Philippe JEAN-PIERRE

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• Type de publi. : Communication dans un congrès
• Date de publi. : 21/10/2007
• Auteurs : Anne-Sophie WalkerVéronique DecognetMarc FermaudAlexandre BoutJohann ConfaisPierre LerouxAngelique GautierFabián MartínezJean RoudetPhilippe C. NicotMarc BardinPhilippe RobinMélody PotronElisabeth Fournier
• Organismes : BIOlogie et GEstion des Risques en agriculture Unité de Pathologie Végétale Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) Institut Sophia Agrobiotech BIOlogie et GEstion des Risques en agriculture BIOlogie et GEstion des Risques en agriculture BIOlogie et GEstion des Risques en agriculture Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) Unité de Pathologie Végétale Unité de Pathologie Végétale BIOlogie et GEstion des Risques en agriculture BIOlogie et GEstion des Risques en agriculture BIOlogie et GEstion des Risques en agriculture

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Fichiers liés : 2007-Walker-Cape Town-pop genet_1.pdf

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• Type de publi. : Article dans une revue
• Date de publi. : 18/10/2007
• Auteurs : Gert SclepJoke AllemeerschRobin LiechtiBjörn de MeyerJim BeynonRishikesh BhaleraoYves MoreauWilfried NietfeldJean-Pierre RenouPhilippe ReymondMartin KuiperPierre Hilson
• Organismes : Universiteit Gent = Ghent University = Université de Gand
• Publié dans BMC Bioinformatics le 01/11/2020

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Résumé : Abstract Background The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries [1] to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research community. The CATMA initiative offers the power and flexibility to regularly update the GST collection according to evolving knowledge about the gene repertoire. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies. This ongoing initiative has already produced approximately 24,000 GSTs that have been made publicly available for spotted microarray printing and RNA interference. Results GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002) were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts, TIGR5 and PSB-EuGène, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an adjusted version of the Specific Primer and Amplicon Design Software (SPADS). A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA. Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 protein-encoding nuclear gene models in the TAIR6 and EuGène genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family Tags or GFTs) to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition. Conclusion To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA repertoire is available through the CATMA database http://www.catma.org.

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Fichiers liés : 2007_Sclep_BMC_Bioinformatics.pdf

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• Type de publi. : Communication dans un congrès
• Date de publi. : 14/10/2007
• Auteurs : Ibrahim CheddadiPierre SaramitoGraner FrançoisPhilippe MarmottantChristophe Raufaste
• Organismes : Modelling, Observations, Identification for Environmental Sciences Modelling, Observations, Identification for Environmental Sciences Laboratoire de Spectrométrie Physique Laboratoire de Spectrométrie Physique Institut de Recherche sur les Phénomènes Hors Equilibre Laboratoire de Spectrométrie Physique Physique et mécanique des milieux hétérogènes

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• Type de publi. : Communication dans un congrès
• Date de publi. : 14/10/2007
• Auteurs : Jean-Philippe TardifPeter SturmSébastien Roy
• Organismes : Département d'Informatique et de Recherche Opérationnelle [Montreal] Interpretation and Modelling of Images and Videos Département d'Informatique et de Recherche Opérationnelle [Montreal]

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Résumé : We present an algorithm for plane-based self-calibration of cameras with radially symmetric distortions given a set of sparse feature matches in at least two views. The projection function of such cameras can be seen as a projection with a pinhole camera, followed by a non-parametric displacement of the image points in the direction of the distortion center. The displacement is a function of the points' distance to the center. Thus, the generated distortion is radially symmetric. Regular cameras, fish-eyes as well as the most popular central catadioptric devices can be described by such a model. Our approach recovers a distortion function consistent with all the views, or estimates one for each view if they are taken by different cameras. We consider a least squares algebraic solution for computing the homography between two views that is valid for rectified (undistorted) point correspondences. We observe that the terms of the function are bilinear in the unknowns of the homography and the distortion coefficient associated to each point. Our contribution is to approximate this non-convex problem by a convex one. To do so, we replace the bilinear terms by a set of new variables and obtain a linear least squares problem. We show that like the distortion coefficients, these variables are subject to monotonicity constraints. Thus, the approximate problem is a convex quadratic program. We show that solving it is sufficient for accurately estimating the distortion parameters. We validate our approach on simulated data as well as on fish-eye and catadioptric cameras. We also compare our solution to three state-of-the-art algorithms and show similar performance.

