diff --git a/_bibliography/citations-eu.bib b/_bibliography/citations-eu.bib index 420765f8..c74d39e7 100644 --- a/_bibliography/citations-eu.bib +++ b/_bibliography/citations-eu.bib @@ -219,6 +219,22 @@ @article{akol_multimodal_2023 year = {2023} } +@article{akpinar_characterization_2024, + abstract = {Xylanases are the main enzymes to hydrolyze xylan, the major hemicellulose found in lignocellulose. Xylanases also have a wide range of industrial applications. Therefore, the discovery of new xylanases has the potential to enhance efficiency and sustainability in many industries. Here, we report a xylanase with thermophilic character and superior biochemical properties for industrial use. The new xylanase is discovered in Anoxybacillus ayderensis as an intracellular xylanase (AAyXYN329) and recombinantly produced. While AAyXYN329 shows significant activity over a wide pH and temperature range, optimum activity conditions were determined as pH 6.5 and 65 °C. The half-life of the enzyme was calculated as 72 h at 65 °C. The enzyme did not lose activity between pH 6.0–9.0 at +4 °C for 75 days. Km, kcat and kcat/Km values of AAyXYN329 were calculated as 4.09824 ± 0.2245 μg/μL, 96.75 1/sec, and 23.61/L/g.s −1, respectively. In conclusion, the xylanase of A. ayderensis has an excellent potential to be utilized in many industrial processes.}, + author = {Akpinar, Zuleyha and Karaoglu, Hakan}, + doi = {10.1016/j.pep.2024.106478}, + issn = {1046-5928}, + journal = {Protein Expression and Purification}, + keywords = {{\textgreater}UseGalaxy.eu, Intracellular, Thermophilic, Xylan, xylanase}, + month = {July}, + pages = {106478}, + title = {Characterization of a highly thermostable recombinant xylanase from \textit{{Anoxybacillu}}s \textit{ayderensis}}, + url = {https://www.sciencedirect.com/science/article/pii/S1046592824000500}, + urldate = {2024-05-17}, + volume = {219}, + year = {2024} +} + @article{alawi_private_2024, abstract = {Water quality testing does not recognise antimicrobial resistance (AMR) and is often limited to indicators of faecal contamination Escherichia coli and Enterococcus species. In Europe, data on AMR in drinking water is scarce. In Ireland, as in many countries, household drinking water is supplied via mains or via private wells or water schemes. Using citizen science, we identified Irish private drinking water supplies as reservoirs of antimicrobial resistant bacteria (ARB). Gram-negative (n = 464) and Gram-positive (n = 72) bacteria were isolated. We identified instances of potentially opportunistic ARB such as Enterobacter cloacae, Acinetobacter baumannii and Enterococcus species. We report reservoirs of multidrug resistance in Enterococcus casseliflavus, E. cloacae, E. coli, Stenotrophomonas maltophilia, and Serratia rubidaea. We also identified linezolid-resistant Enterococcus in Irish drinking water. Linezolid is a last-resort antibiotic used to treat vancomycin-resistant Enterococcus sp. Additionally, we identified mobile AMR in three water samples, two of which were carried on IncF group, one on IncQ and five on Col-like plasmids. Our work suggests that private drinking water is a potential sink and source of AMR pathogens. This highlights a value of drinking water surveillance in a One Health framework as the surveillance would provide information regarding the movement and persistence of ARB and ARGs that are able to survive in drinking water and subsequently have the opportunity to be mobilised through humans; linking the environment to the human and potentially threatening human health.}, author = {Alawi, Marwa and Smyth, Cian and Drissner, David and Zimmerer, Anna and Leupold, Denise and Müller, Daria and Do, Thi Thuy and Velasco-Torrijos, Trinidad and Walsh, Fiona}, @@ -1859,6 +1875,23 @@ @article{candeliere_draft_2020 year = {2020} } +@article{candeliere_genomic_2024, + abstract = {{\textless}p{\textgreater}Mucins are large glycoproteins whose degradation requires the expression of several glycosil hydrolases to catalyze the cleavage of the oligosaccharide chains and release monosaccharides that can be assimilated. In this study, we present a characterization on the strains {\textless}italic{\textgreater}Clostridium celatum{\textless}/italic{\textgreater} WC0700, {\textless}italic{\textgreater}Clostridium tertium{\textless}/italic{\textgreater} WC0709, and {\textless}italic{\textgreater}Paraclostridium bifermentans{\textless}/italic{\textgreater} WC0705. These three strains were previously isolated from enrichment cultures on mucin of fecal samples from healthy subjects and can use mucin as sole carbon and nitrogen source. Genome analysis and {\textless}italic{\textgreater}in vitro{\textless}/italic{\textgreater} functional analysis of these strains elucidated their physiological and biochemical features. {\textless}italic{\textgreater}C. celatum{\textless}/italic{\textgreater} WC0700 harbored the highest number of glycosyl hydrolases specific for mucin degradation, while {\textless}italic{\textgreater}P. bifermentans{\textless}/italic{\textgreater} WC0705 had the least. These predicted differences were confirmed growing the strains on 5 mucin-decorating monosaccharides (L-fucose, N-Acetylneuraminic acid, galactose, N-acetylgalactosamine, and N-acetylglucosamine) as only source of carbon. Fermenting mucin, they all produced formic, acetic, propionic, butyric, isovaleric, and lactic acids, and ethanol; acetic acid was the main primary metabolite. Further catabolic capabilities were investigated, as well as antibiotic susceptibility, biofilm formation, tolerance to oxygen and temperature. The potential pathogenicity of the strains was evaluated through {\textless}italic{\textgreater}in silico{\textless}/italic{\textgreater} research of virulence factors. The merge between comparative and functional genomics and biochemical/physiological characterization provided a comprehensive view of these mucin degraders, reassuring on the safety of these species and leaving ample scope for deeper investigations on the relationship with the host and for assessing if some relevant health-promoting effect could be ascribed to these SCFA producing species.{\textless}/p{\textgreater}}, + author = {Candeliere, Francesco and Musmeci, Eliana and Sola, Laura and Amaretti, Alberto and Raimondi, Stefano and Rossi, Maddalena}, + doi = {10.3389/fmicb.2024.1359726}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Clostridium celatum, Clostridium tertium, Functional Genomics, Paraclostridium bifermentans, human gut microbiota, mucin}, + language = {English}, + month = {March}, + note = {Publisher: Frontiers}, + title = {Genomic and functional analysis of the mucinolytic species {Clostridium} celatum, {Clostridium} tertium, and {Paraclostridium} bifermentans}, + url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1359726/full}, + urldate = {2024-05-17}, + volume = {15}, + year = {2024} +} + @phdthesis{cantarella_insights_2020, abstract = {A large portion of the human genome is composed of repeated sequences, with Alu retrotransposons representing the most abundant repetitive elements. Alu sequences belong to the class of the Short Interspersed Nuclear Elements (SINEs) and depend on the Long Interspersed Nuclear Elements (LINEs) for their mobilization into the genome. The efficiency of Alu amplification during primate evolution suggests a positive driving force for their