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66 results on '"MESH : Phylogeny"'

1. Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens

Author: Du, C, Gryganskyi, G, Tschaplinski, R, Misztal, C, Wu, A, Desirò, I, Vande Pol, I, Du, R, Zienkiewicz, R, Zienkiewicz, G, Tisserant, R, Splivallo, G, Hainaut, R, Henrissat, R, Ohm, R., Kuo, G, Yan, G., Lipzen, G, Nolan, G, LaButti, G, Barry, G, Goldstein, G, Labbe, R., Schadt, R, Tuskan, G., Grigoriev, G, Martin, R, Vilgalys, R., Bonito, G., Du, J., Gryganskyi, A., Du, K., Tschaplinski, T., Misztal, K., Wu, S., Desirò, A., Vande Pol, N., Du, Z., Zienkiewicz, A., Zienkiewicz, K., Morin, E., Tisserant, E., Splivallo, R., Hainaut, M., Henrissat, B., Kuo, A., Yan, J., Lipzen, A., Nolan, M., LaButti, K., Barry, K., Goldstein, A., Labbé, J., Schadt, C., Grigoriev, I., Martin, F., Duke University [Durham], BioSciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, University of California [Berkeley], University of California, Arizona State University [Tempe] (ASU), Deparment of Plant, Soil and Microbial Sciences, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Goethe-University Frankfurt am Main, Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Utrecht University [Utrecht], Genomic Science Program, U.S. Department of Energy, Office of Science - Biological and Environmental Research as part of the Plant Microbe Interfaces Scientific Focus Area at Oak Ridge National Laboratory, U.S. Department of Energy DE-AC05- 00OR22725, DOE Joint Genome Institute by the JGI Community sequencing program 570, Office of Science of the US Department of Energy DE-AC02-05CH11231, EU Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE) ANR-11-LABX-0002-01, Joint Genome Institute (JGI), Northwest Institute for Nonferrous Metal Research (NIN), Laboratorio de Turbulencia, Universidad de Santiago de Chile [Santiago] (USACH), UT-Battelle, LLC, Centre d'études de chimie métallurgique (CECM), Centre National de la Recherche Scientifique (CNRS), Kansas State University, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), United States Department of Energy, Center for Human Genetics, University of Leuven School of Medicine, SCHOOL of MEDICINE [Louvain], Université Catholique de Louvain (UCL)-Université Catholique de Louvain (UCL), DOE Joint Genome Institute [Walnut Creek], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Sub Molecular Microbiology, Molecular Microbiology, Joint Genome Institute ( JGI ), Northwest Institute for Nonferrous Metal Research, Oak Ridge National Laboratory, Duke university [Durham], Centre d'études de chimie métallurgique ( CECM ), Centre National de la Recherche Scientifique ( CNRS ), Interactions Arbres-Microorganismes ( IAM ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), Architecture et fonction des macromolécules biologiques ( AFMB ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA ), UNIVERSITY of LEUVEN SCHOOL of MEDICINE, Institute of Northern Engineering, 455 Duckering Bldg, Lawrence Berkeley National Laboratory [Berkeley] ( LBNL ), Lipides - Nutrition - Cancer (U866) ( LNC ), Université de Bourgogne ( UB ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon ( ENSBANA ), University of California [Berkeley] (UC Berkeley), and University of California (UC)
Subjects: Burkholderiaceae, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, MESH : Symbiosis, MESH: Base Sequence, MESH: Genome, Bacterial, 2.2 Factors relating to physical environment, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, LAND PLANTS, 2.2 Factors relating to the physical environment, MESH : Metagenome, MESH: Animals, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Phylogeny, Phylogeny, MESH: Lipid Metabolism, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Symbiosis, Endosymbiosis, [ SDV.MHEP.ME ] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Bacterial, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], FATTY-ACID BIOSYNTHESIS, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Fungal, [ SDV.NEU.NB ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, MESH: Genome, Fungal, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Infection, Evolution, 030106 microbiology, MESH : Genome, Bacterial, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Microbiology, GENE-TRANSFER, 03 medical and health sciences, MESH : Burkholderiaceae, Botany, MESH : Evolution, Molecular, Ecology, Evolution, Behavior and Systematics, Comparative genomics, [ SDV.IMM.II ] Life Sciences [q-bio]/Immunology/Innate immunity, MESH : Genome, Fungal, Molecular, ENDOBACTERIA, MESH: Burkholderiaceae, DNA, 15. Life on land, Lipid Metabolism, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, INTRACELLULAR BACTERIA, 030104 developmental biology, MESH: Mortierella, Metagenome, MESH : Sequence Analysis, DNA, 0301 basic medicine, MESH: Sequence Analysis, DNA, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, MESH: Carbohydrate Metabolism, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genome, GUT MICROBIOME, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, ARBUSCULAR MYCORRHIZAL FUNGI, [ SDV.BBM.BC ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Mortierella, MESH : Lipid Metabolism, MESH: Evolution, Molecular, 2. Zero hunger, Genetics, biology, Ecology, Fungal genetics, MESH : Carbohydrate Metabolism, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], ESCHERICHIA-COLI, Carbohydrate Metabolism, Sequence Analysis, Metabolic Networks and Pathways, CANDIDATUS GLOMERIBACTER GIGASPORARUM, Bacterial genome size, Symbiosis, Behavior and Systematics, Lipid biosynthesis, Animals, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Evolutionary Biology, Base Sequence, MESH : Metabolic Networks and Pathways, MESH : Phylogeny, [ SDV.BIO ] Life Sciences [q-bio]/Biotechnology, [ SDV.SP.PHARMA ] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, MESH: Metagenome, biology.organism_classification, MESH: Metabolic Networks and Pathways, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, MESH : Base Sequence, BICOLOR S238N, MESH : Animals, MESH : Mortierella, [ SDV.BBM.BS ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract: International audience; Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well-known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. We sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within a lineage of endofungal symbionts that are sister clade to Burkholderia. The genome of M. elongata strain AG77 features a core set of primary metabolic pathways for degradation of simple carbohydrates and lipid biosynthesis, while the M. cysteinexigens (AG77) genome is reduced in size and function. Experiments using antibiotics to cure the endobacterium from the host demonstrate that the fungal host metabolism is highly modulated by presence/absence of M. cysteinexigens. Independent comparative phylogenomic analyses of fungal and bacterial genomes are consistent with an ancient origin for M. elongata - M. cysteinexigens symbiosis, most likely over 350 million years ago and concomitant with the terrestrialization of Earth and diversification of land fungi and plants.
Published: 2017

2. Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes

Author: Spang, Anja, Eme, Laura, Saw, Jimmy H., Caceres, Eva F., Zaremba-Niedzwiedzka, Katarzyna, Lombard, Jonathan, Guy, Lionel, Ettema, Thijs J. G., Biologie Moléculaire du Gène chez les Extrêmophiles ( BMGE ), Institut Pasteur [Paris], Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), COMSATS Institute of Information Technology ( CIIT ), VDC, MG and PF are supported by an European Research Council (ERC) grant from the European Union’s Seventh Framework Program (FP/2007-2013)/ Project EVOMOBIL-ERC Grant Agreement no. 340440. AN is supported by the Higher Education Commission, Pakistan., We are grateful to Gill S., Catchpole R. and Roach D. for comments, and to Poppleton D. and Borrel G. for technical support., European Project : 340440,EC:FP7:ERC,ERC-2013-ADG,EVOMOBIL ( 2014 ), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), COMSATS Institute of Information Technology [Islamabad] (CIIT), and European Project: 340440,EC:FP7:ERC,ERC-2013-ADG,EVOMOBIL(2014)
Subjects: Evolutionary Genetics, [SDV]Life Sciences [q-bio], Gene Expression, Plant Science, QH426-470, Biochemistry, Polymerases, Database and Informatics Methods, Sequence alignment, Genome, Archaeal, MESH : Eukaryota, Macromolecular Structure Analysis, MESH: Phylogeny, MESH: Evolution, Molecular, Data Management, Phylogenetic analysis, Plant Biochemistry, Archaeal Evolution, Eukaryota, MESH: Archaeal Proteins, Genomics, Genomic Databases, Phylogenetics, MESH: Eukaryota, Archaean biology, RNA polymerase, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Sequence Analysis, Research Article, Computer and Information Sciences, Protein Structure, Bioinformatics, MESH: Euryarchaeota, Euryarchaeota, Research and Analysis Methods, Microbiology, Formal Comment, Elongation Factors, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH : Prokaryotic Cells, DNA-binding proteins, Genetics, Gene Regulation, Evolutionary Systematics, Protein structure comparison, MESH : Evolution, Molecular, Molecular Biology, MESH: Prokaryotic Cells, Taxonomy, Evolutionary Biology, [ SDV ] Life Sciences [q-bio], MESH : Euryarchaeota, Organisms, Biology and Life Sciences, Proteins, Computational Biology, MESH : Phylogeny, Genome Analysis, Archaea, Regulatory Proteins, Biological Databases, Prokaryotic Cells, MESH : Archaeal Proteins, Metagenomics
Abstract: The eocyte hypothesis, in which Eukarya emerged from within Archaea, has been boosted by the description of a new candidate archaeal phylum, “Lokiarchaeota”, from metagenomic data. Eukarya branch within Lokiarchaeota in a tree reconstructed from the concatenation of 36 universal proteins. However, individual phylogenies revealed that lokiarchaeal proteins sequences have different evolutionary histories. The individual markers phylogenies revealed at least two subsets of proteins, either supporting the Woese or the Eocyte tree of life. Strikingly, removal of a single protein, the elongation factor EF2, is sufficient to break the Eukaryotes-Lokiarchaea affiliation. Our analysis suggests that the three lokiarchaeal EF2 proteins have a chimeric organization that could be due to contamination and/or homologous recombination with patches of eukaryotic sequences. A robust phylogenetic analysis of RNA polymerases with a new dataset indicates that Lokiarchaeota and related phyla of the Asgard superphylum are sister group to Euryarchaeota, not to Eukarya, and supports the monophyly of Archaea with their rooting in the branch leading to Thaumarchaeota., Author summary Two scenarios have been proposed to describe the history of cellular life on our planet. For some authors, two lineages emerged from the last universal cellular ancestor, one leading to Bacteria, the other one leading to a common ancestor of Archaea and Eukarya (Woese’s hypothesis), while others suggest that Eukaryotes emerged from within an archaeal subgroup (eocyte hypothesis). This latter hypothesis has been boosted by the reconstruction of new archaeal genomes from environmental DNA. These analyses have suggested that eukaryotes originated from complex archaea, called Lokiarchaeota, the first described members of the recently proposed Asgard superphylum. Considering the importance of this question, we performed new analyses of the universal proteins from Lokiarchaea and realized that their affiliation to Eukaryotes was most probably due to different biases, including chimeric sequences and unequal rate of protein evolution. From our results, we suggest here that Lokiarchaea and close relatives are sister group to Euryarchaeota, not to Eukarya. Notably, we also show that the choices of the universal markers to include in one’s analysis will critically impact the scenario supported and that some markers as the RNA polymerase support the traditional Woese’s tree.
Published: 2017

3. Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels

Author: Igor V. Grigoriev, Weihua Wu, John M. Gladden, Sirma Mihaltcheva, Kerrie Barry, Bernard Henrissat, Mary Bao Tran-Gyamfi, Mansi Chovatia, Alan Kuo, Erika Lindquist, Hope Hundley, Ryan W. Davis, Kurt LaButti, US Department of Energy Joint Genome Institute, U.S Department of Energy, U.S. Department of Energy (DOE)-U.S. Department of Energy (DOE), Dept Energy Great Lakes Bioenergy Res Ctr, University of California, Joint Genome Institute, United States Department of Energy, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), U.S. Department of Energy [Washington] (DOE)-U.S. Department of Energy [Washington] (DOE), University of California (UC), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), U.S. Department of Energy ( DOE ) -U.S. Department of Energy ( DOE ), Architecture et fonction des macromolécules biologiques ( AFMB ), and Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA )
Subjects: Ligninolytic enzymes, MESH : Polysaccharides, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Lignin, 7. Clean energy, Terpene, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH : Volatile Organic Compounds, Endophytes, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Phylogeny, Phylogeny, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [ SDV.MHEP.ME ] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], General Medicine, MESH : Glycoside Hydrolases, Volatile organic compound, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [ SDV.NEU.NB ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, MESH: Genome, Fungal, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, CAZy, MESH: Sesquiterpenes, MESH: Fungal Proteins, Genome, Fungal, MESH: Monoterpenes, Sesquiterpenes, MESH: Gene Expression, Glycoside Hydrolases, 030106 microbiology, MESH: Alkyl and Aryl Transferases, MESH : Biofuels, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 03 medical and health sciences, Botany, [ SDV.IMM.II ] Life Sciences [q-bio]/Immunology/Innate immunity, Alkyl and Aryl Transferases, MESH : Genome, Fungal, MESH: Cellulase, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH : Gene Expression, MESH : Monoterpenes, 030104 developmental biology, chemistry, Biofuels, MESH : Cellulases, 0301 basic medicine, MESH: Xylariales, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, MESH : Endophytes, MESH: Cellulases, Gene Expression, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Applied Microbiology and Biotechnology, Endophyte, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, chemistry.chemical_compound, [ SDV.BBM.BC ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Cellulases, MESH : Fungal Proteins, 2. Zero hunger, Xylariales, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Biofuel, Biotechnology, MESH : Sesquiterpenes, Cellulase, Biology, Plant use of endophytic fungi in defense, MESH: Endophytes, MESH: Volatile Organic Compounds, Fungal Proteins, Consolidated bioprocessing, Polysaccharides, MESH : Xylariales, MESH: Glycoside Hydrolases, Bioprocess, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], MESH : Alkyl and Aryl Transferases, MESH: Biofuels, Volatile Organic Compounds, MESH : Lignin, MESH : Phylogeny, [ SDV.BIO ] Life Sciences [q-bio]/Biotechnology, [ SDV.SP.PHARMA ] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, biology.organism_classification, MESH: Lignin, MESH: Polysaccharides, MESH : Cellulase, Monoterpenes, biology.protein, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, [ SDV.BBM.BS ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract: International audience; Recently, several endophytic fungi have been demonstrated to produce volatile organic compounds (VOCs) with properties similar to fossil fuels, called "mycodiesel," while growing on lignocellulosic plant and agricultural residues. The fact that endophytes are plant symbionts suggests that some may be able to produce lignocellulolytic enzymes, making them capable of both deconstructing lignocellulose and converting it into mycodiesel, two properties that indicate that these strains may be useful consolidated bioprocessing (CBP) hosts for the biofuel production. In this study, four endophytes Hypoxylon sp. CI4A, Hypoxylon sp. EC38, Hypoxylon sp. CO27, and Daldinia eschscholzii EC12 were selected and evaluated for their CBP potential. Analysis of their genomes indicates that these endophytes have a rich reservoir of biomass-deconstructing carbohydrate-active enzymes (CAZys), which includes enzymes active on both polysaccharides and lignin, as well as terpene synthases (TPSs), enzymes that may produce fuel-like molecules, suggesting that they do indeed have CBP potential. GC-MS analyses of their VOCs when grown on four representative lignocellulosic feedstocks revealed that these endophytes produce a wide spectrum of hydrocarbons, the majority of which are monoterpenes and sesquiterpenes, including some known biofuel candidates. Analysis of their cellulase activity when grown under the same conditions revealed that these endophytes actively produce endoglucanases, exoglucanases, and β-glucosidases. The richness of CAZymes as well as terpene synthases identified in these four endophytic fungi suggests that they are great candidates to pursue for development into platform CBP organisms.
Published: 2017

4. Broad phylogeny and functionality of cellulosomal components in the bovine rumen microbiome

Author: Bernard Henrissat, Vincent Lombard, Sarah Moraïs, Itzhak Mizrahi, Lizi Bensoussan, Edward A. Bayer, Bareket Dassa, Nir Friedman, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Architecture et fonction des macromolécules biologiques ( AFMB ), and Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA )
Subjects: 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Multienzyme Complexes, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, Cellulosome, [ SDV.BBM.BC ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH : Cattle, MESH : Bacterial Proteins, MESH : Metagenome, MESH: Animals, Fiber degradation, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Protein modules, MESH: Phylogeny, MESH: Bacterial Proteins, Phylogeny, Research Articles, 2. Zero hunger, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH : Gastrointestinal Microbiome, [ SDV.MHEP.ME ] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Hydrolysis, Modular architecture, MESH : Multienzyme Complexes, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Cellulosomes, MESH : Cellulosomes, [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Cattle, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [ SDV.NEU.NB ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Research Article, Rumen, Computational biology, Biology, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Microbiology, MESH: Gastrointestinal Microbiome, 03 medical and health sciences, Bacterial Proteins, Multienzyme Complexes, Phylogenetics, Animals, MESH : Bacteria, MESH : Rumen, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Rumen microorganisms, Cellulose, Ecology, Evolution, Behavior and Systematics, [ SDV.IMM.II ] Life Sciences [q-bio]/Immunology/Innate immunity, Bacteria, MESH : Phylogeny, [ SDV.BIO ] Life Sciences [q-bio]/Biotechnology, [ SDV.SP.PHARMA ] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, MESH: Metagenome, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Gastrointestinal Microbiome, MESH: Bacteria, 030104 developmental biology, MESH: Cellulosomes, Metagenomics, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Metagenome, MESH: Rumen, Cattle, MESH : Animals, Function (biology), [ SDV.BBM.BS ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract: The cellulosome is an extracellular multi-enzyme complex that is considered one of the most efficient plant cell wall-degrading strategies devised by nature. Its unique modular architecture, achieved by high affinity and specific interaction between protein modules (cohesins and dockerins) enables formation of various enzyme combinations. Extensive research has been dedicated to the mechanistic nature of the cellulosome complex. Nevertheless, little is known regarding its distribution and abundance among microbes in natural plant fiber-rich environments. Here, we explored these questions in bovine rumen microbial communities, specialized in efficient degradation of lignocellulosic plant material. We bioinformatically screened for cellulosomal modules in this complex environment using a previously published ultra-deep fiber-adherent rumen metagenome. Intriguingly, a large portion of the functions of the dockerin-containing proteins were related to alternative biological processes, and not necessarily to the classic fiber degradation function. Our analysis was experimentally validated by characterizing specific interactions between selected cohesins and dockerins and revealed that cellulosome is a more generalized strategy employed by diverse bacteria, some of which were not previously associated with cellulosome production. Remarkably, our results provide additional proof of similarity among rumen microbial communities worldwide. This study suggests a broader and widespread role for the cellulosomal machinery in nature. This article is protected by copyright. All rights reserved.
Published: 2017

5. Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements

Author: Eugene V. Koonin, Jaime Iranzo, David Prangishvili, Mart Krupovic, National Center for Biotechnology Information (NCBI), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Institut Pasteur [Paris], National Center for Biotechnology Information ( NCBI ), and Biologie Moléculaire du Gène chez les Extrêmophiles ( BMGE )
Subjects: 0301 basic medicine, Archaeal Viruses, viruses, royalty, Genome, MESH : Archaea, MESH : Biological Evolution, Bacteriophages, Gene Regulatory Networks, Phylogeny, Genetics, Phylogenetic tree, Turriviridae, Biological Evolution, MESH : Bacteriophages, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH : DNA Transposable Elements, MESH : Genome, Viral, Plasmids, Immunology, Genome, Viral, Biology, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Microbiology, 03 medical and health sciences, royalty.royal_line, Caudovirales, Phylogenetics, Virology, MESH : Virion, MESH : Bacteria, Human virome, [ SDV ] Life Sciences [q-bio], Bacteria, Virion, MESH : Phylogeny, Computational Biology, biology.organism_classification, Archaea, MESH : Archaeal Viruses, 030104 developmental biology, Genetic Diversity and Evolution, Evolutionary biology, MESH : Plasmids, MESH : Gene Regulatory Networks, Insect Science, DNA Transposable Elements, Bacterial virus, MESH : Computational Biology
Abstract: Archaea and particularly hyperthermophilic crenarchaea are hosts to many unusual viruses with diverse virion shapes and distinct gene compositions. As is typical of viruses in general, there are no universal genes in the archaeal virosphere. Therefore, to obtain a comprehensive picture of the evolutionary relationships between viruses, network analysis methods are more productive than traditional phylogenetic approaches. Here we present a comprehensive comparative analysis of genomes and proteomes from all currently known taxonomically classified and unclassified, cultivated and uncultivated archaeal viruses. We constructed a bipartite network of archaeal viruses that includes two classes of nodes, the genomes and gene families that connect them. Dissection of this network using formal community detection methods reveals strong modularity, with 10 distinct modules and 3 putative supermodules. However, compared to similar previously analyzed networks of eukaryotic and bacterial viruses, the archaeal virus network is sparsely connected. With the exception of the tailed viruses related to bacteriophages of the order Caudovirales and the families Turriviridae and Sphaerolipoviridae that are linked to a distinct supermodule of eukaryotic and bacterial viruses, there are few connector genes shared by different archaeal virus modules. In contrast, most of these modules include, in addition to viruses, capsidless mobile elements, emphasizing tight evolutionary connections between the two types of entities in archaea. The relative contributions of distinct evolutionary origins, in particular from nonviral elements, and insufficient sampling to the sparsity of the archaeal virus network remain to be determined by further exploration of the archaeal virosphere. IMPORTANCE Viruses infecting archaea are among the most mysterious denizens of the virosphere. Many of these viruses display no genetic or even morphological relationship to viruses of bacteria and eukaryotes, raising questions regarding their origins and position in the global virosphere. Analysis of 5,740 protein sequences from 116 genomes allowed dissection of the archaeal virus network and showed that most groups of archaeal viruses are evolutionarily connected to capsidless mobile genetic elements, including various plasmids and transposons. This finding could reflect actual independent origins of the distinct groups of archaeal viruses from different nonviral elements, providing important insights into the emergence and evolution of the archaeal virome.
Published: 2016

