From e205e58003b8c3195beac0b4889d8dbdf5f6ccd3 Mon Sep 17 00:00:00 2001 From: bgruening Date: Mon, 31 Jul 2023 04:24:27 +0000 Subject: [PATCH] Update citations --- _bibliography/citations-eu.bib | 834 ++++++++++++++++++++++++++++++++- 1 file changed, 816 insertions(+), 18 deletions(-) diff --git a/_bibliography/citations-eu.bib b/_bibliography/citations-eu.bib index 59a584f3b..cbf5170f0 100644 --- a/_bibliography/citations-eu.bib +++ b/_bibliography/citations-eu.bib @@ -74,6 +74,28 @@ @article{aggarwal_role_2021 year = {2021} } +@article{ahmad_biosynthetic_2023, + abstract = {Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73–114 clusters, other lichen associated ascomycetes 8–40, green algae of the genus Trebouxia 14–19, and lichen-associated bacteria 101–105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.}, + author = {Ahmad, Nadim and Ritz, Manfred and Calchera, Anjuli and Otte, Jürgen and Schmitt, Imke and Brueck, Thomas and Mehlmer, Norbert}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/jof9050546}, + issn = {2309-608X}, + journal = {Journal of Fungi}, + keywords = {\textit{Hypogymnia physodes}, \textit{Hypogymnia tubulosa}, {\textgreater}UseGalaxy.eu, biosynthetic gene cluster, lichen, long read sequencing, polyketide synthesis, reference genome}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {546}, + shorttitle = {Biosynthetic {Potential} of {Hypogymnia} {Holobionts}}, + title = {Biosynthetic {Potential} of {Hypogymnia} {Holobionts}: {Insights} into {Secondary} {Metabolite} {Pathways}}, + url = {https://www.mdpi.com/2309-608X/9/5/546}, + urldate = {2023-07-31}, + volume = {9}, + year = {2023} +} + @article{ahmad_development_2019, abstract = {Premise Alkanna tinctoria (Boraginaceae) is an important medicinal herb with its main distribution across the Mediterranean region. To reveal its genetic variation and population structure, microsatellite markers were developed and validated in four Greek populations. Methods and Results RNA-Seq data of the related species Arnebia euchroma and Echium plantagineum were assembled and mined to identify conserved ortholog sets containing simple sequence repeat motifs. Fifty potential loci were identified and then tested on A. tinctoria, of which 17 loci were polymorphic. The number of alleles ranged from one to nine, and the levels of observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.820, respectively. Most of these loci could be successfully amplified in eight other species of Boraginaceae (Alkanna graeca, A. hellenica, A. sfikasiana, Echium vulgare, E. plantagineum, Lithospermum officinale, Borago officinalis, and Anchusa officinalis). Conclusions This study provides the first set of microsatellite loci for studying the genetic variation and population structure of A. tinctoria and shows their potential usefulness in other Boraginaceae species.}, author = {Ahmad, Muhammad and Lazic, Desanka and Hansel‐Hohl, Karin and Lexer, Christian and Sehr, Eva Maria}, @@ -221,6 +243,21 @@ @article{amaral_tcti_2022 year = {2022} } +@article{anbazhagan_comparative_2023, + abstract = {Brucella abortus and Brucella melitensis are the primary etiological agents of brucellosis in large and small ruminants, respectively. There are limited comparative genomic studies involving Brucella strains that explore the relatedness among both species. In this study, we involved strains (n=44) representing standard, vaccine and Indian field origin for pangenome, single nucleotide polymorphism (SNP) and phylogenetic analysis. Both species shared a common gene pool representing 2884 genes out of a total 3244 genes. SNP-based phylogenetic analysis indicated higher SNP diversity among B. melitensis (3824) strains in comparison to B. abortus (540) strains, and a clear demarcation was identified between standard/vaccine and field strains. The analysis for virulence genes revealed that virB3, virB7, ricA, virB5, ipx5, wbkC, wbkB, and acpXL genes were highly conserved in most of the Brucella strains. Interestingly, virB10 gene was found to have high variability among the B. abortus strains. The cgMLST analysis revealed distinct sequence types for the standard/vaccine and field strains. B. abortus strains from north-eastern India fall within similar sequence type differing from other strains. In conclusion, the analysis revealed a highly shared core genome among two Brucella species. SNP analysis revealed B. melitensis strains exhibit high diversity as compared to B. abortus strains. Strains with absence or high polymorphism of virulence genes can be exploited for the development of novel vaccine candidates effective against both B. abortus and B. melitensis.}, + author = {Anbazhagan, S. and Himani, K.M. and Karthikeyan, R. and Prakasan, Lakshmi and Dinesh, M. and Nair, Sonu S. and Lalsiamthara, Jonathan and {Abhishek} and Ramachandra, S.G. and Chaturvedi, V.K. and Chaudhuri, Pallab and Thomas, Prasad}, + doi = {10.1007/s10123-023-00374-w}, + issn = {1618-1905}, + journal = {International Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, B. abortus, B. melitensis, Comparative genomics, Pangenome, Virulence genes}, + language = {en}, + month = {May}, + title = {Comparative genomics of {Brucella} abortus and {Brucella} melitensis unravels the gene sharing, virulence factors and {SNP} diversity among the standard, vaccine and field strains}, + url = {https://doi.org/10.1007/s10123-023-00374-w}, + urldate = {2023-07-31}, + year = {2023} +} + @article{andrade_assessing_2023, author = {Andrade, Luisa and Ryan, Michael P. and Burke, Liam P. and Hynds, Paul and Weatherill, John and O'Dwyer, Jean}, doi = {10.2139/ssrn.4350080}, @@ -298,6 +335,23 @@ @article{arcari_interplay_2022 year = {2022} } +@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}, + journal = {Antimicrobial Agents and Chemotherapy}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {July}, + note = {Publisher: American Society for Microbiology}, + number = {0}, + pages = {e00368--23}, + title = {Multiplicity of {blaKPC} {Genes} and {pKpQIL} {Plasmid} {Plasticity} in the {Development} of {Ceftazidime}-{Avibactam} and {Meropenem} {Coresistance} in {Klebsiella} pneumoniae {Sequence} {Type} 307}, + url = {https://journals.asm.org/doi/full/10.1128/aac.00368-23}, + urldate = {2023-07-31}, + volume = {0}, + year = {2023} +} + @article{ardisasmita_comprehensive_2022, abstract = {The myriad of available hepatocyte in vitro models provides researchers the possibility to select hepatocyte-like cells (HLCs) for specific research goals. However, direct comparison of hepatocyte models is currently challenging. We systematically searched the literature and compared different HLCs, but reported functions were limited to a small subset of hepatic functions. To enable a more comprehensive comparison, we developed an algorithm to compare transcriptomic data across studies that tested HLCs derived from hepatocytes, biliary cells, fibroblasts, and pluripotent stem cells, alongside primary human hepatocytes (PHHs). This revealed that no HLC covered the complete hepatic transcriptome, highlighting the importance of HLC selection. HLCs derived from hepatocytes had the highest transcriptional resemblance to PHHs regardless of the protocol, whereas the quality of fibroblasts and PSC derived HLCs varied depending on the protocol used. Finally, we developed and validated a web application (HLCompR) enabling comparison for specific pathways and addition of new HLCs. In conclusion, our comprehensive transcriptomic comparison of HLCs allows selection of HLCs for specific research questions and can guide improvements in culturing conditions.}, author = {Ardisasmita, Arif Ibrahim and Schene, Imre F. and Joore, Indi P. and Kok, Gautam and Hendriks, Delilah and Artegiani, Benedetta and Mokry, Michal and Nieuwenhuis, Edward E. S. and Fuchs, Sabine A.}, @@ -319,6 +373,25 @@ @article{ardisasmita_comprehensive_2022 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}, + doi = {10.1080/08927022.2023.2228423}, + issn = {0892-7022}, + journal = {Molecular Simulation}, + keywords = {{\textgreater}UseGalaxy.eu, Resistance, molecular docking, molecular dynamics simulation, penicillin−binding proteins, phenolics}, + month = {June}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/08927022.2023.2228423}, + number = {0}, + pages = {1--17}, + title = {Cheminformatics identification of phenolics as modulators of key penicillin−binding proteins of {Escherichia} coli towards interventive antibacterial therapy}, + url = {https://doi.org/10.1080/08927022.2023.2228423}, + urldate = {2023-07-31}, + volume = {0}, + year = {2023} +} + @article{ashrafi_two_2022, 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}, @@ -370,6 +443,25 @@ @incollection{bagnacani_tools_2019 year = {2019} } +@article{baig_genome-wide_2023, + abstract = {β-galactosidase (Lactase), an enzyme belonging to the glycoside hydrolase family causing the hydrolysis and trans-glycosylation of β-D-galactosides, has a vital role in dairy industries. The current investigation emphasizes on in-silico identification and comparative analysis of different fungal lactases present in Aspergillus fumigatus, Aspergillus oryzae, Botrytis cinerea, and Fusarium fujikuroi. Prediction of motifs and domains, chromosomal positioning, gene structure, gene ontology, sub-cellular localization and protein modeling were performed using different bioinformatics tools to have an insight into the structural and functional characteristics of β-galactosidases. Evolutionary and homology relationships were established by phylogenetic and synteny analyses. A total of 14 β-gal genes (GH-35) were identified in these species. Identified lactases, having 5 domains, were predicted to be stable, acidic, non-polar and extracellularly localized with roles in polysaccharide catabolic process. Results showed variable exonic/intronic ratios of the gene structures which were randomly positioned on chromosomes. Moreover, synteny blocks and close evolutionary relationships were observed between Aspergillus fumigatus and Aspergillus oryzae. Structural insights allowed the prediction of best protein models based on the higher ERRAT and Q-MEAN values. And RNA-sequencing analysis, performed on A. fumigatus, elucidated the role of β-gal in germ tube development. This study would pave the way for efficient fungal lactase production as it identified β-gal genes and predicted their various features and also it would provide a road-way to further the understanding of A. fumigatus pathogenicity via the expression insights of β-gal in germ tube development.}, + author = {Baig, Danish Ilyas and Zafar, Zeeshan and Khan, Haris Ahmed and Younus, Amna and Bhatti, Muhammad Faraz}, + 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}, + language = {en}, + month = {June}, + note = {Publisher: Public Library of Science}, + number = {6}, + pages = {e0286428}, + title = {Genome-wide identification and comparative in-silico characterization of β-galactosidase ({GH}-35) in ascomycetes and its role in germ tube development of {Aspergillus} fumigatus via {RNA}-seq analysis}, + url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0286428}, + urldate = {2023-07-31}, + volume = {18}, + year = {2023} +} + @article{baker_no_2020, abstract = {The current state of much of the Wuhan pneumonia virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) 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 10 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 SARS-CoV-2 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and (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 = {Baker, Dannon and Beek, Marius van den and Blankenberg, Daniel and Bouvier, Dave and Chilton, John and Coraor, Nate and Coppens, Frederik and Eguinoa, Ignacio and Gladman, Simon and Grüning, Björn and Keener, Nicholas and Larivière, Delphine and Lonie, Andrew and Pond, Sergei Kosakovsky and Maier, Wolfgang and Nekrutenko, Anton and Taylor, James and Weaver, Steven}, @@ -497,6 +589,28 @@ @article{bartas_changes_2021 year = {2021} } +@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.}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41598-023-34198-5}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Long non-coding RNAs, Transcriptomics}, + language = {en}, + month = {July}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {12051}, + shorttitle = {Discovery of putative long non-coding {RNAs} expressed in the eyes of {Astyanax} mexicanus ({Actinopterygii}}, + title = {Discovery of putative long non-coding {RNAs} expressed in the eyes of {Astyanax} mexicanus ({Actinopterygii}: {Characidae})}, + url = {https://www.nature.com/articles/s41598-023-34198-5}, + urldate = {2023-07-31}, + volume = {13}, + year = {2023} +} + @article{batut_asaim_2018, abstract = {Background. New generations of sequencing platforms coupled to numerous bioinformatics tools have led to rapid technological progress in metagenomics a}, author = {Batut, Bérénice and Gravouil, Kévin and Defois, Clémence and Hiltemann, Saskia and Brugère, Jean-François and Peyretaillade, Eric and Peyret, Pierre}, @@ -580,6 +694,27 @@ @article{bayona-feliu_swisnf_2021 year = {2021} } +@article{bazukyan_silico_2023, + abstract = {A Lactobacillus delbrueckii ssp. lactis strain named A4, isolated from the gut of an Armenian honeybee, was subjected to a probiogenomic characterization because of its unusual origin. A whole-genome sequencing was performed, and the bioinformatic analysis of its genome revealed a reduction in the genome size and the number of the genes—a process typical for the adaptation to endosymbiotic conditions. Further analysis of the genome revealed that Lactobacillus delbrueckii ssp. lactis strain named A4 could play the role of a probiotic endosymbiont because of the presence of intact genetic sequences determining antioxidant properties, exopolysaccharides synthesis, adhesion properties, and biofilm formation, as well as an antagonistic activity against some pathogens which is not due to pH or bacteriocins production. Additionally, the genomic analysis revealed significant potential for stress tolerance, such as extreme pH, osmotic stress, and high temperature. To our knowledge, this is the first report of a potentially endosymbiotic Lactobacillus delbrueckii ssp. lactis strain adapted to and playing beneficial roles for its host.