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3. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

Author

Ying Wang, Chantal Schenowitz, Jeffrey P. Tomkins, Claudine Médigue, Luis Gabriel Wall, Claudio Valverde, Benoit Cournoyer, Nadia Demange, Philippe Normand, Alison M. Berry, Louis S. Tisa, Juliana E. Mastronunzio, David Vallenet, David R. Benson, Pascal Lapierre, Emilie Bagnarol, Tania Rawnsley, Nathalie Choisne, Zoé Rouy, Johann Peter Gogarten, Céline Lavire, Alla Lapidus, Nicole Alloisio, Vincent Daubin, Arnaud Couloux, Stéphane Cruveiller, Ying Huang, Carla A. Bassi, James Niemann, Maria Pilar Francino, Derek M. Bickhart, J Maréchal, Laurent Labarre, Beth C. Mullin, Fernando Tavares, Olga R. Kopp, Michele Martinez, Eugene Goltsman, Anita Sellstedt, Pierre Pujic, 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), Department of Molecular and Cell Biology, University of Connecticut (UCONN), Department of Microbiology, University of New Hampshire (UNH), Department of Plant Sciences [Davis, CA], University of California [Davis] (UC Davis), University of California-University of California, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-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), 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), 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), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Department of Biochemistry & Cellular & Molecular Biology and the Genome Science & Technology Program, The University of Tennessee [Knoxville], Department of Biochemistry & Cellular 1 Molecular Biology and The Genome Science & Technology Program, Department of Plant Physiology, Umeå University, Genomics Institute, Clemson University, Departamento de Ciencia y Tecnología [Buenos Aires], Universidad Nacional de Quilmes (UNQ), 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 ), University of Connecticut ( UCONN ), University of New Hampshire ( UNH ), University of California [Davis] ( UC Davis ), Unité de recherche en génomique végétale ( URGV ), Institut National de la Recherche Agronomique ( INRA ) -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 ), 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 ), 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 ), Department of Energy / Joint Genome Institute ( DOE ), Los Alamos National Laboratory ( LANL ), Programa Interacciones Biologicas, Departamento de Cienca y Tecnologia, Universidad Nacional de Quilmes, 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 la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), 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, Root nodule, Prophages, [SDE.BE.ECOM]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.ecom, Molecular Sequence Data, Frankia, Plant Roots, Genome, Article, Actinobacteria, Evolution, Molecular, Magnoliopsida, 03 medical and health sciences, Symbiosis, Gene Duplication, Nitrogen Fixation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, Genetics, Phylogeny, Genetics (clinical), 030304 developmental biology, 2. Zero hunger, Frankia alni, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, Facultative, Geography, biology, 030306 microbiology, fungi, food and beverages, Sequence Analysis, DNA, 15. Life on land, biology.organism_classification, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], DNA Transposable Elements, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Actinorhizal plant, [ SDE.BE.ECOM ] Environmental Sciences/Biodiversity and Ecology/domain_sde.be.ecom, Gene Deletion, Genome, Bacterial
Abstract

Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N2-fixing root nodules on diverse and globally distributed angiosperms in the “actinorhizal” symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%–98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.

Published
2006
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4. MaGe: a microbial genome annotation system supported by synteny results

Author

Claude Scarpelli, Zoé Rouy, David Vallenet, Laurent Labarre, Stéphanie Bocs, Stéphane Cruveiller, Claudine Médigue, Valérie Barbe, Géraldine Pascal, Aurélie Lajus, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)

Subjects
endocrine system, Biological database, Genomics, Bacterial genome size, Vertebrate and Genome Annotation Project, Biology, Synteny, Genome, Article, User-Computer Interface, 03 medical and health sciences, Annotation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Databases, Genetic, Computer Graphics, Genetics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Internet, 0303 health sciences, 030306 microbiology, Computational Biology, Genome project, Systems Integration, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Database Management Systems, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Bacterial
Abstract

Magnifying Genomes (MaGe) is a microbial genome annotation system based on a relational database containing information on bacterial genomes, as well as a web interface to achieve genome annotation projects. Our system allows one to initiate the annotation of a genome at the early stage of the finishing phase. MaGe's main features are (i) integration of annotation data from bacterial genomes enhanced by a gene coding re-annotation process using accurate gene models, (ii) integration of results obtained with a wide range of bioinformatics methods, among which exploration of gene context by searching for conserved synteny and reconstruction of metabolic pathways, (iii) an advanced web interface allowing multiple users to refine the automatic assignment of gene product functions. MaGe is also linked to numerous well-known biological databases and systems. Our system has been thoroughly tested during the annotation of complete bacterial genomes (Acinetobacter baylyi ADP1, Pseudoalteromonas haloplanktis, Frankia alni) and is currently used in the context of several new microbial genome annotation projects. In addition, MaGe allows for annotation curation and exploration of already published genomes from various genera (e.g. Yersinia, Bacillus and Neisseria). MaGe can be accessed at http://www.genoscope.cns.fr/agc/mage.

