}, + pages = {570}, + title = {Two {Outbreaks} of {Invasive} {Pneumococcal} {Disease} in {Nursing} {Homes} in {Gipuzkoa}, {Northern} {Spain}}, + url = {http://europepmc.org/abstract/MED/40573901}, + volume = {13}, + year = {2025} +} + @article{marisaldi_novo_2021, abstract = {In the present work, we assembled and characterized a de novo larval transcriptome of the Atlantic bluefin tuna Thunnus thynnus by taking advantage of publicly available databases with the goal of better understanding its larval development. The assembled transcriptome comprised 37,117 protein-coding transcripts, of which 13,633 full-length ({\textgreater}80\% coverage), with an Ex90N50 of 3061 bp and 76\% of complete and single-copy core vertebrate genes orthologues. Of these transcripts, 34,980 had a hit against the EggNOG database and 14,983 with the KEGG database. Codon usage bias was identified in processes such as translation and muscle development. By comparing our data with a set of representative fish species, 87.1\% of tuna transcripts were included in orthogroups with other species and 5.1\% in assembly-specific orthogroups, which were enriched in terms related to muscle and bone development, visual system and ion transport. Following this comparative approach, protein families related to myosin, extracellular matrix and immune system resulted significantly expanded in the Atlantic bluefin tuna. Altogether, these results provide a glimpse of how the Atlantic bluefin tuna might have achieved early physical advantages over competing species in the pelagic environment. The information generated lays the foundation for future research on the more detailed exploration of physiological responses at the molecular level in different larval stages and paves the way to evolutionary studies on the Atlantic bluefin tuna.}, author = {Marisaldi, Luca and Basili, Danilo and Gioacchini, Giorgia and Canapa, Adriana and Carnevali, Oliana}, @@ -8743,7 +14489,24 @@ @article{marisaldi_novo_2021 year = {2021} } -@article{martin_pelixirs_2023, +@article{martin_del_pico_fairsoft-practical_2024, + abstract = {{\textless}h4{\textgreater}Motivation{\textless}/h4{\textgreater}Software plays a crucial and growing role in research. Unfortunately, the computational component in Life Sciences research is often challenging to reproduce and verify. It could be undocumented, opaque, contain unknown errors that affect the outcome, or be directly unavailable and impossible to use for others. These issues are detrimental to the overall quality of scientific research. One step to address this problem is the formulation of principles that research software in the domain should meet to ensure its quality and sustainability, resembling the FAIR (findable, accessible, interoperable, and reusable) data principles.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}We present here a comprehensive series of quantitative indicators based on a pragmatic interpretation of the FAIR Principles and their implementation on OpenEBench, ELIXIR's open platform providing both support for scientific benchmarking and an active observatory of quality-related features for Life Sciences research software. The results serve to understand the current practices around research software quality-related features and provide objective indications for improving them.{\textless}h4{\textgreater}Availability and implementation{\textless}/h4{\textgreater}Software metadata, from 11 different sources, collected, integrated, and analysed in the context of this manuscript are available at https://doi.org/10.5281/zenodo.7311067. Code used for software metadata retrieval and processing is available in the following repository: https://gitlab.bsc.es/inb/elixir/software-observatory/FAIRsoft\_ETL.}, + author = {Martín Del Pico, Eva and Gelpí, Josep Lluís and Capella-Gutierrez, Salvador}, + doi = {10.1093/bioinformatics/btae464}, + issn = {1367-4803}, + journal = {Bioinformatics}, + keywords = {{\textgreater}UseGalaxy.eu, Software}, + language = {eng}, + month = {August}, + number = {8}, + pages = {btae464}, + title = {{FAIRsoft}-a practical implementation of {FAIR} principles for research software}, + url = {http://europepmc.org/abstract/MED/39037960}, + volume = {40}, + year = {2024} +} + +@article{martin_elixirs_2023, abstract = {This document lists indicators, and other evidence, used to monitor ELIXIR’s performance and impact, and ultimately its public value as a research infrastructure. The list covers areas of governance, operations, user training, service to users, communications, and policy engagement. Some indicators are monitored and reported on in a systematic manner, whilst others are monitored but not systematically reported on. A number are still in development and/or at the “idea stage”. Altogether, the evidence covered is of varying nature, ranging from quantitative, qualitative, narratives, to simple lists of examples. Due to ELIXIR’s pan-European distributed nature, ownership of indicators is also distributed - this means that the resulting temporal scopes are also quite varied. Some evidence relates to ‘impact’ (i.e. in the infrastructure’s sphere of \textit{interest}) whilst other to ‘performance’ (i.e. the spheres of \textit{control} and \textit{influence}), and there is not always a clear boundary between the two. Mapping against the main ‘impact areas’ of ELIXIR is provided, and so is mapping against the \textit{objectives of greatest relevance for research infrastructures}, as identified by the European Strategy Board on Research Infrastructures (ESFRI).}, author = {Martin, Corinne and Sousoni, Despoina and Balsyte, Erika}, copyright = {https://creativecommons.org/licenses/by/4.0/}, @@ -8756,7 +14519,7 @@ @article{martin_pelixirs_2023 Publisher: F1000 Research Limited}, number = {1512}, pages = {1512}, - title = {{\textless}p{\textgreater}{ELIXIR}’s {List} of indicators, and other evidence, for monitoring performance and impact in a distributed data research infrastructure for the life sciences{\textless}/p{\textgreater}}, + title = {{ELIXIR}’s {List} of indicators, and other evidence, for monitoring performance and impact in a distributed data research infrastructure for the life sciences}, url = {https://f1000research.com/documents/12-1512}, urldate = {2024-11-17}, volume = {12}, @@ -8764,14 +14527,51 @@ @article{martin_pelixirs_2023 } @article{martin_selection_2022, + abstract = {Among the 30 nonsynonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (1) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (2) interactions of Spike with ACE2 receptors, and (3) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any virus within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and, in combination with other mutations, adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron overall previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.}, + author = {Martin, Darren P and Lytras, Spyros and Lucaci, Alexander G and Maier, Wolfgang and Grüning, Björn and Shank, Stephen D and Weaver, Steven and MacLean, Oscar A and Orton, Richard J and Lemey, Philippe and Boni, Maciej F and Tegally, Houriiyah and Harkins, Gordon W and Scheepers, Cathrine and Bhiman, Jinal N and Everatt, Josie and Amoako, Daniel G and San, James Emmanuel and Giandhari, Jennifer and Sigal, Alex and {=NGS-SA} and Williamson, Carolyn and Hsiao, Nei-Yuan and von Gottberg, Anne and De Klerk, Arne and Shafer, Robert W and Robertson, David L and Wilkinson, Robert J and Sewell, B Trevor and Lessells, Richard and Nekrutenko, Anton and Greaney, Allison J and Starr, Tyler N and Bloom, Jesse D and Murrell, Ben and Wilkinson, Eduan and Gupta, Ravindra K and de Oliveira, Tulio and Kosakovsky Pond, Sergei L}, + doi = {10.1093/molbev/msac061}, + issn = {0737-4038}, + journal = {Mol Biol Evol}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19, Spike Glycoprotein, Coronavirus}, + language = {eng}, + month = {April}, + number = {4}, + pages = {msac061}, + title = {Selection {Analysis} {Identifies} {Clusters} of {Unusual} {Mutational} {Changes} in {Omicron} {Lineage} {BA}.1 {That} {Likely} {Impact} {Spike} {Function}}, + url = {http://europepmc.org/abstract/MED/35325204}, + volume = {39}, + year = {2022} +} + +@article{martin_selection_2022, + abstract = {Among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (i) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (ii) interactions of Spike with ACE2 receptors, and (iii) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any genomes within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron over all previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.}, author = {Martin, Darren P and Lytras, Spyro and Lucaci, Alexander G and Maier, Wolfgang and Gruning, Bjorn and Shank, Stephen D and Weaver, Steven and MacLean, Oscar S and Orton, Richard J and Lemey, Philippe and {others}}, + doi = {10.1101/2022.01.14.476382}, journal = {bioRxiv}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, note = {Publisher: Cold Spring Harbor Laboratory}, title = {Selection analysis identifies unusual clustered mutational changes in {Omicron} lineage {BA}. 1 that likely impact {Spike} function}, + url = {http://europepmc.org/abstract/PPR/PPR444222}, year = {2022} } +@article{martin_viral_2021, + abstract = {Despite the reported low expression of the primary SARS-CoV-2 receptor ACE2 in distinct ocular tissues, some clinical evidence suggests that SARS-CoV-2 can infect the eye. In this study, we explored potential entry sites for SARS-CoV-2 by viral S protein histochemistry on various ocular tissues and compared the staining patterns with RNA and protein expression of TMPRSS2 and ACE2. Potential viral entry sites were investigated by histochemistry using tagged recombinant viral S protein on 52 ocular tissue samples including specimens of the cornea, conjunctiva, lid margin, lacrimal gland tissue, retina, choroid, and RPE. In addition, ACE2 and TMPRSS2 immunohistochemistry were performed on the same ocular tissue, each with distinct antibodies binding to different epitopes. Lung tissue samples were used as positive controls. Finally, bulk RNA sequencing (RNA-Seq) was used to determine the expression of ACE2 and its auxiliary factors in the tissues mentioned above. S protein histochemistry revealed a positive staining in lung tissue but absent staining in the cornea, the conjunctiva, eye lid samples, the lacrimal glands, the retina and the optic nerve which was supported by hardly any immunoreactivity for ACE2 and TMPRSS2 and scarce ACE2 and TMPRSS2 RNA expression. Negligible staining with antibodies targeting ACE2 or TMPRSS2 was seen in the main and accessory lacrimal glands. In contrast, ocular staining (S protein, ACE2, TMPRSS2) was distinctly present in pigmented cells of the RPE and choroid, as well as in the ciliary body and the iris stroma. S protein histochemistry revealed hardly any SARS-CoV-2 entry sites in all ocular tissues examined. Similarly, no significant ACE2 or TMPRSS2 expression was found in extra- and intraocular tissue. While this study suggest a rather low risk of ocular infection with SARS-CoV-2, it should be noted, that potential viral entry sites may increase in response to inflammation or in certain disease states.}, + author = {Martin, Gottfried and Wolf, Julian and Lapp, Thabo and Agostini, Hansjürgen T and Schlunck, Günther and Auw-Hädrich, Claudia and Lange, Clemens A K}, + doi = {10.1038/s41598-021-98709-y}, + issn = {2045-2322}, + journal = {Scientific reports}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {September}, + number = {1}, + pages = {19140}, + title = {Viral {S} protein histochemistry reveals few potential {SARS}-{CoV}-2 entry sites in human ocular tissues}, + url = {http://europepmc.org/abstract/MED/34580409}, + volume = {11}, + year = {2021} +} + @phdthesis{martineau_prevalence_2023, abstract = {Les affections respiratoires sont la seconde cause de contre-performance chez le cheval athlète. Elles sont associées à un ensemble de signes cliniques dont certains sont déclenchés ou exacerbés par la présence de micro-organismes dans la sphère respiratoire de l’animal. Les bactéries du genre Mycoplasma, atypiques par leurs caractéristiques phénotypiques et génomiques, ont été décrites comme associées à des infections respiratoires à l'échelle mondiale, tant chez l’homme que les animaux d'élevage. Elles sont retrouvées avec une prévalence proche de 15 \% dans les lavages respiratoires équins reçus pour diagnostic sans que leur rôle clinique ne soit clairement défini. Pour comprendre le rôle de ces bactéries, un protocole mixte, associant culture et amplification génique à partir d’un enrichissement sur bouillon du prélèvement initial, a été validé. Cette méthode a été utilisée sur 1948 échantillons de 1764 chevaux, reçus sur la période 2020-2022. La prévalence des bactéries du genre Mycoplasma a été affinée à 16,1\% avec une prédominance de l’espèce M. equirhinis (85,3\%). La détection de M. equirhinis n’a pas pu être associée à des signes cliniques rapportés par les vétérinaires. Toutefois, une détection plus importante chez les chevaux de races de course et ceux vivant en box, dans les lavages trachéaux, a été mise en évidence. Dans les liquides bronchoalvéolaires, M. equirhinis a été identifié de façon concomitante à une inflammation à médiation neutrophilique. La prévalence de M. equirhinis est augmentée en présence d’autres micro-organismes tels que Streptococcus zooepidemicus, EHV-5 et Actinobacillus equuli. L’analyse des génomes de diverses souches de M. equirhinis montre une homogénéité importante de l’espèce malgré la présence d’éléments génétiques mobiles. Les gènes associés à la virulence retrouvés sont caractéristiques du genre Mycoplasma et très similaires à ceux détectés dans l’espèce M. hominis, un pathogène opportuniste de la sphère génitale chez l’homme, phylogénétiquement très proche de M. equirhinis. Tous ces éléments conduisent donc à considérer M. equirhinis comme un agent opportuniste au sein d’un complexe respiratoire équin, qu’il s’agira de caractériser plus finement par sa détection quantitative dans les prélèvements initiaux et l’analyse plus global du microbiote respiratoire.}, author = {Martineau, Matthieu}, @@ -8804,6 +14604,23 @@ @article{martineau_unravelling_2024 year = {2024} } +@article{martinez-cazorla_early_2025, + abstract = {Bacteriophages must evade bacterial defences to establish successful infections. Type I restriction-modification (RM) systems recognize specific DNA motifs and degrade unmethylated foreign DNA, restricting phage replication. In this study, we detected that Marinomonas mediterranea MMB-2 uses a Type I RM system (Mme2I) to protect against several new phages in the Murciavirus genus within the Autographiviridae family. Whole-genome sequencing and methylation analysis revealed a DNA sequence motif methylated in M. mediterranea MMB-2, which is also present in the phages. Phages lacking the motif within the leading, first injected, region of their genomes, either natural isolates or escape mutants of sensitive phages, successfully infect M. mediterranea MMB-2, despite the presence of the recognition motif elsewhere in their genomes. These results highlight the importance of considering RM motif locations when predicting avoidance of restriction sites as escape mechanisms from RM systems. Additionally, our findings indicate an important role for RM systems in specifically influencing the organization of the leading injected regions of phage genomes, which are highly variable and often encode diverse anti-defence systems.}, + author = {Martinez-Cazorla, Andrea and Martinez-Jimenez, Christian and Elio-Lucas, Patricia and Fineran, Peter C and Jackson, Simon and Sanchez-Amat, Antonio}, + doi = {10.1093/nar/gkaf926}, + issn = {1362-4962}, + journal = {Nucleic Acids Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + number = {18}, + pages = {gkaf926}, + title = {The early injected genomic region determines sensitivity to {Type} {I} restriction-modification defence against {Autographiviridae} phages}, + url = {https://doi.org/10.1093/nar/gkaf926}, + urldate = {2025-10-08}, + volume = {53}, + year = {2025} +} + @misc{martinez-delgado_ehmt2_2024, abstract = {Dysregulation of the epigenetic machinery is associated with neurodevelopmental defects in humans. Kleefstra syndrome (KS) is a neurodevelopmental syndrome caused by heterozygous alterations in the gene EHMT1 that cause loss-of-function. EHTM1 and EHMT2 are highly similar histone methyltransferases that play relevant roles in development. Despite their similarity, individuals with alterations in EHMT2 have never been described. Here, we describe a pediatric patient with a KS-overlapping phenotype and a single base de novo substitution in EHMT2 that causes the amino acid change p.Ala1077Ser in the catalytic SET domain. This change causes a reduction in the affinity of the catalytic domain for the H3 tail and in the activity of the enzyme by three- to five-fold. DNA methylation, histone methylation and gene expression profiles suggest a significant overlap between the EHMT2 p.Ala1077Ser variant and KS. Based on this evidence we suggest that EHMT2 haploinsufficiency causes a Kleefstra-like syndrome. Although we cannot rule out dominant negative effects caused by the EHMT2 p.Ala1077Ser variant, our data and previously published data suggest that loss of EHMT2 function is probably more detrimental to cells than loss of EHMT1, explaining why individuals with alterations in EHMT2 are very rare.}, author = {Martinez-Delgado, Beatriz and Lopez-Martin, Estrella and Kerkhof, Jennifer and Baladron, Beatriz and Mielu, Lidia M. and Sanchez-Ponce, Diana and Bada-Navarro, Ariadna and Herrero-Matesanz, Marina and Lopez-Jimenez, Lidia and Rzasa, Jessica and Rots, Dmitrijs and Fernandez, Marta and Miguel, Esther Hernandez-San and Gomez-Mariano, Gema and Marin-Reina, Purificacion and Cazorla-Calleja, Rosario and Alonso, Javier and Kleefstra, Tjitske and Posada, Manuel and Bermejo-Sanchez, Eva and Sadikovic, Bekim and Barrero, Maria J.}, @@ -8847,12 +14664,13 @@ @article{martins_laminin-2_2024 doi = {10.26508/lsa.202402829}, issn = {2575-1077}, journal = {Life Science Alliance}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Cell Differentiation, Laminin, Muscle, Skeletal, Myoblasts, Oxidative Stress}, language = {en}, month = {December}, note = {Publisher: Life Science Alliance Section: Research Articles}, number = {12}, + pages = {e202402829}, pmid = {39379105}, title = {Laminin-α2 chain deficiency in skeletal muscle causes dysregulation of multiple cellular mechanisms}, url = {https://www.life-science-alliance.org/content/7/12/e202402829}, @@ -8877,7 +14695,7 @@ @article{marzoli_next_2020 abstract = {The predator Asian hornet (Vespa velutina) represents one of the major threats to honeybee survival. Viral spillover from bee to wasp has been supposed in several studies, and this work aims to identify and study the virome of both insect species living simultaneously in the same foraging area. Transcriptomic analysis was performed on V. velutina and Apis mellifera samples, and replicative form of detected viruses was carried out by strand-specific RT-PCR. Overall, 6 and 9 different viral types were reported in V. velutina and A. mellifera, respectively, and five of these viruses were recorded in both hosts. Varroa destructor virus-1 and Cripavirus NB-1/2011/HUN (now classified as Triato-like virus) were the most represented viruses detected in both hosts, also in replicative form. In this investigation, Triato-like virus, as well as Aphis gossypii virus and Nora virus, was detected for the first time in honeybees. Concerning V. velutina, we report for the first time the recently detected honeybee La Jolla virus. A general high homology rate between genomes of shared viruses between V. velutina and A. mellifera suggests the efficient transmission of the virus from bee to wasp. In conclusion, our findings highlight the presence of several known and newly reported RNA viruses infecting A. mellifera and V. velutina. This confirms the environment role as an important source of infection and indicates the possibility of spillover from prey to predator.}, author = {Marzoli, Filippo and Forzan, Mario and Bortolotti, Laura and Pacini, Maria Irene and Rodríguez‐Flores, María Shantal and Felicioli, Antonio and Mazzei, Maurizio}, copyright = {© 2020 Wiley‐VCH GmbH}, - doi = {https://doi.org/10.1111/tbed.13878}, + doi = {10.1111/tbed.13878}, issn = {1865-1682}, journal = {Transboundary and Emerging Diseases}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Vespidae, honey bee viruses, next-generation sequencing, virology}, @@ -8892,6 +14710,34 @@ @article{marzoli_next_2020 year = {2020} } +@article{masangwa_virome_2025, + author = {Masangwa, Johnny Isaac Gregorio and Temple, Coline and Rollin, Johan and Maclot, François and Önder, Serkan and Kamwendo, Jamestone and Mwafongo, Elizabeth and Moses, Philemon and Fandika, Isaac and Massart, Sebastien}, + issn = {1999-4915}, + journal = {Viruses}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {July}, + number = {8}, + title = {Virome {Survey} of {Banana} {Plantations} and {Surrounding} {Plants} in {Malawi}}, + url = {http://europepmc.org/abstract/PMC/PMC12390665}, + volume = {17}, + year = {2025} +} + +@article{mathlouthi_archaeomes_2023, + author = {Mathlouthi, Nour El Houda and Belguith, Imen and Yengui, Mariem and Oumarou Hama, Hamadou and Lagier, Jean-Christophe and Ammar Keskes, Leila and Grine, Ghiles and Gdoura, Radhouane}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {November}, + number = {11}, + title = {The {Archaeome}’s {Role} in {Colorectal} {Cancer}: {Unveiling} the {DPANN} {Group} and {Investigating} {Archaeal} {Functional} {Signatures}}, + url = {http://europepmc.org/abstract/PMC/PMC10673094}, + volume = {11}, + year = {2023} +} + @article{mathlouthi_colorectal_2023, abstract = {Colorectal cancer (CRC) is a serious public health problem known to have a multifactorial etiology. The association between gut microbiota and CRC has been widely studied; however, the link between archaea and CRC has not been sufficiently studied. To investigate the involvement of archaea in colorectal carcinogenesis, we performed a metagenomic analysis of 68 formalin-embedded paraffin fixed tissues from tumoral (n = 33) and healthy mucosa (n = 35) collected from 35 CRC Tunisian patients. We used two DNA extraction methods: Generead DNA FFPE kit (Qiagen, Germantown, MD, USA) and Chelex. We then sequenced the samples using Illumina Miseq. Interestingly, DNA extraction exclusively using Chelex generated enough DNA for sequencing of all samples. After data filtering and processing, we reported the presence of archaeal sequences, which represented 0.33\% of all the reads generated. In terms of abundance, we highlighted a depletion in methanogens and an enrichment in Halobacteria in the tumor tissues, while the correlation analysis revealed a significant association between the Halobacteria and the tumor mucosa (p {\textless} 0.05). We reported a strong correlation between Natrialba magadii, Sulfolobus acidocaldarius, and tumor tissues, and a weak correlation between Methanococcus voltae and healthy adjacent mucosa. Here, we demonstrated the feasibility of archaeome analysis from formol fixed paraffin-embedded (FFPE) tissues using simple protocols ranging from sampling to data analysis, and reported a significant association between Halobacteria and tumor tissues in Tunisian patients with CRC. The importance of our study is that it represents the first metagenomic analysis of Tunisian CRC patients’ gut microbiome, which consists of sequencing DNA extracted from paired tumor-adjacent FFPE tissues collected from CRC patients. The detection of archaeal sequences in our samples confirms the feasibility of carrying out an archaeome analysis from FFPE tissues using a simple DNA extraction protocol. Our analysis revealed the enrichment of Halobacteria, especially Natrialba magadii, in tumor mucosa compared to the normal mucosa in CRC Tunisian patients. Other species were also associated with CRC, including Sulfolobus acidocaldarius and Methanococcus voltae, which is a methanogenic archaea; both species were found to be correlated with adjacent healthy tissues.}, author = {Mathlouthi, Nour El Houda and Oumarou Hama, Hamadou and Belguith, Imen and Charfi, Slim and Boudawara, Tahya and Lagier, Jean-Christophe and Ammar Keskes, Leila and Grine, Ghiles and Gdoura, Radhouane}, @@ -8920,7 +14766,7 @@ @article{mathura_characterization_2023 doi = {10.1371/journal.pone.0288481}, issn = {1932-6203}, journal = {PLOS ONE}, - keywords = {{\textgreater}UseGalaxy.eu, Gene expression, Potato, Protein interaction networks, Sequence motif analysis, Signaling networks, Stress signaling cascade, Sweet potato, Tubers}, + keywords = {{\textgreater}UseGalaxy.eu, Abscisic Acid, Gene expression, Ipomoea batatas, Potato, Protein interaction networks, Sequence motif analysis, Signaling networks, Stress signaling cascade, Sweet potato, Tubers}, language = {en}, month = {March}, note = {Publisher: Public Library of Science}, @@ -8939,7 +14785,7 @@ @article{mathura_genome-wide_2023 doi = {10.1186/s12870-023-04598-w}, issn = {1471-2229}, journal = {BMC Plant Biology}, - keywords = {{\textgreater}UseGalaxy.eu, ARF, Aux/IAA, GH3, SAUR, Sweet potato, Tuberization}, + keywords = {{\textgreater}UseGalaxy.eu, ARF, Aux/IAA, GH3, Ipomoea batatas, SAUR, Sweet potato, Tuberization}, language = {en}, month = {December}, number = {1}, @@ -8972,14 +14818,17 @@ @article{matsuura-suzuki_mirna-mediated_2024 doi = {10.1038/s44318-024-00249-4}, issn = {0261-4189}, journal = {The EMBO Journal}, - keywords = {{\textgreater}UseGalaxy.eu, Development, Drosophila melanogaster, GW182, Gene Silencing, MicroRNA}, + keywords = {{\textgreater}UseGalaxy.eu, Development, Drosophila Proteins, Drosophila melanogaster, GW182, Gene Silencing, Larva, MicroRNA, MicroRNAs}, + language = {eng}, month = {September}, note = {Num Pages: 19 Publisher: John Wiley \& Sons, Ltd}, + number = {23}, pages = {1--19}, title = {{miRNA}-mediated gene silencing in {Drosophila} larval development involves {GW182}-dependent and independent mechanisms}, url = {https://www.embopress.org/doi/full/10.1038/s44318-024-00249-4}, urldate = {2024-10-20}, + volume = {43}, year = {2024} } @@ -8998,19 +14847,86 @@ @misc{matusin_low_2023 year = {2023} } +@article{matusin_prevalence_2025, + abstract = {This is the first genetic study of its kind in Brunei Darussalam. BRCA1 and BRCA2 genes are the most well-known and well described predictors of hereditary breast cancer due to their clinical importance. This study aimed to identify the prevalence and mutation spectrum of the BRCA1 and BRCA2 germline mutations among 120 unselected series of Brunei breast cancer patients. We screened the entire coding region of BRCA1 and BRCA2 gene using Sanger sequencing and next-generation sequencing methods and identified three pathogenic and one likely pathogenic mutations in the BRCA2 gene. Of the 120 patients, 6 (5\%) were BRCA2 carriers which confirm that BRCA2 carriers are more common in the Asian population compared to the Caucasian population. One BRCA2 mutation observed only in the Chinese ethnicity of the Brunei breast cancer population suggest a probability of the mutation being a founder effect in the Southern Chinese population. Brunei BRCA2 carriers were more likely to have a positive family history of breast and/or ovarian cancers and have more than one family members in the first-degree relatives diagnosed with breast cancer.}, + author = {Matusin, Siti Nur Idayu and Mumin, Nuramalina and Zainal Abidin, Hazirah and Mohd Jaya, Fatin Nurizzati and Lu, Zen Huat and Haji Abdul Hamid, Mas Rina Wati}, + doi = {10.1371/journal.pone.0312635}, + issn = {1932-6203}, + journal = {PloS one}, + keywords = {{\textgreater}UseGalaxy.eu, BRCA1 Protein, BRCA2 Protein, Breast Neoplasms, Germ-Line Mutation}, + language = {eng}, + number = {6}, + pages = {e0312635}, + title = {Prevalence and spectrum of germline {BRCA1} and {BRCA2} mutations in multiethnic cohort of breast cancer patients in {Brunei} {Darussalam}}, + url = {http://europepmc.org/abstract/MED/40531958}, + volume = {20}, + year = {2025} +} + @article{mauer_genomics_2021, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Seisonidea (also Seisonacea or Seisonidae) is a group of small animals living on marine crustaceans (Nebalia spec.) with only four species described so far. Its monophyletic origin with mostly free-living wheel animals (Monogononta, Bdelloidea) and endoparasitic thorny-headed worms (Acanthocephala) is widely accepted. However, the phylogenetic relationships inside the Rotifera-Acanthocephala clade (Rotifera sensu lato or Syndermata) are subject to ongoing debate, with consequences for our understanding of how genomes and lifestyles might have evolved. To gain new insights, we analyzed first drafts of the genome and transcriptome of the key taxon Seisonidea.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}Analyses of gDNA-Seq and mRNA-Seq data uncovered two genetically distinct lineages in Seison nebaliae Grube, 1861 off the French Channel coast. Their mitochondrial haplotypes shared only 82\% sequence identity despite identical gene order. In the nuclear genome, distinct linages were reflected in different gene compactness, GC content and codon usage. The haploid nuclear genome spans ca. 46 Mb, of which 96\% were reconstructed. According to {\textasciitilde} 23,000 SuperTranscripts, gene number in S. nebaliae should be within the range published for other members of Rotifera-Acanthocephala. Consistent with this, numbers of metazoan core orthologues and ANTP-type transcriptional regulatory genes in the S. nebaliae genome assembly were between the corresponding numbers in the other assemblies analyzed. We additionally provide evidence that a basal branching of Seisonidea within Rotifera-Acanthocephala could reflect attraction to the outgroup. Accordingly, rooting via a reconstructed ancestral sequence led to monophyletic Pararotatoria (Seisonidea+Acanthocephala) within Hemirotifera (Bdelloidea+Pararotatoria).{\textless}h4{\textgreater}Conclusion{\textless}/h4{\textgreater}Matching genome/transcriptome metrics with the above phylogenetic hypothesis suggests that a haploid nuclear genome of about 50 Mb represents the plesiomorphic state for Rotifera-Acanthocephala. Smaller genome size in S. nebaliae probably results from subsequent reduction. In contrast, genome size should have increased independently in monogononts as well as bdelloid and acanthocephalan stem lines. The present data additionally indicate a decrease in gene repertoire from free-living to epizoic and endoparasitic lifestyles. Potentially, this reflects corresponding steps from the root of Rotifera-Acanthocephala via the last common ancestors of Hemirotifera and Pararotatoria to the one of Acanthocephala. Lastly, rooting via a reconstructed ancestral sequence may prove useful in phylogenetic analyses of other deep splits.}, author = {Mauer, Katharina M. and Schmidt, Hanno and Dittrich, Marco and Fröbius, Andreas C. and Hellmann, Sören Lukas and Zischler, Hans and Hankeln, Thomas and Herlyn, Holger}, doi = {10.1186/s12864-021-07857-y}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {1471-2164}, + journal = {BMC genomics}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Acanthocephala, Rotifera}, + language = {eng}, month = {August}, note = {Publisher: Springer Science and Business Media LLC}, number = {1}, + pages = {604}, title = {Genomics and transcriptomics of epizoic {Seisonidea} ({Rotifera}, syn. {Syndermata}) reveal strain formation and gradual gene loss with growing ties to the host}, url = {https://doi.org/10.1186/s12864-021-07857-y}, volume = {22}, year = {2021} } +@article{mavroidi_genomic_2025, + author = {Mavroidi, Angeliki and Froukala, Elisavet and Spanakis, Nick and Michelaki, Aikaterini and Orfanidou, Maria and Koumaki, Vasiliki and Tsakris, Athanasios}, + issn = {2079-6382}, + journal = {Antibiotics (Basel)}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {July}, + number = {8}, + title = {Genomic {Insights} of {Emerging} {Multidrug}-{Resistant} {OXA}-48-{Producing} {ST135} {Proteus} mirabilis}, + url = {http://europepmc.org/abstract/PMC/PMC12383092}, + volume = {14}, + year = {2025} +} + +@article{mayer_gene_2025, + abstract = {BackgroundProtein kinase CK2 is known to exist as a tetramer of two catalytic α- or α'- subunits and two non-catalytic β-subunits, or as multimers of this tetramer. Moreover, CK2α (CSNK2A1) and CK2α' (CSNK2A2) are also active in the absence of CK2β (CSNK2B). Very little is known about specific functions of the individual subunits of protein kinase CK2.ResultsIn order to study the effects of CK2α and CK2α' on gene expression, we used the Mus musculus pancreatic α-cell line αTC1 and two derivatives with either CK2α (KO1 cells) or CK2α' (KO2 cells) expression knocked-out by CRISPR/Cas technology. We found numerous genes deregulated in both KO1 and KO2 cells compared to the parental cells. Applying stringent thresholds, 266 genes were found down-regulated and 153 genes up-regulated in KO1 cells, 233 genes were found down-regulated and 84 genes up-regulated in KO2 cells. Dozens of genes were found deregulated in a similar fashion in both KO1 and KO2 cells. We found altered expression of genes involved in the differentiation of pancreatic cells, including Hox genes, and in the regulation of glucagon synthesis or secretion. Moreover, many of the deregulated genes play an important role in developmental processes and in neuronal cell biology.ConclusionOur findings reveal individual and shared functions of the CK2α and CK2α' catalytic subunits, in particular regarding their involvement in regulating gene expression.}, + author = {Mayer, Jens and Pack, Mandy and Montenarh, Mathias and Götz, Claudia}, + copyright = {cc by}, + doi = {10.1186/s40659-025-00654-x}, + issn = {0717-6287}, + journal = {Biological research}, + keywords = {{\textgreater}UseGalaxy.eu, Ck2 Knock-out, Ck2α Isoforms, Gene expression profile, Pancreatic Α-cells, protein kinase CK2}, + language = {eng}, + month = {November}, + number = {1}, + pages = {69}, + pmcid = {PMC12616906}, + pmid = {41233858}, + title = {Gene expression changes in pancreatic α-cell lines following knock-out {Of} either {CK2α} or {CK2α}'}, + url = {https://europepmc.org/articles/PMC12616906}, + urldate = {2025-12-26}, + volume = {58}, + year = {2025} +} + +@article{mc_cartney_european_2023, + abstract = {A global genome database of all of Earth's species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all {\textasciitilde}1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 34 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.}, + author = {Mc Cartney, Ann and Formenti, Giulio and Mouton, Alice and De Panis, Diego and De Panis, Diego and Marins, Luisa and Leitao, Henrique and Diedericks, Genevieve and Kirangwa, Joseph and Morselli, Marco and Salces, Judit and Escudero, Nuria and Iannucci, Alessio and Natali, Chiara and Svardal, Hannes and Fernandez, Rosa and De Pooter, Tim and Joris, Geert and Strazisar, Mojca and Wood, Jo and Herron, Katie and Seehausen, Ole and Watts, Phillip and Shaw, Felix and Davey, Robert and Minotto, Alice and Fernandez Gonzalez, Jose Maria and Bohne, Astrid and Alegria, Carla and Alioto, Tyler and Alves, Paulo and Amorim, Isabel and Aury, Jean-Marc and Backstrom, Niclas and Baldrian, Petr and Ballarin, Loriano and Baltrunaite, Laima and Barta, Endre and BedHom, Bertrand and Belser, Caroline and Bergsten, Johannes and Bertrand, Laurie and Bilandija, Helena and Binzer-Panchal, Mahesh and Bista, Iliana and Blaxter, Mark and Borges, Paulo AV and Borges Dias, Guilherme and Bosse, Mirte and Brown, Tom and Bruggmann, Remy and Buena-Atienza, Elena and Burgin, Josephine and Buzan, Elena and Cariani, Alessia and Casadei, Nicolas and Chiara, Matteo and Chozas, Sergio and Ciampor, Fedor and Crottini, Angelica and Cruaud, Corinne and Cruz, Fernando and Dalen, Love and De Biase, Alessio and del Campo, Javier and Delic, Teo and Dennis, Alice and Derks, Martijn FL and Diroma, Maria Angela and Djan, Mihajla and Duprat, Simone and Eleftheriadi, Klara and Feulner, Philine GD and Flot, Jean-Francois and Forni, Giobbe and Fosso, Bruno and Fournier, Pascal and Fournier-Chambrillon, Christine and Gabaldon, Toni and Garg, Shilpa and Gissi, Carmela and Giupponi, Luca and Gomez-Garrido, Jessica and Gonzalez, Josefa and Grilo, Miguel and Gruening, Bjoern and Guerin, Thomas and Guiglielmoni, Nadege and Gut, Marta and Haesler, Marcel and Hahn, Christoph and Halpern, Balint and Harrison, Peter and Heintz, Julia and Hindrikson, Maris and Hoglund, Jacob and Howe, Kerstin and Hughes, Graham and Istace, Benjamin and Cock, Mark and Jancekovic, Franc and Jonsson, Zophonias and Joye-Dind, Sagane and Koskimaki, Janne and Krystufek, Boris and Kubacka, Justyna and Kuhl, Heiner and Kusza, Szilvia and Labadie, Karine and Lahteenaro, Meri and Lantz, Henrik and Lavrinienko, Anton and Leclere, Lucas and Lopes, Ricardo Jorge and Madsen, Ole and Magdelenat, Ghislaine and Magoga, Giulia and Manousaki, Tereza and Mappes, Tapio and Marques, Joao Pedro and Martinez Redondo, Gemma and Maumus, Florian and McCarthy, Shane and Megens, Hendrik-Jan and Melo-Ferreira, Jose and Mendes, Sofia and Montagna, Matteo and Moreno, Joao and Mosbech, Mai-Britt and Moura, Monica and Musilova, Zuzana and Myers, Eugene and Nash, Will and Nater, Alexander and Nicholson, Pamela and Niell, Manuel and Nijland, Reindert and Noel, Benjamin and Noren, Karin and Oliveira, Pedro and Olsen, Remi-Andre and Ometto, Lino and Oomen, Rebekah and Ossowski, Stephan and Palinauskas, Vaidas and Palsson, Snaebjorn and Panibe, Jerome and Pauperio, Joana and Pavlek, Martina and Payen, Emilie and Pawlowska, Julia and Pellicer, Jaume and Pesole, Graziano and Pimenta, Joao and Pippel, Martin and Pirttila, Anna Maria and Poulakakis, Nikos and Rajan, Jeena and Rego, Ruben MC and Resendes, Roberto and Resl, Philipp and Riesgo, Ana and Rodin-Morch, Patrik and Soares, Andre ER and Rodriguez Fernandes, Carlos and Romeiras, Maria and Roxo, Guilherme and Ruber, Lukas and Ruiz-Lopez, Maria Jose and Saarma, Urmas and Silva, Luis and Sim-Sim, Manuela and Soler, Lucile and Sousa, Vitor and Sousa Santos, Carla and Spada, Alberto and Stefanovic, Milomir and Steger, Viktor and Stiller, Josefin and Stock, Matthias and Struck, Torsten Hugo and Sudasinghe, Hiranya and Tapanainen, Riikka and Tellgren-Roth, Christian and Trindade, Helena and Tukalenko, Yevhen and Urso, Ilenia and Vacherie, Benoit and Van Belleghem, Steven and van Oers, Kees and Vargas-Chavez, Carlos and Velickovic, Nevena and Vella, Noel and Vella, Adriana and Vernesi, Cristiano and Vicente, Sara and Villa, Sara and Vinnere Pettersson, Olga and Volckaert, Filip AM and Voros, Judit and Wincker, Patrick and Winkler, Sylke and Ciofi, Claudio and Waterhouse, Robert and Mazzoni, Camila}, + doi = {10.1101/2023.09.25.559365}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {The {European} {Reference} {Genome} {Atlas}: piloting a decentralised approach to equitable biodiversity genomics}, + url = {http://europepmc.org/abstract/PPR/PPR732921}, + year = {2023} +} + @article{mccluskey_predicting_2024, author = {McCluskey, Kevin and Brown, Daren and Bredeweg, Erin and Baker, Scott}, doi = {10.4148/1941-4765.2183}, @@ -9075,12 +14991,14 @@ @article{mcgowan_multi-omics_2020 abstract = {AbstractBackground. Proteogenomics integrates genomics, transcriptomics, and mass spectrometry (MS)-based proteomics data to identify novel protein sequences a}, author = {McGowan, Thomas and Johnson, James E. and Kumar, Praveen and Sajulga, Ray and Mehta, Subina and Jagtap, Pratik D. and Griffin, Timothy J.}, doi = {10.1093/gigascience/giaa025}, + issn = {2047-217X}, journal = {GigaScience}, - keywords = {+Galactic, +IsGalaxy, +RefPublic, +Shared, +Tools, +Visualization, {\textgreater}Galaxy-P, {\textgreater}UseGalaxy.eu}, + keywords = {+Galactic, +IsGalaxy, +RefPublic, +Shared, +Tools, +Visualization, {\textgreater}Galaxy-P, {\textgreater}UseGalaxy.eu, Data Visualization, Proteomics}, language = {en}, month = {April}, note = {Publisher: Oxford Academic}, number = {4}, + pages = {giaa025}, shorttitle = {Multi-omics {Visualization} {Platform}}, title = {Multi-omics {Visualization} {Platform}: {An} extensible {Galaxy} plug-in for multi-omics data visualization and exploration}, url = {https://academic.oup.com/gigascience/article/9/4/giaa025/5813097}, @@ -9089,6 +15007,34 @@ @article{mcgowan_multi-omics_2020 year = {2020} } +@article{mcquarrie_rapid_2024, + abstract = {Seminal fluid proteins (Sfps) are essential for reproductive success and evolve fast, possibly driven by post-copulatory sexual selection (PCSS) originating from sperm competition and cryptic female choice. Counterintuitively, however, the coding region only in few Sfps evolves adaptively. Hence, additional genomic and functional factors must play a role in Sfp evolution independent of the protein coding region. To shed light on drivers of Sfp evolution we focus on those Sfps predominantly expressed in male accessory glands, because this allows examination of their evolution in the tissue which produces the majority of Sfps. Moreover, accessory glands develop normally in hybrids in contrast to testis allowing to control for changes in cellular environment arising during speciation. Here, we discover that Acp promoters contain hot spots for rapid evolution from accumulation of sequence changes and insertions/deletions (indels). We further show that changes in promoter sequences are accompanied by gene expression divergence among closely related Drosophila species. We then validate these observations in Drosophila hybrids to show that species-specific expression divergence of Acps with rapidly evolving promoters are maintained in hybrids for some Acps, while others show dominance of one allele, a phenomenon termed transvection. These results indicate that cis -regulatory evolution, rather than genome background variation, drives Acp expression changes and promotes their rapid evolution.}, + author = {McQuarrie, David and Stephens, Frannie and Ferguson, Alexander and Arnold, Roland and Civetta, Alberto and Soller, Matthias}, + doi = {10.1101/2024.10.14.618274}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Rapid promoter evolution of male accessory gland genes is accompanied by divergent expression in closely {relatedDrosophilaspecies}}, + url = {http://europepmc.org/abstract/PPR/PPR926281}, + year = {2024} +} + +@article{mcquarrie_rapid_2025, + abstract = {Seminal fluid proteins (Sfps) are essential for reproductive success and evolve fast on average, possibly driven by post-copulatory sexual selection (PCSS) originating from sperm competition and cryptic female choice. Counterintuitively, however, the coding region only in few Sfps evolves adaptively. Hence, additional genomic and functional factors must play a role in Sfp evolution independent of the protein coding region. To shed light on drivers of Sfp evolution we focus on those Sfps predominantly expressed in male accessory glands of Drosophila to examine their evolution in the tissue which produces the majority of Sfps. Unlike the testis, the accessory glands are known to develop normally in hybrids, allowing us to control for cellular environment differences arising during speciation. Here, we identify hotspots of rapid evolution in accessory gland protein genes (Acp) promoters, driven by base changes and insertions/deletions (indels). We further show that changes in promoter sequences are accompanied by gene expression divergence among closely related species. Using hybrids, we demonstrate that species-specific expression divergence is maintained for some Acps, while others exhibit dominance of one allele. These results indicate that regulatory evolution, rather than genome background variation, drives Acp expression changes and promotes their rapid evolution.}, + author = {McQuarrie, David W J and Stephens, Frannie H S and Ferguson, Alexander D and Arnold, Roland and Civetta, Alberto and Soller, Matthias}, + doi = {10.1093/genetics/iyaf226}, + issn = {1943-2631}, + journal = {Genetics}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {December}, + number = {4}, + pages = {iyaf226}, + title = {Rapid promoter evolution of male accessory gland genes is accompanied by divergent expression in closely related {Drosophila} species}, + url = {https://doi.org/10.1093/genetics/iyaf226}, + urldate = {2025-12-26}, + volume = {231}, + year = {2025} +} + @article{mcvey_genetic_2024, abstract = {Vascular smooth muscle cell (VSMC) proliferation, migration, and apoptosis play important roles in many physiological processes and pathological conditions. To identify genetic influences on VSMC behavior, we measured these traits and undertook genome-wide association studies in primary umbilical artery-derived VSMCs from {\textgreater}2000 individuals. Although there were no genome-wide significant associations for VSMC proliferation or migration, genetic variants at two genomic loci (7p15.3 and 7q32.3) showed highly significant associations with VSMC apoptosis (P = 1.95 × 10−13 and P = 7.47 × 10−9, respectively). The lead variant at the 7p51.3 locus was associated with increased expression of the GSDME and PALS2 genes in VSMCs. Knockdown of GSDME or PALS2 in VSMCs attenuated apoptotic cell death. A protein co-immunoprecipitation assay indicated that GSDME complexed with PALS2. PALS2 knockdown attenuated activated caspase-3 and GSDME fragmentation, whilst GSDME knockdown also reduced activated caspase-3. These findings provide new insights into the genetic regulation of VSMC apoptosis, with potential utility for therapeutic development.}, author = {McVey, David G. and Andreadi, Catherine and Gong, Peng and Stanczyk, Paulina J. and Solomon, Charles U. and Turner, Lenka and Yan, Liu and Chen, Runji and Cao, Junjun and Nelson, Christopher P. and Thompson, John R. and Yu, Haojie and Webb, Tom R. and Samani, Nilesh J. and Ye, Shu}, @@ -9137,6 +15083,37 @@ @article{meem_exploring_2024 year = {2024} } +@article{mehra_high-quality_2021, + abstract = {Lactobacillus paragasseri was identified as a novel sister taxon of L. gasseri in 2018. Since the reclassification of L. paragasseri, there has been hardly any report describing the probiotic properties of this species. In this study, an L. paragasseri strain UBLG-36 was sequenced and analyzed to determine the molecular basis that may confer the bacteria with probiotic potential. UBLG-36 was previously documented as an L. gasseri strain. Average nucleotide identity and phylogenomic analysis allowed accurate taxonomic identification of UBLG-36 as an L. paragasseri strain. Analysis of the draft genome ({\textasciitilde}1.94 Mb) showed that UBLG-36 contains 5 contigs with an average G+C content of 34.85\%. Genes essential for the biosynthesis of bacteriocins, adhesion to host epithelium, stress resistance, host immunomodulation, defense, and carbohydrate metabolism were identified in the genome. Interestingly, L. paragasseri UBLG-36 also harbored genes that code for enzymes involved in oxalate catabolism, such as formyl coenzyme A transferase (frc) and oxalyl coenzyme A decarboxylase (oxc). In vitro oxalate degradation assay showed that UBLG-36 is highly effective in degrading oxalate (averaging more than 45\% degradation), a feature that has not been reported before. As a recently identified bacterium, there are limited genomic reports on L. paragasseri, and our draft genome sequence analysis is the first to describe and emphasize the probiotic potential and oxalate degrading ability of this species. With results supporting the probiotic functionalities and oxalate catabolism of UBLG-36, we propose that this strain is likely to have immense biotechnological applications upon appropriate characterization.}, + author = {Mehra, Yogita and Viswanathan, Pragasam}, + doi = {10.1371/journal.pone.0260116}, + issn = {1932-6203}, + journal = {PloS one}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + number = {11}, + pages = {e0260116}, + title = {High-quality whole-genome sequence analysis of {Lactobacillus} paragasseri {UBLG}-36 reveals oxalate-degrading potential of the strain}, + url = {http://europepmc.org/abstract/MED/34797858}, + volume = {16}, + year = {2021} +} + +@article{mehta_asaim-mt_2021, + abstract = {The Earth Microbiome Project (EMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the 'microbiome') and microbial diversity patterns across the habitats of our planet. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on the environment and human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). On the other hand, metatranscriptomics, the study of a microbial community's RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome.  In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking.  In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.}, + author = {Mehta, Subina and Crane, Marie and Leith, Emma and Batut, Bérénice and Hiltemann, Saskia and Arntzen, Magnus Ø and Kunath, Benoit J and Pope, Phillip B and Delogu, Francesco and Sajulga, Ray and Kumar, Praveen and Johnson, James E and Griffin, Timothy J and Jagtap, Pratik D}, + doi = {10.12688/f1000research.28608.2}, + issn = {2046-1402}, + journal = {F1000Research}, + keywords = {{\textgreater}UseGalaxy.eu, Metagenomics, Microbiota}, + language = {eng}, + pages = {103}, + title = {{ASaiM}-{MT}: a validated and optimized {ASaiM} workflow for metatranscriptomics analysis within {Galaxy} framework}, + url = {http://europepmc.org/abstract/MED/34484688}, + volume = {10}, + year = {2021} +} + @article{mehta_asaim-mt_2021, abstract = {The Human Microbiome Project (HMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the ‘microbiome’) in human health and disease. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). Conversely, metatranscriptomics, the study of a microbial community’s RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome.  In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking.  In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.}, author = {Mehta, Subina and Crane, Marie and Leith, Emma and Batut, Bérénice and Hiltemann, Saskia and Arntzen, Magnus Ø and Kunath, Benoit J. and Delogu, Francesco and Sajulga, Ray and Kumar, Praveen and Johnson, James E. and Griffin, Timothy J. and Jagtap, Pratik D.}, @@ -9170,6 +15147,7 @@ @article{mehta_catching_2022 pmid = {36298760}, shorttitle = {Catching the {Wave}}, title = {Catching the {Wave}: {Detecting} {Strain}-{Specific} {SARS}-{CoV}-2 {Peptides} in {Clinical} {Samples} {Collected} during {Infection} {Waves} from {Diverse} {Geographical} {Locations}}, + url = {http://europepmc.org/abstract/MED/36298760}, volume = {14}, year = {2022} } @@ -9197,6 +15175,7 @@ @article{mehta_precursor_2020 author = {Mehta, Subina and Easterly, Caleb W. and Sajulga, Ray and Millikin, Robert J. and Argentini, Andrea and Eguinoa, Ignacio and Martens, Lennart and Shortreed, Michael R. and Smith, Lloyd M. and McGowan, Thomas and Kumar, Praveen and Johnson, James E. and Griffin, Timothy J. and Jagtap, Pratik D.}, copyright = {http://creativecommons.org/licenses/by/3.0/}, doi = {10.3390/proteomes8030015}, + issn = {2227-7382}, journal = {Proteomes}, keywords = {+Galactic, +Tools, {\textgreater}Galaxy-P, {\textgreater}UseGalaxy.be, {\textgreater}UseGalaxy.eu, galaxy framework, label-free quantification, proteomics, workflows}, language = {en}, @@ -9247,13 +15226,30 @@ @article{meier_antileukemic_2022 year = {2022} } +@article{merdan_investigation_2022, + abstract = {Candida glabrata is increasingly isolated from blood cultures, and multidrug-resistant isolates have important implications for therapy. This study describes a cholesterol-dependent clinical C. glabrata isolate (ML72254) that did not grow without blood (containing cholesterol) on routine mycological media and that showed azole and amphotericin B (AmB) resistance. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and whole-genome sequencing (WGS) were used for species identification. A modified Etest method (Mueller-Hinton agar supplemented with 5\% sheep blood) was used for antifungal susceptibility testing. WGS data were processed via the Galaxy platform, and the genomic variations of ML72254 were retrieved. A computational biology workflow utilizing web-based applications (PROVEAN, AlphaFold Colab, and Missense3D) was constructed to predict possible deleterious effects of these missense variations on protein functions. The predictive ability of this workflow was tested with previously reported missense variations in ergosterol synthesis genes of C. glabrata. ML72254 was identified as C. glabrata \textit{sensu stricto} with MALDI-TOF, and WGS confirmed this identification. The MICs of fluconazole, voriconazole, and amphotericin B were {\textgreater}256, {\textgreater}32, and {\textgreater}32 μg/mL, respectively. A novel frameshift mutation in the \textit{ERG1} gene (Pro314fs) and many missense variations were detected in the ergosterol synthesis genes. None of the missense variations in the ML72254 ergosterol synthesis genes were deleterious, and the Pro314fs mutation was identified as the causative molecular change for a cholesterol-dependent and multidrug-resistant phenotype. This study verified that web-based computational biology solutions can be powerful tools for examining the possible impacts of missense mutations in C. glabrata. \textbf{IMPORTANCE} In this study, a cholesterol-dependent C. glabrata clinical isolate that confers azole and AmB resistance was investigated using artificial intelligence (AI) technologies and cloud computing applications. This is the first of the known cholesterol-dependent C. glabrata isolate to be found in Turkey. Cholesterol-dependent C. glabrata isolates are rarely isolated in clinical samples; they can easily be overlooked during routine laboratory procedures. Microbiologists therefore need to be alert when discrepancies occur between microscopic examination and growth on routine media. In addition, because these isolates confer antifungal resistance, patient management requires extra care.}, + author = {Merdan, Osman and Şişman, Ayşe Sena and Aksoy, Seçil Ak and Kızıl, Samet and Tüzemen, Nazmiye Ülkü and Yılmaz, Emel and Ener, Beyza}, + doi = {10.1128/spectrum.00776-22}, + issn = {2165-0497}, + journal = {Microbiol Spectr}, + keywords = {{\textgreater}UseGalaxy.eu, Amphotericin B, Candida glabrata}, + language = {eng}, + month = {August}, + number = {4}, + pages = {e0077622}, + title = {Investigation of the {Defective} {Growth} {Pattern} and {Multidrug} {Resistance} in a {Clinical} {Isolate} of {Candida} glabrata {Using} {Whole}-{Genome} {Sequencing} and {Computational} {Biology} {Applications}}, + url = {http://europepmc.org/abstract/MED/35867406}, + volume = {10}, + year = {2022} +} + @article{merida-cerro_rat1_2024, abstract = {Certain DNA sequences can adopt a non-B form in the genome that interfere with DNA-templated processes, including transcription. Among the sequences that are intrinsically difficult to transcribe are those that tend to form R-loops, three-stranded nucleic acid structures formed by a DNA-RNA hybrid and the displaced ssDNA. Here we compared the transcription of an endogenous gene with and without an R-loop-forming sequence inserted. We show that, in agreement with previous in vivo and in vitro analyses, transcription elongation is delayed by R-loops in yeast. Importantly, we demonstrate that the Rat1 transcription terminator factor facilitates transcription throughout such structures by inducing premature termination of arrested RNAPIIs. We propose that RNase H degrades the RNA moiety of the hybrid, providing an entry site for Rat1. Thus, we have uncovered an unanticipated function of Rat1 as a transcription restoring factor opening up the possibility that it may also promote transcription through other genomic DNA structures intrinsically difficult to transcribe. If R-loop-mediated transcriptional stress is not relieved by Rat1, it will cause genomic instability, probably through the increase of transcription-replication conflicts, a deleterious situation that could lead to cancer.}, author = {Mérida-Cerro, José Antonio and Maraver-Cárdenas, Pablo and Rondón, Ana G and Aguilera, Andrés}, doi = {10.1093/nar/gkae033}, issn = {0305-1048}, journal = {Nucleic Acids Research}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Exoribonucleases, R-Loop Structures, Ribonuclease H, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Termination, Genetic}, month = {April}, number = {7}, pages = {3623--3635}, @@ -9270,7 +15266,7 @@ @article{merz_characterization_2024 doi = {10.1186/s12866-024-03231-6}, issn = {1471-2180}, journal = {BMC Microbiology}, - keywords = {{\textgreater}UseGalaxy.eu, AtlC, Autolysis, Knockout mutant, Staphylococcus carnosus}, + keywords = {{\textgreater}UseGalaxy.eu, AtlC, Autolysis, Knockout mutant, N-Acetylmuramoyl-L-alanine Amidase, Staphylococcus, Staphylococcus carnosus}, language = {en}, month = {March}, number = {1}, @@ -9288,7 +15284,7 @@ @article{metris_aircraft_2023 doi = {10.7717/peerj.15171}, issn = {2167-8359}, journal = {PeerJ}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Atmosphere, DNA, Environmental, Environmental Monitoring}, language = {en}, month = {April}, note = {Publisher: PeerJ Inc.}, @@ -9320,11 +15316,27 @@ @article{mevada_variant_2022 year = {2022} } +@article{meyer_wastewater_2025, + abstract = {Synthetic antioxidants (SAOs) are widely used additives in industrial and consumer products, yet their human exposure and fate throughout wastewater treatment remain poorly understood. This study investigates the occurrence of SAOs and their human metabolites in wastewater influent as well as their abatement in three wastewater treatment plants (WWTPs) employing both conventional and advanced treatment technologies. In vitro human liver S9 assays were performed to generate a SAO metabolite MS2 library containing over 2500 potential metabolites, which was matched against wastewater influent data. This approach revealed fenozan, which was detected in the influent of all three WWTPs, as a potential biomarker for five of the seven analyzed 3-(3,5-di-tert-butyl-4-hydroxyphenyl)propionate antioxidants. Detection of the glucuronide conjugate in urinary samples together with the tested high hydrolytic stability of the parent SAOs further qualify fenozan as a potential biomarker. Biological wastewater treatment led to high abatement for most SAOs with a mean value of approximately 70\% across all 18 detected SAOs in the three investigated WWTPs. Subsequent ozonation led to further abatement (≥68\%), particularly for the amine antioxidants. This can be attributed to their aniline-type structures with low pKa values, which render their second-order rate constants with ozone pH-independent at pH values typical for wastewater. For phenolic antioxidants in contrast, the second-order rate constants with ozone are pH-dependent, leading to varying abatements. These results emphasize the important role of wastewater treatment in mitigating SAO pollution. Overall, this study demonstrates the value of wastewater monitoring as a unified approach to assess both human and environmental exposure to SAOs.}, + author = {Meyer, Corina and Bär, Mara L. and Hollender, Juliane}, + doi = {10.1016/j.envint.2025.109709}, + issn = {0160-4120}, + journal = {Environment International}, + keywords = {{\textgreater}UseGalaxy.eu, Human liver S9, Human metabolites, LC-HRMS/MS, MS2 library, Ozonation, Synthetic antioxidants, Wastewater treatment}, + month = {August}, + pages = {109709}, + shorttitle = {Wastewater as a dual indicator of human and environmental exposure to synthetic antioxidants}, + title = {Wastewater as a dual indicator of human and environmental exposure to synthetic antioxidants: {Occurrence} and fate in biological and advanced wastewater treatment}, + url = {https://www.sciencedirect.com/science/article/pii/S016041202500460X}, + urldate = {2025-09-03}, + year = {2025} +} + @article{miao_putative_2020, abstract = {We present a novel method for automated identification of putative cell types from single-cell RNA-seq (scRNA-seq) data. By iteratively applying a machine learning approach to an initial clustering of gene expression profiles of a given set of cells, we simultaneously identify distinct cell groups and a weighted list of feature genes for each group. The feature genes, which are differentially expressed in the particular cell group, jointly discriminate the given cell group from other cells. Each such group of cells corresponds to a putative cell type or state, characterised by the feature genes as markers. To benchmark this approach, we use expert-annotated scRNA-seq datasets from a range of experiments, as well as comparing to existing cell annotation methods, which are all based on a pre-existing reference. We show that our method automatically identifies the 'ground truth' cell assignments with high accuracy. Moreover, our method, Single Cell Clustering Assessment Framework (SCCAF) predicts new putative biologically meaningful cell-states in published data on haematopoiesis and the human cortex. SCCAF is available as an open-source software package on GitHub (https://github.com/SCCAF/sccaf) and as a Python package index and has also been implemented as a Galaxy tool in the Human Cell Atlas.}, author = {Miao, Zhichao and Moreno, Pablo and Huang, Ni and Papatheodorou, Irene and Brazma, Alvis and Teichmann, Sarah A.}, journal = {arXiv}, - keywords = {+RefPublic, +Tools, {\textgreater}UseGalaxy.eu, Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods}, + keywords = {+RefPublic, +Tools, {\textgreater}UseGalaxy.eu, Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods, ⛔ No DOI found}, month = {April}, note = {arXiv: 2004.09847 version: 1}, @@ -9364,13 +15376,24 @@ @article{migur_temperature-regulated_2021 year = {2021} } +@article{miladi_landscape_2020, + abstract = {In 2019 the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the first documented cases of severe lung disease COVID-19. Since then, SARS-CoV-2 has been spreading around the globe resulting in a severe pandemic with over 500.000 fatalities and large economical and social disruptions in human societies. Gaining knowledge on how SARS-Cov-2 interacts with its host cells and causes COVID-19 is crucial for the intervention of novel therapeutic strategies. SARS-CoV-2, like other coronaviruses, is a positive-strand RNA virus. The viral RNA is modified by RNA-modifying enzymes provided by the host cell. Direct RNA sequencing (DRS) using nanopores enables unbiased sensing of canonical and modified RNA bases of the viral transcripts. In this work, we used DRS to precisely annotate the open reading frames and the landscape of SARS-CoV-2 RNA modifications. We provide the first DRS data of SARS-CoV-2 in infected human lung epithelial cells. From sequencing three isolates, we derive a robust identification of SARS-CoV-2 modification sites within a physiologically relevant host cell type. A comparison of our data with the DRS data from a previous SARS-CoV-2 isolate, both raised in monkey renal cells, reveals consistent RNA modifications across the viral genome. Conservation of the RNA modification pattern during progression of the current pandemic suggests that this pattern is likely essential for the life cycle of SARS-CoV-2 and represents a possible target for drug interventions.}, + author = {Miladi, Milad and Fuchs, Jonas and Maier, Wolfgang and Weigang, Sebastian and Pedrosa, Núria Díaz and Weiss, Lisa and Lother, Achim and Nekrutenko, Anton and Ruzsics, Zsolt and Panning, Marcus and Kochs, Georg and Gilsbach, Ralf and Grüning, Björn}, + doi = {10.1101/2020.07.18.204362}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {The landscape of {SARS}-{CoV}-2 {RNA} modifications}, + url = {http://europepmc.org/abstract/PPR/PPR189305}, + year = {2020} +} + @article{minisy_transcription_2024, abstract = {Pregnancy involving intricate tissue transformations governed by the progesterone hormone (P4). P4 signaling via P4 receptors (PRs) is vital for endometrial receptivity, decidualization, myometrial quiescence, and labor initiation. This study explored the role of TCF23 as a downstream target of PR during pregnancy. TCF23 was found to be expressed in female reproductive organs, predominantly in uterine stromal and smooth muscle cells. Tcf23 expression was high during midgestation and was specifically regulated by P4, but not estrogen. The Tcf23 knockout (KO) mouse was generated and analyzed. Female KO mice aged 4-6 months exhibited subfertility, reduced litter size, and defective parturition. Uterine histology revealed disrupted myometrial structure, altered collagen organization, and disarrayed smooth muscle sheets at the conceptus sites of KO mice. RNA-Seq analysis of KO myometrium revealed dysregulation of genes associated with cell adhesion and extracellular matrix organization. TCF23 potentially modulates TCF12 activity to mediate cell-cell adhesion and matrix modulation in smooth muscle cells. Overall, TCF23 deficiency leads to impaired myometrial remodeling, causing parturition delay and fetal demise. This study sheds light on the critical role of TCF23 as a dowstream mediator of PR in uterine remodeling, reflecting the importance of cell-cell communication and matrix dynamics in myometrial activation and parturition.}, author = {Minisy, Fatma M. and Shawki, Hossam H. and Fujita, Tsubasa and Moustafa, Ahmed M. and Sener, Rumeysa and Nishio, Youske and Shimada, Issei S. and Saitoh, Shinji and Sugiura-Ogasawara, Mayumi and Oishi, Hisashi}, doi = {10.1080/10985549.2024.2376146}, issn = {null}, journal = {Molecular and Cellular Biology}, - keywords = {{\textgreater}UseGalaxy.eu, TCF23, bHLH, dystocia, extracellular matrix, myometrium remodeling, parturition, progesterone, resorption, smooth muscle cells}, + keywords = {{\textgreater}UseGalaxy.eu, Myometrium, Parturition, TCF23, bHLH, dystocia, extracellular matrix, myometrium remodeling, parturition, progesterone, resorption, smooth muscle cells}, month = {August}, note = {Publisher: Taylor \& Francis \_eprint: https://doi.org/10.1080/10985549.2024.2376146}, @@ -9405,7 +15428,7 @@ @article{mirmohammadi_silico_2022 doi = {10.1016/j.meegid.2022.105318}, issn = {1567-1348}, journal = {Infection, Genetics and Evolution}, - keywords = {{\textgreater}UseGalaxy.eu, COVID-19, Drug repurposing, In silico, SARS-CoV-2, Transcriptomics}, + keywords = {{\textgreater}UseGalaxy.eu, Antiviral Agents, COVID-19, COVID-19 Drug Treatment, Drug repurposing, Hydrocodone, Hydrocortisone, In silico, SARS-CoV-2, Transcriptomics}, month = {September}, pages = {105318}, shorttitle = {In silico drug repurposing against {SARS}-{CoV}-2 using an integrative transcriptomic profiling approach}, @@ -9431,13 +15454,31 @@ @mastersthesis{missaghimamaghani_evaluation_2023 year = {2023} } +@article{mitra_diversity_2025, + abstract = {IntroductionMobile genetic elements (MGEs) play a crucial role in the spread of carbapenem resistance. A study was undertaken to characterize MGEs and evaluate their contribution to the spread of carbapenem resistance in Escherichia coli and Klebsiella pneumoniae collected from three intensive care units (ICUs) of a tertiary care hospital in Tripura.MethodsIsolates were subjected to susceptibility testing, genotypic detection of carbapenemases and their transmissibility, whole-genome sequencing (WGS), and phylogenomic analysis.ResultsE. coli and K. pneumoniae were the dominant Enterobacterales, exhibiting resistance to the majority of antibiotics. WGS of carbapenemase-producing E. coli (n = 15/48,31\%) and K. pneumoniae (n = 13/26,50\%) revealed the presence of blaNDM-1,5,7 (n = 21), blaKPC-2 (n = 1), and blaOXA-181,232 (n = 8). Isolates were diverse and belonged to different sequence types, including epidemic clones (K. pneumoniae-ST16/101/147/231; E. coli-ST167/410/648). This study has noted the allelic shift of blaNDM-1 to blaNDM-5 similar to global reports. blaNDM-1,5,7-bearing plasmids were conjugative but those carrying blaKPC-2 and blaOXA-181,232 were non-conjugative. blaNDM-1,5,7 were present in diverse replicons: IncF-types (predominant), IncHI1B, IncX3, and IncX4, etc., while blaOXA-181,232 were present in ColKP3, corroborating with global studies. blaNDM-1,5 was associated with intact/truncated ISAba125 in Tn125, blaNDM-7 with IS3000, blaKPC-2 with ISKpn6, and ISKpn7 in Tn4401b, and blaOXA-181,232 with ∆ISEcp1 in Tn2013, depicting an ancestral genetic context noted globally. Study isolates were related to other Indian isolates, primarily from blood.DiscussionThe association with different MGEs noted in the study is similar to those in other parts of India and the globe, signifying that the genetic determinants are part of the global gene pool. These associations can facilitate the spread of carbapenem resistance, leading to outbreaks and treatment failures.}, + author = {Mitra, Shravani and Naha, Sharmi and Chakraborty, Joy and De, Subhadeep and Kaur, Harpreet and Majumdar, Tapan and Basu, Sulagna}, + doi = {10.3389/fmicb.2025.1543427}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {232, 5, 7, {\textgreater}UseGalaxy.eu, blaKPC-2-harboring Escherichia coli, blaNDM-1, blaOXA-181, core genome phylogeny, insertion sequence element, plasmids, transposons}, + language = {English}, + month = {May}, + note = {Publisher: Frontiers}, + title = {Diversity of mobile genetic elements in carbapenem-resistant {Enterobacterales} isolated from the intensive care units of a tertiary care hospital in {Northeast} {India}}, + url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1543427/full}, + urldate = {2025-07-12}, + volume = {16}, + year = {2025} +} + @article{mitrofanov_crisprtracrrna_2022, abstract = {The CRISPR-Cas9 system is a Type II CRISPR system that has rapidly become the most versatile and widespread tool for genome engineering. It consists of two components, the Cas9 effector protein, and a single guide RNA that combines the spacer (for identifying the target) with the tracrRNA, a trans-activating small RNA required for both crRNA maturation and interference. While there are well-established methods for screening Cas effector proteins and CRISPR arrays, the detection of tracrRNA remains the bottleneck in detecting Class 2 CRISPR systems.We introduce a new pipeline CRISPRtracrRNA for screening and evaluation of tracrRNA candidates in genomes. This pipeline combines evidence from different components of the Cas9-sgRNA complex. The core is a newly developed structural model via covariance models from a sequence-structure alignment of experimentally validated tracrRNAs. As additional evidence, we determine the terminator signal (required for the tracrRNA transcription) and the RNA–RNA interaction between the CRISPR array repeat and the 5′-part of the tracrRNA. Repeats are detected via an ML-based approach (CRISPRidenify). Providing further evidence, we detect the cassette containing the Cas9 (Type II CRISPR systems) and Cas12 (Type V CRISPR systems) effector protein. Our tool is the first for detecting tracrRNA for Type V systems.The implementation of the CRISPRtracrRNA is available on GitHub upon requesting the access permission, (https://github.com/BackofenLab/CRISPRtracrRNA). Data generated in this study can be obtained upon request to the corresponding person: Rolf Backofen (backofen@informatik.uni-freiburg.de).Supplementary data are available at Bioinformatics online.}, author = {Mitrofanov, Alexander and Ziemann, Marcus and Alkhnbashi, Omer S and Hess, Wolfgang R and Backofen, Rolf}, doi = {10.1093/bioinformatics/btac466}, issn = {1367-4803}, journal = {Bioinformatics}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, CRISPR-Cas Systems, RNA}, + language = {eng}, month = {September}, number = {Supplement\_2}, pages = {ii42--ii48}, @@ -9449,6 +15490,44 @@ @informatik.uni-freiburg.de).Supplementary year = {2022} } +@article{mitsuwan_recombinant_2025, + abstract = {Background/Objectives: Streptococcus suis is a zoonotic pathogen that causes infections in pigs and humans, leading to significant economic losses. S. suis can evade the immune system of hosts and induce persistent infections. Early detection and vaccination are crucial for controlling the disease in swine industries. This study aimed to investigate candidate recombinant protein for antibodies against S. suis detection and subunit vaccine development. Methods: The whole genome of S. suis BM407 was analyzed using bioinformatic tools to predict suitable proteins and genes for recombinant protein expression. Partial extracellular factor protein (epf) genes of S. suis serotype 2 DMST18783 were amplified. A 3301 bp amplicon was digested, and a specific 615 bp fragment was inserted into a pQE81L-KAN vector. Then, the constructed plasmid was cloned and expressed in Escherichia coli DH10β. Purified protein was analyzed using SDS-PAGE. In addition, translated amino acid sequences were analyzed for immune response properties, molecular docking, molecular dynamic simulation, and epitope prediction. Results: The amino acid sequence of recombinant extracellular factor protein (rEF) was revealed as a promising antigen containing putative protective regions as linear epitopes. Furthermore, the rEF was expressed as a histidine-tagged recombinant protein, and its properties were nearly similar to the predicted rEF using bioinformatic tools. Binding of the recombinant EF (rEF) protein was found to reduce fluctuations in the swine toll-like receptor 2. Furthermore, the rEF contained several regions that were predicted to be epitopes for both B-cells and T-cells. Conclusions: This study indicates that the recombinant EF fragment is a promising candidate for detecting antibodies against S. suis and as a component of a subunit vaccine.}, + author = {Mitsuwan, Watcharapong and Saengsawang, Phirabhat and Boripun, Ratchadaporn and Rodríguez-Ortega, Manuel J and Nwabor, Ozioma F}, + copyright = {cc by}, + doi = {10.3390/vaccines13111128}, + issn = {2076-393X}, + journal = {Vaccines}, + keywords = {{\textgreater}UseGalaxy.eu, Candidate Protein, EPF, Extracellular Factor Protein, Recombinant protein, Streptococcus suis}, + language = {eng}, + month = {November}, + number = {11}, + pages = {1128}, + pmcid = {PMC12656778}, + pmid = {41295502}, + shorttitle = {Recombinant {Extracellular} {Factor} {Protein} of \<i\>{Streptococcus} suis\</i\> as {Potential} {Candidate} {Protein} for {Antibodies} {Against} \<i\>{S}. suis\</i\> {Detection} and {Subunit} {Vaccine} {Development}}, + title = {Recombinant {Extracellular} {Factor} {Protein} of \<i\>{Streptococcus} suis\</i\> as {Potential} {Candidate} {Protein} for {Antibodies} {Against} \<i\>{S}. suis\</i\> {Detection} and {Subunit} {Vaccine} {Development}: \<i\>{In} {Silico}\</i\> and \<i\>{In} {Vitro}\</i\> {Approaches}}, + url = {https://europepmc.org/articles/PMC12656778}, + urldate = {2025-12-26}, + volume = {13}, + year = {2025} +} + +@incollection{mohamad_azmi_molecular_2025, + abstract = {The increasing prevalence of pathogenic Escherichia coli (E. coli) in water and food sources poses a significant threat to public health, necessitating the development of rapid and accurate biosensor detection methods such as aptamer-based biosensors due to their high specificity and sensitivity. Aptamers are nucleic acids that can bind with high affinity and specificity to a range of target molecules. This research aims to investigate biophysical mechanisms by utilizing biophysics simulations such as molecular free energy calculation and molecular docking to elucidate the interaction between specific aptamer with E. coli protein such as Shiga Toxin (Stx). The methodology involves characterizing aptamer-E. coli interactions, identifying key aptamer structural features and docking analysis of binding process between aptamer and E. coli. In conclusion, this research bridges theory for future applications, providing a framework for developing advanced biosensing technologies, by using the in-silico strategies that allowed the detection of aptamer-target interaction during molecular docking processes.}, + author = {Mohamad Azmi, Muhammad Fakhrullah and Wan Ayub, Wan Mardhiyana and Ibrahim, Izzah Afifah and Redzuan, Muhammad Fadzlisyam and Ismadi, Irfan Danial and Mohd Ghazali, Mohd Ifwat and Mohamad Jamali, Muhamad Arif and Azmi, Liyana and Zainal, Nur Zaireena and Abdul Hamid, Nazefah and Abdullah, Shahino Mah}, + isbn = {978-629-95953-0-4}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + note = {Num Pages: 6}, + pages = {157--161}, + publisher = {Universiti Teknologi MARA, Negeri Sembilan}, + shorttitle = {Molecular docking study of aptamer-based biosensor for detection of {Shiga} {Toxin} ({Stx}) protein from {Escherichia} coli {O157}}, + title = {Molecular docking study of aptamer-based biosensor for detection of {Shiga} {Toxin} ({Stx}) protein from {Escherichia} coli {O157}:{H7}}, + url = {https://ir.uitm.edu.my/id/eprint/119544/}, + urldate = {2025-09-03}, + year = {2025} +} + @article{mohamed_candidate_2023, abstract = {Rice tungro disease (RTD), caused by Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV) is one of the most prominent viral diseases in Asian countries. This virus disease problem seems to have been accentuated in those countries by causing a series of outbreaks over the years after being first reported in International Rice Research Institute (IRRI), Philippines, in 1963. One of the effective ways to combat viruses is through RNA silencing. microRNA is an important player in the RNA silencing mechanism. Genome sequences analysis shows RTBV-SP isolate (8 Kb) is composed of four open reading frames (ORF 1, ORF 2, ORF 3, and ORF 4), meanwhile, RTSV-SP (12 Kb) consists of one open reading frame encoded by seven different polyproteins (P1, CP1, CP2, CP3, NTP, Pro, and Rep). Therefore, this study investigated possible rice-encoded miRNAs targeted on RTBV and RTSV using in silico analysis. Five bioinformatics tools were employed using five different prediction algorithms: miRanda, RNA22, RNAhybrid, Tapirhybrid, and psRNATarget. The results revealed each RTBV and RTSV can be silenced by three potentially best candidate rice-encoded miRNA. For RTBV, osa-miR5510 (accession no. MIMAT0022143), osa-miR3980a-3p (accession no. MIMAT0019676), and osa-miR3980b-3p (accession no. MIMAT0019678) are being predicted by all five algorithms. Meanwhile, for RTSV, three miRNAs predicted are osa-miR414 (accession no. MIMAT0001330), osa-miR5505 (accession no. MIMAT00221138) and osa-miR167a-3p (accession no. MIMAT0006780). The predicted data provide useful material for developing RTBV and RTSV-resistant rice varieties.}, author = {Mohamed, Noor Amni and Ngah, Nik Muhammad Faris Nazmie Che and Abas, Azlan and Talip, Noraini and Sarian, Murni Nazira and Hamezah, Hamizah Shahirah and Harun, Sarahani and Bunawan, Hamidun}, @@ -9470,6 +15549,24 @@ @article{mohamed_candidate_2023 year = {2023} } +@article{mohebbi_computer-aided_2025, + abstract = {The primary objective of this study is to harness computer-aided drug repurposing (CADR) techniques to identify existing FDA-approved drugs that can potentially disrupt the assembly of the Hepatitis B Virus (HBV) core protein (HBcAg), an essential process in the virus’s life cycle. By targeting this critical step, our study aims to expand the repertoire of therapeutic options for managing chronic Hepatitis B infection, a major global health challenge. Utilizing a combination of computational methods, including the CavityPlus server for ability to analyze druggable protein cavities and extract pharmacophore features and LigandScout for pharmacophore-based virtual screening of a vast library of FDA-approved drugs was conducted. Molecular dynamic simulation (MDS) was employed to evaluate the stability of HBcAg, complexed with Heteroaryldihydropyrimidine (HAP) and statins exhibiting particularly strong binding energies and conformational compatibility. Our approach focused on identifying pharmacophore features that align with known HBcAg inhibitors. The study identified several promising candidates, including Ciclopirox olamine, Voriconazole, Enasidenib, and statins, demonstrating potential interactions with HBc protein residues. Molecular docking further validated these interactions. The significance of these findings lies in their potential to offer new, effective therapeutic strategies for HBV treatment, particularly as alternatives to current therapies that often suffer from issues of viral resistance and adverse side effects. MDS analysis verified the robustness of HAP and statins by showing a high level of binding energies and compatibility with HBcAg. Our results provide a foundation for further experimental validation and underscore the utility of computer-aided drug repurposing as a rapid, cost-effective approach to drug discovery in antiviral research. This study contributes to our understanding of HBV biology and opens avenues for developing novel anti-HBV therapies based on repurposed drugs. The highlighted compound may also enhance the challenges of drug resistance when used as a combination therapy.}, + author = {Mohebbi, Alireza and Nabavi, Seyed Pooria Tadayon and Naderi, Malihe and Sharifian, Kimia and Behnezhad, Farzane and Mohebbi, Maryam and Gholami, Amytis and Askari, Fatemeh Sana and Mirarab, Azam and Monavari, Seyed Hamidreza}, + doi = {10.1007/s40203-025-00314-8}, + issn = {2193-9616}, + journal = {In Silico Pharmacology}, + keywords = {{\textgreater}UseGalaxy.eu, Antiviral, Capsid protein, Computer-aided drug repurposing, Drug discovery, Hepatitis B, Hepatitis B virus, Medicinal Chemistry, Pharmacophore-based screening, Protein-Ligand Interactions, Structure-Based Drug Design, Virtual Drug Screening}, + language = {en}, + month = {February}, + number = {1}, + pages = {35}, + title = {Computer-aided drug repurposing \& discovery for {Hepatitis} {B} capsid protein}, + url = {https://doi.org/10.1007/s40203-025-00314-8}, + urldate = {2025-02-28}, + volume = {13}, + year = {2025} +} + @article{mohebifar_construction_2023, abstract = {Breast cancer (BC) is one of the leading causes of cancer-related deaths in women. The present study explored the potential role of pseudogenes in BC via construction and analysis of a competing endogenous RNA (ceRNA) network through a three-step process. First, we screened differentially expressed genes in nine BC datasets. Then the gene-pseudogenes pairs (nine hub genes) were selected according to the functional enrichment and correlation analysis. Second, the candidate hub genes and interacting miRNAs were used to construct the ceRNA network. Further analysis of the ceRNA network revealed a crucial ceRNA module with two genes-pseudogene pairs and two miRNAs. The in-depth analysis identified the GBP1/hsa-miR-30d-5p/GBP1P1 axis as a potential tumorigenic axis in BC patients. In the third step, the GBP1/hsa-miR-30d-5p/GBP1P1 axis expression level was assessed in 40 tumor/normal BC patients and MCF-7 cell lines. The expression of GBP1 and GBP1P1 was significantly higher in the tumor compared to the normal tissue. However, the expression of hsa-miR-30d-5p was lower in tumor samples. Then, we introduced the GBP1P1 pseudogene into the MCF-7 cell line to evaluate its effect on GBP1 and hsa-miR-30d-5p expression. As expected, the GBP1 level increased while the hsa-miR-30d-5p level decreased in the GBP1P1-overexprsssing cell line. In addition, the oncogenic properties of MCF-7 (cell viability, clonogenicity, and migration) were improved after GBP1P1 overexpression. In conclusion, we report a ceRNA network that may provide new insight into the role of pseudogenes in BC development.}, author = {Mohebifar, Hossein and Sabbaghian, Amir and Farazmandfar, Touraj and Golalipour, Masoud}, @@ -9524,6 +15621,21 @@ @article{molla_harnessing_2024 year = {2024} } +@article{monteiro_viral_2024, + abstract = {Wild rodents serve as crucial reservoirs for zoonotic viruses. Anthropogenic and environmental disruptions, particularly those induced by mining activities, can destabilize rodent populations and facilitate the emergence of viral agents. In the Canaã dos Carajás and Curionópolis regions of Brazil, significant environmental changes have occurred due to mining expansion, potentially creating conditions conducive to the emergence of rodent-associated viral diseases. This study aimed to investigate the viral diversity in wild rodents captured in Canaã dos Carajás and Curionópolis, Pará, between 2017 and 2019. A total of 102 rodent samples were taxonomically identified through karyotyping and screened for anti-\textit{Orthohantavirus} antibodies using the ELISA method. Subsequently, nucleotide sequencing and bioinformatics analyses were conducted on 14 selected samples to characterize the virome. This selection was based on the most commonly associated rodent genera as reservoirs of \textit{Orthohantavirus} and \textit{Mammarenavirus}. Of the 102 samples tested via ELISA, 100 were negative, and two showed optical density at the cutoff point. Sequencing of the 14 samples generated approximately 520 million reads, with 409 million retained after quality control. These reads were categorized into 53 viral families, including both DNA and RNA viruses, with \textit{Retroviridae, Baculoviridae}, and \textit{Microviridae} being the most abundant. Viral contigs were identified, including one fragment related to \textit{Arenaviridae} and three to \textit{Filoviridae}. Metagenomic analysis revealed high viral diversity in the sampled rodents, with the presence of viral families of public health concern, such as \textit{Arenaviridae} and \textit{Filoviridae}. The findings suggest that increased human activities associated with mining may contribute to the emergence of these viruses, underscoring the need for ongoing surveillance to prevent potential outbreaks.}, + author = {Monteiro, Adriana Freitas Moraes and da Silva, Fábio Silva and Cruz, Ana Cecília Ribeiro and da Silva, Sandro Patroca and Queiroz, Alice Louize Nunes and Casseb, Livia Medeiros Neves and Martins, Livia Carício and Medeiros, Daniele Barbosa de Almeida}, + doi = {10.3389/fmicb.2024.1502462}, + issn = {1664-302X}, + journal = {Frontiers in microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {1502462}, + title = {Viral diversity in wild rodents in the regions of {Canaã} de {Carajás} and {Curionopólis}, {State} of {Pará}, {Brazil}}, + url = {http://europepmc.org/abstract/MED/39839123}, + volume = {15}, + year = {2024} +} + @article{mootapally_sediment_2021, abstract = {Plasmidomes have become the research area of interest for ecologists exploring bacteria rich ecosystems. Marine environments are among such niche that host a huge number of microbes and have a complex environment which pose the need to study these bacterial indicators of horizontal gene transfer events for survival and stability. The plasmid content of the metagenomics data from 8 sediment samples of the Gulfs of Kathiawar and an open Arabian Sea sample was screened. The reads corresponding to hits against the plasmid database were assembled and studied for diversity using Kraken and functional content using MG-RAST. The sequences were also checked for resistome and virulence factors. The replicon hosts were overall dominated by Proteobacteria, Firmicutes, and Actinobacteria while red algae specific to the Kutch samples. The genes encoded were dominant in the flagella motility and type VI secretion systems. Overall, results from the study confirmed that the plasmids encoded traits for metal, antibiotic, and phage resistance along with virulence systems, and these would be conferring benefit to the hosts. The study throws insights into the environmental role of the plasmidome in adaptation of the microbes in the studied sites to the environmental stresses.}, author = {Mootapally, Chandrashekar and Mahajan, Mayur S. and Nathani, Neelam M.}, @@ -9618,7 +15730,7 @@ @article{moris_intrasexual_2023 doi = {10.1038/s42003-022-04370-0}, issn = {2399-3642}, journal = {Communications Biology}, - keywords = {{\textgreater}UseGalaxy.eu, Gene expression, Phylogenetics, RNAi}, + keywords = {{\textgreater}UseGalaxy.eu, Gene expression, Phylogenetics, RNAi, Wasps}, language = {en}, month = {February}, note = {Number: 1 @@ -9638,7 +15750,7 @@ @article{moris_ionizing_2024 doi = {10.1186/s12915-023-01807-8}, issn = {1741-7007}, journal = {BMC Biology}, - keywords = {{\textgreater}UseGalaxy.eu, Antioxidants, Bdelloid rotifers, DNA repair, Desiccation, Radiation}, + keywords = {{\textgreater}UseGalaxy.eu, Antioxidants, Bdelloid rotifers, DNA repair, Desiccation, Radiation, Rotifera}, language = {en}, month = {January}, number = {1}, @@ -9650,6 +15762,23 @@ @article{moris_ionizing_2024 year = {2024} } +@article{moris_rotifers_2025, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}The biological effects of spaceflight remain incompletely understood, even in humans (Homo sapiens), and are largely unexplored in non-traditional models such as bdelloid rotifers.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}This study analyzes the transcriptomic changes experienced by Adineta vaga, a bdelloid rotifer aboard the International Space Station (ISS), using RNA sequencing. The aim was to investigate the overall effect of spaceflight in Low Earth Orbit (LEO) on these organisms. To this end, new hardware was developed to enable autonomous culturing of rotifers with minimal astronaut intervention. The study revealed significant transcriptomic changes, with 18.61\% of genes showing differential expression in response to microgravity and radiation. These changes included upregulation of genes involved in protein synthesis, RNA metabolic processes, and DNA repair. Notably, the study also found a significant enrichment of foreign genes (Horizontal Gene Transfers: HGTs) among the genes that were either over- or under-expressed during spaceflight, suggesting that HGTs play a role in bdelloids' adaptability to new and potentially atypical environments.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}This research not only enhances our understanding of how organisms respond to microgravity but also proposes A. vaga as a valuable model for future studies in space biology.}, + author = {Moris, Victoria C and Bruneau, Lucie and Berthe, Jérémy and Coos, Richard and Baselet, Bjorn and Heuskin, Anne-Catherine and Caplin, Nicol and Demets, René and Krause, Jutta and Zuijderduijn, Lobke and Tortora, Alexandra and Herova, Magdalena and Penninckx, Sébastien and Parmitano, Luca and Tabury, Kevin and Baatout, Sarah and Van Doninck, Karine and Hespeels, Boris}, + doi = {10.1186/s12915-025-02272-1}, + issn = {1741-7007}, + journal = {BMC biology}, + keywords = {{\textgreater}UseGalaxy.eu, Rotifera, Space Flight, Transcriptome, Weightlessness}, + language = {eng}, + month = {July}, + number = {1}, + pages = {182}, + title = {Rotifers in space: transcriptomic response of the bdelloid rotifer {Adineta} vaga aboard the {International} {Space} {Station}}, + url = {http://europepmc.org/abstract/MED/40598353}, + volume = {23}, + year = {2025} +} + @article{morsli_direct_2021, abstract = {The current point-of-care diagnosis of enterovirus meningitis does not identify the viral genotype, which is prognostic. In this case report, more than 81\% of an Echovirus 12 genome were detected and identified by metagenomic next-generation sequencing, directly from the cerebrospinal fluid collected in a 6-month-old child with meningeal syndrome and meningitis: introducing Echovirus 12 as an etiological agent of acute meningitis in the pediatric population.}, author = {Morsli, Madjid and Zandotti, Christine and Morand, Aurelie and Colson, Philippe and Drancourt, Michel}, @@ -9670,6 +15799,22 @@ @article{morsli_direct_2021 year = {2021} } +@article{morsli_real-time_2022, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Point-Of-Care (POC) diagnosis of life-threatening community-acquired meningitis currently relies on multiplexed RT-PCR assays, that lack genotyping and antibiotic susceptibility profiling. We assessed the usefulness of real-time metagenomics (RTM) directly applied to the cerebrospinal fluid (CSF) for the identification, typing and susceptibility profiling of pathogens responsible for community-acquired meningitis.{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}A series of 52 CSF samples from patients suspected of having community-acquired meningitis, were investigated at POC by direct RTM in parallel to routine real-time multiplex PCR (RT-PCR) and bacterial culture, for the detection of pathogens. RTM-generated sequences were blasted in real-time against an in-house database incorporating the panel of 12 most prevalent pathogens and against NCBI using EPI2ME online software, for pathogen identification. In-silico antibiogram and genotype prediction were determined using the ResFinder bio-tool and MLST online software.{\textless}h4{\textgreater}Findings{\textless}/h4{\textgreater}Over eight months, routine multiplex RT-PCR yielded 49/52 positive CSFs, including 21 Streptococcus pneumoniae, nine Neisseria meningitidis, eight Haemophilus influenzae, three Streptococcus agalactiae, three Herpesvirus-1, two Listeria monocytogenes, and one each of Escherichia coli, Staphylococcus aureus and Varicella-Zoster Virus. Parallel RTM agreed with the results of 47/52 CSFs and revealed two discordant multiplex RT-PCR false positives, one H. influenzae and one S. pneumoniae. Both multiplex RT-PCR and RTM agreed on the negativity of three CSFs. While multiplex RT-PCR routinely took 90 min, RTM took 120 min, although the pipeline analysis detected the pathogen genome after 20 min of sequencing in 33 CSF samples; and after two hours in 14 additional CSFs; yielding {\textgreater} 50\% genome coverage in 19 CSFs. RTM identified 14 pathogen genotypes, including a majority of H. influenzae b, N. meningitidis B and S. pneumoniae 11A and 3A. In all 16 susceptible cultured bacteria, the in-silico antibiogram agreed with the in-vitro antibiogram in 10 cases, available within 48 h in routine bacteriology.{\textless}h4{\textgreater}Interpretation{\textless}/h4{\textgreater}In addition to pathogen detection, RTM applied to CSF samples offered supplementary information on bacterial profiling and genotyping. These data provide the proof-of-concept that RTM could be implemented in a POC laboratory for one-shot diagnostic and genomic surveillance of pathogens responsible for life-threatening meningitis.{\textless}h4{\textgreater}Funding{\textless}/h4{\textgreater}This work was supported by the French Government under the Investments in the Future programme managed by the National Agency for Research reference: Méditerranée Infection 10-IAHU-03.}, + author = {Morsli, Madjid and Boudet, Agathe and Kerharo, Quentin and Stephan, Robin and Salipante, Florian and Dunyach-Remy, Catherine and Houhamdi, Linda and Fournier, Pierre-Edouard and Lavigne, Jean Philippe and Drancourt, Michel}, + doi = {10.1016/j.ebiom.2022.104247}, + issn = {2352-3964}, + journal = {EBioMedicine}, + keywords = {{\textgreater}UseGalaxy.eu, Meningitis, Bacterial, Neisseria meningitidis}, + language = {eng}, + month = {October}, + pages = {104247}, + title = {Real-time metagenomics-based diagnosis of community-acquired meningitis: {A} prospective series, southern {France}}, + url = {http://europepmc.org/abstract/MED/36087524}, + volume = {84}, + year = {2022} +} + @article{mossad_gut_2022, abstract = {Microglial function declines during aging. The interaction of microglia with the gut microbiota has been well characterized during development and adulthood but not in aging. Here, we compared microglial transcriptomes from young-adult and aged mice housed under germ-free and specific pathogen-free conditions and found that the microbiota influenced aging associated-changes in microglial gene expression. The absence of gut microbiota diminished oxidative stress and ameliorated mitochondrial dysfunction in microglia from the brains of aged mice. Unbiased metabolomic analyses of serum and brain tissue revealed the accumulation of N6-carboxymethyllysine (CML) in the microglia of the aging brain. CML mediated a burst of reactive oxygen species and impeded mitochondrial activity and ATP reservoirs in microglia. We validated the age-dependent rise in CML levels in the sera and brains of humans. Finally, a microbiota-dependent increase in intestinal permeability in aged mice mediated the elevated levels of CML. This study adds insight into how specific features of microglia from aged mice are regulated by the gut microbiota.}, author = {Mossad, Omar and Batut, Bérénice and Yilmaz, Bahtiyar and Dokalis, Nikolaos and Mezö, Charlotte and Nent, Elisa and Nabavi, Lara Susann and Mayer, Melanie and Maron, Feres José Mocayar and Buescher, Joerg M. and de Agüero, Mercedes Gomez and Szalay, Antal and Lämmermann, Tim and Macpherson, Andrew J. and Ganal-Vonarburg, Stephanie C. and Backofen, Rolf and Erny, Daniel and Prinz, Marco and Blank, Thomas}, @@ -9706,6 +15851,21 @@ @article{mostafa_genome-wide_2024 year = {2024} } +@article{mukhopadhyay_characterization_2025, + abstract = {The \textit{Ophiostomatales} are of economic concern, as many are blue-stain fungi and some are plant pathogens. The mitogenomes of members assigned to this order exhibit size polymorphism despite having highly conserved gene order, owing to the variable number of introns and intron insertion sites. In this work, eleven blue-stain fungi, including nine strains of \textit{Ophiostomaips} with a varied distribution across North America and New Zealand, were sequenced and compared with other members of the \textit{Ophiostomatales}. A pan-mitogenome intron landscape has been prepared to demonstrate the distribution of the mobile genetic elements and to provide insight into the evolutionary dynamics of introns among members of this group of fungi. The size variation among these mitogenomes (from about 23.8 kb to 152 kb) shows high correlation to the presence and absence of introns. Examples of complex or nested introns composed of two or three intron modules have been observed in some \textit{O.ips} strains. RNA-seq data suggests possible splicing pathways with regard to resolving these complex introns. Mitochondrial DNA and RNA data for \textit{O.ips} provides the basis for future studies relating to gene annotation, alternative splicing, evolutionary intron dynamics, and taxonomic investigations for members of the \textit{Ophiostomatales}.}, + author = {Mukhopadhyay, Jigeesha and Wai, Alvan and Lang, B Franz and Hausner, Georg}, + doi = {10.3897/imafungus.16.159349}, + issn = {2210-6340}, + journal = {IMA fungus}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {e159349}, + title = {Characterization of the mitochondrial genomes for \textit{{Ophiostomaips}} and related taxa from various geographic origins and related species: large intron-rich genomes and complex intron arrangements}, + url = {http://europepmc.org/abstract/MED/40741210}, + volume = {16}, + year = {2025} +} + @article{mukhopadhyay_mitogenomes_2023, abstract = {{\textless}sec{\textgreater}{\textless}title{\textgreater}Introduction{\textless}/title{\textgreater}{\textless}p{\textgreater}Many members of the Ophiostomatales are of economic importance as they are bark-beetle associates and causative agents for blue stain on timber and in some instances contribute towards tree mortality. The taxonomy of these fungi has been challenging due to the convergent evolution of many traits associated with insect dispersal and a limited number of morphological characters that happen to be highly pleomorphic. This study examines the mitochondrial genomes for three members of {\textless}italic{\textgreater}Leptographium sensu lato{\textless}/italic{\textgreater} [{\textless}italic{\textgreater}Leptographium aureum{\textless}/italic{\textgreater} (also known as {\textless}italic{\textgreater}Grosmannia aurea{\textless}/italic{\textgreater}), {\textless}italic{\textgreater}Grosmannia fruticeta{\textless}/italic{\textgreater} (also known as {\textless}italic{\textgreater}Leptographium fruticetum{\textless}/italic{\textgreater}), and {\textless}italic{\textgreater}Leptographium{\textless}/italic{\textgreater} sp. WIN(M)1376)].{\textless}/p{\textgreater}{\textless}/sec{\textgreater}{\textless}sec{\textgreater}{\textless}title{\textgreater}Methods{\textless}/title{\textgreater}{\textless}p{\textgreater}Illumina sequencing combined with gene and intron annotations and phylogenetic analysis were performed.{\textless}/p{\textgreater}{\textless}/sec{\textgreater}{\textless}sec{\textgreater}{\textless}title{\textgreater}Results{\textless}/title{\textgreater}{\textless}p{\textgreater}Sequence analysis showed that gene content and gene synteny are conserved but mitochondrial genome sizes were variable: {\textless}italic{\textgreater}G. fruticeta{\textless}/italic{\textgreater} at 63,821 bp, {\textless}italic{\textgreater}Leptographium{\textless}/italic{\textgreater} sp. WIN(M)1376 at 81,823 bp and {\textless}italic{\textgreater}L. aureum{\textless}/italic{\textgreater} at 104,547 bp. The variation in size is due to the number of introns and intron-associated open reading frames. Phylogenetic analysis of currently available mitochondrial genomes for members of the Ophiostomatales supports currently accepted generic arrangements within this order and specifically supports the separation of members with Leptographium-like conidiophores into two genera, with {\textless}italic{\textgreater}L. aureum{\textless}/italic{\textgreater} grouping with {\textless}italic{\textgreater}Leptographium{\textless}/italic{\textgreater} and {\textless}italic{\textgreater}G. fruticeta{\textless}/italic{\textgreater} aligning with {\textless}italic{\textgreater}Grosmannia{\textless}/italic{\textgreater}.{\textless}/p{\textgreater}{\textless}/sec{\textgreater}{\textless}sec{\textgreater}{\textless}title{\textgreater}Discussion{\textless}/title{\textgreater}{\textless}p{\textgreater}Mitochondrial genomes are promising sequences for resolving evolutionary relationships within the Ophiostomatales.{\textless}/p{\textgreater}{\textless}/sec{\textgreater}}, author = {Mukhopadhyay, Jigeesha and Wai, Alvan and Hausner, Georg}, @@ -9781,13 +15941,18 @@ @article{muller_snp_2020 } @article{musmeci_draft_2021, + abstract = {The draft genome sequence of Clostridium tertium WC0709, a gut bacterium able to use mucin in pure culture as the sole carbon and nitrogen source, is presented here. The genome sequence of \textit{C. tertium} will provide valuable references for comparative genome analysis and for studying the relationship with the host.}, author = {Musmeci, Eliana and Candeliere, Francesco and Amaretti, Alberto and Rossi, Maddalena and Raimondi, Stefano}, doi = {10.1128/mra.00642-21}, editor = {Rasko, David}, + issn = {2576-098X}, + journal = {Microbiol Resour Announc}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {August}, note = {Publisher: American Society for Microbiology}, number = {32}, + pages = {e0064221}, title = {Draft {Genome} {Sequence} of the {Mucin} {Degrader} {Clostridium} tertium {WC0709}}, url = {https://doi.org/10.1128/mra.00642-21}, volume = {10}, @@ -9834,7 +15999,7 @@ @article{naimi_direct_2021 doi = {10.1186/s40168-020-00996-6}, issn = {2049-2618}, journal = {Microbiome}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Gastrointestinal Microbiome}, language = {en}, month = {March}, number = {1}, @@ -9853,7 +16018,7 @@ @article{naorem_immunoinformatics_2024 doi = {10.3390/pathogens13100916}, issn = {2076-0817}, journal = {Pathogens}, - keywords = {\textit{Streptococcus mutans}, {\textgreater}UseGalaxy.eu, dental caries, immunoinformatics, molecular docking simulation, molecular dynamic simulation, multiepitope vaccine}, + keywords = {\textit{Streptococcus mutans}, {\textgreater}UseGalaxy.eu, Epitopes, B-Lymphocyte, Epitopes, T-Lymphocyte, Streptococcus mutans, dental caries, immunoinformatics, molecular docking simulation, molecular dynamic simulation, multiepitope vaccine}, language = {en}, month = {October}, note = {Number: 10 @@ -9895,7 +16060,8 @@ @article{nasereddin_concurrent_2022 doi = {10.1186/s13071-022-05388-3}, issn = {1756-3305}, journal = {Parasites \& Vectors}, - keywords = {{\textgreater}UseGalaxy.eu, Amp-NGS, Leishmania, Phlebotomine sand flies, Taxonomy}, + keywords = {{\textgreater}UseGalaxy.eu, Amp-NGS, Leishmania, Parasites, Phlebotomine sand flies, Phlebotomus, Psychodidae, Taxonomy}, + language = {eng}, month = {July}, number = {1}, pages = {262}, @@ -9907,10 +16073,13 @@ @article{nasereddin_concurrent_2022 } @article{nasereddin_identification_2022, + abstract = {COVID-19 is caused by SARS-CoV-2, several virulent variants of which have emerged since 2019. More than 529 million people have been infected, and at least 6 million have died. Our aim was to develop a fast, accurate, low-cost method for detecting and identifying newly emerging variants of concern (VOCs) that could pose a global threat. The 341-bp DNA sequence of a specific region of the SARS-CoV-2's spike protein was amplified by a one-step PCR on RNA samples from 46 patients. The product was sequenced using next-generation sequencing (NGS). DNA sequences from seven genomes, the original Wuhan isolate and six different representative variants obtained from the GISAID website, were used as references. Complete whole-genome sequences from local isolates were also obtained from the GISAID website, and their RNA was used for comparison. We used an amplicon-based NGS method (termed VOC-NGS) for genotyping and successfully identified all 46 samples. Fifteen (32.6\%) were like the original isolate. Twenty-seven were VOCs: nine (19.5\%) Alpha, eight (19\%) Delta, six (14\%) Beta, and four (8.7\%) Omicron. Two were variants of interest (VOI): one (2\%) Kappa and one (2\%) Zeta. Two samples were mixtures of two variants, one of Alpha and Beta and one of Alpha and Delta. The Spearman correlation between whole-genome sequencing (WGS) and VOC-NGS was significant (\textit{P} {\textless} 0.001) with perfect agreement (Kappa = 0.916) for 36/38 (94.7\%) samples with VOC-NGS detecting all the known VOCs. Genotyping by VOC-NGS enables rapid screening of high-throughput clinical samples that includes the identification of VOCs and mixtures of variants, at lower cost than WGS. \textbf{IMPORTANCE} The manuscript described SARS-Cov-2 genotyping by VOC-NGS, which presents an ideal balance of accuracy, rapidity, and cost for detecting and globally tracking VOCs and some VOI of SARS-CoV-2. A large number of clinical samples can be tested together. Rapid introduction of new mutations at a specific site of the spike protein necessitates efficient strain detection and identification to enable choice of treatment and the application of vaccination, as well as planning public health policy.}, author = {Nasereddin, Abdelmajeed and Golan Berman, Hadar and Wolf, Dana G. and Oiknine-Djian, Esther and Adar, Sheera}, doi = {10.1128/spectrum.00736-22}, + issn = {2165-0497}, journal = {Microbiology Spectrum}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19, SARS-CoV-2}, + language = {eng}, month = {June}, note = {Publisher: American Society for Microbiology}, number = {4}, @@ -9922,6 +16091,22 @@ @article{nasereddin_identification_2022 year = {2022} } +@article{nasereddin_tracking_2022, + abstract = {As surges of the COVID-19 pandemic continue globally, including in Palestine, several new SARS-CoV-2 variants have been introduced. This expansion has impacted transmission, disease severity, virulence, diagnosis, therapy, and natural and vaccine-induced immunity. Here, 183 whole genome sequences (WGS) were analyzed, of which 129 were from Palestinian cases, 62 of which were collected in 11 Palestinian districts between October 2020 and April 2021 and sequenced completely. A dramatic shift from the wild type to the Alpha variant (B 1.1.7) was observed within a short period of time. Cluster mapping revealed statistically significant clades in two main Palestinian cities, Al-Khalil (Monte Carlo hypothesis test-Poisson model, P = 0.00000000012) and Nablus (Monte Carlo hypothesis test-Poisson model, P = 0.014 and 0.015). The phylogenetic tree showed three main clusters of SARS-CoV-2 with high bootstrap values ({\textgreater}90). However, population genetics analysis showed a genetically homogenous population supported by low Wright's F-statistic values (Fst {\textless}0.25), high gene flow (Nm {\textgreater} 3), and statistically insignificant Tajima's D values (Tajima's test, neutrality model prediction, P = 0.02). The Alpha variant, rapidly replaced the wild type, causing a major surge that peaked in April 2021, with an increased COVID-19 mortality rate, especially, in the Al-Khalil and Nablus districts. The source of introduction remains uncertain, despite the minimal genetic variation. The study substantiates the use of WGS for SARS-CoV-2 surveillance as an early warning system to track down new variants requiring effective control.