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115 results on '"MESH : Molecular Sequence Data"'

1. Genome sequence of Aedes aegypti, a major arbovirus vector

Author: Sergio Verjovski-Almeida, James E. Galagan, Ryan C. Kennedy, Zhiyong Xi, Jason R. Miller, Eric Eisenstadt, Kyanne R. Reidenbach, Robert V. Bruggner, Yu-Hui Rogers, Hadi Quesneville, Doreen Werner, Owen White, Alexander S. Raikhel, Mario Stanke, J. Spencer Johnston, Diane D. Lovin, Evgenia V. Kriventseva, Ian T. Paulsen, Kathryn S. Campbell, Norman H. Lee, Ewan Birney, Karyn Megy, Hean Koo, David Kulp, Shelby L. Bidwell, Jingsong Zhu, Philip Montgomery, Paolo Amedeo, Yongmei Zhao, Chinnappa D. Kodira, Javier Costas, Michael C. Schatz, Steven P. Sinkins, Claire M. Fraser-Liggett, Martin Shumway, Kurt LaButti, Akio Mori, Brendan J. Loftus, Manfred Grabherr, Eric O. Stinson, Frank H. Collins, Zhijian Jake Tu, Monique R. Coy, Matt Crawford, Janice P. Vanzee, William M. Gelbart, Joshua Orvis, Peter Arensburger, Chunhong Mao, Evgeny M. Zdobnov, Saul A. Kravitz, Suely Lopes Gomes, David DeCaprio, David G. Hogenkamp, Daniel Lawson, Dennis L. Knudson, David W. Severson, George Dimopoulos, Marcelo B. Soares, Sinéad B. O'Leary, Peter W. Atkinson, David M. Jaffe, Becky deBruyn, Martin Hammond, Ana L. T. O. Nascimento, Jim Biedler, Stefan Wyder, Jose M. C. Tubio, Bruce W. Birren, Catherine A. Hill, Chad Nusbaum, Eduardo Lee, Song Li, Susan E. Brown, Jennifer R. Wortman, James R. Hogan, Hamza El-Dorry, Qi Zhao, Linda Hannick, Carlos Frederico Martins Menck, Vishvanath Nene, Jonathan Crabtree, Steven L. Salzberg, Michael H. Holmes, Maria de Fatima Bonaldo, Quinghu Ren, Mihaela Pertea, Charles Roth, Evan Mauceli, Karin Eiglmeier, Horacio Naveira, Brian J. Haas, Qiandong Zeng, Neil F. Lobo, Jennifer R. Schneider, The Institute for Genomic Research, The Institute for Genomic Research, Rockville, European Bioinformatics Institute [Hinxton] ( EMBL-EBI ), European Molecular Biology Laboratory [Hinxton], Broad Institute of MIT and Harvard ( BROAD INSTITUTE ), Broad Institute of MIT and Harvard, Virginia Polytechnic Institute and State University [Blacksburg], University College Dublin [Dublin] ( UCD ), Bloomberg School of Public Health, Johns Hopkins University ( JHU ) -Bloomberg School of Public Health, University of Geneva Medical School, Swiss Institute of Bioinformatics-University of Geneva Medical School, University of Notre Dame ( UND ), Harvard University [Cambridge], College of Agricultural Sciences Colorado State University, Colorado State University [Fort Collins] ( CSU ) -College of Agricultural Sciences, Northwestern University [Evanston], University of California [Riverside] ( UCR ), Department of Atmospheric, Oceanic and Planetary Physics [Oxford] ( AOPP ), University of Oxford [Oxford], Purdue University [West Lafayette], Centro Nacional de Genotipado Fundación Pública Galega de Medicina Xenómica Hospital Clínico Universitario de Santiago, Centro Nacional de Genotipado-Fundación Pública Galega de Medicina Xenómica-Hospital Clínico Universitario de Santiago, Institut Pasteur [Paris], Universidade de Sao Paulo Instituto de Quimica, Universidade de São Paulo ( USP ) -Instituto de Quimica, Texas A&M University [College Station], Joint Technology Center, University of Massachusetts [Amherst] ( UMass Amherst ), Universidade de Sao Paulo, Institute of Biomedical Sciences, Universidade de São Paulo ( USP ) -Institute of Biomedical Sciences, Instituto Butantan [São Paulo], Universidade da Coruña, University of Maryland [College Park], Institut Jacques Monod ( IJM ), Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), University of California [Santa Cruz] ( UCSC ), Complexo Hospitalario Universitario de Santiago, Universität Göttingen, Georg-August-Universität Göttingen, George Washington University Medical Center, George Washington University ( GW ), The Institute for Genomic Research (TIGR), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], University College Dublin [Dublin] (UCD), Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL)-Université de Lausanne (UNIL)-University of Geneva Medical School, University of Notre Dame [Indiana] (UND), Colorado State University [Fort Collins] (CSU)-College of Agricultural Sciences, University of California [Riverside] (UCR), University of California, Department of Atmospheric, Oceanic and Planetary Physics [Oxford] (AOPP), Universidade de São Paulo (USP)-Instituto de Quimica, University of Massachusetts [Amherst] (UMass Amherst), University of Massachusetts System (UMASS), Universidade de São Paulo (USP)-Institute of Biomedical Sciences (ICB/USP), Universidade de São Paulo (USP), University of Maryland System, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), University of California [Santa Cruz] (UCSC), Georg-August-University [Göttingen], The George Washington University (GW), George Washington University (GW), Université de Lausanne = University of Lausanne (UNIL)-Université de Lausanne = University of Lausanne (UNIL)-University of Geneva Medical School, Harvard University, University of California [Riverside] (UC Riverside), University of California (UC), University of Oxford, Institut Pasteur [Paris] (IP), Universidade de São Paulo = University of São Paulo (USP)-Instituto de Quimica, Universidade de São Paulo = University of São Paulo (USP)-Institute of Biomedical Sciences (ICB/USP), Universidade de São Paulo = University of São Paulo (USP), University of California [Santa Cruz] (UC Santa Cruz), Georg-August-University = Georg-August-Universität Göttingen, Zdobnov, Evgeny, and Wyder, Stefan
Subjects: 0106 biological sciences, Male, Transcription, Genetic, Genome, Insect, transposons, receptors, Genes, Insect, Aedes/ genetics/metabolism, MESH: Genes, Insect, Yellow Fever/prevention & control/transmission, MESH: Base Sequence, 01 natural sciences, Dengue/prevention & control/transmission, MESH: Protein Structure, Tertiary, MESH: Arboviruses, MESH : Insect Vectors, MESH: Insect Proteins, MESH : Anopheles gambiae, MESH: Animals, MESH : Arboviruses, insects, MESH: Yellow Fever, superfamily, ddc:616, 0303 health sciences, Anopheles, MESH : Genes, Insect, 3. Good health, yellow-fever mosquito, anopheles-gambiae, drosophila-melanogaster, expression, evolution, organization, Drosophila melanogaster, MESH: DNA Transposable Elements, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Multigene Family, Public Health, MESH : Protein Structure, Tertiary, MESH: Sex Characteristics, Molecular Sequence Data, MESH : Multigene Family, MESH: Sex Determination (Genetics), MESH : Sex Determination (Genetics), Arbovirus, Article, 03 medical and health sciences, Species Specificity, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Anopheles gambiae, Yellow Fever, MESH: Species Specificity, Humans, MESH: Humans, MESH: Molecular Sequence Data, fungi, MESH : Humans, MESH : Sex Characteristics, Membrane Transport Proteins, Sex Determination Processes, medicine.disease, Insect Vectors, Protein Structure, Tertiary, Sex Determination (Genetics), MESH: Multigene Family, MESH: Female, MESH : Sequence Analysis, DNA, MESH: Sequence Analysis, DNA, Drosophila melanogaster/genetics, MESH : Molecular Sequence Data, Odorant binding, Insect Proteins/genetics, Anopheles gambiae, MESH: Dengue, Genome, MESH: Membrane Transport Proteins, Dengue, MESH : Membrane Transport Proteins, Aedes, Insect Vectors/ genetics/metabolism, MESH : Drosophila melanogaster, MESH : Female, Membrane Transport Proteins/genetics, Genetics, MESH : Insect Proteins, Sex Characteristics, Multidisciplinary, MESH: Synteny, MESH: Aedes, MESH : Genome, Insect, MESH : DNA Transposable Elements, Insect Proteins, Female, Orthologous Gene, MESH : Male, MESH : Dengue, Aedes aegypti, MESH: Insect Vectors, Biology, 010603 evolutionary biology, Synteny, MESH: Drosophila melanogaster, Protein Structure, Tertiary/genetics, MESH : Yellow Fever, parasitic diseases, medicine, MESH : Species Specificity, Animals, 030304 developmental biology, MESH : Aedes, Base Sequence, MESH: Genome, Insect, MESH: Transcription, Genetic, MESH : Synteny, MESH : Transcription, Genetic, Sequence Analysis, DNA, biology.organism_classification, MESH: Male, DNA Transposable Elements, MESH : Base Sequence, MESH : Animals, Arboviruses, Anopheles gambiae/genetics/metabolism
Abstract: We present a draft sequence of the genome of Aedes aegypti , the primary vector for yellow fever and dengue fever, which at ∼1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae . Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of ∼4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster . Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of ∼2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.
Published: 2016
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2. Comparative Transcriptomic Analysis of Salt Adaptation in Roots of Contrasting Medicago truncatula Genotypes

Author: Véronique Gruber, Jean-Laurent Ichanté, Axel de Zélicourt, Laura de Lorenzo, Benoit Alunni, Sandrine Imbeaud, Hervé Delacroix, Sandrine Blanchet, Carole Laffont, Mounawer Badri, Anouck Diet, Julie Plet, Esther M. González, Florian Frugier, Ons Zahaf, Martin Crespi, Ana Zabalza, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Génomique Fonctionnelle des Tumeurs Solides (U1162), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de génétique moléculaire (CGM), Université Paris-Sud - Paris 11 (UP11), Laboratoire de physiologie cellulaire végétale ( LPCV ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut National de la Recherche Agronomique ( INRA ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Genomique Fonctionnelle des Tumeurs Solides, Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Paris Descartes - Paris 5 ( UPD5 ) -IFR105-Université Paris Diderot - Paris 7 ( UPD7 ), Centre de génétique moléculaire ( CGM ), and Université Paris-Sud - Paris 11 ( UP11 )
Subjects: 0106 biological sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, MESH : Molecular Sequence Data, MESH : Plant Roots, MESH: Plant Roots, MESH : Genotype, Plant Science, Sodium Chloride, 01 natural sciences, Plant Roots, Transcriptome, MESH: Genotype, Gene Expression Regulation, Plant, MESH: Medicago truncatula, MESH : Adaptation, Physiological, Plant Proteins, 2. Zero hunger, Abiotic component, chemistry.chemical_classification, 0303 health sciences, MESH: Plant Proteins, food and beverages, Adaptation, Physiological, Medicago truncatula, MESH : Sodium Chloride, Soil salinity, MESH: Sodium Chloride, Genotype, Molecular Sequence Data, Biology, 03 medical and health sciences, MESH: Gene Expression Profiling, Auxin, MESH : Plant Proteins, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Gene Expression Regulation, Plant, Gene, Molecular Biology, 030304 developmental biology, MESH: Molecular Sequence Data, Abiotic stress, MESH : Gene Expression Profiling, MESH : Medicago truncatula, Gene Expression Profiling, fungi, 15. Life on land, biology.organism_classification, MESH: Adaptation, Physiological, chemistry, Adaptation, MESH : Gene Expression Regulation, Plant, 010606 plant biology & botany
Abstract: International audience; Evolutionary diversity can be driven by the interaction of plants with different environments. Molecular bases involved in ecological adaptations to abiotic constraints can be explored using genomic tools. Legumes are major crops worldwide and soil salinity is a main stress affecting yield in these plants. We analyzed in the Medicago truncatula legume the root transcriptome of two genotypes having contrasting responses to salt stress: TN1.11, sampled in a salty Tunisian soil, and the reference Jemalong A17 genotype. TN1.11 plants show increased root growth under salt stress as well as a differential accumulation of sodium ions when compared to A17. Transcriptomic analysis revealed specific gene clusters preferentially regulated by salt in root apices of TN1.11, notably those related to the auxin pathway and to changes in histone variant isoforms. Many genes encoding transcription factors (TFs) were also differentially regulated between the two genotypes in response to salt. Among those selected for functional studies, overexpression in roots of the A17 genotype of the bHLH-type TF most differentially regulated between genotypes improved significantly root growth under salt stress. Despite the global complexity of the differential transcriptional responses, we propose that an increase in this bHLH TF expression may be linked to the adaptation of M. truncatula to saline soil environments.
Published: 2012
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3. 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
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4. Functional characterization of the AFF (AF4/FMR2) family of RNA-binding proteins: insights into the molecular pathology of FRAXE intellectual disability

Author: Mireille Melko, Samantha Zongaro, Jozef Gecz, Dominique Douguet, Barbara Bardoni, Céline Verheggen, Mounia Bensaid, Institut de pharmacologie moléculaire et cellulaire ( IPMC ), Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Génétique Moléculaire de Montpellier ( IGMM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Montpellier ( UM ), Department of Genetic Medicine Women's and Children's, University of Adelaide, Université Côte d'Azur ( UCA ), Institut de pharmacologie moléculaire et cellulaire (IPMC), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)
Subjects: MESH : Cell Line, MESH : Molecular Sequence Data, MESH: Sequence Homology, Amino Acid, Gene Expression, RNA-binding protein, MESH: Amino Acid Sequence, MESH: Gene Order, Exon, 0302 clinical medicine, MESH : Protein Transport, Genes, Reporter, Transcription (biology), Gene Order, Genetics (clinical), Genetics, 0303 health sciences, MESH : Amino Acid Sequence, MESH : Sequence Alignment, RNA-Binding Proteins, General Medicine, MESH : Genes, Reporter, Phenotype, MESH : Sequence Homology, Amino Acid, DNA-Binding Proteins, Protein Transport, MESH : Fragile X Syndrome, 030220 oncology & carcinogenesis, RNA splicing, MESH : RNA Splicing, MESH : DNA-Binding Proteins, Intranuclear Space, MESH: Fragile X Syndrome, MESH: Protein Transport, MESH: Gene Expression, RNA Splicing, Molecular Sequence Data, MESH : RNA-Binding Proteins, MESH: Sequence Alignment, MESH: Intranuclear Space, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Cell Line, 03 medical and health sciences, MESH : Fibroblasts, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : HeLa Cells, Amino Acid Sequence, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Gene, 030304 developmental biology, MESH: Molecular Sequence Data, MESH: Humans, MESH : Gene Order, Sequence Homology, Amino Acid, [ SDV.BC ] Life Sciences [q-bio]/Cellular Biology, MESH: Genes, Reporter, MESH : Humans, Alternative splicing, RNA, Fibroblasts, MESH: Cell Line, MESH : Gene Expression, MESH: RNA-Binding Proteins, MESH : Intranuclear Space, MESH: Fibroblasts, Fragile X Syndrome, MESH: HeLa Cells, MESH: RNA Splicing, Sequence Alignment, MESH: DNA-Binding Proteins, HeLa Cells
Abstract: International audience; The AFF (AF4/FMR2) family of genes includes four members: AFF1/AF4, AFF2/FMR2, AFF3/LAF4 and AFF4/AF5q31. AFF2/FMR2 is silenced in FRAXE intellectual disability, while the other three members have been reported to form fusion genes as a consequence of chromosome translocations with the myeloid/lymphoid or mixed lineage leukemia (MLL) gene in acute lymphoblastic leukemias (ALLs). All AFF proteins are localized in the nucleus and their role as transcriptional activators with a positive action on RNA elongation was primarily studied. We have recently shown that AFF2/FMR2 localizes to nuclear speckles, subnuclear structures considered as storage/modification sites of pre-mRNA splicing factors, and modulates alternative splicing via the interaction with the G-quadruplex RNA-forming structure. We show here that similarly to AFF2/FMR2, AFF3/LAF4 and AFF4/AF5q31 localize to nuclear speckles and are able to bind RNA, having a high apparent affinity for the G-quadruplex structure. Interestingly, AFF3/LAF4 and AFF4/AF5q31, like AFF2/FMR2, modulate, in vivo, the splicing efficiency of a mini-gene containing a G-quadruplex structure in one alternatively spliced exon. Furthermore, we observed that the overexpression of AFF2/3/4 interferes with the organization and/or biogenesis of nuclear speckles. These findings fit well with our observation that enlarged nuclear speckles are present in FRAXE fibroblasts. Furthermore, our findings suggest functional redundancy among the AFF family members in the regulation of splicing and transcription. It is possible that other members of the AFF family compensate for the loss of AFF2/FMR2 activity and as such explain the relatively mild to borderline phenotype observed in FRAXE patients.
Published: 2011
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5. Association of Microsatellite Variations of Plasmodium falciparum Na+/H+ Exchanger (Pfnhe-1) Gene with Reduced In Vitro Susceptibility to Quinine: Lack of Confirmation in Clinical Isolates from Africa

Author: Didier Menard, Christiane Bouchier, Jacques Le Bras, Rémy Durand, Véronique Hubert, Stéphane Rabearimanana, Magali Tichit, Valérie Andriantsoanirina, Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), Immunologie moléculaire des parasites, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), 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), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris], Service de Parasitologie [Avicenne], Université Paris 13 (UP13)-Hôpital Avicenne [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Université Paris 13 (UP13)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Avicenne [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut Pasteur de Madagascar - Réseau International des Instituts Pasteur (RIIP), Institut Pasteur [Paris] - Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) - AP-HP - Hôpital Bichat - Claude Bernard [Paris] - Université Paris Descartes - Paris 5 (UPD5), Génomique (Plate-Forme), Assistance publique - Hôpitaux de Paris (AP-HP) - Hôpital Avicenne - Université Paris 13 (UP13), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris]-Université Paris Descartes - Paris 5 (UPD5), and Université Paris 13 (UP13)-Hôpital Avicenne-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)
Subjects: MESH : Molecular Sequence Data, MESH : Polymorphism, Genetic, Drug Resistance, Protozoan Proteins, MESH : Genotype, MESH: Amino Acid Sequence, MESH: Africa, MESH : Microsatellite Repeats, MESH : Malaria, Falciparum, MESH: Genotype, 0302 clinical medicine, MESH : Chloroquine, MESH : Quinine, Polymorphism (computer science), Genotype, MESH : Plasmodium falciparum, MESH: Animals, Malaria, Falciparum, MESH: Protozoan Proteins, MESH: Plasmodium falciparum, MESH: Inhibitory Concentration 50, Genetics, 0303 health sciences, Quinine, biology, MESH : Amino Acid Sequence, MESH : Sequence Alignment, MESH: Malaria, Falciparum, Chloroquine, Articles, MESH: Chloroquine, MESH : Sodium-Hydrogen Antiporter, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, MESH : Inhibitory Concentration 50, MESH: Drug Resistance, Microsatellite, medicine.drug, Sodium-Hydrogen Exchangers, MESH: Quinine, MESH : Africa, Molecular Sequence Data, Plasmodium falciparum, 030231 tropical medicine, MESH: Sequence Alignment, Antimalarials, Inhibitory Concentration 50, 03 medical and health sciences, Virology, MESH: Polymorphism, Genetic, parasitic diseases, Genetic variation, medicine, Animals, Humans, Amino Acid Sequence, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Genotyping, MESH : Protozoan Proteins, MESH : Drug Resistance, Polymorphism, Genetic, MESH: Molecular Sequence Data, MESH: Sodium-Hydrogen Antiporter, MESH: Humans, 030306 microbiology, MESH : Humans, biology.organism_classification, MESH: Antimalarials, Genetic marker, Africa, MESH : Antimalarials, Parasitology, MESH : Animals, MESH: Microsatellite Repeats, Sequence Alignment, Microsatellite Repeats
Abstract: International audience; We sought to test the association of polymorphisms in Plasmodium falciparum nhe-1 (Pfnhe-1, gene PF13_0019) with in vitro susceptibility to quinine, which was previously reported in a limited number of reference strains or culture-adapted isolates. Determination of in vitro susceptibility to quinine, genotyping of Pfnhe-1 ms4760 microsatellite and polymorphism in codon 76 of Pfcrt were performed for 83 isolates obtained from symptomatic malaria-infected travelers returning from various African countries to France or from subjects living in Madagascar. Nineteen different ms4760 microsatellite profiles of Pfnhe-1 were found including 14 not previously described. Multivariate analysis showed no significant association between the in vitro susceptibility to quinine with particular ms4760 profiles. Contrary to previous reports, we only observed that the number of NHNDNHNNDDD repeats was positively associated with the increased IC50 of QN (P = 0.01). We concluded that the studied polymorphisms in Pfnhe-1 did not appear as valid molecular markers of in vitro susceptibility to quinine in P. falciparum isolates from Africa. Because we did not include any isolate of Asian origin in our series, these results did not exclude the possibility of regional associations, for example in South-East Asia.
Published: 2010
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6. Detection and Genomic Characterization of Aichi Viruses in Stool Samples from Children in Monastir, Tunisia

Author: Nabil Sakly, Mouna Hassine, Pierre Pothier, Mohamed Neji Guediche, Katia Ambert-Balay, Mahjoub Aouni, Khira Sdiri-Loulizi, S. Chouchane, Hakima Gharbi-Khelifi, 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: Diarrhea, Microbiology (medical), Kobuvirus, Tunisia, MESH : Molecular Sequence Data, MESH : Prevalence, viruses, Molecular Sequence Data, MESH : Diarrhea, Genome, Viral, MESH : Child, Preschool, Biology, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH : Kobuvirus, Feces, MESH : Child, Virology, MESH : Tunisia, Prevalence, medicine, Humans, Child, Picornaviridae Infections, MESH : Picornaviridae Infections, MESH : Humans, Infant, virus diseases, MESH : Infant, Sequence Analysis, DNA, MESH : Feces, Acute gastroenteritis, biology.organism_classification, Gastroenteritis, MESH : Gastroenteritis, Child, Preschool, medicine.symptom, Aichi virus, MESH : Genome, Viral, MESH : Sequence Analysis, DNA
Abstract: Aichi virus has been associated with acute gastroenteritis in adults and children. Stool samples were collected from 788 Tunisian children suffering from diarrhea. Aichi virus was found in 4.1% of the cases. The high proportion of monoinfections and the high frequency of hospitalizations support the role of Aichi virus in pediatric gastroenteritis.
Published: 2009
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7. Predominance and Circulation of Enteric Viruses in the Region of Greater Cairo, Egypt