6. Evidence of two distinct phylogenetic lineages of dog rabies virus circulating in Cambodia

Author: Paul F. Horwood, Philippe Buchy, Sotheary In, Jean-Marc Reynes, Veasna Duong, Sivuth Ong, Arnaud Tarantola, A. E. Metlin, Hervé Bourhy, Channa Mey, Unité de Virologie, Institut Pasteur du Cambodge-Réseau International des Instituts Pasteur ( RIIP ), Institut Pasteur du Cambodge, Biologie des Infections Virales Émergentes ( UBIVE ), Institut Pasteur [Paris], Dynamique des Lyssavirus et Adaptation à l'Hôte, Unité d'Épidémiologie et de Santé Publique, GlaxoSmithKline, Glaxo Smith Kline, Unité de Virologie / Virology Unit [Phnom Penh], Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Réseau International des Instituts Pasteur (RIIP), Biologie des Infections Virales Émergentes - Biology of Emerging Viral Infections (UBIVE), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP), Dynamique des Lyssavirus et Adaptation à l'Hôte (DyLAH), Institut Pasteur [Paris] (IP), Unité d'Épidémiologie et de Santé Publique [Phnom Penh], Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: 0301 basic medicine, Most recent common ancestor, MESH: Sequence Analysis, DNA, Lineage (evolution), [SDV]Life Sciences [q-bio], MESH : Nucleocapsid Proteins, medicine.disease_cause, MESH: Dogs, MESH : Dogs, MESH : Rabies virus, MESH: Animals, Dog Diseases, Geography, Medical, Clade, Molecular clock, MESH: Phylogeny, Phylogeny, MESH: Evolution, Molecular, Phylogenetic tree, Nucleocapsid Proteins, Rabies virus evolution, MESH: Rabies virus, MESH : Dog Diseases, South-East Asia, [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Infectious Diseases, MESH: RNA, Viral, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, RNA, Viral, Cambodia, Rabies epidemiology, Microbiology (medical), MESH : Geography, Medical, Rabies, MESH: Dog Diseases, 030106 microbiology, Biology, Microbiology, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Evolution, Molecular, 03 medical and health sciences, Dogs, MESH: Rabies, Phylogenetics, MESH: Geography, Medical, Genetics, medicine, Animals, MESH : RNA, Viral, MESH : Evolution, Molecular, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Molecular epidemiology, [ SDV ] Life Sciences [q-bio], MESH : Cambodia, MESH: Cambodia, Rabies virus, MESH : Phylogeny, MESH: Nucleocapsid Proteins, Sequence Analysis, DNA, Virology, 030104 developmental biology, Evolutionary biology, MESH : Rabies, MESH : Animals, Canine rabies, MESH : Sequence Analysis, DNA
Abstract: International audience; This first extensive retrospective study of the molecular epidemiology of dog rabies in Cambodia included 149 rabies virus (RABV) entire nucleoprotein sequences obtained from 1998-2011. The sequences were analyzed in conjunction with RABVs from other Asian countries. Phylogenetic reconstruction confirmed the South-East Asian phylogenetic clade comprising viruses from Cambodia, Vietnam, Thailand, Laos and Myanmar. The present study represents the first attempt to classify the phylogenetic lineages inside this clade, resulting in the confirmation that all the Cambodian viruses belonged to the South-East Asian (SEA) clade. Three distinct phylogenetic lineages in the region were established with the majority of viruses from Cambodia closely related to viruses from Thailand, Laos and Vietnam, forming the geographically widespread phylogenetic lineage SEA1. A South-East Asian lineage SEA2 comprised two viruses from Cambodia was identified, which shared a common ancestor with RABVs originating from Laos. Viruses from Myanmar formed separate phylogenetic lineages within the major SEA clade. Bayesian molecular clock analysis suggested that the time to most recent common ancestor (TMRCA) of all Cambodian RABVs dated to around 1950. The TMRCA of the Cambodian SEA1 lineage was around 1964 and that of the SEA2 lineage was around 1953. The results identified three phylogenetically distinct and geographically separated lineages inside the earlier identified major SEA clade, covering at least five countries in the region. A greater understanding of the molecular epidemiology of rabies in South-East Asia is an important step to monitor progress on the efforts to control canine rabies in the region.
Published: 2016

7. Co-infection of Borrelia afzelii and Bartonella spp. in bank voles from a suburban forest

Author: Dominique Huet, Elise Vaumourin, Patrick Gasqui, Sébastien Masséglia, Elisabeth Ferquel, Lénaïg Halos, Muriel Vayssier-Taussat, Elie Marcheteau, Maud Marsot, Gwenaël Vourc’h, Benoît Pisanu, Jean-Louis Chapuis, Jean-Philippe Buffet, USC INRA Bartonella et Tiques, ANSES - Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail ( ANSES ), Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), Paris-Centre de Recherche Cardiovasculaire ( PARCC - U970 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Hôpital Européen Georges Pompidou [APHP] ( HEGP ), Biologie moléculaire et immunologie parasitaires et fongiques ( BIPAR ), Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -AFSSA-Ecole Nationale Vétérinaire d'Alfort-Institut National de la Recherche Agronomique ( INRA ), Centre d'Ecologie et des Sciences de la COnservation ( CESCO ), Muséum National d'Histoire Naturelle ( MNHN ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de Référence des Borrelia ( CNR ), Institut Pasteur [Paris], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Centre d'Ecologie et des Sciences de la COnservation (CESCO), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence des Borrelia (CNR), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, and Institut Pasteur [Paris] (IP)
Subjects: MESH: Lyme Disease, MESH : Prevalence, [SDV]Life Sciences [q-bio], Human pathogen, medicine.disease_cause, Trees, Bartonella spp, Rodent Diseases, Myodes glareolus, MESH : Trees, Genotype, Prevalence, MESH : Disease Reservoirs, MESH : Epidemiological Monitoring, Immunology and Allergy, MESH: Animals, MESH: Borrelia burgdorferi Group, MESH: Phylogeny, Pathogen, Phylogeny, MESH : Lyme Disease, Lyme Disease, Diversity, 0303 health sciences, MESH: Bartonella Infections, Arvicolinae, Coinfection, Age Factors, MESH : Rodent Diseases, General Medicine, Bacterial Typing Techniques, Co-infection, Bank vole, Infectious Diseases, Epidemiological Monitoring, Borrelia afzelii, MESH: Bartonella, Lyme disease microbiology, France, Bartonella, Immunology, Zoology, Biology, Microbiology, MESH: Bacterial Typing Techniques, 03 medical and health sciences, Borrelia burgdorferi Group, Bartonella Infections, medicine, Animals, Humans, MESH : France, MESH : Bartonella, MESH: Prevalence, Disease Reservoirs, 030304 developmental biology, MESH: Age Factors, MESH: Disease Reservoirs, MESH: Humans, [ SDV ] Life Sciences [q-bio], General Veterinary, Bank voles, 030306 microbiology, MESH : Humans, MESH : Phylogeny, MESH: Arvicolinae, bacterial infections and mycoses, medicine.disease, biology.organism_classification, MESH: Coinfection, MESH: France, MESH: Trees, MESH : Arvicolinae, MESH : Coinfection, MESH : Bartonella Infections, MESH : Bacterial Typing Techniques, MESH: Rodent Diseases, MESH: Epidemiological Monitoring, MESH : Age Factors, MESH : Animals, MESH : Borrelia burgdorferi Group
Abstract: International audience; We report the molecular detection of Borrelia afzelii (11%) and Bartonella spp. (56%) in 447 bank voles trapped in a suburban forest in France. Adult voles were infected by significantly more Borrelia afzelii than juveniles (p
Published: 2012
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8. A single regulatory gene is sufficient to alter Vibrio aestuarianus pathogenicity in oysters

Author: Goudenege, David, Travers, Marie-agnes, Lemire, Astrid, Petton, Bruno, Haffner, Philippe, Labreuche, Yannick, Tourbiez, Delphine, Mangenot, Sophie, Calteau, Alexandra, Mazel, Didier, Nicolas, Jean-louis, Jacq, Annick, Le Roux, Frederique, Unité Physiologie Fonctionnelle des Organismes marins, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Laboratoire de Génétique et Pathologie des Mollusques Marins, 17390 La Tremblade, France. (LGPMM), Santé, Génétique et Microbiologie des Mollusques (IFREMER SG2M), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Plasticité du Génome Bactérien - Bacterial Genome Plasticity (PGB), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), The present study has been supported by the DPMA (Convention DPMA 2013- IFREMER 12/1210320/NYF), the ANR Blanc (11-BSV7-023-01 «VIBRIOGEN», D. G. funding), the EMBRC France (A. L. funding) and the ANR Bioadapt (13-ADAP-0007-01 «OPOPOP»)., We warmly thank Dr Maurizio Labbate (University of Technology, Sydney, Australia), Dr Maxime Bruto (Station Biologique de Roscoff) and Dr Marianne Alunno-Bruscia (Ifremer Argenton) for critically reading the manuscript. We also thank Pr Joël Henry and Dr Céline Zatylny-Gaudin (Université de Caen Basse-Normandie, Institut de Biologie Fondamentale et Appliquée) for kindly performing mass spectrometry analyses. We thank Dr Carla Pruzzo (University of Genoa, Italy) and Dr Ana Roque (IRTA, Spain) for providing U_17 and KB19 strains. We acknowledge the staff of the station Ifremer Argenton, La Tremblade, Bouin, particularly Max Nourry, the ABIMS (SBR Roscoff) and LABGeM (Evry) platforms for technical support., ANR-11-BSV7-0023,VIBRIOGEN,Les vibrios pathogènes d'invertébrés marins : un nouveau regard sur la virulence et les réservoirs de gènes permettant l'adaptation à la niche écologique(2011), ANR-13-ADAP-0007,OPOPOP,Emergence de pathogènes opportunistes d'huîtres dans des populations naturelles de Vibrio(2013), Physiologie Fonctionnelle des Organismes Marins (PFOM), Laboratoire de Génétique et Pathologie des Mollusques Marins (LGPMM), Santé, Génétique et Microbiologie des Mollusques (SGMM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Laboratoire de Biologie Intégrative des Modèles Marins ( LBI2M ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Génomique d'Evry ( IG ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Plasticité du Génome Bactérien, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut de génétique et microbiologie [Orsay] ( IGM ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), ANR-11-BSV7-0023,VIBRIOGEN,Les vibrios pathogènes d'invertébrés marins : un nouveau regard sur la virulence et les réservoirs de gènes permettant l'adaptation à la niche écologique ( 2011 ), ANR-13-ADAP-0007,OPOPOP,Emergence de pathogènes opportunistes d'huîtres dans des populations naturelles de Vibrio ( 2013 ), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: MESH: Genes, Regulator, [SDV]Life Sciences [q-bio], CHOLERAE HEMAGGLUTININ PROTEASE, PACIFIC OYSTERS, MESH : Protein Kinases, MESH: Virulence, MESH: Ostreidae, MESH : Frameshift Mutation, MESH: Vibrio, Genes, Regulator, Animals, LETHALITY, MESH: Animals, MESH : Genes, Regulator, METALLOPROTEASE, MESH : France, Frameshift Mutation, MESH: Phylogeny, MORTALITIES, MESH: Protein Kinases, Phylogeny, Vibrio, CRASSOSTREA-GIGAS, MESH : Ostreidae, [ SDV ] Life Sciences [q-bio], CONSTRUCTION, ACL, MESH: Genomics, MESH : Genomics, ALGORITHMS, MESH : Virulence, MESH: Frameshift Mutation, MESH : Phylogeny, Genomics, Ostreidae, FAMILY, MESH: France, VIRULENCE, MESH : Animals, France, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Protein Kinases, MESH : Vibrio
Abstract: International audience; Oyster diseases caused by pathogenic vibrios pose a major challenge to the sustainability of oyster farming. In France, since 2012 a disease affecting specifically adult oysters has been associated with the presence of Vibrio aestuarianus. Here, by combining genome comparison, phylogenetic analyses and high-throughput infections of strains isolated before or during the recent outbreaks, we show that virulent strains cluster into two V. aestuarianus lineages independently of the sampling dates. The bacterial lethal dose was not different between strains isolated before or after 2012. Hence, the emergence of a new highly virulent clonal strain is unlikely. Each lineage comprises nearly identical strains, the majority of them being virulent, suggesting that within these phylogenetically coherent virulent lineages a few strains have lost their pathogenicity. Comparative genomics allowed the identification of a single frameshift in a non-virulent strain. This mutation affects the varS gene that codes for a signal transduction histidine-protein kinase. Genetic analyses confirmed that varS is necessary for infection of oysters and for a secreted metalloprotease expression. For the first time in a Vibrio species, we show here that VarS is a key factor of pathogenicity.
Published: 2015

9. Special section on Molecular biology of Archaea

Author: David Prangishvili, Simonetta Gribaldo, Bruno Franzetti, Patrick Forterre, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biologie Cellulaire des Archées (ARCHEE), Département Microbiologie (Dpt Microbio), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Biologie Moléculaire du Gène chez les Extrêmophiles ( BMGE ), Institut de biologie structurale ( IBS - UMR 5075 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Biologie Cellulaire des Archées ( ARCHEE ), Département Microbiologie ( Dpt Microbio ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), and Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 )
Subjects: 0303 health sciences, [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], 030302 biochemistry & molecular biology, MESH : Phylogeny, General Medicine, Biology, biology.organism_classification, Archaea, Biochemistry, MESH : Archaea, 03 medical and health sciences, Paleontology, Phylogenetics, Evolutionary biology, MESH: Archaea, Special section, MESH: Phylogeny, Phylogeny, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: International audience
Published: 2015

10. Predominance and Circulation of Enteric Viruses in the Region of Greater Cairo, Egypt

Author: Alexis de Rougemont, Mohamed A. Ali, Gaël Belliot, Hala G. Elnady, Pierre Pothier, A.H. Kamel, Laboratoire Interactions Muqueuses Agents Transmissibles ( LIMA ), Université de Bourgogne ( UB ), Laboratoire de sérologie-virologie (CHU de Dijon), and Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon )
Subjects: Rotavirus, MESH : Molecular Sequence Data, Urban Population, viruses, MESH : Capsid Proteins, MESH : Genotype, Comorbidity, MESH : Child, Preschool, medicine.disease_cause, Feces, fluids and secretions, MESH : Child, Genotype, Cluster Analysis, MESH : Enteritis, Child, Phylogeny, MESH : Viruses, education.field_of_study, virus diseases, MESH : Infant, Enteritis, Virus Diseases, Child, Preschool, Viruses, MESH : Urban Population, MESH : Comorbidity, Egypt, MESH : Mamastrovirus, Microbiology (medical), Adolescent, MESH : Rotavirus, Molecular Sequence Data, Population, Biology, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Virus, Adenoviridae, Microbiology, Astrovirus, Virology, MESH : Adolescent, medicine, Humans, MESH : Cluster Analysis, Typing, MESH : Adenoviridae, education, MESH : Norovirus, Norovirus, MESH : Humans, Infant, MESH : Phylogeny, Sequence Analysis, DNA, MESH : Feces, MESH : Virus Diseases, medicine.disease, biology.organism_classification, MESH : Egypt, Capsid Proteins, Mamastrovirus, MESH : Sequence Analysis, DNA
Abstract: The circulation of enteric viruses among the population of Cairo, Egypt, between March 2006 and February 2007 was studied. At least one virus was detected in 50% of fecal samples, 57.4% of which were positive for rotavirus, 26% for norovirus, 10.4% for adenovirus, and 1.7% for astrovirus. Over 10% of infections were mixed infections. Rotavirus typing showed that G1P[8] and G2P[4] were predominant but that the unusual G12P[4] and G12P[6] reassortants were also present. Among the noroviruses, half belonged to the predominant GGII.4 cluster. The phylogenetic analysis of the capsid gene suggested that GGII.4 strains from Cairo were similar to those circulating elsewhere. It also showed the emergence of new GGII.4 variants that were not associated with any previously known GGII.4 isolate. Further studies are required to assess the disease burden of enteric viruses in Egypt and the impact of atypical strains.
Published: 2009

11. EFD Is an ERF Transcription Factor Involved in the Control of Nodule Number and Differentiation inMedicago truncatula

Author: Françoise de Billy, Andreas Niebel, Tatiana Vernié, Christian Rogers, Florian Frugier, Giles E. D. Oldroyd, Julie Plet, Jean-Philippe Combier, Pascal Gamas, Sandra Moreau, Laboratoire des interactions plantes micro-organismes ( LIPMO ), Institut National de la Recherche Agronomique ( INRA ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: MESH: Signal Transduction, 0106 biological sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Cytokinins, MESH : Molecular Sequence Data, MESH : Transcription Factors, MESH: Feedback, Physiological, Regulator, MESH : Gene Deletion, Plant Science, Plant Root Nodulation, 01 natural sciences, Nod factor, chemistry.chemical_compound, MESH : Nitrogen Fixation, MESH: Phylogeny, MESH: Medicago truncatula, Research Articles, Phylogeny, Plant Proteins, Regulator gene, Feedback, Physiological, MESH : Cell Nucleus, 0303 health sciences, MESH: Plant Proteins, food and beverages, MESH: Transcription Factors, MESH : Feedback, Physiological, MESH : Cytokinins, Medicago truncatula, Cell biology, MESH: Root Nodules, Plant, Multigene Family, Cytokinin, RNA Interference, MESH: Cytokinins, Root Nodules, Plant, MESH: Plant Root Nodulation, Signal Transduction, MESH: Cell Nucleus, MESH: Ethylenes, Molecular Sequence Data, MESH: RNA Interference, MESH : Multigene Family, Biology, MESH: Nitrogen Fixation, MESH: Gene Expression Profiling, MESH : Root Nodules, Plant, 03 medical and health sciences, Nitrogen Fixation, MESH : Plant Proteins, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Transcription factor, 030304 developmental biology, Cell Nucleus, MESH : Signal Transduction, MESH: Molecular Sequence Data, Gene Expression Profiling, MESH : Gene Expression Profiling, MESH : Medicago truncatula, fungi, MESH : Phylogeny, MESH : Sinorhizobium meliloti, Cell Biology, Ethylenes, Meristem, biology.organism_classification, Response regulator, chemistry, MESH: Gene Deletion, MESH: Multigene Family, MESH : RNA Interference, MESH: Sinorhizobium meliloti, MESH : Plant Root Nodulation, Gene Deletion, MESH : Ethylenes, Sinorhizobium meliloti, Transcription Factors, 010606 plant biology & botany
Abstract: Mechanisms regulating legume root nodule development are still poorly understood, and very few regulatory genes have been cloned and characterized. Here, we describe EFD (for ethylene response factor required for nodule differentiation), a gene that is upregulated during nodulation in Medicago truncatula. The EFD transcription factor belongs to the ethylene response factor (ERF) group V, which contains ERN1, 2, and 3, three ERFs involved in Nod factor signaling. The role of EFD in the regulation of nodulation was examined through the characterization of a null deletion mutant (efd-1), RNA interference, and overexpression studies. These studies revealed that EFD is a negative regulator of root nodulation and infection by Rhizobium and that EFD is required for the formation of functional nitrogen-fixing nodules. EFD appears to be involved in the plant and bacteroid differentiation processes taking place beneath the nodule meristem. We also showed that EFD activated Mt RR4, a cytokinin primary response gene that encodes a type-A response regulator. We propose that EFD induction of Mt RR4 leads to the inhibition of cytokinin signaling, with two consequences: the suppression of new nodule initiation and the activation of differentiation as cells leave the nodule meristem. Our work thus reveals a key regulator linking early and late stages of nodulation and suggests that the regulation of the cytokinin pathway is important both for nodule initiation and development.
Published: 2008

12. Genetic diversity of Echinococcus multilocularis on a local scale

Author: Jenny Knapp, Bruno Gottstein, Patrick Giraudoux, M-H Guislain, Francis Raoul, Jean-Mathieu Bart, Renaud Piarroux, Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Institute of Parasitology, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)
Subjects: MESH : Molecular Sequence Data, Range (biology), Foxes, MESH: Base Sequence, MESH : Echinococcus multilocularis, MESH : Microsatellite Repeats, MESH: Variation (Genetics), 0302 clinical medicine, MESH : Genes, Helminth, Parasite hosting, MESH: Animals, MESH : Female, 610 Medicine & health, MESH: Phylogeny, Genes, Helminth, Phylogeny, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, 630 Agriculture, MESH : Variation (Genetics), Ecology, Infectious Diseases, Microsatellite, Female, France, Microbiology (medical), Molecular Sequence Data, 030231 tropical medicine, Zoology, Biology, Echinococcus multilocularis, MESH: Sequence Homology, Nucleic Acid, Microbiology, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, 03 medical and health sciences, Phylogenetics, Sequence Homology, Nucleic Acid, parasitic diseases, Genetic variation, Genetics, Animals, Helminths, MESH : Sequence Homology, Nucleic Acid, MESH : France, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH: Echinococcus multilocularis, MESH : Foxes, Genetic diversity, MESH: Foxes, MESH: Molecular Sequence Data, Base Sequence, Genetic Variation, MESH : Phylogeny, biology.organism_classification, MESH: France, MESH : Base Sequence, MESH: Microsatellite Repeats, MESH : Animals, MESH: Female, Microsatellite Repeats, MESH: Genes, Helminth
Abstract: International audience; Echinococcus multilocularis is the causative agent of human Alveolar Echinococcosis (AE), and it is one of the most lethal zoonotic infections in the Northern Hemisphere. In France, the eastern and central regions are endemic areas; Franche-Comt?Lorraine and Auvergne are particularly contaminated. Recently, several human cases were recorded in the French Ardennes area, a region adjacent to the western border of the E. multilocularis range in France. A previous study in this focus described a prevalence of over 50% of the parasite in red foxes. The present study investigated the genetic diversity of adult worms collected from foxes in a 900km(2) area in the Ardennes. Instead of a conventional mitochondrial target (ATP6), two microsatellite targets (EmsB and NAK1) were used. A total of 140 adult worms isolated from 25 red foxes were genotyped. After hierarchical clustering analyses, the EmsB target enabled us to distinguish two main assemblages, each divided into sub-groups, yielding the differentiation of six clusters or assemblage profiles. Thirteen foxes (52% of the foxes) each harbored worms from at least two different assemblage profiles, suggesting they had become infected by several sources. Using the NAK1 target, we identified 3 alleles, two found in association with the two EmsB assemblages. With the NAK1 target, we investigated the parasite breeding system and the possible causes of genetic diversification. Only one fox harbored hybrid worms, indicative of a possible (and rare) occurrence of recombination, although multiple infections have been observed in foxes. These results confirm the usefulness of microsatellite targets for assessing genetic polymorphism in a geographically restricted local range.
Published: 2008

13. Environmental microbiology as a mosaic of explored ecosystems and issues

Author: Faure , Denis, Bonin , Patricia, Duran , Robert, Bormans , Myriam, Couée , Ivan, Francez , Andre-Jean, Quaiser , Achim, Vandenkoornhuyse , Philippe, Intéractions Plantes-Bactéries ( PBI ), Département Microbiologie ( Dpt Microbio ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Ecosystèmes, biodiversité, évolution [Rennes] ( ECOBIO ), Université de Rennes 1 ( UR1 ), and Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -INEE-Observatoire des Sciences de l'Univers de Rennes ( OSUR ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: MESH : Viruses, Environmental microbiology, MESH : Microbial Interactions, [ SDV ] Life Sciences [q-bio], Microbial ecosystems, MESH : Humans, Critical zone, MESH : Phylogeny, MESH : Archaea, MESH : Environmental Microbiology, Microbial ecology, MESH : Ecosystem, MESH : Bacteria, MESH : Animals, human activities, MESH : Environmental Pollutants
Abstract: International audience; Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium's efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.
Published: 2015

