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1. Ultradeep Pyrosequencing of NS3 To Predict Response to Triple Therapy with Protease Inhibitors in Previously Treated Chronic Hepatitis C Patients

Author

Olivier François, Katia Fusillier, Michael G. B. Blum, Jean-Pierre Zarski, Sylvie Larrat, Pauline Tremeaux, Patrice Morand, Réjane Beugnot, Alice Marlu, Jean-Baptiste Claude, Agnès Plages, Om Kulkarni, Anne Signori-Schmuck, Julien Lupo, Hervé Duborjal, Vincent Leroy, Unit for Virus Host-Cell Interactions [Grenoble] (UVHCI), Centre National de la Recherche Scientifique (CNRS)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Université Joseph Fourier - Grenoble 1 (UJF), Biologie Computationnelle et Mathématique (TIMC-IMAG-BCM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Genostar, GENOME Express (GENOME Express), GENOME Express, Earth and Environmental, AMEC, Biochimie et Génétique Moléculaire, CHU Grenoble-Hôpital Michallon, Pôle Digidune, Pôle DigiDune, Unité de Biophysique, CRSSA, Département d'hépato-gastroentérologie, Université Grenoble Alpes (UGA)-CHU Grenoble, Matière et Systèmes Complexes (MSC (UMR_7057)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), CHU Grenoble-Université Grenoble Alpes (UGA), Université Joseph Fourier - Grenoble 1 (UJF)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Université Joseph Fourier - Grenoble 1 (UJF)-CHU Grenoble, and Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Adult, Male, Microbiology (medical), NS3, medicine.medical_specialty, Entropy, medicine.medical_treatment, Mutation, Missense, Salvage therapy, Viral quasispecies, Viral Nonstructural Proteins, Biology, Antiviral Agents, Peripheral blood mononuclear cell, Gastroenterology, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Virology, Internal medicine, Drug Resistance, Viral, Genotype, medicine, Humans, Protease Inhibitors, Aged, 030304 developmental biology, Aged, 80 and over, Salvage Therapy, 0303 health sciences, Protease, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Genetic Variation, High-Throughput Nucleotide Sequencing, virus diseases, Odds ratio, Hepatitis C, Chronic, Middle Aged, Prognosis, digestive system diseases, Confidence interval, 3. Good health, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], HCV, Immunology, Drug Therapy, Combination, Female, 030211 gastroenterology & hepatology
Abstract

Despite the gain in sustained virological responses (SVR) provided by protease inhibitors (PIs), failures still occur. The aim of this study was to determine if a baseline analysis of the NS3 region using ultradeep pyrosequencing (UDPS) can help to predict an SVR. Serum samples from 40 patients with previously nonresponding genotype 1 chronic hepatitis C who were retreated with triple therapy, including a PI, were analyzed. Baseline UDPS of the NS3 gene was performed on plasma and peripheral blood mononuclear cells (PBMC). Mutations conferring resistance to PIs were sought. The overall diversity of the quasispecies was evaluated by calculating the Shannon entropy (SE). Resistance mutations were found in plasma and PBMC but were not discriminating enough to predict an SVR. NS3 quasispecies heterogeneity was significantly lower at baseline in patients achieving an SVR than in those not achieving an SVR (SE of 26.98 ±16.64 x10^3 versus 44.93 ±19.58 x10^3, P =0.0047). With multivariate analysis, the independent predictors of an SVR were fibrosis of stage F <2 (odds ratio [OR], 13.3; 95% confidence interval [CI], 1.25 to 141.096; P < 0.03) and SE below the median (OR, 5.4; 95% CI, 1.22 to 23.87; P < 0.03). More than the presence of minor mutations at the baseline in plasma or in PBMC, the NS3 viral heterogeneity determined by UDPS is an independent factor for an SVR in previously treated patients receiving triple therapy that includes a PI.&nbsp

Published
2015
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2. Environmentally Selected Aphid Variants in Clonality Context Display Differential Patterns of Methylation in the Genome