}, + author = {Nasereddin, Abedelmajeed and Al-Jawabreh, Amer and Dumaidi, Kamal and Al-Jawabreh, Ahmed and Al-Jawabreh, Hanan and Ereqat, Suheir}, + doi = {10.1016/j.meegid.2022.105279}, + issn = {1567-1348}, + journal = {Infect Genet Evol}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19, SARS-CoV-2}, + language = {eng}, + month = {July}, + pages = {105279}, + title = {Tracking of {SARS}-{CoV}-2 {Alpha} variant ({B}.1.1.7) in {Palestine}}, + url = {http://europepmc.org/abstract/MED/35390503}, + volume = {101}, + year = {2022} +} + @article{nayak_bms345541_2024, abstract = {Glioblastoma (GBM) is one of the most aggressive and fatal cancers, for which Temozolomide (TMZ) chemo drug is commonly used for its treatment. However, patients gradually develop resistance to this drug, leading to tumor relapse. In our previous study, we have identified lncRNAs that regulate chemoresistance through the competing endogenous RNA (ceRNA) mechanism. In this study, we tried to find FDA-approved drugs against the target proteins of these ceRNA networks through drug repurposing using differential gene expression profiles, which could be used to nullify the effect of lncRNAs and promote the sensitivity of TMZ in GBM. We performed molecular docking and simulation studies of predicted repurposed drugs and their targets. Among the predicted repurposed drugs, we found BMS345541 has a higher binding affinity towards its target protein - FOXG1, making it a more stable complex with FOXG1-DNA. The ADMET analysis of this drug BMS345541 shows a higher half-life and lower cytotoxicity level than other predicted repurposed drugs. Hence, we conjecture that this could be a better drug for increasing the sensitivity of TMZ for treating GBM patients.}, author = {Nayak, Rojalin and Mallick, Bibekanand}, @@ -9938,12 +16123,53 @@ @article{nayak_bms345541_2024 year = {2024} } +@article{nazari_comprehensive_2025, + abstract = {Background +Early detection of renal cell carcinoma (RCC) remains a challenge. Identification of novel biomarkers may improve the diagnosis, prognosis, and treatment of RCC. This study aimed to identify potential novel biomarkers for RCC by analyzing gene expression profiles by RNA sequencing (RNA-seq) and validating the results by laboratory tests. +Materials and methods +Data were retrieved from NCBI GEO datasets. After data processing and analysis, two genes with differential expression in RCC were selected: Slc15a3 and Myo1f. Blood samples were then collected from 26 RCC patients and 24 healthy controls. Following the extraction of RNA and the synthesis of cDNA, real-time polymerase chain reaction (PCR) was conducted. The expression of genes was evaluated and analyzed using GraphPad Prism, with a statistical significance threshold of P {\textless} 0.05. +Results +In silico analysis and RNA-seq data revealed that Slc15a3 and Myo1f were differentially expressed in RCC. Real-time PCR results showed a significant increase in Myo1f expression in RCC patients (P {\textless} 0.05), suggesting its potential as a novel biomarker. However, Slc15a3 did not show significant expression differences between RCC patients and controls (P {\textgreater} 0.05), indicating a limited biomarker potential. +Conclusion +This study suggests that Myo1f maybe a promising biomarker for RCC.}, + author = {Nazari, Mahya and Angaji, Seyed Abdolhamid and Beikzadeh, Behnaz and Narouie, Behzad and Mohammadi, Mahdi}, + doi = {10.1016/j.humgen.2025.201422}, + issn = {2773-0441}, + journal = {Human Gene}, + keywords = {{\textgreater}UseGalaxy.eu, Myo1f, RNA sequencing, Renal cell carcinoma, Slc15a3}, + month = {May}, + pages = {201422}, + shorttitle = {Comprehensive analysis of {Slc15a3} and {Myo1f} gene expression in renal carcinoma}, + title = {Comprehensive analysis of {Slc15a3} and {Myo1f} gene expression in renal carcinoma: {Insights} from {RNA}-seq data and validation via {qRT}-{PCR}}, + url = {https://www.sciencedirect.com/science/article/pii/S2773044125000488}, + urldate = {2025-05-28}, + year = {2025} +} + +@article{negrete-mendez_lambda-evo_2025, + abstract = {One of the most significant bacteriophage technologies is phage display, in which heterologous peptides are exhibited on the virion surface. This work describes the display of λ decorative protein Dλ linked to the E protein domain III of Zika virus (Dλ-ZEDIII), to the GFP protein (Dλ-GFP), or to different domain III epitopes of the EZIKV protein (Dλ-TD), exhibited on the surface of an in vitro evolved lambda phage (λevo). This phage harbors a gene D deletion and was subjected to directed evolution using Escherichia coli W3110/pDλ-ZEDIII as background. After 20 days (20 cycles of dilution), the λevo phage developed a {\textasciitilde} 22\% genome deletion affecting the non-essential λ b region, rendering a more stable phage that exhibited fusion proteins Dλ-ZEDIII or Dλ-GFP but not Dλ-TD. Despite the λevo system was able to decorate itself with the Dλ-ZEDIII protein, the production of viral particles was {\textasciitilde} 1000-fold lower than the λ wild-type, due to the unexpected Dλ-ZEDIII protein aggregation into bacterial inclusion bodies. Decorated phages (106 PFU (plaque forming units)/100 µl) were inoculated into BALB/c mice, and subsequent dot blot and Western blot immunoassays proved the production of murine antibodies against ZIKV (Zika virus). This multipurpose λevo phage display platform may be used interchangeably with other more soluble peptides, providing better yields.}, + author = {Negrete-Méndez, Honorio and Valencia-Toxqui, Guadalupe and Martínez-Peñafiel, Eva and Medina-Contreras, Oscar and Fernández-Ramírez, Fernando and Morales-Ríos, Edgar and Navarro-González, Luis Janiel and Torres-Flores, Jesús M. and Kameyama, Luis}, + doi = {10.1007/s00253-024-13380-3}, + issn = {1432-0614}, + journal = {Applied Microbiology and Biotechnology}, + keywords = {{\textgreater}UseGalaxy.eu, Bacteriophage lambda, Cell Surface Display Techniques, Directed evolution, Lambda phage, Lambda-evo phage, Phage display, Recombinant-protein, Viral Envelope Proteins, ZIKV, Zika Virus, λevo}, + language = {en}, + month = {January}, + number = {1}, + pages = {8}, + title = {A {Lambda}-evo (λevo) phage platform for {Zika} virus {EDIII} protein display}, + url = {https://doi.org/10.1007/s00253-024-13380-3}, + urldate = {2025-02-16}, + volume = {109}, + year = {2025} +} + @article{nekrutenko_biology_2018, abstract = {Anton Nekrutenko, Galaxy Team, Jeremy Goecks, James Taylor, Daniel Blankenberg; Biology needs evolutionary software tools: Let’s build them right, Molecular Bi}, author = {Nekrutenko, Anton and Team, Galaxy and Goecks, Jeremy and Taylor, James and Blankenberg, Daniel}, doi = {10.1093/molbev/msy084}, journal = {Molecular Biology and Evolution}, - keywords = {+Galactic, +Project, +RefPublic, +Tools, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au}, + keywords = {+Galactic, +Project, +RefPublic, +Tools, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Biological Evolution, Computational Biology}, language = {en}, month = {April}, shorttitle = {Biology needs evolutionary software tools}, @@ -9953,6 +16179,23 @@ @article{nekrutenko_biology_2018 year = {2018} } +@article{nemours_use_2024, + abstract = {Paclitaxel is a widely used chemotherapeutic agent for the treatment of breast cancer (BC), including as a front-line treatment for triple-negative breast cancer (TNBC) patients. However, resistance to paclitaxel remains one of the major causes of death associated with treatment failure. Multiple studies have demonstrated that miRNAs play a role in paclitaxel resistance and are associated with both disease progression and metastasis. In the present study, we used a miRNA-encoding lentiviral library as a gain-of-function screen for paclitaxel resistance in the MDA-MB-231 TNBC cell line. We identified that \textit{miR-181b}, \textit{miR-29a}, \textit{miR-30c}, \textit{miR-196} and \textit{miR-1295} conferred a resistant phenotype to cells. The expression of \textit{miR-29a} also induced resistance to eribulin and vinorelbine, while \textit{miR-181b} and \textit{miR-30c} induced resistance to vinorelbine. We measured the levels of these miRNAs in breast cancer patients and observed higher levels of \textit{miR-29a} in treatment-refractory patients. Taken together, we suggest that \textit{miR-29a} and \textit{miR-181b} may be good candidates for miRNA inhibition to overcome resistance to chemotherapy.}, + author = {Nemours, Stéphane and Solé, Carla and Goicoechea, Ibai and Armesto, María and Arestin, María and Urruticoechea, Ander and Rezola, Marta and López, Isabel Álvarez and Schaapveld, Roel and Schultz, Iman and Zhang, Lei and Lawrie, Charles H}, + doi = {10.3390/ijms252413630}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Drug Resistance, Neoplasm, Gene Expression Regulation, Neoplastic, MicroRNAs, Paclitaxel, Triple Negative Breast Neoplasms}, + language = {eng}, + month = {December}, + number = {24}, + pages = {13630}, + title = {Use of {Gain}-of-{Function} {Screening} to {Identify} {miRNAs} {Involved} in {Paclitaxel} {Resistance} in {Triple}-{Negative} {Breast} {Cancer}}, + url = {http://europepmc.org/abstract/MED/39769392}, + volume = {25}, + year = {2024} +} + @article{ngo_histone_2022, abstract = {Background @@ -9994,7 +16237,7 @@ @article{nguyen_genomic_2024 doi = {10.1111/1751-7915.70007}, issn = {1751-7915}, journal = {Microbial Biotechnology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Biosynthetic Pathways, Genome, Fungal, Penicillium, Phylogeny, Podophyllotoxin}, language = {en}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1751-7915.70007}, number = {9}, @@ -10006,6 +16249,27 @@ @article{nguyen_genomic_2024 year = {2024} } +@misc{nguyen_single-vessel_2025, + abstract = {Background Capillary malformation (CM) is a congenital vascular anomaly affecting the skin, mucosa, and brain, yet the understanding of its vascular pathogenesis remains limited. +Methods We applied spatial whole-transcriptome profiling (GeoMx) and gene set enrichment analysis within CM lesions at single vasculature level. Differentially expressed genes were validated by immunofluorescence staining. Phosphoproteomics was profiled to uncover lesion-wide phosphorylation sites on proteins. Single-cell RNA sequencing was performed on CM-derived induced pluripotent stem cells (iPSCs) to determine differentiation trajectories of lesional vascular lineages. In silico gene perturbation was used to predict candidate genes for modulating vascular pathological progression, followed by functional validation in CM iPSC-derived endothelial cells (ECs) using a Tet-on system. +Results A spatial transcriptomic atlas was constructed, and pathological landscape of individual CM vasculature was delineated. CM vessels exhibited hallmarks of endothelial-to-mesenchymal transition (EndMT), including disruption of adherens junctions (AJs), vascular identity transitions, and metabolic remodeling. Phosphoproteomics confirmed that differentially phosphorylated proteins were enriched in EndMT- and AJ-related pathways. Aberrant expression of venous transcriptional factor NR2F2 was observed in lesional ECs and correlated with progressive enlargement from capillaries to larger-caliber vessels containing multiple layers of smooth muscle cells (SMCs). In CM iPSCs, differentiation course yielded reduced ECs but increased SMCs. In silico knockout simulation predicted NR2F2 as a crucial regulator of facilitating SMC phenotype in CM. Consistently, enforced NR2F2 expression during iPSC differentiation suppressed endothelial markers while inducing SMC-associated genes. +Conclusions Single CM vasculature displays pathological hallmarks characterized by EndMT and AJ disruption, leading to progressive vascular remodeling. NR2F2 functions as a central regulatory factor orchestrating the acquisition of the SMC phenotype, thereby representing a potential therapeutic target in CM.}, + author = {Nguyen, Vi and Mao, Irving and He, Siwuxie and Castellanos, Isabella and Azuero, Mackenzie and Hochman, Marcelo L. and Rong, Yin and Pernomian, Laena and Chen, Elliott H. and Friedman, Harold I. and Chen, Yan-Hua and Lu, Qun and Fan, Daping and Wenceslau, Camilla F. and Chen, Dong-bao and Nelson, J. Stuart and Jegga, Anil G. and Wang, Yunguan and Tan, Wenbin}, + copyright = {© 2025, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}, + doi = {10.1101/2025.09.02.673874}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {September}, + note = {ISSN: 2692-8205 +Pages: 2025.09.02.673874 +Section: New Results}, + publisher = {bioRxiv}, + title = {Single-vessel transcriptome map pathological landscapes and reveal {NR2F2}-mediated smooth muscle cell phenotype acquisition in capillary malformations}, + url = {https://www.biorxiv.org/content/10.1101/2025.09.02.673874v1}, + urldate = {2025-09-12}, + year = {2025} +} + @article{nicholson_contribution_2024, abstract = {{\textless}p{\textgreater}{\textless}italic{\textgreater}Bordetella bronchiseptica{\textless}/italic{\textgreater} is a highly contagious respiratory bacterial veterinary pathogen. In this study the contribution of the transcriptional regulators BvgR, RisA, RisS, and the phosphorylation of RisA to global gene regulation, intracellular cyclic-di-GMP levels, motility, and biofilm formation were evaluated. Next Generation Sequencing (RNASeq) was used to differentiate the global gene regulation of both virulence-activated and virulence-repressed genes by each of these factors. The BvgAS system, along with BvgR, RisA, and the phosphorylation of RisA served in cyclic-di-GMP degradation. BvgR and unphosphorylated RisA were found to temporally regulate motility. Additionally, BvgR, RisA, and RisS were found to be required for biofilm formation.{\textless}/p{\textgreater}}, author = {Nicholson, Tracy L. and Waack, Ursula and Fleming, Damarius S. and Chen, Qing and Miller, Laura C. and Merkel, Tod J. and Stibitz, Scott}, @@ -10068,6 +16332,89 @@ @article{niemoller_bisulfite-free_2021 year = {2021} } +@article{nieva_de_la_hidalga_facilitating_2025, + abstract = {Publishing supporting data significantly impacts researchers' productivity, especially in experiments requiring extensive tracking of data, processing steps, parameters, and outputs. A managed workflow environment, combined with RO-Crates, addresses these data management challenges. Workflows provide an alternative for handling complex data analyses by orchestrating various processing tools. The RO-Crate format, a community-driven proposal for packaging data, provenance, and workflows, facilitates publishing and reproducibility. The Galaxy workflow management system integrates workflows and RO-Crates, enabling the export of analyses, which can be shared and restored by other users. Using Galaxy, we demonstrate how to improve support for reproducibility. We tested our approach by designing an experiment using diverse supporting data from selected papers. In the experiment, we identified specific FAIRness and completeness issues hindering result reproduction, even when authors made significant efforts to document and publish their supporting data. In comparison, the proposed approach supports reproducibility by packaging datasets in RO-Crate format, streamlining the process. The Galaxy RO-Crates, published as supporting materials, enhance data sharing, transparency, and reproducibility, thus supporting the advancement of FAIR research practices in catalysis research.}, + author = {Nieva de la Hidalga, Abraham and Liborio, Leandro and Austin, Patrick and Devadasan, Subindev and Underwood, Tom and Belozerov, Alexander and Wilding, Martin and Ramanan, Nitya and Catlow, C. Richard A.}, + copyright = {© 2025 Wiley-VCH GmbH}, + doi = {10.1002/cctc.202401676}, + issn = {1867-3899}, + journal = {ChemCatChem}, + keywords = {{\textgreater}UseGalaxy.eu, Data Processing and Analysis, FAIR Data Objects, Reproducibility of Results, Workflow Management System, X-ray absorption spectroscopy}, + language = {en}, + month = {March}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cctc.202401676}, + number = {n/a}, + pages = {e202401676}, + shorttitle = {Facilitating {Reproducibility} in {Catalysis} {Research} with {Managed} {Workflows} and {RO}-{Crates}}, + title = {Facilitating {Reproducibility} in {Catalysis} {Research} with {Managed} {Workflows} and {RO}-{Crates}: {A} {Galaxy} {Case} {Study}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cctc.202401676}, + urldate = {2025-03-29}, + volume = {n/a}, + year = {2025} +} + +@article{nilchi_dissecting_2025, + abstract = {Emerging evidence supports the role of type 2 diabetes (T2D) mellitus as a risk factor for cancer progression. In this study, we investigated and identified biomarkers related to diabetes and pancreatic ductal adenocarcinoma (PDAC) using systems biology to understand better the molecular landscape of PDAC and its connections with T2D.RNA-seq data related to blood samples of diabetes and pancreatic cancer were analyzed using bioinformatics tools in the Galaxy platform. After differential expression analysis using the DESeq2, the co-expression network associated with T2D and PDAC data was reconstructed using the WGCNA. Then, by visualizing the protein-protein interaction network in modules specifically related to T2D and PDAC, the key genes involved in these two diseases were identified, and their interaction network with long non-coding RNAs was reconstructed. Finally, the results of bioinformatics analysis were verified by qPCR in four groups, including T2D, PDAC, PDAC-T2D, and control groups.In this study, 1905 and 18,558 genes with significant differential expression were identified in the data of T2D and PDAC, respectively ({\textbar}logFC{\textbar} {\textgreater} 0.58, adj. p value {\textless} 0.05). The WGCNA showed 32 and 20 co-expression modules in diabetes and pancreatic cancer data, respectively. Among these, 303 genes were co-expressed, related to diabetes and pancreatic cancer. Based on the protein-protein interaction pattern, five hub genes were identified (using the CytoHubba Cytoscape plugin and the Maximal Clique Centrality (MCC) parameter). Finally, the co-expression network was reconstructed between these five genes and other lncRNAs. The qPCR showed that the expression of the CEBPZ gene was significantly increased in the blood samples of the diabetic (log2FC = 1.163, adj. p value = 0.0006), pancreatic cancer (log2FC = 3.22, adj. p value {\textless} 0.0001), and pancreatic cancer-diabetic (log2FC = 2.73, adj. p value {\textless} 0.0001) groups compared to the control group.For the first time, this study suggested that CEBPZ expression may serve as a diagnostic biomarker for assessing PDAC in individuals with T2D, given its differential expression in this specific cohort.}, + author = {Nilchi, Amirhossein Naghsh and Dehghanian, Fariba and Vallian, Sadeq and Bahreini, Amin}, + copyright = {cc by-nc-nd}, + doi = {10.1038/s41598-025-21200-5}, + issn = {2045-2322}, + journal = {Scientific reports}, + keywords = {{\textgreater}UseGalaxy.eu, Cebpz Gene, Co-expression, Differential expression, Pancreatic cancer, Type 2 diabetes, Wgcna}, + language = {eng}, + month = {October}, + number = {1}, + pages = {37288}, + pmcid = {PMC12552502}, + pmid = {41136472}, + title = {Dissecting {lncRNA}-{mRNA} regulatory network in type 2 diabetes as the risk factor of pancreatic cancer}, + url = {https://europepmc.org/articles/PMC12552502}, + urldate = {2025-12-26}, + volume = {15}, + year = {2025} +} + +@book{nilsson_benchmarking_2024, + abstract = {DiVA portal is a finding tool for research publications and student theses written at the following 50 universities and research institutions.}, + author = {Nilsson, Alma}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + shorttitle = {Benchmarking {Bioinformatics} {Workflows} using {Bibliographic} {Networks}}, + title = {Benchmarking {Bioinformatics} {Workflows} using {Bibliographic} {Networks} : {Exploring} {Co}-{Usage} {Information} in {Software} {Co}-{Citation} {Graphs}}, + url = {https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-548528}, + urldate = {2025-02-28}, + year = {2024} +} + +@article{noauthor_58_2025, + issn = {1660-3818}, + journal = {Transfusion medicine and hemotherapy}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {September}, + number = {Suppl 1}, + pages = {1--88}, + pmcid = {PMC12580739}, + title = {58. {Jahrestagung} der {Deutschen} {Gesellschaft} für {Transfusionsmedizin} und {Immunhämatologie} e.{V}. ({DGTI}}, + url = {https://europepmc.org/articles/PMC12580739}, + urldate = {2025-12-26}, + volume = {52}, + year = {2025} +} + +@article{noauthor_abstract_2022, + issn = {2572-9241}, + journal = {Hemasphere}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {June}, + number = {Suppl}, + title = {Abstract {Book} for the 27th {Congress} of the {European} {Hematology} {Association}}, + url = {http://europepmc.org/abstract/PMC/PMC9429973}, + volume = {6}, + year = {2022} +} + @misc{noauthor_amazonian_2024, keywords = {{\textgreater}UseGalaxy.eu}, month = {October}, @@ -10120,6 +16467,48 @@ @article{noauthor_characterization_2023 year = {2023} } +@article{noauthor_cherriaccurate_2024, + issn = {2047-217X}, + journal = {Gigascience}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {January}, + title = {{CheRRI}—{Accurate} classification of the biological relevance of putative {RNA}–{RNA} interaction sites}, + url = {http://europepmc.org/abstract/PMC/PMC11152173}, + volume = {13}, + year = {2024} +} + +@article{noauthor_clostridium_2025, + abstract = {Clostridium tetani (C. tetani) bacteraemia is a rare situation, with only four case reports in the literature. Fourteen teeth from the 1590 plague sit…}, + doi = {10.1016/j.crmicr.2025.100339}, + issn = {2666-5174}, + journal = {Current Research in Microbial Sciences}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en-US}, + month = {January}, + note = {Publisher: Elsevier}, + pages = {100339}, + shorttitle = {Clostridium tetani bacteraemia in the plague area in {France}}, + title = {Clostridium tetani bacteraemia in the plague area in {France}: {Two} cases}, + url = {https://www.sciencedirect.com/science/article/pii/S266651742500001X}, + urldate = {2025-05-29}, + volume = {8}, + year = {2025} +} + +@article{noauthor_dataset_2025, + issn = {2352-3409}, + journal = {Data Brief}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {April}, + title = {Dataset of benthic foraminiferal community structure from sediment {eDNA} of {Sundarbans} mangrove ecosystem}, + url = {http://europepmc.org/abstract/PMC/PMC12048805}, + volume = {60}, + year = {2025} +} + @misc{noauthor_draft_2024, keywords = {{\textgreater}UseGalaxy.eu}, title = {Draft genome sequence of {Streptomyces} poriferorum {RTGN2}, a bacterial endophyte isolated from {Alnus} glutinosa root nodules {\textbar} {Microbiology} {Resource} {Announcements}}, @@ -10147,6 +16536,28 @@ @misc{noauthor_effect_2024 year = {2024} } +@misc{noauthor_erga-bge_2025, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {December}, + title = {{ERGA}-{BGE} reference genome of {Hirudo} verbana, ... {\textbar} {Open} {Research} {Europe}}, + url = {https://open-research-europe.ec.europa.eu/articles/5-395}, + urldate = {2025-12-25}, + year = {2025} +} + +@misc{noauthor_exome_2025, + abstract = {Inherited Retinal Dystrophies (IRD) are rare and heterogeneous blindness-causing diseases caused by pathogenic variants in genes involved in retina function.}, + journal = {Scilit}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {March}, + shorttitle = {Exome sequencing}, + title = {Exome sequencing: a tool for the diagnosis of hereditary retinal dystrophies in {Mexican} patients}, + url = {https://www.scilit.com/publications/d47bdd8a5cfec2f7424314f84159df19}, + urldate = {2025-03-29}, + year = {2025} +} + @misc{noauthor_harmful_2023, abstract = {Explore millions of resources from scholarly journals, books, newspapers, videos and more, on the ProQuest Platform.}, keywords = {{\textgreater}UseGalaxy.eu}, @@ -10290,6 +16701,41 @@ @article{nogell_structure_2024 year = {2024} } +@article{nortje_molecular_2025, + abstract = {The LasR quorum sensing system regulates the virulence factors of Pseudomonas aeruginosa, a multi-drug resistant pathogen. Mangiferin and related compounds have been found to modulate this system as determined by in silico and in vitro experimental procedures. ZINCPharmer was used to compile a library of over 1000 metabolites that were screened to the top five based on shared pharmacophores and drug-like properties with mangiferin. Molecular docking and molecular dynamics simulation (140 ns) showed that ZINC E (− 55.64 ± 2.93 kcal/mol) and ZINC D (− 54.51 ± 2.82 kcal/mol) had significantly lower binding free energy compared to mangiferin-LasR (− 42.24 ± 3.94 kcal/mol) and the reference standard (azithromycin-LasR (− 40.01 ± 6.15 kcal/mol). ZINC D (95.16\%) competed favorably with mangiferin (95.77\%) as potential QS modulators at sub-minimum inhibitory concentrations relative to ZINC E (85.07\%) and azithromycin (85.79\%). These observations suggest mangiferin and related lead compounds as potential drug candidates for P. aeruginosa infection management.}, + author = {Nortje, Nicolas Quinn and Aribisala, Jamiu Olaseni and Pillay, Charlene and Sabiu, Saheed}, + doi = {10.1007/s00203-025-04240-3}, + issn = {1432-072X}, + journal = {Archives of Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Autoinducer, Biofilm, Mangiferin, Molecular dynamics simulation, Pseudomonas aeruginosa, Quorum Sensing, Quorum sensing, Xanthones}, + language = {en}, + month = {February}, + number = {3}, + pages = {53}, + title = {Molecular modelling and experimental validation of mangiferin and its related compounds as quorum sensing modulators of {Pseudomonas} aeruginosa}, + url = {https://doi.org/10.1007/s00203-025-04240-3}, + urldate = {2025-02-16}, + volume = {207}, + year = {2025} +} + +@article{nousias_shotgun_2025, + abstract = {Biodiversity and its associated genetic diversity are being lost at an unprecedented rate. Simultaneously, the distributions of flora, fauna, fungi, microbes and pathogens are rapidly changing. Novel technology can help to capture and record genetic diversity before it is lost and to measure population shifts and pathogen distributions. Here we report the rapid application of shotgun long-read environmental DNA (eDNA) analysis for non-invasive biodiversity, genetic diversity and pathogen assessments from air. We also compared air eDNA with water and soil eDNA. Coupling long-read sequencing with established cloud-based biodiversity pipelines enabled a 2-day turnaround from airborne sample collection to completed analysis by a single investigator. To determine the full utility of airborne eDNA, we also conducted a local bioinformatic analysis and deep short-read shotgun sequencing. From outdoor air eDNA alone, comprehensive genetic analysis was performed, including population genetics (phylogenetic placement) of a charismatic mammal (bobcat, Lynx rufus) and a venomous spider (golden silk orb weaver, Trichonephila clavipes), and haplotyping humans (Homo sapiens) from natural complex community settings, such as subtropical forests and temperate locations. The rich datasets also enabled deeper analysis of specific species and genomic regions of interest, including viral variant calling, human variant analysis and antimicrobial resistance gene surveillance from airborne DNA. Our results highlight the speed, versatility and specificity of pan-biodiversity monitoring via non-invasive eDNA sampling using current benchtop/portable and cloud-based approaches. Furthermore, they reveal the future feasibility of scaling down (equipment and temporally) these approaches for near real-time analysis. Together these approaches can enable rapid simultaneous detection of all life and its genetic diversity from air, water and sediment samples for unbiased non-targeted information-rich genomics-empowered (1) biodiversity monitoring, (2) population genetics, (3) pathogen and disease-vector genomic surveillance, (4) allergen and narcotic surveillance, (5) antimicrobial resistance surveillance and (6) bioprospecting.}, + author = {Nousias, Orestis and McCauley, Mark and Stammnitz, Maximilian R and Farrell, Jessica A and Koda, Samantha A and Summers, Victoria and Eastman, Catherine B and Duffy, Fiona G and Duffy, Isabelle J and Whilde, Jenny and Duffy, David J}, + doi = {10.1038/s41559-025-02711-w}, + issn = {2397-334X}, + journal = {Nat Ecol Evol}, + keywords = {{\textgreater}UseGalaxy.eu, Air Microbiology, Biodiversity, DNA, Environmental, Genetic Variation, Genetics, Population}, + language = {eng}, + month = {June}, + number = {6}, + pages = {1043--1060}, + title = {Shotgun sequencing of airborne {eDNA} achieves rapid assessment of whole biomes, population genetics and genomic variation}, + url = {http://europepmc.org/abstract/MED/40461811}, + volume = {9}, + year = {2025} +} + @article{nugroho_transcriptome_2024, abstract = {Sengon (Falcataria falcata) is an economically important legume tree widely cultivated in community forests, especially in Java Island. However, attacks of gall rust disease by Uromycladium falcatariae is difficult to manage. Understanding sengon genes expressions when artificially infected with gall rust fungi can help unravel its resistance mechanisms. Total RNA was extracted from sengon seedlings samples inoculated with U. falcatariae fungi at 7, 21, and 35 days after inoculation (DAI) and from the control group. Total RNA sequencing was performed using the PCR-cDNA Sequencing protocol (SQK-PCB109) from Oxford Nanopore Technologies. The RNA-Seq obtained varies from 1.3 million to 1.9 million total reads. The assembled full-length transcript was constructed using the RATTLE program, resulting in 21,819 transcripts. The TransDecoder program used to define open reading frames (ORFs) generated 2,342 transcripts, of which 34.15\% were 5′prime\_partial, 8.15\% were 3′prime\_partial, 8.5\% were internal, and 49.14\% were complete. Analysis of differentially expressed genes (DEGs) between resistant and susceptible seedlings, found that 1,013 genes that were up-regulated and 1,130 genes that were down-regulated in the resistant lines. The transcriptome data discussed in this article have been deposited in the DDBJ with accession number DRA015681.}, author = {Nugroho, Aditya and Siregar, Iskandar Zulkarnaen and Matra, Deden Derajat and Siregar, Ulfah Juniarti}, @@ -10297,6 +16743,7 @@ @article{nugroho_transcriptome_2024 issn = {2352-3409}, journal = {Data in Brief}, keywords = {{\textgreater}UseGalaxy.eu, Long-read sequencing, Plant defense, Resistance, Sengon}, + language = {eng}, month = {February}, pages = {109919}, title = {Transcriptome dataset of gall-rust infected {Sengon} (\textit{{Falcataria} falcata}) seedlings using long-read {PCR}-{cDNA} sequencing}, @@ -10307,11 +16754,14 @@ @article{nugroho_transcriptome_2024 } @article{nuhrenberg_impact_2022, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Sepsis is associated with high platelet turnover and elevated levels of immature platelets. Changes in the platelet transcriptome and the specific impact of immature platelets on the platelet transcriptome remain unclear. Thus, this study sought to address whether and how elevated levels of immature platelets affect the platelet transcriptome in patients with sepsis.{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}Blood samples were obtained from patients with sepsis requiring vasopressor therapy (n = 8) and from a control group of patients with stable coronary artery disease and otherwise similar demographic characteristics (n = 8). Immature platelet fraction (IPF) was determined on a Sysmex XE 2100 analyser and platelet function was tested by impedance aggregometry. RNA from leukocyte-depleted platelets was used for transcriptome analysis by Next Generation Sequencing integrating the use of unique molecular identifiers.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}IPF (median [interquartile range]) was significantly elevated in sepsis patients (6.4 [5.3-8.7] \% vs. 3.6 [2.6-4.6] \%, p = 0.005). Platelet function testing revealed no differences in adenosine diphosphate- or thrombin receptor activating peptide-induced platelet aggregation between control and sepsis patients. Putative circular RNA transcripts were decreased in platelets from septic patients. Leukocyte contamination defined by CD45 abundance levels in RNA-sequencing was absent in both groups. Principal component analysis of transcripts showed only partial overlap of clustering with IPF levels. RNA sequencing showed up-regulation of 524 and down-regulation of 118 genes in platelets from sepsis patients compared to controls. Upregulated genes were mostly related to catabolic processes and protein translation. Comparison to published platelet transcriptomes showed a large overlap of changes observed in sepsis and COVID-19 but not with reticulated platelets from healthy donors.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}Patients with sepsis appear to have a less degraded platelet transcriptome as indicated by increased levels of immature platelets and decreased levels of putative circular RNA transcripts. The present data suggests that increased protein translation is a characteristic mechanism of systemic inflammation.}, author = {Nührenberg, Thomas G. and Stöckle, Jasmin and Marini, Federico and Zurek, Mark and Grüning, Björn A. and Benes, Vladimir and Hein, Lutz and Neumann, Franz-Josef and Stratz, Christian and Cederqvist, Marco and Hochholzer, Willibald}, doi = {10.1371/journal.pone.0260222}, editor = {James, Katherine}, + issn = {1932-6203}, journal = {PLOS ONE}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {January}, note = {Publisher: Public Library of Science (PLoS)}, number = {1}, @@ -10327,6 +16777,7 @@ @article{nunez-sanchez_characterizing_2020 author = {Núñez-Sánchez, María A. and Colom, Joan and Walsh, Lauren and Buttimer, Colin and Bolocan, Andrei Sorin and Pang, Rory and Gahan, Cormac G. M. and Hill, Colin}, copyright = {http://creativecommons.org/licenses/by/3.0/}, doi = {10.3390/microorganisms8091374}, + issn = {2076-2607}, journal = {Microorganisms}, keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Enterococcus faecalis, Herelleviridae, IBD, bacteriophage, intestinal model, phage therapy}, language = {en}, @@ -10342,6 +16793,24 @@ @article{nunez-sanchez_characterizing_2020 year = {2020} } +@article{nwankwo_comparative_2025, + abstract = {The soil surrounding plant root harbors a diverse and dynamic microbial community that plays a crucial role in plant growth, health, and nutrient acquisition. This study was aimed at investigating the physicochemical properties and bacterial communities in healthy and infected root soil of plantain (Musa paradisiaca). The physicochemical properties of the soil samples were analyzed using the standard methods. The bacterial communities of the soil samples were determined by the conventional method and the 16S rRNA metagenomics. Both healthy and infected root soils had a pH of 6.18 and 5.56 respectively, and a temperature of 25.7 and 27.6oC respectively. The textural class of both soils is loamy sand. The particle size of healthy root soil (89.1 mg/kg), electrical conductivity (197 μS/cm), alkalinity (12.94 mg/l), organic matter (25.00 mg/l), nitrogen (1.183mg/l), iron (17.01mg/l), magnesium (0.602 mg/l), clay (68\%), coarse sand (2.09\%), fine sand (16.47\%), air porosity (61.41\%), and bulk density (0.803 g/cm3) in healthy root soil were higher than those of infected root soil. Cation exchange capacity (15.88 meq/100g), nitrate (0.731mg/l), phosphate (0.216mg/l), moisture (14.55wt\%), potassium (1.094 mg/l), calcium (0.213 mg/l), copper (0.093 mg/l), zinc (0.189 mg/l), manganese (0.017 mg/l), and silt (36.0 mg/l) were higher in infected than healthy root soil. The isolation and characterization of bacteria reveal 48 bacteria isolates from the healthy and infected root soils respectively, while 42 and 41 predominant fungal isolates were obtained from the healthy and infected root soils. All healthy and infected plantain root bacteria were taxonomically identified by amplifying and sequencing the 16S rRNA genes. A total of 33,198 bacterial taxonomic units comprising 6 phyla, 9 classes, 14 orders, 17 families, 15 genera, and 14 species, were generated from healthy root soil. In contrast, a total of 81,524 bacterial taxonomic units which consist of 11 phyla, 12 classes, 19 orders, 24 families, 31 genera, and 42 species, were generated from infected root soil. The analysis revealed significant differences in the composition and diversity of microbial communities between the two soil types, highlighting the potential role of soil microbiota in influencing the development and progression of Fusarium wilt.}, + author = {Nwankwo, C. C. and Arimaha, C. O. and Ezeonuegbu, B. A.}, + copyright = {Copyright (c) 2025 Scientia Africana}, + issn = {1118-1931}, + journal = {Scientia Africana}, + keywords = {{\textgreater}UseGalaxy.eu, Fusarium wilt, Metagenomics, Physicochemical properties, Plantain, microbes}, + language = {en}, + month = {June}, + number = {2}, + pages = {247--262}, + title = {Comparative analysis of the physiochemical characteristics and bacterial communities of healthy and infected root soil of plantain plant}, + url = {https://www.ajol.info/index.php/sa/article/view/297609}, + urldate = {2025-09-03}, + volume = {24}, + year = {2025} +} + @article{nwankwo_metagenomic_2024, abstract = {Soil contains a great diversity of microorganisms, including bacteria which are known to be drivers of soil ecosystem functions. This study was aimed at investigating the bacterial communities in bulk and rhizosphere soil of Fusarium wilt-infected plantain (Musa paradisiaca). Physicochemical analysis revealed that electrical conductivity (312 µS/cm), cation exchange capacity (15.62 meq/100g), phosphate (0.16 mg/kg), nitrogen (1.53 mg/kg), moisture (19.45 mg/kg), potassium (1.39 mg/kg), magnesium (0.61 mg/kg), clay (60 \%), and silt (35\%) were higher in bulk soil than rhizosphere soil. The 16S rRNA metagenomic sequences quantified a total of 89341 bacterial taxonomic units from bulk soil which consist of 10 phyla, 13 classes, 16 orders, 18 families, 21 genera, and 19 species. A total of 88034 bacterial taxonomic units which comprised of 9 phyla, 13 classes, 23 orders, 22 families, 26 genera, and 25 species, were found in rhizosphere soil. The most abundant phyla in bulk soil are Actinobacteria (31\%), Proteobacteria (26\%), and Gemmatimonadetes (17\%) Acidobacteria (17\%) and Planctomycetes (3\%) while the prominent phyla in rhizosphere soil are Actinobacteria (63\%) Proteobacteria (24\%), Acidobacteria (7\%) and Planctomycetes (3\%). The major functional profiles of bacterial communities in both bulk and rhizosphere soils are metabolism of amino acids, carbohydrates, terpenoids, polyketides, cofactors, and xenobiotic degradation. Alpha diversities among the bacterial community were higher in Simpson’s reciprocal index for both bulk and rhizosphere soils. This study opens up new frontiers in expanding metagenomics studies on environmental samples which would capture and contribute to the identification of soil bacteria useful to ecosystem functions.}, author = {Nwankwo, C. C. and Ezeonuegbu, B. A. and Oranusi, E. C.}, @@ -10380,6 +16849,22 @@ @article{oakes_building_2024 year = {2024} } +@article{ocejo_whole-genome_2024, + author = {Ocejo, Medelin and Mugica, Maitane and Oporto, Beatriz and Lavín, José Luis and Hurtado, Ana}, + doi = {10.1128/spectrum.03672-23}, + journal = {Microbiology Spectrum}, + keywords = {{\textgreater}UseGalaxy.eu, Anti-Infective Agents, Daptomycin, Enterococcus faecium, Gram-Positive Bacterial Infections}, + month = {January}, + note = {Publisher: American Society for Microbiology}, + number = {2}, + pages = {e03672--23}, + title = {Whole-genome long-read sequencing to unveil {Enterococcus} antimicrobial resistance in dairy cattle farms exposed a widespread occurrence of {Enterococcus} lactis}, + url = {https://journals.asm.org/doi/full/10.1128/spectrum.03672-23}, + urldate = {2025-02-28}, + volume = {12}, + year = {2024} +} + @article{oeyen_sawfly_2020, abstract = {Abstract. The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (}, author = {Oeyen, Jan Philip and Baa-Puyoulet, Patrice and Benoit, Joshua B. and Beukeboom, Leo W. and Bornberg-Bauer, Erich and Buttstedt, Anja and Calevro, Federica and Cash, Elizabeth I. and Chao, Hsu and Charles, Hubert and Chen, Mei-Ju May and Childers, Christopher and Cridge, Andrew G. and Dearden, Peter and Dinh, Huyen and Doddapaneni, Harsha Vardhan and Dolan, Amanda and Donath, Alexander and Dowling, Daniel and Dugan, Shannon and Duncan, Elizabeth and Elpidina, Elena N. and Friedrich, Markus and Geuverink, Elzemiek and Gibson, Joshua D. and Grath, Sonja and Grimmelikhuijzen, Cornelis J. P. and Große-Wilde, Ewald and Gudobba, Cameron and Han, Yi and Hansson, Bill S. and Hauser, Frank and Hughes, Daniel S. T. and Ioannidis, Panagiotis and Jacquin-Joly, Emmanuelle and Jennings, Emily C. and Jones, Jeffery W. and Klasberg, Steffen and Lee, Sandra L. and Lesný, Peter and Lovegrove, Mackenzie and Martin, Sebastian and Martynov, Alexander G. and Mayer, Christoph and Montagné, Nicolas and Moris, Victoria C. and Munoz-Torres, Monica and Murali, Shwetha Canchi and Muzny, Donna M. and Oppert, Brenda and Parisot, Nicolas and Pauli, Thomas and Peters, Ralph S. and Petersen, Malte and Pick, Christian and Persyn, Emma and Podsiadlowski, Lars and Poelchau, Monica F. and Provataris, Panagiotis and Qu, Jiaxin and Reijnders, Maarten J. M. F. and von Reumont, Björn Marcus and Rosendale, Andrew J. and Simao, Felipe A. and Skelly, John and Sotiropoulos, Alexandros G. and Stahl, Aaron L. and Sumitani, Megumi and Szuter, Elise M. and Tidswell, Olivia and Tsitlakidis, Evangelos and Vedder, Lucia and Waterhouse, Robert M. and Werren, John H. and Wilbrandt, Jeanne and Worley, Kim C. and Yamamoto, Daisuke S. and van de Zande, Louis and Zdobnov, Evgeny M. and Ziesmann, Tanja and Gibbs, Richard A. and Richards, Stephen and Hatakeyama, Masatsugu and Misof, Bernhard and Niehuis, Oliver}, @@ -10415,6 +16900,22 @@ @article{oger_-cellspecific_2023 year = {2023} } +@article{ogunnupebi_silico_2024, + author = {Ogunnupebi, Temitope A. and Oduselu, Gbolahan O. and Elebiju, Oluwadunni F. and Ajani, Olayinka O. and Adebiyi, Ezekiel}, + doi = {10.3389/fbinf.2024.1428539}, + issn = {2673-7647}, + journal = {Frontiers in Bioinformatics}, + keywords = {{\textgreater}UseGalaxy.eu, ADMET properties, benzothiazole, insecticidal activity, malaria, vector control}, + language = {English}, + month = {August}, + note = {Publisher: Frontiers}, + title = {In silico studies of benzothiazole derivatives as potential inhibitors of {Anopheles} funestus and {Anopheles} gambiae trehalase}, + url = {https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2024.1428539/full}, + urldate = {2025-02-28}, + volume = {4}, + year = {2024} +} + @incollection{ohta_hybrid_2023, abstract = {Galaxy is a web browser-based data analysis platform that is widely used in biology. Public Galaxy instances allow the analysis of data and interpretation of results without requiring software installation. NanoGalaxy is a public Galaxy instance with tools and workflows for nanopore data analysis. This chapter describes the steps involved in performing genome assembly using short and long reads in NanoGalaxy.}, address = {New York, NY}, @@ -10434,6 +16935,25 @@ @incollection{ohta_hybrid_2023 year = {2023} } +@article{okafor_targeting_2025, + abstract = {Plasmodium falciparum subtilisin-like protease 2 (PfSUB2) is responsible for processing Plasmodium falciparum thrombospondin-related apical merozoite protein (PfTRAMP). These proteins are essential for asexual blood stage growth and RBC invasion and have, therefore, been identified as potential drug targets. This study predicted the three-dimensional structure of PfSUB2 and PfTRAMP and identified potential inhibitors using molecular docking methods. Five hundred nineteen compounds were docked against both proteins with AutoDock Vina in PyRx. Compounds 139,974,934 and 154,414,021 exhibited better binding affinities when compared to the standard inhibitors, PMSF, which highlights them as suitable inhibitors and potential antimalarials targeting PfTRAMP and PfSUB2. It also highlights 155,204,487 as a compound with dual antimalarial target potential, exhibiting a better binding affinity to PfTRAMP and PfSUB2. The study recommends 139,974,934, 154,414,021, and 155,204,487 as possible compounds for antimalarial drug development.}, + author = {Okafor, Esther. O. and Bella-Omunagbe, Mercy and Elugbadebo, Temitope and Dokunmu, Titilope M. and Adebiyi, Ezekiel}, + doi = {10.1186/s12879-025-11380-w}, + issn = {1471-2334}, + journal = {BMC Infectious Diseases}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + pages = {1038}, + pmcid = {PMC12366235}, + pmid = {40830840}, + shorttitle = {Targeting invasion-associated proteins {PfSUB2} and {PfTRAMP} in {Plasmodium} falciparum}, + title = {Targeting invasion-associated proteins {PfSUB2} and {PfTRAMP} in {Plasmodium} falciparum: identification of potential inhibitors via molecular docking}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366235/}, + urldate = {2025-09-03}, + volume = {25}, + year = {2025} +} + @article{olagoke_rps6_2023, abstract = {The use of insects to model molecular events that characterize degenerative conditions was originally met with scepticism. However, the discovery of insect insulin-like peptides in the 1970's and the demonstration of evolutionary conservation of insulin-related signalling from insects to mammals have highlighted the importance and reduced cost of insect models in biomedical research. Here, we expand on our earlier described modelling of streptozotocin-induced brain glucose metabolic disruption in Nauphoeta cinerea, using RNA-sequencing analysis to study the transcriptional and genetic signatures of degeneration and stress signalling when glucose levels are elevated in the brain of the lobster cockroach. Nymphs were randomly divided into three groups: Control (0.8\% NaCl), and two single streptozotocin injection doses (74 nmol and 740 nmol). The transcriptional analyses featured a dysregulation of 226 genes at high dose STZ treatment and 278 genes at the low dose. Our mRNA-sequencing data showed that ribosomal protein genes were the most upregulated genes at both 74 and 740 nmol STZ treatment. We therefore used RT-qPCR and relative transcriptional methods to validate our proposed mechanism of brain glucose toxicity-induced degeneration in Nauphoeta cinerea, which involved the upregulation of ribosomal proteins and rpS6 regulators (mTORC1, protein kinases, casein kinase 1 and Death-associated protein kinase), the upregulation of MAPK cascades (RAS, ERK, P38 and JNK), alongside the downregulation of the PI3K/AKT cascade. Taken together, this study highlights the remarkable opportunity for Nauphoeta cinerea use as an experimental organism in hyperglycaemia, degeneration, and stress signalling.}, author = {Olagoke, Olawande C. and Segatto, Ana L. A. and Afolabi, Blessing A. and Ardisson-Araujo, Daniel and Aschner, Michael and Rocha, João B. T.}, @@ -10474,12 +16994,13 @@ @article{oliveira_integrated_2024 doi = {10.26508/lsa.202302358}, issn = {2575-1077}, journal = {Life Science Alliance}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19}, language = {en}, month = {April}, note = {Publisher: Life Science Alliance Section: Research Articles}, number = {4}, + pages = {e202302358}, pmid = {38262689}, title = {Integrated analysis of {RNA}-seq datasets reveals novel targets and regulators of {COVID}-19 severity}, url = {https://www.life-science-alliance.org/content/7/4/e202302358}, @@ -10495,7 +17016,7 @@ @article{olszak-przybys_diversity_2024 doi = {10.3390/pathogens13090769}, issn = {2076-0817}, journal = {Pathogens}, - keywords = {\textit{Glycine max} (L.) Merrill, {\textgreater}UseGalaxy.eu, fungal barcoding, seed-borne fungi, soybean, storage fungi}, + keywords = {\textit{Glycine max} (L.) Merrill, {\textgreater}UseGalaxy.eu, Fungi, Glycine max, Seeds, fungal barcoding, seed-borne fungi, soybean, storage fungi}, language = {en}, month = {September}, note = {Number: 9 @@ -10530,6 +17051,26 @@ @article{olszak-przybys_identification_2023 year = {2023} } +@article{omenge_seor2_2025, + abstract = {The Arabidopsis seor1ko line, which expresses the protein AtSEOR2 free of its bond with AtSEOR1, exhibits a lower phytoplasma titre as compared to wild type plants. In search for mechanism(s) underlying potential SEOR2-mediated defense responses the transcriptome of healthy wild type and Atseor1ko plants was disclosed by RNA sequencing. Comparative transcriptome analysis revealed 1036 differentially expressed genes (DEGs, 893 up- and 143 down-regulated) between the Atseor1ko line and the wild type. Sequence annotation and classification of the up-regulated genes identified “plant-pathogen interaction” among the most enriched clusters. The “plant-pathogen interaction” cluster included genes encoding members of the protein kinase superfamily, actors in calcium/calmodulin signaling transduction and WRKY transcription factors. An interaction network analysis and a host-phytoplasma interaction map demonstrated that AtSEOR2 protein could interact with the calcium-binding proteins CAM2 and TCH3. The latter one also turned out to be an indirect target of the SAP54CY phytoplasma effector, which suggests a SEOR2-mediated role of TCH3 in balancing nutrient investments in plant defense and plant growth.}, + author = {Omenge, Keziah and Viscardo, Ottone Carmelo and De Oliveira Cantao, Fernando Rodrigo and Santi, Simonetta and van Bel, Aart Jan Eeuwe and Musetti, Rita}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-01374-8}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, Arabidopsis Proteins, Calcium, Phytoplasma, Plant Diseases, Plant sciences, Plant stress responses}, + language = {en}, + month = {May}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {17829}, + title = {{SEOR2} in {Arabidopsis} mediates {Ca2}+ dependent defense against phytoplasmas and reduction of plant growth}, + url = {https://www.nature.com/articles/s41598-025-01374-8}, + urldate = {2025-05-28}, + volume = {15}, + year = {2025} +} + @article{omer_acemannan_2023, abstract = {Acemannan, the main polysaccharide in Aloe vera, is a -(1, 4)-acetylated polymannose. According to numerous research findings, acemannan is a viable alternative for the treatment of pathological disorders. Streptozotocin (STZ, 60 mg/kg) administered intraperitoneally caused type 2 diabetes in rats. The current study sought to determine the anti-diabetic efficacy of acemannan (25 and 50 mg/kg) in STZ-injected rats. Different biochemical parameters including HbA1C, glucose and serum insulin, lipid profile, inflammatory markers, antioxidant, oxidative balance, liver function test, glycogen and creatinine, and caspase-3 were evaluated. In addition, a molecular docking study was performed to estimate acemannan's binding affinity to inflammatory markers. Acemannan may be a potent anti-diabetic agent for the treatment of diabetic patients, which will aid in future research into alternative diabetes medications.}, author = {Omer, Asma B. and Altayb, Hisham N. and Al-Abbasi, Fahad A. and Gupta, Gaurav and Ahmed, Mohammed Muqtader and Alghamdi, Amira M. and Alzarea, Sami I. and Sayyed, Nadeem and Nadeem, Muhammad Shahid and Kazmi, Imran}, @@ -10546,10 +17087,25 @@ @article{omer_acemannan_2023 year = {2023} } +@article{oneill_inducible_2021, + abstract = {\textbf{Background:} \textit{Chlamydia trachomatis} is a prolific human pathogen that can cause serious long-term conditions if left untreated. Recent developments in \textit{Chlamydia} genetics have opened the door to conducting targeted and random mutagenesis experiments to identify gene function. In the present study, an inducible transposon mutagenesis approach was developed for \textit{C. trachomatis} using a self-replicating vector to deliver the transposon-transposase cassette - a significant step towards our ultimate aim of achieving saturation mutagenesis of the \textit{Chlamydia} genome. \textbf{Methods:} The low transformation efficiency of \textit{C. trachomatis} necessitated the design of a self-replicating vector carrying the transposon mutagenesis cassette (i.e. the Himar-1 transposon containing the beta lactamase gene as well as a hyperactive transposase gene under inducible control of the \textit{tet} promoter system with the addition of a riboswitch). \textit{Chlamydia} transformed with this vector (pSW2-RiboA-C9Q) were induced at 24 hours post-infection. Through dual control of transcription and translation, basal expression of transposase was tightly regulated to stabilise the plasmid prior to transposition. \textbf{Results:} Here we present the preliminary sequencing results of transposon mutant pools of both \textit{C. trachomatis} biovars, using two plasmid-free representatives: urogenital strain   \textit{C. trachomatis} SWFP- and the lymphogranuloma venereum isolate L2(25667R). DNA sequencing libraries were generated and analysed using Oxford Nanopore Technologies' MinION technology. This enabled 'proof of concept' for the methods as an initial low-throughput screen of mutant libraries; the next step is to employ high throughput sequencing to assess saturation mutagenesis. \textbf{Conclusions:} This significant advance provides an efficient method for assaying \textit{C. trachomatis} gene function and will enable the identification of the essential gene set of \textit{C. trachomatis}. In the long-term, the methods described herein will add to the growing knowledge of chlamydial infection biology leading to the discovery of novel drug or vaccine targets.}, + author = {O'Neill, Colette E and Skilton, Rachel J and Forster, Jade and Cleary, David W and Pearson, Sarah A and Lampe, David J and Thomson, Nicholas R and Clarke, Ian N}, + doi = {10.12688/wellcomeopenres.16068.1}, + issn = {2398-502X}, + journal = {Wellcome open research}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {312}, + title = {An inducible transposon mutagenesis approach for the intracellular human pathogen {Chlamydia} trachomatis}, + url = {http://europepmc.org/abstract/MED/35087955}, + volume = {6}, + year = {2021} +} + @article{ortega_ramirez_molecular_2024, abstract = {open}, author = {ORTEGA RAMÍREZ, JAZMÍN ALEJANDRA}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, language = {it}, month = {December}, note = {Accepted: 2024-12-09T11:07:53Z}, @@ -10559,10 +17115,51 @@ @article{ortega_ramirez_molecular_2024 year = {2024} } +@article{orwa_chaetomium_2025, + abstract = {Late blight is a disease whose causative agent is the oomycete Phytophthora infestans. It is one of the most destructive pathogenic oomycetes and a major challenge to global tomato production. The pathogen is difficult to manage because of its ability to evolve thereby evading host resistance. The aim of this study was to screen for potential antagonists of P. infestans using a combination of culture and microbiome-based approaches. Samples were collected from healthy and P. infestans-infected tomato plants grown in soil collected from two organic tomato growers in the Rhine-Main area in Germany. A total of 246 fungal isolates were screened for their antagonistic activity against P. infestans. Most of the isolates that exhibited in vitro antagonistic activity were from the genera Penicillium, Trichoderma, Chlonostachys, Mortierella, and Pseudogymnoascus. Following a stepwise in vitro screening strategy that accounted for growth features, ecological aspects, taxonomic data, potential health risks, commercial properties, and antagonistic efficacy, five fungal isolates were eventually selected for plant trials. Chaetomium subaffine showed the highest inhibitory effect against P. infestans across three trials whereby the percentage of diseased leaf area reduced by 90\% compared to the control. Chlonostachys and Pseudogymnoascus spp. were effective in two trials, while Trichoderma and Ctenomyces spp. showed weak disease suppressive effects. In parallel, we characterized the fungal microbiome of the rhizosphere, phyllosphere, and endosphere from healthy and diseased tomato plants using ITS-rRNA sequencing. The fungal community differed significantly between the two soil origins, but P. infestans did not significantly influence fungal microbiota composition. Notably, 70\% of our antagonistic fungi from the culture collection were detected in the tomato microbiome. This work identified isolates of Chaetomium subaffine, Clonostachys sp., and Pseudogymnoascus sp. as potential biocontrol candidates promoting plant health. The findings highlight the importance of combined functional screening and microbiome profiling for identifying fungal antagonists.}, + author = {Orwa, Philemon and Kuhl-Nagel, Theresa and Meinhold-Ernst, Rosa and Seyer, Arne and Jehle, Johannes A and Mwirichia, Romano and Linkies, Ada}, + copyright = {cc by}, + doi = {10.1371/journal.pone.0335007}, + issn = {1932-6203}, + journal = {PloS one}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {January}, + number = {10}, + pages = {e0335007}, + pmcid = {PMC12551835}, + pmid = {41134799}, + title = {Chaetomium, {Chlonostachys}, and {Pseudogymnoascus} isolates from tomato tissues significantly suppress {Phytophthora} infestans in tomato}, + url = {https://europepmc.org/articles/PMC12551835}, + urldate = {2025-12-26}, + volume = {20}, + year = {2025} +} + +@article{osca_complete_2022, + abstract = {The complete nucleotide sequence of the mitochondrial (mt) genome of the demersal zebra seabream \textit{Diplodus cervinus} (Lowe, 1838) was determined for the first time. The double stranded circular molecule is 16,559 base pairs (bp) in length and encodes for the typical 37 metazoan mitochondrial genes, and 2 non-coding regions (D-loop and L-origin). The gene arrangement of the \textit{D. cervinus} mt genome follows the usual one for fishes. The nucleotide sequences of the mt protein coding and ribosomal genes of \textit{D. cervinus} mt genome were aligned with orthologous sequences from representatives of the Sparidae family and phylogenetic relationships were inferred. Maximum likelihood analyses placed \textit{D. cervinus} as a sister species of \textit{Diplodus sargus} (Linnaeus, 1758).}, + author = {Osca, David and Caputi, Luigi and Tanduo, Valentina and Sepe, Rosa Maria and Liberti, Assunta and Tiralongo, Francesco and Venuti, Iolanda and Ceruso, Marina and Crocetta, Fabio and Sordino, Paolo and Pepe, Tiziana}, + doi = {10.1080/23802359.2022.2145174}, + issn = {2380-2359}, + journal = {Mitochondrial DNA. Part B, Resources}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + number = {11}, + pages = {2006--2008}, + title = {The complete mitochondrial genome of the zebra seabream {Diplodus} cervinus ({Perciformes}, {Sparidae}) from the {Mediterranean} {Sea}}, + url = {http://europepmc.org/abstract/MED/36451968}, + volume = {7}, + year = {2022} +} + @article{oselusi_cheminformatic_2021, + abstract = {The growing antimicrobial resistance (AMR) of pathogenic organisms to currently prescribed drugs has resulted in the failure to treat various infections caused by these superbugs. Therefore, to keep pace with the increasing drug resistance, there is a pressing need for novel antimicrobial agents, especially from non-conventional sources. Several natural products (NPs) have been shown to display promising in vitro activities against multidrug-resistant pathogens. Still, only a few of these compounds have been studied as prospective drug candidates. This may be due to the expensive and time-consuming process of conducting important studies on these compounds. The present review focuses on applying cheminformatics strategies to characterize, prioritize, and optimize NPs to develop new lead compounds against antimicrobial resistance pathogens. Moreover, case studies where these strategies have been used to identify potential drug candidates, including a few selected open-access tools commonly used for these studies, are briefly outlined.}, author = {Oselusi, Samson Olaitan and Christoffels, Alan and Egieyeh, Samuel Ayodele}, doi = {10.3390/molecules26133970}, + issn = {1420-3049}, + journal = {Molecules (Basel, Switzerland)}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {June}, note = {Publisher: MDPI AG}, number = {13}, @@ -10594,7 +17191,7 @@ @article{ostrovsky_using_2021 abstract = {Modern biology continues to become increasingly computational. Datasets are becoming progressively larger, more complex, and more abundant. The computational savviness necessary to analyze these data creates an ongoing obstacle for experimental biologists. Galaxy (galaxyproject.org) provides access to computational biology tools in a web-based interface. It also provides access to major public biological data repositories, allowing private data to be combined with public datasets. Galaxy is hosted on high-capacity servers worldwide and is accessible for free, with an option to be installed locally. This article demonstrates how to employ Galaxy to perform biologically relevant analyses on publicly available datasets. These protocols use both standard and custom tools, serving as a tutorial and jumping-off point for more intensive and/or more specific analyses using Galaxy. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Finding human coding exons with highest SNP density Basic Protocol 2: Calling peaks for ChIP-seq data Basic Protocol 3: Compare datasets using genomic coordinates Basic Protocol 4: Working with multiple alignments Basic Protocol 5: Single cell RNA-seq}, author = {Ostrovsky, Alexander and Hillman‐Jackson, Jennifer and Bouvier, Dave and Clements, Dave and Afgan, Enis and Blankenberg, Daniel and Schatz, Michael C. and Nekrutenko, Anton and Taylor, James and Team, the Galaxy and Lariviere, Delphine}, copyright = {© 2021 Wiley Periodicals LLC}, - doi = {https://doi.org/10.1002/cpz1.31}, + doi = {10.1002/cpz1.31}, issn = {2691-1299}, journal = {Current Protocols}, keywords = {+Education, +Galactic, +HowTo, +IsGalaxy, +Project, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Galaxy, computational biology, web application}, @@ -10615,7 +17212,7 @@ @article{ou_differences_2024 doi = {10.1101/gr.278131.123}, issn = {1088-9051, 1549-5469}, journal = {Genome Research}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, DNA Transposable Elements, Genome, Plant, Retroelements, Terminal Repeat Sequences, Zea mays}, language = {en}, month = {August}, note = {Company: Cold Spring Harbor Laboratory Press @@ -10651,13 +17248,49 @@ @article{owen_rna-sequencing_2019 year = {2019} } +@article{oyedara_bacterial_2024, + abstract = {Wastewater treatment plants (WWTPs) are hotspots for pathogens, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and horizontal gene transfer because they receive inflow of nutrient-rich organic wastewater from different sources. In this study, bacterial communities and ARGs of raw (influent) and treated (effluent) sewage samples collected from a WWTP in Northern Mexico were studied using nanopore sequencing technology. Proteobacteria (52.56–61.50\%), Bacteroidetes (8.70–15.58\%), Actinobacteria (7.45–12.86\%), and Firmicutes (2.78–21.27\%) were the major phyla detected in all the sewage samples. The genus Arcobacter (15.36–29.11\%) dominated all the sewage samples, except in the effluent collected in 2022, where more abundance of the genus Shewanella (7.51\%) and Aeromonas (6.12\%) was observed. ARGs classes common to the samples include glycopeptide, bacitracin, macrolide, fluoroquinolone, peptide, tetracycline, and phenicol. The members of the clinically relevant ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) group, Escherichia coli, Eubacterium rectale, and Acinetobacter johnsonii with mobile genetic elements carrying ARGs were among the potential human pathogens detected in effluent samples. The release of effluents containing these bacteria or their genomes into the natural environment could have public health implications and aid the spread of ARGs. Better policies and enhanced wastewater treatment strategies are necessary to reduce or eliminate these risks.}, + author = {Oyedara, Omotayo O. and Ruíz-Amaro, Carlos J. and Heredia, Norma and García, Santos}, + doi = {10.1007/s41742-024-00715-1}, + issn = {2008-2304}, + journal = {International Journal of Environmental Research}, + keywords = {{\textgreater}UseGalaxy.eu, Bacteria, Environmental Microbiology, Escherichia Coli, Metagenomics, Microbiome, Nanopore, Resistomes, Sequencing, Wastewater, Water Microbiology}, + language = {en}, + month = {December}, + number = {2}, + pages = {47}, + shorttitle = {Bacterial {Communities}, {Pathogens}, {Resistomes}, and {Mobilomes} {Associated} with a {Wastewater} {Treatment} {Plant} in {Mexico}}, + title = {Bacterial {Communities}, {Pathogens}, {Resistomes}, and {Mobilomes} {Associated} with a {Wastewater} {Treatment} {Plant} in {Mexico}: {A} {Metagenomics} {Approach}}, + url = {https://doi.org/10.1007/s41742-024-00715-1}, + urldate = {2025-02-16}, + volume = {19}, + year = {2024} +} + +@article{ozaki_novel_2020, + abstract = {Cell division requires proper spatial coordination with the chromosome, which undergoes dynamic changes during chromosome replication and segregation. FtsZ is a bacterial cytoskeletal protein that assembles into the Z-ring, providing a platform to build the cell division apparatus. In the model bacterium \textit{Caulobacter crescentus}, the cellular localization of the Z-ring is controlled during the cell cycle in a chromosome replication-coupled manner. Although dynamic localization of the Z-ring at midcell is driven primarily by the replication origin-associated FtsZ inhibitor MipZ, the mechanism ensuring accurate positioning of the Z-ring remains unclear. In this study, we showed that the Z-ring colocalizes with the replication terminus region, located opposite the origin, throughout most of the \textit{C. crescentus} cell cycle. Spatial organization of the two is mediated by ZapT, a previously uncharacterized protein that interacts with the terminus region and associates with ZapA and ZauP, both of which are part of the incipient division apparatus. While the Z-ring and the terminus region coincided with the presence of ZapT, colocalization of the two was perturbed in cells lacking \textit{zapT}, which is accompanied by delayed midcellular positioning of the Z-ring. Moreover, cells overexpressing ZapT showed compromised positioning of the Z-ring and MipZ. These findings underscore the important role of ZapT in controlling cell division processes. We propose that ZapT acts as a molecular bridge that physically links the terminus region to the Z-ring, thereby ensuring accurate site selection for the Z-ring. Because ZapT is conserved in proteobacteria, these findings may define a general mechanism coordinating cell division with chromosome organization.\textbf{IMPORTANCE} Growing bacteria require careful tuning of cell division processes with dynamic organization of replicating chromosomes. In enteric bacteria, ZapA associates with the cytoskeletal Z-ring and establishes a physical linkage to the chromosomal replication terminus through its interaction with ZapB-MatP-DNA complexes. However, because ZapB and MatP are found only in enteric bacteria, it remains unclear how the Z-ring and the terminus are coordinated in the vast majority of bacteria. Here, we provide evidence that a novel conserved protein, termed ZapT, mediates colocalization of the Z-ring with the terminus in \textit{Caulobacter crescentus}, a model organism that is phylogenetically distant from enteric bacteria. Given that ZapT facilitates cell division processes in \textit{C. crescentus}, this study highlights the universal importance of the physical linkage between the Z-ring and the terminus in maintaining cell integrity.}, + author = {Ozaki, Shogo and Jenal, Urs and Katayama, Tsutomu}, + doi = {10.1128/mbio.00487-20}, + issn = {2150-7511}, + journal = {mBio}, + keywords = {{\textgreater}UseGalaxy.eu, Caulobacter crescentus}, + language = {eng}, + month = {April}, + number = {2}, + pages = {e00487--20}, + title = {Novel {Divisome}-{Associated} {Protein} {Spatially} {Coupling} the {Z}-{Ring} with the {Chromosomal} {Replication} {Terminus} in {Caulobacter} crescentus}, + url = {http://europepmc.org/abstract/MED/32345642}, + volume = {11}, + year = {2020} +} + @article{ozkurt_lotus2_2022, abstract = {Amplicon sequencing is an established and cost-efficient method for profiling microbiomes. However, many available tools to process this data require both bioinformatics skills and high computational power to process big datasets. Furthermore, there are only few tools that allow for long read amplicon data analysis. To bridge this gap, we developed the LotuS2 (less OTU scripts 2) pipeline, enabling user-friendly, resource friendly, and versatile analysis of raw amplicon sequences.}, author = {Özkurt, Ezgi and Fritscher, Joachim and Soranzo, Nicola and Ng, Duncan Y. K. and Davey, Robert P. and Bahram, Mohammad and Hildebrand, Falk}, doi = {10.1186/s40168-022-01365-1}, issn = {2049-2618}, journal = {Microbiome}, - keywords = {16S rRNA, {\textgreater}UseGalaxy.eu, Amplicon data analysis, Amplicon sequencing, ITS, Long read, Microbiome, Short read}, + keywords = {16S rRNA, {\textgreater}UseGalaxy.eu, Amplicon data analysis, Amplicon sequencing, ITS, Long read, Microbiome, Short read, Software, Soil}, language = {en}, month = {October}, number = {1}, @@ -10680,6 +17313,7 @@ @article{pachanon_genomic_2024 language = {English}, month = {May}, note = {Publisher: Frontiers}, + pages = {1386496}, title = {Genomic characterization of carbapenem and colistin-resistant {Klebsiella} pneumoniae isolates from humans and dogs}, url = {https://www.frontiersin.org/articles/10.3389/fvets.2024.1386496}, urldate = {2024-06-07}, @@ -10687,11 +17321,31 @@ @article{pachanon_genomic_2024 year = {2024} } +@article{padgett_mitochondrial_2025, + abstract = {The goliath grouper \textit{Epinephelus itajara} (Perciformes: Epinephelidae) is a large, critically endangered fish distributed across coastal habitats in the western Atlantic Ocean, from Florida to southern Brazil, and with additional populations in the eastern Pacific basin. Conservation concerns for this species stem from historical overfishing, habitat loss, and life-history traits such as slow growth and late sexual maturity. In this study, to aid conservation efforts, we assembled and characterized the complete mitochondrial genome of \textit{E. itajara}. The mitochondrial genome of \textit{Epinephelus itajara} is 16,561 bp long and comprises 13 protein-coding genes (PCGs), two ribosomal RNA genes (12S and 16S rRNA), 22 transfer RNA (tRNA) genes, and an 856 bp control region. Gene order is identical to that reported for other congeneric species. The overall A + T content is 56\%, and codon usage shows a preference for A + T-rich codons. All PCGs were found to be under purifying selection, with variation in selective pressure among genes; \textit{cox1} and \textit{nad4} were under the strongest and weakest selection, respectively. Secondary structure analysis of the tRNA genes displayed typical cloverleaf secondary structures, except for trnS1, which lacked a complete D-arm. Comparative analyses between MiTFi and RASP2 revealed that MiTFi provided more accurate predictions of tRNA secondary structures. The control region exhibited a high A + T content (69.9\%), multiple microsatellite motifs, and one tandem repeat, along with hairpin secondary structures. These features mirror findings in closely related species. A maximum likelihood phylogenetic analysis based on translated PCGs did not support the monophyletic status of the genus \textit{Epinephelus} and indicated a sister relationship between \textit{Epinephelus itajara} and \textit{Epinephelus lanceolatus}, another large-bodied grouper from the Indo-Pacific Ocean. The newly sequenced mitochondrial genome of \textit{Epinephelus itajara} provides a new genomic resource that can support future conservation efforts.}, + author = {Padgett, Kyla and Baeza, J Antonio}, + doi = {10.1002/ece3.71795}, + issn = {2045-7758}, + journal = {Ecology and evolution}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {July}, + number = {7}, + pages = {e71795}, + title = {The {Mitochondrial} {Genome} of the {Imperiled} {Goliath} {Grouper} \textit{{Epinephelus} itajara}: {Selective} {Pressures} in {Protein} {Coding} {Genes}, {Secondary} {Structure} of {tRNA} {Genes}, and {Phylogenetic} {Placement}}, + url = {http://europepmc.org/abstract/MED/40692973}, + volume = {15}, + year = {2025} +} + @article{page-karjian_fibropapillomatosis_2021, + abstract = {Fibropapillomatosis (FP), a debilitating, infectious neoplastic disease, is rarely reported in endangered Kemp's ridley sea turtles (\textit{Lepidochelys kempii}). With this study, we describe FP and the associated chelonid alphaherpesvirus 5 (ChHV5) in Kemp's ridley turtles encountered in the United States during 2006-2020. Analysis of 22 case reports of Kemp's ridley turtles with FP revealed that while the disease was mild in most cases, 54.5\% were adult turtles, a reproductively valuable age class whose survival is a priority for population recovery. Of 51 blood samples from tumor-free turtles and 12 tumor samples from turtles with FP, 7.8\% and 91.7\%, respectively, tested positive for ChHV5 DNA via quantitative polymerase chain reaction (qPCR). Viral genome shotgun sequencing and phylogenetic analysis of six tumor samples show that ChHV5 sequences in Kemp's ridley turtles encountered in the Gulf of Mexico and northwestern Atlantic cluster with ChHV5 sequences identified in green (\textit{Chelonia mydas}) and loggerhead (\textit{Caretta caretta}) sea turtles from Hawaii, the southwestern Atlantic Ocean, and the Caribbean. Results suggest an interspecific, spatiotemporal spread of FP among Kemp's ridley turtles in regions where the disease is enzootic. Although FP is currently uncommon in this species, it remains a health concern due to its uncertain pathogenesis and potential relationship with habitat degradation.}, author = {Page-Karjian, Annie and Whitmore, Liam and Stacy, Brian A. and Perrault, Justin R. and Farrell, Jessica A. and Shaver, Donna J. and Walker, J. Shelby and Frandsen, Hilary R. and Rantonen, Elina and Harms, Craig A. and Norton, Terry M. and Innis, Charles and Yetsko, Kelsey and Duffy, David J.}, doi = {10.3390/ani11113076}, + issn = {2076-2615}, journal = {Animals}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {October}, note = {Publisher: MDPI AG}, number = {11}, @@ -10702,6 +17356,26 @@ @article{page-karjian_fibropapillomatosis_2021 year = {2021} } +@article{paiva_ld-transpeptidation_2025, + abstract = {{\textless}h2{\textgreater}Summary{\textless}/h2{\textgreater}{\textless}p{\textgreater}The resistance of \textit{Clostridioides difficile} to the β-lactam antibiotics cephalosporins, which target the peptidoglycan (PG) assembly, is a leading contributor to the development of \textit{C. difficile} infections. \textit{C. difficile} has an original PG structure with a predominance of 3→3 cross-links generated by l,d-transpeptidases (LDTs). \textit{C. difficile} forms spores and we show that the spore cortex PG contains exclusively 3→3 cross-links. PG and spore cortex of \textit{C. difficile} cells were largely unaffected by the deletion of the three predicted LDTs, revealing the implication of a new family of LDTs. The d,d-carboxypeptidases producing the essential LDT substrate were inactivated by cephalosporins, resulting in the inhibition of the l,d-transpeptidation pathway. In contrast, the participation of penicillin-binding proteins (PBPs) to PG cross-linking increased in the presence of the antibiotics. Our findings highlight that cephalosporin resistance is not primarily mediated by LDTs and illustrate the plasticity of the PG biosynthesis machinery in \textit{C. difficile}.{\textless}/p{\textgreater}}, + author = {Paiva, Ana M. Oliveira and Courtin, Pascal and Charpentier, Glenn and Oueled-Chama, Imane and Soutourina, Olga and Chapot-Chartier, Marie-Pierre and Peltier, Johann}, + doi = {10.1016/j.isci.2025.112227}, + issn = {2589-0042}, + journal = {iScience}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {English}, + month = {April}, + note = {Publisher: Elsevier}, + number = {4}, + pages = {112227}, + pmid = {40224013}, + title = {The l,d-transpeptidation pathway is inhibited by antibiotics of the β-lactam class in {Clostridioides} difficile}, + url = {https://www.cell.com/iscience/abstract/S2589-0042(25)00488-2}, + urldate = {2025-05-29}, + volume = {28}, + year = {2025} +} + @article{palacios-rodriguez_antimicrobial_2024, abstract = {Worldwide, bacterial resistance is one of the most severe public health problems. Currently, the failure of antibiotics to counteract superbugs highlights the need to search for new molecules with antimicrobial potential to combat them. The objective of this research was to evaluate the antimicrobial activity of Bacillus amyloliquefaciens BS4 against Gram-negative bacteria. Thirty yeasts and thirty-two Bacillus isolates were tested following the agar well-diffusion method. Four Bacillus sp. strains (BS3, BS4, BS17, and BS21) showed antagonistic activity against E. coli ATCC 25922 using bacterial culture (BC) and the cell-free supernatant (CFS), where the BS4 strain stood out, showing inhibitory values of 20.50 ± 0.70 mm and 19.67 ± 0.58 mm for BC and CFS, respectively. The Bacillus sp. BS4 strain can produce antioxidant, non-hemolytic, and antimicrobial metabolites that exhibit activity against several microorganisms such as Salmonella enterica, Klebsiella pneumoniae, Shigella flexneri, Enterobacter aerogenes, Proteus vulgaris, Yersinia enterocolitica, Serratia marcescens, Aeromonas sp., Pseudomonas aeruginosa, Candida albicans, and Candida tropicalis. According to the characterization of the supernatant, the metabolites could be proteinaceous. The production of these metabolites is influenced by carbon and nitrogen sources. The most suitable medium to produce antimicrobial metabolites was TSB broth. The one-factor-at-a-time method was used to standardize parameters such as pH, agitation, temperature, carbon source, nitrogen source, and salts, resulting in the best conditions of pH 7, 150 rpm, 28 °C, starch (2.5 g/L), tryptone (20 g/L), and magnesium sulfate (0.2 g/L), respectively. Moreover, the co-culture was an excellent strategy to improve antimicrobial activity, achieving maximum antimicrobial activity with an inhibition zone of 21.85 ± 1.03 mm. These findings position the Bacillus amyloliquefaciens BS4 strain as a promising candidate for producing bioactive molecules with potential applications in human health.}, author = {Palacios-Rodriguez, Ana Paula and Espinoza-Culupú, Abraham and Durán, Yerson and Sánchez-Rojas, Tito}, @@ -10723,6 +17397,24 @@ @article{palacios-rodriguez_antimicrobial_2024 year = {2024} } +@article{palamarchuk_comparison_2025, + abstract = {Cancer progression is often accompanied with the acquisition of functional anergy by natural killer (NK) cells and their aging. As a result, persistent herpesviruses, such as hCMV and EBV, reactivate. The catalytic subunit of telomerase encoded by hTERT gene may enhance functional and proliferative activity. We aimed to elucidate if NK cells modified for sustained hTERT expression acquire these beneficial characteristics. We examined the proliferative and functional activities of hTERT-NK cells and combined observations with RNA-seq results. Thus, hTERT-NK cells were characterized with an increase in the expression levels of cell cycle genes and better proliferative activity in the third month after isolation. Increased degranulation upon K562 target cell recognition simultaneously with a higher expression level of granzyme B was observed for hTERT-NK cells. An increased level of IFNγ was also noted in hTERT-NK cells. These results reveal that hTERT-NK cells obtain additional advantages due to the stable hTERT expression. hTERT-NK cells are likely to perform high levels of functional activity over long time periods that are commonly needed during cancer treatment to perform immune surveillance and minimize relapse rates.}, + author = {Palamarchuk, A. I. and Ustiuzhanina, M. O. and Kovalenko, E. I. and Streltsova, M. A.}, + doi = {10.1134/S1990747825700291}, + issn = {1990-7494}, + journal = {Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology}, + keywords = {{\textgreater}UseGalaxy.eu, CMV, EBV, NK cells, hTERT, proliferation, retroviral transduction}, + language = {en}, + month = {September}, + number = {3}, + pages = {338--347}, + title = {Comparison of {Functional} and {Proliferative} {Activity} of {hTERT}-{NK} and {iCasp9}-{NK} {Cells}}, + url = {https://doi.org/10.1134/S1990747825700291}, + urldate = {2025-09-03}, + volume = {19}, + year = {2025} +} + @article{palecanda_increasing_2023, abstract = {Stomatopods are well studied for their unique visual systems, which can consist of up to 16 different photoreceptor types and 33 opsin proteins expressed in the adults of some species. The light-sensing abilities of larval stomatopods are comparatively less well understood with limited information about the opsin repertoire of these early-life stages. Early work has suggested that larval stomatopods may not possess the extensive light detection abilities found in their adult counterparts. However, recent studies have shown that these larvae may have more complex photosensory systems than previously thought. To examine this idea at the molecular level, we characterized the expression of putative light-absorbing opsins across developmental stages, from embryo to adult, in the stomatopod species Pullosquilla thomassini using transcriptomic methods with a special focus on ecological and physiological transition periods. Opsin expression during the transition from the larval to the adult stage was further characterized in the species Gonodactylaceus falcatus. Opsin transcripts from short, middle, and long wavelength-sensitive clades were found in both species, and analysis of spectral tuning sites suggested differences in absorbance within these clades. This is the first study to document the changes in opsin repertoire across development in stomatopods, providing novel evidence for light detection across the visual spectrum in larvae.}, author = {Palecanda, Sitara and Steck, Mireille and Porter, Megan L.}, @@ -10758,11 +17450,16 @@ @article{palecanda_molecular_2023 } @article{pallares-vega_temperature_2021, + abstract = {Plasmid-mediated dissemination of antibiotic resistance among fecal \textit{Enterobacteriaceae} in natural ecosystems may contribute to the persistence of antibiotic resistance genes in anthropogenically impacted environments. Plasmid transfer frequencies measured under laboratory conditions might lead to overestimation of plasmid transfer potential in natural ecosystems. This study assessed differences in the conjugative transfer of an IncP-1 (pKJK5) plasmid to three natural \textit{Escherichia coli} strains carrying extended-spectrum beta-lactamases, by filter mating. Matings were performed under optimal laboratory conditions (rich LB medium and 37°C) and environmentally relevant temperatures (25, 15 and 9°C) or nutrient regimes mimicking environmental conditions and limitations (synthetic wastewater and soil extract). Under optimal nutrient conditions and temperature, two recipients yielded high transfer frequencies (5 × 10$^{\textrm{-1}}$) while the conjugation frequency of the third strain was 1000-fold lower. Decreasing mating temperatures to psychrophilic ranges led to lower transfer frequencies, albeit all three strains conjugated under all the tested temperatures. Low nutritive media caused significant decreases in transconjugants (-3 logs for synthetic wastewater; -6 logs for soil extract), where only one of the strains was able to produce detectable transconjugants. Collectively, this study highlights that despite less-than-optimal conditions, fecal organisms may transfer plasmids in the environment, but the transfer of pKJK5 between microorganisms is limited mainly by low nutrient conditions.}, author = {Pallares-Vega, Rebeca and Macedo, Gonçalo and Brouwer, Michael S. M. and Leal, Lucia Hernandez and Maas, Peter van der and Loosdrecht, Mark C. M. van and Weissbrodt, David G. and Heederik, Dick and Mevius, Dik and Schmitt, Heike}, doi = {10.3389/fmicb.2021.656250}, + issn = {1664-302X}, + journal = {Frontiers in microbiology}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {July}, note = {Publisher: Frontiers Media SA}, + pages = {656250}, title = {Temperature and {Nutrient} {Limitations} {Decrease} {Transfer} of {Conjugative} {IncP}-1 {Plasmid} {pKJK5} to {Wild} {Escherichia} coli {Strains}}, url = {https://doi.org/10.3389/fmicb.2021.656250}, volume = {12}, @@ -10775,7 +17472,7 @@ @article{pan_semibin2_2023 doi = {10.1093/bioinformatics/btad209}, issn = {1367-4811}, journal = {Bioinformatics}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Algorithms, Metagenome}, month = {June}, number = {Supplement\_1}, pages = {i21--i29}, @@ -10787,6 +17484,25 @@ @article{pan_semibin2_2023 year = {2023} } +@article{panagiotopoulou_quorum_2025, + abstract = {The quorum sensing regulated sRNA Lrs1 participates in the adaptation of Pseudomonas aeruginosa in low iron by downregulating the siderophore pyochelin, the Quorum Sensing system PQS, and its associa...}, + author = {Panagiotopoulou, Dimitra and Catalán, Natalia Romo and Wilcox, Max and Halliday, Nigel and Pantalone, Paolo and Lazenby, James and Cámara, Miguel and Heeb, Stephan}, + doi = {10.1111/1758-2229.70090}, + issn = {1758-2229}, + journal = {Environmental Microbiology Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Adaptation, Physiological, Iron, Pseudomonas aeruginosa, Quorum Sensing, RNA, Bacterial, RNA, Small Untranslated}, + language = {en}, + month = {April}, + note = {Publisher: John Wiley \& Sons, Ltd}, + number = {2}, + pages = {e70090}, + title = {The {Quorum} {Sensing} {Regulated} {sRNA} {Lrs1} {Is} {Involved} in the {Adaptation} to {Low} {Iron} in {Pseudomonas} aeruginosa}, + url = {https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1758-2229.70090}, + urldate = {2025-05-29}, + volume = {17}, + year = {2025} +} + @article{pannhorst_non-classical_2023, abstract = {African swine fever virus (ASFV) is a lethal animal pathogen that enters its host cells through endocytosis. So far, host factors specifically required for ASFV replication have been barely identified. In this study a genome-wide CRISPR/Cas9 knockout screen in porcine cells indicated that the genes RFXANK, RFXAP, SLA-DMA, SLA-DMB, and CIITA are important for productive ASFV infection. The proteins encoded by these genes belong to the major histocompatibility complex II (MHC II), or swine leucocyte antigen complex II (SLA II). RFXAP and CIITA are MHC II-specific transcription factors, whereas SLA-DMA/B are subunits of the non-classical MHC II molecule SLA-DM. Targeted knockout of either of these genes led to severe replication defects of different ASFV isolates, reflected by substantially reduced plating efficiency, cell-to-cell spread, progeny virus titers and viral DNA replication. Transgene-based reconstitution of SLA-DMA/B fully restored the replication capacity demonstrating that SLA-DM, which resides in late endosomes, plays a crucial role during early steps of ASFV infection.}, author = {Pannhorst, Katrin and Carlson, Jolene and Hölper, Julia E. and Grey, Finn and Baillie, John Kenneth and Höper, Dirk and Wöhnke, Elisabeth and Franzke, Kati and Karger, Axel and Fuchs, Walter and Mettenleiter, Thomas C.}, @@ -10794,7 +17510,7 @@ @article{pannhorst_non-classical_2023 doi = {10.1038/s41598-023-36788-9}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, High-throughput screening, Virus–host interactions}, + keywords = {{\textgreater}UseGalaxy.eu, African Swine Fever, African Swine Fever Virus, Craniocerebral Trauma, High-throughput screening, Virus–host interactions}, language = {en}, month = {August}, note = {Number: 1 @@ -10808,6 +17524,40 @@ @article{pannhorst_non-classical_2023 year = {2023} } +@article{panzitt_fxr_2025, + abstract = {Metabolic pressure shifts signaling pathways of nuclear receptors, including the bile acid receptor FXR, which are sensitive to nutritional inputs. We performed an FXR ChIP-seq–centered multiomic analysis of liver biopsy samples from individuals with or without obesity, who were treated with either placebo or the FXR agonist obeticholic acid, to define metabolic adaptions of FXR signaling pathways. FXR occupied substantially more DNA binding sites in individuals with obesity, and FXR activation by OCA robustly changed the transcriptional output. Integration of ChIP-seq and RNA-seq data showed that mitochondrial function and substrate oxidation were the top metabolic pathways selectively modulated by FXR activation in individuals with obesity. FXR activation restored compromised substrate oxidation by enhancing β-oxidation and oxidative phosphorylation along with antagonizing ROS production. In line with this, the amount of reduced glutathione in patients with obesity normalized after OCA treatment. In summary, FXR signaling profoundly differs in patients with obesity, consisting of changes in DNA binding profiles and transcriptional programs, which enhance energy substrate utilization in this patient cohort.}, + author = {Panzitt, Katrin and Jungwirth, Emilian and Vosko, Lena E. and Madreiter-Sokolowski, Corina T. and Madl, Tobias and Tawfik, Ines and Habisch, Hansjörg and Krstic, Jelena and Prokesch, Andreas and Karitnig, Robert and Sucher, Robert and Erdogan, Ceyhun Y. and Vallim, Thomas A. and Trauner, Michael and Fickert, Peter and Al-Dury, Samer and Molinaro, Antonio and Moore, David D. and Thallinger, Gerhard G. and Marschall, Hanns-Ulrich and Wagner, Martin}, + doi = {10.1126/scitranslmed.adn4558}, + journal = {Science Translational Medicine}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: American Association for the Advancement of Science}, + number = {811}, + pages = {eadn4558}, + title = {{FXR} adapts hepatic mitochondrial function to increased substrate oxidation in patients with obesity}, + url = {https://www.science.org/doi/full/10.1126/scitranslmed.adn4558}, + urldate = {2025-09-03}, + volume = {17}, + year = {2025} +} + +@article{papakonstantinou_integrative_2025, + abstract = {The increased metastatic ability of small-cell lung cancer (SCLC) necessitates the identification of new prognostic biomarkers for clinical evaluation during the disease course. Our previous research highlighted the clinical relevance of transcription factor JunB (JUNB), C-X-C chemokine receptor type 4 (CXCR4), and programmed cell death 1 ligand 1 (PD-L1) in breast and non-small cell lung cancer (NSCLC) patients. In the current study, we examined these biomarkers in circulating tumor cells (CTCs) and plasma-derived exosomes from 100 treatment-naïve SCLC patients. CTCs were analyzed using the VyCAP system, whereas exosomes were characterized molecularly and transcriptomically. JUNB, CXCR4, and PD-L1 were highly prevalent in CTCs. Patients exhibited significantly increased protein exosomal expression of JUNB and CXCR4 compared to healthy individuals. Overexpression of JUNB and CXCR4 in exosomes can distinguish patients from normal donors, offering an interesting tool for early diagnosis. The presence of JUNB and/or CXCR4 in CTCs correlated with significantly poorer overall survival. CXCR4 exosomal overexpression was associated with CTC presence and their phenotypes. Conclusively, a comprehensive analysis of CTCs and exosomes provides useful prognostic and potential diagnostic tools for SCLC patients.}, + author = {Papakonstantinou, Dimitrios and Roumeliotou, Argyro and Pantazaka, Evangelia and Shaukat, Athanasios-Nasir and Christopoulou, Athina and Koutras, Angelos and Dimitrakopoulos, Foteinos-Ioannis and Georgoulias, Vassilis and Xagara, Anastasia and Chantzara, Evangelia and Koinis, Fillipos and Kotsakis, Athanasios and Stathopoulos, Constantinos and Kallergi, Galatea}, + doi = {10.1002/1878-0261.13765}, + issn = {1574-7891}, + journal = {Mol Oncol}, + keywords = {{\textgreater}UseGalaxy.eu, Exosomes, Lung Neoplasms, Neoplastic Cells, Circulating, Small Cell Lung Carcinoma}, + language = {eng}, + month = {July}, + number = {7}, + pages = {2038--2055}, + title = {Integrative analysis of circulating tumor cells ({CTCs}) and exosomes from small-cell lung cancer ({SCLC}) patients: a comprehensive approach}, + url = {http://europepmc.org/abstract/MED/39575761}, + volume = {19}, + year = {2025} +} + @article{papatheodorou_expression_2019, abstract = {Abstract. Expression Atlas is EMBL-EBI’s resource for gene and protein expression. It sources and compiles data on the abundance and localisation of RNA and pr}, author = {Papatheodorou, Irene and Moreno, Pablo and Manning, Jonathan and Fuentes, Alfonso Muñoz-Pomer and George, Nancy and Fexova, Silvie and Fonseca, Nuno A. and Füllgrabe, Anja and Green, Matthew and Huang, Ni and Huerta, Laura and Iqbal, Haider and Jianu, Monica and Mohammed, Suhaib and Zhao, Lingyun and Jarnuczak, Andrew F. and Jupp, Simon and Marioni, John and Meyer, Kerstin and Petryszak, Robert and Prada Medina, Cesar Augusto and Talavera-López, Carlos and Teichmann, Sarah and Vizcaino, Juan Antonio and Brazma, Alvis}, @@ -10841,6 +17591,22 @@ @article{parenti_mau2_2020 year = {2020} } +@article{parmar_large-scale_2025, + abstract = {Blowflies (Calliphoridae) represent a species-rich group, comprising 9 \% of calyptrate diversity and 1.3 \% of all described Diptera. The blowfly subfamily Calliphorinae, is known for its species of medical, veterinary and forensic importance, which has led to a skew toward these species in publicly available mitochondrial genome data. This skew leaves a significant proportion of this subfamily unrepresented and has resulted in poorly understood inter- and intra-subfamilial relationships, due to restricted taxon sampling. To address this, we assembled mitogenomes for 63 Calliphorinae species across 13 genera and a further 15 species from all remaining calliphorid subfamilies, representing the most comprehensive mitogenomic dataset for blowflies to date. Comparative analysis of mitochondrial DNA revealed structural and functional variations in gene order, base composition, codon usage, evolutionary rates and gene rearrangements across blowfly lineages, including a major rearrangement in Calliphora varifrons. Phylogenetic analysis of 13 mitochondrial protein-coding genes strongly supported the monophyly of Calliphoridae and its subfamilies. Clades Chrysomyinae (Calliphorinae+Luciliinae) and Rhiniinae+Bengaliinae are well-supported, with former subfamilies Melanomyinae and Toxotarsinae nested within Calliphorinae. Ameniinae was paraphyletic in most analyses, with variable placement of Eurychaeta palpalis. Genera Calliphora and Onesia are non-monophyletic, and the synonymisation of Calliphora with Cynomya, Cyanus and Cynomyiomima is suggested.}, + author = {Parmar, Drashti R. and Johnston, Nikolas P. and Szpila, Krzysztof}, + doi = {10.1016/j.ijbiomac.2025.147063}, + issn = {0141-8130}, + journal = {International Journal of Biological Macromolecules}, + keywords = {{\textgreater}UseGalaxy.eu, Calliphoridae, Mitochondrial DNA, Phylogeny}, + month = {August}, + pages = {147063}, + shorttitle = {Large-scale comparative analysis of blowfly mitogenomes, with an emphasis on {Calliphorinae} ({Diptera}}, + title = {Large-scale comparative analysis of blowfly mitogenomes, with an emphasis on {Calliphorinae} ({Diptera}: {Calliphoridae}), provides evolutionary insights into mitochondrial {DNA} structure, gene rearrangements, and inter- and intra-subfamilial relationships among blowflies}, + url = {https://www.sciencedirect.com/science/article/pii/S0141813025076202}, + urldate = {2025-09-03}, + year = {2025} +} + @article{patat_construction_2022, abstract = {Garden cress (Lepidium sativum L.) is a Brassicaceae crop recognized as a healthy vegetable and a medicinal plant. Lepidium is one of the largest genera in Brassicaceae, yet, the genus has not been a focus of extensive genomic research. In the present work, garden cress genome was sequenced using the long read high-fidelity sequencing technology. A de novo, draft genome assembly that spans 336.5 Mb was produced, corresponding to 88.6\% of the estimated genome size and representing 90\% of the evolutionarily expected orthologous gene content. Protein coding gene content was structurally predicted and functionally annotated, resulting in the identification of 25,668 putative genes. A total of 599 candidate disease resistance genes were identified by predicting resistance gene domains in gene structures, and 37 genes were detected as orthologs of heavy metal associated protein coding genes. In addition, 4289 genes were assigned as “transcription factor coding.” Six different machine learning algorithms were trained and tested for their performance in classifying miRNA coding genomic sequences. Logistic regression proved the best performing trained algorithm, thus utilized for pre-miRNA coding loci identification in the assembly. Repetitive DNA analysis involved the characterization of transposable element and microsatellite contents. L. sativum chloroplast genome was also assembled and functionally annotated. Data produced in the present work is expected to constitute a foundation for genomic research in garden cress and contribute to genomics-assisted crop improvement and genome evolution studies in the Brassicaceae family.}, author = {Patat, Aysenur Soyturk and Sen, Fatima and Erdogdu, Behic Selman and Uncu, Ali Tevfik and Uncu, Ayse Ozgur}, @@ -10862,7 +17628,7 @@ @article{patel_bioprospecting_2023 doi = {10.1007/s00894-023-05569-6}, issn = {0948-5023}, journal = {Journal of Molecular Modeling}, - keywords = {{\textgreater}UseGalaxy.eu, ADMET, Drug-likeness study, Molecular docking, Molecular dynamics, Rosmarinus officinalis L., SARS-CoV-2 Mpro}, + keywords = {{\textgreater}UseGalaxy.eu, ADMET, COVID-19, Drug-likeness study, Molecular docking, Molecular dynamics, Rosmarinus, Rosmarinus officinalis L., SARS-CoV-2 Mpro}, language = {en}, month = {April}, number = {5}, @@ -10875,13 +17641,49 @@ @article{patel_bioprospecting_2023 year = {2023} } +@phdthesis{patil_investigating_2025, + abstract = {How a circuit functions can be investigated by examining the organisation of the circuit to be able to decipher the connectivity logic and the logic of information flow within that circuit. Hence, to understand how the sparse coding of the Kenyon cells (KCs) is wired into the circuit, the organisational logic must be resolved. To that effect, a major question emerges - how do KCs find their synaptic partners during development?{\textless}br /{\textgreater} +This thesis aims to answer that question by taking advantage of available transcriptomic datasets (Alyagor et al. 2018; Li et al. 2020; Li et al. 2017; Xie et al. 2021) and focusing on the possible role of cell surface molecules in circuit assembly by means of RNAi-mediated knockdown in the PNs and KC. The effect of the knockdown was analysed by measuring number and distribution of PN boutons, calyx organisation and synapse formation. Based on this primary RNAi screen, candidate molecules that displayed circuit defects in the calyx were isolated and examined for the pattern of expression, the mutant phenotype and its cell autonomy in order to elucidate the role the molecules play in the development of the calyx. In addition, a method for in vivo imaging of the pupa was developed to be able to image developmental milestones in the context of normal development as well as mutants.{\textless}br /{\textgreater} +With this work, we hope to shed light in understanding how the non-stereotypical circuit of the calyx is assembled during development.}, + author = {Patil, Komal B.}, + copyright = {In Copyright}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {March}, + note = {Accepted: 2025-03-11T09:46:02Z}, + school = {Universitäts- und Landesbibliothek Bonn}, + title = {Investigating the molecular mechanisms involved in the developmental assembly of the mushroom body calyx in {\textless}em{\textgreater}{Drosophila} melanogaster{\textless}/em{\textgreater}}, + type = {Thesis}, + url = {https://bonndoc.ulb.uni-bonn.de/xmlui/handle/20.500.11811/12894}, + urldate = {2025-03-29}, + year = {2025} +} + +@article{paula_complete_2024, + abstract = {Carnivorous sponges (Porifera, Demospongiae, Cladorhizidae), contrary to the usual filter-feeding mechanism of sponges, are specialized in catching larger prey through adhesive surfaces or hook-like spicules. The mitochondrial DNA of sponges overall present several divergences from other metazoans, and while presenting unique features among major transitions, such as in calcarean and glass sponges, poriferan mitogenomes are relatively stable within their groups. Here, we report and discuss the mitogenome of Lycopodina hypogea (Vacelet \& Boury-Esnault, 1996), which greatly vary from its subordinal counterparts in both structure and gene order. This mitogenome is seemingly multipartite into three chromosomes, two of them as microDNAs. The main chromosome, chrM1, is unusually large, 31,099 bp in length, has a unique gene order within Poecilosclerida, and presents two rRNA, 13 protein and 19 tRNA coding genes. Intergenic regions comprise approximately 40\% of chrM1, bearing several terminal direct and inverted repeats (TDRr and TIRs) but holding no vestiges of former mitochondrial sequences, pseudogenes, or transposable elements. The nd4l and trnI(gau) genes are likely located in microDNAs thus comprising putative mitochondrial chromosomes chrM2, 291 bp, and chrM3, 140 bp, respectively. It is unclear which processes are responsible for the remarkable features of the of L. hypogea mitogenome, including a generalized gene rearrangement, long IGRs, and putative extrachromosomal genes in microDNAs.}, + author = {Paula, Thiago Silva de and Leite, Dora de Moura Barbosa and Lobo-Hajdu, Gisele and Vacelet, Jean and Thompson, Fabiano and Hajdu, Eduardo}, + doi = {10.7717/peerj.18255}, + issn = {2167-8359}, + journal = {PeerJ}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {November}, + note = {Publisher: PeerJ Inc.}, + pages = {e18255}, + title = {The complete mitochondrial {DNA} of the carnivorous sponge {Lycopodina} hypogea is putatively complemented by {microDNAs}}, + url = {https://peerj.com/articles/18255}, + urldate = {2025-09-03}, + volume = {12}, + year = {2024} +} + @article{pauleikhoff_transcriptional_2023, abstract = {Retinal neovascularization (RNV) is the leading cause of vision loss in diseases like proliferative diabetic retinopathy (PDR). A significant failure rate of current treatments indicates the need for novel treatment targets. Animal models are crucial in this process, but current diabetic retinopathy models do not develop RNV. Although the nondiabetic oxygen-induced retinopathy (OIR) mouse model is used to study RNV development, it is largely unknown how closely it resembles human PDR. We therefore performed RNA sequencing on murine (C57BL/6J) OIR retinas (n = 14) and human PDR RNV membranes (n = 7) extracted during vitrectomy, each with reference to control tissue (n=13/10). Differentially expressed genes (DEG) and associated biological processes were analyzed and compared between human and murine RNV to assess molecular overlap and identify phylogenetically conserved factors. In total, 213 murine- and 1223 human-specific factors were upregulated with a small overlap of 94 DEG (7\% of human DEG), although similar biological processes such as angiogenesis, regulation of immune response, and extracellular matrix organization were activated in both species. Phylogenetically conserved mediators included ANGPT2, S100A8, MCAM, EDNRA, and CCR7. Even though few individual genes were upregulated simultaneously in both species, similar biological processes appeared to be activated. These findings demonstrate the potential and limitations of the OIR model to study human PDR and identify phylogenetically conserved potential treatment targets for PDR.}, author = {Pauleikhoff, Laurenz and Boneva, Stefaniya and Boeck, Myriam and Schlecht, Anja and Schlunck, Günther and Agostini, Hansjürgen and Lange, Clemens and Wolf, Julian}, doi = {10.1167/iovs.64.15.46}, issn = {1552-5783}, journal = {Investigative Ophthalmology \& Visual Science}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Diabetic Retinopathy, Retinal Diseases, Retinal Neovascularization}, month = {December}, number = {15}, pages = {46}, @@ -10933,6 +17735,26 @@ @article{pelos_fast_2023 year = {2023} } +@article{penaranda_dna_2025, + abstract = {Ribosome assembly is a multistep process that ensures a functional ribosome structure. The molecular mechanism that ribosome­associated GTPases (RA­GTPases) use to enhance ribosome assembly accuracy remains largely to be elucidated. Here, we use systematic evolution of ligands by exponential enrichment (SELEX), followed by sequencing, comprehensive bioinformatics analysis, and biochemical characterization to identify aptamers that target the RA-GTPase ERA of Staphylococcus aureus. ELONA and thermophoresis assays show that the AptERA 2 interaction with ERA is in the 200 nM range of affinity, displays a high level of specificity, and depends on the target structure. Docking to ERA suggests that AptERA 2 interacts with the protein’s KH domain, consistent with the aptamer’s similarities with helix 45 of the 16S rRNA. AptERA 2 did interact with the isolated KH domain but did not bind to the ∆KH ERA nor to the similar RA-GTPase RbgA, which shares the GTPase core but lacks the KH domain, confirming that the aptamer recognizes and binds the KH domain of ERA. This interaction leads to a significant reduction of 30S-dependent GTP hydrolysis, indicative of allosteric modulation of the enzyme activity or limiting ERA binding or the KH domain interaction with the 3’ end of the 16S rRNA rather than directly blocking GTP binding. Altogether, this work highlights the versatility of aptamers as tools to understand the complex processes of ribosome biogenesis further, offering new insights into bacterial protein synthesis mechanisms.}, + author = {Peñaranda, Katherin and Pereira, Nicolle and Savva, Orestis and Petrelli, Dezemona and Spurio, Roberto and Corrigan, Rebecca M. and Milon, Pohl}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-15180-9}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Biochemistry, Biological techniques, Biotechnology, Molecular biology}, + language = {en}, + month = {August}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {30879}, + title = {{DNA} aptamer {AptERA} 2 targets {ERA} from {Staphylococcus} aureus and limits {GTP} hydrolysis}, + url = {https://www.nature.com/articles/s41598-025-15180-9}, + urldate = {2025-09-03}, + volume = {15}, + year = {2025} +} + @article{peresh_carbon_2024, abstract = {Carbon quantum dots (CQDs) are promising therapeutic agent due to their pro-oxidant, antioxidant, antiviral, antibacterial, and anticancer properties when exposed to visible light irradiation. Oxidative stress in bacteria is the main reason for bacteria death after exposure to blue light photoexcited quantum dots. Herein, we present the antibacterial activities of hydrophobic carbon quantum dots/polydimethylsiloxane nanocomposites, hydrophilic citric acid CQDs, and combinations of CQDs with methylene blue. We investigated the antirickettsial effect of hydrophilic and hydrophobic CQDs against Rickettsia slovaca, a tick-borne bacterial pathogen. Photodynamic activity against on rickettsiae reached 99.66\% using CQDs with 470 nm blue light irradiation. Combining methylene blue with CQDs further enhanced the effect on rickettsial infection, achieving 99,98\% efficacy. The obtained results reveal the in vitro antirickettsial properties of CQDs. Sequencing analysis on the genomic level of control and treated samples showed single nucleotide variants (SNVs). Based on snippy analysis SNVs were assigned to the rRNA genes, 16S rRNA and 30S rRNA genes. By freebayes analysis in treated samples, a stop-lost mutation was detected in pseudogene (RSL\_RS06070), while the possible effect on down-stream genes including tsaD, acyl-CoA-desaturase, 30S ribosomal protein S6 and DUF424 family protein. The frameshift mutation was localized within clpB pseudogene belonging to stress-response heat-shock proteins.