accumulation, bringing up to 1 million copies in the human genome. For unclear reasons, the majority of Alu sequences is repressed by tight epigenetic silencing, which is released in response to cell stresses such as virus infection and cancer progression. Adenovirus 5 (Ad5) is known to cause an increase of Alu transcription in HeLa, myelogenous leukemia and embryonic kidney cell lines, even though the virus factors that are responsible for this transcriptional enhancement have not been identified yet. Potential candidates could be represented by oncovirus proteins that induce a global remodeling of the host epigenetic landscape. For example, the Adenovirus early E1A protein interacts with the host tumor suppressor Rb, the lysine acetylase p300 and the p400 ATP-dependent chromatin remodeling complex, resulting in the induction of quiescent fibroblasts to enter the S-phase of the cell cycle. The exceptional success of Alu expansion and their retention even at the cost of a strong epigenetic silencing, which is released by virus infection, led us to investigate the molecular mechanism of Alus activation and their potential involvement in various cell processes. @@ -2468,6 +2501,30 @@ @article{de_souza_seeds_2024 year = {2024} } +@article{dehghanian_zfp982_2024, + abstract = {Background +Understanding the genetic underpinnings of protein networks conferring stemness is of broad interest for basic and translational research. +Methods +We used multi-omics analyses to identify and characterize stemness genes, and focused on the zinc finger protein 982 (Zfp982) that regulates stemness through the expression of Nanog, Zfp42, and Dppa3 in mouse embryonic stem cells (mESC). +Results +Zfp982 was expressed in stem cells, and bound to chromatin through a GCAGAGKC motif, for example near the stemness genes Nanog, Zfp42, and Dppa3. Nanog and Zfp42 were direct targets of ZFP982 that decreased in expression upon knockdown and increased upon overexpression of Zfp982. We show that ZFP982 expression strongly correlated with stem cell characteristics, both on the transcriptional and morphological levels. Zfp982 expression decreased with progressive differentiation into ecto-, endo- and mesodermal cell lineages, and knockdown of Zfp982 correlated with morphological and transcriptional features of differentiated cells. Zfp982 showed transcriptional overlap with members of the Hippo signaling pathway, one of which was Yap1, the major co-activator of Hippo signaling. Despite the observation that ZFP982 and YAP1 interacted and localized predominantly to the cytoplasm upon differentiation, the localization of YAP1 was not influenced by ZFP982 localization. +Conclusions +Together, our study identified ZFP982 as a transcriptional regulator of early stemness genes, and since ZFP982 is under the control of the Hippo pathway, underscored the importance of the context-dependent Hippo signals for stem cell characteristics.}, + author = {Dehghanian, Fariba and Bovio, Patrick Piero and Gather, Fabian and Probst, Simone and Naghsh-Nilchi, Amirhosein and Vogel, Tanja}, + doi = {10.1016/j.bbamcr.2024.119686}, + issn = {0167-4889}, + journal = {Biochimica et Biophysica Acta (BBA) - Molecular Cell Research}, + keywords = {{\textgreater}UseGalaxy.eu, Hippo pathway, Nanog, Pluripotency, Stemness, Yap1, ZFP982}, + month = {April}, + number = {4}, + pages = {119686}, + title = {{ZFP982} confers mouse embryonic stem cell characteristics by regulating expression of \textit{{Nanog}}, \textit{{Zfp42}}\textit{,} and \textit{{Dppa3}}}, + url = {https://www.sciencedirect.com/science/article/pii/S0167488924000296}, + urldate = {2024-05-17}, + volume = {1871}, + year = {2024} +} + @article{delandre_long-read_2024, abstract = {Antimalarial drug resistance has become a real public health problem despite WHO measures. New sequencing technologies make it possible to investigate genomic variations associated with resistant phenotypes at the genome-wide scale. Based on the use of hemisynthetic nanopores, the PromethION technology from Oxford Nanopore Technologies can produce long-read sequences, in contrast to previous short-read technologies used as the gold standard to sequence Plasmodium. Two clones of P. falciparum (Pf3D7 and PfW2) were sequenced in long-read using the PromethION sequencer from Oxford Nanopore Technologies without genomic amplification. This made it possible to create a processing analysis pipeline for human Plasmodium with ONT Fastq only. De novo assembly revealed N50 lengths of 18,488 kb and 17,502 kb for the Pf3D7 and PfW2, respectively. The genome size was estimated at 23,235,407 base pairs for the Pf3D7 clone and 21,712,038 base pairs for the PfW2 clone. The average genome coverage depth was estimated at 787X and 653X for the Pf3D7 and PfW2 clones, respectively. This study proposes an assembly processing pipeline for the human Plasmodium genome using software adapted to large ONT data and the high AT percentage of Plasmodium. This search provides all the parameters which were optimized for use with the software selected in the pipeline.}, author = {Delandre, Océane and Lamer, Ombeline and Loreau, Jean-Marie and Papa Mze, Nasserdine and Fonta, Isabelle and Mosnier, Joel and Gomez, Nicolas and Javelle, Emilie and Pradines, Bruno}, @@ -3285,6 +3342,27 @@ @article{figiel_zinc_2023 year = {2023} } +@article{fischer_expanding_2024, + abstract = {Recombinant adenoviruses are widely used in clinical and laboratory applications. Despite the wide variety of available sero- and genotypes, only a fraction is utilized in vivo. As adenoviruses are a large group of viruses, displaying many different tropisms, immune epitopes, and replication characteristics, the merits of translating these natural benefits into vector applications are apparent. This translation, however, proves difficult, since while research has investigated the application of these viruses, there are no universally applicable rules in vector design for non-classical adenovirus types. In this paper, we describe a generalized workflow that allows vectorization, rescue, and cloning of all adenoviral species to enable the rapid development of new vector variants. We show this using human and simian adenoviruses, further modifying a selection of them to investigate their gene transfer potential and build potential vector candidates for future applications.