}, + author = {Bazukyan, Inga and Georgieva-Miteva, Dimitrina and Velikova, Tsvetelina and Dimov, Svetoslav G.}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/insects14060540}, + issn = {2075-4450}, + journal = {Insects}, + keywords = {\textit{L. delbrueckii} ssp. \textit{lactis}, {\textgreater}UseGalaxy.eu, endosymbionts, honeybees, probiogenomic analysis, probiotics, whole-genome sequencing}, + language = {en}, + month = {June}, + note = {Number: 6 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {6}, + pages = {540}, + title = {In {Silico} {Probiogenomic} {Characterization} of {Lactobacillus} delbrueckii subsp. lactis {A4} {Strain} {Isolated} from an {Armenian} {Honeybee} {Gut}}, + url = {https://www.mdpi.com/2075-4450/14/6/540}, + urldate = {2023-07-31}, + volume = {14}, + year = {2023} +} + @article{bazzucchi_near-complete_2020, abstract = {To gain further insight into the genomic features of border disease virus (BDV), we determined the nearly complete genome sequence of isolate TO/121/04 from an aborted ovine fetus. Its genome contains a single open reading frame (ORF), which comprises 11,681 nucleotides encoding a polyprotein of 3893 amino acids. Phylogenetic analysis of the near full-length genome sequence showed that the BDV isolate differed significantly from all ovine pestiviruses identified so far, thus re-affirming the presence in Italy of this novel genetic group, termed BDV-7.}, author = {Bazzucchi, Moira and Pierini, Ilaria and Giammarioli, Monica and De Mia, Gian Mario}, @@ -598,6 +733,17 @@ @article{bazzucchi_near-complete_2020 year = {2020} } +@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.}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {July}, + title = {Enhanced weathering in the {U}.{S}. {Corn} {Belt} delivers carbon removal with agronomic benefits}, + url = {https://www.semanticscholar.org/paper/Enhanced-weathering-in-the-U.S.-Corn-Belt-delivers-Beerling-Epihov/f3467cbb0f578a9bb789a88d6140e1180a57890d}, + urldate = {2023-07-31}, + year = {2023} +} + @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}, @@ -764,6 +910,24 @@ @article{borchel_sex_2022 year = {2022} } +@article{bordel_genome_2023, + abstract = {Keratin-rich wastes, mainly in the form of feathers, are recalcitrant residues generated in high amounts as by-products in chicken farms and food industry. Polylactic acid (PLA) is the second most common biodegradable polymer found in commercial plastics, which is not easily degraded by microbial activity. This work reports the 3.8-Mb genome of Bacillus altitudinis B12, a highly efficient PLA- and keratin-degrading bacterium, with potential for environmental friendly biotechnological applications in the feed, fertilizer, detergent, leather, and pharmaceutical industries. The whole genome sequence of B. altitudinis B12 revealed that this strain (which had been previously misclassified as Bacillus pumilus B12) is closely related to the B. altitudinis strains ER5, W3, and GR-8. A total of 4056 coding sequences were annotated using the RAST server, of which 2484 are core genes of the pan genome of B. altitudinis and 171 are unique to this strain. According to the sequence analysis, B. pumilus B12 has a predicted secretome of 353 proteins, among which a keratinase and a PLA depolymerase were identified by sequence analysis. The presence of these two enzymes could explain the characterized PLA and keratin biodegradation capability of the strain.}, + author = {Bordel, Sergio and Martín-González, Diego and Muñoz, Raúl and Santos-Beneit, Fernando}, + doi = {10.1007/s00438-022-01989-w}, + issn = {1617-4623}, + journal = {Molecular Genetics and Genomics}, + keywords = {{\textgreater}UseGalaxy.eu, Bacillus altitudinis, Keratinases, Pan genome, Polyester biodegradation}, + language = {en}, + month = {March}, + number = {2}, + pages = {389--398}, + title = {Genome sequence analysis and characterization of {Bacillus} altitudinis {B12}, a polylactic acid- and keratin-degrading bacterium}, + url = {https://doi.org/10.1007/s00438-022-01989-w}, + urldate = {2023-07-31}, + volume = {298}, + year = {2023} +} + @article{bose_trna_2020, abstract = {tRNA Adenosine Deaminase 3 helps to sustain telomere tracts in a telomerase-independent fashion, likely through regulating cellular metabolism.}, author = {Bose, Sreyashree and Suescún, Ana Victoria and Song, Jiarui and Castillo-González, Claudia and Aklilu, Behailu Birhanu and Branham, Erica and Lynch, Ryan and Shippen, Dorothy E.}, @@ -833,6 +997,19 @@ @article{bovio_differential_2018 year = {2018} } +@article{bozan_whole-genome_2022, + abstract = {Cyanobacteria are highly promising microorganisms in forthcoming biotechnologies. Besides the systematic development of molecular tools for genetic engineering, the design of chassis strains and novel reactor concepts are in focus. The latter includes capillary biofilm reactors (CBR), which offer a high surface area-to-volume ratio and very high cell densities. In this context, Tolypothrix sp. PCC 7712 was found to be highly suited for this reactor system due to maximal surface coverage, extraordinarily strong biofilm attachment, and high biomass formation. Here, we provide the genome sequence of Tolypothrix sp. PCC 7712 to potentially allow targeted strain engineering. Surprisingly, it was almost identical to an available incomplete genome draft of Tolypothrix sp. PCC 7601. Thus, we completely sequenced this strain as well and compared it in detail to strain PCC 7712. Comparative genome analysis revealed 257 and 80 unique protein-coding sequences for strains PCC 7601 and PCC 7712, respectively. Clustering genomes based on average nucleotide identity (ANI) and 16S rRNA homology showed 99.98\% similarity and only minor distance, respectively, between the two strains in contrast to 21 other cyanobacterial genomes. Despite these high similarities, both strains differ in the ability to fix atmospheric nitrogen and show specific sequence variations, which are discussed in the paper.}, + author = {Bozan, Mahir and Popp, Denny and Kallies, Rene and da Rocha, Ulisses Nunes and Klähn, Stephan and Bühler, Katja}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Whole-genome sequence of the filamentous diazotrophic cyanobacterium {Tolypothrix} sp. {PCC} 7712 and its comparison with non-diazotrophic {Tolypothrix} sp. {PCC} 7601}, + url = {https://www.frontiersin.org/articles/10.3389/fmicb.2022.1042437}, + urldate = {2023-07-31}, + volume = {13}, + year = {2022} +} + @article{bray_chemicaltoolbox_2020, abstract = {Here, we introduce the ChemicalToolbox, a publicly available web server for performing cheminformatics analysis. The ChemicalToolbox provides an intuitive, graphical interface for common tools for downloading, filtering, visualizing and simulating small molecules and proteins. The ChemicalToolbox is based on Galaxy, an open-source web-based platform which enables accessible and reproducible data analysis. There is already an active Galaxy cheminformatics community using and developing tools. Based on their work, we provide four example workflows which illustrate the capabilities of the ChemicalToolbox, covering assembly of a compound library, hole filling, protein-ligand docking, and construction of a quantitative structure-activity relationship (QSAR) model. These workflows may be modified and combined flexibly, together with the many other tools available, to fit the needs of a particular project. The ChemicalToolbox is hosted on the European Galaxy server and may be accessed via https://cheminformatics.usegalaxy.eu.}, author = {Bray, Simon A. and Lucas, Xavier and Kumar, Anup and Grüning, Björn A.}, @@ -943,6 +1120,28 @@ @article{broche_genome-wide_2023 year = {2023} } +@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}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + 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}, + language = {en}, + month = {July}, + note = {Number: 7 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {7}, + pages = {1437}, + shorttitle = {Ploidy in {Vibrio} natriegens}, + title = {Ploidy in {Vibrio} natriegens: {Very} {Dynamic} and {Rapidly} {Changing} {Copy} {Numbers} of {Both} {Chromosomes}}, + url = {https://www.mdpi.com/2073-4425/14/7/1437}, + urldate = {2023-07-31}, + volume = {14}, + year = {2023} +} + @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}, @@ -1349,6 +1548,23 @@ @article{davey_intrinsically_2019 year = {2019} } +@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}, + doi = {10.1016/j.cimid.2023.102027}, + issn = {0147-9571}, + journal = {Comparative Immunology, Microbiology and Infectious Diseases}, + keywords = {{\textgreater}UseGalaxy.eu, Anthrax, One health, WGS, Zoonotic disease}, + language = {en}, + month = {September}, + pages = {102027}, + title = {Whole genome sequencing of {Bacillus} anthracis isolated from animal in the 1960s, {Brazil}, belonging to the {South} {America} subclade}, + url = {https://www.sciencedirect.com/science/article/pii/S0147957123000851}, + urldate = {2023-07-31}, + volume = {100}, + year = {2023} +} + @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}, @@ -1550,6 +1766,27 @@ @article{dvir_uncovering_2021 year = {2021} } +@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.}, + copyright = {2022 The Author(s)}, + doi = {10.1038/s41396-022-01348-y}, + issn = {1751-7370}, + journal = {The ISME Journal}, + keywords = {{\textgreater}UseGalaxy.eu, Bacterial evolution, Bacterial genetics, Microbial ecology}, + language = {en}, + month = {March}, + note = {Number: 3 +Publisher: Nature Publishing Group}, + number = {3}, + pages = {326--339}, + title = {Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium}, + url = {https://www.nature.com/articles/s41396-022-01348-y}, + urldate = {2023-07-31}, + volume = {17}, + year = {2023} +} + @article{eggenhofer_cmv_2018, abstract = {SummaryA standard method for the identification of novel RNAs or proteins is homology search via probabilistic models. One approach relies on the definition of families, which can be encoded as covariance models (CMs) or Hidden Markov Models (HMMs). While being powerful tools, their complexity makes it tedious to investigate them in their (default) tabulated form. This specifically applies to the interpretation of comparisons between multiple models as in family clans. The Covariance model visualization tools (CMV) visualize CMs or HMMs to: I) Obtain an easily interpretable representation of HMMs and CMs; II) Put them in context with the structural sequence alignments they have been created from; III) Investigate results of model comparisons and highlight regions of interest.AvailabilitySource code (http://www.github.com/eggzilla/cmv), web-service (http://rna.informatik.uni-freiburg.de/CMVS) Contactegg@informatik.uni-freiburg.de, choener@bioinf.uni-leipzig.deSupplementary informationSupplementary data available online.}, author = {Eggenhofer, Florian and Hofacker, Ivo L. and Backofen, Rolf and Höner zu Siederdissen, Christian and Valencia, Alfonso}, @@ -1882,6 +2119,53 @@ @article{fernandez-diaz_draft_2023 year = {2023} } +@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 +defects culminate in the loss of fertility when viewed from an evolutionary +perspective, where sperm flagellar function is extremely conserved across all +kingdoms. The model moss Physcomitrium patens has genes copies homologous to +human that are related to the architecture of microtubules that enable sperm motility. +The moss P. patens has been an important model system for studying issues of +evolutionary and developmental biology, as well as being an excellent model for +studies of cellular reprogramming, in addition to collaborating with studies of +flagellated organisms from various domains of biodiversity. Although the genes +involved in the process of organogenesis of the reproductive structures of mosses +are still little explored, it is believed that these may be involved in the construction of +the motility of the flagellum and other elements of the architecture of the tissues and +organs involved in evolution. Based on this hypothesis, our objective is to identify the +genes responsible for the differentiation of reproductive structures and how these +can identify problems in the formation of Organs reproductive organs of mosses. To +achieve the objectives, a differential gene expression analysis was carried out with +the aid of data obtained in the RNA-Seq technique. The reads used were obtained +from the NCBI (National Center for Biotechnology Information) database, on the +Sequence Reads Archives (SRA) platform SRR19502729, SRR19502730, +SRR19502731, SRR19502732, SRR19502733, SRR19502734, SRR4454535 and +SRR9901085. The raw reads were filtered by size and quality (Phred-Score 28) and +then analyzed for transcript counts and differential gene expression analysis (DEGs) +using the Salmon tool. As a result, the genes Pp3c10\_9456v3.1, Pp3c17\_1640V3.1 +and Pp3c17\_13470V3.1 were identified as possible genes involved in the sexual +differentiation between sexual organs of moss, where these genes are +over-expressed when there is formation of antheridia and under-expressed when +there is formation of antheridia. archegoniums. Through the analysis of gene function +and ontology, it was observed that the Pp3c10\_9456v3.1 gene is responsible for the +determination of symmetry, morphogenesis of the anatomical structure, assembly of +cellular components and development of organs in P. patens, being an ideal target +for tests of gene knockout to validate its role in the differentiation of reproductive +organs in this plant.