14. An Atypical Outbreak of Food-Borne Botulism Due to Clostridium botulinum Types B and E from Ham

Author: Christelle Mazuet, Christiane Bouchier, Jean Sautereau, Christine Legeay, Philippe Bouvet, Michel R. Popoff, Bactéries anaérobies et Toxines, Institut Pasteur [Paris], Génomique (Plate-Forme), High-throughput sequencing has been performed on the Genomics Platform, a member of the France Génomique Consortium (ANR10-INBS-09-08)., We thank Benoit Jaulhac, Laboratoire de Bactériologie, Hôpitaux Universitaires, Strasbourg, France, for his assistance., ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique ( 2010 ), Génomique (Plate-Forme) - Genomics Platform, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), and Institut Pasteur [Paris] (IP)
Subjects: Male, MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, MESH : Multilocus Sequence Typing, Sequence Homology, MESH : Genotype, Case Reports, medicine.disease_cause, MESH: Genome, Bacterial, Disease Outbreaks, MESH: Genotype, Cluster Analysis, MESH : DNA, Bacterial, Botulism, MESH : Female, MESH: Sequence Homology, MESH: Clostridium botulinum type A, MESH: Disease Outbreaks, MESH: Phylogeny, MESH: Clostridium botulinum type F, Phylogeny, 0303 health sciences, MESH: Middle Aged, Middle Aged, [ SDV.TOX.TCA ] Life Sciences [q-bio]/Toxicology/Toxicology and food chain, MESH: Multilocus Sequence Typing, MESH : Botulism, Female, Microbiology (medical), Clostridium botulinum type F, DNA, Bacterial, Clostridium botulinum type E, Genotype, Clostridium botulinum type A, MESH : Male, Molecular Sequence Data, MESH : Genome, Bacterial, MESH: Botulism, [SDV.TOX.TCA]Life Sciences [q-bio]/Toxicology/Toxicology and food chain, Biology, Microbiology, 03 medical and health sciences, MESH : Sequence Homology, medicine, Food microbiology, Humans, MESH : Cluster Analysis, MESH : Middle Aged, MESH : Disease Outbreaks, MESH: Food Microbiology, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, MESH: Molecular Sequence Data, 030306 microbiology, MESH : Humans, Outbreak, MESH : Phylogeny, Sequence Analysis, DNA, MESH : Food Microbiology, medicine.disease, Virology, MESH: Cluster Analysis, MESH: DNA, Bacterial, MESH: Male, MESH : Clostridium botulinum type F, Food Microbiology, Multilocus sequence typing, Clostridium botulinum, [ SDV.GEN ] Life Sciences [q-bio]/Genetics, MESH: Female, Genome, Bacterial, MESH : Clostridium botulinum type A, Multilocus Sequence Typing, MESH : Sequence Analysis, DNA
Abstract: An outbreak of human botulism was due to consumption of ham containing botulinum neurotoxins B and E. A Clostridium botulinum type E strain isolated from ham was assigned to a new subtype (E12) based on bont / E gene sequencing and belongs to a new multilocus sequence subtype, as analyzed by whole-genome sequencing.
Published: 2015

15. Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders 'Frankiales' and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov

Author: Vincent Daubin, Philippe Normand, Danis Abrouk, Alison M. Berry, Isaac Gifford, Arnab Sen, Assam University, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Uniformed Services University of the Health Sciences (USUHS), Department of Plant Sciences [Davis, CA], University of California [Davis] (UC Davis), University of California-University of California, Institute of Microelectronics (NCSR), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Armed Forces Radiobiology Research Institute, University of California [Davis] ( UC Davis ), Institute of Microelectronics ( NCSR ), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Sciences [Univ California Davis] (Plant - UC Davis), and University of California (UC)-University of California (UC)
Subjects: DNA, Bacterial, MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, [SDV]Life Sciences [q-bio], Molecular Sequence Data, MESH : Genome, Bacterial, Concatenation, MESH : Actinobacteria, MESH: Genome, Bacterial, Microbiology, Genome, Tree (descriptive set theory), MESH : RNA, Ribosomal, 23S, Phylogenetics, RNA, Ribosomal, 16S, Botany, MESH : DNA, Bacterial, MESH: Phylogeny, Phylogeny, Ecology, Evolution, Behavior and Systematics, Geodermatophilaceae, MESH: Molecular Sequence Data, [ SDV ] Life Sciences [q-bio], Phylogenetic tree, biology, MESH : Phylogeny, Sequence Analysis, DNA, General Medicine, biology.organism_classification, MESH: RNA, Ribosomal, 23S, MESH: DNA, Bacterial, Actinobacteria, MESH : RNA, Ribosomal, 16S, Nakamurellaceae, Kocuria, MESH: RNA, Ribosomal, 16S, RNA, Ribosomal, 23S, Evolutionary biology, Genome, Bacterial, MESH : Sequence Analysis, DNA, MESH: Actinobacteria
Abstract: The phylogeny of the class Actinobacteria remains controversial, essentially because it is very sensitive to the choice of dataset and phylogenetic methods. We used a test proposed recently, based on complete genome data, which chooses among candidate species phylogenies based on the number of lateral gene transfers (LGT) needed to explain the diversity of histories among gene trees for a set of genomes. We used 100 completely sequenced genomes representing 35 families and 17 orders of the class Actinobacteria and evaluated eight different hypotheses for their phylogeny, including one based on a concatenate of 54 conserved proteins present in single copy in all these genomes, trees based on 16S and 23S rRNA gene sequences or their concatenation, and a tree based on the concatenation of MLSA genes (encoding AtpI, GyrA, FtsZ, SecA and DnaK). We used Prunier to infer the number of LGT in 579 proteins (different from those used to build the concatenated tree) present in at least 70 species, using the different hypothetical species trees as references. The best tree, with the lowest number of lateral transfers, was the one based on the concatenation of 54 proteins. In that tree, the orders Bifidobacteriales , Coriobacteriales , ‘Coryneb acteriales’, ‘Micromonosporales’, ‘Propionibacteriales’, ‘Pseudonocardiales’, Streptomycetales and ‘Streptosporangiales’ were recovered while the orders ‘Frankiales’ and Micrococcales were not. It is thus proposed that the order ‘Frankiales’, which has an effectively but not validly published name, be split into Frankiales ord. nov. (type family Frankiaceae ), Geodermatophilales ord. nov. ( Geodermatophilaceae ), Acidothermales ord. nov. ( Acidothermaceae ) and Nakamurellales ord. nov. ( Nakamurellaceae ). The order Micrococcales should also be split into Micrococcales (genera Kocuria , Rothia , Micrococcus , Arthrobacter , Tropheryma , Microbacterium , Leifsonia and Clavibacter ), Cellulomonales ( Beutenbergia , Cellulomonas , Xylanimonas , Jonesia and Sanguibacter ) and Brachybacteriales ( Brachybacterium ) but the formal proposal for this will have to wait until more genomes become available for a significant proportion of strains in this order.
Published: 2014

16. Conserved structure and domain organization among bacterial Slc26 transporters

Author: Martine Moulin, Arnaud Javelle, Heather E. Findlay, Emma L R Compton, David Norman, Michael Haertlein, Kimberly Page, Ulrich Zachariae, Frank Gabel, Lujan Center for Neutron Scattering, LANL, Los Alamos National Laboratory ( LANL ), School of Biochemistry, University of Bristol [Bristol], Unité de recherche Géosciences Marines (Ifremer) ( GM ), Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Institut de biologie structurale ( IBS - UMR 5075 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Los Alamos National Laboratory (LANL), Unité de recherche Géosciences Marines (Ifremer) (GM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Thomas, Frank, Géosciences Marines (GM), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: Models, Molecular, MESH : Molecular Sequence Data, MESH: Yersinia enterocolitica, Biochemistry, Conserved sequence, MESH: Protein Structure, Tertiary, 0302 clinical medicine, MESH : Scattering, Small Angle, MESH : Protein Stability, MESH : Bacterial Proteins, MESH: Phylogeny, MESH: Bacterial Proteins, Conserved Sequence, Phylogeny, 0303 health sciences, MESH: Conserved Sequence, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Protein Stability, MESH: Anion Transport Proteins, MESH : Yersinia enterocolitica, Transmembrane protein, Transport protein, MESH : Protein Structure, Tertiary, MESH: Models, Molecular, Protein family, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], MESH : Models, Molecular, Protein domain, Anion Transport Proteins, Molecular Sequence Data, Biology, RS, 03 medical and health sciences, Bacterial Proteins, Phylogenetics, MESH : Conserved Sequence, MESH: Protein Stability, Scattering, Small Angle, Humans, MESH : Bacteria, Homology modeling, Molecular Biology, MESH: Scattering, Small Angle, 030304 developmental biology, Yersinia enterocolitica, MESH: Humans, MESH: Molecular Sequence Data, Bacteria, MESH : Humans, MESH : Phylogeny, Cell Biology, Protein Structure, Tertiary, MESH: Bacteria, MESH : Anion Transport Proteins, 030217 neurology & neurosurgery, Function (biology), [ SDV.BBM.BS ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract: International audience; The Slc26 proteins are a ubiquitous superfamily of anion transporters conserved from bacteria to humans, among which four have been identified as human disease genes. Our functional knowledge of this protein family has increased but limited structural information is available. These proteins contain a transmembrane (TM) domain and a C-terminal cytoplasmic sulfate transporter and anti-sigma factor (STAS) domain. In a fundamental step towards understanding the structure/function relationships within the family we have used small-angle neutron scattering (SANS) on two distantly related bacterial homologues to show that there is a common, dimeric and structural architecture among Slc26A transporters. Pulsed electron-electron double resonance (PELDOR) spectroscopy supports the dimeric SANS-derived model. Using chimaeric/truncated proteins we have determined the domain organization: the STAS domains project away from the TM core and are essential for protein stability. We use the SANS-generated envelopes to assess a homology model of the TM core.
Published: 2014

17. Candida albicans is not always the preferential yeast colonizing humans: a study in Wayampi Amerindians

Author: Mouna Ben Soltana, Laure Diancourt, Antoine Andremont, Paul-Louis Woerther, Sophie Abélanet, Félix Djossou, Emmanuelle Permal, Cécile Angebault, Christiane Bouchier, Christophe d'Enfert, François Catzeflis, Marie-Elisabeth Bougnoux, CHU Necker - Enfants Malades [AP-HP], Université Paris Descartes - Paris 5 (UPD5), Laboratoire de bactériologie, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris]-Université Paris Diderot - Paris 7 (UPD7), Biologie et Pathogénicité fongiques, Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris], Unité des Maladies Infectieuses et Tropicales [Cayenne, Guyanne Française], Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Génotypage des Pathogènes et Santé Publique (Plate-forme) (PF8), Institut Pasteur [Paris], Génomique (Plate-Forme), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), The ERAES project was supported in part by the Agence Française de Sécurité Sanitaire de l’Environnement et du Travail(contracts ES-05-01 and EST-09-21), the Agence Nationale pour la Recherche (contract 05-9-114), the Institut National de la Santé et de la Recherche Médicale (INSERM, contracts C06-18 and C10-19), the Centre National de Référence' Résistance bactérienne dans les flores commensales, 'the Fondation pour la Recherche Médicale (grants FDM20090615761 andFDM20100619023 to C. A.), and the French government ’ s Investissement d'Avenir program, Laboratoire d’Excellence'Integrative Biology of Emerging Infectious Diseases' (grant ANR-10-LABX-62-IBEID), ANR: the Agence Nationale pour la Recher- che (contract 05-9-114),the Agence Nationale pour la Recher- che (contract 05-9-114),05-9-114 the Agence Nationale pour la Recher- che (contract 05-9-114), ANR-10-LABX-62-IBEID,IBEID,Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010), Assistance publique - Hôpitaux de Paris (AP-HP) - AP-HP - Hôpital Bichat - Claude Bernard [Paris] - Université Paris Diderot - Paris 7 (UPD7), Institut National de la Recherche Agronomique (INRA) - Institut Pasteur [Paris], Institut des Sciences de l'Evolution de Montpellier (ISEM), Université de Montpellier (UM) - Institut de recherche pour le développement [IRD] : UR226 - Centre National de la Recherche Scientifique (CNRS), ANR : the Agence Nationale pour la Recher- che (contract 05-9-114), the Agence Nationale pour la Recher- che (contract 05-9-114), 05-9-114 the Agence Nationale pour la Recher- che (contract 05-9-114), ANR-10-LABX-62-IBEID, IBEID, Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7), Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), Génomique (Plate-Forme) - Genomics Platform, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), 05-9-114 the Agence Nationale pour la Recher- che (contract 05-9-114) the Agence Nationale pour la Recher- che (contract 05-9-114), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Biologie et Pathogénicité fongiques (BPF), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Subjects: Male, MESH : Prevalence, MESH : Multilocus Sequence Typing, MESH : Aged, MESH : Candidiasis, MESH: Aged, 80 and over, Prevalence, Immunology and Allergy, Colonization, MESH : Female, MESH: Animals, Candida albicans, MESH: Phylogeny, Phylogeny, MESH: Evolution, Molecular, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Aged, 80 and over, 2. Zero hunger, MESH : Intestines, MESH: Aged, 0303 health sciences, MESH: Middle Aged, biology, MESH: Yeasts, Candidiasis, intestinal colonization, Middle Aged, MESH : Adult, Corpus albicans, MESH: Candidiasis, French Guiana, Intestines, Infectious Diseases, MESH : Carrier State, MESH: Multilocus Sequence Typing, whole-genome sequencing, MESH: Young Adult, Carrier State, MESH: Genome, Fungal, Female, Genome, Fungal, MESH: Carrier State, MLST, MESH: Intestines, Adult, MESH : French Guiana, Adolescent, Human intestine, MESH : Candida albicans, MESH : Male, Saccharomyces cerevisiae, MESH : Young Adult, yeasts, Microbiology, Evolution, Molecular, Young Adult, 03 medical and health sciences, MESH: Mycoses, Candida krusei, MESH : Adolescent, MESH: French Guiana, Animals, Humans, MESH : Middle Aged, MESH : Evolution, Molecular, MESH : Aged, 80 and over, MESH: Prevalence, Aged, 030304 developmental biology, MESH : Mycoses, MESH: Adolescent, MESH : Yeasts, MESH: Humans, 030306 microbiology, amerindians, MESH : Genome, Fungal, MESH: Candida albicans, MESH : Humans, MESH : Phylogeny, MESH: Adult, biology.organism_classification, [SDV.MP.MYC] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Yeast, MESH: Male, Carriage, Mycoses, candida albicans, MESH : Animals, MESH: Female, Multilocus Sequence Typing
Abstract: Chantier qualité GA; International audience; In industrialized countries Candida albicans is considered the predominant commensal yeast of the human intestine, with approximately 40% prevalence in healthy adults. We discovered a highly original colonization pattern that challenges this current perception by studying in a 4- year interval a cohort of 151 Amerindians living in a remote community (French Guiana), and animals from their environment. The prevalence of C. albicans was persistently low (3% and 7% of yeast carriers). By contrast, Candida krusei and Saccharomyces cerevisiae were detected in over 30% of carriers. We showed that C. krusei and S. cerevisiae carriage was of food or environmental origin, whereas C. albicans carriage was associated with specific risk factors (being female and living in a crowded household). We also showed using whole-genome sequence comparison that C. albicans strains can persist in the intestinal tract of a healthy individual over a 4-year period.
Published: 2013

18. Vallitalea guaymasensis gen. nov., sp nov., isolated from marine sediment

Author: Moktar Hamdi, Anne Godfroy, Marie-Laure Fardeau, Anne Postec, Bernard Ollivier, Raja Lakhal, Nathalie Pradel, Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d' Ecologie & Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie [Tunis] ( INSAT ), Laboratoire de microbiologie des environnements extrêmophiles ( LM2E ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Brest ( UBO ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Institut National des Sciences Appliquées et de Technologie [Tunis] (INSAT), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Arabinose, Geologic Sediments, MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, [SDV]Life Sciences [q-bio], DIVERSITY, Cellobiose, Xylose, chemistry.chemical_compound, RNA, Ribosomal, 16S, WATER, MESH : DNA, Bacterial, Raffinose, MESH: Phylogeny, PHYLOGENIES, MESH : Fatty Acids, Phospholipids, Phylogeny, MESH: Bacteria, Anaerobic, Base Composition, 0303 health sciences, Strain (chemistry), Fatty Acids, General Medicine, 6. Clean water, Bacterial Typing Techniques, MESH: Fatty Acids, MESH: RNA, Ribosomal, 16S, ALIGNMENT, THERMOPHILIC BACTERIUM, Biochemistry, SULFATE-REDUCING BACTERIA, FATTY-ACIDS, DNA, Bacterial, Molecular Sequence Data, MESH : Pacific Ocean, Biology, Microbiology, MESH : Geologic Sediments, MESH: Bacterial Typing Techniques, MESH : Phospholipids, MESH : Base Composition, Bacteria, Anaerobic, 03 medical and health sciences, MESH: Base Composition, MESH : Bacteria, Anaerobic, DEOXYRIBONUCLEIC-ACID, MESH: Pacific Ocean, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, BASIN, MESH: Phospholipids, Pacific Ocean, MESH: Molecular Sequence Data, [ SDV ] Life Sciences [q-bio], 030306 microbiology, MESH : Phylogeny, Sequence Analysis, DNA, Maltose, MESH: Geologic Sediments, MESH: DNA, Bacterial, MESH : RNA, Ribosomal, 16S, chemistry, Galactose, Fermentation, MESH : Bacterial Typing Techniques, MESH : Sequence Analysis, DNA
Abstract: A novel obligately anaerobic, non-spore-forming, rod-shaped mesophilic, halophilic, Gram-stain-negative bacterium, was isolated from sediments of Guaymas Basin. The strain, designated Ra1766G1T, grew at 20–40 °C (optimum, 30–35 °C) and at pH 6.0–8.0 (optimum, pH 6.5–7.5). It required 0.5–7.5 % NaCl (optimum, 2–3 %) for growth. Sulfate, thiosulfate, elemental sulfur, sulfite, fumarate, nitrate and nitrite were not used as terminal electron acceptors. Strain Ra1766G1T used cellobiose, glucose, mannose, maltose, arabinose, raffinose, galactose, ribose, sucrose, pyruvate and xylose as electron donors. The main fermentation product from glucose metabolism was acetate. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso DMA-C15 : 0 and C16 : 0. The main polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, iso-DMA-C15 : 0 glycolipids and phospholipids. The G+C content of the genomic DNA was 31.2 mol%. The closest phylogenetic relatives of strain Ra1766G1T were Natranaerovirga pectinivora AP3T (92.4 % 16S rRNA gene sequence similarity), Natranaerovirga hydrolytica APP2T(90.2 %) and Defluviitalea saccharophila 6LT2T (88.9 %). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766G1T represents a novel species of a new genus for which the name Vallitalea guaymasensis is proposed. The type strain of the type species is Ra1766G1T ( = DSM 24848T = JCM17997T).
Published: 2013

19. Prevalence, genomic and metabolic profiles of Acinetobacter and Asaia associated with field-caught Aedes albopictus from Madagascar

Author: Eléonore Hellard, Fara Nantenaina Raharimalala, Patrick Mavingui, Guillaume Minard, Claire Valiente Moro, Pierre Ravelonandro, Florence Hélène Tran, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Ecoépidémiologie évolutionniste, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre National de Recherche sur l'Environnement (CNRE), Centre National de la Recherche Scientifique, La Region Rhone-Alpes, [FRB-CD-AOOI-07-10], Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre National de Recherche sur l'Environnement, Centre National de recherche sur l'environnement, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: Male, MESH: Sequence Analysis, DNA, MESH : Acetobacteraceae, MESH : Genome Size, [SDV]Life Sciences [q-bio], INSECTS, DIVERSITY, Applied Microbiology and Biotechnology, genomic diversity, MESH: Madagascar, MESH: Genome Size, Genome Size, Aedes, RNA, Ribosomal, 16S, MESH : DNA, Bacterial, MESH : Female, WOLBACHIA, MESH: Animals, MESH: Genetic Variation, MESH: Phylogeny, Phylogeny, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Ecology, biology, Acinetobacter, MESH : Metabolome, MESH: Genomics, Genomics, MESH: Aedes, symbiosis, Electrophoresis, Gel, Pulsed-Field, MESH: RNA, Ribosomal, 16S, MESH: Electrophoresis, Gel, Pulsed-Field, MESH: Acinetobacter, CALCOACETICUS, Acetobacteraceae, Metabolome, Wolbachia, Female, MESH: Metabolome, Plasmids, DNA, Bacterial, Aedes albopictus, DENGUE, MESH : Acinetobacter, MESH : Madagascar, MESH : Male, ACETIC-ACBACTERIA, asian tiger mosquito, Microbiology, Bacterial genetics, 03 medical and health sciences, AEGYPTI, MESH : Genetic Variation, MESH: Plasmids, parasitic diseases, Pulsed-field gel electrophoresis, Madagascar, Animals, Genome size, acetic bacteria, MOSQUITO VECTOR, metabolic repertoire, MESH : Aedes, MESH : Electrophoresis, Gel, Pulsed-Field, 030304 developmental biology, [ SDV ] Life Sciences [q-bio], 030306 microbiology, MESH : Genomics, fungi, MESH : Phylogeny, Genetic Variation, Sequence Analysis, DNA, MESH: Acetobacteraceae, DEGRADATION, biology.organism_classification, 16S ribosomal RNA, MESH: DNA, Bacterial, MESH: Male, MESH : RNA, Ribosomal, 16S, MESH : Plasmids, Vector (epidemiology), MESH : Animals, MESH: Female, PLASMID, MESH : Sequence Analysis, DNA
Abstract: International audience; The presence of cultivable bacteria Acinetobacter and Asaia was recently demonstrated in the mosquito vector Aedes albopictus. However, it is not known how prevalent these bacteria are in field populations. Here, the presence of these bacteria in Ae. albopictus populations from Madagascar was diagnosed by amplification of 16S rRNA gene fragments. Both genera were detected at relatively high frequencies, 46% for Asaia and 74% for Acinetobacter. The prevalence of Acinetobacter correlated significantly with mosquito gender, and the prevalence of Asaia with the interaction between mosquito gender and the sampling site. For each bacterial genus, more male than female mosquitoes were infected. Using pulse field gel electrophoresis, no significant difference in genome size was found between Acinetobacter isolates from mosquitoes compared with free-living Acinetobacter. However, a great diversity was observed in plasmid numbers (from 1 to 12) and sizes (from < 8 to 690 kb). Mosquito isolates utilized fewer substrates than free-living isolates, but some substrates known as blood or plant components were specifically utilized by mosquito isolates. Therefore it is likely that a specific subpopulation of Acinetobacter is selected by Ae. albopictus. Overall, this study emphasizes the need to gain a global view on the bacterial partners in mosquito vectors.
Published: 2013