}, + author = {Fischer, Julian and Fedotova, Ariana and Bühler, Clara and Darriba, Laura and Schreiner, Sabrina and Ruzsics, Zsolt}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/v16050658}, + issn = {1999-4915}, + journal = {Viruses}, + keywords = {{\textgreater}UseGalaxy.eu, human adenoviruses, mutagenesis of viral genomes, replication-competent vectors, transgene insertion sites, viral bacmids}, + language = {en}, + month = {May}, + note = {Number: 5 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {5}, + pages = {658}, + title = {Expanding the {Scope} of {Adenoviral} {Vectors} by {Utilizing} {Novel} {Tools} for {Recombination} and {Vector} {Rescue}}, + url = {https://www.mdpi.com/1999-4915/16/5/658}, + urldate = {2024-05-17}, + volume = {16}, + year = {2024} +} + @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}, @@ -4819,7 +4897,7 @@ @article{jhinjharia_high-throughput_2023 year = {2023} } -@article{joshi_physicochemical_nodate, +@article{joshi_physicochemical_2024, abstract = {Prostate cancer is the most common cancer among men which has major diagnosis in the United States in 2017. Among DYRK class II members, dual specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2) is the functional target for prostate cancer treatment. Studies show that subfamilies of DYRKs are also capable to phosphorylate (tyrosine, serine, and threonine) residues, yet little research has been carried out for its inhibitors. In this article, conceptual density theory is used to estimate the physicochemical properties of 30 experimentally synthesized inhibitors targeting DYRK2. The HOMO–LUMO gap showed low reactivity and high chemical activity for the inhibitors. The biological efficacy of these 30 inhibitors is predicted by bioavailability, mutagenicity, and cardiotoxicity measures. The inhibitors showed low toxicity and no blood brain barrier permeability. Results indicated that the physiological actions of these inhibitors involve multiple target interactions. Since the experimental results of the DYRK2 protein showed great water solubility, favorable safety properties, and potential anti-prostate cancer activities for ligand 24, docking and molecular dynamics simulations from the Galaxy webserver using Gromacs open-source tools are also performed for (DYRK2-24) complex (PDB: 7EJV). (DYRK2-24) showed strong binding affinity and noncovalent interactions.}, author = {Joshi, Sravani and Srivastava, Ruby}, copyright = {© 2024 Vietnam Academy of Science and Technology and Wiley-VCH GmbH.}, @@ -4828,12 +4906,14 @@ @article{joshi_physicochemical_nodate journal = {Vietnam Journal of Chemistry}, keywords = {{\textgreater}UseGalaxy.eu, diagnosis, drugs, dual specificity tyrosine phosphorylation-regulated kinase 2, phosphorylation, prostate cancer}, language = {en}, + month = {April}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/vjch.202300313}, number = {n/a}, title = {Physicochemical properties and biological efficacy of 30 {DYRK2} {Inhibitors} for the treatment of prostate cancer}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/vjch.202300313}, urldate = {2024-05-17}, - volume = {n/a} + volume = {n/a}, + year = {2024} } @article{joshi_tracing_2024, @@ -5359,20 +5439,17 @@ @article{kruse_synaptopodin_2024 @article{kruse_synaptopodin_2024, abstract = {Neurological diseases can lead to the denervation of brain regions caused by demyelination, traumatic injury or cell death. The molecular and structural mechanisms underlying lesion-induced reorganization of denervated brain regions, however, are a matter of ongoing investigation. In order to address this issue, we performed an entorhinal cortex lesion (ECL) in mouse organotypic entorhino-hippocampal tissue cultures of both sexes and studied denervation-induced plasticity of mossy fiber synapses, which connect dentate granule cells (dGCs) with CA3 pyramidal cells (CA3-PCs) and play important roles in learning and memory formation. Partial denervation caused a strengthening of excitatory neurotransmission in dGCs, CA3-PCs and their direct synaptic connections, as revealed by paired recordings (dGC-to-CA3-PC). These functional changes were accompanied by ultrastructural reorganization of mossy fiber synapses, which regularly contain the plasticity-regulating protein synaptopodin and the spine apparatus organelle. We demonstrate that the spine apparatus organelle and synaptopodin are related to ribosomes in close proximity to synaptic sites and reveal a synaptopodin-related transcriptome. Notably, synaptopodin-deficient tissue preparations that lack the spine apparatus organelle failed to express lesion-induced synaptic adjustments. Hence, synaptopodin and the spine apparatus organelle play a crucial role in regulating lesion-induced synaptic plasticity at hippocampal mossy fiber synapses.}, author = {Kruse, Pia and Brandes, Gudrun and Hemeling, Hanna and Huang, Zhong and Wrede, Christoph and Hegermann, Jan and Vlachos, Andreas and Lenz, Maximilian}, - copyright = {http://creativecommons.org/licenses/by/3.0/}, doi = {10.3390/cells13020114}, issn = {2073-4409}, journal = {Cells}, - keywords = {{\textgreater}UseGalaxy.eu, denervation, lesion-induced plasticity, local protein synthesis, synaptopodin}, - language = {en}, + keywords = {{\textgreater}UseGalaxy.eu, Animals, Cell Death, Denervation, Female, Hippocampus, Male, Mice, Mossy Fibers, Hippocampal, Neuronal Plasticity, Synapses, denervation, lesion-induced plasticity, local protein synthesis, synaptopodin}, + language = {eng}, month = {January}, - note = {Number: 2 -Publisher: Multidisciplinary Digital Publishing Institute}, number = {2}, pages = {114}, + pmcid = {PMC10814840}, + pmid = {38247806}, title = {Synaptopodin {Regulates} {Denervation}-{Induced} {Plasticity} at {Hippocampal} {Mossy} {Fiber} {Synapses}}, - url = {https://www.mdpi.com/2073-4409/13/2/114}, - urldate = {2024-01-14}, volume = {13}, year = {2024} } @@ -5380,17 +5457,20 @@ @article{kruse_synaptopodin_2024 @article{kruse_synaptopodin_2024-1, abstract = {Neurological diseases can lead to the denervation of brain regions caused by demyelination, traumatic injury or cell death. The molecular and structural mechanisms underlying lesion-induced reorganization of denervated brain regions, however, are a matter of ongoing investigation. In order to address this issue, we performed an entorhinal cortex lesion (ECL) in mouse organotypic entorhino-hippocampal tissue cultures of both sexes and studied denervation-induced plasticity of mossy fiber synapses, which connect dentate granule cells (dGCs) with CA3 pyramidal cells (CA3-PCs) and play important roles in learning and memory formation. Partial denervation caused a strengthening of excitatory neurotransmission in dGCs, CA3-PCs and their direct synaptic connections, as revealed by paired recordings (dGC-to-CA3-PC). These functional changes were accompanied by ultrastructural reorganization of mossy fiber synapses, which regularly contain the plasticity-regulating protein synaptopodin and the spine apparatus organelle. We demonstrate that the spine apparatus organelle and synaptopodin are related to ribosomes in close proximity to synaptic sites and reveal a synaptopodin-related transcriptome. Notably, synaptopodin-deficient tissue preparations that lack the spine apparatus organelle failed to express lesion-induced synaptic adjustments. Hence, synaptopodin and the spine apparatus organelle play a crucial role in regulating lesion-induced synaptic plasticity at hippocampal mossy fiber synapses.