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6 results on '"espèce modèle"'

1. Sex chromosome and sex locus characterization in the goldfish, Carassius auratus

Author

Hugues Parrinello, Amaury Herpin, Margot Zahm, Romain Feron, Manfred Schartl, Ming Wen, Shawn M. Burgess, Elodie Jouanno, Qiaowei Pan, Yann Guiguen, Laurent Journot, Christophe Klopp, Justine Guguin, Cédric Cabau, John H. Postlethwait, Yoshihiro Omori, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Hunan Normal University, University of Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Department of Ecology and Evolution, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), 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)-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), National Human Genome Research Institute (NHGRI), Nagahama Institute of Bio-Science and Technology, Osaka University, Institute of Neuroscience, University of Oregon [Eugene], University of Würzburg, Texas State University, This project was supported by funds from the 'Agence Nationale de la Recherche' and the 'Deutsche Forschungsgemeinschaft' (ANR/DFG, PhyloSex project, 2014-2016) to MS and YG. Montpellier Genomics (MGX) facility was supported by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). This work was also supported by Grant-in-Aid for Scientific Research (19K22426) to YO, and grants R01OD011116 and 5R01GM085318 from the USA National Institutes of Health to JHP, ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ProdInra, Migration, Blanc – Accords bilatéraux 2013 - Evolution des déterminants majeurs du sexe chez les poissons. - - PhyloSex2013 - ANR-13-ISV7-0005 - Blanc – Accords bilatéraux 2013 - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Hunan Normal University (HNU), Université de Lausanne = University of Lausanne (UNIL), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, male genome assembly, [SDV]Life Sciences [q-bio], marqueur génétique, sex determination, Locus (genetics), [MATH] Mathematics [math], [SDV.GEN] Life Sciences [q-bio]/Genetics, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, [INFO] Computer Science [cs], Biology, Y chromosome, 010603 evolutionary biology, 01 natural sciences, Genome, reproduction, 03 medical and health sciences, poisson, cyprinidae, température, Sex-determination system, chromosome sexuel, [INFO]Computer Science [cs], 14. Life underwater, goldfish, [MATH]Mathematics [math], Gene, poolseq, 030304 developmental biology, Genetics, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, détermination du sexe, génome, carassius auratus, RADseq, Sex reversal, [SDV] Life Sciences [q-bio], poisson rouge, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, espèce modèle, aquaculture, Genetic marker, facteur externe, sex markers, Heterogametic sex
Abstract

BackgroundGoldfish is an important model for various areas of research, including neural development and behavior and a species of significant importance in aquaculture, especially as an ornamental species. It has a male heterogametic (XX/XY) sex determination system that relies on both genetic and environmental factors, with high temperatures being able to produce female-to-male sex reversal. Little, however, is currently known on the molecular basis of genetic sex determination in this important cyprinid model. We used sequencing approaches to better characterize sex determination and sex-chromosomes in goldfish.ResultsOur results confirmed that sex determination in goldfish is a mix of environmental and genetic factors and that its sex determination system is male heterogametic (XX/XY). Using reduced representation (RAD-seq) and whole genome (pool-seq) approaches, we characterized sex-linked polymorphisms and developed male specific genetic markers. These male specific markers were used to distinguish sex-reversed XX neomales from XY males and to demonstrate that XX female-to-male sex reversal could even occur at a relatively low rearing temperature (18°C), for which sex reversal has been previously shown to be close to zero. We also characterized a relatively large non-recombining region (∼11.7 Mb) on goldfish linkage group 22 (LG22) that contained a high-density of male-biased genetic polymorphisms. This large LG22 region harbors 373 genes, including a single candidate as a potential master sex gene, i.e., the anti-Mullerian hormone gene (amh). However, no sex-linked polymorphisms were detected in the goldfish amh gene or its 5 kb proximal promoter sequence.ConclusionsThese results show that goldfish have a relatively large sex locus on LG22, which is likely the goldfish Y chromosome. The presence of a few XX males even at low temperature also suggests that other environmental factors in addition to temperature could trigger female-to-male sex reversal. Finally, we also developed sex-linked genetic markers in goldfish, which will be important for future research on sex determination and aquaculture applications in this species.

