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19 results on '"MESH : Genetic Variation"'

1. Genetic and functional characterisation of the lactococcal P335 phage-host interactions

Author

Laurens Hanemaaijer, Jennifer Mahony, Joana Oliveira, Marco Ventura, Douwe van Sinderen, Horst Neve, Gabriele Andrea Lugli, Barry Collins, Christian Cambillau, Thijs R. H. M. Kouwen, School of Microbiology, University College Cork (UCC), Università degli studi di Parma [Parme, Italie], Dept Microbiol & Biotechnol, Max Rubner Inst, 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), Department of Microbiology, University College Cork, Università degli studi di Parma = University of Parma (UNIPR), University of Parma = Università degli studi di Parma [Parme, Italie], Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), University College Cork ( UCC ), Università degli studi di Parma, 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, viruses, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Proteomics, Siphoviridae, Bacteriophage, Phage group, Bacteriophages, MESH: Genetic Variation, MESH : Viral Proteins, 2. Zero hunger, Genetics, biology, Dairy Fermentation, MESH: Genomics, Genomics, MESH : Host Specificity, MESH : Bacteriophages, Lactococcus lactis, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Calcium, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, DNA microarray, Research Article, Biotechnology, MESH: Host Specificity, Context (language use), [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Host Specificity, Microbiology, Dairy, Viral Proteins, 03 medical and health sciences, MESH : Genetic Variation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Bacteriophages, MESH : Calcium, Host (biology), MESH : Genomics, Genetic Variation, biology.organism_classification, MESH: Viral Proteins, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, MESH: Lactococcus lactis, Fermentation, Receptor-binding protein, Calcium, MESH : Lactococcus lactis
Abstract

Background Despite continuous research efforts, bacterio(phages) infecting Lactococcus lactis starter strains persist as a major threat to dairy fermentations. The lactococcal P335 phages, which are currently classified into four sub-groups (I-IV), are the second most frequently isolated phage group in an industrial dairy context. Results The current work describes the isolation and comparative genomic analysis of 17 novel P335 group phages. Detailed analysis of the genomic region of P335 phages encoding the so-called “baseplate”, which includes the receptor binding protein (RBP) was combined with a functional characterization of the RBP of sub-group III and IV phages. Additionally, calcium-dependence assays revealed a specific requirement for calcium by sub-group IV phages while host range analysis highlighted a higher number of strains with CWPS type A (11 of 39 strains) are infected by the P335 phages assessed in this study than those with a C (five strains), B (three of 39 strains) or unknown (one of 39 strains) CWPS type. Conclusions These analyses revealed significant divergence among RBP sequences, apparently reflecting their unique interactions with the host and particularly for strains with a type A CWPS. The implications of the genomic architecture of lactococcal P335 phages on serving as a general model for Siphoviridae phages are discussed. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3537-5) contains supplementary material, which is available to authorized users.

Published
2017

2. EWET: Data collection and interface for the genetic analysis of Echinococcus multilocularis based on EmsB microsatellite

Author

Raphael Mélior, Jérémy Navion, Vanessa Hormaz, Laurence Millon, Francis Raoul, Jonathan Brillaud, Jenny Knapp, Jean Daniel Tissot, Sylvie Damy, Gérald Umhang, Eve Afonso, Adriano Casulli, Frédéric Dadeau, Bruno Gottstein, Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), UMS THETA (terre, homme, environnement, temps, astronomie) ( OSU-THETA ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Maison des Sciences de l'Homme et de l'Environnement Claude Nicolas Ledoux ( MSHE ), Agence Nationale de Sécurité Sanitaire, de l'Alimentation, de l'environnement et du Travail ( ANSES ), ANSES, Institute of Parasitology, University of Bern, Laboratoire de la rage et pathologie des animaux sauvages ( LERPAS ), Istituto Superiore di Sanità Rome, Rome, Italy, Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies ( FEMTO-ST ), Université de Technologie de Belfort-Montbeliard ( UTBM ) -Ecole Nationale Supérieure de Mécanique et des Microtechniques ( ENSMM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Service de parasitologie et mycologie [CHU de Besançon], Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ), 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), OSU-THETA - Observatoire des Sciences de l'Univers - Terre Homme Environnement Temps Astronomie (OSU-THETA), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Maison des Sciences de l'Homme et de l'Environnement Claude Nicolas Ledoux (MSHE), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de la rage et pathologie des animaux sauvages (LERPAS), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Service de parasitologie et mycologie [CHRU de Besançon], and Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)

Subjects
0301 basic medicine, Epidemiology, Flatworms, lcsh:Medicine, Artificial Gene Amplification and Extension, MESH: Base Sequence, MESH: Genetic Markers, MESH : Echinococcus multilocularis, MESH : Microsatellite Repeats, Polymerase Chain Reaction, Computer Applications, 0302 clinical medicine, Databases, Genetic, MESH : Genes, Helminth, Medicine and Health Sciences, MESH : Genetic Markers, MESH: Animals, MESH: Genetic Variation, lcsh:Science, 610 Medicine & health, Genes, Helminth, MESH: Databases, Genetic, Data Management, Biological data, Multidisciplinary, Geography, 630 Agriculture, Eukaryota, Phylogeography, Biogeography, Genetic Epidemiology, Calibration, Web-Based Applications, Microsatellite, Research Article, Genetic Markers, Genotyping, Computer and Information Sciences, 030231 tropical medicine, Biology, Research and Analysis Methods, Echinococcus multilocularis, MESH: Calibration, [ SDV.EE.SANT ] Life Sciences [q-bio]/Ecology, environment/Health, 03 medical and health sciences, MESH : Genetic Variation, Helminths, Genetic variation, Genetics, Parasitic Diseases, Animals, Molecular Biology Techniques, MESH : Databases, Genetic, Molecular Biology, MESH : Calibration, MESH: Echinococcus multilocularis, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Evolutionary Biology, Genetic diversity, Base Sequence, Population Biology, Ecology and Environmental Sciences, lcsh:R, Organisms, Genetic Variation, Biology and Life Sciences, biology.organism_classification, Invertebrates, Echinococcus, 030104 developmental biology, Genetic distance, Evolutionary biology, Earth Sciences, 570 Life sciences, biology, lcsh:Q, MESH : Base Sequence, MESH: Microsatellite Repeats, MESH : Animals, Population Genetics, Microsatellite Repeats, MESH: Genes, Helminth
Abstract

International audience; Evolution and dispersion history on Earth of organisms can best be studied through biological markers in molecular epidemiological studies. The biological diversity of the cestode Echinococcus multilocularis was investigated in different cladistic approaches. First the morphological aspects were explored in connection with its ecology. More recently, molecular aspects were investigated to better understand the nature of the variations observed among isolates. The study of the tandemly repeated multilocus microsatellite EmsB allowed us to attain a high genetic diversity level where other classic markers have failed. Since 2006, EmsB data have been collected on specimens from various endemic foci of the parasite in Europe (in historic and newly endemic areas), Asia (China, Japan and Kyrgyzstan), and North America (Canada and Alaska). Biological data on the isolates and metadata were also recorded (e.g. host, geographical location, EmsB analysis, citation in the literature). In order to make available the data set of 1,166 isolates from classic and aberrant domestic and wild animal hosts (larval lesions and adult worms) and from human origin, an open web access interface, developed in PHP, and connected to a PostgreSQL database, was developed in the EmsB Website for the Echinococcus Typing (EWET) project. It allows researchers to access data collection, perform genetic analyses online (e.g. defining the genetic distance between their own samples and the samples in the database), consult distribution maps of EmsB profiles, and record and share their new EmsB genotyping data. In order to standardize the EmsB analyses performed in the different laboratories throughout the world, a calibrator was developed. The final aim of this project was to gather and arrange available data to permit to better understand the dispersion and transmission patterns of the parasite among definitive and intermediate hosts, in order to organize control strategies on the ground.

Published
2017
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3. Association of the Pro12Ala and C1431T Variants ofPPARγ and Their Haplotypes with Susceptibility to Gestational Diabetes

Author

Barbara Heude, Jean-François Bedel, Jean-Marc Lacorte, Anne Forhan, Véronique Pelloux, Marie-Aline Charles, Karine Clément, Centre de recherche en épidémiologie et santé des populations (CESP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Sud - Paris 11 (UP11)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Paris Descartes - Paris 5 (UPD5)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service d’Endocrinologie, Métabolisme et Prévention des Risques Cardio-Vasculaires [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Structures bactériennes impliquées dans la modulation de la résistance aux antibiotiques, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR58-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Recherche en épidémiologie et biostatistique, Université Paris-Sud - Paris 11 (UP11)-Institut National de la Santé et de la Recherche Médicale (INSERM), Epidémiologie des maladies infectieuses et modélisation (ESIM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), G. Liccardi, I. Annesi-Maesano 1, A. Salzillo, G. D'amato Liccardi G, Annesi-Maesano I, Salzillo A, D'Amato G. Collaboration, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM), 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), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service d'Endocrinologie, Métabolisme et Prévention des Maladies Cardio-vasculaires [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre de recherche en épidémiologie et santé des populations ( CESP ), Université de Versailles Saint-Quentin-en-Yvelines ( UVSQ ) -Université Paris-Sud - Paris 11 ( UP11 ) -Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale ( INSERM ), 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 ), Service d'endocrinologie-métabolisme [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Pitié-Salpêtrière [APHP], Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IFR58-Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Epidémiologie des maladies infectieuses et modélisation ( ESIM ), and Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM )

Subjects
MESH : DNA, Endocrinology, Diabetes and Metabolism, Clinical Biochemistry, MESH : Genotype, Type 2 diabetes, Biochemistry, Body Mass Index, MESH: Genotype, Cohort Studies, MESH: Pregnancy, 0302 clinical medicine, Endocrinology, Gene Frequency, Pregnancy, Odds Ratio, Medicine, MESH : Female, MESH : Gene Frequency, MESH: Genetic Variation, MESH: Cohort Studies, MESH: Genetic Association Studies, MESH: Diabetes, Gestational, 2. Zero hunger, 0303 health sciences, MESH: Polymorphism, Single Nucleotide, MESH : Polymorphism, Single Nucleotide, MESH: DNA, [ SDV.SPEE ] Life Sciences [q-bio]/Santé publique et épidémiologie, MESH : Adult, 3. Good health, Gestational diabetes, Female, MESH : PPAR gamma, Adult, medicine.medical_specialty, Genotype, MESH : Cohort Studies, 030209 endocrinology & metabolism, Single-nucleotide polymorphism, Polymorphism, Single Nucleotide, MESH: Body Mass Index, 03 medical and health sciences, MESH : Genetic Variation, Diabetes mellitus, Internal medicine, MESH: Gene Frequency, Humans, MESH : Haplotypes, Genetic Association Studies, 030304 developmental biology, MESH: Humans, business.industry, MESH : Humans, Biochemistry (medical), Haplotype, Genetic Variation, MESH: Adult, MESH : Genetic Association Studies, MESH: Haplotypes, DNA, Odds ratio, medicine.disease, Obesity, MESH: Odds Ratio, PPAR gamma, MESH : Body Mass Index, MESH : Pregnancy, Diabetes, Gestational, MESH: PPAR gamma, Haplotypes, MESH : Odds Ratio, MESH : Diabetes, Gestational, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, MESH: Female, Body mass index
Abstract

