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7 results on '"Theoretical Biology and Bioinformatics [Utrecht, The Netherlands]"'

1. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author

Adriaenssens, Evelien M, Sullivan, Matthew B, Knezevic, Petar, van Zyl, Leonardo J, Sarkar, B L, Dutilh, Bas E, Alfenas-Zerbini, Poliane, Łobocka, Małgorzata, Tong, Yigang, Brister, James Rodney, Moreno Switt, Andrea I, Klumpp, Jochen, Aziz, Ramy Karam, Barylski, Jakub, Uchiyama, Jumpei, Kropinski, Andrew M, Petty, Nicola K, Clokie, Martha R J, Kushkina, Alla I, Morozova, Vera V, Duffy, Siobain, Gillis, Annika, Rumnieks, Janis, Kurtböke, İpek, Chanishvili, Nina, Goodridge, Lawrence, Wittmann, Johannes, Lavigne, Rob, Jang, Ho Bin, Prangishvili, David, Enault, Francois, Turner, Dann, Poranen, Minna M, Oksanen, Hanna M, Krupovic, Mart, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Department of Civil, Environmental and Geodetic Engineering [Columbus, USA] (CEGE), Ohio State University [Columbus] (OSU), University of Novi Sad, Institute for Microbial Biotechnology and Metagenomics [Cape Town, South Africa] (IMBM), University of the Western Cape (UWC), National Institute of Cholera and Enteric Diseases, Theoretical Biology and Bioinformatics [Utrecht, The Netherlands], Utrecht University [Utrecht], Radboud University Medical Center [Nijmegen], Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Institute of Biochemistry & Biophysics, Polish Academy of Sciences (PAN), Beijing University of Chemical Technology, National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), Universidad Andrés Bello [Santiago] (UNAB), Institute of Food, Nutrition and Health [Zurich, Suisse] (IFNH), Department of Health Sciences and Technology [ETH Zürich] (D-HEST), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Cairo University, Adam Mickiewicz University in Poznań (UAM), Azabu University, San Diego State University (SDSU), University of Guelph, Ontario Veterinary College [Univ. Guelph, Canada], iThree Institute, University of Technology Sydney (UTS), University of Leicester, D.K. Zabolotny Institute of Microbiology and Virology [Kyiv, Ukraine], National Academy of Sciences of Ukraine (NASU), Institute of Chemical Biology and Fundamental Medicine [Novosibirsk, Russia] (ICBFM SB RAS), Siberian Branch of the Russian Academy of Sciences (SB RAS), Rutgers University [Newark], Rutgers University System (Rutgers), Imperial College London, Latvian Biomedical Research and Study Centre [Rīga], University of the Sunshine Coast (USC), George Eliava Institute of Bacteriophages, Microbiology and Virology [Tbilisi, Georgia], Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Department of Biosystems (BIOSYST), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Ivane Javakhishvili Tbilisi State University (TSU), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Faculty of Health and Applied Sciences [Bristol, UK], University of the West of England [Bristol] (UWE Bristol), Faculty of Biological and Environmental Sciences [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki, This research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent project(s) BBS/E/F/000PR10353. B.E.D. was supported by the Netherlands Organization for Scientific Research (NWO), Vidi Grant 864.14.004. R.A.E was supported by Grant MCB-1330800 from the National Science Foundation. J.R.B. was supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine. R.L. is a member of the PhageBiotics Research Community, supported by FWO Vlaanderen. M.M.P. was supported by the Academy of Finland (272507). H.M.O. was supported by University of Helsinki funding for Instruct-F1 research infrastructure., The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies of their organizations. E.M.A gratefully acknowledges the support of the UK Biotechnology and Biological Sciences Research Council (BBSRC)., UCL - SST/ELI/ELIM - Applied Microbiology, University of the Western Cape, Universidade Federal de Vicosa (UFV), Universidad Andrés Bello - UNAB (CHILE), Institut Pasteur [Paris], University of Helsinki, and Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])

Subjects
06 Biological Sciences, 07 Agricultural and Veterinary Sciences, 11 Medical and Health Sciences, Archaeal Viruses, 0303 health sciences, MESH: Bacteriophages/classification, Bacteria, 030306 microbiology, MESH: Bacteria/virology, Coronacrisis-Taverne, General Medicine, Classification, MESH: Archaeal Viruses/classification, Archaea, 03 medical and health sciences, All institutes and research themes of the Radboud University Medical Center, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], Bacteriophages, MESH: Archaea/virology, MESH: Classification/methods, 030304 developmental biology
Abstract

International audience; This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.