Author

Martine Da Rocha, Neil Ledger, Mathilde Clément, Alain Robichon, Stéphanie Penaud, Maria Capovilla, Aviv Dombrovsky, Claude Pasquier, Corinne Rancurel, Institute of Developmental Biology and Cancer (IBDC), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Volcani Center, GENOME Express (GENOME Express), GENOME Express, 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), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Beckman Coulter Inc, Partenaires INRAE, French National Research Agency (ANR), ANR-11-LABX-0028-01, grant PEPS CNRS, Institut de Biologie Valrose (IBV), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Immunotech-Beckman Coulter, Immunotech, PEPS CNRS 2010, ANR-12-BSV6-0006,methylclonome,Analyse de l'héritabilité des traces épigénétiques dans la reproduction clonale(2012), ANR: 11-LABX-0028,SIGNALIFE,Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie(2011), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA), 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), 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), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), ANR-11-LABX-0028,SIGNALIFE,Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie(2011), Pasquier, Claude, BLANC - Analyse de l'héritabilité des traces épigénétiques dans la reproduction clonale - - methylclonome2012 - ANR-12-BSV6-0006 - BLANC - VALID, Centres d'excellences - Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie - - SIGNALIFE2011 - ANR-11-LABX-0028 - LABX - VALID, Université Nice Sophia Antipolis (1965 - 2019) (UNS), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Scalable and Pervasive softwARe and Knowledge Systems (Laboratoire I3S - SPARKS), 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)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), Université Côte d'Azur (UCA), and 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA)

Subjects
Male, Environmental Impacts, Genome, Insect, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Genome, Epigenesis, Genetic, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Genetics, régulation de l'expression génique, Multidisciplinary, Ecology, Pigmentation, Systems Biology, Founder Effect, Habitats, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Phenotype, DNA methylation, aphidae, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Medicine, Female, Research Article, expression des gènes, méthylation de l'adn, Science, variabilité phénotypique, Genomics, Context (language use), Biology, Environment, Evolution, Molecular, Species Colonization, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Epigenetics, Allele, Selection, Genetic, analyse du transcriptome, Population Biology, Gene Expression Profiling, Ecology and Environmental Sciences, Organisms, Genetic Variation, Biology and Life Sciences, insecta, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Phenotypic trait, DNA Methylation, Gene Ontology, adaptation epigénétique, Aphids, CpG Islands, Adaptation, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

International audience; Heritability of acquired phenotypic traits is an adaptive evolutionary process that appears more complex than the basic allele selection guided by environmental pressure. In insects, the trans-generational transmission of epigenetic marks in clonal and/or sexual species is poorly documented. Aphids were used as a model to explore this feature because their asexual phase generates a stochastic and/or environment-oriented repertoire of variants. The a priori unchanged genome in clonal individuals prompts us to hypothesize whether covalent methyl DNA marks might be associated to the phenotypic variability and fitness selection. The full differential transcriptome between two environmentally selected clonal variants that originated from the same founder mother was mapped on the entire genomic scaffolds, in parallel with the methyl cytosine distribution. Data suggest that the assortments of heavily methylated DNA sites are distinct in these two clonal phenotypes. This might constitute an epigenetic mechanism that confers the robust adaptation of insect species to various environments involving clonal reproduction.

Published
2014
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3. The whole genome of Oenococcus strain IOEB 8413

Author

Dimova, Diliana, Bon, Elisabeth, Lucas, Patrick, Beugnot, R., De Leeuw, Marcel, Lonvaud-Funel, Aline, GENOME Express (GENOME Express), GENOME Express, Modèles et algorithmes pour la Bioinformatique et la Visualisation d'informations, (MABIOVIS), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Institut des Sciences de la Vigne et du Vin (ISVV), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Laboratoire de Biotechnologie et Microbiologie Appliquée (LBMA), Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), and Bon, Elisabeth