International audience; BACKGROUND: The protective role of the Ala allele in the Pro12Ala polymorphism of PPARγ on type 2 diabetes has been well established but not confirmed in the context of pregnancy, for gestational diabetes, a known predictor of later type 2 diabetes onset. Another PPARγ polymorphism, the C1431T, is in strong linkage disequilibrium with Pro12Ala and has been shown to be associated with body weight, but its association with diabetes is controversial. RESEARCH DESIGN AND METHODS: In 1708 women of the EDEN mother-child cohort, the PPARγ Pro12Ala and C1431T polymorphisms were genotyped and analyzed in association with maternal prepregnancy body mass index, obesity before pregnancy, and gestational diabetes, separately and also combined in haplotypes. RESULTS: The prevalence of obesity was significantly higher in mothers with the Ala/Ala genotype compared with carriers of the Pro allele (35 vs. 9%, P < 0.0001), but there was no cases of gestational diabetes in Ala/Ala mothers. Mothers homozygous for the T allele of C1431T were also more obese (24 vs. 9%, P = 0.035), and three times more had gestational diabetes (18 vs. 6%, P = 0.044). Frequencies of haplotypes for these two single-nucleotide polymorphisms differed significantly in mothers with and without gestational diabetes; in comparison with the Pro-C haplotype, the Pro-T haplotype conferred the highest risk [odds ratio (95% CI) = 1.89 (1.05-3.40)], and the Ala-C the lowest risk [odds ratio (95% CI) = 0.12 (0.52-1.70)]. CONCLUSIONS: These results from a haplotype analysis, show for the first time that genetic variations in the PPARγ gene could play a role in the susceptibility to develop gestational diabetes.

Published
2011

4. Characterization of Unique Signature Sequences in the Divergent Maternal Protein Bcl2l10

Author

Germain Gillet, Abdel Aouacheria, François Penin, Aurélie Cornut-Thibaut, Yannis Guillemin, 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), Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Biologie Moléculaire de la Cellule (LBMC), 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), Ganivet, Agnès, 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 ), Centre de Recherche en Cancérologie de Lyon ( CRCL ), Université de Lyon-Université de Lyon-Centre Léon Bérard [Lyon]-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biologie Moléculaire de la Cellule ( LBMC ), 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 ), and École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL)

Subjects
MESH : Cell Line, MESH : Molecular Sequence Data, Amino Acid Motifs, MESH: Amino Acid Sequence, MESH: Base Sequence, MESH : Proto-Oncogene Proteins c-bcl-2, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, MESH: INDEL Mutation, protein sequence, MESH: Amino Acid Motifs, MESH: Protein Structure, Tertiary, 0302 clinical medicine, INDEL Mutation, Databases, Genetic, genetic polymorphism, MESH : Female, MESH: Animals, MESH: Genetic Variation, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Peptide sequence, MESH: Databases, Genetic, MESH: Evolution, Molecular, Sequence Deletion, Genetics, chemistry.chemical_classification, 0303 health sciences, MESH : Amino Acid Sequence, MESH : Sequence Alignment, apoptosis, Vertebrate, MESH: Sequence Deletion, Amino acid, Proto-Oncogene Proteins c-bcl-2, MESH: Calcium, 030220 oncology & carcinogenesis, Female, MESH : Protein Structure, Tertiary, MESH : Amino Acid Motifs, Molecular Sequence Data, MESH: Sequence Alignment, [SDV.CAN]Life Sciences [q-bio]/Cancer, Sequence alignment, Biology, Cell Line, MESH: Oocytes, Evolution, Molecular, 03 medical and health sciences, Bcl-2 family, MESH : Genetic Variation, biology.animal, evolution, [SDV.BDD] Life Sciences [q-bio]/Development Biology, Genetic variation, Homologous chromosome, Animals, Humans, MESH : HeLa Cells, MESH : Evolution, Molecular, Amino Acid Sequence, MESH : Calcium, MESH : Databases, Genetic, Indel, MESH : INDEL Mutation, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH : Mutagenesis, Insertional, calcium, MESH: Humans, MESH: Molecular Sequence Data, Base Sequence, MESH : Sequence Deletion, MESH: Apoptosis, MESH : Humans, MESH : Oocytes, Genetic Variation, Protein Structure, Tertiary, MESH: Cell Line, Mutagenesis, Insertional, MESH: Mutagenesis, Insertional, MESH: Proto-Oncogene Proteins c-bcl-2, chemistry, MESH: HeLa Cells, Oocytes, MESH : Base Sequence, MESH : Animals, Sequence Alignment, MESH: Female, MESH : Apoptosis, HeLa Cells
Abstract

International audience; Insertions or deletions (indels) of amino acids residues have been recognized as an important source of genetic and structural divergence between paralogous Bcl-2 family members. However, these signature sequences have not so far been extensively investigated amongst orthologous Bcl-2 family proteins. Bcl2l10 is an antiapoptotic member of the Bcl-2 family that has evolved rapidly throughout the vertebrate lineage and which shows conserved abundant expression in eggs and oocytes. In this paper, we have unraveled two major sites of divergence between human Bcl2l10 and its vertebrate homologs. The first one provides length variation at the N-terminus (before the BH4 domain) and the second one is located between the predicted α5-α6 pore-forming helices, providing an unprecedented case in the superfamily of helix-bundled pore-forming proteins. These two particular indels were studied phylogenetically and through biochemical and cell biological techniques, including truncation and site-directed mutagenesis. While deletion of the N-terminal extension had no significant functional impact in HeLa cells, our results suggest that the human Bcl2l10 protein evolved a calcium-binding motif in its α5-α6 interhelical region by acquiring critical negatively charged residues. Considering the reliance of female eggs on calcium-dependent proteins and calcium-regulated processes and the exceptional longevity of oocytes in the primate lineage, we propose that this microstructural variation may be an adaptive feature associated with high maternal expression of this Bcl-2 family member.

Published
2011

5. Mutations in DNAH1, which encodes an inner arm heavy chain dynein, lead to male infertility from multiple morphological abnormalities of the sperm flagella

Author

Pierre-Simon Jouk, Nicolas Thierry-Mieg, Pierre F. Ray, Karine Pernet-Gallay, Thomas Karaouzène, Denise Escalier, Charles Coutton, Christophe Arnoult, Virginie Pierre, Marie Bidart, Sylviane Hennebicq, Mariem Ben Khelifa, Raoudha Zouari, Didier Grunwald, John Rendu, Aminata Touré, Julie Delaroche, Sandra Yassine, Laboratoire de Génomique Biomédicale et Oncogénétique - Biomedical Genomics and Oncogenetics Laboratory ( LR11IPT05 ), Université Tunis El Manar ( UTM ) -Institut Pasteur de Tunis-Réseau International des Instituts Pasteur ( RIIP ), Université Joseph Fourier - Grenoble 1 ( UJF ), AGeing and IMagery ( AGIM ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -École pratique des hautes études ( EPHE ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Genetique Chromosomique, CHU Grenoble, Clinique de Promotion des Sciences de la Reproduction - Les Jasmins ( CPSR ), Clinique de Promotion des Sciences de la Reproduction, Grenoble Institut des Neurosciences ( GIN ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -CHU Grenoble-Université Joseph Fourier - Grenoble 1 ( UJF ), Institut de Biologie et de Pathologie ( DBTP ), Laboratoire d’Aide à la Procréation, Département de Génétique et Procréation ( CECOS ), Hôpital Couple Enfant de Grenoble-CHU de Grenoble, Physiopathologie des maladies génétiques d'expression pédiatrique, Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ), Institut Cochin ( 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 ), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications [Grenoble] ( TIMC-IMAG ), 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 ), This work was supported by the research grant ICG2I funded by the program GENOPAT 2009 from the French Research Agency (ANR)., ANR-09-GENO-0013,ICG2I,Identification et Caractérisation de gènes impliqués dans l'infertilité. ( 2009 ), Laboratoire de Génomique Biomédicale et Oncogénétique - Biomedical Genomics and Oncogenetics Laboratory (LR11IPT05), Université de Tunis El Manar (UTM)-Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Université Joseph Fourier - Grenoble 1 (UJF), AGeing and IMagery (AGIM), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génétique Chromosomique [CHU de Grenoble], Clinique de Promotion des Sciences de la Reproduction [Tunis] (CPSR), Polyclinique les Jasmins [Tunis], 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), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-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 Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-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), [GIN] Grenoble Institut des Neurosciences (GIN), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Biologie et de Pathologie (DBTP), Laboratoire d’Aide à la Procréation, Département de Génétique et Procréation (CECOS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), 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), Dynamiques Cellulaire, Tissulaire & Microscopie fonctionnelle (TIMC-IMAG-DyCTiM), ANR-09-GENO-0013,ICG2I,Identification et Caractérisation de gènes impliqués dans l'infertilité.(2009), Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Joseph Fourier - Grenoble 1 (UJF)-Université Pierre Mendès France - Grenoble 2 (UPMF), Clinique de Promotion des Sciences de la Reproduction - Les Jasmins (CPSR), 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), Dynamique Cellulaire et Tissulaire- Interdisciplinarité, Modèles & Microscopies (TIMC-IMAG-DyCTiM), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Université Tunis El Manar (UTM), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-École pratique des hautes études (EPHE)-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), Grenoble Institut des Neurosciences (GIN), and Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF)