}, + author = {Ferreira, Tiego}, + copyright = {Acesso Aberto}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {por}, + month = {February}, + note = {Accepted: 2023-05-25T16:42:56Z +Publisher: Universidade Federal do Pampa}, + title = {Avaliação da expressão diferencial em {Physcomitrium} patens na busca das adaptações moleculares responsivas na arquitetura dos órgãos reprodutivos}, + url = {https://repositorio.unipampa.edu.br/jspui/handle/riu/8369}, + urldate = {2023-07-31}, + year = {2023} +} + @article{fiedler_taxonomic_2021, 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}, @@ -1914,6 +2198,24 @@ @article{figiel_zinc_2023 year = {2023} } +@article{fischer_peptide-mediated_2023, + abstract = {Inhibition of protein-protein interactions (PPIs) via designed peptides is an effective strategy to perturb their biological functions. The Elongin BC heterodimer (ELOB/C) binds to a BC-box motif and is essential for cancer cell growth. Here, we report a peptide that mimics the high-affinity BC-box of the PRC2-associated protein EPOP. This peptide tightly binds to the ELOB/C dimer (kD = 0.46 ± 0.02 nM) and blocks the association of ELOB/C with its interaction partners, both in vitro and in the cellular environment. Cancer cells treated with our peptide inhibitor showed decreased cell viability, increased apoptosis, and perturbed gene expression. Therefore, our work proposes that blocking the BC-box-binding pocket of ELOB/C is a feasible strategy to impair its function and inhibit cancer cell growth. Our peptide inhibitor promises novel mechanistic insights into the biological function of the ELOB/C dimer and offers a starting point for therapeutics linked to ELOB/C dysfunction.}, + author = {Fischer, Sabrina and Trinh, Van Tuan and Simon, Clara and Weber, Lisa M. and Forné, Ignasi and Nist, Andrea and Bange, Gert and Abendroth, Frank and Stiewe, Thorsten and Steinchen, Wieland and Liefke, Robert and Vázquez, Olalla}, + doi = {10.1016/j.chembiol.2023.05.012}, + issn = {2451-9456}, + journal = {Cell Chemical Biology}, + keywords = {{\textgreater}UseGalaxy.eu, EPOP, Elongin BC, VHL, apoptosis, cancer, peptide inhibition, proliferation, protein-protein interactions}, + language = {en}, + month = {July}, + number = {7}, + pages = {766--779.e11}, + title = {Peptide-mediated inhibition of the transcriptional regulator {Elongin} {BC} induces apoptosis in cancer cells}, + url = {https://www.sciencedirect.com/science/article/pii/S2451945623001551}, + urldate = {2023-07-31}, + volume = {30}, + year = {2023} +} + @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}, @@ -2427,6 +2729,24 @@ @article{guendel_group_2020 year = {2020} } +@article{guerler_fast_2023, + abstract = {Protein–protein interactions play a crucial role in almost all cellular processes. Identifying interacting proteins reveals insight into living organisms and yields novel drug targets for disease treatment. Here, we present a publicly available, automated pipeline to predict genome-wide protein–protein interactions and produce high-quality multimeric structural models.}, + author = {Guerler, Aysam and Baker, Dannon and van den Beek, Marius and Gruening, Bjoern and Bouvier, Dave and Coraor, Nate and Shank, Stephen D. and Zehr, Jordan D. and Schatz, Michael C. and Nekrutenko, Anton}, + 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}, + language = {en}, + month = {June}, + number = {1}, + pages = {263}, + title = {Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using {Galaxy}}, + url = {https://doi.org/10.1186/s12859-023-05389-8}, + urldate = {2023-07-31}, + volume = {24}, + year = {2023} +} + @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}, @@ -2495,6 +2815,30 @@ @article{hamprecht_candida_2019 year = {2019} } +@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. +Methods +We utilized apolipoprotein E-deficient mice undergoing one- and six-month high cholesterol diet to model early and advanced atherosclerosis. Aortic macrophages, peritoneal macrophages, and circulating monocytes from each mouse were subjected to bulk RNA-sequencing (RNA-seq). We constructed a comparative directory that profiles lesion- and disease stage-specific transcriptomic regulation of the three cell types in atherosclerosis. Lastly, the regulation of one gene, Gpnmb, whose expression positively correlated with atheroma growth, was validated using single-cell RNA-seq (scRNA-seq) of atheroma plaque from murine and human. +Results +The convergence of gene regulation between the three investigated cell types was surprisingly low. Overall 3245 differentially expressed genes were involved in the biological modulation of aortic macrophages, among which less than 1\% were commonly regulated by the remote monocytes/macrophages. Aortic macrophages regulated gene expression most actively during atheroma initiation. Through complementary interrogation of murine and human scRNA-seq datasets, we showcased the practicality of our directory, using the selected gene, Gpnmb, whose expression in aortic macrophages, and a subset of foamy macrophages in particular, strongly correlated with disease advancement during atherosclerosis initiation and progression. +Conclusions +Our study provides a unique toolset to explore gene regulation of macrophage-related biological processes in and outside the atheromatous plaque at early and advanced disease stages.}, + author = {Härdtner, Carmen and Kumar, Anup and Ehlert, Carolin A. and Vico, Tamara Antonela and Starz, Christopher and von Ehr, Alexander and Krebs, Katja and Dufner, Bianca and Hoppe, Natalie and Stachon, Peter and Heidt, Timo and Wolf, Dennis and von zur Mühlen, Constantin and Grüning, Björn and Robbins, Clinton S. and Maegdefessel, Lars and Westermann, Dirk and Dederichs, Tsai-Sang and Hilgendorf, Ingo}, + doi = {10.1016/j.atherosclerosis.2023.03.006}, + issn = {0021-9150}, + journal = {Atherosclerosis}, + keywords = {{\textgreater}UseGalaxy.eu, Atherosclerosis, Gpnmb, Macrophage, RNA-seq}, + language = {en}, + month = {April}, + pages = {1--13}, + title = {A comparative gene expression matrix in {Apoe}-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages}, + url = {https://www.sciencedirect.com/science/article/pii/S0021915023001041}, + urldate = {2023-06-05}, + volume = {371}, + year = {2023} +} + @article{hedhly_s-locus_2023, abstract = {Self-incompatibility in Prunus species is governed by a single locus consisting of two highly multi-allelic and tightly linked genes, one coding for an F-box protein—i.e., SFB in Prunus- controlling the pollen specificity and one coding for an S-RNase gene controlling the pistil specificity. Genotyping the allelic combination in a fruit tree species is an essential procedure both for cross-based breeding and for establishing pollination requirements. Gel-based PCR techniques using primer pairs designed from conserved regions and spanning polymorphic intronic regions are traditionally used for this task. However, with the great advance of massive sequencing techniques and the lowering of sequencing costs, new genotyping-by-sequencing procedures are emerging. The alignment of resequenced individuals to reference genomes, commonly used for polymorphism detection, yields little or no coverage in the S-locus region due to high polymorphism between different alleles within the same species, and cannot be used for this purpose. Using the available sequences of Japanese plum S-loci concatenated in a rosary-like structure as synthetic reference sequence, we describe a procedure to accurately genotype resequenced individuals that allowed the analysis of the S-genotype in 88 Japanese plum cultivars, 74 of them are reported for the first time. In addition to unraveling two new S-alleles from published reference genomes, we identified at least two S-alleles in 74 cultivars. According to their S-allele composition, they were assigned to 22 incompatibility groups, including nine new incompatibility groups reported here for the first time (XXVII-XXXV).}, author = {Hedhly, Afif and Guerra, María Engracia and Grimplet, Jerome and Rodrigo, Javier}, @@ -2671,6 +3015,19 @@ @phdthesis{holthausen_bermejo_workflow-based_2019 year = {2019} } +@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}, + issn = {1664-8021}, + journal = {Frontiers in Genetics}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Gene expression networks and functionally enriched pathways involved in the response of domestic chicken to acute heat stress}, + url = {https://www.frontiersin.org/articles/10.3389/fgene.2023.1102136}, + urldate = {2023-07-31}, + volume = {14}, + year = {2023} +} + @article{huszarik_external_2023, abstract = {DNA metabarcoding is increasingly used to analyze the diet of arthropods, including spiders. However, high sensitivity to DNA contamination makes it difficult to apply to organisms obtained from mass-sampling methods such as pitfall traps. An alternative is to hand-sample spiders, but it is unclear how effectively this prevents external contamination, especially with new knowledge showing the wide spread of eDNA in the environment. Protocols using bleach to remove external DNA have been tested on several invertebrates, though testing with both mass-sampling methods and spiders is lacking. Here, we used wolf spiders (Lycosidae) to assess the risk of external DNA contamination from pitfall trapping and hand sampling, and the efficacy of bleach decontamination. We first conducted a contamination experiment where we placed spiders in pitfall traps containing trapping medium and a nonprey insect species to simulate external DNA contamination. We also compared sampling methods by collecting spiders using pitfall traps and hand sampling. Spiders from the contamination experiment and sampling method comparison were either bleached or untreated, then metabarcoded using multiple primer pairs. The contamination experiment resulted in the contamination of almost all spiders from pitfall traps, which was successfully eliminated with bleaching. Interestingly, there was no difference in the number of amplicon sequence variants (ASVs) detected per spider between pitfall trapping and hand sampling but bleaching resulted in significantly fewer ASV detections for both methods. Additionally, bleaching, but not sampling method, affected the taxonomic diet composition for both hand-sampled and pitfall-trapped spiders, indicating similar levels of external contamination. Our results are the first to confirm that DNA metabarcoding can be used together with bleaching for spiders sampled from pitfall traps, and that hand sampling does not necessarily exclude external DNA contamination. Thus, diet studies using metabarcoding should address the risk of external contamination with field-sampled arthropods, regardless of sampling method.}, author = {Huszarik, Maike and Röder, Nina and Eberhardt, Linda and Kennedy, Susan and Krehenwinkel, Henrik and Schwenk, Klaus and Entling, Martin H.}, @@ -2917,6 +3274,44 @@ @article{kandinov_azithromycin_2023 year = {2023} } +@article{kandinov_emergence_2023, + abstract = {The goal of this work was to determine the factors affecting the emergence of azithromycin-resistant Neisseria gonorrhoeae isolates in Russia, where azithromycin was never recommended for the treatment of gonococcal infections. Clinical N. gonorrhoeae isolates collected in 2018–2021 (428 isolates) were analyzed. No azithromycin-resistant isolates were found in 2018–2019, but in 2020–2021, a significant increase in the ratio of azithromycin-resistant isolates was observed: 16.8\% and 9.3\%, respectively. A hydrogel DNA microarray was developed for the analysis of resistance determinants: mutations in the genes encoding the mtrCDE efflux system and in all four copies of the 23S rRNA gene (position 2611). A majority of the azithromycin-resistant Russian isolates belonged to the NG-MAST G12302 genogroup, and the resistance was associated with the presence of a mosaic structure of the mtrR gene promoter region with the −35 delA deletion, an Ala86Thr mutation in the mtrR gene, and a mosaic structure of the mtrD gene. A comparative phylogenetic study of modern Russian and European N. gonorrhoeae populations allowed us to conclude that the emergence of azithromycin resistance in Russia in 2020 was the result of the appearance and spread of European N. gonorrhoeae strains belonging to the G12302 genogroup due to possible cross-border transfer.