Published
2019
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2. Genome sequence of the euryhaline Javafish medaka, Oryzias javanicus: a small aquarium fish model for studies on adaptation to salinity

Author

Amaury Herpin, Manfred Schartl, Shigeki Yasumasu, Cédric Cabau, Koji Inoue, Margot Zahm, Kiyoshi Naruse, Céline Roques, Célia Barrachina, Cécile Donnadieu, Yusuke Takehana, Christophe Klopp, Yann Guiguen, Mari Kawaguchi, Chuya Shinzato, Olivier Bouchez, Laurent Journot, Satoshi Ansai, Nagahama Institute of Bio-Science and Technology, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sophia University, Laboratory of Bioresources, National Institute for Basic Biology [Okazaki], Atmosphere and Ocean Research Institute [Kashiwa-shi] (AORI), The University of Tokyo (UTokyo), Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg (JMU), Comprehensive Cancer Center Mainfranken, University Hospital, Hagler Institute for Advanced Study and Department of Biology, Texas A&M University System, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Hunan Normal University (HNU), This work was supported by a 'Projet Incitatif PHASE department 2015' grant (Grant ID ACI_PHASE, Institut National de la Recherche Agronomique) to AH, a NIBB Collaborative Research Initiative to KN, NIBB individual Collaboration Research Project to MK, and Grants-in-Aid for Young Scientists to YT (Grant ID 16K18590) and MK (Grant ID 16K18593). The GeT and MGX core facilities were supported by France Génomique National infrastructure, funded as partof 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). The GeT core facility was also supported by the 409 GET-PACBIO program (« Programme operationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020 »), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-16-COFA-0004,AquaCrispr,Optimization of the CRISPR/Cas9 knock-in technology and application in salmon and trout(2016), ProdInra, Migration, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Optimization of the CRISPR/Cas9 knock-in technology and application in salmon and trout - - AquaCrispr2016 - ANR-16-COFA-0004 - COFA - VALID, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique, 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)-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), The University of Tokyo, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Hunan Normal University, This work was supported by a 'Projet Incitatif PHASE department 2015' grant (Grant ID ACI_PHASE, INRAE) to AH, a NIBB Collaborative Research Initiative to KN, NIBB individual Collaboration Research Project to MK, and Grants-in-Aid for Young Scientists to YT (Grant ID 16K18590) and MK (Grant ID 16K18593). AH was additionally funded by the project AquaCRISPR (ANR-16-COFA-0004-01). The GeT and MGX core facilities were supported by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). The GeT core facility was also supported by the GET-PACBIO program (« Programme opérationnel FEDER-FSE Midi-Pyrénées et Garonne 2014-2020 »), ANR-10- INBS0009,INBS,France-Génomique, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), This work was supported by a 'Projet Incitatif PHASE department 2015' grant (Grant ID ACI_PHASE, INRAE) to AH, a NIBB Collaborative Research Initiative to KN, NIBB individual Collaboration Research Project to MK, and Grants-in-Aid for Young Scientists to YT (Grant ID 16K18590) and MK (Grant ID 16K18593). AH was additionally funded by the project AquaCRISPR (ANR-16-COFA-0004-01). The GeT and MGX core facilities were supported by France Génomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). The GeT core facility was also supported by the GET-PACBIO program (« Programme operationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020 »), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), 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)-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), and Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE)

Subjects
0106 biological sciences, Salinity, carte génétique, Evolution, [SDV]Life Sciences [q-bio], séquençage du génome complet, Sequence assembly, [SDV.GEN] Life Sciences [q-bio]/Genetics, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, QH426-470, Long reads, [INFO] Computer Science [cs], 010603 evolutionary biology, 01 natural sciences, Genome, identification de gènes, adaptation comportementale, 03 medical and health sciences, Genetic map, Genome editing, poisson, Genetics, [INFO]Computer Science [cs], 14. Life underwater, adrianichthyidae, Adaptation, 030304 developmental biology, Whole genome sequencing, tolérance à la salinité, 0303 health sciences, whole genome sequencing, Whole genome sequencing WGS, [SDV.GEN]Life Sciences [q-bio]/Genetics, Phylogenetic tree, biology, Euryhaline, biology.organism_classification, Medaka, osmorégulation, [SDV] Life Sciences [q-bio], [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, espèce modèle, séquençage du génome, eau de mer, Evolutionary biology, Oryzias javanicus, Transcriptome
Abstract