Subjects
Male, MESH: Sequence Analysis, DNA, Axoneme, MESH : RNA, Messenger, [SDV]Life Sciences [q-bio], MESH: RNA Splice Sites, Male infertility, 0302 clinical medicine, MESH : Axoneme, Testis, MESH : Infertility, Male, Genetics(clinical), MESH: Genetic Variation, Genetics (clinical), Sperm motility, Primary ciliary dyskinesia, Genetics, 0303 health sciences, 030219 obstetrics & reproductive medicine, MESH: Testis, Cilium, Homozygote, MESH : Kartagener Syndrome, MESH: Sperm Motility, MESH: Axoneme, MESH : Axonemal Dyneins, Flagella, Sperm Motility, MESH: Axonemal Dyneins, MESH : Mutation, MESH : RNA Splice Sites, MESH: Homozygote, Infertility, MESH: Mutation, MESH : Male, Dynein, Flagellum, Biology, MESH: Infertility, Male, MESH: Flagella, 03 medical and health sciences, MESH : Cilia, MESH : Homozygote, MESH: Cilia, MESH : Genetic Variation, Report, medicine, Humans, Cilia, RNA, Messenger, Infertility, Male, 030304 developmental biology, MESH: RNA, Messenger, MESH : Testis, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, Sperm flagellum, Kartagener Syndrome, MESH : Humans, MESH : Sperm Tail, Genetic Variation, Axonemal Dyneins, Sequence Analysis, DNA, medicine.disease, MESH: Male, MESH: Sperm Tail, MESH : Sperm Motility, Sperm Tail, Mutation, MESH: Kartagener Syndrome, RNA Splice Sites, MESH : Flagella, [ SDV.GEN ] Life Sciences [q-bio]/Genetics, MESH : Sequence Analysis, DNA
Abstract

International audience; Ten to fifteen percent of couples are confronted with infertility and a male factor is involved in approximately half the cases. A genetic etiology is likely in most cases yet only few genes have been formally correlated with male infertility. Homozygosity mapping was carried out on a cohort of 20 North African individuals, including 18 index cases, presenting with primary infertility resulting from impaired sperm motility caused by a mosaic of multiple morphological abnormalities of the flagella (MMAF) including absent, short, coiled, bent, and irregular flagella. Five unrelated subjects out of 18 (28%) carried a homozygous variant in DNAH1, which encodes an inner dynein heavy chain and is expressed in testis. RT-PCR, immunostaining, and electronic microscopy were carried out on samples from one of the subjects with a mutation located on a donor splice site. Neither the transcript nor the protein was observed in this individual, confirming the pathogenicity of this variant. A general axonemal disorganization including mislocalization of the microtubule doublets and loss of the inner dynein arms was observed. Although DNAH1 is also expressed in other ciliated cells, infertility was the only symptom of primary ciliary dyskinesia observed in affected subjects, suggesting that DNAH1 function in cilium is not as critical as in sperm flagellum.

Published
2014

6. A multi-locus inference of the evolutionary diversification of extant flamingos (Phoenicopteridae)

Author

Brittney Ferrari, Marcel van Tuinen, Lisa M. Ogawa, Christopher R. Torres, Mark A. F. Gillingham, Department of Biology and Marine Biology, University of North Carolina Wilmington, Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de recherche de la Tour du Valat, Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, and Financial support from the College of Arts and Sciences and Department of Biology and Marine Biology at UNCW, the Conseil Régional de Bourgogne, and the Total Foundation.

Subjects
Bill, Biogeography, Population, MESH : Multilocus Sequence Typing, Zoology, Metapopulation, Mirandornithes, Birds, Evolution, Molecular, MESH : Bayes Theorem, Phylogenetics, MESH : Genetic Variation, MESH : Biological Evolution, MESH : Phylogeography, Animals, MESH : Evolution, Molecular, MESH : Birds, education, Divergence time, Ecology, Evolution, Behavior and Systematics, Phylogeny, Cell Nucleus, education.field_of_study, MESH : Cell Nucleus, biology, Phylogenetic tree, Fossils, Genetic Variation, Bayes Theorem, Fossil, biology.organism_classification, Biological Evolution, Phoenicoparrus, Phoenicopteridae, Phylogeography, Flamingo, Evolutionary biology, Filter feeding, MESH : Fossils, MESH : Animals, [ SDV.BID.SPT ] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Multilocus Sequence Typing, Research Article
Abstract

9 pages; International audience; BACKGROUND: Modern flamingos (Phoenicopteridae) occupy a highly specialized ecology unique among birds and represent a potentially powerful model system for informing the mechanisms by which a lineage of birds adapts and radiates. However, despite a rich fossil record and well-studied feeding morphology, molecular investigations of the evolutionary progression among modern flamingos have been limited. Here, using three mitochondrial (mtDNA) markers, we present the first DNA sequence-based study of population genetic variation in the widely distributed Chilean Flamingo and, using two mtDNA and 10 nuclear (nDNA) markers, recover the species tree and divergence time estimates for the six extant species of flamingos. Phylogenetic analyses include likelihood and Bayesian frameworks and account for potential gene tree discordance. Analyses of divergence times are fossil calibrated at the divergence of Mirandornithes (flamingos + grebes) and the divergence of crown grebes. RESULTS: mtDNA sequences confirmed the presence of a single metapopulation represented by two minimally varying mtDNA barcodes in Chilean flamingos. Likelihood and Bayesian methods recovered identical phylogenies with flamingos falling into shallow-keeled (comprising the Greater, American and Chilean Flamingos) and deep-keeled (comprising the Lesser, Andean and James's Flamingos) sub-clades. The initial divergence among flamingos occurred at or shortly after the Mio-Pliocene boundary (6-3 Ma) followed by quick consecutive divergences throughout the Plio-Pleistocene. There is significant incongruence between the ages recovered by the mtDNA and nDNA datasets, likely due to mutational saturation occurring in the mtDNA loci. CONCLUSION: The finding of a single metapopulation in the widespread Chilean Flamingo confirms similar findings in other widespread flamingo species. The robust species phylogeny is congruent with previous classifications of flamingos based on feeding morphology. Modern phoenicopterids likely originated in the New World with each sub-clade dispersing across the Atlantic at least once. Our divergence time estimates place flamingos among the youngest families of birds, counter to the classical notion of flamingos as among the oldest based on biogeography and the fossil record. Finally, we designate 'Phoeniconaias' as a junior synonym of 'Phoenicoparrus' and redefine the latter genus as containing all flamingos more closely related to Phoenicoparrus andinus than Phoenicopterus roseus.

Published
2014

7. 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

8. HBVdb: a knowledge database for Hepatitis B Virus

Author

Fabien Zoulim, Fanny Jadeau, Gilbert Deléage, Juliette Hayer, Alan Kay, Christophe Combet, Bases moléculaires et structurales des systèmes infectieux ( BMSSI ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), Institut de biologie et chimie des protéines [Lyon] ( IBCP ), Centre de Recherche en Cancérologie de Lyon ( CRCL ), Université de Lyon-Université de Lyon-Centre Léon Bérard [Lyon]-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Bases moléculaires et structurales des systèmes infectieux (BMSSI), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de biologie et chimie des protéines [Lyon] (IBCP), Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Genotyping Techniques, [SDV]Life Sciences [q-bio], Reading frame, MESH : Hepatitis B virus, MESH : Molecular Sequence Annotation, medicine.disease_cause, Genome, User-Computer Interface, 0302 clinical medicine, Databases, Genetic, MESH: Genetic Variation, MESH : Viral Proteins, MESH: Databases, Genetic, 0303 health sciences, MESH: Drug Resistance, Viral, MESH : Genotyping Techniques, DNA virus, Articles, 3. Good health, MESH: Hepatitis B virus, MESH : Drug Resistance, Viral, MESH: Internet, 030211 gastroenterology & hepatology, MESH: Genome, Viral, MESH : Internet, MESH : Genome, Viral, Hepatitis B virus, Sequence analysis, MESH: Molecular Sequence Annotation, Genome, Viral, Biology, 03 medical and health sciences, Viral Proteins, MESH : Genetic Variation, MESH: Genotyping Techniques, Drug Resistance, Viral, Genetics, medicine, MESH : User-Computer Interface, MESH : Databases, Genetic, Genotyping, 030304 developmental biology, MESH: User-Computer Interface, Internet, [ SDV ] Life Sciences [q-bio], Genetic Variation, Molecular Sequence Annotation, Virology, MESH: Viral Proteins, Reverse transcriptase
Abstract

International audience; We have developed a specialized database, HBVdb (http://hbvdb.ibcp.fr), allowing the researchers to investigate the genetic variability of Hepatitis B Virus (HBV) and viral resistance to treatment. HBV is a major health problem worldwide with more than 350 million individuals being chronically infected. HBV is an enveloped DNA virus that replicates by reverse transcription of an RNA intermediate. HBV genome is optimized, being circular and encoding four overlapping reading frames. Indeed, each nucleotide of the genome takes part in the coding of at least one protein. However, HBV shows some genome variability leading to at least eight different genotypes and recombinant forms. The main drugs used to treat infected patients are nucleos(t)ides analogs (reverse transcriptase inhibitors). Unfortunately, HBV mutants resistant to these drugs may be selected and be responsible for treatment failure. HBVdb contains a collection of computer-annotated sequences based on manually annotated reference genomes. The database can be accessed through a web interface that allows static and dynamic queries and offers integrated generic sequence analysis tools and specialized analysis tools (e.g. annotation, genotyping, drug resistance profiling).

Published
2012

9. Genetic variability of the mTOR pathway and prostate cancer risk in the European Prospective Investigation on Cancer (EPIC)