}, + author = {Kandinov, Ilya and Dementieva, Ekaterina and Filippova, Marina and Vinokurova, Alexandra and Gorshkova, Sofya and Kubanov, Alexey and Solomka, Victoria and Shagabieva, Julia and Deryabin, Dmitry and Shaskolskiy, Boris and Gryadunov, Dmitry}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/microorganisms11051226}, + issn = {2076-2607}, + journal = {Microorganisms}, + keywords = {\textit{Neisseria gonorrhoeae}, {\textgreater}UseGalaxy.eu, G12302 genogroup, NG-MAST, azithromycin resistance, genetic determinants of antimicrobial resistance, phylogenetic analysis}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {1226}, + title = {Emergence of {Azithromycin}-{Resistant} {Neisseria} gonorrhoeae {Isolates} {Belonging} to the {NG}-{MAST} {Genogroup} 12302 in {Russia}}, + url = {https://www.mdpi.com/2076-2607/11/5/1226}, + urldate = {2023-07-31}, + volume = {11}, + year = {2023} +} + +@article{karthik_foremost_2023, + abstract = {Several Pasteurella like organisms isolated from various avian species were recently reclassified into new genus based on whole genome sequence analysis. One such Pasteurella like organism, Bisgaard taxon 14 was classified as Spirabiliibacterium mucosae. In the present study, a Gram-negative organism was isolated from ailing pigeons with respiratory infection from a farm in Tamil Nadu, India and the organism was misidentified as Burkholderia mallei by Vitek 2 compact system based on biochemical characterization. Since, B. mallei is highly pathogenic and zoonotic, to further confirm, 16S rDNA sequencing and analysis was carried out which revealed that the strain belonged to Bisgaard taxon 14 (Spirabiliibacterium mucosae). To further confirm the findings, whole genome sequencing of the isolate was performed. Whole genome phylogeny and average nucleotide identity (ANI) analysis showed that the genome was closely matching with Spirabiliibacterium mucosae type strain 20,609 /3. Hence, the strain from pigeon was named as Spirabiliibacterium mucosae TN\_CUL\_2021 and the genome was submitted in NCBI SRA database. The genome of S. mucosase TN\_CUL\_2021 is only the second genome available worldwide in the NCBI database. Comparative genome analysis of 26 Pasteurellaceae family strains revealed 1101 genes specific for Spirabiliibacterium mucosae. Similarly, luxS virulence gene was found only in S. mucosae and Bisgaardia hudsonensis strains. Since there are only 2 genomes available in the NCBI genome database, further studies on isolation of S. mucosae needs to be carried out to identify its epidemiology and pathogenesis so as to develop better diagnostic assays and vaccines.}, + author = {Karthik, Kumaragurubaran and Anbazhagan, Subbaiyan and Ananda Chitra, Murugesan and Ramya, Rajendran and Sridhar, Ramaswamy and Dhinakar Raj, Gopal}, + doi = {10.1016/j.gene.2023.147359}, + issn = {0378-1119}, + journal = {Gene}, + keywords = {{\textgreater}UseGalaxy.eu, Comparative genomics, India, Pigeon, Vitek 2}, + language = {en}, + month = {May}, + pages = {147359}, + title = {Foremost report of the whole genome of {Spirabiliibacterium} mucosae from {India} and comparative genomics of the novel genus {Spirabiliibacterium}}, + url = {https://www.sciencedirect.com/science/article/pii/S0378111923002007}, + urldate = {2023-07-31}, + volume = {867}, + year = {2023} +} + @article{katsanos_gene_2021, 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}, @@ -2973,6 +3368,21 @@ @article{kavas_genome-wide_2022 year = {2022} } +@phdthesis{kefi_improving_2023, + abstract = {The Human Genome Annotation (HGA) file is a database where different features describing elements of the genome (genes, transcripts, etc) are stored. HGA is the process of identifying those elements, characterizing them and elucidating their roles. Currently, HGA is still incomplete because it suffers from missed annotation and mis-annotation. Mis-annotation happens when some elements are wrongly annotated or labeled. Missed annotation happens when some elements are absent from the annotation files due to the limitations of analytical and experimental procedures. On one hand, improved identification of novel genome elements is required to help solve the problem of missed annotation. On the other hand, to address the problem of mis-annotation, better classification methods are needed to characterize and validate the novel elements. This thesis addresses the problem of incomplete human genome annotation and proposes an improved identification and validation approach via integration of second and third generation of sequencing. We apply this integrative approach to detect novel mono-exonic genes (MNEGs) and confirm their transcription and translation. Up until recent studies, MNEGs were thought to be artifacts and were discarded. However, our integrative analysis provided additional evidence for the genuine existence of these genes. In the second part of this project, we used computational methods based on a deep learning framework to validate these findings by characterizing MNEG types and classifying them into either proteins coding RNAs (pcRNAs) or long non-coding RNAs (lncRNAs). Our results showed that the majority of MNEGs are classified as lncRNAs and further investigation suggested that some of them are circRNAs. Finally, this work provides an innovative approach and a unique computational framework to address the problem of incomplete HGA and could be adopted by the annotators in their pipelines. This study is an important step towards the completion and the improvement of the human genome annotation.}, + address = {Ann Arbor, United States}, + author = {Kefi, Amira}, + copyright = {Database copyright ProQuest LLC; ProQuest does not claim copyright in the individual underlying works.}, + keywords = {{\textgreater}UseGalaxy.eu, Deep learning, Genome annotation, ISOseq, Machine learning, RNAseq, Ribo-seq}, + language = {Englisch}, + note = {ISBN: 9798379745967}, + title = {Improving the {Human} {Genome} {Annotation} {Using} {Integrative} {Analysis} and {Deep} {Learning} {Methods}}, + type = {Ph.{D}.}, + url = {https://www.proquest.com/docview/2830283170/abstract/B6B2BD2F6A44FF9PQ/1}, + urldate = {2023-07-31}, + year = {2023} +} + @article{khan_comparative_2023, abstract = {Very long-chain fatty acids (VLCFAs) possess more than twenty carbon atoms and are the major components of seed storage oil, wax, and lipids. FAE (Fatty Acid Elongation) like genes take part in the biosynthesis of VLCFAs, growth regulation, and stress responses, and are further comprised of KCS (Ketoacyl-CoA synthase) and ELO (Elongation Defective Elongase) sub-gene families. The comparative genome-wide analysis and mode of evolution of KCS and ELO gene families have not been investigated in tetraploid Brassica carinata and its diploid progenitors. In this study, 53 KCS genes were identified in B. carinata compared to 32 and 33 KCS genes in B. nigra and B. oleracea respectively, which suggests that polyploidization might has impacted the fatty acid elongation process during Brassica evolution. Polyploidization has also increased the number of ELO genes in B. carinata (17) over its progenitors B. nigra (7) and B. oleracea (6). Based on comparative phylogenetics, KCS, and ELO proteins can be classified into eight and four major groups, respectively. The approximate date of divergence for duplicated KCS and ELO genes varied from 0.03 to 3.20 million years ago (MYA). Gene structure analysis indicated that the maximum number of genes were intron-less and remained conserved during evolution. The neutral type of selection seemed to be predominant in both KCS and ELO genes evolution. String-based protein-protein interaction analysis suggested that bZIP53, a transcription factor might be involved in the activation of transcription of ELO/KCS genes. The presence of biotic and abiotic stress-related cis-regulatory elements in the promoter region suggests that both KCS and ELO genes might also play their role in stress tolerance. The expression analysis of both gene family members reflect their preferential seed-specific expression, especially during the mature embryo development stage. Furthermore, some KCS and ELO genes were found to be specifically expressed under heat stress, phosphorus starvation, and Xanthomonas campestris infection. The current study provides a basis to understand the evolution of both KCS and ELO genes in fatty acid elongation and their role in stress tolerance.}, author = {Khan, Uzair Muhammad and Rana, Iqrar Ahmad and Shaheen, Nabeel and Raza, Qasim and Rehman, Hafiz Mamoon and Maqbool, Rizwana and Khan, Iqrar Ahmad and Atif, Rana Muhammad}, @@ -2994,6 +3404,27 @@ @article{khan_comparative_2023 year = {2023} } +@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}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41598-023-32406-w}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Environmental sciences, Evolution, Genetics, Microbiology}, + language = {en}, + month = {March}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {5124}, + title = {Comparative genomic analysis of {Colistin} resistant {Escherichia} coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm}, + url = {https://www.nature.com/articles/s41598-023-32406-w}, + urldate = {2023-07-31}, + volume = {13}, + year = {2023} +} + @article{kim_complete_2022, abstract = {Metabacillus litoralis is part of the newly proposed genus Metabacillus. The bacterium was first isolated from a Yellow Sea tidal flat in 2005. As of May 2022, there are five genomic assemblies deposited in GenBank. We report the 5.2-Mbp genome sequence of M. litoralis strain NCTR108, from commercial tattoo ink.}, author = {Kim, Sung Guk and Summage-West, Christine V. and Reyna, Mariela and Kim, Seong-Jae and Foley, Steven L.}, @@ -3427,6 +3858,24 @@ @article{lange_expression_2020 year = {2020} } +@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}, + doi = {10.1016/j.gene.2023.147547}, + issn = {0378-1119}, + journal = {Gene}, + keywords = {{\textgreater}UseGalaxy.eu, Horizontal Gene Transfer, Immune effectors, Insects, RNA -glycosidase, Ribosome Inactivating Proteins}, + language = {en}, + month = {August}, + pages = {147547}, + shorttitle = {Ribosome inactivating proteins in insects}, + title = {Ribosome inactivating proteins in insects: {HGT}, gene expression, and functional implications}, + url = {https://www.sciencedirect.com/science/article/pii/S0378111923003888}, + urldate = {2023-07-31}, + volume = {877}, + year = {2023} +} + @article{larsen_identification_2019, abstract = {C-type lectin-like domain containing proteins (CTLDcps) mainly bind carbohydrate-based ligands, but also other ligands. CTLDcps are involved in several biological processes including cell adhesion, cell-cell interactions, and pathogen recognition. Pathogen recognition by myeloid cells, e.g. dendritic cells (DCs), can be facilitated through cell surface expressed CTLDcps. Cell surface expressed CTLDcps have been exploited in vaccine designs for specific targeting of human and mouse DCs using antibodies. In recent years, however, DC targeting using carbohydrate-based vaccines has gained interest due to low production cost, limited immunogenicity, and possibility of multivalent adjustment. In chicken, however, only a few CTLDcps have been identified. Identifying and annotating additional chicken CTLDcps (chCTLDcps) is needed to exploit carbohydrate-mediated DC targeting in chicken. Therefore, we searched the chicken GRCg6a assembly for novel chCTLDcps. We identified 28 chCTLDcps of which 10 had previously been described and also experimentally validated. RNA-seq and RT-qPCR confirmed mRNA expression of the remaining 18 identified chCTLDcps. A group of highly related chCTLDcps, moreover, was shown to be avian-specific and comprise novel members mapped to the proposed chicken natural killer gene complex. Two chCTLDcps, chCLEC17AL-A and chCLEC17AL-B, were found to share a recent common ancestor with CLEC17A. Putative mannose or fucose-binding sequence motifs, EPN and WND, were found in the CTLD of chCLEC17AL-A. Both contained intracellular internalisation and signalling sequence motifs. In conclusion, several chCTLDcps were identified and their expression confirmed. Both chCLEC17AL-A and -B showed promise as potential targets in carbohydrate-based chicken vaccine strategies. Determination of DC-specific expression of chCLEC17AL-A and -B, thus, might prove useful in chicken vaccinology.}, author = {Larsen, Frederik T. and Bed’Hom, Bertrand and Guldbrandtsen, Bernt and Dalgaard, Tina S.