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Fichiers liés : TardifSturmRoy-iccv2007.pdf

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• Type de publi. : Article dans une revue
• Date de publi. : 12/10/2007
• Auteurs : Sabeeha S MerchantSimon E ProchnikOlivier VallonElizabeth H HarrisSteven J KarpowiczGeorge B WitmanAstrid TerryAsaf SalamovLillian K Fritz-LaylinLaurence Maréchal-DrouardWallace F MarshallLiang-Hu QuDavid R NelsonAnton A SanderfootMartin H SpaldingVladimir V KapitonovQinghu RenPatrick FerrisErika LindquistHarris ShapiroSusan M LucasJane GrimwoodJeremy SchmutzPierre CardolHeriberto CeruttiGuillaume ChanfreauChun-Long ChenValérie CognatMartin T CroftRachel DentSusan DutcherEmilio FernándezHideya FukuzawaDavid González-BallesterDiego González-HalphenArmin HallmannMarc HanikenneMichael HipplerWilliam InwoodKamel JabbariMing KalanonRichard KurasPaul A LefebvreStéphane D. LemaireAlexey V LobanovMartin LohrAndrea ManuellIris MeierLaurens MetsMaria MittagTelsa MittelmeierJames V MoroneyJeffrey MoseleyCarolyn NapoliAurora M NedelcuKrishna K NiyogiSergey V NovoselovIan T PaulsenGreg PazourSaul PurtonJean-Philippe RalDiego Mauricio Riaño-PachónWayne RiekhofLinda RymarquisMichael SchrodaDavid L. SternJames UmenRobert WillowsNedra WilsonSara Lana ZimmerJens AllmerJanneke BalkKaterina BisovaChong-Jian ChenMarek EliasKarla GendlerCharles HauserMary Rose LambHeidi LedfordJoanne C LongJun MinagawaM Dudley PageJunmin PanWirulda PootakhamSanja RojeAnnkatrin RoseEric StahlbergAimee M TerauchiPinfen YangSteven BallChris BowlerCarol L DieckmannVadim N GladyshevPamela GreenRichard JorgensenStephen MayfieldBernd Mueller-RoeberSathish RajamaniRichard T SayrePeter BroksteinInna DubchakDavid GoodsteinLeila Hornicky Wayne HuangJinal JhaveriYigong LuoDiego MartínezWing Chi Abby NgauBobby OtillarAlexander PoliakovAaron PorterLukasz SzajkowskiGregory WernerKemin ZhouIgor V GrigorievDaniel S RokhsarArthur R Grossman
• Organismes : Department of Chemistry and Biochemistry Department of Energy / Joint Genome Institute Physiologie membranaire et moléculaire du chloroplaste Department of Biology Department of Chemistry and Biochemistry Department of Cell Biology Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Molecular & Cell Biology [Berkeley] Institut de Biologie Moléculaire des Plantes Department of Biochemistry and Biophysics Biotechnology Research Center Department of Molecular Sciences and Center of Excellence in Genomics and Bioinformatics Department of Plant Biology Department of Genetics, Development, and Cell Biology Genetic Information Research Institute The Institute for Genomic Research Plant Biology Laboratory Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Stanford School of Medicine [Stanford] Stanford School of Medicine [Stanford] Physiologie membranaire et moléculaire du chloroplaste Plant Biology Institute, Department of Life Sciences School of Biological Sciences–Plant Science Initiative Department of Chemistry and Biochemistry Biotechnology