}, author = {Peresh, Yevheniy-Yuliy and Šoltys, Katarína and Kľúčár, Ľuboš and Beke, Gábor and Kováčová, Mária and Špitalský, Zdenko and Špitalská, Eva}, @@ -10955,7 +17777,7 @@ @article{perez-schindler_characterization_2022 doi = {10.1038/s41598-022-15731-4}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, Cell biology, Genetics, Molecular biology, Molecular medicine}, + keywords = {{\textgreater}UseGalaxy.eu, Cell biology, Genetics, Molecular biology, Molecular medicine, Non-alcoholic Fatty Liver Disease}, language = {en}, month = {July}, note = {Number: 1 @@ -10981,9 +17803,13 @@ @article{perez-schindler_discovery_2021 } @article{perez-schindler_rna-bound_2021, + abstract = {Plasticity of cells, tissues, and organs is controlled by the coordinated transcription of biological programs. However, the mechanisms orchestrating such context-specific transcriptional networks mediated by the dynamic interplay of transcription factors and coregulators are poorly understood. The peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) is a prototypical master regulator of adaptive transcription in various cell types. We now uncovered a central function of the C-terminal domain of PGC-1α to bind RNAs and assemble multiprotein complexes including proteins that control gene transcription and RNA processing. These interactions are important for PGC-1α recruitment to chromatin in transcriptionally active liquid-like nuclear condensates. Notably, such a compartmentalization of active transcription mediated by liquid-liquid phase separation was observed in mouse and human skeletal muscle, revealing a mechanism by which PGC-1α regulates complex transcriptional networks. These findings provide a broad conceptual framework for context-dependent transcriptional control of phenotypic adaptations in metabolically active tissues.}, author = {Pérez-Schindler, Joaquín and Kohl, Bastian and Schneider-Heieck, Konstantin and Leuchtmann, Aurel B. and Henríquez-Olguín, Carlos and Adak, Volkan and Maier, Geraldine and Delezie, Julien and Sakoparnig, Thomas and Vargas-Fernández, Elyzabeth and Karrer-Cardel, Bettina and Ritz, Danilo and Schmidt, Alexander and Hondele, Maria and Jensen, Thomas E. and Hiller, Sebastian and Handschin, Christoph}, doi = {10.1073/pnas.2105951118}, + issn = {0027-8424}, + journal = {Proc Natl Acad Sci U S A}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {August}, note = {Publisher: Proceedings of the National Academy of Sciences}, number = {36}, @@ -10994,6 +17820,17 @@ @article{perez-schindler_rna-bound_2021 year = {2021} } +@article{perez-sisques_deficiency_2024, + abstract = {Loss-of-function mutations in genes encoding lysine methyltransferases (KMTs) and demethylases (KDMs) responsible for regulating the trimethylation of histone 3 on lysine 4 (H3K4me3) are associated with neurodevelopmental conditions, including autism spectrum disorder and intellectual disability. To study the specific role of H3K4me3 demethylation, we investigated neurodevelopmental phenotypes in mice without KDM5B demethylase activity. These mice exhibited autism-like behaviours and increased brain size. H3K4me3 levels and the expression of neurodevelopmental genes were increased in the developing Kdm5b mutant neocortex. These included elevated expression of Grin2d . The Grin2d gene product NMDAR2D was increased in synaptosomes isolated from the Kdm5b -deficient neocortex and treating mice with the NMDAR antagonist memantine rescued deficits in ultrasonic vocalisations and reduced repetitive digging behaviours. These findings suggest that increased H3K4me3 levels and associated Grin2d gene upregulation disrupt brain development and function, leading to socio-communication deficits and repetitive behaviours, and identify a potential therapeutic target for neurodevelopmental disorders associated with KDM5B deficiency.}, + author = {Pérez-Sisqués, Leticia and Bhatt, Shail and Caruso, Angela and Ahmed, Mohi and Gileadi, Talia and Spring, Shoshana and Hendy, Eleanor and Taylor-Papadimitriou, Joyce and Cash, Diana and Clifton, Nicholas and Ellegood, Jacob and Andreae, Laura and Lerch, Jason and Scattoni, Maria Luisa and Giese, Peter and Fernandes, Cathy and Basson, Albert}, + doi = {10.1101/2024.05.28.596232}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Deficiency of the histone lysine demethylase {KDM5B} causes autism-like phenotypes via increased {NMDAR} signalling}, + url = {http://europepmc.org/abstract/PPR/PPR859099}, + year = {2024} +} + @article{perez-sisques_intellectual_2024, abstract = {The histone lysine demethylase KDM5B is implicated in recessive intellectual disability disorders, and heterozygous, protein-truncating variants in KDM5B are associated with reduced cognitive function in the population. The KDM5 family of lysine demethylases has developmental and homeostatic functions in the brain, some of which appear to be independent of lysine demethylase activity. To determine the functions of KDM5B in hippocampus-dependent learning and memory, we first studied male and female mice homozygous for a Kdm5bΔARID allele that lacks demethylase activity. Kdm5bΔARID/ΔARID mice exhibited hyperactivity and long-term memory deficits in hippocampus-dependent learning tasks. The expression of immediate early, activity-dependent genes was downregulated in these mice and hyperactivated upon a learning stimulus compared with wild-type (WT) mice. A number of other learning-associated genes were also significantly dysregulated in the Kdm5bΔARID/ΔARID hippocampus. Next, we knocked down Kdm5b specifically in the adult, WT mouse hippocampus with shRNA. Kdm5b knockdown resulted in spontaneous seizures, hyperactivity, and hippocampus-dependent long-term memory and long-term potentiation deficits. These findings identify KDM5B as a critical regulator of gene expression and synaptic plasticity in the adult hippocampus and suggest that at least some of the cognitive phenotypes associated with KDM5B gene variants are caused by direct effects on memory consolidation mechanisms.}, author = {Pérez-Sisqués, Leticia and Bhatt, Shail U. and Matuleviciute, Rugile and Gileadi, Talia E. and Kramar, Eniko and Graham, Andrew and Garcia, Franklin G. and Keiser, Ashley and Matheos, Dina P. and Cain, James A. and Pittman, Alan M. and Andreae, Laura C. and Fernandes, Cathy and Wood, Marcelo A. and Giese, K. Peter and Basson, M. Albert}, @@ -11001,12 +17838,13 @@ @article{perez-sisques_intellectual_2024 doi = {10.1523/JNEUROSCI.1544-23.2024}, issn = {0270-6474, 1529-2401}, journal = {Journal of Neuroscience}, - keywords = {{\textgreater}UseGalaxy.eu, KDM5B, chromatin, hippocampus, histone lysine demethylase, learning, memory, mouse}, + keywords = {{\textgreater}UseGalaxy.eu, Hippocampus, Intellectual Disability, Jumonji Domain-Containing Histone Demethylases, KDM5B, Memory Consolidation, Memory, Long-Term, chromatin, hippocampus, histone lysine demethylase, learning, memory, mouse}, language = {en}, month = {May}, note = {Publisher: Society for Neuroscience Section: Research Articles}, number = {19}, + pages = {e1544232024}, pmid = {38575342}, title = {The {Intellectual} {Disability} {Risk} {Gene} {Kdm5b} {Regulates} {Long}-{Term} {Memory} {Consolidation} in the {Hippocampus}}, url = {https://www.jneurosci.org/content/44/19/e1544232024}, @@ -11042,7 +17880,7 @@ @article{perezriverol_scalable_2019 doi = {10.1002/pmic.201900147}, issn = {1615-9861}, journal = {PROTEOMICS}, - keywords = {+Galactic, +IsGalaxy, +RefPublic, +Reproducibility, +Tools, {\textgreater}Galaxy-P, {\textgreater}PhenoMeNal, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}Workflow4Metabolomics}, + keywords = {+Galactic, +IsGalaxy, +RefPublic, +Reproducibility, +Tools, {\textgreater}Galaxy-P, {\textgreater}PhenoMeNal, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}Workflow4Metabolomics, Software}, language = {en}, month = {October}, number = {n/a}, @@ -11096,18 +17934,42 @@ @article{pessoa_rodrigues_histone_2021 } @article{peters_metabolic_2021, + abstract = {Chronic diseases affecting the central nervous system (CNS) like Alzheimer's or Parkinson's disease typically develop with advanced chronological age. Yet, aging at the metabolic level has been explored only sporadically in humans using biofluids in close proximity to the CNS such as the cerebrospinal fluid (CSF). We have used an untargeted liquid chromatography high-resolution mass spectrometry (LC-HRMS) based metabolomics approach to measure the levels of metabolites in the CSF of non-neurological control subjects in the age of 20 up to 74. Using a random forest-based feature selection strategy, we extracted 69 features that were strongly related to age (p$_{\textrm{age}}$ {\textless} 0.001, r$_{\textrm{age}}$ = 0.762, R$^{\textrm{2}}$$_{\textrm{Boruta age}}$ = 0.764). Combining an in-house library of known substances with in silico chemical classification and functional semantic annotation we successfully assigned putative annotations to 59 out of the 69 CSF metabolites. We found alterations in metabolites related to the Cytochrome P450 system, perturbations in the tryptophan and kynurenine pathways, metabolites associated with cellular energy (NAD+, ADP), mitochondrial and ribosomal metabolisms, neurological dysfunction, and an increase of adverse microbial metabolites. Taken together our results point at a key role for metabolites found in CSF related to the Cytochrome P450 system as most often associated with metabolic aging.}, author = {Peters, Kristian and Herman, Stephanie and Khoonsari, Payam Emami and Burman, Joachim and Neumann, Steffen and Kultima, Kim}, doi = {10.1038/s41598-021-97491-1}, + issn = {2045-2322}, + journal = {Scientific reports}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {September}, note = {Publisher: Springer Science and Business Media LLC}, number = {1}, + pages = {18822}, title = {Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid}, url = {https://doi.org/10.1038/s41598-021-97491-1}, volume = {11}, year = {2021} } +@article{petroll_enhanced_2025, + abstract = {Transcription-associated proteins (TAPs) fulfill multiple functions in regulatory and developmental processes and display lineage-specific evolution. TAPscan is a comprehensive and highly reliable tool for genome-wide TAP annotation via domain profiles. Here, we present TAPscan v4, including an updated web interface (https://tapscan.plantcode.cup.uni-freiburg.de/), which enables an in-depth representation of the distribution of 138 TAP families across 678 species from diverse groups of organisms, with a focus on Archaeplastida (plants in the wide sense). With this release, we also make the underlying “Genome Zoo” available, a curated protein data set with scripts and metadata. Eighteen new TAP (sub)families were added as part of the update. Nine of those were gained in the most recent common ancestor of the Streptophyta (comprising streptophyte algae and land plants), or within the streptophyte algae. More than one-third of all detected TAP family gains were identified during the evolution of streptophyte algae, before the emergence of land plants, and are thus likely to have been significant for plant terrestrialization. The TAP complement of the Zygnematophyceae was identified to be the most similar to that of land plants, consistent with the finding that this lineage is sister to land plants. Overall, our data retrace the evolution of streptophyte TAPs, allowing us to pinpoint the regulatory repertoire of the earliest land plants.}, + author = {Petroll, Romy and Varshney, Deepti and Hiltemann, Saskia and Finke, Hermann and Schreiber, Mona and de Vries, Jan and Rensing, Stefan A.}, + copyright = {© 2024 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.}, + doi = {10.1111/tpj.17184}, + issn = {1365-313X}, + journal = {The Plant Journal}, + keywords = {{\textgreater}UseGalaxy.eu, Evolution, Molecular, Streptophyte algae, Transcription Factors, annotation, evolution, terrestrialization, transcription factor}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.17184}, + number = {1}, + pages = {e17184}, + title = {Enhanced sensitivity of {TAPscan} v4 enables comprehensive analysis of streptophyte transcription factor evolution}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.17184}, + urldate = {2025-02-16}, + volume = {121}, + year = {2025} +} + @article{pfaffle_14-day_2024, abstract = {Despite substantial heterogeneity of studies, there is evidence that antibiotics commonly used in primary care influence the composition of the gastrointestinal microbiota in terms of changing their composition and/or diversity. Benzyl isothiocyanate (BITC) from the food and medicinal plant nasturtium (Tropaeolum majus) is known for its antimicrobial activity and is used for the treatment of infections of the draining urinary tract and upper respiratory tract. Against this background, we raised the question of whether a 14 d nasturtium intervention (3 g daily, N = 30 healthy females) could also impact the normal gut microbiota composition. Spot urinary BITC excretion highly correlated with a weak but significant antibacterial effect against Escherichia coli. A significant increase in human beta defensin 1 as a parameter for host defense was seen in urine and exhaled breath condensate (EBC) upon verum intervention. Pre-to-post analysis revealed that mean gut microbiome composition did not significantly differ between groups, nor did the circulating serum metabolome. On an individual level, some large changes were observed between sampling points, however. Explorative Spearman rank correlation analysis in subgroups revealed associations between gut microbiota and the circulating metabolome, as well as between changes in blood markers and bacterial gut species.}, author = {Pfäffle, Simon P. and Herz, Corinna and Brombacher, Eva and Proietti, Michele and Gigl, Michael and Hofstetter, Christoph K. and Mittermeier-Kleßinger, Verena K. and Claßen, Sophie and Tran, Hoai T. T. and Dawid, Corinna and Kreutz, Clemens and Günther, Stefan and Lamy, Evelyn}, @@ -11115,7 +17977,7 @@ @article{pfaffle_14-day_2024 doi = {10.3390/nu16030373}, issn = {2072-6643}, journal = {Nutrients}, - keywords = {\textit{Escherichia coli}, {\textgreater}UseGalaxy.eu, BITC, antimicrobial, gut microbiome, human beta defensin 1, metabolome, nasturtium}, + keywords = {\textit{Escherichia coli}, {\textgreater}UseGalaxy.eu, BITC, Gastrointestinal Microbiome, Nasturtium, Tropaeolum, antimicrobial, gut microbiome, human beta defensin 1, metabolome, nasturtium}, language = {en}, month = {January}, note = {Number: 3 @@ -11135,14 +17997,17 @@ @article{pham_epigenetic_2024 doi = {10.1038/s44321-024-00152-9}, issn = {1757-4676}, journal = {EMBO Molecular Medicine}, - keywords = {{\textgreater}UseGalaxy.eu, CBX7, Cerebral Cavernous Malformation, KLF2, WNT9, endoMT}, + keywords = {{\textgreater}UseGalaxy.eu, CBX7, Cerebral Cavernous Malformation, Epigenesis, Genetic, Hemangioma, Cavernous, Central Nervous System, KLF2, Polycomb Repressive Complex 1, WNT9, Zebrafish, Zebrafish Proteins, endoMT}, + language = {eng}, month = {October}, note = {Num Pages: 29 Publisher: Springer Nature}, + number = {11}, pages = {1--29}, title = {Epigenetic regulation by polycomb repressive complex 1 promotes cerebral cavernous malformations}, url = {https://www.embopress.org/doi/full/10.1038/s44321-024-00152-9}, urldate = {2024-10-20}, + volume = {16}, year = {2024} } @@ -11182,6 +18047,23 @@ @article{phillip_molecular_2023 year = {2023} } +@article{phumthanakorn_prevalence_2025, + abstract = {In Thailand, small- to medium-scale (SM) dairy farms typically have fewer than 100 cows. They are often family-owned or independently operated, and vary in infrastructure and mechanization depending on their size. In contrast, large-scale (L) farms, with more than 100 cows, are more industrialized, utilizing advanced technology, higher production systems, and usually employ multiple workers. To date, few studies have reported the prevalence of methicillin-resistant staphylococci (MRS) and methicillin-susceptible staphylococci (MSS) and their antimicrobial resistance (AMR) at different farm scales. This study aimed to investigate the prevalence of Staphylococcus spp., MRS, MSS and their AMR as well as their genetic backgrounds on SM and L dairy farms in Thailand. A total of 157 mastitis milk samples were collected from 106 cows on 42 SM farms, and 65 samples from 37 cows on one L farm, all located in Kanchanaburi Province. Antimicrobial susceptibility testing was conducted by determining the minimum inhibitory concentration. Whole-genome sequencing and analysis were performed for genetic characterization. There was a significant difference in the prevalence of Staphylococcus spp. on L farm (26.2\%) and SM farms (14\%) (P = 0.031, χ² test). The phenotypic resistance of trimethoprim/sulfamethoxazole in L farm (58.8\%) was significantly greater than that in SM farms (27.3\%) (P = 0.049, χ² test). Six methicillin-resistant staphylococci (27.3\%), including Staph. haemolyticus sequence type (ST) 3 (N=1) and ST42 (N=3) and Staph. epidermidis ST59 (N=2) were discovered on SM farms, whereas a single Staph. aureus ST398 (5.9\%, N=1) was found on an L farm. These strains were multidrug-resistant and carried multiple, diverse antimicrobial resistance genes, including β-lactam resistance genes (mecA, blaZ), tetracycline resistance genes [tet(K), tet(M)], and macrolide resistance genes [msr(A), mph(C)]. Compared with MRS, MSS carried fewer diverse antimicrobial resistance genes and had distinct STs at both farm scales. At each farm scale, a particular type of resistance may originate from a certain species or specific ST. In conclusion, the prevalence of Staphylococcus spp. and their resistance traits and genetic background on SM and L farms differ according to different production farm scales. The specific management and monitoring of the information on Staphylococcus spp. circulated on each farm type could help to limit the spread of antimicrobial-resistant staphylococci.}, + author = {Phumthanakorn, Nathita and Thanasak, Jitkamol}, + doi = {10.1093/tas/txaf081}, + issn = {2573-2102}, + journal = {Translational Animal Science}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {June}, + pages = {txaf081}, + title = {Prevalence and {Antimicrobial} {Resistance} of {Methicillin}-{Resistant} and {Methicillin}-{Susceptible} {Staphylococcus} in {Small}- to {Medium}-{Scale} and {Large}-{Scale} {Dairy} {Farms} in {Thailand}}, + url = {https://doi.org/10.1093/tas/txaf081}, + urldate = {2025-07-12}, + volume = {9}, + year = {2025} +} + @article{pick_complete_2024, author = {Pick, Kat and Stothard, Paul and Raivio, Tracy L.}, doi = {10.1128/mra.01216-23}, @@ -11204,7 +18086,7 @@ @article{pietroforte_meiotic_2024 doi = {10.1007/s10815-024-03160-3}, issn = {1573-7330}, journal = {Journal of Assisted Reproduction and Genetics}, - keywords = {{\textgreater}UseGalaxy.eu, Bovine, Meiosis, Oocyte, Oocyte competence, Primary ovarian insufficiency, Transcriptome}, + keywords = {{\textgreater}UseGalaxy.eu, Bovine, Meiosis, Oocyte, Oocyte competence, Oocytes, Primary Ovarian Insufficiency, Primary ovarian insufficiency, Transcriptome}, language = {en}, month = {August}, number = {8}, @@ -11217,6 +18099,39 @@ @article{pietroforte_meiotic_2024 year = {2024} } +@article{pilla_virulence_2022, + abstract = {\textit{Shigella flexneri} is a major health burden in low- and middle-income countries, where it is a leading cause of mortality associated with diarrhoea in children, and shows an increasing incidence among travellers and men having sex with men. Like all \textit{Shigella} spp., \textit{S. flexneri} has evolved from commensal \textit{Escherichia coli} following the acquisition of a large plasmid pINV, which contains genes essential for virulence. Current sequence typing schemes of \textit{Shigella} are based on combinations of chromosomal genetic loci, since pINV-encoded virulence genes are often lost during growth in the laboratory, making these elements inappropriate for sequence typing. By performing comparative analysis of pINVs from \textit{S. flexneri} strains isolated from different geographical regions and belonging to different serotypes, we found that in contrast to plasmid-encoded virulence genes, plasmid maintenance genes are highly stable pINV-encoded elements. For the first time, to our knowledge, we have developed a \textit{S. flexneri} plasmid multilocus sequence typing (pMLST) method based on different combinations of alleles of the \textit{vapBC} and \textit{yacAB} toxin-antitoxin (TA) systems, and the \textit{parAB} partitioning system. This enables typing of \textit{S. flexneri} pINV plasmids into distinct 'virulence sequence types' (vSTs). Furthermore, the phylogenies of vST alleles and bacterial host core genomes suggests an intimate co-evolution of pINV with the chromosome of its bacterial host, consistent with previous findings. This work demonstrates the potential of plasmid maintenance loci as genetic characteristics to study as well as to trace the molecular phylogenesis of \textit{S. flexneri} pINV and the phylogenetic relationship of this plasmid with its bacterial host.}, + author = {Pilla, Giulia and Arcari, Gabriele and Tang, Christoph M and Carattoli, Alessandra}, + doi = {10.1099/mgen.0.000846}, + issn = {2057-5858}, + journal = {Microb Genom}, + keywords = {{\textgreater}UseGalaxy.eu, Shigella, Shigella flexneri}, + language = {eng}, + month = {June}, + number = {6}, + title = {Virulence plasmid {pINV} as a genetic signature for \textit{{Shigella} flexneri} phylogeny}, + url = {http://europepmc.org/abstract/MED/35759406}, + volume = {8}, + year = {2022} +} + +@article{pilliol_candidatus_2024, + abstract = {\textit{Methanosphaera stadtmanae} was the sole \textit{Methanosphaera} representative to be cultured and detected by molecular methods in the human gut microbiota, further associated with digestive and respiratory diseases, leaving unknown the actual diversity of human-associated \textit{Methanosphaera} species. Here, a novel \textit{Methanosphaera} species, \textit{Candidatus} Methanosphaera massiliense (\textit{Ca}. M. massiliense) sp. nov. was isolated by culture using a hydrogen- and carbon dioxide-free medium from one human feces sample. \textit{Ca}. M. massiliense is a non-motile, 850 nm Gram-positive coccus autofluorescent at 420 nm. Whole-genome sequencing yielded a 29.7\% GC content, gapless 1,785,773 bp genome sequence with an 84.5\% coding ratio, encoding for alcohol and aldehyde dehydrogenases promoting the growth of \textit{Ca}. M. massiliense without hydrogen. Screening additional mammal and human feces using a specific genome sequence-derived DNA-polymerase RT-PCR system yielded a prevalence of 22\% in pigs, 12\% in red kangaroos, and no detection in 149 other human samples. This study, extending the diversity of \textit{Methanosphaera} in human microbiota, questions the zoonotic sources of \textit{Ca}. M. massiliense and possible transfer between hosts.IMPORTANCEMethanogens are constant inhabitants in the human gut microbiota in which \textit{Methanosphaera stadtmanae} was the only cultivated \textit{Methanosphaera} representative. We grew \textit{Candidatus} Methanosphaera massiliense sp. nov. from one human feces sample in a novel culture medium under a nitrogen atmosphere. Systematic research for methanogens in human and animal fecal samples detected \textit{Ca}. M. massiliense in pig and red kangaroo feces, raising the possibility of its zoonotic acquisition. Host specificity, source of acquisition, and adaptation of methanogens should be further investigated.}, + author = {Pilliol, Virginie and Morsli, Madjid and Terlier, Laureline and Hassani, Yasmine and Malat, Ihab and Guindo, Cheick Oumar and Davoust, Bernard and Lamglait, Benjamin and Drancourt, Michel and Aboudharam, Gérard and Grine, Ghiles and Terrer, Elodie}, + doi = {10.1128/spectrum.05141-22}, + issn = {2165-0497}, + journal = {Microbiol Spectr}, + keywords = {{\textgreater}UseGalaxy.eu, Macropodidae, Methanobacteriaceae}, + language = {eng}, + month = {February}, + number = {2}, + pages = {e0514122}, + title = {Candidatus {Methanosphaera} massiliense sp. nov., a methanogenic archaeal species found in a human fecal sample and prevalent in pigs and red kangaroos}, + url = {http://europepmc.org/abstract/MED/38189277}, + volume = {12}, + year = {2024} +} + @article{pilliol_methanobrevibacter_2024, abstract = {Among oral microbiota methanogens, Methanobrevibacter massiliense (M. massiliense) has remained less studied than the well-characterised and cultivated methanogens Methanobrevibacter oralis and Methanobrevibacter smithii. M. massiliense has been associated with different oral pathologies and was co-isolated with the Synergistetes bacterium Pyramidobacter piscolens (P. piscolens) in one case of severe periodontitis. Here, reporting on two additional necrotic pulp cases yielded the opportunity to characterise two co-cultivated M. massiliense isolates, both with P. piscolens, as non-motile, 1–2-µm-long and 0.6–0.8-µm-wide Gram-positive coccobacilli which were autofluorescent at 420 nm. The two whole genome sequences featured a 31.3\% GC content, gapless 1,834,388-base-pair chromosome exhibiting an 85.9\% coding ratio, encoding a formate dehydrogenase promoting M. massiliense growth without hydrogen in GG medium. These data pave the way to understanding a symbiotic, transkingdom association with P. piscolens and its role in oral pathologies.}, author = {Pilliol, Virginie and Beye, Mamadou and Terlier, Laureline and Balmelle, Julien and Kacel, Idir and Lan, Romain and Aboudharam, Gérard and Grine, Ghiles and Terrer, Elodie}, @@ -11280,7 +18195,7 @@ @article{pinter_maxquant_2022 doi = {10.1021/acs.jproteome.2c00051}, issn = {1535-3893}, journal = {Journal of Proteome Research}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {+IsGalaxy, {\textgreater}UseGalaxy.eu}, month = {May}, note = {Publisher: American Chemical Society}, title = {{MaxQuant} and {MSstats} in {Galaxy} {Enable} {Reproducible} {Cloud}-{Based} {Analysis} of {Quantitative} {Proteomics} {Experiments} for {Everyone}}, @@ -11318,7 +18233,7 @@ @article{pirnay_personalized_2024 doi = {10.1038/s41564-024-01705-x}, issn = {2058-5276}, journal = {Nature Microbiology}, - keywords = {{\textgreater}UseGalaxy.eu, Antimicrobial resistance, Bacterial genetics, Bacterial infection, Bacteriophages}, + keywords = {{\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Antimicrobial resistance, Bacterial Infections, Bacterial genetics, Bacterial infection, Bacteriophages, Phage Therapy}, language = {en}, month = {June}, note = {Publisher: Nature Publishing Group}, @@ -11332,12 +18247,83 @@ @article{pirnay_personalized_2024 year = {2024} } +@misc{pishan_role_2025, + abstract = {The production rate of Polyethylene (PE), has escalated to a concerning level, necessitating the development of effective strategies to reduce its environmental consequences. This paper aims to investigate the role of LMCO1 in oxidative degradation of polyethylene, through comprehensive examination that includes machine learning analysis, recombinant expression, biochemical and biological assays. To do so, the available RNA-seq data related to Rhodococcus opacus R7 grown on PE was analysed using several attribute weighting algorithms to explore the discriminative role of LMCO1 in PE degradation. Further, the recombinant LMCO1 was evaluated and found to have a substantial degrading impact on the polyethylene films. The findings indicated that Cu²⁺ increased the activity of LMCO1 in the crude extract by 490\%, with peak activity occurring at a pH of 8 and an optimal temperature of 60°C. Oxidative degradation of PE samples was evaluated by measuring loss weight rate, assessment of water contact angle measuring, Fourier transform infrared spectroscopy and scanning electron microscopy analysis. The findings from the polyethylene degradation experiments conducted over 72 hours indicated that a weight loss rate of 17.11\% was observed in polyethylene, accompanied by a reduction in the water contact angle to 74.22°C. Fourier transform infrared spectroscopy analysis revealed the existence of various polar functional groups on the surface of polyethylene, such as carbonyl, carboxyl, and hydroxyl groups. Significant damage to the polyethylene surface, including cracks, pitting, and roughness, as well as internal aspects such as structural weakening and material degradation, was identified through scanning electron microscopy. Overall, this study presented the high potential of LMCO1 to degrade polyethylene film and particle in short time.}, + address = {Rochester, NY}, + author = {Pishan, Mahboobeh and Sazegari, Sima and Niazi, Ali and Majdinasab, Marjan and Zinati, Zahra and Eskandari, Mohammad Hadi}, + doi = {10.2139/ssrn.5280412}, + keywords = {{\textgreater}UseGalaxy.eu, Biodegradation, Polyethylene, Rhodococcus opacus R7, plastic waste}, + language = {en}, + month = {June}, + publisher = {Social Science Research Network}, + title = {The {Role} of {Rhodococcus} {Opacus} {R7} {Laccase}-{Like} {Multicopper} {Oxidase} ({Lmco1}) {Enzyme} {In} {Biodegradation} of {Polyethylene} {Polymer}}, + type = {{SSRN} {Scholarly} {Paper}}, + url = {https://papers.ssrn.com/abstract=5280412}, + urldate = {2025-07-12}, + year = {2025} +} + +@article{pitt_aquirufa_2025, + abstract = {Within a citizen science project, 112 freshwater habitats in Austria were sampled to get bacterial cultures belonging to the genus Aquirufa using a strategy for targeted isolation. We focused on these bacteria because they are widespread and represent typical freshwater bacteria and, furthermore, the typic red pigmentation facilitates preselection. Among the 113 obtained Aquirufa strains were HETE-83DT, KTFRIE-69FT, OSTEICH-129VT and PLAD-142S6KT, originating from small ponds and a creek. Phylogenetic reconstructions with 16S rRNA gene sequences and genome-based analyses with amino acid sequences of 501 core genes showed that all four strains belonged to the A. antheringensis branch of the genus Aquirufa. Calculation of whole-genome average nucleotide identity values and digital DNA-DNA hybridization values revealed that they represent in each case a new species. The genome sizes of the four strains were between 2.5 and 2.8 Mbp and the G + C values were between 41.4 and 41.8\%. Like all type strains of the genus Aquirufa, cells were rod-shaped, and liquid cultures and colonies on agar plates were red-pigmented, likely due to carotenoids. All strains except OSTEICH-129VT showed gliding motility on soft agar plates. All strains grew aerobically but only PLAD-142S6KT could grow weakly under anaerobic conditions. We propose here to establish the names Aquirufa esocilacus sp. nov. for strain HETE-83DT (= DSM 118087T = JCM 37094T), Aquirufa originis sp. nov. for KTFRIE-69FT (= DSM 117798T = JCM 37095T), Aquirufa avitistagni for OSTEICH-129VT (= DSM 118088T = JCM 37100T) and Aquirufa echingensis sp. nov. for PLAD-142S6KT (= DSM 117799T = JCM 37096T).}, + author = {Pitt, Alexandra and Lienbacher, Stefan and Schmidt, Johanna and Neumann-Schaal, Meina and Wolf, Jacqueline and Oren, Aharon and Reichl, Sophia and Hahn, Martin W.}, + doi = {10.1007/s00203-025-04275-6}, + issn = {1432-072X}, + journal = {Archives of Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Aquirufa, Citizen science, Fresh Water, Freshwater bacteria, Genome, Genome size, Spirosomataceae}, + language = {en}, + month = {February}, + number = {4}, + pages = {71}, + title = {Aquirufa esocilacus sp. nov., {Aquirufa} originis sp. nov., {Aquirufa} avitistagni, and {Aquirufa} echingensis sp. nov. discovered in small freshwater habitats in {Austria} during a citizen science project}, + url = {https://doi.org/10.1007/s00203-025-04275-6}, + urldate = {2025-02-28}, + volume = {207}, + year = {2025} +} + +@article{pitt_biodiversity_2025, + abstract = {During a citizen science project, four freshwater habitats in a riparian forest restoration area in Salzburg, Austria, were sampled. The primary aim was to obtain bacterial strains of the genus Aquirufa, a group of typical and widespread freshwater bacteria. Numerous pure cultures of Aquirufa strains could be obtained, three of them originating from the river Salzach, a newly created pond and the lake Ausee represented new species. Strain 1-SAACH-A3T was characterized by a genome size of 3.2 Mbp and a G + C value of 38.4 mol\% and encoded genes predicted for nitrate uptake and nitrous oxide utilization. Strains BAHN-186BT and 2-AUSEE-184A6 were characterized by a genome size of 2.4 Mbp and a G + C value of 42.4 and 42.2 mol\%, respectively, and encoded genes predicted for the light-harvesting rhodopsin system. Calculated whole-genome average nucleotide identity values with Aquirufa type strains resulted in a maximum value of 93.65\% for comparison of strain 1-SAACHT with the type strain of Aquirufa ecclesiirivi, which is slightly under the proposed threshold of species demarcation. The calculated gANI value comparing strains BAHN-186BT and 2-AUSEE-184A6 revealed 95.76\%, thus a value slightly above the threshold. Further analyses revealed that the three new strains represent two new species, proposed here as Aquirufa salirivi sp. nov. with type strain 1-SAACH-A3T (= DSM 117800 T = JCM 37097 T) and Aquirufa novilacunae sp. nov. with type strain BAHN-186BT (= DSM 118143 T = JCM 37099 T). Analyses of 123 publicly available metagenomes and a metagenome of the lake Ausee resulted in no detection of A. salirivi sp. nov. In contrast, A. novilacunae sp. nov. could be detected in 15 water samples of rivers, mainly from Asia, but also from North America and Australia. The analyses suggested that the species occurs in most of these samples in low relative abundance, detections derived from metagenomes of water samples from the river Yangtze in the subtropical zone could be interpreted as occurrence in higher abundances.}, + author = {Pitt, Alexandra and Lienbacher, Stefan and Schmidt, Johanna and Neumann-Schaal, Meina and Wolf, Jacqueline and Wenng, Hannah and Oren, Aharon and Huber, Zoe and Hahn, Martin W.}, + doi = {10.1007/s10123-025-00642-x}, + issn = {1618-1905}, + journal = {International Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Aquirufa, Citizen science, Freshwater bacteria, Genome size, Metagenome, Riparian forest, Spirosomataceae}, + language = {en}, + month = {February}, + title = {Biodiversity of strains belonging to the freshwater genus {Aquirufa} in a riparian forest restoration area in {Salzburg}, {Austria}, with a focus on the description of {Aquirufa} salirivi sp. nov. and {Aquirufa} novilacunae sp. nov}, + url = {https://doi.org/10.1007/s10123-025-00642-x}, + urldate = {2025-02-28}, + year = {2025} +} + +@article{plata_suarez_unlocking_2025, + abstract = {Phage therapy has emerged as a promising alternative for combating infections caused by drug-resistant pathogens. Among these, Enterococcus faecalis remains a significant public health concern due to its persistence in clinical settings and frequent involvement in healthcare-associated infections (HAIs). In this study, we report the characterization of the lytic bacteriophage vB\_EfaS\_LOK1, isolated from urban sewage using E. faecalis strain IIH-74.4 as the host. Transmission electron microscopy revealed morphological features consistent with the phages formerly classified within the Siphoviridae family. The phage exhibited high thermal and pH stability, remaining viable up to 70 °C and within a pH range of 4-11. It displayed a latent period of 20 min and a burst size of 72 PFU/cell. Notably, vB\_EfaS\_LOK1 exhibited a narrow host range, lysing only the strain used for their isolation. Genomic analysis revealed a 41.2 kb double-stranded DNA genome devoid of known virulence or antibiotic resistance genes. Phylogenomic analysis classified the phage within the genus Efquatrovirus (Caudoviricetes), suggesting it represents a newly isolated bacteriophage species. Functional annotation identified genes related to DNA replication, host interaction, and bacterial lysis, including endolysins and holins with putative antimicrobial properties. Long-term stability assays demonstrated that tryptic soy broth (TSB) with CaCl2/MgCl2 at 4 °C maintained viability for at least 90 days. Collectively, these findings support the potential of vB\_EfaS\_LOK1 as a potential candidate for the development of phage-based therapies targeting E. faecalis.}, + author = {Plata Suarez, Laura Marcela and Del Valle Balbuena, Salvador and Becerra Mejía, Isamar Leticia and Loera Piedra, Alejandra Aidee and Domínguez Espinoza, Cristina and Ángeles González, Arantxa Monserrat and Contreras Rodríguez, Araceli and Aquino Andrade, Alejandra and Martínez Díaz, Sergio Francisco and Aguilera Arreola, Ma Guadalupe}, + copyright = {cc by}, + doi = {10.3390/microorganisms13102414}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu, Antibiotic Resistance, Bacteriophages, Enterococcus Faecalis Phage, Phage Therapy, Phylogenomic Analysis, Whole Genome Sequencing}, + language = {eng}, + month = {October}, + number = {10}, + pages = {2414}, + pmcid = {PMC12566377}, + pmid = {41156872}, + shorttitle = {Unlocking the {Potential} of \<i\>{vB}\</i\>\_\<i\>{EfaS}\</i\>\_\<i\>{LOK1}\</i\>}, + title = {Unlocking the {Potential} of \<i\>{vB}\</i\>\_\<i\>{EfaS}\</i\>\_\<i\>{LOK1}\</i\>: {A} {Newly} {Isolated} {Bacteriophage} {Against} \<i\>{Enterococcus} faecalis\</i\>}, + url = {https://europepmc.org/articles/PMC12566377}, + urldate = {2025-12-26}, + volume = {13}, + year = {2025} +} + @article{plaza_genomic_2023, author = {Plaza, David Fernando and Zerebinski, Julia and Broumou, Ioanna and Lautenbach, Maximilian Julius and Ngasala, Billy and Sundling, Christopher and Färnert, Anna}, doi = {10.1016/j.crmeth.2023.100574}, issn = {2667-2375}, journal = {Cell Reports Methods}, - keywords = {{\textgreater}UseGalaxy.eu, CP: Biotechnology, CP: Microbiology, antigen discovery, circumsporozoite protein, genomic surveillance, glutamate-rich protein, long-read sequencing, malaria epidemiology, merozoite surface protein 1, merozoite surface protein 2}, + keywords = {{\textgreater}UseGalaxy.eu, CP: Biotechnology, CP: Microbiology, Malaria, Falciparum, Plasmodium, antigen discovery, circumsporozoite protein, genomic surveillance, glutamate-rich protein, long-read sequencing, malaria epidemiology, merozoite surface protein 1, merozoite surface protein 2}, language = {English}, month = {August}, note = {Publisher: Elsevier}, @@ -11349,6 +18335,22 @@ @article{plaza_genomic_2023 year = {2023} } +@article{plaza_protocol_2025, + abstract = {Here, we present a protocol that identifies and classifies structurally diverse variants of msp1, msp2, glurp, and csp in Plasmodium falciparum using an amplicon-based long-read sequencing platform. We describe steps for PCR barcoding, PacBio circular consensus sequencing (CCS), in silico PCR-based size variant calling, and advanced data analysis in Galaxy. By resolving full-length sequences for each antigenic clone, this approach measures infection complexity, constructs isolate phylogenies, and supports vaccine design. For complete details on the use and execution of this protocol, please refer to Plaza et al.\<sup\>1\</sup\>.}, + author = {Plaza, David Fernando}, + doi = {10.1016/j.xpro.2025.104093}, + issn = {2666-1667}, + journal = {STAR protocols}, + keywords = {{\textgreater}UseGalaxy.eu, Bioinformatics, Genomics, Microbiology, Molecular biology, Sequencing}, + month = {September}, + number = {4}, + pages = {104093}, + title = {Protocol for genomic surveillance of {Plasmodium} falciparum antigens using amplicon-based {PacBio} long-read sequencing}, + url = {https://europepmc.org/articles/PMC12464706}, + volume = {6}, + year = {2025} +} + @article{plazas_avila_introduccion_2023, abstract = {Desde el descubrimiento de la estructura del ácido desoxirribonucleico (ADN) por Watson, Crick y Franklin en 1953, la comunidad científica ha realizado continuos esfuerzos para secuenciar el ADN. La primera tecnología de Sanger era increíblemente precisa, pero requería mucho tiempo de preparación, lo que aumentaba el coste del proceso y de los secuenciadores. Sin embargo, la secuenciación del ADN ha avanzado mucho desde Sanger. Las tecnologías de secuenciación de nueva generación (NGS) consiguieron reducir drásticamente el coste del procesado y aumentaron el rendimiento por muestra, pero no el coste de los secuenciadores. En este sentido, la secuenciación genómica de tercera generación Nanopore ha revolucionado el mercado debido a su bajo coste, alta repetibilidad y facilidad de preparación de muestras. En especial, el secuenciador MinION desarrollado por Oxford Nanopore Technologies es un dispositivo económico, portátil y de mecanismo sencillo para la secuenciación de ADN en tiempo real. En este artículo proponemos un modelo que une conceptos experimentales y bioinformáticos utilizando el MinION para determinar el perfil microbiano de diferentes muestras de suelo gracias a las regiones conservadas y variables del gen ARNr 16S.}, author = {Plazas Ávila, María de la O. and Arrones Olmo, Andrea and Vilanova Navarro, Santiago}, @@ -11365,13 +18367,30 @@ @article{plazas_avila_introduccion_2023 year = {2023} } +@article{polisetti_transcriptomic_2022, + abstract = {Limbal stem cell deficiency (LSCD) is a complex, multifactorial disease affecting limbal epithelial progenitor cells (LEPC), which are essential for maintaining corneal stability and transparency. Human induced pluripotent stem cell-derived (hiPSC-) LEPC are a promising cell source for the treatment of LSCD. However, their similarity to native tissue-derived (T-) LEPC and their functional characterization has not been studied in detail. Here, we show that hiPSC-LEPC and T-LEPC have rather similar gene expression patterns, colony-forming ability, wound-healing capacity, and melanosome uptake. In addition, hiPSC-LEPC exhibited lower immunogenicity and reduced the proliferation of peripheral blood mononuclear cells compared with T-LEPC. Similarly, the hiPSC-LEPC secretome reduced the proliferation of vascular endothelial cells more than the T-LEPC secretome. Moreover, hiPSC-LEPC successfully repopulated decellularized human corneolimbal (DHC/L) scaffolds with multilayered epithelium, while basal deposition of fibrillary material was observed. These findings suggest that hiPSC-LEPC exhibited functional properties close to native LEPC and that hiPSC-LEPC-DHC/L scaffolds might be feasible for transplantation in patients suffering from LSCD in the future. Although hiPSC-LEPC-based stem cell therapy is promising, the current study also revealed new challenges, such as abnormal extracellular matrix deposition, that need to be overcome before hiPSC-LEPC-based stem cell therapies are viable.}, + author = {Polisetti, Naresh and Rapp, Julian and Liang, Paula and Dettmer-Monaco, Viviane and Bucher, Felicitas and Pruszak, Jan and Schlötzer-Schrehardt, Ursula and Cathomen, Toni and Schlunck, Günther and Reinhard, Thomas}, + doi = {10.3390/cells11233752}, + issn = {2073-4409}, + journal = {Cells}, + keywords = {{\textgreater}UseGalaxy.eu, Epithelium, Corneal, Induced Pluripotent Stem Cells, Limbus Corneae}, + language = {eng}, + month = {November}, + number = {23}, + pages = {3752}, + title = {Transcriptomic {Landscape} and {Functional} {Characterization} of {Human} {Induced} {Pluripotent} {Stem} {Cell}-{Derived} {Limbal} {Epithelial} {Progenitor} {Cells}}, + url = {http://europepmc.org/abstract/MED/36497012}, + volume = {11}, + year = {2022} +} + @article{potgieter_metanovo_2023, abstract = {Background Microbiome research is providing important new insights into the metabolic interactions of complex microbial ecosystems involved in fields as diverse as the pathogenesis of human diseases, agriculture and climate change. Poor correlations typically observed between RNA and protein expression datasets make it hard to accurately infer microbial protein synthesis from metagenomic data. Additionally, mass spectrometry-based metaproteomic analyses typically rely on focused search sequence databases based on prior knowledge for protein identification that may not represent all the proteins present in a set of samples. Metagenomic 16S rRNA sequencing only targets the bacterial component, while whole genome sequencing is at best an indirect measure of expressed proteomes. Here we describe a novel approach, MetaNovo, that combines existing open-source software tools to perform scalable de novo sequence tag matching with a novel algorithm for probabilistic optimization of the entire UniProt knowledgebase to create tailored sequence databases for target-decoy searches directly at the proteome level, enabling metaproteomic analyses without prior expectation of sample composition or metagenomic data generation and compatible with standard downstream analysis pipelines. Results We compared MetaNovo to published results from the MetaPro-IQ pipeline on 8 human mucosal-luminal interface samples, with comparable numbers of peptide and protein identifications, many shared peptide sequences and a similar bacterial taxonomic distribution compared to that found using a matched metagenome sequence database—but simultaneously identified many more non-bacterial peptides than the previous approaches. MetaNovo was also benchmarked on samples of known microbial composition against matched metagenomic and whole genomic sequence database workflows, yielding many more MS/MS identifications for the expected taxa, with improved taxonomic representation, while also highlighting previously described genome sequencing quality concerns for one of the organisms, and identifying an experimental sample contaminant without prior expectation. Conclusions By estimating taxonomic and peptide level information directly on microbiome samples from tandem mass spectrometry data, MetaNovo enables the simultaneous identification of peptides from all domains of life in metaproteome samples, bypassing the need for curated sequence databases to search. We show that the MetaNovo approach to mass spectrometry metaproteomics is more accurate than current gold standard approaches of tailored or matched genomic sequence database searches, can identify sample contaminants without prior expectation and yields insights into previously unidentified metaproteomic signals, building on the potential for complex mass spectrometry metaproteomic data to speak for itself.}, author = {Potgieter, Matthys G. and Nel, Andrew J. M. and Fortuin, Suereta and Garnett, Shaun and Wendoh, Jerome M. and Tabb, David L. and Mulder, Nicola J. and Blackburn, Jonathan M.}, doi = {10.1371/journal.pcbi.1011163}, issn = {1553-7358}, journal = {PLOS Computational Biology}, - keywords = {{\textgreater}UseGalaxy.eu, BLAST algorithm, Database searching, Metagenomics, Microbiome, Open source software, Proteomes, Sequence databases, Taxonomy}, + keywords = {{\textgreater}UseGalaxy.eu, BLAST algorithm, Database searching, Metagenomics, Microbiome, Microbiota, Open source software, Proteomes, Sequence databases, Tandem Mass Spectrometry, Taxonomy}, language = {en}, month = {June}, note = {Publisher: Public Library of Science}, @@ -11402,7 +18421,8 @@ @article{pranomphon_oviduct_2024 doi = {10.1186/s40659-024-00555-5}, issn = {0717-6287}, journal = {Biological Research}, - keywords = {{\textgreater}UseGalaxy.eu, Cattle, Embryo, In vitro embryo production, Oviduct, Oxidative stress, RNA-seq, Spheroids, Transcriptome}, + keywords = {{\textgreater}UseGalaxy.eu, Blastocyst, Cattle, Embryo, Embryo Culture Techniques, In vitro embryo production, Oviduct, Oxidative Stress, Oxidative stress, RNA-seq, Spheroids, Transcriptome}, + language = {eng}, month = {October}, number = {1}, pages = {73}, @@ -11413,6 +18433,40 @@ @article{pranomphon_oviduct_2024 year = {2024} } +@article{prasad_fused_2022, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Use of next-generation sequencing technologies to transcriptomics (RNA-seq) for gene expression profiling has found widespread application in studying different biological conditions including cancers. However, RNA-seq experiments are still small sample size experiments due to the cost. Recently, an increased focus has been on meta-analysis methods for integrated differential expression analysis for exploration of potential biomarkers. In this study, we propose a p-value combination method for meta-analysis of multiple independent but related RNA-seq studies that accounts for sample size of a study and direction of expression of genes in individual studies.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}The proposed method generalizes the inverse-normal method without an increase in statistical or computational complexity and does not pre- or post-hoc filter genes that have conflicting direction of expression in different studies. Thus, the proposed method, as compared to the inverse-normal, has better potential for the discovery of differentially expressed genes (DEGs) with potentially conflicting differential signals from multiple studies related to disease. We demonstrated the use of the proposed method in detection of biologically relevant DEGs in glioblastoma (GBM), the most aggressive brain cancer. Our approach notably enabled the identification of over-expressed tumour suppressor gene RAD51 in GBM compared to healthy controls, which has recently been shown to be a target for inhibition to enhance radiosensitivity of GBM cells during treatment. Pathway analysis identified multiple aberrant GBM related pathways as well as novel regulators such as TCF7L2 and MAPT as important upstream regulators in GBM.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}The proposed meta-analysis method generalizes the existing inverse-normal method by providing a way to establish differential expression status for genes with conflicting direction of expression in individual RNA-seq studies. Hence, leading to further exploration of them as potential biomarkers for the disease.}, + author = {Prasad, Birbal and Li, Xinzhong}, + doi = {10.1186/s12859-022-04859-9}, + issn = {1471-2105}, + journal = {BMC bioinformatics}, + keywords = {{\textgreater}UseGalaxy.eu, Brain Neoplasms, Glioblastoma}, + language = {eng}, + month = {August}, + number = {1}, + pages = {320}, + title = {Fused inverse-normal method for integrated differential expression analysis of {RNA}-seq data}, + url = {http://europepmc.org/abstract/MED/35931958}, + volume = {23}, + year = {2022} +} + +@article{prasad_transcriptional_2025, + abstract = {Drought hinders growth, development, and productivity of higher plants. While the physiological and molecular background of plant responses to drought has been extensively studied, the role of post-translational modifications of histones or DNA methylation in response to dehydration remains largely elusive. In this study, we deciphered genome-wide changes in transcriptome and histone modifications in response to dehydration in rapeseed (Brassica napus L.). High-throughput transcript profiling (RNA-seq) and ChIP followed by sequencing (ChIP-seq) of polyethylene glycol (PEG)-treated rapeseed plants revealed genome-scale changes in transcription and histone methylation patterns, specifically in histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 tri-methylated lysine 27 (H3K27me3) sites. We have identified gene sets with altered transcript profiles as well as histone methylation marks in response to osmotic stress. Several proline biosynthesis regulatory genes coding for Delta 1-Pyrroline-5-Carboxylate Synthetases (P5CS) displayed changes in H3K4me3 and/or H3K36me3 enrichment post-PEG treatment. Targeted bisulfite sequencing further identified stress-dependent gene body DNA methylation in one of the BnP5CSA gene copies that correlates with its stress-induced activation. By integrating physiological, transcriptional, and epigenomic data, our study contributes to a better understanding of the drought response control in crop plants.}, + author = {Prasad, Melvin and Shetty, Prateek and Pal, Avik Kumar and Rigó, Gábor and Kant, Kamal and Zsigmond, Laura and Nagy, István and Shivaprasad, Padubidri V and Szabados, László}, + doi = {10.1093/jxb/eraf123}, + issn = {0022-0957}, + journal = {J Exp Bot}, + keywords = {{\textgreater}UseGalaxy.eu, Brassica napus, Epigenesis, Genetic, Osmotic Pressure, Polyethylene Glycols, Transcriptome}, + language = {eng}, + month = {June}, + number = {9}, + pages = {2535--2556}, + title = {Transcriptional and epigenomic changes in response to polyethylene glycol-triggered osmotic stress in {Brassica} napus {L}}, + url = {http://europepmc.org/abstract/MED/40178034}, + volume = {76}, + year = {2025} +} + @article{prislan_proof_2019, author = {Prislan, Iztok and Sajko, Sara and Poklar Ulrih, Nataša and Fürst, Luka}, doi = {10.1039/C9RA09800C}, @@ -11428,6 +18482,21 @@ @article{prislan_proof_2019 year = {2019} } +@article{proenca_bacterial_2019, + abstract = {Pine Wilt Disease (PWD) is caused by \textit{Bursaphelenchus xylophilus}, the pinewood nematode, and affects several species of pine trees worldwide. The ecosystem of the \textit{Pinus pinaster} trees was investigated as a source of bacteria producing metabolites affecting this ecosystem: \textit{P. pinaster} trees as target-plant, nematode as disease effector and its insect-vector as shuttle. For example, metals and metal-carrying compounds contribute to the complex tree-ecosystems. This work aimed to detect novel secondary metabolites like metallophores and related molecules produced under iron limitation by PWD-associated bacteria and to test their activity on nematodes. After screening 357 bacterial strains from Portugal and United States, two promising metallophore-producing strains \textit{Erwinia} sp. A41C3 and \textit{Rouxiella} sp. Arv20\#4.1 were chosen and investigated in more detail. The genomes of these strains were sequenced, analyzed, and used to detect genetic potential for secondary metabolite production. A combinatorial approach of liquid chromatography-coupled tandem mass spectrometry (LC-MS) linked to molecular networking was used to describe these compounds. Two major metabolites were detected by HPLC analyses and described. One HPLC fraction of strain Arv20\#4.1 showed to be a hydroxamate-type siderophore with higher affinity for chelation of Cu. The HPLC fraction of strain A41C3 with highest metal affinity showed to be a catecholate-type siderophore with higher affinity for chelation of Fe. LC-MS allowed the identification of several desferrioxamines from strain Arv20\#4.1, in special desferrioxamine E, but no hit was obtained in case of strain A41C3 which might indicate that it is something new. Bacteria and their culture supernatants showed ability to attract \textit{C. elegans}. HPLC fractions of those supernatant-extracts of \textit{Erwinia} strain A41C3, enriched with secondary metabolites such as siderophores, were able to kill pinewood nematode. These results suggest that metabolites secreted under iron limitation have potential to biocontrol \textit{B. xylophilus} and for management of Pine Wilt Disease.}, + author = {Proença, Diogo Neves and Heine, Thomas and Senges, Christoph H R and Bandow, Julia E and Morais, Paula V and Tischler, Dirk}, + doi = {10.3389/fmicb.2019.02166}, + issn = {1664-302X}, + journal = {Frontiers in microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {2166}, + title = {Bacterial {Metabolites} {Produced} {Under} {Iron} {Limitation} {Kill} {Pinewood} {Nematode} and {Attract} {Caenorhabditis} elegans}, + url = {http://europepmc.org/abstract/MED/31608025}, + volume = {10}, + year = {2019} +} + @article{pt_whole_2023, author = {P.t, Waseem Mirsab}, keywords = {{\textgreater}UseGalaxy.eu}, @@ -11446,7 +18515,7 @@ @article{punyawatthananukool_prostaglandin_2024 doi = {10.1038/s41467-024-53706-3}, issn = {2041-1723}, journal = {Nature Communications}, - keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Cancer, Chronic inflammation, Immune evasion, Tumour immunology}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Cancer, Chronic inflammation, Dinoprostone, Energy Metabolism, Immune evasion, Receptors, Prostaglandin E, EP2 Subtype, Receptors, Prostaglandin E, EP4 Subtype, Ribosomes, Signal Transduction, Tumor Microenvironment, Tumour immunology}, language = {en}, month = {November}, note = {Publisher: Nature Publishing Group}, @@ -11465,7 +18534,7 @@ @article{pustam_comparative_2023 doi = {10.1371/journal.pone.0283583}, issn = {1932-6203}, journal = {PLOS ONE}, - keywords = {{\textgreater}UseGalaxy.eu, Bacterial pathogens, Caribbean, Genomics, Klebsiella pneumoniae, Mobile genetic elements, Pathogenesis, Secretion systems, Virulence factors}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial pathogens, Caribbean, Genomics, Klebsiella Infections, Klebsiella pneumoniae, Mobile genetic elements, Pathogenesis, Secretion systems, Virulence factors}, language = {en}, month = {October}, note = {Publisher: Public Library of Science}, @@ -11509,6 +18578,7 @@ @article{pyles_altered_2024 language = {English}, month = {March}, note = {Publisher: Frontiers}, + pages = {1341808}, title = {The altered {TBI} fecal microbiome is stable and functionally distinct}, url = {https://www.frontiersin.org/articles/10.3389/fnmol.2024.1341808}, urldate = {2024-05-17}, @@ -11549,6 +18619,23 @@ @article{qi_secreted_2020 year = {2020} } +@article{qi_secreted_2021, + abstract = {Multicellular organisms coordinate tissue specific responses to environmental information via both cell-autonomous and non-autonomous mechanisms. In addition to secreted ligands, recent reports implicated release of small RNAs in regulating gene expression across tissue boundaries. Here, we show that the conserved poly-U specific endoribonuclease ENDU-2 in C. elegans is secreted from the soma and taken-up by the germline to ensure germline immortality at elevated temperature. ENDU-2 binds to mature mRNAs and negatively regulates mRNA abundance both in the soma and the germline. While ENDU-2 promotes RNA decay in the soma directly via its endoribonuclease activity, ENDU-2 prevents misexpression of soma-specific genes in the germline and preserves germline immortality independent of its RNA-cleavage activity. In summary, our results suggest that the secreted RNase ENDU-2 regulates gene expression across tissue boundaries in response to temperature alterations and contributes to maintenance of stem cell immortality, probably via retaining a stem cell specific program of gene expression.}, + author = {Qi, Wenjing and Gromoff, Erika D V and Xu, Fan and Zhao, Qian and Yang, Wei and Pfeifer, Dietmar and Maier, Wolfgang and Long, Lijiang and Baumeister, Ralf}, + doi = {10.1038/s41467-021-21516-6}, + issn = {2041-1723}, + journal = {Nature communications}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {February}, + number = {1}, + pages = {1262}, + title = {The secreted endoribonuclease {ENDU}-2 from the soma protects germline immortality in {C}. elegans}, + url = {http://europepmc.org/abstract/MED/33627668}, + volume = {12}, + year = {2021} +} + @article{qiu_smcyp71d373_2024, abstract = {Salvia miltiorrhiza is one of the most commonly used Chinese medicinal herbs. Tanshinone I and tanshinone IIB with anti-inflammatory, anti-bacterial, anti-oxidative, anti-neoplastic, neuron protective, and heart protective properties are valuable active components in it. However, the biosynthetic pathway of tanshinone IIB and tanshinone I has not been completely elucidated. Here, we identified a tanshinone IIA 19-hydroxylase from S. miltiorrhiza. In vitro and in vivo analyses showed that SmCYP71D373 could hydroxylate tanshinone IIA at C-19 position to produce tanshinone IIB. Reaction conditions optimization demonstrated that the catalytic efficiency of SmCYP71D373 was the highest using the substrate-feeding method under the following conditions, fed the tanshinone IIA into the Saccharomyces cerevisiae expressing codon-optimized SmCYP71D373 at 28℃ for 24 hours. And the yield of tanshinone IIB was up to 6.38\%. Furthermore, N121 and S210 of SmCYP71D373 were verified as the key amino acid residues responsible for its catalytic activity for tanshinone IIA by molecular docking and site-directed mutagenesis. The results not only lay a foundation for the elucidation of tanshinone I synthesis pathway, but also provide the theoretical support to improve the catalytic efficiency of SmCYP71D373 for tanshinone IIB production.}, author = {Qiu, Xiaoping and Zhang, Yi and Luo, Yinggang and Zhang, Yongmei}, @@ -11565,6 +18652,27 @@ @article{qiu_smcyp71d373_2024 year = {2024} } +@article{quinto_genomic_2025, + abstract = {Background/Objectives: Streptococcus uberis is a Gram-positive bacterium and a major cause of bovine mastitis. The use of antimicrobial treatments raises concerns about resistance. This study aimed to characterize S. uberis isolates from one of the ten largest milk-producing regions in Europe. Methods: Thirty-six isolates from 36 cows with mastitis were identified using MALDI-TOF and VITEK®MS. Susceptibility to 9 antibiotics (penicillin G, ampicillin, tetracycline, erythromycin, clindamycin, cefotaxime, ceftriaxone, levofloxacin, and moxifloxacin) was determined with VITEK®2. Whole-genome sequencing was performed using MinION Mk1C. Results: Alleles were identified for 7 loci: arcC, ddl, gki, recP, tdk, tpi, and yqiL. Only 10 isolates had alleles for all the loci. The loci with the highest number of alleles were ddl and tdk (33/36 strains), while arcC had the fewest (19/36). Four isolates were assigned to known sequence types (ST6, ST307, and ST184), and novel alleles were detected in 32 of the 36 isolates. Twelve isolates showed phenotypic resistance to one or more of the following antibiotics: tetracycline, erythromycin, clindamycin, and ceftriaxone. The lnu was the most frequently detected resistance gene (27 out of 102 total gene appearances). A total of 19 virulence factors were identified. All strains were predicted to be capable of infecting human hosts. Conclusions: Streptococcus uberis is a potential reservoir of antimicrobial resistance genes. The use of antimicrobials to treat bovine mastitis has reduced the susceptibility of this microorganism to several antibiotics, underscoring the importance of monitoring antimicrobial use in veterinary practice. The results also highlight the high genetic diversity of the isolates, suggesting a strong capacity to adapt to different environmental conditions.}, + author = {Quinto, Emiliano J and Redondo Del Río, Paz and de Mateo Silleras, Beatriz and Prieto, Alberto and López-Lorenzo, Gonzalo and Franco, Carlos M and Vázquez, Beatriz I}, + copyright = {cc by}, + doi = {10.3390/antibiotics14111059}, + issn = {2079-6382}, + journal = {Antibiotics (Basel, Switzerland)}, + keywords = {{\textgreater}UseGalaxy.eu, Antimicrobial resistance, Bovine Mastitis, Streptococcus Uberis, virulence factors}, + language = {eng}, + month = {October}, + number = {11}, + pages = {1059}, + pmcid = {PMC12649216}, + pmid = {41301555}, + title = {Genomic {Characterization} and {Antimicrobial} {Resistance} {Profile} of \<i\>{Streptococcus} uberis\</i\> {Strains} {Isolated} from {Cows} with {Mastitis} from {Northwestern} {Spain}}, + url = {https://europepmc.org/articles/PMC12649216}, + urldate = {2025-12-26}, + volume = {14}, + year = {2025} +} + @mastersthesis{rabbas_surveillance_2024, abstract = {The discovery of antibiotics has radically changed the treatment of bacterial infections, making the increasing antibiotic resistance one of the top ten greatest threats to the global health. The main focus of antibiotic resistance research has, until recently, been focused on clinical settings and human and veterinary aspects. It has become more evident that the environment plays a vital role in the evolution, dissemination and prevalence of antibiotic resistant bacteria and genes. Aquatic ecosystems are a known mixing ground for clinical and environmental bacteria and can be a source and reservoir for resistance genes. The transfer of resistance between environmental and clinically important bacteria occurs, and surveillance of the environment is therefore important to better understand this flow of resistance. @@ -11609,6 +18717,17 @@ @article{rahman_mobilisation_2024 year = {2024} } +@article{rajczewski_rigorous_2021, + abstract = {The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world’s population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. In this study we have compiled a list of 639 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639 peptide possibilities to 87 peptides which were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Applying stringent statistical scoring thresholds, combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from a variety of sample types. We also contend that samples taken from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.}, + author = {Rajczewski, Andrew and Mehta, Subina and Nguyen, Dinh Duy An and Grüning, Björn and Johnson, James and McGowan, Thomas and Griffin, Timothy and Jagtap, Pratik}, + doi = {10.1101/2021.02.09.21251427}, + journal = {medRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {A rigorous evaluation of optimal peptide targets for {MS}-based clinical diagnostics of {Coronavirus} {Disease} 2019 ({COVID}-19)}, + url = {http://europepmc.org/abstract/PPR/PPR282374}, + year = {2021} +} + @article{rajczewski_rigorous_2021, abstract = {The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc.}, author = {Rajczewski, Andrew T. and Mehta, Subina and Nguyen, Dinh Duy An and Grüning, Björn and Johnson, James E. and McGowan, Thomas and Griffin, Timothy J. and Jagtap, Pratik D.}, @@ -11616,6 +18735,7 @@ @article{rajczewski_rigorous_2021 issn = {1559-0275}, journal = {Clinical Proteomics}, keywords = {+Galactic, +Methods, +Shared, +UsePublic, {\textgreater}UseGalaxy.eu, Bioinformatics, Mass spectrometry, Pandemic, Peptide-detection, Viral proteome, Workflows}, + language = {eng}, month = {May}, number = {1}, pages = {15}, @@ -11641,6 +18761,22 @@ @article{ramos_mobilome_2024 year = {2024} } +@article{ran_mitochondrial_2025, + abstract = {This study sequenced the complete mitochondrial genomes of three Camaenidae snail species (\<i\>Acusta ravida\</i\>, \<i\>Bradybaena similaris\</i\>, and \<i\>Trichobradybaena submissa\</i\>). Each mitogenome contained the typical 37 genes (13 PCGs, 22 tRNAs, and 2 rRNAs), with most tRNAs forming clover structures (except trnK, trnH, trnN, trnS1, trnS2, and trnR). Comparative analysis with nine existing Camaenidae mitogenomes revealed: (1) The nucleotide composition of mitochondrial genes was significantly skewed toward A and T; (2) Most protein genes used ATN start codons and TAA/T- stop codons; (3) Synonymous codons ending with T/A were dominant. Analyses (PR2-plot, neutrality plot) indicated codon usage was influenced by both mutation pressure and natural selection. Phylogenetically, the three newly sequenced species clustered within Bradybaeninae of Camaenidae, consistent with previous classifications. The results support Hygromiidae and Geomitridae as sister groups and identify Polygyridae as the sister clade to Camaenidae. Additionally, they also partially support elevating Satsuma and its subgenus to subfamily status. This study enriches mitogenomic resources for Camaenidae and provides foundational data for future research on codon usage, adaptive evolution, and phylogenetics within this family.}, + author = {Ran, Xing-Ming and He, Hai-Yong and Yang, Lin and Long, Jian-Kun and Chang, Zhi-Min and Li, Zhong and Gao, Junyi and Chen, Xiang-Sheng}, + doi = {10.1002/ece3.72282}, + issn = {2045-7758}, + journal = {Ecology and evolution}, + keywords = {{\textgreater}UseGalaxy.eu, Camaenidae, Codon usage bias, Phylogenetic analysis}, + month = {October}, + number = {10}, + pages = {e72282}, + title = {Mitochondrial {Genomes} of {Three} {Species} of the {Family} {Camaenidae} ({Gastropoda}: {Stylommatophora}): {Structural} {Features}, {Codon} {Usage} {Patterns}, and {Phylogenetic} {Implications}}, + url = {https://europepmc.org/articles/PMC12515985}, + volume = {15}, + year = {2025} +} + @inproceedings{ranawaka_custos_2022, abstract = {Custos is open source software that provides user, group, and resource credential management services for science gateways. This paper describes the resource credential, or secrets, management service in Custos that allows science gateways to safely manage security tokens, SSH keys, and passwords on behalf of users. Science gateways such as Galaxy are well-established mechanisms for researchers to access cyberinfrastructure and, increasingly, couple it with other online services, such as user-provided storage or compute resources. To support this use case, science gateways need to operate on behalf of the users to connect, acquire, and release these resources, which are protected by a variety of authentication and access mechanisms. Storing and managing the credentials associated with these access mechanisms must be done using “best of breed” software and established security protocols. The Custos Secrets Service allows science gateways to store and retrieve these credentials using secure protocols and APIs while the data is protected at rest. Here, we provide implementation details for the service, describe the available APIs and SDKs, and discuss integration with Galaxy as a use case.}, address = {New York, NY, USA}, @@ -11661,24 +18797,64 @@ @inproceedings{ranawaka_custos_2022 } @article{ranchou-peyruse_microbial_2021, + abstract = {Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial ecosystems that participate in physicochemical balances. These microorganisms can positively or negatively interfere with subsurface (i) energy storage (CH$_{\textrm{4}}$ and H$_{\textrm{2}}$), (ii) CO$_{\textrm{2}}$ sequestration; and (iii) resource (water, rare metals) exploitation. The aquifer studied here (720m deep, 37°C, 88bar) is naturally oligotrophic, with a total organic carbon content of {\textless}1mg.L$^{\textrm{-1}}$ and a phosphate content of 0.02mg.L$^{\textrm{-1}}$. The influence of natural gas storage locally generates different pressures and formation water displacements, but it also releases organic molecules such as monoaromatic hydrocarbons at the gas/water interface. The hydrocarbon biodegradation ability of the indigenous microbial community was evaluated in this work. The \textit{in situ} microbial community was dominated by sulfate-reducing (e.g., Sva0485 lineage, Thermodesulfovibriona, \textit{Desulfotomaculum}, \textit{Desulfomonile}, and \textit{Desulfovibrio}), fermentative (e.g., \textit{Peptococcaceae} SCADC1\_2\_3, Anaerolineae lineage and \textit{Pelotomaculum}), and homoacetogenic bacteria ("\textit{Candidatus} Acetothermia") with a few archaeal representatives (e.g., \textit{Methanomassiliicoccaceae}, \textit{Methanobacteriaceae}, and members of the Bathyarcheia class), suggesting a role of H$_{\textrm{2}}$ in microenvironment functioning. Monoaromatic hydrocarbon biodegradation is carried out by sulfate reducers and favored by concentrated biomass and slightly acidic conditions, which suggests that biodegradation should preferably occur in biofilms present on the surfaces of aquifer rock, rather than by planktonic bacteria. A simplified bacterial community, which was able to degrade monoaromatic hydrocarbons at atmospheric pressure over several months, was selected for incubation experiments at \textit{in situ} pressure (i.e., 90bar). These showed that the abundance of various bacterial genera was altered, while taxonomic diversity was mostly unchanged. The candidate phylum Acetothermia was characteristic of the community incubated at 90bar. This work suggests that even if pressures on the order of 90bar do not seem to select for obligate piezophilic organisms, modifications of the thermodynamic equilibria could favor different microbial assemblages from those observed at atmospheric pressure.}, author = {Ranchou-Peyruse, Magali and Guignard, Marion and Casteran, Franck and Abadie, Maïder and Defois, Clémence and Peyret, Pierre and Dequidt, David and Caumette, Guilhem and Chiquet, Pierre and Cézac, Pierre and Ranchou-Peyruse, Anthony}, doi = {10.3389/fmicb.2021.688929}, + issn = {1664-302X}, + journal = {Frontiers in microbiology}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {October}, note = {Publisher: Frontiers Media SA}, + pages = {688929}, title = {Microbial {Diversity} {Under} the {Influence} of {Natural} {Gas} {Storage} in a {Deep} {Aquifer}}, url = {https://doi.org/10.3389/fmicb.2021.688929}, volume = {12}, year = {2021} } +@article{ranganathan_targets_2025, + abstract = {Branchio-otic (BOS) and branchio-oto-renal (BOR) syndromes are autosomal dominant disorders featuring multiple birth defects including ear, renal and branchial malformations. Mutations in the homeodomain transcription factor SIX1 and its co-factor EYA1 have been identified in about 50\% of individuals with BOS or BOR, while causative mutations are unknown in the other half. We hypothesise that SIX1 target genes represent new BOS and BOR candidates. Using published transcriptomic and epigenomic data from chick ear progenitors, we first identify putative Six1 targets. Next, we provide evidence that Six1 directly regulates some of these candidates: Six1 binds to their enhancers, and functional experiments in Xenopus and chick confirm that Six1 controls their expression. Finally, we show that most putative chick Six1 targets are also expressed in the human developing ear and are associated with known deafness loci. Together, our results not only characterise the molecular mechanisms that mediate Six1 function in the developing ear, but also provide new candidates for human congenital deafness.}, + author = {Ranganathan, Ramya and Sari, Fereshteh and Wang, Scarlet Xiaoyan and Thiery, Alexandre and Buzzi, Ailin Leticia and Guerra, Rosalinda and Moody, Sally A. and Streit, Andrea}, + doi = {10.1242/dev.204533}, + issn = {0950-1991}, + journal = {Development}, + keywords = {{\textgreater}UseGalaxy.eu, Deafness, Homeodomain Proteins, Xenopus Proteins}, + month = {April}, + number = {7}, + pages = {dev204533}, + title = {Targets of the transcription factor {Six1} identify previously unreported candidate deafness genes}, + url = {https://doi.org/10.1242/dev.204533}, + urldate = {2025-04-15}, + volume = {152}, + year = {2025} +} + +@article{ranta_isolation_2025, + abstract = {Pseudomonas aeruginosa is an opportunistic pathogen that causes a wide variety of infections, and belongs to the group of ESKAPE pathogens that are the leading cause of healthcare-associated infections and have high level of antibiotic resistance. The treatment of infections caused by antibiotic-resistant P. aeruginosa is challenging, which makes it a common target for phage therapy. The successful utilization of phage therapy requires a collection of well characterized phages.}, + author = {Ranta, Kira and Skurnik, Mikael and Kiljunen, Saija}, + doi = {10.1186/s12985-025-02679-w}, + issn = {1743-422X}, + journal = {Virology Journal}, + keywords = {{\textgreater}UseGalaxy.eu, Flagellum-dependent, Jumbo phage, Phage resistance, Phage therapy, Phage-binding receptor, PhiKZ, Pseudomonas Phages, Pseudomonas aeruginosa}, + language = {en}, + month = {March}, + number = {1}, + pages = {55}, + title = {Isolation and characterization of {fMGyn}-{Pae01}, a {phiKZ}-like jumbo phage infecting {Pseudomonas} aeruginosa}, + url = {https://doi.org/10.1186/s12985-025-02679-w}, + urldate = {2025-03-18}, + volume = {22}, + year = {2025} +} + @article{rapp_oncostatin_2024, abstract = {Continuous vision loss due to vasoproliferative eye disease still represents an unsolved issue despite anti-vascular endothelial growth factor (VEGF) therapy. The impact of signal transducer and activator of transcription 3 (STAT3) signaling on retinal angiogenesis and its potential use as a therapeutic target remain controversial. In vitro, oncostatin M (OSM), as a strong STAT3 activator, possesses robust proangiogenic activity. This study investigated to what extent the proangiogenic effects of OSM translate to the in vivo setting of vasoproliferative eye disease. The in vitro effect of OSM on endothelial cells was investigated in the spheroid sprouting assay and through RNA sequencing. The mouse model for oxygen-induced retinopathy (OIR) was used to evaluate the impact of OSM in vivo. Signaling patterns were measured by western blot and retinal cryosections. Primary Müller cell cultures were used to evaluate the effect of OSM on the Müller cell secretome. Murine retinal vascular endothelial cells were isolated from OIR retinas using fluorescence-activated cell sorting (FACS) and were used for RNA sequencing. Although OSM induced pro-angiogenic responses in vitro, in the OIR model intravitreal injection of OSM reduced retinal neovascularization by 65.2\% and vaso-obliteration by 45.5\% in Müller cells. Injecting OSM into the vitreous activated the STAT3 signaling pathway in multiple retinal cell types, including Müller cells. In vitro, OSM treatment increased CXCL10 secretion. RNA sequencing of sorted vascular endothelial cells at OIR P17 following OSM treatment indicated downregulation of angiogenesis- and mitosis-associated genes. In vivo, OSM reveals a beneficial angiomodulatory effect by activating Müller cells and changing their secretome. The data highlight contradictions between cytokine-induced effects in vitro and in vivo depending on the cell types mediating the effect.}, author = {Rapp, Julian and Hospach, Alban and Liang, Paula and Schwämmle, Melanie and Renz, Lisa and Agostini, Hansjürgen and Schlunck, Günther and Bucher, Felicitas}, doi = {10.1167/iovs.65.1.22}, issn = {1552-5783}, journal = {Investigative Ophthalmology \& Visual Science}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Neovascularization, Pathologic, Oncostatin M, Retinal Diseases}, month = {January}, number = {1}, pages = {22}, @@ -11710,12 +18886,14 @@ @article{rasche_galactic_2020 abstract = {AbstractBackground. Circos is a popular, highly flexible software package for the circular visualization of complex datasets. While especially popular in the f}, author = {Rasche, Helena and Hiltemann, Saskia}, doi = {10.1093/gigascience/giaa065}, + issn = {2047-217X}, journal = {GigaScience}, - keywords = {+Education, +Galactic, +IsGalaxy, +RefPublic, +Shared, +Tools, +Visualization, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au}, + keywords = {+Education, +Galactic, +IsGalaxy, +RefPublic, +Shared, +Tools, +Visualization, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Software}, language = {en}, month = {June}, note = {Publisher: Oxford Academic}, number = {6}, + pages = {giaa065}, shorttitle = {Galactic {Circos}}, title = {Galactic {Circos}: {User}-friendly {Circos} plots within the {Galaxy} platform}, url = {https://academic.oup.com/gigascience/article/9/6/giaa065/5856406}, @@ -11742,6 +18920,22 @@ @article{rasche_training_2020 year = {2020} } +@article{rasche_training_2022, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Hands-on training, whether in bioinformatics or other domains, often requires significant technical resources and knowledge to set up and run. Instructors must have access to powerful compute infrastructure that can support resource-intensive jobs running efficiently. Often this is achieved using a private server where there is no contention for the queue. However, this places a significant prerequisite knowledge or labor barrier for instructors, who must spend time coordinating deployment and management of compute resources. Furthermore, with the increase of virtual and hybrid teaching, where learners are located in separate physical locations, it is difficult to track student progress as efficiently as during in-person courses.{\textless}h4{\textgreater}Findings{\textless}/h4{\textgreater}Originally developed by Galaxy Europe and the Gallantries project, together with the Galaxy community, we have created Training Infrastructure-as-a-Service (TIaaS), aimed at providing user-friendly training infrastructure to the global training community. TIaaS provides dedicated training resources for Galaxy-based courses and events. Event organizers register their course, after which trainees are transparently placed in a private queue on the compute infrastructure, which ensures jobs complete quickly, even when the main queue is experiencing high wait times. A built-in dashboard allows instructors to monitor student progress.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}TIaaS provides a significant improvement for instructors and learners, as well as infrastructure administrators. The instructor dashboard makes remote events not only possible but also easy. Students experience continuity of learning, as all training happens on Galaxy, which they can continue to use after the event. In the past 60 months, 504 training events with over 24,000 learners have used this infrastructure for Galaxy training.}, + author = {Rasche, Helena and Hyde, Cameron and Davis, John and Gladman, Simon and Coraor, Nate and Bretaudeau, Anthony and Cuccuru, Gianmauro and Bacon, Wendi and Serrano-Solano, Beatriz and Hillman-Jackson, Jennifer and Hiltemann, Saskia and Zhou, Miaomiao and Grüning, Björn and Stubbs, Andrew}, + doi = {10.1093/gigascience/giad048}, + issn = {2047-217X}, + journal = {Gigascience}, + keywords = {{\textgreater}UseGalaxy.eu, Learning, Software}, + language = {eng}, + month = {December}, + pages = {giad048}, + title = {Training {Infrastructure} as a {Service}}, + url = {http://europepmc.org/abstract/MED/37395629}, + volume = {12}, + year = {2022} +} + @article{rasche_usegalaxyeu_2019, abstract = {Read this work by Rasche H, at F1000Research.}, author = {Rasche, Helena and Europe, Galaxy Project}, @@ -11773,6 +18967,53 @@ @article{rasheed_metagenomic_2023 year = {2023} } +@article{rashid_shotgun_2025, + abstract = {Clinical endometritis (CE) is associated with bacterial pathogens while the same has not been proved about subclinical endometritis (SCE). We aimed to use shotgun metagenomic sequencing to investigate the associations between potentially unidentified pathogens and SCE. Uterine cytobrush samples from multiparous Holstein cows (n = 23) were taken at 21 days in milk (DIM) and sequenced via the Illumina shotgun platform. At 36 DIM, the cows were diagnosed as CE (n = 7), SCE (n = 7), or healthy (n = 9). We did not find differences in the alpha and beta diversity of bacteria and eukaryotes among the health groups. Relative abundance of typical pathogens i.e. Fusobacterium, Peptoniphilus, Peptostreptococcus, and Trueperella was greater in CE than healthy controls. We did not find evidence of eukaryotic or viral association in infection, yet, distinct patterns of bacterial co-occurrence were observed among pathogenic and non-pathogenic bacteria. In CE cows, Wnt/catenin pathway had lower abundance than SCE or healthy cows. Our findings support that CE is characterized by domination of pathogenic bacteria that intercorrelate, whereas SCE is not associated with bacterial colonization.}, + author = {Rashid, Muhammad Hussnain and Pascottini, Osvaldo Bogado and Xie, Lei and Niazi, Mehrnaz and Lietaer, Leen and Comlekcioglu, Ugur and Opsomer, Geert}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-03265-4}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Cattle Diseases, Endometritis, Infertility, Metagenomics, Microbial Interactions, Microbiota, Uterus}, + language = {en}, + month = {May}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {18274}, + title = {Shotgun metagenomic composition, microbial interactions and functional insights into the uterine microbiome of postpartum dairy cows with clinical and subclinical endometritis}, + url = {https://www.nature.com/articles/s41598-025-03265-4}, + urldate = {2025-05-28}, + volume = {15}, + year = {2025} +} + +@article{ratchasong_bactericidal_2025, + author = {Ratchasong, Kunchaphorn and Saengsawang, Phirabhat and Yusakul, Gorawit and Makkliang, Fonthip and Lakhanapuram, Hemanth Kumar and Wintachai, Phitchayapak and Thomrongsuwannakij, Thotsapol and Nwabor, Ozioma Forstinus and Punyapornwithaya, Veerasak and Romyasamit, Chonticha and Mitsuwan, Watcharapong}, + issn = {2079-6382}, + journal = {Antibiotics (Basel, Switzerland)}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + number = {8}, + title = {Bactericidal {Activities} of {Nanoemulsion} {Containing} {Piper} betle {L}. {Leaf} and {Hydroxychavicol} {Against} {Avian} {Pathogenic} {Escherichia} coli and {Modelling} {Simulation} of {Hydroxychavicol} {Against} {Bacterial} {Cell} {Division} {Proteins}}, + url = {https://europepmc.org/articles/PMC12382705}, + volume = {14}, + year = {2025} +} + +@article{ratchasong_bactericidal_2025, + author = {Ratchasong, Kunchaphorn and Saengsawang, Phirabhat and Yusakul, Gorawit and Makkliang, Fonthip and Lakhanapuram, Hemanth Kumar and Wintachai, Phitchayapak and Thomrongsuwannakij, Thotsapol and Nwabor, Ozioma Forstinus and Punyapornwithaya, Veerasak and Romyasamit, Chonticha and Mitsuwan, Watcharapong}, + issn = {2079-6382}, + journal = {Antibiotics (Basel)}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {August}, + number = {8}, + title = {Bactericidal {Activities} of {Nanoemulsion} {Containing} {Piper} betle {L}. {Leaf} and {Hydroxychavicol} {Against} {Avian} {Pathogenic} {Escherichia} coli and {Modelling} {Simulation} of {Hydroxychavicol} {Against} {Bacterial} {Cell} {Division} {Proteins}}, + url = {http://europepmc.org/abstract/PMC/PMC12382705}, + volume = {14}, + year = {2025} +} + @article{raubenolt_generalized_2024, abstract = {Viral helicases are promising targets for the development of antiviral therapies. Given their vital function of unwinding double-stranded nucleic acids, inhibiting them blocks the viral replication cycle. Previous studies have elucidated key structural details of these helicases, including the location of substrate binding sites, flexible domains, and the discovery of potential inhibitors. Here we present a series of new Galaxy tools and workflows for performing and analyzing molecular dynamics simulations of viral helicases. We first validate them by demonstrating recapitulation of data from previous simulations of Zika (NS3) and SARS-CoV-2 (NSP13) helicases in apo and complex with inhibitors. We further demonstrate the utility and generalizability of these Galaxy workflows by applying them to new cases, proving their usefulness as a widely accessible method for exploring antiviral activity.}, author = {Raubenolt, Bryan and Blankenberg, Daniel}, @@ -11806,6 +19047,23 @@ @article{rauschmeier_bhlhe40_2019 year = {2019} } +@article{rauschmeier_bhlhe40_2022, + abstract = {The generation of high-affinity antibodies against pathogens and vaccines requires the germinal center (GC) reaction, which relies on a complex interplay between specialized effector B and CD4 T lymphocytes, the GC B cells and T follicular helper (TFH) cells. Intriguingly, several positive key regulators of the GC reaction are common for both cell types. Here, we report that the transcription factor Bhlhe40 is a crucial cell-intrinsic negative regulator affecting both the B and T cell sides of the GC reaction. In activated CD4 T cells, Bhlhe40 was required to restrain proliferation, thus limiting the number of TFH cells. In B cells, Bhlhe40 executed its function in the first days after immunization by selectively restricting the generation of the earliest GC B cells but not of early memory B cells or plasmablasts. Bhlhe40-deficient mice with progressing age succumbed to a B cell lymphoma characterized by the accumulation of monoclonal GC B-like cells and polyclonal TFH cells in various tissues.}, + author = {Rauschmeier, René and Reinhardt, Annika and Gustafsson, Charlotte and Glaros, Vassilis and Artemov, Artem V and Dunst, Josefine and Taneja, Reshma and Adameyko, Igor and Månsson, Robert and Busslinger, Meinrad and Kreslavsky, Taras}, + doi = {10.1084/jem.20211406}, + issn = {0022-1007}, + journal = {J Exp Med}, + keywords = {{\textgreater}UseGalaxy.eu, Disease Susceptibility}, + language = {eng}, + month = {February}, + number = {2}, + pages = {e20211406}, + title = {Bhlhe40 function in activated {B} and {TFH} cells restrains the {GC} reaction and prevents lymphomagenesis}, + url = {http://europepmc.org/abstract/MED/34919144}, + volume = {219}, + year = {2022} +} + @article{rauschmeier_cell-intrinsic_2021, abstract = {{\textless}h3{\textgreater}ABSTRACT{\textless}/h3{\textgreater} {\textless}p{\textgreater}The generation of high-affinity antibodies against pathogens and vaccines requires the germinal center (GC) reaction – a process that relies on a complex interplay between specialized effector subsets of B and CD4 T lymphocytes – GC B cells and T follicular helper (T$_{\textrm{FH}}$) cells. Intriguingly, several key positive regulators of the GC reaction are common for both cell types. Here, we report that the transcription factor Bhlhe40 is a crucial cell-intrinsic negative regulator affecting both the B and T cell sides of the GC reaction. In activated CD4 T cells, Bhlhe40 was required to restrain proliferation thus limiting the number of T$_{\textrm{FH}}$ cells. In B cells, Bhlhe40 executed its function in the first days after immunization by selectively restricting the generation of the earliest GC B cells but not of early memory B cells or plasmablasts. Conditional Bhlhe40 inactivation confirmed cell-autonomous functions of Bhlhe40 in both GC B and T$_{\textrm{FH}}$ cells, while the GC phenotype was further enhanced upon loss of Bhlhe40 in both cell types. This negative regulation of the GC reaction by Bhlhe40 was of crucial importance, as Bhlhe40-deficient mice with progressing age succumbed to a B cell lymphoma characterized by accumulation of monoclonal GC B-like cells and polyclonal T$_{\textrm{FH}}$ cells in various tissues.{\textless}/p{\textgreater}}, author = {Rauschmeier, René and Reinhardt, Annika and Gustafsson, Charlotte and Glaros, Vassilis and Artemov, Artem V. and Taneja, Reshma and Adameyko, Igor and Månsson, Robert and Busslinger, Meinrad and Kreslavsky, Taras}, @@ -11824,6 +19082,21 @@ @article{rauschmeier_cell-intrinsic_2021 year = {2021} } +@article{rauterberg_pcsk9-antibodies_2024, + abstract = {{\textless}h4{\textgreater}Background and aims{\textless}/h4{\textgreater}Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a crucial role in cholesterol homeostasis by regulating low-density lipoprotein (LDL) receptor levels. Despite its known effects on cholesterol metabolism, the role of PCSK9 in cardiac function, especially post-myocardial infarction (MI), remains unclear. This study investigates the impact of PCSK9 on heart function post-MI and evaluates the effects of PCSK9 inhibition via Alirocumab.{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}We used PCSK9 knockout (KO) mice and wildtype (WT) mice and \textit{in vivo} treatment with Alirocumab to analyze cardiac function and survival post-MI induced by permanent ligation of the left anterior descending artery. PCSK9 and LDL receptor levels were measured using ELISA and qRT-PCR. Cardiac function was assessed via echocardiography and isolated working heart model experiments. Gene expression changes were evaluated using RNA sequencing, and inflammatory responses in bone marrow-derived macrophages (BMDMs) were analyzed \textit{in vitro}.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}PCSK9 was expressed in murine heart tissue at levels comparable to the liver, despite minimal heart RNA expression. PCSK9 KO mice had lower plasma cholesterol levels and showed reduced cardiac functions in the working heart model compared to WT mice. Post-MI, PCSK9 KO mice demonstrated significantly improved survival and reduced ventricular rupture compared to WT mice. Alirocumab treatment, while effective in lowering plasma cholesterol, did not replicate the survival benefits seen in PCSK9 KO mice and even worsened cardiac function post-MI. \textit{In vitro}, PCSK9 induced significant inflammatory responses in macrophages, which were not mitigated by Alirocumab.{\textless}h4{\textgreater}Conclusion{\textless}/h4{\textgreater}PCSK9 accumulation in the heart post-MI contributes to adverse cardiac remodeling and inflammation. Genetic deletion of PCSK9 confers protection against post-infarct mortality, whereas pharmacological inhibition with Alirocumab fails to reproduce these benefits and may exacerbate cardiac dysfunction. These findings highlight the complex role of PCSK9 in cardiac pathology and caution against the assumption that PCSK9 inhibitors will necessarily yield cardiovascular benefits similar to genetic PCSK9 deficiency.}, + author = {Rauterberg, Simon and Härdtner, Carmen and Hein, Jennifer and Schrepf, Paola and Peyronnet, Remi and Koentges, Christoph and Vico, Tamara A and Ehlert, Carolin and Dufner, Bianca and Lindner, Diana and von Zur Mühlen, Constantin and Wolf, Dennis and Westermann, Dirk and Hilgendorf, Ingo and von Ehr, Alexander}, + doi = {10.3389/fcvm.2024.1463844}, + issn = {2297-055X}, + journal = {Frontiers in cardiovascular medicine}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {1463844}, + title = {{PCSK9}-antibodies fail to block {PCSK9}-induced inflammation in macrophages and cannot recapitulate protective effects of {PCSK9}-deficiency in experimental myocardial infarction}, + url = {http://europepmc.org/abstract/MED/39906341}, + volume = {11}, + year = {2024} +} + @article{ravindran_multifaceted_2024, abstract = {Cardiovascular disease (CVD) remains a global economic burden even in the 21st century with 85\% of deaths resulting from heart attacks. Despite efforts in reducing the risk factors, and enhancing pharmacotherapeutic strategies, challenges persist in early identification of disease progression and functional recovery of damaged hearts. Targeting mitochondrial dysfunction, a key player in the pathogenesis of CVD has been less successful due to its role in other coexisting diseases. Additionally, it is the only organelle with an agathokakological function that is a remedy and a poison for the cell. In this review, we describe the origins of cardiac mitochondria and the role of heteroplasmy and mitochondrial subpopulations namely the interfibrillar, subsarcolemmal, perinuclear, and intranuclear mitochondria in maintaining cardiac function and in disease-associated remodeling. The cumulative evidence of mitochondrial retrograde communication with the nucleus is addressed, highlighting the need to study the genotype-phenotype relationships of specific organelle functions with CVD by using approaches like genome-wide association study (GWAS). Finally, we discuss the practicality of computational methods combined with single-cell sequencing technologies to address the challenges of genetic screening in the identification of heteroplasmy and contributory genes towards CVD.}, author = {Ravindran, Sriram and Rau, Christoph D.}, @@ -11842,6 +19115,24 @@ @article{ravindran_multifaceted_2024 year = {2024} } +@article{raymond_targeting_2025, + abstract = {Sex inequalities in cancer are well documented, but the current limited understanding is hindering advances in precision medicine and therapies1. Consideration of ethnicity, age and sex is essential for the management of cancer patients because they underlie important differences in both incidence and response to treatment2,3. Age-related hormone production, which is a consistent divergence between the sexes, is underestimated in cancers that are not recognized as being hormone dependent4–6. Here, we show that premenopausal women have increased vulnerability to cancers, and we identify the cell–cell adhesion molecule E-cadherin as a crucial component in the oestrogen response in various cancers, including melanoma. In a mouse model of melanoma, we discovered an oestrogen-sensitizing pathway connecting E-cadherin, β-catenin, oestrogen receptor-α and GRPR that promotes melanoma aggressiveness in women. Inhibiting this pathway by targeting GRPR or oestrogen receptor-α reduces metastasis in mice, indicating its therapeutic potential. Our study introduces a concept linking hormone sensitivity and tumour phenotype in which hormones affect cell phenotype and aggressiveness. We have identified an integrated pro-tumour pathway in women and propose that targeting a G-protein-coupled receptor with drugs not commonly used for cancer treatment could be more effective in treating E-cadherin-dependent cancers in women. This study emphasizes the importance of sex-specific factors in cancer management and offers hope of improving outcomes in various cancers.}, + author = {Raymond, Jérémy H. and Aktary, Zackie and Pouteaux, Marie and Petit, Valérie and Luciani, Flavie and Wehbe, Maria and Gizzi, Patrick and Bourban, Claire and Decaudin, Didier and Nemati, Fariba and Martianov, Igor and Davidson, Irwin and Tomasetto, Catherine-Laure and White, Richard M. and Mahuteau-Betzer, Florence and Vergier, Béatrice and Larue, Lionel and Delmas, Véronique}, + copyright = {2025 The Author(s), under exclusive licence to Springer Nature Limited}, + doi = {10.1038/s41586-025-09111-x}, + issn = {1476-4687}, + journal = {Nature}, + keywords = {{\textgreater}UseGalaxy.eu, Cadherins, Gonadal Steroid Hormones, Melanoma, Molecular Targeted Therapy, Transcription}, + language = {en}, + month = {June}, + note = {Publisher: Nature Publishing Group}, + pages = {1--9}, + title = {Targeting {GRPR} for sex hormone-dependent cancer after loss of {E}-cadherin}, + url = {https://www.nature.com/articles/s41586-025-09111-x}, + urldate = {2025-06-17}, + year = {2025} +} + @article{rebollo_identification_2024, author = {Rebollo, Rita and Gerenton, Pierre and Cumunel, Eric and Mary, Arnaud and Sabot, François and Burlet, Nelly and Gillet, Benjamin and Hughes, Sandrine and S. Oliveira, Daniel and Goubert, Clément and Fablet, Marie and Vieira, Cristina and Lacroix, Vincent}, doi = {10.24072/pcjournal.457}, @@ -11856,6 +19147,34 @@ @article{rebollo_identification_2024 year = {2024} } +@article{recio_thermotolerant_2025, + author = {Recio, Maria‐Isabel and Gavira, José A. and de La Torre, Jesús and Cano‐Muñoz, Mario and Martínez‐Rodriguez, Sergio and Daddaoua, Abdelali and Duque, Estrella and Ramos, Juan L.}, + issn = {0961-8368}, + journal = {Protein Sci}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {August}, + number = {9}, + title = {Thermotolerant class {A} acid phosphatase active across broad {pH} range and diverse substrates}, + url = {http://europepmc.org/abstract/PMC/PMC12356135}, + volume = {34}, + year = {2025} +} + +@misc{redonion_clinical_2025, + abstract = {La medicina personalizzata aumenta l’efficacia di diagnosi, prevenzione e cura delle malattie. Scopri come la genetica medica trasforma la sanità moderna.}, + author = {redonion}, + journal = {TomaLab}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {it-IT}, + month = {March}, + shorttitle = {Clinical validation of 13-gene {DNA} methylation analysis in oral brushing samples for detection of oral carcinoma}, + title = {Clinical validation of 13-gene {DNA} methylation analysis in oral brushing samples for detection of oral carcinoma: {An} {Italian} multicenter study}, + url = {https://tomalab.it/clinical-validation-of-13-gene-dna-methylation-analysis-in-oral-brushing-samples-for-detection-of-oral-carcinoma-an-italian-multicenter-study/}, + urldate = {2025-03-30}, + year = {2025} +} + @article{rehm_analyse_2023, abstract = {Humane Papillomviren (HPV) infizieren Keratinozyten der Haut- und Schleimhaut. Die Hochrisiko-Typen (HR) der alpha-Gattung verursachen dadurch anogenitalen- und oropharyngalen-Krebs. Vorherrschend dabei ist das Zervixkarzinom, welches zu 70 \% von HPV16 und HPV18 ausgelöst wird. Im Gegensatz dazu sind die onkogenen Eigenschaften der beta-HPV Gattung weniger gut erforscht. Bei Patienten mit der seltenen Erbkrankheit Epidermodysplasia Verruciformis (EV) und Organtransplantatempfängern (OTRs) wird ein Zusammenhang zwischen beta-HPV-Infektionen und der Entstehung von kutanen Plattenepithelkarzinomen vermutet. Bisher wurden die Eigenschaften von beta-HPV vor allem durch retrovirale Expression der E6 und E7 Onkogene in Keratinozyten, durch Transfektion der Osteosarkomzelllinie U2OS mit beta-HPV Genomen und in transgenen Mausmodellen untersucht, aber nicht mit vollständigen viralen Genomen in normalen humanen Keratinozyten (NHK), den natürlichen Zielzellen. Im Rahmen meiner Dissertation konnte ich zeigen, dass HPV8-, 38- und 49-Genome in humanen Keratinozyten mindestens neun Tage lang transkriptionell aktiv sind und replizieren. Durch Inaktivierung des viralen E8{\textasciicircum}E2 Repressors (E8-/E8{\textasciicircum}E2-) erhält das HPV49 Genom die Fähigkeit NHK zu immortalisieren. Die immortalisierten HPV49 E8- Zelllinien enthalten große Mengen an episomalen Virusgenomen und viralen Transkripten und behalten diese in Kultur über einen langen Zeitraum. Nicht nur der Verlust der E6 und E7 Onkogene, sondern auch eine Inaktivierung der E1 oder E2 Replikationsgene verhindern die Immortalisierung. Die E8-/E1- und E8-/E2- Genome zeigen deutlich niedrigere E6 und E7 Transkriptmengen in transienten Experimenten. Dies legt nahe, dass für die Immortalisierung eine starke E6 und E7 Expression von extrachromosomalen Virusgenomen erforderlich ist. Die Notwendigkeit für eine Inaktivierung von E8 im Kontext von intakten E1 und E2 Genen für die Immortalisierung von NHK zeigt, dass E8{\textasciicircum}E2 eine wichtige Rolle bei der Kontrolle der Onkogenität von beta-HPV spielen könnte, und weist auf grundlegende Unterschiede zwischen HPV49 und HR-HPV Genomen hin. Durch RNA-Sequenzierung der HPV49 E8- positiven Zelllinien konnten bekannte Spleißverknüpfungen bestätigt, das frühe Polyadenylierungssignal lokalisiert und Hinweise auf unterschiedliche virale Promotoren erhalten werden. Außerdem wurden neue Spleißverbindungen kartiert und ein neuer Spleißdonor im E6 Gen funktionell untersucht. Dieser beeinflusst die Menge an E6 Protein und vermutlich dadurch die Immortalisierung durch das HPV49 E8- Genom. @@ -11875,6 +19194,60 @@ @article{rehm_analyse_2023 year = {2023} } +@article{rehm_splice_2025, + author = {Rehm, Tina M. and Iftner, Thomas and Stubenrauch, Frank}, + doi = {10.1128/jvi.01640-24}, + journal = {Journal of Virology}, + keywords = {{\textgreater}UseGalaxy.eu, Betapapillomavirus, Cell Transformation, Viral, Keratinocytes, Oncogene Proteins, Viral, RNA Splice Sites}, + month = {January}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e01640--24}, + title = {A splice donor in {E6} influences keratinocyte immortalization by beta-{HPV49}}, + url = {https://journals.asm.org/doi/full/10.1128/jvi.01640-24}, + urldate = {2025-02-16}, + volume = {0}, + year = {2025} +} + +@phdthesis{reichenbach_einfluss_2024, + abstract = {Vitamin D nimmt nicht nur eine wichtige Funktion im Knochenstoffwechsel ein, es spielt darüber hinaus eine bedeutende Rolle bei der angeborenen und adaptiven Immunabwehr 3 und auch bei malignen Neoplasien ist der Vitamin D Serumspiegel der Patienten von prognostischer Relevanz 7, 37. Bei B Zell Lymphomen konnte gezeigt werden, dass ein höherer Vitamin D Spiegel mit einem besseren Überleben assoziiert ist, vor allem wenn die Patienten mit dem monoklonalen Antikörper Rituximab behandelt wurden 6. Die Wirkung monoklonaler Antikörper, die heute in der Tumortherapie routinemäßig eingesetzt werden, ist von der antikörperabhängigen zellvermittelten Zytotoxizität der natürlichen Killerzellen abhängig 60, 75. Basierend auf den Ergebnissen der Ricover 60 Studie konnten Bittenbring et al. bei sieben Probanden nach Supplementation von Vitamin D und Normalisierung des 25 Hydroxyvitamin D-Spiegels eine signifikant höhere antikörperabhängige zellvermittelte Zytotoxizität nachweisen 6. +Für die vorliegende Arbeit wurden zehn Probanden (fünf Frauen und fünf Männer) mit einem Vitamin D-Mangel beziehungsweise einer Vitamin D-Insuffizienz rekrutiert. Nach erfolgter Vitamin D-Supplementation lag der Vitamin D-Serumspiegel aller zehn Probanden im suffizienten Bereich (71,48 ng/ml ± 9,47 ng/ml). Die Aktivität der antikörperabhängigen zellvermittelten Zytotoxizität stieg bei allen Probanden nach Supplementation an, ein signifikanter Anstieg konnte bei acht von zehn Probanden nachgewiesen werden. +Es muss folglich angenommen werden, dass die Supplementation von Vitamin D Einfluss auf die Transkription von Genen der natürlichen Killerzellen nimmt, die für die Abwehrfunktion ausschlaggebend sind. Deshalb wurde in dieser Studie die Genexpression an Target-Zellen aktivierter und nicht aktivierter (passiver) natürlicher Killerzellen vor und nach in vivo Vitamin D Supplementation mittels RNA Sequenzierung untersucht. +Diese Arbeit konnte sowohl bei passiven als auch bei aktivierten natürlichen Killerzellen nach im Vergleich zu vor in vivo Vitamin D Supplementation Veränderungen im Transkriptom nachweisen, insbesondere aber bei aktivierten natürlichen Killerzellen. Auch bei den zusätzlich durchgeführten Vergleichen aktivierter versus passiver natürlicher Killerzellen jeweils vor und nach Vitamin D Supplementation zeigten sich zahlreiche Gene differentiell exprimiert. Wobei bei diesen beiden Vergleichen viele der hoch- und runterregulierten Gene unabhängig vom Vitamin D Status übereinstimmen und somit auf die Aktivierung der natürlichen Killerzellen zurückzuführen sind. 2.440 Gene wiesen jedoch eine signifikante Änderung der Expression nach Aktivierung der natürlichen Killerzellen nur nach Vitamin D Supplementation auf, diese Gene könnten von besonderem Interesse sein. +Da nicht einzelne differenziell exprimierte Gene die Funktion einer Zelle ausmachen, sondern das Zusammenspiel vieler Transkripte, die sich innerhalb einer Zelle unter verschiedenen Bedingungen zu biologischen Pfaden (engl. Pathways) organisieren, erfolgte zudem eine Genmengen Anreicherungsanalyse. Damit konnte nachgewiesen werden, dass zentrale Pfade der Immunabwehr und der Signaltransduktion bei den verschiedenen Vergleichen angereichert werden. Hervorzuheben ist, dass sowohl bei passiven als auch bei aktivierten natürlichen Killerzellen nach Vitamin D Supplementation der “Cytokine-cytokine receptor interaction“ Pathway signifikant stärker exprimiert wird. Dieser Pathway ist entscheidend für die intrazelluläre Regulation von Zellen, die an der angeborenen und der adaptiven Immunabwehr beteiligt sind 17. Bereits bei peripheren mononukleären Zellen konnte eine Anreicherung des “Cytokine-cytokine receptor interaction“ Pathways nach ex vivo Vitamin D Supplementation nachgewiesen werden 24. +Darüber hinaus konnte in der vorliegenden Arbeit gezeigt werden, dass der Pathway “natural killer cell mediated cytotoxicity“ bei passiven und aktivierten natürlichen Killerzellen nach Vitamin D Supplementation angereichert wird. Dieser biologische Pfad beinhaltet sowohl die Kaskaden der aktivierenden und inhibierenden Rezeptoren von natürlichen Killerzellen im Allgemeinen, als auch die der antikörperabhängigen zellvermittelten Zytotoxizität im Speziellen 47.}, + author = {Reichenbach, Franziska Julia}, + doi = {10.22028/D291-43528}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {de}, + note = {Accepted: 2024-11-28T11:00:30Z}, + school = {Saarländische Universitäts- und Landesbibliothek}, + shorttitle = {Der {Einfluss} von {Vitamin} {D} auf die {Genexpression} aktivierter und nicht aktivierter natürlicher {Killerzellen}}, + title = {Der {Einfluss} von {Vitamin} {D} auf die {Genexpression} aktivierter und nicht aktivierter natürlicher {Killerzellen} : {Transkriptomanalyse} mittels {RNA}-{Sequenzierung}}, + type = {{doctoralThesis}}, + url = {https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/39054}, + urldate = {2025-09-03}, + year = {2024} +} + +@article{reimann_specificities_2020, + abstract = {Many bacteria and archaea possess an RNA-guided adaptive and inheritable immune system that consists of clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. In most CRISPR-Cas systems, the maturation of CRISPR-derived small RNAs (crRNAs) is essential for functionality. Cas6 endonucleases function as the most frequent CRISPR RNA maturation enzymes. In the cyanobacterium \textit{Anabaena} sp. PCC 7120, ten CRISPR loci are present, but only two \textit{cas} gene cassettes plus a Tn7-associated eleventh array. In this study, we deleted the two \textit{cas6} genes \textit{alr1482} (Type III-D) or \textit{alr1566} (Type I-D) and tested the specificities of the two corresponding enzymes in the resulting mutant strains, as recombinant proteins and in a cell-free transcription-translation system. The results assign the direct repeats (DRs) to three different groups. While Alr1566 is specific for one group, Alr1482 has a higher preference for the DRs of the second group but can also cleave those of the first group. We found that this cross-recognition limits crRNA accumulation for the Type I-D system \textit{in vivo}. We also show that the DR of the \textit{cas} gene-free CRISPR array of cyanophage N-1 is processed by these enzymes, suggesting that it is fully competent in association with host-encoded Cas proteins. The data support the functionality of CRISPR arrays that frequently appear fragmented to multiple genomic loci in multicellular cyanobacteria and disfavour other possibilities, such as the nonfunctionality of these orphan repeat-spacer arrays. Our results show the functional coordination of Cas6 endonucleases with both neighbouring and remote repeat-spacer arrays in the CRISPR-Cas system of cyanobacteria.