}, @@ -3481,6 +3930,28 @@ @article{latif_nfatc1_2022 year = {2022} } +@article{le_corre_mechanism-based_2023, + abstract = {Hydrogen sulfide (H2S) is a gaseous signaling molecule that participates in various signaling functions in health and diseases. The tetrameric cystathionine γ-lyase (CSE) contributes to H2S biogenesis and several investigations provide evidence on the pharmacological modulation of CSE as a potential target for the treatment of a multitude of conditions. D-penicillamine (D-pen) has recently been reported to selectively impede CSE-catalyzed H2S production but the molecular bases for such inhibitory effect have not been investigated. In this study, we report that D-pen follows a mixed-inhibition mechanism to inhibit both cystathionine (CST) cleavage and H2S biogenesis by human CSE. To decipher the molecular mechanisms underlying such a mixed inhibition, we performed docking and molecular dynamics (MD) simulations. Interestingly, MD analysis of CST binding reveals a likely active site configuration prior to gem-diamine intermediate formation, particularly H-bond formation between the amino group of the substrate and the O3′ of PLP. Similar analyses realized with both CST and D-pen identified three potent interfacial ligand-binding sites for D-pen and offered a rational for D-pen effect. Thus, inhibitor binding not only induces the creation of an entirely new interacting network at the vicinity of the interface between enzyme subunits, but it also exerts long range effects by propagating to the active site. Overall, our study paves the way for the design of new allosteric interfacial inhibitory compounds that will specifically modulate H2S biogenesis by cystathionine γ-lyase.}, + author = {Le Corre, Laurent and Padovani, Dominique}, + copyright = {2023 The Author(s)}, + doi = {10.1038/s41598-023-34405-3}, + issn = {2045-2322}, + journal = {Scientific Reports}, + keywords = {{\textgreater}UseGalaxy.eu, Biochemistry, Chem-informatics, Enzyme mechanisms, Enzymes, Mechanism of action, Small molecules, chemicaltoolbox}, + language = {en}, + month = {May}, + note = {Number: 1 +Publisher: Nature Publishing Group}, + number = {1}, + pages = {7287}, + shorttitle = {Mechanism-based and computational modeling of hydrogen sulfide biogenesis inhibition}, + title = {Mechanism-based and computational modeling of hydrogen sulfide biogenesis inhibition: interfacial inhibition}, + url = {https://www.nature.com/articles/s41598-023-34405-3}, + urldate = {2023-07-31}, + volume = {13}, + year = {2023} +} + @article{lengfelder_complex_2019, abstract = {Inflammatory bowel diseases (IBD) are associated with compositional and functional changes of the intestinal microbiota, but specific contributions of individual bacteria to chronic intestinal inflammation remain unclear. Enterococcus faecalis is a resident member of the human intestinal core microbiota that has been linked to the pathogenesis of IBD and induces chronic colitis in susceptible monoassociated IL-10-deficient (IL-10-/-) mice. In this study, we characterized the colitogenic activity of E. faecalis as part of a simplified human microbial consortium based on seven enteric bacterial strains (SIHUMI). RNA sequencing analysis of E. faecalis isolated from monoassociated wild type and IL-10-/- mice identified 408 genes including 14 genes of the ethanolamine utilization (eut) locus that were significantly up-regulated in response to inflammation. Despite considerable up-regulation of eut genes, deletion of ethanolamine utilization (∆eutVW) had no impact on E. faecalis colitogenic activity in monoassociated IL-10-/- mice. However, replacement of the E. faecalis wild type bacteria by a ∆eutVW mutant in SIHUMI-colonized IL-10-/- mice resulted in exacerbated colitis, suggesting protective functions of E. faecalis ethanolamine utilization in complex bacterial communities. To better understand E. faecalis gene response in the presence of other microbes, we purified wild type E. faecalis cells from the colon content of SIHUMI-colonized wild type and IL-10-/- mice using immuno-magnetic separation and performed RNA sequencing. Transcriptional profiling revealed that the bacterial environment reprograms E. faecalis gene expression in response to inflammation, with the majority of differentially expressed genes not being shared between monocolonized and SIHUMI conditions. While in E. faecalis monoassociation a general bacterial stress response could be observed, expression of E. faecalis genes in SIHUMI-colonized mice was characterized by up-regulation of genes involved in growth and replication. Interestingly, in mice colonized with SIHUMI lacking E. faecalis enhanced inflammation was observed in comparison to SIHUMI-colonized mice, supporting the hypothesis that E. faecalis ethanolamine metabolism protects against colitis in complex consortia. In conclusion, this study demonstrates that complex bacterial consortia interactions reprogram the gene expression profile and colitogenic activity of the opportunistic pathogen E. faecalis towards a protective function.}, author = {Lengfelder, Isabella and Sava, Irina G. and Hansen, Jonathan J. and Kleigrewe, Karin and Herzog, Jeremy and Neuhaus, Klaus and Hofmann, Thomas and Sartor, R. Balfour and Haller, Dirk}, @@ -3496,6 +3967,29 @@ @article{lengfelder_complex_2019 year = {2019} } +@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.}, + author = {Lenz, Maximilian and Eichler, Amelie and Kruse, Pia and Galanis, Christos and Kleidonas, Dimitrios and Andrieux, Geoffroy and Boerries, Melanie and Jedlicka, Peter and Müller, Ulrike and Deller, Thomas and Vlachos, Andreas}, + copyright = {Copyright © 2023 the authors. SfN exclusive license.}, + 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}, + language = {en}, + month = {July}, + note = {Publisher: Society for Neuroscience +Section: Research Articles}, + number = {29}, + pages = {5290--5304}, + pmid = {37369586}, + title = {The {Amyloid} {Precursor} {Protein} {Regulates} {Synaptic} {Transmission} at {Medial} {Perforant} {Path} {Synapses}}, + url = {https://www.jneurosci.org/content/43/29/5290}, + urldate = {2023-07-31}, + volume = {43}, + year = {2023} +} + @article{lenz_denervated_2023, abstract = {Structural, functional, and molecular reorganization of denervated neural networks is often observed in neurological conditions. The loss of input is accompanied by homeostatic synaptic adaptations, which can affect the reorganization process. A major ...}, author = {Lenz, Maximilian and Eichler, Amelie and Kruse, Pia and Stöhr, Phyllis and Kleidonas, Dimitrios and Galanis, Christos and Lu, Han and Vlachos, Andreas}, @@ -3930,6 +4424,21 @@ @article{marzoli_next_2020 year = {2020} } +@article{mathura_genome-wide_2023, + abstract = {Auxin is a plant phytohormone that is essential for the initiation of tuberization in sweet potato (Ipomoea batatas (L.) Lam.). Auxin exerts these effects via polar auxin transport facilitated by various auxin influx and efflux carriers. It is unclear which members of the auxin transporter families: PIN, PILS, Aux/LAX, and ABCB, are involved in sweet potato tuber initiation and development. Therefore, a genome-wide analysis of the I. batatas auxin transporter genes was conducted, and their expression patterns during storage root initiation and development were analyzed. Five IbLAX, 16 IbPIN, 12 IbPILS, and 34 IbABCB family members were identified. These genes showed high conservation among families based on their intron-exon structure, motif composition, and phylogenetic analysis. Additionally, the promoter regions of these genes had various cis-acting regulatory elements involved in hormone, light, and developmental responses. The auxin transporter genes were expressed in various sweet potato tissues, and many were differentially expressed during storage root development. IbLAX1, IbPIN13, IbPILS7, IbABCB1, and IbABCB14 showed up-regulated expression during tuber initiation. This study characterizes these auxin transporter gene families for the first time. These results are an important reference for validation studies to determine the specific functions of these genes and their auxin transporting capability.}, + author = {Mathura, Sarah R. and Sutton, Fedora and Bowrin, Valerie}, + doi = {10.1007/s12042-023-09333-1}, + issn = {1935-9764}, + journal = {Tropical Plant Biology}, + keywords = {{\textgreater}UseGalaxy.eu, ABCB, Aux/LAX, Ipomoea batatas, PILS, PIN}, + language = {en}, + month = {June}, + title = {Genome-wide {Identification} of the {Auxin} {Transporter} {Gene} {Families} in {Sweet} {Potato} ({Ipomoea} batatas) and their {Expression} {During} {Tuberization}}, + url = {https://doi.org/10.1007/s12042-023-09333-1}, + urldate = {2023-07-31}, + year = {2023} +} + @article{mauer_genomics_2021, 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}, @@ -4591,6 +5100,21 @@ @article{niemoller_bisulfite-free_2021 year = {2021} } +@article{noauthor_characterization_2023, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Characterization of the {Italian} population of {Ciborinia} camelliae}, + url = {https://air.unimi.it/handle/2434/980235}, + urldate = {2023-07-31}, + year = {2023} +} + +@misc{noauthor_proceedings_nodate, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Proceedings of the {Joint} 3rd {International} {Conference} on {Bioinformatics} and {Data} {Science} ({ICBDS} 2022), {ISBN} 9789464631630 - {Better} {Read} {Than} {Dead} {Bookstore} {Newtown}}, + url = {https://www.betterread.com.au/book/proceedings-of-the-joint-3rd-international-conference-on-bioinformatics-and-data-science-icbds-2022.do}, + urldate = {2023-07-31} +} + @article{nuhrenberg_impact_2022, 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}, @@ -4645,6 +5169,23 @@ @article{oeyen_sawfly_2020 year = {2020} } +@article{oger_-cellspecific_2023, + abstract = {The loss of pancreatic β-cell identity has emerged as an important feature of type 2 diabetes development, but the molecular mechanisms are still elusive. Here, we explore the cell-autonomous role of the cell-cycle regulator and transcription factor E2F1 in the maintenance of β-cell identity, insulin secretion, and glucose homeostasis. We show that the β-cell–specific loss of E2f1 function in mice triggers glucose intolerance associated with defective insulin secretion, altered endocrine cell mass, downregulation of many β-cell genes, and concomitant increase of non–β-cell markers. Mechanistically, epigenomic profiling of the promoters of these non–β-cell upregulated genes identified an enrichment of bivalent H3K4me3/H3K27me3 or H3K27me3 marks. Conversely, promoters of downregulated genes were enriched in active chromatin H3K4me3 and H3K27ac histone marks. We find that specific E2f1 transcriptional, cistromic, and epigenomic signatures are associated with these β-cell dysfunctions, with E2F1 directly regulating several β-cell genes at the chromatin level. Finally, the pharmacological inhibition of E2F transcriptional activity in human islets also impairs insulin secretion and the expression of β-cell identity genes. Our data suggest that E2F1 is critical for maintaining β-cell identity and function through sustained control of β-cell and non–β-cell transcriptional programs.β-Cell–specific E2f1 deficiency in mice impairs glucose tolerance.Loss of E2f1 function alters the ratio of α- to β-cells but does not trigger β-cell conversion into α-cells.Pharmacological inhibition of E2F activity inhibits glucose-stimulated insulin secretion and alters β- and α-cell gene expression in human islets.E2F1 maintains β-cell function and identity through control of transcriptomic and epigenetic programs.}, + author = {Oger, Frédérik and Bourouh, Cyril and Friano, Marika Elsa and Courty, Emilie and Rolland, Laure and Gromada, Xavier and Moreno, Maeva and Carney, Charlène and Rabhi, Nabil and Durand, Emmanuelle and Amanzougarene, Souhila and Berberian, Lionel and Derhourhi, Mehdi and Blanc, Etienne and Hannou, Sarah Anissa and Denechaud, Pierre-Damien and Benfodda, Zohra and Meffre, Patrick and Fajas, Lluis and Kerr-Conte, Julie and Pattou, François and Froguel, Philippe and Pourcet, Benoit and Bonnefond, Amélie and Collombat, Patrick and Annicotte, Jean-Sébastien}, + doi = {10.2337/db22-0604}, + issn = {0012-1797}, + journal = {Diabetes}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {May}, + number = {8}, + pages = {1112--1126}, + title = {β-{Cell}–{Specific} {E2f1} {Deficiency} {Impairs} {Glucose} {Homeostasis}, β-{Cell} {Identity}, and {Insulin} {Secretion}}, + url = {https://doi.org/10.2337/db22-0604}, + urldate = {2023-07-31}, + volume = {72}, + year = {2023} +} + @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}, @@ -4879,6 +5420,29 @@ @article{perezriverol_scalable_2019 year = {2019} } +@phdthesis{peschel_molekulare_2023, + abstract = {Metastasierung und Therapieresistenz stellen die wesentlichen Hindernisse bei der kurativen Behandlung des Kolorektalkarzinoms (KRK) dar und sind Hauptursache für die krebsbedingte Sterblichkeit. Bei etwa einem Viertel der KRK-Patient*innen liegen bei Erstdiagnose Fernmetastasen vor, bei ca. der Hälfte der Erkrankten treten im Verlauf Fernmetastasen auf (Kumbrink et al., 2021; Van Cutsem \& Oliveira, 2009; Vatandoust et al., 2015). +Fluoropyrimidin-basierte Chemotherapieregime sind das Grundgerüst der systemischen KRK-Therapie, welche durch weitere klassische Zytostatika sowie Antikörper-basierte Wirkstoffe erweitert werden kann. Das Kombinationsschema bestehend aus 5-Fluoruracil, Irinotecan und Leucovorin – syn. FOLFIRI – wird bei metastasiertem KRK (mKRK) als Erst- oder Zweitlinientherapie eingesetzt (Leitlinienprogramm Onkologie (Deutsche Krebsgesellschaft, 2019). Trotz der Wirksamkeit dieser Kombinationsbehandlung, durch die die Überlebensrate deutlich verbessert