BackgroundThe genus Oryzias is constituted of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behaviour, morphology or adaptation through comparative genomic approaches, all medaka species share many advantages of experimental model organisms including small size and short generation time, transparent embryos and genome editing tools for reverse and forward genetic studies. The Java medaka, Oryzias javanicus, is one of the two species of medaka perfectly adapted for living in brackish/sea-waters. Being an important component of the mangrove ecosystem, O. javanicus is also used as a valuable marine test-fish for ecotoxicology studies. Here, we sequenced and assembled the whole genome of O. javanicus, and anticipate this resource will be catalytic for a wide range of comparative genomic, phylogenetic and functional studies.FindingsComplementary sequencing approaches including long-read technology and data integration with a genetic map allowed the final assembly of 908 Mbp of the O. javanicus genome. Further analyses estimate that the O. javanicus genome contains 33% of repeat sequences and has a heterozygosity of 0.96%. The achieved draft assembly contains 525 scaffolds with a total length of 809.7 Mbp, a N50 of 6.3 Mbp and a L50 of 37 scaffolds. We identified 21454 expressed transcripts for a total transcriptome size of 57, 146, 583 bps.ConclusionsWe provide here a high-quality draft genome assembly of the euryhaline Javafish medaka, and give emphasis on the evolutionary adaptation to salinity.

Published
2019
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3. What can a weevil teach a fly, and reciprocally? Interaction of host immune systems with endosymbionts in Glossina and Sitophilus

Author

Brian L. Weiss, Abdelaziz Heddi, Anna Zaidman-Rémy, Aurélien Vigneron, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), French ANR-13-BSV7–0016-01 (IMetSym), NIH/NIAID (AI051584), Ambrose Monell Foundation, International Atomic Energy Agency (IAEA), Zaidman-Remy, Anna, and Heddi, Abdelaziz

Subjects
0301 basic medicine, Biodiversité et Ecologie, [SDV]Life Sciences [q-bio], lcsh:QR1-502, Review, Wigglesworthia glossinidia, Cereal weevil, lcsh:Microbiology, Homeostasis, 2. Zero hunger, Tsetse fly, endosymbiosis, immunity, evolution, insects, homeostasis, biology, Sitophilus, Sodalis glossinidius, food and beverages, Biological Evolution, Insects, espèce modèle, Wolbachia, symbiose, Microbiology (medical), Sodalis, food.ingredient, Tsetse Flies, Evolution, 030106 microbiology, Zoology, Microbiology, Biodiversity and Ecology, 03 medical and health sciences, food, Enterobacteriaceae, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Symbiosis, Wigglesworthia, Host Microbial Interactions, Obligate, Endosymbiosis, Host (biology), fungi, Immunity, mouche tsé tsé, 15. Life on land, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, 030104 developmental biology, Weevils, bacteria, Pest Control, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; The tsetse fly (Glossina genus) is the main vector of African trypanosomes, which are protozoan parasites that cause human and animal African trypanosomiases in Sub-Saharan Africa. In the frame of the IAEA/FAO program 'Enhancing Vector Refractoriness to Trypanosome Infection', in addition to the tsetse, the cereal weevil Sitophilus has been introduced as a comparative system with regards to immune interactions with endosymbionts. The cereal weevil is an agricultural pest that destroys a significant proportion of cereal stocks worldwide. Tsetse flies are associated with three symbiotic bacteria, the multifunctional obligate Wigglesworthia glossinidia, the facultative commensal Sodalis glossinidius and the parasitic Wolbachia. Cereal weevils house an obligatory nutritional symbiosis with the bacterium Sodalis pierantonius, and occasionally Wolbachia. Studying insect host-symbiont interactions is highly relevant both for understanding the evolution of symbiosis and for envisioning novel pest control strategies. In both insects, the long co-evolution between host and endosymbiont has led to a stringent integration of the host-bacteria partnership. These associations were facilitated by the development of specialized host traits, including symbiont-housing cells called bacteriocytes and specific immune features that enable both tolerance and control of the bacteria. In this review, we compare the tsetse and weevil model systems and compile the latest research findings regarding their biological and ecological similarities, how the immune system controls endosymbiont load and location, and how host-symbiont interactions impact developmental features including cuticle synthesis and immune system maturation. We focus mainly on the interactions between the obligate symbionts and their host's immune systems, a central theme in both model systems. Finally, we highlight how parallel studies on cereal weevils and tsetse flies led to mutual discoveries and stimulated research on each model, creating a pivotal example of scientific improvement through comparison between relatively distant models.