}, + author = {Reimann, Viktoria and Ziemann, Marcus and Li, Hui and Zhu, Tao and Behler, Juliane and Lu, Xuefeng and Hess, Wolfgang R}, + doi = {10.1080/15476286.2020.1774197}, + issn = {1547-6286}, + journal = {RNA Biol}, + keywords = {{\textgreater}UseGalaxy.eu, CRISPR-Cas Systems}, + language = {eng}, + month = {October}, + number = {10}, + pages = {1442--1453}, + title = {Specificities and functional coordination between the two {Cas6} maturation endonucleases in {Anabaena} sp. {PCC} 7120 assign orphan {CRISPR} arrays to three groups}, + url = {http://europepmc.org/abstract/MED/32453626}, + volume = {17}, + year = {2020} +} + @article{retamal-morales_draft_2018, abstract = {Biosurfactants are amphipathic molecules with relevance in biotechnology due to their structural diversity, low toxicity and biodegradability. The genus Rhodococcus has extensively been studied because of its capacity to produce trehalose-containing surfactants as well as trehalose lipids as potential pathogenic factor. Here we present the draft genome sequence of Rhodococcus erythropolis B7g isolated with toluene from fuel-contaminated soil. The genome comprises 7,175,690 bp in 121 contigs, a G + C content of 62,4\% and 7,153 coding DNA sequences (CDSs), and it contains genes for trehalose biosynthesis and surfactant production. Additionally, genes for the production of trehalose-tetraester biosurfactant were identified, whose function was experimentally verified making the strain B7g a potential candidate for use in bioremediation applications or in biosurfactant exploration.}, author = {Retamal-Morales, Gerardo and Heine, Thomas and Tischler, Judith S. and Erler, Beate and Gröning, Janosch A. D. and Kaschabek, Stefan R. and Schlömann, Michael and Levicán, Gloria and Tischler, Dirk}, @@ -11904,6 +19277,24 @@ @article{reyes_characterization_2023 year = {2023} } +@article{reyes_loaiciga_comprehensive_2025, + abstract = {In the budding yeast Saccharomyces cerevisiae, the widespread adoption of ribosome profiling technology has allowed the discovery of evidence of transcription and translation for thousands of small proteins or microproteins whose importance was once disregarded. Both conserved and evolutionarily short-lived microproteins have demonstrated relevant involvement in biological functions. However, sequences exist in a broad spectrum of conservation. Here, we tested whether these small proteins in yeast detected by ribosome profiling technology have different properties across their levels of conservation, and how do these properties compare with the canonical small protein-coding sequences.}, + author = {Reyes Loaiciga, Cristopher and Li, Weiyi and Zhao, Xin-Qing and Li, Jing}, + doi = {10.1186/s12864-025-12064-0}, + issn = {1471-2164}, + journal = {BMC Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, De novo origination, Fungi, Microprotein, Phylostratigraphy, Ribo-seq, Saccharomyces cerevisiae, Sequence evolution}, + language = {en}, + month = {September}, + number = {1}, + pages = {856}, + title = {Comprehensive profiling of ribo-seq detected small sequences in yeast reveals robust conservation patterns and their potential mechanisms of origin}, + url = {https://doi.org/10.1186/s12864-025-12064-0}, + urldate = {2025-10-03}, + volume = {26}, + year = {2025} +} + @article{richter_genome_2024, abstract = {{\textless}p{\textgreater}{\textless}italic{\textgreater}Diplocarpon coronariae{\textless}/italic{\textgreater} is a fungal pathogen that is prevalent in low-input apple production. Over the past 15 years, it has become increasingly distributed in Europe. However, comprehensive insights into its biology and pathogenicity remain limited. One particular aspect is the rarity of the sexual morph of this pathogen, a phenomenon hitherto unobserved in Europe. {\textless}italic{\textgreater}Diplocarpon coronariae{\textless}/italic{\textgreater} reproduces through a heterothallic mating system requiring at least two different mating types for sexual reproduction. Genes determining the mating types are located on the mating-type locus. In this study, {\textless}italic{\textgreater}D. coronariae{\textless}/italic{\textgreater} strain DC1\_JKI from Dresden, Germany, was sequenced and used to unravel the structure of the mating type locus. Using short-read and long-read sequencing methods, the first gapless and near-complete telomere-to-telomere genome assembly of {\textless}italic{\textgreater}D. coronariae{\textless}/italic{\textgreater} was achieved. The assembled genome spans 51.2 Mbp and comprises 21 chromosome-scale contigs of high completeness. The generated genome sequence was used to {\textless}italic{\textgreater}in silico{\textless}/italic{\textgreater} elucidate the structure of the mating-type locus, identified as MAT1-2. Furthermore, an examination of MAT1-1 and MAT1-2 frequency across a diverse set of samples sourced from Europe and Asia revealed the exclusive presence of MAT1-2 in European samples, whereas both MAT loci were present in Asian counterparts. Our findings suggest an explanation for the absence of the sexual morph, potentially linked to the absence of the second mating idiomorph of {\textless}italic{\textgreater}D. coronariae{\textless}/italic{\textgreater} in European apple orchards.{\textless}/p{\textgreater}}, author = {Richter, Sophie and Kind, Sabine and Oberhänsli, Thomas Wolfgang and Schneider, Michael and Nenasheva, Natalia and Hoff, Katharina and Keilwagen, Jens and Yeon, Il-Kweon and Philion, Vincent and Moriya, Shigeki and Flachowsky, Henryk and Patocchi, Andrea and Wöhner, Thomas Wolfgang}, @@ -11927,7 +19318,7 @@ @article{richter_genomic_2024 doi = {10.1021/acs.est.4c02431}, issn = {0013-936X}, journal = {Environmental Science \& Technology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Escherichia coli, beta-Lactamases}, month = {August}, note = {Publisher: American Chemical Society}, number = {32}, @@ -11941,9 +19332,13 @@ @article{richter_genomic_2024 } @article{riediger_analysis_2020, + abstract = {Although regulatory small RNAs have been reported in photosynthetic cyanobacteria, the lack of clear RNA chaperones involved in their regulation poses a conundrum. Here, we analyzed the full complement of cellular RNAs and proteins using gradient profiling by sequencing (Grad-seq) in Synechocystis 6803. Complexes with overlapping subunits such as the CpcG1-type versus the CpcL-type phycobilisomes or the PsaK1 versus PsaK2 photosystem I pre(complexes) could be distinguished, supporting the high quality of this approach. Clustering of the in-gradient distribution profiles followed by several additional criteria yielded a short list of potential RNA chaperones that include an YlxR homolog and a cyanobacterial homolog of the KhpA/B complex. The data suggest previously undetected complexes between accessory proteins and CRISPR-Cas systems, such as a Csx1-Csm6 ribonucleolytic defense complex. Moreover, the exclusive association of either RpoZ or 6S RNA with the core RNA polymerase complex and the existence of a reservoir of inactive sigma-antisigma complexes is suggested. The Synechocystis Grad-seq resource is available online at https://sunshine.biologie.uni-freiburg.de/GradSeqExplorer/ providing a comprehensive resource for the functional assignment of RNA-protein complexes and multisubunit protein complexes in a photosynthetic organism.}, author = {Riediger, Matthias and Spät, Philipp and Bilger, Raphael and Voigt, Karsten and Maček, Boris and Hess, Wolfgang R.}, doi = {10.1093/plcell/koaa017}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {1040-4651}, + journal = {Plant Cell}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Photosynthesis, Sequence Analysis, RNA}, + language = {eng}, month = {December}, note = {Publisher: Oxford University Press (OUP)}, number = {2}, @@ -11961,7 +19356,7 @@ @article{riesle_activator-blocker_2023 doi = {10.1038/s41467-023-41507-z}, issn = {2041-1723}, journal = {Nature Communications}, - keywords = {{\textgreater}UseGalaxy.eu, Development, Differential equations, Gastrulation, Gene expression profiling, Transcriptional regulatory elements}, + keywords = {{\textgreater}UseGalaxy.eu, Development, Differential equations, Gastrulation, Gene expression profiling, Histones, Transcriptional regulatory elements, Zebrafish}, language = {en}, month = {September}, note = {Publisher: Nature Publishing Group}, @@ -11995,13 +19390,47 @@ @article{ristinmaa_resin_2023 year = {2023} } +@article{ritson_repeated_2025, + abstract = {The mechanism by which chronic systemic inflammation contributes to cerebral endothelial dysfunction and neurological disorders is unclear, although endothelial inflammatory signalling is considered a cornerstone of this process. Here, we have performed transcriptomic analysis of published RNASeq datasets and identified consistent upregulation of the Tumour Necrosis Factor—C-X-C Motif Chemokine Ligand 10 (TNF-CXCL10) signalling pathway in mouse cerebral endothelial cells following a single inflammatory challenge. We subsequently investigated the effects of repeated low-level inflammation on the modulation of this pathway in a mouse cerebral endothelial cell line, analysing the effect on markers of endothelial cell activation and changes in cellular function, as a potential mechanism underlying the cerebrovascular response to low-level systemic inflammation. Mouse cerebral endothelial cells (bEnd.3) were exposed to hour-long treatments with phosphate buffered saline (PBS), a single low concentration of TNF (0.5 ng/mL), repeated low-concentration TNF (0.5 ng/mL, 1 h × 4 days) or a single cumulative concentration of TNF (2.0 ng/mL). RNA and protein were extracted 4 and 24 h after the final treatment for analysis of gene/protein expression using qRT-PCR and western blotting. Repeated inflammatory challenge significantly upregulated both Intercellular Adhesion Molecule 1 (ICAM1) and CXCL10 at the mRNA and protein levels. Signal transducer and activator of transcription 1 (STAT1) and phosphorylated-STAT1 (pSTAT1) protein levels were also increased at 4 and 24 h. Differentially, tumor necrosis factor receptor-associated factor 2 (TRAF2) and Interferon gamma (IFNγ) gene expression were decreased at 4 h, returning to control levels at 24 h. Functional analysis revealed significant increases in endothelial cell proliferation and apoptosis in the presence of repeated TNF exposure. CXCL10 knockdown with small interfering RNA (siRNA) reduced mean caspase 3/7 activity induced by the repeated inflammatory paradigm. These data suggest an upregulation of the TNF-CXCL10 pathway in response to low-level repetitive inflammation in mouse cerebral endothelial cells. Modulation of this pathway may represent a broad therapeutic target for neurovascular disease.}, + author = {Ritson, Megan and Xia, Dong and Wheeler-Jones, Caroline and Stolp, Helen B.}, + copyright = {© 2025 The Author(s). Journal of Neurochemistry published by John Wiley \& Sons Ltd on behalf of International Society for Neurochemistry.}, + doi = {10.1111/jnc.70130}, + issn = {1471-4159}, + journal = {Journal of Neurochemistry}, + keywords = {{\textgreater}UseGalaxy.eu, Chemokine CXCL10, Endothelial Cells, Inflammation, Signal Transduction, Tumor Necrosis Factor-alpha, apoptosis, cerebrovascular, endothelium, inflammation, proliferation}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jnc.70130}, + number = {6}, + pages = {e70130}, + title = {Repeated {Low}-{Level} {Inflammatory} {Challenge} {Leads} to {Alterations} in the {TNF}-{CXCL10} {Signalling} {Pathway} in {Mouse} {Cerebral} {Endothelial} {Cells} {In} {Vitro}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jnc.70130}, + urldate = {2025-07-12}, + volume = {169}, + year = {2025} +} + +@article{robinson_deciphering_2025, + abstract = {For 25 years, analysis of the \textit{gp60} gene has been the cornerstone of \textit{Cryptosporidium} subtyping, particularly for \textit{Cryptosporidium hominis} and \textit{Cryptosporidium parvum}, during population-based and epidemiological studies. This gene, which encodes a 60 kDa glycoprotein, is highly polymorphic with several variable features that make it particularly useful for differentiating within \textit{Cryptosporidium} species. However, while this variability has proven useful for subtyping, it has on occasion resulted in alternative interpretations, and descriptions of novel and unusual features have been added to the nomenclature system, resulting in inconsistency and confusion. The components of the \textit{gp60} gene sequence used in the nomenclature that are discussed here include "R" repeats, "r" repeats, alphabetical suffixes, "variant" designations, and the use of the Greek alphabet as a family designation. As the subtyping scheme has expanded over the years, its application to different \textit{Cryptosporidium} species has also made the scheme more complex. For example, key features may be absent, such as the typical TCA/TCG/TCT serine microsatellite that forms a major part of the nomenclature in \textit{C. hominis} and \textit{C. parvum}. As is to be expected in such a variable gene, different primer sets have been developed for the amplification of the \textit{gp60} in various species and these have been collated. Here we bring together all the current components of \textit{gp60}, including a guide to the nomenclature in various species, software to assist in analysing sequences, and links to useful reference resources with an aim to promote standardisation of this subtyping tool.}, + author = {Robinson, Guy and Chalmers, Rachel M and Elwin, Kristin and Guy, Rebecca A and Bessonov, Kyrylo and Troell, Karin and Xiao, Lihua}, + doi = {10.1016/j.crpvbd.2025.100257}, + issn = {2667-114X}, + journal = {Current research in parasitology \& vector-borne diseases}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {100257}, + title = {Deciphering a cryptic minefield: {A} guide to \textit{{Cryptosporidium} gp60} subtyping}, + url = {http://europepmc.org/abstract/MED/40256454}, + volume = {7}, + year = {2025} +} + @article{robson_environmental_2024, abstract = {Formation of functional pollen and successful fertilization rely on the spatial and temporal regulation of anther and pollen development. This process responds to environmental cues to maintain optimal fertility despite climatic changes. Arabidopsis transcription factors basic helix–loop–helix (bHLH) 10, 89, and 91 were previously thought to be functionally redundant in their control of male reproductive development, however here we show that they play distinct roles in the integration of light signals to maintain pollen development under different environmental conditions. Combinations of the double and triple bHLH10,89,91 mutants were analysed under normal (200 μmol m–2 s–1) and low (50 μmol m–2 s–1) light conditions to determine the impact on fertility. Transcriptomic analysis of a new conditionally sterile bhlh89,91 double mutant shows differential regulation of genes related to sexual reproduction, hormone signal transduction, and lipid storage and metabolism under low light. Here we have shown that bHLH89 and bHLH91 play a role in regulating fertility in response to light, suggesting that they function in mitigating environmental variation to ensure fertility is maintained under environmental stress.}, author = {Robson, Jordan K and Tidy, Alison C and Thomas, Stephen G and Wilson, Zoe A}, doi = {10.1093/jxb/erad480}, issn = {0022-0957}, journal = {Journal of Experimental Botany}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, Arabidopsis Proteins}, month = {March}, number = {7}, pages = {1934--1947}, @@ -12012,6 +19441,22 @@ @article{robson_environmental_2024 year = {2024} } +@article{rocha_escherichia_2025, + abstract = {Escherichia coli sequence type 131:H:22 is a consequential lineage of extraintestinal pathogenic E. coli, associated with human pyelonephritis and sepsis. We report the transmission of avian pathogenic E. coli in a parrot rehabilitation center in Brazil and the presence of a high-risk zoonotic lineage of extraintestinal pathogenic E. coli sequence type 131-H22.}, + author = {Rocha, Victoria Galdino Pavlenco and Barbosa, Fernanda Borges and Ruiz, Joaquim and Christensen, Henrik and Knöbl, Terezinha}, + doi = {10.3201/eid3110.241279}, + issn = {1080-6040}, + journal = {Emerging infectious diseases}, + keywords = {{\textgreater}UseGalaxy.eu, APEC, Bacteria, Bacterial infections, Brazil, Escherichia Coli, Expec, High-risk, Parrots, St131-h22, Zoonoses, Zoonotic Lineage}, + month = {October}, + number = {10}, + pages = {2025--2028}, + title = {Escherichia coli {Sequence} {Type} 131-{H22} in {Parrots} from {Illegal} {Pet} {Trade}, {Brazil}, 2024}, + url = {https://europepmc.org/articles/PMC12483012}, + volume = {31}, + year = {2025} +} + @article{rodrigues_alves_barbosa_phenotypic_2024, abstract = {Essential genes are deemed crucial for survival and/or reproductive success, hence, their loss of function leads to lethality. However, gene essentiality is not static, but dependent on multiple factors, including the genetic background. The genetic background affects gene essentiality through genetic modifiers, second-site variants capable of interacting with the primary variant and altering phenotype. Genetic modifiers can act as suppressors, alleviating the phenotype, or enhancers, exacerbating the phenotype. The plasticity (modification) of gene essentiality caused by genetic modifiers has been shown in multiple species. In Caenorhabditis elegans, recent evidence shows phenotypic variability for knock-down of essential genes in two natural isolates: N2 and CB4856. N2 represents the laboratory-cultivated strain, while CB4856 is one of the strains with most diverse genome in comparison to N2. Much has been explored for these two genetic backgrounds, but little is known about the plasticity of gene essentiality in other C. elegans wild isolates. Thus, I here explore the effect of the genetic background on the plasticity of two genes, known as essential in the N2 background, but potentially dispensable in CB4856: the Metaphase-to-Anaphase Transition Defect gene (mat-1), and the Conserved Germline Helicase (cgh-1). These are involved in cell division and posttranscriptional regulation, respectively. Here, I further investigate the plasticity of mat-1 and cgh-1 in N2 and CB4856 backgrounds, and also include four other wild isolate backgrounds from diverse geographical locations (GXW1, KR314, JU1400, and AB1). Using hatch rate and propagation assays, I explored the phenotype of mat-1 and cgh-1 knockdowns across the six natural isolates using temperature-sensitive alleles and uncovered phenotypic variability for the embryonic lethal phenotype, suggestively due to influence of each genetic background. Next, bioinformatics and genomics tools were utilized for identification of candidate genetic modifiers for mat-1 and cgh-1 and led to prioritization of eight extragenic variants. Out of these, none showed notable modifying activity when studied in isolation. Importantly, this work shows the challenges associated with identifying true genetic modifiers in genomes with substantial variation. Undeniably, understanding more about a gene and its phenotype under different conditions and genetic backgrounds may be fundamental for elucidating fixed and plastic genetic interactions.}, author = {Rodrigues Alves Barbosa, Victoria}, @@ -12024,10 +19469,97 @@ @article{rodrigues_alves_barbosa_phenotypic_2024 year = {2024} } +@misc{rodriguez-alarcon_microbial_2024, + abstract = {This study aimed to investigate the microbial diversity of bacteria in the +composite microbial community associated with Culicoides reevesi biting +midges from Buenaventura municipality in the state of Chihuahua, Mexico, +using a Sanger sequencing 16s rRNA metagenomics approach. Adult +females of Culicoides reevesi were collected by human landing catches +in the rainy season of 2023 and morphologically identified. They were +grouped into pools of 25 individuals from which genomic DNA (gDNA) was +extracted. Sanger sequencing of 16S rRNA was performed for a total of +4 pools, and the amplicon sequencing of the V3-V4 hypervariable region +was done on Illumina Mseq platform to detect bacterial communities. The +bioinformatic analysis included quality assessment, taxonomic classification, +and visualization. The evaluation of the microbial community involved +assessing taxa abundance and diversity using Mothur and QIIME2 software +included in Galaxy Tool Shed (https://usegalaxy.eu/). Our study presents, +for the first time in México and worldwide, an in-depth analysis of the +bacteriome composition in C. reevesi, utilizing a 16S rRNA metagenomic +approach. We emphasize the prevalence of dominant bacterial phyla, +particularly Proteobacteria, alongside varying abundances of Actinobacteria, +Firmicutes, Acidobacteria, and Bacteroidota, with a notable occurrence +of Tenericutes. We identified intriguing species of both human and animal +pathogenic bacteria. Moreover, we observed the absence of unidentified +bacterial sequences, alongside the presence of other bacterial groups +associated with the environment or plants. This has implications for both +healthcare and ecological management, potentially simplifying control +measures but also posing risks if the dominant species are harmful. This +research enhances our understanding of the microbiome associated with +Culicoides species, such as Culicoides reevesi, underscoring the need for +further investigation to fully grasp their ecological importance and impact on +public health.}, + author = {Rodríguez-Alarcón, Carlos Arturo and Garza Hernandez, Javier Alfonso and Gonzalez Peña, Rodolfo and Hidalgo Martínez, David Orlando and Huerta, Herón and Adame Gallegos, Jaime R. and De Luna Santillana, Erick J. and Laredo-Tiscareño, Stephanie Viridiana and García Rejón, Julian E. and Hernández-Triana, Luis M.}, + copyright = {CC0 1.0 Universal}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en\_US}, + month = {November}, + note = {Accepted: 2025-01-20T21:38:58Z}, + shorttitle = {{MICROBIAL} {DIVERSITY} {OF} {CULICOIDES} {REEVESI} {FROM} {CHIHUAHUA}, {MEXICO}}, + title = {{MICROBIAL} {DIVERSITY} {OF} {CULICOIDES} {REEVESI} {FROM} {CHIHUAHUA}, {MEXICO}: {A} {METAGENOMIC} {ANALYSIS} {OF} {RRNA} {16S}}, + type = {Memoria en abstract}, + url = {https://cathi.uacj.mx/handle/20.500.11961/30964}, + urldate = {2025-01-28}, + year = {2024} +} + +@article{rodriguez-outeirino_mir-106b_2022, + abstract = {Satellite cells (SCs), muscle stem cells, display functional heterogeneity, and dramatic changes linked to their regenerative capabilities are associated with muscle-wasting diseases. SC behavior is related to endogenous expression of the myogenic transcription factor MYF5 and the propensity to enter into the cell cycle. Here, we report a role for miR-106b reinforcing MYF5 inhibition and blocking cell proliferation in a subset of highly quiescent SC population. miR-106b down-regulation occurs during SC activation and is required for proper muscle repair. In addition, miR-106b is increased in dystrophic mice, and intramuscular injection of antimiR in injured mdx mice enhances muscle regeneration promoting transcriptional changes involved in skeletal muscle differentiation. miR-106b inhibition promotes the engraftment of human muscle stem cells. Furthermore, miR-106b is also high in human dystrophic muscle stem cells and its inhibition improves intrinsic proliferative defects and increases their myogenic potential. This study demonstrates that miR-106b is an important modulator of SC quiescence, and that miR-106b may be a new target to develop therapeutic strategies to promote muscle regeneration improving the regenerative capabilities of injured dystrophic muscle.}, + author = {Rodriguez-Outeiriño, Lara and Hernandez-Torres, Francisco and Ramirez de Acuña, Felicitas and Rastrojo, Alberto and Creus, Carlota and Carvajal, Alejandra and Salmeron, Luis and Montolio, Marisol and Soblechero-Martin, Patricia and Arechavala-Gomeza, Virginia and Franco, Diego and Aranega, Amelia Eva}, + doi = {10.1016/j.omtn.2022.08.025}, + issn = {2162-2531}, + journal = {Molecular therapy. Nucleic acids}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {September}, + pages = {769--786}, + title = {{miR}-106b is a novel target to promote muscle regeneration and restore satellite stem cell function in injured {Duchenne} dystrophic muscle}, + url = {http://europepmc.org/abstract/MED/36159592}, + volume = {29}, + year = {2022} +} + +@article{rogg_arp23-dependent_2025, + abstract = {Proteinuric kidney disease substantially affects renal tubules through incompletely understood mechanisms. We identify elongation of primary cilia in distal renal tubules in the context of glomerular nephropathy. In renal biopsies and mouse models, tubular injury correlates with ciliary elongation, tubule dilation, and disruption of the cortical actin cytoskeleton. In vitro studies implicate biophysical cues of the glomerular filtrate and subsequent dysregulation of the actin cytoskeleton as contributing factors, confirmed by conditional deletion of N-WASP and Arp2/3 in vivo and in vitro. Electron and fluorescence microscopy revealed enlarged ciliary pockets, basal body mislocalization, and intracellular cilia formation in +Arp3 +knockout conditions. Transcriptome analysis identifies the essential role of cilia in maintaining adaptive tubular cell states, while persistent activation leads to disease progression through extracellular matrix remodeling, exemplified by Tenascin-C. Our findings establish cilia as central mediators of tubular adaptation to injury and identify the Arp2/3-dependent actin cytoskeleton as a critical regulator, providing essential insights into the pathogenesis of chronic kidney disease. + +, +Proteinuria causes ciliary elongation and actin cytoskeleton remodeling, revealing a key mechanism in kidney disease progression.}, + author = {Rogg, Manuel and Weißer, Lisa and Maier, Jasmin I. and Sigle, August and Helmstädter, Martin and Stigler, Marlene and Sammarco, Alena and Gräwe, Katja and Andreev, Grigor and Kark, Charlotte and Ramakrishnan, Suresh K. and Özel, Cem and Butt, Linus and Arnold, Frederic and Bechtel-Walz, Wibke and Schilling, Oliver and Tanriver, Yakup and Brinkkötter, Paul and Grabbert, Markus and Simons, Matias and Werner, Martin and Kretz, Oliver and Benzing, Thomas and Huber, Tobias B. and Schell, Christoph}, + doi = {10.1126/sciadv.ady1623}, + issn = {2375-2548}, + journal = {Science Advances}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {November}, + number = {48}, + pages = {eady1623}, + title = {Arp2/3-dependent regulation of ciliogenesis governs adaptive distal tubular epithelial cell states in kidney disease}, + url = {https://www.science.org/doi/10.1126/sciadv.ady1623}, + urldate = {2025-12-01}, + volume = {11}, + year = {2025} +} + @article{rogg_srgap1_2021, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Previous research demonstrated that small Rho GTPases, modulators of the actin cytoskeleton, are drivers of podocyte foot-process effacement in glomerular diseases, such as FSGS. However, a comprehensive understanding of the regulatory networks of small Rho GTPases in podocytes is lacking.{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}We conducted an analysis of podocyte transcriptome and proteome datasets for Rho GTPases; mapped \textit{in vivo}, podocyte-specific Rho GTPase affinity networks; and examined conditional knockout mice and murine disease models targeting \textit{Srgap1}. To evaluate podocyte foot-process morphology, we used super-resolution microscopy and electron microscopy; \textit{in situ} proximity ligation assays were used to determine the subcellular localization of the small GTPase-activating protein SRGAP1. We performed functional analysis of CRISPR/Cas9-generated \textit{SRGAP1} knockout podocytes in two-dimensional and three-dimensional cultures and quantitative interaction proteomics.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}We demonstrated SRGAP1 localization to podocyte foot processes \textit{in vivo} and to cellular protrusions \textit{in vitro}. \textit{Srgap1$^{\textrm{fl/fl}}$*Six2Cre} but not \textit{Srgap1$^{\textrm{fl/fl}}$*hNPHS2Cre} knockout mice developed an FSGS-like phenotype at adulthood. Podocyte-specific deletion of \textit{Srgap1} by \textit{hNPHS2Cre} resulted in increased susceptibility to doxorubicin-induced nephropathy. Detailed analysis demonstrated significant effacement of podocyte foot processes. Furthermore, \textit{SRGAP1}-knockout podocytes showed excessive protrusion formation and disinhibition of the small Rho GTPase machinery \textit{in vitro}. Evaluation of a SRGAP1-dependent interactome revealed the involvement of SRGAP1 with protrusive and contractile actin networks. Analysis of glomerular biopsy specimens translated these findings toward human disease by displaying a pronounced redistribution of SRGAP1 in FSGS.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}SRGAP1, a podocyte-specific RhoGAP, controls podocyte foot-process architecture by limiting the activity of protrusive, branched actin networks. Therefore, elucidating the complex regulatory small Rho GTPase affinity network points to novel targets for potentially precise intervention in glomerular diseases.}, author = {Rogg, Manuel and Maier, Jasmin I. and Dotzauer, Robert and Artelt, Nadine and Kretz, Oliver and Helmstädter, Martin and Abed, Ahmed and Sammarco, Alena and Sigle, August and Sellung, Dominik and Dinse, Patrick and Reiche, Karoline and Yasuda-Yamahara, Mako and Biniossek, Martin L. and Walz, Gerd and Werner, Martin and Endlich, Nicole and Schilling, Oliver and Huber, Tobias B. and Schell, Christoph}, doi = {10.1681/asn.2020081126}, + issn = {1046-6673}, + journal = {J Am Soc Nephrol}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {January}, note = {Publisher: American Society of Nephrology (ASN)}, number = {3}, @@ -12059,6 +19591,37 @@ @article{rogg_yaptazarhgap29rhoa_2023 year = {2023} } +@article{rohrbach_microplastic_2025, + abstract = {Unmanaged plastic waste in Sub-Saharan Africa pollutes large areas and degrades into microplastics (MPs). Surfaces of MP are colonized by bacteria and fungi, resulting in the plastisphere. Plastispheres from high population hotspots on the African continent enrich pathogenic fungi, posing a potential threat to human health. Prokaryotes in such plastispheres are unknown to date. Thus, we analysed the prokaryotic microbiome of native plastisphere and soil by 16S rRNA gene amplicon sequencing, with a focus on community assembly mechanisms and putative pathogenic bacteria. A strong plastic-dependent depletion of archaeal ammonia oxidizing Nitrososphaeraceae was observed. Prokaryotic but not archaeal beta diversity significantly differed between plastisphere and soil microbiomes. The prokaryotic pathogenic potential in the plastisphere was marginally increased relative to soil, suggesting that MP is a driver for fungal rather than bacterial pathogens. Null model comparisons revealed a moderately stronger effect of deterministic selection events in the plastisphere than in soil. We observed a severe disruption of cooccurrence network connectivity in plastisphere communities in contrast to bulk soil communities. This study closes the knowledge gap on plastic debris in Sub-Saharan terrestrial environments, and the observed effects on archaea and cooccurrence networks suggest negative impacts on nitrification and stability of microbial communities.}, + author = {Rohrbach, Stephan and Gkoutselis, Gerasimos and Hink, Linda and Weig, Alfons R and Rambold, Gerhard and Horn, Marcus A}, + doi = {10.1093/femsec/fiaf085}, + issn = {0168-6496}, + journal = {FEMS microbiology ecology}, + keywords = {{\textgreater}UseGalaxy.eu, Community Assembly Mechanisms, Metabarcoding, Microplastics, Plastisphere, pathogens, terrestrial ecosystems}, + month = {September}, + number = {10}, + pages = {fiaf085}, + title = {Microplastic impacts archaeal abundance, microbial communities, and their network connectivity in a {Sub}-{Saharan} soil environment}, + url = {https://europepmc.org/articles/PMC12481198}, + volume = {101}, + year = {2025} +} + +@article{rojas_galaxy_2025, + abstract = {High-performance computing (HPC) environments are crucial for computational research, including quantum chemistry (QC), but pose challenges for non-expert users. Researchers with limited computational knowledge struggle to utilise domain-specific software and access mass spectra prediction for \textit{in silico} annotation. Here, we provide a robust workflow that leverages interoperable file formats for molecular structures to ensure integration across various QC tools. The quantum chemistry package for mass spectral predictions after electron ionization or collision-induced dissociation has been integrated into the Galaxy platform, enabling automated analysis of fragmentation mechanisms. The extended tight binding quantum chemistry package, chosen for its balance between accuracy and computational efficiency, provides molecular geometry optimisation. A Docker image encapsulates the necessary software stack. We demonstrated the workflow for four molecules, highlighting the scalability and efficiency of our solution via runtime performance analysis. This work shows how non-HPC users can make these predictions effortlessly, using advanced computational tools without needing in-depth expertise.}, + author = {Rojas, Wudmir Y and Ahmad, Zargham and Jakiela, Julia and Hecht, Helge and Klánová, Jana and Price, Elliott J}, + doi = {10.46471/gigabyte.160}, + issn = {2709-4715}, + journal = {GigaByte (Hong Kong, China)}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {gigabyte160}, + title = {Galaxy {QCxMS} for straightforward semi-empirical quantum mechanical {EI}-{MS} prediction}, + url = {http://europepmc.org/abstract/MED/40661852}, + volume = {2025}, + year = {2025} +} + @article{roland_wirth_microbiomes_2020, abstract = {Background: Comparison of the microbiomes in supragingival biofilm and saliva samples collected from juvenile patients developing induced or spontaneous gingivitis with healthy controls.Results: 36 supragingival biofilm samples from 9 a...}, author = {{Roland Wirth}}, @@ -12079,19 +19642,55 @@ @article{roncoroni_sars-cov-2_2021 doi = {10.1093/bioinformatics/btab421}, issn = {1367-4803}, journal = {Bioinformatics}, - keywords = {+Stellar, +Tools, +UsePublic, {\textgreater}ENA-Submission, {\textgreater}UseGalaxy.eu}, + keywords = {+Stellar, +Tools, +UsePublic, {\textgreater}ENA-Submission, {\textgreater}UseGalaxy.eu, COVID-19, Software}, + language = {eng}, month = {June}, number = {btab421}, + pages = {3983--3985}, title = {A {SARS}-{CoV}-2 sequence submission tool for the {European} {Nucleotide} {Archive}}, url = {https://doi.org/10.1093/bioinformatics/btab421}, urldate = {2021-08-16}, + volume = {37}, year = {2021} } +@article{ronspies_crispr-casmediated_2025, + abstract = {The genome of +Arabidopsis thaliana +consists of 10 chromosomes. By inducing CRISPR-Cas–mediated breaks at subcentromeric and subtelomeric sequences, we fused entire chromosome arms, obtaining two eight-chromosome lines. In one line, both arms of chromosome 3 were fused to chromosome 1. In another line, the arms were transferred to chromosomes 1 and 5. Both chromosome number–reduced lines were fertile. Phenotypic and transcriptional analyses revealed no differences compared with wild-type plants. After crossing with the wild type, the progeny showed reduced fertility. The meiotic recombination patterns of the transferred chromosome arms were substantially changed. Directed chromosome number changes in plants may enable new breeding strategies, redefining linkage groups and establishing genetic barriers. Moreover, our data indicate that plants are highly robust to engineered karyotype changes. + +, +Editor’s summary + +Restructuring chromosomes alters inheritance patterns of genetic information. In plants, chromosomal rearrangements can reproductively isolate engineered plants from wild relatives or can change the inheritance of desirable agronomic traits. Rönspies +et al +. used the model plant +Arabidopsis thaliana +as a testbed to implement CRISPR-Cas technology to fuse chromosomes together (see the Perspective by Zhang and Dawe). The researchers generated plants with eight chromosomes instead of 10, which appeared to be phenotypically normal and were self-fertile. Altered recombination patterns illustrated the changes to genetic inheritance rules. This work opens avenues for large-scale chromosomal changes in plants and provides insights into the plasticity of plant genomes. —Madeleine Seale}, + author = {Rönspies, Michelle and Khosravi, Solmaz and Helia, Ondřej and Valisi, Alessandro and Fajkus, Jiří and Fojtová, Miloslava and Houben, Andreas and Puchta, Holger}, + doi = {10.1126/science.adz8505}, + issn = {0036-8075, 1095-9203}, + journal = {Science}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {November}, + number = {6775}, + pages = {843--848}, + title = {{CRISPR}-{Cas}–mediated heritable chromosome fusions in \textit{{Arabidopsis}}}, + url = {https://www.science.org/doi/10.1126/science.adz8505}, + urldate = {2025-11-24}, + volume = {390}, + year = {2025} +} + @article{roquis_genomic_2021, + abstract = {Transposable elements (TEs) have long been known to be major contributors to plant evolution, adaptation and crop domestication. Stress-induced TE mobilization is of particular interest because it may result in novel gene regulatory pathways responding to stresses and thereby contribute to stress adaptation. Here, we investigated the genomic impacts of stress induced TE mobilization in wild type Arabidopsis plants. We find that the heat-stress responsive ONSEN TE displays an insertion site preference that is associated with specific chromatin states, especially those rich in H2A.Z histone variant and H3K27me3 histone mark. In order to better understand how novel ONSEN insertions affect the plant's response to heat stress, we carried out an in-depth transcriptomic analysis. We find that in addition to simple gene knockouts, ONSEN can produce a plethora of gene expression changes such as: constitutive activation of gene expression, alternative splicing, acquisition of heat-responsiveness, exonisation and genesis of novel non-coding and antisense RNAs. This report shows how the mobilization of a single TE-family can lead to a rapid rise of its copy number increasing the host's genome size and contribute to a broad range of transcriptomic novelty on which natural selection can then act.}, author = {Roquis, David and Robertson, Marta and Yu, Liang and Thieme, Michael and Julkowska, Magdalena and Bucher, Etienne}, doi = {10.1093/nar/gkab828}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {0305-1048}, + journal = {Nucleic Acids Res}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Retroelements, Transcriptome}, + language = {eng}, month = {September}, note = {Publisher: Oxford University Press (OUP)}, number = {18}, @@ -12102,13 +19701,48 @@ @article{roquis_genomic_2021 year = {2021} } +@article{rossitto_trim28-dependent_2022, + abstract = {Gonadal sexual fate in mammals is determined during embryonic development and must be actively maintained in adulthood. In the mouse ovary, oestrogen receptors and FOXL2 protect ovarian granulosa cells from transdifferentiation into Sertoli cells, their testicular counterpart. However, the mechanism underlying their protective effect is unknown. Here, we show that TRIM28 is required to prevent female-to-male sex reversal of the mouse ovary after birth. We found that upon loss of Trim28, ovarian granulosa cells transdifferentiate to Sertoli cells through an intermediate cell type, different from gonadal embryonic progenitors. TRIM28 is recruited on chromatin in the proximity of FOXL2 to maintain the ovarian pathway and to repress testicular-specific genes. The role of TRIM28 in ovarian maintenance depends on its E3-SUMO ligase activity that regulates the sex-specific SUMOylation profile of ovarian-specific genes. Our study identifies TRIM28 as a key factor in protecting the adult ovary from the testicular pathway.}, + author = {Rossitto, Moïra and Déjardin, Stephanie and Rands, Chris M and Le Gras, Stephanie and Migale, Roberta and Rafiee, Mahmoud-Reza and Neirijnck, Yasmine and Pruvost, Alain and Nguyen, Anvi Laetitia and Bossis, Guillaume and Cammas, Florence and Le Gallic, Lionel and Wilhelm, Dagmar and Lovell-Badge, Robin and Boizet-Bonhoure, Brigitte and Nef, Serge and Poulat, Francis}, + doi = {10.1038/s41467-022-32061-1}, + issn = {2041-1723}, + journal = {Nature communications}, + keywords = {{\textgreater}UseGalaxy.eu, Ovary, Sumoylation}, + language = {eng}, + month = {July}, + number = {1}, + pages = {4412}, + title = {{TRIM28}-dependent {SUMOylation} protects the adult ovary from activation of the testicular pathway}, + url = {http://europepmc.org/abstract/MED/35906245}, + volume = {13}, + year = {2022} +} + +@article{rothschild-rodriguez_klebphacol_2025, + abstract = {The growing threat of multidrug-resistant Klebsiella pneumoniae, coupled with its role in gut colonisation, has intensified the search for new treatments, including bacteriophage therapy. Despite increasing documentation of Klebsiella-targeting phages, clinical applications remain limited, with key phage–bacteria interactions still poorly understood. A major obstacle is fragmented access to well-characterised phage–bacteria pairings, restricting the collective advancement of therapeutic and mechanistic insights. To address this gap, we created the Klebsiella Phage Collection (KlebPhaCol), an open resource comprising 52 phages and 74 Klebsiella isolates, characterised at phenotypic and genomic levels. These phages span six families—including a novel family, Felixviridae, associated with the human gut—and target 20 sequence types (including ST258, ST11, and ST14) and 19 capsular-locus types (including KL1 and KL2), across 6 Klebsiella species. Freely accessible at www.klebphacol.org, KlebPhaCol invites the scientific community to both use and contribute to this resource, fostering collaborative research and a deeper understanding of Klebsiella-phage interactions beyond therapeutic use.Multidrug-resistant Klebsiella pneumoniae is a critical global health challenge. Bacteriophages (phages) could offer new therapies, but progress has been slowed by fragmented resources. KlebPhaCol addresses this gap as the first open, community-driven Klebsiella phage collection. It brings together physical samples (52 phages and 74 Klebsiella isolates) alongside extensive genomic, phenotypic, and host-range data, all freely accessible via www.klebphacol.org. The collection includes globally relevant clones, spans six phage families, and revealed a new gut-associated phage family, Felixviridae. Crucially, KlebPhaCol is designed to grow: researchers worldwide can deposit new strains and phages or add fresh analyses to existing ones, creating a sustainable platform for therapeutic development and fundamental microbiology.}, + author = {Rothschild-Rodriguez, Daniela and Lambon, Kai S and Kushwaha, Simran Krishnakant and Garushyants, Sofya K and Ertelt, Moritz and Latka, Agnieszka and Costa, Ana Rita and Mantzouratou, Anna and King, Claire and Boeckaerts, Dimitri and Sheridan, Elizabeth and Koonin, Eugene V and Merrick, Francesca and Drobniewski, Francis and De Angelis, Ilaria and Saeed, Kordo and Martin, Macy and Sutton, J Mark and Wand, Matthew E and Andrew, Michael and Hedges, Morgen and Brouns, Stan J J and Haas, Pieter-Jan and Lawson, Sophie T and Fordham, Stephen M E and Lee, Yan-Jiun and Wu, Yi and Briers, Yves and Braun, Peter and Weigele, Peter R and Nobrega, Franklin L}, + doi = {10.1093/nar/gkaf1122}, + issn = {1362-4962}, + journal = {Nucleic Acids Research}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {November}, + number = {21}, + pages = {gkaf1122}, + shorttitle = {{KlebPhaCol}}, + title = {{KlebPhaCol}: a community-driven resource for {Klebsiella} research identified a novel phage family}, + url = {https://doi.org/10.1093/nar/gkaf1122}, + urldate = {2025-12-26}, + volume = {53}, + year = {2025} +} + @article{roux_dna_2023, abstract = {Unintegrated HIV DNA represents between 20\% and 35\% of the total viral DNA in infected patients. Only the linear forms (unintegrated linear DNAs [ULDs]) can be substrates for integration and for the completion of a full viral cycle. In quiescent cells, these ULDs may be responsible for pre-integrative latency. However, their detection remains difficult due to the lack of specificity and sensitivity of existing techniques. We developed an ultra-sensitive, specific, and high-throughput technology for ULD quantification called DUSQ (DNA ultra-sensitive quantification) combining linker-mediated PCR and next-generation sequencing (NGS) using molecular barcodes. Studying cells with different activity levels, we determined that the ULD half-life goes up to 11 days in resting CD4+ T cells. Finally, we were able to quantify ULDs in samples from patients infected with HIV-1, providing a proof of concept for the use of DUSQ in vivo to track pre-integrative latency. DUSQ can be adapted to the detection of other rare DNA molecules.}, author = {Roux, Hélène Marie and Figueiredo, Suzanne and Sareoua, Lucas and Salmona, Maud and Hamroune, Juliette and Adoux, Lucie and Migraine, Julie and Hance, Allan and Clavel, François and Cheynier, Rémi and Dutrieux, Jacques}, doi = {10.1016/j.crmeth.2023.100443}, issn = {2667-2375}, journal = {Cell Reports Methods}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, HIV Seropositivity, HIV-1}, language = {en}, month = {April}, number = {4}, @@ -12158,13 +19792,47 @@ @article{royaux_genetic_2024 year = {2024} } +@misc{ruider_accelerated_2025, + abstract = {Droplet-based organoid culture offers several advantages over conventional bulk organoid culture, such as improved yield, reproducibility, and throughput. However, organoids grown in droplets typically display only a spherical geometry and lack the intricate structural complexity found in native tissue. By incorporating singularized pancreatic ductal adenocarcinoma cells into collagen droplets, we achieve the growth of branched structures, indicating a more complex interaction with the surrounding hydrogel. A comparison of organoid growth in droplets of different diameters showed that while geometrical confinement improves organoid homogeneity, it also impairs the formation of more complex organoid morphologies. Thus, only in 750 µm diameter collagen droplets did we achieve the consistent growth of highly branched structures with a morphology closely resembling the structural complexity achieved in traditional bulk organoid culture. Moreover, our analysis of organoid morphology and transcriptomic data suggests an accelerated maturation of organoids cultured in collagen droplets, highlighting a shift in developmental timing compared to traditional systems.}, + author = {Ruider, Iris and Pastucha, Anna and Raich, Marion K. and Xu, Wentao and Liu, Yan and Reichert, Maximilian and Weitz, David and Bausch, Andreas R.}, + copyright = {© 2025, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/}, + doi = {10.1101/2025.03.24.644794}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {March}, + note = {Pages: 2025.03.24.644794 +Section: New Results}, + publisher = {bioRxiv}, + title = {Accelerated maturation of branched organoids confined in collagen droplets}, + url = {https://www.biorxiv.org/content/10.1101/2025.03.24.644794v1}, + urldate = {2025-04-02}, + year = {2025} +} + +@article{ruiz-mena_comparative_2024, + abstract = {Using next-generation sequencing data, the complete mitogenomes of six species from the genus \textit{Tapinoma} were assembled. This study explores the mitochondrial genomes of \textit{Tapinoma} species, among them the five species from the \textit{Tapinoma nigerrimum} complex, comparing them with each other and with other species from Dolichoderinae subfamily to understand their evolutionary relationships and evolution. \textit{Tapinoma} mitochondrial genomes contain the typical set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and the A + T-rich control region. A phylogenetic analysis using the protein-coding gene sequences from available Dolichoderinae mitogenomes supports the monophyletic nature of the genus \textit{Tapinoma}, with the \textit{T. nigerrimum} complex forming a well-supported clade. Key findings include genetic traits unique to the \textit{T. nigerrimum} complex, such as a start codon in the \textit{atp8} gene and a complete stop codon in \textit{cox1}, distinguishing them from other \textit{Tapinoma} species. Additionally, a gene rearrangement involving \textit{tRNA-Trp}, \textit{tRNA-Cys}, and \textit{tRNA-Tyr} was found exclusively in the \textit{Tapinoma} species, suggesting a potential phylogenetic marker for the genus.}, + author = {Ruiz-Mena, Areli and Mora, Pablo and Rico-Porras, José M and Kaufmann, Bernard and Seifert, Bernhard and Palomeque, Teresa and Lorite, Pedro}, + doi = {10.3390/insects15120957}, + issn = {2075-4450}, + journal = {Insects}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {December}, + number = {12}, + pages = {957}, + title = {A {Comparative} {Analysis} of {Mitogenomes} in {Species} of the {Tapinoma} nigerrimum {Complex} and {Other} {Species} of the {Genus} {Tapinoma} ({Formicidae}, {Dolichoderinae})}, + url = {http://europepmc.org/abstract/MED/39769559}, + volume = {15}, + year = {2024} +} + @article{rukminiati_first_2024, abstract = {Recent spoligotyping results in the island nation of Indonesia had revealed the existence of Mycobacterium tuberculosis complex lineage 3 (MTBC L3) or Central Asian (CAS) strains. In this work, whole-genome sequencing (WGS) – based methods were used to search for the presence of MTBC L3.}, author = {Rukminiati, Yuni and Mesak, Felix and Lolong, Dina and Sudarmono, Pratiwi}, doi = {10.1186/s13104-024-06825-5}, issn = {1756-0500}, journal = {BMC Research Notes}, - keywords = {{\textgreater}UseGalaxy.eu, Phylogenomic, Tuberculosis, Whole genome sequencing}, + keywords = {{\textgreater}UseGalaxy.eu, Genome, Bacterial, Mycobacterium tuberculosis, Phylogenomic, Tuberculosis, Whole Genome Sequencing, Whole genome sequencing}, language = {en}, month = {June}, number = {1}, @@ -12183,7 +19851,7 @@ @article{russo_excrete_2024 doi = {10.1038/s42003-024-06910-2}, issn = {2399-3642}, journal = {Communications Biology}, - keywords = {{\textgreater}UseGalaxy.eu, Bacterial secretion, Proteomic analysis}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial Proteins, Bacterial secretion, Proteomic analysis, Proteomics, Workflow}, language = {en}, month = {September}, note = {Publisher: Nature Publishing Group}, @@ -12234,6 +19902,23 @@ @article{sabbaghian_panel_2022 year = {2022} } +@article{sabelleck_thiamine_2025, + abstract = {Thiamine (vitamin B1) is an essential micronutrient in all forms of life that serves as a cofactor for several enzymes in primary metabolism. Plant-pathogenic and obligate biotrophic powdery mildew fungi appear to be auxotrophic for the micronutrient, as they have lost the majority of the genes needed for thiamine biosynthesis. Using the barley powdery mildew pathogen, \textit{Blumeria hordei}, as a study object, we found that (1) asexual conidiospores contain detectable levels of thiamine, (2) the \textit{B. hordei THI80} gene encodes a functional thiamine pyrophosphokinase, and (3) \textit{B. hordei} has a functional DUR31-like thiamine transporter likely localizing to the cell surface. We further demonstrated a requirement of the metabolite for the activity of \textit{B. hordei} transketolase, an enzyme of central carbon metabolism known to be thiamine-dependent in other organisms. Taken together, our data suggest that thiamine is a vitamin for \textit{B. hordei} and, thus, likely all powdery mildew fungi.}, + author = {Sabelleck, Björn and Freh, Matthias and Lammertz, Meltem and Browatzki, Jennifer and Vllaho, Anna-Maria and Piślewska-Bednarek, Mariola and Bednarek, Paweł and Panstruga, Ralph}, + doi = {10.1016/j.isci.2025.113123}, + issn = {2589-0042}, + journal = {iScience}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {August}, + number = {8}, + pages = {113123}, + title = {Thiamine is a vitamin for plant-pathogenic powdery mildew fungi}, + url = {http://europepmc.org/abstract/MED/40777049}, + volume = {28}, + year = {2025} +} + @phdthesis{sabrina_statistical_2020, abstract = {Protein-RNA interactions play an important role in all post-transcriptional regulatory processes. High throughput detection of protein-RNA interactions has been facilitated by the emerging CLIP-seq (crosslinking and immunoprecipitation combined with high-throughput sequencing) techniques. Enrichments in mapped reads as well as base transitions or deletions at crosslink sites can be used to infer binding regions. Single-nucleotide resolution techniques (iCLIP and eCLIP) have been achieved by capturing high fractions of cDNAs which are truncated at protein-RNA crosslink sites. Increasing numbers of datasets and derivatives of these protocols have been published in recent years, requiring tailored computational analyses. Existing methods unfortunately do not explicitly model the specifics of truncation patterns and possible biases caused by background binding or crosslinking sequence preferences. We present PureCLIP, a hidden Markov model based approach, which simultaneously performs peak calling and individual crosslink site detection. It is capable of incorporating external data to correct for non-specific background signals and, for the first time, for the crosslinking biases. We devised a comprehensive evaluation based on three strategies. Firstly, we developed a workflow to simulate iCLIP data, which starts from real RNA-seq data and known binding regions and then mimics the experimental steps of the iCLIP protocol, including the generation of background signals. Secondly, we used experimental iCLIP and eCLIP datasets, using the proteins’ known predominant binding regions. And thirdly, we assessed the agreement of called sites between replicates, assuming target-specific signals are reproducible between replicates. @@ -12276,7 +19961,7 @@ @article{saddiqa_discovery_2024 doi = {10.1038/s41598-024-69721-9}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, Cancer, Computational biology and bioinformatics, Oncology}, + keywords = {{\textgreater}UseGalaxy.eu, Cancer, Computational biology and bioinformatics, Oncology, Receptors, Estrogen, Triple Negative Breast Neoplasms}, language = {en}, month = {September}, note = {Publisher: Nature Publishing Group}, @@ -12289,13 +19974,46 @@ @article{saddiqa_discovery_2024 year = {2024} } +@article{sadler_complete_2025, + author = {Sadler, Michael C. and Mino, Sayaka and Morris, Robert M.}, + doi = {10.1128/mra.00158-25}, + journal = {Microbiology Resource Announcements}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e00158--25}, + title = {Complete genome sequences of 34 {Arctic} marine bacteria}, + url = {https://journals.asm.org/doi/full/10.1128/mra.00158-25}, + urldate = {2025-09-03}, + volume = {0}, + year = {2025} +} + +@article{sadler_genomic_2025, + author = {Sadler, Michael C. and Wietz, Matthias and Mino, Sayaka and Morris, Robert M.}, + doi = {10.1128/mbio.01555-25}, + journal = {mBio}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e01555--25}, + title = {Genomic diversity and adaptation in {Arctic} marine bacteria}, + url = {https://journals.asm.org/doi/10.1128/mbio.01555-25}, + urldate = {2025-09-03}, + volume = {0}, + year = {2025} +} + @article{sageman-furnas_detailing_2024, abstract = {Shoot growth directly impacts plant productivity. Plants adjust their shoot growth in response to varying environments to maximize resource capture and stress resilience. While several factors controlling shoot growth are known, the complexity of the regulation and the input of the environment are not fully understood. We have investigated shoot growth repression induced by low ambient temperatures in hybrids of Arabidopsis thaliana Kro-0 and BG-5 accessions. To continue our previous studies, we confirmed that the Kro-0 allele of DYNAMIN-RELATED PROTEIN 3B causes stunted shoot growth in the BG-5 background. We also found that shoot growth repression was most pronounced near the apex at a lower temperature and that the cells in the hybrid stem failed to elongate correctly. Furthermore, we observed that shoot growth repression in hybrids depended on light availability. Global gene expression analysis indicated the involvement of hormones, especially strigolactone, associated with the dwarf phenotype. Altogether, this study enhances our knowledge on the genetic, physiological and environmental factors associated with shoot growth regulation.}, author = {Sageman-Furnas, Katelyn and Duarte, Gustavo T and Laitinen, Roosa A E}, doi = {10.1093/pcp/pcad167}, issn = {1471-9053}, journal = {Plant and Cell Physiology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, Arabidopsis Proteins}, + language = {eng}, month = {March}, number = {3}, pages = {420--427}, @@ -12390,6 +20108,24 @@ @incollection{saleh_nascent_2021 year = {2021} } +@article{salem_comparative_2025, + abstract = {Acinetobacter baumannii (A. baumannii) has emerged as a major public health threat in low- and middle-income countries (LMICs), particularly in Egypt, due to its remarkable ability to acquire and transfer resistance genes, as highlighted in the WHO bacterial Priority Pathogens List 2024 classification. This pilot study aimed to characterize 18 A. baumannii isolates from Egyptian healthcare settings, focusing on clonal lineages, antibiotic resistance determinants, horizontal gene transfer potential, and the presence of virulence factors and chromosomal mutations.}, + author = {Salem, Salma and Osama, Dina and Abdelsalam, Nehal Adel and Shata, Ahmed H. and Mouftah, Shaimaa F. and Elhadidy, Mohamed}, + doi = {10.1186/s12879-025-11185-x}, + issn = {1471-2334}, + journal = {BMC Infectious Diseases}, + keywords = {{\textgreater}UseGalaxy.eu, Acinetobacter Infections, Acinetobacter baumannii, Antibacterial drug resistance, Antimicrobial Resistance, Antimicrobial resistance, Bacillus subtilis, Bacterial Genetics, Bacterial Genomics, Clonal selection, Drug Resistance, Multiple, Bacterial, Egypt, International clones, Mobile genetic elements}, + language = {en}, + month = {June}, + number = {1}, + pages = {803}, + title = {Comparative genomics of {Acinetobacter} baumannii from {Egyptian} healthcare settings reveals high-risk clones and resistance gene mobilization}, + url = {https://doi.org/10.1186/s12879-025-11185-x}, + urldate = {2025-07-12}, + volume = {25}, + year = {2025} +} + @book{salerno_metaproteomics_2024, abstract = {This volume provides references for methods about the proteomics of microbial communities, also called metaproteomics. Chapters guide readers first through specific protein extractions from different environments and/or ecological niches crowded by heterogeneous microbial communities, then deepening the possible complete metaproteomic workflows in several situations or conditions. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Metaproteomics: Methods and Protocols aims to ensure successful results in the further study of this vital field.}, author = {Salerno, Carlo}, @@ -12403,6 +20139,44 @@ @book{salerno_metaproteomics_2024 year = {2024} } +@article{salinas_genetic_2025, + author = {Salinas, Claudia and Rodriguez, Fátima and Muñoz-Barrera, Adrián and Lorenzo Salazar, José Miguel and González-Montelongo, Rafaela and Flores, Carlos and Guillén, Rosa}, + doi = {10.1128/spectrum.00596-25}, + journal = {Microbiology Spectrum}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e00596--25}, + title = {Genetic variability of {Shiga} toxin-producing {Escherichia} coli strains isolated from {Paraguayan} cattle}, + url = {https://journals.asm.org/doi/10.1128/spectrum.00596-25}, + urldate = {2025-09-03}, + volume = {0}, + year = {2025} +} + +@article{samanic_characterisation_2025, + abstract = {This study examines the genomic composition and resistance potential of eight putative plasmid-derived contig assemblies reconstructed from marine Enterobacterales isolated in the central Adriatic Sea. Using a combination of Illumina-based whole genome sequencing, de novo assembly, and a multi-tool bioinformatics pipeline, we annotated antimicrobial resistance genes (ARGs), insertion sequences (ISs), and plasmid replicon types. Clinically significant resistance markers such as blaKPC, blaTEM, aacA4, tetA, and folP were identified, frequently co-localised with mobile genetic elements including IS110, IS4, and IS1182. The plasmid-associated contigs were assigned to MOBP and MOBQ types and contained replicon markers (IncP6, IncA/C2) characteristic of broad-host-range plasmids. Our findings provide valuable insight into the plasmidome of environmental Enterobacterales, emphasising the role of coastal pollution in shaping the distribution and potential mobility of antimicrobial resistance genes. This supports the One Health framework by linking environmental reservoirs to clinically relevant resistance mechanisms.}, + author = {Šamanić, Ivica and Dželalija, Mia and Bellulovich, Ema and Kalinić, Hrvoje and Jozić, Slaven and Ordulj, Marin and Udiković-Kolić, Nikolina and Maravić, Ana}, + copyright = {cc by}, + doi = {10.3390/ijms262210910}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Adriatic Sea, Coastal Enterobacterales, Mobile genetic elements, One Health, Plasmid-associated Resistance, Replicon Typing}, + language = {eng}, + month = {November}, + number = {22}, + pages = {10910}, + pmcid = {PMC12652098}, + pmid = {41303395}, + shorttitle = {Characterisation of {Plasmid}-{Associated} {Antimicrobial} {Resistance} {Genes} in {Coastal} {Marine} \<i\>{Enterobacterales}\</i\> from the {Central} {Adriatic} {Sea}}, + title = {Characterisation of {Plasmid}-{Associated} {Antimicrobial} {Resistance} {Genes} in {Coastal} {Marine} \<i\>{Enterobacterales}\</i\> from the {Central} {Adriatic} {Sea}: {De} {Novo} {Assembly} and {Bioinformatic} {Profiling}}, + url = {https://europepmc.org/articles/PMC12652098}, + urldate = {2025-12-26}, + volume = {26}, + year = {2025} +} + @article{sanchez-leon_heteroresistance_2023, abstract = {Heteroresistance to colistin can be defined as the presence of resistant subpopulations in an isolate that is susceptible to this antibiotic. Colistin resistance in Gram-negative bacteria is more frequently related to chromosomal mutations and insertions. This work aimed to study heteroresistance in nine clinical isolates of Klebsiella pneumoniae producing OXA-48 and to describe genomic changes in mutants with acquired resistance in vitro. Antimicrobial susceptibility was determined by broth microdilution (BMD) and heteroresistance by population analysis profiling (PAP). The proteins related to colistin resistance were analyzed for the presence of mutations. Additionally, PCR of the mgrB gene was performed to identify the presence of insertions. In the nine parental isolates, the PAP method showed colistin heteroresistance of colonies growing on plates with concentrations of up to 64 mg/L, corresponding to stable mutant subpopulations. The MICs of some mutants from the PAP plate containing 4×MIC of colistin had absolute values of ≤2 mg/L that were higher than the parental MICs and were defined as persistent variants. PCR of the mgrB gene identified an insertion sequence that inactivated the gene in 21 mutants. Other substitutions in the investigated mutants were found in PhoP, PhoQ, PmrB, PmrC, CrrA and CrrB proteins. Colistin heteroresistance in K. pneumoniae isolates was attributed mainly to insertions in the mgrB gene and point mutations in colistin resistance proteins. The results of this study will improve understanding regarding the mechanisms of colistin resistance in mutants of K. pneumoniae producing OXA-48.}, author = {Sánchez-León, Irene and García-Martínez, Teresa and Diene, Seydina M. and Pérez-Nadales, Elena and Martínez-Martínez, Luis and Rolain, Jean-Marc}, @@ -12438,16 +20212,34 @@ @article{sanchez-leon_heterorresistencia_2024 year = {2024} } +@article{sanchez_arnold_2022, + abstract = {Living systems exhibit an unmatched complexity, due to countless, entangled interactions across scales. Here, we aim to understand a complex system, that is, segmentation timing in mouse embryos, without a reference to these detailed interactions. To this end, we develop a coarse-grained approach, in which theory guides the experimental identification of the segmentation clock entrainment responses. We demonstrate period- and phase-locking of the segmentation clock across a wide range of entrainment parameters, including higher-order coupling. These quantifications allow to derive the phase response curve (PRC) and Arnold tongues of the segmentation clock, revealing its essential dynamical properties. Our results indicate that the somite segmentation clock has characteristics reminiscent of a highly non-linear oscillator close to an infinite period bifurcation and suggests the presence of long-term feedbacks. Combined, this coarse-grained theoretical-experimental approach reveals how we can derive simple, essential features of a highly complex dynamical system, providing precise experimental control over the pace and rhythm of the somite segmentation clock.}, + author = {Sanchez, Paul Gerald Layague and Mochulska, Victoria and Mauffette Denis, Christian and Mönke, Gregor and Tomita, Takehito and Tsuchida-Straeten, Nobuko and Petersen, Yvonne and Sonnen, Katharina and François, Paul and Aulehla, Alexander}, + doi = {10.7554/elife.79575}, + issn = {2050-084X}, + journal = {eLife}, + keywords = {{\textgreater}UseGalaxy.eu, Somites, Tongue}, + language = {eng}, + month = {October}, + pages = {e79575}, + title = {Arnold tongue entrainment reveals dynamical principles of the embryonic segmentation clock}, + url = {http://europepmc.org/abstract/MED/36223168}, + volume = {11}, + year = {2022} +} + @article{sanchez_pathwaymatcher_2019, abstract = {AbstractBackground. Mapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers (e.g., g}, author = {Sánchez, Luis Francisco Hernández and Burger, Bram and Horro, Carlos and Fabregat, Antonio and Johansson, Stefan and Njølstad, Pål Rasmus and Barsnes, Harald and Hermjakob, Henning and Vaudel, Marc}, doi = {10.1093/gigascience/giz088}, + issn = {2047-217X}, journal = {GigaScience}, - keywords = {+Tools, {\textgreater}UseGalaxy.eu}, + keywords = {+Tools, {\textgreater}UseGalaxy.eu, Gene Regulatory Networks, Signal Transduction, Software}, language = {en}, month = {August}, note = {Publisher: Oxford Academic}, number = {8}, + pages = {giz088}, shorttitle = {{PathwayMatcher}}, title = {{PathwayMatcher}: proteoform-centric network construction enables fine-granularity multiomics pathway mapping}, url = {https://academic.oup.com/gigascience/article/8/8/giz088/5541632}, @@ -12456,6 +20248,45 @@ @article{sanchez_pathwaymatcher_2019 year = {2019} } +@article{sandybayev_next_2022, + abstract = {The COVID-19 pandemic and heightened perception of the risk of emerging viral infections have boosted the efforts to better understand the virome or complete repertoire of viruses in health and disease, with a focus on infectious respiratory diseases. Next-generation sequencing (NGS) is widely used to study microorganisms, allowing the elucidation of bacteria and viruses inhabiting different body systems and identifying new pathogens. However, NGS studies suffer from a lack of standardization, in particular, due to various methodological approaches and no single format for processing the results. Here, we review the main methodological approaches and key stages for studies of the human virome, with an emphasis on virome changes during acute respiratory viral infection, with applications for clinical diagnostics and epidemiologic analyses.}, + author = {Sandybayev, Nurlan and Beloussov, Vyacheslav and Strochkov, Vitaliy and Solomadin, Maxim and Granica, Joanna and Yegorov, Sergey}, + doi = {10.3390/microorganisms10122327}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {November}, + number = {12}, + pages = {2327}, + title = {Next {Generation} {Sequencing} {Approaches} to {Characterize} the {Respiratory} {Tract} {Virome}}, + url = {http://europepmc.org/abstract/MED/36557580}, + volume = {10}, + year = {2022} +} + +@article{santos_wastewater_2025, + abstract = {This study investigates viral composition in wastewater through metagenomic analysis, evaluating the performance of four bioinformatic tools—Genome Detective, CZ.ID, INSaFLU-TELEVIR and Trimmomatic + Kraken2—on samples collected from four sites in each of two wastewater treatment plants (WWTPs) in Lisbon, Portugal in April 2019. From each site, we collected and processed separately three replicates and one pool of nucleic acids extracted from the replicates. A total of 32 samples were processed using sequence-independent single-primer amplification (SISPA) and sequenced on an Illumina MiSeq platform. Across the 128 sample–tool combinations, viral read counts varied widely, from 3 to 288,464. There was a lack of consistency between replicates and their pools in terms of viral abundance and diversity, revealing the heterogeneity of the wastewater matrix and the variability in sequencing effort. There was also a difference between software tools highlighting the impact of tool selection on community profiling. A positive correlation between crAssphage and human pathogens was found, supporting crAssphage as a proxy for public health surveillance. A custom Python pipeline automated viral identification report processing, taxonomic assignments and diversity calculations, streamlining analysis and ensuring reproducibility. These findings emphasize the importance of sequencing depth, software tool selection and standardized pipelines in advancing wastewater-based epidemiology.}, + author = {Santos, André F. B. and Nunes, Mónica and Filipa-Silva, Andreia and Pimentel, Victor and Pingarilho, Marta and Abrantes, Patrícia and Miranda, Mafalda N. S. and Crespo, Maria Teresa Barreto and Abecasis, Ana B. and Parreira, Ricardo and Seabra, Sofia G.}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijerph22050707}, + issn = {1660-4601}, + journal = {International Journal of Environmental Research and Public Health}, + keywords = {{\textgreater}UseGalaxy.eu, Computational Biology, Metagenomics, Virome, Viruses, Wastewater, environmental surveillance, metagenomic analysis, next generation sequencing, wastewater}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {707}, + shorttitle = {Wastewater {Metavirome} {Diversity}}, + title = {Wastewater {Metavirome} {Diversity}: {Exploring} {Replicate} {Inconsistencies} and {Bioinformatic} {Tool} {Disparities}}, + url = {https://www.mdpi.com/1660-4601/22/5/707}, + urldate = {2025-05-02}, + volume = {22}, + year = {2025} +} + @incollection{saracchi_characterization_2023, abstract = {8}, author = {Saracchi, M. and Kunova, A. and Valenti, I. and Degradi, L. and Pizzatti, C. and Corneo, A. and Cortesi, P. and Pasquali, M.}, @@ -12521,6 +20352,43 @@ @article{sarkar_junb_2024 year = {2024} } +@misc{sarker_genetic_2024, + abstract = {This study evaluated the prevalence of methicillin-resistant Staphylococcus aureus (MRSA), examined transmission pathways between pets, owners, and veterinary professionals, and assessed antimicrobial resistance determinants in MRSA isolates. Between July 2022 and June 2024, 213 human and 191 animal samples, including nasal, pus, and wound swabs, were collected from two veterinary hospitals. Staphylococcus aureus was isolated using selective media and confirmed by Gram staining, biochemical tests, and PCR for the nuc gene. Methicillin resistance was verified by cefoxitin disk diffusion and PCR detection of the mecA gene. Antimicrobial susceptibility was tested against 15 antibiotics, and whole genome sequencing (WGS) identified Staphylococcal Cassette Chromosome mec (SCCmec) types. The prevalence of S. aureus was 31.92\% in humans, 18.18\% in cats, and 32.43\% in dogs, with MRSA detected in 15.02\% of humans, 5.84\% of cats, and 13.51\% of dogs. All MRSA isolates were resistant to cefoxitin, with high resistance to penicillin (94.87\%), azithromycin (82.00\%), and ciprofloxacin (53.85\%) but were sensitive to amikacin, clindamycin, linezolid, and vancomycin. Genetic analysis revealed four sequence types (ST), predominantly ST6 (66.67\%), and clonal relationships between pet-owner MRSA pairs. Virulence profiling showed the presence of hemolysins, Panton-Valentine Leukocidin, and toxic shock syndrome toxin genes in select isolates. Detection of diverse MRSA lineages, including ST88 and ST6-t304, highlights the need for targeted MRSA surveillance and effective infection control. Collaboration between veterinary and human healthcare sectors through a One Health approach is crucial to managing MRSA spread and associated risks.}, + address = {Rochester, NY}, + author = {Sarker, Himangsu and Hassan, Jayedul and Rahman, A. K. M. Anisur and Korber, Darren R. and Alam, Md Mahbub}, + doi = {10.2139/ssrn.5053279}, + keywords = {{\textgreater}UseGalaxy.eu, MRSA, Nasal swabs, One Health, Pets, human, pus, wound}, + language = {en}, + month = {December}, + publisher = {Social Science Research Network}, + title = {Genetic {Evidence} of {Methicillin} {Resistant} {Staphylococcus} {Aureus} {Transmission} between {Pets} and {Their} {Owners}}, + type = {{SSRN} {Scholarly} {Paper}}, + url = {https://papers.ssrn.com/abstract=5053279}, + urldate = {2025-09-03}, + year = {2024} +} + +@article{sarker_zoonotic_2025, + abstract = {This study investigated the prevalence of methicillin-resistant Staphylococcus aureus (MRSA), their antimicrobial resistance, virulence determinants, and potential zoonotic potential between pets, owners, and veterinary professionals. From July 2022 to June 2024, 213 human and 191 animal samples (nasal, pus, and wound swabs) were collected from two veterinary hospitals. Staphylococcus aureus was isolated using conventional cultural method and subsequently confirmed through Gram staining, biochemical tests, and PCR targeting the nuc gene. Methicillin resistance was confirmed using the cefoxitin disk diffusion method and PCR for the mecA gene. Antimicrobial susceptibility testing was performed using the disc diffusion method against 15 antibiotics. Additionally, whole genome sequencing (WGS) was conducted on selected MRSA isolates from pets and their owners to study clonal transmission and virulence factors. The prevalence of MRSA in humans was 15.0\%, in cats was 5.8\% and in dogs was 13.5\%. The MRSA isolates exhibited resistance to penicillin (94.9\%), azithromycin (82\%), and ciprofloxacin (53.9\%), in addition to their intrinsic resistance to cefoxitin. Multidrug resistance was observed in 94.9\% of MRSA isolates, though all were sensitive to amikacin, clindamycin, linezolid, and vancomycin. Notably, six dogs and cats, along with their respective owners, tested positive for MRSA. WGS analysis of these six pairs (12 isolates) showed four sequence types (ST), with ST6 being the most common (66.7\%). There were also four spa types identified, with t304 being the predominant (58.3\%). Within four pairs, identical ST-spa patterns were observed, except for the pair C52-P52 and D88-P88. Two pairs of isolates, C134-P134 and C185-P185, showed clonality based on whole genome and core genome SNP analysis, and other genetic parameters, suggesting clonal transmission between the pets and their respective owners. Virulence profiling revealed the presence of hemolysins, Panton-Valentine Leukocidin, and toxic shock syndrome toxin genes in selected isolates. The detection of diverse MRSA lineages, including human lineages ST80, ST88 and ST6-t304 in pets, indicates their zoonotic potential, and emphasizes the necessity for targeted MRSA surveillance and effective infection control measures. A collaborative One Health approach is therefore imperative to address the spread of MRSA between pets and their owners, thereby mitigating associated risks. The detection of diverse MRSA lineages, including human lineages ST80, ST88, and ST6-t304 in pets, underscores their zoonotic potential and emphasizes the necessity for targeted MRSA surveillance and effective infection control measures. A collaborative One Health approach is therefore imperative to address the spread of MRSA between pets and their owners, thereby mitigating associated risks.}, + author = {Sarker, Himangsu and Hassan, Jayedul and Rahman, A K M Anisur and Korber, Darren R and Alam, Md Mahbub}, + copyright = {cc by-nc-nd}, + doi = {10.1038/s41598-025-02638-z}, + issn = {2045-2322}, + journal = {Scientific reports}, + keywords = {{\textgreater}UseGalaxy.eu, MRSA, One Health, Owners, Pets, Zoonotic Potential}, + language = {eng}, + month = {October}, + number = {1}, + pages = {37002}, + pmcid = {PMC12550073}, + pmid = {41130984}, + title = {Zoonotic potential of methicillin-resistant {Staphylococcus} aureus isolated from pets and their owners in {Bangladesh}}, + url = {https://europepmc.org/articles/PMC12550073}, + urldate = {2025-12-26}, + volume = {15}, + year = {2025} +} + @article{sauriol_modeling_2020, abstract = {Cancer cell lines are amongst the most important pre-clinical models. In the context of epithelial ovarian cancer, a highly heterogeneous disease with diverse subtypes, it is paramount to study a wide panel of models in order to draw a representative picture of the disease. As this lethal gynaecological malignancy has seen little improvement in overall survival in the last decade, it is all the more pressing to support future research with robust and diverse study models. Here, we describe ten novel spontaneously immortalized patient-derived ovarian cancer cell lines, detailing their respective mutational profiles and gene/biomarker expression patterns, as well as their in vitro and in vivo growth characteristics. Eight of the cell lines were classified as high-grade serous, while two were determined to be of the rarer mucinous and clear cell subtypes, respectively. Each of the ten cell lines presents a panel of characteristics reflective of diverse clinically relevant phenomena, including chemotherapeutic resistance, metastatic potential, and subtype-associated mutations and gene/protein expression profiles. Importantly, four cell lines formed subcutaneous tumors in mice, a key characteristic for pre-clinical drug testing. Our work thus contributes significantly to the available models for the study of ovarian cancer, supplying additional tools to better understand this complex disease.}, author = {Sauriol, Alexandre and Simeone, Kayla and Portelance, Lise and Meunier, Liliane and Leclerc-Desaulniers, Kim and de Ladurantaye, Manon and Chergui, Meriem and Kendall-Dupont, Jennifer and Rahimi, Kurosh and Carmona, Euridice and Provencher, Diane M. and Mes-Masson, Anne-Marie}, @@ -12579,7 +20447,7 @@ @article{schafer_practical_2024 doi = {10.1099/mgen.0.001173}, issn = {2057-5858}, journal = {Microbial Genomics}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Algorithms, Genome, Bacterial}, note = {Publisher: Microbiology Society,}, number = {1}, pages = {001173}, @@ -12616,7 +20484,7 @@ @article{schildhauer_glycation_2023 doi = {10.3390/cells12232758}, issn = {2073-4409}, journal = {Cells}, - keywords = {{\textgreater}UseGalaxy.eu, astrocytes, glioblastoma, glioma, glycation, methylglyoxal, polysialylation, sialyltransferases}, + keywords = {{\textgreater}UseGalaxy.eu, Glioblastoma, Glioma, astrocytes, glioblastoma, glioma, glycation, methylglyoxal, polysialylation, sialyltransferases}, language = {en}, month = {January}, note = {Number: 23 @@ -12636,7 +20504,7 @@ @article{schiml_integrative_2023 doi = {10.1186/s40793-023-00514-9}, issn = {2524-6372}, journal = {Environmental Microbiome}, - keywords = {{\textgreater}UseGalaxy.eu, Bioinformatics, Galaxy, Integrated meta-omics, Metagenomics, Metaproteomics, Metatrascriptomics}, + keywords = {+Galactic, {\textgreater}UseGalaxy.eu, Bioinformatics, Galaxy, Integrated meta-omics, Metagenomics, Metaproteomics, Metatrascriptomics}, language = {en}, month = {July}, number = {1}, @@ -12648,6 +20516,55 @@ @article{schiml_integrative_2023 year = {2023} } +@article{schlecht_immunosenescence_2021, + abstract = {Immunosenescence is considered a possible factor in the development of age-related macular degeneration and choroidal neovascularization (CNV). However, age-related changes of myeloid cells (MCs), such as microglia and macrophages, in the healthy retina or during CNV formation are ill-defined. In this study, \textit{Cx3cr1}-positive MCs were isolated by fluorescence-activated cell sorting from six-week (young) and two-year-old (old) \textit{Cx3cr1$^{\textrm{GFP}}$}$^{\textrm{/+}}$ mice, both during physiological aging and laser-induced CNV development. High-throughput RNA-sequencing was performed to define the age-dependent transcriptional differences in MCs during physiological aging and CNV development, complemented by immunohistochemical characterization and the quantification of MCs, as well as CNV size measurements. These analyses revealed that myeloid cells change their transcriptional profile during both aging and CNV development. In the steady state, senescent MCs demonstrated an upregulation of factors contributing to cell proliferation and chemotaxis, such as \textit{Cxcl13 and Cxcl14}, as well as the downregulation of microglial signature genes. During CNV formation, aged myeloid cells revealed a significant upregulation of angiogenic factors such as \textit{Arg1} and \textit{Lrg1} concomitant with significantly enlarged CNV and an increased accumulation of MCs in aged mice in comparison to young mice. Future studies need to clarify whether this observation is an epiphenomenon or a causal relationship to determine the role of immunosenescence in CNV formation.}, + author = {Schlecht, Anja and Thien, Adrian and Wolf, Julian and Prinz, Gabriele and Agostini, Hansjürgen and Schlunck, Günther and Wieghofer, Peter and Boneva, Stefaniya and Lange, Clemens}, + doi = {10.3390/ijms222413318}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Down-Regulation}, + language = {eng}, + month = {December}, + number = {24}, + pages = {13318}, + title = {Immunosenescence in {Choroidal} {Neovascularization} ({CNV})-{Transcriptional} {Profiling} of {Naïve} and {CNV}-{Associated} {Retinal} {Myeloid} {Cells} during {Aging}}, + url = {http://europepmc.org/abstract/MED/34948115}, + volume = {22}, + year = {2021} +} + +@article{schlecht_secreted_2020, + abstract = {Age-related macular degeneration (AMD) represents the most common cause of blindness in the elderly in the Western world. An impairment of the outer blood-retina barrier and a localized inflammatory microenvironment cause sprouting of choroidal neovascular membranes (CNV) in neovascular AMD that are in intimate contact with surrounding myeloid cells, such as retinal microglia, and ultimately lead to visual impairment. The discovery of novel target molecules to interfere with angiogenesis and inflammation is vital for future treatment approaches in AMD patients. To explore the transcriptional profile and the function of retinal microglia at sites of CNV, we performed a comprehensive RNA-seq analysis of retinal microglia in the mouse model of laser-induced choroidal neovascularization (mCNV). Here, we identified the angiogenic factor Osteopontin (\textit{Opn}), also known as "secreted phosphoprotein 1" (\textit{Spp1}), as one of the most highly expressed genes in retinal microglia in the course of CNV formation. We confirmed the presence of SPP1 at the lesion site in recruited retinal microglia in \textit{Cx3cr1} $^{\textrm{CreER}}$:\textit{Rosa26-tdTomato} reporter mice by confocal microscopy and in whole retinal tissue lysates by ELISA highlighting a massive local production of SPP1. Inhibition of SPP1 by intravitreal injection of an anti-SPP1 antibody significantly increased the lesion size compared to IgG-treated control eyes. In line with our results in rodents, we found an increased \textit{SPP1} mRNA expression in surgically extracted human choroidal neovascular (hCNV) membranes by the quantitative RNA-seq approach of massive analysis of cDNA ends (MACE). Numerous IBA1$^{\textrm{+}}$SPP1$^{\textrm{+}}$ myeloid cells were detected in human CNV membranes. Taken together, these results highlight the importance of SPP1 in the formation of CNV and potentially offer new opportunities for therapeutic intervention by modulating the SPP1 pathway.}, + author = {Schlecht, Anja and Zhang, Peipei and Wolf, Julian and Thien, Adrian and Rosmus, Dennis-Dominik and Boneva, Stefaniya and Schlunck, Günther and Lange, Clemens and Wieghofer, Peter}, + doi = {10.3389/fcell.2020.618598}, + issn = {2296-634X}, + journal = {Frontiers in cell and developmental biology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {618598}, + title = {Secreted {Phosphoprotein} 1 {Expression} in {Retinal} {Mononuclear} {Phagocytes} {Links} {Murine} to {Human} {Choroidal} {Neovascularization}}, + url = {http://europepmc.org/abstract/MED/33585455}, + volume = {8}, + year = {2020} +} + +@article{schlecht_transcriptional_2022, + abstract = {Macular neovascularization type 3, formerly known as retinal angiomatous proliferation (RAP), is a hallmark of age-related macular degeneration and is associated with an accumulation of myeloid cells, such as microglia (MG) and infiltrating blood-derived macrophages (MAC). However, the contribution of MG and MAC to the myeloid cell pool at RAP sites and their exact functions remain unknown. In this study, we combined a microglia-specific reporter mouse line with a mouse model for RAP to identify the contribution of MG and MAC to myeloid cell accumulation at RAP and determined the transcriptional profile of MG using RNA sequencing. We found that MG are the most abundant myeloid cell population around RAP, whereas MAC are rarely, if ever, associated with late stages of RAP. RNA sequencing of RAP-associated MG showed that differentially expressed genes mainly contribute to immune-associated processes, including chemotaxis and migration in early RAP and proliferative capacity in late RAP, which was confirmed by immunohistochemistry. Interestingly, MG upregulated only a few angiomodulatory factors, suggesting a rather low angiogenic potential. In summary, we showed that MG are the dominant myeloid cell population at RAP sites. Moreover, MG significantly altered their transcriptional profile during RAP formation, activating immune-associated processes and exhibiting enhanced proliferation, however, without showing substantial upregulation of angiomodulatory factors.}, + author = {Schlecht, Anja and Wolf, Julian and Boneva, Stefaniya and Prinz, Gabriele and Braunger, Barbara M and Wieghofer, Peter and Agostini, Hansjürgen and Schlunck, Günther and Lange, Clemens}, + doi = {10.3390/ijms23073443}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Macular Degeneration, Retinal Neovascularization}, + language = {eng}, + month = {March}, + number = {7}, + pages = {3443}, + title = {Transcriptional and {Distributional} {Profiling} of {Microglia} in {Retinal} {Angiomatous} {Proliferation}}, + url = {http://europepmc.org/abstract/MED/35408803}, + volume = {23}, + year = {2022} +} + @article{schlecht_transcriptomic_2020, abstract = {Recent studies have deciphered the transcriptional profile of choroidal neovascularisation (CNV) in body donor eyes with neovascular age-related macular degeneration (nAMD) and were thus limited by the time span from death to preservation and the associated 5'-RNA degradation. Therefore, this study used CNV and control specimens which had been formalin-fixed and paraffin-embedded immediately after surgical extraction and analyzed them using a 3’ RNA sequencing approach. Transcriptome profiles were analyzed and used to estimate content of immune and stromal cells and to define disease-associated gene signatures using statistical and bioinformatic methods. We identified 158 differentially-expressed genes (DEG) that were significantly increased in CNV compared to control tissue. Cell type enrichment analysis revealed a diverse cellular landscape with an enrichment of immune and stroma cell types in CNV including endothelial cells, macrophages, T cells and NKT cells. Gene ontology enrichment analysis demonstrated that DEG contributed to Blood Vessel Development, Extracellular Structure Organization, Response to Wounding and several immune-related terms. The S100 calcium-binding protein A8 (S100A8) and S100A9 emerged among the top DEG, as confirmed by immunohistochemistry on CNV tissue and protein analysis of vitreous samples. This study provides a high-resolution RNA-sequencing-based transcriptional signature of human CNV, characterizes its compositional pattern of immune and stromal cells and reveals S100A8/A9 as a novel biomarker and promising target for AMD-directed therapeutics and diagnostics.}, author = {Schlecht, Anja and Boneva, Stefaniya and Gruber, Markus and Zhang, Peipei and Horres, Ralf and Bucher, Felicitas and Auw-Haedrich, Claudia and Hansen, Lutz and Stahl, Andreas and Hilgendorf, Ingo and Agostini, Hansjürgen and Wieghofer, Peter and Schlunck, Günther and Wolf, Julian and Lange, Clemens AK.}, @@ -12688,7 +20605,7 @@ @article{schneider_crispr-cas9_2023 doi = {10.3390/ijms241713207}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {\textit{KMT2A}-rearranged, {\textgreater}UseGalaxy.eu, ARID4B, BMPR2, CRISPR-Cas9, MBD3, epigenome, infant, kinome, leukemia}, + keywords = {\textit{KMT2A}-rearranged, {\textgreater}UseGalaxy.eu, ARID4B, BMPR2, CRISPR-Cas Systems, CRISPR-Cas9, MBD3, Precursor Cell Lymphoblastic Leukemia-Lymphoma, epigenome, infant, kinome, leukemia}, language = {en}, month = {January}, note = {Number: 17 @@ -12702,6 +20619,23 @@ @article{schneider_crispr-cas9_2023 year = {2023} } +@article{schoellkopf_genome_2022, + abstract = {PMT is a protein toxin produced by Pasteurella multocida serotypes A and D. As causative agent of atrophic rhinitis in swine, it leads to rapid degradation of the nasal turbinate bone. The toxin acts as a deamidase to modify a crucial glutamine in heterotrimeric G proteins, which results in constitutive activation of the G proteins and permanent stimulation of numerous downstream signaling pathways. Using a lentiviral based genome wide CRISPR knockout screen in combination with a lethal toxin chimera, consisting of full length inactive PMT and the catalytic domain of diphtheria toxin, we identified the LRP1 gene encoding the Low-Density Lipoprotein Receptor-related protein 1 as a critical host factor for PMT function. Loss of LRP1 reduced PMT binding and abolished the cellular response and deamidation of heterotrimeric G proteins, confirming LRP1 to be crucial for PMT uptake. Expression of LRP1 or cluster 4 of LRP1 restored intoxication of the knockout cells. In summary our data demonstrate LRP1 as crucial host entry factor for PMT intoxication by acting as its primary cell surface receptor.}, + author = {Schoellkopf, Julian and Mueller, Thomas and Hippchen, Lena and Mueller, Teresa and Reuten, Raphael and Backofen, Rolf and Orth, Joachim and Schmidt, Gudula}, + doi = {10.1371/journal.ppat.1010781}, + issn = {1553-7366}, + journal = {PLoS pathogens}, + keywords = {{\textgreater}UseGalaxy.eu, Heterotrimeric GTP-Binding Proteins, Pasteurella multocida}, + language = {eng}, + month = {December}, + number = {12}, + pages = {e1010781}, + title = {Genome wide {CRISPR} screen for {Pasteurella} multocida toxin ({PMT}) binding proteins reveals {LDL} {Receptor} {Related} {Protein} 1 ({LRP1}) as crucial cellular receptor}, + url = {http://europepmc.org/abstract/MED/36516199}, + volume = {18}, + year = {2022} +} + @article{schoof_mouse_2023, abstract = {Pediatric high-grade gliomas of the subclass MYCN (HGG-MYCN) are highly aggressive tumors frequently carrying MYCN amplifications, TP53 mutations, or both alterations. Due to their rarity, such tumors have only recently been identified as a distinct entity, and biological as well as clinical characteristics have not been addressed specifically. To gain insights into tumorigenesis and molecular profiles of these tumors, and to ultimately suggest alternative treatment options, we generated a genetically engineered mouse model by breeding hGFAP-cre::Trp53Fl/Fl::lsl-MYCN mice. All mice developed aggressive forebrain tumors early in their lifetime that mimic human HGG-MYCN regarding histology, DNA methylation, and gene expression. Single-cell RNA sequencing revealed a high intratumoral heterogeneity with neuronal and oligodendroglial lineage signatures. High-throughput drug screening using both mouse and human tumor cells finally indicated high efficacy of Doxorubicin, Irinotecan, and Etoposide as possible therapy options that children with HGG-MYCN might benefit from.}, author = {Schoof, Melanie and Godbole, Shweta and Albert, Thomas K. and Dottermusch, Matthias and Walter, Carolin and Ballast, Annika and Qin, Nan and Olivera, Marlena Baca and Göbel, Carolin and Neyazi, Sina and Holdhof, Dörthe and Kresbach, Catena and Peter, Levke-Sophie and Epplen, Gefion Dorothea and Thaden, Vanessa and Spohn, Michael and Blattner-Johnson, Mirjam and Modemann, Franziska and Mynarek, Martin and Rutkowski, Stefan and Sill, Martin and Varghese, Julian and Afflerbach, Ann-Kristin and Eckhardt, Alicia and Münter, Daniel and Verma, Archana and Struve, Nina and Jones, David T. W. and Remke, Marc and Neumann, Julia E. and Kerl, Kornelius and Schüller, Ulrich}, @@ -12723,6 +20657,24 @@ @article{schoof_mouse_2023 year = {2023} } +@article{schroder_eomes_2024, + author = {Schröder, Chiara M. and Zissel, Lea and Mersiowsky, Sophie-Luise and Tekman, Mehmet and Probst, Simone and Schüle, Katrin M. and Preissl, Sebastian and Schilling, Oliver and Timmers, H. Th Marc and Arnold, Sebastian J.}, + doi = {10.1016/j.devcel.2024.11.014}, + issn = {1534-5807}, + journal = {Developmental Cell}, + keywords = {{\textgreater}UseGalaxy.eu, Eomes, SWI/SNF complex, Tbx factors, cell fate decision, chromatin accessibility, enhancer regulation, epigenetic remodeling, gastrulation}, + language = {English}, + month = {December}, + note = {Publisher: Elsevier}, + number = {0}, + pmid = {39662466}, + title = {{EOMES} establishes mesoderm and endoderm differentiation potential through {SWI}/{SNF}-mediated global enhancer remodeling}, + url = {https://www.cell.com/developmental-cell/abstract/S1534-5807(24)00696-8}, + urldate = {2025-03-09}, + volume = {0}, + year = {2024} +} + @article{schule_eomes_2023, author = {Schüle, Katrin M. and Weckerle, Jelena and Probst, Simone and Wehmeyer, Alexandra E. and Zissel, Lea and Schröder, Chiara M. and Tekman, Mehmet and Kim, Gwang-Jin and Schlägl, Inga-Marie and Sagar and Arnold, Sebastian J.}, doi = {10.1016/j.devcel.2023.07.023}, @@ -12792,6 +20744,40 @@ @article{schwabenland_neonatal_2023 year = {2023} } +@patent{schwarz_biotechnological_2022, + assignee = {S2B Gmbh \& Co. Kg}, + author = {Schwarz, Christoph and PREUSS, Christian and ANTELMANN, Amira}, + keywords = {{\textgreater}UseGalaxy.eu, cytochrome, microorganism, nucleic acid, seq, synthase}, + language = {en}, + month = {November}, + nationality = {WO}, + number = {WO2022229378A1}, + title = {Biotechnological production of terpenes}, + url = {https://patents.google.com/patent/WO2022229378A1/en?q=(%22usegalaxy.eu%22+OR+%22European+Galaxy%22)&oq=%22usegalaxy.eu%22+OR+%22European+Galaxy%22}, + urldate = {2025-04-14}, + year = {2022} +} + +@article{seah_maternal_2025, + abstract = {PR/SET domain-containing (PRDM) proteins are metazoan-specific transcriptional regulators that play diverse roles in mammalian development and disease. Several members such as PRDM1, PRDM14 and PRDM9, have been implicated in germ cell specification and homoeostasis and are essential to fertility-related processes. Others, such as PRDM14, PRDM15 and PRDM10 play a role in early embryogenesis and embryonic stem cell maintenance. Here, we describe the first PRDM family member with a maternal effect. Absence of maternal Prdm10 results in catastrophic failure of oocyte-to-embryo transition and complete arrest at the 2-cell stage. We describe multiple defects in oocytes, zygotes and 2-cell stage embryos relating to the failure to accumulate PRDM10 target gene transcripts in the egg. Transcriptomic analysis and integration of genome-wide chromatin-binding data reveals new and essential PRDM10 targets, including the cytoskeletal protein encoding gene Septin11. We demonstrate that the failure to express maternal Septin11, in the absence of maternal PRDM10, disrupts Septin-complex assembly at the polar body extrusion site in MII oocytes. Our study sheds light into the essentiality of maternal PRDM10, the requirement of the maternal Septin-complex and the likely evolutionary conservation of this regulatory axis in human female germ cells.}, + author = {Seah, Michelle K. Y. and Han, Brenda Y. and Huang, Yan and Rasmussen, Louise J. H. and Stäubli, Andrina J. and Bello-Rodríguez, Judith and Chan, Andrew Chi-Ho and Gasnier, Maxime and Wollmann, Heike and Guccione, Ernesto and Messerschmidt, Daniel M.}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41467-025-56991-8}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Embryonic induction, Meiosis, Transcription}, + language = {en}, + month = {February}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {1939}, + title = {Maternal {PRDM10} activates essential genes for oocyte-to-embryo transition}, + url = {https://www.nature.com/articles/s41467-025-56991-8}, + urldate = {2025-02-27}, + volume = {16}, + year = {2025} +} + @article{seckin_dinler_regulation_2023, abstract = {Plant hormones and antioxidant system changes occur during plants' exposure to stress conditions. Although the interactions of some plant hormones (abscisic acid, salicylic acid, jasmonic acid, nitric oxide, and ethylene) with the glutathione s-transferase (GST) enzyme, which is one of the antioxidant enzymes, have already been reported, the influence of gibberellic acid (GA3) on this enzyme under saline conditions has not yet been reported. Plant material for the experiments was obtained from M14G144 cultivar of maize (Zea mays L.) plants grown as a soil culture in growth chambers at 22 °C, 65–70\% moisture, 16-h light/8-h dark conditions, and with full strength Hoagland solution for 8 days under controlled growth conditions. Then, the plants were exposed to salt stress (350 mM NaCl and 100, 300, and 500 ppm GA3) simultaneously. In maize leaves, GA3 treatment alleviated the physiological parameters under salt stress. Specifically, the treatments with 100 and 500 ppm of GA3 were able to trigger GST enzyme and isoenzyme activities as well as hydrogen sulfide accumulation and anthocyanin content, although the lowest malondialdehyde, hydrogen peroxide, and superoxide radical content were under the treatment of 300 ppm of GA3. Besides this, GST gene expression levels were found to be upregulated between 1.5 and fourfold higher in all the plants treated with GA3 at different concentrations in proportion to salt stress. These results first indicated that the reason for the changes in GA3-treated plants was the stimulating role of this hormone to maintain GST regulation in maize plants.}, author = {Seckin Dinler, Burcu and Cetinkaya, Hatice and Secgin, Zafer}, @@ -12810,6 +20796,40 @@ @article{seckin_dinler_regulation_2023 year = {2023} } +@article{semail_genomic_2025, + abstract = {Burkholderia pseudomallei is a highly infectious bacterium responsible for melioidosis, a systemic disease prevalent in Northern Australia and Southeast Asia. Melioidosis is a community-acquired infectious disease caused by B. pseudomallei, which thrives in tropical regions. This study presents the complete genome sequences of 18 B. pseudomallei isolates from clinical and environmental settings in Kelantan, Malaysia. Clinical isolates were characterized based on patient outcomes: recovery (n=6), relapse (n=4), and death due to melioidosis (n=6), with two environmental isolates that were obtained from soil samples. Draft genome sequences of the isolates were generated using Illumina HiSeq sequencing technology. The 18 B. pseudomallei genomes have an average length of 7,823, 977 bp (7,587,408-8,243,305 bp), an average GC content of 67.4\%, with a mean N50 length and contigs of 47,798 bp and 2,882, respectively. RAST identified an average of 9,671 CDS and 64 RNAs per genome. A total of 144 virulence genes were identified across the dataset, including bimA, bipD, bopA, hcp, and vgrG genes. Antimicrobial resistance gene detection revealed a predicted resistance profile involving the blaOXA-59 gene, conferring resistance to beta-lactam antibiotics, present in all 18 genomes. MLST profiles revealed ST54 as the most common sequence type, corresponding to isolates USM003, USM010, USM011, USM013, and USM014. The 18 draft genomes also showed a close phylogenetic relationship with other genomes from Southeast Asia. In summary, the complete genome sequences of 18 B. pseudomallei isolates have been elucidated and provide a valuable resource to investigate the genetic diversity and virulence profiles of B. pseudomallei.}, + author = {Semail, Noreafifah and Zuraina, Nik Mohd Noor Nik and Ismadi, Yasmin Khairani Muhammad and Harun, Azian and Aziah, Ismail and Deris, Zakuan Zainy}, + doi = {10.1016/j.crmicr.2025.100397}, + issn = {2666-5174}, + journal = {Current Research in Microbial Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Genome annotation, Genome assembly, Melioidosis, Whole genome sequencing}, + language = {eng}, + month = {January}, + pages = {100397}, + title = {Genomic dataset of eighteen \textit{{Burkholderia} pseudomallei} strains isolated from clinical and environmental settings in {Malaysia}}, + url = {https://www.sciencedirect.com/science/article/pii/S2666517425000598}, + urldate = {2025-05-28}, + volume = {8}, + year = {2025} +} + +@article{semenzato_endophytic_2022, + abstract = {Seed-associated microbiota are believed to play a crucial role in seed germination, seedling establishment, and plant growth and fitness stimulation, due to the vertical transmission of a core microbiota from seeds to the next generations. It might be hypothesized that medicinal and aromatic plants could use the seeds as vectors to vertically transfer beneficial endophytes, providing plants with metabolic pathways that could influence phytochemicals production. Here, we investigated the localization, the structure and the composition of the bacterial endophytic population that resides in \textit{Origanum heracleoticum} L. seeds. Endocellular bacteria, surrounded by a wall, were localized close to the aleurone layer when using light and transmission electron microscopy. From surface-sterilized seeds, cultivable endophytes were isolated and characterized through RAPD analysis and 16S RNA gene sequencing, which revealed the existence of a high degree of biodiversity at the strain level and the predominance of the genus \textit{Pseudomonas}. Most of the isolates grew in the presence of six selected antibiotics and were able to inhibit the growth of clinical and environmental strains that belong to the \textit{Burkholderia cepacia} complex. The endophytes production of antimicrobial compounds could suggest their involvement in plant secondary metabolites production and might pave the way to endophytes exploitation in the pharmaceutical field.}, + author = {Semenzato, Giulia and Faddetta, Teresa and Falsini, Sara and Del Duca, Sara and Esposito, Antonia and Padula, Anna and Greco, Claudia and Mucci, Nadia and Zaccaroni, Marco and Puglia, Anna Maria and Papini, Alessio and Fani, Renato}, + doi = {10.3390/microorganisms10102086}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {October}, + number = {10}, + pages = {2086}, + title = {Endophytic {Bacteria} {Associated} with {Origanum} heracleoticum {L}. ({Lamiaceae}) {Seeds}}, + url = {http://europepmc.org/abstract/MED/36296360}, + volume = {10}, + year = {2022} +} + @article{semenzato_genomic_2022, abstract = {Multidrug-resistant pathogens represent a serious threat to human health. The inefficacy of traditional antibiotic drugs could be surmounted through the exploitation of natural bioactive compounds of which medicinal plants are a great reservoir. The finding that bacteria living inside plant tissues, (i.e., the endophytic bacterial microbiome) can influence the synthesis of the aforementioned compounds leads to the necessity of unraveling the mechanisms involved in the determination of this symbiotic relationship. Here, we report the genome sequence of four endophytic bacterial strains isolated from the medicinal plant Origanum vulgare L. and able to antagonize the growth of opportunistic pathogens of cystic fibrosis patients. The in silico analysis revealed the presence of gene clusters involved in the production of antimicrobial compounds, such as paeninodin, paenilarvins, polymyxin, and paenicidin A. Endophytes’ adaptation to the plant microenvironment was evaluated through the analysis of the presence of antibiotic resistance genes in the four genomes. The diesel fuel degrading potential was also tested. Strains grew in minimum media supplemented with diesel fuel, but no n-alkanes degradation genes were found in their genomes, suggesting that diesel fuel degradation might occur through other steps involving enzymes catalyzing the oxidation of aromatic compounds.}, author = {Semenzato, Giulia and Alonso-Vásquez, Tania and Del Duca, Sara and Vassallo, Alberto and Riccardi, Christopher and Zaccaroni, Marco and Mucci, Nadia and Padula, Anna and Emiliani, Giovanni and Palumbo Piccionello, Antonio and Puglia, Anna Maria and Fani, Renato}, @@ -12836,7 +20856,7 @@ @article{semenzato_genomic_2023 doi = {10.3390/ijms24054845}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {{\textgreater}UseGalaxy.eu, endophytes, essential oil, genome, plant microbiota, volatile organic compounds}, + keywords = {{\textgreater}UseGalaxy.eu, Arthrobacter, Oils, Volatile, Origanum, Plants, Medicinal, endophytes, essential oil, genome, plant microbiota, volatile organic compounds}, language = {en}, month = {January}, note = {Number: 5 @@ -12855,7 +20875,7 @@ @article{senapathi_biomolecular_2019 author = {Senapathi, Tharindu and Bray, Simon and Barnett, Christopher B. and Grüning, Björn and Naidoo, Kevin J.}, doi = {10.1093/bioinformatics/btz107}, journal = {Bioinformatics}, - keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}BRIDGE, {\textgreater}UseGalaxy.eu}, + keywords = {+Galactic, +IsGalaxy, +Tools, {\textgreater}BRIDGE, {\textgreater}UseGalaxy.eu, Software}, language = {en}, month = {February}, title = {Biomolecular {Reaction} \& {Interaction} {Dynamics} {Global} {Environment} ({BRIDGE})}, @@ -12949,7 +20969,7 @@ @article{shaikh_stcdf1_2024 doi = {10.1111/nph.20186}, issn = {1469-8137}, journal = {New Phytologist}, - keywords = {{\textgreater}UseGalaxy.eu, DAP-seq, Solanum tuberosum L., StCDF1 transcription factor, nitrate reductase, promoter polymorphism}, + keywords = {{\textgreater}UseGalaxy.eu, DAP-seq, Gene Expression Regulation, Plant, Nitrates, Plant Proteins, Solanum tuberosum, Solanum tuberosum L., StCDF1 transcription factor, nitrate reductase, promoter polymorphism}, language = {en}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20186}, number = {n/a}, @@ -12976,6 +20996,23 @@ @article{shankar_structure_2023 year = {2023} } +@article{shao_pegr_2022, + abstract = {Reproducibility is a significant challenge in (epi)genomic research due to the complexity of experiments composed of traditional biochemistry and informatics. Recent advances have exacerbated this as high-throughput sequencing data is generated at an unprecedented pace. Here, we report the development of a Platform for Epi-Genomic Research (PEGR), a web-based project management platform that tracks and quality controls experiments from conception to publication-ready figures, compatible with multiple assays and bioinformatic pipelines. It supports rigor and reproducibility for biochemists working at the bench, while fully supporting reproducibility and reliability for bioinformaticians through integration with the Galaxy platform.