werden konnte, führen intrinsische und erworbene Resistenzmechanismen zur Progression der Krankheit (Jensen et al., 2015; Lyskjær et al., 2019). + +Um molekularen Mechanismen und Biomarker der FOLFIRI-Resistenz auf Transkriptomebene zu identifizieren, wurden aus den KRK -Zelllinien Colo205, HT29 und SW480 drei FOLFIRI-resistente Subzelllinien durch kontinuierliche Behandlung mit steigenden FOLFIRI-Konzentrationen hergestellt. Als biologische Effekte der FOLFIRI-Resistenz konnten Änderungen in der Genexpression, morphologische Veränderungen sowie Anpassung des Zellzyklus und Zelltod-Resistenz beobachtet werden. + +Zur Identifikation von resistenz-assoziierten Expressionssignaturen oder potentiell prognostischen Biomarkern wurde eine RNA-Sequenzierung der parentalen sowie der resistenten Zelllinien durchgeführt. +Insgesamt 284 differentiell exprimierte Gene (DEGs) wurden nach der bioinformatischen Analyse der RNA-Sequenzierung von 24 Proben ermittelt (Colo205: 222 Gene, HT29: 47 Gene, SW480: 30 Gene). Anschließend wurden diese DEGs miteinander abgeglichen und 12 DEGs identifiziert, die in zwei oder allen drei Zelllinien konsistent dysreguliert waren. Mittels Kaplan-Meier (KM-) Überlebenszeitanalyse des Kolon-Adenokarzinom-Datensatz (COAD) des Krebsgenomatlas (The Cancer Genome Atlas, TCGA, PanCancer Atlas Datenset ) wurden hieraus drei prognostisch relevante Gene (TACSTD2, PERP und CAV2) identifiziert, die sich signifikant mit kürzerem Überleben bei KRK assoziiert zeigten. +Diese Ergebnisse wurden mit den Ergebnissen einer klinischen Studie (GSE62322) abgeglichen. In dieser Studie wurden von 21 Chemotherapie-naiven KRK-Patient*innen Tumorproben entnommen, worauf eine postoperative Chemotherapie mit FOLFIRI folgte. Um eine Gensignatur zu identifizieren, die das Ansprechen auf FOLFIRI vorhersagen soll, wurden im nächsten Schritt die Expressionsdaten der auf FOLFIRI ansprechenden Patient*innen mit denen der nicht auf FOLFIRI ansprechenden Patient*innen verglichen. +Im Abgleich mit diesen Expressionsdaten konnten die drei Gene TACSTD2, PERP und CAV2 nicht als signifikant dysreguliert bzw. als Teil der Gensignatur nachgewiesen werden. Jedoch konnten die Gene SERPINE2 und TNC aus der Liste aller 284 DEGs in den klinischen Tumorproben ebenfalls als signifikant differentiell exprimiert nachgewiesen werden und mittels KM-Überlebenszeitanalyse als prognostisch relevant eingestuft werden. +Diese drei bzw. fünf identifizierten Gene können nun Grundlage für weitere experimentelle Schritte sein, um neue diagnostische und prognostische Biomarker für die klinische Praxis zu etablieren.}, + author = {Peschel, Christiane}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {de}, + month = {March}, + school = {Ludwig-Maximilians-Universität München}, + title = {Molekulare {Mechanismen} der pharmakologischen {Resistenz} kolorektaler {Karzinomzelllinien} gegen das {Chemotherapieregime} {FOLFIRI}}, + type = {Text.{PhDThesis}}, + url = {https://edoc.ub.uni-muenchen.de/31524/}, + urldate = {2023-07-31}, + year = {2023} +} + @article{pessoa_rodrigues_histone_2021, abstract = {Noncommunicable diseases (NCDs) account for over 70\% of deaths world-wide. Previous work has linked NCDs such as type 2 diabetes (T2D) to disruption of chromatin regulators. However, the exact molecular origins of these chronic conditions remain elusive. Here, we identify the H4 lysine 16 acetyltransferase MOF as a critical regulator of central carbon metabolism. High-throughput metabolomics unveil a systemic amino acid and carbohydrate imbalance in Mof deficient mice, manifesting in T2D predisposition. Oral glucose tolerance testing (OGTT) reveals defects in glucose assimilation and insulin secretion in these animals. Furthermore, Mof deficient mice are resistant to diet-induced fat gain due to defects in glucose uptake in adipose tissue. MOF-mediated H4K16ac deposition controls expression of the master regulator of glucose metabolism, Pparg and the entire downstream transcriptional network. Glucose uptake and lipid storage can be reconstituted in MOF-depleted adipocytes in vitro by ectopic Glut4 expression, PPARγ agonist thiazolidinedione (TZD) treatment or SIRT1 inhibition. Hence, chronic imbalance in H4K16ac promotes a destabilisation of metabolism triggering the development of a metabolic disorder, and its maintenance provides an unprecedented regulatory epigenetic mechanism controlling diet-induced obesity.}, author = {Pessoa Rodrigues, Cecilia and Chatterjee, Aindrila and Wiese, Meike and Stehle, Thomas and Szymanski, Witold and Shvedunova, Maria and Akhtar, Asifa}, @@ -5201,6 +5765,19 @@ @article{retamal-morales_draft_2018 year = {2018} } +@article{reyes_characterization_2023, + abstract = {IntroductionTheobroma cacao, the cocoa tree, is a target for pathogens, such as fungi from the genera Phytophthora, Moniliophthora, Colletotrichum, Ceratocystis, among others. Some cacao pathogens are restricted to specific regions of the world, such as the Cacao swollen shoot virus (CSSV) in West African countries, while others are expanding geographically, such as Moniliophthora roreri in the Americas. M. roreri is one of the most threatening cacao pathogens since it directly attacks the cacao pods driving a significant reduction in production, and therefore economic losses. Despite its importance, the knowledge about the microenvironment of this pathogen and the cocoa pods is still poorly characterized.MethodsHerein we performed RNA sequencing of spores in differential stages of culture in a medium supplemented with cacao pod extract and mycelium collected of the susceptible variety ICT 7121 naturally infected by the pathogen to evaluate the diversity and transcriptional activity of microorganisms associated with the in vitro sporulation of M. roreri.ResultsOur data revealed a great variety of fungi and bacteria associated with M. roreri, with an exceptional diversity of individuals from the genus Trichoderma sp. Interestingly, the dynamics of microorganisms from different kingdoms varied proportionally, suggesting they are somehow affected by M. roreri culture time. We also identified three sequences similar to viral genomes from the Narnaviridae family, posteriorly confirmed by phylogenetic analysis as members of the genus Narnavirus. Screening of M. roreri public datasets indicated the virus sequences circulating in samples from Ecuador, suggesting a wide spread of these elements. Of note, we did not identify traces of the viral sequences in the M. roreri genome or DNA sequencing, restricting the possibility of these sequences representing endogenized elements.DiscussionTo the best of our knowledge, this is the first report of viruses infecting the fungus of the genus Moniliophthora and only the third description of viruses that are able to parasite elements from the Marasmiaceae family.}, + author = {Reyes, Brayan Maudiel Diaz and Fonseca, Paula Luize Camargos and Heming, Neander Marcel and Conceição, Lucas Barbosa de Amorim and Nascimento, Katiucia Ticila de Souza and Gramacho, Karina Peres and Arevalo-Gardini, Enrique and Pirovani, Carlos Priminho and Aguiar, Eric Roberto Guimarães Rocha}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + title = {Characterization of the microbiota dynamics associated with {Moniliophthora} roreri, causal agent of cocoa frosty pod rot disease, reveals new viral species}, + url = {https://www.frontiersin.org/articles/10.3389/fmicb.2022.1053562}, + urldate = {2023-07-31}, + volume = {13}, + year = {2023} +} + @article{riediger_analysis_2020, author = {Riediger, Matthias and Spät, Philipp and Bilger, Raphael and Voigt, Karsten and Maček, Boris and Hess, Wolfgang R.}, doi = {10.1093/plcell/koaa017}, @@ -5422,6 +5999,24 @@ @article{schafer_glassgo_2020 year = {2020} } +@article{schiml_integrative_2023, + abstract = {‘Omics methods have empowered scientists to tackle the complexity of microbial communities on a scale not attainable before. Individually, omics analyses can provide great insight; while combined as “meta-omics”, they enhance the understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize environmental nutrients. Here we present three integrative meta-omics workflows, developed in Galaxy, for enhanced analysis and integration of metagenomics, metatranscriptomics, and metaproteomics, combined with our newly developed web-application, ViMO (Visualizer for Meta-Omics) to analyse metabolisms in complex microbial communities.}, + author = {Schiml, Valerie C. and Delogu, Francesco and Kumar, Praveen and Kunath, Benoit and Batut, Bérénice and Mehta, Subina and Johnson, James E. and Grüning, Björn and Pope, Phillip B. and Jagtap, Pratik D. and Griffin, Timothy J. and Arntzen, Magnus Ø.}, + 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}, + language = {en}, + month = {July}, + number = {1}, + pages = {56}, + title = {Integrative meta-omics in {Galaxy} and beyond}, + url = {https://doi.org/10.1186/s40793-023-00514-9}, + urldate = {2023-07-31}, + volume = {18}, + year = {2023} +} + @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.}, @@ -5729,6 +6324,27 @@ @article{soriano-sexto_identification_2022 year = {2022} } +@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}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/plants12081600}, + issn = {2223-7747}, + journal = {Plants}, + keywords = {{\textgreater}UseGalaxy.eu, artichoke ecotype, artichoke transcriptome, bioactive compounds, lignin, peroxidase, virus sanitation}, + language = {en}, + month = {January}, + note = {Number: 8 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {8}, + pages = {1600}, + title = {Comparative {Analysis} of {Bioactive} {Compounds} in {Two} {Globe} {Artichoke} {Ecotypes} {Sanitized} and {Non}-{Sanitized} from {Viral} {Infections}}, + url = {https://www.mdpi.com/2223-7747/12/8/1600}, + urldate = {2023-07-31}, + volume = {12}, + year = {2023} +} + @article{spradling_mitochondrial_2021, author = {Spradling, Theresa A. and Place, Alexandra C. and Campbell, Ashley L. and Demastes, James W.}, doi = {10.1371/journal.pone.0254138}, @@ -5804,6 +6420,25 @@ @article{strateva_analysis_2023 year = {2023} } +@article{strateva_genotypic_2023, + abstract = {Abstract The present study aimed to explore the virulence characteristics in 221 Bulgarian nosocomial Stenotrophomonas maltophilia isolates (2011–2022) via screening for the presence of virulence genes, their mutational variability, and the corresponding enzyme activity. PCR amplification, enzymatic assays, whole-genome sequencing (WGS), and biofilm quantification on a polystyrene plate were performed. The incidence of virulence determinants was as follows: stmPr1 (encoding for the major extracellular protease StmPr1) 87.3\%, stmPr2 (minor extracellular protease StmPr2) 99.1\%, Smlt3773 locus (outer membrane esterase) 98.2\%, plcN1 (non-hemolytic phospholipase C) 99.1\%, and smf-1 (type-1 fimbriae, biofilm-related gene) 96.4\%. The 1621-bp allele of stmPr1 was most frequently found (61.1\%), followed by the combined allelic variant (17.6\%), stmPr1-negative genotype (12.7\%), and 868-bp allele (8.6\%). Protease, esterase, and lecithinase activity was observed in 95\%, 98.2\%, and 17.2\% of the isolates, respectively. The WGS-subjected isolates (n = 9) formed two groups. Five isolates possessed only the 1621-bp variant of stmPr1, higher biofilm formation ability (Optical Density at λ = 550 nm (OD550): 1.253–1.789), as well as a low number of mutations in the protease genes and smf-1. Three other isolates had only the 868-bp variant, weaker biofilm production (OD550: 0.788–1.108), and higher number of mutations within these genes. The only weak biofilm producer (OD550 = 0.177) had no stmPr1 alleles. In conclusion, the similar PCR detection rates did not allow differentiation of the isolates. In contrast, WGS permitted stmPr1 alleles-based differentiation. To the best of our knowledge, this is the first Bulgarian study presenting genotypic and phenotypic insights into virulence factors of S. maltophilia isolates.}, + author = {Strateva, Tanya and Trifonova, Angelina and Stratev, Alexander and Peykov, Slavil}, + doi = {10.1556/030.2023.02059}, + issn = {1217-8950, 1588-2640}, + journal = {Acta Microbiologica et Immunologica Hungarica}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {en}, + month = {July}, + note = {Publisher: Akadémiai Kiadó +Section: Acta Microbiologica et Immunologica Hungarica}, + number = {aop}, + title = {Genotypic and phenotypic insights into virulence factors of nosocomial {Stenotrophomonas} maltophilia isolates collected in {Bulgaria} (2011–2022)}, + url = {https://akjournals.com/view/journals/030/aop/article-10.1556-030.2023.02059/article-10.1556-030.2023.02059.xml}, + urldate = {2023-07-31}, + volume = {-1}, + year = {2023} +} + @article{subramoney_identification_2022, abstract = {The circulation of Omicron BA.1 led to the rapid increase in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases in South Africa in November 2021, which warranted the use of more rapid detection methods. We, therefore, assessed the ability to detect Omicron BA.1 using genotyping assays to identify specific mutations in SARS-CoV-2 positive samples, Gauteng province, South Africa. The TaqPath™ COVID-19 real-time polymerase chain reaction assay was performed on all samples selected to identify spike gene target failure (SGTF). SARS-CoV-2 genotyping assays were used for the detection of del69/70 and K417N mutation. Whole-genome sequencing was performed on a subset of genotyped samples to confirm these findings. Of the positive samples received, 11.0\% (175/1589) were randomly selected to assess if SGTF and genotyping assays, that detect del69/70 and K417N mutations, could identify Omicron BA.1. We identified SGTF in 98.9\% (173/175) of samples, of which 88.0\% (154/175) had both the del69/70 and K417N mutation. The genotyped samples (45.7\%; 80/175) that were sequenced confirmed Omicron BA.1 (97.5\%; 78/80). Our data show that genotyping for the detection of the del69/70 and K417N coupled with SGTF is efficient to exclude Alpha and Beta variants and rapidly detect Omicron BA.1. However, we still require assays for the detection of unique mutations that will allow for the differentiation between other Omicron sublineages. Therefore, the use of genotyping assays to detect new dominant or emerging lineages of SARS-CoV-2 will be beneficial in limited-resource settings.