Subjects
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

International audience; Taking advantage of recent technology developments of 454 pyrosequencing we have undertaken whole genome sequencing of O. oeni strain IOEB 8413. This strain performs malolactic fermentation, but has a relatively low level of adaptation to oenological environment. The genome draft was obtained with Genome Sequencer FLX System (Roche). The generated 111 Mb of raw data (406 255 individual reads) was processed with Newbler Assembler through two different modes. The assembly resulting from the "de novo" mode consisted of 39 major contigs attaining an average 50x coverage. Manual draft inspection revealed that, independently of the number of contigs, it contained only 19 real gaps. Cumulated size of missing fractions was estimated to be less than 10 kb, thus allowing us one-step finishing by Sanger sequencing. For the second assembly mode, particularly indicated for resequencing projects, we have used as a reference the recently achieved genome of strain ATCC BAA-1163 (LAB9, communication Bon et al.). The 1,8-Mb chromosome is covered by 90% of all mapped reads, whereas the fully covered 3,9-kb high-copy plasmid monopolizes the remaining 10%. More than 97% of all reads were fully mapped to the reference (chromosome or plasmid) and organized in 18 "mapping" contigs. Less than 2% of reads aligned partially at the oriC linearization site or corresponded to repeat regions (rRNA operons). Only 429 reads are unique meaning that both strains have very close nucleotide content. Preliminary evaluation of the two genomes indicates no significant large-scale rearrangements. Functional annotation as well as further comparative analyses between available strains (including PSU-1) will await completion of the strain IOEB 8413 genome.

Published
2008

4. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding

Author

Gérard Corthier, Christian Brochmann, Thierry Vermat, François Pompanon, Alice Valentini, Ludovic Gielly, Christian Miquel, Eske Willerslev, Pierre Taberlet, Eric Coissac, Laboratoire d'Ecologie Alpine (LECA), 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), Computer science and genomics (HELIX), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-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-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), Dipartimento di Ecologia e Sviluppo Economico Sostenibile (DECOS), Università degli studi della Tuscia [Viterbo], Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences (NMBU), GENOME Express (GENOME Express), GENOME Express, Unité de recherche d'Écologie et Physiologie du Système Digestif (UEPSD), Institut National de la Recherche Agronomique (INRA), National Centre for Biosystematics (NCB), University of Oslo (UiO), Center for Ancient Genetics, University of Copenhagen = Københavns Universitet (KU), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Taberlet, Pierre, Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), and University of Copenhagen = Københavns Universitet (UCPH)

Subjects
0106 biological sciences, code barre adn, Biodiversité et Ecologie, Molecular Sequence Data, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Polymerase Chain Reaction, 010603 evolutionary biology, 01 natural sciences, DNA barcoding, law.invention, Conserved sequence, Biodiversity and Ecology, 03 medical and health sciences, chemistry.chemical_compound, law, Genetics, Conserved Sequence, Polymerase chain reaction, DNA Primers, 030304 developmental biology, 2. Zero hunger, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Base Sequence, chloroplaste, DNA, Chloroplast, Intron, Sequence Analysis, DNA, Plants, Introns, Chloroplast, puissance, Ancient DNA, chemistry, Evolutionary biology, GenBank, plante, Methods Online, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Databases, Nucleic Acid, DNA
Abstract

Times Cited: 4; International audience; DNA barcoding should provide rapid, accurate and automatable species identifications by using a standardized DNA region as a tag. Based on sequences available in GenBank and sequences produced for this study, we evaluated the resolution power of the whole chloroplast trnL (UAA) intron (254-767 bp) and of a shorter fragment of this intron (the P6 loop, 10-143 bp) amplified with highly conserved primers. The main limitation of the whole trnL intron for DNA barcoding remains its relatively low resolution (67.3% of the species from GenBank unambiguously identified). The resolution of the P6 loop is lower (19.5% identified) but remains higher than those of existing alternative systems. The resolution is much higher in specific contexts such as species originating from a single ecosystem, or commonly eaten plants. Despite the relatively low resolution, the whole trnL intron and its P6 loop have many advantages: the primers are highly conserved, and the amplification system is very robust. The P6 loop can even be amplified when using highly degraded DNA from processed food or from permafrost samples, and has the potential to be extensively used in food industry, in forensic science, in diet analyses based on feces and in ancient DNA studies.