}, + author = {Shao, Danying and Kellogg, Gretta D and Nematbakhsh, Ali and Kuntala, Prashant K and Mahony, Shaun and Pugh, B Franklin and Lai, William K M}, + doi = {10.1186/s13059-022-02671-5}, + issn = {1474-7596}, + journal = {Genome biology}, + keywords = {{\textgreater}UseGalaxy.eu, Epigenomics, Genomics}, + language = {eng}, + month = {April}, + number = {1}, + pages = {99}, + title = {{PEGR}: a flexible management platform for reproducible epigenomic and genomic research}, + url = {http://europepmc.org/abstract/MED/35440038}, + volume = {23}, + year = {2022} +} + @article{sharaf_bridging_2023, abstract = {The Open Institute of the African BioGenome Project empowers African scientists and institutions with the skill sets, capacity and infrastructure to advance scientific knowledge and innovation and drive economic growth.}, author = {Sharaf, Abdoallah and Ndiribe, Charlotte C. and Omotoriogun, Taiwo Crossby and Abueg, Linelle and Badaoui, Bouabid and Badiane Markey, Fatu J. and Beedessee, Girish and Diouf, Diaga and Duru, Vincent C. and Ebuzome, Chukwuike and Eziuzor, Samuel C. and Jaufeerally Fakim, Yasmina and Formenti, Giulio and Ghanmi, Nidhal and Guerfali, Fatma Zahra and Houaga, Isidore and Ideozu, Justin Eze and Katee, Sally Mueni and Khayi, Slimane and Kuja, Josiah O. and Kwon-Ndung, Emmanuel Hala and Marks, Rose A. and Moila, Acclaim M. and Mungloo-Dilmohamud, Zahra and Muzemil, Sadik and Nigussie, Helen and Osuji, Julian O. and Ras, Verena and Tchiechoua, Yves H. and Zoclanclounon, Yedomon Ange Bovys and Tolley, Krystal A. and Ziyomo, Cathrine and Mapholi, Ntanganedzeni and Muigai, Anne W. T. and Djikeng, Appolinaire and Ebenezer, ThankGod Echezona}, @@ -12997,6 +21034,57 @@ @article{sharaf_bridging_2023 year = {2023} } +@article{sharifian_genetic_2025, + abstract = {BackgroundLeishmaniasis is a major public health concern, with a high annual incidence and extensive geographical distribution. This parasitic disease is transmitted through the bite of specific species of sand flies and is caused by flagellated protozoa. Leishmania major is one of the main causes of cutaneous leishmaniasis (CL) in Iran, with diverse clinical manifestations. This research seeks to explore the impact of genetic diversity on clinical differences by investigating variations in chromosomal count and analyzing single nucleotide polymorphisms (SNPs) and insertions/deletions (Indels).Materials and methodsThe whole genome of the Iranian Leishmania major strain MRHO/IR/75/ER has been sequenced using next-generation sequencing. Data alignment to the reference genome, variant calling, and SNP, Indel, and chromosomal variation identification were carried out using bioinformatics tools.ResultsThe findings indicated notable karyotypic variations in the Iranian Leishmania major strain, specifically demonstrating monosomy on chromosome 2 and trisomy on chromosomes 5, 13, 28, and 31. The analysis of SNPs and INDELs revealed 144,509 genetic variants, with 99\% situated within coding regions. Significant changes were observed in MRPA, HSP70.4, GP63, and CPA, which may affect drug resistance and pathogenicity.ConclusionThis research clarifies the genetic diversity of L. major and its consequences for disease development and resistance to treatment. Further functional studies are essential to validate these genetic discoveries and their implications for clinical practice.}, + author = {Sharifian, Hanieh and Khalafiyan, Anis and Fadaie, Mahmood and Khanahmad, Hossein and Shahmoradi, Zabihollah and Zaker, Erfan and Mousavi, Parisa and Pourmoshir, Nadia and Zolfaghari, Azadeh}, + copyright = {cc by-nc-sa}, + doi = {10.4103/abr.abr_172_25}, + issn = {2277-9175}, + journal = {Advanced biomedical research}, + keywords = {{\textgreater}UseGalaxy.eu, Cutaneous Leishmaniasis, Leishmania Major, Variant Calling, Whole Genome Sequencing}, + language = {eng}, + month = {January}, + pages = {112}, + pmcid = {PMC12543250}, + pmid = {41132223}, + shorttitle = {Genetic {Diversity} and {Chromosomal} {Variations} in the {Iranian} \<i\>{Leishmania} major\</i\> {Strain}}, + title = {Genetic {Diversity} and {Chromosomal} {Variations} in the {Iranian} \<i\>{Leishmania} major\</i\> {Strain}: {Insights} into {Pathogenicity} and {Drug} {Resistance}}, + url = {https://europepmc.org/articles/PMC12543250}, + urldate = {2025-12-26}, + volume = {14}, + year = {2025} +} + +@article{sharma_cytokinesis_2025, + abstract = {The polarized architecture of neurons is intricately associated with modulation of microtubule dynamics. Over the years several microtubule-associated-factors that modulate neuronal polarity have been identified. However, the precise details of how microtubule arrangement and stability is established in axon and dendrites is not clearly understood. To uncover relevant factors involved in the biological pathways governing microtubule regulation in neuron, we conducted a suppressor screen using the neuronal ectopic extension phenotype caused due to loss of kinesin-13 family microtubule depolymerizing protein KLP-7 in C. elegans . Interestingly, apart from eleven variants of α ( mec-12 ) and β ( mec-7 ) tubulins, we isolated a variant of cytokinesis associated protein, W02B8.2/citk-1, the kinase-less worm orthologue of mammalian citron-rho interacting kinase (CIT). Little is known about the role of CITK in microtubule regulation in post-mitotic neurons. In this study, we found that the kinase-less worm orthologues of CIT, citk-1 and citk-2 redundantly modulate microtubule stability in the axon-like anterior process and maintain the population of plus-end-out microtubules in the dendrite-like posterior process of the PLM mechanosensory neurons in a cell autonomous manner. In the absence of citk-1 , PLM neurons exhibit variable morphological defects including defects in migration, growth, and guidance. Moreover, the neuronal and microtubule phenotypes of loss of both citk-1 and citk-2 were phenocopied by the mutant animals of aspm-1, the worm homolog of abnormal spindle-like microcephaly-associated protein (ASPM), suggesting a genetic association, similar to their association in dividing mammalian cells. These observations suggest that the cytokinesis associated citron kinase and ASPM-1 have non-mitotic roles in C. elegans mechanosensory neurons in the regulation of microtubules.}, + author = {Sharma, Sunanda and Ponniah, Keerthana and Ghosh-Roy, Anindya}, + doi = {10.1101/2025.04.24.650367}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {The cytokinesis associated proteins {CITK} and {ASPM}-1 regulate neuronal microtubule dynamics and polarity in {C}. elegans}, + url = {http://europepmc.org/abstract/PPR/PPR1010293}, + year = {2025} +} + +@article{sharma_multi-omic_2025, + abstract = {Sperm DNA methylation changes have been implicated in the increased adverse pregnancy and offspring disease risks associated with advanced paternal age. Here, an analysis of diverse, publicly available human multi-omic data is presented that assesses the mechanistic plausibility for these changes to exert cross-generational developmental and health effects. First, differentially methylated CpGs in aging sperm DNA were found to specifically overrepresent differentially methylated CpGs in aging and disease soma. Next, sperm and soma common CpGs, compared to sperm and soma unique CpGs, showed higher enrichment for regulatory regions of developmental genes. Further, genes associated with the common CpGs, compared to the unique CpGs, showed higher enrichment for genes differentially expressed during both preimplantation and postimplantation development, and most crucially for epigenetic inheritance amenability, in early embryos known to undergo paternal methylation-associated gene regulation and in epigenetically reprogrammed primordial germ cells. Higher enrichment is likewise also observed for aging- and disease-associated genes. These results suggest that aging sperm methylation marks may possibly affect early embryonic gene expression, with downstream somatic and germline gene regulatory consequences leading to reestablishment of methylation marks, developmental anomalies, and inheritance of disease phenotypes. This data-grounded mechanistic possibility could be relevant in epigenetic inheritance in general.}, + author = {Sharma, Abhay}, + copyright = {© 2025 The New York Academy of Sciences.}, + doi = {10.1111/nyas.70056}, + issn = {1749-6632}, + journal = {Annals of the New York Academy of Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, DNA methylation, aging, disease, embryonic development, epigenetic inheritance, gene expression, sperm}, + language = {en}, + month = {September}, + note = {\_eprint: https://nyaspubs.onlinelibrary.wiley.com/doi/pdf/10.1111/nyas.70056}, + number = {n/a}, + title = {Multi-{Omic} {Data} {Analysis} {Supporting} the {Plausibility} of {Human} {Aging} {Sperm}–{Mediated} {Epigenetic} {Inheritance}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nyas.70056}, + urldate = {2025-10-02}, + volume = {n/a}, + year = {2025} +} + @article{sharma_pan-cancer_2019, abstract = {Synonymous mutations have been viewed as silent mutations, since they only affect the DNA and mRNA, but not the amino acid sequence of the resulting protein. Nonetheless, recent studies suggest their significant impact on splicing, RNA stability, RNA folding, translation or co-translational protein folding. Hence, we compile 659194 synonymous mutations found in human cancer and characterize their properties. We provide the user-friendly, comprehensive resource for synonymous mutations in cancer, SynMICdb (http://SynMICdb.dkfz.de), which also contains orthogonal information about gene annotation, recurrence, mutation loads, cancer association, conservation, alternative events, impact on mRNA structure and a SynMICdb score. Notably, synonymous and missense mutations are depleted at the 5'-end of the coding sequence as well as at the ends of internal exons independent of mutational signatures. For patient-derived synonymous mutations in the oncogene KRAS, we indicate that single point mutations can have a relevant impact on expression as well as on mRNA secondary structure., Synonymous mutations do not alter amino acid sequence but may exert oncogenic effects in other ways. Here, the authors present a catalogue of synonymous mutations in cancer and characterise their properties.}, author = {Sharma, Yogita and Miladi, Milad and Dukare, Sandeep and Boulay, Karine and Caudron-Herger, Maiwen and Groß, Matthias and Backofen, Rolf and Diederichs, Sven}, @@ -13020,7 +21108,7 @@ @article{sheikh_volatile_2023 author = {Sheikh, Taha Majid Mahmood and Zhou, Dongmei and Ali, Haider and Hussain, Sarfraz and Wang, Nan and Chen, Siqiao and Zhao, Yishen and Wen, Xian and Wang, Xiaoyu and Zhang, Jinfeng and Wang, Lunji and Deng, Sheng and Feng, Hui and Raza, Waseem and Fu, Pengxiao and Peng, Hao and Wei, Lihui and Daly, Paul}, doi = {10.1128/spectrum.01510-23}, journal = {Microbiology Spectrum}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Pythium, Volatile Organic Compounds, Zingiber officinale}, month = {August}, note = {Publisher: American Society for Microbiology}, number = {0}, @@ -13032,6 +21120,21 @@ @article{sheikh_volatile_2023 year = {2023} } +@article{sherwood_transcriptional_2025, + abstract = {The frequency of extreme precipitation events is predicted to increase owing to climate change, leading to soil waterlogging and crop yield losses, particularly in the case of susceptible species, such as barley (Hordeum vulgare). Aerenchyma formation is a key morphological adaptation to waterlogging stress and hypoxic conditions; however, its genetic regulation in barley remains largely unresolved. The aim of this study was to address this knowledge gap and characterize the transcriptional signatures associated with the waterlogging stress response and aerenchyma formation in barley roots.Two barley cultivars (Franklin and Yerong) were subjected to waterlogging stress, followed by analysis of phenotypic traits, including root aerenchyma formation, and transcriptomic profiling of root tissue. Differential gene expression analysis and gene regulatory network construction were carried out using generated RNA-sequencing datasets.Performed analyses identified genes transcriptionally responsive to 24 and 72 h of waterlogging in both cultivars and highlighted metabolic adaptations, regulation of reactive oxygen species signalling and management of stress responses as key elements of the waterlogging response in barley roots. Large intra-individual variation was observed for root aerenchyma formation. This variation was exploited to identify 81 candidate aerenchyma-associated genes and ascertain pathways involved in aerenchyma formation. Furthermore, network analyses suggested that the DNA damage response gene DRT100 and the cell wall-modifying genes XTH16 and XTH15 are regulatory hub genes in aerenchyma formation.This study provides new insights into transcriptional signatures associated with waterlogging responses and aerenchyma formation in barley roots. The identified candidate aerenchyma-associated genes offer new targets for future research and breeding efforts aimed at enhancing waterlogging tolerance in this crop species.}, + author = {Sherwood, Orla L and Burke, Rory and O’Rourke, Jennifer and Whelan, Conor V and Downey, Frances and Ryan, Louise and McCabe, Eoin F and Huang, Zixia and Ng, Carl K Y and McCabe, Paul F and Kacprzyk, Joanna}, + doi = {10.1093/aob/mcaf104}, + issn = {0305-7364}, + journal = {Annals of Botany}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {June}, + pages = {mcaf104}, + title = {Transcriptional signatures associated with waterlogging stress responses and aerenchyma formation in barley root tissue}, + url = {https://doi.org/10.1093/aob/mcaf104}, + urldate = {2025-07-12}, + year = {2025} +} + @article{shi_modeling_2023, abstract = {Background Ischemia of the bile duct is a common feature in liver disease and transplantation, which represents a major cause of morbidity and mortality, especially after liver transplantation. Detailed knowledge of its pathogenesis remains incomplete due to the lack of appropriate in vitro models. @@ -13059,10 +21162,13 @@ @article{shi_modeling_2023 } @article{shi_recapitulating_2022, + abstract = {{\textless}h4{\textgreater}Background \& aims{\textless}/h4{\textgreater}Liver and bile duct diseases often are associated with extensive cell death of cholangiocytes. Necroptosis represents a common mode of programmed cell death in cholangiopathy, however, detailed mechanistic knowledge is limited owing to the lack of appropriate in vitro models. To address this void, we investigated whether human intrahepatic cholangiocyte organoids (ICOs) can recapitulate cholangiopathy-associated necroptosis and whether this model can be used for drug screening.{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}We evaluated the clinical relevance of necroptosis in end-stage liver diseases and liver transplantation by immunohistochemistry. Cholangiopathy-associated programmed cell death was evoked in ICOs derived from healthy donors or patients with primary sclerosing cholangitis or alcoholic liver diseases by the various stimuli.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}The expression of key necroptosis mediators, receptor-interacting protein 3 and phosphorylated mixed lineage kinase domain-like, in cholangiocytes during end-stage liver diseases was confirmed. The phosphorylated mixed lineage kinase domain-like expression was etiology-dependent. Gene expression analysis confirmed that primary cholangiocytes are more prone to necroptosis compared with primary hepatocytes. Both apoptosis and necroptosis could be specifically evoked using tumor necrosis factor α and second mitochondrial-derived activator of caspases mimetic, with or without caspase inhibition in healthy and patient-derived ICOs. Necroptosis also was induced by ethanol metabolites or human bile in ICOs from donors and patients. The organoid cultures further uncovered interdonor variable and species-specific drug responses. Dabrafenib was identified as a potent necroptosis inhibitor and showed a protective effect against ethanol metabolite toxicity.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}Human ICOs recapitulate cholangiopathy-associated necroptosis and represent a useful in vitro platform for the study of biliary cytotoxicity and preclinical drug evaluation.}, author = {Shi, Shaojun and Verstegen, Monique M. A. and Roest, Henk P. and Ardisasmita, Arif I. and Cao, Wanlu and Roos, Floris J. M. and Ruiter, Petra E. de and Niemeijer, Marije and Pan, Qiuwei and IJzermans, Jan N. M. and Laan, Luc J. W. van der}, doi = {10.1016/j.jcmgh.2021.10.009}, + issn = {2352-345X}, journal = {Cellular and Molecular Gastroenterology and Hepatology}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Necroptosis, Organoids}, + language = {eng}, note = {Publisher: Elsevier BV}, number = {2}, pages = {541--564}, @@ -13072,6 +21178,42 @@ @article{shi_recapitulating_2022 year = {2022} } +@article{shiekh_suliman_taxonomic_2025, + author = {Shiekh Suliman, Nagham and Talaei-Hassanloui, Reza and Abachi, Hamid and Zarei, Sadegh and Osdaghi, Ebrahim}, + doi = {10.3389/fmicb.2025.1518307}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Bacillus, Bacillus cereus, bacterial taxonomy, biological control, phylotaxonomy}, + language = {English}, + month = {February}, + note = {Publisher: Frontiers}, + title = {Taxonomic refinement of {Bacillus} thuringiensis}, + url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1518307/full}, + urldate = {2025-02-23}, + volume = {16}, + year = {2025} +} + +@article{shinge_inspired_2025, + abstract = {Garuga pinnata a tree spotted in the Asian continent constitutes of constellation of phytochemicals in the whole tree from which the alcoholic extract of the leaf is the abundant source. The phytochemicals namely Amentoflavone, Garuganin-1, Garuganin-3, Garuganin-4, and Garuganin-5 were considered for the study as they have the anti-Alzheimer’s potential but the biological target has not been reported. So, to identify the target the phytochemicals were scrutinized by employing in silico methodologies namely molecular docking, molecular dynamics simulation, and ADMET prediction. Molecular docking revealed that Amentoflavone occupied the active site of the NMDA, and established interactions with Gln110, Glu236, Ile133, and Asp136 with an excellent docking score of −8.535 kcal/mol. Amentoflavone with the best docking score was selected for molecular dynamics which revealed that Amentoflavone maintained stability in the active site of the NMDA receptor with three hydrogen bond interactions in 100 ns time scale of the trajectory. Amentoflavone demonstrated an encouraging ADMET profile as compared to other phytochemicals. In the nut shell Amentoflavone displayed excellent in silico results and further may demonstrate an excellent in vitro NMDA inhibitory potential.}, + author = {Shinge, Jagannath and , Amol, Muthal and , Vinayak, Walhekar and , Chandrakant, Bagul and , Dileep, Kumar and , Chandrashekar, V. M. and , Baswaraj, Macha and , Vaibhav, Shinde and , Mahesh, Palled and and Kulkarni, Ravindra}, + doi = {10.1080/07391102.2025.2477776}, + issn = {0739-1102}, + journal = {Journal of Biomolecular Structure and Dynamics}, + keywords = {{\textgreater}UseGalaxy.eu, Garuga pinnata, NMDA receptors, amentoflavone, molecular docking, molecular dynamics simulation}, + month = {April}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/07391102.2025.2477776}, + number = {0}, + pages = {1--15}, + pmid = {40166865}, + title = {Inspired by molecular dynamic simulation, exploring chemical constituents of alcoholic extract of {Garuga} pinnata computationally as inhibitors of {GluN2B}-containing {NMDA} receptors}, + url = {https://doi.org/10.1080/07391102.2025.2477776}, + urldate = {2025-04-21}, + volume = {0}, + year = {2025} +} + @article{shipman_combined_2024, abstract = {Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is a serious disease that threatens banana production worldwide. It is a long-standing problem in Hawaii, but previously, there was little knowledge of the causal pathogen. We isolated a strain of Foc, named Foc-UH, from a field experiencing the disease epidemic in Hawaii. Infection assays of a diverse panel of 26 banana clones, including varieties used for differentiating pathogen races and fruit production, revealed that Foc-UH has a race 1 pathogenic phenotype with an intermediate race 2 virulence and revealed the differential resistance of varieties to infection. Separate phylogenetic analyses using the barcoding regions of three nuclear genes, seven complete nuclear genes, and single-nucleotide polymorphisms within conserved whole-genome protein coding sequences placed Foc-UH into recently proposed taxonomic frameworks relevant to Foc and the F. oxysporum species complex. Screening of the 99.7\% complete draft genome identified five secreted in xylem (SIX) gene homologs: SIX1d, SIX1f, SIX9a, SIX9b, and SIX13a. This profile is similar to that of several race 1 isolates except for the absence of SIX4 and SIX6. Foc-UH was morphologically dissimilar to the nearest related isolates. Altogether, this study identified a unique isolate that causes banana Fusarium wilt, which represents the first characterization of the causal pathogen in Hawaii. The findings and genomic resources generated in this study are expected to guide banana breeding and cultivar deployment in Hawaii and beyond and contribute to further understanding of the pathogenicity and evolutionary systematics of Foc.}, author = {Shipman, Aaron and Tian, Miaoying}, @@ -13090,6 +21232,21 @@ @article{shipman_combined_2024 year = {2024} } +@article{showers_scuba_2024, + abstract = {While robust tools exist for the analysis of single-cell datasets in both Python and R, interoperability is limited, and analysis tools generally only accept one object class. Considerable programming expertise is required to integrate tools across package ecosystems into a comprehensive analysis, due to their differing languages and internal data structures. This complicates validation of results and leads to inconsistent visualizations between analysis suites. Conversion between object formats is the most common solution, but this is difficult and error-prone due to the rapid pace of development of the analysis suites and their underlying data structures. To address this, we created SCUBA (Single-Cell Unified Backend API), an R package that implements a unified data access API for all common R and Python single-cell object formats. SCUBA extends the data access approach from the widely used Seurat package to SingleCellExperiment and anndata objects. SCUBA also implements new data-specific access functions for all supported object types. Performance scales well across all SCUBA-supported formats. In addition to performance, SCUBA offers several advantages over object conversion for the visualization and further analysis of pre-processed single-cell data. First, SCUBA extracts only data required for the operation at hand, leaving the original object unmodified. This process is simpler, less error prone, and less memory intensive than object conversion, which operates on the entire dataset. Second, code written with SCUBA can use any supported object class as input, with simple and consistent syntax across object formats. This allows a single analysis script or package (like our interactive single-cell browser, scExploreR) to work seamlessly with multiple object types, reducing the complexity of the code and improving both readability and reproducibility. Adoption of SCUBA will ultimately improve collaboration and reproducible research in single-cell analysis by lowering the barriers between package ecosystems.}, + author = {Showers, William M and Desai, Jairav and Engel, Krysta L and Smith, Clayton and Jordan, Craig T and Gillen, Austin E}, + doi = {10.12688/f1000research.154675.2}, + issn = {2046-1402}, + journal = {F1000Research}, + keywords = {{\textgreater}UseGalaxy.eu, Information Storage and Retrieval, Programming Languages, Single-Cell Analysis, Software}, + language = {eng}, + pages = {1256}, + title = {{SCUBA} implements a storage format-agnostic {API} for single-cell data access in {R}}, + url = {http://europepmc.org/abstract/MED/40822437}, + volume = {13}, + year = {2024} +} + @article{siatra_return_2023, abstract = {The single curative measure for heart failure patients is a heart transplantation, which is limited due to a shortage of donors, the need for immunosuppression and economic costs. Therefore, there is an urgent unmet need for identifying cell populations capable of cardiac regeneration that we will be able to trace and monitor. Injury to the adult mammalian cardiac muscle, often leads to a heart attack through the irreversible loss of a large number of cardiomyocytes, due to an idle regenerative capability. Recent reports in zebrafish indicate that Tbx5a is a vital transcription factor for cardiomyocyte regeneration. Preclinical data underscore the cardioprotective role of Tbx5 upon heart failure. Data from our earlier murine developmental studies have identified a prominent unipotent Tbx5-expressing embryonic cardiac precursor cell population able to form cardiomyocytes, in vivo, in vitro and ex vivo. Using a developmental approach to an adult heart injury model and by employing a lineage-tracing mouse model as well as the use of single-cell RNA-seq technology, we identify a Tbx5-expressing ventricular cardiomyocyte-like precursor population, in the injured adult mammalian heart. The transcriptional profile of that precursor cell population is closer to that of neonatal than embryonic cardiomyocyte precursors. Tbx5, a cardinal cardiac development transcription factor, lies in the center of a ventricular adult precursor cell population, which seems to be affected by neurohormonal spatiotemporal cues. The identification of a Tbx5-specific cardiomyocyte precursor-like cell population, which is capable of dedifferentiating and potentially deploying a cardiomyocyte regenerative program, provides a clear target cell population for translationally-relevant heart interventional studies.}, author = {Siatra, Panagiota and Vatsellas, Giannis and Chatzianastasiou, Athanasia and Balafas, Evangelos and Manolakou, Theodora and Papapetropoulos, Andreas and Agapaki, Anna and Mouchtouri, Eleni-Taxiarchia and Ruchaya, Prashant J. and Korovesi, Artemis G. and Mavroidis, Manolis and Thanos, Dimitrios and Beis, Dimitris and Kokkinopoulos, Ioannis}, @@ -13134,7 +21291,7 @@ @article{silva_comparative_2024 doi = {10.3390/ijms25084228}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {\textit{Blattabacterium}, \textit{Blattella germanica}, {\textgreater}UseGalaxy.eu, antimicrobial peptides, cuticle, fat body, metabolite transporters, peptidoglycan-recognition proteins, transcriptome, tyrosine metabolism, uricolytic pathway}, + keywords = {\textit{Blattabacterium}, \textit{Blattella germanica}, {\textgreater}UseGalaxy.eu, Fat Body, Symbiosis, Transcriptome, antimicrobial peptides, cuticle, fat body, metabolite transporters, peptidoglycan-recognition proteins, transcriptome, tyrosine metabolism, uricolytic pathway}, language = {en}, month = {January}, note = {Number: 8 @@ -13148,6 +21305,25 @@ @article{silva_comparative_2024 year = {2024} } +@article{silva_exploring_2025, + abstract = {Compelling evidence supports the potential application of wild crop relatives in Solanum breeding. Efforts have been made to generate genomic data from wild Solanum plants to assess the insertion of advantageous traits into crop species. South America hosts a broad range of plants that have not been widely evaluated at the molecular level. Solanum sessiliflorum is a wild species that shows tolerance to Ralstonia solanacearum and nematode infections. The Illumina platform was used to construct the transcriptome of S. sessiliflorum. The data were analyzed using bioinformatics tools for both phylogenetic comparison and bioprospecting of disease-related genes. Our leaf transcriptome assembly of S. sessiliflorum enables phylogenetic comparisons and stress-tolerant gene bioprospecting. De novo assembly generated 114,184 unigenes. A comparison of the S. sessiliflorum unigene dataset with other Solanum nucleotide genomic resources revealed greater similarity with Solanum tuberosum than with Solanum melongena. Additionally, S. sessiliflorum within the Leptostemonum group, along with S. melongena, possesses features related to Solanum clade evolution. Bioprospection of disease response targets identified 122 potential candidate unigenes retrieved from the S. sessiliflorum dataset. The abundant expression of fragments of disease-related and hormonal defense genes appears to constitute a housekeeping mechanism to avoid pathogen attacks on leaves. In total, 1091 unigenes were classified as transcription factors (TFs), with a large number of TFs associated with biotic resilience. These results highlight the potential for exploring the genomic diversity of S. sessiliflorum, which will be useful for applications in breeding programs.}, + author = {Silva, Priscila O. and Silva, Lucas Eduardo R. and Gouveia, Débora G. and Rodrigues, Priscila M. and Gonçalves, José Francisco C. and Nunes-Nesi, Adriano and Araújo, Wagner L. and Cavalcanti, João Henrique F.}, + copyright = {© 2025 The Author(s). Crop Science published by Wiley Periodicals LLC on behalf of Crop Science Society of America.}, + doi = {10.1002/csc2.70036}, + issn = {1435-0653}, + journal = {Crop Science}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/csc2.70036}, + number = {2}, + pages = {e70036}, + title = {Exploring the genomic diversity and breeding applications of the {Solanum} sessiliflorum transcriptome via phylogenetic analysis}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/csc2.70036}, + urldate = {2025-04-21}, + volume = {65}, + year = {2025} +} + @article{sime_microbial_2024, abstract = {The global over-reliance on non-renewable fossil fuels has led to the emission of greenhouse gases, creating a critical global environmental challenge. There is an urgent need for alternative solutions like biofuels. Advanced biofuel is a renewable sustainable energy generated from lignocellulosic plant materials, which can significantly contribute to mitigating CO2 emissions. Microbial Carbohydrate Active Enzymes (CAZymes) are the most crucial enzymes for the generation of sustainable biofuel energy. The present study designed shotgun metagenomics approaches to assemble, predict, and annotate, aiming to gain an insight into the taxonomic diversity, annotate CAZymes, and identify carbohydrate hydrolyzing CAZymes from microbiomes in Menagesha suba forest soil for the first time.}, author = {Sime, Amsale Melkamu and Kifle, Bezayit Amare and Woldesemayat, Adugna Abdi and Gemeda, Mesfin Tafesse}, @@ -13182,6 +21358,23 @@ @article{simon-chica_novel_2021 year = {2021} } +@article{simonis_persistent_2025, + abstract = {Immune memory plays a critical role in the development of durable antimicrobial immune responses. How precisely mRNA vaccines train innate immune cells to shape protective host defense mechanisms remains unknown. Here we show that SARS-CoV-2 mRNA vaccination significantly establishes histone H3 lysine 27 acetylation (H3K27ac) at promoters of human monocyte-derived macrophages, suggesting epigenetic memory. However, we found that two consecutive vaccinations were required for the persistence of H3K27ac, which matched with pro-inflammatory innate immune-associated transcriptional changes and antigen-mediated cytokine secretion. H3K27ac at promoter regions were preserved for six months and a single mRNA booster vaccine potently restored their levels and release of macrophage-derived cytokines. Interestingly, we found that H3K27ac at promoters is enriched for G-quadruplex DNA secondary structure-forming sequences in macrophage-derived nucleosome-depleted regions, linking epigenetic memory to nucleic acid structure. Collectively, these findings reveal that mRNA vaccines induce a highly dynamic and persistent training of innate immune cells enabling a sustained pro-inflammatory immune response.}, + author = {Simonis, Alexander and Theobald, Sebastian J and Koch, Anna E and Mummadavarapu, Ram and Mudler, Julie M and Pouikli, Andromachi and Göbel, Ulrike and Acton, Richard and Winter, Sandra and Albus, Alexandra and Holzmann, Dmitriy and Albert, Marie-Christine and Hallek, Michael and Walczak, Henning and Ulas, Thomas and Koch, Manuel and Tessarz, Peter and Hänsel-Hertsch, Robert and Rybniker, Jan}, + doi = {10.1038/s44320-025-00093-6}, + issn = {1744-4292}, + journal = {Molecular Systems Biology}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19, COVID-19 Vaccines, Epigenesis, Genetic, Epigenetic Memory, G-quadruplex, H3K27ac, Immunologic Memory, Macrophages, SARS-CoV-2, SARS-Cov-2 mRNA Vaccination, Trained Innate Immunity}, + month = {March}, + note = {Num Pages: 20 +Publisher: John Wiley \& Sons, Ltd}, + pages = {1--20}, + title = {Persistent epigenetic memory of {SARS}-{CoV}-2 {mRNA} vaccination in monocyte-derived macrophages}, + url = {https://www.embopress.org/doi/full/10.1038/s44320-025-00093-6}, + urldate = {2025-03-29}, + year = {2025} +} + @article{singh_biophysical_2024, abstract = {Tetramethrin (TMT) is a commonly used insecticide and has a carcinogenic and neurodegenerative effect on humans. The binding mechanism and toxicological implications of TMT to human serum albumin (HSA) were examined in this study employing a combination of biophysical and computational methods indicating moderate binding affinity and potential hepato and renal toxicity. Fluorescence quenching experiments showed that TMT binds to HSA with a moderate affinity, and the binding process was spontaneous and predominantly enthalpy-driven. Circular dichroism spectroscopy revealed that TMT binding did not induce any significant conformational changes in HSA, resulting in no changes in its alpha-helix content. The binding site and modalities of TMT interactions with HSA as computed by molecular docking and molecular dynamics simulations revealed that it binds to Sudlow site II of HSA via hydrophobic interactions through its dimethylcyclopropane carboxylate methyl propanyl group. The structural dynamics of TMT induce proper fit into the binding site creating increased and stabilizing interactions. Additionally, molecular mechanics–Poisson Boltzmann surface area calculations also indicated that non-polar and van der Waals were found to be the major contributors to the high binding free energy of the complex. Quantum mechanics (QM) revealed the conformational energies of the binding confirmation and the degree of deviation from the global minimum energy conformation of TMT. The results of this study provide a comprehensive understanding of the binding mechanism of TMT with HSA, which is important for evaluating the toxicity of this insecticide in humans.}, author = {Singh, Pratik and Gopi, Priyanka and Rani, Majji Sai Sudha and Singh, Shweta and Pandya, Prateek}, @@ -13254,6 +21447,23 @@ @techreport{singh_identification_2022 year = {2022} } +@article{singh_nrd1p_2021, + abstract = {Nuclear degradation of aberrant mRNAs in Saccharomyces cerevisiae is accomplished by the nuclear exosome and its cofactors TRAMP/CTEXT. Evidence from this investigation establishes a universal role of the Nrd1p-Nab3p-Sen1p (NNS) complex in the nuclear decay of all categories of aberrant mRNAs. In agreement with this, both nrd1-1 and nrd1-2 mutations impaired the decay of all classes of aberrant messages. This phenotype is similar to that displayed by GAL::RRP41 and rrp6-Δ mutant yeast strains. Remarkably, however, nrd1ΔCID mutation (lacking the C-terminal domain required for interaction of Nrd1p with RNAPII) only diminished the decay of aberrant messages with defects occurring during the early stage of mRNP biogenesis, without affecting other messages with defects generated later in the process. Co-transcriptional recruitment of Nrd1p on the aberrant mRNAs was vital for their concomitant decay. Strikingly, this recruitment on to mRNAs defective in the early phases of biogenesis is solely dependent upon RNAPII. In contrast, Nrd1p recruitment onto export-defective transcripts with defects occurring in the later stage of biogenesis is independent of RNAPII and dependent on the CF1A component, Pcf11p, which explains the observed characteristic phenotype of nrd1ΔCID mutation. Consistently, pcf11-2 mutation displayed a selective impairment in the degradation of only the export-defective messages.}, + author = {Singh, Pragyan and Chaudhuri, Anusha and Banerjea, Mayukh and Marathe, Neeraja and Das, Biswadip}, + doi = {10.1093/nar/gkab930}, + issn = {0305-1048}, + journal = {Nucleic Acids Res}, + keywords = {{\textgreater}UseGalaxy.eu, Post-Transcriptional, RNA Processing}, + language = {eng}, + month = {November}, + number = {20}, + pages = {11512--11536}, + title = {Nrd1p identifies aberrant and natural exosomal target messages during the nuclear {mRNA} surveillance in {Saccharomyces} cerevisiae}, + url = {http://europepmc.org/abstract/MED/34664673}, + volume = {49}, + year = {2021} +} + @article{skalon_expression_2024, abstract = {Background: Transposable elements (TEs) are major components of eukaryotic genomes. The extensive body of evidence suggests that although they were once considered “genomic parasites”, transposons and their transcripts perform specific functions, such as regulation of early embryo development. Understanding the role of TEs in such parasites as trematodes is becoming critically important. Fasciola hepatica, a parasite affecting humans and livestock, undergoes a complex life cycle in diverse environments and hosts, and knowledge about its life cycle regulation is scarce so far. Methods: We summarized the data regarding the repetitive elements in F. hepatica and conducted bulk RNA-seq analysis across its life cycle stages. TE expression profiles were analyzed, focusing on differential expression and potential homology with previously described long non-coding RNAs (lncRNAs). Results: Differential expression analysis revealed stage-specific TE transcription patterns, notably peaking during egg and metacercariae stages. Some TEs showed homology with known lncRNAs and contained putative transcription factor binding sites. Interestingly, TE transcription levels were highest in eggs and metacercariae compared to adults, suggesting regulatory roles in trematode life cycle transitions. Conclusions: These findings suggest that TEs may play roles in regulating trematode life cycle transitions. Moreover, TE homology with lncRNAs underscores their significance in gene regulation.}, author = {Skalon, Elizaveta K. and Panyushev, Nick V. and Podgornaya, Olga I. and Smolyaninova, Anastasia R. and Solovyeva, Anna I.}, @@ -13275,10 +21485,60 @@ @article{skalon_expression_2024 year = {2024} } +@article{skarlatoudi_escherichia_2025, + author = {Skarlatoudi, Theodora and Anagnostou, Glykeria-Myrto and Theodorakis, Vasileios and Bosnea, Loulouda and Mataragas, Marios}, + issn = {2306-7381}, + journal = {Vet Sci}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {August}, + number = {8}, + title = {Escherichia coli {Strains} {Originating} from {Raw} {Sheep} {Milk}, with {Special} {Reference} to {Their} {Genomic} {Characterization}, {Such} as {Virulence} {Factors} ({VFs}) and {Antimicrobial} {Resistance} ({AMR}) {Genes}, {Using} {Whole}-{Genome} {Sequencing} ({WGS})}, + url = {http://europepmc.org/abstract/PMC/PMC12390150}, + volume = {12}, + year = {2025} +} + +@article{sliti_whole_2025, + abstract = {Lacticaseibacillus paracasei is widely used as a probiotic supplement and food additive in the medicinal and food industries. However, its application requires careful evaluation of safety traits associated with probiotic pathogenesis, including the transfer of antibiotic-resistance genes, the presence of virulence and pathogenicity factors, and the potential disruptions of the gut microbiome and immune system. In this study, we conducted whole genome sequencing (WGS) of L. paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules and performed genome annotation to assess its probiotic and safety attributes. Our comparative genomic analysis assessed this novel strain's genetic attributes and functional diversity and unraveled its evolutionary relationships with other L. paracasei strains. The assembly yielded three contigs: one corresponding to the chromosome and two corresponding to plasmids. Genome annotation revealed the presence of 2,838 DNA-coding sequences (CDS), 78 ribosomal RNAs (rRNAs), 60 transfer RNAs (tRNAs), three non-coding RNAs (ncRNAs), and 126 pseudogenes. The strain lacked antibiotic resistance genes and pathogenicity factors. Two intact prophages, one Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, and three antimicrobial peptide gene clusters were identified, highlighting the genomic stability and antimicrobial potential of the strain. Furthermore, genes linked to probiotic functions, such as mucosal colonization, stress resistance, and biofilm formation, were characterized. The pan-genome analysis identified 3,358 orthologous clusters, including 1,775 single-copy clusters, across all L. paracasei strains. Notably, L. paracasei FMT2 contained many unique singleton genes, potentially contributing to its distinctive probiotic properties. Our findings confirm the potential of L. paracasei FMT2 for food and therapeutic applications based on its probiotic profile and safety.}, + author = {Sliti, Amani and Kim, Ryeong-Hui and Lee, Dokyung and Shin, Jae-Ho}, + doi = {10.1016/j.micpath.2025.107405}, + issn = {0882-4010}, + journal = {Microbial Pathogenesis}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}nano, FMT, WGS, food additive, pathogenesis, probiotic, therapeutic applications}, + month = {February}, + pages = {107405}, + title = {Whole {Genome} {Sequencing} and \textit{{In} {Silico}} {Analysis} of the {Safety} and {Probiotic} {Features} of \textit{{Lacticaseibacillus} paracasei} {FMT2} {Isolated} from {Fecal} {Microbiota} {Transplantation} ({FMT}) {Capsules}}, + url = {https://www.sciencedirect.com/science/article/pii/S0882401025001305}, + urldate = {2025-03-04}, + year = {2025} +} + +@article{smith_autocrine_2020, + abstract = {Although accumulation of myeloid-derived suppressor cells (MDSC) is a hallmark of cancer, the underlying mechanism of this accumulation within the tumor microenvironment remains incompletely understood. We report here that TNFα-RIP1-mediated necroptosis regulates accumulation of MDSCs. In tumor-bearing mice, pharmacologic inhibition of DNMT with the DNA methyltransferease inhibitor decitabine (DAC) decreased MDSC accumulation and increased activation of antigen-specific cytotoxic T lymphocytes. DAC-induced decreases in MDSC accumulation correlated with increased expression of the myeloid cell lineage-specific transcription factor IRF8 in MDSCs. However, DAC also suppressed MDSC-like cell accumulation in IRF8-deficient mice, indicating that DNA methylation may regulate MDSC survival through an IRF8-independent mechanism. Instead, DAC decreased MDSC accumulation by increasing cell death via disrupting DNA methylation of RIP1-dependent targets of necroptosis. Genome-wide DNA bisulfite sequencing revealed that the \textit{Tnf} promoter was hypermethylated in tumor-induced MDSCs \textit{in vivo}. DAC treatment dramatically increased TNFα levels in MDSC \textit{in vitro}, and neutralizing TNFα significantly increased MDSC accumulation and tumor growth in tumor-bearing mice \textit{in vivo}. Recombinant TNFα induced MDSC cell death in a dose- and RIP1-dependent manner. IL6 was abundantly expressed in MDSCs in tumor-bearing mice and patients with human colorectal cancer. \textit{In vitro}, IL6 treatment of MDSC-like cells activated STAT3, increased expression of DNMT1 and DNMT3b, and enhanced survival. Overall, our findings reveal that MDSCs establish a STAT3-DNMT epigenetic axis, regulated by autocrine IL6, to silence TNFα expression. This results in decreased TNFα-induced and RIP1-dependent necroptosis to sustain survival and accumulation. SIGNIFICANCE: These findings demonstrate that targeting IL6 expression or function represent potentially effective approaches to suppress MDSC survival and accumulation in the tumor microenvironment.}, + author = {Smith, Alyssa D and Lu, Chunwan and Payne, Daniela and Paschall, Amy V and Klement, John D and Redd, Priscilla S and Ibrahim, Mohammed L and Ibrahim, Mohammed L and Yang, Dafeng and Han, Qimei and Liu, Zhuoqi and Shi, Huidong and Hartney, Thomas J and Nayak-Kapoor, Asha and Liu, Kebin}, + doi = {10.1158/0008-5472.can-19-3670}, + issn = {0008-5472}, + journal = {Cancer Res}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {August}, + number = {15}, + pages = {3145--3156}, + title = {Autocrine {IL6}-{Mediated} {Activation} of the {STAT3}-{DNMT} {Axis} {Silences} the {TNFα}-{RIP1} {Necroptosis} {Pathway} to {Sustain} {Survival} and {Accumulation} of {Myeloid}-{Derived} {Suppressor} {Cells}}, + url = {http://europepmc.org/abstract/MED/32554751}, + volume = {80}, + year = {2020} +} + @article{soares_hierarchical_2021, + abstract = {During mitosis, chromatin condensation is accompanied by a global arrest of transcription. Recent studies suggest transcriptional reactivation upon mitotic exit occurs in temporally coordinated waves, but the underlying regulatory principles have yet to be elucidated. In particular, the contribution of sequence-specific transcription factors (TFs) remains poorly understood. Here we report that Brn2, an important regulator of neural stem cell identity, associates with condensed chromatin throughout cell division, as assessed by live-cell imaging of proliferating neural stem cells. In contrast, the neuronal fate determinant Ascl1 dissociates from mitotic chromosomes. ChIP-seq analysis reveals that Brn2 mitotic chromosome binding does not result in sequence-specific interactions prior to mitotic exit, relying mostly on electrostatic forces. Nevertheless, surveying active transcription using single-molecule RNA-FISH against immature transcripts reveals differential reactivation kinetics for key targets of Brn2 and Ascl1, with transcription onset detected in early (anaphase) versus late (early G1) phases, respectively. Moreover, by using a mitotic-specific dominant-negative approach, we show that competing with Brn2 binding during mitotic exit reduces the transcription of its target gene \textit{Nestin} Our study shows an important role for differential binding of TFs to mitotic chromosomes, governed by their electrostatic properties, in defining the temporal order of transcriptional reactivation during mitosis-to-G1 transition.}, author = {Soares, Mário A. F. and Soares, Diogo S. and Teixeira, Vera and Heskol, Abeer and Bressan, Raul Bardini and Pollard, Steven M. and Oliveira, Raquel A. and Castro, Diogo S.}, doi = {10.1101/gad.348174.120}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {0890-9369}, + journal = {Genes Dev}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Mitosis, Neural Stem Cells}, + language = {eng}, month = {June}, note = {Publisher: Cold Spring Harbor Laboratory}, number = {13-14}, @@ -13311,7 +21571,7 @@ @article{soleau_first_2024 doi = {10.3390/ijms25105428}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {{\textgreater}UseGalaxy.eu, Shiga-toxin-producing \textit{Escherichia coli} (STEC), characterization, emerging pathogen, first isolation, serotype O80:H2, whole-genome sequencing}, + keywords = {{\textgreater}UseGalaxy.eu, Escherichia coli Infections, Genome, Bacterial, Phylogeny, Shiga-Toxigenic Escherichia coli, Shiga-toxin-producing \textit{Escherichia coli} (STEC), Whole Genome Sequencing, characterization, emerging pathogen, first isolation, serotype O80:H2, whole-genome sequencing}, language = {en}, month = {January}, note = {Number: 10 @@ -13345,7 +21605,7 @@ @article{soorni_genome-wide_2023 doi = {10.1186/s12870-022-04031-8}, issn = {1471-2229}, journal = {BMC Plant Biology}, - keywords = {{\textgreater}UseGalaxy.eu, Bolting, Lettuce, Long non-coding RNA, Regulation}, + keywords = {{\textgreater}UseGalaxy.eu, Bolting, Lactuca, Lettuce, Long non-coding RNA, RNA, Long Noncoding, Regulation}, language = {en}, month = {January}, number = {1}, @@ -13364,7 +21624,7 @@ @article{soriano-sexto_identification_2022 doi = {10.3390/ijms232112850}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {{\textgreater}UseGalaxy.eu, allelic expression imbalance, differential gene expression, inherited metabolic disorders, multi-omics, targeted transcriptomics}, + keywords = {{\textgreater}UseGalaxy.eu, Maple Syrup Urine Disease, Metabolism, Inborn Errors, allelic expression imbalance, differential gene expression, inherited metabolic disorders, multi-omics, targeted transcriptomics}, language = {en}, month = {January}, note = {Number: 21 @@ -13378,6 +21638,23 @@ @article{soriano-sexto_identification_2022 year = {2022} } +@article{soumia_unravelling_2025, + author = {Soumia, P. S. and Shirsat, Dhananjay V. and Karuppaiah, Vadivelu and Divekar, Pratap A. and Mahajan, Vijay}, + doi = {10.3389/finsc.2025.1536160}, + issn = {2673-8600}, + journal = {Frontiers in Insect Science}, + keywords = {{\textgreater}UseGalaxy.eu, Thrips parvispinus, Thrips tabaci, invasive pest, mitochondrial genome, phylogeny}, + language = {English}, + month = {February}, + note = {Publisher: Frontiers}, + shorttitle = {Unravelling the complete mitochondrial genomes of {Thrips} tabaci {Lindeman} and {Thrips} parvispinus {Karny} ({Thysanoptera}}, + title = {Unravelling the complete mitochondrial genomes of {Thrips} tabaci {Lindeman} and {Thrips} parvispinus {Karny} ({Thysanoptera}: {Thripidae}) and their phylogenetic implications}, + url = {https://www.frontiersin.org/journals/insect-science/articles/10.3389/finsc.2025.1536160/full}, + urldate = {2025-03-29}, + volume = {5}, + year = {2025} +} + @phdthesis{souza_effect_2024, abstract = {In this thesis, we investigated the relationship between increasing plant richness and the diversity and composition of soil and endophytic microbiome and its importance to stress response. We made use of a plant richness diversity gradient established in a long-term biodiversity experiment (the Jena experiment) to access the changes on seed microbiome of a model plant, Plantago lanceolata and the effect of this diversity gradient on the soil bacterial community after long term drought stress.}, author = {Souza, De and Alves, Yuri Pinheiro}, @@ -13389,6 +21666,41 @@ @phdthesis{souza_effect_2024 year = {2024} } +@article{souza_new_2025, + author = {Souza, Júlia W. and Henriques, Lethícia R. and Carlson, Roger M. and Botelho, Bruna B. F. and Carvalho, João Victor R. P. and Santos, João Pedro N. and Aguiar, Eric R. G. R. and Agarkova, Irina V. and Van Etten, James L. and Dunigan, David D. and Rodrigues, Rodrigo A. L.}, + issn = {1999-4915}, + journal = {Viruses}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {August}, + number = {8}, + title = {New {Isolates} of {Betachloroviruses} {Shed} {Light} on the {Diversity} and {Biological} {Complexity} of an {Unexplored} {Group} of {Giant} {Algal} {Viruses}}, + url = {http://europepmc.org/abstract/PMC/PMC12390592}, + volume = {17}, + year = {2025} +} + +@article{souza_new_2025, + abstract = {Satellite DNAs (satDNAs) play a crucial role in understanding chromosomal evolution and the differentiation of sex chromosomes across diverse taxa, particularly when high karyotypic diversity occurs. The Physalaemus cuvieri–Physalaemus ephippifer species complex comprises at least seven divergent lineages, each exhibiting specific karyotypic signatures. The group composed of Ph. ephippifer, Lineage 1B of ‘Ph. cuvieri’ (L1B), and a lineage resulting from their secondary contact is especially intriguing due to varying degrees of sex chromosome heteromorphism. In this study, we characterized the satellitome of Ph. ephippifer in order to identify novel satDNAs that may provide insights into chromosomal evolution, particularly concerning sex chromosomes. We identified 62 satDNAs in Ph. ephippifer, collectively accounting for approximately 10\% of the genome. Notably, nine satDNA families were shared with species from distantly related clades, raising questions about their potential roles in anurans genomes. Among the seven satDNAs mapped via fluorescent in situ hybridization, PepSat3 emerged as a strong candidate for the centromeric sequence in this group. Additionally, PepSat11 and PepSat24 provided evidence supporting a translocation involving both arms of the W chromosome in Ph. ephippifer. Furthermore, a syntenic block composed of PepSat3, PcP190, and PepSat11 suggested an inversion event during the divergence of Ph. ephippifer and L1B. The variation in signal patterns of satDNAs associated with nucleolar organizer regions (NORs) highlights the complexity of NOR evolution in this species complex, which exhibits substantial diversity in this genomic region. Additionally, our findings for PepSat30-350 emphasize the importance of validating the sex-biased abundance of satDNAs.}, + author = {Souza, Lucas H. B. and Ferro, Juan M. and Milanez, Helena M. and Haddad, Célio F. B. and Lourenço, Luciana B.}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/biom15060876}, + issn = {2218-273X}, + journal = {Biomolecules}, + keywords = {{\textgreater}UseGalaxy.eu, Anura, DNA, Satellite, Evolution, Molecular, Sex Chromosomes, chromosomal homologies, chromosomal rearrangements, nucleolar organizer region, repetitive elements, satellitome}, + language = {en}, + month = {June}, + note = {Number: 6 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {6}, + pages = {876}, + title = {New {Insights} into the {Sex} {Chromosome} {Evolution} of the {Common} {Barker} {Frog} {Species} {Complex} ({Anura}, {Leptodactylidae}) {Inferred} from {Its} {Satellite} {DNA} {Content}}, + url = {https://www.mdpi.com/2218-273X/15/6/876}, + urldate = {2025-06-20}, + volume = {15}, + year = {2025} +} + @mastersthesis{soyland_mapping_2024, abstract = {The last few decades have seen a massive use of antibiotics worldwide, in all from human health care and veterinary use to agriculture and aquaculture. This has led to a rise in emergence of antibiotic resistant bacteria (ARB), where bacteria harbouring genes for extended-spectrum β-lactamases (ESBL) and carbapenem resistance are of particular concern. Infectious diseases caused by these bacteria can be very challenging to treat, and a staggering number of deaths every year result directly or indirectly from antibiotic resistance. With no measurements taken to stop the ARB spread, this problem will only keep on growing. @@ -13424,6 +21736,25 @@ @article{sozzoni_chromosome-level_2023 year = {2023} } +@article{sozzoni_quaternary_2025, + abstract = {Quaternary climatic fluctuations had a substantial influence on ecosystems, species distribution, phenology and genetic diversity, driving extinction, adaptation and demographic shifts during glacial periods and postglacial expansions. Integration of genomic data and environmental niche modelling can provide valuable insights on how organisms responded to past environmental variations and contribute to assessing vulnerability and resilience to ongoing climatic challenges. Among vertebrates, turtles are particularly vulnerable to habitat changes because of distinctive life history traits and the effect of environmental conditions on physiology and survival. We estimated contemporary heterozygosity (H) and effective population size (Ne) using a high-quality chromosome-level reference genome we produced for the European pond turtle (Emys orbicularis) and reference genomes and whole genome sequence data available for 21 species of tortoises and freshwater turtles. We implemented environmental niche modelling (ENM) to estimate past habitat dynamics. We found recurrent cycles of population expansion and contraction over the last 10 Mya in all species, with a general pattern of decrease in Ne correlated with temperature reduction after the last interglacial period. No correlation was found between habitat fluctuations during the Quaternary and past Ne. Moreover, neither H nor mean Ne was correlated to threat status as defined by IUCN Red List categories. Our results add to studies on other vertebrates showing the extent to which genetic parameters can aid the assessment of conservation status, and although genomic data may not always be consistent indicators of the level of threat, investigations of which genomic parameters could best represent essential biodiversity variables should be consistently supported.}, + author = {Sozzoni, Marcella and Balacco, Jennifer and Bellavita, Massimo and Brüniche-Olsen, Anna and Formenti, Giulio and Jain, Nivesh and Koo, Bonhwang and Mountcastle, Jacquelyn and Palmada-Flores, Marc and Trifonov, Vladimir and Chelazzi, Guido and Fratini, Sara and Jarvis, Erich D. and Natali, Chiara and Nespoli, Davide and Ciofi, Claudio and Iannucci, Alessio}, + copyright = {© 2025 The Author(s). Molecular Ecology Resources published by John Wiley \& Sons Ltd.}, + doi = {10.1111/1755-0998.70040}, + issn = {1755-0998}, + journal = {Molecular Ecology Resources}, + keywords = {{\textgreater}UseGalaxy.eu, ENM, Emys orbicularis, PSMC, effective population size, population genomics, reptiles}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.70040}, + number = {n/a}, + pages = {e70040}, + title = {Quaternary {Habitat} {Fluctuations} and {Demographic} {Dynamics} in {Turtles} {Inferred} {From} {Environmental} {Niche} {Modelling} and {Whole} {Genome} {Data}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.70040}, + urldate = {2025-09-10}, + volume = {n/a}, + year = {2025} +} + @article{spano_comparative_2023, abstract = {Globe artichoke ecotypes sanitized from plant pathogen infections are characterized by high vegetative vigor, productivity, and quality of capitula. The recent availability on the market of these plants has renewed the interest of farmers and pharmaceutical industries in the crop. Globe artichoke exhibits interesting nutraceutical properties due to the high content of health-promoting bioactive compounds (BACs), such as polyphenols, that could be extracted from waste biomass. The production of BACs depends on several factors including the plant portion considered, the globe artichoke variety/ecotype, and the physiological status of the plants, linked to biotic and abiotic stresses. We investigated the influence of viral infections on polyphenol accumulation in two Apulian late-flowering ecotypes “Locale di Mola tardivo” and “Troianella”, comparing sanitized virus-free material (S) vs. naturally virus-infected (non-sanitized, NS) plants. Transcriptome analysis of the two ecotypes highlighted that differentially expressed genes (DEGs), in the two tested conditions, were mainly involved in primary metabolism and processing of genetic/environmental information. The up-regulation of the genes related to the biosynthesis of secondary metabolites and the analysis of peroxidase activity suggested that their modulation is influenced by the phytosanitary status of the plant and is ecotype-dependent. Conversely, the phytochemical analysis showed a remarkable decrease in polyphenols and lignin accumulation in S artichokes compared to NS plants. This unique study analyzes the potential of growing vigorous, sanitized plants, in order to have high amounts of ‘soft and clean’ biomass, finalized for BAC extraction for nutraceutical purposes. This, in turn, opens new perspectives for a circular economy of sanitized artichokes, in line with the current phytosanitary standards and sustainable development goals.}, author = {Spanò, Roberta and Fortunato, Stefania and Linsalata, Vito and D’Antuono, Isabella and Cardinali, Angela and de Pinto, Maria Concetta and Mascia, Tiziana}, @@ -13486,10 +21817,14 @@ @article{spano_spotlight_2024 } @article{spradling_mitochondrial_2021, + abstract = {Parasitic lice demonstrate an unusual array of mitochondrial genome architectures and gene arrangements. We characterized the mitochondrial genome of Geomydoecus aurei, a chewing louse (Phthiraptera: Trichodectidae) found on pocket gophers (Rodentia: Geomyidae) using reads from both Illumina and Oxford Nanopore sequencing coupled with PCR, cloning, and Sanger sequencing to verify structure and arrangement for each chromosome. The genome consisted of 12 circular mitochondrial chromosomes ranging in size from 1,318 to 2,088 nucleotides (nt). Total genome size was 19,015 nt. All 37 genes typical of metazoans (2 rRNA genes, 22 tRNA genes, and 13 protein-coding genes) were present. An average of 26\% of each chromosome was composed of non-gene sequences. Within the non-gene region of each chromosome, there was a 79-nt nucleotide sequence that was identical among chromosomes and a conserved sequence with secondary structure that was always followed by a poly-T region. We hypothesize that these regions may be important in the initiation of transcription and DNA replication, respectively. The G. aurei genome shares 8 derived gene clusters with other chewing lice of mammals, but in G. aurei, genes on several chromosomes are not contiguous.}, author = {Spradling, Theresa A. and Place, Alexandra C. and Campbell, Ashley L. and Demastes, James W.}, doi = {10.1371/journal.pone.0254138}, editor = {Waller, Ross Frederick}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {1932-6203}, + journal = {PloS one}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Genome, Mitochondrial}, + language = {eng}, month = {July}, note = {Publisher: Public Library of Science (PLoS)}, number = {7}, @@ -13517,6 +21852,68 @@ @article{stachurova_beta-lactam_2021 year = {2021} } +@article{staehle_lysine-specific_2025, + abstract = {The lysine-specific demethylase 1 (LSD1) regulates hematopoietic stem cell differentiation and has been identified as a therapeutic target in hematological disorders. LSD1 demethylates mono and dimethylated histones 3 at lysine 4 and 9. In addition, it acts as a scaffold for the formation of chromatin-modifying complexes that regulates the transcription of myeloid-lineage-specific genes in complex with GFI1, a transcriptional repressor. While both enzymatic and non-enzymatic functions of LSD1 have been well defined, the relative importance of these two functions in hematopoiesis remains incompletely understood. Here, we investigated the contribution of enzymatic and non-enzymatic functions of LSD1 to myelopoiesis. We show that myeloid differentiation is independent of the enzymatic functions of LSD1 but requires the non-enzymatic, scaffolding function, which directs GFI1 binding to target sequences. In the absence of the LSD1 protein, GFI1 DNA binding is diminished, and myeloid cell differentiation arrests at an immature, myelomonocytic-like cell stage, which overexpresses Prtn3. We provide functional data implicating Prtn3 as an effector of the stem cell expansion and myeloid maturation block caused by the loss of LSD1.}, + author = {Staehle, Hans Felix and Koellerer, Christoph and Staehle, Anne Marie and Schulze, Jana and Eble, Philipp and Müller, Anja and Zell, Franziska and Müller, Judith M. and Perner, Florian and Attia, Aya and Mallm, Jan-Philipp and Pozdnyakova, Olga and Rippe, Karsten and Brors, Benedikt and Feuerbach, Lars and Imbusch, Charles D. and Metzger, Eric and Schüle, Roland and Pahl, Heike L. and Jutzi, Jonas S.}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41419-025-07951-z}, + issn = {2041-4889}, + journal = {Cell Death \& Disease}, + keywords = {{\textgreater}UseGalaxy.eu, Epigenetics, Haematopoietic stem cells, Myelopoiesis, Transcriptomics}, + language = {en}, + month = {August}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {619}, + title = {Lysine-specific demethylase 1 regulates hematopoietic stem cell expansion and myeloid cell differentiation}, + url = {https://www.nature.com/articles/s41419-025-07951-z}, + urldate = {2025-08-20}, + volume = {16}, + year = {2025} +} + +@article{stafiniak_stabilizing_2025, + abstract = {Accurate normalization is crucial for reliable gene expression quantification and depends on stably expressed housekeeping genes (HKGs) as internal controls. However, HKGs expression varies with developmental stage, tissue type, and treatments, potentially introducing bias and compromising data accuracy. Thus, validating candidate reference genes under defined conditions is essential. Reynoutria, also known as giant Asian knotweeds, is a Polygonaceae family genus of several medicinal plants producing a diverse array of specialized metabolites of pharmacological interest. Outside their native range, these plants are also noxious invasive weeds, causing significant environmental and economic threats. Research on stable reference genes in these species is limited, with a primary focus on R. japonica. To enable accurate gene expression analysis related to specialized metabolism and natural product biosynthesis, we aimed to identify the most stable reference genes across the most common species: R. japonica Houtt., R. sachalinensis (F. Schmidt) Nakai, and their hybrid—R. × bohemica Chrtek \& Chrtková. In this study, we evaluated twelve candidate HKGs (ACT, TUA, TUB, GAPDH, EF-1γ, UBQ, UBC, 60SrRNA, eIF6A, SKD1, YLS8, and NDUFA13) across three tissue types (rhizomes, leaves, and flowers) from three Reynoutria species sampled at peak flowering. Primer specificity and amplification efficiency were confirmed through standard-curve analysis. We assessed expression stability using ΔCt, geNorm, NormFinder, and BestKeeper, and generated comprehensive rankings with RefFinder. Our integrated analysis revealed organ- and species-dependent stability differences, yet identified up to three reference genes suitable for interspecific normalization in Reynoutria. This represents the first systematic, comparative validation of HKGs across closely related knotweed species, providing a robust foundation for future transcriptomic and functional studies of their specialized metabolism and other biological processes.}, + author = {Stafiniak, Marta and Makowski, Wojciech and Matkowski, Adam and Bielecka, Monika}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms26178265}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {\textit{Reynoutria}, {\textgreater}UseGalaxy.eu, housekeeping genes, invasive species, qRT-PCR normalization, reference-gene validation}, + language = {en}, + month = {January}, + note = {Publisher: Multidisciplinary Digital Publishing Institute}, + number = {17}, + pages = {8265}, + shorttitle = {Stabilizing the {Baseline}}, + title = {Stabilizing the {Baseline}: {Reference} {Gene} {Evaluation} in {Three} {Invasive} {Reynoutria} {Species}}, + url = {https://www.mdpi.com/1422-0067/26/17/8265}, + urldate = {2025-09-12}, + volume = {26}, + year = {2025} +} + +@article{stefanovska_fibroblast_2025, + abstract = {During aging, peripheral nerves undergo structural and cellular changes that trigger loss of function, impair quality of life, and increase disease risk. During peripheral nerve aging there are cellular and molecular changes, such as increased extracellular matrix deposition. The mechanisms behind these aging-induced alterations remain unclear. Here, we profile mouse sciatic nerves using single nucleus transcriptomics and unravel changes in macrophage subtypes during nerve aging. Phagocytic macrophage numbers increase at the onset of aging, followed by higher numbers of chronic inflammatory macrophages. Based on ligand-receptor analysis, we predict that increased fibroblast growth factor (FGF) signaling from adipocytes activates a chondrocyte-like neural fibroblast state during peripheral nerve aging. Finally, we show that FGF2 induces the co-expression of the chondrocyte markers SOX9 and FOXC2 in senescent human perineurial fibroblast, that can be blocked with FGF1. In conclusion, our findings reveal some of the molecular mechanisms of peripheral nerve aging by FGF-regulated induction of a chondrocyte-like fibroblast state.}, + author = {Stefanovska, Dragana and Sassu, Eliza and Tekman, Mehmet and Naghsh Nilchi, Amirhossein and Haider, Severin and Domisch, Claudia and Hossfeld, Madelon and Perez-Feliz, Stefanie and Miarka, Lauritz and Schneider-Warme, Franziska and Arnold, Sebastian J and Prinz, Marco and Grüning, Björn and Preissl, Sebastian and Hortells, Luis}, + copyright = {cc by}, + doi = {10.1038/s41467-025-65297-8}, + issn = {2041-1723}, + journal = {Nature communications}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {November}, + number = {1}, + pages = {10020}, + pmcid = {PMC12618493}, + pmid = {41238529}, + title = {Fibroblast growth factor signaling induces a chondrocyte-like state of peripheral nerve fibroblast during aging}, + url = {https://europepmc.org/articles/PMC12618493}, + urldate = {2025-12-26}, + volume = {16}, + year = {2025} +} + @article{stein_single-cell_2021, author = {Stein, Catarina M. and Weiskirchen, Ralf and Damm, Frederik and Strzelecka, Paulina M.}, doi = {10.1002/jcb.30134}, @@ -13529,16 +21926,40 @@ @article{stein_single-cell_2021 } @article{stephen_jr_comparative_2022, + abstract = {Black-rot disease caused by the phytopathogen \textit{Xanthomonas campestris} pv. \textit{campestris} (Xcc) continues to have considerable impacts on the productivity of cruciferous crops in Trinidad and Tobago and the wider Caribbean region. While the widespread occurrence of resistance of Xcc against bactericidal agrochemicals can contribute to the high disease burdens, the role of virulence and pathogenicity features of local strains on disease prevalence and severity has not been investigated yet. In the present study, a comparative genomic analysis was performed on 6 pathogenic Xcc and 4 co-isolated non-pathogenic \textit{Xanthomonas melonis} (Xmel) strains from diseased crucifer plants grown in fields with heavy chemical use in Trinidad. Native isolates were grouped into two known and four newly assigned ribosomal sequence types (rST). Mobile genetic elements were identified which belonged to the IS3, IS5 family, Tn3 transposon, resolvases, and \textit{tra} T4SS gene clusters. Additionally, exogenous plasmid derived sequences with origins from other bacterial species were characterised. Although several instances of genomic rearrangements were observed, native Xcc and Xmel isolates shared a significant level of structural homology with reference genomes, Xcc ATCC 33913 and Xmel CFBP4644, respectively. Complete T1SS \textit{hlyDB}, T2SS, T4SS \textit{vir} and T5SS \textit{xadA}, \textit{yapH} and \textit{estA} gene clusters were identified in both species. Only Xmel strains contained a complete T6SS but no T3SS. Both species contained a complex repertoire of extracellular cell wall degrading enzymes. Native Xcc strains contained 37 T3SS and effector genes but a variable and unique profile of 8 \textit{avr}, 4 \textit{xop} and 1 \textit{hpa} genes. Interestingly, Xmel strains contained several T3SS effectors with low similarity to references including \textit{avrXccA1} ({\textasciitilde}89\%), \textit{hrpG} ({\textasciitilde}73\%), \textit{hrpX} ({\textasciitilde}90\%) and \textit{xopAZ} ({\textasciitilde}87\%). Furthermore, only Xmel genomes contained a CRISPR-Cas I-F array, but no lipopolysaccharide \textit{wxc} gene cluster. Xmel strains were confirmed to be non-pathogenic by pathogenicity assays. The results of this study will be useful to guide future research into virulence mechanisms, agrochemical resistance, pathogenomics and the potential role of the co-isolated non-pathogenic \textit{Xanthomonas} strains on Xcc infections.}, author = {Stephen Jr, DB and Jayaraman, Jayaraj and Ramsubhag, Adesh and {others}}, + doi = {10.7717/peerj.12632}, + issn = {2167-8359}, journal = {PeerJ}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, note = {Publisher: PeerJ Inc.}, pages = {e12632}, title = {Comparative genomics of the black rot pathogen {Xanthomonas} campestris pv. campestris and non-pathogenic co-inhabitant {Xanthomonas} melonis from {Trinidad} reveal unique pathogenicity determinants and secretion system profiles}, + url = {http://europepmc.org/abstract/MED/35036136}, volume = {9}, year = {2022} } +@article{sterling_revision_2025, + abstract = {The genus Topiris Walker, 1863 is revised. This genus, previously neglected or deemed unrecognisable, comprised only Walker’s damaged and misrepaired type specimen of Topiris candidella Walker, 1863. Evidence is provided that this specimen was collected by Alfred Russel Wallace in 1855–56 in Sarawak, Malaysian Borneo. The mitogenome of this specimen was assembled using low coverage whole genome sequencing (genome skimming). The COI-5P portion of this mitogenome (658 bp) differs by 1–3 bp from two haplotypes sequenced from early 1990’s Brunei specimens. Another specimen recently discovered at NHMUK with an identical label to that of the type perfectly matches the Brunei specimens in its genitalia. Based on these four specimens, we present a fuller description of the morphology of T. candidella. Topiris includes the following additional species authored by Sterling and Lees: Topiris albidella sp. nov., T. albogrisella sp. nov., T. cinderella sp. nov., T. digiticosta sp. nov., T. lacteella sp. nov., T. madonna sp. nov., T. meyricki sp. nov., T. ochrotincta sp. nov., T. schneeweissella sp. nov., T. sericella sp. nov., and T. thunbergella sp. nov. The following new combinations are also established: T. salva (Meyrick, 1932), comb. nov. and T. sampitella (Lvovsky, 2014), comb. nov. The type of Athrypsiastis salva Meyrick is confirmed as lost and so a neotype and paraneotype of this species are designated. A published mitogenome of “Linoclostis gonatias” is shown to be correctly identified as T. salva, and references to L. gonatias, identified in some literature as a pest of Theaceae, are likely misidentified. The genus Topiris is divided into three groups, the candidella group, the salva group, and the albidella group, based on characters in the male genitalia. The candidella group and albidella group are supported sub-clades of Topiris. The phylogenetic placement of Topiris and Athrypsiastis within ‘core’ Xyloryctidae (as subtended by its type species, X. luteotactella) is confirmed by analysis of COI and seven nuclear genes, whereas the genera Eumenodora Meyrick, 1906 and Izatha Walker, 1864 do not fall within this clade. The morphology of Athrypsiastis phaeoleuca Meyrick, 1910 (the type species of Athrypsiastis; Xyloryctidae) is more fully described. The following new species authored by Sterling and Lees are described: Athrypsiastis cheesmanae sp. nov., A. edelweissella sp. nov., and A. penumbrella sp. nov. Two taxa are newly combined: Athrypsiastis halmaherella (Lvovsky, 2014), comb. nov. and Paralecta rosiflora (Meyrick, 1930), comb. nov.}, + author = {Sterling, Mark J. and Price, Ben W. and Lees, David C.}, + copyright = {2025 Mark J. Sterling, Ben W. Price, David C. Lees}, + doi = {10.3897/zookeys.1229.119155}, + issn = {1313-2970}, + journal = {ZooKeys}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {March}, + note = {Publisher: Pensoft Publishers}, + pages = {297--368}, + title = {A revision of the hitherto neglected genus {Topiris} {Walker}, 1863 ({Lepidoptera}, {Xyloryctidae}) with taxonomic notes on the genus {Athrypsiastis} {Meyrick}, 1910}, + url = {https://zookeys.pensoft.net/article/119155/}, + urldate = {2025-03-09}, + volume = {1229}, + year = {2025} +} + @article{stillger_neoadjuvant_2024, abstract = {Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer, often diagnosed at stages that dis-qualify for surgical resection. Neoadjuvant therapies offer potential tumor regression and improved resectability. Although features of the tumor biology (e.g., molecular markers) may guide adjuvant therapy, biological alterations after neoadjuvant therapy remain largely unexplored. We performed mass spectrometry to characterize the proteomes of 67 PDAC resection specimens of patients who received either neoadjuvant chemo (NCT) or chemo-radiation (NCRT) therapy. We employed data-independent acquisition (DIA), yielding a proteome coverage in excess of 3500 proteins. Moreover, we successfully integrated two publicly available proteome datasets of treatment-naïve PDAC to unravel proteome alterations in response to neoadjuvant therapy, highlighting the feasibility of this approach. We found highly distinguishable proteome profiles. Treatment-naïve PDAC was characterized by enrichment of immunoglobulins, complement and extracellular matrix (ECM) proteins. Post-NCT and post-NCRT PDAC presented high abundance of ribosomal and metabolic proteins as compared to treatment-naïve PDAC. Further analyses on patient survival and protein expression identified treatment-specific prognostic candidates. We present the first proteomic characterization of the residual PDAC mass after NCT and NCRT, and potential protein candidate markers associated with overall survival. We conclude that residual PDAC exhibits fundamentally different proteome profiles as compared to treatment-naïve PDAC, influenced by the type of neoadjuvant treatment. These findings may impact adjuvant or targeted therapy options.}, author = {Stillger, Maren N. and Kurowski, Konrad and Bronsert, Peter and Brombacher, Eva and Kreutz, Clemens and Werner, Martin and Tang, Laura and Timme-Bronsert, Sylvia and Schilling, Oliver}, @@ -13565,7 +21986,7 @@ @article{stojkovic_targeted_2024 doi = {10.3390/ijms25053016}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {{\textgreater}UseGalaxy.eu, PBMCs, ferroptosis, gene expression, multiple sclerosis, severity, targeted RNAseq}, + keywords = {{\textgreater}UseGalaxy.eu, Ferroptosis, Multiple Sclerosis, PBMCs, ferroptosis, gene expression, multiple sclerosis, severity, targeted RNAseq}, language = {en}, month = {January}, note = {Number: 5 @@ -13579,6 +22000,50 @@ @article{stojkovic_targeted_2024 year = {2024} } +@article{stoof_mechanisms_2025, + abstract = {Pancreatic ductal adenocarcinoma (PDAC) is a highly fatal disease with limited treatment options. PARP inhibitors (PARPi) have shown promise in treating PDAC with homologous recombination deficiency (HRD), but rapid acquisition of resistance limits their efficacy. Our objective is to investigate mechanisms of resistance to PARPi in BRCA2-mutant PDAC cells and identify potential therapeutic targets to modulate this resistance. We developed olaparib- and talazoparib-resistant Capan-1 cell lines and characterised their resistance profiles using viability assays, RNA sequencing and metabolomic profiling. We also developed a cisplatin-resistant Capan-1 cell line to compare resistance mechanisms between PARPi and platinum agents. Both olaparib- and talazoparib-resistant cells showed cross-resistance to other PARPi and oxaliplatin, but not to gemcitabine or 5-FU. Talazoparib-resistant cells exhibited a similar resistance profile to cisplatin-resistant cells, including decreased PARP1 expression and altered metabolomic profiles. RNA sequencing and metabolomic profiling revealed significant enrichment of metabolic pathways, including oxidative phosphorylation and glycolysis, in resistant cells. Our study highlights the complexity of resistance mechanisms to PARPi in PDAC and identifies potential therapeutic targets in metabolism. The differences in the resistance profiles between olaparib and talazoparib suggest that PARP-trapping potency may play a role in resistance development. Further research is needed to validate these findings and explore novel therapeutic strategies to overcome resistance to PARPi in PDAC.}, + author = {Stoof, Jojanneke and Andrieu, Charlotte and O'Connell, Fiona and O'Sullivan, Jacintha and Lowery, Maeve A. and Walsh, Naomi}, + doi = {10.1111/jcmm.70816}, + issn = {1582-4934}, + journal = {Journal of Cellular and Molecular Medicine}, + keywords = {{\textgreater}UseGalaxy.eu, PARP inhibitor, cisplatin, metabolism, pancreatic ductal adenocarcinoma, resistance}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jcmm.70816}, + number = {16}, + pages = {e70816}, + title = {Mechanisms of {Resistance} to {PARPi} in {Pancreatic} {Ductal} {Adenocarcinoma}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jcmm.70816}, + urldate = {2025-09-03}, + volume = {29}, + year = {2025} +} + +@article{storer_sex-lethal_2025, + abstract = {The RNA-binding protein Sex-lethal (Sxl) is classically known as a master regulator of sex determination and mRNA splicing in Drosophila melanogaster . However, this role is not conserved across species, and functions beyond this canonical pathway remain poorly understood. In this study, we uncover a splicing-independent role for Sxl at the chromatin level in the Drosophila brain. Using Targeted DamID (TaDa) profiling in neurons, we identify widespread recruitment of Sxl to promoter regions, independent of sex or RNA binding activity. Notably, Sxl chromatin occupancy exhibits near-complete overlap with Polr3E (RPC37), an RNA Polymerase III subunit, with Sxl binding abolished upon Polr3E knockdown. Depletion of Sxl in mature male neurons induces widespread transcriptional changes, particularly in metabolic genes, and improves negative geotaxis during ageing, phenotypes that closely mirror Polr3E knockdown. Conversely, overexpression of the brain-specific Sxl RAC transcript leads to enhanced tRNA synthesis and upregulated metabolic gene expression. Together, these findings reveal a previously unrecognised role for Sxl in regulating Pol III activity via Polr3E, regulating tRNA synthesis and supporting neuronal metabolism. Given the emerging tie between Pol III regulation and neuronal ageing, our study highlights Sxl as a novel modulator of neuronal homeostasis.}, + author = {Storer, Freya and McClure, Colin and Gomez, Alicia Estacio and Wong, Tsz Lam and Minkley, Lucy and Southall, Tony}, + doi = {10.1101/2025.04.25.650657}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Sex-lethal is recruited to chromatin to promote neuronal {tRNA} synthesis in males through {RNA} {Polymerase} {III} regulation}, + url = {http://europepmc.org/abstract/PPR/PPR1010171}, + year = {2025} +} + +@article{storms_influenza_2024, + abstract = {{\textless}h4{\textgreater}Introduction{\textless}/h4{\textgreater}Influenza A virus in swine (IAV-S) is common in the United States commercial swine population and has the potential for zoonotic transmission.{\textless}h4{\textgreater}Objective{\textless}/h4{\textgreater}To elucidate influenza shedding the domestic pig population, we evaluated two commercial swine farms in Illinois, United States, for 7 weeks. Farm 1 had a recent IAV-S outbreak. Farm 2 has had IAV-S circulating for several years.{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}Forty post-weaning pigs on Farm 1 and 51 pigs from Farm 2 were individually monitored and sampled by nasal swabs for 7 weeks.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}RT-PCR results over time showed most piglets shed in the first 2 weeks post weaning, with 91.2\% shedding in week one, and 36.3\% in week two. No difference in the number of pigs shedding was found between the two nurseries. Reinfection events did differ between the farms, with 30\% of piglets on Farm 1 becoming reinfected, compared to 7.8\% on Farm 2. In addition, whole genome sequencing of nasal swab samples from each farm showed identical viruses circulating between the initial infection and the reinfection periods. Sequencing also allowed for nucleic and amino acid mutation analysis in the circulating viruses, as well the identification of a potential reverse zoonosis event. We saw antigenic site mutations arising in some pigs and MxA resistance genes in almost all samples.{\textless}h4{\textgreater}Conclusion{\textless}/h4{\textgreater}This study provided information on IAV-S circulation in nurseries to aid producers and veterinarians to screen appropriately for IAV-S, determine the duration of IAV-S shedding, and predict the occurrence of reinfection in the nursery period.}, + author = {Storms, Suzanna M and Leonardi-Cattolica, Antonio and Prezioso, Tara and Varga, Csaba and Wang, Leyi and Lowe, James}, + doi = {10.3389/fvets.2024.1482225}, + issn = {2297-1769}, + journal = {Frontiers in veterinary science}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {1482225}, + title = {Influenza {A} virus shedding and reinfection during the post-weaning period in swine: longitudinal study of two nurseries}, + url = {http://europepmc.org/abstract/MED/39606665}, + volume = {11}, + year = {2024} +} + @article{strateva_analysis_2023, abstract = {Abstract The present study aimed to explore the genotypic and phenotypic characteristics of biofilm formation in Bulgarian nosocomial Stenotrophomonas maltophilia isolates (n = 221) during the period 2011–2022, by screening for the presence of biofilm-associated genes (BAG) (spgM, rmlA and rpfF), their mutational variability, and assessment of the adherent growth on a polystyrene surface. The methodology included: PCR amplification, whole-genome sequencing (WGS) and crystal violet microtiter plate assay for biofilm quantification. The overall incidence of BAG was: spgM 98.6\%, rmlA 86\%, and rpfF 66.5\%. The most prevalent genotype was spgM+/rmlA+/rpfF+ (56.1\%), followed by spgM+/rmlA+/rpfF- (28.5\%), and spgM+/rmlA-/rpfF+ (9.5\%), with their significant predominance in lower respiratory tract isolates compared to those with other origin (P {\textless} 0.001). All strains examined were characterized as strong biofilm producers (OD550 from 0.224 ± 0.049 to 2.065 ± 0.023) with a single exception that showed a weak biofilm-forming ability (0.177 ± 0.024). No significant differences were observed in the biofilm formation according to the isolation source, as well as among COVID-19 and non-COVID-19 isolates (1.256 ± 0.028 vs. 1.348 ± 0.128, respectively). Also, no correlation was found between the biofilm amounts and the corresponding genotypes. WGS showed that the rmlA accumulated a larger number of variants (0.0086 per base) compared to the other BAG, suggesting no critical role of its product to the biofilm formation. Additionally, two of the isolates were found to harbour class 1 integrons (7-kb and 2.6-kb sized, respectively) containing sul1 in their 3′ conservative ends, which confers sulfonamide resistance. To the best of our knowledge, this is the first study on S. maltophilia biofilm formation in Bulgaria, which also identifies novel sequence types (ST819, ST820 and ST826). It demonstrates the complex nature of this adaptive mechanism in the multifactorial pathogenesis of biofilm-associated infections.}, author = {Strateva, Tanya and Trifonova, Angelina and Sirakov, Ivo and Borisova, Dayana and Stancheva, Mikaela and Keuleyan, Emma and Setchanova, Lena and Peykov, Slavil}, @@ -13619,6 +22084,27 @@ @article{strateva_first_2024 year = {2024} } +@article{strateva_first_2025, + abstract = {Linezolid is an oxazolidinone antibiotic and is considered a last-resort treatment option for serious infections caused by problematic Gram-positive pathogens, including vancomycin-resistant enterococci. The present study aimed to explore the linezolid resistance mechanisms and genomic characteristics of two vancomycin-susceptible Enterococcus faecalis isolates from Bulgaria. The strains designated Efs2503-bg (inpatient from Pleven) and Efs966-bg (outpatient from Varna) were recovered from wounds in 2018 and 2023, respectively. Antimicrobial susceptibility testing, whole-genome sequencing, multilocus sequence typing, and phylogenomic analysis based on 332 linezolid-resistant E. faecalis genomes were performed. Efs2503-bg was high-level resistant to linezolid (MIC {\textgreater} 256 mg/L) and displayed the G2576T mutation affecting three of the four 23S rDNA loci. Efs966-bg (MIC = 8 mg/L) carried a plasmid-located optrA determinant surrounded by fexA and ermA. No mutations in the genes encoding for ribosomal proteins L3, L4, and L22 were detected. The isolates belonged to the sequence types ST6 (Efs2503-bg) and ST1102 (Efs966-bg). Phylogenomic analysis revealed that Efs2503-bg and Efs966-bg are genetically distinct, with a difference of 12,051 single-nucleotide polymorphisms. To our knowledge, this is the first report of linezolid-resistant enterococci in Bulgaria. Although the global incidence of linezolid-resistant enterococci is still low, their emergence is alarming and poses a growing clinical threat to public health.}, + author = {Strateva, Tanya V. and Hristova, Preslava and Stoeva, Temenuga J. and Hitkova, Hristina and Peykov, Slavil}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/microorganisms13010195}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {\textit{Enterococcus faecalis}, \textit{optrA}, {\textgreater}UseGalaxy.eu, G2576T mutation, ST1102, hospital-adapted ST6 lineage, linezolid resistance, pAR0780 plasmid, whole-genome sequencing}, + language = {en}, + month = {January}, + note = {Number: 1 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {1}, + pages = {195}, + title = {First {Detection} and {Genomic} {Characterization} of {Linezolid}-{Resistant} {Enterococcus} faecalis {Clinical} {Isolates} in {Bulgaria}}, + url = {https://www.mdpi.com/2076-2607/13/1/195}, + urldate = {2025-02-11}, + volume = {13}, + year = {2025} +} + @article{strateva_genomic_2024, abstract = {Extensively drug-resistant P. aeruginosa (XDR-PA) has been highlighted as a serious public health threat. The present study aimed to explore the genomic characteristics of two Vietnamese extended-spectrum β-lactamase-9 (VEB-9)-producing XDR-PA isolates from Bulgaria in comparison to all blaVEB-9-positive strains with available genomes. The isolates designated Pae51 and Pae52 were obtained from tracheobronchial aspirates of intensive care unit (ICU) patients. Antimicrobial susceptibility testing, whole-genome sequencing, RT-qPCR, and phylogenomic analysis were performed. Pae51 and Pae52 were resistant to most antipseudomonal β-lactams including carbapenems, aminoglycosides, and fluoroquinolones but remained susceptible to colistin and cefiderocol. Numerous resistance determinants were detected: blaVEB-9, blaPDC-3, blaOXA-10, blaOXA-50, aac(6′)-II, ant(2″)-Ia, ant(3″)-IIa, aph(3′)-IIb, cprP, catB7, dfrB2, sul1, fosA, and tet(A). Both isolates carried complex integrons with blaVEB-9 and tet(A) embedded next to the conservative 3′ end sequences. A variety of virulence factors were also identified, including the type III secretion system exotoxin U. Pae51 and Pae52 differed by only four SNPs and belonged to the high-risk clone ST357. To our knowledge, this is the first report of blaVEB-9-positive XDR-PA isolates in Bulgaria presenting a detailed genomic analysis. The development of novel antimicrobial strategies for such pathogens should be an essential part of infection control stewardship practices in ICU wards.}, author = {Strateva, Tanya and Stratev, Alexander and Peykov, Slavil}, @@ -13626,7 +22112,7 @@ @article{strateva_genomic_2024 doi = {10.3390/pathogens13090719}, issn = {2076-0817}, journal = {Pathogens}, - keywords = {\textit{Pseudomonas aeruginosa}, {\textgreater}UseGalaxy.eu, VEB-9 extended-spectrum β-lactamase, carbapenem resistance, exotoxin U, extensive drug resistance, high-risk clone ST357, phylogenomic analysis, whole-genome sequencing}, + keywords = {\textit{Pseudomonas aeruginosa}, {\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Drug Resistance, Multiple, Bacterial, Intensive Care Units, Microbial Sensitivity Tests, Pseudomonas Infections, Pseudomonas aeruginosa, VEB-9 extended-spectrum β-lactamase, beta-Lactamases, carbapenem resistance, exotoxin U, extensive drug resistance, high-risk clone ST357, phylogenomic analysis, whole-genome sequencing}, language = {en}, month = {September}, note = {Number: 9 @@ -13680,11 +22166,49 @@ @article{strateva_phenotypic_2023 year = {2023} } +@article{strepis_benchamrking_2025, + abstract = {The Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) networks ‘Seq4AMR’ and ‘B2B2B AMR Dx’ were established to promote collaboration between microbial whole genome sequencing (WGS) and antimicrobial resistance (AMR) stakeholders. A key topic discussed was the frequent variability in results obtained between different microbial WGS-related AMR gene prediction workflows. Further, comparative benchmarking studies are difficult to perform due to differences in AMR gene prediction accuracy and a lack of agreement in the naming of AMR genes (semantic conformity) for the results obtained. To illustrate this problem, and as a capacity-building exercise to encourage stakeholder involvement, a comparative Galaxy-based BenchAMRking platform was developed and validated using datasets from bacterial species with PCR-verified AMR gene presence or absence information from abritAMR.}, + author = {Strepis, Nikolaos and Dollee, Dennis and Vrins, Donny and Vanneste, Kevin and Bogaerts, Bert and Carrillo, Catherine and Bharat, Amrita and Horan, Kristy and Sherry, Norelle L. and Seemann, Torsten and Howden, Benjamin P. and Hiltemann, Saskia and Chindelevitch, Leonid and Stubbs, Andrew P. and Hays, John P.}, + doi = {10.1186/s12864-024-11158-5}, + issn = {1471-2164}, + journal = {BMC Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Antimicrobial resistance, Bacteria, Benchmarking, Computational Biology, Drug Resistance, Bacterial, Galaxy, Genes, Bacterial, Microbial whole genome sequencing, Software, Workflows}, + language = {en}, + month = {January}, + number = {1}, + pages = {27}, + shorttitle = {{BenchAMRking}}, + title = {{BenchAMRking}: a {Galaxy}-based platform for illustrating the major issues associated with current antimicrobial resistance ({AMR}) gene prediction workflows}, + url = {https://doi.org/10.1186/s12864-024-11158-5}, + urldate = {2025-02-28}, + volume = {26}, + year = {2025} +} + +@article{su_c13-deacylase_2025, + abstract = {The enzyme C13DAc, isolated and characterized from Nocardioides albus ATCC 55425, represents a novel hydrolase with a classical Ser-His-Asp catalytic triad. Notably, it displays a distinct substrate profile, exhibiting no activity toward conventional esterase substrates such as p-nitrophenyl esters or cinnamate esters. Instead, C13DAc hydrolyzes compounds with a taxane core (e.g., paclitaxel), indicating a specialized biocatalytic function. Computational models provided critical insights into the architecture of the enzyme's active site. Molecular docking simulations revealed the catalytic triad positioned within a hydrophobic pocket and identified hydrophobic residues essential for substrate binding. The mutagenesis of a tyrosine residue led to the complete abolition of activity, thereby indicating an essential role for stabilizing the oxyanion intermediate. The substrate spectrum of C13DAc has been found to correlate with ligand hydrophobicity and structural specificity, thereby supporting the predicted binding mode and suggesting potential substrate combinations for synthetic applications. While transesterification reactions are feasible, the enzymatic esterification required for paclitaxel synthesis remains a significant challenge. These results underscore the potential of C13DAc as a promising candidate for biotransformation processes, particularly in the modification of complex natural products such as paclitaxel derivatives.}, + author = {Su, Jinfen and Schell, Eugen and Heine, Thomas and Ansorge-Schumacher, Marion B.}, + doi = {10.1002/cctc.202500567}, + issn = {1867-3899}, + journal = {ChemCatChem}, + keywords = {{\textgreater}UseGalaxy.eu, Biocatalysis, Deacylase, Hydrolysis, Paclitaxel, Protein models}, + language = {en}, + month = {December}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cctc.202500567}, + number = {n/a}, + pages = {e00567}, + title = {C13-{Deacylase} from {Nocardioides} albus {Resp}. {Streptomyces} sp., {Catalyzing} {Side} {Chain} {Hydrolysis} on the {Taxane} {Core}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cctc.202500567}, + urldate = {2025-06-11}, + volume = {n/a}, + year = {2025} +} + @article{subramani_genetic_2023, author = {Subramani, Prabha and Menichincheri, Gaia and Pirolo, Mattia and Arcari, Gabriele and Kudirkiene, Egle and Polani, Riccardo and Carattoli, Alessandra and Damborg, Peter and Guardabassi, Luca}, doi = {10.1128/aem.00559-23}, journal = {Applied and Environmental Microbiology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Enteritis, Enterotoxigenic Escherichia coli, Escherichia coli Infections}, month = {October}, note = {Publisher: American Society for Microbiology}, number = {10}, @@ -13702,7 +22226,7 @@ @article{subramoney_identification_2022 doi = {10.1002/jmv.27797}, issn = {1096-9071}, journal = {Journal of Medical Virology}, - keywords = {{\textgreater}UseGalaxy.eu, Omicron BA.1, SARS-CoV-2, genotyping, variants of concern}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19, Omicron BA.1, SARS-CoV-2, genotyping, variants of concern}, language = {en}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/jmv.27797}, number = {8}, @@ -13734,9 +22258,13 @@ @article{subramoney_sars-cov-2_2023 } @article{sun_complete_2021, + abstract = {Here, we reported the complete mitochondrial genome of \textit{Antheraea yamamai} Guérin-Méneville (1861) collected in Heilongjiang Province, China. The mitochondrial genome is 15,341 bp and encodes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Sequence comparison identified 22 SNVs in the \textit{A. yamamai} mitochondrial genomes between Chinese and Korean populations, indicating a low intraspecific variation between the two populations . Phylogenetic analyses with maximum-likelihood and Bayesian inference methods revealed a close relationship between \textit{A. yamamai} and \textit{Antheraea frithi} and supported the relationship among \textit{Antheraea} species (((\textit{A. yamamai} + \textit{A. frithi}) + \textit{A. pernyi}) + \textit{A. assamensis}).}, author = {Sun, Shu-Wei and Huang, Jing-Chao and Liu, Yan-Qun}, doi = {10.1080/23802359.2021.1945975}, + issn = {2380-2359}, + journal = {Mitochondrial DNA. Part B, Resources}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {July}, note = {Publisher: Informa UK Limited}, number = {8}, @@ -13747,6 +22275,22 @@ @article{sun_complete_2021 year = {2021} } +@article{sun_first_2021, + abstract = {This study reports the first complete mitochondrial genome of \textit{Antheraea pernyi} Guérin-Méneville 1855 (Lepidoptera: Saturniidae) strain Dingzhou\_1, a silkworm resource serving silk production in North Korea. The mitochondrial genome is circular with 15,573 bp in length encoding 37 typical mitochondrial genes (13 protein-coding genes, two ribosomal \textit{RNA} genes, and 22 transfer \textit{RNA} genes). The 553-bp A + T-rich region harbors a repeat region composed of 6 ∼ 38 bp tandem repeat units, as found in other known inbred strains from Chinese populations. The phylogenetic analysis clustered Dingzhou\_1 from North Korea together with Chinese Liaoning population, suggesting that oak silkworm in North Korea might be introduced from her neighbor China Liaoning.}, + author = {Sun, Shu-Wei and Tan, En-Guang and Liu, Yan-Qun}, + doi = {10.1080/23802359.2021.2002216}, + issn = {2380-2359}, + journal = {Mitochondrial DNA. Part B, Resources}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + number = {12}, + pages = {3480--3481}, + title = {First complete mitochondrial genome of {Antheraea} pernyi {Guérin}-{Méneville} 1855 ({Lepidoptera}: {Saturniidae}) from {North} {Korea}}, + url = {http://europepmc.org/abstract/MED/34869883}, + volume = {6}, + year = {2021} +} + @article{sun_stencil_2022, author = {Sun, Qi and Nematbakhsh, Ali and Kuntala, Prashant K. and Kellogg, Gretta and Pugh, B. Franklin and Lai, William K. M.}, doi = {10.1371/journal.pcbi.1009859}, @@ -13778,6 +22322,41 @@ @article{sundar_-silico_2023 year = {2023} } +@article{suresh_comparative_2025, + abstract = {Parvimonas micra is a Gram-positive, anaerobic bacterium commonly found in the oral cavity, skin and gastrointestinal tract. While typically a harmless organism, it can cause infections in individuals with weakened immune systems, leading to conditions like periodontitis and deep-tissue abscesses. This study focuses on the comparative genomic analysis of P. micra to explore its evolutionary relationships, antimicrobial resistance profiles and functional diversity by assessing phylogenetic analyses, resistance genes, virulence factors, mobile genetic elements, carbohydrate-active enzymes and pan-genome analysis. Comparative genomic analysis of 11 P. micra strains reveals significant functional variations among the strains, indicating notable interspecies diversity. Phylogenetic and comparative genome analysis revealed that strain JM503A is taxonomically distinct from the P. micra species, with genome similarity ranging from 54\% to 61\%. The 16S rRNA sequence similarity of strain JM503A is 98.28\%, indicating a distinct phylogenetic position. The average nucleotide identity value ranging from 91.32\% to 91.7\% and digital DNA–DNA hybridization values ranging from 43.00\% to 44.00\% of JM503A with other strains are below the cutoff values \<95\% and \<70\%, respectively, which confirms JM503A as a novel species. Based on its evolutionary relationships, strain JM503A is identified as a potential new species of Parvimonas, providing important evidence for its reclassification as a new species within the genus Parvimonas.}, + author = {Suresh, Roja and Jayachandiran, Susanthika and Balu, Pratebha and Ranganadin, Pajanivel and Dhamodharan, Ramasamy}, + doi = {10.1099/mgen.0.001511}, + issn = {2057-5858}, + journal = {Microbial Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Antimicrobial resistance, Comparative genomics, Novel Species, Pan-genome Analysis, Parvimonas Micra, Phylogenetic analysis, virulence factors}, + note = {Publisher: Microbiology Society,}, + number = {9}, + pages = {001511}, + title = {Comparative genome analysis of human pathogen {Parvimonas} micra revealed strain {JM503A} as potential novel species in the genus {Parvimonas} and high intra-species functional diversity}, + url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001511}, + urldate = {2025-10-03}, + volume = {11}, + year = {2025} +} + +@article{suresh_comparative_2025, + abstract = {The genus Arachnia, including Arachnia propionica and Arachnia rubra, are part of the normal oral and respiratory microbiota but can act as opportunistic pathogens in humans. This study investigates the functional, phylogenomic and taxonomic characteristics of 10 completely sequenced Arachnia strains, to elucidate their evolutionary relationships and divergence patterns, focusing on genomic variability and functional diversity. Phylogenetic analyses revealed distinct patterns, with Arachnia propionica strains showing significant divergence compared to the conserved Arachnia rubra strains. Notably, E10012 (=NBRC 14587) emerged as a distinct lineage with unique adaptations, while NCTC11666 exhibited a unique phylogenetic position, suggesting subspecies-level classification. Functional analyses highlighted variability among Arachnia propionica strains, with E10012 (=NBRC 14587) showing genes linked to choline metabolism and metal resistance, and NCTC11666 enriched in carbohydrate-active enzymes like GH179. In contrast, Arachnia rubra demonstrated genomic conservation, indicative of evolutionary specialization. This study reveals that strains E10012 (=NBRC 14587) and NCTC11666 displayed unique genomic features and distinct phylogenetic positioning, suggesting their reclassification as potential novel species and subspecies respectively. This underscores the balance between genomic conservation and diversification in Arachnia, reflecting their ecological adaptability and functional roles in the oral microbiome.}, + author = {Suresh, Roja and Jayachandiran, Susanthika and Balu, Pratebha and Ramasamy, Dhamodharan}, + doi = {10.1007/s00203-025-04302-6}, + issn = {1432-072X}, + journal = {Archives of Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Arachnia, Arachnia propionica, Arachnia rubra, Biological Taxonomy, Comparative genomics, Drosophila, Fungal evolution, Fungal genetics, Fungal genomics, Novel species, Phylogenomic analysis, Phylogeny}, + language = {en}, + month = {March}, + number = {4}, + pages = {93}, + title = {Comparative genomics reveals genetic diversity and differential metabolic potentials of the species of {Arachnia} and suggests reclassification of {Arachnia} propionica {E10012} (={NBRC}\_14587) as novel species}, + url = {https://doi.org/10.1007/s00203-025-04302-6}, + urldate = {2025-03-28}, + volume = {207}, + year = {2025} +} + @incollection{suzuki_genomic_2023, abstract = {Antimicrobial-resistant (AMR) bacterial infections caused by clinically important bacteria, including ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and mycobacteria (Mycobacterium tuberculosis and nontuberculous mycobacteria), have become a global public health threat. Their epidemic and pandemic clones often accumulate useful accessory genes in their genomes, such as AMR genes (ARGs) and virulence factor genes (VFGs). This process is facilitated by horizontal gene transfer among microbial communities via mobile genetic elements (MGEs), such as plasmids and phages. Nanopore long-read sequencing allows easy and inexpensive analysis of complex bacterial genome structures, although some aspects of sequencing data calculation and genome analysis methods are not systematically understood. Here we describe the latest and most recommended experimental and bioinformatics methods available for the construction of complete bacterial genomes from nanopore sequencing data and the detection and classification of genotypes of bacterial chromosomes, ARGs, VFGs, plasmids, and other MGEs based on their genomic sequences for genomic epidemiological analysis of AMR bacteria.}, address = {New York, NY}, @@ -13797,6 +22376,35 @@ @incollection{suzuki_genomic_2023 year = {2023} } +@article{sweatman_setd1a-dependent_2024, + abstract = {{\textless}h4{\textgreater}ABSTRACT{\textless}/h4{\textgreater} {\textless}h4{\textgreater}Background{\textless}/h4{\textgreater} Cells deficient in DNA repair factors breast cancer susceptibility 1/2 (BRCA1/2) or ataxia-telangiectasia mutated (ATM) are sensitive to poly-ADP ribose polymerase (PARP) inhibitors. Building on our previous findings, we asked how the lysine methyltransferase SETD1A contributed to PARP inhibitor-mediated cell death and determined the mechanisms responsible. {\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater} We used cervical, breast, lung and ovarian cancer cells bearing mutations in BRCA1 or ATM and depleted SETD1A using siRNA or CRISPR/Cas9. We assessed the effects of the PARPi Olaparib on cell viability, homologous recombination, and DNA repair. We assessed underlying transcriptional perturbations using RNAseq. We also used data from The Cancer Genomics Atlas (TCGA) to investigate overall patient survival. {\textless}h4{\textgreater}Results{\textless}/h4{\textgreater} Loss of SETD1A from both BRCA1-deficient and ATM-deficient cancer cells was associated with resistance to Olaparib, explained by an partial restoration of homologous recombination. Mechanistically, SETD1A-dependent transcription of the crossover junction endonuclease EME1 correlated with sensitivity to Olaparib in these cells. Accordingly, when SETD1A or EME1 was lost, BRCA1 or ATM-mutated cells became resistant to Olaparib, and homologous recombination was partially restored. {\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater} Loss of SETD1A or EME1 may explain why patients develop resistance to PARP inhibitors in the clinic.