}, author = {Subramoney, Kathleen and Mtileni, Nkhensani and Bharuthram, Avani and Davis, Ashlyn and Kalenga, Beauty and Rikhotso, Mikateko and Maphahlele, Mpho and Giandhari, Jennifer and Naidoo, Yeshnee and Pillay, Sureshnee and Ramphal, Upasana and Ramphal, Yajna and Tegally, Houriiyah and Wilkinson, Eduan and Mohale, Thabo and Ismail, Arshad and Mashishi, Bonolo and Mbenenge, Nonhlanhla and de Oliveira, Tulio and Makatini, Zinhle and Fielding, Burtram C. and Treurnicht, Florette K. and Africa, Network for Genomics Surveillance in South}, @@ -5871,6 +6506,21 @@ @article{sun_stencil_2022 year = {2022} } +@article{sundar_-silico_2023, + abstract = {The emergence of drug resistant Mycobacterium tuberculosis strains increases the burden on the treatment of tuberculosis. In this study, through in-silico transcriptome analysis of drug-treated M. tuberculosis samples, novel drug targets for the treatment of drug resistance in tuberculosis were identified. Gene expression datasets of tuberculosis patients samples treated with different antibiotics (Isoniazid, Rifampicin, Pyrazinamide, Bedaquiline and Linezolid) were considered in this study. DESeq2 was used to identify the differentially regulated genes. Novel genes which were up-regulated during antibiotic treatment were identified which could be antibiotic resistance factors. Further, to understand the resistance mechanism of the novel genes, we performed gene ontology and gene network analysis for the differentially up-regulated genes. Thus, the in-silico transcriptome analysis paves way for a deeper understanding of the antibiotic resistance in M. tuberculosis.}, + author = {Sundar, Shobana}, + doi = {10.1016/j.ijtb.2023.06.010}, + issn = {0019-5707}, + journal = {Indian Journal of Tuberculosis}, + keywords = {{\textgreater}UseGalaxy.eu, Antibiotic resistance, Transcriptome}, + language = {en}, + month = {June}, + title = {In-silico transcriptome analysis of antibiotic-treated {Mycobacterium} tuberculosis identifies novel antibiotic resistance factors}, + url = {https://www.sciencedirect.com/science/article/pii/S0019570723001166}, + urldate = {2023-07-31}, + year = {2023} +} + @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}, @@ -5879,7 +6529,7 @@ @incollection{suzuki_genomic_2023 doi = {10.1007/978-1-0716-2996-3_16}, editor = {Arakawa, Kazuharu}, isbn = {978-1-07-162996-3}, - keywords = {{\textgreater}UseGalaxy.eu, Antimicrobial resistance, Chromosome, ESKAPE pathogens, Mobile genetic element, Mycobacteria, Phage, Plasmid, Virulence}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, Antimicrobial resistance, Chromosome, ESKAPE pathogens, Mobile genetic element, Mycobacteria, Phage, Plasmid, Virulence}, language = {en}, pages = {227--246}, publisher = {Springer US}, @@ -5929,6 +6579,24 @@ @article{tabarelli_chasing_2022 year = {2022} } +@article{tajuddin_genomic_2023, + abstract = {Vibrio alginolyticus is a Gram-negative bacterium commonly associated with mackerel poisoning. A bacteriophage that specifically targets and lyses this bacterium could be employed as a biocontrol agent for treating the bacterial infection or improving the shelf-life of mackerel products. However, only a few well-characterized V. alginolyticus phages have been reported in the literature. In this study, a novel lytic phage, named ΦImVa-1, specifically infecting V. alginolyticus strain ATCC 17749, was isolated from Indian mackerel. The phage has a short latent period of 15 min and a burst size of approximately 66 particles per infected bacterium. ΦImVa-1 remained stable for 2 h at a wide temperature (27–75 °C) and within a pH range of 5 to 10. Transmission electron microscopy revealed that ΦImVa-1 has an icosahedral head of approximately 60 nm in diameter with a short tail, resembling those in the Schitoviridae family. High throughput sequencing and bioinformatics analysis elucidated that ΦImVa-1 has a linear dsDNA genome of 77,479 base pairs (bp), with a G + C content of {\textasciitilde} 38.72\% and 110 predicted gene coding regions (106 open reading frames and four tRNAs). The genome contains an extremely large virion-associated RNA polymerase gene and two smaller non-virion-associated RNA polymerase genes, which are hallmarks of schitoviruses. No antibiotic genes were found in the ΦImVa-1 genome. This is the first paper describing the biological properties, morphology, and the complete genome of a V. alginolyticus-infecting schitovirus. When raw mackerel fish flesh slices were treated with ΦImVa-1, the pathogen loads reduced significantly, demonstrating the potential of the phage as a biocontrol agent for V. alginolyticus strain ATCC 17749 in the food.}, + author = {Tajuddin, Sofiah and Khan, Asif M. and Chong, Li Chuin and Wong, Chuan Loo and Tan, Jia Sen and Ina-Salwany, Md Yasin and Lau, Han Yih and Ho, Kok Lian and Mariatulqabtiah, Abdul Razak and Tan, Wen Siang}, + doi = {10.1007/s00253-022-12312-3}, + issn = {1432-0614}, + journal = {Applied Microbiology and Biotechnology}, + keywords = {{\textgreater}Pasteur, {\textgreater}UseGalaxy.eu, Bacteriophage, Biocontrol, Bioinformatics, Food poisoning, Genome, Schitoviridae, Vibrio alginolyticus, Vibriosis}, + language = {en}, + month = {February}, + number = {2}, + pages = {749--768}, + title = {Genomic analysis and biological characterization of a novel {Schitoviridae} phage infecting {Vibrio} alginolyticus}, + url = {https://doi.org/10.1007/s00253-022-12312-3}, + urldate = {2023-07-31}, + volume = {107}, + year = {2023} +} + @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}, @@ -6054,6 +6722,26 @@ @article{tosar_ri-sec-seq_2021 year = {2021} } +@article{trifonova_combination_2023, + abstract = {Background The SARS-CoV-2 virus significantly changed our knowledge about coronaviruses. The interplay between SARS-CoV-2 and the human host, the infection ranges from asymptomatic to lethal, and differences in the degree of disease severity are important examples.Methods In this retrospective study, 24 nasopharyngeal swabs from 21 out of 457 patients with SARS-CoV-2 infection were analysed by whole-genome sequencing. The principal selection criteria were the duration of infection and disease severity.Results Two co-occurring rare mutations in the SARS-CoV-2 M gene were detected in six samples. Three of these samples were collected from an immunocompromised patient with fatal outcome, two from an immunocompetent patient, and one from a patient with severe disease and fatal outcome, all with a prolonged course of infection.Conclusions Although this interesting finding was demonstrated in a small number of patients, the results increase the knowledge regarding the significance of mutations in the M gene of SARS-CoV-2 in the context of persistent infection and viral escape mechanisms.}, + author = {Trifonova, Angelina and Syarov, Atanas and Takov, Svetlomir and Angelov, Krassimir and Vazharova, Radoslava and Terzieva, Velislava}, + doi = {10.1080/23744235.2023.2238077}, + issn = {2374-4235}, + journal = {Infectious Diseases}, + keywords = {{\textgreater}UseGalaxy.eu, COVID-19, M gene, SARS-CoV-2, mutation, prolonged infection}, + month = {July}, + note = {Publisher: Taylor \& Francis +\_eprint: https://doi.org/10.1080/23744235.2023.2238077}, + number = {0}, + pages = {1--5}, + pmid = {37493404}, + title = {Combination of two rare mutations in the {SARS}-{CoV}-2 {M} gene in patients with severe and prolonged {COVID}-19}, + url = {https://doi.org/10.1080/23744235.2023.2238077}, + urldate = {2023-07-31}, + volume = {0}, + year = {2023} +} + @article{tsai_biogenesis_2022, author = {Tsai, Hsin-Yue and Cheng, Hsian-Tang and Tsai, Yi-Ting}, doi = {10.1126/sciadv.abm0699}, @@ -6105,6 +6793,24 @@ @article{uellendahl-werth_benchmark_2020 year = {2020} } +@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}, + doi = {10.1007/s10722-022-01480-w}, + issn = {1573-5109}, + journal = {Genetic Resources and Crop Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org, {\textgreater}UseGalaxy.org.au, MACE, O. ficus-indica, O. joconostle, O. robusta, RNA-seq}, + language = {en}, + month = {March}, + number = {3}, + pages = {951--970}, + title = {The first transcriptomic analyses of fruits and cladodes for comparison between three species of {Opuntia}}, + url = {https://doi.org/10.1007/s10722-022-01480-w}, + urldate = {2023-07-31}, + volume = {70}, + year = {2023} +} + @article{valsecchi_rna_2020, 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}, doi = {10.1038/s41586-020-2935-z}, @@ -6132,23 +6838,6 @@ @article{vaquero-sedas_epigenetic_2022 year = {2022} } -@article{vaquero-sedas_epigenetic_2023, - 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}, - month = {January}, - number = {1}, - pages = {47--55}, - title = {Epigenetic nature of {Arabidopsis} thaliana telomeres}, - url = {https://doi.org/10.1093/plphys/kiac471}, - urldate = {2023-03-15}, - volume = {191}, - year = {2023} -} - @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}, @@ -6246,6 +6935,27 @@ @article{villa_degradation_2020 year = {2020} } +@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}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/antibiotics12071179}, + issn = {2079-6382}, + journal = {Antibiotics}, + keywords = {{\textgreater}UseGalaxy.eu, VOCs, biosynthesis pathways, endophyte, medicinal plants}, + language = {en}, + month = {July}, + note = {Number: 7 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {7}, + pages = {1179}, + title = {Employing {Genome} {Mining} to {Unveil} a {Potential} {Contribution} of {Endophytic} {Bacteria} to {Antimicrobial} {Compounds} in the {Origanum} vulgare {L}. {Essential} {Oil}}, + url = {https://www.mdpi.com/2079-6382/12/7/1179}, + urldate = {2023-07-31}, + volume = {12}, + year = {2023} +} + @article{voelker_high-quality_2021, author = {Voelker, Julia and Shepherd, Mervyn and Mauleon, Ramil}, doi = {10.46471/gigabyte.28}, @@ -6259,6 +6969,24 @@ @article{voelker_high-quality_2021 year = {2021} } +@article{voelker_terpene_2023, + abstract = {Terpene synthases (TPS) are responsible for the terminal biosynthetic step of terpenoid production. They are encoded by a highly diverse gene family believed to evolve by tandem duplication in response to adaptive pressures. Taxa in the Myrtaceae family are renowned for their diversity of terpenoid-rich essential oils, and among them, the tribe Eucalypteae has the largest TPS gene family found in any plant ({\textgreater} 100 TPS). In this study, comparative analysis of Melaleuca alternifolia (tea tree), from the related tribe Melaleuceae, revealed some Myrtaceae have smaller TPS families, as a total of 58 putatively functional full-length TPS genes, and 21 pseudogenes were identified by manual annotation of a newly released long-read assembly of the genome. The TPS-a and TPS-b2 subfamilies that synthesise secondary compounds often mediating plant-environment interactions were more diminutive than those in eucalypts, probably reflecting key differences in the evolutionary histories of the two lineages. Of the putatively functional TPS-b1, 13 clustered into a region of around 400 kb on one scaffold. The organisation of these TPS suggested that tandem duplication was instrumental in the evolution and diversity of terpene chemistry in Melaleuca. Four TPS-b1 likely to catalyse the synthesis of the three monoterpenoid components that are used to classify tea tree chemotypes were encoded within a single small region of 87 kb in the larger cluster of TPS-b1, raising the possibility that coregulation and linkage may lead to their behaviour as a single locus, providing an explanation for the categorical inheritance of complex multiple-component chemotypes in the taxon.}, + author = {Voelker, Julia and Mauleon, Ramil and Shepherd, Mervyn}, + doi = {10.1007/s00606-023-01847-1}, + issn = {1615-6110}, + journal = {Plant Systematics and Evolution}, + keywords = {{\textgreater}UseGalaxy.eu, {\textgreater}UseGalaxy.org.au, Eucalypts, Genetics, Monoterpenes, Myrtaceae, TPS manual annotation, Tea tree}, + language = {en}, + month = {April}, + number = {3}, + pages = {13}, + title = {The terpene synthase genes of {Melaleuca} alternifolia (tea tree) and comparative gene family analysis among {Myrtaceae} essential oil crops}, + url = {https://doi.org/10.1007/s00606-023-01847-1}, + urldate = {2023-07-31}, + volume = {309}, + year = {2023} +} + @article{volkova_radiosensitivity_2021, author = {Volkova, Polina Yu and Duarte, Gustavo T. and Kazakova, Elizaveta A. and Makarenko, Ekaterina S. and Bitarishvili, Sofia V. and Bondarenko, Vladimir S. and Perevolotskii, Alexander N. and Geras'kin, Stanislav A. and Garbaruk, Dmitrii K. and Turchin, Larisa M.