Published
2018
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4. An inconvenient truth about xylem resistance to embolism in the model species for refilling Laurus nobilis L

Author

José M. Torres-Ruiz, Régis Burlett, Steven Jansen, Kathy Steppe, Laurent J. Lamarque, Ya Zhang, Nicolas Martin-StPaul, Nicolas Lenoir, Gregory A. Gambetta, Timothy J. Brodribb, Guillaume Charrier, Hervé Cochard, Jan Van den Bulcke, Brendan Choat, Sylvain Delzon, Eric Badel, Andrew King, Déborah Corso, Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Unité de Recherches Forestières Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), project 20150954, Ecophysiologie et Génomique Fonctionnelle de la Vigne (EGFV), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut des Sciences de la Vigne et du Vin (ISVV)-Université de Bordeaux (UB), and Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, 0301 basic medicine, TREE MORTALITY, [SDV]Life Sciences [q-bio], Hydraulics, Safety margin, 01 natural sciences, Microtomographie, Refilling, Xylème, Ecology, Drought resistance, food and beverages, Forestry, Horticulture, Donnée optique, Espèce modèle, NEGATIVE-PRESSURE, Stomatal conductance, TOMOGRAPHIC RECONSTRUCTION, STOMATAL CONDUCTANCE, VULNERABILITY CURVES, Biology, 03 medical and health sciences, Laurus nobilis, food, Embolie, Laurus Nobilis, medicine, CAVITATION RESISTANCE, Desiccation, HYDRAULIC SAFETY MARGIN, Resistance (ecology), fungi, Xylem embolism, X-RAY MICROTOMOGRAPHY, Biology and Life Sciences, Xylem, 15. Life on land, medicine.disease, food.food, 030104 developmental biology, Résistance à la sécheresse, Embolism, Earth and Environmental Sciences, Laurel, Fonctionnement hydraulique, OPEN VESSEL ARTIFACT, CURRENT CONTROVERSIES, 010606 plant biology & botany
Abstract

Key message: Direct, non-invasive X-ray microtomography and optical technique observations applied in stems and leaves of intact seedlings revealed that laurel is highly resistant to drought-induced xylem embolism. Contrary to what has been brought forward, daily cycles of embolism formation and refilling are unlikely to occur in this species and to explain how it copes with drought. Context: There has been considerable controversy regarding xylem embolism resistance for long-vesselled angiosperm species and particularly for the model species for refilling (Laurus nobilis L.). Aims: The purpose of this study was to resolve the hydraulic properties of this species by documenting vulnerability curves of different organs in intact plants. Methods: Here, we applied a direct, non-invasive method to visualize xylem embolism in stems and leaves of intact laurel seedlings up to 2-m tall using X-ray microtomography (microCT) observations and the optical vulnerability technique. These approaches were coupled with complementary centrifugation measurements performed on 1-m long branches sampled from adult trees and compared with additional microCT analyses carried out on 80-cm cut branches. Results: Direct observations of embolism spread during desiccation of intact laurels revealed that 50% loss of xylem conductivity (Psi(50)) was reached at - 7.9 +/- 0.5 and - 8.4 +/- 0.3 MPa in sterns and leaves, respectively, while the minimum xylem water potentials measured in the field were - 4.2 MPa during a moderate drought season. Those findings reveal that embolism formation is not routine in Laurus nobilis contrary to what has been previously reported. These Psi(50) values were close to those based on the flow-centrifuge technique (- 9.2 +/- 0.2 MPa), but at odds with microCT observations of cut branches (- 4.0 +/- 0.5 MPa). Conclusion: In summary, independent methods converge toward the same conclusion that laurel is highly resistant to xylem embolism regardless its development stage. Under typical growth conditions without extreme drought events, this species maintains positive hydraulic safety margin, while daily cycles of embolism formation and refilling are unlikely to occur in this species.