Published
2006
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5. L’annotationin silicodes séquences génomiques

Author

David Vallenet, Catherine Mathé, Stéphanie Bocs, Laurent Labarre, and Claudine Médigue

Subjects
Annotation, In silico, General Medicine, Biology, Molecular biology, General Biochemistry, Genetics and Molecular Biology
Abstract

Depuis 1995, nous avons acces a l’information genetique complete d’un nombre croissant d’organismes vivants tres divers. Cette explosion d’informations impose des changements profonds dans de nombreuses disciplines scientifiques, particulierement en bio-informatique et en genetique moleculaire. L’un des plus importants defis est de predire et d’annoter les fonctions de la plupart des produits de genes de facon a la fois rapide et exhaustive, en tenant compte des interactions moleculaires entre les differents elements predits (expression de la regulation des genes et donnees metaboliques). Au-dela de l’information fournie par la sequence complete des genomes, ces dernieres analyses requierent des donnees complementaires issues de l’etude du transcriptome et du proteome. Aussi, de nouvelles infrastructures informatiques, integrant differents niveaux d’annotation de sequences et de prediction des fonctions biologiques, vont devenir indispensables. Cette revue est destinee a decrire les demarches permettant l’annotation in silico des sequences genomiques d’organismes procaryotes et euca-ryotes. Un regard specifique est porte sur les problemes auxquels se heurte tout annotateur, ainsi que les voies de recherches actuelles dans ce domaine.

Published
2002
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6. Transcriptome analysis of Yersinia pestis in human plasma: an approach for discovering bacterial genes involved in septicaemic plague

Author

Michael Marceau, Elisabeth Carniel, Jeannine Foulon, Marie-Laure Rosso, Michel Simonet, Sylvie Chauvaux, Céline Lacroix, Claudine Médigue, Marie-Agnès Dillies, Laurent Labarre, Angèle Schiavo, Lionel Frangeul, Jean-Yves Coppée, Yersinia, Institut Pasteur [Paris], Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP), Intégration et Analyse Génomique (Plate-Forme 4) (PF4), Puces à ADN (Plate-Forme 2) (PF2), 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), This work was supported in part by grant 02 34 021 from the ‘Délégation Générale pour l'Armement’ and grant PTR88 from the ‘Programmes transversaux de recherche’, Institut Pasteur., and Institut Pasteur [Paris] (IP)

Subjects
Proteome, Transcription, Genetic, Yersinia pestis, Bacteremia, MESH: Genome, Bacterial, Yersiniabactin, Virulence factor, Transcriptome, chemistry.chemical_compound, Plasma, MESH: Reverse Transcriptase Polymerase Chain Reaction, MESH: Bacteremia, Pathogen, MESH: Bacterial Proteins, Oligonucleotide Array Sequence Analysis, 0303 health sciences, MESH: Gene Expression Regulation, Bacterial, biology, Reverse Transcriptase Polymerase Chain Reaction, Yersiniosis, MESH: Proteome, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Yersinia pestis, Virulence, Microbiology, MESH: Plague, 03 medical and health sciences, QRT-PCR, MESH: Gene Expression Profiling, Bacterial Proteins, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Humans, quantitative real-time PCR, Gene, MESH: Plasma, 030304 developmental biology, Plague, MESH: Humans, 030306 microbiology, Gene Expression Profiling, MESH: Transcription, Genetic, Gene Expression Regulation, Bacterial, medicine.disease, biology.organism_classification, Culture Media, chemistry, MESH: Oligonucleotide Array Sequence Analysis, MESH: Culture Media, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Bacterial
Abstract