}, doi = {10.1016/j.scitotenv.2021.146206}, @@ -6304,6 +7032,27 @@ @techreport{vorobyeva_suhw_2023 year = {2023} } +@article{voronezhskaya_multi-omics_2023, + abstract = {Our understanding of the long-term consequences of chronic ionising radiation for living organisms remains scarce. Modern molecular biology techniques are helpful tools for researching pollutant effects on biota. To reveal the molecular phenotype of plants growing under chronic radiation exposure, we sampled Vicia cracca L. plants in the Chernobyl exclusion zone and areas with normal radiation backgrounds. We performed a detailed analysis of soil and gene expression patterns and conducted coordinated multi-omics analyses of plant samples, including transcriptomics, proteomics, and metabolomics. Plants growing under chronic radiation exposure showed complex and multidirectional biological effects, including significant alterations in the metabolism and gene expression patterns of irradiated plants. We revealed profound changes in carbon metabolism, nitrogen reallocation, and photosynthesis. These plants showed signs of DNA damage, redox imbalance, and stress responses. The upregulation of histones, chaperones, peroxidases, and secondary metabolism was noted.}, + author = {Voronezhskaya, Viktoria and Volkova, Polina and Bitarishvili, Sofia and Shesterikova, Ekaterina and Podlutskii, Mikhail and Clement, Gilles and Meyer, Christian and Duarte, Gustavo Turqueto and Kudin, Maksim and Garbaruk, Dmitrii and Turchin, Larisa and Kazakova, Elizaveta}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/plants12122318}, + issn = {2223-7747}, + journal = {Plants}, + keywords = {\textit{Fabaceae}, {\textgreater}UseGalaxy.eu, abiotic stress, low doses, metabolomics, proteomics, transcriptomics}, + language = {en}, + month = {January}, + note = {Number: 12 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {12}, + pages = {2318}, + title = {Multi-{Omics} {Analysis} of {Vicia} cracca {Responses} to {Chronic} {Radiation} {Exposure} in the {Chernobyl} {Exclusion} {Zone}}, + url = {https://www.mdpi.com/2223-7747/12/12/2318}, + urldate = {2023-07-31}, + volume = {12}, + year = {2023} +} + @article{vukovikj_-depth_2023, abstract = {The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a persistent negative impact on both the public health and the global economy. To comprehend the origin, transmission routes and discover the mutations that alter the virus’s transmissibility and pathogenicity, full-length SARS-CoV-2 genomes have to be molecularly characterized. Focusing on a two-year time frame (2020-2021), we provide an in-depth virologic and epidemiological overview of the SARS-CoV-2 pandemic in the Republic of North Macedonia by assessing the frequency and distribution of the circulating SARS-CoV-2 variants. Using genetic characterization and phylogenetic analysis we shed light on the molecular evolution of the virus as well as test for a possible connection between specific SARS-CoV-2 haplotypes and the severity of the clinical symptoms. Our results show that one fifth (21.51\%) of the tested respiratory samples for SARS-CoV-2 were positive. A noticeable trend in the incidence and severity of the COVID-19 infections was observed in the 60+ age group between males and females. Of the total number of positive cases, the highest incidence of SARS-CoV-2 was noticed in 60+ males (4,170.4/100,000), with a statistically significant (0,0001) difference between the two sexes. Additionally, a 1.8x increase in male mortality and consequentially significantly higher number of death cases was observed compared to females of the same age group (0.001). A total of 327 samples were sequenced in the period March 2020 - August 2021, showing the temporal distribution of SARS-CoV-2 variants circulating in North Macedonia. The phylogenetic analysis showed that most of the viral genomes were closely related and clustered in four distinctive lineages, B.1, B.1.1.7, B.1.351 and B.1.617.2. A statistically significant difference was observed in the 2C\_1 haplotype (p=0.0013), where 10.5\% of the patients were hospitalized due to severe clinical condition. By employing genetic sequencing, coupled with epidemiological investigations, we investigated viral distribution patterns, identified emerging variants and detected vaccine breakthrough infections. The present work is the first molecular study giving a comprehensive overview of the genetic landscape of circulating SARS-CoV-2 viruses in North Macedonia in a period of two years.}, author = {Vukovikj, Maja and Boshevska, Golubinka and Janchevska, Elizabeta and Buzharova, Teodora and Preshova, Ardian and Simova, Milica and Peshnacka, Aneta and Kocinski, Dragan and Kuzmanovska, Gordana and Memeti, Shaban and Gjorgoski, Icko}, @@ -6578,6 +7327,23 @@ @article{wittenburg_canonical_2022 year = {2022} } +@article{wittke_eodie_2023, + abstract = {Remote sensing satellites provide a vast amount of data to monitor and observe Earth’s surface and events on it. To use these data efficiently in subsequent analysis and decision-making, highly automated easy-to-use tools are needed. Here, we present Earth Observation Data Information Extractor (EODIE). EODIE is a toolkit to extract object-level time-series information from several multispectral satellite remote sensing platforms and to produce analysis-ready products for subsequent data analysis. EODIE has a modular design that makes it adjustable for end-user requirements. Users have a possibility to exchange and add modules in EODIE for flexible processing in different computing environments. With EODIE, remote sensing data can be processed to object level array, geotiff or statistics information of different (vegetation) indices or plain wavelength intervals.}, + author = {Wittke, Samantha and Fouilloux, Anne and Lehti, Petteri and Varho, Juuso and Kivimäki, Arttu and Karhu, Maiju and Karjalainen, Mika and Vaaja, Matti and Puttonen, Eetu}, + doi = {10.1016/j.softx.2023.101421}, + issn = {2352-7110}, + journal = {SoftwareX}, + keywords = {{\textgreater}UseGalaxy.eu, Big data processing, Earth observation, Open-source software, Remote sensing}, + language = {en}, + month = {July}, + pages = {101421}, + title = {{EODIE} — {Earth} {Observation} {Data} {Information} {Extractor}}, + url = {https://www.sciencedirect.com/science/article/pii/S2352711023001176}, + urldate = {2023-07-31}, + volume = {23}, + year = {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}, @@ -6770,6 +7536,19 @@ @incollection{wolfien_workflow_2019 year = {2019} } +@article{wolkowicz_utility_2017, + abstract = {Modern diagnostics is in general based on molecular biology methods. Nowadays sequencing-based methods, especially whole genome sequencing, are becoming increasingly important. Implementation of such methods into routine diagnostic of highly dangerous pathogens, like Bacillus anthracis, Francisella tularensis, Yersinia pestis, Ebola virus, MERS, Lassa virus etc. would be very helpful. The best diagnostic strategy would be the metagenomic sequencing directly from the clinical sample. Implementation of majority of currently available WGS platforms inside the BSL-3 or 4 laboratory is impractical because of the size of the equipment and time consuming wet lab part (e.g. library preparation). Nowadays there is a possibility to implement pocket size MinION - real time whole genome sequencer into BSL-3 and 4 laboratory for rapid and precise diagnostic purposes.}, + author = {Wołkowicz, Tomasz}, + doi = {10.1093/bfgp/elx033}, + journal = {Briefings in Functional Genomics}, + keywords = {+Workbench, {\textgreater}UseGalaxy.eu}, + month = {November}, + title = {The utility and perspectives of {NGS}-based methods in {BSL}-3 and {BSL}-4 laboratory – sequencing and analysis strategies}, + url = {https://academic.oup.com/bfg/advance-article/doi/10.1093/bfgp/elx033/4616141}, + urldate = {2017-12-01}, + year = {2017} +} + @article{wright*_structure_2018, abstract = {Many years of research in RNA biology have soundly established the importance of RNA-based regulation far beyond most early traditional presumptions. Importantly, the advances in “wet” laboratory techniques have produced unprecedented amounts of data that require efficient and precise computational analysis schemes and algorithms. Hence, many in silico methods that attempt topological and functional classification of novel putative RNA-based regulators are available. In this review, we technically outline thermodynamics-based standard RNA secondary structure and RNA-RNA interaction prediction approaches that have proven valuable to the RNA research community in the past and present. For these, we highlight their usability with a special focus on prokaryotic organisms and also briefly mention recent advances in whole-genome interactomics and how this may influence the field of predictive RNA research.}, author = {Wright*, Patrick R. and Mann*, Martin and Backofen*, Rolf}, @@ -7058,6 +7837,25 @@ @article{zilbauer_roadmap_2023 } @article{zirngibl_triose_2023, + abstract = {Plants have evolved multiple strategies to cope with rapid changes in the environment. During high light (HL) acclimation, the biosynthesis of photoprotective flavonoids, such as anthocyanins, is induced. However, the exact nature of the signal and downstream factors for HL induction of flavonoid biosynthesis (FB) is still under debate. Here, we show that carbon fixation in chloroplasts, subsequent export of photosynthates by triose phosphate/phosphate translocator (TPT), and rapid increase in cellular sugar content permit the transcriptional and metabolic activation of anthocyanin biosynthesis during HL acclimation. In combination with genetic and physiological analysis, targeted and whole-transcriptome gene expression studies suggest that reactive oxygen species and phytohormones play only a minor role in rapid HL induction of the anthocyanin branch of FB. In addition to transcripts of FB, sugar-responsive genes showed delayed repression or induction in tpt-2 during HL treatment, and a significant overlap with transcripts regulated by SNF1-related protein kinase 1 (SnRK1) was observed, including a central transcription factor of FB. Analysis of mutants with increased and repressed SnRK1 activity suggests that sugar-induced inactivation of SnRK1 is required for HL-mediated activation of anthocyanin biosynthesis. Our study emphasizes the central role of chloroplasts as sensors for environmental changes as well as the vital function of sugar signaling in plant acclimation.}, + author = {Zirngibl, Max-Emanuel and Araguirang, Galileo Estopare and Kitashova, Anastasia and Jahnke, Kathrin and Rolka, Tobias and Kühn, Christine and Nägele, Thomas and Richter, Andreas S.}, + 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}, + language = {en}, + month = {January}, + number = {1}, + pages = {100423}, + series = {Focus {Issue} on {Chloroplast} {Biology}}, + title = {Triose phosphate export from chloroplasts and cellular sugar content regulate anthocyanin biosynthesis during high light acclimation}, + url = {https://www.sciencedirect.com/science/article/pii/S2590346222002553}, + urldate = {2023-07-31}, + volume = {4}, + year = {2023} +} + +@article{zirngibl_triose_2023-1, abstract = {Plants have evolved multiple strategies to cope with rapid changes in the environment. During high light (HL) acclimation, the biosynthesis of photoprotective flavonoids, such as anthocyanins, is induced. However, the exact nature of the signal and downstream factors for HL induction of flavonoid biosynthesis (FB) is still under debate. Here, we show that carbon fixation in chloroplasts, subsequent export of photosynthates by triose phosphate/phosphate translocator (TPT), and rapid increase in cellular sugar content permit the transcriptional and metabolic activation of anthocyanin biosynthesis during HL acclimation. In combination with genetic and physiological analysis, targeted and whole-transcriptome gene expression studies suggest that reactive oxygen species and phytohormones play only a minor role in rapid HL induction of the anthocyanin branch of FB. In addition to transcripts of FB, sugar-responsive genes showed delayed repression or induction in tpt-2 during HL treatment, and a significant overlap with transcripts regulated by SNF1-related protein kinase 1 (SnRK1) was observed, including a central transcription factor of FB. Analysis of mutants with increased and repressed SnRK1 activity suggests that sugar-induced inactivation of SnRK1 is required for HL-mediated activation of anthocyanin biosynthesis. Our study emphasizes the central role of chloroplasts as sensors for environmental changes as well as the vital function of sugar signaling in plant acclimation.}, author = {Zirngibl, Max-Emanuel and Araguirang, Galileo Estopare and Kitashova, Anastasia and Jahnke, Kathrin and Rolka, Tobias and Kühn, Christine and Nägele, Thomas and Richter, Andreas S.}, doi = {10.1016/j.xplc.2022.100423},