Author

Laudina Rodríguez, Anika Hüsing, Isabelle Romieu, Rudolf Kaaks, Naomi E. Allen, Heiner Boeing, Federico Canzian, Carlotta Sacerdote, Kim Overvad, Núria Sala, David G. Cox, Elio Riboli, José María Huerta, Henk J. van Kranen, Lucie Dostal, H. Bas Bueno-de-Mesquita, Jane Nautrup Østergaard, Afshan Siddiq, Ruth C. Travis, María José Sánchez, Nerea Larrañaga, Anne Tjønneland, Angelika Stein, Göran Hallmans, Nicholas J. Wareham, Daniele Campa, Antonia Trichopoulou, Nina Roswall, Rosario Tumino, Pagona Lagiou, Mazda Jenab, Dimitrios Trichopoulos, Aurelio Barricarte, Mattias Johansson, Kay-Tee Khaw, Domenico Palli, Tobias Pischon, Sabina Sieri, [Campa, Daniele, Huesing, Anika, Stein, Angelika, Dostal, Lucie, Canzian, Federico, Kaaks, Rudolf] German Canc Res Ctr, Heidelberg, Germany. [Boeing, Heiner, Pischon, Tobias] Deutsch Inst Ernahrungsforsch, Dept Epidemiol, Potsdam, Germany. [Tjonneland, Anne, Roswall, Nina] Danish Canc Soc, Inst Canc Epidemiol, Copenhagen, Denmark. [Overvad, Kim, Ostergaard, Jane Nautrup] Aarhus Univ Hosp, Dept Cardiol, Cardiovasc Res Ctr, Aalborg Hosp, Aalborg, Denmark. [Overvad, Kim, Ostergaard, Jane Nautrup] Aarhus Univ, Dept Epidemiol, Sch Publ Hlth, DK-8000 Aarhus C, Denmark. [Rodriguez, Laudina] Hlth & Hlth Care Serv Council, Publ Hlth & Participat Directorate, Asturias, Spain. [Sala, Nuria] ICO IDIBELL, Barcelona, Spain. [Sanchez, Maria-Jose] Andalusian Sch Publ Hlth, Granada, Spain. [Sanchez, Maria-Jose, Larranaga, Nerea, Maria Huerta, Jose, Barricarte, Aurelio] Consortium Biomed Res Epidemiol & Publ Hlth CIBER, Madrid, Spain. [Larranaga, Nerea] Basque Govt, Publ Hlth Dept Gipuzkoa, Gipuzkoa, Spain. [Maria Huerta, Jose] Murcia Reg Hlth Author, Dept Epidemiol, Murcia, Spain. [Barricarte, Aurelio] Navarre Publ Hlth Inst, Pamplona, Spain. [Khaw, Kay-Tee] Univ Cambridge, Sch Clin Med, Cambridge, England. [Wareham, Nicholas] MRC Epidemiol Unit, Cambridge, England. [Travis, Ruth C., Allen, Naomi E.] Univ Oxford, Nuffield Dept Clin Med, Canc Epidemiol Unit, Oxford, England. [Lagiou, Pagona, Trichopoulou, Antonia] Univ Athens, Sch Med, WHO Collaborating Ctr Food & Nutr Policies, Dept Hyg Epidemiol & Med Stat, GR-11527 Athens, Greece. [Lagiou, Pagona, Trichopoulos, Dimitrios] Harvard Univ, Sch Publ Hlth, Dept Epidemiol, Boston, MA 02115 USA. [Trichopoulou, Antonia] Hellen Hlth Fdn, Athens, Greece. [Trichopoulos, Dimitrios] Acad Athens, Bur Epidemiol Res, Athens, Greece. [Palli, Domenico] Canc Res & Prevent Inst ISPO, Mol & Nutr Epidemiol Unit, Florence, Italy. [Sieri, Sabina] Fdn IRCCS Ist Nazl Tumori, Milan, Italy. [Tumino, Rosario] Civile MP Arezzo Hosp, Canc Registry, Ragusa, Italy. [Tumino, Rosario] Civile MP Arezzo Hosp, Histopathol Unit, Ragusa, Italy. [Sacerdote, Carlotta] Ctr Canc Prevent CPO Piemonte, Turin, Italy. [Sacerdote, Carlotta] Human Genet Fdn HuGeF, Turin, Italy. [van Kranen, Henk, Bueno-de-Mesquita, H. Bas] Natl Inst Publ Hlth & Environm, Ctr Nutr & Hlth CVG, Bilthoven, Netherlands. [Hallmans, Goran, Johansson, Mattias] Umea Univ, Dept Publ Hlth & Clin Med, Umea, Sweden. [Johansson, Mattias, Romieu, Isabelle, Jenab, Mazda] Int Agcy Res Canc, F-69372 Lyon, France. [Cox, David G., Siddiq, Afshan, Riboli, Elio] Univ London Imperial Coll Sci Technol & Med, London, England. [Cox, David G.] Ctr Leon Berard, INSERM, F-69373 Lyon, France., Specific results of this study were obtained with financial support from the US Army Medical Research and Material Command (W81XWH-05-1-0156). http://cdmrp.army.mil/pcrp/default.shtml. The EPIC study was funded by 'Europe Against Cancer' Programme of the European Commission (SANCO), Ligue contre le Cancer (France), Société 3M (France), Mutuelle Générale de l'Education Nationale, Institut National de la Santé et de la Recherche Médicale (INSERM), German Cancer Aid, German Cancer Research Center, German Federal Ministry of Education and Research, Danish Cancer Society, Health Research Fund (FIS) of the Spanish Ministry of Health, the participating regional governments and institutions of Spain, Cancer Research UK, Medical Research Council, UK, Hellenic Ministry of Health and Social Solidarity, the Stavros Niarchos Foundation and the Hellenic Health Foundation, Italian Association for Research on Cancer, Italian National Research Council, Dutch Ministry of Public Health, Welfare and Sports (VWS), Dutch Ministry of Health, Netherlands Cancer Registry (NKR), LK Research Funds, Dutch Prevention Funds, Dutch ZON (Zorg Onderzoek Nederland), World Cancer Research Fund (WCRF) (The Netherlands), Statistics Netherlands, Swedish Cancer Society, Swedish Scientific Council, Regional Government of Skane, Sweden, Norwegian Cancer Society, Department of Cancer Epidemiology, German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), German Institute of Human Nutrition Potsdam-Rehbrücke, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Department of Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Cancer Epidemiology Institute, Department of Cardiology, Aarhus University Hospital, Public Health and Participation Directorate, Health and Health Care Services Council, Catalan Institute of Oncology, Consorcio de Investigación Biomédica en Red especializado en Epidemiología y Salud Pública (CIBERESP), Los Centros de Investigación Biomédica en Red (CIBER), Granada Cancer Registry, Andalusian School of Public Health [Granada], Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), CIBER de Epidemiología y Salud Pública (CIBERESP), Murcia Regional Health Authority, Public Health Institute of Navarra, School of Clinical Medicine, University of Cambridge [UK] (CAM), Epidemiology Unit, Medical Research Council, Cancer Epidemiology Unit, University of Oxford [Oxford]-Cancer Epidemiology Unit, WHO Collaborating Center for Food and Nutrition Policies, Department of Hygiene-Epidemiology and Medical Statistics-Athens Medical School, Department of Hygiene, Epidemiology and Medical Statistics, Harvard School of Public Health, Bureau of Epidemiologic Research, Academy of Athens, Molecular and Nutritional Epidemiology Unit, ISPO-Cancer Research and Prevention Institute, Nutritional Epidemiology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Cancer Registry, Civile - M.P.Arezzo Hospital, CPO Piemonte, National Institute for Public Health and the Environment [Bilthoven] (RIVM), Department of Public Health and Clinical Medicine/Nutritional Research, Umeå University, Nutrition and Metabolism Section, International Agency for Cancer Research (IACR), Unit of Nutrition, Environment, and Cancer, Equipe 6, Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Genomics of Common Disease, Imperial College London-School of public health, The University of Hong Kong (HKU)-The University of Hong Kong (HKU), Department of Epidemiology and Biostatistics, Imperial College London-Faculty of Medicine-School of public health, Department of Epidemiology and Public Health, Imperial College London, Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Aalborg Hospital-Aarhus University Hospital, Consorcio de Investigación Biomédica en Red especializado en Epidemiología y Salud Pública ( CIBERESP ), Andalusian School of Public Health, University of Cambridge [UK] ( CAM ), Azienda Ospedaliera 'Civile M.P.Arezzo', National Institute for Public Health and the Environment [Bilthoven] ( RIVM ), University of Umeå, International Agency for Research on Cancer, Centre de Recherche en Cancérologie de Lyon ( CRCL ), Centre Léon Bérard [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 ) -Centre Léon Bérard [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 )

Subjects
Oncology, Male, MESH: Carcinoma, Epidemiology, protein p53, MESH : Aged, PROTEIN, Genome-wide association study, MESH : Genotype, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, KAPPA-B ACTIVATION, MESH: Genotype, 0302 clinical medicine, PKC-IOTA, Epidemiology of cancer, Multicenter Studies as Topic, TUBEROUS SCLEROSIS, MESH: Genetic Variation, lcsh:Science, MESH : Isoenzymes, 0303 health sciences, MESH: Middle Aged, MESH : Carcinoma, TOR Serine-Threonine Kinases, Cancer Risk Factors, target of rapamycin kinase, MTOR protein, MESH: Case-Control Studies, 3. Good health, 030220 oncology & carcinogenesis, Medicine, Science & Technology - Other Topics, MESH : Genome-Wide Association Study, Phenomena and Processes::Genetic Phenomena::Genetic Variation [Medical Subject Headings], MESH : Prostatic Neoplasms, Phenomena and Processes::Chemical Phenomena::Chemical Processes::Biochemical Processes::Signal Transduction [Medical Subject Headings], medicine.medical_specialty, MESH : Case-Control Studies, Genotype, Single-nucleotide polymorphism, Variación genética, 03 medical and health sciences, Genetics, Cancer Genetics, Humans, MESH : Middle Aged, human, Biology, mammalian target of rapamycin, Aged, Estudio Multicéntrico, Science & Technology, MESH: Humans, MULTIDISCIPLINARY SCIENCES, lcsh:R, MESH : Humans, Genetic Variation, medicine.disease, MESH : Neoplasms, Genitourinary Tract Tumors, Genetic epidemiology, Cardiovascular and Metabolic Diseases, Case-Control Studies, KINASE-C-IOTA, MESH: Genome-Wide Association Study, MESH: Multicenter Studies as Topic, lcsh:Q, MESH : Genetic Predisposition to Disease, RAPAMYCIN, Lifestyle Causes of Cancer, MESH: Signal Transduction, Health Care::Environment and Public Health::Public Health::Epidemiologic Methods::Epidemiologic Study Characteristics as Topic::Clinical Trials as Topic::Multicenter Studies as Topic [Medical Subject Headings], lcsh:Medicine, Bioinformatics, MESH : Multicenter Studies as Topic, Prostate cancer, Risk Factors, MESH: Risk Factors, Neoplasms, Clinical Epidemiology, MESH: Neoplasms, Protein Kinase C, MESH: Aged, Multidisciplinary, Prostate Cancer, MESH: Genetic Predisposition to Disease, Middle Aged, MESH : Risk Factors, European Prospective Investigation into Cancer and Nutrition, Europe, Isoenzymes, Diseases::Male Urogenital Diseases::Urogenital Neoplasms::Genital Neoplasms, Male::Prostatic Neoplasms [Medical Subject Headings], Genetic Epidemiology, protein kinase C lambda, MESH: Isoenzymes, MESH : TOR Serine-Threonine Kinases, isoenzyme, Cancer Epidemiology, Signal Transduction, Research Article, MESH : Male, Genetic Causes of Cancer, MESH : Europe, [SDV.CAN]Life Sciences [q-bio]/Cancer, Neoplasias de la Próstata, Genetic polymorphisms, Serina-Treonina Quinasas TOR, Health Care::Environment and Public Health::Public Health::Epidemiologic Methods::Epidemiologic Study Characteristics as Topic::Epidemiologic Studies::Case-Control Studies [Medical Subject Headings], Diseases::Pathological Conditions, Signs and Symptoms::Pathologic Processes::Disease Attributes::Disease Susceptibility::Genetic Predisposition to Disease [Medical Subject Headings], LUNG-CANCER, MESH : Genetic Variation, Internal medicine, medicine, Chemicals and Drugs::Amino Acids, Peptides, and Proteins::Proteins::Intracellular Signaling Peptides and Proteins::TOR Serine-Threonine Kinases [Medical Subject Headings], Genetic Predisposition to Disease, MESH : Protein Kinase C, PI3K/AKT/mTOR pathway, Genetic Association Studies, MESH: TOR Serine-Threonine Kinases, 030304 developmental biology, MESH : Signal Transduction, COMPLEX, Càncer de pròstata, Polimorfisme genètic, Carcinoma, MTOR protein, human, protein kinase C, Cancer, Prostatic Neoplasms, Cancers and Neoplasms, Human Genetics, MESH: Protein Kinase C, MESH: Male, MAMMALIAN TARGET, MESH: Prostatic Neoplasms, CELL-GROWTH, MESH: Europe, EPIC, Genome-Wide Association Study
Abstract