International audience; Yersinia pestis is the aetiologic agent of plague. Without appropriate treatment, the pathogen rapidly causes septicaemia, the terminal and fatal phase of the disease. In order to identify bacterial genes which are essential during septicaemic plague in humans, we performed a transcriptome analysis on the fully virulent Y. pestis CO92 strain grown in either decomplemented human plasma or Luria-Bertani medium, incubated at either 28 or 37 degrees C and harvested at either the mid-exponential or the stationary growth phase. Y. pestis genes involved in 12 iron-acquisition systems and one iron-storage system (bfr, bfd) were specifically induced in human plasma. Of these, the ybt and tonB genes (encoding the yersiniabactin siderophore virulence factor and the siderophore transporter, respectively) were induced at 37 degrees C, i.e. under conditions mimicking the mammalian environment. Growth in human plasma also upregulated genes involved in the synthesis of five fimbrial-like structures (including the Psa virulence factor), and in purine/pyrimidine metabolism (the nrd genes). Genes known to play a role in the virulence of several bacterial pathogens (such as those encoding the Lpp lipoprotein and non-iron metal-uptake proteins) were induced in human plasma, during either the exponential or the stationary phase. Finally, 120 genes encoding proteins of unknown function were upregulated in human plasma. Eleven of these genes were specifically transcribed at 37 degrees C and may thus represent new virulence factors that are important during the septicaemic phase of human plague.

Published
2007
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7. Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data

Author

Anne Morgat, Laurent Labarre, Joël Pothier, Frédéric Boyer, and Alain Viari

Subjects
Statistics and Probability, Theoretical computer science, Source code, media_common.quotation_subject, Biochemistry, Models, Biological, Evolution, Molecular, RNA, Transfer, Protein Interaction Mapping, Computer Graphics, Escherichia coli, Cluster Analysis, Databases, Protein, Molecular Biology, media_common, Mathematics, Connected component, Comparative genomics, Biological data, Genome, Models, Statistical, Models, Genetic, Multigraph, Computational Biology, Genomics, Graph, Computer Science Applications, Computational Mathematics, Exact algorithm, Computational Theory and Mathematics, restrict, Genes, Bacterial, RNA, Ribosomal, Algorithms, Genome, Bacterial, Software
Abstract

Motivation: Modern comparative genomics does not restrict to sequence but involves the comparison of metabolic pathways or protein--protein interactions as well. Central in this approach is the concept of neighbourhood between entities (genes, proteins, chemical compounds). Therefore there is a growing need for new methods aiming at merging the connectivity information from different biological sources in order to infer functional coupling. Results: We present a generic approach to merge the information from two or more graphs representing biological data. The method is based on two concepts. The first one, the correspondence multigraph, precisely defines how correspondence is performed between the primary data-graphs. The second one, the common connected components, defines which property of the multigraph is searched for. Although this problem has already been informally stated in the past few years, we give here a formal and general statement together with an exact algorithm to solve it. Availability: The algorithm presented in this paper has been implemented in C. Source code is freely available for download at: http://www.inrialpes.fr/helix/people/viari/cccpart Contact: Alain.Viari@inrialpes.fr

Published
2005

8. Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium

Author

Philippe Marlière, Catherine Robert, Sophie Oztas, Stéphane Cruveiller, Patrick Wincker, David Vallenet, Claudine Médigue, L. Nicholas Ornston, Nuria Fonknechten, Jean Weissenbach, Laurent Labarre, Georges N. Cohen, Simone Duprat, Annett Kreimeyer, and Valérie Barbe

Subjects
Molecular Sequence Data, Coenzymes, Genome, Synteny, Evolution, Molecular, Polysaccharides, Nucleic Acids, Genetics, Amino Acids, Gene, Nitrites, Whole genome sequencing, Nitrates, biology, Acinetobacter, Base Sequence, Sulfates, Circular bacterial chromosome, Pseudomonas, Biological Transport, Articles, Vitamins, biology.organism_classification, Pseudomonas putida, Aerobiosis, Transformation, Bacterial, Energy Metabolism, GC-content, Genome, Bacterial
Abstract

Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for genetic manipulation. The circular chromosome of the Acinetobacter ADP1, presented here, encodes 3325 predicted coding sequences, of which 60% have been classified based on sequence similarity to other documented proteins. The close evolutionary proximity of Acinetobacter and Pseudomonas species, as judged by the sequences of their 16S RNA genes and by the highest level of bidirectional best hits, contrasts with the extensive divergence in the GC content of their DNA (40 versus 62%). The chromosomes also differ significantly in size, with the Acinetobacter ADP1 chromosome

Published
2004

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