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

Author: Françoise de Billy, Andreas Niebel, Tatiana Vernié, Christian Rogers, Florian Frugier, Giles E. D. Oldroyd, Julie Plet, Jean-Philippe Combier, Pascal Gamas, Sandra Moreau, Laboratoire des interactions plantes micro-organismes ( LIPMO ), Institut National de la Recherche Agronomique ( INRA ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: MESH: Signal Transduction, 0106 biological sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Cytokinins, MESH : Molecular Sequence Data, MESH : Transcription Factors, MESH: Feedback, Physiological, Regulator, MESH : Gene Deletion, Plant Science, Plant Root Nodulation, 01 natural sciences, Nod factor, chemistry.chemical_compound, MESH : Nitrogen Fixation, MESH: Phylogeny, MESH: Medicago truncatula, Research Articles, Phylogeny, Plant Proteins, Regulator gene, Feedback, Physiological, MESH : Cell Nucleus, 0303 health sciences, MESH: Plant Proteins, food and beverages, MESH: Transcription Factors, MESH : Feedback, Physiological, MESH : Cytokinins, Medicago truncatula, Cell biology, MESH: Root Nodules, Plant, Multigene Family, Cytokinin, RNA Interference, MESH: Cytokinins, Root Nodules, Plant, MESH: Plant Root Nodulation, Signal Transduction, MESH: Cell Nucleus, MESH: Ethylenes, Molecular Sequence Data, MESH: RNA Interference, MESH : Multigene Family, Biology, MESH: Nitrogen Fixation, MESH: Gene Expression Profiling, MESH : Root Nodules, Plant, 03 medical and health sciences, Nitrogen Fixation, MESH : Plant Proteins, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Transcription factor, 030304 developmental biology, Cell Nucleus, MESH : Signal Transduction, MESH: Molecular Sequence Data, Gene Expression Profiling, MESH : Gene Expression Profiling, MESH : Medicago truncatula, fungi, MESH : Phylogeny, MESH : Sinorhizobium meliloti, Cell Biology, Ethylenes, Meristem, biology.organism_classification, Response regulator, chemistry, MESH: Gene Deletion, MESH: Multigene Family, MESH : RNA Interference, MESH: Sinorhizobium meliloti, MESH : Plant Root Nodulation, Gene Deletion, MESH : Ethylenes, Sinorhizobium meliloti, Transcription Factors, 010606 plant biology & botany
Abstract: Mechanisms regulating legume root nodule development are still poorly understood, and very few regulatory genes have been cloned and characterized. Here, we describe EFD (for ethylene response factor required for nodule differentiation), a gene that is upregulated during nodulation in Medicago truncatula. The EFD transcription factor belongs to the ethylene response factor (ERF) group V, which contains ERN1, 2, and 3, three ERFs involved in Nod factor signaling. The role of EFD in the regulation of nodulation was examined through the characterization of a null deletion mutant (efd-1), RNA interference, and overexpression studies. These studies revealed that EFD is a negative regulator of root nodulation and infection by Rhizobium and that EFD is required for the formation of functional nitrogen-fixing nodules. EFD appears to be involved in the plant and bacteroid differentiation processes taking place beneath the nodule meristem. We also showed that EFD activated Mt RR4, a cytokinin primary response gene that encodes a type-A response regulator. We propose that EFD induction of Mt RR4 leads to the inhibition of cytokinin signaling, with two consequences: the suppression of new nodule initiation and the activation of differentiation as cells leave the nodule meristem. Our work thus reveals a key regulator linking early and late stages of nodulation and suggests that the regulation of the cytokinin pathway is important both for nodule initiation and development.
Published: 2008
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9. Primary cystic lung light chain deposition disease: a clinicopathologic entity derived from unmutated B cells with a stereotyped IGHV4-34/IGKV1 receptor

Author: Marc Stern, Marie-Hélène Delfau-Larue, Hervé Mal, Diane Damotte, Magali Colombat, Michel Fournier, Patrice Callard, Jacques Diebold, Jean-Pierre Farcet, Christiane Copie-Bergman, Service d'anatomie pathologique [CHU Tenon], Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Tenon [APHP], Service de pneumologie B, Assistance publique - Hôpitaux de Paris (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris]-Université Paris Diderot - Paris 7 ( UPD7 ), Service d'anatomie pathologique, Assistance publique - Hôpitaux de Paris (AP-HP)-Hôtel-Dieu, Département de pathologie [Mondor], Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ), Service d'anatomo-pathologie [CHU HEGP], Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Européen Georges Pompidou [APHP] ( HEGP ), Service d'immunologie biologique, Service de pneumologie, and Hôpital Foch [Suresnes]
Subjects: Lung Diseases, Pathology, MESH : Molecular Sequence Data, MESH : DNA, medicine.medical_treatment, Immunoglobulin Variable Region, Paraproteinemias, MESH : Immunoglobulin Heavy Chains, Plasma cell, Biochemistry, 0302 clinical medicine, MESH : Female, MESH : Immunoglobulin Variable Region, B-Lymphocytes, 0303 health sciences, MESH : Lung Diseases, Cysts, MESH : Amino Acid Sequence, Hematology, MESH : Adult, MESH : Immunoglobulin Light Chains, 3. Good health, medicine.anatomical_structure, MESH : Paraproteinemias, 030220 oncology & carcinogenesis, MESH : Lung Transplantation, Female, Genes, Immunoglobulin Light Chain, Immunoglobulin Heavy Chains, Lung Transplantation, Adult, medicine.medical_specialty, Genes, Immunoglobulin Heavy Chain, Molecular Sequence Data, Immunology, MESH : Genes, Immunoglobulin Heavy Chain, MESH : Cysts, Biology, Immunoglobulin light chain, Article, Light chain deposition disease, MESH : B-Lymphocytes, Lung Disorder, Immunoglobulin kappa-Chains, 03 medical and health sciences, MESH : Immunoglobulin kappa-Chains, medicine, Humans, Lung transplantation, Amino Acid Sequence, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Genes, Immunoglobulin Light Chain, 030304 developmental biology, Lung, Base Sequence, MESH : Humans, DNA, Cell Biology, medicine.disease, Immunoglobulin heavy chain, MESH : Base Sequence, Immunoglobulin Light Chains, CD5
Abstract: We have recently described a new form of light chain deposition disease (LCDD) presenting as a severe cystic lung disorder requiring lung transplantation. There was no bone marrow plasma cell proliferation. Because of the absence of disease recurrence after bilateral lung transplantation and of serum-free light chain ratio normalization after the procedure, we hypothesized that monoclonal light chain synthesis occurred within the lung. The aim of this study was to look for the monoclonal B-cell component in 3 patients with cystic lung LCDD. Histologic examination of the explanted lungs showed diffuse nonamyloid κ light chain deposits associated with a mild lymphoid infiltrate composed of aggregates of small CD20+, CD5−, CD10− B lymphocytes reminiscent of bronchus-associated lymphoid tissue. Using polymerase chain reaction (PCR), we identified a dominant B-cell clone in the lung in the 3 studied patients. The clonal expansion of each patient shared an unmutated antigen receptor variable region sequence characterized by the use of IGHV4-34 and IGKV1 subgroups with heavy and light chain CDR3 sequences of more than 80% amino acid identity, a feature evocative of an antigen-driven process. Combined with clinical and biologic data, our results strongly argue for a new antigen-driven primary pulmonary lymphoproliferative disorder.
Published: 2008
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10. A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis

Author: Carine Tisné, Yves Mechulam, Frédéric Dardel, Pierre Barraud, Emmanuelle Schmitt, Laboratoire de cristallographie et RMN biologiques ( LCRB - UMR 8015 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biochimie de l'Ecole polytechnique ( BIOC ), École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de cristallographie et RMN biologiques (LCRB - UMR 8015), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biochimie de l'Ecole polytechnique (BIOC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), and Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)
Subjects: Models, Molecular, MESH : Escherichia coli, MESH : Molecular Sequence Data, MESH : Nucleic Acid Conformation, MESH: Base Sequence, Crystallography, X-Ray, chemistry.chemical_compound, MESH : Anticodon, Protein biosynthesis, MESH : RNA, Transfer, Met, Peptide Chain Initiation, Translational, 0303 health sciences, MESH: Escherichia coli, 030302 biochemistry & molecular biology, Stem-loop, RNA, Bacterial, MESH: Nucleic Acid Conformation, Biochemistry, Transfer RNA, MESH: RNA, Bacterial, MESH: Models, Molecular, MESH: Peptide Chain Initiation, Translational, RNA, Transfer, Met, MESH : Models, Molecular, Base pair, Stereochemistry, Molecular Sequence Data, Biology, 03 medical and health sciences, Eukaryotic translation, Anticodon, Escherichia coli, MESH: Anticodon, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, MESH: Molecular Sequence Data, Methionine, Base Sequence, MESH: RNA, Transfer, Met, RNA, MESH : RNA, Bacterial, MESH: Crystallography, X-Ray, chemistry, Helix, Nucleic Acid Conformation, MESH : Base Sequence, MESH : Crystallography, X-Ray, MESH : Peptide Chain Initiation, Translational
Abstract: International audience; In all organisms, translational initiation takes place on the small ribosomal subunit and two classes of methionine tRNA are present. The initiator is used exclusively for initiation of protein synthesis while the elongator is used for inserting methionine internally in the nascent polypeptide chain. The crystal structure of Escherichia coli initiator tRNA(f)(Met) has been solved at 3.1 A resolution. The anticodon region is well-defined and reveals a unique structure, which has not been described in any other tRNA. It encompasses a Cm32*A38 base pair with a peculiar geometry extending the anticodon helix, a base triple between A37 and the G29-C41 pair in the major groove of the anticodon stem and a modified stacking organization of the anticodon loop. This conformation is associated with the three GC basepairs in the anticodon stem, characteristic of initiator tRNAs and suggests a mechanism by which the translation initiation machinery could discriminate the initiator tRNA from all other tRNAs.
Published: 2008
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11. Genetic diversity of Echinococcus multilocularis on a local scale

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

Author: Robert Barouki, Etienne Blanc, Nathalie M. Mazure, Fabrice Lecuru, Marie-Claude Fulchignoni-Lataud, Marie-Aude Le Frere Belda, Anne Dreiem, Thérèse Hervèe Mayi, Charbel Massaad, Vincent Favaudon, Liliane Massaad-Massade, Ramzi Seifeddine, Laboratoire de Détection et de Géophysique (CEA) (LDG), DAM Île-de-France (DAM/DIF), Direction des Applications Militaires (DAM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction des Applications Militaires (DAM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), IFR50, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Faculté de Médecine Nice, Institut de signalisation, biologie du développement et cancer (ISBDC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Génotoxicologie, signalisation et radiothérapie expérimentale, Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Biophysique moléculaire, Régulation de la transcription et maladies génétiques (RTMG), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Stéroïdes et système nerveux : physiopathologie moléculaire et clinique, Institut National de la Santé et de la Recherche Médicale (INSERM), Faculté de Médecine Paris-Sud, Université Paris-Sud - Paris 11 (UP11), Toxicologie Moleculaire (U490), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Laboratoire de Détection et de Géophysique (CEA) ( LDG ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Hôpital Européen Georges Pompidou [APHP] ( HEGP ), Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Faculté de Médecine Nice, Institut de signalisation, biologie du développement et cancer ( ISBDC ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -INSTITUT CURIE, Régulation de la transcription et maladies génétiques ( RTMG ), Centre National de la Recherche Scientifique ( CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université Paris-Sud - Paris 11 ( UP11 ), Toxicologie Moleculaire, Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Faculté de Médecine Nice, Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Curie
Subjects: Cancer Research, Hypoxia-Inducible Factor 1, MESH : Molecular Sequence Data, MESH : RNA, Messenger, Transcription, Genetic, MESH : Immunohistochemistry, MESH: Cell Hypoxia, Electrophoretic Mobility Shift Assay, MESH: Cell Cycle, RNA polymerase II, MESH : Blotting, Western, MESH : Breast Neoplasms, MESH: Base Sequence, MESH : RNA, Small Interfering, MESH: Down-Regulation, MESH : Down-Regulation, 0302 clinical medicine, Transcription (biology), MESH: Reverse Transcriptase Polymerase Chain Reaction, Enhancer binding, MESH: RNA, Small Interfering, Gene expression, MESH: CCAAT-Enhancer-Binding Protein-alpha, MESH : CCAAT-Enhancer-Binding Protein-alpha, RNA, Small Interfering, Promoter Regions, Genetic, 0303 health sciences, Gene knockdown, Reverse Transcriptase Polymerase Chain Reaction, Cell Cycle, MESH : Reverse Transcriptase Polymerase Chain Reaction, Immunohistochemistry, Cell Hypoxia, 3. Good health, MESH: Promoter Regions (Genetics), Oncology, MESH : Electrophoretic Mobility Shift Assay, 030220 oncology & carcinogenesis, MESH: Cell Growth Processes, MESH : Cell Hypoxia, MESH : Transfection, Subcellular Fractions, medicine.medical_specialty, MESH : Hypoxia-Inducible Factor 1, alpha Subunit, MESH: Cell Line, Tumor, Blotting, Western, Molecular Sequence Data, MESH : Deferoxamine, Down-Regulation, Breast Neoplasms, Cell Growth Processes, MESH : Subcellular Fractions, Deferoxamine, Biology, Transfection, MESH: Hypoxia-Inducible Factor 1, alpha Subunit, 03 medical and health sciences, Cell Line, Tumor, Internal medicine, MESH : Cell Cycle, CCAAT-Enhancer-Binding Protein-alpha, medicine, Humans, MESH: Blotting, Western, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA, Messenger, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Transcription factor, MESH: RNA, Messenger, 030304 developmental biology, MESH: Humans, MESH: Molecular Sequence Data, Base Sequence, MESH : Cell Line, Tumor, MESH: Transcription, Genetic, MESH: Transfection, MESH : Humans, MESH : Transcription, Genetic, MESH: Immunohistochemistry, MESH: Deferoxamine, Hypoxia-Inducible Factor 1, alpha Subunit, MESH : Promoter Regions (Genetics), Molecular biology, Endocrinology, HIF1A, MESH : Cell Growth Processes, MESH: Subcellular Fractions, MESH: Electrophoretic Mobility Shift Assay, biology.protein, MESH : Base Sequence, MESH: Breast Neoplasms
Abstract: International audience; The transcription factor CCAAT/enhancer binding protein-alpha (C/EBP alpha) is involved in the control of cell differentiation and proliferation, and has been suggested to act as a tumor suppressor in several cancers. By using microarray analysis, we have previously shown that hypoxia and estrogen down-regulate C/EBP alpha mRNA in T-47D breast cancer cells. Here, we have examined the mechanism by which the down-regulation by hypoxia takes place. Using the specific RNA polymerase II inhibitor 5,6-dichlorobenzimidazole-1-beta-D-ribofuranoside, the mRNA stability was analyzed under normoxia or hypoxia by quantitative reverse transcription-PCR. Hypoxia reduced the half-life of C/EBP alpha mRNA by approximately 30%. C/EBP alpha gene promoter studies indicated that hypoxia also repressed the transcription of the gene and identified a hypoxia-responsive element (-522; -527 bp), which binds to hypoxia-inducible factor (HIF)-1 alpha, as essential for down-regulation of C/EBP alpha transcription in hypoxia. Immunocytochemical analysis showed that C/EBP alpha was localized in the nucleus at 21% O(2), but was mostly cytoplasmic under 1% O(2). Knockdown of HIF-1 alpha by RNAi restored C/EBP alpha to normal levels under hypoxic conditions. Immunohistochemical studies of 10 tumor samples did not show any colocalization of C/EBP alpha and glucose transporter 1 (used as a marker for hypoxia). Taken together, these results show that hypoxia down-regulates C/EBP alpha expression in breast cancer cells by several mechanisms, including transcriptional and posttranscriptional effects. The down-regulation of C/EBP alpha in hypoxia is mediated by HIF-1.
Published: 2008
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13. Auxin Influx Activity Is Associated with Frankia Infection during Actinorhizal Nodule Formation in Casuarina glauca

Author: Ranjan Swarup, Florence Auguy, Didier Bogusz, Benjamin Péret, Gaëlle Devos, Leentje Jansen, Myriam Collin, Laurent Laplaze, Malcolm J. Bennett, Carole Santi, Valérie Hocher, Claudine Franche, Centre for Plant Integrative Biology [Nothingham] (CPIB), University of Nottingham, UK (UON), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Diversité et adaptation des plantes cultivées (UMR DIAPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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 Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre for Plant Integrative Biology [Nothingham] ( CPIB ), University of Nottingham, UK ( UON ), UMR - Interactions Plantes Microorganismes Environnement ( UMR IPME ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université de Montpellier ( UM ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), 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 ), Diversité, adaptation, développement des plantes ( DIADE ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), Laboratoire Génome et développement des plantes ( LGDP ), Université de Perpignan Via Domitia ( UPVD ) -Centre National de la Recherche Scientifique ( CNRS ), Diversité et adaptation des plantes cultivées ( DIAPC ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ), and 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)
Subjects: 0106 biological sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, MESH : Molecular Sequence Data, Casuarinaceae, Root nodule, NODULATION, MESH: Sequence Homology, Amino Acid, Physiology, MESH: Glycolates, Frankia, Arabidopsis, MESH : Symbiosis, Gene Expression, MESH: Amino Acid Sequence, Plant Science, 01 natural sciences, MESH : Arabidopsis Proteins, MESH : Arabidopsis, MESH: Genes, Plant, Arabidopsis thaliana, MESH: Arabidopsis, MESH: Angiosperms, chemistry.chemical_classification, MESH: Genetic Complementation Test, 0303 health sciences, MESH: Symbiosis, biology, MESH : Amino Acid Sequence, food and beverages, MESH: Frankia, MESH : Indoleacetic Acids, Arts and Architecture, MESH : Sequence Homology, Amino Acid, Cell biology, MESH: Root Nodules, Plant, MESH : Angiosperms, Multigene Family, WHITE CLOVER, MESH : Carrier Proteins, Root Nodules, Plant, Actinorhizal plant, Research Article, EXPRESSION, Auxin influx, MESH: Indoleacetic Acids, MESH: Gene Expression, Molecular Sequence Data, MESH : Multigene Family, MESH: Carrier Proteins, MESH: Arabidopsis Proteins, TREE ALLOCASUARINA-VERTICILLATA, Genes, Plant, MESH : Glycolates, Magnoliopsida, MESH : Root Nodules, Plant, 03 medical and health sciences, Auxin, Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, CORTICAL-CELLS, Amino Acid Sequence, Symbiosis, LATERAL ROOT DEVELOPMENT, MESH : Genes, Plant, 030304 developmental biology, MESH: Molecular Sequence Data, FUNCTIONAL-ANALYSIS, Indoleacetic Acids, Sequence Homology, Amino Acid, MESH : Genetic Complementation Test, Arabidopsis Proteins, MESH : Frankia, Genetic Complementation Test, fungi, MEDICAGO-TRUNCATULA, biology.organism_classification, TRANSPORT, Glycolates, MESH : Gene Expression, chemistry, ARABIDOPSIS-THALIANA, MESH: Multigene Family, Carrier Proteins, 010606 plant biology & botany
Abstract: Plants from the Casuarinaceae family enter symbiosis with the actinomycete Frankia leading to the formation of nitrogen-fixing root nodules. We observed that application of the auxin influx inhibitor 1-naphtoxyacetic acid perturbs actinorhizal nodule formation. This suggests a potential role for auxin influx carriers in the infection process. We therefore isolated and characterized homologs of the auxin influx carrier (AUX1-LAX) genes in Casuarina glauca. Two members of this family were found to share high levels of deduced protein sequence identity with Arabidopsis (Arabidopsis thaliana) AUX-LAX proteins. Complementation of the Arabidopsis aux1 mutant revealed that one of them is functionally equivalent to AUX1 and was named CgAUX1. The spatial and temporal expression pattern of CgAUX1 promoter:β-glucuronidase reporter was analyzed in Casuarinaceae. We observed that CgAUX1 was expressed in plant cells infected by Frankia throughout the course of actinorhizal nodule formation. Our data suggest that auxin plays an important role during plant cell infection in actinorhizal symbioses.
Published: 2007
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14. Binding interface between the Salmonella σ(S)/RpoS subunit of RNA polymerase and Crl: hints from bacterial species lacking crl