International audience; The mTOR (mammalian target of rapamycin) signal transduction pathway integrates various signals, regulating ribosome biogenesis and protein synthesis as a function of available energy and amino acids, and assuring an appropriate coupling of cellular proliferation with increases in cell size. In addition, recent evidence has pointed to an interplay between the mTOR and p53 pathways. We investigated the genetic variability of 67 key genes in the mTOR pathway and in genes of the p53 pathway which interact with mTOR. We tested the association of 1,084 tagging SNPs with prostate cancer risk in a study of 815 prostate cancer cases and 1,266 controls nested within the European Prospective Investigation into Cancer and Nutrition (EPIC). We chose the SNPs (n = 11) with the strongest association with risk (p

Published
2011

10. The EmsB tandemly repeated multilocus microsatellite: a new tool to investigate genetic diversity of Echinococcus granulosus sensu lato

Author

Bruno Gottstein, Renaud Piarroux, M. C. Benchikh-Elfegoun, I. Colovic, S. Ma, Karen Luisa Haag, Jenny Knapp, S. Maillard, Institut de l'Ouest : Droit et Europe ( IODE ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), Institute of Parasitology, University of Bern, Laboratoire Evolution, Génomes et Spéciation ( LEGS ), Centre National de la Recherche Scientifique ( CNRS ), The Institute of Automation of the Chinese Academy of Sciences ( CASIA ), Chinese Academy of Sciences [Beijing] ( CAS ), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Infections Parasitaires : Transmission, Physiopathologie et Thérapeutiques ( IP-TPT ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Assistance Publique - Hôpitaux de Marseille ( APHM ) -Service de Santé des Armées-Université de Montpellier ( UM ), Millon, Laurence, Institut de l'Ouest : Droit et Europe (IODE), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), The Institute of Automation of the Chinese Academy of Sciences (CASIA), Chinese Academy of Sciences [Beijing] (CAS), 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), Infections Parasitaires : Transmission, Physiopathologie et Thérapeutiques (IP-TPT), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Service de Santé des Armées, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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), and Service de Santé des Armées-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)

Subjects
MESH : Algeria, MESH : Genotype, MESH: DNA, Helminth, MESH : Romania, MESH : Microsatellite Repeats, MESH : Echinococcosis, MESH: Echinococcus granulosus, 030308 mycology & parasitology, MESH: Genotype, MESH: Dogs, MESH : Dogs, MESH : Mauritania, MESH : Cattle, MESH : DNA, Helminth, Genotype, Cluster Analysis, MESH: Animals, MESH: Genetic Variation, Echinococcus granulosus, Genetics, 0303 health sciences, biology, Mauritania, MESH: Camels, DNA, Helminth, Echinococcosis, MESH: China, 3. Good health, MESH: Cattle, Microsatellite, MESH : Sensitivity and Specificity, MESH: Algeria, Serbia, Brazil, MESH: Mauritania, Microbiology (medical), China, Camelus, MESH: Sheep, MESH : Sheep, Sensitivity and Specificity, MESH: Romania, [ SDV.EE.SANT ] Life Sciences [q-bio]/Ecology, environment/Health, 03 medical and health sciences, MESH: Echinococcosis, Dogs, Sensu, MESH : Genetic Variation, Genetic variation, parasitic diseases, medicine, Animals, Humans, [SDV.EE.SANT] Life Sciences [q-bio]/Ecology, environment/Health, MESH : Brazil, MESH : China, MESH : Cluster Analysis, Genotyping, MESH : Serbia, 030304 developmental biology, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Genetic diversity, Sheep, MESH: Humans, MESH : Camels, Romania, MESH : Echinococcus granulosus, MESH : Humans, Genetic Variation, medicine.disease, biology.organism_classification, MESH: Cluster Analysis, MESH: Sensitivity and Specificity, MESH: Serbia, Evolutionary biology, Algeria, Cattle, Parasitology, MESH: Microsatellite Repeats, MESH : Animals, MESH: Brazil, Microsatellite Repeats
Abstract

Cystic echinococcosis (CE) is a widespread and severe zoonotic disease caused by infection with the larval stage of the eucestode Echinococcus granulosus sensu lato. The polymorphism exhibited by nuclear and mitochondrial markers conventionally used for the genotyping of different parasite species and strains does not reach the level necessary for the identification of genetic variants linked to restricted geographical areas. EmsB is a tandemly repeated multilocus microsatellite that proved its usefulness for the study of genetic polymorphisms within the species E. multilocularis , the causative agent of alveolar echinococcosis. In the present study, EmsB was used to characterize E. granulosus sensu lato samples collected from different host species (sheep, cattle, dromedaries, dogs, and human patients) originating from six different countries (Algeria, Mauritania, Romania, Serbia, Brazil, and the People's Republic of China). The conventional mitochondrial cox1 and nad1 markers identified genotypes G1, G3, G5, G6, and G7, which are clustered into three groups corresponding to the species E. granulosus sensu stricto, E. ortleppi , and E. canadensis . With the same samples, EmsB provided a higher degree of genetic discrimination and identified variations that correlated with the relatively small-scale geographic origins of the samples. In addition, one of the Brazilian single hydatid cysts presented a hybrid genotypic profile that suggested genetic exchanges between E. granulosus sensu stricto and E. ortleppi . In summary, the EmsB microsatellite exhibits an interesting potential for the elaboration of a detailed map of the distribution of genetic variants and therefore for the determination and tracking of the source of CE.

Published
2009

11. The genetic diversity of three peculiar populations descending from the slave trade: Gm study of Noir Marron from French Guiana

Author

Patricia Tortevoye, Georges Larrouy, Antoine Gessain, Evelyne Guitard, Sabine Plancoulaine, Nicolas Brucato, Jean-Michel Dugoujon, Alicia Sanchez-Mazas, Laboratoire d'Anthropobiologie (LA), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique Humaine des Maladies Infectieuses (Inserm U980), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Département d'anthropologie et d'écologie, Université de Genève (UNIGE), Laboratoire d'Anthropobiologie ( LA ), École des hautes études en sciences sociales ( EHESS ) -Université Toulouse - Jean Jaurès ( UT2J ) -Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique ( CNRS ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Génétique Humaine des Maladies Infectieuses ( Inserm U980 ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Paris Descartes - Paris 5 ( UPD5 ), Université de Genève ( UNIGE ), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)

Subjects
Male, Latin Americans, Ethnic group, Population genetics, Ethnic origin, MESH: Founder Effect, Gene flow, MESH: Indians, South American, Consanguinity, Human genetics, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Ethnicity, MESH : Female, MESH: Genetic Variation, Marriage, ddc:599.9, 0303 health sciences, biology, 030305 genetics & heredity, General Medicine, MESH: European Continental Ancestry Group, Founder Effect, French Guiana, MESH : Africa, Western, Europe, Africa, Western, Geography, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Ethnology, Female, MESH: Ethnic Groups, Gene pool, General Agricultural and Biological Sciences, Atlantic slave trade, MESH : Cultural Characteristics, African population, MESH : Ethnic Groups, MESH : French Guiana, MESH : Male, MESH : Europe, MESH : Founder Effect, MESH: Cultural Characteristics, Black People, MESH : Immunoglobulin Gm Allotypes, Marron, General Biochemistry, Genetics and Molecular Biology, White People, MESH : African Continental Ancestry Group, MESH : European Continental Ancestry Group, 03 medical and health sciences, Immunoglobulin Gm Allotypes, MESH : Genetic Variation, MESH: Africa, Western, MESH : Consanguinity, MESH: French Guiana, Humans, MESH: Immunoglobulin Gm Allotypes, MESH : Haplotypes, MESH : Marriage, 030304 developmental biology, MESH: Consanguinity, Cultural Characteristics, MESH: Humans, General Immunology and Microbiology, Indians, South American, MESH : Humans, MESH : Indians, South American, Genetic Variation, MESH: Haplotypes, biology.organism_classification, Polymorhism, MESH: Marriage, MESH: Male, Haplotypes, MESH: African Continental Ancestry Group, MESH: Europe, MESH: Female
Abstract

International audience; The Noir Marron communities are the direct descendants of African slaves brought to the Guianas during the four centuries (16th to 19th) of the Atlantic slave trade. Among them, three major ethnic groups have been studied: the Aluku, the Ndjuka and the Saramaka. Their history led them to share close relationships with Europeans and Amerindians, as largely documented in their cultural records. The study of Gm polymorphisms of immunoglobulins may help to estimate the amount of gene flow linked to these cultural exchanges. Surprisingly, very low levels of European contribution (2.6%) and Amerindian contribution (1.7%) are detected in the Noir Marron gene pool. On the other hand, an African contribution of 95.7% redraws their origin to West Africa (F(ST) < or = 0.15). This highly preserved African gene pool of the Noir Marron is unique in comparison to other African American populations of Latin America, who are notably more admixed.