}, + author = {Sweatman, Ellie and Bayley, Rachel and Selemane, Richad and Higgs, Martin}, + doi = {10.1101/2024.06.16.599181}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {{SETD1A}-dependent {EME1} transcription drives {PARPi} sensitivity in {HR} deficient tumour cells}, + url = {http://europepmc.org/abstract/PPR/PPR868361}, + year = {2024} +} + +@article{sweatman_setd1a-dependent_2025, + abstract = {Cells deficient in DNA repair factors breast cancer susceptibility 1/2 (BRCA1/2) or ataxia-telangiectasia mutated (ATM) are sensitive to poly-ADP ribose polymerase (PARP) inhibitors. Building on our previous findings, we asked how the lysine methyltransferase SETD1A contributed to PARP inhibitor-mediated cell death in these contexts and determined the mechanisms responsible.}, + author = {Sweatman, Ellie and Bayley, Rachel and Selemane, Richad and Higgs, Martin R.}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41416-025-02963-0}, + issn = {1532-1827}, + journal = {British Journal of Cancer}, + keywords = {{\textgreater}UseGalaxy.eu, Cancer therapeutic resistance, Histone-Lysine N-Methyltransferase, Methylation, Neoplasms, Poly(ADP-ribose) Polymerase Inhibitors}, + language = {en}, + month = {February}, + note = {Publisher: Nature Publishing Group}, + pages = {1--13}, + title = {{SETD1A}-dependent {EME1} transcription drives {PARPi} sensitivity in {HR} deficient tumour cells}, + url = {https://www.nature.com/articles/s41416-025-02963-0}, + urldate = {2025-02-28}, + year = {2025} +} + @article{szachniuk_rnapolis:_2019, author = {Szachniuk, Marta}, doi = {10.2478/fcds-2019-0012}, @@ -13821,7 +22429,7 @@ @article{tabarelli_chasing_2022 doi = {10.3390/genes13101696}, issn = {2073-4425}, journal = {Genes}, - keywords = {\textit{Malus} × \textit{domestica}, \textit{TCP} gene family, {\textgreater}UseGalaxy.eu, GDDH13v1.1 genome assembly}, + keywords = {\textit{Malus} × \textit{domestica}, \textit{TCP} gene family, {\textgreater}UseGalaxy.eu, Arabidopsis, GDDH13v1.1 genome assembly, Malus}, language = {en}, month = {October}, note = {Number: 10 @@ -13854,16 +22462,77 @@ @article{tajuddin_genomic_2023 year = {2023} } +@article{talubo_qsar-based_2025, + abstract = {Background/Objectives: The molecular heterogeneity and metabolic flexibility of Hepatocellular Carcinoma (HCC) pose significant challenges to the efficacy of systemic therapy for advanced cases. Early screening difficulties often delay diagnosis, leading to more advanced stages at presentation. Combined with the inconsistent responses to current systemic therapies, HCC continues to have one of the highest mortality rates among cancers. Thus, this paper seeks to contribute to the development of systemic therapy options through the consideration of HCC’s metabolic vulnerabilities and lay the groundwork for future in vitro studies. Methods: Transcriptomic data were used to calculate single and double knockout options for HCC using genetic Minimal Cut Sets. Furthermore, using QSAR modeling, drug repositioning opportunities were assessed to inhibit the selected genes. Results: Two single knockout options that were also annotated as essential pairs were found within the pyrimidine metabolism pathway of HCC, wherein the knockout of either DHODH or TYMS is potentially disruptive to proliferation. The result of the flux balance analysis and gene knockout simulation indicated a significant decrease in biomass production. Three machine learning algorithms were assessed for their performance in predicting the pIC50 of a given compound for the selected genes. SVM-rbf performed the best on unseen data achieving an R2 of 0.82 for DHODH and 0.81 for TYMS. For DHODH, the drugs Oteseconazole, Tipranavir, and Lusutrombopag were identified as potential inhibitors. For TYMS, the drugs Tadalafil, Dabigatran, Baloxavir Marboxil, and Candesartan Cilexetil showed promise as inhibitors. Conclusions: Overall, this study suggests in vitro testing of the identified drugs to assess their capabilities in inducing pyrimidine starvation on HCC.}, + author = {Talubo, Nicholas Dale D. and Dela Cruz, Emery Wayne B. and Fowler, Peter Matthew Paul T. and Tsai, Po-Wei and Tayo, Lemmuel L.}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/cancers17050903}, + issn = {2072-6694}, + journal = {Cancers}, + keywords = {{\textgreater}UseGalaxy.eu, QSAR, drug repurposing, hepatocellular carcinoma, pyrimidine metabolism}, + language = {en}, + month = {January}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {903}, + title = {{QSAR}-{Based} {Drug} {Repurposing} and {RNA}-{Seq} {Metabolic} {Networks} {Highlight} {Treatment} {Opportunities} for {Hepatocellular} {Carcinoma} {Through} {Pyrimidine} {Starvation}}, + url = {https://www.mdpi.com/2072-6694/17/5/903}, + urldate = {2025-05-29}, + volume = {17}, + year = {2025} +} + +@article{tamang_analysis_2025, + abstract = {Tempe, a fermented soybean product, plays a significant role in Indonesian dietary culture. Currently, there have been no studies that classify tempe as a functional food using up-to-date genomic data. This research used an Illumina-based meta-transcriptomic method to explore the microbial communities that mainly contribute to tempe fermentation and their functions related to its health benefits. The analysis revealed 8 phyla, 19 families, 20 genera, and 28 species of both bacteria and fungi. The dominant species found were Klebsiella africana, followed by Rhizopus microsporus, Klebsiella pneumoniae, Rhizopus oligosporus, Propionibacterium humerusii, and Lactobacillus brevis. Klebsiella and Propionibacterium are involved in vitamin B12 production, while Rhizopus is associated with GABA production and isoflavones like genistein and daidzein, along with spermidine, caffeic acid, and chlorogenic acid. Lactobacillus contributes proteases, GABA, and beta-glucosidase. The study also strengthened the link between microbes and health benefits by identifying certain microbial genes and their expression levels in the samples. Changes in gene expression reveal how fermentation environments affect diversity and functionality. Overall, finding a variety of bioactive compounds and their genetic backgrounds supports tempe’s position as a functional superfood that could gain global popularity through further research and development.}, + author = {Tamang, Jyoti Prakash and Das, Souvik and Lama, Sonam and Utama, Gemiilang Lara and Safitri, Ratu and Balia, Roostita Lobo and Thapa, Namrata}, + doi = {10.1016/j.foodres.2025.115757}, + issn = {0963-9969}, + journal = {Food Research International}, + keywords = {{\textgreater}UseGalaxy.eu, Gene expression, Meta-transcriptome, RNA-seq}, + month = {February}, + pages = {115757}, + title = {Analysis of meta-transcriptomics and identification of genes linked to bioactive peptides and vitamins in {Indonesian} \textit{tempe}}, + url = {https://www.sciencedirect.com/science/article/pii/S0963996925000948}, + urldate = {2025-02-16}, + volume = {202}, + year = {2025} +} + +@article{tang_denser_2025, + abstract = {The superfamily Tellinoidea is one of the most diverse groups of marine bivalves, with significant ecological and economic value. To date, the availability of complete mitochondrial genome data within Tellinoidea remains limited, and the taxonomic coverage is still insufficient to resolve its internal controversies. The current study aims to further explore the phylogenetic relationships within Tellinoidea through denser sampling. We have newly sequenced the mitochondrial genomes of 13 species, among which seven genera are being published for the first time. Combined with the published mitogenomes and transcriptomic data, we constructed the most comprehensive Tellinoidea phylogeny to date through maximum likelihood and Bayesian Inference analyses. Our findings support the monophyly of the superfamily Tellinoidea, with Semelidae nesting as a monophyletic group within Tellinidae. We also support the paraphyly of Tellinidae based on the mitochondrial genome data for the first time, identifying that the two subfamilies (Macominae and Tellininae) are polyphyletic. Gene rearrangement analysis reveals a relatively high degree of variation in Semelidae. By expanding the mitochondrial genome dataset, this study provides new insights into the phylogeny of Tellinoidea and underscores the need for further sampling of species to reassess the phylogenetic relationships of Tellinidae and the entire Tellinoidea.}, + author = {Tang, Weikang and Xu, Tao and Gong, Jihang and Kong, Lingfeng}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/d17050303}, + issn = {1424-2818}, + journal = {Diversity}, + keywords = {{\textgreater}UseGalaxy.eu, Mollusca, Tellinoidea, mitogenome, phylogeny}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {303}, + shorttitle = {Denser {Mitogenomic} {Sampling} for {Exploring} the {Phylogeny} of {Tellinoidea} ({Mollusca}}, + title = {Denser {Mitogenomic} {Sampling} for {Exploring} the {Phylogeny} of {Tellinoidea} ({Mollusca}: {Bivalvia})}, + url = {https://www.mdpi.com/1424-2818/17/5/303}, + urldate = {2025-05-29}, + volume = {17}, + year = {2025} +} + @article{tangaro_laniakea_2020, abstract = {AbstractBackground. While the popular workflow manager Galaxy is currently made available through several publicly accessible servers, there are scenarios wher}, author = {Tangaro, Marco Antonio and Donvito, Giacinto and Antonacci, Marica and Chiara, Matteo and Mandreoli, Pietro and Pesole, Graziano and Zambelli, Federico}, doi = {10.1093/gigascience/giaa033}, + issn = {2047-217X}, journal = {GigaScience}, - keywords = {+Cloud, +Galactic, +IsGalaxy, +RefPublic, {\textgreater}GVL-Unspecified, {\textgreater}Laniakea, {\textgreater}PhenoMeNal, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au}, + keywords = {+Cloud, +Galactic, +IsGalaxy, +RefPublic, {\textgreater}GVL-Unspecified, {\textgreater}Laniakea, {\textgreater}PhenoMeNal, {\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Software, Workflow}, language = {en}, month = {April}, note = {Publisher: Oxford Academic}, number = {4}, + pages = {giaa033}, shorttitle = {Laniakea}, title = {Laniakea: an open solution to provide {Galaxy} “on-demand” instances over heterogeneous cloud infrastructures}, url = {https://academic.oup.com/gigascience/article/9/4/giaa033/5816668}, @@ -13872,6 +22541,24 @@ @article{tangaro_laniakea_2020 year = {2020} } +@article{tangermann_saturation_2025, + abstract = {Variants of uncertain significance represent the biggest challenge for genomics-based precision oncology. Activated fibroblast growth factor receptors (FGFRs) frequently drive tumorigenesis by different genetic aberrations. However, it remains unknown which of the many point mutations affecting FGFR1, FGFR2, FGFR3 or FGFR4 in cancer are druggable, that is, activating signaling while not mediating FGFR inhibitor resistance. Here we implemented a saturation mutational scanning platform to screen all 11,520 possible point mutations covering the kinase domains of FGFR1–4. Pooled positive selection screens identified 474 activating and 738 mutations mediating resistance to the FGFR inhibitors pemigatinib and futibatinib, together revealing 301 druggable FGFR mutations analogous to a strong PS3/BS3 evidence level. The screens also identified loss-of-function mutations and an association of gain-of-function mutations with hydrophobic changes. The functional screens identified 97\% of acquired resistance mutations in clinical trials. Our comprehensive catalog of every druggable mutation in the FGFR kinase domains is readily available for clinical decision support.}, + author = {Tangermann, Carla and Ghosh, Avantika and Ziegler, Martin and Facchinetti, Francesco and Stappenbeck, Jannis and Carus Sahin, Yagmur Oyku and Riester, Marisa and Viardot, Luise Carmina and Zundel, Tobias and Friboulet, Luc and Hollebecque, Antoine and Naveja, José J. and Wanninger, Angela and Hess, Maria Elena and Brummer, Tilman and Boerries, Melanie and Loges, Sonja and Loriot, Yohann and Illert, Anna L. and Diederichs, Sven}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41588-025-02431-8}, + issn = {1546-1718}, + journal = {Nature Genetics}, + keywords = {{\textgreater}UseGalaxy.eu, Mutagenesis, Oncogenes, Targeted therapies}, + language = {en}, + month = {December}, + note = {Publisher: Nature Publishing Group}, + pages = {1--12}, + title = {Saturation mutagenesis identifies activating and resistance-inducing {FGFR} kinase domain mutations}, + url = {https://www.nature.com/articles/s41588-025-02431-8}, + urldate = {2025-12-10}, + year = {2025} +} + @article{tapia_nanopore_2024, author = {Tapia, Stephanie and Orellana, Joseph and Duran, Yerson and Rodriguez, Jose and Angulo, Derly and Dominguez-Mendoza, Luz and Grabiel, Sandra and Silva, Jose and Caballero, Romina and Zapata, Katherine and Gómez, Muriel and Tataje-Lavanda, Luis and Velazco, Rodolfo}, doi = {10.1128/mra.00190-24}, @@ -13905,13 +22592,36 @@ @article{tari_u2af65_2019 year = {2019} } +@article{tascini_oxa-carbapenemases_2025, + abstract = {Objective +Carbapenem- resistant A. baumannii (CRAB) isolates represent a serious public health concern. Recently, a novel molecule, the cefiderocol (FDC), has emerged as promising therapeutic option for CRAB infections. In the present study, we analyzed the genomes of five A. baumannii ST2 isolated from four hospitalized patients. All patients were treated with FDC and ampicillin/sulbactam (AMP/SUL) combination. +Methods +Whole-genome sequencing of the five CRAB isolates was performed using an Illumina MiSeq instrument. A detailed bioinformatic analysis was carried out to acquire information about genotyping, antimicrobial resistance genes (ARGs), virulence associated genes (VAGs), single nucleotide polymorphisms (SNPs) and phylogenetic tree of the five CRAB isolates. +Results +Among the five CRAB isolates, only three (Ab.2, Ab.3 and Ab.4) exhibited resistance to FDC. The genomes of all isolates were highly similar, and MLST analysis indicated they all belong to sequence type 2 (ST2), corresponding to international clone 2. Phylogenetic analysis suggests that isolates Ab.2, Ab.3 and Ab.4 may share a common ancestor or be linked by a possible transmission event. In contrast, isolates Ab.1 and Ab.5 were more divergent from the other three. Nevertheless, all five isolates harbored the same ARGs and VAGs. The OXA-23, OXA-66 and ADC-25 β-lactamases were detected in all strains. The FDC-non-susceptible isolates showed K235N/H370Y double mutation within PBP3, along with a G370C substitution in PBP1a. +Conclusion +The four clinical cases described in this study represent an important example of efficacy and good practice of FDC plus AMP/SUL combination in the treatment of critical patients suffering from CRAB infections.}, + author = {Tascini, C. and Giuliano, S. and Martini, L. and Carannante, N. and Mariano, B. and Perilli, M. and Piccirilli, A.}, + doi = {10.1016/j.jgar.2025.06.014}, + issn = {2213-7165}, + journal = {Journal of Global Antimicrobial Resistance}, + keywords = {{\textgreater}UseGalaxy.eu, FDC, PBPs, carbapenemases, whole-genome sequencing}, + month = {June}, + shorttitle = {{OXA}-carbapenemases and mutations within {PBPs} in {ST2} carbapenem-resistant \textit{{A}. baumannii}}, + title = {{OXA}-carbapenemases and mutations within {PBPs} in {ST2} carbapenem-resistant \textit{{A}. baumannii}: evaluating the efficacy of cefiderocol and ampicillin-sulbactam combination therapy}, + url = {https://www.sciencedirect.com/science/article/pii/S221371652500147X}, + urldate = {2025-07-12}, + year = {2025} +} + @article{taylor_whirly_2023, abstract = {The WHIRLY (WHY) family of DNA/RNA binding proteins fulfil multiple but poorly characterised functions in plants. We analysed WHY protein functions in the Arabidopsis Atwhy1, Atwhy3, Atwhy1why3 single and double mutants and wild type controls. The Atwhy3 and Atwhy1why3 double mutants showed a significant delay in flowering, having more siliques per plant but with fewer seeds per silique than the wild type. While germination was similar in the unaged high-quality seeds of all lines, significant decreases in vigour and viability were observed in the aged mutant seeds compared with the wild type. Imbibition of unaged high-quality seeds was characterised by large increases in transcripts that encode proteins involved in oxygen sensing and responses to hypoxia. Seed aging resulted in a disruption of the imbibition-induced transcriptome profile such that transcripts encoding RNA metabolism and processing became the most abundant components of the imbibition signature. The imbibition-related profile of the Atwhy1why3 mutant seeds, was characterised by decreased expression of hypoxia-related and oxygen metabolism genes even in the absence of aging. Seed aging further decreased the abundance of hypoxia-related and oxygen metabolism transcripts relative to the wild type. These findings suggest that the WHY1 and WHY3 proteins regulate the imbibition-induced responses to oxygen availability and hypoxia. Loss of WHY1 and WHY3 functions decreases the ability of Arabidopsis seeds to resist the adverse effects of seed aging.}, author = {Taylor, Rachel E. and Waterworth, Wanda and West, Christopher E and Foyer, Christine H.}, doi = {10.1042/BCJ20230008}, issn = {0264-6021}, journal = {Biochemical Journal}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, Arabidopsis Proteins}, + language = {eng}, month = {July}, number = {13}, pages = {941--956}, @@ -13958,9 +22668,11 @@ @article{tekman_single-cell_2020 doi = {10.1093/gigascience/giaa102}, issn = {2047-217X}, journal = {GigaScience}, - keywords = {+Education, +Galactic, +IsGalaxy, +Project, +RefPublic, +Tools, {\textgreater}Human Cell Atlas, {\textgreater}Live EU, {\textgreater}SingleCell}, + keywords = {+Education, +Galactic, +IsGalaxy, +Project, +RefPublic, +Tools, {\textgreater}Human Cell Atlas, {\textgreater}Live EU, {\textgreater}SingleCell, Ecosystem, Software}, + language = {eng}, month = {October}, number = {10}, + pages = {giaa102}, title = {A single-cell {RNA}-sequencing training and analysis suite using the {Galaxy} framework}, url = {https://doi.org/10.1093/gigascience/giaa102}, urldate = {2021-10-03}, @@ -13968,6 +22680,26 @@ @article{tekman_single-cell_2020 year = {2020} } +@article{teng_tgf-_2025, + abstract = {Cancer cells infiltrating surrounding tissue frequently undergo partial epithelial-mesenchymal transitions (pEMT) and employ a collective mode of invasion. How these phenotypic traits are regulated and interconnected remains underexplored. Here, we used intestinal organoids with colorectal cancer (CRC) driver mutations as model system to investigate the mechanistic basis of TGF-β1-induced pEMT and collective invasion. By scRNA-seq we identified multiple cell subpopulations representing a broad pEMT spectrum, where the most advanced pEMT state correlated with the transcriptional profiles of leader cells in collective invasion and a poor prognosis mesenchymal subtype of human CRC. Bioinformatic analyses pinpointed Sox11 as a transcription factor gene whose expression peaked in the potential leader/pEMThigh cells. Immunofluorescence staining confirmed Sox11 expression in cells at the invasive front of TGF-β1-treated organoids. Loss-of-function and overexpression experiments showed that Sox11 is necessary, albeit not sufficient, for TGF-β1-induced pEMT and collective invasion. In human CRC samples, elevated SOX11 expression was associated with advanced tumor stages and worse prognosis. Unexpectedly, aside from orchestrating the organoid response to TGF-β1, Sox11 controlled expression of genes related to normal gut function and tumor suppression. Apparently, Sox11 is embedded in several distinct gene regulatory circuits, contributing to intestinal tissue homeostasis, tumor suppression, and TGF-β-mediated cancer cell invasion.}, + author = {Teng, Yu-Hsiang and Appiah, Bismark and Andrieux, Geoffroy and Schrempp, Monika and Rose, Katja and Hofmann, Angelika Susanna and Ku, Manching and Beyes, Sven and Boerries, Melanie and Hecht, Andreas}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41389-025-00560-7}, + issn = {2157-9024}, + journal = {Oncogenesis}, + keywords = {{\textgreater}UseGalaxy.eu, Cancer, Growth factor signalling}, + language = {en}, + month = {May}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {1--14}, + title = {{TGF}-β signaling redirects {Sox11} gene regulatory activity to promote partial {EMT} and collective invasion of oncogenically transformed intestinal organoids}, + url = {https://www.nature.com/articles/s41389-025-00560-7}, + urldate = {2025-05-23}, + volume = {14}, + year = {2025} +} + @article{tensen_dark_2024, abstract = {\textit{African Journal of Wildlife Research} is a multidisciplinary journal that has been published since 1971 and covers the scientific, applied, managerial, methodological, and sociological issues related to wildlife research.}, author = {Tensen, Laura and Camacho, Gerrie}, @@ -13993,7 +22725,8 @@ @article{tetzlaff_small_2024 editor = {Nicolás, Marisa and Sussel, Lori}, issn = {2050-084X}, journal = {eLife}, - keywords = {{\textgreater}UseGalaxy.eu, Toxoplasma gondii, mitochondria, mitogenome, polysomes, rRNA, rribosome}, + keywords = {{\textgreater}UseGalaxy.eu, Genome, Mitochondrial, RNA, Small Untranslated, Toxoplasma gondii, mitochondria, mitogenome, polysomes, rRNA, rribosome}, + language = {eng}, month = {February}, note = {Publisher: eLife Sciences Publications, Ltd}, pages = {e95407}, @@ -14007,7 +22740,7 @@ @article{tetzlaff_small_2024 @article{teznerova_ago-hook_2023, abstract = {Metylace DNA řízená malými RNA (RdDM) je důležitá dráha, jež prostřednictvím navození metylace DNA reguluje genovou expresi a podílí se na obraně proti invazivním DNA elementům (zejména transposonům). Klíčovou roli v RdDM dráze hrají proteiny Argonaut (AGO) s malými RNA (sRNA), které jsou k cílové DNA sekvenčně komplementární. S proteiny Argonaut jsou schopné interagovat domény zvané AGO-hooky. U rostlin se v RdDM dráze uplatňují dva proteiny s AGO-hook doménami: NRPE1 a SPT5L. Na řešitelském pracovišti bylo nedávno objeveno, že součástí komplexu Pol V (stejně jako zmíněné dva proteiny) je ještě třetí protein SPT6L. Role SPT6L role dosud nebyla popsána, ale předpokládáme, že rovněž hraje roli v RdDM dráze. Tato práce se zabývá studiem všech tří AGO-hook domén přítomných v Pol V komplexu a jejich rolí v RdDM dráze u rostliny Arabidopsis thaliana, od přípravy mutantů postrádajících různé kombinace uvedených AGO-hook domén po studium jejich role a zastupitelnosti při metylaci DNA v různých lokusech. Klíčová slova AGO-hook, Arabidopsis thaliana, NRPE1, SPT5L, SPT6L, siRNA, epigenetické značení chromatinu, protein Argonaut}, author = {Teznerová, Kateřina}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, language = {cs\_CZ}, month = {September}, note = {Accepted: 2024-09-12T06:33:52Z @@ -14018,6 +22751,23 @@ @article{teznerova_ago-hook_2023 year = {2023} } +@article{thakur_comparative_2022, + abstract = {\textit{Trueperella pyogenes} is a Gram-positive opportunistic pathogen that causes severe cases of mastitis, metritis, and pneumonia in a wide range of animals, resulting in significant economic losses. Although little is known about the virulence factors involved in the disease pathogenesis, a comprehensive comparative genome analysis of \textit{T. pyogenes} genomes has not been performed till date. Hence, present investigation was carried out to characterize and compare 19 \textit{T. pyogenes} genomes originating in different geographical origins including the draftgenome of the first Indian origin strain \textit{T. pyogenes} Bu5. Additionally, candidate virulence determinants that could be crucial for their pathogenesis were also detected and analyzed by using various bioinformatics tools. The pan-genome calculations revealed an open pan-genome of \textit{T. pyogenes}. In addition, an inventory of virulence related genes, 190 genomic islands, 31 prophage sequences, and 40 antibiotic resistance genes that could play a significant role in organism's pathogenicity were detected. The core-genome based phylogeny of \textit{T. pyogenes} demonstrates a polyphyletic, host-associated group with a high degree of genomic diversity. The identified core-genome can be further used for screening of drug and vaccine targets. The investigation has provided unique insights into pan-genome, virulome, mobiliome, and resistome of \textit{T. pyogenes} genomes and laid the foundation for future investigations.}, + author = {Thakur, Zoozeal and Vaid, Rajesh Kumar and Anand, Taruna and Tripathi, Bhupendra Nath}, + doi = {10.3390/antibiotics12010024}, + issn = {2079-6382}, + journal = {Antibiotics (Basel, Switzerland)}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {December}, + number = {1}, + pages = {24}, + title = {Comparative {Genome} {Analysis} of 19 {Trueperella} pyogenes {Strains} {Originating} from {Different} {Animal} {Species} {Reveal} a {Genetically} {Diverse} {Open} {Pan}-{Genome}}, + url = {http://europepmc.org/abstract/MED/36671226}, + volume = {12}, + year = {2022} +} + @article{thangameeran_examining_2024, abstract = {Intracerebral hemorrhage (ICH) is a life-threatening condition associated with significant morbidity and mortality. This study investigates transcriptomic alterations in rodent models of ICH and severe ICH to shed light on the genetic pathways involved in hemorrhagic brain injury. We performed principal component analysis, revealing distinct principal component segments of normal rats compared to ICH and severe ICH rats. We employed heatmaps and volcano plots to identify differentially expressed genes and utilized bar plots and KEGG pathway analysis to elucidate the molecular pathways involved. We identified a multitude of differentially expressed genes in both the ICH and severe ICH models. Our results revealed 5679 common genes among the normal, ICH, and severe ICH groups in the upregulated genes group, and 1196 common genes in the downregulated genes, respectively. A volcano plot comparing these groups further highlighted common genes, including PDPN, TIMP1, SERPINE1, TUBB6, and CD44. These findings underscore the complex interplay of genes involved in inflammation, oxidative stress, and neuronal damage. Furthermore, pathway enrichment analysis uncovered key signaling pathways, including the TNF signaling pathway, protein processing in the endoplasmic reticulum, MAPK signaling pathway, and Fc gamma R-mediated phagocytosis, implicated in the pathogenesis of ICH.}, author = {Thangameeran, Shaik Ismail Mohammed and Tsai, Sheng-Tzung and Liew, Hock-Kean and Pang, Cheng-Yoong}, @@ -14025,7 +22775,7 @@ @article{thangameeran_examining_2024 doi = {10.3390/biom14060678}, issn = {2218-273X}, journal = {Biomolecules}, - keywords = {{\textgreater}UseGalaxy.eu, gene expression, intracerebral hemorrhage, neuroinflammation, severe intracerebral hemorrhage, transcriptomics}, + keywords = {{\textgreater}UseGalaxy.eu, Cerebral Hemorrhage, Disease Models, Animal, Rats, Sprague-Dawley, Transcriptome, gene expression, intracerebral hemorrhage, neuroinflammation, severe intracerebral hemorrhage, transcriptomics}, language = {en}, month = {June}, note = {Number: 6 @@ -14039,12 +22789,23 @@ @article{thangameeran_examining_2024 year = {2024} } -@article{thanki_aequatus:_2018, +@article{thanki_aequatus_2016, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater} Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral gene duplication events as well as regions under positive or purifying selection within lineages. Gene family and orthogroup characterisation enables the identification of syntenic blocks, which can then be visualised with various tools. Unfortunately, currently available tools display only an overview of syntenic regions as a whole, limited to the gene level, and none provide further details about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. {\textless}h4{\textgreater}Findings{\textless}/h4{\textgreater} We present Aequatus, a standalone web-based tool that provides an in-depth view of gene structure across gene families, with various options to render and filter visualisations. It relies on pre-calculated alignment and gene feature information typically held in, but not limited to, the Ensembl Compara and Core databases. We also offer Aequatus.js, a reusable JavaScript module that fulfils the visualisation aspects of Aequatus, available within the Galaxy web platform as a visualisation plugin, which can be used to visualise gene trees generated by the GeneSeqToFamily workflow. {\textless}h4{\textgreater}Availability{\textless}/h4{\textgreater} Aequatus is an open-source tool freely available to download under the MIT license at https://github.com/TGAC/Aequatus . A demo server is available at http://aequatus.earlham.ac.uk/ . A publicly available instance of the GeneSeqToFamily workflow to generate gene tree information and visualise it using Aequatus is available on the Galaxy EU server at https://usegalaxy.eu . {\textless}h4{\textgreater}Contacts{\textless}/h4{\textgreater} Anil.Thanki@earlham.ac.uk and Robert.Davey@earlham.ac.uk}, + author = {Thanki, Anil and Soranzo, Nicola and Herrero, Javier and Haerty, Wilfried and Davey, Robert}, + doi = {10.1101/055632}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Aequatus: {An} open-source homology browser}, + url = {http://europepmc.org/abstract/PPR/PPR9505}, + year = {2016} +} + +@article{thanki_aequatus_2018, abstract = {Background. Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, inclu}, author = {Thanki, Anil S. and Soranzo, Nicola and Herrero, Javier and Haerty, Wilfried and Davey, Robert P.}, doi = {10.1093/gigascience/giy128}, journal = {GigaScience}, - keywords = {+Galactic, +RefPublic, +Tools, {\textgreater}UseGalaxy.eu}, + keywords = {+Galactic, +RefPublic, +Tools, {\textgreater}UseGalaxy.eu, Software}, language = {en}, month = {November}, shorttitle = {Aequatus}, @@ -14054,11 +22815,48 @@ @article{thanki_aequatus:_2018 year = {2018} } +@article{thaqi_non-rhizobial_2025, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Non-rhizobial endophytes (NREs) support plant health and nodule function by enhancing symbiotic interactions and nitrogen fixation. However, their recruitment dynamics under fertilizers of varying phosphorus solubility remain poorly understood. This study investigated how four P fertilization treatments-no phosphorus (P0), bone char (BC), surface-modified bone char plus (BC$^{\textrm{plus}}$), and triple superphosphate (TSP)-with increasing solubility influence microbial recruitment and diversity in Pisum sativum, leading to differences in plant-available phosphorus across bulk soil, rhizosphere, roots, and nodules.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}Using 16S rRNA amplicon sequencing, we found that nodule-associated microbial communities were primarily recruited from unknown sources, likely seeds, followed by roots, especially under BC$^{\textrm{plus}}$. Phosphorus solubility of treatments significantly influenced recruitment patterns, with solubility further shaping microbial diversity. BC$^{\textrm{plus}}$ recruited beneficial taxa like Beijerinckiaceae and Flavobacteriaceae, which are associated with nitrogen fixation and biocontrol. In contrast, the highly soluble TSP treatment expanded recruitment from the rhizosphere, reflecting less stringent environmental filtering and promoting taxa like Steroidobacteraceae and Blastocatellaceae, known for nutrient cycling and pathogen suppression. In the absence of P fertilization (P0), recruitment relied heavily on seeds and roots, with arbuscular mycorrhizal fungi colonization prioritized over nodulation. Notably, TSP supported significantly more nodules with greater microbial diversity, potentially enhanced by NREs.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}Phosphorus solubility of the applied fertilizers strongly influences NRE recruitment dynamics in P. sativum. Seeds and roots act as primary reservoirs, while highly soluble fertilizers promote broader recruitment from the rhizosphere and increase microbial diversity in nodules. These results underscore the importance of the fertilization form in modulating NRE recruitment.}, + author = {Thaqi, Stefanie Katharina and Hensel, Natalia and Vitow, Nora and Baum, Christel and Streb, Lisa-Marie and Kublik, Susanne and Leinweber, Peter and Panten, Kerstin and Schloter, Michael and Schulz, Stefanie}, + doi = {10.1186/s40793-025-00751-0}, + issn = {2524-6372}, + journal = {Environmental microbiome}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {July}, + number = {1}, + pages = {92}, + title = {Non-rhizobial endophyte recruitment and diversity in {Pisum} sativum are strongly shaped by phosphorus fertilizer form}, + url = {http://europepmc.org/abstract/MED/40696482}, + volume = {20}, + year = {2025} +} + +@article{then_plant_2021, + abstract = {Alighting aphids probe a new host plant by intracellular test punctures for suitability. These induce immediate calcium signals that emanate from the punctured sites and might be the first step in plant recognition of aphid feeding and the subsequent elicitation of plant defence responses. Calcium is also involved in the transmission of non-persistent plant viruses that are acquired by aphids during test punctures. Therefore, we wanted to determine whether viral infection alters calcium signalling. For this, calcium signals triggered by aphids were imaged on transgenic \textit{Arabidopsis} plants expressing the cytosolic FRET-based calcium reporter YC3.6-NES and infected with the non-persistent viruses cauliflower mosaic (CaMV) and turnip mosaic (TuMV), or the persistent virus, turnip yellows (TuYV). Aphids were placed on infected leaves and calcium elevations were recorded by time-lapse fluorescence microscopy. Calcium signal velocities were significantly slower in plants infected with CaMV or TuMV and signal areas were smaller in CaMV-infected plants. Transmission tests using CaMV-infected \textit{Arabidopsis} mutants impaired in pathogen perception or in the generation of calcium signals revealed no differences in transmission efficiency. A transcriptomic meta-analysis indicated significant changes in expression of receptor-like kinases in the BAK1 pathway as well as of calcium channels in CaMV- and TuMV-infected plants. Taken together, infection with CaMV and TuMV, but not with TuYV, impacts aphid-induced calcium signalling. This suggests that viruses can modify plant responses to aphids from the very first vector/host contact.}, + author = {Then, Christiane and Bellegarde, Fanny and Schivre, Geoffrey and Martinière, Alexandre and Macia, Jean-Luc and Xiong, Tou Cheu and Drucker, Martin}, + doi = {10.3390/cells10123534}, + issn = {2073-4409}, + journal = {Cells}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {December}, + number = {12}, + pages = {3534}, + title = {Plant {Viruses} {Can} {Alter} {Aphid}-{Triggered} {Calcium} {Elevations} in {Infected} {Leaves}}, + url = {http://europepmc.org/abstract/MED/34944040}, + volume = {10}, + year = {2021} +} + @article{thompson_draft_2023, + abstract = {Here, we report the draft genome sequence of \textit{Amycolatopsis} camponoti RTGN1, a bacterial endophyte of \textit{Alnus glutinosa} root nodules, collected from Saltwell Park, United Kingdom. The genome is 11.9 Mbp in size, composed of 147 contigs, with an N$_{\textrm{50}}$ of 179,211 bp and presenting a GC content of 70.9\%.}, author = {Thompson, Ryan Michael and Fox, Edward M. and Montero-Calasanz, Maria del Carmen}, doi = {10.1128/mra.00470-23}, + issn = {2576-098X}, journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, month = {December}, note = {Publisher: American Society for Microbiology}, number = {1}, @@ -14088,36 +22886,57 @@ @article{thompson_draft_2023 @article{thompson_draft_2024, author = {Thompson, Ryan Michael and Fox, Edward M. and Montero-Calasanz, Maria del Carmen}, - doi = {10.1128/mra.01131-23}, + doi = {10.1128/mra.01132-23}, journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, - month = {February}, + month = {January}, note = {Publisher: American Society for Microbiology}, - number = {3}, - pages = {e01131--23}, - title = {Draft genome sequences of two {Micromonospora} strains isolated from the root nodules of {Alnus} glutinosa}, - url = {https://journals.asm.org/doi/full/10.1128/mra.01131-23}, - urldate = {2024-11-17}, + number = {2}, + pages = {e01132--23}, + title = {Draft genome sequences of five {Mycobacterium} strains, isolated from {Alnus} glutinosa root nodules}, + url = {https://journals.asm.org/doi/full/10.1128/mra.01132-23}, + urldate = {2024-05-17}, volume = {13}, year = {2024} } @article{thompson_draft_2024-1, author = {Thompson, Ryan Michael and Fox, Edward M. and Montero-Calasanz, Maria del Carmen}, - doi = {10.1128/mra.01132-23}, + doi = {10.1128/mra.01131-23}, journal = {Microbiology Resource Announcements}, keywords = {{\textgreater}UseGalaxy.eu}, - month = {January}, + month = {February}, note = {Publisher: American Society for Microbiology}, - number = {2}, - pages = {e01132--23}, - title = {Draft genome sequences of five {Mycobacterium} strains, isolated from {Alnus} glutinosa root nodules}, - url = {https://journals.asm.org/doi/full/10.1128/mra.01132-23}, - urldate = {2024-05-17}, + number = {3}, + pages = {e01131--23}, + title = {Draft genome sequences of two {Micromonospora} strains isolated from the root nodules of {Alnus} glutinosa}, + url = {https://journals.asm.org/doi/full/10.1128/mra.01131-23}, + urldate = {2024-11-17}, volume = {13}, year = {2024} } +@article{thompson_pollution_2025, + abstract = {Actinorhizal plants, such as Alnus glutinosa, play a critical role in ecosystem restoration, particularly in metal-contaminated soils, yet their nodule microbiome remains largely unexplored beyond Frankiaceae endosymbionts. This study presents the first comprehensive analysis of A. glutinosa root nodules under heavy metal stress, focusing on a 30-year-old chronosequence planted upon opencast coal mine spoil. Microbial diversity analysis revealed that A. glutinosa nodules harbour a distinct and conserved microbiome, dominated by Frankiaceae but also enriched with plant growth-promoting bacteria such as Bradyrhizobium, Mycobacterium, and Actinoplanes. Additionally, despite similar beta diversity between the nodules and soil, significant compositional differences were observed, reinforcing the selective nature of the nodules. However, functional profiling indicated that metabolic pathways were largely shared between nodule and soil microbiomes. Overall, this study provides new insights into the resilience and specialisation of the A. glutinosa nodule microbiome and its potential role in bioremediation within heavy metal-contaminated environments.}, + author = {Thompson, Ryan Michael and del Carmen Montero-Calasanz, Maria and George, David and Fox, Edward M.}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-07006-5}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Alnus, Environmental microbiology, Microbial communities, Microbial ecology, Microbiota, Root Nodules, Plant}, + language = {en}, + month = {July}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {23373}, + shorttitle = {From pollution to reforestation}, + title = {From pollution to reforestation: the hidden microbiome of {Alnus} glutinosa nodules over 30 years}, + url = {https://www.nature.com/articles/s41598-025-07006-5}, + urldate = {2025-07-12}, + volume = {15}, + year = {2025} +} + @article{thongbunrod_potential_2024, abstract = {Anaerobic lignocellulosic microbial consortia are known to be prodigiously efficient at converting lignocellulosic biomass to methane. In this study, the efficacy of anaerobic fungal consortia (AFC) from five different inocula, including Bubalus bubalis rumen fluid (RU), in degrading filter paper, microcrystalline cellulose, and rice straw (RS), was screened. The AFC from RU performed best in lignocellulosic material degradation and methane production; thus, RU was selected for further experiments. Consecutive batch subculturing (CBS) was performed in RU to enrich and stabilize the dominant and key microorganisms categorized as anaerobic fungi, using the addition of antibacterial agents to suppress the growth of untargeted bacteria. After the CBS, subculture E19 proved the most efficient, with RS degradation of 84\% and a methane yield of 310 mL/g VSadded, representing 1.83- and 2.25-fold increases compared to the initial seed, respectively. The microbial community of E19 consisted of anaerobic fungi (uncultured Neocallimastigales, Anaeromyces sp., Orpinomyces sp., and Feramyces sp.) coexisting with anaerobic bacteria (streptomycin resistant Proteiniphilum acetatigenes), and methanogens. The E19 consortium was able to use various carbon sources (87.5\%) and contained potential genes encoding enzymes involved in RS degradation. The microbial community of E19 was highly stable, making it a promising inoculum for biomass degradation, especially for anaerobic digestion to produce biogas.}, author = {Thongbunrod, Nitiya and Chaiprasert, Pawinee}, @@ -14156,6 +22975,38 @@ @article{tiwari_innate_2024 year = {2024} } +@article{tomasello_erga-bge_2025, + abstract = {The +Xanthium orientale +subsp. +italicum +(Asterales: Asteraceae: Asteroideae) reference genome offers a valuable resource for understanding the genetic basis of invasiveness and fitness differences among congeneric species. The entirety of the genome sequence was assembled into 18 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 2.26 Gb, composed of 46 contigs and 32 scaffolds, with contig and scaffold N50 values of 98.8 Mb and 124 Mb, respectively.}, + author = {Tomasello, Salvatore and Manzo, Eleonora and Monteiro, Rita and Böhne, Astrid and Marcussen, Thomas and Struck, Torsten H and Oomen, Rebekah A and {Genoscope Sequencing Team} and Moussy, Alice and Cruaud, Corinne and Labadie, Karine and Demirdjian, Lola and N’dar, Adama and Wincker, Patrick and Oliveira, Pedro H and Aury, Jean-Marc and Barrera Enriquez, Vianey Paola and Haggerty, Leanne and Martin, Fergal and Brown, Tom}, + doi = {10.12688/openreseurope.21891.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {November}, + pages = {367}, + title = {{ERGA}-{BGE} genome of {Xanthium} orientale subsp. italicum ({Moretti}) {Greuter}. {A} plant of {American} origin, now widespread and, in some cases, invasive in {Europe}}, + url = {https://open-research-europe.ec.europa.eu/articles/5-367/v1}, + urldate = {2025-11-30}, + volume = {5}, + year = {2025} +} + +@patent{toni_truly_2019, + address = {EP}, + author = {Toni, Cathomen and Alexandra, Haas Simone and Markus, Hildenbeutel and Claudio, Mussolino and Melanie, Börries and Geoffroy, Andrieux}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {October}, + number = {EP 3812472 B1}, + title = {A {Truly} {Unbiased} {In} {Vitro} {Assay} {To} {Profile} {Off}-target {Activity} {Of} {One} {Or} {More} {Target}-specific {Programmable} {Nucleases} {In} {Cells} (abnoba-seq)}, + url = {https://lens.org/083-085-839-746-016}, + year = {2019} +} + @article{torres-paz_maternally_2019, abstract = {Sequential developmental events, starting from the moment of fertilization, are crucial for the acquisition of animal body plan. Subtle modifications in such early events are likely to have major impacts in later morphogenesis, bringing along morphological diversification. Here, comparing the blind cave and the surface morphotypes of Astyanax mexicanus fish, we found heterochronies during gastrulation that produce organizer and axial mesoderm tissues with different properties (including differences in the expression of dkk1b) that may have contributed to cavefish brain evolution. These variations observed during gastrulation depend fully on maternal factors. The developmental evolution of retinal morphogenesis and hypothalamic patterning are among those traits that retained significant maternal influence at larval stages. Transcriptomic analysis of fertilized eggs from both morphotypes and reciprocal F1 hybrids showed a strong and specific maternal signature. Our work strongly suggests that maternal effect genes and developmental heterochronies that occur during gastrulation have impacted morphological brain change during cavefish evolution.}, author = {Torres-Paz, Jorge and Leclercq, Julien and Rétaux, Sylvie}, @@ -14163,7 +23014,8 @@ @article{torres-paz_maternally_2019 editor = {Bronner, Marianne E and Podrabsky, Jason E}, issn = {2050-084X}, journal = {eLife}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Astyanax mexicanus, developmental evolution, dkk1b, heterocrhony, maternal transcriptome, prechordal plate}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Astyanax mexicanus, Biological Evolution, developmental evolution, dkk1b, heterocrhony, maternal transcriptome, prechordal plate}, + language = {eng}, month = {October}, pages = {e50160}, title = {Maternally regulated gastrulation as a source of variation contributing to cavefish forebrain evolution}, @@ -14173,12 +23025,34 @@ @article{torres-paz_maternally_2019 year = {2019} } +@article{torres-tiji_bioinformatic_2024, + abstract = {Algae biotechnology holds immense promise for revolutionizing the bioeconomy through the sustainable and scalable production of various bioproducts. However, their development has been hindered by the lack of advanced genetic tools. This study introduces a synthetic biology approach to develop such tools, focusing on the construction and testing of synthetic promoters. By analyzing conserved DNA motifs within the promoter regions of highly expressed genes across six different algal species, we identified cis-regulatory elements (CREs) associated with high transcriptional activity. Combining the algorithms POWRS, STREME, and PhyloGibbs, we predicted 1511 CREs and inserted them into a minimal synthetic promoter sequence in 1, 2, or 3 copies, resulting in 4533 distinct synthetic promoters. These promoters were evaluated in vivo for their capacity to drive the expression of a transgene in a high-throughput manner through next-generation sequencing post antibiotic selection and fluorescence-activated cell sorting. To validate our approach, we sequenced hundreds of transgenic lines showing high levels of GFP expression. Further, we individually tested 14 identified promoters, revealing substantial increases in GFP expression─up to nine times higher than the baseline synthetic promoter, with five matching or even surpassing the performance of the native AR1 promoter. As a result of this study, we identified a catalog of CREs that can now be used to build superior synthetic algal promoters. More importantly, here we present a validated pipeline to generate building blocks for innovative synthetic genetic tools applicable to any algal species with a sequenced genome and transcriptome data set.}, + author = {Torres-Tiji, Y and Sethuram, H and Gupta, A and McCauley, J and Dutra-Molino, J-V and Pathania, R and Saxton, L and Kang, K and Hillson, NJ and Mayfield, SP}, + doi = {10.1021/acssynbio.4c00199}, + issn = {2161-5063}, + journal = {ACS Synth Biol}, + keywords = {{\textgreater}UseGalaxy.eu, Computational Biology, Promoter Regions, Genetic, Synthetic Biology}, + language = {eng}, + month = {July}, + number = {7}, + pages = {2150--2165}, + title = {Bioinformatic {Prediction} and {High} {Throughput} {In} {Vivo} {Screening} to {Identify} {Cis}-{Regulatory} {Elements} for the {Development} of {Algal} {Synthetic} {Promoters}}, + url = {http://europepmc.org/abstract/MED/38986010}, + volume = {13}, + year = {2024} +} + @article{tosar_ri-sec-seq_2021, + abstract = {Exosomes and other extracellular vesicles (EVs) are considered the main vehicles transporting RNAs in extracellular samples, including human bodily fluids. However, a major proportion of extracellular RNAs (exRNAs) do not copurify with EVs and remain in ultracentrifugation supernatants of cell-conditioned medium or blood serum. We have observed that nonvesicular exRNA profiles are highly biased toward those RNAs with intrinsic resistance to extracellular ribonucleases. These highly resistant exRNAs are interesting from a biomarker point of view, but are not representative of the actual bulk of RNAs released to the extracellular space. In order to understand exRNA dynamics and capture both stable and unstable RNAs, we developed a method based on size-exclusion chromatography (SEC) fractionation of RNase inhibitor (RI)-treated cell-conditioned medium (RI-SEC-seq). This method has allowed us to identify and study extracellular ribosomes and tRNAs, and offers a dynamical view of the extracellular RNAome which can impact biomarker discovery in the near future. \textbf{Graphical abstract:} \textbf{Overview of the RI-SEC-seq protocol: sequencing of size-exclusion chromatography fractions from nonvesicular extracellular samples treated or not with RNase inhibitors (+/- RI)}.}, author = {Tosar, Juan and Gámbaro, Fabiana and Castellano, Mauricio and Cayota, Alfonso}, doi = {10.21769/bioprotoc.3918}, + issn = {2331-8325}, + journal = {Bio-protocol}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, note = {Publisher: Bio-Protocol, LLC}, number = {4}, + pages = {e3918}, title = {{RI}-{SEC}-seq: {Comprehensive} {Profiling} of {Nonvesicular} {Extracellular} {RNAs} with {Different} {Stabilities}}, url = {https://doi.org/10.21769/bioprotoc.3918}, volume = {11}, @@ -14227,6 +23101,22 @@ @article{toth_genomic_2024 year = {2024} } +@article{tran_bacteriophage_2025, + abstract = {Bacteriophage (phage) therapy is a promising means to combat drug-resistant bacterial pathogens. Infection by phage can select for mutations in bacterial populations that confer resistance against phage infection. However, resistance against phage can yield evolutionary trade-offs of biomedical relevance. Here, we report the discovery that infection by certain staphylococcal phages sensitizes different strains of methicillin-resistant \textit{Staphylococcus aureus} (MRSA) to β-lactams, a class of antibiotics against which MRSA is typically resistant. MRSA cells that survive infection by these phages display significant reductions in minimal inhibitory concentration against different β-lactams compared to uninfected bacteria. Transcriptomic profiling reveals that these evolved MRSA strains possess highly modulated transcriptional profiles, where numerous genes involved in \textit{S. aureus} virulence are downregulated. Phage-treated MRSA exhibited attenuated virulence phenotypes in the form of reduced hemolysis and clumping. Despite sharing similar phenotypes, whole-sequencing analysis revealed that the different MRSA strains evolved unique genetic profiles during infection. These results suggest complex evolutionary trajectories in MRSA during phage predation and open up new possibilities to reduce drug resistance and virulence in MRSA infections.}, + author = {Tran, My and Hernandez Viera, Angel J and Tran, Patricia Q and Nilsen, Erick D and Tran, Lily and Mo, Charlie Y}, + doi = {10.7554/elife.102743}, + issn = {2050-084X}, + journal = {eLife}, + keywords = {{\textgreater}UseGalaxy.eu, Anti-Bacterial Agents, Methicillin-Resistant Staphylococcus aureus, Staphylococcus Phages, beta-Lactam Resistance, beta-Lactams}, + language = {eng}, + month = {July}, + pages = {RP102743}, + title = {Bacteriophage infection drives loss of β-lactam resistance in methicillin-resistant \textit{{Staphylococcus} aureus}}, + url = {http://europepmc.org/abstract/MED/40637714}, + volume = {13}, + year = {2025} +} + @article{tregear_micro-rna-regulated_2022, abstract = {Sexual differentiation of inflorescences and flowers is important for reproduction and affects crop plant productivity. We report here on a molecular study of the process of sexual differentiation in the immature inflorescence of oil palm (Elaeis guineensis). This species is monoecious and exhibits gender diphasy, producing male and female inflorescences separately on the same plant in alternation. Three main approaches were used: small RNA-seq to characterise and study the expression of miRNA genes; RNA-seq to monitor mRNA accumulation patterns; hormone quantification to assess the role of cytokinins and auxins in inflorescence differentiation. Our study allowed the characterisation of 30 previously unreported palm MIRNA genes. In differential gene and miRNA expression studies, we identified a number of key developmental genes and miRNA-mRNA target modules previously described in relation to their developmental regulatory role in the cereal panicle, notably the miR156/529/535-SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) gene regulatory module. Gene enrichment analysis highlighted the importance of hormone-related genes, and this observation was corroborated by the detection of much higher levels of cytokinins in the female inflorescence. Our data illustrate the importance of branching regulation within the developmental window studied, during which the female inflorescence, unlike its male counterpart, produces flower clusters on new successive axes by sympodial growth.}, author = {Tregear, James W. and Richaud, Frédérique and Collin, Myriam and Esbelin, Jennifer and Parrinello, Hugues and Cochard, Benoît and Nodichao, Leifi and Morcillo, Fabienne and Adam, Hélène and Jouannic, Stefan}, @@ -14241,6 +23131,7 @@ @article{tregear_micro-rna-regulated_2022 pmcid = {PMC8912876}, pmid = {35270155}, title = {Micro-{RNA}-{Regulated} {SQUAMOSA}-{PROMOTER} {BINDING} {PROTEIN}-{LIKE} ({SPL}) {Gene} {Expression} and {Cytokinin} {Accumulation} {Distinguish} {Early}-{Developing} {Male} and {Female} {Inflorescences} in {Oil} {Palm} ({Elaeis} guineensis)}, + url = {http://europepmc.org/abstract/MED/35270155}, volume = {11}, year = {2022} } @@ -14265,6 +23156,44 @@ @article{trifonova_combination_2023 year = {2023} } +@article{trifonova_expansion_2025, + abstract = {Lessons from the COVID-19 outbreak suggest a highly variable individual clinical course of infection and unpredictable outcomes among infected individuals. In this retrospective study, we examined the intra-host viral evolution in an immunocompromised patient with B-cell lymphoma, severe COVID-19, and a two-stage, long-lasting in-hospital period with lethal outcome. The whole-genome sequencing profile demonstrated a dynamic accumulation of new viral mutations in the entire viral genome, mainly in S1-RBD and Nsp12, against the background of antiviral treatment and convalescent plasma transfusion. Long range-PCR and nanopore sequencing of ACE2, TLR7, TLR8, TLR4, DDX58, and IFIH1 genes revealed single nucleotide substitutions in the ACE2, TLR4, DDX58, IFIH1, and TLR7 receptors, negatively affecting the disease course from the onset. Our results demonstrate that genetic variations in host innate immunity and impaired adaptive immunity facilitate the accumulation of viral mutations that overcome antiviral treatment and passive antibody transfer, affecting the course of SARS-CoV-2 infection.}, + author = {Trifonova, Angelina and Yosifova, Adelina and Syarov, Atanas and Velichkov, Andrey and Pasev, Martin and Takov, Svetlomir and Madarzhieva, Kalina and Angelov, Krassimir and Vazharova, Radoslava and Terzieva, Velislava}, + doi = {10.1016/j.clicom.2025.02.001}, + issn = {2772-6134}, + journal = {Clinical Immunology Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Immunocompromised patient, Sars-cov-2, Toll-like receptors, Viral mutations, Virus-host interactions}, + month = {June}, + pages = {47--54}, + shorttitle = {Expansion of {SARS}-{CoV}-2 mutations in patient with {B}-cell lymphoma and rare combination of {ACE2}, {TLR4}, {DDX58} and {IFIH1} variations}, + title = {Expansion of {SARS}-{CoV}-2 mutations in patient with {B}-cell lymphoma and rare combination of {ACE2}, {TLR4}, {DDX58} and {IFIH1} variations: {A} retrospective analysis of the virus-host interplay}, + url = {https://www.sciencedirect.com/science/article/pii/S2772613425000034}, + urldate = {2025-03-09}, + volume = {7}, + year = {2025} +} + +@article{triggiano_clinical_2025, + abstract = {Chryseobacterium spp. are Gram-negative, opportunistic pathogens antibiotic-resistant commonly found in the environment. The aim of this study was to investigate potential sources of Chryseobacterium infections in healthcare settings by comparing clinical and environmental isolates using phenotypic and genotypic analyses. Between June and July 2023, six cases of infection with Chryseobacterium spp. were identified in a hospital in Apulia, southern Italy. Environmental sampling (air, surfaces and water) was performed in parallel with routine clinical investigations. Isolates were subjected to antibiotic susceptibility testing and genotypic analysis using Sanger and Next-Generation Sequencing. Five cases of Chryseobacterium spp. infection were recorded in the Gastroenterology Department (Pavilion A) and one in the Vertebral Surgery Department (Pavilion B). C. indologenes was identified in blood and tracheal aspirate samples using MALDI-TOF MS. Environmental analysis carried out in the pavilions A and B isolated C. indologenes from sink tap in Pavilion B. Subsequently, genome sequencing revealed that Chryseobacterium strains misidentified as C. indologenes were more closely related to C. arthrosphaerae. Genetic analysis confirmed the cluster hypothesis involving four patients from the pavilion A, while no genetic link was found between the environmental and clinical strains. Innovative molecular methods in clinical and environmental investigations have allowed more accurate identification of the etiologic agent and possibly tracing the source of infection in the nosocomial setting. Control measures, such as patient isolation and room disinfection, have prevented the spread of infection.}, + author = {Triggiano, Francesco and Caggiano, Giuseppina and Capozzi, Loredana and Castellana, Stefano and Diella, Giusy and Furio, Alessandro and Cantalice, Michele Alberto and Manicone, Anna Lucia and Savino, Antonella Francesca and Mosca, Adriana and De Carlo, Carmela and Sparapano, Eleonora and Dalfino, Lidia and Saracino, Annalisa and Di Gennaro, Francesco and Principi, Maria Beatrice and Parisi, Antonio and Montagna, Maria Teresa and Tafuri, Silvio and De Giglio, Osvalda}, + copyright = {cc by-nc-nd}, + doi = {10.1038/s41598-025-24632-1}, + issn = {2045-2322}, + journal = {Scientific reports}, + keywords = {{\textgreater}UseGalaxy.eu, C. Indologenes, Chryseobacterium Spp., Environmental Surveillance, Genome sequencing, Hospital Infections, bacteremia}, + language = {eng}, + month = {November}, + number = {1}, + pages = {39814}, + pmcid = {PMC12615676}, + pmid = {41233552}, + title = {Clinical and environmental investigation of six cases of {Chryseobacterium} arthrosphaerae infections in a {Southern} {Italian} hospital}, + url = {https://europepmc.org/articles/PMC12615676}, + urldate = {2025-12-26}, + volume = {15}, + year = {2025} +} + @article{trinh-minh_effect_2024, abstract = {Objective.S100A4 is a DAMP protein. S100A4 is overexpressed in patients with systemic sclerosis (SSc), andlevels correlate with organ involvement and disease activity. S100A4−/−mice are protected fromfibrosis. The aim ofthis study was to assess the antifibrotic effects of anti-S100A4 monoclonal antibody (mAb) in murine models of SScand in precision cut skin slices of patients with SSc.Methods.The effects of anti-S100A4 mAbs were evaluated in a bleomycin-induced skinfibrosis model and inTsk-1 mice with a therapeutic dosing regimen. In addition, the effects of anti-S100A4 mAbs on precision cut SSc skinslices were analyzed by RNA sequencing.Results.Inhibition of S100A4 was effective in the treatment of pre-established bleomycin-induced skinfibrosis andin regression of pre-establishedfibrosis with reduced dermal thickening, myofibroblast counts, and collagen accumu-lation. Transcriptional profiling demonstrated targeting of multiple profibrotic and proinflammatory processes relevantto the pathogenesis of SSc on targeted S100A4 inhibition in a bleomycin-induced skinfibrosis model. Moreover, tar-geted S100A4 inhibition also modulated inflammation- andfibrosis-relevant gene sets in precision cut SSc skin slicesin an ex vivo trial approach. Selected downstream targets of S100A4, such as AMP-activated protein kinase,calsequestrin-1, and phosphorylated STAT3, were validated on the protein level, and STAT3 inhibition was shown toprevent the profibrotic effects of S100A4 onfibroblasts in human skin.Conclusion.Inhibition of S100A4 confers dual targeting of inflammatory andfibrotic pathways in complementarymouse models offibrosis and in SSc skin. These effects support the further development of anti-S100A4 mAbs asdisease-modifying targeted therapies for SSc.}, author = {Trinh-Minh, Thuong and Györfi, Andrea Hermina and Tomcik, Michal and Tran-Manh, Cuong and Zhou, Xiang and Dickel, Nicholas and Tümerdem, Bilgesu Safak and Kreuter, Alexander and Burmann, Sven Niklas and Borchert, Signe Vedel and Hussain, Rizwan Iqbal and Hallén, Jonas and Klingelhöfer, Jörg and Kunz, Meik and Distler, Jörg H.W.}, @@ -14280,6 +23209,40 @@ @article{trinh-minh_effect_2024 year = {2024} } +@article{trouillon_determination_2021, + abstract = {Pseudomonas aeruginosa possesses one of the most complex bacterial regulatory networks, which largely contributes to its success as a pathogen. However, most of its transcription factors (TFs) are still uncharacterized and the potential intra-species variability in regulatory networks has been mostly ignored so far. Here, we used DAP-seq to map the genome-wide binding sites of all 55 DNA-binding two-component systems (TCSs) response regulators (RRs) across the three major P. aeruginosa lineages. The resulting networks encompass about 40\% of all genes in each strain and contain numerous new regulatory interactions across most major physiological processes. Strikingly, about half of the detected targets are specific to only one or two strains, revealing a previously unknown large functional diversity of TFs within a single species. Three main mechanisms were found to drive this diversity, including differences in accessory genome content, as exemplified by the strain-specific plasmid in IHMA87 outlier strain which harbors numerous binding sites of conserved chromosomally-encoded RRs. Additionally, most RRs display potential auto-regulation or RR-RR cross-regulation, bringing to light the vast complexity of this network. Overall, we provide the first complete delineation of the TCSs regulatory network in P. aeruginosa that will represent an important resource for future studies on this pathogen.}, + author = {Trouillon, Julian and Imbert, Lionel and Villard, Anne-Marie and Vernet, Thierry and Attrée, Ina and Elsen, Sylvie}, + doi = {10.1093/nar/gkab928}, + issn = {0305-1048}, + journal = {Nucleic Acids Res}, + keywords = {{\textgreater}UseGalaxy.eu, Gene Regulatory Networks}, + language = {eng}, + month = {November}, + number = {20}, + pages = {11476--11490}, + title = {Determination of the two-component systems regulatory network reveals core and accessory regulations across {Pseudomonas} aeruginosa lineages}, + url = {http://europepmc.org/abstract/MED/34718721}, + volume = {49}, + year = {2021} +} + +@article{trouillon_transcription_2021, + abstract = {Transcription factors (TFs) are instrumental in the bacterial response to new environmental conditions. They can act as direct signal sensors and subsequently induce changes in gene expression leading to physiological adaptation. Here, by combining transcriptome sequencing (RNA-seq) and cistrome determination (DAP-seq), we studied a family of eight TFs in \textit{Pseudomonas aeruginosa} This family, encompassing TFs with XRE-like DNA-binding and cupin signal-sensing domains, includes the metabolic regulators ErfA, PsdR, and PauR and five so-far-unstudied TFs. The genome-wide delineation of their regulons identified 39 regulatory interactions with genes mostly involved in metabolism. We found that the XRE-cupin TFs are inhibitors of their neighboring genes, forming local, functional units encoding proteins with functions in condition-specific metabolic pathways. Growth phenotypes of isogenic mutants highlighted new roles for PauR and PA0535 in polyamines and arginine metabolism. The phylogenetic analysis of this family of regulators across the bacterial kingdom revealed a wide diversity of such metabolic regulatory modules and identified species with potentially higher metabolic versatility. Numerous genes encoding uncharacterized XRE-cupin TFs were found near metabolism-related genes, illustrating the need of further systematic characterization of transcriptional regulatory networks in order to better understand the mechanisms of bacterial adaptation to new environments.\textbf{IMPORTANCE} Bacteria of the \textit{Pseudomonas} genus, including the major human pathogen \textit{Pseudomonas aeruginosa}, are known for their complex regulatory networks and high number of transcription factors, which contribute to their impressive adaptive ability. However, even in the most studied species, most of the regulators are still uncharacterized. With the recent advances in high-throughput sequencing methods, it is now possible to fill this knowledge gap and help the understanding of how bacteria adapt and thrive in new environments. By leveraging these methods, we provide an example of a comprehensive analysis of an entire family of transcription factors and bring new insights into metabolic and regulatory adaptation in the \textit{Pseudomonas} genus.}, + author = {Trouillon, Julian and Ragno, Michel and Simon, Victor and Attrée, Ina and Elsen, Sylvie}, + doi = {10.1128/msystems.00753-20}, + issn = {2379-5077}, + journal = {mSystems}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {January}, + number = {1}, + pages = {e00753--20}, + title = {Transcription {Inhibitors} with {XRE} {DNA}-{Binding} and {Cupin} {Signal}-{Sensing} {Domains} {Drive} {Metabolic} {Diversification} in {Pseudomonas}}, + url = {http://europepmc.org/abstract/MED/33436508}, + volume = {6}, + year = {2021} +} + @article{tsai_biogenesis_2022, author = {Tsai, Hsin-Yue and Cheng, Hsian-Tang and Tsai, Yi-Ting}, doi = {10.1126/sciadv.abm0699}, @@ -14296,10 +23259,35 @@ @article{tsai_biogenesis_2022 year = {2022} } +@article{tsangaras_crossing_2025, + abstract = {Wallace’s line is a biogeographical barrier to faunal movements between Southeast Asia and the Australo-Papuan region. There are exceptions among rodents and bats, few of which have crossed Wallace’s line. The gibbon ape leukemia viruses (GALV) and koala retrovirus (KoRV) have only been identified in wildlife on the Australo-Papuan side of Wallaces’s Line with the potential exception of partial sequences identified in two microbat fecal samples from China and a recently described GALV relative in a rodent from Africa. Here we describe a group of GALV-like endogenous retroviral sequences from the Southeast Asian flying lemur (Cynocephalus volans) representing the first known description of a primate relative which has been infected, and the germline colonized, by GALVs on the Southeast Asian side of Wallace’s Line.}, + author = {Tsangaras, Kyriakos and Mayer, Jens and Greenwood, Alex D.}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-94582-1}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Endogenous Retroviruses, Evolution, Genomics, Leukemia Virus, Gibbon Ape}, + language = {en}, + month = {March}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {9790}, + shorttitle = {Crossing {Wallace}’s line}, + title = {Crossing {Wallace}’s line: an evolutionarily young gibbon ape leukemia virus like endogenous retrovirus identified from the {Philippine} flying lemur ({Cynocephalus} volans)}, + url = {https://www.nature.com/articles/s41598-025-94582-1}, + urldate = {2025-03-23}, + volume = {15}, + year = {2025} +} + @article{tu_molecular_2021, + abstract = {Bacterial endospores (spores) are among the most resistant living forms on earth. Spores of \textit{Bacillus subtilis} A163 show extremely high resistance to wet heat compared to spores of laboratory strains. In this study, we found that spores of \textit{B. subtilis} A163 were indeed very wet heat resistant and released dipicolinic acid (DPA) very slowly during heat treatment. We also determined the proteome of vegetative cells and spores of \textit{B. subtilis} A163 and the differences in these proteomes from those of the laboratory strain PY79, spores of which are much less heat resistant. This proteomic characterization identified 2011 proteins in spores and 1901 proteins in vegetative cells of \textit{B. subtilis} A163. Surprisingly, spore morphogenic protein SpoVM had no homologs in \textit{B. subtilis} A163. Comparing protein expression between these two strains uncovered 108 proteins that were differentially present in spores and 93 proteins differentially present in cells. In addition, five of the seven proteins on an operon in strain A163, which is thought to be primarily responsible for this strain's spores high heat resistance, were also identified. These findings reveal proteomic differences of the two strains exhibiting different resistance to heat and form a basis for further mechanistic analysis of the high heat resistance of \textit{B. subtilis} A163 spores.}, author = {Tu, Zhiwei and Setlow, Peter and Brul, Stanley and Kramer, Gertjan}, doi = {10.3390/microorganisms9030667}, + issn = {2076-2607}, + journal = {Microorganisms}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {March}, note = {Publisher: MDPI AG}, number = {3}, @@ -14310,6 +23298,26 @@ @article{tu_molecular_2021 year = {2021} } +@article{ueira-vieira_deep_2025, + abstract = {Characterizing the complex web of ecological interactions is a central challenge in molecular ecology. Shotgun metagenomics of environmental samples offers a powerful, high-resolution approach, yet its potential for simultaneously generating multiple genomic resources from different trophic levels remains underexplored. This study serves as a proof-of-concept, using deep sequencing of a single, complex sample—the larval food of the stingless bee Tetragonisca angustula—to demonstrate the method's capacity to recover genomic information across varying template abundances. We successfully assembled three genomes of different completeness levels: a near-complete bacterial genome (Acetilactobacillus jinshanensis, 2,097,977 bp with 0.002\% ambiguous bases), a draft mitochondrial genome (T. angustula, 15,498–15,549 bp), and a fragmented chloroplast genome (Lactuca sativa, 130,532 bp with 23.47\% ambiguous bases). The assembly quality gradient, observed from complete to fragmented, directly reflects the relative abundance of each DNA template in the environmental sample, demonstrating the method's sensitivity and ecological informativeness. Beyond these genomic resources, the data provided a comprehensive biodiversity profile, revealing DNA from seven major taxonomic groups, including 209 bacterial genera, 123 plant families, and 55 insect taxa. Additionally, genomic comparisons using Average Nucleotide Identity (ANI) and digital DNA–DNA Hybridization (dDDH) analyses suggest that the dominant bacterial strain represents a putative novel species within the genus Acetilactobacillus. This approach simultaneously provided insights into host genetics, food sources, and microbial communities, illustrating the potential of single metagenomic datasets to generate multiple valuable genomic resources for molecular ecology research.}, + author = {Ueira-Vieira, Carlos and Santos, Ana Carolina Costa and Araújo, Thayane Nogueira and Augusto, Solange Cristina and de Avila, Natanael Borges and Bonetti, Ana Maria and dos Santos, Anderson Rodrigues}, + copyright = {© 2025 The Author(s). Ecology and Evolution published by British Ecological Society and John Wiley \& Sons Ltd.}, + doi = {10.1002/ece3.72546}, + issn = {2045-7758}, + journal = {Ecology and Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, NGS, genome assembly, genomic resources, pollinator, proof-of-concept, stingless bee}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.72546}, + number = {12}, + pages = {e72546}, + shorttitle = {A {Deep} {Metagenomic} {Snapshot} as a {Proof}-of-{Concept} for {Resource} {Generation}}, + title = {A {Deep} {Metagenomic} {Snapshot} as a {Proof}-of-{Concept} for {Resource} {Generation}: {Simultaneous} {Assembly} of {Host}, {Food}, and {Microbiome} {Genomes} {From} {Stingless} {Bee} {Larval} {Food}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.72546}, + urldate = {2025-12-26}, + volume = {15}, + year = {2025} +} + @article{uellendahl-werth_benchmark_2020, abstract = {RNA-Sequencing (RNA-Seq) of peripheral blood can be a valuable source of information for investigating the status and mechanism of diseases. However, blood contains 50–80\% unwanted hemoglobin (Hb) transcripts. Lexogen’s QuantSeq mRNA-Seq-Kit for Illumina RNA-Seq features a ‘Globin Block’ (GB) module that depletes Hb cDNAs during library preparation. Here, we aimed to assess GB’s effectiveness and checked for technical biases attributable to GB. Using whole blood total RNA samples of 91 healthy individuals, we sequenced 91 pairs of GB and non-blocked samples (noGB) on Illumina HiSeq2500 and 8 pairs of GB/noGB technical replicates on HiSeq4000. GB reduced the fraction of Hb transcripts from 43\% (s.d. 14\%) to 8.0\% (s.d. 4.3\%). From GB samples we detected 1,397 more expressed genes at approximately 11 million reads per RNA-isolate. Enrichment and differential expression analyses did not reveal significant differences for GB and noGB samples with respect to molecular function. In contrast to results from studies that have examined the performance of GB during RNA isolation, we were able to assign GB to corresponding noGB samples (from multiple sequencing runs on HiSeq2500) with at least 89.8\% accuracy from the complete correlation matrix of all GB/GB, noGB/noGB and GB/noGB pairs. However, the use of different sequencers (HiSeq2500 vs HiSeq4000) impaired assignment of technical replicates, whereas assignment of GB to corresponding noGB samples worked perfectly when sequencing on one lane on HiSeq4000. Lexogen’s GB RNA-Seq module is a valuable addition during mRNA-Seq library preparation which works even with low amounts of input total RNA (50 ng per sample). GB facilitated the detection of low abundant transcripts and yielded more non-hemoglobin reads, while preserving biological information. We observed that differences in sequencing run and platform have a far greater effect on technical variation than the use of GB.}, author = {Uellendahl-Werth, Florian and Wolfien, Markus and Franke, Andre and Wolkenhauer, Olaf and Ellinghaus, David}, @@ -14331,6 +23339,44 @@ @article{uellendahl-werth_benchmark_2020 year = {2020} } +@article{uhl_improving_2020, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Current peak callers for identifying RNA-binding protein (RBP) binding sites from CLIP-seq data take into account genomic read profiles, but they ignore the underlying transcript information, that is information regarding splicing events. So far, there are no studies available that closer observe this issue.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}Here we show that current peak callers are susceptible to false peak calling near exon borders. We quantify its extent in publicly available datasets, which turns out to be substantial. By providing a tool called CLIPcontext for automatic transcript and genomic context sequence extraction, we further demonstrate that context choice affects the performances of RBP binding site prediction tools. Moreover, we show that known motifs of exon-binding RBPs are often enriched in transcript context sites, which should enable the recovery of more authentic binding sites. Finally, we discuss possible strategies on how to integrate transcript information into future workflows.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}Our results demonstrate the importance of incorporating transcript information in CLIP-seq data analysis. Taking advantage of the underlying transcript information should therefore become an integral part of future peak calling and downstream analysis tools.}, + author = {Uhl, Michael and Tran, Van Dinh and Backofen, Rolf}, + doi = {10.1186/s12864-020-07297-0}, + issn = {1471-2164}, + journal = {BMC genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Chromatin Immunoprecipitation Sequencing, Data Analysis}, + language = {eng}, + month = {December}, + number = {1}, + pages = {894}, + title = {Improving {CLIP}-seq data analysis by incorporating transcript information}, + url = {http://europepmc.org/abstract/MED/33334306}, + volume = {21}, + year = {2020} +} + +@article{uluar_mitogenomics_2025, + abstract = {Advances in DNA sequencing technologies have made comparative mitogenome studies available. However, studies on intraspecific mitogenome variation are still rare. This study reports total mitogenome of Psorodonotus ebneri Brunner von Wattenwyl, 1861 (Orthoptera: Tettigoniidae), highlighting selection profile and intraspecific and interspecific divergence in protein-coding genes (PCGs). To this end, two datasets were analysed, one including five P. ebneri mitogenomes and the other additionally possessing a mitogenome of P. venosus (Fischer von Waldheim, 1839). Results showed that the mitogenome of P. ebneri consists of 37 genes and an AT-rich region, ordering as in Pancrustacean, constituting 15645-15668 base pairs. Among 38 gene borders, eight had intergenic sequences (IGS) and seven overlapping (OR). All tRNAs exhibited the typical clover-leaf structure except for trnS1. Pairwise distance ranges between 0.001-0.003 among sequences of P. ebneri and {\textasciitilde}0.12 between P. ebneri and P. venosus. The dN/dS and neutrality index indicated purifying selection in PCGs. We arrived at the following conclusions: (i) P. ebneri mitogenomes show characteristics of Orthoptera and Pancrustacea, (ii) IGS and OR appear conserved in Tettigoniidae, (iii) low intraspecific variation is likely due to small population size, and (iv) most of the PCGs evolved under purifying selection suggesting no specific adaptation to montane habitats.}, + author = {Uluar, Onur and Yartaş, Mustafa and Yahyaoğlu, Özgül and Çıplak, Battal}, + doi = {10.15671/hjbc.1661824}, + issn = {2687-475X, 2687-475X}, + journal = {Hacettepe Journal of Biology and Chemistry}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {July}, + note = {Number: 3 +Publisher: Hacettepe University}, + number = {3}, + pages = {81--96}, + shorttitle = {Mitogenomics of {Psorodonotus} ebneri {Brunner} von {Wattenwyl}, 1861 ({Orthoptera}}, + title = {Mitogenomics of {Psorodonotus} ebneri {Brunner} von {Wattenwyl}, 1861 ({Orthoptera}: {Tettigoniidae}): {Selection} profile and patterns of intraspecific and interspecific divergence}, + url = {https://dergipark.org.tr/en/pub/hjbc/issue/92227/1661824}, + urldate = {2025-07-12}, + volume = {53}, + year = {2025} +} + @phdthesis{ummethum_proximity_2024, author = {Ummethum, Henning}, keywords = {{\textgreater}UseGalaxy.eu}, @@ -14345,10 +23391,13 @@ @phdthesis{ummethum_proximity_2024 } @article{umpeleva_identification_2024, + abstract = {Collecting data on rare \textit{Mycobacterium tuberculosis} (\textit{Mtb}) clinical isolates with resistance to the new anti-tuberculosis drug bedaquiline is an important task for improving antimicrobial susceptibility testing methods. Nanopore whole genome sequencing, the proportion method on Middlebrook 7H11 medium, and BACTEC MGIT 960 assays were used to analyze genotypic and phenotypic resistance to bedaquiline. We found four mutations: \textit{atpE} I66M, \textit{atpE} А63Р, \textit{Rv0678} А36Т, and \textit{Rv0678} S53P in five isolates with different levels of phenotypic bedaquiline resistance.{\textless}h4{\textgreater}Importance{\textless}/h4{\textgreater}Bedaquiline (BDQ) is a new anti-tuberculosis drug. The phenotypic and genotypic data describing the mechanism of drug resistance are critical for the design of rapid and accurate diagnostic tests. We consider that our work, which describes genotypic and phenotypic resistance to BDQ, can contribute to the standardization of drug susceptibility testing.}, author = {Umpeleva, Tatiana and Chetverikova, Elena and Belyaev, Danila and Eremeeva, Natalya and Boteva, Tatiana and Golubeva, Ludmila and Vakhrusheva, Diana and Vasilieva, Irina}, doi = {10.1128/spectrum.03749-23}, + issn = {2165-0497}, journal = {Microbiology Spectrum}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Diarylquinolines, Mycobacterium tuberculosis, Tuberculosis, Multidrug-Resistant}, + language = {eng}, month = {February}, note = {Publisher: American Society for Microbiology}, number = {3}, @@ -14397,6 +23446,23 @@ @article{urrutia-angulo_unravelling_2024 year = {2024} } +@article{uyar_flexynesis_2025, + abstract = {Accurate decision making in precision oncology depends on integration of multimodal molecular information, for which various deep learning methods have been developed. However, most deep learning-based bulk multi-omics integration methods lack transparency, modularity, deployability, and are limited to narrow tasks. To address these limitations, we introduce Flexynesis, which streamlines data processing, feature selection, hyperparameter tuning, and marker discovery. Users can choose from deep learning architectures or classical supervised machine learning methods with a standardized input interface for single/multi-task training and evaluation for regression, classification, and survival modeling. We showcase the tool's capability across diverse use-cases in precision oncology. To maximize accessibility, Flexynesis is available on PyPi, Guix, Bioconda, and the Galaxy Server ( https://usegalaxy.eu/ ). This toolset makes deep-learning based bulk multi-omics data integration in clinical/pre-clinical research more accessible to users with or without deep-learning experience. Flexynesis is available at https://github.com/BIMSBbioinfo/flexynesis .}, + author = {Uyar, Bora and Savchyn, Taras and Naghsh Nilchi, Amirhossein and Sarigun, Ahmet and Wurmus, Ricardo and Shaik, Mohammed Maqsood and Grüning, Björn and Franke, Vedran and Akalin, Altuna}, + doi = {10.1038/s41467-025-63688-5}, + issn = {2041-1723}, + journal = {Nature communications}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {September}, + number = {1}, + pages = {8261}, + title = {Flexynesis: {A} deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond}, + url = {http://europepmc.org/abstract/MED/40940333}, + volume = {16}, + year = {2025} +} + @article{valadez-moctezuma_first_2023, abstract = {Although Opuntia is one of the most emblematic and promising crops in Mexico, no extensive genomic resources are available. Herein, we present the first transcriptomic datasets of three species of Opuntia. Comparative transcriptome profiling provides insights into the molecular and physiological functions between species and tissues. Total RNA from young cladodes and developing fruits of O. ficus-indica, O. robusta and O. joconostle was purified and sequenced by Massive Analysis of cDNA Ends technology, an RNA-seq variant. A total of 8383, 7890, and 5300 transcripts and GC content of 40.1, 39.9 and 40.1\% were obtained for the de novo assembly of O. ficus-indica, O. robusta and O. joconostle, respectively. For annotations, about 22.2–23.7\% of transcripts had matches in the UniProtKB/Swiss-Prot database. Moreover, the enriched 21 COG categories, 282 KEGG pathways and 2793 GO terms revealed that the transcriptomes obtained included functionally diverse genes in Opuntia. Differentially expressed transcripts (DETs) between fruit and cladode resulted in the enrichment of 13 significant KEGG pathways and 80 GO terms, where some genes viz. FULL, CYP75B1, and CMB1 were upregulated in the fruits of the three species. Between species, the most enriched GOs fell into the category of “Cellular Components”, which would explain the morphological and physiological differences between the three species. Moreover, DETs comparisons between fruit types and between cladodes were also reported. Overall, the transcriptomic data generated in this study provide the initial resources to understand the biology of Opuntia, offering new insight to understand its morphology, systematic and adaptation.}, author = {Valadez-Moctezuma, Ernestina and Samah, Samir and Mascorro-Gallardo, J. Oscar and Marbán-Mendoza, Nahum and Aranda-Osorio, Gilberto and Flores-Girón, Emmanuel and Brito-Nájera, Guadalupe and Rodríguez de la O, José Luis}, @@ -14430,13 +23496,46 @@ @article{valadez-moctezuma_novo_2023 year = {2023} } +@article{valenti_first_2021, + abstract = {\textit{Ciborinia camelliae} is the causal agent of camellia flower blight (CFB). It is a hemibiotrophic pathogen, inoperculate Discomycete of the family Sclerotiniaceae. It shows host and organ specificity infecting only flowers of species belonging to the genus \textit{Camellia}, causing serious damage to the ornamental component of the plant. In this work, the first mitochondrial genome of \textit{Ciborinia camellia} is reported. The mitogenome was obtained by combining Illumina short read and Nanopore long read technology. To resolve repetitive elements, specific primers were designed and used for Sanger sequencing. The manually curated mitochondrial DNA (mtDNA) of the Italian strain DSM 112729 is a circular sequence of 114,660 bp, with 29.6\% of GC content. It contains two ribosomal RNA genes, 33 transfer RNAs, one RNase P gene, and 62 protein-coding genes. The latter include one gene coding for a ribosomal protein (\textit{rps3}) and the 14 typical proteins involved in the oxidative metabolism. Moreover, a partial mtDNA assembled from a contig list was obtained from the deposited genome assembly of a New Zealand strain of \textit{C. camelliae}. The present study contributes to understanding the mitogenome arrangement and the evolution of this phytopathogenic fungus in comparison to other Sclerotiniaceae species and confirms the usefulness of mitochondrial analysis to define phylogenetic positioning of this newly sequenced species.}, + author = {Valenti, Irene and Degradi, Luca and Kunova, Andrea and Cortesi, Paolo and Pasquali, Matias and Saracchi, Marco}, + doi = {10.3389/ffunb.2021.802511}, + issn = {2673-6128}, + journal = {Frontiers in fungal biology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {802511}, + title = {The {First} {Mitochondrial} {Genome} of {Ciborinia} camelliae and {Its} {Position} in the {Sclerotiniaceae} {Family}}, + url = {http://europepmc.org/abstract/MED/37744111}, + volume = {2}, + year = {2021} +} + +@article{valer_pi3k_2025, + abstract = {Heterotopic ossification (HO) occurs following mechanical trauma and burns, or congenitally in patients suffering from fibrodysplasia ossificans progressiva (FOP). Recently, we demonstrated that inhibitors of phosphatidylinositol 3-kinase alpha (PI3Kα) may be a useful therapy for patients undergoing HO. In this study, using the already marketed BYL719/Alpelisib/Piqray drug, we have further confirmed these results, detailed the underlying mechanisms of action, and optimized the timing of the administration of BYL719. We found that BYL719 effectively prevents HO even when administered up to 3–7 days after injury. We demonstrate in cell cultures and in a mouse model of HO that the major actions of BYL719 are on-target effects through the inhibition of PI3Kα, without directly affecting ACVR1 or FOP-inducing ACVR1R206H kinase activities. In vivo, we found that a lack of PI3Kα in progenitors at injury sites is sufficient to prevent HO. Moreover, time course assays in HO lesions demonstrate that BYL719 not only blocks osteochondroprogenitor specification but also reduces the inflammatory response. BYL719 inhibits the migration, proliferation, and expression of pro-inflammatory cytokines in monocytes and mast cells, suggesting that BYL719 hampers the hyper-inflammatory status of HO lesions. Altogether, these results highlight the potential of PI3Kα inhibition as a safe and effective therapeutic strategy for HO.}, + author = {Valer, José Antonio and Deber, Alexandre and Wits, Marius and Pimenta-Lope, Carolina and Goumans, Marie-José and Rosa, Jose Luis and Sánchez-Duffhues, Gonzalo and Ventura, Francesc}, + doi = {10.7554/eLife.91779}, + editor = {Tanaka, Sakae and Weigel, Detlef}, + issn = {2050-084X}, + journal = {eLife}, + keywords = {{\textgreater}UseGalaxy.eu, Class I Phosphatidylinositol 3-Kinases, Inflammation, Ossification, Heterotopic, Phosphoinositide-3 Kinase Inhibitors, fibrodysplasia ossificans progressiva, heterotopic bone, mesenchymal progenitors, rare diseases}, + month = {June}, + note = {Publisher: eLife Sciences Publications, Ltd}, + pages = {RP91779}, + title = {{PI3Kα} inhibition blocks osteochondroprogenitor specification and the hyper-inflammatory response to prevent heterotopic ossification}, + url = {https://doi.org/10.7554/eLife.91779}, + urldate = {2025-07-12}, + volume = {12}, + year = {2025} +} + @article{vallecillo-garcia_mesenchymal_2024, abstract = {The lymphatic system is formed during embryonic development by the commitment of specialized lymphatic endothelial cells (LECs) and their subsequent assembly in primary lymphatic vessels. Although lymphatic cells are in continuous contact with mesenchymal cells during development and in adult tissues, the role of mesenchymal cells in lymphatic vasculature development remains poorly characterized. Here, we show that a subpopulation of mesenchymal cells expressing the transcription factor Osr1 are in close association with migrating LECs and established lymphatic vessels in mice. Lineage tracing experiments revealed that Osr1+ cells precede LEC arrival during lymphatic vasculature assembly in the back of the embryo. Using Osr1-deficient embryos and functional in vitro assays, we show that Osr1 acts in a non-cell-autonomous manner controlling proliferation and early migration of LECs to peripheral tissues. Thereby, mesenchymal Osr1+ cells control, in a bimodal manner, the production of extracellular matrix scaffold components and signal ligands crucial for lymphatic vessel formation.}, author = {Vallecillo-García, Pedro and Kühnlein, Mira Nicola and Orgeur, Mickael and Hansmeier, Nils Rouven and Kotsaris, Georgios and Meisen, Zarah Gertrud and Timmermann, Bernd and Giesecke-Thiel, Claudia and Hägerling, René and Stricker, Sigmar}, doi = {10.1242/dev.202747}, issn = {0950-1991}, journal = {Development}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Endothelial Cells, Lymphangiogenesis, Lymphatic Vessels, Transcription Factors}, month = {September}, number = {17}, pages = {dev202747}, @@ -14447,6 +23546,20 @@ @article{vallecillo-garcia_mesenchymal_2024 year = {2024} } +@article{valouzi_virome_2025, + author = {Valouzi, Hajar and Dizadji, Akbar and Golnaraghi, Alireza and Salami, Seyed Alireza and Fontdevila Pareta, Nuria and Önder, Serkan and Selmi, Ilhem and Rollin, Johan and Berhal, Chadi and Tamisier, Lucie and Maclot, François and Wang, Long and Zhang, Rui and Bahlolzada, Habibullah and Lefeuvre, Pierre and Massart, Sébastien}, + issn = {1999-4915}, + journal = {Viruses}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {August}, + number = {8}, + title = {A {Virome} {Scanning} of {Saffron} ({Crocus} sativus {L}.) at the {National} {Scale} in {Iran} {Using} {High}-{Throughput} {Sequencing} {Technologies}}, + url = {http://europepmc.org/abstract/PMC/PMC12390696}, + volume = {17}, + year = {2025} +} + @article{valsecchi_rna_2021, abstract = {Confinement of the X chromosome to a territory for dosage compensation is a prime example of how subnuclear compartmentalization is used to regulate transcription at the megabase scale. In Drosophila melanogaster, two sex-specific non-coding RNAs (roX1 and roX2) are transcribed from the X chromosome. They associate with the male-specific lethal (MSL) complex1, which acetylates histone H4 lysine 16 and thereby induces an approximately twofold increase in expression of male X-linked genes2,3. Current models suggest that X-over-autosome specificity is achieved by the recognition of cis-regulatory DNA high-affinity sites (HAS) by the MSL2 subunit4,5. However, HAS motifs are also found on autosomes, indicating that additional factors must stabilize the association of the MSL complex with the X chromosome. Here we show that the low-complexity C-terminal domain (CTD) of MSL2 renders its recruitment to the X chromosome sensitive to roX non-coding RNAs. roX non-coding RNAs and the MSL2 CTD form a stably condensed state, and functional analyses in Drosophila and mammalian cells show that their interactions are crucial for dosage compensation in vivo. Replacing the CTD of mammalian MSL2 with that from Drosophila and expressing roX in cis is sufficient to nucleate ectopic dosage compensation in mammalian cells. Thus, the condensing nature of roX–MSL2CTD is the primary determinant for specific compartmentalization of the X chromosome in Drosophila.}, author = {Valsecchi, Claudia Isabelle Keller and Basilicata, M. Felicia and Georgiev, Plamen and Gaub, Aline and Seyfferth, Janine and Kulkarni, Tanvi and Panhale, Amol and Semplicio, Giuseppe and Manjunath, Vinitha and Holz, Herbert and Dasmeh, Pouria and Akhtar, Asifa}, @@ -14468,21 +23581,75 @@ @article{valsecchi_rna_2021 year = {2021} } +@article{van_bree_hidden_2022, + abstract = {Genome-wide association studies (GWAS) have been highly informative in discovering disease-associated loci but are not designed to capture all structural variations in the human genome. Using long-read sequencing data, we discovered widespread structural variation within SINE-VNTR-\textit{Alu} (SVA) elements, a class of great ape-specific transposable elements with gene-regulatory roles, which represents a major source of structural variability in the human population. We highlight the presence of structurally variable SVAs (SV-SVAs) in neurological disease-associated loci, and we further associate SV-SVAs to disease-associated SNPs and differential gene expression using luciferase assays and expression quantitative trait loci data. Finally, we genetically deleted SV-SVAs in the \textit{BIN1} and \textit{CD2AP} Alzheimer's disease-associated risk loci and in the \textit{BCKDK} Parkinson's disease-associated risk locus and assessed multiple aspects of their gene-regulatory influence in a human neuronal context. Together, this study reveals a novel layer of genetic variation in transposable elements that may contribute to identification of the structural variants that are the actual drivers of disease associations of GWAS loci.}, + author = {van Bree, Elisabeth J and Guimarães, Rita L F P and Lundberg, Mischa and Blujdea, Elena R and Rosenkrantz, Jimi L and White, Fred T G and Poppinga, Josse and Ferrer-Raventós, Paula and Schneider, Anne-Fleur E and Clayton, Isabella and Haussler, David and Reinders, Marcel J T and Holstege, Henne and Ewing, Adam D and Moses, Colette and Jacobs, Frank M J}, + doi = {10.1101/gr.275515.121}, + issn = {1088-9051}, + journal = {Genome Res}, + keywords = {{\textgreater}UseGalaxy.eu, DNA Transposable Elements, Genome-Wide Association Study}, + language = {eng}, + month = {April}, + number = {4}, + pages = {656--670}, + title = {A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci}, + url = {http://europepmc.org/abstract/MED/35332097}, + volume = {32}, + year = {2022} +} + +@article{van_den_bossche_critical_2021, + abstract = {Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.}, + author = {Van Den Bossche, Tim and Kunath, Benoit J and Schallert, Kay and Schäpe, Stephanie S and Abraham, Paul E and Armengaud, Jean and Arntzen, Magnus Ø and Bassignani, Ariane and Benndorf, Dirk and Fuchs, Stephan and Giannone, Richard J and Griffin, Timothy J and Hagen, Live H and Halder, Rashi and Henry, Céline and Hettich, Robert L and Heyer, Robert and Jagtap, Pratik and Jehmlich, Nico and Jensen, Marlene and Juste, Catherine and Kleiner, Manuel and Langella, Olivier and Lehmann, Theresa and Leith, Emma and May, Patrick and Mesuere, Bart and Miotello, Guylaine and Peters, Samantha L and Pible, Olivier and Queiros, Pedro T and Reichl, Udo and Renard, Bernhard Y and Schiebenhoefer, Henning and Sczyrba, Alexander and Tanca, Alessandro and Trappe, Kathrin and Trezzi, Jean-Pierre and Uzzau, Sergio and Verschaffelt, Pieter and von Bergen, Martin and Wilmes, Paul and Wolf, Maximilian and Martens, Lennart and Muth, Thilo}, + doi = {10.1038/s41467-021-27542-8}, + issn = {2041-1723}, + journal = {Nature communications}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {December}, + number = {1}, + pages = {7305}, + title = {Critical {Assessment} of {MetaProteome} {Investigation} ({CAMPI}): a multi-laboratory comparison of established workflows}, + url = {http://europepmc.org/abstract/MED/34911965}, + volume = {12}, + year = {2021} +} + @article{vaquero-sedas_epigenetic_2022, abstract = {The epigenetic features of defined chromosomal domains condition their biochemical and functional properties. Therefore, there is considerable interest in studying the epigenetic marks present at relevant chromosomal loci. Telomeric regions, which include telomeres and subtelomeres, have been traditionally considered heterochromatic. However, whereas the heterochromatic nature of subtelomeres has been widely accepted, the epigenetic status of telomeres remains controversial. Here, we studied the epigenetic features of Arabidopsis (Arabidopsis thaliana) telomeres by analyzing multiple genome-wide ChIP-seq experiments. Our analyses revealed that Arabidopsis telomeres are not significantly enriched either in euchromatic marks like H3K4me2, H3K9ac, and H3K27me3 or in heterochromatic marks such as H3K27me1 and H3K9me2. Thus, telomeric regions in Arabidopsis have a bimodal chromatin organization with telomeres lacking significant levels of canonical euchromatic and heterochromatic marks followed by heterochromatic subtelomeres. Since heterochromatin is known to influence telomere function, the heterochromatic modifications present at Arabidopsis subtelomeres could play a relevant role in telomere biology.}, author = {Vaquero-Sedas, María I and Vega-Palas, Miguel A}, doi = {10.1093/plphys/kiac471}, issn = {0032-0889}, journal = {Plant Physiology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis}, + language = {eng}, month = {October}, + number = {1}, pages = {kiac471}, title = {Epigenetic nature of {Arabidopsis} thaliana telomeres}, url = {https://doi.org/10.1093/plphys/kiac471}, urldate = {2022-11-06}, + volume = {191}, year = {2022} } +@article{varga_transposon_2025, + abstract = {The maternal-effect mutation ichabod (ich) results in ventralized zebrafish embryos due to impaired induction of the dorsal canonical Wnt-signaling pathway. While previous studies linked the phenotype to reduced ctnnb2 transcript levels, the causative mutation remained unidentified. Using long-read sequencing, we discovered that the ich phenotype stems from the insertion of a non-autonomous CMC-Enhancer/Suppressor-mutator (CMC-EnSpm) transposon in the 3’UTR of the gene. Through reporter assays, we demonstrate that while wild type ctnnb2 mRNAs exhibit remarkably high stability throughout the early stages of development, the insertion of the transposon dramatically reduces transcript stability. Genome-wide mapping of the CMC-EnSpm transposons across multiple zebrafish strains also indicated ongoing transposition activity in the zebrafish genome. Our findings not only resolve the molecular basis of the ich mutation but also highlight the continuing mutagenic potential of endogenous transposons and reveal unexpected aspects of maternal transcript regulation during early zebrafish development.}, + author = {Varga, Zsombor and Kagan, Ferenc and Maegawa, Shingo and Nagy, Ágnes and Okendo, Javan and Burgess, Shawn M. and Weinberg, Eric S. and Varga, Máté}, + doi = {10.1016/j.bbagrm.2025.195104}, + issn = {1874-9399}, + journal = {Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {September}, + number = {3}, + pages = {195104}, + title = {Transposon insertion causes \textit{ctnnb2} transcript instability that results in the maternal effect zebrafish \textit{ichabod} (\textit{ich}) mutation}, + url = {https://www.sciencedirect.com/science/article/pii/S187493992500029X}, + urldate = {2025-07-12}, + volume = {1868}, + year = {2025} +} + @inproceedings{varshney_madland_2024, author = {Varshney, D. and Hiltemann, S. and Petroll, R. and Fernandez-Pozo, N. and Grüning, B. A. and Rensing, S. A.}, keywords = {{\textgreater}UseGalaxy.eu}, @@ -14494,6 +23661,18 @@ @inproceedings{varshney_madland_2024 year = {2024} } +@article{vasileiadou_erga-bge_2025, + author = {Vasileiadou, K and Dailianis, T and Skouradakis, G and Vernadou, E and Karakasi, D and B�hne, A and Monteiro, R and Fern�ndez, R and Escudero, N and Manousaki, T and Moussy, A and Cruaud, C and Labadie, K and Demirdjian, L and Ndar, A and Wincker, P and H Oliveira, P and Aury, JM and Bortoluzzi, C}, + doi = {10.12688/openreseurope.20841.1}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + number = {297}, + title = {{ERGA}-{BGE} reference genome of {Holothuria} ({Platyperona}) sanctori: a sea cucumber from the {Mediterranean} {Sea} [version 1; peer review: awaiting peer review]}, + url = {https://open-research-europe.ec.europa.eu/articles/5-297/v1}, + volume = {5}, + year = {2025} +} + @article{vecchi_mitogenome_2024, abstract = {Ramazzottius is a widespread genus of tardigrades with extreme cryptobiotic capabilities. Thanks to its ability to survive desiccation and freezing, this genus is usually recorded from harsh habitats such as exposed mosses and lichens and rock pools. In the last years, research focused on both describing Ramazzottius diversity and revealing the molecular mechanisms behind their cryptobiotic capabilities. Despite the research efforts in these fields, much still remains to be discovered. Here we describe a new Ramazzottius species from an Italian rock pool by means of integrative taxonomy (morphology, morphometry, and DNA sequencing) and sequenced its genome with Nanopore technology to provide an assembled mitogenome and annotate its Temperature and Desiccation Resistance Proteins (TDPR) repertoire. The new gonochoric species is phylogenetically close to the parthenogenetic R. varieornatus, a strain of which (YOKOZUNA-1) has been adopted as model organism for the study of cryptobiosis. The mitogenome of the new species shows perfect synteny with R. varieornatus and shares with it most of the TDPR genes. The relative genetic similarity of the new species to the model R. varieornatus, combined with unique biological traits (for example the difference in reproductive mode and the unique habitat it colonizes), makes the new species a potential new addition to the range of model tardigrade species.}, author = {Vecchi, Matteo and Stec, Daniel}, @@ -14510,6 +23689,45 @@ @article{vecchi_mitogenome_2024 year = {2024} } +@article{velasquez_emerging_2025, + abstract = {Blueberry cultivation has recently become a rapidly expanding export industry in Peru. With few to no official records of phytosanitary problems up to date. Nevertheless, as observed in other major blueberry producer countries, pests occurrences have been already reported. This study presents a comprehensive biological and molecular characterization of a novel blueberry pest, identifying it as a member of the Tortricidae family in the genus Platynota. The insect’s average life cycle was determined to be 46.3 days for males and 48.6 days for females, with the larval stage being the longest (25.4 days on average), and the most destructive due to its feeding behavior, which significantly damages buds and fruits. Morphological analysis of the genitalia, along with a comparison of its complete mitochondrial DNA, further supports the conclusion that this pest is a new species. These findings represent the first report of a tortricid pest affecting blueberries in Peru and offer crucial insights for developing effective pest management strategies, contributing to the sustainable growth of blueberry production and exports in the region.}, + author = {Velasquez, Ricardo and Leiva, Ana Maria and Gil-Ordóñez, Alejandra and Perez-Fuentes, Lady Susan and Domínguez, Viviana and Cuellar, Wilmer J.}, + doi = {10.3389/finsc.2025.1593907}, + issn = {2673-8600}, + journal = {Frontiers in Insect Science}, + keywords = {{\textgreater}UseGalaxy.eu, biological cycle, diagnostics, emerging pests, mitogenome, taxonomy}, + language = {English}, + month = {June}, + note = {Publisher: Frontiers}, + shorttitle = {An emerging {Platynota} sp. ({Lepidoptera}}, + title = {An emerging {Platynota} sp. ({Lepidoptera}: {Tortricidae}) infesting blueberry ({Vaccinium} corymbosum) in the central coast of {Peru}}, + url = {https://www.frontiersin.org/journals/insect-science/articles/10.3389/finsc.2025.1593907/full}, + urldate = {2025-07-12}, + volume = {5}, + year = {2025} +} + +@article{verdes_erga-bge_2025, + abstract = {Hanak's bat ( +Pipistrellus hanaki +Hulva and Benda 2004) is one of the most range restricted mammals in Europe, since it occurs only in Cyrenaica, Libya, and Crete (Greece). It is currently classified as 'Vulnerable' on the IUCN Red List, with its foraging habitat threatened by a number of human activities. The reference genome of Hanak's bat ( +Pipistrellus hanaki +) will provide a crucial resource for uncovering the species phylogenetic history and will help assess the degree of genetic isolation among its populations. A total of 23 contiguous chromosomal pseudomolecules (sex chromosomes included) were assembled from the genome sequence. This chromosome-level assembly encompasses 1.9 Gb, composed of 447 contigs and 141 scaffolds, with contig and scaffold N50 values of 48.7 Mb and 89.1 Mb, respectively.}, + author = {Verdes, Aida and Alvarez-Campos, Patricia and Conejero, María and Riesgo, Ana and Böhne, Astrid and Monteiro, Rita and Palma-Guerrero, Javier and Fernández, Rosa and Gut, Marta and Aguilera, Laura and Câmara Ferreira, Francisco and Cruz, Fernando and Gómez-Garrido, Jèssica and S. Alioto, Tyler and Bortoluzzi, Chiara}, + doi = {10.12688/openreseurope.21501.1}, + issn = {2732-5121}, + journal = {Open Research Europe}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {October}, + pages = {317}, + title = {{ERGA}-{BGE} reference genome of the lineid heteronemertean {Lineus} lacteus ({Pilidiophora}, {Nemertea})}, + url = {https://open-research-europe.ec.europa.eu/articles/5-317/v1}, + urldate = {2025-10-19}, + volume = {5}, + year = {2025} +} + @article{vergata_how_2023, abstract = {Phylloremediation for the reduction of air particulate matter (PM) is an interesting opportunity to significantly contribute to improve the air quality of urban environment. The aim of this study was to: 1) gain insight into the gene regulatory networks modulating leaf responses to polluted air, 2) identify possible changes in the leaf microbiome due to particulate matter in the real urban environment. The leaf transcriptome and microbiome were analyzed for Photinia x fraseri L. plants cultivated for three months in pots in two close-by areas under different levels of air PMs (low and high). PCA and heat map analysis showed that 28 differentially expressed genes in common between the three pairwise comparisons were able to clearly discriminate plants under higher PM levels. The pollutants were mainly sensed by plants through a restructuring modification of cell wall and membrane due to the main repression of lipid desaturases. In addition, high PMs showed a clear repression of genes belonging to primary metabolism pathways involved in C assimilation. Microbiome analysis showed no significant changes in taxonomic diversity indexes for the bacterial communities, whereas fungi belonging to the genera Epicoccum and Dioszegia were differently affected by the different exposure to PM levels. A model of transcriptional regulation to air PMs in plants has been proposed.