Research Center Institut de Biologie Moléculaire des Plantes Department of Plant Sciences Department of Plant and Microbial Biology [Berkeley] Department of Genetics Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Graduate School of Biostudies Department of Plant Biology [Carnegie] Departamento de Genética Molecular, Instituto de Fisiología Celular Department of Cellular and Developmental Biology of Plants Plant Biology Institute, Department of Life Sciences Institute for Plant Biochemistry and Biotechnology Department of Plant and Microbial Biology [Berkeley] Institut Jacques Monod Plant Cell Biology Research Centre, The School of Botany Physiologie membranaire et moléculaire du chloroplaste Department of Plant Biology Institut de biotechnologie des plantes Department of Biochemistry Institut für Allgemeine Botanik Department of Cell Biology and Skaggs Institute for Chemical Biology PCMB and Plant Biotechnology Center Molecular Genetics and Cell Biology Institut für Allgemeine Botanik und Pflanzenphysiologie Department of Molecular and Cellular Biology [University of Arizona] Department of Biological Science Department of Plant Biology [Carnegie] Biology Institute Department of Biology Department of Plant and Microbial Biology [Berkeley] Department of Biochemistry The Institute for Genomic Research Department of Physiology Department of Biology Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 University of Potsdam = Universität Potsdam Department of Medicine Delaware Biotechnology Institute Institute of Biology II/Plant Biochemistry Boyce Thompson Institute [Ithaca] Plant Biology Laboratory Department of Chemistry and Biomolecular Sciences Department of Anatomy and Cell Biology Boyce Thompson Institute [Ithaca] Izmir Ekonomi Universitesi Department of Plant Sciences Institute of Microbiology Biotechnology Research Center Department of Plant Physiology, Faculty of Sciences Biology Institute Bioinformatics Program Department of Biology Department of Plant and Microbial Biology [Berkeley] Department of Chemistry and Biochemistry Institute of Low-Temperature Science Department of Chemistry and Biochemistry Department of Biology Department of Plant Biology [Carnegie] Institute of Biological Chemistry Appalachian State University PCMB and Plant Biotechnology Center Department of Chemistry and Biochemistry Department of Biology Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 Institut Jacques Monod Cell Signaling Laboratory Department of Molecular and Cellular Biology [University of Arizona] Department of Biochemistry Delaware Biotechnology Institute Biology Institute Department of Cell Biology and Skaggs Institute for Chemical Biology University of Potsdam = Universität Potsdam Graduate Program in Biophysics PCMB and Plant Biotechnology Center Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Energy / Joint Genome Institute Department of Molecular & Cell Biology [Berkeley] Department of Plant Biology [Carnegie]
• Publié dans Science le 22/10/2020