Published
2009

12. Comparative analysis of oncogenic properties and nuclear factor-kappaB activity of latent membrane protein 1 natural variants from Hodgkin's lymphoma's Reed-Sternberg cells and normal B-lymphocytes

Author

Fabienne Meggetto, Alan Bénard, Nadine Cogne, Aurélie Chanut, Nathalie Faumont, Georges Delsol, Jean Feuillard, Physiologie Moléculaire de la Réponse Immune et des Lymphoproliférations (PMRIL), Université de Limoges (UNILIM)-Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST FR CNRS 3503)-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 Physiopathologie Toulouse Purpan ex IFR 30 et IFR 150 (CPTP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-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-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 Physiopathologie Toulouse Purpan (CPTP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Physiologie Moléculaire de la Réponse Immune et des Lymphoproliférations ( PMRIL ), Université de Limoges ( UNILIM ) -Génomique, Environnement, Immunité, Santé, Thérapeutique ( GEIST FR CNRS 3503 ) -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 Physiopathologie Toulouse Purpan, and Université Paul Sabatier - Toulouse 3 ( UPS ) -IFR30-IFR150-Institut National de la Santé et de la Recherche Médicale ( INSERM )

Subjects
MESH : Cell Line, MESH : Molecular Sequence Data, DNA Mutational Analysis, MESH: NF-kappa B, Apoptosis, MESH: Base Sequence, medicine.disease_cause, 0302 clinical medicine, MESH : Tumor Cells, Cultured, MESH: Luciferases, Renilla, immune system diseases, hemic and lymphatic diseases, MESH : Hodgkin Disease, Tumor Cells, Cultured, [ SDV.IMM ] Life Sciences [q-bio]/Immunology, MESH: Animals, MESH : Viral Matrix Proteins, MESH: Genetic Variation, Reed-Sternberg Cells, MESH: DNA Mutational Analysis, MESH : Immunoblotting, MESH: Reed-Sternberg Cells, Oncogene Proteins, Genetics, B-Lymphocytes, 0303 health sciences, Mutation, MESH: Immunoblotting, MESH : Oncogene Proteins, NF-kappa B, Hematology, Transfection, Hodgkin Disease, MESH: Hodgkin Disease, MESH : NF-kappa B, 030220 oncology & carcinogenesis, [SDV.IMM]Life Sciences [q-bio]/Immunology, MESH : Mutation, MESH : Transfection, MESH: Mutation, MESH : Recombinant Fusion Proteins, Recombinant Fusion Proteins, Immunoblotting, Molecular Sequence Data, MESH : Luciferases, Renilla, MESH : DNA Mutational Analysis, Biology, MESH: Sequence Homology, Nucleic Acid, MESH : B-Lymphocytes, Cell Line, Viral Matrix Proteins, 03 medical and health sciences, MESH: Oncogene Proteins, stomatognathic system, MESH : Genetic Variation, Sequence Homology, Nucleic Acid, MESH: B-Lymphocytes, medicine, otorhinolaryngologic diseases, MESH: Recombinant Fusion Proteins, Animals, Humans, Hodgkin's Lymphoma, MESH : Sequence Homology, Nucleic Acid, MESH: Tumor Cells, Cultured, Luciferases, Renilla, 030304 developmental biology, MESH: Viral Matrix Proteins, MESH: Molecular Sequence Data, MESH: Humans, MESH : Reed-Sternberg Cells, Base Sequence, MESH: Apoptosis, MESH: Transfection, MESH : Humans, Genetic Variation, medicine.disease, Hodgkin's lymphoma, Epstein–Barr virus, Lymphoma, MESH: Cell Line, stomatognathic diseases, Reed–Sternberg cell, Cell culture, Cancer research, MESH : Base Sequence, MESH : Animals, Carcinogenesis, MESH : Apoptosis
Abstract

International audience; BACKGROUND: In Epstein-Barr virus-associated Hodgkin's lymphomas, neoplastic Reed-Sternberg cells and surrounding non-tumor B-cells contain different variants of the LMP1-BNLF1 oncogene. In this study, we raised the question of functional properties of latent membrane protein 1 (LMP1) natural variants from both Reed-Sternberg and non-tumor B-cells. DESIGN AND METHODS: Twelve LMP1 natural variants from Reed-Sternberg cells, non-tumor B-cells of Hodgkin's lymphomas and from B-cells of benign reactive lymph nodes were cloned, sequenced and stably transfected in murine recombinant interleukin-3-dependent Ba/F3 cells to search for relationships between LMP1 cellular origin and oncogenic properties as well as nuclear factor-kappaB activation, and apoptosis protection. RESULTS: LMP1 variants of Reed-Sternberg cell origin were often associated with increased mutation rate and with recurrent genetic events, such as del15bp associated with S to N replacement at codon 309, and four substitutions I85L, F106Y, I122L, and M129I. Oncogenic potential (growth factor-independence plus clonogenicity) was consistently associated with LMP1 variants from Reed-Sternberg cells, but inconstantly for LMP1-variants from non-tumor B-cells. Analysis of LMP1 variants from both normal B-cells and Reed-Sternberg cells indicates that protection against apoptosis through activation of nuclear factor-kappaB - whatever the cellular origin of LMP1 - was maintained intact, regardless of the mutational pattern. CONCLUSIONS: Taken together, our results demonstrate that preserved nuclear factor-kappaB activity and protection against apoptosis would be the minimal prerequisites for all LMP1 natural variants from both normal and tumor cells in Hodgkin's lymphomas, and that oncogenic potential would constitute an additional feature for LMP1 natural variants in Reed-Sternberg cells.

Published
2009

13. 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

14. Molecular epidemiology of norovirus gastroenteritis investigated using samples collected from children in Tunisia during a four-year period: detection of the norovirus variant GGII.4 Hunter as early as January 2003

Author

Sdiri-Loulizi , Khira, Ambert-Balay , Katia, Gharbi-Khelifi , Hakima, Sakly , Nabil, Hassine , Mouna, Chouchane , Slaheddine, Guediche , Mohamed Neji, Pothier , Pierre, Aouni , Mahjoub, 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
MESH : Molecular Sequence Data, MESH : Norovirus, MESH : Prevalence, MESH : Molecular Epidemiology, MESH : Humans, MESH : Reverse Transcriptase Polymerase Chain Reaction, MESH : Infant, MESH : Feces, MESH : Adult, MESH : Child, Preschool, bacterial infections and mycoses, MESH : Infant, Newborn, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH : Gastroenteritis, MESH : Child, MESH : Genetic Variation, MESH : Tunisia, MESH : RNA, Viral, MESH : Cluster Analysis, MESH : Caliciviridae Infections, MESH : Sequence Analysis, DNA
Abstract

International audience; Human noroviruses (NoVs) cause epidemic and endemic acute gastroenteritis in children and adults. To study the prevalence and genetic diversity of NoV in children in Tunisia, a total of 788 fecal samples were collected during a 4-year period in the region of Monastir, from children 12 years of age or younger, hospitalized or presenting in dispensaries with symptoms of acute gastroenteritis. NoV was detected by reverse transcription-PCR and confirmed by sequence analysis. This is the first report that describes the molecular epidemiology of NoV in Tunisian children: NoVs were characterized as the causative agent in 128 (16.2%) of the samples. Fourteen samples contained a mixture of two NoVs, and 33 samples were coinfected with additional enteric viruses. Eight distinct NoV genotypes were detected (GGI.2, GGI.4, GGII.1, GGII.4, GGII.8, GGII.14, GGIIb/GGII.2, and GGIIb/GGII.3). GGII.4 was the most prevalent genotype, accounting for 83 (64.8%) cases. Interestingly the GGII.4 variant Hunter, described as spreading all over the world in 2004, was found in Tunisia as early as January 2003. The delay of 1 year between the isolation in Tunisia and the worldwide emergence is somewhat surprising, considering the importance of the contacts between North Africa and Europe particularly. Nevertheless, this illustrates the idea that sporadic gastroenteritis cases may be a reservoir for emerging epidemic NoV strains.

Published
2009

15. Genetic diversity of the cestode Echinococcus multilocularis in red foxes at a continental scale in Europe

Author

Thomas Romig, Patrick Giraudoux, Renaud Piarroux, Jenny Knapp, Francis Raoul, Marie-Hélène Guislain, Peter Deplazes, Bruno Gottstein, Karel Martinek, Jean-Mathieu Bart, Florence Cliquet, Marie-Louise Glowatzki, Isabelle Breyer, Georg Gerhard Duscher, Pavol Dubinsky, A. Malczewski, Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Institute of Parasitology, University of Bern, University of Zürich [Zürich] ( UZH ), Institute of Parasitology [Vienna], University of Veterinary Medicine, Vienna, Department of Biology [Pilsen], University of West Bohemia [Plzeň ], Slovak Academy of Sciences, Slovak Academy of Science [Bratislava] ( SAS ), Laboratoire d'études et de recherches sur la rage et la pathologie des animaux sauvages, AFSSA, University of Hohenheim, Witold Stefanski Institute of Parasitology, Polska Akademia Nauk ( PAN ), 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), Vetsuisse Faculty, Universität Zürich [Zürich] = University of Zurich (UZH), Slovak Academy of Sciences (SAS), Centre de Recherche et de Formation en Eco-éthologie (2C2A-CERFE), Université de Reims Champagne-Ardenne (URCA), Polska Akademia Nauk = Polish Academy of Sciences (PAN), Infections Parasitaires : Transmission, Physiopathologie et Thérapeutiques (IP-TPT), Service de Santé des Armées-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), University of Zurich, Knapp, J, Laboratoire Chrono-environnement (UMR 6249) (LCE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Service de Santé des Armées, Laboratoire Chrono-environnement - CNRS - UFC (UMR 6249) (LCE), University of Zürich [Zürich] (UZH), Agence Française de Sécurité Sanitaire des Aliments (AFSSA), Institut Universitaire de France ( IUF ), Ministère de l'Éducation nationale, de l’Enseignement supérieur et de la Recherche ( M.E.N.E.S.R. ), Centre Marc Bloch ( CMB ), Ministère de l'Europe et des Affaires étrangères ( MEAE ) -Bundesministerium für Bildung und Forschung-Ministère de l'Éducation nationale, de l’Enseignement supérieur et de la Recherche ( M.E.N.E.S.R. ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de Recherche et de Formation en Eco-éthologie ( 2C2A-CERFE ), Université de Reims Champagne-Ardenne ( URCA ), Combi, Laboratoire d'Informatique de Nantes Atlantique ( LINA ), Mines Nantes ( Mines Nantes ) -Université de Nantes ( UN ) -Centre National de la Recherche Scientifique ( CNRS ) -Mines Nantes ( Mines Nantes ) -Université de Nantes ( UN ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Parsitology [Stuttgart], Infections Parasitaires : Transmission, Physiopathologie et Thérapeutiques ( IP-TPT ), and Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Assistance Publique - Hôpitaux de Marseille ( APHM ) -Service de Santé des Armées-Université de Montpellier ( UM )

Subjects
10078 Institute of Parasitology, MESH: Geography, Population genetics, Foxes, MESH : Echinococcus multilocularis, MESH : Microsatellite Repeats, MESH : Echinococcosis, 0302 clinical medicine, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, 600 Technology, MESH: DNA Fingerprinting, Cluster Analysis, MESH: Animals, MESH: Genetic Variation, 0303 health sciences, education.field_of_study, Molecular Epidemiology, 630 Agriculture, Geography, Ecology, lcsh:Public aspects of medicine, MESH : Geography, MESH : DNA Fingerprinting, 3. Good health, Europe, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Research Article, lcsh:Arctic medicine. Tropical medicine, lcsh:RC955-962, 030231 tropical medicine, Population, MESH : Molecular Epidemiology, MESH : Europe, Zoology, 610 Medicine & health, Biology, Echinococcus multilocularis, [ SDV.EE.SANT ] Life Sciences [q-bio]/Ecology, environment/Health, 03 medical and health sciences, MESH: Echinococcosis, MESH : Genetic Variation, Echinococcosis, Genetic variation, Ecology/Evolutionary Ecology, Genetics and Genomics/Population Genetics, MESH : Cluster Analysis, Animals, MESH: Molecular Epidemiology, education, 030304 developmental biology, MESH : Foxes, MESH: Echinococcus multilocularis, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Genetic diversity, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, MESH: Foxes, Public Health, Environmental and Occupational Health, Genetic Variation, lcsh:RA1-1270, 2739 Public Health, Environmental and Occupational Health, 2725 Infectious Diseases, biology.organism_classification, DNA Fingerprinting, MESH: Cluster Analysis, Phylogeography, Genetic epidemiology, 570 Life sciences, biology, MESH : Animals, MESH: Microsatellite Repeats, MESH: Europe, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Founder effect, Microsatellite Repeats
Abstract