}, author = {Vergata, Chiara and Contaldi, Felice and Baccelli, Ivan and Basso, Marcos Fernando and Santini, Alberto and Pecori, Francesco and Buti, Matteo and Mengoni, Alessio and Vaccaro, Francesca and Moura, Barbara Basso and Ferrini, Francesco and Martinelli, Federico}, @@ -14527,6 +23745,23 @@ @article{vergata_how_2023 year = {2023} } +@article{verma_genomic_2021, + abstract = {In Drosophila, expression of eyeless (ey) gene is restricted to the developing eyes and central nervous system. However, the flanking genes, myoglianin (myo), and bent (bt) have different temporal and spatial expression patterns as compared to the ey. How distinct regulation of ey is maintained is mostly unknown. Earlier, we have identified a boundary element intervening myo and ey genes (ME boundary) that prevents the crosstalk between the cis-regulatory elements of myo and ey genes. In the present study, we further searched for the cis-elements that define the domain of ey and maintain its expression pattern. We identify another boundary element between ey and bt, the EB boundary. The EB boundary separates the regulatory landscapes of ey and bt genes. The two boundaries, ME and EB, show a long-range interaction as well as interact with the nuclear architecture. This suggests functional autonomy of the ey locus and its insulation from differentially regulated flanking regions. We also identify a new Polycomb Response Element, the ey-PRE, within the ey domain. The expression state of the ey gene, once established during early development is likely to be maintained with the help of ey-PRE. Our study proposes a general regulatory mechanism by which a gene can be maintained in a functionally independent chromatin domain in gene-rich euchromatin.}, + author = {Verma, Shreekant and Pathak, Rashmi U and Mishra, Rakesh K}, + doi = {10.1093/g3journal/jkab338}, + issn = {2160-1836}, + journal = {G3 (Bethesda)}, + keywords = {{\textgreater}UseGalaxy.eu, Drosophila Proteins, Drosophila melanogaster}, + language = {eng}, + month = {December}, + number = {12}, + pages = {jkab338}, + title = {Genomic organization of the autonomous regulatory domain of eyeless locus in {Drosophila} melanogaster}, + url = {http://europepmc.org/abstract/MED/34570231}, + volume = {11}, + year = {2021} +} + @article{verma_identification_2022, author = {Verma, Divya and Bagchi, Preenon and IA, Shylesh Murthy}, doi = {10.21203/rs.3.rs-1253773/v1}, @@ -14555,13 +23790,31 @@ @inproceedings{verma_identification_2023 year = {2023} } +@article{vidal-quist_stage-specific_2025, + abstract = {House dust mites (HDMs) such as Dermatophagoides pteronyssinus are major allergy elicitors worldwide, yet their gene expression across developmental stages remains underexplored. Herein, we report a comprehensive RNAseq analysis of larvae, nymphs, and adult males and females, mapped to a recently published high-quality genome with extended functional annotations.}, + author = {Vidal-Quist, José Cristian and Ortego, Félix and Lambrecht, Bart N. and Rombauts, Stephane and Hernández-Crespo, Pedro}, + doi = {10.1186/s12864-025-11703-w}, + issn = {1471-2164}, + journal = {BMC Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Allergen, Cuticular protein, Dermatophagoides pteronyssinus, Development, Ecdysteroid, Fungal Genes, Gene Expression, Gene Transcription, Genome-wide analysis of gene expression, Horizontal gene transfer, House dust mite, Insect Hormone, RNAseq, Reproduction, Seminal fluid protein, Transcriptomics}, + language = {en}, + month = {May}, + number = {1}, + pages = {527}, + title = {Stage-specific transcriptomic analysis reveals insights into the development, reproduction and biological function of allergens in the {European} house dust mite {Dermatophagoides} pteronyssinus}, + url = {https://doi.org/10.1186/s12864-025-11703-w}, + urldate = {2025-05-29}, + volume = {26}, + year = {2025} +} + @article{videm_chira_2021, abstract = {With the advances in next-generation sequencing technologies, it is possible to determine RNA-RNA interaction and RNA structure predictions on a genome-wide level. The reads from these experiments usually are chimeric, with each arm generated from one of the interaction partners. Owing to short read lengths, often these sequenced arms ambiguously map to multiple locations. Thus, inferring the origin of these can be quite complicated. Here we present ChiRA, a generic framework for sensitive annotation of these chimeric reads, which in turn can be used to predict the sequenced hybrids.Grouping reference loci on the basis of aligned common reads and quantification improved the handling of the multi-mapped reads in contrast to common strategies such as the selection of the longest hit or a random choice among all hits. On benchmark data ChiRA improved the number of correct alignments to the reference up to 3-fold. It is shown that the genes that belong to the common read loci share the same protein families or similar pathways. In published data, ChiRA could detect 3 times more new interactions compared to existing approaches. In addition, ChiRAViz can be used to visualize and filter large chimeric datasets intuitively.ChiRA tool suite provides a complete analysis and visualization framework along with ready-to-use Galaxy workflows and tutorials for RNA-RNA interactome and structurome datasets. Common read loci built by ChiRA can rescue multi-mapped reads on paralogous genes without requiring any information on gene relations. We showed that ChiRA is sensitive in detecting new RNA-RNA interactions from published RNA-RNA interactome datasets.}, author = {Videm, Pavankumar and Kumar, Anup and Zharkov, Oleg and Grüning, Björn Andreas and Backofen, Rolf}, doi = {10.1093/gigascience/giaa158}, issn = {2047-217X}, journal = {GigaScience}, - keywords = {+Education, +Galactic, +Shared, +Tools, {\textgreater}RNA Workbench}, + keywords = {+Education, +Galactic, +IsGalaxy, +Shared, +Tools, {\textgreater}RNA Workbench}, month = {February}, number = {giaa158}, shorttitle = {{ChiRA}}, @@ -14578,7 +23831,8 @@ @article{vieira_da_cruz_pyridylpiperazine_2024 doi = {10.1038/s44321-023-00007-9}, issn = {1757-4676}, journal = {EMBO Molecular Medicine}, - keywords = {{\textgreater}UseGalaxy.eu, AcrAB-TolC, Antibiotic Efflux Pump, Antimicrobial Resistance, Cryo-EM, Efflux Pump Inhibitor}, + keywords = {{\textgreater}UseGalaxy.eu, AcrAB-TolC, Anti-Bacterial Agents, Antibiotic Efflux Pump, Antimicrobial Resistance, Cryo-EM, Efflux Pump Inhibitor, Escherichia coli Proteins}, + language = {eng}, month = {January}, note = {Num Pages: 111 Publisher: Springer Nature}, @@ -14613,6 +23867,28 @@ @article{vieira_polymyxin_2024 year = {2024} } +@article{vijayanathan_auxin_2025, + abstract = {The critically important YUCCA (YUC) gene family is highly conserved and specific to the plant kingdom, primarily responsible for the final and rate-limiting step for indole-3-acetic acid (IAA) biosynthesis. IAA is an essential phytohormone, involved in virtually all aspects of plant growth and development. In addition, IAA is involved in fine-tuning plant responses to biotic and abiotic interactions and stresses. While the YUC gene family has significantly expanded throughout the plant kingdom, a detailed analysis of the evolutionary patterns driving this diversification has not been performed. Here, we present a comprehensive phylogenetic analysis of the YUC family, combining YUCs from species representing key evolutionary plant lineages. The evolutionary history of YUCs is complex and suggests multiple recruitment events via horizontal gene transfer from bacteria. We identify and hierarchically classify the YUC family into an early diverging grade, five distinct classes and 41 subclasses. Angiosperm YUC diversity and expansion are explained in the context of protein sequence conservation, as well as spatial and gene expression patterns. The presented YUC gene landscape offers new perspectives on the distribution and evolutionary trends of this crucial family, which facilitates further YUC characterization within plant development and response to environmental change.}, + author = {Vijayanathan, Mallika and Faryad, Amna and Abeywickrama, Thanusha D and Christensen, Joachim Møller and Jakobsen Neilson, Elizabeth H}, + copyright = {cc by-nc-nd}, + doi = {10.1111/tpj.70563}, + issn = {1365-313X}, + journal = {The Plant journal}, + keywords = {{\textgreater}UseGalaxy.eu, Evolution, Flavin‐containing Monooxygenase, Fmo, Yucca, auxin}, + language = {eng}, + month = {November}, + number = {4}, + pages = {e70563}, + pmcid = {PMC12659883}, + pmid = {41308173}, + shorttitle = {The auxin gatekeepers}, + title = {The auxin gatekeepers: {Evolution} and diversification of the {YUCCA} family}, + url = {https://europepmc.org/articles/PMC12659883}, + urldate = {2025-12-26}, + volume = {124}, + year = {2025} +} + @article{vijaykrishna_expanding_2022, abstract = {Summary: Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows users to easily organize, retrieve and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. In addition, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenie's remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS (CernVM File System) repository from GalaxyProject.org, with mirrors across the USA, Canada, Europe and Australia, enabling easy use outside of Galaxy. Availability and implementation: The ability of Galaxy to use refgenie assets was added to the core Galaxy framework in version 22.01, which is available from https://github.com/galaxyproject/galaxy under the Academic Free License version 3.0. The refgenie Data Manager tool can be installed via the Galaxy ToolShed, with source code managed at https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data\_managers/data\_manager\_refgenie\_pull and released using an MIT license. Access to existing data is also available through CVMFS, with instructions at https://galaxyproject.org/admin/reference-data-repo/. No new data were generated or analyzed in support of this research.}, @@ -14627,10 +23903,29 @@ @article{vijaykrishna_expanding_2022 pmcid = {PMC9155181}, pmid = {35669346}, title = {Expanding the {Galaxy}'s reference data}, + url = {http://europepmc.org/abstract/MED/35669346}, volume = {2}, year = {2022} } +@article{vila-luna_draft_2025, + abstract = {Phytoplasmas are phloem-restricted plant pathogens that infect different plant species, causing severe symptoms in agricultural and ornamental crops. ´Candidatus Phytoplasma palmae’ strain LY-C2 is associated with the coconut lethal yellowing disease, a devastating disease for coconut palm. Currently, many phytoplasma genomes have been reported in the literature. One of these corresponds to the draft genome of ‘Ca. P. palmae’, strain ACPD, which is associated with the Texas Phoenix Palm Decline phytoplasma and belongs to the 16SrIV-D subgroup. The genome of ‘Ca. P. palmae’, strain ACPD has been sequenced but not thoroughly analyzed. In this study, we present the draft genome of ‘Ca. P. palmae’-LY-C2, which belongs to the 16SrIV-A subgroup. It consists of 49 scaffolds, totaling 434,453 bp in length, and contains 412 coding-genes, with 365 of them being protein-coding genes. Fifty-four effectors were predicted, 24 of which are unique to this phytoplasma and 11 share homology with effectors of the Texas Phoenix Palm Decline phytoplasma. Some effectors have protein motifs in common with those of other phytoplasmas, but five new protein motifs exclusive to ‘Ca. P. palmae’-LY-C2 were identified. This study also highlights similarities and differences between ‘Ca. P. palmae’-LY-C2 and other phytoplasmas, including ‘Ca. P. palmae’ ACPD, providing new insights into this pathogen. The availability of these draft genomes lay the groundwork for further research on the pathogenic mechanisms and evolution of ‘Ca. P. palmae’.}, + author = {Vila-Luna, Sara Elena and Carreón-Anguiano, Karla Gisel and Córdova-Lara, Iván and Sáenz-Carbonell, Luis and Oropeza-Salín, Carlos and Canto-Canché, Blondy}, + doi = {10.1007/s11274-025-04418-3}, + issn = {1573-0972}, + journal = {World Journal of Microbiology and Biotechnology}, + keywords = {16SrIV group phytoplasma, {\textgreater}UseGalaxy.eu, Coconut lethal yellowing phytoplasma, Coconut phytoplasma genome, Fungal Genes, Fungal genomics, Genome, Neurospora crassa, Phytoplasma, ‘Ca. phytoplasma palmae’-LY-C2}, + language = {en}, + month = {July}, + number = {7}, + pages = {242}, + title = {The draft genome of ‘{Candidatus} {Phytoplasma} palmae’ strain {LY}-{C2}, the phytoplasma associated with coconut lethal yellowing disease, reveals insights into its biological characteristics}, + url = {https://doi.org/10.1007/s11274-025-04418-3}, + urldate = {2025-07-12}, + volume = {41}, + year = {2025} +} + @article{viljoen_rabies-related_2023, author = {Viljoen, Natalie and Ismail, Arshad and Weyer, Jacqueline and Markotter, Wanda}, doi = {10.1128/MRA.00621-23}, @@ -14682,6 +23977,45 @@ @article{villa_degradation_2020 year = {2020} } +@article{villa_first_2025, + abstract = {The sweet chestnut (Castanea sativa Mill.) is one of the most widespread cultivated temperate trees in Europe, valued both for its edible nuts and high-quality timber. Due to its ecological, economic, and cultural importance, it has been the focus of extensive genetic studies. However, its mitochondrial genome has remained largely unexplored. Here, we present the first complete mitochondrial genome of C. sativa (cultivar ‘Marrone di Chiusa Pesio’), assembled using high-throughput sequencing and characterised through comparative analyses with closely related species. The final assembly consists of six contigs with a total length of 402,729 bp, comprising 35 protein-coding genes, 33 tRNA genes, and 3 rRNA genes. Compared to the congeneric C. mollissima, C. sativa shows a relatively low repeat content in terms of both number and length. Codon usage patterns were found to be highly similar among C. sativa, C. mollissima, and C. henryi. Additionally, homologous fragments between the plastid and mitochondrial genomes were identified, totaling 4,671 bp (1.16\% of the mitogenome), and including several tRNA genes. A phylogenetic analysis based on mitochondrial coding sequences from C. sativa and 11 other Fagaceae species confirmed its close relationship with C. mollissima, C. henryi, and Castanopsis carlesii. Discrepancies observed among mitochondrial, plastid, and nuclear gene trees likely reflect either inherent genomic characteristics or extensive hybridisation, particularly within the genus Quercus.}, + author = {Villa, Sara and Marchesini, Alexis and Torre, Sara and Bianco, Luca and Fontana, Paolo and De Quattro, Concetta and Moser, Mirko and Piazza, Stefano and Alessandri, Sara and Pavese, Vera and Pollegioni, Paola and Vernesi, Cristiano and Malnoy, Mickael and Marinoni, Daniela Torello and Murolo, Sergio and Dondini, Luca and Mattioni, Claudia and Botta, Roberto and Micheletti, Diego and Palmieri, Luisa and Sebastiani, Federico}, + doi = {10.1007/s11295-025-01707-8}, + issn = {1614-2950}, + journal = {Tree Genetics \& Genomes}, + keywords = {{\textgreater}UseGalaxy.eu, Castanea sativa mill, Conservation genomics, Gene transfer, Genome, Genome assembly algorithms, Mitochondrial genome, Organellar DNA, Phylogenetic analysis, Plant Genetics}, + language = {en}, + month = {July}, + number = {4}, + pages = {22}, + shorttitle = {First complete mitogenome assembly of {Castanea} sativa}, + title = {First complete mitogenome assembly of {Castanea} sativa: structure, comparative genomics, and phylogeny}, + url = {https://doi.org/10.1007/s11295-025-01707-8}, + urldate = {2025-07-30}, + volume = {21}, + year = {2025} +} + +@article{virgili_paedomorphic_2025, + abstract = {Inhabiting soft substrates presents complex challenges for some groups of sessile filter feeders. Among these, ascidians have independently evolved traits and strategies to live in such habitats. Paedomorphosis, the retention of juvenile features of the ancestor into the adult stage, has been associated with taxa living freely within the sediment, including species of the pyurid genus Heterostigma Ärnbäck-Christie-Linde, 1924 (Ascidiacea: Stolidobranchia: Pyuridae). These poorly known solitary ascidians display peculiar morphological adaptations deemed for an interstitial lifestyle, although complete knowledge of their biology is still lacking. We hereby describe Heterostigma monniotae sp. nov., a new pyurid species from the littoral soft bottoms of Napoli (central Tyrrhenian Sea, Mediterranean Sea). An updated taxonomic table, built on the literature and the screening of types and unpublished material, clarified differences within the known species of the genus. Multilocus phylogenetic analyses based on single genes and the complete mitochondrial genome of the new species provided the first molecular information on this group and resolved its position as sister to the other Stolidobranchia. Finally, morphological and behavioural acquired adaptations were observed in live specimens of H. monniotae, revealing the shift from a sessile to a paedomorphic motile phenotype in mature specimens. This adaptive strategy was never documented before in sessile ascidians, appearing as an extreme strategy to survive in unstable habitats, although its inducing factors are still unclear. The motility of adults was filmed here for the first time. These findings challenge previous assumptions of these species’ lifestyle and behaviour, contributing to the understanding of the development and ecology of this group of sand-living ascidians. Finally, the comparison with closely related species highlighted how ontogenetic processes may have contributed to the radiation of sand-living tunicates. ZooBank: urn:lsid:zoobank.org:pub:FBC89E26-9213-4E40-81D1-36E686B118FC}, + author = {Virgili, Riccardo and Tanduo, Valentina and D’Aniello, Salvatore and Fontana, Angelo and Turon, Xavier and Crocetta, Fabio}, + doi = {10.1071/IS24103}, + issn = {1447-2600}, + journal = {Invertebrate Systematics}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {July}, + note = {Publisher: CSIRO PUBLISHING}, + number = {7}, + pages = {NULL--NULL}, + shorttitle = {Paedomorphic adaptations in a new {Heterostigma} species}, + title = {Paedomorphic adaptations in a new {Heterostigma} species: a novel strategy for ascidians to live in soft-bottom habitats}, + url = {https://www.publish.csiro.au/is/IS24103}, + urldate = {2025-07-12}, + volume = {39}, + year = {2025} +} + @article{vitali_employing_2023, abstract = {Essential oils (EOs) from medicinal plants have long been used in traditional medicine for their widely known antimicrobial properties and represent a promising reservoir of bioactive compounds against multidrug-resistant pathogens. Endophytes may contribute to the yield and composition of EOs, representing a useful tool for biotechnological applications. In this work, we investigated the genomic basis of this potential contribution. The annotated genomes of four endophytic strains isolated from Origanum vulgare L. were used to obtain KEGG ortholog codes, which were used for the annotation of different pathways in KEGG, and to evaluate whether endophytes might harbor the (complete) gene sets for terpene and/or plant hormone biosynthesis. All strains possessed ortholog genes for the mevalonate-independent pathway (MEP/DOXP), allowing for the production of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) precursors. Ortholog genes for the next steps in terpenoid biosynthesis were scarce. All the strains possess potential plant growth promotion (PGP) ability, as shown by the presence of orthologous genes involved in the biosynthesis of indoleacetic acid. The main contribution of endophytes to the yield and composition of O. vulgare EO very likely resides in their PGP activities and in the biosynthesis of precursors of bioactive compounds.}, author = {Vitali, Francesco and Frascella, Arcangela and Semenzato, Giulia and Del Duca, Sara and Palumbo Piccionello, Antonio and Mocali, Stefano and Fani, Renato and Emiliani, Giovanni}, @@ -14703,6 +24037,26 @@ @article{vitali_employing_2023 year = {2023} } +@article{viushkov_influence_2025, + abstract = {Cohesin organizes the genome into spatially segregated loops and topologically associated domains by loop extrusion. In addition, it ensures cohesion of sister chromatids after replication. Thus, cohesin is expected to limit chromatin dynamics by ensuring cohesion and compacting chromatin in the interphase. Nonetheless, loop extrusion is an example of chromatin dynamics; thus, cohesin could promote the dynamics of genomic loci at the scale of individual loops and contact domains. Moreover, given that the extruding activity of cohesin after replication is supplemented by its cohesive activity, the impact of cohesin on chromatin dynamics in different phases of the cell cycle may vary. Of particular interest is the cohesin’s role in the regulation of the dynamics of damaged chromatin, which remains insufficiently studied. Here, we visualized a genomic locus using the CRISPR-Sirius system in human cells with auxin-induced depletion of the cohesin subunit RAD21. Cohesin depletion increased the local spatial dynamics of the visualized locus on a time scale of fractions of a second to one minute. This effect was observed in both replicated and unreplicated chromatin. However, the increase in the mobility of the visualized locus upon cohesin depletion was more pronounced in the former. In addition, we showed that cohesin depletion did not affect the local mobility of double-strand break repair foci visualized using a fluorescent fragment of the repair factor 53BP1. Cohesin depletion did not affect the local mobility of repair foci in either replicated or unreplicated chromatin. The results indicate that cohesin constrains local spatial dynamics of genomic loci. At the same time, cohesive activity of cohesin is not indispensable for restricting chromatin dynamics, although it enhances the confinement effect. On the other hand, repair foci are less mobile structures than point chromatin loci, and cohesin does not affect their dynamics on the studied time scales.}, + author = {Viushkov, Vladimir S. and Lomov, Nikolai A. and Kalitina, Polina O. and Potashnikova, Daria M. and Shtompel, Anastasia S. and Ulianov, Sergey V. and Razin, Sergey V. and Rubtsov, Mikhail A.}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ijms26188837}, + issn = {1422-0067}, + journal = {International Journal of Molecular Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Auxin-inducible Degron, CRISPR-Sirius, Chromatin Dynamics, Cohesin, Crispr-sirius, Double-strand Breaks Repair, Live-cell Imaging, RAD21, Rad21, auxin-inducible degron, chromatin dynamics, cohesin, double-strand breaks repair, live-cell imaging}, + language = {en}, + month = {January}, + note = {Publisher: Multidisciplinary Digital Publishing Institute}, + number = {18}, + pages = {8837}, + title = {The {Influence} of {Cohesin} on the {Short}-{Scale} {Dynamics} of {Intact} and {Damaged} {Chromatin} in {Different} {Phases} of the {Cell} {Cycle}}, + url = {https://www.mdpi.com/1422-0067/26/18/8837}, + urldate = {2025-09-15}, + volume = {26}, + year = {2025} +} + @article{voelker_high-quality_2021, author = {Voelker, Julia and Shepherd, Mervyn and Mauleon, Ramil}, doi = {10.46471/gigabyte.28}, @@ -14747,6 +24101,22 @@ @article{voelker_terpene_2023 year = {2023} } +@article{voigt_genetic_2025, + abstract = {The rapid emergence of mineralized structures in diverse animal groups during the late Ediacaran and early Cambrian periods likely resulted from modifications of pre-adapted biomineralization genes inherited from a common ancestor. As the oldest extant phylum with mineralized structures, sponges are key to understanding animal biomineralization. Yet, the biomineralization process in sponges, particularly in forming spicules, is not well understood. To address this, we conducted transcriptomic, genomic, and proteomic analyses on the calcareous sponge \textit{Sycon ciliatum}, supplemented by \textit{in situ} hybridization. We identified 829 genes overexpressed in regions of increased calcite spicule formation, including 17 calcarins-proteins analogous to corals' galaxins localized in the spicule matrix and expressed in sclerocytes. Their expression varied temporally and spatially, specific to certain spicule types, indicating that fine-tuned gene regulation is crucial for biomineralization control. Similar subtle expression changes are also relevant in stony coral biomineralization. Tandem gene arrangements and expression changes suggest that gene duplication and neofunctionalization have significantly shaped \textit{S. ciliatum}'s biomineralization, similar to that in corals. These findings suggest a parallel evolution of carbonate biomineralization in the calcitic \textit{S. ciliatum} and aragonitic corals, exemplifying the evolution of mechanisms crucial for animals to act as ecosystem engineers and form reef structures.}, + author = {Voigt, Oliver and Wilde, Magdalena V and Fröhlich, Thomas and Fradusco, Benedetta and Vargas, Sergio and Wörheide, Gert}, + doi = {10.7554/elife.106239}, + issn = {2050-084X}, + journal = {eLife}, + keywords = {{\textgreater}UseGalaxy.eu, Anthozoa, Biomineralization, Calcareous Sponges, Convergent Evolution, Corals, Evolutionary Biology, Gene duplication, Porifera, Sycon Ciliatum}, + language = {eng}, + month = {September}, + pages = {RP106239}, + title = {Genetic parallels in biomineralization of the calcareous sponge \textit{{Sycon} ciliatum} and stony corals}, + url = {http://europepmc.org/abstract/MED/40922549}, + volume = {14}, + year = {2025} +} + @article{volkova_multi-omics_2024, abstract = {Barley is a resilient crop with high nutritional value and adaptability, making it a promising candidate for phytoremediation and space agriculture. The study presents a comprehensive multi-omics analysis of the impact of ionising radiation (IR) on barley seedlings, intending to identify candidate pathways for creating radiation-resilient barley plants. We found that different IR treatments (gamma, electron, proton, neutron) increased the intensity of protein catabolism and led to the attenuation of translation. The impact of IRs on protein synthesis and degradation was accompanied by rearrangements in energy metabolism and reallocation of nitrogen, probably due to enhanced protein catabolism. At least partially, those changes seem to fuel secondary metabolites production, including riboflavin, various phytoalexins, phytosiderophores, ferulic and sinapic acids, kaempferol, quercetin, nictoflorin, gallate, and podophyllotoxin. Many of these compounds have antioxidant or radioprotective properties. To focus on possible targets for gene editing, we identified genes differentially regulated after all types of IR exposure and potential transcription factors regulating secondary metabolism, including AP2/ERF, WRKY, bHLH, bZIP, MYB, and NAC families.}, author = {Volkova, Polina and Prazyan, Alexandr and Podlutskii, Mikhail and Saburov, Vyacheslav and Kazakova, Elizaveta and Bitarishvili, Sofia and Duarte, Gustavo T. and Shesterikova, Ekaterina and Makarenko, Ekaterina and Lychenkova, Maria and Ben, Cécile and Gentzbittel, Laurent and Kazakov, Evgenii and Moiseev, Alexandr and Diuzhenko, Sergei and Korol, Marina and Bondarenko, Ekaterina}, @@ -14776,6 +24146,29 @@ @article{volkova_radiosensitivity_2021 year = {2021} } +@article{von_ehr_experimental_2025, + abstract = {Background and aims +Atherosclerosis, driven by inflammation, is a leading cause of cardiovascular events. Recent clinical trials have highlighted the therapeutic potential of anti-inflammatory treatments. Consequently, colchicine is being recommended for secondary prevention in current guidelines, although the drug's mechanistic actions are not fully understood. +Methods +To this end, we conducted a multiomic investigation of colchicine's effect on human carotid plaques. Sections from endarterectomy specimens were exposed to colchicine at concentrations of 2 ng/ml and 10 ng/ml ex vivo for 24 h and compared to untreated segments of the same plaque. Gene expression changes were analyzed by bulk RNA sequencing, and plaque secretomes underwent mass spectrometry for proteomic analysis. In situ cell proliferation was assessed by histology. +Results +Our data indicate, that colchicine suppresses neutrophil and platelet degranulation and activation, collagen degradation and atheromatous plaque macrophage proliferation in a dose-dependent manner in human plaques, while stimulating myofibroblast activation. Unexpectedly, interleukine (IL)-1beta release from colchicine treated plaques was not reduced. These results indicate that the inflammasome may not be the predominant target of low-dose colchicine in human carotid artery plaques. +Conclusion +Our study identifies multifactorial pathways through which colchicine, the first cardiovascular guideline-recommended anti-inflammatory drug, predominantly acts on human atherosclerotic lesions beyond the inflammasome. Targeting neutrophil and platelet degranulation, collagen degradation and macrophage proliferation, selectively, may provide substantial therapeutic benefit in atherosclerotic cardiovascular disease without colchicine's undesired side effects.}, + author = {von Ehr, Alexander and Steenbuck, Ines Derya and Häfele, Charlotte and Remmersmann, Felix and Vico, Tamara A. and Ehlert, Carolin and Lindner, Diana and Wolf, Dennis and Tholen, Stefan and Schilling, Oliver and Czerny, Martin and Westermann, Dirk and Hilgendorf, Ingo}, + doi = {10.1016/j.atherosclerosis.2025.119239}, + issn = {0021-9150}, + journal = {Atherosclerosis}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {July}, + pages = {119239}, + title = {Experimental evidence on colchicine's mode of action in human carotid artery plaques}, + url = {https://www.sciencedirect.com/science/article/pii/S0021915025001376}, + urldate = {2025-05-28}, + volume = {406}, + year = {2025} +} + @incollection{von_suchodoletz_lessons_2020, author = {Von Suchodoletz, Dirk and Bauer, Jonathan and Zharkov, Oleg}, booktitle = {E-{Science}-{Tage} 2019}, @@ -14860,6 +24253,17 @@ @article{vukovikj_-depth_2023 year = {2023} } +@article{wadhawan_e_2022, + abstract = {{\textless}h4{\textgreater}Summary{\textless}/h4{\textgreater} Enterococcus faecalis is a normal member of the gut microbiota and an opportunistic pathogen of many animals, including mammals, birds, and insects. It is a common cause of nosocomial infections, and is particularly troublesome due to extensive intrinsic and acquired antimicrobial resistance. Using experimental evolution, we generated Drosophila -adapted E. faecalis strains, which exhibited immune resistance, resulting in increased in vivo growth and virulence. Resistance was characterised by mutations in bacterial pathways responsive to cell envelope stress. Drosophila -adapted strains exhibited changes in sensitivity to relevant antimicrobials, including daptomycin and vancomycin. Evolved daptomycin-resistant strains harboured mutations in the same signalling systems, with some strains showing increased virulence similar to Drosophila -adapted strains. Our results show that common mechanisms provide a route to resistance to both antimicrobials and host immunity in E. faecalis and demonstrate that the selection and emergence of antibiotic resistance in vivo does not require antibiotic exposure. {\textless}h4{\textgreater}One sentence summary{\textless}/h4{\textgreater} Host interaction can promote antimicrobial resistance and antimicrobial treatment can promote virulence in E. faecalis .}, + author = {Wadhawan, Ashima and Simoes da Silva, Carolina and Nunes, Catarina and Edwards, Andrew and Dionne, Marc}, + doi = {10.1101/2022.08.17.504265}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {E. faecalisacquires resistance to antimicrobials and insect immunity via common mechanisms}, + url = {http://europepmc.org/abstract/PPR/PPR533230}, + year = {2022} +} + @phdthesis{wadhawan_investigating_2022, abstract = {Enterococcus faecalis is a Gram-positive bacterium found in the normal gut microbiota of diverse species, including vertebrates and invertebrates, as well as being common in the environment. It is also an opportunistic pathogen with a broad host range. One of the hosts E. faecalis can infect is the fruit fly, Drosophila melanogaster. The Drosophila immune response is distinct from that of humans and interacts with E. faecalis differently. To study this interaction we carried out experimental evolution via serial passage of E. faecalis in Drosophila. We generated E. faecalis strains with much-enhanced ability to survive and proliferate within this host. Strains selected in this way are specifically resistant to the Toll-induced Bomanin family of effector peptides, resulting not only in higher E. faecalis numbers but also in a significant increase in pathogenicity. Many of these Drosophila-selected strains also exhibit marked increases or decreases in antimicrobial resistance. Whole genome sequencing showed that most selected strains carried single mutations and that many of these mutations were in genes encoding proteins known to be involved in bacterial surface characteristics and antimicrobial resistance (mprF\_2, liaF, yxdM, croS, bgsA). To test if Drosophila antimicrobial peptides kill E. faecalis using mechanisms similar to antibiotics we generated E. faecalis strains that were resistant to daptomycin. Some of these daptomycin-adapted strains also acquired resistance to the Drosophila immune response. Daptomycin-adapted E. faecalis strains have mutations in the same genes or the same regulatory systems as were observed in Drosophila-adapted strains. As common genetic mechanisms underlie the resistance of E. faecalis to daptomycin and the Drosophila immune response, these results indicate these two systems target the same conserved bacterial properties in E. faecalis. They also demonstrate that the selection and emergence of antibiotic resistance in vivo does not require antibiotic exposure.}, author = {Wadhawan, Ashima Deepak}, @@ -14875,6 +24279,44 @@ @phdthesis{wadhawan_investigating_2022 year = {2022} } +@article{wahlberg_genome_2025, + abstract = {High-throughput sequencing has transformed molecular systematics. This study presents a semi-automated pipeline for genome skimming in Thysanoptera, an insect order known for challenging species identification and cryptic relationships. By efficiently obtaining mitochondrial genomes and nuclear genes from multiple thrips specimens, the study evaluates the limitations of traditional barcoding and the data required for accurate species delimitation. The results highlight the importance of the sequencing data volume and this pipeline in reconstructing Thysanoptera phylogeny. This research also showcases the potential of advanced sequencing techniques for species delimitation and phylogenetics.}, + author = {Wahlberg, Emma}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/d17040226}, + issn = {1424-2818}, + journal = {Diversity}, + keywords = {{\textgreater}UseGalaxy.eu, Thysanoptera, genome skimming, high-throughput sequencing, mitochondrial genome, phylogeny, species delimitation}, + language = {en}, + month = {April}, + note = {Number: 4 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {4}, + pages = {226}, + title = {Genome {Skimming} of {Thysanoptera} ({Arthropoda}, {Insecta}) and {Its} {Taxonomic} and {Systematic} {Applications}}, + url = {https://www.mdpi.com/1424-2818/17/4/226}, + urldate = {2025-03-29}, + volume = {17}, + year = {2025} +} + +@article{wambreuse_carotenoid-based_2025, + abstract = {Sea cucumbers are marine deuterostomes possessing a complex innate immune system composed of a wide diversity of immune cells—coelomocytes—making them compelling models for exploring the evolution of immunity. This study investigates the functional specialisation of coelomocytes within the two main echinoderm body fluids, namely, the perivisceral fluid (PF) from the perivisceral cavity and the hydrovascular fluid (HF) from the hydrovascular–ambulacral system. Given their distribution restricted to the HF, haemocyte-like cells (HELs) are particularly investigated. In echinoderms, haemocytes have been described as reddish cells containing haemoglobin and thus presenting a function in oxygen transport. Using an integrative approach that combines cell morphological analyses, pigment profiling, and multi-omics technologies, we demonstrate in the sea cucumber Holothuria forskali that HELs harbour exceptionally high concentrations of carotenoids, primarily canthaxanthin and astaxanthin, potent antioxidant molecules responsible for their pigmentation. Transcriptomics and proteomics analyses reveal that HELs express candidate genes involved in the carotenoid metabolism pathway as well as catalase, an antioxidant enzyme. Additionally, spectral flow cytometry assays reveal that HELs do not produce reactive oxygen species (ROS) in contrast to most coelomocyte types, reinforcing the hypothesis of their antioxidant function. HELs also contribute to the formation of large red bodies (i.e., coelomocyte aggregates) and increase in concentration following lipopolysaccharide injections, indicating an active role in immunity. Given these results, we hypothesise that these cells act after the culmination of the immune response, forming an antioxidant shell around the cellular aggregates to mitigate oxidative stress from ROS produced while encapsulating pathogens, thus protecting the host tissues. The discovery of carotenoid-carrying coelomocytes constitutes the first report of pigmented coelomocytes in sea cucumbers (except respiratory pigments), challenging the long-standing assumption that these cells contain haemoglobin. Therefore, we propose renaming haemocytes into carotenocytes, at least in this species. However, we believe that this newly described coelomocyte type has been misidentified as haemoglobin-containing cells in many previous studies and may be present in many other holothuroid species. Our findings thus establish a new paradigm in the study of coelomocytes in echinoderms, as well as in the function of the hydrovascular system, which is unique to this phylum.}, + author = {Wambreuse, Noé and Bossiroy, Estelle and David, Frank and Vanwinge, Céline and Fievez, Laurence and Bureau, Fabrice and Gabriele, Sylvain and Karasiewicz, Tania and Mascolo, Cyril and Wattiez, Ruddy and Eeckhaut, Igor and Caulier, Guillaume and Delroisse, Jérôme}, + doi = {10.3389/fimmu.2025.1668167}, + issn = {1664-3224}, + journal = {Frontiers in Immunology}, + keywords = {{\textgreater}UseGalaxy.eu, Echinodermata, antioxidant, deuterostome, gene expression, haemocyte, hydrovascular system, immune cell, reactive oxygen species}, + language = {English}, + month = {November}, + note = {Publisher: Frontiers}, + title = {Carotenoid-based immune response in sea cucumbers relies on newly identified coelomocytes—the carotenocytes}, + url = {https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2025.1668167/full}, + urldate = {2025-12-26}, + volume = {16}, + year = {2025} +} + @misc{wambreuse_morpho-functional_2023, abstract = {Holothuria scabra is one of the most valuable species of sea cucumber owing to its exploitation as a seafood product. This study aims to describe the main molecular and cellular actors in the immunology of the holothuroid H. scabra. First of all, a detailed description of the immune cells – the cœlomocytes – is provided, highlighting five main cell types including phagocytes, small round cells (SRCs), spherulocytes, fusiform cells, and crystal cells, with a further five subtypes identified using transmission electron microscopy. Cœlomocyte aggregates were also described morphologically, yielding two main types, one comprising three successive maturation stages. A comparison of the concentration and proportion of cell populations was carried out between the two main body fluids, namely the hydrovascular fluid of the Polian vesicle (HF) and the perivisceral fluid of the general cavity (PF), and no clear relation could be revealed. Next, the cœlomocyte immune response was studied 24 hours after a lipopolysaccharide (LPS) injection. Firstly, the fluctuation in cell populations was assessed, and despite a high inter-individual variability, it shows a decrease in the phagocyte proportion and an increase in the SRC proportion. Secondly, the differential gene expression of PF cœlomocytes was studied by de novo RNA-sequencing between LPS-injected and control-injected individuals: 945 genes were differentially expressed, including 673 up-regulated and 272 down-regulated in the LPS-injected individuals. Among these genes, 80 had a presumed function in immunity based on their annotation, covering a wide range of immune mechanisms. Overall, this study reveals a complex immune system at both molecular and cellular levels and constitutes a baseline reference on H. scabra immunity, which may be useful for the development of sustainable aquaculture and provides valuable data for comparative immunology.}, address = {Rochester, NY}, @@ -14892,6 +24334,47 @@ @misc{wambreuse_morpho-functional_2023 year = {2023} } +@article{wambreuse_morpho-functional_2025, + abstract = {Holothuria scabra is one of the most valuable species of sea cucumber owing to its exploitation as a seafood product. This study aims to describe the main molecular and cellular actors in the immunology of this species. First, a detailed description of the immune cells – the cœlomocytes – is provided, highlighting five main cell types including phagocytes, small round cells (SRCs), spherulocytes, fusiform cells, and crystal cells, with a further five subtypes identified using transmission electron microscopy. Cœlomocyte aggregates were also described morphologically, yielding two main types, one comprising three successive maturation stages. A comparison of the concentration and proportion of cell populations was carried out between the two main body fluids, namely the hydrovascular fluid of the Polian vesicle (HF) and the perivisceral fluid of the general cavity (PF), and no clear relation could be highlighted. Next, the cœlomocyte immune response was studied 24 h after lipopolysaccharide (LPS) injection in the two body fluids. Firstly, the fluctuation in cell populations was assessed, and despite a high inter-individual variability, it shows a decrease in the phagocyte proportion and an increase in the SRC proportion. Secondly, the differential gene expression of PF cœlomocytes was studied by de novo RNA-sequencing between LPS-injected and control-injected individuals: 945 genes were differentially expressed, including 673 up-regulated and 272 down-regulated in the LPS-injected individuals. Among these genes, 80 had a presumed function in immunity based on their annotation, covering a wide range of immune mechanisms. Overall, this study reveals a complex immune system at both molecular and cellular levels and constitutes a baseline reference on H. scabra immunity, which may be useful for the development of sustainable aquaculture and provides valuable data for comparative immunology.}, + author = {Wambreuse, Noé and Caulier, Guillaume and Eeckhaut, Igor and Borrello, Laura and Bureau, Fabrice and Fievez, Laurence and Delroisse, Jérôme}, + doi = {10.1016/j.fsi.2025.110144}, + issn = {1050-4648}, + journal = {Fish \& Shellfish Immunology}, + keywords = {{\textgreater}UseGalaxy.eu, Cellular response, Echinodermata, Humoral response, Immune cells, Immune genes, Lipopolysaccharide, RNA-Sequencing, Transcriptomics}, + month = {March}, + pages = {110144}, + shorttitle = {Morpho-functional characterisation of cœlomocytes in the aquacultivated sea cucumber \textit{{Holothuria} scabra}}, + title = {Morpho-functional characterisation of cœlomocytes in the aquacultivated sea cucumber \textit{{Holothuria} scabra}: {From} cell diversity to transcriptomic immune response}, + url = {https://www.sciencedirect.com/science/article/pii/S1050464825000336}, + urldate = {2025-02-16}, + volume = {158}, + year = {2025} +} + +@article{wan_immunogenic_2025, + abstract = {This work utilized an ORFeome phage display platform to systematically identify antigenic +epitopes produced by Streptococcus equi subspecies equi (S. equi), an important equine pathogen and the causative agent of horses strangles. Three +major S. equi surface proteins were identified: a novel proline-rich repeat domain protein, a serine +peptidase, and the M-like protein SeM. The proline-rich repeat protein and serine +peptidase were confirmed to be immunogenic in horses with strangles, and their sequences +were shown to be conserved in global S. equi genomes, in contrast to their diversity in S. equi subsp. zooepidemicus. With the well-characterized S. equi immunogenic protein SeM, this paper identified an immunogenic region outside of the +reported critical IgG-binding region. This work provides novel insights to the understanding +of the S. equi immunogenic proteins and provides peptide regions that could serve as vaccine candidates +against S. equi or as diagnostic markers to specifically identify S. equi infections.}, + author = {Wan, Joshua and Weldon, Evan and Ganser, Gabriella and Morris, Ellen Ruth A. and Hughes, Emma V. and Bordin, Angela I. and Heine, Philip Alexander and Hust, Michael and Cohen, Noah D. and Gill, Jason J. and Liu, Mei}, + copyright = {Copyright © 2025 Wan et al.}, + doi = {10.1128/msphere.00626-25}, + journal = {mSphere}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {EN}, + month = {December}, + note = {Publisher: American Society for Microbiology1752 N St., N.W., Washington, DC}, + title = {Immunogenic {Streptococcus} equi cell surface proteins identified by {ORFeome} phage display}, + url = {https://journals.asm.org/doi/10.1128/msphere.00626-25}, + urldate = {2025-12-26}, + year = {2025} +} + @phdthesis{wang_application_2024, abstract = {VEZF1 is a highly conserved vertebrate transcription factor that has ubiquitous expression in vertebrates. VEZF1 is essential for the barrier activity of the chicken ẞ globin HS4 insulator, where it prevents de novo DNA methylation. Knock-out of VEZF1 results in lethal haemorrhaging and edema in murine embryos, indicating a role for VEZF1 in the maintenance of vascular integrity. @@ -14910,6 +24393,22 @@ @phdthesis{wang_application_2024 year = {2024} } +@article{wang_exploring_2025, + abstract = {Perlidae represents one of the most diverse and ecologically important groups within the order Plecoptera. However, the phylogenetic relationships within Perlidae remain unresolved due to morphological plasticity and the limited availability of molecular data. Here we sequenced and assembled the mitogenome of \<i\>Hemacroneuria ovalis\</i\> and \<i\>Hesperoperla pacifica\</i\>. By comparing with other published Acroneuriinae mitogenomes, we found that minimal length variation in protein-coding genes (PCGs), transfer RNA genes (tRNAs), and ribosomal RNA genes (rRNAs), whereas the control region (CR) exhibits considerable length divergence. Meanwhile, the mitogenome of Acroneuriinae species is relatively conserved in nucleotide composition and codon usage. The nucleotide diversity (Pi) and Ka/Ks values indicated that the \<i\>ND6\</i\> gene evolves at a faster rate than the \<i\>COI\</i\> gene, and all 13 PCGs are under purifying selection. We also identified gene rearrangement in these two mitogenomes, representing the first report of such events in the order Plecoptera. Phylogenetic results support the monophyly of the tribes Claasseniini, Neoperlini, and Kiotinini, as well as the subfamily Perlinae. Trees from the PCG and PCG12 datasets exhibited more congruent and well accepted topologies. Although both Acroneuriini and Perlini failed to demonstrate monophyly, the phylogenetic relationships among the five families of Perlidae were still reconstructed as (((Perlini + Neoperlini) + Claasseniini) + Kiotinini) + Acroneuriini.}, + author = {Wang, Ying and Niu, Yannan and Qin, Baoni and Cao, Jinjun and Li, Weihai and Murányi, Dávid}, + doi = {10.1002/ece3.72309}, + issn = {2045-7758}, + journal = {Ecology and evolution}, + keywords = {{\textgreater}UseGalaxy.eu, Mitochondrial genome, Phylogeny, Stonefly, gene rearrangement}, + month = {October}, + number = {10}, + pages = {e72309}, + title = {Exploring the {Mitogenomes} of {Acroneuriinae}: {The} {First} {Report} of {Gene} {Rearrangements} in {Plecoptera} {Species} and {Phylogenetic} {Analyses} of {Perlidae}}, + url = {https://europepmc.org/articles/PMC12508255}, + volume = {15}, + year = {2025} +} + @article{wang_genome_2024, abstract = {The co-evolution between symbionts and their insect hosts has led to intricate functional interdependencies. Advances in DNA-sequencing technologies have not only reduced the cost of sequencing but, with the advent of highly accurate long-read methods, have also enabled facile genome assembly even using mixed genomic input, thereby allowing us to more easily assess the contribution of symbionts to their insect hosts. In this study, genomic data recently generated from Peregrinus maidis was used to assemble the genome of a bacterial symbiont, Pm Arsenophonus sp. This {\textasciitilde}4.9-Mb assembly is one of the largest Arsenophonus genomes reported to date. The Benchmarking Universal Single-Copy Orthologs (BUSCO) result indicates that this Pm Arsenophonus assembly has a high degree of completeness, with 96\% of the single-copy Enterobacterales orthologs found. The identity of the Pm Arsenophonus sp. was further confirmed by phylogenetic analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicates a major contribution by Pm Arsenophonus sp. to the biosynthesis of B vitamins and essential amino acids in P. maidis, where threonine and lysine production is carried out solely by Pm Arsenophonus sp. This study not only provides deeper insights into the evolutionary relationships between symbionts and their insect hosts, but also adds to our understanding of insect biology, potentially guiding the development of novel pest control methods.}, author = {Wang, Yu-Hui and Mikaelyan, Aram and Coates, Brad S. and Lorenzen, Marcé}, @@ -14938,7 +24437,7 @@ @article{wang_growth_2024 doi = {10.3390/biom14020148}, issn = {2218-273X}, journal = {Biomolecules}, - keywords = {{\textgreater}UseGalaxy.eu, CAZymes, XYR1/XlnR/XLR-1, cellulose, transcriptional regulation}, + keywords = {{\textgreater}UseGalaxy.eu, CAZymes, Cellulases, Hypocreales, XYR1/XlnR/XLR-1, cellulose, transcriptional regulation}, language = {en}, month = {February}, note = {Number: 2 @@ -14952,6 +24451,17 @@ @article{wang_growth_2024 year = {2024} } +@article{wang_rab7_2024, + abstract = {Cell surface receptors such as integrins are repeatedly internalized from and recycled back to the plasma membrane before routed to lysosomes for degradation. In search for modulators of β1 integrin surface stability, we identified the Rab7 small GTPase, believed to be required for lysosome biogenesis, as integrin stabilizer. We show that Rab7 deficiency produces late endosomes and lysosomes with acidic pH, lysosome-specific proteins and membrane architectures that are functional in protein degradation and organelle fusion. Furthermore, Rab7-deficient lysosomes form from Rab4- and transferrin receptor-positive recycling endosomes, resulting in the degradation of proteins designated for recycling. Finally, we also found that overexpression of Rab4 can direct lysosome formation from recycling endosomes in absence as well as presence of Rab7, however, the latter to a much lesser extent. Our findings reveal a lysosome biogenesis and lysosomal protein degradation pathway that becomes dominant in absence of Rab7 or when Rab4 is highly abundant.}, + author = {Wang, Guan and Xu, Peng and Yu, Kaikai and Guo, Shiny Shengzhen and Faessler, Reinhard}, + doi = {10.1101/2024.05.13.593900}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Rab7 deficiency induces lysosome formation from recycling endosomes leading to an increased degradation of cell surface proteins}, + url = {http://europepmc.org/abstract/PPR/PPR853032}, + year = {2024} +} + @article{wang_systems-level_2023, abstract = {Chemical modifications of transcripts with a 5′ cap occur in all organisms and function in many aspects of RNA metabolism. To facilitate analysis of RNA caps, we developed a systems-level mass spectrometry-based technique, CapQuant, for accurate and sensitive quantification of the cap epitranscriptome. The protocol includes the addition of stable isotope-labeled cap nucleotides (CNs) to RNA, enzymatic hydrolysis of endogenous RNA to release CNs, and off-line enrichment of CNs by ion-pairing high-pressure liquid chromatography, followed by a 17 min chromatography-coupled tandem quadrupole mass spectrometry run for the identification and quantification of individual CNs. The total time required for the protocol can be up to 7 d. In this approach, 26 CNs can be quantified in eukaryotic poly(A)-tailed RNA, bacterial total RNA and viral RNA. This protocol can be modified to analyze other types of RNA and RNA from in vitro sources. CapQuant stands out from other methods in terms of superior specificity, sensitivity and accuracy, and it is not limited to individual caps nor does it require radiolabeling. Thanks to its unique capability of accurately and sensitively quantifying RNA caps on a systems level, CapQuant can reveal both the RNA cap landscape and the transcription start site distribution of capped RNA in a broad range of settings.}, author = {Wang, Jin and Chew, Bing Liang Alvin and Lai, Yong and Dong, Hongping and Xu, Luang and Liu, Yu and Fu, Xin-Yuan and Lin, Zhenguo and Shi, Pei-Yong and Lu, Timothy K. and Luo, Dahai and Jaffrey, Samie R. and Dedon, Peter C.}, @@ -14970,6 +24480,38 @@ @article{wang_systems-level_2023 year = {2023} } +@misc{wasfy_first_2025, + abstract = {{\textless}div{\textgreater}{\textless}p{\textgreater}Background: Numerous bacterial taxa in the human microbiome have yet to be cultured, such as the CPR superphylum (͠͠ ͠͠ around 25\% of bacterial diversity). What we know about CPR is at the genomic level. The role of Candidatus Saccharibacteria in gut microbiota has been described as predominantly anti-inflammatory. However, detection of CPR in HBV infection has not been reported till now. Methodology: Different methods using standard PCR, qPCR, 16S rRNA sequencing, whole genome sequencing, and electron microscopy were used.{\textless}/p{\textgreater}{\textless}p{\textgreater}Results: Correlation analysis showed a significant negative correlation with the prothrombin index, indicating their role should be further investigated in hepatic diseases through developing specific culture methods. Conclusion: Our study proved for the first time a significant abundance of the CPR phyla, particularly Candidatus Saccharibacteria, in HBVinfected patients.{\textless}/p{\textgreater}{\textless}/div{\textgreater}}, + author = {Wasfy, Reham Magdy and Benseddik, Fatma and Zgheib, Rita and Borentain, Patrick and Alou, Maryam Tidjani and Andrieu, Claudia and Caputo, Aurelia and Raoult, Didier and Gerolami, Rene and Million, Matthieu}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {March}, + shorttitle = {First {Evidence} of {Candidate} {Phyla} {Radiation} in {Chronic} {Hepatitis} {B} {Virus}-{Infected} {Patients}}, + title = {First {Evidence} of {Candidate} {Phyla} {Radiation} in {Chronic} {Hepatitis} {B} {Virus}-{Infected} {Patients}: {A} {Case}-{Control} {Metagenomic} {Study}}, + url = {https://amu.hal.science/hal-04975154}, + urldate = {2025-03-29}, + year = {2025} +} + +@article{waterhouse_elixir_2024, + abstract = {Biodiversity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the Earth’s biosphere and human health and well-being. ELIXIR can help address the technical challenges of biodiversity science, through leveraging its suite of services and expertise to enable data management and analysis activities that enhance our understanding of life on Earth and facilitate biodiversity preservation and restoration. This white paper, prepared by the ELIXIR Biodiversity Community, summarises the current status and responses, and presents a set of plans, both technical and community-oriented, that should both enhance how ELIXIR Services are applied in the biodiversity field and how ELIXIR builds connections across the many other infrastructures active in this area. We discuss the areas of highest priority, how they can be implemented in cooperation with the ELIXIR Platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for a Biodiversity Community in ELIXIR and is an appeal to identify and involve new stakeholders.}, + author = {Waterhouse, Robert M. and Adam-Blondon, Anne-Françoise and Balech, Bachir and Barta, Endre and Ying Shi Chua, Physilia and Di Cola, Valeria and Heil, Katharina F. and Hughes, Graham M. and Jermiin, Lars S. and Kalaš, Matúš and Lanfear, Jerry and Pafilis, Evangelos and Palagi, Patricia M. and Papageorgiou, Aristotelis C. and Paupério, Joana and Psomopoulos, Fotis and Raes, Niels and Burgin, Josephine and Gabaldón, Toni}, + doi = {10.12688/f1000research.133724.2}, + issn = {2046-1402}, + journal = {F1000Research}, + keywords = {{\textgreater}UseGalaxy.eu, Biodiversity}, + month = {May}, + pages = {ELIXIR--499}, + pmcid = {PMC11179050}, + pmid = {38882711}, + shorttitle = {The {ELIXIR} {Biodiversity} {Community}}, + title = {The {ELIXIR} {Biodiversity} {Community}: {Understanding} short- and long-term changes in biodiversity}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11179050/}, + urldate = {2025-02-28}, + volume = {12}, + year = {2024} +} + @article{watson_modification_2024, abstract = {Single-cell RNA sequencing (scRNAseq) is a rapidly advancing field enabling the characterisation of heterogeneous gene expression profiles within a population. The cell cycle phase is a major contributor to gene expression variance between cells and computational analysis tools have been developed to assign cell cycle phases to cells within scRNAseq datasets. Whilst these tools can be extremely useful, all have the drawback that they classify cells as only G1, S or G2/M. Existing discrete cell phase assignment tools are unable to differentiate between G2 and M and continuous-phase-assignment tools are unable to identify a region corresponding specifically to mitosis in a pseudo-timeline for continuous assignment along the cell cycle. In this study, bulk RNA sequencing was used to identify differentially expressed genes between mitotic and interphase cells isolated based on phospho-histone H3 expression using fluorescence-activated cell sorting. These gene lists were used to develop a methodology which can distinguish G2 and M phase cells in scRNAseq datasets. The phase assignment tools present in Seurat were modified to allow for cell cycle phase assignment of all stages of the cell cycle to identify a mitotic-specific cell population.}, author = {Watson, Steven and Porter, Harry and Sudbery, Ian and Thompson, Ruth}, @@ -14977,7 +24519,7 @@ @article{watson_modification_2024 doi = {10.3390/ijms25094589}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {{\textgreater}UseGalaxy.eu, RNA sequencing, bioinformatics, cell cycle, mitosis, phase assignment}, + keywords = {{\textgreater}UseGalaxy.eu, G2 Phase, Mitosis, RNA sequencing, bioinformatics, cell cycle, mitosis, phase assignment}, language = {en}, month = {January}, note = {Number: 9 @@ -14997,7 +24539,8 @@ @article{weber_histone_2023 doi = {10.1093/nar/gkac1188}, issn = {0305-1048}, journal = {Nucleic Acids Research}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Chromatin, Histone Acetyltransferases, Histones}, + language = {eng}, month = {January}, number = {2}, pages = {574--594}, @@ -15009,8 +24552,27 @@ @article{weber_histone_2023 } @article{weigang_within-host_2021, + abstract = {The origin of SARS-CoV-2 variants of concern remains unclear. Here, we test whether intra-host virus evolution during persistent infections could be a contributing factor by characterizing the long-term SARS-CoV-2 infection dynamics in an immunosuppressed kidney transplant recipient. Applying RT-qPCR and next-generation sequencing (NGS) of sequential respiratory specimens, we identify several mutations in the viral genome late in infection. We demonstrate that a late viral isolate exhibiting genome mutations similar to those found in variants of concern first identified in UK, South Africa, and Brazil, can escape neutralization by COVID-19 antisera. Moreover, infection of susceptible mice with this patient's escape variant elicits protective immunity against re-infection with either the parental virus and the escape variant, as well as high neutralization titers against the alpha and beta SARS-CoV-2 variants, B.1.1.7 and B.1.351, demonstrating a considerable immune control against such variants of concern. Upon lowering immunosuppressive treatment, the patient generated spike-specific neutralizing antibodies and resolved the infection. Our results suggest that immunocompromised patients could be a source for the emergence of potentially harmful SARS-CoV-2 variants.}, + author = {Weigang, Sebastian and Fuchs, Jonas and Zimmer, Gert and Schnepf, Daniel and Kern, Lisa and Beer, Julius and Luxenburger, Hendrik and Ankerhold, Jakob and Falcone, Valeria and Kemming, Janine and Hofmann, Maike and Thimme, Robert and Neumann-Haefelin, Christoph and Ulferts, Svenja and Grosse, Robert and Hornuss, Daniel and Tanriver, Yakup and Rieg, Siegbert and Wagner, Dirk and Huzly, Daniela and Schwemmle, Martin and Panning, Marcus and Kochs, Georg}, + doi = {10.1038/s41467-021-26602-3}, + issn = {2041-1723}, + journal = {Nature communications}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {November}, + number = {1}, + pages = {6405}, + title = {Within-host evolution of {SARS}-{CoV}-2 in an immunosuppressed {COVID}-19 patient as a source of immune escape variants}, + url = {http://europepmc.org/abstract/MED/34737266}, + volume = {12}, + year = {2021} +} + +@article{weigang_within-host_2021, + abstract = {The recent emergence of SARS-CoV-2 variants showing increased transmissibility and immune escape is a matter of global concern. Their origin remains unclear, but intra-host virus evolution during persistent infections could be a contributing factor. Here, we studied the long-term SARS-CoV-2 infection in an immunosuppressed organ transplant recipient. Frequent respiratory specimens were tested for variant viral genomes by RT-qPCR, next-generation sequencing (NGS), and virus isolation. Late in infection, several virus variants emerged which escaped neutralization by COVID-19 convalescent and vaccine-induced antisera and had acquired genome mutations similar to those found in variants of concern first identified in UK, South Africa, and Brazil. Importantly, infection of susceptible hACE2-transgenic mice with one of the patient’s escape variants elicited protective immunity against re-infection with either the parental virus, the escape variant or the South African variant of concern, demonstrating broad immune control. Upon lowering immunosuppressive treatment, the patient generated spike-specific neutralizing antibodies and resolved the infection. Our results indicate that immunocompromised patients are an alarming source of potentially harmful SARS-CoV-2 variants and open up new avenues for the updating of COVID-19 vaccines.}, author = {Weigang, Sebastian and Fuchs, Jonas and Zimmer, Gert and Schnepf, Daniel and Kern, Lisa and Beer, Julius and Luxenburger, Hendrik and Ankerhold, Jakob and Falcone, Valeria and Kemming, Janine and Hofmann, Maike and Thimme, Robert and Neumann-Haefelin, Christoph and Ulferts, Svenja and Grosse, Robert and Hornuss, Daniel and Tanriver, Yakup and Rieg, Siegbert and Wagner, Dirk and Huzly, Daniela and Schwemmle, Martin and Panning, Marcus and Kochs, Georg}, doi = {10.1101/2021.04.30.21256244}, + journal = {medRxiv}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {May}, note = {Publisher: Cold Spring Harbor Laboratory}, @@ -15053,6 +24615,23 @@ @article{weise_foxg1_2018 year = {2018} } +@article{weise_identification_2021, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater}Cancer metastases are the main cause of lethality. The five-year survival rate for patients diagnosed with advanced stage oral cancer is 30\%. Hence, the identification of novel therapeutic targets is an urgent need. However, tumors are comprised of a heterogeneous collection of cells with distinct genetic and molecular profiles that can differentially promote metastasis making therapy development a challenging task. Here, we leveraged intratumoral heterogeneity in order to identify drivers of cancer cell motility that might be druggable targets for anti-metastasis therapy.{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}We used 2D migration and 3D matrigel-based invasion assays to characterize the invasive heterogeneity among and within four human oral cancer cell lines in vitro. Subsequently, we applied mRNA-sequencing to map the transcriptomes of poorly and strongly invasive subclones as well as primary tumors and matched metastasis.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}We identified SAS cells as a highly invasive oral cancer cell line. Clonal analysis of SAS yielded a panel of 20 subclones with different invasive capacities. Integrative gene expression analysis identified the Lymphocyte cell-specific protein-tyrosine kinase (LCK) as a druggable target gene associated with cancer cell invasion and metastasis. Inhibition of LCK using A-770041 or dasatinib blocked invasion of highly aggressive SAS cells. Interestingly, reduction of LCK activity increased the formation of adherens junctions and induced cell differentiation.{\textless}h4{\textgreater}Conclusion{\textless}/h4{\textgreater}Analysis of invasive heterogeneity led to the discovery of LCK as an important regulator of motility in oral cancer cells. Hence, small molecule mediated inhibition of LCK could be a promising anti-metastasis therapy option for oral cancer patients.}, + author = {Weiße, Jonas and Rosemann, Julia and Müller, Lisa and Kappler, Matthias and Eckert, Alexander W and Glaß, Markus and Misiak, Danny and Hüttelmaier, Stefan and Ballhausen, Wolfgang G and Hatzfeld, Mechthild and Haemmerle, Monika and Gutschner, Tony}, + doi = {10.1186/s12943-021-01384-w}, + issn = {1476-4598}, + journal = {Molecular cancer}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {June}, + number = {1}, + pages = {88}, + title = {Identification of lymphocyte cell-specific protein-tyrosine kinase ({LCK}) as a driver for invasion and migration of oral cancer by tumor heterogeneity exploitation}, + url = {http://europepmc.org/abstract/MED/34116687}, + volume = {20}, + year = {2021} +} + @article{weise_trusted_2024, abstract = {Trusted Research Environments (TREs) enable the analysis of sensitive data under strict security assertions that protect the data with technical, organizational, and legal measures from (accidentally) being leaked outside the facility. While many TREs exist in Europe, little information is available publicly on the architecture and descriptions of their building blocks and their slight technical variations. To highlight on these problems, an overview of the existing, publicly described TREs and a bibliography linking to the system description are provided. Their technical characteristics, especially in commonalities and variations, are analysed, and insight is provided into their data type characteristics and availability. The literature study shows that 47 TREs worldwide provide access to sensitive data, of which two-thirds provide data predominantly via secure remote access. Statistical offices (SOs) make the majority of sensitive data records included in this study available.}, author = {Weise, Martin and Rauber, Andreas}, @@ -15088,6 +24667,23 @@ @article{wennmann_distribution_2024 year = {2024} } +@article{werner_mitochondrial_2022, + abstract = {Prolonged manganese exposure causes manganism, a neurodegenerative movement disorder. The identity of adaptive and nonadaptive cellular processes targeted by manganese remains mostly unexplored. Here we study mechanisms engaged by manganese in genetic cellular models known to increase susceptibility to manganese exposure, the plasma membrane manganese efflux transporter SLC30A10 and the mitochondrial Parkinson's gene PARK2. We found that SLC30A10 and PARK2 mutations as well as manganese exposure compromised the mitochondrial RNA granule composition and function, resulting in disruption of mitochondrial transcript processing. These RNA granule defects led to impaired assembly and function of the mitochondrial respiratory chain. Notably, cells that survived a cytotoxic manganese challenge had impaired RNA granule function, thus suggesting that this granule phenotype was adaptive. CRISPR gene editing of subunits of the mitochondrial RNA granule, FASTKD2 or DHX30, as well as pharmacological inhibition of mitochondrial transcription-translation, were protective rather than deleterious for survival of cells acutely exposed to manganese. Similarly, adult \textit{Drosophila} mutants with defects in the mitochondrial RNA granule component \textit{scully} were safeguarded from manganese-induced mortality. We conclude that impairment of the mitochondrial RNA granule function is a protective mechanism for acute manganese toxicity.}, + author = {Werner, E and Gokhale, A and Ackert, M and Xu, C and Wen, Z and Roberts, AM and Roberts, BR and Vrailas-Mortimer, A and Crocker, A and Faundez, V}, + doi = {10.1091/mbc.e22-03-0096}, + issn = {1059-1524}, + journal = {Mol Biol Cell}, + keywords = {{\textgreater}UseGalaxy.eu, Cytoplasmic Ribonucleoprotein Granules, Manganese}, + language = {eng}, + month = {October}, + number = {12}, + pages = {ar108}, + title = {The mitochondrial {RNA} granule modulates manganese-dependent cell toxicity}, + url = {http://europepmc.org/abstract/MED/35921164}, + volume = {33}, + year = {2022} +} + @article{werner_mitochondrial_2022, author = {Werner, Erica and Gokhale, Avanti and Ackert, Molly and Xu, Chongchong and Wen, Zhexing and Roberts, Anne M and Roberts, Blaine R and Vrailas-Mortimer, Alysia R and Crocker, Amanda J and Faundez, Victor}, journal = {bioRxiv}, @@ -15103,7 +24699,7 @@ @article{werner_targeted_2023 doi = {10.1016/j.neo.2022.100871}, issn = {1476-5586}, journal = {Neoplasia}, - keywords = {{\textgreater}UseGalaxy.eu, FFPE, KLK, Mass Spectrometry, PDAC}, + keywords = {{\textgreater}UseGalaxy.eu, Carcinoma, Pancreatic Ductal, FFPE, KLK, Mass Spectrometry, PDAC, Pancreatic Neoplasms, Pancreatitis, Chronic}, language = {en}, month = {February}, pages = {100871}, @@ -15114,6 +24710,23 @@ @article{werner_targeted_2023 year = {2023} } +@article{wess_versatile_2025, + abstract = {Clear cell renal cell carcinoma (ccRCC) is the most prevalent renal malignancy with a poor prognosis when metastasized. The invasive growth of cancer cells relates to membrane-damaging forces, but the relevance of plasma membrane repair machinery in ccRCC remains incompletely understood. Employing proteomics, analysis of scRNA-sequencing data, and multiplex imaging, we identified ANXA4 as selectively expressed in ccRCC, with distinct localization patterns at the plasma and nuclear membranes. Genetic titration studies demonstrated that reduced ANXA4 expression impairs membrane repair and invasive capabilities. Further segmentation analysis of ANXA4-low tumors showed a distinct composition of the tumor microenvironment, with increased tumor-infiltrating lymphocytes and acellular extracellular matrix deposition. Transcriptomic analysis demonstrated alterations in epithelial-mesenchymal transition and immune signaling signatures in ANXA4-low tumors. Transcription factor enrichment analysis identified ELF3 as a regulator of invasive properties. Our integrative approach uncovered multiple roles for ANXA4 in modulating membrane repair, transcriptional regulation, and shaping the ccRCC tumor microenvironment composition.}, + author = {Wess, Maximilian and Rogg, Manuel and Gueib-Picard, Constance and Merz, Annika and Kössinger, Anna L and Feilen, Tobias and Andreev, Grigor and Werner, Martin and Frew, Ian J and Grabbert, Markus and Schilling, Oliver and Schell, Christoph}, + doi = {10.1016/j.isci.2025.112198}, + issn = {2589-0042}, + journal = {iScience}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {April}, + number = {4}, + pages = {112198}, + title = {Versatile roles of annexin {A4} in clear cell renal cell carcinoma: {Impact} on membrane repair, transcriptional signatures, and composition of the tumor microenvironment}, + url = {http://europepmc.org/abstract/MED/40212597}, + volume = {28}, + year = {2025} +} + @article{weterings_duration_2021, abstract = {Background Escherichia coli sequence type ST131 is a recently emerged worldwide pandemic clonal group. Antibiotic resistance, virulence factors or colonisation fitness are mentioned among other as possible factors contributing to the worldwide success. In this study, we assessed the duration of rectal ESBL- producing E. coli colonisation in the residents, and compare duration of colonisation for ESBL-ST131 versus ESBL-non-ST131.MethodsRectal or faecal samples were obtained from residents of nursing home A between 2013 and 2019 and nursing home B between 2017 and 2019, with repeated point prevalence surveys at intervals of three to six months. Extended-spectrum β-lactamase (ESBL)-producing strains of E. coli were identified on selective culture and selective\&nbsp;enrichment\&nbsp;broth, and examined by antimicrobial susceptibility testing. In nursing home A multilocus sequence typing (MLST) and cluster analyse was performed by respectively O25:ST131-specific PCR and amplified fragment length polymorphism (AFLP). In nursing home B whole genome sequencing data were used to determine MLST and to perform a cluster analyse. Kaplan Meier survival analysis was performed to calculate the median time of rectal colonisation of ESBL-EC with a Log-Rank analysis to test for differences between ESBL-ST131 and ESBL-non-ST131.ResultsA total of 144 residents were included: 84 residents (58\%) with ESBL-ST131 rectal colonisation and 60 residents (42\%) with ESBL-non-ST131 rectal colonisation. Survival analysis showed a median colonisation length of 13 months for ESBL-ST131 (95\%CI: 7,2 – 18,7) versus 8,3 months (95\%CI: 2,8 – 13,8) for ESBL-non-ST131 (p = 0,028). Remarkably, in the subgroup ST131 the median colonisation length was significantly longer in female than in males: 25,7 months versus 8,1 months (p = 0,013).ConclusionHere we found a prolonged colonisation duration of ESBL-ST131 compared to ESBL-non-ST131 in residents of Dutch nursing homes. Prolonged colonisation duration complicates the controlling and ending an ESBL-ST131 outbreak, especially in long stay settings such as nursing homes.\&nbsp;}, author = {Weterings, Veronica and Goede, Tineke de and Hendriks, Yvonne and Kilsdonk, Linda and Mulders, Ans and Wier, Bregje van de and Kluytmans, Jan}, @@ -15129,6 +24742,23 @@ @article{weterings_duration_2021 year = {2021} } +@article{whitmore_evolutionary_2021, + abstract = {The spreading global sea turtle fibropapillomatosis (FP) epizootic is threatening some of Earth's ancient reptiles, adding to the plethora of threats faced by these keystone species. Understanding this neoplastic disease and its likely aetiological pathogen, chelonid alphaherpesvirus 5 (ChHV5), is crucial to understand how the disease impacts sea turtle populations and species and the future trajectory of disease incidence. We generated 20 ChHV5 genomes, from three sea turtle species, to better understand the viral variant diversity and gene evolution of this oncogenic virus. We revealed previously underappreciated genetic diversity within this virus (with an average of 2035 single nucleotide polymorphisms (SNPs), 1.54\% of the ChHV5 genome) and identified genes under the strongest evolutionary pressure. Furthermore, we investigated the phylogeny of ChHV5 at both genome and gene level, confirming the propensity of the virus to be interspecific, with related variants able to infect multiple sea turtle species. Finally, we revealed unexpected intra-host diversity, with up to 0.15\% of the viral genome varying between ChHV5 genomes isolated from different tumours concurrently arising within the same individual. These findings offer important insights into ChHV5 biology and provide genomic resources for this oncogenic virus.}, + author = {Whitmore, Liam and Yetsko, Kelsey and Farrell, Jessica A and Page-Karjian, Annie and Daniel, Whitney and Shaver, Donna J and Frandsen, Hilary R and Walker, Jennifer Shelby and Crowder, Whitney and Bovery, Caitlin and Rollinson Ramia, Devon and Burkhalter, Brooke and Ryan, Elizabeth and Duffy, David J}, + doi = {10.3390/ani11092489}, + issn = {2076-2615}, + journal = {Animals : an open access journal from MDPI}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {August}, + number = {9}, + pages = {2489}, + title = {Evolutionary {Comparisons} of {Chelonid} {Alphaherpesvirus} 5 ({ChHV5}) {Genomes} from {Fibropapillomatosis}-{Afflicted} {Green} ({Chelonia} mydas), {Olive} {Ridley} ({Lepidochelys} olivacea) and {Kemp}'s {Ridley} ({Lepidochelys} kempii) {Sea} {Turtles}}, + url = {http://europepmc.org/abstract/MED/34573455}, + volume = {11}, + year = {2021} +} + @article{whitmore_inadvertent_2023, abstract = {The field of environmental DNA (eDNA) is advancing rapidly, yet human eDNA applications remain underutilized and underconsidered. Broader adoption of eDNA analysis will produce many well-recognized benefits for pathogen surveillance, biodiversity monitoring, endangered and invasive species detection, and population genetics. Here we show that deep-sequencing-based eDNA approaches capture genomic information from humans (Homo sapiens) just as readily as that from the intended target species. We term this phenomenon human genetic bycatch (HGB). Additionally, high-quality human eDNA could be intentionally recovered from environmental substrates (water, sand and air), holding promise for beneficial medical, forensic and environmental applications. However, this also raises ethical dilemmas, from consent, privacy and surveillance to data ownership, requiring further consideration and potentially novel regulation. We present evidence that human eDNA is readily detectable from ‘wildlife’ environmental samples as human genetic bycatch, demonstrate that identifiable human DNA can be intentionally recovered from human-focused environmental sampling and discuss the translational and ethical implications of such findings.}, author = {Whitmore, Liam and McCauley, Mark and Farrell, Jessica A. and Stammnitz, Maximilian R. and Koda, Samantha A. and Mashkour, Narges and Summers, Victoria and Osborne, Todd and Whilde, Jenny and Duffy, David J.}, @@ -15136,7 +24766,7 @@ @article{whitmore_inadvertent_2023 doi = {10.1038/s41559-023-02056-2}, issn = {2397-334X}, journal = {Nature Ecology \& Evolution}, - keywords = {{\textgreater}NanoGalaxy, {\textgreater}UseGalaxy.eu, Ecological genetics, Science, Sequencing, Zoology, technology and society}, + keywords = {{\textgreater}NanoGalaxy, {\textgreater}UseGalaxy.eu, DNA, Ecological genetics, Environmental, Science, Sequencing, Zoology, technology and society}, language = {en}, month = {May}, note = {Publisher: Nature Publishing Group}, @@ -15170,7 +24800,8 @@ @article{wicaksono_genome-wide_2024 doi = {10.1186/s12864-024-10893-z}, issn = {1471-2164}, journal = {BMC Genomics}, - keywords = {{\textgreater}UseGalaxy.eu, Calcium signaling, Fabaceae, Legumes, Seed, Transcription factor, Vigna radiata}, + keywords = {{\textgreater}UseGalaxy.eu, Calcium Signaling, Calcium signaling, Fabaceae, Gene Expression Regulation, Plant, Legumes, Light, Plant Proteins, Seed, Seedlings, Transcription factor, Vigna, Vigna radiata}, + language = {eng}, month = {October}, number = {1}, pages = {992}, @@ -15181,12 +24812,37 @@ @article{wicaksono_genome-wide_2024 year = {2024} } +@article{wicaksono_hairpin_2025, + abstract = {Rafflesiaceae is a family of endangered plants whose members are solely parasitic to the tropical grape vine Tetrastigma (Vitaceae). Currently, the genetics of their crosstalk with the host remains unexplored. In this study, we use homology-based in silico approaches to characterize micro-RNAs (miRNAs) expressed by Sapria himalayana and Rafflesia cantleyi from published omics data. Derived from secondary structures or hairpins, miRNAs are small regulators of gene expression. We found that some plant-conserved miRNA still exists in Rafflesiaceae. Out of 9 highly conserved miRNA families in plants, 7 families (156/157, 159/319, 160, 165/166, 171, 172, 390) were identified with a total of 22 variants across Rafflesiaceae. Some miRNAs were missing endogenous targets and may have evolved to target host miRNA, though this requires experimental verification. Rafflesiaceae miRNA promoters are mostly inducible by ethylene that mediates stress response in the host but could be perceived by the parasites as a signal for growth. This study provides evidence that certain miRNAs with ancient origins in land plants still exist in Rafflesiaceae, though some may have been coopted by parasites to target host genes.}, + author = {Wicaksono, Adhityo and Meitha, Karlia and Wan, Kiew-Lian and Isa, Mohd Noor Mat and Parikesit, Arli Aditya and Molina, Jeanmaire}, + copyright = {De Gruyter expressly reserves the right to use all content for commercial text and data mining within the meaning of Section 44b of the German Copyright Act.}, + doi = {10.1515/biol-2022-1033}, + issn = {2391-5412}, + journal = {Open Life Sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Malpighiales, RNAi, gene regulation, ncRNA, small RNA}, + language = {en}, + month = {January}, + note = {Publisher: De Gruyter Open Access}, + number = {1}, + shorttitle = {Hairpin in a haystack}, + title = {Hairpin in a haystack: {In} silico identification and characterization of plant-conserved {microRNA} in {Rafflesiaceae}}, + url = {https://www.degruyter.com/document/doi/10.1515/biol-2022-1033/html}, + urldate = {2025-02-12}, + volume = {20}, + year = {2025} +} + @article{wichers_common_2021, + abstract = {Sequestration of \textit{Plasmodium falciparum}(\textit{P. falciparum})-infected erythrocytes to host endothelium through the parasite-derived \textit{P. falciparum} erythrocyte membrane protein 1 (\textit{Pf}EMP1) adhesion proteins is central to the development of malaria pathogenesis. \textit{Pf}EMP1 proteins have diversified and expanded to encompass many sequence variants, conferring each parasite a similar array of human endothelial receptor-binding phenotypes. Here, we analyzed RNA-seq profiles of parasites isolated from 32 \textit{P. falciparum-}infected adult travellers returning to Germany. Patients were categorized into either malaria naive (n = 15) or pre-exposed (n = 17), and into severe (n = 8) or non-severe (n = 24) cases. For differential expression analysis, \textit{Pf}EMP1-encoding \textit{var} gene transcripts were de novo assembled from RNA-seq data and, in parallel, \textit{var-}expressed sequence tags were analyzed and used to predict the encoded domain composition of the transcripts. Both approaches showed in concordance that severe malaria was associated with \textit{Pf}EMP1 containing the endothelial protein C receptor (EPCR)-binding CIDRα1 domain, whereas CD36-binding \textit{Pf}EMP1 was linked to non-severe malaria outcomes. First-time infected adults were more likely to develop severe symptoms and tended to be infected for a longer period. Thus, parasites with more pathogenic \textit{Pf}EMP1 variants are more common in patients with a naive immune status, and/or adverse inflammatory host responses to first infections favor the growth of EPCR-binding parasites.}, author = {Wichers, J. Stephan and Tonkin-Hill, Gerry and Thye, Thorsten and Krumkamp, Ralf and Kreuels, Benno and Strauss, Jan and Thien, Heidrun von and Scholz, Judith AM and Hansson, Helle Smedegaard and Jensen, Rasmus Weisel and Turner, Louise and Lorenz, Freia-Raphaella and Schöllhorn, Anna and Bruchhaus, Iris and Tannich, Egbert and Fendel, Rolf and Otto, Thomas D. and Lavstsen, Thomas and Gilberger, Tim W. and Duffy, Michael F. and Bachmann, Anna}, doi = {10.7554/elife.69040}, + issn = {2050-084X}, + journal = {eLife}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + language = {eng}, month = {April}, note = {Publisher: eLife Sciences Publications, Ltd}, + pages = {e69040}, title = {Common virulence gene expression in adult first-time infected malaria patients and severe cases}, url = {https://doi.org/10.7554/elife.69040}, volume = {10}, @@ -15194,10 +24850,13 @@ @article{wichers_common_2021 } @article{wight_anthropogenic_2024, + abstract = {Antimicrobial resistance (AMR) is an ever-present threat to the treatment of infectious diseases. However, the potential relevance of this phenomenon in environmental reservoirs still raises many questions. Detection of antimicrobial-resistant bacteria in the environment is a critical aspect for understanding the prevalence of resistance outside of clinical settings, as detection in the environment indicates that resistance is likely already widespread. We isolated antimicrobial-resistant \textit{Escherichia coli} from three urban waterbodies over a 15-month time series, determined their antimicrobial susceptibilities, investigated their population structure, and identified genetic determinants of resistance. We found that \textit{E. coli} populations at each site were composed of different dominant phylotypes and showed distinct patterns of antimicrobial and multidrug resistance, despite close geographic proximity. Many strains that were genome-sequenced belonged to sequence types of international concern, particularly the ST131 clonal complex. We found widespread resistance to clinically important antimicrobials such as amoxicillin, cefotaxime, and ciprofloxacin, but found that all strains were susceptible to amikacin and the last-line antimicrobials meropenem and fosfomycin. Resistance was most often due to acquirable antimicrobial resistance genes, while chromosomal mutations in \textit{gyrA}, \textit{parC}, and \textit{parE} conferred resistance to quinolones. Whole-genome analysis of a subset of strains further revealed the diversity of the population of \textit{E. coli} present, with a wide array of AMR and virulence genes identified, many of which were present on the chromosome, including \textit{bla$_{\textrm{CTX-M}}$}. Finally, we determined that environmental persistence, transmission between sites, most likely mediated by wild birds, and transfer of mobile genetic elements likely contributed significantly to the patterns observed.IMPORTANCEA One Health perspective is crucial to understand the extent of antimicrobial resistance (AMR) globally, and investigation of AMR in the environment has been increasing in recent years. However, most studies have focused on waterways that are directly polluted by sewage, industrial manufacturing, or agricultural activities. Therefore, there remains a lack of knowledge about more natural, less overtly impacted environments. Through phenotypic and genotypic investigation of AMR in \textit{Escherichia coli}, this study adds to our understanding of the extent and patterns of resistance in these types of environments, including over a time series, and showed that complex biotic and abiotic factors contribute to the patterns observed. Our study further emphasizes the importance of incorporating the surveillance of microbes in freshwater environments in order to better comprehend potential risks for both human and animal health and how the environment may serve as a sentinel for potential future clinical infections.}, author = {Wight, Jordan and Byrne, Alexander S. and Tahlan, Kapil and Lang, Andrew S.}, doi = {10.1128/aem.01809-23}, + issn = {0099-2240}, journal = {Applied and Environmental Microbiology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Anti-Infective Agents, Escherichia coli Infections}, + language = {eng}, month = {February}, note = {Publisher: American Society for Microbiology}, number = {3}, @@ -15209,13 +24868,25 @@ @article{wight_anthropogenic_2024 year = {2024} } +@article{williams_discovery_2022, + abstract = {The deep sea is known to host novel bacteria with the potential to produce a diverse array of undiscovered natural products. Understanding these bacteria is thus of broad interest in ecology and could also underpin applied drug discovery, specifically in the area of antimicrobials. Here, we isolate a new strain of Streptomyces from the tissue of the deep-sea sponge Polymastia corticata collected at a depth of 1869 m from the Gramberg seamount in the Atlantic Ocean. This strain, which was given the initial designation A15ISP2-DRY2 T , has a genome size of 9.29 Mb with a GC content of 70.83\%. Phylogenomics determined that A15ISP2-DRY2 T represents a novel species within the genus Streptomyces as part of the Streptomyces aurantiacus clade. The biosynthetic potential of A15ISP2-DRY2 T was assessed relative to other members of the aurantiacus clade via comparative gene cluster family (GCF) analysis. This revealed a clear congruent relationship between phylogeny and GCF content. A15ISP2-DRY2 T contains six unique GCFs absent elsewhere in the clade. Culture-based assays were used to demonstrate the antibacterial activity of A15ISP2-DRY2 T against two drug-resistant human pathogens. We thus determine A15ISP2-DRY2 T to be a novel bacterial species with considerable biosynthetic potential and propose the systematic name Streptomyces ortus sp. nov. {\textless}h4{\textgreater}Impact Statement{\textless}/h4{\textgreater} The Streptomyces genus has contributed more to our antibiotic arsenal than any other group of bacteria or fungi. Despite decades of exploration, global analysis has suggested they still possess more undiscovered biosynthetic diversity than any other bacterial group. Isolating novel species of Streptomyces is therefore a priority for antibiotic discovery. Here we isolate a novel strain from a deep-sea sponge and use comparative cluster analysis to identify six biosynthetic clusters unique to our deep-sea strain. This work demonstrates the utility of continuing to isolate novel Streptomyces strains for antibiotic discovery and, for the first time, we used species tree-gene cluster tree reconciliation to assess the contribution of vertical evolution on the biosynthetic gene cluster content of Streptomyces .}, + author = {Williams, Sam and Back, Catherine and Best, Eleanor and Mantell, Judith and Stach, James and Williams, Tom and Race, Paul and Curnow, Paul}, + doi = {10.1101/2022.11.21.517041}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Discovery and biosynthetic assessment {ofStreptomyces} ortussp nov. isolated from a deep-sea sponge}, + url = {http://europepmc.org/abstract/PPR/PPR574300}, + year = {2022} +} + @article{williams_discovery_2023, abstract = {The deep sea is known to host novel bacteria with the potential to produce a diverse array of undiscovered natural products. Thus, understanding these bacteria is of broad interest in ecology and could also underpin applied drug discovery, specifically in the area of antimicrobials....}, author = {Williams, Sam E. and Back, Catherine R. and Best, Eleanor and Mantell, Judith and Stach, James E. M. and Williams, Tom A. and Race, Paul R. and Curnow, Paul}, doi = {10.1099/mgen.0.000996}, issn = {2057-5858}, journal = {Microbial Genomics}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Porifera, Streptomyces}, + language = {eng}, month = {May}, number = {5}, pages = {mgen000996}, @@ -15246,6 +24917,22 @@ @article{willnow_nuclear_2024 year = {2024} } +@article{wingfield_ima_2022, + author = {Wingfield, Brenda D and Berger, Dave K and Coetzee, Martin P A and Duong, Tuan A and Martin, Anke and Pham, Nam Q and van den Berg, Noelani and Wilken, P Markus and Arun-Chinnappa, Kiruba Shankari and Barnes, Irene and Buthelezi, Sikelela and Dahanayaka, Buddhika Amarasinghe and Durán, Alvaro and Engelbrecht, Juanita and Feurtey, Alice and Fourie, Arista and Fourie, Gerda and Hartley, Jesse and Kabwe, Eugene N K and Maphosa, Mkhululi and Narh Mensah, Deborah L and Nsibo, David L and Potgieter, Lizel and Poudel, Barsha and Stukenbrock, Eva H and Thomas, Chanel and Vaghefi, Niloofar and Welgemoed, Tanya and Wingfield, Michael J}, + doi = {10.1186/s43008-022-00104-3}, + issn = {2210-6340}, + journal = {IMA fungus}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {November}, + number = {1}, + pages = {19}, + title = {{IMA} genome‑{F17} : {Draft} genome sequences of an {Armillaria} species from {Zimbabwe}, {Ceratocystis} colombiana, {Elsinoë} necatrix, {Rosellinia} necatrix, two genomes of {Sclerotinia} minor, short‑read genome assemblies and annotations of four {Pyrenophora} teres isolates from barley grass, and a long-read genome assembly of {Cercospora} zeina}, + url = {http://europepmc.org/abstract/MED/36411457}, + volume = {13}, + year = {2022} +} + @article{winkler_contrast_2020, abstract = {Mass spectrometry imaging (MSI) enables the unbiased characterization of surfaces with respect to their chemical composition. In biological MSI, zones with differentialmass profiles hint towards localized physiological processes, such as the tissue-specific accumulation of secondary metabolites, or diseases, such as cancer. Thus, the efficientdiscovery of ‘regions of interest’ (ROI) is of utmost importance in MSI. However, often the discovery of ROIs is hampered by high background noise and artifact signals. Especially in ambient ionization MSI, unmasking biologically relevant information from crude data sets is challenging. Therefore, we implemented a Threshold Intensity Quantization (TrIQ) algorithm for augmenting the contrast in MSI data visualizations. The simple algorithm reduces the impact of extreme values (‘outliers’) and rescales the dynamic range of mass signals. We provide an R script for post-processing MSI data in the imzML community format (https://bitbucket.org/lababi/msi.r) and implemented the TrIQ in our open-source imaging software RmsiGUI (https://bitbucket.org/lababi/rmsigui/). Applying these programs to different biological MSI data sets demonstrated the universal applicability of TrIQ for improving the contrast in the MSI data visualization. We show that TrIQ improves a subsequent detection of ROIs by sectioning. In addition, the adjustment of the dynamic signal intensity range makes MSI data sets comparable.}, author = {Winkler, Robert and Rosas-Román, Ignacio}, @@ -15262,8 +24949,10 @@ @article{winkler_contrast_2020 } @article{winkler_gene_2021, + abstract = {{\textless}h4{\textgreater}Background: {\textless}/h4{\textgreater} We previously reported that a Human Ro52 gene sequence (TRIM21) produced a significant stretch of protein sequence homologous to T . cruzi Antigen 36 (Ag 36) protein sequence, when Ag 36 was translated in the second reading frame. Comparison of their respective DNA sequences demonstrated a 114 nucleotide region of both genes having {\textasciitilde} 70 percent partial homology. After Ro52 was shown to be an E3 Ubiquitin dependent Type I ligase for transcription factors for Interferon genes, we proposed that the Ag 36 gene, which contains a repetitive motif within it, may function to repress Ro52 in the human heart through RNA interference, or other unknown mechanism, giving rise to autoimmunity found in Chronic Chagas Cardiomyopathy (CCC). Results To test that hypothesis, we compared various mammalian TRIM genes to the T . cruzi Ag 36 DNA sequence using the Needleman-Wunsch algorithm in the http:{\textbackslash}{\textbackslash}usegalaxy.eu bioinformatics tool base. In addition to human and chimpanzee, TRIM21 comparable gene regions from canine, shrew, ferret, bat, feline, and armadillo, and aardvark showed homology to the gene for Ag 36 ranging from 68 to 30 percent. However, mouse and eight other mammalian species showed no significant homology. Since mice have been shown to have severe cardiac cardiomyopathy after infection, but their TRIM21 was not homologous to Ag 36 in this study, we conclude that the gene homology has no causative link to CCC. Conclusions In addition to human TRIM21, eight mammalian species showed partial gene homology to T. cruzi Ag 36, and some of these have been demonstrated to have CCC. However, rats and mice TRIM21 showed no partial homology to Ag 36. Since these species have been demonstrated to have CCC, the partial gene homology between Ag36 and TRIM 21 may not be causative or associated with CCC, as was originally hypothesized.}, author = {Winkler, Martin A. and Pan, Alfred A.}, doi = {10.21203/rs.3.rs-553828/v2}, + journal = {Research Square}, keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, month = {July}, note = {Publisher: Research Square Platform LLC}, @@ -15272,6 +24961,45 @@ @article{winkler_gene_2021 year = {2021} } +@article{winkler_molecular_2024, + abstract = {Initial studies using bioinformatics analysis revealed DNA sequence similarities between Trypanosoma cruzi GenBank® M21331, coding for Antigen 36 (Ag 36), and tripartite motif (TRIM) genes. TRIM40 showed 9.7\% identity to GenBank M21331, and four additional TRIM genes had identities greater than 5.0\%. TRIM37 showed a continuous stretch of identity of 12 nucleotides, that is, at least 25\% longer than any of the other TRIMs. When we extended our analysis on the relationships of GenBank M21331 to further innate immune genes, using the Needleman-Wunsch (NW) algorithm for alignment, identities to human IFN-α, IFN-β, and IFN-γ genes of 13.6\%, 12.6\%, and 17.9\%, respectively, were found. To determine the minimum number of genes coding for proteins closely related to Ag 36, a BLAST-p search was conducted with it versus the T. cruzi genome. The BLAST-p search revealed that T. cruzi GenBank M21331 had 14 gene sequences homologous to microtubule-associated protein (MAP) genes with 100\% amino acid sequence identity. To verify the similarities in non-human genes, a study comparing TRIM21 region sequences among mammalian species to the comparable human TRIM21 region showed that related sequences were also present in 11 mammalian species. The MAP genes homologous to Ag 36 form a family of at least 14 genes which mimic human immune genes in the IFN and TRIM families. This mimicry is of gene sequences and not their protein products or epitopes. These results appear to be the first description of molecular mimicry of immune genes in humans by a protozoan parasite.}, + author = {Winkler, Martin A. and Pan, Alfred A.}, + doi = {10.1007/s00436-024-08329-4}, + issn = {1432-1955}, + journal = {Parasitology Research}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, Antigen 36, Interferons, Molecular mimicry, TRIM genes, Trypanosoma cruzi}, + language = {en}, + month = {September}, + number = {9}, + pages = {319}, + title = {Molecular similarities between the genes for {Trypanosoma} cruzi microtubule-associated proteins, mammalian interferons, and {TRIMs}}, + url = {https://doi.org/10.1007/s00436-024-08329-4}, + urldate = {2024-10-20}, + volume = {123}, + year = {2024} +} + +@article{winkler_molecular_2025, + abstract = {Trypanosoma cruzi GenBank® M21331 encodes for Antigen 36 (Ag 36), which is a tandemly repeated T. cruzi antigen. GenBank M21331 has a gene sequence similarity to human immune genes IFN-α, IFN-β, and IFN-γ, as well as to human TRIM genes. A BLAST-p search revealed that T. cruzi GenBank M21331 had seven gene sequences homologous to microtubule-associated protein (MAP) genes with a 100\% amino acid sequence identity. There are 36 genes in the T. cruzi genome with {\textgreater}94\% identity to GenBank M21331, and these genes encode proteins ranging in size from 38 to 2011 amino acids in length, the largest containing 20, 25, and 30 repeats of the Ag 36 thirty-eight-amino-acid-sequence motif. The purpose of this study was to perform a genetic and molecular comparative analysis of T. cruzi GenBank M21331 to determine if this gene sequence is unique to the T. cruzi clade, present in the T. brucei clade, and/or exists in other trypanosomatids. There are seven homologous genes to GenBank M21331 in T. cruzi, but only one homolog found of this gene in T. brucei. The MAP genes in T. cruzi appear to have expanded at least eleven-fold in number compared to similar MAP genes in T. brucei. The DNA sequences and functions of these MAP genes in their respective species and clades will be discussed and are a fascinating area for further scientific study.}, + author = {Winkler, Martin A. and Pan, Alfred A.}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/pathogens14050476}, + issn = {2076-0817}, + journal = {Pathogens}, + keywords = {\textit{Trypanosoma brucei}, \textit{Trypanosoma cruzi}, {\textgreater}UseGalaxy.eu, Chagas disease, Microtubule-Associated Proteins, Protozoan Proteins, Trypanosoma cruzi, antigen 36, genetic diversity, microtubule associated protein, molecular bioinformatics}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {476}, + title = {Molecular and {Genetic} {Analysis} of the {Increased} {Number} of {Genes} for {Trypanosoma} cruzi {Microtubule} {Associated} {Proteins} in the {Class} {Kinetoplastida}}, + url = {https://www.mdpi.com/2076-0817/14/5/476}, + urldate = {2025-05-29}, + volume = {14}, + year = {2025} +} + @article{wirth_characterization_2019, abstract = {Microalgal biomass is an alternative feedstock for biogas production although its C/N ratio is usually lower than optimal, therefore co-fermentation is recommended. Identification of the core microbiome by metagenome analysis and prediction of functional characteristics are essential to make microalgal feedstock more sustainable and economically feasible. Biogas production from photoautotrophically grown Chlorella vulgaris (Ch. vulgaris) biomass (240 mL CH4 g oTS-1) and co-fermentation with maize silage (330 mL CH4 g oTS-1) has been studied in semi continuous laboratory biogas fermenters. Maize silage control yielded 310 mL CH4 g oTS-1. The microbial community and the read-based functional profiles, derived from these data, were examined during the process by using next-generation metagenome Ion Torrent sequencing technology. The read-based core microbiome consisted of 92 genera from which 60 abundant taxa were directly associated with the microbial methane producing food chain. The data-set was also analyzed in a genome-based approach. 65 bins were assembled, 52 of them belonged in the core biogas producing genera identified by the read-based metagenomes. The read-based and genome-based approaches complemented and verified each other. The functional profiles indicated a variety of glycoside hydrolases. Substantial rearrangements of the methanogen functions have also been observed. Co-fermentation of algal biomass and plant biomass can be carried out for an extended period of time without process failure. The microbial members of the inoculum are well conserved, feedstock composition cause relative abundance changes in the core microbiome.}, author = {Wirth, Roland and Böjti, Tamás and Lakatos, Gergely and Maróti, Gergely and Bagi, Zoltán and Rákhely, Gábor and Kovács, Kornél L.}, @@ -15391,9 +25119,12 @@ @article{wittke_eodie_2023 @article{wolf_-depth_2022, abstract = {Microglia are the tissue-resident macrophages of the retina and brain, being critically involved in organ development, tissue homeostasis, and response to cellular damage. Until now, little is known about the molecular signature of human retinal microglia and how it differs from the one of brain microglia and peripheral monocytes. In addition, it is not yet clear to what extent murine retinal microglia resemble those of humans, which represents an important prerequisite for translational research. The present study applies fluorescence-activated cell sorting to isolate human retinal microglia from enucleated eyes and compares their transcriptional profile with the one of whole retinal tissue, human brain microglia as well as classical, intermediate and non-classical monocytes. Finally, human retinal microglia are compared to murine retinal microglia, isolated from Cx3cr1GFP/+ mice. Whereas human retinal microglia exhibited a high grade of similarity in comparison to their counterparts in the brain, several enriched genes were identified in retinal microglia when compared to whole retinal tissue, as well as classical, intermediate, and non-classical monocytes. In relation to whole retina sequencing, several risk genes associated with age-related macular degeneration (AMD) and diabetic retinopathy (DR) were preferentially expressed in retinal microglia, indicating their potential pathophysiological involvement. Although a high degree of similarity was observed between human and murine retinal microglia, several species-specific genes were identified, which should be kept in mind when employing mouse models to investigate retinal microglia biology. In summary, this study provides detailed insights into the molecular profile of human retinal microglia, identifies a plethora of tissue-specific and species-specific genes in comparison to human brain microglia and murine retinal microglia, and thus highlights the significance of retinal microglia in human retinal diseases and for translational research approaches.}, author = {Wolf, Julian and Boneva, Stefaniya and Rosmus, Dennis-Dominik and Agostini, Hansjürgen and Schlunck, Günther and Wieghofer, Peter and Schlecht, Anja and Lange, Clemens}, + doi = {10.3389/fimmu.2022.863158}, issn = {1664-3224}, journal = {Frontiers in Immunology}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Macular Degeneration, Microglia}, + language = {eng}, + pages = {863158}, title = {In-{Depth} {Molecular} {Profiling} {Specifies} {Human} {Retinal} {Microglia} {Identity}}, url = {https://www.frontiersin.org/articles/10.3389/fimmu.2022.863158}, urldate = {2022-09-24}, @@ -15401,6 +25132,21 @@ @article{wolf_-depth_2022 year = {2022} } +@article{wolf_characterization_2021, + abstract = {With a worldwide prevalence of {\textasciitilde}12\%, pterygium is a common degenerative and environmentally triggered ocular surface disorder characterized by wing-shaped growth of conjunctival tissue onto the cornea that can lead to blindness if left untreated. This study characterizes the transcriptional profile and the cellular microenvironment of conjunctival pterygia and identifies novel pterygia-specific biomarkers. Formalin-fixed and paraffin-embedded pterygia as well as healthy conjunctival specimens were analyzed using MACE RNA sequencing (\textit{n} = 8 each) and immunohistochemistry (pterygia \textit{n} = 7, control \textit{n} = 3). According to the bioinformatic cell type enrichment analysis using xCell, the cellular microenvironment of pterygia was characterized by an enrichment of myofibroblasts, T-lymphocytes and various antigen-presenting cells, including dendritic cells and macrophages. Differentially expressed genes that were increased in pterygia compared to control tissue were mainly involved in autophagy (including \textit{DCN, TMBIM6}), cellular response to stress (including \textit{TPT1, DDX5}) as well as fibroblast proliferation and epithelial to mesenchymal transition (including \textit{CTNNB1, TGFBR1, and FN1}). Immunohistochemical analysis confirmed a significantly increased FN1 stromal immunoreactivity in pterygia when compared to control tissue. In addition, a variety of factors involved in apoptosis were significantly downregulated in pterygia, including \textit{LCN2, CTSD}, and \textit{NISCH}. Furthermore, 450 pterygia-specific biomarkers were identified by including transcriptional data of different ocular surface pathologies serving as controls (training group), which were then validated using transcriptional data of cultured human pterygium cells. Among the most pterygia-specific factors were transcripts such as \textit{AHNAK, RTN4, TPT1, FSTL1}, and \textit{SPARC}. Immunohistochemical validation of SPARC revealed a significantly increased stromal immunoreactivity in pterygia when compared to controls, most notably in vessels and intravascular vessel wall-adherent mononuclear cells. Taken together, the present study provides new insights into the cellular microenvironment and the transcriptional profile of pterygia, identifies new and specific biomarkers and in addition to fibrosis-related genes, uncovers autophagy, stress response and apoptosis modulation as pterygium-associated processes. These findings expand our understanding of the pathophysiology of pterygia, provide new diagnostic tools, and may enable new targeted therapeutic options for this common and sight-threatening ocular surface disease.}, + author = {Wolf, Julian and Hajdu, Rozina Ida and Boneva, Stefaniya and Schlecht, Anja and Lapp, Thabo and Wacker, Katrin and Agostini, Hansjürgen and Reinhard, Thomas and Auw-Hädrich, Claudia and Schlunck, Günther and Lange, Clemens}, + doi = {10.3389/fmed.2021.714458}, + issn = {2296-858X}, + journal = {Frontiers in medicine}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {714458}, + title = {Characterization of the {Cellular} {Microenvironment} and {Novel} {Specific} {Biomarkers} in {Pterygia} {Using} {RNA} {Sequencing}}, + url = {http://europepmc.org/abstract/MED/35174178}, + volume = {8}, + year = {2021} +} + @article{wolf_comparative_2021, abstract = {{\textless}h3{\textgreater}Abstract{\textless}/h3{\textgreater} {\textless}h3{\textgreater}Background{\textless}/h3{\textgreater} {\textless}p{\textgreater}Visual outcome of patients with neovascular age-related macular degeneration has significantly improved during the last years following the introduction of anti-vascular endothelial growth factor (VEGF) therapy. However, about one third of patients show persistent exudation and decreasing visual acuity despite recurrent anti-VEGF treatment, which implies a role of other, still unknown proangiogenic mediators.