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Résumé : Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.

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• Type de publi. : Communication dans un congrès
• Date de publi. : 04/10/2007
• Auteurs : Nicolas BellegardePhilippe DessanteJean-Claude VannierPierre Vidal
• Organismes : SUPELEC-Campus Gif SUPELEC-Campus Gif SUPELEC-Campus Gif SUPELEC-Campus Gif

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Résumé : This paper is about a modelling and an optimisation of an electromechanical drive system. The device consists of a DC source, a power converter, a linear actuator and its load. The aim of the system is to drive a load along a linear displacement. The two main objectives are to reduce the actuator volume and the copper losses, which are contrary objectives. Here, we present an analytical modelling of the system and afterwards an optimisation of the linear actuator main dimensions in order to carry out the previous objectives.

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Fichiers liés : 5_N.Bellegarde_Supelec.pdf

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• Type de publi. : Article dans une revue
• Date de publi. : 01/10/2007
• Auteurs : C. CombadiereCharles FeumiWilliam RaoulNicole KellerMathieu P RoderoAdeline PézardSophie LavaletteMarianne HoussierLaurent JonetÉmilie PicardPatrice DebréMirna SirinyanPhilippe DeterreTania FerroukhiSalomon-Yves CohenDominique ChauvaudJean-Claude JeannySylvain ChemtobFrancine Behar-CohenFlorian Sennlaub
• Organismes : Immunologie cellulaire et tissulaire AP-HP - Hôpital de la Pitié Salpêtrière Centre de Recherche des Cordeliers Centre de Recherche des Cordeliers Centre de Recherche des Cordeliers Immunologie cellulaire et tissulaire Immunologie cellulaire et tissulaire Centre de Recherche des Cordeliers Centre de Recherche des Cordeliers Centre de Recherche des Cordeliers Centre de Recherche des Cordeliers Immunologie cellulaire et tissulaire AP-HP - Hôpital de la Pitié Salpêtrière Department of Pediatrics, Ophthalmology and Pharmacology Immunologie cellulaire et tissulaire Immunologie cellulaire et tissulaire Centre d'Angiographie et de Laser Service d'ophtalmologie [Hôtel-Dieu - Paris] Centre de Recherche des Cordeliers Department of Pediatrics, Ophthalmology and Pharmacology Centre de Recherche des Cordeliers Service d'ophtalmologie [Hôtel-Dieu - Paris] Centre de Recherche des Cordeliers
• Publié dans Journal of Clinical Investigation le 24/10/2020

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Résumé : The role of retinal microglial cells (MCs) in age-related macular degeneration (AMD) is unclear. Here we demonstrated that all retinal MCs express CX3C chemokine receptor 1 (CX3CR1) and that homozygosity for the CX3CR1 M280 allele, which is associated with impaired cell migration, increases the risk of AMD. In humans with AMD, MCs accumulated in the subretinal space at sites of retinal degeneration and choroidal neovascularization (CNV). In CX3CR1-deficient mice, MCs accumulated subretinally with age and albino background and after laser impact preceding retinal degeneration. Raising the albino mice in the dark prevented both events. The appearance of lipid-bloated subretinal MCs was drusen-like on funduscopy of senescent mice, and CX3CR1-dependent MC accumulation was associated with an exacerbation of experimental CNV. These results show that CX3CR1-dependent accumulation of subretinal MCs evokes cardinal features of AMD. These findings reveal what we believe to be a novel pathogenic process with important implications for the development of new therapies for AMD.

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Fichiers liés : Combadiere_JCI_07.pdf

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• Type de publi. : Article dans une revue
• Date de publi. : 01/10/2007
• Auteurs : Estelle Jumas-BilakJean-Philippe CarlierHélène Jean-PierreFrancine MoryCorinne TeyssierBernard GayJosiane CamposH. Marchandin
• Organismes : Laboratoire universitaire d'antibiologie Laboratoire de Bactériologie Department of Geology and Geophysics Institut de Recherche en Infectiologie de Montpellier Facultat de Fisica, Departament Universitari d'Optica Laboratoire universitaire d'antibiologie Laboratoire de Bactériologie
• Publié dans International Journal of Systematic and Evolutionary Microbiology le 31/10/2020

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Résumé : Eleven strains of a hitherto unknown, Gram-negative, anaerobic coccus were recovered from various human clinical samples of patients hospitalized in two geographically distant French hospitals. These strains displayed the morphology and growth characteristics of those related to the genus Acidaminococcus. The clinical isolates shared at least 99.9 and 99.7 % of their nucleotide positions in the 16S and 23S rRNA gene sequences, respectively. They displayed 95.6 and 88.9 % 16S and 23S rRNA gene sequence similarities, respectively, with Acidaminococcus fermentans. The 16S rRNA-based phylogeny revealed that all the clinical isolates grouped in a statistically well supported cluster separate from A. fermentans. Enzymic activity profiles as well as metabolic end product patterns, including propionic acid production, differentiated the novel bacteria from A. fermentans. Finally, phenotypic, genotypic and phylogenetic data, including large-scale chromosome structure and DNA G+C content, supported the proposal of a novel species of the genus Acidaminococcus, for which the name Acidaminococcus intestini sp. nov. is proposed. The type strain is ADV 255.99(T) (=AIP 283.01(T)=CIP 108586(T)=CCUG 50930(T)).