Background Alveolar echinococcosis (AE) is a severe helminth disease affecting humans, which is caused by the fox tapeworm Echinococcus multilocularis. AE represents a serious public health issue in larger regions of China, Siberia, and other regions in Asia. In Europe, a significant increase in prevalence since the 1990s is not only affecting the historically documented endemic area north of the Alps but more recently also neighbouring regions previously not known to be endemic. The genetic diversity of the parasite population and respective distribution in Europe have now been investigated in view of generating a fine-tuned map of parasite variants occurring in Europe. This approach may serve as a model to study the parasite at a worldwide level. Methodology/Principal Findings The genetic diversity of E. multilocularis was assessed based upon the tandemly repeated microsatellite marker EmsB in association with matching fox host geographical positions. Our study demonstrated a higher genetic diversity in the endemic areas north of the Alps when compared to other areas. Conclusions/Significance The study of the spatial distribution of E. multilocularis in Europe, based on 32 genetic clusters, suggests that Europe can be considered as a unique global focus of E. multilocularis, which can be schematically drawn as a central core located in Switzerland and Jura Swabe flanked by neighbouring regions where the parasite exhibits a lower genetic diversity. The transmission of the parasite into peripheral regions is governed by a “mainland–island” system. Moreover, the presence of similar genetic profiles in both zones indicated a founder event., Author Summary Echinococcus multilocularis is a tapeworm of the red fox, which represents a considerable health threat to respectively infected humans. Main endemic areas are located in China, Siberia, and central Europe. Alarmed by an emerging or reemerging situation in Europe, the question of how the parasite gets spatially and temporally spread and transmitted becomes essential to prepare appropriate control programs. The question was tackled by using genetic data on a large sample size of E. multilocularis adult stage tapeworms, combined with geographical site location data input. The historically documented endemic area, represented by the northern Alpine arch, was shown to harbour the highest genetic richness and diversity, as compared to surrounding areas in northern and eastern Europe. The spatial and temporal spread of different E. multilocularis genotypes in Europe seems to be ruled by a founder event, linked to exportation of parasites from the central core to newly identified (western and eastern) areas or subregions, where these parasites could subsequently disseminate under geographical separation from the original foci.

Published
2009

16. Innate immunity in ocular Chlamydia trachomatis infection: contribution of IL8 and CSF2 gene variants to risk of trachomatous scarring in Gambians

Author

David Mabey, Dominic P. Kwiatkowski, Gaia Luoni, Matthew J. Burton, Hassan Joof, Kirk A. Rockett, Robin L. Bailey, Martin J. Holland, Jeremy Hull, Angels Natividad, BMC, Ed., London School of Hygiene and Tropical Medicine (LSHTM), Génétique Humaine des Maladies Infectieuses (Inserm U980), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), The Wellcome Trust Centre for Human Genetics [Oxford], University of Oxford, Medical Research Council Laboratories, This work was supported by the Medical Research Council, UK and The Wellcome Trust, UK., Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5), University of Oxford [Oxford], London School of Hygiene and Tropical Medicine ( LSHTM ), Génétique Humaine des Maladies Infectieuses ( Inserm U980 ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Paris Descartes - Paris 5 ( UPD5 ), and Wellcome Trust Centre for Human Genetics

Subjects
Male, MESH : Aged, MESH: Base Sequence, Blindness, Linkage Disequilibrium, MESH: Blindness, MESH : Child, MESH : Gambia, MESH: Child, MESH: Epistasis, Genetic, Genetics(clinical), MESH: Genetic Variation, Child, Aged, 80 and over, 0303 health sciences, education.field_of_study, MESH: Middle Aged, MESH: Polymorphism, Single Nucleotide, MESH : Trachoma, MESH: Granulocyte-Macrophage Colony-Stimulating Factor, MESH : Granulocyte-Macrophage Colony-Stimulating Factor, MESH: Case-Control Studies, 3. Good health, MESH: Linkage Disequilibrium, MESH: Young Adult, Child, Preschool, Chromosomes, Human, Pair 5, Gambia, Chromosomes, Human, Pair 4, MESH: Trachoma, MESH : Case-Control Studies, MESH : Young Adult, Locus (genetics), 03 medical and health sciences, Cicatrix, MESH : Adolescent, Genetics, Humans, MESH : Middle Aged, MESH : Aged, 80 and over, education, lcsh:RC31-1245, MESH : Haplotypes, Trichiasis, Alleles, Aged, MESH: Adolescent, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, 030306 microbiology, MESH : Humans, MESH: Child, Preschool, Genetic Variation, Epistasis, Genetic, MESH: Adult, MESH: Matrix Metalloproteinase 9, MESH: Haplotypes, MESH : Cicatrix, medicine.disease, Immunity, Innate, MESH: Interleukin-8, Case-Control Studies, MESH : Blindness, Immunology, MESH : Alleles, [ SDV.GEN ] Life Sciences [q-bio]/Genetics, Chlamydia trachomatis, MESH: Female, Linkage disequilibrium, [SDV.GEN] Life Sciences [q-bio]/Genetics, MESH : Child, Preschool, medicine.disease_cause, MESH : Chromosomes, Human, Pair 5, MESH: Aged, 80 and over, MESH : Chromosomes, Human, Pair 4, Risk Factors, MESH: Risk Factors, MESH : Female, MESH : Matrix Metalloproteinase 9, Genetics (clinical), Keratoconjunctivitis, MESH : Epistasis, Genetic, MESH: Aged, MESH : Linkage Disequilibrium, MESH : Polymorphism, Single Nucleotide, MESH : Adult, MESH : Immunity, Innate, Middle Aged, MESH : Risk Factors, Trachoma, Matrix Metalloproteinase 9, Female, MESH: Immunity, Innate, Adult, MESH: Chromosomes, Human, Pair 5, MESH : Interleukin-8, lcsh:Internal medicine, MESH: Chromosomes, Human, Pair 4, Adolescent, lcsh:QH426-470, MESH : Male, Population, Biology, Polymorphism, Single Nucleotide, Young Adult, MESH : Genetic Variation, Research article, medicine, Allele, 030304 developmental biology, MESH: Cicatrix, Base Sequence, MESH: Alleles, Interleukin-8, Granulocyte-Macrophage Colony-Stimulating Factor, MESH: Male, lcsh:Genetics, MESH: Gambia, Haplotypes, MESH : Base Sequence
Abstract

Background: Trachoma, a chronic keratoconjunctivitis caused by Chlamydia trachomatis, is the world's commonest infectious cause of blindness. Blindness is due to progressive scarring of the conjunctiva (trachomatous scarring) leading to in-turning of eyelashes (trichiasis) and corneal opacification. We evaluated the contribution of genetic variation across the chemokine and cytokine clusters in chromosomes 4q and 5q31 respectively to risk of scarring trachoma and trichiasis in a large case-control association study in a Gambian population. Methods: Linkage disequilibrium (LD) mapping was used to investigate risk effects across the 4q and 5q31 cytokine clusters in relation to the risk of scarring sequelae of ocular Ct infection. Disease association and epistatic effects were assessed in a population based study of 651 case-control pairs by conditional logistic regression (CLR) analyses. Results: LD mapping suggested that genetic effects on risk within these regions mapped to the pro-inflammatory innate immune genes interleukin 8 (IL8) and granulocyte-macrophage colony stimulatory factor (CSF2) loci. The IL8-251 rare allele (IL8-251 TT) was associated with protection from scarring trachoma (OR = 0.29 p = 0.027). The intronic CSF2_27348 A allele in chromosome 5q31 was associated with dose dependent protection from trichiasis, with each copy of the allele reducing risk by 37% (p = 0.005). There was evidence of epistasis, with effects at IL8 and CSF2 loci interacting with those previously reported at the MMP9 locus, a gene acting downstream to IL8 and CSF2 in the inflammatory cascade. Conclusion: innate immune response SNP-haplotypes are linked to ocular Ct sequelae. This work illustrates the first example of epistatic effects of two genes on trachoma.

Published
2009

17. Contribution of energy restriction and macronutrient composition to changes in adipose tissue gene expression during dietary weight-loss programs in obese women