Author: Christina Sizun, Jacques Bellalou, Claudine Mayer, Véronique Monteil, Mireille Nowakowski, Fabienne Levi-Acobas, Françoise Norel, François Bontems, Paola Cavaliere, Systèmes macromoléculaires et Signalisation, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Production de Protéines Recombinantes (Plate-Forme) (PRPF), Université Paris Diderot - Paris 7 (UPD7), Microbiologie structurale - Structural Microbiology (Microb. Struc. (UMR_3528 / U-Pasteur_5)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the French National Research Agency [grant ANR- 11-BSV3-009], the IR-RMN-THC (CNRS FR3050) for access to the 950 MHz spectrometer at Gif-sur-Yvette for preliminary experiments and by grants from the Institut Pasteur and the Centre National de la Recherche Scientifique. The WeNMR project (European FP7 e-Infrastructure grant, contract no. 261572, www.wenmr.eu), supported by the European Grid Initiative (EGI) through the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan, the Latin America GRID infrastructure via the Gisela project and the US Open Science Grid (OSG) are acknowledged for the use of web portals, computing and storage facilities., ANR-11-BSV3-0009,SIGMADAPT,Rôle de SigmaS dans la compétitivité et l'adaptation des bactéries à l'environnement(2011), European Project: 261572,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-2,WENMR(2010), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut de Chimie des Substances Naturelles ( ICSN ), Centre National de la Recherche Scientifique ( CNRS ), Production de Protéines Recombinantes (Plate-Forme) ( PRPF ), Université Paris Diderot - Paris 7 ( UPD7 ), Microbiologie structurale, ANR-11-BSV3-0009,SIGMADAPT,Rôle de SigmaS dans la compétitivité et l'adaptation des bactéries à l'environnement ( 2011 ), European Project : 261572,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-2,WENMR ( 2010 ), Institut Pasteur [Paris] - Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), ANR-11-BSV3-0009, SIGMADAPT, Rôle de SigmaS dans la compétitivité et l'adaptation des bactéries à l'environnement(2011), and European Project : 261572, EC:FP7:INFRA, FP7-INFRASTRUCTURES-2010-2, WENMR(2010)
Subjects: MESH : Models, Chemical, MESH: Pseudomonas aeruginosa/metabolism, MESH : Molecular Sequence Data, Protein Conformation, MESH : Protein Subunits, Plasma protein binding, MESH: Amino Acid Sequence, MESH: DNA-Directed RNA Polymerases/chemistry, chemistry.chemical_compound, Protein structure, MESH: Protein Conformation, MESH: Structure-Activity Relationship, MESH : Sigma Factor/ultrastructure, MESH: Bacterial Proteins/ultrastructure, Salmonella, Sigma factor, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, RNA polymerase, MESH: Sigma Factor/metabolism, MESH: DNA-Directed RNA Polymerases/metabolism, MESH : Structure-Activity Relationship, MESH : Protein Conformation, Genetics, Multidisciplinary, MESH : Amino Acid Sequence, MESH: Models, Chemical, food and beverages, MESH : Protein Binding, DNA-Directed RNA Polymerases, MESH: Protein Subunits, MESH : Bacterial Proteins/ultrastructure, MESH: Amino Acid Substitution, Molecular Docking Simulation, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, Pseudomonas aeruginosa, MESH : Molecular Docking Simulation, MESH: Bacterial Proteins/metabolism, Protein Binding, MESH: Bacterial Proteins/chemistry, MESH : Salmonella/metabolism, MESH : Pseudomonas aeruginosa/metabolism, MESH : Sigma Factor/chemistry, Protein subunit, Molecular Sequence Data, MESH : DNA-Directed RNA Polymerases/chemistry, Sigma Factor, Biology, Article, Structure-Activity Relationship, MESH: DNA-Directed RNA Polymerases/ultrastructure, MESH : DNA-Directed RNA Polymerases/ultrastructure, MESH : Amino Acid Substitution, Bacterial Proteins, Species Specificity, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Molecular Docking Simulation, MESH: Sigma Factor/chemistry, MESH : Species Specificity, MESH : Bacterial Proteins/chemistry, MESH: Protein Binding, MESH: Species Specificity, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, MESH : DNA-Directed RNA Polymerases/metabolism, Binding site, Gene, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Binding Sites, MESH: Molecular Sequence Data, fungi, MESH : Sigma Factor/metabolism, Protein Subunits, Amino Acid Substitution, Models, Chemical, chemistry, MESH: Binding Sites, MESH : Bacterial Proteins/metabolism, MESH: Salmonella/metabolism, rpoS, MESH : Binding Sites, MESH: Sigma Factor/ultrastructure
Abstract: International audience; In many Gram-negative bacteria, including Salmonella enterica serovar Typhimurium (S. Typhimurium), the sigma factor RpoS/σ S accumulates during stationary phase of growth, and associates with the core RNA polymerase enzyme (E) to promote transcription initiation of genes involved in general stress resistance and starvation survival. Whereas σ factors are usually inactivated upon interaction with anti-σ proteins, σ S binding to the Crl protein increases σ S activity by favouring its association to E. Taking advantage of evolution of the σ S sequence in bacterial species that do not contain a crl gene, like Pseudomonas aeruginosa, we identified and assigned a critical arginine residue in σ S to the S. Typhimurium σ S-Crl binding interface. We solved the solution structure of S. Typhimurium Crl by NMR and used it for NMR binding assays with σ S and to generate in silico models of the σ S-Crl complex constrained by mutational analysis. The σ S-Crl models suggest that the identified arginine in σ S interacts with an aspartate of Crl that is required for σ S binding and is located inside a cavity enclosed by flexible loops, which also contribute to the interface. This study provides the basis for further structural investigation of the σ S-Crl complex. In bacteria, a primary housekeeping sigma factor and one or more alternative σ factors associate with the catalytically active RNA polymerase (RNAP) core enzyme (α 2β β 'ω , E), to form the holoenzyme Eσ , and direct transcription initiation of specific subsets of genes 1,2. In many Gram-negative bacteria, σ S /RpoS is produced during late exponential phase, or in response to stress, to modify global gene transcription and to allow stationary phase survival and general stress resistance 3–5. In the wide host-range pathogen S. Typhimurium, σ S is not only required for general stress resistance, but also for virulence, biofilm formation and development of the red dry and rough (rdar) morphotype, a colony morphology caused by the production of amyloid fibers (curli) and cellulose 6–8. The efficiency of formation of the housekeeping and alternative Eσ can be modulated by regulatory factors that bind E and/or σ 5,9. So far, Crl is the only known σ S-dedicated regulatory factor that enhances σ S activity through a direct interaction, favouring Eσ S formation 7,10–15. Analyses of sequenced bacterial genomes revealed that crl is less widespread and less conserved at the sequence level than
Published: 2015
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15. A vanG-type locus in Clostridium argentinense

Author: Christine Legeay, Michel-Robert Popoff, Philippe Bouvet, Christelle Mazuet, Patrice Courvalin, Bruno Périchon, Christiane Bouchier, Nicolas Berthet, Diana Chapeton-Montes, Centre International de Recherches Médicales de Franceville (CIRMF), Agents antibactériens, Institut Pasteur [Paris], Bactéries anaérobies et Toxines, Génomique (Plate-Forme) - Genomics Platform, This work was supported by Institut Pasteur funding. The ‘Plateforme de Génomique’ of the Institut Pasteur was supported in part by France-Genomique. N. B. was supported in part by the Elisabeth Taub award from the Académie Nationale de Médecine., Institut Pasteur [Paris] (IP), Centre International de Recherches Médicales de Franceville, and Génomique (Plate-Forme)
Subjects: MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, vancomycin, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, C. argentinense, MESH: Genome, Bacterial, Polymerase Chain Reaction, law.invention, MESH: Gene Order, Clostridium, Clostridium argentinense, MESH : Genetic Loci, law, Disk Diffusion Antimicrobial Tests, MESH : Clostridium, Gene cluster, Gene Order, MESH : DNA, Bacterial, Pharmacology (medical), MESH : Anti-Bacterial Agents, MESH : Polymerase Chain Reaction, Polymerase chain reaction, 0303 health sciences, biology, Teicoplanin, MESH : Genes, Bacterial, Glycopeptides, Glycopeptide, Anti-Bacterial Agents, Infectious Diseases, MESH: Disk Diffusion Antimicrobial Tests, MESH: Vancomycin Resistance, MESH: Genes, Bacterial, medicine.drug, Microbiology (medical), DNA, Bacterial, MESH : Glycopeptides, MESH : Vancomycin Resistance, MESH : Genome, Bacterial, Molecular Sequence Data, Locus (genetics), MESH: Genetic Loci, Microbiology, resistance, 03 medical and health sciences, MESH: Anti-Bacterial Agents, medicine, Humans, MESH : Disk Diffusion Antimicrobial Tests, Gene, 030304 developmental biology, MESH: Glycopeptides, Pharmacology, MESH : Gene Order, MESH: Humans, MESH: Molecular Sequence Data, 030306 microbiology, MESH: Clostridium, MESH : Humans, Vancomycin Resistance, MESH: Polymerase Chain Reaction, Sequence Analysis, DNA, biology.organism_classification, MESH: DNA, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genes, Bacterial, Genetic Loci, Genome, Bacterial, MESH : Sequence Analysis, DNA
Abstract: Objectives The objective was to study a new vanG-type locus in Clostridium argentinense vanGCar and to determine its impact on glycopeptide susceptibility of the host. Methods The whole genome of C. argentinense NCIB 10714 was sequenced using Illumina single-reads sequencing technology. The presence of vanGCar in seven C. argentinense strains was tested by PCR and its expression was tested by quantitative RT–PCR (qRT–PCR). Glycopeptide susceptibility was determined by the Etest procedure. Results The vanGCar locus contained four genes encoding a carboxypeptidase, a d-alanine:d-serine ligase, a serine transporter and a serine racemase, and was present in the seven C. argentinense studied. An AraC-type transcriptional regulator was found upstream from the genes. C. argentinense NCIB 10714 was susceptible to vancomycin and to teicoplanin. qRT–PCR experiments revealed that vanGCar was not expressed without or with induction by a subinhibitory concentration of vancomycin. Conclusions The new vanGCar locus was cryptic in C. argentinense and intrinsic to this species. Emergence of vancomycin resistance in C. argentinense due to decryptification of the vanGCar gene cluster could occur.
Published: 2015
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16. Shifted, the Drosophila Ortholog of Wnt Inhibitory Factor-1, Controls the Distribution and Movement of Hedgehog

Author: Michael A. Halbisen, Bruno Glise, Alain Vincent, Michèle Crozatier, Steve Wise, Catherine A. Miller, David J. Olson, Seth S. Blair, Institut de Recherches et d'Etudes sur le Monde Arabe et Musulman (IREMAM), Sciences Po Aix - Institut d'études politiques d'Aix-en-Provence (IEP Aix-en-Provence)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre de biologie du développement (CBD), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Anatomopathologie Haut-Lévêque (ANATOMOPATHOLOGIE), CHU, Clinical Neurology Oxford (CLINICAL NEUROLOGY), Hospital, Departement /u661 : Endocrinologie, Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de synthèse organique (DCSO), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), FLAveur, VIsion et Comportement du consommateur (FLAVIC), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Institut de Recherches et d'Etudes sur les Mondes Arabes et Musulmans (IREMAM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), École polytechnique (X)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherches et d'Etudes sur le Monde Arabe et Musulman ( IREMAM ), Sciences Po Aix - Institut d'études politiques d'Aix-en-Provence ( IEP Aix-en-Provence ) -Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de biologie du développement ( CBD ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Bordelais de Recherche en Informatique ( LaBRI ), Centre National de la Recherche Scientifique ( CNRS ) -École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Institut de Génomique Fonctionnelle ( IGF ), Centre National de la Recherche Scientifique ( CNRS ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Montpellier 1 ( UM1 ) -Université de Montpellier ( UM ), Anatomopathologie Haut-Lévêque ( ANATOMOPATHOLOGIE ), Clinical Neurology Oxford ( CLINICAL NEUROLOGY ), Université Montpellier 1 ( UM1 ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de synthèse organique ( DCSO ), École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), FLAveur, VIsion et Comportement du consommateur ( FLAVIC ), Etablissement National d'Enseignement Supérieur Agronomique de Dijon ( ENESAD ) -Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Université de Bourgogne (UB)
Subjects: Male, MESH: Signal Transduction, MESH : Molecular Sequence Data, MESH: Sequence Homology, Amino Acid, MESH: Drosophila, MESH : Animals, Genetically Modified, Sequence Homology, MESH : Models, Biological, MESH: Amino Acid Sequence, Wing, MESH: Cholesterol, 0302 clinical medicine, Models, Drosophila Proteins, MESH : Female, MESH: Animals, MESH : Cholesterol, Genetics, 0303 health sciences, biology, MESH : Amino Acid Sequence, Wnt signaling pathway, Signal transducing adaptor protein, MESH : Sequence Homology, Amino Acid, Hedgehog signaling pathway, Cell biology, MESH : Phenotype, Amino Acid, Imaginal disc, Cholesterol, Phenotype, MESH: Repressor Proteins, Drosophila, Female, MESH : Mutation, MESH : Repressor Proteins, MESH : Carrier Proteins, Drosophila melanogaster, Signal transduction, MESH : Heparan Sulfate Proteoglycans, Drosophila Protein, Signal Transduction, MESH: Mutation, animal structures, MESH: Drosophila Proteins, MESH : Male, Molecular Sequence Data, MESH : Wing, Genetically Modified, MESH: Carrier Proteins, MESH: Phenotype, General Biochemistry, Genetics and Molecular Biology, MESH: Animals, Genetically Modified, 03 medical and health sciences, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, MESH : Drosophila, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Hedgehog, Alleles, 030304 developmental biology, MESH : Signal Transduction, MESH: Humans, MESH: Molecular Sequence Data, MESH: Alleles, MESH : Humans, MESH: Models, Biological, Cell Biology, MESH : Drosophila Proteins, Biological, MESH: Wing, biology.organism_classification, MESH: Male, Repressor Proteins, Mutation, MESH: Heparan Sulfate Proteoglycans, MESH : Animals, MESH : Alleles, Carrier Proteins, MESH: Female, Heparan Sulfate Proteoglycans, 030217 neurology & neurosurgery, Developmental Biology
Abstract: SummaryWe here identify and characterize an extracellular modulator of Hedgehog signaling in Drosophila, Shifted. Shifted is required for high levels of long-range signaling in the developing wing imaginal disc. Surprisingly, shifted encodes the only Drosophila ortholog of the secreted vertebrate protein Wnt Inhibitory Factor-1 (WIF-1), whose known role is to bind to extracellular Wnts and inhibit their activity. However, Shifted does not regulate Hedgehog signaling by affecting Wingless or Wnt signaling. We show instead that Shifted is a secreted protein that acts over a long distance and is required for the normal accumulation of Hh protein and its movement in the wing. Our data further indicate that Shf interacts with Hh and the heparan sulfate proteoglycans. Therefore, we propose that Shf stabilizes the interaction between Hh and the proteoglycans, an unexpected role for a member of the WIF-1 family.
Published: 2005
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17. Foot Infection by Clostridium sordellii: Case Report and Review of 15 Cases in France

Author: Michel-R. Popoff, Jean Sautereau, Christiane Bouchier, Alain Le Coustumier, Francine Mory, Philippe Bouvet, Centre National de Référence des Bactéries Anaérobies et Botulisme - National Reference Center Anaerobic Bacteria and Botulism (CNR), Institut Pasteur [Paris], Centre hospitalier Jean Rougier, Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Génomique (Plate-Forme) - Genomics Platform, We thank French private and hospital laboratories for sending Clostridium sordellii isolates to the NRC. Maria Manich, Marie Bedora-Faure, and Guylène K'Ouas from the NRC are warmly thanked for excellent technical assistance., Centre National de Référence des Bactéries Anaérobies et du Botulisme - Bactéries Anaérobies et Toxines ( CNR ), Centre Hospitalier Régional Universitaire de Nancy ( CHRU Nancy ), Génomique (Plate-Forme), and Institut Pasteur [Paris] (IP)
Subjects: Male, MESH : Molecular Sequence Data, MESH: Clostridium sordellii, [ SDV.TOX ] Life Sciences [q-bio]/Toxicology, MESH : Aged, Clostridium sordellii, Case Reports, 0302 clinical medicine, MESH: Aged, 80 and over, Medicine, MESH : Female, 030212 general & internal medicine, MESH : Anti-Bacterial Agents, Aged, 80 and over, MESH: Aged, 0303 health sciences, MESH: Middle Aged, biology, Clostridium Infections, MESH : Adult, Middle Aged, 3. Good health, Anti-Bacterial Agents, [SDV.TOX]Life Sciences [q-bio]/Toxicology, Female, France, Foot (unit), Microbiology (medical), Adult, MESH : Male, MESH: Clostridium Infections, Molecular Sequence Data, MESH: Foot Diseases, Microbiology, Foot Diseases, 03 medical and health sciences, MESH: Anti-Bacterial Agents, Humans, MESH : Middle Aged, Lethal toxin, MESH : Aged, 80 and over, MESH : Foot Diseases, MESH : France, Aged, MESH: Molecular Sequence Data, MESH: Humans, 030306 microbiology, business.industry, MESH : Humans, MESH: Adult, MESH : Clostridium sordellii, biology.organism_classification, Virology, MESH: Male, Clostridium septicum, MESH : Clostridium Infections, MESH: France, business, MESH: Female
Abstract: We report a case of foot infection by Clostridium sordellii and review 15 human infections registered at a Reference Center in France during the period 1998 to 2011. All strains were found nontoxigenic, lacking the lethal toxin gene coding for TcsL. Like Clostridium septicum , several C. sordellii infections were associated with intestinal neoplasms.
Published: 2015
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18. An Atypical Outbreak of Food-Borne Botulism Due to Clostridium botulinum Types B and E from Ham

Author: Christelle Mazuet, Christiane Bouchier, Jean Sautereau, Christine Legeay, Philippe Bouvet, Michel R. Popoff, Bactéries anaérobies et Toxines, Institut Pasteur [Paris], Génomique (Plate-Forme), High-throughput sequencing has been performed on the Genomics Platform, a member of the France Génomique Consortium (ANR10-INBS-09-08)., We thank Benoit Jaulhac, Laboratoire de Bactériologie, Hôpitaux Universitaires, Strasbourg, France, for his assistance., ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique ( 2010 ), Génomique (Plate-Forme) - Genomics Platform, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), and Institut Pasteur [Paris] (IP)
Subjects: Male, MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, MESH : Multilocus Sequence Typing, Sequence Homology, MESH : Genotype, Case Reports, medicine.disease_cause, MESH: Genome, Bacterial, Disease Outbreaks, MESH: Genotype, Cluster Analysis, MESH : DNA, Bacterial, Botulism, MESH : Female, MESH: Sequence Homology, MESH: Clostridium botulinum type A, MESH: Disease Outbreaks, MESH: Phylogeny, MESH: Clostridium botulinum type F, Phylogeny, 0303 health sciences, MESH: Middle Aged, Middle Aged, [ SDV.TOX.TCA ] Life Sciences [q-bio]/Toxicology/Toxicology and food chain, MESH: Multilocus Sequence Typing, MESH : Botulism, Female, Microbiology (medical), Clostridium botulinum type F, DNA, Bacterial, Clostridium botulinum type E, Genotype, Clostridium botulinum type A, MESH : Male, Molecular Sequence Data, MESH : Genome, Bacterial, MESH: Botulism, [SDV.TOX.TCA]Life Sciences [q-bio]/Toxicology/Toxicology and food chain, Biology, Microbiology, 03 medical and health sciences, MESH : Sequence Homology, medicine, Food microbiology, Humans, MESH : Cluster Analysis, MESH : Middle Aged, MESH : Disease Outbreaks, MESH: Food Microbiology, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, MESH: Molecular Sequence Data, 030306 microbiology, MESH : Humans, Outbreak, MESH : Phylogeny, Sequence Analysis, DNA, MESH : Food Microbiology, medicine.disease, Virology, MESH: Cluster Analysis, MESH: DNA, Bacterial, MESH: Male, MESH : Clostridium botulinum type F, Food Microbiology, Multilocus sequence typing, Clostridium botulinum, [ SDV.GEN ] Life Sciences [q-bio]/Genetics, MESH: Female, Genome, Bacterial, MESH : Clostridium botulinum type A, Multilocus Sequence Typing, MESH : Sequence Analysis, DNA
Abstract: An outbreak of human botulism was due to consumption of ham containing botulinum neurotoxins B and E. A Clostridium botulinum type E strain isolated from ham was assigned to a new subtype (E12) based on bont / E gene sequencing and belongs to a new multilocus sequence subtype, as analyzed by whole-genome sequencing.
Published: 2015
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19. Haemorrhagic toxin and lethal toxin from C lostridium sordellii strain vpi9048: molecular characterization and comparative analysis of substrate specificity of the large clostridial glucosylating toxins

Author: Harald, Genth, Serge, Pauillac, Ilona, Schelle, Philippe, Bouvet, Christiane, Bouchier, Carolina, Varela-Chavez, Ingo, Just, Michel R, Popoff, Hannover Medical School [Hannover] ( MHH ), Bactéries anaérobies et Toxines, Institut Pasteur [Paris], Génomique (Plate-Forme), This work is supported by VW Vorab from Lower Saxony (TP5) and Institute Pasteur funding., Hannover Medical School [Hannover] (MHH), Institut Pasteur [Paris] (IP), and Génomique (Plate-Forme) - Genomics Platform
Subjects: DNA, Bacterial, MESH: Sequence Analysis, DNA, Glycosylation, MESH : Molecular Sequence Data, MESH: Sequence Homology, Amino Acid, MESH: Clostridium sordellii, Bacterial Toxins, Molecular Sequence Data, [ SDV.TOX ] Life Sciences [q-bio]/Toxicology, MESH: Monomeric GTP-Binding Proteins, Substrate Specificity, MESH : DNA, Bacterial, Clostridium sordellii, Monomeric GTP-Binding Proteins, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Molecular Sequence Data, Sequence Homology, Amino Acid, MESH : Substrate Specificity, MESH : Glycosylation, Sequence Analysis, DNA, MESH : Clostridium sordellii, MESH: Glycosylation, MESH: DNA, Bacterial, MESH : Sequence Homology, Amino Acid, MESH: Bacterial Toxins, [SDV.TOX]Life Sciences [q-bio]/Toxicology, MESH : Bacterial Toxins, MESH : Monomeric GTP-Binding Proteins, MESH: Substrate Specificity, [ SDV.GEN ] Life Sciences [q-bio]/Genetics, MESH : Sequence Analysis, DNA
Abstract: International audience; Large clostridial glucosylating toxins (LCGTs) are produced by toxigenic strains of Clostridium difficile, Clostridium perfringens, Clostridium novyi and Clostridium sordellii. While most C. sordellii strains solely produce lethal toxin (TcsL), C. sordellii strain VPI9048 co-produces both hemorrhagic toxin (TcsH) and TcsL. Here, the sequences of TcsH-9048 and TcsL-9048 are provided, showing that both toxins retain conserved LCGT features and that TcsL and TcsH are highly related to Toxin A (TcdA) and Toxin B (TcdB) from C. difficile strain VPI10463. The substrate profile of the toxins was investigated with recombinant LCGT transferase domains (rN) and a wide panel of small GTPases. rN-TcsH-9048 and rN-TcdA-10463 glucosylated preferably Rho-GTPases but also Ras-GTPases to some extent. In this respect, rN-TcsH-9048 and rN-TcdA-10463 differ from the respective full-length TcsH-9048 and TcdA-10463, which exclusively glucosylate Rho-GTPases. rN-TcsL-9048 and full length TcsL-9048 glucosylate both Rho- and Ras-GTPases, whereas rN-TcdB-10463 and full length TcdB-10463 exclusively glucosylate Rho-GTPases. Vero cells treated with full length TcsH-9048 or TcdA-10463 also showed glucosylation of Ras, albeit to a lower extent than of Rho-GTPases. Thus, in vitro analysis of substrate spectra using recombinant transferase domains corresponding to the auto-proteolytically cleaved domains, predicts more precisely the in vivo substrates than the full length toxins. Except for TcdB-1470, all LCGTs evoked increased expression of the small GTPase RhoB, which exhibited cytoprotective activity in cells treated with TcsL isoforms, but pro-apoptotic activity in cells treated with TcdA, TcdB, and TcsH. All LCGTs induced a rapid dephosphorylation of pY118-paxillin and of pS144/141-PAK1/2 prior to actin filament depolymerization indicating that disassembly of focal adhesions is an early event leading to the disorganization of the actin cytoskeleton.
Published: 2014
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20. Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders 'Frankiales' and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov

Author: Vincent Daubin, Philippe Normand, Danis Abrouk, Alison M. Berry, Isaac Gifford, Arnab Sen, Assam University, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Uniformed Services University of the Health Sciences (USUHS), Department of Plant Sciences [Davis, CA], University of California [Davis] (UC Davis), University of California-University of California, Institute of Microelectronics (NCSR), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Armed Forces Radiobiology Research Institute, University of California [Davis] ( UC Davis ), Institute of Microelectronics ( NCSR ), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Sciences [Univ California Davis] (Plant - UC Davis), and University of California (UC)-University of California (UC)
Subjects: DNA, Bacterial, MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, [SDV]Life Sciences [q-bio], Molecular Sequence Data, MESH : Genome, Bacterial, Concatenation, MESH : Actinobacteria, MESH: Genome, Bacterial, Microbiology, Genome, Tree (descriptive set theory), MESH : RNA, Ribosomal, 23S, Phylogenetics, RNA, Ribosomal, 16S, Botany, MESH : DNA, Bacterial, MESH: Phylogeny, Phylogeny, Ecology, Evolution, Behavior and Systematics, Geodermatophilaceae, MESH: Molecular Sequence Data, [ SDV ] Life Sciences [q-bio], Phylogenetic tree, biology, MESH : Phylogeny, Sequence Analysis, DNA, General Medicine, biology.organism_classification, MESH: RNA, Ribosomal, 23S, MESH: DNA, Bacterial, Actinobacteria, MESH : RNA, Ribosomal, 16S, Nakamurellaceae, Kocuria, MESH: RNA, Ribosomal, 16S, RNA, Ribosomal, 23S, Evolutionary biology, Genome, Bacterial, MESH : Sequence Analysis, DNA, MESH: Actinobacteria
Abstract: The phylogeny of the class Actinobacteria remains controversial, essentially because it is very sensitive to the choice of dataset and phylogenetic methods. We used a test proposed recently, based on complete genome data, which chooses among candidate species phylogenies based on the number of lateral gene transfers (LGT) needed to explain the diversity of histories among gene trees for a set of genomes. We used 100 completely sequenced genomes representing 35 families and 17 orders of the class Actinobacteria and evaluated eight different hypotheses for their phylogeny, including one based on a concatenate of 54 conserved proteins present in single copy in all these genomes, trees based on 16S and 23S rRNA gene sequences or their concatenation, and a tree based on the concatenation of MLSA genes (encoding AtpI, GyrA, FtsZ, SecA and DnaK). We used Prunier to infer the number of LGT in 579 proteins (different from those used to build the concatenated tree) present in at least 70 species, using the different hypothetical species trees as references. The best tree, with the lowest number of lateral transfers, was the one based on the concatenation of 54 proteins. In that tree, the orders Bifidobacteriales , Coriobacteriales , ‘Coryneb acteriales’, ‘Micromonosporales’, ‘Propionibacteriales’, ‘Pseudonocardiales’, Streptomycetales and ‘Streptosporangiales’ were recovered while the orders ‘Frankiales’ and Micrococcales were not. It is thus proposed that the order ‘Frankiales’, which has an effectively but not validly published name, be split into Frankiales ord. nov. (type family Frankiaceae ), Geodermatophilales ord. nov. ( Geodermatophilaceae ), Acidothermales ord. nov. ( Acidothermaceae ) and Nakamurellales ord. nov. ( Nakamurellaceae ). The order Micrococcales should also be split into Micrococcales (genera Kocuria , Rothia , Micrococcus , Arthrobacter , Tropheryma , Microbacterium , Leifsonia and Clavibacter ), Cellulomonales ( Beutenbergia , Cellulomonas , Xylanimonas , Jonesia and Sanguibacter ) and Brachybacteriales ( Brachybacterium ) but the formal proposal for this will have to wait until more genomes become available for a significant proportion of strains in this order.
Published: 2014
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21. Conserved structure and domain organization among bacterial Slc26 transporters

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

22. Merkel Cell Polyomavirus Strains in Patients with Merkel Cell Carcinoma

Author: Pierre Coursaget, Christine Clavel, Emmanuelle Le Bidre, Julien Gaitan, Antoine Touzé, Gérard Lorette, Anne Durlach, François Aubin, Angélique Doussinaud, Annabel Maruani, Serge Guyétant, Plasticité de l'épithélium respiratoire dans les conditions normales et pathologiques - UMR-S 903 (PERPMP), Université de Reims Champagne-Ardenne (URCA)-Centre Hospitalier Universitaire de Reims (CHU Reims)-Institut National de la Santé et de la Recherche Médicale (INSERM)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV), Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC (EA 3181) (CEF2P / CARCINO), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Département de dermatologie, Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Hôpital Saint-Jacques-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Pathologies Respiratoires : Protéolyse et Aérosolthérapie, Université de Tours-Institut National de la Santé et de la Recherche Médicale (INSERM), Plasticité de l'épithélium respiratoire dans les conditions normales et pathologiques - UMR-S 903 ( PERPMP ), Université de Reims Champagne-Ardenne ( URCA ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne ( URCA ) -Université de Picardie Jules Verne ( UPJV ) -Université de Reims Champagne-Ardenne ( URCA ) -Université de Picardie Jules Verne ( UPJV ) -CHU de Reims - Hôpital Maison Blanche, Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC ( CEF2P / CARCINO ), Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ) -Université Bourgogne Franche-Comté ( UBFC ) -Université de Franche-Comté ( UFC ), Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ) -Hôpital Saint-Jacques-Université de Franche-Comté ( UFC ), Université de Tours-Institut National de la Santé et de la Recherche Médicale ( INSERM ), SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre Hospitalier Universitaire de Reims (CHU Reims)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Reims Champagne-Ardenne (URCA), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Université de Franche-Comté (UFC), and Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Male, MESH: Sequence Analysis, DNA, Pathology, Skin Neoplasms, MESH : Molecular Sequence Data, Epidemiology, MESH: Polyomavirus, MESH : Aged, MESH : Capsid Proteins, lcsh:Medicine, Merkel cell polyomavirus, Polymerase Chain Reaction, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, MESH: Aged, 80 and over, 0302 clinical medicine, MESH : Female, MESH : DNA, Viral, MESH : Carcinoma, Merkel Cell, Dna viral, MESH : Polymerase Chain Reaction, MESH: Capsid Proteins, Aged, 80 and over, MESH: Aged, 0303 health sciences, MESH: Middle Aged, integumentary system, biology, Merkel cell carcinoma, Dispatch, virus diseases, food and beverages, Middle Aged, MESH : Polyomavirus, 3. Good health, Neuroendocrine Carcinomas, Infectious Diseases, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Female, France, MESH : Merkel Cells, Merkel cell, Microbiology (medical), medicine.medical_specialty, virus transforming agent, MESH : Male, Molecular Sequence Data, MESH: Polyomavirus Infections, polyomavirus, [SDV.CAN]Life Sciences [q-bio]/Cancer, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, medicine, Carcinoma, Humans, lcsh:RC109-216, viruses, MESH : Middle Aged, In patient, MESH : Aged, 80 and over, MESH : France, Aged, 030304 developmental biology, Polyomavirus Infections, MESH: Molecular Sequence Data, MESH: Humans, MESH: Skin Neoplasms, lcsh:R, MESH : Skin Neoplasms, MESH : Humans, MESH: Tumor Virus Infections, MESH: Polymerase Chain Reaction, MESH: Carcinoma, Merkel Cell, Sequence Analysis, DNA, biology.organism_classification, medicine.disease, Merkel cells, MESH: Male, MESH : Polyomavirus Infections, MESH: DNA, Viral, Carcinoma, Merkel Cell, MESH: France, Tumor Virus Infections, MESH: Merkel Cells, DNA, Viral, Capsid Proteins, MESH : Tumor Virus Infections, MESH: Female, MESH : Sequence Analysis, DNA
Abstract: International audience; We investigated whether Merkel cell carcinoma (MCC) patients in France carry Merkel cell polyomavirus (MCPyV) and then identified strain variations. All frozen MCC specimens and 45% of formalin-fixed and paraffin-embedded specimens, but none of the non-MCC neuroendocrine carcinomas specimens, had MCPyV. Strains from France and the United States were similar.
Published: 2009
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23. VEB-1 in Achromobacter xylosoxidans from Cystic Fibrosis Patient, France

Author: Eliane Siebor, Carine Freby, André Pechinot, Frédéric Huet, Agathe Ogier-Desserrey, Anne Houzel, Stéphanie Perez-Martin, Jean-Marie Duez, Catherine Neuwirth, UFR des Sciences de Santé (Université de Bourgogne), Université de Bourgogne ( UB ), Laboratoire de Microbiologie Médicale et Moléculaire, Laboratoire de Bactériologie (CHU Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Humbert, Murielle, Université de Bourgogne (UB), Laboratoire de bactériologie (CHU Dijon), Plateau technique de Biologie [CHU de Dijon], Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon)-Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), and Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon)
Subjects: Male, MESH : Molecular Sequence Data, integron, MESH: beta-Lactamases, lcsh:Medicine, MESH: Base Sequence, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Integron, Cystic fibrosis, Integrons, cystic fibrosis, ComputingMilieux_MISCELLANEOUS, MESH: Microbial Sensitivity Tests, 0303 health sciences, education.field_of_study, biology, Escherichia coli Proteins, MESH : beta-Lactamases, Achromobacter denitrificans, dispatch, Achromobacter xylosoxidans, MESH: Integrons, 3. Good health, MESH : Achromobacter denitrificans, France, medicine.symptom, MESH : Integrons, MESH: Cystic Fibrosis, Adolescent, MESH : Male, Molecular Sequence Data, Population, Microbial Sensitivity Tests, beta-Lactamases, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, MESH : Adolescent, MESH : Cystic Fibrosis, medicine, Humans, Base sequence, lcsh:RC109-216, education, 030304 developmental biology, MESH: Adolescent, MESH: Humans, MESH: Molecular Sequence Data, Base Sequence, 030306 microbiology, business.industry, MESH : Humans, lcsh:R, Extended-spectrum beta-lactamase VEB-1, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Male, MESH: Achromobacter denitrificans, biology.protein, Sputum, MESH : Base Sequence, MESH : Microbial Sensitivity Tests, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, business
Abstract: Multidrug-resistant Achromobacter xylosoxidans was recovered from the sputum of a patient with cystic fibrosis. The VEB-1 extended-spectrum β-lactamase was detected on a class 1 integron. This first report of a VEB-1–producing isolate in this population requires further investigation to determine its distribution.
Published: 2006

24. Insights into bacteriophage T5 structure from analysis of its morphogenesis genes and protein components

Author: Luc Ponchon, Alexis Huet, Madalena Renouard, Cécile Breyton, Rudi Lurz, Pascale Boulanger, Fabrice Confalonieri, Alan R. Davidson, Mohamed Chami, Yvan Zivanovic, Ali Flayhan, Paulette Decottignies, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de cristallographie et RMN biologiques (LCRB - UMR 8015), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre d'études et de recherche en informatique et communications (CEDRIC), Ecole Nationale Supérieure d'Informatique pour l'Industrie et l'Entreprise (ENSIIE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire pour l'utilisation du rayonnement électromagnétique (LURE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-MENRT-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN), Institut de biochimie et biophysique moléculaire et cellulaire (IBBMC), Laboratoire de Réactivité de Surface (LRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), Institut de biologie structurale (IBS - UMR 5075), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut de génétique et microbiologie [Orsay] ( IGM ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de cristallographie et RMN biologiques ( LCRB - UMR 8015 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Centre National de la Recherche Scientifique ( CNRS ), Centre d'étude et de recherche en informatique et communications ( CEDRIC ), Ecole Nationale Supérieure d'Informatique pour l'Industrie et l'Entreprise ( ENSIIE ) -Conservatoire National des Arts et Métiers [CNAM] ( CNAM ), Institut de biologie structurale ( IBS - UMR 5075 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Université Joseph Fourier - Grenoble 1 ( UJF ), Laboratoire pour l'utilisation du rayonnement électromagnétique ( LURE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -MENRT-Centre National de la Recherche Scientifique ( CNRS ), Muséum National d'Histoire Naturelle ( MNHN ), Institut de biochimie et biophysique moléculaire et cellulaire ( IBBMC ), Laboratoire de Réactivité de Surface ( LRS ), and Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: MESH : Escherichia coli, MESH : Molecular Sequence Data, viruses, MESH: Amino Acid Sequence, Siphoviridae, Genome, chemistry.chemical_compound, MESH: Capsid, Bacteriophages, MESH : Viral Proteins, Bacteriophage T5, MESH : Siphoviridae, 0303 health sciences, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], MESH: Escherichia coli, MESH : Amino Acid Sequence, MESH : Sequence Alignment, 030302 biochemistry & molecular biology, MESH : Bacteriophages, Cell biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Capsid, Lytic cycle, MESH : Capsid, Molecular Sequence Data, Immunology, MESH: Sequence Alignment, MESH: Microscopy, Electron, Microbiology, Viral Proteins, 03 medical and health sciences, Virology, Escherichia coli, MESH: Siphoviridae, Amino Acid Sequence, MESH: Bacteriophages, Gene, 030304 developmental biology, MESH: Molecular Sequence Data, Structure and Assembly, biology.organism_classification, Molecular biology, MESH: Viral Proteins, MESH : Microscopy, Electron, Microscopy, Electron, chemistry, Cytoplasm, Insect Science, Sequence Alignment, DNA, [ SDV.BBM.BS ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract: Bacteriophage T5 represents a large family of lytic Siphoviridae infecting Gram-negative bacteria. The low-resolution structure of T5 showed the T=13 geometry of the capsid and the unusual trimeric organization of the tail tube, and the assembly pathway of the capsid was established. Although major structural proteins of T5 have been identified in these studies, most of the genes encoding the morphogenesis proteins remained to be identified. Here, we combine a proteomic analysis of T5 particles with a bioinformatic study and electron microscopic immunolocalization to assign function to the genes encoding the structural proteins, the packaging proteins, and other nonstructural components required for T5 assembly. A head maturation protease that likely accounts for the cleavage of the different capsid proteins is identified. Two other proteins involved in capsid maturation add originality to the T5 capsid assembly mechanism: the single head-to-tail joining protein, which closes the T5 capsid after DNA packaging, and the nicking endonuclease responsible for the single-strand interruptions in the T5 genome. We localize most of the tail proteins that were hitherto uncharacterized and provide a detailed description of the tail tip composition. Our findings highlight novel variations of viral assembly strategies and of virion particle architecture. They further recommend T5 for exploring phage structure and assembly and for deciphering conformational rearrangements that accompany DNA transfer from the capsid to the host cytoplasm.
Published: 2014
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25. SUN proteins belong to a novel family of β-(1,3)-glucan-modifying enzymes involved in fungal morphogenesis

Author: Christine Schmitt, Christophe d'Enfert, Audrey Nesseir, Anne Beauvais, Patrick England, Vishukumar Aimanianda, Rémi Beau, Arnaud Firon, Marie-Christine Prévost, Amandine Gastebois, Sophie Bachellier-Bassi, Jean-Paul Latgé, Isabelle Mouyna, Aspergillus, Institut Pasteur [Paris], Biologie et Pathogénicité fongiques, Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), Microscopie ultrastructurale (plate-forme), Biochimie et Biophysique des Macromolécules (Plate-forme), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This work was supported by grants from the European Commission (Galar Fungail 2, MRTN-CT-2003-504148, FINSysB, PITN-GA-2008-214004) (to C. d. E.) and the European Science Foundation (ESF) Fuminomics, Partenariat Sanofi-aventis-Aviesan (ITMO Maladies Infectieuses, Sanofi Aventis Research & Development TSU ID (SAR&D) TSU ID/Sanofi-Pasteur), and Agence Nationale de Recherches (ANR) (Grant 09-BLAN-0287) (to J. P. L.), ANR-09-BLAN-0287,REMODELE,Nouvelles voies métaboliques essentielles pour la biosynthèse de la paroi des champignons(2009), European Project: 214004,PEOPLE,FP7-PEOPLE-2007-1-1-ITN,FINSYSB(2008), Institut Pasteur [Paris] (IP), Biologie et Pathogénicité fongiques (BPF), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris], Biophysique des macromolécules et de leurs interactions, ANR Grant 09-BLAN-0287,ANR Grant 09-BLAN-0287,Grant 09-BLAN-0287, Institut National de la Recherche Agronomique (INRA) - Institut Pasteur [Paris], Microscopie ultrastructurale - Ultrapole (CITECH), Biophysique des macromolécules et leurs interactions, and Institut Pasteur [Paris] - Centre National de la Recherche Scientifique (CNRS)
Subjects: Hyphal growth, MESH : Spores, Fungal, MESH : Molecular Sequence Data, Glycosylation, MESH: Sequence Homology, Amino Acid, Conidiation, Gene Expression, Oligosaccharides, Glycobiology and Extracellular Matrices, MESH: Amino Acid Sequence, Biochemistry, Aspergillus fumigatus, Cell Wall, Gene Expression Regulation, Fungal, Candida albicans, Morphogenesis, MESH : Fungal Proteins, skin and connective tissue diseases, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 0303 health sciences, integumentary system, MESH : Amino Acid Sequence, Hydrolysis, MESH : Glycosylation, Glucan Hydrolase Activity, SUN, MESH : Protein Binding, MESH : Glycoside Hydrolases, Spores, Fungal, MESH: Glycosylation, MESH : Sequence Homology, Amino Acid, Cell biology, [SDV] Life Sciences [q-bio], Aspergillus, CELL-WALL BIOGENESIS, MOTOR-LIKE DOMAIN, ASPERGILLUS-FUMIGATUS, CANDIDA-ALBICANS, SCHIZOSACCHAROMYCES-POMBE, SACCHAROMYCES-CEREVISIAE, BIOFILM FORMATION, BETA-GLUCOSIDASE, CHITIN SYNTHASES, GENE, MESH: Fungal Proteins, MESH: Aspergillus fumigatus, MESH: Gene Expression Regulation, Fungal, MESH: Hydrolysis, Protein Binding, CAZy, MESH: Gene Expression, Hypha, MESH : Candida albicans, Glycoside Hydrolases, Molecular Sequence Data, Hyphae, MESH: Glycoproteins, Biology, Microbiology, Cell wall, Fungal Proteins, 03 medical and health sciences, MESH : Hydrolysis, MESH: Hyphae, MESH: Spores, Fungal, MESH : Gene Expression Regulation, Fungal, MESH: Glycoside Hydrolases, MESH: Protein Binding, Amino Acid Sequence, Molecular Biology, 030304 developmental biology, MESH : Protein Processing, Post-Translational, Glycoproteins, MESH: Molecular Sequence Data, Sequence Homology, Amino Acid, 030306 microbiology, MESH: Candida albicans, MESH : Oligosaccharides, Cell Biology, biology.organism_classification, MESH : Glycoproteins, [SDV.MP.MYC] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Yeast, MESH: Morphogenesis, MESH : Gene Expression, MESH : Morphogenesis, MESH : Aspergillus fumigatus, MESH: Protein Processing, Post-Translational, MESH : Hyphae, Carbohydrate-binding Protein, Protein Processing, Post-Translational, MESH: Oligosaccharides, Biogenesis
Abstract: International audience; BACKGROUND:SUN proteins are involved in yeast morphogenesis, but their function is unknown.RESULTS:SUN protein plays a role in the Aspergillus fumigatus morphogenesis. Biochemical properties of recombinant SUN proteins were elucidated.CONCLUSION:Both Candida albicans and Aspergillus fumigatus sun proteins show a β-(1,3)-glucanase activity.SIGNIFICANCE:The mode of action of SUN proteins on β-(1,3)-glucan is unique, new, and original. In yeasts, the family of SUN proteins has been involved in cell wall biogenesis. Here, we report the characterization of SUN proteins in a filamentous fungus, Aspergillus fumigatus. The function of the two A. fumigatus SUN genes was investigated by combining reverse genetics and biochemistry. During conidial swelling and mycelial growth, the expression of AfSUN1 was strongly induced, whereas the expression of AfSUN2 was not detectable. Deletion of AfSUN1 negatively affected hyphal growth and conidiation. A closer examination of the morphological defects revealed swollen hyphae, leaky tips, intrahyphal growth, and double cell wall, suggesting that, like in yeast, AfSun1p is associated with cell wall biogenesis. In contrast to AfSUN1, deletion of AfSUN2 either in the parental strain or in the AfSUN1 single mutant strain did not affect colony and hyphal morphology. Biochemical characterization of the recombinant AfSun1p and Candida albicans Sun41p showed that both proteins had a unique hydrolysis pattern: acting on β-(1,3)-oligomers from dimer up to insoluble β-(1,3)-glucan. Referring to the CAZy database, it is clear that fungal SUN proteins represent a new family of glucan hydrolases (GH132) and play an important morphogenetic role in fungal cell wall biogenesis and septation.
Published: 2013
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26. Vallitalea guaymasensis gen. nov., sp nov., isolated from marine sediment