Published
2007
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5. GenoLink: A graph-based querying and browsing system for investigating the function of genes and proteins

Author

Durand, Patrick, Labarre, Laurent, Meil, Alain, Divo1, Jean-Louis, Viari, Alain, Wojcik, Jérôme, Vert, Jean-Philippe, Foveau, Nicolas, Lajaunie, Christian, Vandenbrouck, Yves, 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 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, Institut National de Recherche en Informatique et en Automatique (Inria), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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-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), Hybrigenics [Paris], Hybrigenics, Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale (ERABLE), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Quartzbio, Geneva, Centre de Bioinformatique (CBIO), MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Laboratoire Biologie-Informatique-Mathématique (LBIM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre de Géosciences (GEOSCIENCES), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-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)-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), GENOME Express (GENOME Express), GENOME Express, DRDC/BIM [Grenoble], CEA-Grenoble, Computer science and genomics (HELIX), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-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-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), Serono Genetics Institute S.A.[Evry], Serono Genetics Institute, 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, 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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Theoretical computer science, Computer science, [SDV]Life Sciences [q-bio], Gene Expression, 02 engineering and technology, computer.software_genre, lcsh:Computer applications to medicine. Medical informatics, Biochemistry, Computer graphics, User-Computer Interface, 03 medical and health sciences, Software, Text mining, Structural Biology, 020204 information systems, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Databases, Genetic, Computer Graphics, 0202 electrical engineering, electronic engineering, information engineering, Computer Simulation, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, Molecular Biology, lcsh:QH301-705.5, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Biological data, Parsing, business.industry, Applied Mathematics, Graph based, Proteins, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Graph, Computer Science Applications, Vertex (geometry), Genes, Data model, lcsh:Biology (General), Database Management Systems, Graph (abstract data type), lcsh:R858-859.7, Isomorphism, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, Graph operations, computer, Signal Transduction
Abstract

Background A large variety of biological data can be represented by graphs. These graphs can be constructed from heterogeneous data coming from genomic and post-genomic technologies, but there is still need for tools aiming at exploring and analysing such graphs. This paper describes GenoLink, a software platform for the graphical querying and exploration of graphs. Results GenoLink provides a generic framework for representing and querying data graphs. This framework provides a graph data structure, a graph query engine, allowing to retrieve sub-graphs from the entire data graph, and several graphical interfaces to express such queries and to further explore their results. A query consists in a graph pattern with constraints attached to the vertices and edges. A query result is the set of all sub-graphs of the entire data graph that are isomorphic to the pattern and satisfy the constraints. The graph data structure does not rely upon any particular data model but can dynamically accommodate for any user-supplied data model. However, for genomic and post-genomic applications, we provide a default data model and several parsers for the most popular data sources. GenoLink does not require any programming skill since all operations on graphs and the analysis of the results can be carried out graphically through several dedicated graphical interfaces. Conclusion GenoLink is a generic and interactive tool allowing biologists to graphically explore various sources of information. GenoLink is distributed either as a standalone application or as a component of the Genostar/Iogma platform. Both distributions are free for academic research and teaching purposes and can be requested at academy@genostar.com. A commercial licence form can be obtained for profit company at info@genostar.com. See also http://www.genostar.org.

Published
2006
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6. Quantitative Single-letter Sequencing: a method for simultaneously monitoring numerous known allelic variants in single DNA samples

Author

Stéphane Blanc, Baptiste Monsion, Hervé Duborjal, Biologie et Génétique des Interactions Plantes-Agents Pathogènes, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Montpellier (ENSA M)-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), and GENOME Express