}, author = {Kruse, Pia and Brandes, Gudrun and Hemeling, Hanna and Huang, Zhong and Wrede, Christoph and Hegermann, Jan and Vlachos, Andreas and Lenz, Maximilian}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, doi = {10.3390/cells13020114}, issn = {2073-4409}, journal = {Cells}, - keywords = {{\textgreater}UseGalaxy.eu, Animals, Cell Death, Denervation, Female, Hippocampus, Male, Mice, Mossy Fibers, Hippocampal, Neuronal Plasticity, Synapses, denervation, lesion-induced plasticity, local protein synthesis, synaptopodin}, - language = {eng}, + keywords = {{\textgreater}UseGalaxy.eu, denervation, lesion-induced plasticity, local protein synthesis, synaptopodin}, + language = {en}, month = {January}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, number = {2}, pages = {114}, - pmcid = {PMC10814840}, - pmid = {38247806}, title = {Synaptopodin {Regulates} {Denervation}-{Induced} {Plasticity} at {Hippocampal} {Mossy} {Fiber} {Synapses}}, + url = {https://www.mdpi.com/2073-4409/13/2/114}, + urldate = {2024-01-14}, volume = {13}, year = {2024} } @@ -6001,6 +6081,17 @@ @article{liang_reciprocal_2020 year = {2020} } +@phdthesis{link_characterization_2024, + abstract = {{\textless}em{\textgreater}T. halophilus{\textless}/em{\textgreater} and {\textless}em{\textgreater}D. hansenii{\textless}/em{\textgreater} are key players in the fermentation of lupine moromi. Comparative genomic analyses and transcriptomic profiling of {\textless}em{\textgreater}T. halophilus{\textless}/em{\textgreater} strains isolated from lupine moromi led to the identification of genes beneficial in this environment. Further, the competitiveness of isolated {\textless}em{\textgreater}T. halophilus{\textless}/em{\textgreater} strains in a lupine moromi model fermentation was investigated. The {\textless}em{\textgreater}D. hansenii{\textless}/em{\textgreater} strain that dominated the lupine moromi fermentation was fully sequenced and genomically analyzed.}, + author = {Link, Tobias}, + keywords = {{\textgreater}UseGalaxy.eu}, + school = {Technische Universität München}, + title = {Characterization and habitat adaptation of {\textless}em{\textgreater}{Tetragenococcus} halophilus{\textless}/em{\textgreater} and {\textless}em{\textgreater}{Debaryomyces} hansenii{\textless}/em{\textgreater} from a lupine seasoning sauce fermentation}, + url = {https://mediatum.ub.tum.de/1713925}, + urldate = {2024-05-17}, + year = {2024} +} + @article{liu_comparative_2022, abstract = {In 2016, a 68-year-old patient with a disseminated multidrug-resistant Acinetobacter baumannii infection was successfully treated using lytic bacteriophages. Here we report the genomes of the nine phages used for treatment and three strains of A. baumannii isolated prior to and during treatment. The phages used in the initial treatment are related, T4-like myophages. Analysis of 19 A. baumannii isolates collected before and during phage treatment shows that resistance to the T4-like phages appeared two days following the start of treatment. We generate complete genomic sequences for three A. baumannii strains (TP1, TP2 and TP3) collected before and during treatment, supporting a clonal relationship. Furthermore, we use strain TP1 to select for increased resistance to five of the phages in vitro, and identify mutations that are also found in phage-insensitive isolates TP2 and TP3 (which evolved in vivo during phage treatment). These results support that in vitro investigations can produce results that are relevant to the in vivo environment.}, author = {Liu, Mei and Hernandez-Morales, Adriana and Clark, James and Le, Tram and Biswas, Biswajit and Bishop-Lilly, Kimberly A. and Henry, Matthew and Quinones, Javier and Voegtly, Logan J. and Cer, Regina Z. and Hamilton, Theron and Schooley, Robert T. and Salka, Scott and Young, Ry and Gill, Jason J.}, @@ -7208,6 +7299,23 @@ @article{ngo_histone_2022 year = {2022} } +@article{nicholson_contribution_2024, + abstract = {{\textless}p{\textgreater}{\textless}italic{\textgreater}Bordetella bronchiseptica{\textless}/italic{\textgreater} is a highly contagious respiratory bacterial veterinary pathogen. In this study the contribution of the transcriptional regulators BvgR, RisA, RisS, and the phosphorylation of RisA to global gene regulation, intracellular cyclic-di-GMP levels, motility, and biofilm formation were evaluated. Next Generation Sequencing (RNASeq) was used to differentiate the global gene regulation of both virulence-activated and virulence-repressed genes by each of these factors. The BvgAS system, along with BvgR, RisA, and the phosphorylation of RisA served in cyclic-di-GMP degradation. BvgR and unphosphorylated RisA were found to temporally regulate motility. Additionally, BvgR, RisA, and RisS were found to be required for biofilm formation.{\textless}/p{\textgreater}}, + author = {Nicholson, Tracy L. and Waack, Ursula and Fleming, Damarius S. and Chen, Qing and Miller, Laura C. and Merkel, Tod J. and Stibitz, Scott}, + doi = {10.3389/fmicb.2024.1305097}, + issn = {1664-302X}, + journal = {Frontiers in Microbiology}, + keywords = {{\textgreater}UseGalaxy.eu, Bordetella bronchiseptica, RNA-Seq, and biofilm, cyclic-di-GMP, motility}, + language = {English}, + month = {March}, + note = {Publisher: Frontiers}, + title = {The contribution of {BvgR}, {RisA}, and {RisS} to global gene regulation, intracellular cyclic-di-{GMP} levels, motility, and biofilm formation in {Bordetella} bronchiseptica}, + url = {https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1305097/full}, + urldate = {2024-05-17}, + volume = {15}, + year = {2024} +} + @article{nielsen_delayed_2023, author = {Nielsen, Carolyn M. and Barrett, Jordan R. and Davis, Christine and Fallon, Jonathan K. and Goh, Cyndi and Michell, Ashlin R. and Griffin, Catherine and Kwok, Andrew and Loos, Carolin and Darko, Samuel and Laboune, Farida and Tekman, Mehmet and Diouf, Ababacar and Miura, Kazutoyo and Francica, Joseph R. and Ransier, Amy and Long, Carole A. and Silk, Sarah E. and Payne, Ruth O. and Minassian, Angela M. and Lauffenburger, Douglas A. and Seder, Robert A. and Douek, Daniel C. and Alter, Galit and Draper, Simon J.}, doi = {10.1172/jci.insight.163859}, @@ -8157,6 +8265,23 @@ @article{pustam_whole_2024 year = {2024} } +@article{pyles_altered_2024, + abstract = {Patients who suffer a traumatic brain injury (TBI) often experience chronic and sometimes debilitating sequelae. Recent reports have illustrated both acute and long-term dysbiosis of the gastrointestinal microbiome with significant alterations in composition and predicted functional consequences. Working with participants from past research, metagenomic stability of the TBIassociated fecal microbiome (FMB) was evaluated by custom qPCR array comparing a fecal sample from 2015 to one collected in 2020. A remarkably stable FMB metagenome with significant similarity (two-tail Spearman nonparametric correlation p80\% of the samples in only one of the cohorts (binary distinction). Functional differences included amino acid metabolism, energy and carbon source usage, fatty acid metabolism, bacterial cell wall component production and nucleic acid synthesis and processing pathways. Together these data shed light on the functional consequences of the dysbiotic TBI FMB decades after injury.}, + author = {Pyles, Richard B. and Miller, Aaron L. and Urban, Randall J. and Sheffield-Moore, Melinda and Wright, Traver J. and Maxwell, Carrie A. and Randolph, Kathleen M. and Danesi, Christopher P. and McGovern, Kristen A. and Vargas, Jayson and Armstrong, Peyton and Kreber, Lisa and Cumpa, Giuliana and Randall, Kevin and Morrison, Melissa and Masel, Brent E.