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Methods{\textless}/h3{\textgreater} {\textless}p{\textgreater}The present study applied transcriptional profiling of human and mouse (C57BL/6J wildtype) choroidal neovascularization (CNV) membranes each with reference to healthy control tissue to identify yet unrecognized mediators of CNV formation. Key factors were further investigated by immunohistochemistry as well as by intravitreal inhibition experiments and multiplex protein assays in the laser-induced CNV mouse model.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Results{\textless}/h3{\textgreater} {\textless}p{\textgreater}Transcriptional profiles of CNV membranes were characterized by enhanced activation of blood vessel development, cytoskeletal organization, and cytokine production, with angiogenesis and wound healing processes predominating in humans and activation of immune processes in mice. Besides several species-specific factors, 95 phylogenetically conserved CNV-associated genes were detected, among which fibroblast growth factor inducible-14 (FN14), a member of the tumor necrosis factor (TNF) receptor family, was identified as a key player of CNV formation. Blocking the pathway by intravitreal injection of a FN14 decoy receptor modulated the cytokine profile - most notably IL-6 - and led to a significant reduction of CNV size \textit{in vivo}.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Conclusions{\textless}/h3{\textgreater} {\textless}p{\textgreater}This study characterizes the transcriptome of human and mouse CNV membranes in an unprejudiced manner and identifies FN14 as a phylogenetically conserved mediator of CNV formation and a promising new therapeutic target for neovascular AMD.{\textless}/p{\textgreater}{\textless}h3{\textgreater}Funding{\textless}/h3{\textgreater} {\textless}p{\textgreater}This study was funded by the Helmut-Ecker-Stiftung and the Volker-Homann-Stiftung.{\textless}/p{\textgreater}}, author = {Wolf, Julian and Schlecht, Anja and Rosmus, Dennis-Dominik and Boneva, Stefaniya and Agostini, Hansjürgen and Schlunck, Günther and Wieghofer, Peter and Lange, Clemens}, @@ -15464,7 +25210,8 @@ @article{wolf_deciphering_2022 doi = {10.1167/iovs.63.3.9}, issn = {1552-5783}, journal = {Investigative Ophthalmology \& Visual Science}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Monocytes, Vitreous Body}, + language = {eng}, month = {March}, number = {3}, pages = {9}, @@ -15488,6 +25235,35 @@ @article{wolf_human_2022 year = {2022} } +@article{wolf_proteotranscriptomic_2025, + abstract = {Background +Retinoblastoma is a rare pediatric eye cancer caused by mutations in the RB1 gene, which regulates retinal cell growth. Early detection and treatment are critical for preventing vision loss and improving survival outcomes. This study aimed to perform an integrated proteotranscriptomic characterization of human retinoblastoma to provide a deeper understanding of disease biology and to identify novel therapeutic targets. + +Methods +Paired tumor and adjacent retinal tissue samples were dissected from seven eyes. RNA sequencing and liquid chromatography-mass spectrometry were performed on the same samples. The spatially resolved cellular landscape was assessed using Imaging Mass Cytometry (IMC). + +Results +The correlation between RNA and protein level was moderate with variations across different pathways, underscoring the value of an integrated proteotranscriptomic approach. IMC identified more than 67,000 single cells in 11 distinct clusters, including antigen presenting cells, T cells, stroma cells, vascular cells and two clusters of proliferating and CD44/c-Myc positive tumor cells. Antigen presenting cells expressed higher levels of CD68 in retinoblastoma compared to controls. + +Conclusions +CD44+ and high-c-Myc-expressing tumor cells may represent cancer stem cells with possible involvement in metastasis, warranting further validation. Our multilayered approach could pave the way for enhanced molecular assessments and novel targeted therapies for human retinoblastoma.}, + author = {Wolf, Julian and Hajdu, Rozina Ida and Boneva, Stefaniya and Godbole, Ira and Stürzbecher, Lucas and Auw-Haedrich, Claudia and Lagrèze, Wolf A. and Agostini, Hansjürgen and Reinhard, Thomas and Tholen, Stefan and Schilling, Oliver and Schlunck, Günther and Bengsch, Bertram and Lange, Clemens}, + doi = {10.3389/fonc.2025.1571702}, + issn = {2234-943X}, + journal = {Frontiers in Oncology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {May}, + pages = {1571702}, + pmcid = {PMC12088971}, + pmid = {40395327}, + title = {A proteotranscriptomic approach to dissect the molecular landscape of human retinoblastoma}, + url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12088971/}, + urldate = {2025-05-28}, + volume = {15}, + year = {2025} +} + @article{wolf_transcriptional_2020, abstract = {This study characterizes the transcriptome and the cellular tumor microenvironment (TME) of conjunctival melanoma (CM) and identifies prognostically relevant biomarkers. 12 formalin-fixed and paraffin-embedded CM were analyzed by MACE RNA sequencing, including six cases each with good or poor clinical outcome, the latter being defined by local recurrence and/or systemic metastases. Eight healthy conjunctival specimens served as controls. The TME of CM, as determined by bioinformatic cell type enrichment analysis, was characterized by the enrichment of melanocytes, pericytes and especially various immune cell types, such as plasmacytoid dendritic cells, natural killer T cells, B cells and mast cells. Differentially expressed genes between CM and control were mainly involved in inhibition of apoptosis, proteolysis and response to growth factors. POU3F3, BIRC5 and 7 were among the top expressed genes associated with inhibition of apoptosis. 20 genes, among them CENPK, INHA, USP33, CASP3, SNORA73B, AAR2, SNRNP48 and GPN1, were identified as prognostically relevant factors reaching high classification accuracy (area under the curve: 1.0). The present study provides new insights into the TME and the transcriptional profile of CM and additionally identifies new prognostic biomarkers. These results add new diagnostic tools and may lead to new options of targeted therapy for CM.}, author = {Wolf, Julian and Auw-Haedrich, Claudia and Schlecht, Anja and Boneva, Stefaniya and Mittelviefhaus, Hans and Lapp, Thabo and Agostini, Hansjürgen and Reinhard, Thomas and Schlunck, Günther and Lange, Clemens A. K.}, @@ -15495,7 +25271,7 @@ @article{wolf_transcriptional_2020 doi = {10.1038/s41598-020-72864-0}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Gene Expression Regulation, Neoplastic}, language = {en}, month = {October}, note = {Number: 1 @@ -15509,6 +25285,23 @@ @article{wolf_transcriptional_2020 year = {2020} } +@article{wolf_transcriptional_2022, + abstract = {Corneal transplantation is one of the most common forms of tissue transplantation worldwide. Donor corneal tissue used in transplantation is provided by eye banks, which store the tissue in culture medium after procurement. To date, the effects of cell culture on human corneal tissue have not been fully elucidated. Using the 3' RNA sequencing method for massive analysis of cDNA ends (MACE), we show that cultivation of corneal tissue leads to significant changes in a variety of molecular processes in human corneal tissue that go well beyond aspects of previously known culture effects. Functionally grouped network analysis revealed nine major groups of biological processes that were affected by corneal organ culture, among them keratinization, hypoxia, and angiogenesis, with genes from each group being affected by culture time. A cell type deconvolution analysis revealed significant modulations of the corneal immune cell profile in a time dependent manner. The results suggest that current culture conditions should be further refined and that prolonged cultivation may be detrimental. Recently, we showed that MACE enables transcriptional profiling of formalin-fixed and paraffin-embedded (FFPE) conjunctival tissue with high accuracy even after more than 10 years of storage. Here we demonstrate that MACE provides comparable results for native and FFPE corneal tissue, confirming that the technology is suitable for transcriptome analysis of a wide range of archived diseased corneal samples stored in histological archives. Finally, our data underscore the feasibility of bioinformatics cell-type enrichment analysis in bulk RNA-seq data to profile immune cell composition in fixed and archived corneal tissue samples, for which RNA-seq analysis of individual cells is often not possible.}, + author = {Wolf, Julian and Kammrath Betancor, Paola and Maier, Philip and Heinzelmann, Sonja Ute and Jiang, Jana and Lange, Clemens and Reinhard, Thomas and Schlunck, Günther and Lapp, Thabo}, + doi = {10.3390/ijms232314507}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Eye Banks, Organ Preservation}, + language = {eng}, + month = {November}, + number = {23}, + pages = {14507}, + title = {Transcriptional {Profiling} {Provides} {New} {Insights} into {Organ} {Culture}-{Induced} {Changes} in {Human} {Donor} {Corneas}}, + url = {http://europepmc.org/abstract/MED/36498835}, + volume = {23}, + year = {2022} +} + @article{wolf_transcriptional_2023, abstract = {This study characterizes the transcriptional profile and the cellular tumor microenvironment of conjunctival extranodal marginal zone lymphoma (EMZL) and identifies prognostically relevant biomarkers. Ten formalin-fixed and paraffin-embedded conjunctival EMZL and eight healthy conjunctival specimens were analyzed by Massive Analysis of cDNA Ends (MACE) RNA sequencing. The 3417 upregulated genes in conjunctival EMZL were involved in processes such as B cell proliferation and Rac protein signaling, whereas the 1188 downregulated genes contributed most significantly to oxidative phosphorylation and UV protection. The tumor microenvironment, as determined by deconvolution analysis, was mainly composed of multiple B cell subtypes which reflects the tumor’s B cell lineage. However, several T cell types, including T helper 2 cells and regulatory T cells, as well as innate immune cell types, such as anti-inflammatory macrophages and plasmacytoid dendritic cells, were also strongly enriched in conjunctival EMZL. A 13-biomarker prognostic panel, including S100A8 and S100A9, classified ocular and extraocular tumor recurrence, exceeded prognostic accuracy of Ann Arbor and American Joint Committee on Cancer (AJCC) staging, and demonstrated prognostic value for patient survival in 21 different cancer types in a database of 12,332 tumor patients. These findings may lead to new options of targeted therapy and may improve prognostic prediction for conjunctival EMZL.}, author = {Wolf, Julian and Reinhard, Thomas and Hajdu, Rozina Ida and Schlunck, Günther and Auw-Haedrich, Claudia and Lange, Clemens}, @@ -15516,7 +25309,7 @@ @article{wolf_transcriptional_2023 doi = {10.3390/biom13010115}, issn = {2218-273X}, journal = {Biomolecules}, - keywords = {{\textgreater}UseGalaxy.eu, EMZL, RNA sequencing, cellular tumor microenvironment, conjunctival lymphoma, formalin-fixation and paraffin-embedding (FFPE), prognosis, recurrence}, + keywords = {{\textgreater}UseGalaxy.eu, Conjunctival Neoplasms, EMZL, Lymphoma, B-Cell, Marginal Zone, RNA sequencing, cellular tumor microenvironment, conjunctival lymphoma, formalin-fixation and paraffin-embedding (FFPE), prognosis, recurrence}, language = {en}, month = {January}, note = {Number: 1 @@ -15610,6 +25403,81 @@ @article{wright*_structure_2018 year = {2018} } +@article{wu_atlas_2025, + abstract = {We present an atlas of genes that respond to thyroid hormone in the adult mouse mediobasal hypothalamus. Based on droplet-based single nuclei RNA-seq method and batch transcriptome analyses, the atlas lists putative target genes of the hormone nuclear receptors in 20 different types of neuronal and glial cells. The transcriptional regulation of these genes varies extensively across neuronal and glial cell types. However, while astrocytes appear to be highly sensitive to thyroid hormone stimulation, differentiated oligodendrocytes are relatively insensitive. This atlas is expected to promote future investigations into the molecular and cellular mechanisms that underlie the numerous functions of thyroid hormone in the hypothalamic circuits.}, + author = {Wu, Shijia and Dellinger, Julien and Markossian, Suzy and Dusabyinema, Yves and Guyot, Romain and Hughes, Sandrine and Aubert, Denise and Fackeure, Marie and Gauthier, Karine and Gillet, Benjamin and Jiang, Wenzheng and Flamant, Frédéric}, + doi = {10.1210/endocr/bqaf084}, + issn = {0013-7227}, + journal = {Endocrinology}, + keywords = {{\textgreater}UseGalaxy.eu, Gene Expression Regulation, Hypothalamus, Thyroid Hormones}, + language = {eng}, + month = {June}, + number = {6}, + pages = {bqaf084}, + title = {An {Atlas} of {Thyroid} {Hormone} {Responsive} {Genes} in {Adult} {Mouse} {Hypothalamus}}, + url = {https://doi.org/10.1210/endocr/bqaf084}, + urldate = {2025-05-28}, + volume = {166}, + year = {2025} +} + +@article{wu_comparative_2025, + abstract = {This study explores the phylogeny and mitochondrial genomics of Ovulidae, a family of marine gastropods related to Cypraeidae, by analyzing mitochondrial genomes from 14 of 15 species collected off C...}, + author = {Wu, Qiong and Xiang, Peng and Fan, ShiHao and Chen, GuangCheng and Xing, BingPeng}, + doi = {10.1002/ece3.71224}, + issn = {2045-7758}, + journal = {Ecology and Evolution}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {April}, + note = {Publisher: John Wiley \& Sons, Ltd}, + number = {4}, + pages = {e71224}, + shorttitle = {Comparative {Genomic} and {Mitochondrial} {Phylogenetic} {Relationships} of {Ovulidae} ({Mollusca}}, + title = {Comparative {Genomic} and {Mitochondrial} {Phylogenetic} {Relationships} of {Ovulidae} ({Mollusca}: {Gastropoda}) {Along} the {Chinese} {Coast}}, + url = {https://onlinelibrary.wiley.com/doi/10.1002/ece3.71224}, + urldate = {2025-05-29}, + volume = {15}, + year = {2025} +} + +@article{wu_differential_2025, + abstract = {As ectotherms highly sensitive to environmental temperature fluctuations, skinks (a small lizard) are increasingly vulnerable to population instability due to global heatwaves. A clade model analysis of four Chinese skink species (Plestiodon capito, Plestiodon chinensis, Sphenomorphus indicus, and Scincella modesta) revealed positive selection acting on the ND6 gene in Sp. indicus. This species exhibits codon alterations in ND6, shifts its expression pathway and potentially decouples ND6 from high-temperature stress response mechanisms. To validate these findings, transcriptomic profiling was conducted to assess mitochondrial protein-coding gene (PCG) expression patterns under thermal stress. Using RT-qPCR, liver mitochondrial PCG transcript levels were compared between high-temperature (34 °C) and control (25 °C) groups in skink populations from distinct latitudes. Low-latitude species (P. chinensis and Sc. modesta) exhibited metabolic downregulation, characterized by a significant suppression of mitochondrial gene expression. Specifically, P. chinensis showed the downregulation of six mitochondrial genes (COII, COIII, ATP6, ND2, ND4, ND6) while upregulating one (ND1). By contrast, Sc. modesta showed the downregulation of nine genes (COI, COII, COIII, ATP8, ND1, ND3, ND4, ND4L, CYTB) and upregulated two (ND5, ND6). By contrast, high-latitude species exhibited divergent patterns: P. capito downregulated four genes (COI, COII, COIII, ND4L) and upregulated four others (ND1, ND2, ND3, ND4), whereas Sp. indicus downregulated six genes (COI, COII, ND2, ND3, ND4, ND4L) and upregulated one (ND5). These regulatory disparities suggest that low-latitude skinks have a greater capacity for metabolic depression to cope with chronic stress, whereas their high-latitude counterparts exhibit different adaptations. The findings provide valuable insights into assessing the adaptive potential of species in warming environments, particularly for ectotherms with limited thermoregulatory capacities.}, + author = {Wu, Xuxiang and Zhan, Lemei and Storey, Kenneth B. and Zhang, Jiayong and Yu, Danna}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/ani15070999}, + issn = {2076-2615}, + journal = {Animals}, + keywords = {\textit{RT}-qPCR, {\textgreater}UseGalaxy.eu, high-temperature stress, mitochondrial genome expression, selection pressure, skink}, + language = {en}, + month = {January}, + note = {Number: 7 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {7}, + pages = {999}, + title = {Differential {Mitochondrial} {Genome} {Expression} of {Four} {Skink} {Species} {Under} {High}-{Temperature} {Stress} and {Selection} {Pressure} {Analyses} in {Scincidae}}, + url = {https://www.mdpi.com/2076-2615/15/7/999}, + urldate = {2025-05-29}, + volume = {15}, + year = {2025} +} + +@article{wu_genome_2025, + author = {Wu, Jingtong and Wen, Yongxian and You, Lv and Wei, Xiaoyu and Wang, Junhua and Zhu, Ge and Li, Shijun}, + doi = {10.3389/fmicb.2025.1498995}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Salmonella, colistin-resistant, mcr-1.1, multidrug resistance, whole-genome sequence}, + language = {English}, + month = {January}, + note = {Publisher: Frontiers}, + title = {Genome analysis of colistin-resistant {Salmonella} isolates from human sources in {Guizhou} of southwestern {China}, 2019–2023}, + url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1498995/full}, + urldate = {2025-02-16}, + volume = {16}, + year = {2025} +} + @article{wurzbacher_planctoellipticum_2024, abstract = {In the present study, we characterise a strain isolated from the wastewater aeration lagoon of a sugar processing plant in Schleswig (Northern Germany) by Heinz Schlesner. As a pioneer in planctomycetal research, he isolated numerous strains belonging to the phylum Planctomycetota from aquatic habitats around the world. Phylogenetic analyses show that strain SH412T belongs to the family Planctomycetaceae and shares with 91.6\% the highest 16S rRNA gene sequence similarity with Planctopirus limnophila DSM 3776T. Its genome has a length of 7.3 Mb and a G + C content of 63.6\%. Optimal growth of strain SH412T occurs at pH 7.0–7.5 and 28 °C with its pigmentation depending on sunlight exposure. Strain SH412T reproduces by polar asymmetric division (“budding”) and forms ovoid cells. The cell size determination was performed using a semi-automatic pipeline, which we first evaluated with the model species P. limnophila and then applied to strain SH412T. Furthermore, the data acquired during time-lapse analyses suggests a lifestyle switch from flagellated daughter cells to non-flagellated mother cells in the subsequent cycle. Based on our data, we suggest that strain SH412T represents a novel species within a novel genus, for which we propose the name Planctoellipticum variicoloris gen. nov., sp. nov., with strain SH412T (= CECT 30430T = STH00996T, the STH number refers to the Jena Microbial Resource Collection JMRC) as the type strain of the new species.}, author = {Wurzbacher, Carmen E. and Haufschild, Tom and Hammer, Jonathan and van Teeseling, Muriel C. F. and Kallscheuer, Nicolai and Jogler, Christian}, @@ -15617,7 +25485,7 @@ @article{wurzbacher_planctoellipticum_2024 doi = {10.1038/s41598-024-56373-y}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, Bacterial genomics, Bacterial physiology}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial genomics, Bacterial physiology, Fatty Acids, Wastewater}, language = {en}, month = {March}, note = {Publisher: Nature Publishing Group}, @@ -15636,7 +25504,7 @@ @article{wylie_whole-genome_2019 doi = {10.3389/fcimb.2019.00014}, issn = {2235-2988}, journal = {Frontiers in Cellular and Infection Microbiology}, - keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Klebsiella pneumoniae, Strain tracking, Urinary tract infection (UTI), single nucleotide variants (SNVs), whole genome sequencing}, + keywords = {+Methods, +UsePublic, {\textgreater}UseGalaxy.eu, Klebsiella pneumoniae, Strain tracking, Urinary tract infection (UTI), Whole Genome Sequencing, single nucleotide variants (SNVs), whole genome sequencing}, language = {English}, title = {Whole-{Genome} {Sequencing} of {Klebsiella} pneumoniae {Isolates} to {Track} {Strain} {Progression} in a {Single} {Patient} {With} {Recurrent} {Urinary} {Tract} {Infection}}, url = {https://www.frontiersin.org/articles/10.3389/fcimb.2019.00014/full}, @@ -15652,7 +25520,8 @@ @article{wynne_apoe_2023 editor = {Chacinska, Agnieszka and Pfeffer, Suzanne R and Chacinska, Agnieszka}, issn = {2050-084X}, journal = {eLife}, - keywords = {{\textgreater}UseGalaxy.eu, APOE, alzheimer's disease, mitochondria}, + keywords = {{\textgreater}UseGalaxy.eu, APOE, Apolipoprotein E4, Mitochondria, alzheimer's disease, mitochondria}, + language = {eng}, month = {May}, note = {Publisher: eLife Sciences Publications, Ltd}, pages = {e85779}, @@ -15663,6 +25532,87 @@ @article{wynne_apoe_2023 year = {2023} } +@article{xavier_diversity_2025, + abstract = {\textit{Pseudomonas aeruginosa} is a major pathogen associated with hospital-acquired infections, and the spread of carbapenem-resistant isolates highlights the urgency of developing non-conventional therapies, such as phage therapy. For this alternative to be effective, understanding phage-host interactions is crucial for the selection of candidate phages and offers new insights into these dynamics. \textbf{Background/Objectives}: This study aimed to characterize prophage diversity in clinical \textit{P. aeruginosa} genomes, assess the relationship between phages and the CRISPR/Cas system, and investigate the potential role of prophages in disseminating resistance genes. \textbf{Methods}: A total of 141 genomes from Brazilian hospitals were analyzed. Prophage detection was performed using VIBRANT, and in silico analyses were conducted to evaluate taxonomic diversity, the presence of resistance genes, phage life cycle, genomic distribution, and the presence of the CRISPR/Cas system. \textbf{Results}: A total of 841 viral sequences were identified by the VIBRANT tool, of which 498 were confirmed by CheckV, with a predominance of the class Caudoviricetes and high overall phage diversity. No statistically significant difference was observed in the number of prophages between isolates with and without CRISPR/Cas systems. Prophages carrying resistance genes such as \textit{rsmA}, \textit{OXA-56}, \textit{SPM-1}, and others were detected in isolates harboring the type I-C CRISPR/Cas system. Additionally, prophages showed no preference for specific insertion sites along the bacterial genome. \textbf{Conclusions}: These findings provide evidence of a well-established phage-host relationship. The dual role of prophages-as vectors of antimicrobial resistance and as potential therapeutic agents-reflects their dynamic impact on bacterial communities and reinforces their importance in developing new strategies to combat antimicrobial resistance.}, + author = {Xavier, Keyla Vitória Marques and Silva, Adrianne Maria de Albuquerque and Luz, Ana Carolina de Oliveira and da Silva, Felipe Santana Caboclo and de Melo, Beatriz Souza Toscano and Pitta, João Luiz de Lemos Padilha and Leal-Balbino, Tereza Cristina}, + doi = {10.3390/genes16060656}, + issn = {2073-4425}, + journal = {Genes}, + keywords = {{\textgreater}UseGalaxy.eu, Drug Resistance, Bacterial, Prophages, Pseudomonas aeruginosa}, + language = {eng}, + month = {May}, + number = {6}, + pages = {656}, + title = {Diversity and {Role} of {Prophages} in \textit{{Pseudomonas} aeruginosa}: {Resistance} {Genes} and {Bacterial} {Interactions}}, + url = {http://europepmc.org/abstract/MED/40565548}, + volume = {16}, + year = {2025} +} + +@article{xie_benchmarking_2025, + abstract = {CRISPR/Cas9 has facilitated yeast functional genomics by generating a large number +of precise genetic variants in a very short period of time. This enabled the interrogation +of reconstituted natural genetic variants across different genetic backgrounds or +entirely synthetic mutations to discover novel or improved functions. However, Cas9 +only targets a limited genomic sequence space due to its preference for G-rich PAM +sequences. In this study, we close this gap by developing a CRISPR/Cas12a-based system +to engineer user-defined genetic variants targeting T-rich PAM sequences. Our system +adopts a homology-integrated design and the most PAM-relaxed Cas12a characterized +in yeast to date. These features collectively enabled the creation of genetic variant +libraries and multiplex edited strains. This genome editing tool can be used together +with Cas9-based tools to interrogate a greater genomic sequence space.}, + author = {Xie, Weiyu and Cai, Zhenkun and Bao, Zehua}, + copyright = {Copyright © 2025 Xie et al.}, + doi = {10.1128/aem.01618-25}, + journal = {Applied and Environmental Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {EN}, + month = {December}, + note = {Publisher: American Society for Microbiology1752 N St., N.W., Washington, DC}, + title = {Benchmarking the {PAM} compatibility of {Cas12a} variants for high-throughput yeast genetic variant engineering}, + url = {https://journals.asm.org/doi/10.1128/aem.01618-25}, + urldate = {2025-12-26}, + year = {2025} +} + +@article{xu_characterization_2025, + abstract = {To enhance our understanding of the phylogenetics and evolutionary processes within Dacinae, we sequenced and analyzed four complete mitogenomes for the first time, specifically Acroceratitis separata, Acrotaeniostola quadrivittata, Gastrozona parviseta, and Paragastrozona vulgaris, which represent Gastrozonini species. Our results indicated that these four mitogenomes, including A. separata, A. quadrivittata, G. parviseta, and P. vulgaris, comprised 37 mitochondrial genes and an A+T-control region, with a total length of 16,603 bp, 16,112 bp, 16,691 bp, and 16,594 bp, revealing a notably high AT content reaching 77.4\%, 78.4\%, 75.1\%, and 75.1\%, respectively. Our phylogenetic analyses using Bayesian inference and Maximum Likelihood methods under site-homogeneous models consistently demonstrated their superiority over the site-heterogeneous mixture model CAT + GTR, given the currently accepted phylogenetic framework. Apart from a few species demonstrating unstable placements, the inferred phylogenetic relationships among the three tribes were strongly supported as monophyletic groups, with the topology represented as ((Ceratitidini + Gastrozonini) + Dacini), and most branches displaying moderate-to-high support values, of which four newly sequenced mitogenomes and A. dissimilis robustly formed a single clade representing Gastrozonini. This study substantially augments the existing mitogenome data, thereby providing more profound insight into the evolutionary history and higher-level phylogenetic structure within the Dacinae.}, + author = {Xu, Deliang and Ding, Shuangmei and Zeng, Xiaojie and Du, Lele}, + copyright = {cc by}, + doi = {10.3390/ani15223301}, + issn = {2076-2615}, + journal = {Animals}, + keywords = {{\textgreater}UseGalaxy.eu, Gastrozonini, Mitochondrial genome, Phylobayes, True Fruit Flies}, + language = {eng}, + month = {November}, + number = {22}, + pages = {3301}, + pmcid = {PMC12649545}, + pmid = {41302010}, + shorttitle = {Characterization of the {Complete} {Mitogenomes} of {Four} {Dacinae} {Species} ({Diptera}}, + title = {Characterization of the {Complete} {Mitogenomes} of {Four} {Dacinae} {Species} ({Diptera}: {Tephritidae}) with {Phylogenetic} {Analysis}}, + url = {https://europepmc.org/articles/PMC12649545}, + urldate = {2025-12-26}, + volume = {15}, + year = {2025} +} + +@article{xu_mitogenomic_2025, + abstract = {Mitochondrial genomes are powerful tools for taxonomic delimitation and species identification, yet they remain scarce for Chironomidae (Diptera). In this study, we assembled and annotated 63 new mitochondrial genomes, encompassing 63 species within 39 genera in Orthocladiinae \<i\>sensu lato\</i\> (including Prodiamesinae and Orthocladiinae) and Chironominae by whole-genome sequencing, marking the first report of mitochondrial genome data for the Xiaomyini. Comparative analyses revealed structural variation, including transfer RNA gene rearrangements, along with strong nucleotide composition bias, codon usage patterns, and gene-specific selection pressure differences. Distinct evolutionary dynamics were detected among protein-coding genes, ribosomal RNAs, transfer RNAs, and the control region. Heterogeneity analyses and phylogenetic analyses showed that amino acid datasets perform better for basal branch of Orthocladiinae relationships, although the resolution within non-basal branches of Orthocladiinae remains limited. By substantially increasing both the number and taxonomic breadth of mitochondrial genomes in Chironomidae, this study delivers a vital foundation for future multi-marker phylogenetic reconstruction, taxonomic revision, and rapid species identification, with direct applications to biodiversity conservation and freshwater ecosystem monitoring.}, + author = {Xu, Hai-Feng and Xiao, Xiu-Ru and Zhang, Zhi-Chao and Li, Yu-Fan and Lin, Xiao-Long}, + doi = {10.3390/biology14091178}, + issn = {2079-7737}, + journal = {Biology}, + keywords = {{\textgreater}UseGalaxy.eu, Mitogenome, Ngs, Rearrangement}, + month = {September}, + number = {9}, + pages = {1178}, + title = {Mitogenomic {Insights} into {Orthocladiinae} ({Diptera}: {Chironomidae}): {Structural} {Diversity} and {Phylogenetic} {Implications}}, + url = {https://europepmc.org/articles/PMC12467726}, + volume = {14}, + year = {2025} +} + @article{xu_reprogramming_2023, abstract = {Xu and colleagues report that the poly-U-specific endoribonuclease ENDU-2/ENDOU activates a transcriptional reprogramming after a brief heat shock and this has a long-term beneficial effect in the model organism C. elegans.}, author = {Xu, Fan and Li, Ruoyao and von Gromoff, Erika D. and Drepper, Friedel and Knapp, Bettina and Warscheid, Bettina and Baumeister, Ralf and Qi, Wenjing}, @@ -15670,7 +25620,7 @@ @article{xu_reprogramming_2023 doi = {10.1038/s41467-023-39882-8}, issn = {2041-1723}, journal = {Nature Communications}, - keywords = {{\textgreater}UseGalaxy.eu, Cell biology, Cell signalling, Genetics}, + keywords = {{\textgreater}UseGalaxy.eu, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Cell biology, Cell signalling, Genetics}, language = {en}, month = {July}, note = {Number: 1 @@ -15684,6 +25634,27 @@ @article{xu_reprogramming_2023 year = {2023} } +@article{yaghoubi_khanghahi_transcriptomic_2025, + abstract = {This study investigates the efficacy of plant growth-promoting bacteria (PGPB) in improving stress tolerance in plants by analyzing the molecular and biochemical bases in durum wheat grain. An experiment was conducted where soil and seeds were inoculated with PGPB, under drought and salinity stress. 16 S rRNA sequencing indicated no change in grain bacterial communities in response to biofertilizers and stress. However, a genome-wide analysis identified 153 up-regulated and 33 down-regulated plant genes in response to PGPB, predominantly enriched in stress-related biological processes. These genes specifically encode for proteins involved in metabolite interconversion enzyme, chaperone, protein modifying enzyme, and transporters, which are functionally related groups assisting protein folding in the cell under stress conditions. Moreover, pathway analysis confirmed related changes at the metabolite and enzyme activity levels. In this regard, PGPB-treated plants exhibited heightened activity of both enzymatic and non-enzymatic (e.g., thioredoxins, peroxiredoxins, etc.) antioxidants under stress, showcasing significant enhancements ranging from + 27\% to + 283\% and + 36\% to + 266\%, respectively. Further elucidation of biochemical pathways revealed alterations in the activation of non-antioxidant enzymes in PGPB-treated plants, exemplified by increased activities of glutamate synthase (40-44\%) and decreased activities of protein-tyrosine-phosphatase (29-31\%) under both stresses, as well as elevated activities of anthocyanidin reductase (91\%) and lipoxygenases (18\%) specifically under drought. Overall, the present research highlighted the potential of beneficial bacteria in improving plant stress tolerance, especially under drought, through shifting transcriptome expression of plant genes and employing multiple protective strategies which can complement each other.Supplementary informationThe online version contains supplementary material available at 10.1007/s12298-025-01686-z.}, + author = {Yaghoubi Khanghahi, Mohammad and AbdElgawad, Hamada and Curci, Maddalena and Garrigues, Romain and Korany, Shereen Magdy and Alsherif, Emad A and Verbruggen, Erik and Spagnuolo, Matteo and Addesso, Rosangela and Sofo, Adriano and Beemster, Gerrit T S and Crecchio, Carmine}, + copyright = {cc by}, + doi = {10.1007/s12298-025-01686-z}, + issn = {0974-0430}, + journal = {Physiology and molecular biology of plants}, + keywords = {{\textgreater}UseGalaxy.eu, Durum Wheat Grain, Endophytic Bacterial Community, Plant Growth-promoting Bacteria, Stress, Transcriptomics}, + language = {eng}, + month = {December}, + number = {12}, + pages = {2121--2143}, + pmcid = {PMC12715099}, + pmid = {41425608}, + title = {Transcriptomic, biochemical, and microbiome assessments into drought and salinity tolerance in durum wheat mediated by plant growth-promoting bacteria}, + url = {https://europepmc.org/articles/PMC12715099}, + urldate = {2025-12-26}, + volume = {31}, + year = {2025} +} + @article{yan_diet-like_2023, abstract = {Direct interspecies electron transfer (DIET) has been demonstrated to be an efficient type of mutualism in methanogenesis. However, few studies have reported its presence in mixed microbial communities and its trigger mechanism in the natural environment and engineered systems. Here, we reported DIET-like mutualism of Geobacter and methanogens in the planktonic microbiome for the first time in anaerobic electrochemical digestion (AED) fed with propionate, potentially triggered by excessive cathodic hydrogen (56 times higher than the lowest) under the electrochemical condition. In contrast with model prediction without DIET, the highest current density and hydrogen and methane production were concurrently observed at −0.2 V where an abundance of Geobacter (49\%) and extracellular electron transfer genes were identified in the planktonic microbiome via metagenomic analysis. Metagenomic assembly genomes annotated to Geobacter anodireducens were identified alongside two methanogens, Methanothrix harundinacea and Methanosarcina mazei, which were previously identified to participate in DIET. This discovery revealed that DIET-like mutualism could be triggered without external conductive materials, highlighting its potentially ubiquitous presence. Such mutualism simultaneously boosted methane and hydrogen production, thereby demonstrating the potential of AED in engineering applications.}, author = {Yan, Yuqing and Zhang, Jiayao and Tian, Lili and Yan, Xuejun and Du, Lin and Leininger, Aaron and Zhang, Mou and Li, Nan and Ren, Zhiyong Jason and Wang, Xin}, @@ -15700,6 +25671,58 @@ @article{yan_diet-like_2023 year = {2023} } +@article{yang_complete_2025, + abstract = {The snapping shrimp Alpheus is the genus with most species in the Alpheidae family. In this study, the mitochondrial genome of Alpheus brevicristatus De Haan, 1844 has been sequenced and analyzed. The circular mitogenome was 15,705 bp in length with an A+T content of 62.64\%. It contained 37 genes typically found in metazoans, and one non-coding region. Phylogenetic analysis highly supported the placement of A. brevicristatus within Alpheidae. This study provides important mitochondrial genome data that could be used for further phylogenetic and evolutionary study of caridean snapping shrimps.}, + author = {Yang, Yan-Bin and Zhu, Fang-Chao and Liu, Xin and Zhao, Lin-Tao and Yu, Shuo and Chen, Xu-Yang}, + doi = {10.1080/23802359.2025.2487072}, + issn = {null}, + journal = {Mitochondrial DNA Part B}, + keywords = {{\textgreater}UseGalaxy.eu, Alpheus brevicristatus, Mitochondrial genome, phylogenetic analysis, snapping shrimp}, + month = {July}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/23802359.2025.2487072}, + number = {7}, + pages = {554--557}, + pmid = {40503060}, + title = {The complete mitochondrial genome of the snapping shrimp, {Alpheus} brevicristatus {De} {Haan}, 1844 ({Crustacea}, {Decapoda}, {Alpheidae})}, + url = {https://doi.org/10.1080/23802359.2025.2487072}, + urldate = {2025-07-12}, + volume = {10}, + year = {2025} +} + +@article{yang_opposing_2025, + abstract = {Gene duplication generates gene paralogs that may undergo diverse fates during evolution, and thus serves as a potent catalyst of biological complexity. Genetic paralogs frequently share redundant functions and may also exhibit antagonistic activities by competing for common interaction partners. Here we show that the gene paralogs NRBP1 and NRBP2 oppositely regulate long interspersed nuclear element-1 (L1) retrotransposition, via influencing integrity of the L1 ribonucleoprotein complex. We demonstrate that the opposing roles of NRBP1 and NRBP2 are not results of a competitive mechanism, but rather due to targeting NRBP1 for degradation by NRBP2, probably through heterodimer formation. Moreover, our phylogenetic analysis shows that the regulatory function of NRBP2 may be acquired later during evolution, suggesting that evolutionary pressure has favored this functional fine-tuning of NRBP1. In summary, our findings not only identify NRBP1/2 as L1 regulators and implicate their involvement in human pathogenesis, but also provide a mechanistic insight into the regulatory details arising from gene duplication.}, + author = {Yang, Wei and Cong, Shaobo and Li, Ruoyao and Schwarz, Jennifer and Schulze, Thilo and Gevelhoff, Raban A. and Chen, Xinyan and Ullrich, Sara and Falkenstein, Kristina and Ott, Denis and Eixmann, Pia and Trentino, Angelica and Thien, Antje and Heidmann, Thierry and Schulze, Ekkehard and Warscheid, Bettina and Baumeister, Ralf and Qi, Wenjing}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41467-025-61626-z}, + issn = {2041-1723}, + journal = {Nature Communications}, + keywords = {{\textgreater}UseGalaxy.eu, Long Interspersed Nucleotide Elements, Molecular Chaperones, Nuclear Pore Complex Proteins, Protein quality control, Transposition}, + language = {en}, + month = {July}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {6327}, + title = {Opposing roles of pseudokinases {NRBP1} and {NRBP2} in regulating {L1} retrotransposition}, + url = {https://www.nature.com/articles/s41467-025-61626-z}, + urldate = {2025-09-03}, + volume = {16}, + year = {2025} +} + +@patent{yanniv_floe1-mediated_2021, + address = {US}, + assignee = {The Board Of Trustees Of The Leland Stanford Junior University}, + author = {Yanniv, Dorone and Steven, Boeynaems and D, Gitler Aaron and Yon, Rhee Seung}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {August}, + number = {US 2023/0416772 A1}, + title = {Floe1-mediated {Modulation} {Of} {Seed} {Longevity} {And} {Germination} {Rates}}, + url = {https://lens.org/027-218-608-757-880}, + year = {2021} +} + @article{yanta_cryptogenotyper_2021, abstract = {Cryptosporidium is a protozoan parasite that is transmitted to both humans and animals through zoonotic or anthroponotic means. When a host is infected with this parasite, it causes a gastrointestinal disease known as cryptosporidiosis. To understand the transmission dynamics of Cryptosporidium, the small subunit (SSU or 18S) rRNA and gp60 genes are commonly studied through PCR analysis and conventional Sanger sequencing. However, analyzing sequence chromatograms manually is both time consuming and prone to human error, especially in the presence of poorly resolved, heterozygous peaks and the absence of a validated database. For this study, we developed a Cryptosporidium genotyping tool, called CryptoGenotyper, which has the capability to read raw Sanger sequencing data for the two common Cryptosporidium gene targets (SSU rRNA and gp60) and classify the sequence data into standard nomenclature. The CryptoGenotyper has the capacity to perform quality control and properly classify sequences using a high quality, manually curated reference database, saving users' time and removing bias during data analysis. The incorporated heterozygous base calling algorithms for the SSU rRNA gene target resolves double peaks, therefore recovering data previously classified as inconclusive. The CryptoGenotyper successfully genotyped 99.3\% (428/431) and 95.1\% (154/162) of SSU rRNA chromatograms containing single and mixed sequences, respectively, and correctly subtyped 95.6\% (947/991) of gp60 chromatograms without manual intervention. This new, user-friendly tool can provide both fast and reproducible analyses of Sanger sequencing data for the two most common Cryptosporidium gene targets.}, author = {Yanta, Christine A. and Bessonov, Kyrylo and Robinson, Guy and Troell, Karin and Guy, Rebecca A.}, @@ -15718,6 +25741,54 @@ @article{yanta_cryptogenotyper_2021 year = {2021} } +@article{yao_genome_2025, + abstract = {The biodegradation of lignite (brown coal) by microorganisms has the potential for bioremediation of contaminated mining sites and to generate alternative ways to valorize lignite, such as by producing humic acids or building block chemicals. Previously, a lignite-degrading strain of Trichoderma was isolated, but the genomic and transcriptomic basis of its lignite-degrading ability remained unknown. Here we report that the sequenced genome of the T. cf. simile WF8 strain encoded for enzymes with roles in the degradation of lignite, and potentially tolerance to lignite-breakdown products. There was only a small number of annotated unique genes in the T. cf. simile WF8 genome compared to other fungi, and likely the expression of gene families shared with other fungi is a key factor in lignite biosolubilization by T. cf. simile. The transcriptomes were analyzed of T. cf. simile cultured at two time-points with the lignite-breakdown model compounds 4-phenoxybenzoic acid (which was growth inhibitory), and phenetole and 9-10-dibutoxyanthracene (neither of which inhibited growth), and showed ∼20\% of genes up-regulated by one or more of these compounds. The analysis highlights candidates for characterization and engineering enzyme over-expressing T. cf. simile strains with potentially improved degradation capacity, e.g., laccases and peroxidases, or tolerance and catabolism of breakdown products, e.g., cytochrome P450s, and ring cleavage dioxygenases.}, + author = {Yao, Jinghua and Chen, Yajuan and Zhuo, Deyu and Chen, Siqiao and Xu, Baichao and Yan, Congwei and Li, Wanrong and Feng, Hui and Deng, Sheng and Cai, Feng M. and Steindorff, Andrei S. and Druzhinina, Irina S. and Xiao, Lei and Wei, Lihui and Daly, Paul}, + doi = {10.1016/j.ibiod.2025.105997}, + issn = {0964-8305}, + journal = {International Biodeterioration \& Biodegradation}, + keywords = {{\textgreater}UseGalaxy.eu, Comparative genomics, Lignite biodegradation, Polyaromatic compounds}, + month = {February}, + pages = {105997}, + title = {Genome and transcriptome analysis of the lignite-degrading \textit{{Trichoderma}} cf. \textit{simile} {WF8} strain highlights potential degradation mechanisms}, + url = {https://www.sciencedirect.com/science/article/pii/S0964830525000010}, + urldate = {2025-02-16}, + volume = {198}, + year = {2025} +} + +@article{yerlikaya_enhanced_2025, + abstract = {PvMLP19 overexpression in Arabidopsis enhances proline accumulation, mitigates oxidative stress, improves water retention, delays germination, and stimulates root growth under drought and salt stress conditions.}, + author = {Yerlikaya, Bayram Ali and Yerlikaya, Seher and Aydin, Abdullah and Yilmaz, Nisa Nur and Bahadır, Sibel and Abdulla, Mohamed Farah and Mostafa, Karam and Kavas, Musa}, + doi = {10.1007/s00299-025-03520-y}, + issn = {1432-203X}, + journal = {Plant Cell Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, Climate resilience, Common bean, Drought tolerance, Ectopic Gene Expression, Plant Biotechnology, Plant Molecular Biology, Plant Physiology, Plant Proteins, Plant Stress Responses, Plant stem cell, PvMLP19, Root development, Salt Tolerance, Seed germination}, + language = {en}, + month = {May}, + number = {6}, + pages = {130}, + title = {Enhanced drought and salt stress tolerance in {Arabidopsis} via ectopic expression of the {PvMLP19} gene}, + url = {https://doi.org/10.1007/s00299-025-03520-y}, + urldate = {2025-05-28}, + volume = {44}, + year = {2025} +} + +@article{yinsai_genomic_2025, + author = {Yinsai, Orathai and Yuantrakul, Sastra and Srisithan, Punnaporn and Zhou, Wenting and Chittaprapan, Sorawit and Intajak, Natthawat and Kruayoo, Thanakorn and Khamnoi, Phadungkiat and Tongjai, Siripong and Daungsonk, Kwanjit}, + issn = {2079-6382}, + journal = {Antibiotics (Basel)}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {July}, + number = {8}, + title = {Genomic {Insights} into {Emerging} {Multidrug}-{Resistant} {Chryseobacterium} indologenes {Strains}: {First} {Report} from {Thailand}}, + url = {http://europepmc.org/abstract/PMC/PMC12382657}, + volume = {14}, + year = {2025} +} + @article{yol_high-density_2021, author = {Yol, Engin and Basak, Merve and Kızıl, Sibel and Lucas, Stuart James and Uzun, Bulent}, doi = {10.3389/fpls.2021.679659}, @@ -15767,6 +25838,32 @@ @article{yoshida_dataset_2020 year = {2020} } +@article{young_transcriptional_2024, + abstract = {The activation of IP$_{\textrm{3}}$ receptor (IP$_{\textrm{3}}$R) Ca$^{\textrm{2+}}$ channels generates agonist-mediated Ca$^{\textrm{2+}}$ signals that are critical for the regulation of a wide range of biological processes. It is therefore surprising that CRISPR induced loss of all three IP$_{\textrm{3}}$R isoforms (TKO) in HEK293 and HeLa cell lines yields cells that can survive, grow and divide, albeit more slowly than wild-type cells. In an effort to understand the adaptive mechanisms involved, we have examined the activity of key Ca$^{\textrm{2+}}$ dependent transcription factors (NFAT, CREB and AP-1) and signaling pathways using luciferase-reporter assays, phosphoprotein immunoblots and whole genome transcriptomic studies. In addition, the diacylglycerol arm of the signaling pathway was investigated with protein kinase C (PKC) inhibitors and siRNA knockdown. The data showed that agonist-mediated NFAT activation was lost but CREB activation was maintained in IP$_{\textrm{3}}$R TKO cells. Under base-line conditions transcriptome analysis indicated the differential expression of 828 and 311 genes in IP$_{\textrm{3}}$R TKO HEK293 or HeLa cells, respectively, with only 18 genes being in common. Three main adaptations in TKO cells were identified in this study: 1) increased basal activity of NFAT, CREB and AP-1; 2) an increased reliance on Ca$^{\textrm{2+}}$- insensitive PKC isoforms; and 3) increased production of reactive oxygen species and upregulation of antioxidant defense enzymes. We suggest that whereas wild-type cells rely on a Ca$^{\textrm{2+}}$ and DAG signal to respond to stimuli, the TKO cells utilize the adaptations to allow key signaling pathways (e.g., PKC, Ras/MAPK, CREB) to transition to the activated state using a DAG signal alone.}, + author = {Young, Michael and Booth, David M and Smith, David and Tigano, Marco and Hajnóczky, György and Joseph, Suresh K}, + doi = {10.3389/fcell.2024.1473210}, + issn = {2296-634X}, + journal = {Frontiers in cell and developmental biology}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + pages = {1473210}, + title = {Transcriptional regulation in the absence of inositol trisphosphate receptor calcium signaling}, + url = {http://europepmc.org/abstract/MED/39712573}, + volume = {12}, + year = {2024} +} + +@article{yousif_molecular_2022, + abstract = {The use of wastewater for SARS-CoV-2 surveillance is a useful complementary tool to clinical surveillance. The aims of this study were to characterize SARS-CoV-2 from wastewater samples, and to identify variants of concern present in samples collected from wastewater treatment plants in South African urban metros from April 2021 to January 2022. A total of 325 samples were collected from 15 wastewater treatment plants. Nucleic acids were extracted from concentrated samples, and subjected to amplicon-based whole genome sequencing. To identify variants of concerns and lineages, we used the Freyja tool ( https://github.com/andersen-lab/Freyja ), which assigns each sample with the prevalence of each variant present. We also used signature mutation analysis to identify variants in each wastewater treatment site. A heatmap was generated to identify patterns of emerging mutations in the spike gene using Excel conditional formatting. Using the Freyja tool, the Beta variant was detected and became predominate from April to June 2021 followed by the Delta variant and lastly the Omicron variant. Our heatmap approach was able to identify a pattern during the changes of predominate variant in wastewater with the emergence of mutations and the loss of others. In conclusion, sequencing of SARS-CoV-2 from wastewater largely corresponded with sequencing from clinical specimens. Our heatmap has the potential to detect new variants prior to emergence in clinical samples and this may be particularly useful during times of low disease incidence between waves, when few numbers of positive clinical samples are collected and submitted for testing. A limitation of wastewater sequencing is that it is not possible to identify new variants, as variants are classified based on known mutations in clinical strains.}, + author = {Yousif, Mukhlid and Rachida, Said and Taukobong, Setshaba and Ndlovu, Nkosenhle and Iwu-Jaja, Chinwe and Howard, Wayne and Moonsamy, Shelina and Mhlambi, Nompilo and Gwala, Sipho and Levy, Joshua and Andersen, Kristian and Scheepers, Cathrine and Gottberg, Anne von and Wolter, Nicole and Ismail, Arshad and Suchard, Melinda and McCarthy, Kerrigan and {=the SACCESS network}}, + doi = {10.1101/2022.12.15.22283506}, + journal = {medRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Molecular identification of {SARS}-{CoV}-2 variants of concern at urban wastewater treatment plants across {South} {Africa}}, + url = {http://europepmc.org/abstract/PPR/PPR585861}, + year = {2022} +} + @article{yousif_sars-cov-2_2023, abstract = {As global SARS-CoV-2 burden and testing frequency have decreased, wastewater surveillance has emerged as a key tool to support clinical surveillance efforts. The aims of this study were to identify and characterize SARS-CoV-2 variants in wastewater samples collected from urban centers across South Africa. Here we show that wastewater sequencing analyses are temporally concordant with clinical genomic surveillance and reveal the presence of multiple lineages not detected by clinical surveillance. We show that wastewater genomics can support SARS-CoV-2 epidemiological investigations by reliably recovering the prevalence of local circulating variants, even when clinical samples are not available. Further, we find that analysis of mutations observed in wastewater can provide a signal of upcoming lineage transitions. Our study demonstrates the utility of wastewater genomics to monitor evolution and spread of endemic viruses.}, author = {Yousif, Mukhlid and Rachida, Said and Taukobong, Setshaba and Ndlovu, Nkosenhle and Iwu-Jaja, Chinwe and Howard, Wayne and Moonsamy, Shelina and Mhlambi, Nompilo and Gwala, Sipho and Levy, Joshua I. and Andersen, Kristian G. and Scheepers, Cathrine and von Gottberg, Anne and Wolter, Nicole and Bhiman, Jinal N. and Amoako, Daniel Gyamfi and Ismail, Arshad and Suchard, Melinda and McCarthy, Kerrigan}, @@ -15774,7 +25871,7 @@ @article{yousif_sars-cov-2_2023 doi = {10.1038/s41467-023-41369-5}, issn = {2041-1723}, journal = {Nature Communications}, - keywords = {{\textgreater}UseGalaxy.eu, Epidemiology, Genomics, SARS-CoV-2}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19, Epidemiology, Genomics, SARS-CoV-2, Wastewater}, language = {en}, month = {October}, note = {Number: 1 @@ -15824,6 +25921,22 @@ @article{yu_bromodomain-containing_2021 year = {2021} } +@article{yu_complete_2024, + abstract = {The leaf beetles have important economic and ecological significance. \textit{Phyllobrotica} \textit{signata} belongs to the subfamily Galerucinae. In this study, the complete mitogenome of \textit{P. signata} has been obtained by the next-generation sequencing. The length of the new complete mitogenome is 16,207 bp containing 37 genes and a control region. Fourteen species from Galerucinae and Alticinae were selected as ingroups for phylogenetic analysis based on mitogenomic data. The results supported that \textit{P. signata and P. quadrimaculata} were sister groups. The mitochondrial genome of P. signata will provide valuable genetic information for exploring the phylogenetic relationships in the family Chrysomelidae.}, + author = {Yu, Xiao-Xuan and Jin, Xu and Lin, Xiao-Ling and Liu, Li-Na and Nie, Rui-E}, + doi = {10.1080/23802359.2024.2439465}, + issn = {2380-2359}, + journal = {Mitochondrial DNA. Part B, Resources}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + number = {12}, + pages = {1688--1692}, + title = {The complete mitochondrial genome of {Phyllobrotica} signata ({Mannerheim}, 1825) ({Coleoptera}: {Chrysomelidae}: {Galerucinae}): characterization and phylogenetic implications}, + url = {http://europepmc.org/abstract/MED/39687443}, + volume = {9}, + year = {2024} +} + @article{yu_grace_2023, abstract = {Large-scale single-cell RNA sequencing (scRNA-seq) has emerged as a robust method for dissecting cellular heterogeneity at single-cell resolution. However, to meet the increasingly high computational demands of non-programming experts, a user-friendly, scalable, and accessible online platform for analyzing scRNA-seq data is urgently needed. Here, we have developed a web-based platform GRACE (GRaphical Analyzing Cell Explorer) (http://grace.flowhub.com.cn or http://grace.jflab.ac.cn:28080) that enables online massive single-cell transcriptome analysis, improving interactivity and reproducibility using high-quality visualization frameworks. GRACE provides easy access to interactive visualization, customized parameters, and publication-quality graphs. Furthermore, it comprehensively integrates preprocessing, clustering, developmental trajectory inference, cell-cell communication, cell-type annotation, subcluster analysis, and pathway enrichment. In addition to the website platform, we also provide a Docker version that can be easily deployed on private servers. The source code for GRACE is freely available at (https://github.com/th00516/GRACE). Documentation and video tutorials are accessible from website homepage (http://grace.flowhub.com.cn). GRACE can analyze massive scRNA-seq data more flexibly and be accessible to the scientific community. This platform fulfills the major gap that exists between experimental (wet lab) and bioinformatic (dry lab) research.}, author = {Yu, Hao and Wang, Yuqing and Zhang, Xi and Wang, Zheng}, @@ -15842,13 +25955,32 @@ @article{yu_grace_2023 year = {2023} } +@article{yu_pseudomonas_2025, + abstract = {Nodules harbour microbial communities composed of rhizobia and other lower-abundance bacteria. These non-rhizobial bacteria can promote plant growth. However, their genomic diversity and how this relates to their plant growth-promoting traits remain poorly investigated. Here, we isolated 14 Pseudomonas strains from the nodules of Lotus plants, sequenced their genomes, analysed their genomic and phylogenetic diversity, and assessed their ability to promote plant growth. We identified five distinct species, including a novel species named Pseudomonas monachiensis sp. nov., with strain PLb12AT, as the type strain. Genome analysis of these nodule-isolated Pseudomonas revealed an abundance of genes associated to plant growth-promoting traits, especially auxin-related genes, compared to closely related type strains. In accordance, most nodule-isolated Pseudomonas strains enhanced shoot growth of Lotus burttii, while only some promoted root growth or early onset of root hair proliferation. However, none of the strains significantly affected the ability to form nodules. Overall, our findings highlight the genotypic diversity and the plant growth-promoting potential of nodule-isolated Pseudomonas and underscore their possible applications in mixed inocula with rhizobia.}, + author = {Yu, Yu-Hsiang and Kurtenbach, Julian and Crosbie, Duncan and Brachmann, Andreas and Marín Arancibia, Macarena}, + copyright = {© 2025 The Author(s). Environmental Microbiology published by John Wiley \& Sons Ltd.}, + doi = {10.1111/1462-2920.70066}, + issn = {1462-2920}, + journal = {Environmental Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Lotus, Mesorhizobium, Pseudomonas genomic diversity, plant growth-promotion, root nodule symbiosis}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.70066}, + number = {3}, + pages = {e70066}, + title = {Pseudomonas {Species} {Isolated} {From} {Lotus} {Nodules} {Are} {Genetically} {Diverse} and {Promote} {Plant} {Growth}}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.70066}, + urldate = {2025-03-18}, + volume = {27}, + year = {2025} +} + @article{yu_usp1246_2024, abstract = {The functions of integrins are tightly regulated via multiple mechanisms including trafficking and degradation. Integrins are repeatedly internalized, routed into the endosomal system and either degraded by the lysosome or recycled back to the plasma membrane. The ubiquitin system dictates whether internalized proteins are degraded or recycled. Here, we use a genetic screen and proximity-dependent biotin identification to identify deubiquitinase(s) that control integrin surface levels. We find that a ternary deubiquitinating complex, comprised of USP12 (or the homologous USP46), WDR48 and WDR20, stabilizes β1 integrin (Itgb1) by preventing ESCRT-mediated lysosomal degradation. Mechanistically, the USP12/46-WDR48-WDR20 complex removes ubiquitin from the cytoplasmic tail of internalized Itgb1 in early endosomes, which in turn prevents ESCRT-mediated sorting and Itgb1 degradation.}, author = {Yu, Kaikai and Wang, Guan M and Guo, Shiny Shengzhen and Bassermann, Florian and Fässler, Reinhard}, doi = {10.1038/s44319-024-00300-9}, issn = {1469-221X}, journal = {EMBO reports}, - keywords = {{\textgreater}UseGalaxy.eu, DUB, ESCRT, Integrin, USP12/USP46, Ubiquitination}, + keywords = {{\textgreater}UseGalaxy.eu, DUB, ESCRT, Endosomal Sorting Complexes Required for Transport, Integrin, Integrin beta1, Lysosomes, Proteolysis, USP12/USP46, Ubiquitination}, month = {November}, note = {Num Pages: 32 Publisher: John Wiley \& Sons, Ltd}, @@ -15866,7 +25998,7 @@ @article{yuan_ezh2_2022 doi = {10.1038/s41418-022-00992-3}, issn = {1476-5403}, journal = {Cell Death \& Differentiation}, - keywords = {{\textgreater}UseGalaxy.eu, Epigenetics, Inflammasome}, + keywords = {{\textgreater}UseGalaxy.eu, Epigenetics, Inflammasome, Long Noncoding, RNA}, language = {en}, month = {October}, note = {Number: 10 @@ -15916,6 +26048,26 @@ @article{zafar_identification_2024 year = {2024} } +@article{zakir_cohesive_2025, + abstract = {Breast cancer is the most prevalent and lethal form of cancer being the utmost common medical concern of women. Breast cancer etiology implicates numerous cellular protein receptors such as estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor/receptor 2 (HER2) which turn on oncogenic cascade often attributed to certain genetic variations. Breast Cancer is thus classified into ER + /-, PR + /-, HER2 ± and Triple Negative types. This study seeks to build upon our current knowledge of HER2 + and TNBC BC types to discover novel patterns for diagnosis and prognosis. The study exploits wealth of HER2 + and TNBC transcriptome (RNA Seq) data to elucidate the key hub genes, their associated networks, pathways, stage-wise expression profile, role in prognosis and survival expectancy, and regulatory transcription factors. The study also employs machine learning models including support vector machine (SVM), XGBoost, Random Forest, k nearest neighbor (kNN), Naïve Bayes and Voting Classifier to distinguish between HER2 + and TNBC transcriptomes which is a key variable for early detection and choice of therapeutic alternatives. RNA Seq datasets consisting of 49 HER2 + and 44 TNBC breast tumor samples were retrieved and pre-processed. Differentially Expressed Genes (DEGs) along with their logFC and p-values were fetched. The KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) analyses of DEGs were conducted on DAVID (the Database for Annotation, Visualization and Integrated Discovery) and interaction network was constructed through Cytoscape. Ten hub genes were obtained based on maximum clique centrality (MCC), maximum neighborhood component (MNC), degree, closeness and betweenness using cytoHubba which included ACTB, ATM, ESR1, GAPDH, HNRNPK, KRAS, MDM2, SIRT1, TP53, and H3F3C (H3-5). These hub genes were found to be associated with cell proliferation, invasion and migration. Transcription factors and association of the expression profile of these hub genes with survival expectancy was also determined. Among the ML models, SVM stood out, exhibiting classification success between HER2 + and TNBC transcriptomes with an accuracy of 90\%. The findings of this study can therefore effectively aid in tracing the initial prognosis of BC and identify biomarkers for the personalized prevention, prediction, diagnosis, and treatment of BC.}, + author = {Zakir, Mahrukh and Saddiqa, Alishbah and Sheikh, Mawara and Zakir, Lalarukh and Sami, Fatima and Ahmad, Faisal Sardar and Rauf, Sadaf Abdul and Ali, Iqra and Muneer, Zahid and Alonazi, Wadi B. and Siddiqi, Abdul Rauf}, + copyright = {2025 The Author(s)}, + doi = {10.1038/s41598-025-94084-0}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Breast Neoplasms, Breast cancer, Cancer, Receptor, erbB-2, Triple Negative Breast Neoplasms}, + language = {en}, + month = {July}, + note = {Publisher: Nature Publishing Group}, + number = {1}, + pages = {23675}, + title = {Cohesive data analysis for the identification of prognostic hub genes and significant pathways associated with {HER2} + and {TN} breast cancer types}, + url = {https://www.nature.com/articles/s41598-025-94084-0}, + urldate = {2025-07-12}, + volume = {15}, + year = {2025} +} + @article{zaman_tolperisone_2024, abstract = {The mitogen-activated protein kinase (MAPK) signaling pathway, particularly the p38 MAPK and ERK1/2, has been implicated in the pathogenesis of Parkinson's disease (PD). Recent studies have shown that MAPK signaling pathway can influence the expression of matrix metalloproteinase 9 (MMP-9), known for its involvement in various physiological and pathological processes, including neurodegenerative diseases. This study explores the modulation of MMP-9 expression via the MAPK/ERK signaling cascade and its potential therapeutic implications in the context of PD-associated motor dysfunction. Here, tolperisone hydrochloride (TL), a muscle relaxant that blocks voltage-gated sodium and calcium channels, was used as a treatment to observe its effect on MAPK signaling and MMP-9 expression. Rotenone (RT) exposure in mice resulted in a significant reduction in substantia nigra and primary motor cortex neurons, which were further evidenced by impairments in motor function. When TL was administered, neuron count was restored (89.0 ± 4.78 vs 117.0 ± 4.46/mm2), and most of the motor dysfunction was alleviated. Mechanistically, TL reduced the protein expression of phospho-p38MAPK (1.06 fold vs 1.00 fold) and phospho-ERK1/2 (1.16 fold vs 1.02 fold), leading to the inhibition of MAPK signaling, as well as reduced MMP-9 concentrations (2.76 ± 0.10 vs 1.94 ± 0.10 ng/mL) in the process of rescuing RT-induced neuronal cell death and motor dysfunction. Computational analysis further revealed TL’s potential inhibitory properties against MMP-9 along with N and L-type calcium channels. These findings shed light on TL's neuroprotective effects via MMP-9 inhibition and MAPK signaling downregulation, offering potential therapeutic avenues for PD-associated motor dysfunction.}, author = {Zaman, Bushra and Mostafa, Irona and Hassan, Tazree and Ahmed, Shamim and Esha, Nusrat Jahan Ikbal and Chowdhury, Fowzia Afsana and Bosu, Tory and Chowdhury, Humayra Noor and Mallick, Anup and Islam, MM Shanjid and Sharmin, Ayesha and Uddin, Kabir M. and Hossain, Md. Mainul and Rahman, Mahbubur}, @@ -15932,6 +26084,57 @@ @article{zaman_tolperisone_2024 year = {2024} } +@article{zapata-garcia_comparative_2022, + abstract = {Acute lymphoblastic leukemia (ALL) in children or adults is characterized by structural and numeric aberrations in chromosomes; these anomalies strongly correlate with prognosis and clinical outcome. Therefore, this work aimed to identify the genes present in chromosomal gain regions found more frequently in patients with acute lymphoblastic leukemia (ALL) and ALL-derived cell lines using comparative genomic hybridization (CGH). In addition, validation of the genes found in these regions was performed utilizing RNAseq from JURKAT, CEM, and SUP-B15 cell lines, as well as expression microarrays derived from a MILE study. Chromosomes with common gain zones that were maintained in six or more samples were 14, 17, and 22, in which a total of 22 genes were identified. From them, \textit{NT5C3B}, \textit{CNP}, \textit{ACLY}, and \textit{GNB1L} maintained overexpression at the mRNA level in the cell lines and in patients with ALL. It is noteworthy that \textit{SALL2} showed very high expression in T-ALL, while \textit{JUP} was highly expressed in B-ALL lineages. Interestingly, the latter correlated with worse survival in patients. This provided evidence that the measurement of these genes has high potential for clinical utility; however, their expressions should first be evaluated with a sensitive test in a more significant number of patients.}, + author = {Zapata-García, Jessica Alejandra and Riveros-Magaña, Alma Rocío and Ortiz-Lazareno, Pablo Cesar and Hernández-Flores, Georgina and Jave-Suárez, Luis Felipe and Aguilar-Lemarroy, Adriana}, + doi = {10.3390/diagnostics12112788}, + issn = {2075-4418}, + journal = {Diagnostics (Basel, Switzerland)}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {November}, + number = {11}, + pages = {2788}, + title = {Comparative {Genomic} {Hybridization} and {Transcriptome} {Sequencing} {Reveal} {Genes} with {Gain} in {Acute} {Lymphoblastic} {Leukemia}: {JUP} {Expression} {Emerges} as a {Survival}-{Related} {Gene}}, + url = {http://europepmc.org/abstract/MED/36428851}, + volume = {12}, + year = {2022} +} + +@article{zapata_garcia_alterations_2025, + abstract = {Endometrial cancer is the fifth most common cancer worldwide, with one of the highest incidence and mortality rates. Its incidence is projected to increase 55\% by 2030. Currently, the techniques used for its detection are heterogeneous and can be invasive and nonspecific. In this context, omics studies have gained relevance, providing solutions that have improved patient diagnosis and prognosis. In this study, we used data from the GSE268888 study as discovery cohort and data from the TCGA consortium as a validation cohort. Expression analyses were performed to identify miRNAs overexpressed in endometrial cancer. These miRNAs were then analyzed in relation to diagnostic and prognostic clinical variables. The target genes of these miRNAs were identified using bioinformatic tools, and functional enrichment analyses were conducted with this gene set to explore their involvement in relevant oncogenic signaling pathways. We also calculated the structural topology of the miRNA-target complexes and computed their correlation coefficients. We found that hsa-miR-182 and hsa-miR-760 had diagnostic and prognostic relevance and interacted with the p53 signaling pathway. Specifically, hsa-miR-449a was associated with diagnosis, but not with prognosis. Furthermore, we found that these miRNAs share \textit{TP53INP1} as a common target gene and estimated a high probability of complex formation, along with a positive correlation between these miRNAs and \textit{TP53INP1} in more advanced stages of the disease. These findings suggest that this miRNA signature has potential to be used as a diagnostic and prognostic biomarker and could serve as a foundation for future therapeutic strategies for endometrial cancer. However, further experimental validation is needed to confirm its clinical applicability.}, + author = {Zapata García, Jessica Alejandra}, + doi = {10.3390/ijms26115215}, + issn = {1422-0067}, + journal = {International journal of molecular sciences}, + keywords = {{\textgreater}UseGalaxy.eu, Endometrial Neoplasms, Gene Expression Regulation, Neoplastic, MicroRNAs, Signal Transduction, Tumor Suppressor Protein p53}, + language = {eng}, + month = {May}, + number = {11}, + pages = {5215}, + title = {Alterations in the {Expression} of a {Set} of {miRNAs} in {Endometrial} {Cancer} and {Their} {Correlation} with {Clinical} {Variables} and the p53 {Signaling} {Pathway}}, + url = {http://europepmc.org/abstract/MED/40508024}, + volume = {26}, + year = {2025} +} + +@article{zavala-alvarado_oxidative_2021, + abstract = {Pathogenic Leptospira are the causative agents of leptospirosis, the most widespread zoonotic infectious disease. Leptospirosis is a potentially severe and life-threatening emerging disease with highest burden in sub-tropical areas and impoverished populations. Mechanisms allowing pathogenic Leptospira to survive inside a host and induce acute leptospirosis are not fully understood. The ability to resist deadly oxidants produced by the host during infection is pivotal for Leptospira virulence. We have previously shown that genes encoding defenses against oxidants in L. interrogans are repressed by PerRA (encoded by LIMLP\_10155), a peroxide stress regulator of the Fur family. In this study, we describe the identification and characterization of another putative PerR-like regulator (LIMLP\_05620) in L. interrogans. Protein sequence and phylogenetic analyses indicated that LIMLP\_05620 displayed all the canonical PerR amino acid residues and is restricted to pathogenic Leptospira clades. We therefore named this PerR-like regulator PerRB. In L. interrogans, the PerRB regulon is distinct from that of PerRA. While a perRA mutant had a greater tolerance to peroxide, inactivating perRB led to a higher tolerance to superoxide, suggesting that these two regulators have a distinct function in the adaptation of L. interrogans to oxidative stress. The concomitant inactivation of perRA and perRB resulted in a higher tolerance to both peroxide and superoxide and, unlike the single mutants, a double perRAperRB mutant was avirulent. Interestingly, this correlated with major changes in gene and non-coding RNA expression. Notably, several virulence-associated genes (clpB, ligA/B, and lvrAB) were repressed. By obtaining a double mutant in a pathogenic Leptospira strain, our study has uncovered an interplay of two PerRs in the adaptation of Leptospira to oxidative stress with a putative role in virulence and pathogenicity, most likely through the transcriptional control of a complex regulatory network.}, + author = {Zavala-Alvarado, Crispin and G Huete, Samuel and Vincent, Antony T and Sismeiro, Odile and Legendre, Rachel and Varet, Hugo and Bussotti, Giovanni and Lorioux, Céline and Lechat, Pierre and Coppée, Jean-Yves and Veyrier, Frédéric J and Picardeau, Mathieu and Benaroudj, Nadia}, + doi = {10.1371/journal.ppat.1009087}, + issn = {1553-7366}, + journal = {PLoS pathogens}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {eng}, + month = {December}, + number = {12}, + pages = {e1009087}, + title = {The oxidative stress response of pathogenic {Leptospira} is controlled by two peroxide stress regulators which putatively cooperate in controlling virulence}, + url = {http://europepmc.org/abstract/MED/34855911}, + volume = {17}, + year = {2021} +} + @article{zavala-alvarado_transcriptional_2020, abstract = {Pathogenic Leptospira spp. are the causative agents of the waterborne zoonotic disease leptospirosis. Leptospira are challenged by numerous adverse conditions, including deadly reactive oxygen species (ROS), when infecting their hosts. Withstanding ROS produced by the host innate immunity is an important strategy evolved by pathogenic Leptospira for persisting in and colonizing hosts. In L. interrogans, genes encoding defenses against ROS are repressed by the peroxide stress regulator, PerR. In this study, RNA sequencing was performed to characterize both the L. interrogans response to low and high concentrations of hydrogen peroxide and the PerR regulon. We showed that Leptospira solicit three main peroxidase machineries (catalase, cytochrome C peroxidase and peroxiredoxin) and heme to detoxify oxidants produced during peroxide stress. In addition, canonical molecular chaperones of the heat shock response and DNA repair proteins from the SOS response were required for Leptospira recovering from oxidative damage. Identification of the PerR regulon upon exposure to H2O2 allowed to define the contribution of this regulator in the oxidative stress response. This study has revealed a PerR-independent regulatory network involving other transcriptional regulators, two-component systems and sigma factors as well as non-coding RNAs that putatively orchestrate, in concert with PerR, the oxidative stress response. We have shown that PerR-regulated genes encoding a TonB-dependent transporter and a two-component system (VicKR) are involved in Leptospira tolerance to superoxide. This could represent the first defense mechanism against superoxide in L. interrogans, a bacterium lacking canonical superoxide dismutase. Our findings provide an insight into the mechanisms required by pathogenic Leptospira to overcome oxidative damage during infection-related conditions. This will participate in framing future hypothesis-driven studies to identify and decipher novel virulence mechanisms in this life-threatening pathogen.}, author = {Zavala-Alvarado, Crispin and Sismeiro, Odile and Legendre, Rachel and Varet, Hugo and Bussotti, Giovanni and Bayram, Jan and Huete, Samuel G. and Rey, Guillaume and Coppée, Jean-Yves and Picardeau, Mathieu and Benaroudj, Nadia}, @@ -15974,7 +26177,7 @@ @article{zehr_patterns_2023 abstract = {Viruses may acquire mutations that result in a tropism shift. RNA viruses, such as Coronaviruses (CoVs), are susceptible to tropism shifts. A tropism shift occurs when a virus alters the tissue or cell type it infects, which can have important implications for disease pathogenesis, virulence, transmission, and treatment control. Tropism shifts can occur after cross-species jumps, as well as result from within-host evolution. Beyond the human host, CoVs can be highly pathogenic to a wide variety of wildlife and companion animals. A spillover event from animals to humans, resulting in a tropism shift, has occurred at some point in the evolutionary history of all three highly pathogenic human CoVs: severe acute respiratory syndrome coronavirus (SARS-CoV), middle eastern respiratory syndrome coronavirus (MERS), and severe acute respiratory syndrome 2 (SARS-CoV-2). Therefore, studying the evolution of CoVs in non-human animals may be of critical importance for pandemic prevention. This was the focus of my dissertation, to apply state-of-the-art codon models of evolution to a variety of CoV viral sequences to identify how natural selection may alter viral proteins priming them for tropism shifts. Statistical codon models can infer both which codon sites and genes have been subject to positive or negative selection, effectively differentiating signal between random mutations and those that may impact fitness. These models may also compare selection at homologous sites between different phenotypes (i.e., Spike protein sequences isolated from the gastrointestinal tract and those from macrophages) to identify where selection is acting differently between the phenotypes. In chapter 2 I examined a CoV sequence isolated from hospitalized humans in Malaysia that resembled a Canine Coronavirus (CCoV) to investigate how natural selection had shaped the Spike protein sequence in related animal CoV sequences priming it to jump into humans. In chapter 3 I compared the natural selection signals at specific codon positions in the Spike protein from sequences isolated from two separate feline tropisms (gastrointestinal and macrophage) to identity which adaptive mutations may be associated with the tropism shift and subsequent shift in virulence. This was performed on Feline Coronavirus (FCoVs), where almost 90\% of all wild and domestic cats are gastrointestinally infected with FCoVs, and infection becomes highly pathogenic as a result of the shift in tropism to the macrophages. Since intra-host evolution can impact tropism shifts, in Chapter 4 I performed a detailed high-throughout analysis of intra-host evolution of RNAseq data of Equine Coronavirus (ECoV), as well as natural selection analyses of related embecoviruses that have colonized the human host. Taken together, I report on novel signals of natural selection across viral proteins, with an emphasis on Spike, on a diverse set of CoV clades that shed light on the complexities of coronavirus evolution as it relates to tropism shifts.}, author = {Zehr, Jordan}, copyright = {http://rightsstatements.org/vocab/InC/1.0/}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, language = {eng}, month = {May}, note = {Accepted: 2023-09-03T14:54:54Z @@ -15986,10 +26189,13 @@ @article{zehr_patterns_2023 } @article{zehr_positive_2024, + abstract = {There are several examples of coronaviruses in the Betacoronavirus subgenus \textit{Embecovirus} that have jumped from an animal to the human host. Studying how evolutionary factors shape coronaviruses in non-human hosts may provide insight into the coronavirus host-switching potential. Equids, such as horses and donkeys, are susceptible to equine coronaviruses (ECoVs). With increased testing prevalence, several ECoV genome sequences have become available for molecular evolutionary analyses, especially those from the United States of America (USA). To date, no analyses have been performed to characterize evolution within coding regions of the ECoV genome. Here, we obtain and describe four new ECoV genome sequences from infected equines from across the USA presenting clinical symptoms of ECoV, and infer ECoV-specific and \textit{Embecovirus}-wide patterns of molecular evolution. Within two of the four data sets analyzed, we find evidence of intra-host evolution within the nucleocapsid (N) gene, suggestive of quasispecies development. We also identify 12 putative genetic recombination events within the ECoV genome, 11 of which fall in ORF1ab. Finally, we infer and compare sites subject to positive selection on the ancestral branch of each major \textit{Embecovirus} member clade. Specifically, for the two currently identified human coronavirus (HCoV) embecoviruses that have spilled from animals to humans (HCoV-OC43 and HCoV-HKU1), we find that there are 42 and 2 such sites, respectively, perhaps reflective of the more complex ancestral evolutionary history of HCoV-OC43, which involves several different animal hosts.IMPORTANCEThe Betacoronavirus subgenus \textit{Embecovirus} contains coronaviruses that not only pose a health threat to animals and humans, but also have jumped from animal to human host. Equids, such as horses and donkeys are susceptible to equine coronavirus (ECoV) infections. No studies have systematically examined evolutionary patterns within ECoV genomes. Our study addresses this gap and provides insight into intra-host ECoV evolution from infected horses. Further, we identify and report natural selection pattern differences between two embecoviruses that have jumped from animals to humans [human coronavirus OC43 and HKU1 (HCoV-OC43 and HCoV-HKU1, respectively)], and hypothesize that the differences observed may be due to the different animal host(s) that each virus circulated in prior to its jump into humans. Finally, we contribute four novel, high-quality ECoV genomes to the scientific community.}, author = {Zehr, Jordan D. and Kosakovsky Pond, Sergei L. and Shank, Stephen D. and McQueary, Holly and Grenier, Jennifer K. and Whittaker, Gary R. and Stanhope, Michael J. and Goodman, Laura B.}, doi = {10.1128/spectrum.00867-24}, + issn = {2165-0497}, journal = {Microbiology Spectrum}, - keywords = {{\textgreater}UseGalaxy.eu}, + keywords = {{\textgreater}UseGalaxy.eu, Evolution, Molecular, Genome, Viral, Phylogeny, Recombination, Genetic, Selection, Genetic}, + language = {eng}, month = {October}, note = {Publisher: American Society for Microbiology}, number = {0}, @@ -16001,6 +26207,17 @@ @article{zehr_positive_2024 year = {2024} } +@article{zerebinski_uncovering_2025, + abstract = {Genetic diversity in Plasmodium falciparum poses a significant challenge to malaria control and elimination. This is particularly important for developing fully efficacious vaccines, which should include valuable blood stage antigens. Several antigen candidates are highly diverse and require further understanding. We surveyed the genetic diversity of the highly polymorphic merozoite surface protein 2 (MSP2) in 2761 P. falciparum isolates collected across Sub-Saharan Africa. Using PCR-based genotyping and long-read sequencing, we identified extensive diversity among msp2 size variants and sequences. Some size variants were more prevalent than others across different geographical regions, transmission intensities, and time points. These variants comprised multiple unique sequences, of which several were geographically and temporally widespread. Our study reveals greater msp2 sequence diversity than previously known, while also identifying interesting similarities in sequence and gene length across Sub-Saharan Africa. These findings support the further exploration of common msp2 variants in relation to parasite virulence and vaccine development.}, + author = {Zerebinski, Julia and Broumou, Ioanna and Kimenyi, Kelvin and Aklilu, Eleni and Andrade, Carolina and Babiker, Hamza and Bejon, Philip and Cherif, Mariama and Crompton, Peter and Fançony, Cláudia and Foroogh, Fariba and Gil, José Pedro and Kapulu, Melissa and Kiwuwa, Steven and Kweku, Margaret and Liljander, Anne and Lopes, Dinora and Marsh, Kevin and Mutemi, Doreen and Ngasala, Billy and Normark, Johan and Orikiiriza, Judy and Persson, Kristina E.M. and Portugal, Silvia and Ribacke, Ulf and Sirima, Sodiomon and Sondén, Klara and de Sousa, Taís and Traore, Boubacar and Tijani, Muyideen Kolapo and Eckerdal, Nils and Villner, Pär and Ochola-Oyier, Lynette Isabella and Plaza, David and Färnert, Anna}, + doi = {10.1101/2025.07.23.666329}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Uncovering the genetic diversity of the malaria parasite antigen {MSP2} across {Sub}-{Saharan} {Africa}}, + url = {http://europepmc.org/abstract/PPR/PPR1054411}, + year = {2025} +} + @article{zerouki_whole-genome_2023, abstract = {Phacidium infestans (synonym Gremmenia infestans) is a significant pathogen that impacts Pinus species across the northern regions of Europe and Asia. This study introduces the genome sequence of P. infestans Karsten DSM 5139 (Phain), obtained through Pacbio technology. The assembly resulted in 44 contigs, with a total genome size of 36,805,277 bp and a Guanine–Cytosine content of 46.4\%. Genome-mining revealed numerous putative biosynthetic gene clusters that code for virulence factors and fungal toxins. The presence of the enzyme pisatin demethylase was indicative of the potential of Phain to detoxify its environment from the terpenoid phytoalexins produced by its host as a defense mechanism. Proteomic analysis revealed the potential survival strategies of Phain under the snow, which included the production of antifreeze proteins, trehalose synthesis enzymes, desaturases, proteins related to elongation of very long-chain fatty acids, and stress protein responses. Study of protein GH11 endoxylanase expressed in Escherichia coli showed an acidic optimum pH (pH 5.0) and a low optimum temperature (45 °C), which is reflective of the living conditions of the fungus. Mass spectrometry analysis of the methanol extract of Phain, incubated at − 3 °C and 22 °C, revealed differences in the produced metabolites. Both genomic and mass spectrometry analyses showed the ability of Phain to adapt its metabolic processes and secretome to freezing temperatures through the production of osmoprotectant and cryoprotectant metabolites. This comprehensive exploration of Phain's genome sequence, proteome, and secretome not only advances our understanding of its unique adaptive mechanisms but also expands the possibilities of biotechnological applications.}, author = {Zerouki, C. and Chakraborty, K. and Kuittinen, S. and Pappinen, A. and Turunen, O.}, @@ -16023,7 +26240,7 @@ @article{zhan_comparison_2024 doi = {10.3390/ijms251910637}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, - keywords = {\textit{RT}-qPCR, {\textgreater}UseGalaxy.eu, latitudinal pattern, low-temperature stress, mitochondrial genome expression, skink}, + keywords = {\textit{RT}-qPCR, {\textgreater}UseGalaxy.eu, Genome, Mitochondrial, Lizards, latitudinal pattern, low-temperature stress, mitochondrial genome expression, skink}, language = {en}, month = {January}, note = {Number: 19 @@ -16065,7 +26282,7 @@ @article{zhang_deciphering_2024 doi = {10.1038/s44318-024-00302-2}, issn = {0261-4189}, journal = {The EMBO Journal}, - keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, Cell-specific Transcriptomic and Epigenetic Profiling, Root, Stem Cells Organizer, WOX5}, + keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, Arabidopsis Proteins, Cell-specific Transcriptomic and Epigenetic Profiling, Gene Expression Regulation, Plant, Plant Roots, Root, Stem Cells, Stem Cells Organizer, WOX5}, month = {November}, note = {Num Pages: 23 Publisher: John Wiley \& Sons, Ltd}, @@ -16083,7 +26300,7 @@ @article{zhang_first_2024 doi = {10.3390/genes15020254}, issn = {2073-4425}, journal = {Genes}, - keywords = {\textit{L. scaber}, {\textgreater}UseGalaxy.eu, Diplopoda, genomic features, mitochondrial genome, phylogenetic analysis}, + keywords = {\textit{L. scaber}, {\textgreater}UseGalaxy.eu, Arthropods, Diplopoda, Genome, Mitochondrial, genomic features, mitochondrial genome, phylogenetic analysis}, language = {en}, month = {February}, note = {Number: 2 @@ -16098,6 +26315,26 @@ @article{zhang_first_2024 year = {2024} } +@article{zhang_irf4_2025, + abstract = {Natural killer (NK) cells are essential for controlling tumor metastasis, but their protective capacity diminishes when entering an exhaustion state. The mechanisms underlying NK cell exhaustion are incompletely understood. Here, we show that the susceptibility of NK cells to exhaustion is predetermined early during their development and is governed by the transcription factor IRF4. Notably, IRF4 is highly expressed in CD27−CD24+ NK precursors but is nearly absent in immature and mature NK cells. Deletion of IRF4 redirects NK cell development, enabling NK precursors to generate more mature NK cells that resist exhaustion, thereby decreasing melanoma lung metastasis. This resistance to exhaustion is evident by increased effector molecule production and decreased expression of inhibitory receptors such as TIGIT and Pik3ip1. Deleting Pik3ip1 also enhances NK cell ability to counteract melanoma lung metastasis. These findings enhance our understanding of NK cell exhaustion and have implications for preventing cancer metastasis using NK cells.}, + author = {Zhang, Xiaolong and Yin, Zheng and Wu, Jie and Xiang, Xiao and Zou, Dawei and Wang, Guangchuan and Fu, Jinfei and Lan, Peixiang and Minze, Laurie J. and Li, Xian C. and Chen, Wenhao}, + copyright = {2025 The Author(s), under exclusive licence to Springer Nature America, Inc.}, + doi = {10.1038/s41590-025-02176-w}, + issn = {1529-2916}, + journal = {Nature Immunology}, + keywords = {{\textgreater}UseGalaxy.eu, NK cells, Tumour immunology}, + language = {en}, + month = {July}, + note = {Publisher: Nature Publishing Group}, + number = {7}, + pages = {1062--1073}, + title = {{IRF4} expression by {NK} precursors predetermines exhaustion of {NK} cells during tumor metastasis}, + url = {https://www.nature.com/articles/s41590-025-02176-w}, + urldate = {2025-07-12}, + volume = {26}, + year = {2025} +} + @article{zhang_nfatc1_2023, abstract = {Background \& Aims Loss of AT-rich interactive domain-containing protein 1A (ARID1A) fosters acinar-to-ductal metaplasia (ADM) and pancreatic carcinogenesis by down-regulating transcription programs controlling acinar cell identity. However, how ARID1A reacts to metaplasia-triggering environmental cues remains elusive. Here, we aimed to elucidate the role of ARID1A in controlling ductal pancreatic gene signatures and deciphering hierarchical signaling cues determining ARID1A-dependent chromatin regulation during acinar cell reprogramming. @@ -16111,12 +26348,15 @@ @article{zhang_nfatc1_2023 doi = {10.1016/j.jcmgh.2023.01.015}, issn = {2352-345X}, journal = {Cellular and Molecular Gastroenterology and Hepatology}, - keywords = {{\textgreater}UseGalaxy.eu, ARID1A, Acinar-to-Ductal Metaplasia, EGFR, NFATc1, Pancreas, Transcription}, + keywords = {{\textgreater}UseGalaxy.eu, ARID1A, Acinar-to-Ductal Metaplasia, Carcinoma, Pancreatic Ductal, EGFR, NFATc1, Pancreas, Pancreatic Neoplasms, Transcription}, language = {en}, month = {February}, + number = {5}, + pages = {1219--1246}, title = {{NFATc1} {Is} a {Central} {Mediator} of {EGFR}-{Induced} {ARID1A} {Chromatin} {Dissociation} {During} {Acinar} {Cell} {Reprogramming}}, url = {https://www.sciencedirect.com/science/article/pii/S2352345X23000188}, urldate = {2023-03-15}, + volume = {15}, year = {2023} } @@ -16127,7 +26367,7 @@ @article{zhang_replication_2022 doi = {10.1038/s41467-022-34577-y}, issn = {2041-1723}, journal = {Nature Communications}, - keywords = {{\textgreater}UseGalaxy.eu, Cancer epigenetics, Cancer stem cells, Mechanisms of disease}, + keywords = {{\textgreater}UseGalaxy.eu, Adult Stem Cells, Cancer epigenetics, Cancer stem cells, Histone-Lysine N-Methyltransferase, Mechanisms of disease}, language = {en}, month = {November}, note = {Number: 1 @@ -16182,6 +26422,33 @@ @article{zhao_rrm_2024 year = {2024} } +@article{zhong_distinct_2025, + abstract = {\<h4\>Background\</h4\>We investigate the flow of genetic information from DNA to RNA to protein as described by the Central Dogma in molecular biology, to determine the impact of intermediate genomic levels on plant protein expression.\<h4\>Results\</h4\>We perform genomic profiling of rosette leaves in two Arabidopsis accessions, Col-0 and Can-0, and assemble their genomes using long reads and chromatin interaction data. We measure gene and protein expression in biological replicates grown in a controlled environment, also measuring CpG methylation, ribosome-associated transcript levels, and tRNA abundance. Each omic level is highly reproducible between biological replicates and between accessions despite their 1\% sequence divergence; the single best predictor of any level in one accession is the corresponding level in the other. Within each accession, gene codon frequencies accurately model both mRNA and protein expression. The effects of a codon on mRNA and protein expression are highly correlated but independent of genome-wide codon frequencies or tRNA levels which instead match genome-wide amino acid frequencies. Ribosome-associated transcripts closely track mRNA levels.\<h4\>Conclusions\</h4\>DNA codon frequencies and mRNA expression levels are the main predictors of protein abundance. In the absence of environmental perturbation neither gene-body methylation, tRNA abundance nor ribosome-associated transcript levels add appreciable information. The impact of constitutive gene-body methylation is mostly explained by gene codon composition. tRNA abundance tracks overall amino acid demand. However, genetic differences between accessions associate with differential gene-body methylation by inflating differential expression variation. Our data show that the dogma holds only if both sequence and abundance information in mRNA are considered.}, + author = {Zhong, Ziming and Bailey, Mark and Kim, Yong-In and Afsharyan, Nazanin P and Parker, Briony and Arathoon, Louise and Li, Xiaowei and Rundle, Chelsea A and Behrens, Andrew and Nedialkova, Danny and Slavov, Gancho and Hassani-Pak, Keywan and Lilley, Kathryn S and Theodoulou, Frederica L and Mott, Richard}, + doi = {10.1186/s13059-025-03741-0}, + issn = {1474-7596}, + journal = {Genome biology}, + keywords = {{\textgreater}UseGalaxy.eu, Central dogma, Chromatin Interaction, Data-independent Acquisition, Gene Expression, Gene-body Methylation, Genome Assembly, Long Reads, Mim-trnaseq, Protein expression, Ribosome-associated Expression, Rnaseq}, + month = {September}, + number = {1}, + pages = {319}, + title = {The distinct roles of genome, methylation, transcription, and translation on protein expression in {Arabidopsis} thaliana resolve the {Central} {Dogma}'s information flow}, + url = {https://europepmc.org/articles/PMC12477803}, + volume = {26}, + year = {2025} +} + +@article{zhong_revisiting_2025, + abstract = {{\textless}h4{\textgreater}Background{\textless}/h4{\textgreater} We investigated the flow of information from genome sequence to protein expression implied by the Central Dogma, to determine the impact of intermediate genomic levels in plants. {\textless}h4{\textgreater}Results{\textless}/h4{\textgreater} We performed genomic profiling of rosettes in two Arabidopsis accessions, Col-0 and Can-0, and assembled their genomes using long reads and chromatin interaction data. We measured gene and protein expression in biological replicates grown in a controlled environment, also measuring CpG methylation, ribosome-associated transcript levels and tRNA abundance. Each omic level is highly reproducible between biological replicates and between accessions despite their 0.5\% sequence divergence; the single best predictor of any level in one accession is the corresponding level in the other. Within each accession, gene codon frequencies accurately model both mRNA and protein expression. The effects of a codon on mRNA and protein expression are highly correlated but are unrelated to genome-wide codon frequencies or to tRNA levels which instead match genome-wide amino acid frequencies. Ribosome-associated transcripts closely track mRNA levels. {\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater} In the absence of environmental perturbation, neither methylation, tRNA nor ribosome-associated transcript levels add appreciable information about constitutive protein abundance beyond that in DNA codon frequencies and mRNA expression levels. The impact of constitutive gbM is mostly explained by gene codon composition. tRNA abundance tracks overall amino acid demand. However, genetic differences between accessions associate with differential gbM by inflating differential expression variation. Our data show that the Central Dogma holds only if both sequence and abundance information in mRNA are considered.}, + author = {Zhong, Ziming and Bailey, Mark and Kim, Yong-In and Afsharyan, Nazanin and Parker, Briony and Arathoon, Louise and Li, Xiaowei and Rundle, Chelsea and Behrens, Andrew and Nedialkova, Danny and Slavov, Gancho and Hassani-Pak, Keywan and Lilley, Kathryn and Theodoulou, Frederica and Mott, Richard}, + doi = {10.1101/2025.01.08.631880}, + journal = {bioRxiv}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Revisiting the {Central} {Dogma}: the distinct roles of genome, methylation, transcription, and translation on protein expression in {Arabidopsis} thaliana}, + url = {http://europepmc.org/abstract/PPR/PPR964854}, + year = {2025} +} + @article{zhou_toxic_2023, abstract = {Benzophenones (BPs) are commonly used in personal care products like sunscreens and are increasingly being released into the environment, raising concerns about their potential ecotoxic effects. BPs as emerging environmental contaminants, little is known about their toxic effects on estuarine organisms. This study firstly investigated the toxic effects of five commonly used BPs on mud crabs (Scylla paramamosain). The crabs were exposed to varying concentrations of BPs for 14 days. The results showed that BPs caused damage to antioxidant systems in crabs. Transcriptome sequencing revealed that BP-3 and BP-1 had a greater impact on the crabs compared to the other BPs. Specifically, BP-1 and BP-3 caused severe damage to organelles and ribosomes. BP affected catalytic activity and hydrolase activity, BP-2 affected phosphoenolpyruate carboxykinase activity, and BP-4 affected tRNA aminoacylation and hydrolase activity. These findings can enhance our understanding of the ecotoxicity of BPs and may help to protect estuarine ecosystems.}, author = {Zhou, Yi-Lian and Dong, Wei-Ren and Shu, Miao-An}, @@ -16199,11 +26466,12 @@ @article{zhou_toxic_2023 } @article{zhu_bas_2024, + abstract = {Brassinosteroid (BR) signaling leads to the nuclear accumulation of the BRASSINAZOLE-RESISTANT 1 (BZR1) transcription factor, which plays dual roles in activating or repressing the expression of thousands of genes. BZR1 represses gene expression by recruiting histone deacetylases, but how it activates transcription of BR-induced genes remains unclear. Here, we show that BR reshapes the genome-wide chromatin accessibility landscape, increasing the accessibility of BR-induced genes and reducing the accessibility of BR-repressed genes in Arabidopsis. BZR1 physically interacts with the BRAHMA-associated SWI/SNF (BAS)-chromatin-remodeling complex on the genome and selectively recruits the BAS complex to BR-activated genes. Depletion of BAS abrogates the capacities of BZR1 to increase chromatin accessibility, activate gene expression, and promote cell elongation without affecting BZR1's ability to reduce chromatin accessibility and expression of BR-repressed genes. Together, these data identify that BZR1 recruits the BAS complex to open chromatin and to mediate BR-induced transcriptional activation of growth-promoting genes.}, author = {Zhu, Tao and Wei, Chuangqi and Yu, Yaoguang and Zhang, Zhenzhen and Zhu, Jiameng and Liang, Zhenwei and Song, Xin and Fu, Wei and Cui, Yuhai and Wang, Zhi-Yong and Li, Chenlong}, doi = {10.1016/j.devcel.2024.01.021}, issn = {1534-5807}, journal = {Developmental Cell}, - keywords = {{\textgreater}UseGalaxy.eu, BAS-chromatin-remodeling complexes, BZR1, Brassinosteroid, SWI/SNF, chromatin accessibility, growth and development, phytohormone}, + keywords = {{\textgreater}UseGalaxy.eu, Arabidopsis, Arabidopsis Proteins, BAS-chromatin-remodeling complexes, BZR1, Brassinosteroid, SWI/SNF, chromatin accessibility, growth and development, phytohormone}, language = {English}, month = {April}, note = {Publisher: Elsevier}, @@ -16218,14 +26486,20 @@ @article{zhu_bas_2024 } @article{zhuang_time-_2021, + abstract = {{\textless}h4{\textgreater}Purpose{\textless}/h4{\textgreater}The pattern of immune cells infiltrating the corneal stroma has been extensively studied in mice, but data on human tissue have been far less elaborate. To further characterize the number and differentiation state of resident immune cells in organ-cultured human corneal tissue, we employed a comprehensive bioinformatic deconvolution (xCell) of bulk RNA-sequencing (RNA-seq) data, immunohistochemistry (IHC), and flow cytometry (FC).{\textless}h4{\textgreater}Methods{\textless}/h4{\textgreater}A transcriptome-based analysis of immune cell types in human corneal samples was performed. The results were validated by IHC, focusing on the identification of pro-inflammatory (M1) and regulatory (M2) macrophages. A protocol was established to identify these 2 different macrophage populations in human corneal tissue by means of FC. Subsequently, corneal samples in organ culture were differentially stimulated by IL-10, IL-4 \& IL-13, or LPS and macrophage populations were evaluated regarding their response to these stimuli. Furthermore, cell survival was analyzed in correlation with time in organ culture.{\textless}h4{\textgreater}Results{\textless}/h4{\textgreater}xCell-based mathematical deconvolution of bulk RNA-seq data revealed the presence of CD8 T cells, Th17 cells, dendritic cells, and macrophages as the predominant immune cell types in organ-cultured human corneal tissue. Furthermore, RNA-seq allowed the detection of different macrophage marker genes in corneal samples, including PTPRC (CD45), ITGAM (CD11b), CD14, and CD74. Our RNA-seq data showed no evidence of a relevant presence of monocytes in human corneal tissue. The presence of different macrophage subtypes was confirmed by IHC. The disintegration and subsequent FC analysis of human corneal samples showed the presence of both M1 (HLA-DR+, CD282+, CD86+, and CD284+) and M2 (CD163+ and CD206+) macrophage subtypes. Furthermore, we found that the total number of macrophages in corneal samples decreased more than the total cell count with increasing tissue culture time. Treatment with IL-10 led to higher total cell counts per cornea and to an increased expression of the M2 marker CD163 (p {\textless} 0.05) while expression levels of various M1 macrophage markers were not significantly reduced by interleukin treatment.{\textless}h4{\textgreater}Conclusions{\textless}/h4{\textgreater}Regarding different macrophage populations, untreated human corneas showed more M1 than M2 macrophages. With increasing organ culture time, these macrophages decreased. In terms of cell dynamics, adding interleukins to the organ culture medium influenced the phenotype of macrophages within the cornea as detected by FC. Modifying the immunomodulatory properties of human grafts appears a promising approach to further reduce the risk of graft rejection in patients. In this context, treatment with interleukins was more effective in upregulating M2 macrophages than in suppressing M1 macrophages in corneal tissue.}, author = {Zhuang, Xinyu and Schlunck, Günther and Wolf, Julian and Rosmus, Dennis-Dominik and Bleul, Tim and Luo, Ren and Böhringer, Daniel and Wieghofer, Peter and Lange, Clemens and Reinhard, Thomas and Lapp, Thabo}, doi = {10.1159/000516669}, - keywords = {+UsePublic, {\textgreater}UseGalaxy.eu}, + issn = {1662-8128}, + journal = {J Innate Immun}, + keywords = {+UsePublic, {\textgreater}UseGalaxy.eu, Macrophages, Monocytes}, + language = {eng}, month = {June}, note = {Publisher: S. Karger AG}, + number = {2}, pages = {1--14}, title = {Time- and {Stimulus}-{Dependent} {Characteristics} of {Innate} {Immune} {Cells} in {Organ}-{Cultured} {Human} {Corneal} {Tissue}}, url = {https://doi.org/10.1159/000516669}, + volume = {14}, year = {2021} } @@ -16254,7 +26528,7 @@ @article{zinati_deciphering_2023 doi = {10.1038/s41598-023-40189-3}, issn = {2045-2322}, journal = {Scientific Reports}, - keywords = {{\textgreater}UseGalaxy.eu, Computational biology and bioinformatics, Molecular biology}, + keywords = {{\textgreater}UseGalaxy.eu, Computational biology and bioinformatics, Cucumis sativus, Molecular biology}, language = {en}, month = {August}, note = {Number: 1 @@ -16274,7 +26548,7 @@ @article{zirngibl_triose_2023 doi = {10.1016/j.xplc.2022.100423}, issn = {2590-3462}, journal = {Plant Communications}, - keywords = {{\textgreater}UseGalaxy.eu, SnRK1, acclimation, anthocyanin, flavonoid biosynthesis, high light, sugar signaling}, + keywords = {{\textgreater}UseGalaxy.eu, Anthocyanins, SnRK1, Sugars, acclimation, anthocyanin, flavonoid biosynthesis, high light, sugar signaling}, language = {en}, month = {January}, number = {1}, @@ -16286,3 +26560,32 @@ @article{zirngibl_triose_2023 volume = {4}, year = {2023} } + +@article{zubaer_comparative_2025, + abstract = {Leptographium wingfieldii is a fungal associate of Tomicus piniperda (the pine shoot beetle) and pathogen of pines and this species is an agent of blue stain in sapwood on infected trees. This fungus was first reported from Europe and has been recently introduced to Canadian forests. Ten new mitogenomes have been sequenced and characterized, including seven strains of L. wingfieldii, two strains of L. procerum and one strain of L. terebrantis. The data were combined with other members of the Ophiostomatales collected from NCBI to gain more insight into the genetic diversity, evolution, and systematics of these fungi. The size of the studied mitogenomes of Leptographium species ranged from 41 to 126 kb with the number of potential mobile introns embedded within these mitogenomes ranging from 13 to 45. These data show that introns generate genetic diversity and confirms the contribution of mobile introns in genome expansion in Ophiostomatales fungi. This study also uncovered complex intron arrangements (twintrons) suggesting the potential of mobile introns generating complex ribozymes that may have implications in gene regulation.}, + author = {Zubaer, Abdullah and Wai, Alvan and Hausner, Georg}, + doi = {10.1139/cjm-2024-0179}, + issn = {0008-4166}, + journal = {Canadian Journal of Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {January}, + note = {Publisher: NRC Research Press}, + pages = {1--13}, + title = {Comparative mitogenomics of {Leptographium} procerum, {Leptographium} terebrantis, and {Leptographium} wingfieldii, an invasive fungal species in {Canadian} forests}, + url = {https://cdnsciencepub.com/doi/abs/10.1139/cjm-2024-0179}, + urldate = {2025-09-03}, + volume = {71}, + year = {2025} +} + +@article{zubaer_genome_2025, + abstract = {Leptographium wingfieldii is an invasive fungal species in Canadian forests which was originally isolated in Europe (France and Greece). Leptographium wingfieldii and other fungi in the order Ophiostomatales (Ascomycota) are vectored by arthropods, and they can be either pathogenic to tree species or cause blue stain on sapwood in conifer (and hardwood) species. These fungi are ecologically and economically significant due to their impact on forest ecosystems and lumber industry. Whole genome sequences were obtained from Leptographium wingfieldii and related fungi (including Leptographium procerum, Leptographium terebrantis, Grosmannia aureum, Ophiostoma minus, and Ophiostoma piliferum). The mitochondrial genomes of these fungi were assembled and found to contain autocatalytic group I and group II introns, intron-encoded homing endonucleases along with intron-encoded reverse transcriptase enzymes that have applications in genome editing. These elements contribute toward the genetic diversity observed among the mitochondrial genomes studied. The study provided information to generate a mitochondrial intron landscape, identified complex intron arrangements, and demonstrated the correlation of mitogenome expansion with the number of introns. The whole genome sequence data were also analyzed with regards to the presence of nuclear genome encoded biosynthetic gene clusters (BGCs). This effort identified the presence of 205 BGCs categorized into PKS I, PKS III, NRPS, RiPPS, Terpenes, and hybrid types and these could be sources for potential antimicrobials and industrially important chemical compounds. The study provides a platform for downstream biochemical characterization and heterologous expression of the identified genetic elements, facilitating their functional annotation and explore their potential for industrial applications.}, + author = {Zubaer, Abdullah}, + keywords = {{\textgreater}UseGalaxy.eu, ⛔ No DOI found}, + language = {eng}, + month = {May}, + title = {Genome mining of {Leptographium} wingfieldii, an invasive species in {Canadian} forests, and related taxa in the order {Ophiostomatales} for the characterization of secondary metabolites and ribozymes}, + url = {http://hdl.handle.net/1993/39115}, + urldate = {2025-07-12}, + year = {2025} +}