Subjects
Genetic Markers, lcsh:QH426-470, lcsh:Biotechnology, Molecular Sequence Data, variabilité génétique, Population, Genomics, Genome, Viral, Biology, Polymerase Chain Reaction, Genome, CAULIFLOWER MOSAIC VIRUS, law.invention, 03 medical and health sciences, pcr, Caulimovirus, law, lcsh:TP248.13-248.65, Genetics, education, pathologie végétale, Alleles, Polymerase chain reaction, DNA Primers, 030304 developmental biology, locus, 0303 health sciences, education.field_of_study, [SDV.GEN]Life Sciences [q-bio]/Genetics, Base Sequence, 030306 microbiology, Methodology Article, Genetic Variation, DNA, Sequence Analysis, DNA, Electropherogram, méthode de détection, lcsh:Genetics, Genetic marker, DNA, Viral, Primer (molecular biology), DNA microarray, Plasmids, Biotechnology
Abstract

Background Pathogens such as fungi, bacteria and especially viruses, are highly variable even within an individual host, intensifying the difficulty of distinguishing and accurately quantifying numerous allelic variants co-existing in a single nucleic acid sample. The majority of currently available techniques are based on real-time PCR or primer extension and often require multiplexing adjustments that impose a practical limitation of the number of alleles that can be monitored simultaneously at a single locus. Results Here, we describe a novel method that allows the simultaneous quantification of numerous allelic variants in a single reaction tube and without multiplexing. Quantitative Single-letter Sequencing (QSS) begins with a single PCR amplification step using a pair of primers flanking the polymorphic region of interest. Next, PCR products are submitted to single-letter sequencing with a fluorescently-labelled primer located upstream of the polymorphic region. The resulting monochromatic electropherogram shows numerous specific diagnostic peaks, attributable to specific variants, signifying their presence/absence in the DNA sample. Moreover, peak fluorescence can be quantified and used to estimate the frequency of the corresponding variant in the DNA population. Using engineered allelic markers in the genome of Cauliflower mosaic virus, we reliably monitored six different viral genotypes in DNA extracted from infected plants. Evaluation of the intrinsic variance of this method, as applied to both artificial plasmid DNA mixes and viral genome populations, demonstrates that QSS is a robust and reliable method of detection and quantification for variants with a relative frequency of between 0.05 and 1. Conclusion This simple method is easily transferable to many other biological systems and questions, including those involving high throughput analysis, and can be performed in any laboratory since it does not require specialized equipment.

Published
2008
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7. Rerouting of pyruvate metabolism during acid adaptation in Lactobacillus bulgaricus

Author

S. Penaud, Emmanuelle Maguin, Maarten van de Guchte, Jun Ogawa, Annabelle Fernandez, Dusko Ehrlich, Samira Boudebbouze, Unité de recherche Génétique Microbienne (UGM), Institut National de la Recherche Agronomique (INRA), Bactéries Lactiques et Pathogènes Opportunistes (UBLO), Kyoto University [Kyoto], GENOME Express, Danone Vitapole, Microbiota Interaction with Human and Animal (MIHA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Streptococcus thermophilus, pyruvate metabolism, [SDV]Life Sciences [q-bio], acid adaptation, Models, Biological, Polymerase Chain Reaction, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, Lactobacillus bulgaricus, Pyruvic Acid, Chaperonin 10, Electrophoresis, Gel, Two-Dimensional, Glycolysis, Molecular Biology, Heat-Shock Proteins, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, acid stress, food and beverages, Chaperonin 60, Gene Expression Regulation, Bacterial, Hydrogen-Ion Concentration, biology.organism_classification, Adaptation, Physiological, GroEL, Culture Media, Lactic acid, Lactobacillus, chemistry, Fermentation, NAD+ kinase, Pyruvic acid, Lactobacillus delbrueckii subsp. bulgaricus
Abstract

International audience; Lactic acid bacteria (LAB) gradually acidify their environment through the conversion of pyruvate to lactate, an essential process to regenerate NAD(+) used during glycolysis. A clear demonstration of acidification can be found in yogurt, the product of milk fermentation by the LAB Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) and Streptococcus thermophilus, where the pH falls to 4.2. Acid adaptation therefore plays an important role in the physiology of LAB. Here we present the results of a proteomic approach to reveal cellular changes associated with acid adaptation in L. bulgaricus. These results were complemented with transcription data for selected genes to show three major effects: (i) induction of the chaperones GroES, GroEL, HrcA, GrpE, DnaK, DnaJ, ClpE, ClpP, and ClpL, and the repression of ClpC; (ii) induction of genes involved in the biosynthesis of fatty acids (fabH, accC, fabI); (iii) repression of genes involved in the mevalonate pathway of isoprenoid synthesis (mvaC, mvaS). Together with changes in the expression of other genes from the local metabolic network, these results for the first time show a coherent picture of changes in gene expression expected to result in a rerouting of pyruvate metabolism to favor fatty acid biosynthesis, and thereby affect membrane fluidity.