Published
2020
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2. Binomial nomenclature for virus species: a consultation

Author

Siddell, Stuart G, Walker, Peter J, Lefkowitz, Elliot J, Mushegian, Arcady R, Dutilh, Bas E, Harrach, Balázs, Harrison, Robert L, Junglen, Sandra, Knowles, Nick J, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Nibert, Max L, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Varsani, Arvind, Zerbini, Francisco Murilo, Davison, Andrew J, Sub Bioinformatics, Theoretical Biology and Bioinformatics, School of Cellular and Molecular Medicine [Bristol] (CellModMed), University of Bristol [Bristol], School of Biological Sciences [Brisbane], University of Queensland [Brisbane], University of Alabama at Birmingham [ Birmingham] (UAB), Division of Molecular and Cellular Biosciences [Alexandria, USA] (MCB), National Science Foundation [Arlington] (NSF), Theoretical Biology and Bioinformatics [Utrecht, The Netherlands], Utrecht University [Utrecht], Radboud University Medical Center [Nijmegen], Institute for Veterinary Medical Research [Budapest] (AOTI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Invasive Insect Biocontrol and Behavior Laboratory [Beltsville, USA], USDA Agricultural Research Service [Beltsville, Maryland], USDA-ARS : Agricultural Research Service-USDA-ARS : Agricultural Research Service, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Berlin Institute of Health (BIH), The Pirbright Institute, Biotechnology and Biological Sciences Research Council (BBSRC), University of Guelph, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), Blavatnik Institute [Boston], Harvard Medical School [Boston] (HMS), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology [Mstate, USA] (BCH-EPP), Mississippi State University [Mississippi], Nuffield Department of Clinical Medicine [Oxford], University of Oxford, School of Life Sciences [Tempe, USA], Arizona State University [Tempe] (ASU), Departamento de Fitopatologia [Viçosa, Brazil] (BIOAGRO), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), MRC - University of Glasgow Centre for Virus Research, A.D. is supported by Medical Research Council programme Grant MC_UU_12014/3. B.E.D. is supported by the Netherlands Organization for Scientific Research (NWO) Vidi Grant 864.14.004. B.H. is supported by National Research, Development and Innovation Office–NKFIH, NN128309. N.J.K. is funded by the Department for Environment, Food and Rural Affairs (Defra), UK (Grant no. SE2944), work at the Pirbright Institute is supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/E/I/00007035, BB/E/I/00007036 and BBS/E/I/00007037). J.H.K is supported through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract no. HHSN272200700016I. S.S. acknowledges partial financial support from Mississippi Agricultural and Forestry Experiment Station (MAFES), Mississippi State University., The authors acknowledge the contribution of ICTV Life Member, Dr. Mike Adams, to previous discussions on the need for a standard binomial nomenclature for virus species., Institute for Animal Health, the Pirbright Institute, Institut Pasteur [Paris], Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), Consiglio Nazionale delle Ricerche (CNR), University of Oxford [Oxford], Universidade Federal de Vicosa (UFV), Sub Bioinformatics, and Theoretical Biology and Bioinformatics

Subjects
Library science, Biology, MESH: Terminology as Topic, Binomial species names, Executive committee, International committee on taxonomy of viruses (ICTV), 03 medical and health sciences, Virology Division News, Terminology as Topic, Virology, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], Nomenclature, Virus classification, 030304 developmental biology, 0303 health sciences, 030306 microbiology, Binomial nomenclature, Virus taxonomy, Species nomenclature, General Medicine, Classification, MESH: Viruses/classification, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Taxonomy (biology), MESH: Classification/methods
Abstract