20. Identification of novel paramyxoviruses in insectivorous bats of the Southwest Indian Ocean

Author: Sarah Temmam, Jean-Michel Heraud, Koussay Dellagi, Beza Ramasindrazana, Hervé Pascalis, Steven M. Goodman, Julia Guillebaud, Julien Chotte, Erwan Lagadec, Camille Lebarbenchon, Xavier de Lamballerie, David A. Wilkinson, Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien (CRVOI), Université de La Réunion (UR), Cyclotron Réunion Océan Indien (CYROI), Université de La Réunion (UR)-Centre Hospitalier Universitaire de La Réunion (CHU La Réunion), Institut de Recherche pour le Développement (IRD), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Association Vahatra, Association Vahatra [Antananarivo, Madagascar], Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), Emergence des Pathologies Virales (EPV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM), Field Museum of Natural History [Chicago, USA], D.A. Wilkinson and C. Lebarbenchon post-doctoral fellowships were funded by 'RUN-Emerge: European project funded by European Commission under FP7 program'., Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Centre de Recherche et de Veille sur les Maladies Émergentes dans l'Océan Indien ( CRVOI ), Université de la Réunion ( UR ), Cyclotron Réunion Océan Indien ( CYROI ), Université de la Réunion ( UR ) -Centre Hospitalier Universitaire de La Réunion ( CHU La Réunion ), Institut de Recherche pour le Développement ( IRD ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Station de la Bretagne ( CIRAD ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ), Institut Pasteur de Madagascar-Réseau International des Instituts Pasteur ( RIIP ), Emergence des Pathologies Virales ( EPV ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Assistance Publique - Hôpitaux de Marseille ( APHM ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Field Museum of Natural History, Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Cancer Research, Lineage (evolution), viruses, [SDV]Life Sciences [q-bio], MESH: Indian Ocean, Bats viruses, Paramyxovirus, Cytopathogenic Effect, Viral, Chiroptera, Chlorocebus aethiops, MESH: Animals, MESH : Viral Proteins, MESH: Phylogeny, Indian Ocean, Phylogeny, MESH : Paramyxovirinae, 0303 health sciences, Paramyxoviridae Infections, Phylogenetic tree, Ecology, MESH: Chiroptera, MESH : Indian Ocean, Infectious Diseases, Paramyxovirinae, Mauritius, MESH: Virion, Identification (biology), MESH : Chiroptera, animal structures, Zoology, MESH: Vero Cells, Biology, 03 medical and health sciences, Viral Proteins, MESH: Paramyxovirinae, Phylogenetics, Virology, MESH : Virion, Madagascar, Animals, Union of Comoros, Vero Cells, Viral isolation, 030304 developmental biology, [ SDV ] Life Sciences [q-bio], 030306 microbiology, Virion, MESH : Phylogeny, Insectivore, MESH : Paramyxoviridae Infections, MESH: Cytopathogenic Effect, Viral, MESH: Cercopithecus aethiops, MESH: Viral Proteins, Indian ocean, Paramyxovirus infection, MESH : Cytopathogenic Effect, Viral, MESH: Paramyxoviridae Infections, MESH : Animals, MESH : Cercopithecus aethiops, MESH : Vero Cells
Abstract: International audience; Bats are reservoirs for many emerging zoonotic viruses. In this study, we screened 197 animals from 15 different bat species of the Southwest Indian Ocean for paramyxovirus infection and identified paramyxoviruses in five insectivorous bat-species from the Union of the Comoros (3/66), Mauritius (1/55) and Madagascar (4/76). Viral isolation was possible via cell culture and phylogenetic analysis revealed these viruses clustered in a Morbillivirus-related lineage, with relatively high nucleotide sequence similarity to other recently discovered insectivorous-bat paramyxoviruses but distinct from those known to circulate in frugivorous bats.
Published: 2012

21. Using a Multi-Locus Microsatellite Typing method improved phylogenetic distribution of Candida albicans isolates but failed to demonstrate association of some genotype with the commensal or clinical origin of the isolates

Author: Marie-Elisabeth Bougnoux, Christophe d'Enfert, Frédéric Dalle, Ahmed Jebrane, Alain Bonnin, Catherine Labruère, Coralie L'Ollivier, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire de parasitologie mycologie (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Institut de Mathématiques de Bourgogne [Dijon] (IMB), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université de Bourgogne (UB), Cellule Pasteur, Université Paris Diderot - Paris 7 (UPD7)-PRES Sorbonne Paris Cité, Biologie et Pathogénicité fongiques, Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), This study was supported by a grant from the French Ministry of Health: PHRC regional 2005., Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), Institut de Mathématiques de Bourgogne [Dijon] ( IMB ), Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Université Paris Diderot - Paris 7 ( UPD7 ) -PRES Sorbonne Paris Cité, Institut National de la Recherche Agronomique ( INRA ) -Institut Pasteur [Paris], Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Biologie et Pathogénicité fongiques (BPF), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP), and Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris]
Subjects: MESH: Genetic Markers, MESH : Microsatellite Repeats, MESH : Candidiasis, Genotype, Candida albicans, MESH : Genetic Markers, DNA, Fungal, Mycological Typing Techniques, MESH : Mycological Typing Techniques, MESH: Phylogeny, Phylogeny, [ SDV.MP.MYC ] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Genetics, 0303 health sciences, biology, Candidiasis, Fungal genetics, Allelic frequencies, MESH: Case-Control Studies, Corpus albicans, MESH: Candidiasis, Infectious Diseases, MESH : Carrier State, Carrier State, Microsatellite, MESH: Carrier State, Genetic Markers, Microbiology (medical), MESH : Case-Control Studies, Genotyping, MESH : Candida albicans, Genes, Fungal, Microbiology, 03 medical and health sciences, MESH: Mycological Typing Techniques, Humans, Pathogenicity, Typing, Lineages, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH: Humans, 030306 microbiology, MESH: Candida albicans, MESH : Humans, UPGMA, MESH : Phylogeny, biology.organism_classification, MESH: DNA, Fungal, Case-Control Studies, Multilocus sequence typing, MLMT, MESH : Genes, Fungal, MESH: Microsatellite Repeats, MESH : DNA, Fungal, MESH: Genes, Fungal, Microsatellite Repeats
Abstract: EA MERS CT3 Enjeu 3; International audience; The dimorphic yeast Candida albicans is a component of the normal microflora at the mucosal surfaces of healthy individuals. It possesses an array of phenotypic properties considered as virulence traits that contribute to pathogenicity of the yeast in immuno-compromised patients. We addressed the question of the pathogenicity of lineages of C. albicans with regard to their genotype in three series of C. albicans isolates (a series of commensal isolates collected in healthy individuals, a group of bloodstream isolates and a group of non-bloodstream clinical isolates) using a Multi-Locus Microsatellite Typing (MLMT) approach based on the analysis of the polymorphism of 11 microsatellite loci. The MLMT analysis of the three series, corresponding to 174 C. albicans isolates, gave a 100% typability to the method, with a DP index of 0.999. The UPGMA analysis showed that the isolates segregated in eight phylogenetic groups. Interestingly, the clustering was comparable when using NJ and MS-tree algorithms and a good concordance index of the clustering was observed with MLST. All in all our data strongly indicated MLMT as a reliable tool for DNA-typing studies in C. albicans. Isolates from healthy and non-healthy individuals segregated at the same proportions into the eight phylogenetic groups, suggesting that isolates of different origin share the same overall pathogenicity. Surprisingly allelic frequencies at the HIS3 microsatellite differed significantly in commensal isolates (group A) from pooled groups B and C (clinical isolates), raising the possibility that some individual alleles at the HIS3 microsatellite may be associated with distinct pathogenic profiles in C. albicans.
Published: 2012

22. Betaproteobacteria dominance and diversity shifts in the bacterial community of a PAH-contaminated soil exposed to phenanthrene

Author: Yves Jouanneau, Florence Martin, Denis Le Paslier, Agnès Barbance, Fabrice Martin-Laurent, David Bru, Roberto A. Geremia, Stéphane Torelli, Gérard Blake, Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Département de Chimie Moléculaire (DCM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Joseph Fourier - Grenoble 1 (UJF), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Laboratoire Optimisation de la Conception et Ingénierie de l'Environnement (LOCIE), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie et Biologie des Métaux ( LCBM - UMR 5249 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Département de Chimie Moléculaire ( DCM ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire d'Ecologie Alpine ( LECA ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Optimisation de la Conception et Ingénierie de l'Environnement ( LOCIE ), Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)
Subjects: phenanthrene, MESH : Molecular Sequence Data, Health, Toxicology and Mutagenesis, Stable-isotope probing, 010501 environmental sciences, Toxicology, 01 natural sciences, MESH: Biodegradation, Environmental, 16S rRNA sequences, MESH : Soil Pollutants, chemistry.chemical_compound, [ SDV.BBM.BC ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Hydrogenophaga, MESH : Biodiversity, Soil Pollutants, PAH degradation, Polycyclic Aromatic Hydrocarbons, MESH: Betaproteobacteria, MESH: Phylogeny, stable isotope probing, Betaproteobacteria, Phylogeny, Soil Microbiology, MESH : Betaproteobacteria, 0303 health sciences, education.field_of_study, biology, Chemistry, General Medicine, Biodiversity, Pollution, Soil contamination, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Biodegradation, Environmental, Environmental chemistry, Soil microbiology, Population, Molecular Sequence Data, MESH : Biodegradation, Environmental, MESH : Soil Microbiology, betaproteobacteria, MESH: Biodiversity, 03 medical and health sciences, MESH: Polycyclic Hydrocarbons, Aromatic, Rhodoferax, MESH: Phenanthrenes, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], education, MESH : Phenanthrenes, 030304 developmental biology, 0105 earth and related environmental sciences, MESH: Soil Pollutants, MESH: Molecular Sequence Data, MESH : Phylogeny, Phenanthrene, Phenanthrenes, biology.organism_classification, MESH : Polycyclic Hydrocarbons, Aromatic, MESH: Soil Microbiology, 13. Climate action
Abstract: International audience; In this study, the PAH-degrading bacteria of a constructed wetland collecting road runoff has been studied through DNA stable isotope probing. Microcosms were spiked with (13)C-phenanthrene at 34 or 337 ppm, and bacterial diversity was monitored over a 14-day period. At 337 ppm, PAH degraders became dominated after 5 days by Betaproteobacteria, including novel Acidovorax, Rhodoferax and Hydrogenophaga members, and unknown bacteria related to Rhodocyclaceae. The prevalence of Betaproteobacteria was further demonstrated by phylum-specific quantitative PCR, and was correlated with a burst of phenanthrene mineralization. Striking shifts in the population of degraders were observed after most of the phenanthrene had been removed. Soil exposed to 34 ppm phenanthrene showed a similar population of degraders, albeit only after 14 days. Results demonstrate that specific Betaproteobacteria are involved in the main response to soil PAH contamination, and illustrate the potential of SIP approaches to investigate PAH biodegradation in soil.
Published: 2012

23. Desulfovibrio piezophilus sp. nov., a piezophilic, sulfate-reducing bacterium isolated from wood falls in the Mediterranean Sea

Author: Jean Luc Cayol, Françoise Gaill, Marc Garel, Bernard Ollivier, Marie Laure Fardeau, Saber Khelaifia, Clement Aussignargues, Christian Tamburini, Nathalie Pradel, Sylvie M. Gaudron, Laboratoire de Microbiologie et Biotechnologie des Environnements Chauds, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Systématique, adaptation, évolution ( SAE ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Oxidation-Reduction, 0106 biological sciences, Geologic Sediments, MESH : Molecular Sequence Data, Sodium Chloride, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, 7. Clean energy, chemistry.chemical_compound, MESH : Mediterranean Sea, Lactate oxidation, MESH : Seawater: microbiology, Nitrite, MESH: Phylogeny, Phylogeny, Thiosulfate, 0303 health sciences, Base Composition, Strain (chemistry), biology, Sulfates, Fatty Acids, MESH : Sulfates: metabolism, General Medicine, MESH: Seawater: microbiology, Biochemistry, GROWTH, Desulfovibrio, FATTY-ACIDS, Energy source, Oxidation-Reduction, MESH: Geologic Sediments: microbiology, MESH: Mediterranean Sea, Stereochemistry, MESH: Sulfates: metabolism, Molecular Sequence Data, chemistry.chemical_element, PRESSURE, 010603 evolutionary biology, Microbiology, MESH : Sodium Chloride: metabolism, MESH: Sodium Chloride: metabolism, MESH : Base Composition, 03 medical and health sciences, MESH: Base Composition, Sulfite, MESH : Geologic Sediments: microbiology, Mediterranean Sea, Seawater, 14. Life underwater, MESH : Fatty Acids: metabolism, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH : Oxidation-Reduction, MESH: Molecular Sequence Data, 030306 microbiology, MESH: Fatty Acids: metabolism, MESH: Desulfovibrio: chemistry,classification,genetics,isolation & purification, MESH : Phylogeny, biology.organism_classification, Sulfur, chemistry, MESH : Desulfovibrio: chemistry,classification,genetics,isolation & purification, Bacteria, [ SDV.BID.SPT ] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Abstract: A novel sulfate-reducing bacterium, designated C1TLV30T, was isolated from wood falls at a depth of 1693 m in the Mediterranean Sea. Cells were motile vibrios (2–4×0.5 µm). Strain C1TLV30T grew at temperatures between 15 and 45 °C (optimum 30 °C) and at pH 5.4–8.6 (optimum 7.3). It required NaCl for growth (optimum at 25 g NaCl l−1) and tolerated up to 80 g NaCl l−1. Strain C1TLV30T used as energy sources: lactate, fumarate, formate, malate, pyruvate and ethanol. The end products from lactate oxidation were acetate, H2S and CO2 in the presence of sulfate as terminal electron acceptor. Besides sulfate, thiosulfate and sulfite were also used as terminal electron acceptors, but not elemental sulfur, fumarate, nitrate or nitrite. Strain C1TLV30T possessed desulfoviridin and was piezophilic, growing optimally at 10 MPa (range 0–30 MPa). The membrane lipid composition of this strain was examined to reveal an increase in fatty acid chain lengths at high hydrostatic pressures. The G+C content of the genomic DNA was 49.6 % and the genome size was estimated at 3.5±0.5 Mb. Phylogenetic analysis of the SSU rRNA gene sequence indicated that strain C1TLV30T was affiliated to the genus Desulfovibrio with Desulfovibrio profundus being its closest phylogenetic relative (similarity of 96.4 %). On the basis of SSU rRNA gene sequence comparisons and physiological characteristics, strain C1TLV30T ( = DSM 21447T = JCM 1548T) is proposed to be assigned to a novel species of the genus Desulfovibrio, Desulfovibrio piezophilus sp. nov.
Published: 2011

24. Caldicoprobacter algeriensis sp. nov. a new thermophilic anaerobic, xylanolytic bacterium isolated from an Algerian hot spring

Author: Jean Luc Cayol, Bernard Ollivier, Marie-Laure Fardeau, Tahar Benayad, Salima Kebbouche-Gana, Manon Joseph, Patrick Gregoire, Hocine Hacene, Amel Bouanane-Darenfed, Université des Sciences et de la Technologie Houari Boumediene [Alger] (USTHB), Laboratoire de Microbiologie et Biotechnologie des Environnements Chauds, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, Laboratoire de Biologie Cellulaire et Moléculaire, Laboratoire de Biologie Cellulaire et Moleculaire, Université du Québec, Laboratoire de la sécurité Alimentaire et de l'environnement, LBCM, and Université des Sciences et de la Technologie Houari Boumediene = University of Sciences and Technology Houari Boumediene [Alger] (USTHB)
Subjects: MESH: Hydrogen-Ion Concentration, MESH: Sequence Analysis, DNA, MESH : Algeria, MESH : Molecular Sequence Data, Hot Temperature, MESH: Gram-Positive Bacteria: classification,genetics,isolation & purification,physiology, MESH: Carbohydrate Metabolism, Cellobiose, Xylose, Sodium Chloride, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Applied Microbiology and Biotechnology, MESH: DNA, Bacterial: chemistry,genetics, Hot Springs, MESH: Hot Springs: microbiology, MESH : Anaerobiosis, MESH : DNA, Bacterial: chemistry,genetics, chemistry.chemical_compound, RNA, Ribosomal, 16S, MESH : Sodium Chloride: toxicity, Cluster Analysis, Anaerobiosis, Raffinose, Lactose, MESH: Phylogeny, Phylogeny, 0303 health sciences, Base Composition, Strain (chemistry), General Medicine, Hydrogen-Ion Concentration, MESH : Carbohydrate Metabolism, Bacterial Typing Techniques, Biochemistry, Carbohydrate Metabolism, Xylans, MESH : Hot Temperature, MESH : Gram-Positive Bacteria: classification,genetics,isolation & purification,physiology, MESH: Algeria, MESH: RNA, Ribosomal, 16S: genetics, DNA, Bacterial, Molecular Sequence Data, Biology, MESH: DNA, Ribosomal: chemistry,genetics, MESH: Hot Temperature, Gram-Positive Bacteria, Microbiology, DNA, Ribosomal, MESH: Bacterial Typing Techniques, MESH: Fermentation, MESH : Base Composition, 03 medical and health sciences, MESH: Base Composition, MESH : Xylans: metabolism, MESH : Hydrogen-Ion Concentration, MESH : DNA, Ribosomal: chemistry,genetics, MESH : Fermentation, MESH: Anaerobiosis, MESH : Cluster Analysis, MESH : Hot Springs: microbiology, Melibiose, 030304 developmental biology, MESH: Molecular Sequence Data, 030306 microbiology, MESH: Sodium Chloride: toxicity, MESH: Xylans: metabolism, MESH : Phylogeny, Maltose, Sequence Analysis, DNA, MESH: Cluster Analysis, chemistry, MESH : RNA, Ribosomal, 16S: genetics, Algeria, Fermentation, MESH : Bacterial Typing Techniques, [ SDV.BID.SPT ] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, MESH : Sequence Analysis, DNA
Abstract: A thermophilic anaerobic bacterium (strain TH7C1(T)) was isolated from the hydrothermal hot spring of Guelma in the northeast of Algeria. Strain TH7C1(T) stained Gram-positive, was a non-motile rod appearing singly, in pairs, or as long chains (0.7-1 x 2-6 mu m(2)). Spores were never observed. It grew at temperatures between 55 and 75A degrees C (optimum 65A degrees C) and at pH between 6.2 and 8.3 (optimum 6.9). It did not require NaCl for growth, but tolerated it up to 5 g l(-1). Strain TH7C1(T) is an obligatory heterotroph fermenting sugars including glucose, galactose, lactose, raffinose, fructose, ribose, xylose, arabinose, maltose, mannitol, cellobiose, mannose, melibiose, saccharose, but also xylan, and pyruvate. Fermentation of sugars only occurred in the presence of yeast extract (0.1%). The end-products from glucose fermentation were acetate, lactate, ethanol, CO2, and H-2. Nitrate, nitrite, thiosulfate, elemental sulfur, sulfate, and sulfite were not used as electron acceptors. The G+C content of the genomic DNA was 44.7 mol% (HPLC techniques). Phylogenetic analysis of the small-subunit ribosomal RNA (rRNA) gene sequence indicated that strain TH7C1(T) was affiliated to Firmicutes, order Clostridiales, family Caldicoprobacteraceae, with Caldicoprobacter oshimai (98.5%) being its closest relative. Based on phenotypic, phylogenetic, and genetic characteristics, strain TH7C1(T) is proposed as a novel species of genus Caldicoprobacter, Caldicoprobacter algeriensis, sp. nov. (strain TH7C1(T) = DSM 22661(T) = JCM 16184(T)).
Published: 2011

25. An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection research

Author: Christelle Monsempes, Fabrice Legeai, Julie Poulain, Marie-Christine François, Christine Merlin, Nicolas Montagné, Frédérick Gavory, Sébastien Malpel, Martine Maïbèche-Coisne, Emmanuelle Jacquin-Joly, François Cousserans, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Développement et Communication Chimique chez les Insectes (DCCI), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Physiologie de l'Insecte : Signalisation et Communication (PISC), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech, Biologie Intégrative et Virologie des Insectes [Univ. de Montpellier II] (BIVI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Universite Pierre et Marie Curie (UPMC) ANR-07-NEURO-037-01 ANR-09-BLAN0239-01, Jacquin Joly, Emmanuelle, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Biologie des organismes et des populations appliquées à la protection des plantes ( BIO3P ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, Biological systems and models, bioinformatics and sequences ( SYMBIOSE ), Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National des Sciences Appliquées - Rennes ( INSA Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National des Sciences Appliquées - Rennes ( INSA Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ) -Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique ( Inria ), Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Développement et Communication Chimique chez les Insectes ( DCCI ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Physiologie de l'Insecte : Signalisation et Communication ( PISC ), Institut National de la Recherche Agronomique ( INRA ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -AgroParisTech, Biologie Intégrative et Virologie des Insectes [Univ. de Montpellier II] ( BIVI ), Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)
Subjects: Male, MESH: Sequence Analysis, DNA, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, MESH : Arthropod Antennae, détection olfactive, MESH : Molecular Sequence Annotation, Genes, Insect, Insect, MESH: Genes, Insect, MESH : Pheromones, Pheromones, 0302 clinical medicine, Arthropod Antennae, Databases, Genetic, MESH: Smell, MESH: Animals, MESH: Phylogeny, Phylogeny, MESH: Databases, Genetic, media_common, Expressed Sequence Tags, 0303 health sciences, Expressed sequence tag, MESH: Pheromones, noctuelle, MESH: Spodoptera, MESH : Expressed Sequence Tags, MESH : Genes, Insect, food and beverages, Smell, Sex pheromone, Pheromone, Biotechnology, Research Article, papillon de nuit, lcsh:QH426-470, MESH : Male, lcsh:Biotechnology, media_common.quotation_subject, Gene prediction, Olfaction, Computational biology, MESH: Molecular Sequence Annotation, Biology, Spodoptera, MESH : Spodoptera, MESH: Expressed Sequence Tags, 03 medical and health sciences, MESH: Gene Expression Profiling, lcsh:TP248.13-248.65, Botany, MESH: Gene Library, Genetics, Animals, MESH : Databases, Genetic, Spodoptera littoralis, 030304 developmental biology, Gene Library, MESH: Arthropod Antennae, MESH : Gene Expression Profiling, Gene Expression Profiling, séquence génomique, fungi, MESH : Phylogeny, Molecular Sequence Annotation, Sequence Analysis, DNA, MESH : Gene Library, biology.organism_classification, MESH: Male, lcsh:Genetics, MESH : Smell, MESH : Animals, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 030217 neurology & neurosurgery, MESH : Sequence Analysis, DNA
Abstract: Background Nocturnal insects such as moths are ideal models to study the molecular bases of olfaction that they use, among examples, for the detection of mating partners and host plants. Knowing how an odour generates a neuronal signal in insect antennae is crucial for understanding the physiological bases of olfaction, and also could lead to the identification of original targets for the development of olfactory-based control strategies against herbivorous moth pests. Here, we describe an Expressed Sequence Tag (EST) project to characterize the antennal transcriptome of the noctuid pest model, Spodoptera littoralis, and to identify candidate genes involved in odour/pheromone detection. Results By targeting cDNAs from male antennae, we biased gene discovery towards genes potentially involved in male olfaction, including pheromone reception. A total of 20760 ESTs were obtained from a normalized library and were assembled in 9033 unigenes. 6530 were annotated based on BLAST analyses and gene prediction software identified 6738 ORFs. The unigenes were compared to the Bombyx mori proteome and to ESTs derived from Lepidoptera transcriptome projects. We identified a large number of candidate genes involved in odour and pheromone detection and turnover, including 31 candidate chemosensory receptor genes, but also genes potentially involved in olfactory modulation. Conclusions Our project has generated a large collection of antennal transcripts from a Lepidoptera. The normalization process, allowing enrichment in low abundant genes, proved to be particularly relevant to identify chemosensory receptors in a species for which no genomic data are available. Our results also suggest that olfactory modulation can take place at the level of the antennae itself. These EST resources will be invaluable for exploring the mechanisms of olfaction and pheromone detection in S. littoralis, and for ultimately identifying original targets to fight against moth herbivorous pests.
Published: 2011