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

Author: Claire Prigent-Combaret, Ouafa Zghidi-Abouzid, Géraldine Effantin, Philippe Lejeune, Sylvie Reverchon, William Nasser, 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), Trafic et signalisation membranaires chez les bactéries (MTSB), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Chromatine et Régulation de la Pathogénie bactérienne (CRP), 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), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-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 ), Microbiologie, adaptation et pathogénie ( MAP ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), and Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: MESH : Operator Regions, Genetic, Operator Regions, Genetic, MESH : Molecular Sequence Data, MESH : Operon, MESH : Solanum tuberosum, MESH: Base Sequence, MESH: Virulence, Chicory, MESH: Plant Diseases, Genes, Reporter, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, MESH: Cellulose, MESH: Gene Expression Regulation, Bacterial, Virulence, MESH : Plant Diseases, MESH : Virulence, MESH : beta-Galactosidase, MESH : Enterobacteriaceae, MESH : Genes, Reporter, MESH: beta-Galactosidase, MESH : Biofilms, MESH: Repressor Proteins, MESH: Transcription Initiation Site, Transcription Initiation Site, MESH : Repressor Proteins, MESH : Gene Expression Regulation, Bacterial, MESH: Operon, Molecular Sequence Data, MESH: Biofilms, MESH: Solanum tuberosum, MESH: Artificial Gene Fusion, MESH: Enterobacteriaceae, Enterobacteriaceae, Operon, Cellulose, Plant Diseases, Solanum tuberosum, MESH: Molecular Sequence Data, Base Sequence, MESH : Cellulose, MESH: Genes, Reporter, Gene Expression Regulation, Bacterial, beta-Galactosidase, Artificial Gene Fusion, MESH : Chicory, Repressor Proteins, MESH : Artificial Gene Fusion, MESH : Transcription Initiation Site, MESH: Operator Regions, Genetic, Biofilms, MESH: Chicory, MESH : Base Sequence, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Bacteria use biofilm structures to colonize surfaces and to survive in hostile conditions, and numerous bacteria produce cellulose as a biofilm matrix polymer. Hence, expression of the bcs operon, responsible for cellulose biosynthesis, must be finely regulated in order to allow bacteria to adopt the proper surface-associated behaviours. Here we show that in the phytopathogenic bacterium, Dickeya dadantii, production of cellulose is required for pellicle-biofilm formation and resistance to chlorine treatments. Expression of the bcs operon is growth phase-regulated and is stimulated in biofilms. Furthermore, we unexpectedly found that the nucleoid-associated protein and global regulator of virulence functions, Fis, directly represses bcs operon expression by interacting with an operator that is absent from the bcs operon of animal pathogenic bacteria and the plant pathogenic bacterium Pectobacterium. Moreover, production of cellulose enhances plant surface colonization by D. dadantii. Overall, these data suggest that cellulose production and biofilm formation may be important factors for surface colonization by D. dadantii and its subsequent survival in hostile environments. This report also presents a new example of how bacteria can modulate the action of a global regulator to co-ordinate basic metabolism, virulence and modifications of lifestyle.
Published: 2012

28. Three cases of post-cataract surgery endophthalmitis due to Rhizobium (Agrobacterium) radiobacter

Author: Pierre Loïc Cornut, Max Maurin, Sandrine Boisset, Viviane Moreau-Gaudry, Yvonne Benito, Alain M. Bron, Christophe Chiquet, Jacques Croize, François Vandenesch, Department of Ophtalmology, CHU Grenoble, Université Joseph Fourier - Grenoble 1 (UJF), Laboratoire de Bactériologie, Hospices Civils de Lyon (HCL), Centre National de référence des Staphylocoques, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL), CHU Dijon, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-CHU Grenoble, Université Joseph Fourier - Grenoble 1 ( UJF ), Hospices Civils de Lyon ( HCL ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Hospices Civils de Lyon ( HCL ), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), and Université Joseph Fourier - Grenoble 1 ( UJF ) -CHU Grenoble
Subjects: Male, MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, genetic structures, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, medicine.medical_treatment, MESH : Aged, Vitrectomy, Case Reports, MESH : Gram-Negative Bacterial Infections, MESH: Molecular Diagnostic Techniques, 0302 clinical medicine, Endophthalmitis, MESH: Aged, 80 and over, RNA, Ribosomal, 16S, 80 and over, MESH: Gram-Negative Bacterial Infections, MESH : Female, Aged, 80 and over, MESH: Aged, 0303 health sciences, MESH: Cataract Extraction, MESH: Agrobacterium tumefaciens, Bacterial, 3. Good health, MESH: RNA, Ribosomal, 16S, RNA, Bacterial, MESH : Agrobacterium tumefaciens, medicine.anatomical_structure, Molecular Diagnostic Techniques, Rhizobium, Female, MESH: RNA, Bacterial, Sequence Analysis, Bacterial dna, Microbiology (medical), Pars plana, MESH : Cataract Extraction, 16S, medicine.medical_specialty, MESH : Male, Molecular Sequence Data, MESH : Endophthalmitis, Cataract Extraction, Biology, 03 medical and health sciences, medicine, Humans, MESH: Endophthalmitis, MESH : Aged, 80 and over, Aged, Ribosomal, MESH: Molecular Sequence Data, MESH: Humans, Gram-negative bacterial infections, 030306 microbiology, MESH : Humans, Sequence Analysis, DNA, DNA, MESH : RNA, Bacterial, Cataract surgery, biology.organism_classification, medicine.disease, eye diseases, MESH: Male, Surgery, MESH : RNA, Ribosomal, 16S, Agrobacterium tumefaciens, 030221 ophthalmology & optometry, RNA, sense organs, Gram-Negative Bacterial Infections, MESH: Female, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, MESH : Molecular Diagnostic Techniques, MESH : Sequence Analysis, DNA, Agrobacterium radiobacter
Abstract: We present three unrelated post-cataract surgery endophthalmitis cases caused by Rhizobium radiobacter , hospitalized in three different hospitals. Early diagnosis was obtained in two cases by bacterial DNA detection in vitreous samples. All patients recovered from infection, but pars plana vitrectomy was needed in two patients due to rapid clinical deterioration.
Published: 2012
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29. Betaproteobacteria dominance and diversity shifts in the bacterial community of a PAH-contaminated soil exposed to phenanthrene

Author: Yves Jouanneau, Florence Martin, Denis Le Paslier, Agnès Barbance, Fabrice Martin-Laurent, David Bru, Roberto A. Geremia, Stéphane Torelli, Gérard Blake, Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Département de Chimie Moléculaire (DCM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Joseph Fourier - Grenoble 1 (UJF), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Laboratoire Optimisation de la Conception et Ingénierie de l'Environnement (LOCIE), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie et Biologie des Métaux ( LCBM - UMR 5249 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Département de Chimie Moléculaire ( DCM ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire d'Ecologie Alpine ( LECA ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Optimisation de la Conception et Ingénierie de l'Environnement ( LOCIE ), Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)
Subjects: phenanthrene, MESH : Molecular Sequence Data, Health, Toxicology and Mutagenesis, Stable-isotope probing, 010501 environmental sciences, Toxicology, 01 natural sciences, MESH: Biodegradation, Environmental, 16S rRNA sequences, MESH : Soil Pollutants, chemistry.chemical_compound, [ SDV.BBM.BC ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Hydrogenophaga, MESH : Biodiversity, Soil Pollutants, PAH degradation, Polycyclic Aromatic Hydrocarbons, MESH: Betaproteobacteria, MESH: Phylogeny, stable isotope probing, Betaproteobacteria, Phylogeny, Soil Microbiology, MESH : Betaproteobacteria, 0303 health sciences, education.field_of_study, biology, Chemistry, General Medicine, Biodiversity, Pollution, Soil contamination, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Biodegradation, Environmental, Environmental chemistry, Soil microbiology, Population, Molecular Sequence Data, MESH : Biodegradation, Environmental, MESH : Soil Microbiology, betaproteobacteria, MESH: Biodiversity, 03 medical and health sciences, MESH: Polycyclic Hydrocarbons, Aromatic, Rhodoferax, MESH: Phenanthrenes, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], education, MESH : Phenanthrenes, 030304 developmental biology, 0105 earth and related environmental sciences, MESH: Soil Pollutants, MESH: Molecular Sequence Data, MESH : Phylogeny, Phenanthrene, Phenanthrenes, biology.organism_classification, MESH : Polycyclic Hydrocarbons, Aromatic, MESH: Soil Microbiology, 13. Climate action
Abstract: International audience; In this study, the PAH-degrading bacteria of a constructed wetland collecting road runoff has been studied through DNA stable isotope probing. Microcosms were spiked with (13)C-phenanthrene at 34 or 337 ppm, and bacterial diversity was monitored over a 14-day period. At 337 ppm, PAH degraders became dominated after 5 days by Betaproteobacteria, including novel Acidovorax, Rhodoferax and Hydrogenophaga members, and unknown bacteria related to Rhodocyclaceae. The prevalence of Betaproteobacteria was further demonstrated by phylum-specific quantitative PCR, and was correlated with a burst of phenanthrene mineralization. Striking shifts in the population of degraders were observed after most of the phenanthrene had been removed. Soil exposed to 34 ppm phenanthrene showed a similar population of degraders, albeit only after 14 days. Results demonstrate that specific Betaproteobacteria are involved in the main response to soil PAH contamination, and illustrate the potential of SIP approaches to investigate PAH biodegradation in soil.
Published: 2012
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30. Ex vivo and in vivo inhibition of human rhinovirus replication by a new pseudosubstrate of viral 2A protease

Author: Fatma Berri, Bruno Lina, Didier Decimo, Jean-Claude Cortay, Sébastien Violot, Isabelle Schuffenecker, Béatrice Riteau, Florence Morfin, Théophile Ohlmann, Marie-Laure Foucault-Grunenwald, Nisrine Falah, Virologie et pathologie humaine (VirPath), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Virologie humaine, École normale supérieure - Lyon (ENS Lyon)-IFR128-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Biologie et Pathologie Est, Bron, Laboratory of Virology East, Hospices Civils de Lyon (HCL), Microbiologie moléculaire et biochimie structurale / Molecular Microbiology and Structural Biochemistry (MMSB), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), National Reference Center of Enteroviruses, Institut de Veille Sanitaire, Agence Nationale de la Recherche (ANR), Virologie et pathologie humaine ( VirPath ), Université Claude Bernard Lyon 1 ( UCBL ), Laboratoire de physiologie cellulaire végétale ( LPCV ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut National de la Recherche Agronomique ( INRA ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), École normale supérieure - Lyon ( ENS Lyon ) -IFR128-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Hospices Civils de Lyon ( HCL ), École normale supérieure de Lyon (ENS de Lyon)-IFR128-Institut National de la Santé et de la Recherche Médicale (INSERM), and Centre de Biologie et Pathologie Est [Bron] (CBPE)
Subjects: MESH : Molecular Sequence Data, Rhinovirus, AIRWAY INFLAMMATION, medicine.medical_treatment, [SDV]Life Sciences [q-bio], Peptide, POLIOVIRUS, MESH: Amino Acid Sequence, medicine.disease_cause, Virus Replication, MESH: Down-Regulation, Substrate Specificity, MESH : Down-Regulation, Mice, MESH: Picornaviridae Infections, MESH : Female, MESH: Animals, MESH : Viral Proteins, Peptide sequence, chemistry.chemical_classification, MESH : Picornaviridae Infections, 0303 health sciences, Mice, Inbred BALB C, MESH: Rhinovirus, MESH : Substrate Specificity, MESH : Peptides, MESH: Peptides, MESH : Amino Acid Sequence, MESH : Sequence Alignment, 030302 biochemistry & molecular biology, MESH : Protein Binding, PEPTIDES, Cysteine protease, 3. Good health, MESH : Rhinovirus, MESH : Virus Replication, Cysteine Endopeptidases, INFECTIONS, MESH : Cysteine Endopeptidases, Female, Protein Binding, Immunology, Molecular Sequence Data, MESH: Mice, Inbred BALB C, MESH: Sequence Alignment, Down-Regulation, Biology, Microbiology, 03 medical and health sciences, Viral Proteins, In vivo, Virology, Vaccines and Antiviral Agents, MESH : Mice, medicine, Animals, Humans, MESH: Protein Binding, Amino Acid Sequence, MESH: Mice, MESH : Mice, Inbred BALB C, 030304 developmental biology, Protease, Picornaviridae Infections, MESH: Humans, MESH: Molecular Sequence Data, [ SDV ] Life Sciences [q-bio], STABILITY, CLEAVAGE, PROTEINASES, MESH : Humans, COXSACKIEVIRUS, MESH: Virus Replication, MESH: Viral Proteins, Viral replication, chemistry, Insect Science, RNA, MESH: Substrate Specificity, MESH : Animals, TRANSLATION, Sequence Alignment, MESH: Female, Ex vivo, MESH: Cysteine Endopeptidases
Abstract: Human rhinoviruses (HRVs) remain a significant public health problem as they are the major cause of both upper and lower respiratory tract infections. Unfortunately, to date no vaccine or antiviral against these pathogens is available. Here, using a high-throughput yeast two-hybrid screening, we identified a 6-amino-acid hit peptide, LVLQTM, which acted as a pseudosubstrate of the viral 2A cysteine protease (2A pro ) and inhibited its activity. This peptide was chemically modified with a reactive electrophilic fluoromethylketone group to form a covalent linkage with the nucleophilic active-site thiol of the enzyme. Ex vivo and in vivo experiments showed that thus converted, LVLQTM was a strong inhibitor of HRV replication in both A549 cells and mice. To our knowledge, this is the first report validating a compound against HRV infection in a mouse model.
Published: 2012
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31. Autoimmune mediated regulation of ovarian tumor growth

Author: Vincent K. Tuohy, Cengiz Z. Altuntas, Ritika Jaini, Daniel Jane-wit, Pavani Kesaraju, Christopher A. Flask, Jean Yves Picard, Martin Dutertre, Kelly K Covey, Justin M. Johnson, Lerner Research Institute, Cleveland Clinic, Equipe 7, 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), Endocrinologie et Génétique de la Reproduction et du Développement, Université Paris-Sud - Paris 11 (UP11)-IFR13-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche en Cancérologie de Lyon ( CRCL ), Université Claude Bernard Lyon 1 ( UCBL ), 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 ) -Université Claude Bernard Lyon 1 ( UCBL ), 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 ), and Université Paris-Sud - Paris 11 ( UP11 ) -IFR13-Institut National de la Santé et de la Recherche Médicale ( INSERM )
Subjects: MESH : Molecular Sequence Data, endocrine system diseases, Autoimmunity, MESH: Amino Acid Sequence, medicine.disease_cause, HER2/neu, MESH: Cancer Vaccines, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, Ovarian tumor, Mice, 0302 clinical medicine, MESH: Autoimmune Diseases, MESH : Autoimmunity, MESH : Female, MESH: Animals, MESH: Peptide Fragments, Ovarian Neoplasms, 0303 health sciences, biology, MESH : Amino Acid Sequence, MESH : Cancer Vaccines, Obstetrics and Gynecology, Anti-Müllerian hormone, MESH : Mice, Transgenic, female genital diseases and pregnancy complications, 3. Good health, Premature ovarian failure, MESH: Ovarian Neoplasms, medicine.anatomical_structure, Oncology, 030220 oncology & carcinogenesis, MESH: Cell Growth Processes, Female, endocrine system, MESH: Mice, Transgenic, Molecular Sequence Data, Ovary, Mice, Transgenic, [SDV.CAN]Life Sciences [q-bio]/Cancer, Cell Growth Processes, MESH : Mice, Inbred C57BL, Cancer Vaccines, Article, Autoimmune Diseases, 03 medical and health sciences, Immune system, MESH : Autoimmune Diseases, MESH: Mice, Inbred C57BL, MESH : Mice, MESH: Autoimmunity, medicine, Animals, Humans, Inhibins, Amino Acid Sequence, MESH: Mice, 030304 developmental biology, MESH: Molecular Sequence Data, MESH: Humans, MESH : Inhibins, business.industry, MESH : Ovarian Neoplasms, MESH : Peptide Fragments, MESH : Humans, MESH: Inhibins, medicine.disease, MESH : Disease Models, Animal, Peptide Fragments, Mice, Inbred C57BL, Disease Models, Animal, MESH : Cell Growth Processes, Immunology, biology.protein, Cancer vaccine, MESH : Animals, MESH: Disease Models, Animal, business, MESH: Female
Abstract: International audience; OBJECTIVES: An immune response sufficient to induce organ failure may provide protection and therapy against tumors derived from the targeted organ particularly when removal or ablation of the organ is part of the standard therapy and does not threaten survival. We have previously shown that a targeted immune response directed against the ovarian-specific protein, inhibin-α, causes ovarian failure. Here we determined whether inhibin-α autoimmunity is effective in both prevention and treatment of ovarian tumors. METHODS: A transgene consisting of the SV40 large tumor transformation antigen under the regulation of an anti-Mullerian hormone promoter (AMH-SV40Tag) was transferred by backcrossing for 12 generations to SJL/J mice producing SJL.AMH-SV40Tag (H-2(s)) females that develop a high incidence of autochthonous granulosa cell tumors. We determined whether immunization of SJL.AMH-SV40Tag female mice with the IA(s)-restricted p215-234 peptide of mouse inhibin-α was capable of preventing and treating these ovarian tumors. RESULTS: The growth of autochthonous ovarian granulosa cell tumors in SJL.AMH-SV40Tag transgenic mice was significantly inhibited in mice immunized with Inα 215-234. In addition, significant inhibition of tumor growth occurred when mice with established ovarian granulosa cell tumors were therapeutically vaccinated with Inα 215-234. CONCLUSIONS: Our results indicate that induction of ovarian-specific autoimmunity may serve as an effective way to prevent the emergence of autochthonous ovarian tumors and control the growth of established ovarian malignancies.
Published: 2012
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32. Desulfovibrio piezophilus sp. nov., a piezophilic, sulfate-reducing bacterium isolated from wood falls in the Mediterranean Sea

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

Author: Rabhi, Makhlouf, Espéli, Olivier, Schwartz, Annie, Cayrol, Bastien, Rahmouni, a Rachid, Arluison, Véronique, Boudvillain, Marc, Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire Bioénergétique Membranaire et Stress (LBMS), Département Biochimie, Biophysique et Biologie Structurale (B3S), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre de biophysique moléculaire ( CBM ), Université d'Orléans ( UO ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Bioénergétique, Métalloprotéines et Stress ( LBMS ), Département Biochimie, Biophysique et Biologie Structurale ( B3S ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), and Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH : Escherichia coli, MESH : Molecular Sequence Data, Transcription, Genetic, MESH : Transcription Factors, MESH: Peptide Elongation Factors, Molecular Sequence Data, Electrophoretic Mobility Shift Assay, MESH: Terminator Regions, Genetic, MESH: Escherichia coli Proteins, MESH: Host Factor 1 Protein, Host Factor 1 Protein, MESH: Base Sequence, Article, Escherichia coli, MESH: Adenosine Triphosphatases, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Peptide Elongation Factors, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Adenosine Triphosphatases, Terminator Regions, Genetic, MESH: Gene Expression Regulation, Bacterial, MESH: Molecular Sequence Data, Base Sequence, MESH : Adenosine Triphosphatases, MESH : Terminator Regions, Genetic, MESH: RNA Helicases, MESH: Escherichia coli, Escherichia coli Proteins, MESH : Escherichia coli Proteins, MESH: Transcription, Genetic, MESH : Host Factor 1 Protein, MESH : Molecular Chaperones, MESH : Transcription, Genetic, Gene Expression Regulation, Bacterial, MESH: Transcription Factors, MESH : RNA, Bacterial, Peptide Elongation Factors, MESH : RNA Helicases, RNA, Bacterial, MESH : Electrophoretic Mobility Shift Assay, MESH: Electrophoretic Mobility Shift Assay, MESH : Base Sequence, MESH: Molecular Chaperones, MESH: RNA, Bacterial, RNA Helicases, Molecular Chaperones, Transcription Factors, MESH : Gene Expression Regulation, Bacterial
Abstract: International audience; In Escherichia coli, the essential motor protein Rho promotes transcription termination in a tightly controlled manner that is not fully understood. Here, we show that the general post-transcriptional regulatory protein Hfq associates with Rho to regulate Rho function. The Hfq:Rho complex can be further stabilized by RNA bridging both factors in a configuration that inhibits the ATP hydrolysis and duplex unwinding activities of Rho and that mediates transcription antitermination at Rho-dependent terminators in vitro and in vivo. Antitermination at a prototypical terminator (λtR1) requires Hfq binding to an A/U-rich transcript region directly upstream from the terminator. Antitermination is modulated by trans-acting factors (NusG or nucleic acid competitors) that affect Hfq association with Rho or RNA. These data unveil a new Hfq function and a novel transcription regulatory mechanism with potentially important implications for bacterial RNA metabolism, gene silencing, and pathogenicity.
Published: 2011
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34. The glutaredoxin ATGRXS13 is required to facilitate Botrytis cinerea infection of Arabidopsis thaliana plants