Erratum in : Correction to: Binomial nomenclature for virus species: a consultation. [Arch Virol. 2020]; International audience; The Executive Committee of the International Committee on Taxonomy of Viruses (ICTV) recognizes the need for a standardized nomenclature for virus species. This article sets out the case for establishing a binomial nomenclature and presents the advantages and disadvantages of different naming formats. The Executive Committee understands that adopting a binomial system would have major practical consequences, and invites comments from the virology community before making any decisions to change the existing nomenclature. The Executive Committee will take account of these comments in deciding whether to approve a standardized binomial system at its next meeting in October 2020. Note that this system would relate only to the formal names of virus species and not to the names of viruses.

Published
2020
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3. A quick and robust MHC typing method for free-ranging and captive primate species

Author

K. Stanbury, N. Poirier, N. G. de Groot, Ronald E. Bontrop, N.G. de Groot, G. Blancho, G.G.M. Doxiadis, A. J. M. de Vos-Rouweler, C. de Luna, Department of Comparative Genetics and Refinement [Rijswijk, The Netherlands], Biomedical Primate Research Centre [Rijswijk] (BPRC), Writtle College [Essex, UK], University of Essex, Centre de Recherche en Transplantation et Immunologie (U1064 Inserm - CRTI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Institut de transplantation urologie-néphrologie (ITUN), Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes), Theoretical Biology and Bioinformatics [Utrecht, The Netherlands], Utrecht University [Utrecht], NIH/NIAID project HHSN272201100013C., and Le Bihan, Sylvie

Subjects
0301 basic medicine, Primates, Male, DNA Copy Number Variations, Genotype, Population, Immunology, Pre-clinical research, Major histocompatibility complex, Major Histocompatibility Complex, 03 medical and health sciences, Hylobates, Genetics, Animals, Humans, Typing, Copy-number variation, education, Microsatellites, Gene, Genotyping, Phylogeny, education.field_of_study, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Polymorphism, Genetic, biology, Conservation biology, biology.organism_classification, 030104 developmental biology, biology.protein, Microsatellite, Original Article, Female, MHC, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Microsatellite Repeats
Abstract

Gene products of the major histocompatibility complex (MHC) of human and non-human primates play a crucial role in adaptive immunity, and most of the relevant genes not only show a high degree of variability (polymorphism) but also copy number variation (CNV) is observed. Due to this diversity, MHC proteins influence the capability of individuals to cope with various pathogens. MHC and/or MHC-linked gene products such as odorant receptor genes are thought to influence mate choice and reproductive success. Therefore, MHC typing of wild and captive primate populations is considered to be useful in conservation biology, which is, however, often hampered by the need of invasive and time-consuming methods. All intact Mhc-DRB genes in primates appear to possess a complex and highly divergent microsatellite, DRB-STR. A panel of 154 pedigreed olive baboons (Papio anubis) was examined for their DRB content by DRB-STR analysis of genomic DNA. Using the same methodology on DNA of feces samples, DRB variability of a silvery gibbon population (Hylobates moloch) (N = 24), an endangered species, could successfully be studied. In both species, length determination of the DRB-STR resulted in the definition of unique genotyping patterns that appeared to be specific for a certain chromosome. Moreover, the different STR lengths were shown to segregate with the allelic variation of the respective gene. The results obtained expand data gained previously on DRB-STR typing in macaques, great apes, and humans and strengthen the conclusion that this protocol is applicable in molecular ecology, conservation biology, and colony management, especially of endangered primate species. Electronic supplementary material The online version of this article (doi:10.1007/s00251-016-0968-0) contains supplementary material, which is available to authorized users.