Published
2008
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8. Genes involved in conceptus-endometrial interactions in ruminants: insights from reductionism and thoughts on holistic approaches

Author

Thomas E. Spencer, Eckhard Wolf, Olivier Sandra, Texas A&M University System, Biologie du développement et reproduction (BDR), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Ludwig Maximilians University of Munich, Gene Center, Ludwig Maximilians University, Department of Agriculture Cooperative State Research, Education, and Extension Service and National Institutes of Health, the European EMBIC network (contract no. 512040) and French National Institute for Agricultural Research (INRA), and the German Research Council (DFG), the Bavarian Research Foundation (BFS), and the German Federal Ministry of Science (BMBF). This article is based on research presented at the 2nd International Meeting on Mammalian Embryogenomics, which was sponsored by the Organisation for Economic Co-operation and Development (OECD), Le conseil Régional Ile-de-France, the Institut National de la Recherche Agronomique (INRA), Cogenics-Genome Express, Eurogentac, Proteigene, Sigma-Aldrich France and Diagenode sa, and Organisation de Coopération et de Développement Economiques. FRA.

Subjects
Embryology, Somatomammotropin, Biology, Pregnancy Maintenance, 03 medical and health sciences, 0302 clinical medicine, Endocrinology, Pregnancy, medicine, Conceptus, Animals, Blastocyst, Embryo Implantation, Placental lactogen, reproductive and urinary physiology, 030304 developmental biology, Oligonucleotide Array Sequence Analysis, Regulation of gene expression, 0303 health sciences, 030219 obstetrics & reproductive medicine, Sheep, urogenital system, Gene Expression Profiling, Obstetrics and Gynecology, Trophoblast, Gene Expression Regulation, Developmental, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Cell Biology, Ruminants, medicine.disease, Cell biology, medicine.anatomical_structure, Reproductive Medicine, embryonic structures, Pregnancy, Animal, Cattle, Female, Hormone
Abstract

National audience; This review summarizes new knowledge on expression of genes and provides insights into approaches for study of conceptus-endometrial interactions in ruminants with emphasis on the peri-implantation stage of pregnancy. Conceptus-endometrial interactions in ruminants are complex and involve carefully orchestrated temporal and spatial alterations in gene expression regulated by hormones from the ovary and conceptus. Progesterone is the hormone of pregnancy and acts on the uterus to stimulate blastocyst survival, growth, and development. Inadequate progesterone levels or a delayed rise in progesterone is associated with pregnancy loss. The mononuclear trophectoderm cells of the elongating blastocyst synthesize and secrete interferon-tau (IFNT), the pregnancy recognition signal. Trophoblast giant binucleate cells begin to differentiate and produce hormones including chorionic somatomammotropin 1 (CSH1 or placental lactogen). A number of genes, induced or stimulated by progesterone, IFNT, and/or CSH1 in a cell-specific manner, are implicated in trophectoderm adhesion to the endometrial luminal epithelium and regulation of conceptus growth and differentiation. Transcriptional profiling experiments are beginning to unravel the complex dynamics of conceptus-endometrial interactions in cattle and sheep. Future experiments should incorporate physiological models of pregnancy loss and be complemented by metabolomic studies of uterine lumen contents to more completely define factors required for blastocyst survival, growth, and implantation. Both reduction and holistic approaches will be important to understand the multifactorial phenomenon of recurrent pregnancy loss and provide a basis for new strategies to improve pregnancy outcome and reproductive efficiency in cattle and other domestic animals.