Published
2018
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5. The BioMart community portal: an innovative alternative to large, centralized data repositories

Author

Byung Woo Han, Jose Manuel Garcia-Manteiga, Alejandro Maass, Jayson Harshbarger, Daniel M. Staines, Zhengyan Kan, Davide Rambaldi, Dong Jin Han, Richard Baldock, Ji Hyun Lee, Merideth Bonierbale, Hadi Quesneville, Anthony Esposito, Thomas Letellier, Jun Wang, Steven Rosanoff, Céline Noirot, Richard D. Hayes, Sarah W. Burge, Anthony J. Brookes, Gabriele Bucci, Giulia Barbiera, Elia Stupka, Olivier Arnaiz, Thomas Maurel, Shen Hu, Olivier Sallou, Emanuela Gadaleta, Jérôme Mariette, Rosalind J. Cutts, Joseph W. Carlson, Damian Smedley, Robert C. Free, James E. Allen, Simon A. Forbes, Kevin R. Stone, Jie Luo, Andrew Blake, Chu Jun Liu, Takatomo Fujisawa, Jon W. Teague, Cristian Perez-Llamas, Rebecca Shepherd, Julio Fernandez-Banet, Raul Cordova, David Goodstein, Shi Jian Zhang, Ken Youens-Clark, Cédric Cabau, José Afonso Guerra-Assunção, Iwan Buetti, Stefania Merella, Delphine Steinbach, Linda Sperling, Robert K. Hastings, Abu Z. Dayem Ullah, Claude Chelala, Erik Dassi, Eduardo Eyras, Sunghoon Kim, Kristian Gray, Dejan Lazarevic, Luca Pandini, Azza M. Mohamed, Doreen Ware, William Spooner, Alex Di Genova, Daniel Lawson, Alessandro Quattrone, Davide Cittaro, Heather Estrella, Rhoda Kinsella, Chuan-Yun Li, Christophe Klopp, Aminah Keliet, Michela Riba, Zhi-Liang Hu, Hideya Kawaji, Arnaud Kerhornou, James M. Reecy, Tim Beck, Charalambos Chrysostomou, François Moreews, Nelson Ndegwa, Arek Kasprzyk, Michael Primig, Claire Hoede, Ibounyamine Nabihoudine, Amonida Zadissa, Paolo Provero, Reinhard Simon, Todd W. Harris, Bernard Haggarty, Lucie N. Hutchins, Marie Wong-Erasmus, Philippe Bardou, Elisa Salas, Lei Kong, Anis Djari, Syed Haider, Steffen Durinck, Mohammad Awedh, Pietro Liò, Amna A. Saddiq, Olivier Collin, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Computer Laboratory [Cambridge], University of Cambridge [UK] (CAM), Genentech, Inc., Genentech, Inc. [San Francisco], San Raffaele Scientific Institute, Vita-Salute San Raffaele University and Center for Translational Genomics and Bioinformatics, Genetics, Biology and Biochemistry, Molecular Biotechnology Centre, Centre de génétique moléculaire (CGM), Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), King Abdulaziz University, MRC Human Genetics Unit, University of Edinburgh-Western General Hospital, Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Department of Genetics [Leicester], University of Leicester, Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Medical Research Counc, International Potato Center, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Centre for Molecular Oncology and Imaging, Centre for Molecular Oncology and Imaging, Barts Cancer Institute, Plateforme bioinformatique GenOuest [Rennes], Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Plateforme Génomique Santé Biogenouest®-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec, University of Trento [Trento], University of Chile [Santiago], Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Pfizer Oncology, Institució Catalana de Recerca i Estudis Avançats (ICREA), Cancer Genome Project, The Wellcome Trust Sanger Institute [Cambridge], Kasuza DNA Research Institute, Seoul National University [Seoul] (SNU), Cold Spring Harbor Laboratory (CSHL), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), School of Dentistry and Dental Research Institute [UCLA], University of California [Los Angeles] (UCLA), University of California-University of California, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University (ISU), Mouse Genomic Informatics Group (MGI), The Jackson Laboratory, Unité de Recherche Génomique Info (URGI), Center for Bioinformatics [Pekin], Peking University [Beijing], Division of Industrial Ecology (KTH), Royal Institute of Technology [Stockholm] (KTH ), Institute of Molecular Medicine, Universidad de Santiago de Chile [Santiago] (USACH), Centro de Regulación Génica (CRG), Pontificia Universidad Católica de Chile (UC)-Universidad Andrés Bello [Santiago] (UNAB)-Universidad de Santiago de Chile [Santiago] (USACH), Centre de Modélisation Mathématique / Centro de Modelamiento Matemático (CMM), Centre National de la Recherche Scientifique (CNRS), Unité Mathématiques et Informatique Appliquées de Toulouse (MIAT), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Mathématiques et Informatique Appliquées Toulouse, Universitat Pompeu Fabra [Barcelona], Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Department of Animal Science, Eagle Genomics Ltd, Eagle Genomics, State Key Laboratory of Lithospheric Evolution (SKL), Institute of Geology and Geophysics [Beijing] (IGG), Chinese Academy of Sciences [Beijing] (CAS)-Chinese Academy of Sciences [Beijing] (CAS), University of the Chinese Academy of Sciences, Ontario Institute for Cancer Research [Canada] (OICR), Ontario Institute for Cancer Research, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, International Potato Center [Lima] (CIP), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Universidad de Chile = University of Chile [Santiago] (UCHILE), The Jackson Laboratory [Bar Harbor] (JAX), Center for Bioinformatics [Peking], Pontificia Universidad Católica de Chile (UC)-Universidad Andrés Bello [Santiago] (UNAB), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Universitat Pompeu Fabra [Barcelona] (UPF), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Santé et de la Recherche Médicale (INSERM)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université d'Angers (UA), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), University of California (UC)-University of California (UC), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Jonchère, Laurent, CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Lio, Pietro [0000-0002-0540-5053], and Apollo - University of Cambridge Repository