26. Borrelia crocidurae infection of Ornithodoros erraticus (Lucas, 1849) ticks in Tunisia

Author: Danièle Postic, Youmna M’ghirbi, Martine Garnier, M’hammed Sarih, Lise Gern, Ali Bouattour, Elisabeth Ferquel, Muriel Cornet, Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP), Centre National de Référence des Borrelia (CNR), Institut Pasteur [Paris], Institut Pasteur du Maroc, Laboratoire d'Eco-Epidémiologie des Parasites, Université de Neuchâtel (UNINE), Microbiologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Descartes - Paris 5 (UPD5), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris Descartes - Paris 5 (UPD5), Institut Pasteur [Paris] (IP), Institut Pasteur de Tunis - Réseau International des Instituts Pasteur (RIIP), Réseau International des Instituts Pasteur (RIIP) - Institut Pasteur du Maroc, Université de Neuchâtel, and Assistance publique - Hôpitaux de Paris (AP-HP) - Université Paris Descartes - Paris 5 (UPD5)
Subjects: Male, MESH : Molecular Sequence Data, relapsing fever, law.invention, 0302 clinical medicine, law, RNA, Ribosomal, 16S, MESH : Female, MESH: Animals, MESH: Borrelia, MESH: Phylogeny, Ornithodoros, Polymerase chain reaction, Phylogeny, 0303 health sciences, biology, Phylogenetic tree, Arthropod Vectors, MESH : Arthropod Vectors, 3. Good health, MESH: RNA, Ribosomal, 16S, Infectious Diseases, MESH : Borrelia, Female, MESH: Tunisia, Tunisia, MESH : Male, 030231 tropical medicine, Molecular Sequence Data, Microbiology, MESH : Ornithodoros, 03 medical and health sciences, Virology, Borrelia, MESH : Tunisia, MESH: Ornithodoros, medicine, Animals, Ornithodoros erraticus, MESH: Arthropod Vectors, MESH: Molecular Sequence Data, 030306 microbiology, MESH : Phylogeny, Ribosomal RNA, 16S ribosomal RNA, medicine.disease, biology.organism_classification, bacterial infections and mycoses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Male, MESH : RNA, Ribosomal, 16S, MESH : Animals, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Female
Abstract: International audience; Tick-borne relapsing fever (TBRF) is caused by Borrelia species transmitted to humans by infected Ornithodoros sp. ticks. The disease has been rarely described in North Africa, and in Tunisia the local transmission of TBRF seems to have disappeared or is undiagnosed. A longitudinal study was conducted in 14 sites located in four different bioclimatic zones of Tunisia to assess both the distribution of Ornithodoros sp. and their infection rate with the relapsing fever Borrelia sp. Three polymerase chain reaction methods targeting the 16S rRNA, the intergenic spacer, and the fla (flagellin) genes were used and phylogenetic analyses were carried out. Three hundred and fifty-eight specimens of Ornithodoros were collected: O. erraticus (previously termed "small variety") (n = 190) and O. normandi (n = 168). Borrelia crocidurae DNA was detected in 15.1% of O. erraticus (small variety) (24 out of the 159 randomly selected for testing) collected in rodent burrows situated in the arid and Saharan areas in southern Tunisia. Molecular analysis targeting the 16S rRNA gene and the noncoding intergenic spacer domain showed good resolution for this Borrelia sp., although no molecular polymorphism was evidenced according to location. In contrast, none of the 133 O. normandi, also randomly selected for testing, was infected by Borrelia sp. and these ticks were restricted to the subhumid and semiarid zones in northern Tunisia. Both O. erraticus (small variety) and O. normandi were found in Tunisia and the high B. crocidurae infection rate found in O. erraticus highlights the risk of TBRF transmission in the southern part of the country.
Published: 2010

27. Genome-wide analysis of plant metal transporters, with an emphasis on poplar

Author: Malcolm M. Campbell, Barbara Montanini, Pierre Richaud, Aude Migeon, Damien Blaudez, Olivia Wilkins, Sébastien Thomine, Michel Chalot, Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Biologie végétale et microbiologie environnementale - UMR7265 ( BVME ), Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Aix Marseille Université ( AMU ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Chrono-environnement ( LCE ), and Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC )
Subjects: 0106 biological sciences, Populus trichocarpa, MESH: Genome, Plant, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, MESH : Populus, MESH : Saccharomyces cerevisiae, MESH: Plants, Chlamydomonas reinhardtii, MESH: Carrier Proteins, Saccharomyces cerevisiae, MESH : Plants, Physcomitrella patens, 01 natural sciences, Genome, Fungal Proteins, 03 medical and health sciences, Cellular and Molecular Neuroscience, Selaginella moellendorffii, Botany, Arabidopsis thaliana, Gene family, MESH : Fungal Proteins, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Phylogeny, Molecular Biology, Gene, Phylogeny, 030304 developmental biology, Pharmacology, 0303 health sciences, MESH: Metals, biology, MESH : Metals, MESH : Phylogeny, food and beverages, Cell Biology, Plants, biology.organism_classification, MESH: Saccharomyces cerevisiae, MESH : Genome, Plant, MESH: Populus, Populus, Metals, Molecular Medicine, MESH: Fungal Proteins, MESH : Carrier Proteins, Carrier Proteins, Genome, Plant, 010606 plant biology & botany
Abstract: International audience; The specific transport of metal ions, mediated by membrane-localized metal transporters, is of fundamental importance in all eukaryotes. Genome-wide analysis of metal transporters was undertaken, making use of whole genome sequences of the green alga Chlamydomonas reinhardtii, the moss Physcomitrella patens, the lycophyte Selaginella moellendorffii, the monocots rice and sorghum, and the dicots Arabidopsis thaliana, poplar, grapevine, as well as of the yeast Saccharomyces cerevisiae. A repertoire of 430 metal transporters was found in total across eight photosynthetic plants, as well as in S. cerevisiae. Seventy-two full-length metal transporter genes were identified in the Populus genome alone, which is the largest number of metal transporters genes identified in any single species to date. Diversification of some transporter family gene clusters appears to have occurred in a lineage-specific manner. Expression analysis of Populus metal transporters indicates that some family members show tissue-specific transcript abundance. Taken together, the data provide a picture into the diversification of these important gene families.
Published: 2010

28. Immunoglobulin heavy chain V-D-J gene rearrangement and mutational status in Uruguayan patients with chronic lymphocytic leukemia

Author: Guillermo Dighiero, Sergio Bianchi, Hugo Naya, Pilar Moreno, Raul Gabus, Ana Inés Landoni, Otto Pritsch, Pablo Oppezzo, Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur ( RIIP ) -Institut Pasteur de Montevideo, Departamento de Fisiopatología, Universidad de la República-Hospital de Clinicas, Servicio de Hematología, Hospital Maciel, Departamento de Inmunobiología, and Universidad de la República-Facultad de Medicina
Subjects: Male, Cancer Research, Chronic lymphocytic leukemia, DNA Mutational Analysis, MESH : Aged, Gene Rearrangement, B-Lymphocyte, Heavy Chain, Immunoglobulin Variable Region, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, Gene Frequency, hemic and lymphatic diseases, MESH : Female, MESH : Gene Frequency, MESH : Immunoglobulin Variable Region, MESH : Uruguay, Phylogeny, Genetics, education.field_of_study, Geography, Incidence (epidemiology), MESH : Geography, Hematology, MESH : Adult, MESH : Leukemia, Lymphocytic, Chronic, B-Cell, Middle Aged, Oncology, Chronic leukemia, Female, MESH : Mutation, IGHV@, Adult, MESH : Male, Genes, Immunoglobulin Heavy Chain, Population, MESH : Genes, Immunoglobulin Heavy Chain, MESH : DNA Mutational Analysis, Biology, MESH : Gene Rearrangement, B-Lymphocyte, Heavy Chain, medicine, Humans, MESH : Middle Aged, education, Gene, Aged, MESH : Humans, MESH : Phylogeny, Gene rearrangement, medicine.disease, Leukemia, Lymphocytic, Chronic, B-Cell, Immunology, Mutation, Immunoglobulin heavy chain, Uruguay, [ SDV.GEN ] Life Sciences [q-bio]/Genetics
Abstract: International audience; B-cell chronic lymphocytic leukemia (CLL) is characterized by the accumulation of long-lived circulating clonal leukemic B-cells, although the etiopathogenesis remains unclear. The incidence of CLL is variable in different regions around the world. While it is the most frequent chronic leukemia in Western countries, it has a low incidence in Asia. In this work we have investigated the immunoglobulin heavy chain gene rearrangements and mutational status in 80 Uruguayan patients with CLL, and compared these results with those obtained in other geographic regions. Our results demonstrate that Uruguayan patients with CLL display an IGHV gene usage which resembles that observed in Mediterranean countries and exhibits certain differences compared with Brazilian and Asian series, as expected, considering the ethnic basis of the Uruguayan population. This suggests that genetic influences could be important in the development and etiopathogenesis of CLL, but larger studies are necessary to substantiate this possibility.
Published: 2010

29. Phylogenetic relationships within Echinococcus and Taenia tapeworms (Cestoda: Taeniidae): an inference from nuclear protein-coding genes

Author: Jenny Knapp, Akira Ito, Minoru Nakao, Antti Lavikainen, Tetsuya Yanagida, Urmas Saarma, Munehiro Okamoto, Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Asahikawa Medical University, Primate Research Institute, Kyoto University [Kyoto], Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)
Subjects: Paraphyly, MESH: Sequence Analysis, DNA, Time Factors, MESH : Polymorphism, Genetic, MESH: Echinococcus, Helminth genetics, MESH: Base Sequence, MESH: DNA, Helminth, MESH: Genetic Markers, Polymerase Chain Reaction, 030308 mycology & parasitology, MESH : Taenia, MESH : DNA, Helminth, MESH : Genes, Helminth, MESH : Echinococcus, MESH : Genetic Markers, MESH: Animals, MESH: Phylogeny, Clade, MESH : Polymerase Chain Reaction, Genes, Helminth, Phylogeny, 0303 health sciences, Likelihood Functions, Phylogenetic tree, biology, Nuclear Proteins, DNA, Helminth, MESH: Taenia, MESH : RNA Polymerase II, RNA Polymerase II, MESH : Likelihood Functions, MESH : Time Factors, Genetic Markers, MESH: Bayes Theorem, Zoology, MESH : Open Reading Frames, [ SDV.EE.SANT ] Life Sciences [q-bio]/Ecology, environment/Health, 03 medical and health sciences, Open Reading Frames, MESH : Bayes Theorem, Phylogenetics, MESH: Polymorphism, Genetic, parasitic diseases, Genetics, Animals, Humans, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, MESH: Humans, Polymorphism, Genetic, Base Sequence, Taenia, MESH: Time Factors, MESH : Humans, MESH : Phylogeny, MESH : Nuclear Proteins, MESH: Polymerase Chain Reaction, Bayes Theorem, Sequence Analysis, DNA, MESH: Open Reading Frames, biology.organism_classification, MESH: RNA Polymerase II, Echinococcus, Taeniidae, MESH: Likelihood Functions, MESH : Base Sequence, MESH : Animals, MESH: Nuclear Proteins, MESH: Genes, Helminth, MESH : Sequence Analysis, DNA
Abstract: International audience; The family Taeniidae of tapeworms is composed of two genera, Echinococcus and Taenia, which obligately parasitize mammals including humans. Inferring phylogeny via molecular markers is the only way to trace back their evolutionary histories. However, molecular dating approaches are lacking so far. Here we established new markers from nuclear protein-coding genes for RNA polymerase II second largest subunit (rpb2), phosphoenolpyruvate carboxykinase (pepck) and DNA polymerase delta (pold). Bayesian inference and maximum likelihood analyses of the concatenated gene sequences allowed us to reconstruct phylogenetic trees for taeniid parasites. The tree topologies clearly demonstrated that Taenia is paraphyletic and that the clade of Echinococcus oligarthrus and Echinococcusvogeli is sister to all other members of Echinococcus. Both species are endemic in Central and South America, and their definitive hosts originated from carnivores that immigrated from North America after the formation of the Panamanian land bridge about 3 million years ago (Ma). A time-calibrated phylogeny was estimated by a Bayesian relaxed-clock method based on the assumption that the most recent common ancestor of E. oligarthrus and E. vogeli existed during the late Pliocene (3.0 Ma). The results suggest that a clade of Taenia including human-pathogenic species diversified primarily in the late Miocene (11.2 Ma), whereas Echinococcus started to diversify later, in the end of the Miocene (5.8 Ma). Close genetic relationships among the members of Echinococcus imply that the genus is a young group in which speciation and global radiation occurred rapidly.
Published: 2010

30. State-of-the-art Echinococcus and Taenia: phylogenetic taxonomy of human-pathogenic tapeworms and its application to molecular diagnosis

Author: Yasuhito Sako, Agathe Nkouawa, Jenny Knapp, Minoru Nakao, Tetsuya Yanagida, Munehiro Okamoto, Akira Ito, Asahikawa Medical University, Primate Research Institute, Kyoto University [Kyoto], Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)
Subjects: Microbiology (medical), 030231 tropical medicine, Zoology, MESH: Cestode Infections, MESH: Echinococcus, MESH: Molecular Diagnostic Techniques, Microbiology, 030308 mycology & parasitology, [ SDV.EE.SANT ] Life Sciences [q-bio]/Ecology, environment/Health, 03 medical and health sciences, 0302 clinical medicine, MESH : Cestode Infections, MESH : Taenia, Phylogenetics, parasitic diseases, Genetics, medicine, Taeniasis, Animals, Humans, MESH : Echinococcus, MESH: Animals, MESH: Phylogeny, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Phylogeny, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 0303 health sciences, MESH: Humans, Molecular epidemiology, Phylogenetic tree, biology, Taenia, MESH : Humans, MESH : Phylogeny, medicine.disease, biology.organism_classification, Cestode Infections, Cladistics, Echinococcus, Infectious Diseases, Molecular Diagnostic Techniques, Evolutionary biology, MESH: Taenia, MESH : Animals, MESH : Molecular Diagnostic Techniques, Phylogenetic nomenclature
Abstract: International audience; The taxonomy of tapeworms belonging to the family Taeniidae has been controversial because of the paucity of adult phenotypic characters and the great plasticity of larvae in intermediate hosts. The family consists of the medically important two genera Echinococcus and Taenia, which are closely related to each other. Cladistic approaches using the molecular data of DNA and the numerical data of morphologic characters are clarifying phylogenetic relationships among the members of these genera. The nucleotide data of worldwide taeniid parasites accumulated in public DNA databases may provide a basis for the development of molecular diagnostic tools, and make it possible to identify the parasites, at least the human Taenia spp. by non-morphologists. Furthermore, the detection of intraspecific genetic variations prompts evolutionary and ecological studies to address fundamental questions of parasite distributional patterns. Here, we introduce the recent advances of taeniid phylogeny and its application to molecular diagnosis.
Published: 2010

31. Identification of relations between risk factors and their pathologies or health conditions by mining scientific literature

Author: Hamon, Thierry, Graña, Martin, Raggio, Víctor, Grabar, Natalia, Naya, Hugo, Laboratoire d'Informatique Médicale et de BIOinformatique (LIM&BIO), Université Paris 13 (UP13), Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP), Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Laboratoire d'Informatique Médicale et de BIOinformatique ( LIM&BIO ), Université Paris 13 ( UP13 ), Réseau International des Instituts Pasteur ( RIIP ) -Institut Pasteur de Montevideo, Centre de Recherche des Cordeliers ( CRC (UMR_S 872) ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), and Hôpital Européen Georges Pompidou [APHP] ( HEGP )
Subjects: MESH : Quantitative Trait Loci, MESH: Abstracting and Indexing as Topic, MESH : Saccharomyces cerevisiae, MESH : Microsatellite Repeats, MESH: Semantics, MESH: Natural Language Processing, Medical Subject Headings, MESH: Saccharomyces cerevisiae Proteins, Risk Factors, MESH: Risk Factors, MESH: Disease, Data Mining, Disease, MESH : Semantics, MESH : Mycological Typing Techniques, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Phylogeny, MESH : Minisatellite Repeats, MESH : Trans-Activators, MESH: Polymorphism, Single Nucleotide, MESH : Polymorphism, Single Nucleotide, MESH : Natural Language Processing, MESH : Databases, Bibliographic, MESH : Risk Factors, MESH: Saccharomyces cerevisiae, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Semantics, MESH : Disease, MESH : Abstracting and Indexing as Topic, MESH : United States, Abstracting and Indexing, MESH: Trans-Activators, MESH : Medical Subject Headings, MESH: Medical Subject Headings, MESH : Saccharomyces cerevisiae Proteins, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Mycological Typing Techniques, MESH: United States, Natural Language Processing, MESH : Data Mining, MESH: Data Mining, MESH : Nuclear Proteins, MESH : Phylogeny, Databases, Bibliographic, United States, MESH: Quantitative Trait Loci, MESH: Databases, Bibliographic, MESH: Minisatellite Repeats, MESH: Microsatellite Repeats, MESH : Databases as Topic, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Databases as Topic, MESH: Nuclear Proteins
Abstract: International audience; Risk factors discovery and prevention is an active research field within the biomedical domain. Despite abundant existing information on risk factors, as found in bibliographical databases or on several websites, accessing this information may be difficult. Methods from Natural Language Processing and Information Extraction can be helpful to access it more easily. Specifically, we show a procedure for analyzing massive amounts of scientific literature and for detecting linguistically marked associations between pathologies and risk factors. This approach allowed us to extract over 22,000 risk factors and associated pathologies. The performed evaluations pointed out that (1) over 88% of risk factors for coronary heart disease are correct, (2) associated pathologies, when they could be compared to MeSH indexing, are correct in about 70%, and (3) in existing terminologies links between risk factors and their pathologies are seldom recorded.
Published: 2010

32. Evidence of Emergence of New GGII.4 Norovirus Variants from Gastroenteritis Outbreak Survey in France during the 2007-to-2008 and 2008-to-2009 Winter Seasons ▿

Author: Pierre Pothier, Katia Ambert-Balay, Marie Estienney, A.H. Kamel, Gaël Belliot, Laboratoire de sérologie-virologie (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), Laboratoire Interactions Muqueuses Agents Transmissibles ( LIMA ), and Université de Bourgogne ( UB )
Subjects: Microbiology (medical), MESH : Molecular Sequence Data, Genotype, MESH : Molecular Epidemiology, Molecular Sequence Data, MESH : Genotype, Biology, medicine.disease_cause, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Disease Outbreaks, Virology, medicine, MESH : Cluster Analysis, MESH : RNA, Viral, Cluster Analysis, Humans, MESH : Disease Outbreaks, MESH : France, Phylogeny, Caliciviridae Infections, Molecular Epidemiology, MESH : Seasons, Molecular epidemiology, MESH : Norovirus, MESH : Humans, Norovirus, MESH : Phylogeny, Outbreak, Sequence Analysis, DNA, biology.organism_classification, Caliciviridae, Gastroenteritis, MESH : Gastroenteritis, Gastroenteritis outbreak, RNA, Viral, France, Seasons, MESH : Caliciviridae Infections, MESH : Sequence Analysis, DNA
Abstract: Analysis of 316 outbreaks of gastroenteritis in France from September 2007 through March 2009 showed that genogroup II.4 (GGII.4) noroviruses were predominant and mostly belonged to the 2006b variant. However, the new GGII.4 variants, variant 2008 and the newly discovered Cairo variant from the Middle East, were also detected. The epidemiological survey suggests that these new variants might become the next predominant strains.
Published: 2009

33. Low prevalence of HIV type 1 drug resistance mutations in untreated, recently infected patients from Burkina Faso, Côte d'Ivoire, Senegal, Thailand, and Vietnam: the ANRS 12134 study