Published
2007
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9. Transcriptome analysis of wood formation in maritime pine

Author

Frigerio Cantón, Grégoire Le Provost, Garcia, V., Barre, A., Jean-Marc Frigerio, Jorge Almiro Paiva, Fevereiro, P., Avila, C., Mouret, J. F., Jean Brach, Daruvar, A., Canovas, F. M., christophe plomion, Universidad de Málaga [Málaga] = University of Málaga [Málaga], Biodiversité, Gènes et Ecosystèmes (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Instituto de Technologia Quimica e Biologica, GENOME Express, and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], PIN MARITIME, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2002

10. Identification of genes involved in ceramide-dependent neuronal apoptosis using cDNA arrays

Author

Decraene, C., Brugg, B., Ruberg, M., Eveno, E., Matingou, C., Tahi, F., Jean Mariani, Auffray, C., Pietu, G., Genexpress, Centre National de la Recherche Scientifique (CNRS), Service de Génomique Fonctionnelle, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Neurobiologie des processus adaptatifs (NPA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Neurologie Expérimentale et Thérapeutique, IFR70-Institut National de la Santé et de la Recherche Médicale (INSERM), Université d'Évry-Val-d'Essonne (UEVE), This work was supported by the CNRS and grants from European Union to J.M. (TMR projet Neuril) and BIOMED2 programs (EURO-IMAGE Consortium, BMH4-CT-97-2284) to C.A. C.M. was supported by Genome Express and C.D. acknowledges fellowships from the Fédération Française des Groupements Parkinsoniens (FFGP) and the Association pour la Recherche sur le Cancer (ARC)., and Maylin, Françoise

Subjects
MESH: Signal Transduction, MESH: Cell Differentiation, MESH: Rats, MESH: Neurons, Apoptosis, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, PC12 Cells, MESH: Nucleic Acid Hybridization, MESH: Gene Expression Profiling, Sphingosine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, MESH: PC12 Cells, MESH: Animals, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Oligonucleotide Array Sequence Analysis, Neurons, Research, Gene Expression Profiling, MESH: Apoptosis, Nucleic Acid Hybridization, Cell Differentiation, MESH: Genes, Rats, Genes, MESH: Oligonucleotide Array Sequence Analysis, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], MESH: Sphingosine, Signal Transduction
Abstract

A cell-culture model was used to establish a profile of gene expression during the effector phase of ceramide-mediated cell death. Of the 239 genes that met the criteria for differential hybridization, 10 correspond to genes previously involved in C2-ceramide or TNF-α signaling pathways and 20 in neuronal disorders, oncogenesis or more broadly in the regulation of proliferation., Background Ceramide is important in many cell responses, such as proliferation, differentiation, growth arrest and apoptosis. Elevated ceramide levels have been shown to induce apoptosis in primary neuronal cultures and neuronally differentiated PC 12 cells. Results To investigate gene expression during ceramide-dependent apoptosis, we carried out a global study of gene expression in neuronally differentiated PC 12 cells treated with C2-ceramide using an array of 9,120 cDNA clones. Although the criteria adopted for differential hybridization were stringent, modulation of expression of 239 genes was identified during the effector phase of C2-ceramide-induced cell death. We have made an attempt at classifying these genes on the basis of their putative functions, first with respect to known effects of ceramide or ceramide-mediated transduction systems, and then with respect to regulation of cell growth and apoptosis. Conclusions Our cell-culture model has enabled us to establish a profile of gene expression during the effector phase of ceramide-mediated cell death. Of the 239 genes that met the criteria for differential hybridization, 10 correspond to genes previously involved in C2-ceramide or TNF-α signaling pathways and 20 in neuronal disorders, oncogenesis or more broadly in the regulation of proliferation. The remaining 209 genes, with or without known functions, constitute a pool of genes potentially implicated in the regulation of neuronal cell death.