}, + doi = {10.3389/fnmol.2024.1341808}, + issn = {1662-5099}, + journal = {Frontiers in Molecular Neuroscience}, + keywords = {{\textgreater}UseGalaxy.eu, BIAFAC, Traumatic Brain Injury, fecal microbiome, metatranscriptome, microbiome}, + language = {English}, + month = {March}, + note = {Publisher: Frontiers}, + title = {The altered {TBI} fecal microbiome is stable and functionally distinct}, + url = {https://www.frontiersin.org/articles/10.3389/fnmol.2024.1341808}, + urldate = {2024-05-17}, + volume = {17}, + year = {2024} +} + @article{qi_secreted_2020, abstract = {{\textless}p{\textgreater}Multicellular organisms coordinate tissue specific response to environmental information via both cell-autonomous and non-autonomous mechanisms. In addition to secreted ligands, secreted small RNAs have recently been reported to regulate gene expression across tissue boundaries. Here we show that the conserved poly-U specific endoribonuclease ENDU-2 is secreted from the soma and taken-up by the germline to ensure germline immortality at elevated temperature in C. elegans. ENDU-2 binds to mature mRNAs and negatively regulates mRNA abundance both in the soma and the germline. While ENDU-2 promotes RNA decay in the soma directly via its endoribonuclease activity, ENDU-2 prevents misexpression of soma-specific genes in the germline and preserves germline immortality independent of its RNA-cleavage activity. In summary, our results suggest that the secreted RNase ENDU-2 transmits environmental information across tissue boundaries and contributes to maintenance of stem cell immortality probably via retaining a stem cell specific program of gene expression.{\textless}/p{\textgreater}}, author = {Qi, Wenjing and Gromoff, Erika D. v and Xu, Fan and Zhao, Qian and Yang, Wei and Pfeifer, Dietmar and Maier, Wolfgang and Long, Lijiang and Baumeister, Ralf}, @@ -8175,6 +8300,22 @@ @article{qi_secreted_2020 year = {2020} } +@article{qiu_smcyp71d373_2024, + abstract = {Salvia miltiorrhiza is one of the most commonly used Chinese medicinal herbs. Tanshinone I and tanshinone IIB with anti-inflammatory, anti-bacterial, anti-oxidative, anti-neoplastic, neuron protective, and heart protective properties are valuable active components in it. However, the biosynthetic pathway of tanshinone IIB and tanshinone I has not been completely elucidated. Here, we identified a tanshinone IIA 19-hydroxylase from S. miltiorrhiza. In vitro and in vivo analyses showed that SmCYP71D373 could hydroxylate tanshinone IIA at C-19 position to produce tanshinone IIB. Reaction conditions optimization demonstrated that the catalytic efficiency of SmCYP71D373 was the highest using the substrate-feeding method under the following conditions, fed the tanshinone IIA into the Saccharomyces cerevisiae expressing codon-optimized SmCYP71D373 at 28℃ for 24 hours. And the yield of tanshinone IIB was up to 6.38\%. Furthermore, N121 and S210 of SmCYP71D373 were verified as the key amino acid residues responsible for its catalytic activity for tanshinone IIA by molecular docking and site-directed mutagenesis. The results not only lay a foundation for the elucidation of tanshinone I synthesis pathway, but also provide the theoretical support to improve the catalytic efficiency of SmCYP71D373 for tanshinone IIB production.}, + author = {Qiu, Xiaoping and Zhang, Yi and Luo, Yinggang and Zhang, Yongmei}, + doi = {10.1016/j.indcrop.2024.118323}, + issn = {0926-6690}, + journal = {Industrial Crops and Products}, + keywords = {{\textgreater}UseGalaxy.eu, Biosynthesis pathway, CYP450, Hydroxylation, Tanshinone IIB}, + month = {June}, + pages = {118323}, + title = {{SmCYP71D373} of \textit{{Salvia} miltiorrhiza} catalyzes the methyl oxidation reaction of tanshinone {IIA}-19 position}, + url = {https://www.sciencedirect.com/science/article/pii/S0926669024003005}, + urldate = {2024-05-17}, + volume = {212}, + year = {2024} +} + @article{ragot_edna_2022, author = {Ragot, Rose and Villemur, Richard}, journal = {Environmental monitoring and assessment}, @@ -8633,6 +8774,23 @@ @article{sacco_outbreak_2022 year = {2022} } +@article{sageman-furnas_detailing_2024, + abstract = {Shoot growth directly impacts plant productivity. Plants adjust their shoot growth in response to varying environments to maximize resource capture and stress resilience. While several factors controlling shoot growth are known, the complexity of the regulation and the input of the environment are not fully understood. We have investigated shoot growth repression induced by low ambient temperatures in hybrids of Arabidopsis thaliana Kro-0 and BG-5 accessions. To continue our previous studies, we confirmed that the Kro-0 allele of DYNAMIN-RELATED PROTEIN 3B causes stunted shoot growth in the BG-5 background. We also found that shoot growth repression was most pronounced near the apex at a lower temperature and that the cells in the hybrid stem failed to elongate correctly. Furthermore, we observed that shoot growth repression in hybrids depended on light availability. Global gene expression analysis indicated the involvement of hormones, especially strigolactone, associated with the dwarf phenotype. Altogether, this study enhances our knowledge on the genetic, physiological and environmental factors associated with shoot growth regulation.}, + author = {Sageman-Furnas, Katelyn and Duarte, Gustavo T and Laitinen, Roosa A E}, + doi = {10.1093/pcp/pcad167}, + issn = {1471-9053}, + journal = {Plant and Cell Physiology}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {March}, + number = {3}, + pages = {420--427}, + title = {Detailing {Early} {Shoot} {Growth} {Arrest} in {Kro}-0 x {BG}-5 {Hybrids} of {Arabidopsis} thaliana}, + url = {https://doi.org/10.1093/pcp/pcad167}, + urldate = {2024-05-17}, + volume = {65}, + year = {2024} +} + @article{sajulga_survey_2020, abstract = {To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.}, author = {Sajulga, Ray and Easterly, Caleb and Riffle, Michael and Mesuere, Bart and Muth, Thilo and Mehta, Subina and Kumar, Praveen and Johnson, James and Gruening, Bjoern Andreas and Schiebenhoefer, Henning and Kolmeder, Carolin A. and Fuchs, Stephan and Nunn, Brook L. and Rudney, Joel and Griffin, Timothy J. and Jagtap, Pratik D.}, @@ -9374,6 +9532,25 @@ @article{stephen_jr_comparative_2022 year = {2022} } +@article{stillger_neoadjuvant_2024, + abstract = {Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer, often diagnosed at stages that dis-qualify for surgical resection. Neoadjuvant therapies offer potential tumor regression and improved resectability. Although features of the tumor biology (e.g., molecular markers) may guide adjuvant therapy, biological alterations after neoadjuvant therapy remain largely unexplored. We performed mass spectrometry to characterize the proteomes of 67 PDAC resection specimens of patients who received either neoadjuvant chemo (NCT) or chemo-radiation (NCRT) therapy. We employed data-independent acquisition (DIA), yielding a proteome coverage in excess of 3500 proteins. Moreover, we successfully integrated two publicly available proteome datasets of treatment-naïve PDAC to unravel proteome alterations in response to neoadjuvant therapy, highlighting the feasibility of this approach. We found highly distinguishable proteome profiles. Treatment-naïve PDAC was characterized by enrichment of immunoglobulins, complement and extracellular matrix (ECM) proteins. Post-NCT and post-NCRT PDAC presented high abundance of ribosomal and metabolic proteins as compared to treatment-naïve PDAC. Further analyses on patient survival and protein expression identified treatment-specific prognostic candidates. We present the first proteomic characterization of the residual PDAC mass after NCT and NCRT, and potential protein candidate markers associated with overall survival. We conclude that residual PDAC exhibits fundamentally different proteome profiles as compared to treatment-naïve PDAC, influenced by the type of neoadjuvant treatment. These findings may impact adjuvant or targeted therapy options.