Published
2017

4. IMGT, the international ImMunoGeneTics database

Author

Giudicelli, V., Chaume, D., Bodmer, J., Muller, W., Busin, C., Marsh, S., Bontrop, R., Marc, L., Malik, A., Lefranc, M. P., Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Christchurch] (DPA), University of Canterbury [Christchurch], Department of Comparative Genetics and Refinement [Rijswijk, The Netherlands], Biomedical Primate Research Centre [Rijswijk] (BPRC), Theoretical Biology and Bioinformatics [Utrecht, The Netherlands], Utrecht University [Utrecht], Institut de Génétique Moléculaire de Montpellier (IGMM), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)

Subjects
Models, Molecular, Databases, Factual, Molecular Sequence Data, Receptors, Antigen, T-Cell, Immunoglobulins, Information Storage and Retrieval, chemical and pharmacologic phenomena, Major Histocompatibility Complex, Computer Communication Networks, 03 medical and health sciences, 0302 clinical medicine, Terminology as Topic, Immunogenetics, Genetics, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, 030304 developmental biology, Internet, 0303 health sciences, Base Sequence, Genes, Immunoglobulin, Data Collection, Genetic Variation, 3. Good health, Genes, T-Cell Receptor, Genes, Vertebrates, France, Sequence Analysis, Research Article, 030215 immunology
Abstract

IMGT, the international ImMunoGeneTics database, is an integrated database specializing in immunoglobulins, T-cell receptors (TcR) and major histocompatibility complex (MHC) of all vertebrate species, initiated and co-ordinated by Marie-Paule Lefranc, CNRS, Montpellier II University, Montpellier, France (lefranc@ligm.crbm.cnrs-mop.fr). IMGT includes two databases: LIGM-DB (for immunoglobulins and TcR) and MHC/HLA-DB. IMGT comprises expertly annotated sequences and alignment tables. LIGM-DB contains more than 19 000 immunoglobulin and TcR sequences from 78 species. MHC/HLA-DB contains class I and class II human leukocyte antigen alignment tables. An IMGT tool, DNAPLOT, developed for immunoglobulins, TcR and MHC sequence alignments, is also available. IMGT works in close collaboration with the EMBL database. IMGT goals are to establish a common data access to all immunogenetics data, including sequences, oligonucleotide primers, gene maps and other genetic data of immunoglobulins, TcR and MHC molecules, and to provide a graphical user-friendly data access. IMGT will have important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas), therapeutical approaches (antibody engineering), genome diversity and genome evolution studies. IMGT can be accessed at http://imgt.cnusc.fr:8104 and http://www.ebi.ac.uk/IMGT

Published
1997
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5. A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen.

Author

Feurtey A, Lorrain C, McDonald MC, Milgate A, Solomon PS, Warren R, Puccetti G, Scalliet G, Torriani SFF, Gout L, Marcel TC, Suffert F, Alassimone J, Lipzen A, Yoshinaga Y, Daum C, Barry K, Grigoriev IV, Goodwin SB, Genissel A, Seidl MF, Stukenbrock EH, Lebrun MH, Kema GHJ, McDonald BA, and Croll D

Subjects
Humans, Virulence genetics, Genomics, Plant Diseases microbiology, Adaptation, Physiological, Acclimatization
Abstract

Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of crop pathogens. Here, we address this by assembling a global thousand-genome panel of Zymoseptoria tritici, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen., (© 2023. The Author(s).)

Published
2023
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7. Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review.

Author

Coutinho FH, Meirelles PM, Moreira AP, Paranhos RP, Dutilh BE, and Thompson FL

Abstract

Associations between microorganisms occur extensively throughout Earth's oceans. Understanding how microbial communities are assembled and how the presence or absence of species is related to that of others are central goals of microbial ecology. Here, we investigate co-occurrence associations between marine prokaryotes by combining 180 new and publicly available metagenomic datasets from different oceans in a large-scale meta-analysis. A co-occurrence network was created by calculating correlation scores between the abundances of microorganisms in metagenomes. A total of 1,906 correlations amongst 297 organisms were detected, segregating them into 11 major groups that occupy distinct ecological niches. Additionally, by analyzing the oceanographic parameters measured for a selected number of sampling sites, we characterized the influence of environmental variables over each of these 11 groups. Clustering organisms into groups of taxa that have similar ecology, allowed the detection of several significant correlations that could not be observed for the taxa individually.

Published
2015
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