Author: Dominique Costagliola, Coumba Toure Kane, Nicole Ngo-Giang-Huong, Eric Delaporte, Diane Valéa, Halimatou Diop, Eitel Mpoudi Ngole, Truong Xuan Lien, Avelin F. Aghokeng, Dominique Joulia-Ekaza, Eric Nerrienet, Laurence Vergne, Marie-Laure Chaix, Janin Nouhin, Ahidjo Ayouba, François Rouet, Thomas d. 'Aquin Toni, Martine Peeters, VIH/SIDA et maladies associées, Université Montpellier 1 (UM1), Institut Pasteur d'Ho Chi Minh Ville, Réseau International des Instituts Pasteur (RIIP), Institut Pasteur du Cambodge, CRESAR/IMPM/IRD - Virology, CRESAR/IMPM/IRD, Épidémiologie clinique, santé mère-enfant et VIH en Asie du Sud-Est (IRD_PHPT), Harvard University [Cambridge]-Chiang Mai university (Thaïlande), Laboratoire Bactériologie-Virologie, Hôpital Aristide-Le-Dantec, Institut de Recherche en Sciences de la Santé (IRSS) / Centre Muraz, Centre de recherche et de Diagnostic sur le Sida (CeDreS), CHU Treichville, Epidémiologie Clinique et Traitement de l'Infection à VIH, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Virologie, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP], Université Montpellier 1 ( UM1 ), Réseau International des Instituts Pasteur ( RIIP ) -Institut Pasteur d'Ho Chi Minh Ville, Institut Pasteur du Cambodge-Réseau International des Instituts Pasteur ( RIIP ), Épidémiologie clinique, santé mère-enfant et VIH en Asie du Sud-Est ( IRD_PHPT ), Centre de recherche et de Diagnostic sur le Sida ( CeDreS ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IFR113-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Assistance publique - Hôpitaux de Paris (AP-HP)-Université Paris Descartes - Paris 5 ( UPD5 ) -CHU Necker - Enfants Malades [AP-HP], Harvard University [Cambridge]-Chiang Mai University (CMU), Centre de recherche et de Diagnostic sur le Sida [Abidjan, Côte d'Ivoire] (CeDreS), Centre Hospitalier Universitaire de Treichville [Abidjan, Côte d'Ivoire] (CHU de Treichville), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), and Harvard University-Chiang Mai University (CMU)
Subjects: MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, MESH : Prevalence, MESH : Genotype, HIV Infections, Drug resistance, 030312 virology, MESH: HIV-1, MESH: Genotype, 0302 clinical medicine, MESH: Pregnancy, HIV Protease, Pregnancy, Genotype, Epidemiology, Prevalence, Medicine, MESH : HIV Reverse Transcriptase, MESH : Female, 030212 general & internal medicine, MESH: Anti-HIV Agents, Pregnancy Complications, Infectious, MESH: Phylogeny, Phylogeny, 0303 health sciences, MESH: Drug Resistance, Viral, biology, virus diseases, MESH: HIV Infections, MESH : Adult, Thailand, MESH : Senegal, HIV Reverse Transcriptase, Senegal, 3. Good health, MESH : Drug Resistance, Viral, Infectious Diseases, Vietnam, MESH: Young Adult, Lentivirus, Female, Sample collection, MESH : Mutation, HIV drug resistance, MESH : HIV-1, Adult, medicine.medical_specialty, MESH: Mutation, MESH: Cote d'Ivoire, MESH: HIV Reverse Transcriptase, Anti-HIV Agents, Immunology, Molecular Sequence Data, MESH : Young Adult, Cote d ivoire, Context (language use), 03 medical and health sciences, MESH: HIV Protease, Young Adult, MESH: Senegal, Virology, [ SDV.MHEP ] Life Sciences [q-bio]/Human health and pathology, parasitic diseases, Burkina Faso, Drug Resistance, Viral, MESH : HIV Infections, Humans, MESH: Pregnancy Complications, Infectious, MESH: Burkina Faso, MESH : Burkina Faso, MESH: Thailand, MESH: Prevalence, MESH: Humans, MESH: Molecular Sequence Data, business.industry, MESH : Anti-HIV Agents, MESH : Humans, MESH : Phylogeny, MESH: Adult, MESH : Vietnam, MESH : Cote d'Ivoire, Sequence Analysis, DNA, biology.organism_classification, MESH : Thailand, MESH : HIV Protease, MESH : Pregnancy, Cote d'Ivoire, MESH : Pregnancy Complications, Infectious, Mutation, HIV-1, MESH: Vietnam, business, MESH: Female, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, MESH : Sequence Analysis, DNA
Abstract: International audience; The frequency of transmitted HIV drug resistance (HIVDR) was evaluated in the context of rapid scale-up of antiretroviral treatment in Thailand, Vietnam, Burkina Faso, Côte d'Ivoire, and Senegal by using an adaptation of the WHO generic protocol of the HIV Drug Resistance Threshold Survey (HIVDR-TS) for sample collection and classification. Resistance-associated mutations were interpreted using the 2009 WHO list for epidemiological surveys. We included 266 subjects from the five study sites. Of the 266 RT and PR sequences analyzed, two from Vietnam harbored virus with major drug resistance mutations (G190A in RT for one individual and M46I in PR for the second individual). Phylogenetic analysis revealed that CRF01_AE predominates (>90%) in Thailand and Vietnam. CRF02 (>65%) cocirculates with other HIV-1 variants in Senegal and Côte d'Ivoire. The prevalence of HIVDRM is scored as low (< or = 5%) in all the five sites for the three drug classes analyzed. A continuous population survey for HIVDRM will provide a rational basis for maintaining or changing the current first line regimen in these countries.
Published: 2009

34. Molecular epidemiology of human astrovirus and adenovirus serotypes 40/41 strains related to acute diarrhea in Tunisian children

Author: Nabil Sakly, Mahjoub Aouni, Alexis de Rougemont, Katia Ambert-Balay, S. Chouchane, Hakima Gharbi-Khelifi, Khira Sdiri-Loulizi, Pierre Pothier, Mouna Hassine, Mohamed Neji Guediche, Laboratoire Interactions Muqueuses Agents Transmissibles ( LIMA ), Université de Bourgogne ( UB ), Laboratoire de sérologie-virologie (CHU de Dijon), and Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon )
Subjects: Serotype, Male, MESH : Molecular Sequence Data, Sequence Homology, MESH : Diarrhea, MESH : Genotype, MESH : Child, Preschool, medicine.disease_cause, Adenovirus Infections, Human, Feces, MESH : Child, Rotavirus, Astroviridae Infections, Genotype, Cluster Analysis, MESH : Female, Child, Phylogeny, MESH : Adenoviruses, Human, Molecular Epidemiology, biology, MESH : Infant, MESH : Adenovirus Infections, Human, Diarrhea, Infectious Diseases, Child, Preschool, Female, medicine.symptom, MESH : Mamastrovirus, Tunisia, MESH : Male, Molecular Sequence Data, MESH : Molecular Epidemiology, MESH : Infant, Newborn, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Astrovirus, MESH : Astroviridae Infections, MESH : Sequence Homology, Virology, MESH : Tunisia, medicine, Humans, MESH : Cluster Analysis, Molecular epidemiology, Adenoviruses, Human, MESH : Humans, Infant, Newborn, Infant, MESH : Phylogeny, Sequence Analysis, DNA, MESH : Feces, biology.organism_classification, Mastadenovirus, Norovirus, Mamastrovirus, MESH : Sequence Analysis, DNA
Abstract: Human astrovirus (AstV) and adenovirus types 40 and 41 (AdV 40/41) are responsible for epidemic and endemic acute gastroenteritis in children and adults. The present study was designed to evaluate the prevalence and genetic diversity of enteric viruses in children in Tunisia. A total of 788 fecal samples were collected during a 4-year period in the region of Monastir, from children under 12 years old, hospitalized or presenting in dispensaries with symptoms of acute gastroenteritis. AstV and AdV40/41 were detected by immunoenzymatic methods and confirmed by PCR/RT-PCR and sequence analysis. Phylogenetic analyses were performed for nucleotide homology with reference strains. AstV and AdV40/41 were characterized as a causative agent in 28 (3.6%) and 18 (2.3%) of the fecal samples, respectively. Phylogenetic analysis showed that the AstVs belonged to the serotypes 3 (n = 4; 14.3%) and 1 (n = 24; 85.7%), and the enteric AdVs to the serotypes 40 (n = 1; 5.6%) and 41 (n = 17; 94.4%). This is the first report that describes the molecular epidemiology of AstV and AdV40/41 in Tunisian children. Their respective detection rate was very low, far below that of rotavirus and norovirus. The genetic diversity among these two viruses is relatively limited and varies depending on the area. J. Med. Virol. 81:1895–1902, 2009. © 2009 Wiley-Liss, Inc.
Published: 2009

35. Polyphasic characterization of xanthomonads pathogenic to members of the Anacardiaceae and their relatedness to species of Xanthomonas

Author: Olivier Pruvost, Xavier Nesme, Nathalie Ah-You, Pierre Lefeuvre, Christian Vernière, L. Bui Thi Ngoc, Frédéric Chiroleu, Emmanuel Jouen, Sylvain Brisse, Lionel Gagnevin, Patrick A. D. Grimont, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Biodiversité des Bactéries Pathogènes Émergentes, Institut Pasteur [Paris], Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Institut Pasteur [Paris] (IP), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), UMR Peuplements végétaux et bioagresseurs en milieu tropical ( UMR PVBMT - Université de La Réunion ), Université de la Réunion ( UR ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de La Réunion (UR)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, Xanthomonas citri, RNA, Ribosomal, 16S, Genotype, Anacardiaceae, MESH: Genetic Variation, Amplified Fragment Length Polymorphism Analysis, MESH: Phylogeny, Phylogeny, 0303 health sciences, biology, Phylogenetic tree, [ SDV.BV.PEP ] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, General Medicine, MESH: RNA, Ribosomal, 16S, Pathovar, Sequence Analysis, 16S, Xanthomonas, Molecular Sequence Data, MESH: Amplified Fragment Length Polymorphism Analysis, [SDV.BID]Life Sciences [q-bio]/Biodiversity, MESH: Xanthomonas, Microbiology, 03 medical and health sciences, MESH : Xanthomonas, Phylogenetics, MESH : Genetic Variation, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, H20 - Maladies des plantes, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, Ribosomal, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, MESH: Molecular Sequence Data, MESH : Anacardiaceae, 030306 microbiology, MESH : Amplified Fragment Length Polymorphism Analysis, MESH : Phylogeny, Genetic Variation, Sequence Analysis, DNA, DNA, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, MESH : RNA, Ribosomal, 16S, MESH: Anacardiaceae, RNA, Amplified fragment length polymorphism, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, MESH : Sequence Analysis, DNA
Abstract: International audience; We have used amplified fragment length polymorphism (AFLP), multilocus sequence analysis (MLSA) and DNA-DNA hybridization for genotypic classification of Xanthomonas pathovars associated with the plant family Anacardiaceae. AFLP and MLSA results showed congruent phylogenetic relationships of the pathovar mangiferaeindicae (responsible for mango bacterial canker) with strains of Xanthomonas axonopodis subgroup 9.5. This subgroup includes X. axonopodis pv. citri (synonym Xanthomonas citri). Similarly, the pathovar anacardii, which causes cashew bacterial spot in Brazil, was included in X. axonopodis subgroup 9.6 (synonym Xanthomonas fuscans). Based on the thermal stability of DNA reassociation, consistent with the AFLP and MLSA data, the two pathovars share a level of similarity consistent with their being members of the same species. The recent proposal to elevate X. axonopodis pv. citri to species level as X. citri is supported by our data. Therefore, the causal agents of mango bacterial canker and cashew bacterial spot should be classified as pathovars of X. citri, namely X. citri pv. mangiferaeindicae (pathotype strain CFBP 1716) and X. citri pv. anacardii (pathotype strain CFBP 2913), respectively. Xanthomonas fuscans should be considered to be a later heterotypic synonym of Xanthomonas citri.
Published: 2009

36. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths

Author: Edouard Bingen, Olivier Clermont, Chantal Le Bouguénec, Zoé Rouy, Sophie Oztas, James R. Johnson, Anne-Marie Gilles, Erick Denamur, Marie Touchon, Olivier Tenaillon, David Vallenet, Valérie Barbe, Marie-Agnès Petit, Meriem El Karoui, Stéphane Bonacorsi, Dominique Schneider, Louis Garry, Eduardo P. C. Rocha, Alexandra Calteau, Antoine Danchin, Xavier Nassif, Ivan Matic, Vanessa Martinez-Jéhanne, Jérôme Tourret, Sophie Mangenot, Christophe Pichon, Jean Marc Ghigo, Claude Saint Ruf, Philippe Bidet, Claire Hoede, Eric Frapy, Christiane Bouchier, Simon Baeriswyl, Benoit Vacherie, Stéphane Cruveiller, Mathilde Lescat, Odile Bouvet, Carole Dossat, Claudine Médigue, Médéric Diard, Hélène Chiapello, Atelier de BioInformatique (ABI), Université Pierre et Marie Curie - Paris 6 (UPMC), Génomique évolutive des microbes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Ecologie et Evolution des Microorganismes (EEM), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génétique moléculaire, évolutive et médicale, IFR65-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris 7, Hôpital Robert Debré-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris] (IP), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Mathématique, Informatique, et Génomique, Institut National de la Recherche Agronomique (INRA), Génétique des Génomes Bactériens, Pathogénie des infections systémiques (UMR_S 570), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génétique des Biofilms, Veterans Affairs Medical Center, Department of Medecine, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Pathogénie Bactérienne des Muqueuses, Unité des Bactéries Lactiques et Pathogènes Opportunistes, Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Gagnon, Jean, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7)-Université Paris 13 (UP13)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique (Plate-Forme), Institut Pasteur [Paris], University of Minnesota [Twin Cities], IFR65-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Atelier de BioInformatique ( ABI ), Université Pierre et Marie Curie - Paris 6 ( UPMC ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Ecologie et Evolution des Microorganismes ( EEM ), Université Paris 13 ( UP13 ) -Université Paris Diderot - Paris 7 ( UPD7 ) -Université Sorbonne Paris Cité ( USPC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), IFR65-Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Hôpital Robert Debré-Université Paris Diderot - Paris 7 ( UPD7 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut National de la Recherche Agronomique ( INRA ), Pathogénie des infections systémiques ( UMR_S 570 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), University of Minnesota [Minneapolis], Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] ( LAPM ), and Université Joseph Fourier - Grenoble 1 ( UJF ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: MESH : Escherichia coli, Cancer Research, MESH : Polymorphism, Genetic, MESH : Recombination, Genetic, MESH : Models, Genetic, MESH : Models, Biological, MESH: Genome, Bacterial, Genome, MESH: Genetics, Gene flow, MESH : Genetics, MESH: Models, Genetic, MESH: Phylogeny, bioinformatique, Phylogeny, Genetics (clinical), MESH: Evolution, Molecular, Recombination, Genetic, bactérie, 2. Zero hunger, Genetics, Likelihood Functions, 0303 health sciences, Phylogenetic tree, MESH: Escherichia coli, MESH: Genomics, Genomics, Genome project, Evolutionary Biology/Microbial Evolution and Genomics, MESH: DNA Transposable Elements, MESH : DNA Transposable Elements, MESH: Recombination, Genetic, escherichia coli, MESH : Likelihood Functions, Research Article, lcsh:QH426-470, MESH : Genome, Bacterial, Biology, Models, Biological, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, MESH: Polymorphism, Genetic, Escherichia coli, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Genome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Evolution, Molecular, Gene conversion, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Comparative genomics, Polymorphism, Genetic, Evolutionary Biology/Evolutionary and Comparative Genetics, Models, Genetic, 030306 microbiology, génome, MESH : Genomics, MESH: Models, Biological, MESH : Phylogeny, Microbiology/Medical Microbiology, lcsh:Genetics, DNA Transposable Elements, MESH: Likelihood Functions, MESH : Genome, Genome, Bacterial
Abstract: The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome., Author Summary Although abundant knowledge has been accumulated regarding the E. coli laboratory strain K-12, little is known about the evolutionary trajectories that have driven the high diversity observed among natural isolates of the species, which encompass both commensal and highly virulent intestinal and extraintestinal pathogenic strains. We have annotated or re-annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Although recombination rates are much higher than mutation rates, we were able to reconstruct a robust phylogeny based on the ∼2,000 genes common to all strains. Based on this phylogeny, we established the evolutionary scenario of gains and losses of thousands of specific genes, identifying functional classes under opposite selection pressures. This genome flux is confined to very few positions in the chromosome, which are the same for every genome. Notably, we identified few or no extraintestinal virulence-specific genes. We also defined a long-scale structure of recombination in the genome with lower recombination rates at the terminus of replication. These findings demonstrate that, despite a very high gene flow, genes can co-exist in an organised genome.
Published: 2009

37. Epidemiological surveillance of mycoplasmas belonging to the 'Mycoplasma mycoides' cluster: is DGGE fingerprinting of 16S rRNA genes suitable?

Author: Laure Maigre, François Poumarat, A. Tricot, Florence Tardy, Patrice Gaurivaud, Laboratoire d'études et de recherches en pathologie bovine et hygiène des viandes, AFSSA, Mycoplasmoses des ruminants [Lyon], Université de Lyon-VetAgro Sup ( VAS ), Agence Française de Sécurité Sanitaire des Aliments (AFSSA), Mycoplasmoses des Ruminants - UMR (MYCO), and Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: MESH : Mycoplasma Infections, MESH : Molecular Sequence Data, 16SrRNA gene, MESH: Base Sequence, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, medicine.disease_cause, Applied Microbiology and Biotechnology, strains detection and identification, MESH: Mycoplasma, Mycoplasma, MESH : Cattle, RNA, Ribosomal, 16S, MESH: Cattle Diseases, MESH: DNA Fingerprinting, MESH : DNA, Ribosomal, MESH : DNA, Bacterial, MESH: Animals, 1UMYCOPLASME, DGGE, MESH: Phylogeny, Phylogeny, MESH: DNA, Ribosomal, biology, Phylogenetic tree, MESH : Sequence Alignment, Goats, epidemiological surveillance, [ SDV.SPEE ] Life Sciences [q-bio]/Santé publique et épidémiologie, MESH : DNA Fingerprinting, MESH: RNA, Ribosomal, 16S, MESH: Cattle, "Mycoplasma mycoides" cluster, Electrophoresis, Polyacrylamide Gel, Mycoplasma mycoides, Temperature gradient gel electrophoresis, DNA, Bacterial, Sequence analysis, Molecular Sequence Data, MESH: Sequence Alignment, Cattle Diseases, MESH : Goat Diseases, MESH: Goat Diseases, MESH : Electrophoresis, Polyacrylamide Gel, MESH: Goats, DNA, Ribosomal, MYCOPLASME, Microbiology, Phylogenetics, medicine, Animals, Humans, Mycoplasma Infections, MESH : Cattle Diseases, MESH: Humans, MESH: Molecular Sequence Data, MESH : Mycoplasma, Goat Diseases, Base Sequence, MESH : Humans, MESH : Phylogeny, Ribosomal RNA, MESH: Mycoplasma Infections, biology.organism_classification, 16S ribosomal RNA, MESH: DNA, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, DNA Fingerprinting, MESH : RNA, Ribosomal, 16S, MESH : Goats, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Mycoplasma mycoides" cluster, MESH : Base Sequence, Cattle, MESH : Animals, Sequence Alignment, MESH: Electrophoresis, Polyacrylamide Gel
Abstract: Aims: The analysis by Denaturing Gradient Gel Electrophoresis (DGGE) of the PCR-amplified V3 region of 16S rRNA gene was previously shown to detect and differentiate a large number of human and animal mycoplasmas. In this study, we further assessed the suitability of the technique for epidemiological surveillance of mycoplasmas belonging to the ‘Mycoplasma mycoides’ cluster, a phylogenetic group that includes major ruminant pathogens. Methods and Results: The V3 region of 16S rRNA genes from approx. 50 field strains was amplified and analysed by DGGE. Detection and identification results were compared with the ones obtained by antigenic testing and sequence analysis. Conclusions: The DGGE technique is robust and valuable as a first-line test, but the patterns obtained for strains belonging to the ‘M. mycoides’ cluster were too variable within a taxon and in contrast too conserved between taxa to allow an unequivocal identification of isolates without further analysis. Significance and Impact of the Study: Issues raised by the quest for a single universal test able to detect and identify any mycoplasma in one clinical sample are thoroughly documented.
Published: 2008

38. Phylogenetic analysis of viridans group streptococci causing endocarditis

Author: Marie Francoise Tripodi, Mercedes Marín, Tony M. Korman, Patrick Plésiat, L. Barth Reller, Efthymia Giannitsioti, Thanh Doco-Lecompte, David R. Murdoch, Christopher W. Woods, Dannah Wray, Selwyn Lang, Stanley Mirrett, Lori Hall, Keith E. Simmon, Suzanne Ryan, Phillip Jones, Riccardo Utili, Francesc Marco, David L. Gordon, Arjana Tambic, Arthur J. Morris, Cathy A. Petti, Christopher H. Cabell, Suzanne F. Bradley, Bruno Hoen, José M. Miró, Service des maladies infectieuses et tropicales, Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Hôpital Saint-Jacques, Agents pathogènes et inflammation - UFC (EA 4266) (API), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ) -Hôpital Saint-Jacques, Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Agents pathogènes et inflammation - UFC (EA 4266) ( API ), Université de Franche-Comté ( UFC ), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Simmon, Ke, Hall, L, Woods, Cw, Marco, F, Miro, Jm, Cabell, C, Hoen, B, Marin, M, Utili, Riccardo, Giannitsioti, E, DOCO LECOMPTE, T, Bradley, S, Mirrett, S, Tambic, A, Ryan, S, Gordon, D, Jones, P, Korman, T, Wray, D, Reller, Lb, Tripodi, Mf, Plesiat, P, Morris, Aj, Lang, S, Murdoch, Dr, Petti, Ca, and INTERNATIONAL COLLABORATION ON ENDOCARDITIS MICROBIOLOGY, Investigators
Subjects: Microbiology (medical), MESH: Sequence Analysis, DNA, Sequence analysis, Concordance, MESH : Streptococcal Infections, Biology, Microbiology, 03 medical and health sciences, Species level, MESH: Streptococcal Infections, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Phylogenetics, Streptococcal Infections, medicine, Humans, Endocarditis, MESH : Viridans Streptococci, MESH: Endocarditis, Bacterial, MESH : Endocarditis, Bacterial, MESH: Phylogeny, Clinical syndrome, Phylogeny, 030304 developmental biology, Genetics, 0303 health sciences, MESH: Humans, Phylogenetic tree, 030306 microbiology, MESH: Viridans Streptococci, MESH : Humans, MESH : Phylogeny, Bacteriology, Endocarditis, Bacterial, Sequence Analysis, DNA, Viridans Streptococci, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Identification (biology), MESH : Sequence Analysis, DNA
Abstract: Identification of viridans group streptococci (VGS) to the species level is difficult because VGS exchange genetic material. We performed multilocus DNA target sequencing to assess phylogenetic concordance of VGS for a well-defined clinical syndrome. The hierarchy of sequence data was often discordant, underscoring the importance of establishing biological relevance for finer phylogenetic distinctions.
Published: 2008

39. Delivery of mengovirus-derived RNA replicons into tumoural liver enhances the anti-tumour efficacy of a peripheral peptide-based vaccine