Subjects
Proteomics, Interface (Java), Data management, [SDV]Life Sciences [q-bio], génomique fonctionnelle, Biology, Ontology (information science), computer.software_genre, World Wide Web, Genomics, Humans, Internet, Neoplasms, Database Management Systems, Genetics, cancer, Web Server issue, protéomique, ontologie, ComputingMilieux_MISCELLANEOUS, base de données, business.industry, Toolbox, [SDV] Life Sciences [q-bio], espèce modèle, Scalability, The Internet, Web service, business, Host (network), computer
Abstract

International audience; The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.

Published
2015
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6. The LOU/c/jall Rat as an Animal Model of Healthy Aging?

Author

Gisèle Pickering, Josette Alliot, Didier Jourdan, Stéphane Boghossian, Dominique Meynial-Denis, N. Gaumet, Christelle Veyrat-Durebex, Laboratory of Neuroendocrinology of Aging, Université Blaise Pascal - Clermont-Ferrand 2 (UBP), EMI 9004, Department of Clinical Pharmacology, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Metabolisme Mineral, Institut National de la Recherche Agronomique (INRA), Université Blaise Pascal (Clermont Ferrand 2) (UBP), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), and Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université-Institut National de la Recherche Agronomique (INRA)

Subjects
Male, Aging, medicine.medical_specialty, Cross-sectional study, media_common.quotation_subject, [SDV]Life Sciences [q-bio], Sensitivity and Specificity, Body Mass Index, sexe, 03 medical and health sciences, Sex Factors, 0302 clinical medicine, Weight loss, Internal medicine, Weight Loss, medicine, Animals, rat, Rats, Wistar, Probability, 030304 developmental biology, media_common, Analysis of Variance, 0303 health sciences, Behavior, Animal, business.industry, Age Factors, Longevity, Rats, Inbred Strains, Feeding Behavior, vieillissement, medicine.disease, Adaptation, Physiological, Obesity, Rats, Cross-Sectional Studies, Endocrinology, Physiological Aging, espèce modèle, Ageing, ageing, Models, Animal, Female, Analysis of variance, Geriatrics and Gerontology, medicine.symptom, business, Body mass index, 030217 neurology & neurosurgery
Abstract

We propose the LOU/c/jall rat as a possible model for research into aging. Physiological and behavioral data have been collected over the past 5 years, using lifelong and cross-sectional studies. The median life span of the rats was 29 months in males and 33-34 months in females. A low level of body fat throughout life was observed in both sexes. Basic phenomena of aging such as body weight loss, decrease in caloric intake, and dramatic drop in protein selection were noted from the age of 18 months in males and 28 months in females. A decline in muscle mass, depending on the sex and the type of muscle, was seen. These data allowed us to demonstrate physiological aging in male and female LOU/c/jall rats. The most interesting characteristics of this strain of rat for aging studies are longevity, and the absence of obesity and of severe pathologies. Further studies are required in order to confirm this last point.

Published
2002
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