}, + author = {Stillger, Maren N. and Kurowski, Konrad and Bronsert, Peter and Brombacher, Eva and Kreutz, Clemens and Werner, Martin and Tang, Laura and Timme-Bronsert, Sylvia and Schilling, Oliver}, + copyright = {© 2024 The Authors. International Journal of Cancer published by John Wiley \& Sons Ltd on behalf of UICC.}, + doi = {10.1002/ijc.34867}, + issn = {1097-0215}, + journal = {International Journal of Cancer}, + keywords = {{\textgreater}UseGalaxy.eu, data-independent acquisition, mass spectrometry, neoadjuvant therapy, pancreatic ductal adenocarcinoma, proteogenomics}, + language = {en}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ijc.34867}, + number = {12}, + pages = {2162--2175}, + title = {Neoadjuvant chemo- or chemo-radiation-therapy of pancreatic ductal adenocarcinoma differentially shift {ECM} composition, complement activation, energy metabolism and ribosomal proteins of the residual tumor mass}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ijc.34867}, + urldate = {2024-05-17}, + volume = {154}, + year = {2024} +} + @article{stojkovic_targeted_2024, abstract = {Detrimental molecular processes in multiple sclerosis (MS) lead to the cellular accumulation of lipid peroxidation products and iron in the CNS, which represents the main driving force for ferroptosis. Ferroptosis is an iron-dependent form of regulated cell death, with proposed roles in neurodegeneration, oligodendrocyte loss and neuroinflammation in the pathogenesis of MS. Ferroptosis-related gene expression signature and molecular markers, which could reflect MS severity and progression, are currently understudied in humans. To tackle these challenges, we have applied a curated approach to create and experimentally analyze a comprehensive panel of ferroptosis-related genes covering a wide range of biological processes associated with ferroptosis. We performed the first ferroptosis-related targeted RNAseq on PBMCs from highly distinctive MS phenotype groups: mild relapsing–remitting (RR) (n = 24) and severe secondary progressive (SP) (n = 24), along with protein detection of GPX4 and products of lipid peroxidation (MDA and 4-HNE). Out of 138 genes, 26 were differentially expressed genes (DEGs), indicating changes in both pro- and anti-ferroptotic genes, representing a molecular signature associated with MS severity. The top three DEGs, as non-core ferroptosis genes, CDKN1A, MAP1B and EGLN2, were replicated by qPCR to validate findings in independent patient groups (16 RR and 16 SP MS). Co-expression and interactions of DEGs were presented as additional valuable assets for deeper understanding of molecular mechanisms and key targets related to MS severity. Our study integrates a wide genetic signature and biochemical markers related to ferroptosis in easily obtainable PBMCs of MS patients with clinical data and disease severity, thus providing novel molecular markers which can complement disease-related changes in the brain and undergo further research as potential therapeutic targets.}, author = {Stojkovic, Ljiljana and Jovanovic, Ivan and Dincic, Evica and Djordjevic, Ana and Kuveljic, Jovana and Djuric, Tamara and Stankovic, Aleksandra and Vojinovic, Slobodan and Zivkovic, Maja}, @@ -9803,6 +9980,27 @@ @article{tosar_ri-sec-seq_2021 year = {2021} } +@article{toth_genomic_2024, + abstract = {Extended-spectrum β-lactamase-producing Escherichia coli ST131 has become widespread worldwide. This study aims to characterize the virulome, resistome, and population structure of E. coli ST131 isolates from clinical blood samples in Hungary. A total of 30 C2/H30Rx and 33 C1-M27 ST131 isolates were selected for Illumina MiSeq sequencing and 30 isolates for MinION sequencing, followed by hybrid de novo assembly. Five C2/H30Rx and one C1-M27 cluster were identified. C1-M27 isolates harbored the F1:A2:B20 plasmid in 93.9\% of cases. Long-read sequencing revealed that blaCTX-M-27 was on plasmids. Among the C2/H30Rx isolates, only six isolates carried the C2-associated F2:A1:B- plasmid type. Of 19 hybrid-assembled C2/H30Rx genomes, the blaCTX-M-15 gene was located on plasmid only in one isolate, while in the other isolates, ISEcp1 or IS26-mediated chromosomal integration of blaCTX-M-15 was detected in unique variations. In one isolate a part of F2:A1:B- plasmid integrated into the chromosome. These results suggest that CTX-M-15-producing C2/H30Rx and CTX-M-27-producing C1-M27 subclades may have emerged and spread in different ways in Hungary. While blaCTX-M-27 was carried mainly on the C1/H30R-associated F1:A2:B20 plasmid, the IncF-like plasmids of C2/H30Rx or its composite transposons have been incorporated into the chromosome through convergent evolutionary processes.}, + author = {Tóth, Kinga and Damjanova, Ivelina and Laczkó, Levente and Buzgó, Lilla and Lesinszki, Virág and Ungvári, Erika and Jánvári, Laura and Hanczvikkel, Adrienn and Tóth, Ákos and Szabó, Dóra}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/antibiotics13040363}, + issn = {2079-6382}, + journal = {Antibiotics}, + keywords = {\textit{Escherichia coli}, \textit{bla}$_{\textrm{CTX-M-15}}$, \textit{bla}$_{\textrm{CTX-M-27}}$, {\textgreater}UseGalaxy.eu, C1-M27, C2/H30RX, ST131, long-read sequencing, whole genome sequencing (WGS)}, + language = {en}, + month = {April}, + note = {Number: 4 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {4}, + pages = {363}, + title = {Genomic {Epidemiology} of {C2}/{H30Rx} and {C1}-{M27} {Subclades} of {Escherichia} coli {ST131} {Isolates} from {Clinical} {Blood} {Samples} in {Hungary}}, + url = {https://www.mdpi.com/2079-6382/13/4/363}, + urldate = {2024-05-17}, + volume = {13}, + year = {2024} +} + @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}, @@ -9889,6 +10087,35 @@ @article{uellendahl-werth_benchmark_2020 year = {2020} } +@phdthesis{ummethum_proximity_2024, + author = {Ummethum, Henning}, + keywords = {{\textgreater}UseGalaxy.eu}, + language = {de}, + month = {February}, + school = {Ludwig-Maximilians-Universität München}, + title = {Proximity labeling as a tool to study transcription-replication interference}, + type = {Text.{PhDThesis}}, + url = {https://edoc.ub.uni-muenchen.de/33323/}, + urldate = {2024-05-17}, + year = {2024} +} + +@article{umpeleva_identification_2024, + author = {Umpeleva, Tatiana and Chetverikova, Elena and Belyaev, Danila and Eremeeva, Natalya and Boteva, Tatiana and Golubeva, Ludmila and Vakhrusheva, Diana and Vasilieva, Irina}, + doi = {10.1128/spectrum.03749-23}, + journal = {Microbiology Spectrum}, + keywords = {{\textgreater}UseGalaxy.eu}, + month = {February}, + note = {Publisher: American Society for Microbiology}, + number = {3}, + pages = {e03749--23}, + title = {Identification of genetic determinants of bedaquiline resistance in {Mycobacterium} tuberculosis in {Ural} region, {Russia}}, + url = {https://journals.asm.org/doi/full/10.1128/spectrum.03749-23}, + urldate = {2024-05-17}, + volume = {12}, + year = {2024} +} + @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}, @@ -10013,6 +10240,28 @@ @article{vieira_da_cruz_pyridylpiperazine_2024 year = {2024} } +@article{vieira_polymyxin_2024, + abstract = {Until 2015, polymyxin resistance was primarily attributed to chromosomal mutations. However, with the first report of mobile colistin resistance (mcr-1) in commensal Escherichia coli from food animals in