Author: La Camera, Sylvain, L'Haridon, Floriane, Astier, Jérémy, Zander, Mark, Abou-Mansour, Eliane, Page, Gonzague, Thurow, Corinna, Wendehenne, David, Gatz, Christiane, Métraux, Jean-Pierre, Lamotte, Olivier, PhyMoTS, Laboratoire de catalyse en chimie organique (LACCO), Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers, Plante - microbe - environnement : biochimie, biologie cellulaire et écologie (PMEBBCE), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Management et Relations internationales, ESG, Catalyse en chimie organique ( LACCO ), Université de Poitiers-Centre National de la Recherche Scientifique ( CNRS ) -Université de Poitiers-Centre National de la Recherche Scientifique ( CNRS ), Plante - microbe - environnement : biochimie, biologie cellulaire et écologie ( PMEBBCE ), Etablissement National d'Enseignement Supérieur Agronomique de Dijon ( ENESAD ) -Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Equipe Physiologie Moléculaire du Transport de Sucres (PhyMoTS), Université de Poitiers-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)
Subjects: MESH: Signal Transduction, MESH : Molecular Sequence Data, MESH : Transcription Factors, Arabidopsis, MESH : Alternative Splicing, MESH: Amino Acid Sequence, MESH: RNA, Plant, MESH : Arabidopsis Proteins, necrotrophic pathogen, MESH : Arabidopsis, MESH: Plant Diseases, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Gene Expression Regulation, Plant, MESH: Arabidopsis, Cloning, Molecular, Disease Resistance, Oligonucleotide Array Sequence Analysis, MESH : Amino Acid Sequence, MESH : Plant Diseases, MESH: Alternative Splicing, MESH : Oxylipins, food and beverages, MESH : Glutaredoxins, MESH: Transcription Factors, MESH : Oligonucleotide Array Sequence Analysis, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, RNA, Plant, MESH: Salicylic Acid, Botrytis, botrytis cinerea, Salicylic Acid, Signal Transduction, MESH : Botrytis, MESH : Cloning, Molecular, MESH: Oxylipins, MESH: Glutaredoxins, Molecular Sequence Data, MESH: Disease Resistance, MESH: Arabidopsis Proteins, Cyclopentanes, MESH: Botrytis, MESH : Disease Resistance, MESH: Cloning, Molecular, Amino Acid Sequence, Oxylipins, MESH: Gene Expression Regulation, Plant, Glutaredoxins, Plant Diseases, MESH : Signal Transduction, MESH : Mutagenesis, Insertional, MESH: Molecular Sequence Data, MESH : RNA, Plant, MESH : Salicylic Acid, Arabidopsis Proteins, jasmonic acid, fungi, glutaredoxin, Alternative Splicing, Mutagenesis, Insertional, MESH: Mutagenesis, Insertional, MESH: Oligonucleotide Array Sequence Analysis, MESH: Cyclopentanes, MESH : Cyclopentanes, MESH : Gene Expression Regulation, Plant, Transcription Factors
Abstract: International audience; Botrytis cinerea is a major pre- and post-harvest necrotrophic pathogen with a broad host range that causes substantial crop losses. The plant hormone jasmonic acid (JA) is involved in the basal resistance against this fungus. Despite basal resistance, virulent strains of B. cinerea can cause disease on Arabidopsis thaliana and virulent pathogens can interfere with the metabolism of the host in a way to facilitate infection of the plant. However, plant genes that are required by the pathogen for infection remain poorly described. To find such genes, we have compared the changes in gene expression induced in A. thaliana by JA with those induced after B. cinerea using genome-wide microarrays. We have identified genes that are repressed by JA but that are induced by B. cinerea. In this study, we describe one candidate gene, ATGRXS13, that encodes for a putative glutaredoxin and that exhibits such a crossed expression. In plants that are infected by this necrotrophic fungus, ATGRXS13 expression was negatively controlled by JA and TGA transcription factors but also through a JA-salicylic acid (SA) cross-talk mechanism as B. cinerea induced SA production that positively controlled ATGRXS13 expression. Furthermore, plants impaired in ATGRXS13 exhibited resistance to B. cinerea. Finally, we present a model whereby B. cinerea takes advantage of defence signalling pathways of the plant to help the colonization of its host.
Published: 2011
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35. A phosphorylation cycle shapes gradients of the DYRK family kinase Pom1 at the plasma membrane

Author: Kyriakos Kokkoris, Vincent Vincenzetti, Josselin Moosbrugger, Olivier Hachet, Sophie G. Martin, Martine Berthelot-Grosjean, Université de Lausanne, Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Université de Lausanne (UNIL), Centre National de la Recherche Scientifique (CNRS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), and Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS )
Subjects: MESH : Molecular Sequence Data, [SDV]Life Sciences [q-bio], Cell, MESH: Cell Cycle, MESH: Amino Acid Sequence, Amino Acid Sequence, Cell Cycle, Cell Membrane/metabolism, Microtubule-Associated Proteins/metabolism, Molecular Sequence Data, Phosphorylation, Protein Kinases/chemistry, Protein Kinases/metabolism, Schizosaccharomyces/cytology, Schizosaccharomyces/metabolism, Schizosaccharomyces pombe Proteins/metabolism, Sequence Alignment, MESH : Phosphorylation, 0302 clinical medicine, 0303 health sciences, Kinase, MESH : Amino Acid Sequence, MESH : Sequence Alignment, Cortical gradient, MESH : Schizosaccharomyces pombe Proteins, Fission yeast, Cell biology, medicine.anatomical_structure, MESH: Schizosaccharomyces, Pom1, Microtubule-Associated Proteins, MESH : Cell Membrane, MESH: Sequence Alignment, MESH : Protein Kinases, Biology, General Biochemistry, Genetics and Molecular Biology, Dephosphorylation, 03 medical and health sciences, Microtubule, MESH : Cell Cycle, Schizosaccharomyces, Cell cortex, medicine, Mitosis, MESH: Protein Kinases, 030304 developmental biology, MESH: Molecular Sequence Data, [ SDV ] Life Sciences [q-bio], Phosphorylation cycle, MESH: Phosphorylation, Biochemistry, Genetics and Molecular Biology(all), Cell Membrane, MESH: Schizosaccharomyces pombe Proteins, MESH: Microtubule-Associated Proteins, MESH : Schizosaccharomyces, MESH : Microtubule-Associated Proteins, Schizosaccharomyces pombe Proteins, DYRK family kinase, Protein Kinases, 030217 neurology & neurosurgery, MESH: Cell Membrane
Abstract: http://linkinghub.elsevier.com/; International audience; Concentration gradients regulate many cell biological and developmental processes. In rod-shaped fission yeast cells, polar cortical gradients of the DYRK family kinase Pom1 couple cell length with mitotic commitment by inhibiting a mitotic inducer positioned at midcell. However, how Pom1 gradients are established is unknown. Here, we show that Tea4, which is normally deposited at cell tips by microtubules, is both necessary and, upon ectopic cortical localization, sufficient to recruit Pom1 to the cell cortex. Pom1 then moves laterally at the plasma membrane, which it binds through a basic region exhibiting direct lipid interaction. Pom1 autophosphorylates in this region to lower lipid affinity and promote membrane release. Tea4 triggers Pom1 plasma membrane association by promoting its dephosphorylation through the protein phosphatase 1 Dis2. We propose that local dephosphorylation induces Pom1 membrane association and nucleates a gradient shaped by the opposing actions of lateral diffusion and autophosphorylation-dependent membrane detachment.
Published: 2011
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36. Spectrum of mutations in Gitelman syndrome

Author: Annabelle Venisse, Diana Kahila, Claire Rigothier, Bernard Grisart, Bruno Moulin, Marie-Christine Vantyghem, Ivan Tack, Anne-Paule Gimenez-Roqueplo, Franck Bridoux, Jean-Philippe Haymann, Olivier Devuyst, Hubert Nivet, Rosa Vargas-Poussou, Laurence Dubourg, Eva Riveira-Munoz, Anne Blanchard, Karin Dahan, Michel Godin, Pascal Houillier, Huguette Debaix, Bertrand Dussol, Robert J. Unwin, Xavier Jeunemaitre, Service de néphrologie - hémodialyse et transplantation rénale, Université de Poitiers-Centre hospitalier universitaire de Poitiers ( CHU Poitiers ), Contrôle de la Réponse Immune B et des Lymphoproliférations ( CRIBL ), Université de Limoges ( UNILIM ) -Génomique, Environnement, Immunité, Santé, Thérapeutique ( GEIST FR CNRS 3503 ) -Centre National de la Recherche Scientifique ( CNRS ), Institute of Physiology, University of Zürich [Zürich] ( UZH ) -Zurich Center for Integrative Human Physiology, Klinik für Nephrologie, UniversitätsSpital, Division of Nephrology, UCL Medical School, Paris-Centre de Recherche Cardiovasculaire ( PARCC - U970 ), Hôpital Européen Georges Pompidou [APHP] ( HEGP ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université Paris Descartes - Paris 5 ( UPD5 ), Hôpital Européen Georges Pompidou [APHP] ( HEGP ), Centre hospitalier universitaire de Poitiers (CHU Poitiers), Contrôle de la Réponse Immune B et des Lymphoproliférations (CRIBL), Université de Limoges (UNILIM)-Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST FR CNRS 3503)-Centre National de la Recherche Scientifique (CNRS), University of Zürich [Zürich] (UZH)-Zurich Center for Integrative Human Physiology, Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Université Paris Descartes - Paris 5 (UPD5)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5), Hôpital Européen Georges Pompidou [APHP] (HEGP), Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Universität Zürich [Zürich] = University of Zurich (UZH)-Zurich Center for Integrative Human Physiology, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Européen Georges Pompidou [APHP] (HEGP), and Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)
Subjects: Male, MESH : Molecular Sequence Data, MESH : Retrospective Studies, Receptors, Drug, Gene Dosage, 030232 urology & nephrology, MESH: Base Sequence, MESH : Child, Preschool, medicine.disease_cause, MESH: Gitelman Syndrome, MESH: Gene Dosage, MESH : Chloride Channels, 0302 clinical medicine, MESH : Child, MESH: Child, Missense mutation, [ SDV.IMM ] Life Sciences [q-bio]/Immunology, Solute Carrier Family 12, Member 3, MESH : Female, MESH : Gene Dosage, Child, Gene Rearrangement, Genetics, 0303 health sciences, Mutation, MESH: Middle Aged, Symporters, MESH: Genetic Testing, MESH: Genetic Predisposition to Disease, General Medicine, Middle Aged, MESH : Adult, 3. Good health, Nephrology, MESH: Young Adult, Child, Preschool, MESH : Symporters, MESH: Solute Carrier Family 12, Member 3, MESH : Gitelman Syndrome, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, MESH : Mutation, MESH : Sensitivity and Specificity, Gitelman Syndrome, Adult, MESH: Symporters, MESH: Mutation, Adolescent, MESH: Gene Rearrangement, MESH : Male, Molecular Sequence Data, Non-allelic homologous recombination, MESH : Young Adult, MESH : Solute Carrier Family 12, Member 3, Biology, Sensitivity and Specificity, Gene dosage, Young Adult, 03 medical and health sciences, Chloride Channels, MESH: Receptors, Drug, MESH : Adolescent, MESH : Genetic Testing, medicine, Humans, Genetic Predisposition to Disease, MESH : Middle Aged, Genetic Testing, Multiplex ligation-dependent probe amplification, Allele, Alleles, Retrospective Studies, 030304 developmental biology, MESH: Adolescent, MESH: Humans, MESH: Molecular Sequence Data, Base Sequence, MESH : Receptors, Drug, MESH: Alleles, MESH: Child, Preschool, MESH: Chloride Channels, MESH : Humans, MESH: Adult, MESH: Retrospective Studies, Gene rearrangement, MESH : Gene Rearrangement, Gitelman syndrome, medicine.disease, MESH: Male, MESH: Sensitivity and Specificity, Basic Research, MESH : Genetic Predisposition to Disease, MESH : Base Sequence, MESH : Alleles, MESH: Female
Abstract: International audience; Gitelman's syndrome (GS) is a rare, autosomal recessive, salt-losing tubulopathy caused by mutations in the SLC12A3 gene, which encodes the thiazide-sensitive NaCl cotransporter (NCC). Because 18 to 40% of suspected GS patients carry only one SLC12A3 mutant allele, large genomic rearrangements may account for unidentified mutations. Here, we directly sequenced genomic DNA from a large cohort of 448 unrelated patients suspected of having GS. We found 172 distinct mutations, of which 100 were unreported previously. In 315 patients (70%), we identified two mutations; in 81 patients (18%), we identified one; and in 52 patients (12%), we did not detect a mutation. In 88 patients, we performed a search for large rearrangements by multiplex ligation-dependent probe amplification (MLPA) and found nine deletions and two duplications in 24 of the 51 heterozygous patients. A second technique confirmed each rearrangement. Based on the breakpoints of seven deletions, nonallelic homologous recombination by Alu sequences and nonhomologous end-joining probably favor these intragenic deletions. In summary, missense mutations account for approximately 59% of the mutations in Gitelman's syndrome, and there is a predisposition to large rearrangements (6% of our cases) caused by the presence of repeated sequences within the SLC12A3 gene.
Published: 2011
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37. Caldicoprobacter algeriensis sp. nov. a new thermophilic anaerobic, xylanolytic bacterium isolated from an Algerian hot spring

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

Author: Slobodan Culina, Vedran Brezar, Thomas Osterbye, Yann Verdier, Giovanni Chiappetta, F. Susan Wong, Joëlle Vinh, Roberto Mallone, Søren Buus, François Guillonneau, VINH, Joëlle, Immunologie et génétique du diabète de type 1, génétique multifactorielle en endocrinologie pédiatrique (U986), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratory of Experimental Immunology [Copenhagen], Department of Immunology and Microbiology [Copenhagen], Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Plateforme protéomique 3P5 [Institut Cochin] (3P5), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Spectrométrie de Masse Biologique et Protéomique (USR3149 / FRE2032) (SMBP), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Centre for Endocrine and Diabetes Sciences, Cardiff University, This research was supported by the Juvenile Diabetes Research Foundation (JDRF grant 1-2008-106), the European Foundation for the Study ofDiabetes (EFSD/JDRF/Novo Nordisk European Programme in Type 1 Diabetes Research 2007) and the Domaine d’Inte´reˆt Majeur: Cardiovasculaire – Obe´site´ –Diabe`te (Ile-de-France CODDIM), Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris Descartes - Paris 5 (UPD5), Institut des Maladies Emergentes et des Thérapies Innovantes (IMETI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Verdier, Yann, Physiopathologie et immunothérapies dans l’infection VIH, GHU A. Chenevier - Henri Mondor (Inserm U955, équipe 16), Neurobiologie et diversité cellulaire (NDC), Benaroya Research Institute at Virginia Mason and Department of Immunology, University of Washington School of Medicine, Service de diabétologie [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], CHU Cochin [AP-HP], Université Paris Descartes - Paris 5 ( UPD5 ), Institut des Maladies Emergentes et des Thérapies Innovantes ( IMETI ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Laboratory of Experimental Immunology, University of Copenhagen ( KU ), Plateforme protéomique 3P5 [Institut Cochin] ( 3P5 ), 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 ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Unité de Spectrométrie de Masse Biologique et Protéomique, ESPCI ParisTech-Centre National de la Recherche Scientifique ( CNRS ), CNRS/ESPCI ParisTech USR 3149, Centre National de la Recherche Scientifique ( CNRS ), Department of Cellular and Molecular Medicine, University of Bristol, University Walk, Faculty of Health Sciences-University of Copenhagen ( KU ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique (CNRS)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)
Subjects: Proteomics, Mouse, MESH: Mice, Inbred NOD, MESH: Sequence Analysis, Protein, Autoimmunity, Peptide, MESH: Amino Acid Sequence, MESH : Glucose-6-Phosphatase, CD8-Positive T-Lymphocytes, Mass Spectrometry, Epitope, MESH : Proteins, Mice, 0302 clinical medicine, Mice, Inbred NOD, Sequence Analysis, Protein, MESH: Animals, MESH: Proteins, Immune Response, Peptide sequence, chemistry.chemical_classification, 0303 health sciences, MESH : Peptides, MESH: Peptides, MESH : Amino Acid Sequence, MESH: CD8-Positive T-Lymphocytes, 3. Good health, MESH: Reproducibility of Results, [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Glucose-6-Phosphatase, Medicine, endocrine system, [SDV.IMM] Life Sciences [q-bio]/Immunology, Immune Cells, Science, Molecular Sequence Data, Immunology, Endocrine System, Immunodominance, Mass spectrometry, Immune Activation, Interferon-gamma, Islets of Langerhans, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, MESH : Islets of Langerhans, Amino Acid Sequence, Biology, MESH: Mass Spectrometry, MESH: Humans, MESH: Molecular Sequence Data, MESH : Mice, Inbred NOD, MESH : Reproducibility of Results, MESH: Islets of Langerhans, MESH : Humans, Histocompatibility Antigens Class I, Immunity, MESH : Clone Cells, Proteins, R1, MESH: Glucose-6-Phosphatase, Clone Cells, chemistry, Peptides, MESH : Sequence Analysis, Protein, MESH : Molecular Sequence Data, Anatomy and Physiology, Epitopes, T-Lymphocyte, MESH: Histocompatibility Antigens Class I, Interferon gamma, Multidisciplinary, T Cells, Animal Models, MESH : CD8-Positive T-Lymphocytes, [SDV.IMM.IA] Life Sciences [q-bio]/Immunology/Adaptive immunology, [SDV.IMM]Life Sciences [q-bio]/Immunology, MESH : Histocompatibility Antigens Class I, Research Article, medicine.drug, MESH: Interferon-gamma, Major histocompatibility complex, MESH: Epitopes, T-Lymphocyte, MESH : Mass Spectrometry, Model Organisms, MESH : Mice, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, medicine, Animals, Synthetic Peptide, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Epitopes, T-Lymphocyte, MESH: Mice, MESH : Interferon-gamma, 030304 developmental biology, Diabetic Endocrinology, MESH: Clone Cells, Reproducibility of Results, Molecular biology, biology.protein, MESH : Animals, CD8, 030215 immunology
Abstract: International audience; Synthetic peptides are widely used in immunological research as epitopes to stimulate their cognate T cells. These preparations are never completely pure, but trace contaminants are commonly revealed by mass spectrometry quality controls. In an effort to characterize novel major histocompatibility complex (MHC) Class I-restricted β-cell epitopes in non-obese diabetic (NOD) mice, we identified islet-infiltrating CD8+ T cells recognizing a contaminating peptide. The amount of this contaminant was so small to be undetectable by direct mass spectrometry. Only after concentration by liquid chromatography, we observed a mass peak corresponding to an immunodominant islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP)$_{206-214}$ epitope described in the literature. Generation of CD8+ T-cell clones recognizing IGRP$_{206-214}$) using a novel method confirmed the identity of the contaminant, further underlining the immunodominance of IGRP$_{206-214}$. If left undetected, minute impurities in synthetic peptide preparations may thus give spurious results.
Published: 2011
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39. Genotype-phenotype correlations of TGFBI p.Leu509Pro, p.Leu509Arg, p.Val613Gly, and the allelic association of p.Met502Val-p.Arg555Gln mutations

Author: Niel-Butschi F, Kantelip B, Iwaszkiewicz J, Zoete V, Boimard M, Delpech M, Jl, Bourges, Renard G, D'Hermies F, Pj, Pisella, Hamel C, Delbosc B, Sophie Valleix, Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC ( CEF2P / CARCINO ), Université Bourgogne Franche-Comté ( UBFC ) -Université de Franche-Comté ( UFC ) -Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ), Laboratoire d'anatomie pathologique [Besancon], Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ) -Hôpital Jean Minjoz-Université de Franche-Comté ( UFC ), Hôtel-Dieu, Assistance publique - Hôpitaux de Paris (AP-HP)-Hôtel-Dieu-Université Paris Descartes - Paris 5 ( UPD5 ), Centre de référence des affections sensorielles d'origine génétique, Centre Hospitalier Régional Universitaire [Montpellier] ( CHRU Montpellier ) -Hôpital Gui De Chaulliac, Service d'ophtalmologie [Besançon], Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ) -Hôpital Jean Minjoz, Laboratoire de Biochimie et Génétique Moléculaire, Assistance publique - Hôpitaux de Paris (AP-HP)-Université Paris Descartes - Paris 5 ( UPD5 ), Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC (EA 3181) (CEF2P / CARCINO), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Service d'Anatomie pathologique [CHRU Besançon], Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôtel-Dieu-Université Paris Descartes - Paris 5 (UPD5), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Gui De Chaulliac, Service d'ophtalmologie [CHRU Besançon], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Descartes - Paris 5 (UPD5), Viala, Pascale, Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre Hospitalier Régional Universitaire [Besançon] (CHRU Besançon)-Université de Franche-Comté (UFC), Centre Hospitalier Régional Universitaire [Besançon] (CHRU Besançon)-Hôpital Jean Minjoz-Université de Franche-Comté (UFC), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôtel-Dieu-Université Paris Descartes - Paris 5 (UPD5), Centre Hospitalier Régional Universitaire [Besançon] (CHRU Besançon)-Hôpital Jean Minjoz, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris Descartes - Paris 5 (UPD5), Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC (EA 3181) ( CEF2P / CARCINO ), and Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ) -Université Bourgogne Franche-Comté [COMUE] ( UBFC ) -Université de Franche-Comté ( UFC )
Subjects: Male, Models, Molecular, MESH: Extracellular Matrix Proteins, MESH : Molecular Sequence Data, MESH : Algeria, Genetic Linkage, MESH : Genotype, MESH: Amino Acid Sequence, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, MESH: Genotype, MESH: Aged, 80 and over, Gene Frequency, Transforming Growth Factor beta, MESH : Gene Frequency, MESH : Female, Bowman Membrane, MESH: Genetic Association Studies, Aged, 80 and over, Corneal Dystrophies, Hereditary, Extracellular Matrix Proteins, MESH: Middle Aged, MESH : Amino Acid Sequence, MESH : Infant, Middle Aged, MESH : Adult, MESH: Infant, Pedigree, MESH : Phenotype, Phenotype, Female, France, MESH : Mutation, MESH: Algeria, MESH: Models, Molecular, Research Article, Adult, MESH: Mutation, Genotype, MESH: Pedigree, MESH : Models, Molecular, MESH : Bowman Membrane, MESH : Male, Molecular Sequence Data, MESH: Genetic Linkage, MESH: Corneal Dystrophies, Hereditary, [SDV.CAN]Life Sciences [q-bio]/Cancer, MESH: Phenotype, MESH : Extracellular Matrix Proteins, [SDV.CAN] Life Sciences [q-bio]/Cancer, Algeria/ethnology, Alleles, Amino Acid Sequence, Bowman Membrane/metabolism, Bowman Membrane/pathology, Corneal Dystrophies, Hereditary/classification, Corneal Dystrophies, Hereditary/epidemiology, Corneal Dystrophies, Hereditary/ethnology, Corneal Dystrophies, Hereditary/genetics, Corneal Dystrophies, Hereditary/pathology, Extracellular Matrix Proteins/genetics, Extracellular Matrix Proteins/metabolism, France/epidemiology, Genetic Association Studies, Humans, Infant, Mutation, Transforming Growth Factor beta/genetics, Transforming Growth Factor beta/metabolism, MESH: Gene Frequency, MESH : Middle Aged, MESH : Aged, 80 and over, MESH : France, MESH: Transforming Growth Factor beta, MESH: Humans, MESH: Molecular Sequence Data, MESH: Alleles, MESH : Humans, MESH: Adult, MESH : Genetic Association Studies, MESH : Genetic Linkage, MESH: Male, eye diseases, MESH: France, MESH : Transforming Growth Factor beta, Algeria, MESH : Pedigree, MESH : Corneal Dystrophies, Hereditary, MESH : Alleles, MESH: Female, MESH: Bowman Membrane
Abstract: International audience; PURPOSE: Investigate the genotype-phenotype correlations for five TGFBI (transforming growth factor, beta-induced) mutations including one novel pathogenic variant and one complex allele affecting the fourth FAS1 domain of keratoepithelin, and their potential effects on the protein's structure. METHODS: Three unrelated families were clinically diagnosed with lattice corneal dystrophy (CD) and one with an unclassified CD of Bowman's layer. Mutations in the TGFBI gene were detected by direct sequencing, and the functional impact of each variant was predicted using in silico algorithms. Corneal phenotypes, including histological examinations, were compared with the literature data. Furthermore, molecular modeling studies of these mutations were performed. RESULTS: Two distinct missense mutations affecting the same residue at position 509 of keratoepithelin: p.Leu509Pro (c.1526T>C) and p.Leu509Arg (c.1526T>G) were found to be associated with a lattice-type CD. The novel p.Val613Gly (c.1828T>G) TGFBI mutation was found in a sporadic case of an Algerian individual affected by lattice CD. Finally, the Bowman's layer CD was linked to the association in cis of the p.Met502Val and p.Arg555Gln variants, leading to the reclassification of this CD as atypical Thiel-Behnke CD. Structural modeling of these TGFBI mutations argues in favor of these mutations being responsible for instability and/or incorrect folding of keratoepithelin, predictions that are compatible with the clinical diagnoses. CONCLUSIONS: Description of a novel TGFBI mutation and a complex TGFBI allele further extends the mutational spectrum of TGFBI. Moreover, we show convincing evidence that TGFBI mutations affecting Leu509 are linked to the lattice phenotype in two unrelated French families, contrasting with findings previously reported. The p.Leu509Pro was reported to be associated with both amyloid and non-amyloid aggregates, whereas p.Leu509Arg has been described as being responsible for Epithelial Basement Membrane Dystrophy (EBMD).
Published: 2011