Author: Sylvie van der Werf, Mireille Viguier, Carmen Marchiol, Didier Fradelizi, Anne-Marie Crain, Jean-Pierre Couty, Sarah Boudaly, Marilyne Labasque, Marco Vignuzzi, Catherine Guettier, Nicolas Escriou, Sylvie Gerbaud, Institut Cochin (UMR_S567 / UMR 8104), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5), Université Paris Diderot - Paris 7 (UPD7), Génétique Moléculaire des Virus Respiratoires, Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Pathologie cellulaire : aspects moléculaires et viraux / Pathologie et Virologie Moléculaire, Institut Universitaire d'Hématologie (IUH), Université Paris Diderot - Paris 7 (UPD7)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Anatomie Pathologique, Hôpital Paul Brousse, Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Institut Pasteur [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut Cochin ( UMR_S567 / UMR 8104 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Cochin ( UM3 (UMR 8104 / U1016) ), Université Paris Descartes - Paris 5 ( UPD5 ), Université Paris Diderot - Paris 7 ( UPD7 ), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Immunologie Cellulaire et Immunopathologie de l'Ecole Pratique des Hautes Etudes, Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Université Paris Diderot - Paris 7 (UPD7)-Université Paris Diderot - Paris 7 (UPD7)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Male, MESH : Prevalence, MESH: Immunotherapy, medicine.medical_treatment, MESH: Flow Cytometry, Epitope, MESH: Cancer Vaccines, Mice, 0302 clinical medicine, MESH: Liver Neoplasms, Cytotoxic T cell, MESH: Animals, Replicon, MESH : Influenza A Virus, H9N2 Subtype, MESH: Phylogeny, MESH: Treatment Outcome, 0303 health sciences, MESH : Peptides, MESH: Peptides, Liver Neoplasms, MESH : Reverse Transcriptase Polymerase Chain Reaction, Flow Cytometry, MESH : Influenza in Birds, 3. Good health, MESH : Influenza A virus, MESH : Immunotherapy, Oncology, MESH: RNA, Viral, MESH : Animal Migration, Immunotherapy, Carcinoma, Hepatocellular, T cell, Immunology, MESH: Replicon, 03 medical and health sciences, MESH: Species Specificity, MESH: Animals, Wild, MESH : Birds, MESH: Prevalence, Histocompatibility Antigens Class I, Mengovirus, RNA, MESH : Disease Models, Animal, Mice, Inbred C57BL, MESH: Disease Models, Animal, Peptides, MESH: Female, Cancer Research, MESH : Liver Neoplasms, MESH : Mengovirus, MESH: Histocompatibility Antigens Class I, MESH: Reverse Transcriptase Polymerase Chain Reaction, Immunology and Allergy, MESH : Female, MESH: Carcinoma, Hepatocellular, MESH : Animals, Wild, MESH : Cloaca, biology, MESH : Cancer Vaccines, MESH: Animal Migration, medicine.anatomical_structure, Treatment Outcome, MESH: Birds, MESH: Sentinel Surveillance, RNA, Viral, MESH : Histocompatibility Antigens Class I, MESH : Replicon, MESH : Carcinoma, Hepatocellular, MESH : Sentinel Surveillance, MESH : Flow Cytometry, MESH : Male, MESH: Influenza A virus, MESH : Mice, Inbred C57BL, MESH : Treatment Outcome, Cancer Vaccines, MESH: Influenza in Birds, MESH: Mice, Inbred C57BL, MESH : Mice, medicine, MESH : Species Specificity, MESH : RNA, Viral, Animals, MESH : France, MESH: Mice, 030304 developmental biology, MESH : Phylogeny, biology.organism_classification, MESH: Male, MESH: Cloaca, MESH: Influenza A Virus, H9N2 Subtype, MESH: France, Disease Models, Animal, MESH : Animals, CD8, MESH: Mengovirus, 030215 immunology
Abstract: International audience; Hepatocellular carcinoma is a deadly cancer with growing incidence for which immunotherapy is one of the most promising therapeutic approach. Peptide-based vaccines designed to induce strong, sustained CD8+ T cell responses are effective in animal models and cancer patients. We demonstrated the efficacy of curative peptide-based immunisation against a unique epitope of SV40 tumour antigen, through the induction of a strong CD8+ T cell-specific response, in our liver tumour model. However, as in human clinical trials, most tumour antigen epitopes did not induce a therapeutic effect, despite inducing strong CD8+ T cell responses. We therefore modified the tumour environment to enhance peptide-based vaccine efficacy by delivering mengovirus (MV)-derived RNA autoreplicating sequences (MV-RNA replicons) into the liver. The injection of replication-competent RNA replicons into the liver converted partial tumour regression into tumour eradication, whereas non-replicating RNA had no such effect. Replicating RNA replicon injection induced local recruitment of innate immunity effectors (NK and NKT) to the tumour and did not affect specific CD8+ T cell populations or other myelolymphoid subsets. The local delivery of such RNA replicons into tumour stroma is therefore a promising strategy complementary to the use of peripheral peptide-based vaccines for treating liver tumours.
Published: 2008

40. Tetrameric and homodimeric camelid IgGs originate from the same IgH locus

Author: Pierre Lafaye, Patricia Cavelier, Ikbel Achour, François Rougeon, Christiane Bouchier, Magali Tichit, Génétique et Biochimie du Développement, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut de Génétique Moléculaire de Montpellier ( IGMM ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Génomique (Plate-Forme), Institut Pasteur [Paris], Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris] (IP), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Subjects: MESH: Immunoglobulins, MESH : Molecular Sequence Data, MESH: Amino Acid Sequence, MESH: Base Sequence, MESH : Immunoglobulins, 0302 clinical medicine, Immunology and Allergy, MESH: Animals, MESH: Phylogeny, Peptide sequence, Phylogeny, Genetics, 0303 health sciences, B-Lymphocytes, biology, MESH : Amino Acid Sequence, MESH: Camels, MESH : Protein Binding, Translocon, medicine.anatomical_structure, MESH : Dimerization, Cosmid, MESH: Camelids, New World, Antibody, Camelids, New World, Dimerization, Protein Binding, Camelus, MESH : Cell Membrane, Immunology, Molecular Sequence Data, Immunoglobulins, [ SDV.IMM.IMM ] Life Sciences [q-bio]/Immunology/Immunotherapy, MESH : B-Lymphocytes, 03 medical and health sciences, Complementary DNA, MESH: B-Lymphocytes, medicine, MESH: Protein Binding, Animals, Amino Acid Sequence, Gene, B cell, 030304 developmental biology, MESH: Molecular Sequence Data, MESH : Camels, Base Sequence, Cell Membrane, MESH : Phylogeny, [SDV.IMM.IMM]Life Sciences [q-bio]/Immunology/Immunotherapy, Molecular biology, MESH : Camelids, New World, Chromosome 4, MESH: Dimerization, biology.protein, MESH : Base Sequence, MESH : Animals, 030215 immunology, MESH: Cell Membrane
Abstract: In addition to producing conventional tetrameric IgGs, camelids have the particularity of producing a functional homodimeric IgG type lacking L (light) chains and only made up of two H (heavy) chains. This nonconventional IgG type is characterized by variable and constant regions referred to as VHH and CHH, respectively, and which differ from conventional VH and CH counterparts. Although the structural properties of homodimeric IgGs have been well investigated, the genetic bases involved in their generation are still largely unknown. In this study, we characterized the organization of genes coding for the H chains of tetrameric and homodimeric IgGs by constructing an alpaca (Lama pacos) genomic cosmid library. We showed that a single IgH locus in alpaca chromosome 4 contains all of the genetic elements required for the generation of the two types of Igs. The alpaca IgH locus is composed of a V region that contains both VHH and VH genes followed by a unique DH-JH cluster and C region genes, which include both CHH and CH genes. Although this general gene organization greatly resembles that of other typical mammalian Vn-Dn-Jn-Cn translocon IgH loci, the intermixed gene organization within the alpaca V and C regions reveals a new type of translocon IgH locus. Furthermore, analyses of cDNA coding for the membrane forms of IgG and IgM present in alpaca peripheral blood B cells are most consistent with the notion that the development of a B cell bearing homodimeric IgG passes through an IgM+ stage, similar to the case for conventional IgG.
Published: 2008

41. Diversity surveys and evolutionary relationships of aoxB genes in aerobic arsenite-oxidizing bacteria

Author: Marianne Quéméneur, Michel Jauzein, Audrey Heinrich-Salmeron, Didier Lièvremont, Catherine Joulian, Daniel Muller, Philippe N. Bertin, Francis Garrido, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire de Biologie Tumorale, CRLCC Paul Strauss, XLIM (XLIM), Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Génétique moléculaire, génomique, microbiologie ( GMGM ), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), XLIM ( XLIM ), Université de Limoges ( UNILIM ) -Centre National de la Recherche Scientifique ( CNRS ), and Bureau de Recherches Géologiques et Minières (BRGM) ( BRGM )
Subjects: Chemoautotrophic Growth, MESH: Sequence Analysis, Protein, MESH: Amino Acid Sequence, MESH: Base Sequence, Polymerase Chain Reaction, MESH : Arsenites, Conserved sequence, Sequence Analysis, Protein, RNA, Ribosomal, 16S, MESH : Genetic Markers, MESH : DNA, Bacterial, Soil Pollutants, MESH: Genetic Variation, MESH: Phylogeny, MESH : Proteobacteria, Phylogeny, 0303 health sciences, MESH: Conserved Sequence, MESH : Amino Acid Sequence, MESH : Genes, Bacterial, Bacterial, MESH : Oxidoreductases, MESH: RNA, Ribosomal, 16S, MESH : DNA Primers, MESH: Arsenites, Proteobacteria, Genetic Markers, MESH: DNA Primers, 16S, Sequence analysis, Arsenites, MESH : Soil Microbiology, Molecular Sequence Data, MESH: Biodiversity, 03 medical and health sciences, Phylogenetics, MESH : Conserved Sequence, MESH : Bacteria, Amino Acid Sequence, MESH: Oxidoreductases, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Oxidation-Reduction, Ribosomal, MESH: Soil Pollutants, MESH: Molecular Sequence Data, Bacteria, 030306 microbiology, Alphaproteobacteria, Genetic Variation, MESH: Polymerase Chain Reaction, DNA, Ribosomal RNA, MESH: DNA, Bacterial, Genes, MESH : Sequence Analysis, Protein, MESH : Sequence Analysis, DNA, MESH: Oxidation-Reduction, MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, MESH: Genetic Markers, Applied Microbiology and Biotechnology, MESH : Soil Pollutants, MESH : Biodiversity, MESH : Polymerase Chain Reaction, Betaproteobacteria, Conserved Sequence, Soil Microbiology, Genetics, Ecology, biology, Biodiversity, MESH: Genes, Bacterial, Oxidoreductases, Oxidation-Reduction, Sequence Analysis, Biotechnology, DNA, Bacterial, MESH : Chemoautotrophic Growth, Microbial Ecology, MESH : Genetic Variation, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, DNA Primers, Base Sequence, Protein, MESH : Phylogeny, Sequence Analysis, DNA, MESH: Proteobacteria, biology.organism_classification, 16S ribosomal RNA, MESH: Chemoautotrophic Growth, MESH : RNA, Ribosomal, 16S, MESH: Bacteria, MESH: Soil Microbiology, Genes, Bacterial, RNA, MESH : Base Sequence, Food Science
Abstract: A new primer set was designed to specifically amplify ca. 1,100 bp of aoxB genes encoding the As(III) oxidase catalytic subunit from taxonomically diverse aerobic As(III)-oxidizing bacteria. Comparative analysis of AoxB protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. AoxB phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16S rRNA phylogeny. Alphaproteobacteria -, Betaproteobacteria -, and Gammaproteobacteria -related sequences were retrieved from environmental surveys, demonstrating their prevalence in mesophilic As-contaminated soils. Our study underlines the usefulness of the aoxB gene as a functional marker of aerobic As(III) oxidizers.
Published: 2008

42. Genotypic diversity of coagulase-negative staphylococci causing endocarditis: a global perspective

Author: Cathy A. Petti, Efthymia Giannitsioti, Dannah Wray, Bruno Hoen, Tony M. Korman, Emilio Bouza, Thanh Doco-Lecompte, Jerome J. Federspiel, Patrick Plésiat, Riccardo Utili, L. Barth Reller, Eugene Athan, Arthur J. Morris, David R. Murdoch, Suzanne F. Bradley, Suzanne Ryan, José M. Miró, Annibale Raglio, Francesca Tripodi, Francesc Marco, Christopher W. Woods, K. Boisson, Vivian H. Chu, Porl Reinbott, Cristina Garcia-de-la-Maria, David L. Gordon, Selwyn Lang, Keith E. Simmon, Vance G. Fowler, Suzana Bukovski, Service des maladies infectieuses et tropicales, Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Hôpital Saint-Jacques, Agents pathogènes et inflammation - UFC (EA 4266) (API), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ) -Hôpital Saint-Jacques, Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Agents pathogènes et inflammation - UFC (EA 4266) ( API ), Université de Franche-Comté ( UFC ), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Petti, Ca, Simmon, Ke, Miro, Jm, Hoen, B, Marco, F, Chu, Vh, Athan, E, Bukovski, S, Bouza, E, Bradley, S, Fowler, Vg, Giannitsioti, E, Gordon, D, Reinbott, P, Korman, T, Lang, S, DE LA MARIA, Cg, Raglio, A, Morris, Aj, Plesiat, P, Ryan, S, DOCO LECOMPTE, T, Tripodi, F, Utili, Riccardo, Wray, D, Federspiel, Jj, Boisson, K, Reller, Lb, Murdoch, Dr, Woods, Cw, and THE ICE MICRO, Investigators
Subjects: MESH: Sequence Analysis, DNA, Epidemiology, MESH : Polymorphism, Genetic, Staphylococcus, MESH : Aged, MESH : Coagulase, Sequence Homology, MESH : Genotype, MESH: Genotype, endocarditis, coagulase-negative staphylococci, DNA target sequencing, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genotype, MESH : DNA, Ribosomal, MESH : DNA, Bacterial, MESH: Sequence Homology, MESH : Anti-Bacterial Agents, MESH : Endocarditis, Bacterial, MESH: Phylogeny, Phylogeny, Genetics, MESH: Aged, 0303 health sciences, MESH: Microbial Sensitivity Tests, MESH: Middle Aged, MESH: DNA, Ribosomal, MESH: Staphylococcus, DNA-Directed RNA Polymerases, Middle Aged, 3. Good health, Anti-Bacterial Agents, Bacterial Typing Techniques, [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Infective endocarditis, Coagulase, MESH: Coagulase, Microbiology (medical), DNA, Bacterial, Sequence analysis, Microbial Sensitivity Tests, Biology, Peptide Elongation Factor Tu, DNA, Ribosomal, MESH: Bacterial Typing Techniques, Microbiology, Bacterial genetics, 03 medical and health sciences, MESH : Sequence Homology, MESH : DNA-Directed RNA Polymerases, MESH: Anti-Bacterial Agents, MESH: Peptide Elongation Factor Tu, MESH: Polymorphism, Genetic, medicine, Endocarditis, Humans, MESH : Middle Aged, MESH: Endocarditis, Bacterial, 030304 developmental biology, Aged, MESH : Staphylococcus, Genetic diversity, Polymorphism, Genetic, MESH: Humans, 030306 microbiology, MESH : Humans, MESH : Phylogeny, Endocarditis, Bacterial, Sequence Analysis, DNA, medicine.disease, rpoB, MESH: DNA, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: DNA-Directed RNA Polymerases, MESH : Bacterial Typing Techniques, MESH : Microbial Sensitivity Tests, MESH : Peptide Elongation Factor Tu, MESH : Sequence Analysis, DNA
Abstract: Coagulase-negative staphylococci (CNS) are important causes of infective endocarditis (IE), but their microbiological profiles are poorly described. We performed DNA target sequencing and susceptibility testing for 91 patients with definite CNS IE who were identified from the International Collaboration on Endocarditis—Microbiology, a large, multicenter, multinational consortium. A hierarchy of gene sequences demonstrated great genetic diversity within CNS from patients with definite endocarditis that represented diverse geographic regions. In particular, rpoB sequence data demonstrated unique genetic signatures with the potential to serve as an important tool for global surveillance.
Published: 2008

43. Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times

Author: Calvignac, Sébastien, Hughes, Sandrine, Tougard, Christelle, Michaux, Jacques, Thevenot, Michel, Philippe, Michel, Hamdine, Watik, Hänni, Catherine, Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Conservation et d'Étude sur les Collections (CCEC), Muséeum d'Histoire Naturelle, Work supported by the CNRS (eclipse program), University Lyon I and the programme ‘Dynamique évolutive des espèces fractionnées, insulaires et invasives' of the EPHE. Contribution ISEM 2006–085., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Génomique Fonctionnelle de Lyon ( IGFL ), École normale supérieure - Lyon ( ENS Lyon ) -Institut National de la Recherche Agronomique ( INRA ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Institut des Sciences de l'Evolution de Montpellier ( ISEM ), Université de Montpellier ( UM ) -Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique ( CNRS ), Centre d’Ecologie Fonctionnelle et Evolutive ( CEFE ), Université Paul-Valéry - Montpellier 3 ( UM3 ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -École pratique des hautes études ( EPHE ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), and Centre de Conservation et d'Étude sur les Collections ( CCEC )
Subjects: MESH : Molecular Sequence Data, MESH : Cytochromes b, MESH: Africa, Northern, brown bear, phylogeography, MESH: Base Sequence, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Polymerase Chain Reaction, MESH: Fossils, MESH: Variation (Genetics), MESH: Extinction, Biological, Africa, Northern, MESH : DNA, Mitochondrial, MESH: Animals, MESH: Phylogeny, MESH : Ursidae, MESH : Polymerase Chain Reaction, Phylogeny, [ SDU.STU.PG ] Sciences of the Universe [physics]/Earth Sciences/Paleontology, MESH : Variation (Genetics), Fossils, mtDNA, MESH : Sequence Alignment, Cytochromes b, MESH: Cytochromes b, MESH : Africa, Northern, [ SDV.GEN.GPO ] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], MESH : Extinction, Biological, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Ursidae, MESH: Ursidae, Molecular Sequence Data, MESH: Sequence Alignment, Extinction, Biological, DNA, Mitochondrial, Animals, ancient DNA, MESH: Molecular Sequence Data, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Base Sequence, Holocene, MESH: DNA, Mitochondrial, MESH : Phylogeny, Genetic Variation, MESH: Polymerase Chain Reaction, North Africa, MESH : Fossils, MESH : Base Sequence, MESH : Animals, Sequence Alignment, human activities, [ SDV.BID.SPT ] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Abstract: 9 pages; International audience; The genetic diversity of present-day brown bears (Ursus arctos) has been extensively studied over the years and appears to be geographically structured into five main clades. The question of the past diversity of the species has been recently addressed by ancient DNA studies that concluded to a relative genetic stability over the last 35,000 years. However, the post-last glacial maximum genetic diversity of the species still remains poorly documented, notably in the Old World. Here, we analyse Atlas brown bears, which became extinct during the Holocene period. A divergent brown bear mitochondrial DNA lineage not present in any of the previously studied modern or ancient bear samples was uncovered, suggesting that the diversity of U. arctos was larger in the past than it is now. Specifically, a significant portion (with respect to sequence divergence) of the intraspecific diversity of the brown bear was lost with the extinction of the Atlas brown bear after the Pleistocene/Holocene transition.
Published: 2008

44. Molecular and biochemical characterization of a cathepsin B-like protease family unique to Trypanosoma congolense

Author: Edith Authié, Théo Baltz, Theresa H.T. Coetzer, Nicolas Biteau, Virginie Coustou, C. Giroud, Carlos Mendoza-Palomares, Alain Boulangé, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Microbiologie cellulaire et moléculaire et pathogénicité (MCMP), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire biologie moléculaire et immunologie de protozoaires parasites, Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5) - Centre National de la Recherche Scientifique (CNRS), Université Bordeaux Segalen - Bordeaux 2 - Centre National de la Recherche Scientifique (CNRS), Université de Lyon - Université de Lyon - Centre National de la Recherche Scientifique (CNRS), ProdInra, Migration, Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Programme forêts naturelles (Cirad-Forêt programme Forêts naturelles), Département Forêt (Cirad-FORET), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Infectiologie Animale et Santé Publique (UR IASP), Institut National de la Recherche Agronomique (INRA), UMR Trypanosomes, Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)
Subjects: MESH : Molecular Sequence Data, Trypanosoma congolense, [SDV]Life Sciences [q-bio], Cathepsin E, MESH: Amino Acid Sequence, Cathepsin F, L73 - Maladies des animaux, Cathepsin A, Cathepsin B, Cathepsin C, MESH: Recombinant Proteins, 0302 clinical medicine, Cathepsin O, Cathepsin H, Cathepsin L1, Immunologie, MESH: Animals, MESH: Phylogeny, Phylogeny, 0303 health sciences, MESH : Amino Acid Sequence, MESH : Sequence Alignment, Contrôle de maladies, MESH : Trypanosoma congolense, Cystéine, General Medicine, Articles, MESH: Trypanosoma congolense, Recombinant Proteins, 3. Good health, [SDV] Life Sciences [q-bio], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, PCR, Biochemistry, Multigene Family, Protéase, MESH : Recombinant Proteins, 030231 tropical medicine, Molecular Sequence Data, MESH : Multigene Family, MESH: Sequence Alignment, MESH : Cathepsins, Biology, Microbiology, 03 medical and health sciences, Animals, Peptidase, Amino Acid Sequence, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Molecular Biology, 030304 developmental biology, MESH: Molecular Sequence Data, Anticorps, MESH : Phylogeny, Molecular biology, Cathepsins, MESH: Cathepsins, MESH: Multigene Family, MESH : Animals, Sequence Alignment
Abstract: Cysteine proteases have been shown to be essential virulence factors and drug targets in trypanosomatids and an attractive antidisease vaccine candidate forTrypanosoma congolense. Here, we describe an important amplification of genes encoding cathepsin B-like proteases unique toT. congolense. More than 13 different genes were identified, whereas only one or two highly homologous genes have been identified in other trypanosomatids. These proteases grouped into three evolutionary clusters: TcoCBc1 to TcoCBc5 and TcoCBc6, which possess the classical catalytic triad (Cys, His, and Asn), and TcoCBs7 to TcoCBs13, which contains an unusual catalytic site (Ser, Xaa, and Asn). Expression profiles showed that members of the TcoCBc1 to TcoCBc5 and the TcoCBs7 to TcoCBs13 groups are expressed mainly in bloodstream forms and localize in the lysosomal compartment. The expression of recombinant representatives of each group (TcoCB1, TcoCB6, and TcoCB12) as proenzymes showed that TcoCBc1 and TcoCBc6 are able to autocatalyze their maturation 21 and 31 residues, respectively, upstream of the predicted start of the catalytic domain. Both displayed a carboxydipeptidase function, while only TcoCBc1 behaved as an endopeptidase. TcoCBc1 exhibited biochemical differences regarding inhibitor sensitivity compared to that of other cathepsin B-like proteases. Recombinant pro-TcoCBs12 did not automature in vitro, and the pepsin-matured enzyme was inactive in tests with cathepsin B fluorogenic substrates. In vivo inhibition studies using CA074Me (a cell-permeable cathepsin B-specific inhibitor) demonstrated that TcoCB are involved in lysosomal protein degradation essential for survival in bloodstream form. Furthermore, TcoCBc1 elicited an important immune response in experimentally infected cattle. We propose this family of proteins as a potential therapeutic target and as a plausible antigen forT. congolensediagnosis.
Published: 2008