Author

Claus Holst, Nathalie Vega, Moira A. Taylor, J. Alfredo Martínez, Eva Klimcakova, Thorkild I. A. Sørensen, Dominique Langin, Sébastien Déjean, Jean M. Oppert, Peter Arner, Hubert Vidal, Nathalie Viguerie, Karine Clément, Frédéric Capel, Wim H. M. Saris, Institut de médecine moléculaire de Rangueil (I2MR), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-IFR150-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Recherche sur les obésités, CHU Toulouse [Toulouse]-Laboratoire, IFR 31 Louis Bugnard (IFR 31), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Toulouse [Toulouse]-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Service d'anatomie et cytologie pathologiques [Purpan], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse], Franco-Czech Laboratory for Clinical Research on Obesity, Charles University [Prague] (CU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Faculté de Médecine Lyon-Sud, FACULTE DE LYON, Centre de Recherche en Nutrition Humaine, Hospices Civils de Lyon (HCL), Régulations métaboliques, nutrition et diabètes - UM55 (RMND UM55), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA), Institut de Mathématiques de Toulouse UMR5219 (IMT), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Department of Midicine Karolinska Institute, Karolinska University Hospital Huddinge, Department of Sports Medicine of Charles University, Faculty of Medicine Charles University, Department of Physiology and nutrition University of Navarra, Universidad de Navarra [Pamplona] (UNAV), Department of Human Biology Nutrition and Toxicology Research Institute, Maastricht University [Maastricht], The Netherlands Institute of Preventive Medicine, Institute of Preventive Medicine, School of Biomedical Sciences Queen's Medical Center, University of Nottingham Medical School, 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), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre Hospitalier Universitaire de Toulouse, Charles University [Prague]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Department of Nutrition and Endocrinology AP / HP, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Institut de médecine moléculaire de Rangueil ( I2MR ), Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-IFR150-Institut National de la Santé et de la Recherche Médicale ( INSERM ), IFR 31 Louis Bugnard ( IFR 31 ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Charles University [Prague]-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Hospices Civils de Lyon ( HCL ), Régulations métaboliques, nutrition et diabètes - UM55 ( RMND UM55 ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Hospices Civils de Lyon ( HCL ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Institut National de la Recherche Agronomique ( INRA ), Institut de Mathématiques de Toulouse UMR5219 ( IMT ), Université Toulouse 1 Capitole ( UT1 ) -Université Toulouse - Jean Jaurès ( UT2J ) -Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-PRES Université de Toulouse-Institut National des Sciences Appliquées - Toulouse ( INSA Toulouse ), Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Universidad de Navarra [Pamplona] ( UNAV ), 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 ), Assistance publique - Hôpitaux de Paris (AP-HP), Humane Biologie, RS: NUTRIM - R1 - Metabolic Syndrome, Université de Toulouse (UT)-Université de Toulouse (UT)- Institut Fédératif de Recherche Bio-médicale Institution (IFR150)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service Endocrinologie, maladies métaboliques et nutrition [CHU Toulouse], Pôle Cardiovasculaire et Métabolique [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service Anatomie et cytologie pathologiques [CHU Toulouse], Pôle Biologie [CHU Toulouse], Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Transcription, Genetic, Endocrinology, Diabetes and Metabolism, MESH: Energy Intake, Biochemistry, Body Mass Index, 0302 clinical medicine, Endocrinology, Gene expression, MESH: Genetic Variation, MESH : Adaptor Proteins, Signal Transducing, Oligonucleotide Array Sequence Analysis, 0303 health sciences, Addipose tissue, Reducing, MESH: Mitochondrial Proteins, [ SDV.MHEP.EM ] Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, [SDV.MHEP.EM]Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, 3. Good health, MESH : Oligonucleotide Array Sequence Analysis, Adipose Tissue, Body Composition, MESH: Adipose Tissue, medicine.medical_specialty, Diet, Reducing, MESH : Body Composition, MESH : Adipose Tissue, MESH: Body Mass Index, MESH : Receptors, Glucocorticoid, 03 medical and health sciences, MESH: Weight Loss, Genetic, Humans, MESH : Fatty Acid-Binding Proteins, MESH : Mitochondrial Proteins, MESH: Adaptor Proteins, Signal Transducing, MESH: Humans, MESH : Humans, Signal Transducing, Genetic Variation, MESH: Adult, Autophagy-Related Protein 8 Family, MESH: Body Composition, medicine.disease, Obesity, MESH : Energy Metabolism, MESH : Body Mass Index, Energy intake, Body mass index, MESH: Female, Candidate gene, MESH: Receptors, Glucocorticoid, Clinical Biochemistry, Adipose tissue, Blood lipids, Glucocorticoid, Weight loss, Sirtuin 3, Receptors, MESH : RNA, Sirtuins, MESH: Obesity, MESH : Female, Nutrición y dietética [Ciencias de la Salud], MESH : Diet, Reducing, 2. Zero hunger, MESH : Sirtuins, MESH: Diet, Reducing, Microfilament Proteins, MESH: Energy Metabolism, Adaptor Proteins, MESH : Adult, MESH: Sirtuins, MESH : Obesity, Female, medicine.symptom, Transcription, Adult, MESH : Microfilament Proteins, 030209 endocrinology & metabolism, Context (language use), Biology, Fatty Acid-Binding Proteins, MESH: Fatty Acid-Binding Proteins, Mitochondrial Proteins, MESH: Microfilament Proteins, Receptors, Glucocorticoid, MESH : Genetic Variation, MESH: RNA, Internal medicine, Weight Loss, medicine, 030304 developmental biology, Adaptor Proteins, Signal Transducing, MESH: Transcription, Genetic, Biochemistry (medical), MESH : Transcription, Genetic, MESH : Energy Intake, Diet, MESH: Oligonucleotide Array Sequence Analysis, RNA, MESH : Weight Loss, Energy Intake, Energy Metabolism
Abstract

Context: Hypoenergetic diets are used to reduce body fat mass and metabolic risk factors in obese subjects. The molecular changes in adipose tissue associated with weight loss and specifically related to the dietary composition are poorly understood. Objective: We investigated adipose tissue gene expression from human obese women according to energy deficit and, the fat and carbohydrate content of the diet. Design & setting: Obese subjects recruited among 8 European clinical centers followed 10 weeks of either a low fat (high carbohydrate) or a moderate fat (low carbohydrate) hypoenergetic diet. Subjects: Two sets of 47 women in each dietary arm were selected among 648 subjects matched for anthropometric and biological parameters. Main Outcome Measure: We measured adipose tissue gene expression changes in one set using a candidate gene approach. The other set was used to survey 24469 transcripts using DNA microarrays. Results were analyzed using dedicated statistical methods. Diet-sensitive regulations were confirmed on the other set of subjects. Results: The two diets induced similar weight loss and similar changes for most of the biological variables except for components of the blood lipid profile. A thousand genes were regulated by energy restriction. We validated an effect of the fat-to-carbohydrate ratio for five genes (FABP4, NR3C1, SIRT3, FNTA and GABARAPL2) with increased expression during the moderate fat diet. Conclusions: Energy restriction had a more pronounced impact on variations in human adipose tissue gene expression than macronutrient composition. The macronutrient-sensitive regulation of a subset of genes may influence adipose tissue function and metabolic response. AD - INSERM, U858, Laboratoire de Recherches sur les Obesites, Institut de Medecine Moleculaire de Rangueil, Toulouse; Universite Paul Sabatier, Institut Louis Bugnard IFR31, Toulouse; Centre Hospitalier Universitaire de Toulouse, France; Franco-Czech Laboratory for Clinical Research on Obesity, Prague, Czech Republic; INSERM, UMR -870; INRA U-1235; Faculte de Medecine Lyon-Sud universite de Lyon 1; Centre de Recherche en Nutrition Humaine, Hospices civils de Lyon; Lyon, France; Institut de Mathematiques de Toulouse UMR 5219, Universite Paul-Sabatier, Toulouse, France; Department of Medicine, Karolinska Institute, Karolinska University Hospital Huddinge, Stockholm, Sweden; Department of Sports Medicine, Centre of Preventive Medicine, Third Faculty of Medicine, Charles University, Prague, Czech Republic; Franco-Czech Laboratory for Clinical Research on Obesity, Prague, Czech Republic; Department of Physiology and Nutrition, University of Navarra, Pamplona, Spain; Department of Human Biology, Nutrition and Toxicology Research Institute Maastricht (NUTRIM), Maastricht University, Maastricht, The Netherlands; Institute of Preventive Medicine, Centre for Health and Society, Copenhagen University Hospital, Copenhagen, Denmark; School of Biomedical Sciences, Queen's Medical Centre, University of Nottingham Medical School, Nottingham, United Kingdom; INSERM, Nutriomique U872 (Team 7), 75004 Paris, France; Universites Pierre et Marie Curie-Paris6, UMR-S 872, Cordelier Research Center & Paris Descartes, 75006 Paris; and Assistance Publique/Hopitaux de Paris (AP-HP), Pitie Salpetriere Hospital, Nutrition and Endocrinology department, 75013 Paris, France.

Published
2008

18. 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

19. Evaluation of the intra- and inter-specific genetic variability of Plasmodium lactate dehydrogenase

Author

Arthur M. Talman, Seiha Yen, Frédéric Ariey, Véronique Hubert, Sandrine Houzé, Jacques Le Bras, Linda Duval, David Bell, Eric Legrand, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Division of Cell and Molecular Biology, Imperial College London, Institut Pasteur de la Guyane, Centre National de Référence du Paludisme, 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 Descartes - Paris 5 (UPD5), Malaria and other Vector-borne and parasitic diseases, Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris]-Université Paris Descartes - Paris 5 (UPD5), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Institut Pasteur du Cambodge - Réseau International des Instituts Pasteur (RIIP), Assistance publique - Hôpitaux de Paris (AP-HP) - AP-HP - Hôpital Bichat - Claude Bernard [Paris] - Université Paris Descartes - Paris 5 (UPD5), WHO(OMS), and Assistance publique - Hôpitaux de Paris (AP-HP) - AP-HP - Hôpital Bichat - Claude Bernard [Paris]

Subjects
Plasmodium, MESH: Sequence Analysis, DNA, Plasmodium ovale, Plasmodium vivax, Plasmodium malariae, MESH : Malaria, 0302 clinical medicine, MESH : Plasmodium malariae, MESH : Plasmodium falciparum, MESH: Animals, MESH: Genetic Variation, 030212 general & internal medicine, MESH: Plasmodium falciparum, MESH: Plasmodium malariae, Genetics, biology, MESH: Plasmodium vivax, 3. Good health, Infectious Diseases, MESH : Plasmodium vivax, MESH : Sensitivity and Specificity, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, MESH: L-Lactate Dehydrogenase, lcsh:Arctic medicine. Tropical medicine, lcsh:RC955-962, Plasmodium falciparum, MESH: Malaria, 030231 tropical medicine, Sensitivity and Specificity, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Species Specificity, MESH : Genetic Variation, MESH : Plasmodium ovale, parasitic diseases, Genetic variation, medicine, MESH : Species Specificity, Animals, Humans, MESH: Species Specificity, lcsh:RC109-216, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Genetic variability, MESH : L-Lactate Dehydrogenase, MESH: Humans, L-Lactate Dehydrogenase, MESH: Plasmodium, Research, MESH : Humans, Genetic Variation, Sequence Analysis, DNA, biology.organism_classification, medicine.disease, Virology, MESH: Sensitivity and Specificity, Malaria, MESH : Plasmodium, MESH: Plasmodium ovale, Parasitology, MESH : Animals, MESH : Sequence Analysis, DNA
Abstract

Background Malaria diagnosis is vital to efficient control programmes and the recent advent of malaria rapid diagnostic tests (RDTs) provides a reliable and simple diagnostic method. However a characterization of the efficiency of these tests and the proteins they detect is needed to maximize RDT sensitivity. Methods Plasmodial lactate dehydrogenase (pLDH) gene of wild isolates of the four human species of Plasmodium from a variety of malaria endemic settings were sequenced and analysed. Results No variation in nucleotide was found within Plasmodium falciparum, synonymous mutations were found for Plasmodium malariae and Plasmodium. vivax; and three different types of amino acid sequence were found for Plasmodium ovale. Conserved and variable regions were identified within each species. Conclusion The results indicate that antigen variability is unlikely to explain variability in performance of RDTs detecting pLDH from cases of P. falciparum, P. vivax or P. malariae malaria, but may contribute to poor detection of P. ovale.

Published
2007

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