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

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

Author: Palmer Taylor, Pascale Marchot, Géraldine Ferracci, Sandrine Conrod, Philippe Leone, Yves Bourne, Davide Comoletti, Simon U Garcia, 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), Université de Provence - Aix-Marseille 1, Department of pharmacology, University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), University of California-University of California, Architecture et fonction des macromolécules biologiques ( AFMB ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA ), University of California [San Diego] ( UC San Diego ), Centre de recherche en neurobiologie - neurophysiologie de Marseille ( CRN2M ), and Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: Models, Molecular, MESH : Molecular Sequence Data, Neurexin, MESH : Alternative Splicing, Neuroligin, Plasma protein binding, MESH: Amino Acid Sequence, Crystallography, X-Ray, MESH: Synapses, MESH: Protein Structure, Tertiary, [ SDV.BBM.BC ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 0302 clinical medicine, MESH: Nerve Tissue Proteins, Surface plasmon resonance, MESH : Nerve Tissue Proteins, 0303 health sciences, MESH : Amino Acid Sequence, MESH : Sequence Alignment, General Neuroscience, MESH: Alternative Splicing, MESH : Protein Binding, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], MESH: Surface Plasmon Resonance, Dissociation constant, Biochemistry, MESH: Membrane Proteins, MESH : Surface Plasmon Resonance, MESH : Carrier Proteins, MESH : Protein Structure, Tertiary, MESH : Synapses, MESH: Models, Molecular, Protein Binding, MESH : Models, Molecular, Cell Adhesion Molecules, Neuronal, Molecular Sequence Data, MESH: Sequence Alignment, Sequence alignment, Nerve Tissue Proteins, MESH: Carrier Proteins, Biology, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Humans, MESH: Protein Binding, Amino Acid Sequence, Binding site, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, MESH : Protein Processing, Post-Translational, 030304 developmental biology, Binding Sites, MESH: Humans, MESH: Molecular Sequence Data, General Immunology and Microbiology, MESH : Humans, Alternative splicing, Membrane Proteins, Surface Plasmon Resonance, MESH: Crystallography, X-Ray, Protein Structure, Tertiary, Alternative Splicing, MESH: Binding Sites, MESH : Membrane Proteins, MESH: Protein Processing, Post-Translational, Synapses, Biophysics, MESH : Crystallography, X-Ray, Carrier Proteins, Protein Processing, Post-Translational, Sequence Alignment, MESH : Binding Sites, 030217 neurology & neurosurgery
Abstract: International audience; The extracellular domains of neuroligins and neurexins interact through Ca(2+) to form flexible trans-synaptic associations characterized by selectivity for neuroligin or neurexin subtypes. This heterophilic interaction, essential for synaptic maturation and differentiation, is regulated by gene selection, alternative mRNA splicing and post-translational modifications. A new, 2.6 A-resolution crystal structure of a soluble neurexin-1beta-neuroligin-4 (Nrx1beta-NL4) complex permits a detailed description of the Ca(2+)-coordinated interface and unveils concerted positional rearrangements of several residues of NL4, not observed in neuroligin-1, associated with Nrx1beta binding. Surface plasmon resonance analysis of the binding of structure-guided Nrx1beta mutants towards NL4 and neuroligin-1 shows that flexibility of the Nrx1beta-binding site in NL4 is reflected in a greater dissociation constant of the complex and higher sensitivity to ionic strength and pH variations. Analysis of neuroligin mutants points to critical functions for two respective residues in neuroligin-1 and neuroligin-2 in governing the affinity of the complexes. Although neuroligin-1 and neuroligin-2 have pre-determined conformations that respectively promote and prevent Nrx1beta association, unique conformational reshaping of the NL4 surface is required to permit Nrx1beta association.
Published: 2010
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42. Comprehensive diagnostic strategy for blood culture-negative endocarditis: a prospective study of 819 new cases

Author: Jean-Paul Casalta, Pierre-Edouard Fournier, Jean-Pierre Arzouni, Franck Thuny, Hervé Richet, Didier Raoult, Jean-Luc Mainardi, Marie Célard, Thierry Caus, Gilbert Habib, Frederic Collart, Max Maurin, Hubert Lepidi, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Service de cardiologie, Université de la Méditerranée - Aix-Marseille 2-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), Fédération de Microbiologie Clinique, Hôpital de la Timone [CHU - APHM] (TIMONE), Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), CHU Grenoble, Université Joseph Fourier - Grenoble 1 (UJF)-CHU Grenoble, Laboratoire de microbiologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5), Affectations Mineralisantes du Systeme Cardiovasculaire : Calcifications Arterielles et Valvulaires Aortiques, Université de Picardie Jules Verne (UPJV)-Institut National de la Santé et de la Recherche Médicale (INSERM), Chirurgie cardiaque, CHU Amiens-Picardie, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes ( URMITE ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -IFR48, INSB-INSB-Centre National de la Recherche Scientifique ( CNRS ), Université de la Méditerranée - Aix-Marseille 2-Assistance Publique - Hôpitaux de Marseille ( APHM ) - Hôpital de la Timone [CHU - APHM] ( TIMONE ), Hôpital de la Timone [CHU - APHM] ( TIMONE ), Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] ( LAPM ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Centre National de la Recherche Scientifique ( CNRS ), Université Joseph Fourier - Grenoble 1 ( UJF ) -CHU Grenoble, Assistance publique - Hôpitaux de Paris (AP-HP)-Hôpital Européen Georges Pompidou [APHP] ( HEGP ) -Université Paris Descartes - Paris 5 ( UPD5 ), Université de Picardie Jules Verne ( UPJV ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, MESH: Endocarditis, MESH : Molecular Sequence Data, MESH : Pathology, Molecular, MESH : Immunohistochemistry, MESH : Prospective Studies, MESH : Aged, MESH: Molecular Diagnostic Techniques, 030204 cardiovascular system & hematology, Polymerase Chain Reaction, Serology, 0302 clinical medicine, MESH: Aged, 80 and over, MESH : Child, Neoplasms, MESH: Autoimmune Diseases, MESH: Child, Blood culture, MESH : Female, MESH: Neoplasms, 030212 general & internal medicine, Prospective Studies, Pathology, Molecular, Child, MESH : Polymerase Chain Reaction, Aged, 80 and over, Immunoassay, MESH: Aged, MESH: Middle Aged, medicine.diagnostic_test, biology, Endocarditis, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Bacterial Infections, Middle Aged, MESH : Adult, MESH : Immunoassay, Immunohistochemistry, MESH : Endocarditis, 3. Good health, MESH : Bacterial Infections, Infectious Diseases, [ SDV.BID.EVO ] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Molecular Diagnostic Techniques, MESH: Young Adult, Female, MESH: Immunoassay, Bartonella Infection, Microbiology (medical), Bartonella, Adult, Adolescent, MESH: Bacterial Infections, MESH : Male, Molecular Sequence Data, MESH : Young Adult, Q fever, Autoimmune Diseases, Tropheryma whipplei, 03 medical and health sciences, Young Adult, MESH : Autoimmune Diseases, MESH : Adolescent, medicine, Humans, MESH : Middle Aged, MESH : Aged, 80 and over, Aged, MESH: Pathology, Molecular, MESH: Adolescent, MESH: Molecular Sequence Data, MESH: Humans, business.industry, MESH : Humans, MESH: Adult, MESH: Immunohistochemistry, MESH: Polymerase Chain Reaction, medicine.disease, biology.organism_classification, Coxiella burnetii, Virology, MESH : Neoplasms, MESH: Male, MESH: Prospective Studies, business, MESH: Female, MESH : Molecular Diagnostic Techniques
Abstract: International audience; BACKGROUND. Blood culture-negative endocarditis (BCNE) may account for up to 31% of all cases of endocarditis. METHODS. We used a prospective, multimodal strategy incorporating serological, molecular, and histopathological assays to investigate specimens from 819 patients suspected of having BCNE. RESULTS. Diagnosis of endocarditis was first ruled out for 60 patients. Among 759 patients with BCNE, a causative microorganism was identified in 62.7%, and a noninfective etiology in 2.5%. Blood was the most useful specimen, providing a diagnosis for 47.7% of patients by serological analysis (mainly Q fever and Bartonella infections). Broad-range polymerase chain reaction (PCR) of blood and Bartonella-specific Western blot methods diagnosed 7 additional cases. PCR of valvular biopsies identified 109 more etiologies, mostly streptococci, Tropheryma whipplei, Bartonella species, and fungi. Primer extension enrichment reaction and autoimmunohistochemistry identified a microorganism in 5 additional patients. No virus or Chlamydia species were detected. A noninfective cause of endocarditis, particularly neoplasic or autoimmune disease, was determined by histological analysis or by searching for antinuclear antibodies in 19 (2.5%) of the patients. Our diagnostic strategy proved useful and sensitive for BCNE workup. CONCLUSIONS. We highlight the major role of zoonotic agents and the underestimated role of noninfective diseases in BCNE. We propose serological analysis for Coxiella burnetii and Bartonella species, detection of antinuclear antibodies and rheumatoid factor as first-line tests, followed by specific PCR assays for T. whipplei, Bartonella species, and fungi in blood. Broad-spectrum 16S and 18S ribosomal RNA PCR may be performed on valvular biopsies, when available.
Published: 2010
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43. Structural and catalytic properties of the D-3-hydroxybutyrate dehydrogenase from Pseudomonas aeruginosa

Author: M'Hammed Saïd El Kebbaj, Norbert Latruffe, Mustapha Cherkaoui-Malki, Pierre Andreoletti, Driss Mountassif, Laboratoire Biochimie et Biologie Moléculaire ( LBBM ), Université Hassan II, Mathématiques - Analyse, Probabilités, Modélisation - Orléans ( MAPMO ), Université d'Orléans ( UO ) -Centre National de la Recherche Scientifique ( CNRS ), Lipides - Nutrition - Cancer (U866) ( LNC ), Université de Bourgogne ( UB ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon ( ENSBANA ), Laboratoire de Biochimie Moléculaire et Cellulaire ( LBMC ), Université de Bourgogne ( UB ), Laboratoire Biochimie et Biologie Moléculaire (LBBM), Université Hassan II [Casablanca] (UH2MC), Mathématiques - Analyse, Probabilités, Modélisation - Orléans (MAPMO), Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO), Lipides - Nutrition - Cancer (U866) (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA), Laboratoire de Biochimie Moléculaire et Cellulaire (LBMC), and Université de Bourgogne (UB)
Subjects: Models, Molecular, MESH : Molecular Weight, MESH : Molecular Sequence Data, MESH : NAD, Protein Conformation, MESH: Amino Acid Sequence, Applied Microbiology and Biotechnology, Chromatography, Affinity, Protein structure, MESH: Protein Conformation, MESH: 3-Hydroxybutyric Acid, MESH : Bacterial Proteins, MESH : DNA, Bacterial, Peptide sequence, Polyacrylamide gel electrophoresis, MESH: Bacterial Proteins, MESH : Protein Conformation, chemistry.chemical_classification, 0303 health sciences, MESH : Sepharose, 3-Hydroxybutyric Acid, MESH: Molecular Weight, Sepharose, MESH : Amino Acid Sequence, MESH: NAD, General Medicine, MESH: Chromatography, Affinity, MESH : Pseudomonas aeruginosa, MESH : Chromatography, Affinity, Amino acid, Biochemistry, MESH: Pseudomonas aeruginosa, Pseudomonas aeruginosa, Electrophoresis, Polyacrylamide Gel, MESH: Biocatalysis, MESH: Models, Molecular, DNA, Bacterial, MESH: Sepharose, MESH : Models, Molecular, Molecular Sequence Data, MESH : Hydroxybutyrate Dehydrogenase, Biology, MESH : Electrophoresis, Polyacrylamide Gel, Microbiology, Cofactor, 03 medical and health sciences, Hydroxybutyrate Dehydrogenase, Affinity chromatography, Bacterial Proteins, MESH : 3-Hydroxybutyric Acid, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, MESH: Molecular Sequence Data, 030306 microbiology, NAD, MESH: DNA, Bacterial, MESH: Hydroxybutyrate Dehydrogenase, Molecular Weight, Open reading frame, chemistry, biology.protein, Biocatalysis, NAD+ kinase, MESH : Biocatalysis, MESH: Electrophoresis, Polyacrylamide Gel
Abstract: International audience; To put forward BDH from Pseudomonas aeruginosa's enzymatic properties, we report a two-step purification of BDH and its gene sequencing allowing the investigation of its structural properties. Purification of BDH was achieved, using ammonium sulfate fractionation and Blue Sepharose CL-6B affinity chromatography. SDS-PAGE analysis reveals a MM of 29 kDa, whereas the native enzyme showed a MM of 120 kDa suggesting a homotetrameric structure. BDH encoding gene sequence shows a nucleotide open reading frame sequence of 771 bp encoding a 265 amino acid residues polypeptide chain. The modeling analysis of the three dimensional structure fits with the importance of amino acids in the catalysis reaction especially a strictly conserved tetrad. Amino-acid residues in interaction with the coenzyme NAD(+) were also identified.
Published: 2010
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44. Mining protein loops using a structural alphabet and statistical exceptionality

Author: Leslie Regad, Anne-Claude Camproux, Gregory Nuel, Juliette Martin, Molécules Thérapeutiques in silico (MTI), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de Mathématique, Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), 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), Mathématiques Appliquées Paris 5 (MAP5 - UMR 8145), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Mathématiques et de leurs Interactions (INSMI)-Université Paris Descartes - Paris 5 (UPD5), LR had a grant from the Ministère de la Recherche. JM had a grant from INRA., Université Paris Descartes - Paris 5 (UPD5)-Institut National des Sciences Mathématiques et de leurs Interactions (INSMI)-Centre National de la Recherche Scientifique (CNRS), Molécules Thérapeutique in silico, Recherche de molécules à visée thérapeutique par approches In Silico ( MTI ), Université Paris Diderot - Paris 7 ( UPD7 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Unité de Mathématique, Informatique et Génome ( MIG ), Institut National de la Recherche Agronomique ( INRA ), 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 ), Mathématiques Appliquées à Paris 5 ( MAP5 - UMR 8145 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National des Sciences Mathématiques et de leurs Interactions-Centre National de la Recherche Scientifique ( CNRS ), BMC, Ed., and Unité Mathématique Informatique et Génome (MIG)
Subjects: Models, Molecular, Secondary, MESH : Molecular Sequence Data, Amino Acid Motifs, MESH: Protein Structure, Secondary, MESH: Amino Acid Sequence, Bioinformatics, Biochemistry, Protein Structure, Secondary, MESH : Proteins, MESH: Amino Acid Motifs, Protein structure, Structural Biology, Models, Data Mining, MESH: Proteins, Structural motif, Databases, Protein, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], lcsh:QH301-705.5, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Complement (set theory), 0303 health sciences, Sequence, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Applied Mathematics, MESH : Amino Acid Sequence, 030302 biochemistry & molecular biology, String (computer science), [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], lcsh:R858-859.7, Bio-informatique, Algorithm, MESH: Models, Molecular, MESH: Databases, Protein, Loop (graph theory), Protein Structure, MESH : Amino Acid Motifs, Sequence analysis, MESH : Models, Molecular, Structural alignment, Molecular Sequence Data, Biology, lcsh:Computer applications to medicine. Medical informatics, 03 medical and health sciences, Databases, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Research article, Amino Acid Sequence, MESH : Databases, Protein, Molecular Biology, Protein, Molecular, Proteins, 030304 developmental biology, MESH: Molecular Sequence Data, MESH : Data Mining, MESH: Data Mining, SDV:BBM:GTP, lcsh:Biology (General), MESH : Protein Structure, Secondary, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], SDV:BIBS
Abstract: Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 Å). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. Conclusions We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/.
Published: 2010
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45. Toxicity at three years with and without irradiation of the internal mammary and medial supraclavicular lymph node chain in stage I to III breast cancer (EORTC trial 22922/10925)

Author: Matzinger, O., Heimsoth, I., Poortmans, P., Collette, L., Struikmans, H., Bogaert, W. van den, Fourquet, A., Bartelink, H., Ataman, F., Gulyban, A., Pierart, M., Tienhoven, G. van, EORTC Radiation Oncology Grp, Breast Canc Grp, CCA -Cancer Center Amsterdam, Radiotherapy, Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC (EA 3181) (CEF2P / CARCINO), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Carcinogénèse épithéliale : facteurs prédictifs et pronostiques - UFC ( CEF2P / CARCINO ), and Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ) -Université Bourgogne Franche-Comté ( UBFC ) -Université de Franche-Comté ( UFC )
Subjects: Oncology, MESH: Radiotherapy, MESH: Lymphatic Metastasis, MESH: Mastectomy, medicine.medical_treatment, MESH : Aged, MESH: Amino Acid Sequence, MESH : Breast Neoplasms, Severity of Illness Index, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, MESH: Protein Conformation, 0302 clinical medicine, MESH : Neoplasm Staging, MESH: Animals, Mastectomy, MESH : Protein Conformation, health care economics and organizations, MESH: Middle Aged, MESH : Amino Acid Sequence, Heart, MESH : Chemotherapy, Adjuvant, MESH : Lymphatic Metastasis, General Medicine, 3. Good health, MESH : Diabetes Mellitus, Medial supraclavicular lymph node, 030220 oncology & carcinogenesis, MESH: Diabetes Mellitus, Type 2, medicine.medical_specialty, MESH: Diabetes Mellitus, MESH: Receptor, Insulin, 03 medical and health sciences, MESH : Amyloid, Breast cancer, MESH: Severity of Illness Index, Severity of illness, Humans, MESH : Middle Aged, MESH : Islets of Langerhans, Aged, Pneumonitis, MESH: Humans, MESH: Molecular Sequence Data, MESH : Glucose, MESH : Radiotherapy, MESH: Islets of Langerhans, MESH : Humans, MESH: Adult, medicine.disease, MESH: Heart, Radiation therapy, MESH: Female, MESH: Combined Modality Therapy, MESH : Molecular Sequence Data, Pulmonary Fibrosis, 030218 nuclear medicine & medical imaging, MESH : Diabetes Mellitus, Type 2, MESH : Female, quality-assurance cardiac toxicity randomized-trial high-risk postoperative radiotherapy adjuvant radiotherapy premenopausal women radiation chemotherapy management, MESH: Aged, MESH: Neoplasm Staging, Hematology, Middle Aged, MESH : Adult, Combined Modality Therapy, humanities, MESH: Glucose, Chemotherapy, Adjuvant, MESH: Chemotherapy, Adjuvant, Lymphatic Metastasis, MESH: Monosaccharide Transport Proteins, Toxicity, Female, MESH : Severity of Illness Index, MESH : Mastectomy, Adult, Breast Neoplasms, [SDV.CAN]Life Sciences [q-bio]/Cancer, MESH : Pulmonary Fibrosis, MESH: Sequence Homology, Nucleic Acid, MESH : Heart, Internal medicine, medicine, Radiology, Nuclear Medicine and imaging, MESH : Sequence Homology, Nucleic Acid, Neoplasm Staging, MESH : Monosaccharide Transport Proteins, MESH: Amyloid, Radiotherapy, MESH: Pulmonary Fibrosis, Performance status, business.industry, MESH : Receptor, Insulin, MESH : Animals, MESH : Combined Modality Therapy, business, MESH: Breast Neoplasms
Abstract: National audience; INTRODUCTION: The EORTC 22922/10925 trial investigated the potential survival benefit and toxicity of elective irradiation of the internal mammary and medial supraclavicular (IM-MS) nodes Accrual completed in January 2004 and first results are expected in 2012. We present the toxicity reported until year 3 after treatment. PATIENTS AND METHODS: At each visit, toxicity was reported but severity was not graded routinely. Toxicity rates and performance status (PS) changes at three years were compared by chi(2) tests and logistic regression models in all the 3,866 of 4,004 patients eligible to the trial who received the allocated treatment. RESULTS: Only lung (fibrosis; dyspnoea; pneumonitis; any lung toxicities) (4.3% vs. 1.3%; p < 0.0001) but not cardiac toxicity (0.3% vs. 0.4%; p = 0.55) significantly increased with IM-MS treatment. No significant worsening of the PS was observed (p = 0.79), suggesting that treatment-related toxicity does not impair patient's daily activities. CONCLUSIONS: IM-MS irradiation seems well tolerated and does not significantly impair WHO PS at three years. A follow-up period of at least 10 years is needed to determine whether cardiac toxicity is increased after radiotherapy.
Published: 2010
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46. Identification of small RNAs in Francisella tularensis