45. A novel nonsymbiotic hemoglobin from oak: cellular and tissue specificity of gene expression

Author: Audrey Berger, James F. Dat, Pierre-Marie Badot, Hélène Folzer, Nicolas Capelli, Michèle Crèvecoeur, Claire Parent, Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Département de Botanique et Biologie Végétale, Université de Genève ( UNIGE ), Institut Méditerranéen d'Ecologie et de Paléoécologie ( IMEP ), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Université d'Avignon et des Pays de Vaucluse ( UAPV ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Université de Genève (UNIGE), Institut Méditerranéen d'Ecologie et de Paléoécologie (IMEP), Université Paul Cézanne - Aix-Marseille 3-Centre National de la Recherche Scientifique (CNRS)-Avignon Université (AU)-Université de Provence - Aix-Marseille 1, Laboratoire Chrono-environnement (UMR 6249) (LCE), Université de Genève = University of Geneva (UNIGE), and Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, MESH : Molecular Sequence Data, MESH : Oxygen, Physiology, MESH: Plant Shoots, MESH : Plant Roots, MESH: Plant Roots, Plant Science, MESH: Amino Acid Sequence, MESH: RNA, Plant, MESH : Hemoglobins, 01 natural sciences, Plant Roots, Hemoglobins, Quercus, Gene Expression Regulation, Plant, Gene expression, Cloning, Molecular, Hypoxia, MESH: Phylogeny, Peptide sequence, Phylogeny, MESH: Organ Specificity, Plant Proteins, 0303 health sciences, Oak (Quercus petraea, Quercus robur), MESH: Plant Proteins, MESH : Amino Acid Sequence, MESH : In Situ Hybridization, nonsymbiotic hemoglobin, MESH : Plant Shoots, MESH : Water, ddc:580, MESH: Hemoglobins, Organ Specificity, RNA, Plant, Quercus petraea, oak (Quercus petraea, In situ hybridization, Quercus robur), Plant Shoots, MESH: Oxygen, MESH : Cloning, Molecular, Molecular Sequence Data, education, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Quercus robur, MESH : Organ Specificity, 03 medical and health sciences, MESH: Gene Expression Profiling, MESH: In Situ Hybridization, ddc:570, MESH: Quercus, MESH : Plant Proteins, Botany, MESH: Water, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Cloning, Molecular, Northern blot, Amino Acid Sequence, MESH: Gene Expression Regulation, Plant, Gene, 030304 developmental biology, MESH: Molecular Sequence Data, hypoxia, MESH : RNA, Plant, [ SDV.BC ] Life Sciences [q-bio]/Cellular Biology, Gene Expression Profiling, MESH : Gene Expression Profiling, Water, MESH : Phylogeny, Meristem, biology.organism_classification, Molecular biology, Oxygen, Nonsymbiotic hemoglobin, gene expression, in situ hybridization, MESH : Quercus, MESH : Gene Expression Regulation, Plant, 010606 plant biology & botany
Abstract: International audience; This study presents the isolation and characterization of a novel nonsymbiotic Hb gene from sessile oak (Quercus petraea) seedlings, herein designated QpHb1. The cellular and tissue expression of QpHb1 was analysed by Northern blotting and in situ hybridization. The encoded protein was predicted to consist of 161 amino acid residues, and shares 71 and 51% amino acid sequence identity with the Arabidopsis class 1 and 2 nonsymbiotic Hb, respectively. Northern blot analysis revealed that QpHb1 was strongly expressed in roots. Spatial expression analysis of QpHb1 in the root apical region of sessile oak by in situ hybridization indicated that transcripts were mostly abundant in protoxylem cell initials, some cortical cells and the protoderm. In addition, when comparing the expression profile of QpHb1 in sessile and pedunculate oak (Quercus robur), two species with contrasted hypoxia tolerance, the transcript level of QpHb1 rose early in the most flood-tolerant species, pedunculate oak, during root submergence. The spatial-temporal expression of QpHb1 suggests that this gene could participate in perception and signalling during hypoxia.
Published: 2008

46. Molluscan shell proteins: primary structure, origin, and evolution

Author: Marin , Frédéric, Luquet , Gilles, Marie , Benjamin, Medakovic , Davorin, Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Center for Marine Research Rovinj, Ruder Boskovic Institute, ‘‘Aide Concertée Incitative Jeunes Chercheurs' (ACI JC 3049) awarded by the French ‘‘Ministère Délégué à la Recherche et aux Nouvelles Technologies' ANR project (ACCRO–Earth, ref. BLAN06–2_159971, coordinator Gilles Ramstein, LSCE, Gif/Yvette) Financial supports provided by the ‘‘Conseil Régional de Bourgogne' (Dijon, France), Gerald P. Schatten, Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and Rudjer Boskovic Institute [Zagreb]
Subjects: MESH: Hydrogen-Ion Concentration, MESH: Molecular Structure, MESH : Calcification, Physiologic, MESH: Calcification, Physiologic, Evolution, Molecular, MESH : Proteins, Calcification, Physiologic, MESH : Hydrogen-Ion Concentration, Animals, MESH: Animals, MESH: Proteins, MESH : Evolution, Molecular, MESH: Phylogeny, [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, Phylogeny, MESH: Evolution, Molecular, Molecular Structure, Proteins, MESH : Phylogeny, Hydrogen-Ion Concentration, [ SDV.IB.BIO ] Life Sciences [q-bio]/Bioengineering/Biomaterials, MESH: Mollusca, Mollusca, MESH : Animals, MESH : Mollusca, MESH : Molecular Structure
Abstract: 68 pages; International audience; In the last few years, the field of molluscan biomineralization has known a tremendous mutation, regarding fundamental concepts on biomineralization regulation as well as regarding the methods of investigation. The most recent advances deal more particularly with the structure of shell biominerals at nanoscale and the identification of an increasing number of shell matrix protein components. Although the matrix is quantitatively a minor constituent in the shell of mollusks (less than 5% w/w), it is, however, the major component that controls different aspects of the shell formation processes: synthesis of transient amorphous minerals and evolution to crystalline phases, choice of the calcium carbonate polymorph (calcite vs aragonite), organization of crystallites in complex shell textures (microstructures). Until recently, the classical paradigm in molluscan shell biomineralization was to consider that the control of shell synthesis was performed primarily by two antagonistic mechanisms: crystal nucleation and growth inhibition. New concepts and emerging models try now to translate a more complex reality, which is remarkably illustrated by the wide variety of shell proteins, characterized since the mid-1990s, and described in this chapter. These proteins cover a broad spectrum of pI, from very acidic to very basic. The primary structure of a number of them is composed of different modules, suggesting that these proteins are multifunctional. Some of them exhibit enzymatic activities. Others may be involved in cell signaling. The oldness of shell proteins is discussed, in relation with the Cambrian appearance of the mollusks as a mineralizing phylum and with the Phanerozoic evolution of this group. Nowadays, the extracellular calcifying shell matrix appears as a whole integrated system, which regulates protein-mineral and protein-protein interactions as well as feedback interactions between the biominerals and the calcifying epithelium that synthesized them. Consequently, the molluscan shell matrix may be a source of bioactive molecules that would offer interesting perspectives in biomaterials and biomedical fields.
Published: 2008

47. Detection and characterization of Human caliciviruses associated with sporadic acute diarrhea in adults in Djibouti (horn of Africa)

Author: Katia Ambert-Balay, Jérôme Kaplon, Evelyne Kohli, Christine Fouet, Rachel Haus, Jérôme Maslin, Pierre Pothier, Elisabeth Nicand, Humbert, Murielle, Fédération des laboratoires ( HIA ), Hopital d'Instruction des Armées Saint Anne HIA, Policlinique, Département de consultations et de santé publique, Hôpital Max Fourestier, Laboratoire Interactions Muqueuses Agents Transmissibles ( LIMA ), Université de Bourgogne ( UB ), Laboratoire de sérologie-virologie (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), Fédération des laboratoires (HIA), Laboratoire Interactions Muqueuses Agents Transmissibles (LIMA), Université de Bourgogne (UB), and Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon)
Subjects: Male, Acute diarrhea, MESH: Caliciviridae, viruses, MESH : Diarrhea, Feces, fluids and secretions, Genotype, MESH : Female, MESH: Phylogeny, MESH: Caliciviridae Infections, Phylogeny, Caliciviridae Infections, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Middle Aged, MESH: Feces, virus diseases, Middle Aged, MESH : Adult, Diarrhea, MESH: Diarrhea, Infectious Diseases, MESH : Caliciviridae, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Djibouti, Female, medicine.symptom, MESH : Caliciviridae Infections, Caliciviridae, Adult, Adolescent, MESH : Male, Biology, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Virus, Virology, MESH : Adolescent, medicine, Humans, MESH : Middle Aged, Genotyping, MESH: Adolescent, Genetic diversity, MESH: Humans, MESH : Humans, MESH : Phylogeny, MESH: Adult, MESH: Djibouti, MESH : Feces, Molecular diagnostics, biology.organism_classification, MESH: Male, MESH : Djibouti, Parasitology, MESH: Female
Abstract: International audience; Recent advances in molecular diagnostics have allowed us to recognize Human caliciviruses (HuCVs) as important agents of acute diarrhea in industrialized countries. Their prevalence and genetic diversity in developing countries remains unknown. We report on the characterization of HuCVs among adults presenting acute diarrheas in Djibouti; 108 stool samples collected were screened by EIA, RTPCR, or cell cultures for the group A Rotaviruses, Adenoviruses, Astroviruses, and HuCVs, which were further characterized by genotyping. Among stool samples screened for HuCVs, 25.3% were positive. The other enteric viruses were less prevalent. The 11 HuCV strains sequenced revealed a large diversity (3 sapoviruses and 8 noroviruses). GII strains noroviruses were predominant, five were newly described genotypes, and two were recombinant with a pol gene related to GGIIb strains with the particularity to associate a unique pol gene to different capsid genes. These results could help to the knowledge of HuCV infections in Tropical Africa.
Published: 2008

48. Extraintestinal virulence is a coincidental by-product of commensalism in B2 phylogenetic group Escherichia coli strains

Author: Olivier Clermont, Stéphanie Gouriou, Olivier Tenaillon, Tony Le Gall, Bertrand Picard, Xavier Nassif, Erick Denamur, Ecologie et Evolution des Microorganismes ( EEM ), Université Paris Diderot - Paris 7 ( UPD7 ) -Université Paris 13 ( UP13 ) -Université Sorbonne Paris Cité ( USPC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Génétique moléculaire et génétique épidémiologique, Université de Brest ( UBO ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire de Microbiologie, Centre Hospitalier Régional Universitaire de Brest ( CHRU Brest ), Pathogénie des infections systémiques ( UMR_S 570 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie et Evolution des Microorganismes (EEM), Université Paris Diderot - Paris 7 (UPD7)-Université Paris 13 (UP13)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Pathogénie des infections systémiques (UMR_S 570), and Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Sequence Analysis, DNA, commensalism, MESH : Escherichia coli, MESH : Genotype, MESH: Virulence, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Genome, Bacterial, medicine.disease_cause, MESH: Genotype, Mice, MESH : DNA, Bacterial, MESH: Animals, MESH : Female, MESH: Phylogeny, Pathogen, MESH: Evolution, Molecular, Phylogeny, 2. Zero hunger, Genetics, 0303 health sciences, Phylogenetic tree, Virulence, coincidental by-product, MESH: Escherichia coli, MESH : Genes, Bacterial, MESH : Virulence, extraintestinal virulence, 3. Good health, MESH : Phenotype, Phenotype, Female, Gene pool, MESH: Genes, Bacterial, DNA, Bacterial, Genotype, MESH : Genome, Bacterial, Biology, MESH: Phenotype, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, MESH : Mice, medicine, Escherichia coli, Animals, Humans, MESH : Evolution, Molecular, MESH: Mice, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH: Humans, 030306 microbiology, MESH : Humans, MESH : Phylogeny, Sequence Analysis, DNA, Commensalism, MESH: DNA, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genes, Bacterial, Multilocus sequence typing, MESH : Animals, MESH: Female, Genome, Bacterial, MESH : Sequence Analysis, DNA
Abstract: This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Molecular Biology and Evolution following peer review. The definitive publisher-authenticated version Mol. Biol. Evol. 24(11):2373–2384. 2007 is available online at: http://mbe.oxfordjournals.org/content/24/11/2373.full.pdf+html.; International audience; The selective pressures leading to the evolution and maintenance of virulence in the case of facultative pathogens are quite unclear. For example, Escherichia coli, a commensal of the gut of warm-blooded animals and humans, can cause severe extraintestinal diseases, such as septicemia and meningitis, which represent evolutionary dead ends for the pathogen as they are associated to rapid host death and poor interhost transmission. Such infectious process has been linked to the presence of so-called "virulence genes." To understand the evolutionary forces that select and maintain these genes, we focused our study on E. coli B2 phylogenetic group strains that encompass both commensal and pathogenic (extra- and intraintestinal) strains. Multilocus sequence typing (MLST), comparative genomic hybridization of the B2 flexible gene pool, and quantification of extraintestinal virulence using a mouse model of septicemia were performed on a panel of 60 B2 strains chosen for their genetic and ecologic diversity. The phylogenetic history of the strains reconstructed from the MLST data indicates the emergence of at least 9 subgroups of strains. A high polymorphism is observed in the B2 flexible gene pool among the strains with a good correlation between the MLST-inferred phylogenetic history of the strains and the presence/absence of specific genomic regions, indicating coevolution between the chromosomal background and the flexible gene pool. Virulence in the mouse model is a highly prevalent and widespread character present in all subgroups except one. Association studies reveal that extraintestinal virulence is a multigenic process with a common set of "virulence determinants" encompassing genes involved in transcriptional regulation, iron metabolism, adhesion, lipopolysaccharide (LPS) biosynthesis, and the recently reported peptide polyketide hybrid synthesis system. Interestingly, these determinants can also be viewed as intestinal colonization and survival factors linked to commensalism as they can increase the fitness of the strains within the normal gut environment. Altogether, these data argue for an ancestral emergence of the extraintestinal virulence character that is a coincidental by-product of commensalism. Furthermore, the phenotypic and genotypic markers identified in this work will allow further epidemiological studies devoted to test the niche specialization hypothesis for the B2 phylogenetic subgroups.
Published: 2007

49. A tale of two oxidation states: bacterial colonization of arsenic-rich environments

Author: Caroline Dossat, Barbara Schoepp, Jean Weissenbach, Yuko Makita, Valérie Barbe, Patricia Siguier, Béatrice Segurens, Michael Chandler, Wolfgang Nitschke, Sophie Mangenot, Zoé Rouy, Stéphanie Weiss, David Vallenet, Benoit Cournoyer, Diliana D. Simeonova, Philippe Ortet, Antoine Danchin, Florence Arsène-Ploetze, Sandrine Koechler, Christine Carapito, Mohamed Barakat, Evelyne Krin, Didier Lièvremont, Daniel Muller, Emmanuelle Leize, Simon Duval, Philippe N. Bertin, Marie-Claire Lett, Nicolas Perdrial, Michaël Heymann, Stéphane Cruveiller, Aurélie Lieutaud, Violaine Bonnefoy, Evelyne Turlin, Claudine Médigue, Emmanuel Talla, Alain Van Dorsselaer, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pluridisciplinaire Hubert Curien (IPHC), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre de géochimie de la surface (CGS), Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut national des sciences de l'Univers (INSU - CNRS), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Génétique moléculaire, génomique, microbiologie ( GMGM ), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes ( LEMIRE ), Université de la Méditerranée - Aix-Marseille 2-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de chimie bactérienne ( LCB ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut Pluridisciplinaire Hubert Curien ( IPHC ), Laboratoire de microbiologie et génétique moléculaires ( LMGM ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Centre de géochimie de la surface ( CGS ), Institut national des sciences de l'Univers ( INSU - CNRS ) -Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Structure et évolution des génomes ( SEG ), and CNS-Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: MESH: Oxidation-Reduction, Cancer Research, Drug Resistance, MESH : Models, Biological, QH426-470, MESH : Carbon, MESH : Drug Resistance, Bacterial, MESH: Genome, Bacterial, Arsenic, Bacteria, Biodegradation, Environmental, Carbon, Bacterial, Energy Metabolism, Genome, Metals, Models, Biological, Oxidation-Reduction, Phylogeny, MESH: Biodegradation, Environmental, 0302 clinical medicine, Herminiimonas arsenicoxydans, MESH: Phylogeny, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), 0303 health sciences, Ecology, MESH: Energy Metabolism, MESH : Arsenic, 6. Clean water, Biodegradation, Environmental, Research Article, inorganic chemicals, MESH : Biodegradation, Environmental, MESH : Genome, Bacterial, Energy metabolism, chemistry.chemical_element, MESH: Carbon, Biology, Genomic databases, Microbiology, Models, Biological, 03 medical and health sciences, Bacterial colonization, Bioremediation, Drug Resistance, Bacterial, MESH: Arsenic, MESH: Drug Resistance, Bacterial, SDV:BBM, Genetics, MESH : Bacteria, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH : Oxidation-Reduction, MESH: Metals, 030306 microbiology, MESH : Metals, MESH: Models, Biological, MESH : Phylogeny, Computational Biology, Oxidation reduction, Genetics and Genomics, biology.organism_classification, Archaea, MESH : Energy Metabolism, Eubacteria, MESH: Bacteria, Positive chemotaxis, chemistry, 13. Climate action, Genome, Bacterial, 030217 neurology & neurosurgery
Abstract: Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments—including ground and surface waters—from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the β-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth., Author Summary Microorganisms play a crucial role in nutrient biogeochemical cycles. Arsenic is found throughout the environment from both natural and anthropogenic sources. Its inorganic forms are highly toxic and impair the physiology of most higher organisms. Arsenic contamination of groundwater supplies is giving rise to increasingly severe human health problems in both developing and industrial countries. In the present work, we investigated the metabolism of this metalloid in Herminiimonas arsenicoxydans, a representative organism of a novel bacterial genus widespread in aquatic environments. Examination of the genome sequence and experimental evidence revealed that it is remarkably capable of coping with arsenic. Our observations support the existence of multiple strategies allowing arsenic-metabolizing microbes to efficiently colonize toxic environments. In particular, arsenic oxidation and scavenging may have played a crucial role in the development of early stages of life on Earth. Such mechanisms may one day be exploited as part of a potential bioremediation strategy in toxic environments.
Published: 2007

50. Identification of cellulolytic bacteria in soil by stable isotope probing

Author: Christine Marol, Richard Christen, Marie-France Marais, Jérôme Balesdent, Christophe Mougel, Odile Berge, Feth el Zahar Haichar, Lionel Ranjard, Wafa Achouak, Thierry Heulin, Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de signalisation, biologie du développement et cancer (ISBDC), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Centre de Recherches sur les Macromolécules Végétales (CERMAV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Microbiologie du Sol et de l'Environnement (MSE), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes ( LEMIRE ), Université de la Méditerranée - Aix-Marseille 2-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de signalisation, biologie du développement et cancer ( ISBDC ), Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de recherches sur les macromolécules végétales ( CERMAV ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Centre National de la Recherche Scientifique ( CNRS ), Microbiologie du Sol et de l'Environnement ( MSE ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)
Subjects: MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, Microorganism, DNA-SIP, Stable-isotope probing, CELLULOSE DEGRADATION, chemistry.chemical_compound, MESH: Centrifugation, Density Gradient, MESH : Ecosystem, RNA, Ribosomal, 16S, MESH : DNA, Bacterial, MESH: Ecosystem, Food science, MESH: Cellulose, MESH : DNA, Ribosomal Spacer, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Phylogeny, ComputingMilieux_MISCELLANEOUS, Phylogeny, Soil Microbiology, 0303 health sciences, Carbon Isotopes, biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: RNA, Ribosomal, 16S, Electrophoresis, Polyacrylamide Gel, MESH : Carbon Isotopes, Temperature gradient gel electrophoresis, DNA, Bacterial, Ribosomal Intergenic Spacer analysis, MESH : Soil Microbiology, Molecular Sequence Data, chemistry.chemical_element, MESH : Electrophoresis, Polyacrylamide Gel, Microbiology, 03 medical and health sciences, Botany, DNA, Ribosomal Spacer, Centrifugation, Density Gradient, MESH : Bacteria, Cellulose, MESH: DNA, Ribosomal Spacer, Ecology, Evolution, Behavior and Systematics, Ecosystem, 030304 developmental biology, MESH: Molecular Sequence Data, Bacteria, 030306 microbiology, MESH : Cellulose, MESH : Phylogeny, MESH: Carbon Isotopes, Sequence Analysis, DNA, 15. Life on land, biology.organism_classification, MESH: DNA, Bacterial, MESH : RNA, Ribosomal, 16S, RELATION SOL MICRO-ORGANISME, MESH: Bacteria, chemistry, MESH: Soil Microbiology, MESH : Centrifugation, Density Gradient, ACETOBACTER XYLINUS, BACTERIAL POPULATIONS, Carbon, DNA, MESH : Sequence Analysis, DNA, MESH: Electrophoresis, Polyacrylamide Gel
Abstract: Plant residues, mainly made up of cellulose, are the largest fraction of organic carbon material in terrestrial ecosystems. Soil microorganisms are mainly responsible for the transfer of this carbon to the atmosphere, but their contribution is not accurately known. The aim of the present study was to identify bacterial populations that are actively involved in cellulose degradation, using the DNA-stable isotope probing (DNA-SIP) technique. (13)C-cellulose was produced by Acetobacter xylinus and incubated in soil for 7, 14, 30 and 90 days. Total DNA was extracted from the soil, the (13)C-labelled (heavy) and unlabelled (light) DNA fractions were separated by ultracentrifugation, and the structure of active bacterial communities was analysed by bacterial-automated ribosomal intergenic spacer analysis (B-ARISA) and characterized with denaturing gradient gel electrophoresis (DGGE). Cellulose degradation was associated with significant changes in bacterial community structure issued from heavy DNA, leading to the appearance of new bands and increase in relative intensities of other bands until day 30. The majority of bands decreased in relative intensity at day 90. Sequencing and phylogenetic analysis of 10 of these bands in DGGE profiles indicated that most sequences were closely related to sequences from organisms known for their ability to degrade cellulose or to uncultured soil bacteria.
Published: 2007

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