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• Type de publi. : Article dans une revue
• Date de publi. : 01/10/2007
• Auteurs : Benoît RousseauLudovic MénardValérie HaurieDanièle TarasJean-Frédéric BlancFrançois Moreau-GaudryPhilippe MetzlerMichel HuguesSandrine BoyaultSylvie LemièreXavier CanronPierre CostetMichael ColeCharles BalabaudPaulette Bioulac-SageJessica Zucman-RossiJean Rosenbaum
• Organismes : Fibrose hépatique et cancer du foie Fibrose hépatique et cancer du foie Fibrose hépatique et cancer du foie Fibrose hépatique et cancer du foie Fibrose hépatique et cancer du foie Service d'Hépato-Gastro-Entérologie Transfert de Genes a Visee Therapeutique Dans les Cellules Souches Fibrose hépatique et cancer du foie Fibrose hépatique et cancer du foie Génomique Fonctionnelle des Tumeurs Solides Mecanismes Moleculaires de l'Angiogenese Mecanismes Moleculaires de l'Angiogenese Animalerie spécialisée Department of Pharmacology and of Genetics Fibrose hépatique et cancer du foie Service d'Hépato-Gastro-Entérologie Fibrose hépatique et cancer du foie Service d'Hépato-Gastro-Entérologie Génomique Fonctionnelle des Tumeurs Solides Fibrose hépatique et cancer du foie
• Publié dans Hepatology le 30/10/2020

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Résumé : Using a proteomic analysis of human hepatocellular carcinoma (HCC), we identified the overexpression in 4 tumors of RuvB-like 2 (RUVBL2), an ATPase and putative DNA helicase known to interact with beta-catenin and cellular v-myc myelocytomatosis viral oncogene homolog (c-myc). RUVBL2 expression was further analyzed in tumors with quantitative reverse-transcription polymerase chain reaction analysis and immunohistochemistry; in addition, RUVBL2 expression in a HuH7 cell line was silenced by small interfering RNA or increased with a lentiviral vector. RUVBL2 messenger RNA overexpression was confirmed in 72 of 96 HCC cases, and it was associated with poorly differentiated tumors (P = 0.02) and a poor prognosis (P = 0.02) but not with beta-catenin mutations or c-myc levels. Although RUVBL2 was strictly nuclear in normal hepatocytes, tumoral hepatocytes exhibited additional cytoplasmic staining. There was no mutation in the coding sequence of RUVBL2 in 10 sequenced cases. Silencing RUVBL2 in HuH7 HCC cells reduced cell growth (P < 0.001) and increased apoptosis, as shown by DNA fragmentation (P < 0.001) and caspase 3 activity (P < 0.005). This was associated with an increased expression of several proapoptotic genes and with an increased conformational activation of Bak-1 and Bax. On the other hand, HuH7 cells with an overexpression of RUVBL2 grew better in soft agar (P < 0.03), had increased resistance to C2 ceramide-induced apoptosis (P < 0.001), and gave rise to significantly larger tumors when injected into immunodeficient Rag2/gammac mice (P = 0.016). CONCLUSION: RUVBL2 is overexpressed in a large majority of HCCs. RUVBL2 overexpression enhances tumorigenicity, and RUVBL2 is required for tumor cell viability. These results argue for a major role of RUVBL2 in liver carcinogenesis.

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Fichiers liés : Rousseau.pdf

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• Type de publi. : Article dans une revue
• Date de publi. : 01/10/2007
• Auteurs : Emmanuelle LacazeJean-Philippe MichelMichel AlbaMichel Goldmann
• Organismes : Institut des Nanosciences de Paris Institut des Nanosciences de Paris Laboratoire Léon Brillouin Institut des Nanosciences de Paris
• Publié dans Physical Review E : Statistical, Nonlinear, and Soft Matter Physics [2001-2015] le 01/11/2020

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Résumé : We study ultrathin films of 8CB in planar anchoring on a MoS(2) inorganic substrate. We evidence an anchoring breakage for 60-nm-thick films, in favor of the homeotropic anchoring at the air interface. This allows one to determine the 8CB-MoS(2) smectic anchoring energy. We then demonstrate for films thinner than 60 nm that, under the homeotropic bulk, an intermediate film remains in planar anchoring, associated with a melting of the smectic layers close to the substrate. Such a melting could be general for planar or tilted anchorings and we show that, for strong anchorings, the anchoring energy can be driven by the deformations of this intermediate nematic film.

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