China, the landscape has changed. To evaluate the presence of polymyxin resistance in Salmonella spp., a drop screening test for colistin and polymyxin B was carried out on 1156 isolates of non-human origin (animals, food, and the environment), received in Brazil, between 2016 and 2021. Subsequently, 210 isolates with resistant results in the drop test were subjected to the gold-standard test (broth microdilution) for both colistin and polymyxin B. Whole-genome sequencing (WGS) of 102 resistant isolates was performed for a comprehensive analysis of associated genes. Surprisingly, none of the isolates resistant to colistin in the drop test harbored any of the mcr variants (mcr-1 to mcr-10). WGS identified that the most common mutations were found in pmrA (n= 22; T89S) and pmrB (n = 24; M15T, G73S, V74I, I83A, A111V). Other resistance determinants were also detected, such as the aac(6′)-Iaa gene in 72 isolates, while others carried beta-lactamase genes (blaTEM-1 blaCTX-M-2, blaCMY-2). Additionally, genes associated with fluoroquinolone resistance (qnrB19, qnrS1, oqxA/B) were detected in 11 isolates. Colistin and polymyxin B resistance were identified among Salmonella from non-human sources, but not associated with the mcr genes. Furthermore, the already-described mutations associated with polymyxin resistance were detected in only a small number of isolates, underscoring the need to explore and characterize unknown genes that contribute to resistance.}, + author = {Vieira, Thais and Dos Santos, Carla Adriana and de Jesus Bertani, Amanda Maria and Costa, Gisele Lozano and Campos, Karoline Rodrigues and Sacchi, Cláudio Tavares and Cunha, Marcos Paulo Vieira and Carvalho, Eneas and da Costa, Alef Janguas and de Paiva, Jacqueline Boldrin and Rubio, Marcela da Silva and Camargo, Carlos Henrique and Tiba-Casas, Monique Ribeiro}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/antibiotics13020110}, + issn = {2079-6382}, + journal = {Antibiotics}, + keywords = {\textit{Salmonella} spp., {\textgreater}UseGalaxy.eu, antimicrobial resistance, colistin, polymyxin}, + language = {en}, + month = {February}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {2}, + pages = {110}, + shorttitle = {Polymyxin {Resistance} in {Salmonella}}, + title = {Polymyxin {Resistance} in {Salmonella}: {Exploring} {Mutations} and {Genetic} {Determinants} of {Non}-{Human} {Isolates}}, + url = {https://www.mdpi.com/2079-6382/13/2/110}, + urldate = {2024-05-17}, + volume = {13}, + year = {2024} +} + @article{vijaykrishna_expanding_2022, abstract = {Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows users to easily organize, retrieve and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. In addition, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenie’s remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS (CernVM File System) repository from GalaxyProject.org, with mirrors across the USA, Canada, Europe and Australia, enabling easy use outside of Galaxy.The ability of Galaxy to use refgenie assets was added to the core Galaxy framework in version 22.01, which is available from https://github.com/galaxyproject/galaxy under the Academic Free License version 3.0. The refgenie Data Manager tool can be installed via the Galaxy ToolShed, with source code managed at https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data\_managers/data\_manager\_refgenie\_pull and released using an MIT license. Access to existing data is also available through CVMFS, with instructions at https://galaxyproject.org/admin/reference-data-repo/. No new data were generated or analyzed in support of this research.}, author = {VijayKrishna, Nagampalli and Joshi, Jayadev and Coraor, Nate and Hillman-Jackson, Jennifer and Bouvier, Dave and van den Beek, Marius and Eguinoa, Ignacio and Coppens, Frederik and Davis, John and Stolarczyk, Michał and Sheffield, Nathan C and Gladman, Simon and Cuccuru, Gianmauro and Grüning, Björn and Soranzo, Nicola and Rasche, Helena and Langhorst, Bradley W and Bernt, Matthias and Fornika, Dan and de Lima Morais, David Anderson and Barrette, Michel and van Heusden, Peter and Petrillo, Mauro and Puertas-Gallardo, Antonio and Patak, Alex and Hotz, Hans-Rudolf and Blankenberg, Daniel}, @@ -10150,6 +10399,22 @@ @article{volkova_multi-omics_2024 } @article{volkova_multi-omics_2024-1, + abstract = {Barley is a resilient crop with high nutritional value and adaptability, making it a promising candidate for phytoremediation and space agriculture. The study presents a comprehensive multi-omics analysis of the impact of ionising radiation (IR) on barley seedlings, intending to identify candidate pathways for creating radiation-resilient barley plants. We found that different IR treatments (gamma, electron, proton, neutron) increased the intensity of protein catabolism and led to the attenuation of translation. The impact of IRs on protein synthesis and degradation was accompanied by rearrangements in energy metabolism and reallocation of nitrogen, probably due to enhanced protein catabolism. At least partially, those changes seem to fuel secondary metabolites production, including riboflavin, various phytoalexins, phytosiderophores, ferulic and sinapic acids, kaempferol, quercetin, nictoflorin, gallate, and podophyllotoxin. Many of these compounds have antioxidant or radioprotective properties. To focus on possible targets for gene editing, we identified genes differentially regulated after all types of IR exposure and potential transcription factors regulating secondary metabolism, including AP2/ERF, WRKY, bHLH, bZIP, MYB, and NAC families.}, + author = {Volkova, Polina and Prazyan, Alexandr and Podlutskii, Mikhail and Saburov, Vyacheslav and Kazakova, Elizaveta and Bitarishvili, Sofia and Duarte, Gustavo T. and Shesterikova, Ekaterina and Makarenko, Ekaterina and Lychenkova, Maria and Ben, Cécile and Gentzbittel, Laurent and Kazakov, Evgenii and Moiseev, Alexandr and Diuzhenko, Sergei and Korol, Marina and Bondarenko, Ekaterina}, + doi = {10.1016/j.envexpbot.2023.105600}, + issn = {0098-8472}, + journal = {Environmental and Experimental Botany}, + keywords = {{\textgreater}UseGalaxy.eu, Barley, Ionising radiation, Metabolomics, Multi-omics, Phytoremediation, Proteomics, Radioresistance, Secondary metabolites, Transcriptomics, Translation}, + month = {February}, + pages = {105600}, + title = {Multi-omics responses of barley seedlings to low and high linear energy transfer irradiation}, + url = {https://www.sciencedirect.com/science/article/pii/S0098847223003957}, + urldate = {2024-05-17}, + volume = {218}, + year = {2024} +} + +@article{volkova_multi-omics_2024-2, abstract = {Barley is a resilient crop with high nutritional value and adaptability, making it a promising candidate for phytoremediation and space agriculture. The study presents a comprehensive multi-omics analysis of the impact of ionising radiation (IR) on barley seedlings, intending to identify candidate pathways for creating radiation-resilient barley plants. We found that different IR treatments (gamma, electron, proton, neutron) increased the intensity of protein catabolism and led to the attenuation of translation. The impact of IRs on protein synthesis and degradation was accompanied by rearrangements in energy metabolism and reallocation of nitrogen, probably due to enhanced protein catabolism. At least partially, those changes seem to fuel secondary metabolites production, including riboflavin, various phytoalexins, phytosiderophores, ferulic and sinapic acids, kaempferol, quercetin, nictoflorin, gallate, and podophyllotoxin. Many of these compounds have antioxidant or radioprotective properties. To focus on possible targets for gene editing, we identified genes differentially regulated after all types of IR exposure and potential transcription factors regulating secondary metabolism, including AP2/ERF, WRKY, bHLH, bZIP, MYB, and NAC families.