Published
2002

11. Genepi: a blackboard framework for genome annotation.

Author

Descorps-Declère S, Ziébelin D, Rechenmann F, and Viari A

Subjects
Base Sequence, Genome genetics, Molecular Sequence Data, Algorithms, Chromosome Mapping methods, Databases, Genetic, Information Storage and Retrieval methods, Sequence Analysis, DNA methods, Software, User-Computer Interface
Abstract

Background: Genome annotation can be viewed as an incremental, cooperative, data-driven, knowledge-based process that involves multiple methods to predict gene locations and structures. This process might have to be executed more than once and might be subjected to several revisions as the biological (new data) or methodological (new methods) knowledge evolves. In this context, although a lot of annotation platforms already exist, there is still a strong need for computer systems which take in charge, not only the primary annotation, but also the update and advance of the associated knowledge. In this paper, we propose to adopt a blackboard architecture for designing such a system, Results: We have implemented a blackboard framework (called Genepi) for developing automatic annotation systems. The system is not bound to any specific annotation strategy. Instead, the user will specify a blackboard structure in a configuration file and the system will instantiate and run this particular annotation strategy. The characteristics of this framework are presented and discussed. Specific adaptations to the classical blackboard architecture have been required, such as the description of the activation patterns of the knowledge sources by using an extended set of Allen's temporal relations. Although the system is robust enough to be used on real-size applications, it is of primary use to bioinformatics researchers who want to experiment with blackboard architectures., Conclusion: In the context of genome annotation, blackboards have several interesting features related to the way methodological and biological knowledge can be updated. They can readily handle the cooperative (several methods are implied) and opportunistic (the flow of execution depends on the state of our knowledge) aspects of the annotation process.

Published
2006
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12. Large functional range of steady-state levels of nuclear and mitochondrial transcripts coding for the subunits of the human mitochondrial OXPHOS system.

Author

Duborjal H, Beugnot R, Mousson de Camaret B, and Issartel JP

Subjects
Cell Nucleus metabolism, Cell Nucleus physiology, Cells, Cultured, Codon metabolism, Codon physiology, Gene Expression Profiling methods, Genetic Variation genetics, Humans, Mitochondria metabolism, Mitochondria physiology, Multienzyme Complexes genetics, Multienzyme Complexes metabolism, Multienzyme Complexes physiology, Oxidoreductases genetics, Oxidoreductases metabolism, Oxidoreductases physiology, RNA metabolism, RNA physiology, RNA, Mitochondrial, RNA, Nuclear metabolism, RNA, Nuclear physiology, Reverse Transcriptase Polymerase Chain Reaction methods, Skin cytology, Skin enzymology, Skin metabolism, Tumor Cells, Cultured, Cell Nucleus genetics, Codon genetics, Mitochondria genetics, Oxidative Phosphorylation, RNA genetics, RNA, Nuclear genetics, Transcription, Genetic
Abstract

We have measured, by reverse transcription and real-time quantitative PCR, the steady-state levels of the mitochondrial and nuclear transcripts encoding several subunits of the human oxidative phosphorylation (OXPHOS) system, in different normal tissues (muscle, liver, trachea, and kidney) and in cultured cells (normal fibroblasts, 143B osteosarcoma cells, 143B206 rho(0) cells). Five mitochondrial transcripts and nine nuclear transcripts were assessed. The measured amounts of these OXPHOS transcripts in muscle samples corroborated data obtained by others using the serial analysis of gene expression (SAGE) method to appraise gene expression in the same type of tissue. Steady-state levels for all the transcripts were found to range over more than two orders of magnitude. Most of the time, the mitochondrial H-strand transcripts were present at higher levels than the nuclear transcripts. The mitochondrial L-strand transcript ND6 was usually present at a low level. Cultured 143B cells contained significantly reduced amounts of mitochondrial transcripts in comparison with the tissue samples. In 143B206 rho(0) cells, fully depleted of mitochondrial DNA, the levels of nuclear OXPHOS transcripts were not modified in comparison with the parental cells. This observation indicated that nuclear transcription is not coordinated with mitochondrial transcription. We also observed that in the different tissues and cells, there is a transcriptional coregulation of all the investigated nuclear genes. Nuclear OXPHOS gene expression seems to be finely regulated.

Published
2002
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