Author: Guillaume Postic, Eric Frapy, Marion Dupuis, Alain Charbit, Jonathan Livny, Iharilalao Dubail, Karin L. Meibom, Pathogénie des infections systémiques ( UMR_S 570 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Broad Institute of MIT and Harvard ( BROAD INSTITUTE ), Harvard Medical School [Boston] ( HMS ) -Massachusetts General Hospital [Boston] ( MGH ) -Massachusetts Institute of Technology ( MIT ), Channing Laboratories, Brigham and Women's Hospital [Boston], Pathogénie des infections systémiques (UMR_S 570), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], and BMC, Ed.
Subjects: MESH : Molecular Sequence Data, MESH : DNA, Complementary, MESH : Nucleic Acid Conformation, Intracellular Space, MESH : Intracellular Space, MESH: Base Sequence, Genome, RNA Transport, Mice, MESH: RNA Transport, MESH: Reverse Transcriptase Polymerase Chain Reaction, MESH: Animals, Cloning, Molecular, Francisella tularensis, MESH : RNA Transport, Oligonucleotide Array Sequence Analysis, MESH : Macrophages, Genetics, 0303 health sciences, MESH: Gene Expression Regulation, Bacterial, MESH : Francisella tularensis, Reverse Transcriptase Polymerase Chain Reaction, MESH : Blotting, Northern, MESH : Reverse Transcriptase Polymerase Chain Reaction, Bacterial vaccine, MESH: Reproducibility of Results, RNA, Bacterial, MESH : Oligonucleotide Array Sequence Analysis, MESH: Nucleic Acid Conformation, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Bacterial Vaccines, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Intracellular Space, DNA microarray, MESH : Mutation, MESH: RNA, Bacterial, Biotechnology, Research Article, MESH: Computational Biology, MESH : Gene Expression Regulation, Bacterial, DNA, Complementary, MESH: Mutation, lcsh:QH426-470, MESH : Cloning, Molecular, lcsh:Biotechnology, In silico, Molecular Sequence Data, Context (language use), Biology, Vaccines, Attenuated, 03 medical and health sciences, MESH: Gene Expression Profiling, MESH: Francisella tularensis, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Vaccines, Attenuated, MESH : Mice, Animals, MESH: Blotting, Northern, MESH: Cloning, Molecular, MESH : Vaccines, Attenuated, MESH: Mice, 030304 developmental biology, MESH: Molecular Sequence Data, Base Sequence, 030306 microbiology, Gene Expression Profiling, Macrophages, MESH : Reproducibility of Results, MESH : Gene Expression Profiling, RNA, Computational Biology, Reproducibility of Results, MESH: Macrophages, Gene Expression Regulation, Bacterial, MESH: DNA, Complementary, MESH : RNA, Bacterial, biology.organism_classification, Blotting, Northern, Gene expression profiling, MESH : Bacterial Vaccines, lcsh:Genetics, Mutation, MESH: Oligonucleotide Array Sequence Analysis, Nucleic Acid Conformation, MESH : Base Sequence, MESH : Animals, MESH: Bacterial Vaccines, MESH : Computational Biology
Abstract: Background Regulation of bacterial gene expression by small RNAs (sRNAs) have proved to be important for many biological processes. Francisella tularensis is a highly pathogenic Gram-negative bacterium that causes the disease tularaemia in humans and animals. Relatively little is known about the regulatory networks existing in this organism that allows it to survive in a wide array of environments and no sRNA regulators have been identified so far. Results We have used a combination of experimental assays and in silico prediction to identify sRNAs in F. tularensis strain LVS. Using a cDNA cloning and sequencing approach we have shown that F. tularensis expresses homologues of several sRNAs that are well-conserved among diverse bacteria. We have also discovered two abundant putative sRNAs that share no sequence similarity or conserved genomic context with any previously annotated regulatory transcripts. Deletion of either of these two loci led to significant changes in the expression of several mRNAs that likely include the cognate target(s) of these sRNAs. Deletion of these sRNAs did not, however, significantly alter F. tularensis growth under various stress conditions in vitro, its replication in murine cells, or its ability to induce disease in a mouse model of F. tularensis infection. We also conducted a genome-wide in silico search for intergenic loci that suggests F. tularensis encodes several other sRNAs in addition to the sRNAs found in our experimental screen. Conclusion Our findings suggest that F. tularensis encodes a significant number of non-coding regulatory RNAs, including members of well conserved families of structural and housekeeping RNAs and other poorly conserved transcripts that may have evolved more recently to help F. tularensis deal with the unique and diverse set of environments with which it must contend.
Published: 2010
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47. Human mucosal associated invariant T cells detect bacterially infected cells

Author: Wei Jen Chua, Marielle C. Gold, Deborah A. Lewinsohn, Olivier Lantz, Stefania Cerri, Megan D. Null, David M. Lewinsohn, Ted H. Hansen, Todd M. Vogt, Gwendolyn Swarbrick, Matthew S. Cook, Susan Smyk-Pearson, Jacob Delepine, Yik Y. L. Yu, Melanie J. Harriff, David B. Jacoby, Ervina Winata, Meghan E. Cansler, Division of Pulmonary and Critical Care Medicine, Oregon Health & Science University [Portland] ( OHSU ), Portland Veterans Administration Medical Center, Department of Pediatrics, Department of Pathology and Immunology, Washington University School of Medicine, Immunité et cancer ( U932 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut Curie-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Department of Molecular Microbiology and Immunology, Funding was provided in part by the Department of Veterans Affairs and with resources and the use of facilities at the Portland VA Medical Center, National Institutes of Health (NIH) grant AI48090, and NIH contract HHSN266200400081C., Autard, Delphine, Oregon Health and Science University [Portland] (OHSU), Immunité et cancer (U932), and Université Paris Descartes - Paris 5 (UPD5)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: MESH: Mycobacterium tuberculosis, MESH : Molecular Sequence Data, Immunology/Innate Immunity, Microbiology/Innate Immunity, MESH: Amino Acid Sequence, CD8-Positive T-Lymphocytes, Respiratory Medicine/Respiratory Infections, MESH : Receptors, Antigen, T-Cell, Infectious Diseases/Bacterial Infections, MESH: Cross Reactions, 0302 clinical medicine, MESH : HLA Antigens, HLA Antigens, Cytotoxic T cell, [ SDV.IMM ] Life Sciences [q-bio]/Immunology, IL-2 receptor, MESH : Mucous Membrane, Biology (General), MESH: HLA Antigens, 0303 health sciences, biology, General Neuroscience, MESH : Amino Acid Sequence, MESH : Cross Reactions, MESH: Receptors, Antigen, T-Cell, respiratory system, MESH : CD8-Positive T-Lymphocytes, Natural killer T cell, MESH: CD8-Positive T-Lymphocytes, Microbiology/Immunity to Infections, 3. Good health, Immunology/Antigen Processing and Recognition, MESH: Complementarity Determining Regions, [SDV.IMM]Life Sciences [q-bio]/Immunology, General Agricultural and Biological Sciences, Research Article, [SDV.IMM] Life Sciences [q-bio]/Immunology, QH301-705.5, Immunology, Molecular Sequence Data, Antigen presentation, Receptors, Antigen, T-Cell, CD1, MESH : Complementarity Determining Regions, chemical and pharmacologic phenomena, Mucosal associated invariant T cell, Cross Reactions, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, MESH : Mycobacterium tuberculosis, Immunology/Immunity to Infections, Humans, Amino Acid Sequence, Clone Cells, Complementarity Determining Regions, Mucous Membrane, Mycobacterium tuberculosis, Agricultural and Biological Sciences (all), Biochemistry, Genetics and Molecular Biology (all), Immunology and Microbiology (all), Neuroscience (all), Antigen-presenting cell, 030304 developmental biology, CD40, MESH: Humans, MESH: Molecular Sequence Data, General Immunology and Microbiology, Infectious Diseases/Respiratory Infections, MESH: Clone Cells, MESH : Humans, MESH: Mucous Membrane, MESH : Clone Cells, Immunology/Immune Response, biology.protein, 030215 immunology
Abstract: A first indication of the biological role of mucosal associated invariant T (MAIT) cells reveals that this discrete T cell subset is broadly reactive to bacterial infection. In particular MAIT cells recognize Mycobacterium tuberculosis-infected lung airway epithelial cells via the most evolutionarily conserved major histocompatibility molecule., Control of infection with Mycobacterium tuberculosis (Mtb) requires Th1-type immunity, of which CD8+ T cells play a unique role. High frequency Mtb-reactive CD8+ T cells are present in both Mtb-infected and uninfected humans. We show by limiting dilution analysis that nonclassically restricted CD8+ T cells are universally present, but predominate in Mtb-uninfected individuals. Interestingly, these Mtb-reactive cells expressed the Vα7.2 T-cell receptor (TCR), were restricted by the nonclassical MHC (HLA-Ib) molecule MR1, and were activated in a transporter associated with antigen processing and presentation (TAP) independent manner. These properties are all characteristics of mucosal associated invariant T cells (MAIT), an “innate” T-cell population of previously unknown function. These MAIT cells also detect cells infected with other bacteria. Direct ex vivo analysis demonstrates that Mtb-reactive MAIT cells are decreased in peripheral blood mononuclear cells (PBMCs) from individuals with active tuberculosis, are enriched in human lung, and respond to Mtb-infected MR1-expressing lung epithelial cells. Overall, these findings suggest a generalized role for MAIT cells in the detection of bacterially infected cells, and potentially in the control of bacterial infection., Author Summary About one-third of the world's population is infected with Mycobacterium tuberculosis (Mtb), yet thanks to a robust immune response most infected people remain healthy. CD8 T cells are unique in detecting intracellular infections. Surprisingly, Mtb-reactive CD8 T cells are found in humans with no prior exposure to Mtb. We show that mucosal associated invariant T (MAIT) cells, which have no previously known in vivo function, make up a proportion of these Mtb-reactive CD8 T cells and detect Mtb-infected cells via a specific major histocompatibility molecule called MHC-related molecule 1, which is evolutionarily conserved among mammals. Mtb-reactive MAIT cells are enriched in lung and detect primary Mtb-infected lung epithelial cells from the airway where initial exposure to Mtb occurs. We go on to show that MAIT cells are not specific for Mtb since they can detect cells infected with a variety of other bacteria. Curiously, Mtb-reactive MAIT cells are absent in the blood of individuals with active tuberculosis. We postulate that MAIT cells are innate detectors of bacterial infection poised to play a role in control of intracellular infection.
Published: 2010
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48. Evidence of Emergence of New GGII.4 Norovirus Variants from Gastroenteritis Outbreak Survey in France during the 2007-to-2008 and 2008-to-2009 Winter Seasons ▿

Author: Pierre Pothier, Katia Ambert-Balay, Marie Estienney, A.H. Kamel, Gaël Belliot, Laboratoire de sérologie-virologie (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand ( CHU Dijon ), Laboratoire Interactions Muqueuses Agents Transmissibles ( LIMA ), and Université de Bourgogne ( UB )
Subjects: Microbiology (medical), MESH : Molecular Sequence Data, Genotype, MESH : Molecular Epidemiology, Molecular Sequence Data, MESH : Genotype, Biology, medicine.disease_cause, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Disease Outbreaks, Virology, medicine, MESH : Cluster Analysis, MESH : RNA, Viral, Cluster Analysis, Humans, MESH : Disease Outbreaks, MESH : France, Phylogeny, Caliciviridae Infections, Molecular Epidemiology, MESH : Seasons, Molecular epidemiology, MESH : Norovirus, MESH : Humans, Norovirus, MESH : Phylogeny, Outbreak, Sequence Analysis, DNA, biology.organism_classification, Caliciviridae, Gastroenteritis, MESH : Gastroenteritis, Gastroenteritis outbreak, RNA, Viral, France, Seasons, MESH : Caliciviridae Infections, MESH : Sequence Analysis, DNA
Abstract: Analysis of 316 outbreaks of gastroenteritis in France from September 2007 through March 2009 showed that genogroup II.4 (GGII.4) noroviruses were predominant and mostly belonged to the 2006b variant. However, the new GGII.4 variants, variant 2008 and the newly discovered Cairo variant from the Middle East, were also detected. The epidemiological survey suggests that these new variants might become the next predominant strains.
Published: 2009
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49. Low prevalence of HIV type 1 drug resistance mutations in untreated, recently infected patients from Burkina Faso, Côte d'Ivoire, Senegal, Thailand, and Vietnam: the ANRS 12134 study

Author: Dominique Costagliola, Coumba Toure Kane, Nicole Ngo-Giang-Huong, Eric Delaporte, Diane Valéa, Halimatou Diop, Eitel Mpoudi Ngole, Truong Xuan Lien, Avelin F. Aghokeng, Dominique Joulia-Ekaza, Eric Nerrienet, Laurence Vergne, Marie-Laure Chaix, Janin Nouhin, Ahidjo Ayouba, François Rouet, Thomas d. 'Aquin Toni, Martine Peeters, VIH/SIDA et maladies associées, Université Montpellier 1 (UM1), Institut Pasteur d'Ho Chi Minh Ville, Réseau International des Instituts Pasteur (RIIP), Institut Pasteur du Cambodge, CRESAR/IMPM/IRD - Virology, CRESAR/IMPM/IRD, Épidémiologie clinique, santé mère-enfant et VIH en Asie du Sud-Est (IRD_PHPT), Harvard University [Cambridge]-Chiang Mai university (Thaïlande), Laboratoire Bactériologie-Virologie, Hôpital Aristide-Le-Dantec, Institut de Recherche en Sciences de la Santé (IRSS) / Centre Muraz, Centre de recherche et de Diagnostic sur le Sida (CeDreS), CHU Treichville, Epidémiologie Clinique et Traitement de l'Infection à VIH, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Virologie, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP], Université Montpellier 1 ( UM1 ), Réseau International des Instituts Pasteur ( RIIP ) -Institut Pasteur d'Ho Chi Minh Ville, Institut Pasteur du Cambodge-Réseau International des Instituts Pasteur ( RIIP ), Épidémiologie clinique, santé mère-enfant et VIH en Asie du Sud-Est ( IRD_PHPT ), Centre de recherche et de Diagnostic sur le Sida ( CeDreS ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IFR113-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Assistance publique - Hôpitaux de Paris (AP-HP)-Université Paris Descartes - Paris 5 ( UPD5 ) -CHU Necker - Enfants Malades [AP-HP], Harvard University [Cambridge]-Chiang Mai University (CMU), Centre de recherche et de Diagnostic sur le Sida [Abidjan, Côte d'Ivoire] (CeDreS), Centre Hospitalier Universitaire de Treichville [Abidjan, Côte d'Ivoire] (CHU de Treichville), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), and Harvard University-Chiang Mai University (CMU)
Subjects: MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, MESH : Prevalence, MESH : Genotype, HIV Infections, Drug resistance, 030312 virology, MESH: HIV-1, MESH: Genotype, 0302 clinical medicine, MESH: Pregnancy, HIV Protease, Pregnancy, Genotype, Epidemiology, Prevalence, Medicine, MESH : HIV Reverse Transcriptase, MESH : Female, 030212 general & internal medicine, MESH: Anti-HIV Agents, Pregnancy Complications, Infectious, MESH: Phylogeny, Phylogeny, 0303 health sciences, MESH: Drug Resistance, Viral, biology, virus diseases, MESH: HIV Infections, MESH : Adult, Thailand, MESH : Senegal, HIV Reverse Transcriptase, Senegal, 3. Good health, MESH : Drug Resistance, Viral, Infectious Diseases, Vietnam, MESH: Young Adult, Lentivirus, Female, Sample collection, MESH : Mutation, HIV drug resistance, MESH : HIV-1, Adult, medicine.medical_specialty, MESH: Mutation, MESH: Cote d'Ivoire, MESH: HIV Reverse Transcriptase, Anti-HIV Agents, Immunology, Molecular Sequence Data, MESH : Young Adult, Cote d ivoire, Context (language use), 03 medical and health sciences, MESH: HIV Protease, Young Adult, MESH: Senegal, Virology, [ SDV.MHEP ] Life Sciences [q-bio]/Human health and pathology, parasitic diseases, Burkina Faso, Drug Resistance, Viral, MESH : HIV Infections, Humans, MESH: Pregnancy Complications, Infectious, MESH: Burkina Faso, MESH : Burkina Faso, MESH: Thailand, MESH: Prevalence, MESH: Humans, MESH: Molecular Sequence Data, business.industry, MESH : Anti-HIV Agents, MESH : Humans, MESH : Phylogeny, MESH: Adult, MESH : Vietnam, MESH : Cote d'Ivoire, Sequence Analysis, DNA, biology.organism_classification, MESH : Thailand, MESH : HIV Protease, MESH : Pregnancy, Cote d'Ivoire, MESH : Pregnancy Complications, Infectious, Mutation, HIV-1, MESH: Vietnam, business, MESH: Female, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, MESH : Sequence Analysis, DNA
Abstract: International audience; The frequency of transmitted HIV drug resistance (HIVDR) was evaluated in the context of rapid scale-up of antiretroviral treatment in Thailand, Vietnam, Burkina Faso, Côte d'Ivoire, and Senegal by using an adaptation of the WHO generic protocol of the HIV Drug Resistance Threshold Survey (HIVDR-TS) for sample collection and classification. Resistance-associated mutations were interpreted using the 2009 WHO list for epidemiological surveys. We included 266 subjects from the five study sites. Of the 266 RT and PR sequences analyzed, two from Vietnam harbored virus with major drug resistance mutations (G190A in RT for one individual and M46I in PR for the second individual). Phylogenetic analysis revealed that CRF01_AE predominates (>90%) in Thailand and Vietnam. CRF02 (>65%) cocirculates with other HIV-1 variants in Senegal and Côte d'Ivoire. The prevalence of HIVDRM is scored as low (< or = 5%) in all the five sites for the three drug classes analyzed. A continuous population survey for HIVDRM will provide a rational basis for maintaining or changing the current first line regimen in these countries.
Published: 2009
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50. HIV-1 gp41-specific monoclonal mucosal IgAs derived from highly exposed but IgG-seronegative individuals block HIV-1 epithelial transcytosis and neutralize CD4(+) cell infection: an IgA gene and functional analysis

Author: L. Diomede, Tudor D, C Moog, Reynes Jm, Anne Sophie Drillet, Houimel M, Lucia Lopalco, Morgane Bomsel, Derrien M, Institut Cochin (UMR_S567 / UMR 8104), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Pathogénie des infections Virales Persistantes, Université Louis Pasteur - Strasbourg I-Faculté de Médecine-Institut de Virologie, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Institut Cochin ( UMR_S567 / UMR 8104 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Pasteur du Cambodge-Réseau International des Instituts Pasteur ( RIIP ), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)
Subjects: Immunoglobulin A, Sexually transmitted disease, CD4-Positive T-Lymphocytes, MESH : Molecular Sequence Data, MESH: HIV Envelope Protein gp41, MESH: Virus Internalization, Sequence Homology, MESH : Vagina, HIV Infections, Cervix Uteri, MESH : Sexual Partners, MESH: Amino Acid Sequence, HIV Antibodies, MESH: Antibodies, Monoclonal, MESH: HIV-1, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Immunology and Allergy, MESH: Sexual Partners, MESH : Female, MESH : Mucous Membrane, MESH: Sequence Homology, Gene Rearrangement, B-Lymphocyte, MESH: Peptide Fragments, MESH : HIV Seronegativity, Conserved Sequence, MESH: HIV Seronegativity, MESH: Conserved Sequence, biology, MESH : Amino Acid Sequence, MESH : Sequence Alignment, MESH: Gene Rearrangement, B-Lymphocyte, MESH : Immunoglobulin A, Secretory, Antibodies, Monoclonal, MESH: CD4-Positive T-Lymphocytes, Environmental exposure, MESH: HIV Infections, MESH: Cervix Uteri, MESH : Adult, MESH : Immunity, Innate, HIV Envelope Protein gp41, MESH: Immunoglobulin Fab Fragments, Sexual Partners, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Transcytosis, MESH : Antibodies, Monoclonal, MESH : CD4-Positive T-Lymphocytes, Monoclonal, Vagina, Female, MESH: Immunity, Innate, Antibody, MESH : HIV-1, Adult, Immunology, Molecular Sequence Data, MESH: Environmental Exposure, MESH: Sequence Alignment, Gp41, Immunoglobulin Fab Fragments, MESH : HIV Antibodies, MESH : Immunoglobulin Fab Fragments, Peptide Library, MESH : Peptide Library, MESH : Sequence Homology, MESH : Conserved Sequence, HIV Seronegativity, MESH : HIV Infections, MESH : Virus Internalization, Humans, Amino Acid Sequence, Mucous Membrane, MESH: Molecular Sequence Data, MESH: Humans, MESH: HIV Antibodies, MESH : Humans, MESH : Peptide Fragments, MESH: Mucous Membrane, MESH: Adult, Gene rearrangement, Environmental Exposure, Virus Internalization, Virology, Immunity, Innate, Peptide Fragments, MESH : HIV Envelope Protein gp41, MESH: Immunoglobulin A, Secretory, MESH : Gene Rearrangement, B-Lymphocyte, MESH: Vagina, MESH : Cervix Uteri, Immunoglobulin A, Secretory, biology.protein, HIV-1, MESH: Peptide Library, Sequence Alignment, MESH : Environmental Exposure, MESH: Female
Abstract: International audience; AIDS is mainly a sexually transmitted disease, and accordingly, mucosal tissues are the primary sites of natural human immunodeficiency virus type-1 (HIV-1) transmission. Mucosal immunoglobulin A (IgA) antibody specific for HIV-1 envelope gp41 subunit is one correlate of protection in individuals who are highly sexually exposed to HIV-1 but remain persistently IgG seronegative (HEPS). Understanding these peculiar IgAs at the gene and functional level is possible only with monoclonal IgAs. We have constructed a mucosal Fab IgA library from HEPS and have characterized a series of HIV-1 IgAs specific for gp41 that, in vitro, are transcytosis-blocking and infection-neutralizing. Characterization of their IgA genes shows that Fab specific for the gp41 membrane-proximal region harbors a long heavy-chain CDR3 loop (CDRH3) similar to the two broadly neutralizing IgG monoclonal antibodies, 2F5 and 4E10. Furthermore, the selected Fab IgA shows extensive somatic mutations that cluster in the CDR regions, indicating that affinity maturation due to an antigen-driven process had occurred in HEPS individuals, presumably upon multiple exposures to HIV. This analysis of HEPS monoclonal IgA gives a unique opportunity to correlate an antibody function (resistance to a pathogen in vivo) with an antibody gene. Such neutralizing monoclonal IgAs could be used in microbicide formulation.
Published: 2009
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