}, author = {Volkova, Polina and Prazyan, Alexandr and Podlutskii, Mikhail and Saburov, Vyacheslav and Kazakova, Elizaveta and Bitarishvili, Sofia and Duarte, Gustavo T. and Shesterikova, Ekaterina and Makarenko, Ekaterina and Lychenkova, Maria and Ben, Cécile and Gentzbittel, Laurent and Kazakov, Evgenii and Moiseev, Alexandr and Diuzhenko, Sergei and Korol, Marina and Bondarenko, Ekaterina}, doi = {10.1016/j.envexpbot.2023.105600}, @@ -10277,6 +10542,48 @@ @phdthesis{wadhawan_investigating_2022 year = {2022} } +@article{wang_genome_2024, + abstract = {The co-evolution between symbionts and their insect hosts has led to intricate functional interdependencies. Advances in DNA-sequencing technologies have not only reduced the cost of sequencing but, with the advent of highly accurate long-read methods, have also enabled facile genome assembly even using mixed genomic input, thereby allowing us to more easily assess the contribution of symbionts to their insect hosts. In this study, genomic data recently generated from Peregrinus maidis was used to assemble the genome of a bacterial symbiont, Pm Arsenophonus sp. This {\textasciitilde}4.9-Mb assembly is one of the largest Arsenophonus genomes reported to date. The Benchmarking Universal Single-Copy Orthologs (BUSCO) result indicates that this Pm Arsenophonus assembly has a high degree of completeness, with 96\% of the single-copy Enterobacterales orthologs found. The identity of the Pm Arsenophonus sp. was further confirmed by phylogenetic analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicates a major contribution by Pm Arsenophonus sp. to the biosynthesis of B vitamins and essential amino acids in P. maidis, where threonine and lysine production is carried out solely by Pm Arsenophonus sp. This study not only provides deeper insights into the evolutionary relationships between symbionts and their insect hosts, but also adds to our understanding of insect biology, potentially guiding the development of novel pest control methods.}, + author = {Wang, Yu-Hui and Mikaelyan, Aram and Coates, Brad S. and Lorenzen, Marcé}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/insects15020113}, + issn = {2075-4450}, + journal = {Insects}, + keywords = {\textit{Arsenophonus} sp., \textit{Peregrinus maidis}, {\textgreater}UseGalaxy.eu, genome assembly, hemiptera}, + language = {en}, + month = {February}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {2}, + pages = {113}, + title = {The {Genome} of {Arsenophonus} sp. and {Its} {Potential} {Contribution} in the {Corn} {Planthopper}, {Peregrinus} maidis}, + url = {https://www.mdpi.com/2075-4450/15/2/113}, + urldate = {2024-05-17}, + volume = {15}, + year = {2024} +} + +@article{wang_growth_2024, + abstract = {The regulation of plant biomass degradation by fungi is critical to the carbon cycle, and applications in bioproducts and biocontrol. Trichoderma harzianum is an important plant biomass degrader, enzyme producer, and biocontrol agent, but few putative major transcriptional regulators have been deleted in this species. The T. harzianum ortholog of the transcriptional activator XYR1/XlnR/XLR-1 was deleted, and the mutant strains were analyzed through growth profiling, enzymatic activities, and transcriptomics on cellulose. From plate cultures, the Δxyr1 mutant had reduced growth on D-xylose, xylan, and cellulose, and from shake-flask cultures with cellulose, the Δxyr1 mutant had {\textasciitilde}90\% lower β-glucosidase activity, and no detectable β-xylosidase or cellulase activity. The comparison of the transcriptomes from 18 h shake-flask cultures on D-fructose, without a carbon source, and cellulose, showed major effects of XYR1 deletion whereby the Δxyr1 mutant on cellulose was transcriptionally most similar to the cultures without a carbon source. The cellulose induced 43 plant biomass-degrading CAZymes including xylanases as well as cellulases, and most of these had massively lower expression in the Δxyr1 mutant. The expression of a subset of carbon catabolic enzymes, other transcription factors, and sugar transporters was also lower in the Δxyr1 mutant on cellulose. In summary, T. harzianum XYR1 is the master regulator of cellulases and xylanases, as well as regulating carbon catabolic enzymes.}, + author = {Wang, Lunji and Zhao, Yishen and Chen, Siqiao and Wen, Xian and Anjago, Wilfred Mabeche and Tian, Tianchi and Chen, Yajuan and Zhang, Jinfeng and Deng, Sheng and Jiu, Min and Fu, Pengxiao and Zhou, Dongmei and Druzhinina, Irina S. and Wei, Lihui and Daly, Paul}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + doi = {10.3390/biom14020148}, + issn = {2218-273X}, + journal = {Biomolecules}, + keywords = {{\textgreater}UseGalaxy.eu, CAZymes, XYR1/XlnR/XLR-1, cellulose, transcriptional regulation}, + language = {en}, + month = {February}, + note = {Number: 2 +Publisher: Multidisciplinary Digital Publishing Institute}, + number = {2}, + pages = {148}, + title = {Growth, {Enzymatic}, and {Transcriptomic} {Analysis} of xyr1 {Deletion} {Reveals} a {Major} {Regulator} of {Plant} {Biomass}-{Degrading} {Enzymes} in {Trichoderma} harzianum}, + url = {https://www.mdpi.com/2218-273X/14/2/148}, + urldate = {2024-05-17}, + volume = {14}, + year = {2024} +} + @article{wang_systems-level_2023, abstract = {Chemical modifications of transcripts with a 5′ cap occur in all organisms and function in many aspects of RNA metabolism. To facilitate analysis of RNA caps, we developed a systems-level mass spectrometry-based technique, CapQuant, for accurate and sensitive quantification of the cap epitranscriptome. The protocol includes the addition of stable isotope-labeled cap nucleotides (CNs) to RNA, enzymatic hydrolysis of endogenous RNA to release CNs, and off-line enrichment of CNs by ion-pairing high-pressure liquid chromatography, followed by a 17 min chromatography-coupled tandem quadrupole mass spectrometry run for the identification and quantification of individual CNs. The total time required for the protocol can be up to 7 d. In this approach, 26 CNs can be quantified in eukaryotic poly(A)-tailed RNA, bacterial total RNA and viral RNA. This protocol can be modified to analyze other types of RNA and RNA from in vitro sources. CapQuant stands out from other methods in terms of superior specificity, sensitivity and accuracy, and it is not limited to individual caps nor does it require radiolabeling. Thanks to its unique capability of accurately and sensitively quantifying RNA caps on a systems level, CapQuant can reveal both the RNA cap landscape and the transcription start site distribution of capped RNA in a broad range of settings.}, author = {Wang, Jin and Chew, Bing Liang Alvin and Lai, Yong and Dong, Hongping and Xu, Luang and Liu, Yu and Fu, Xin-Yuan and Lin, Zhenguo and Shi, Pei-Yong and Lu, Timothy K. and Luo, Dahai and Jaffrey, Samie R. and Dedon, Peter C.},