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1. The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses.

Author

Stelzer G, Rosen N, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, Stein TI, Nudel R, Lieder I, Mazor Y, Kaplan S, Dahary D, Warshawsky D, Guan-Golan Y, Kohn A, Rappaport N, Safran M, and Lancet D

Subjects
High-Throughput Nucleotide Sequencing, Humans, Phenotype, Proteome, Software standards, Data Mining methods, Databases, Genetic, Genomics methods, Sequence Analysis methods
Abstract

GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It automatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. VarElect's capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses. © 2016 by John Wiley & Sons, Inc., (Copyright © 2016 John Wiley & Sons, Inc.)

Published
2016
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2. α-Fucosidases with different substrate specificities from two species of Fusarium

Author

Jonathan D. Walton, Janet M. Paper, John S. Scott-Craig, Mareike Bongers, Richard E. Wiemels, Ahmed Faik, David Cavalier, and Melissa S. Borrusch

Subjects
alpha-L-Fucosidase, Genetics, Subfamily, Sequence Homology, Amino Acid, Sequence analysis, Molecular Sequence Data, Fungal genetics, food and beverages, Sequence alignment, Sequence Analysis, DNA, General Medicine, Biology, biology.organism_classification, Applied Microbiology and Biotechnology, Substrate Specificity, Pichia pastoris, Microbiology, Fusarium, Fusarium oxysporum, Glycosides, DNA, Fungal, Sequence Alignment, Gene, Trichoderma reesei, Biotechnology
Abstract

Two fungal-secreted α-fucosidases and their genes were characterized. FoFCO1 was purified from culture filtrates of Fusarium oxysporum strain 0685 grown on l-fucose and its encoding gene identified in the sequenced genome of strain 4287. FoFCO1 was active on p-nitrophenyl-α-fucoside (pNP-Fuc), but did not defucosylate a nonasaccharide (XXFG) fragment of pea xyloglucan. A putative α-fucosidase gene (FgFCO1) from Fusarium graminearum was expressed in Pichia pastoris. FgFCO1 was ∼1,800 times less active on pNP-Fuc than FoFCO1, but was able to defucosylate the XXFG nonasaccharide. Although FgFCO1 and FoFCO1 both belong to Glycosyl Hydrolase family 29, they share

Published
2012

3. Urban Environmental Improvement on the Falling Birthrate and Parenting Support: History as Seen from the Structural Analysis and Sequence Analysis of the Measures

Author

Departmental Bulletin Paper and 鹿児島純心女子大学

Subjects
少子化対策、子育て支援、子育てバリアフリー、シークエンス分析, Parenting support, Childcare for barrier-free, Sequence Analysis, Falling birthrate
Abstract

Recently，the concept of barrier-free and universal design has been focused on the urban environmental improvement.This study, following up on my previous study in 2010,fucuses on the viewpoint about child and child care in the city planning in Japan. The gavernment documents were analyzed by the structural analysis and sequence analysis. Falling birthrate and Parenting support on Government policy.A typical keyword is home, residence, road, theatre, park, and, the childcare for barrier-free including toilet, nursing room, elimination of steps. Particularly, on the "Plus one of falling birthrate"(2000), The term of Childcare for barrier-free came to be used. "Support plan on child and child care" are proposed to support the most detailed, Then Development along with the central issue is gone but hardly enough. In this study, The cause of low fertility can not say the urban environment are in place.But Depend on future research on hearing the needs of users.

Published
2012

4. BMC Genomics

Author

Grace C. Davey, Penelope K. Lindeque, Richard Reinhardt, Christophe Klopp, Pascal Favrel, Dario Moraga, Pierre Boudry, Sylvie Lapegue, Patrick Prunet, Arnaud Huvet, Julien de Lorgeril, Jeanne Moal, Viviane Boulo, Elodie Fleury, Christophe Lelong, Christopher Sauvage, Patrick Wincker, François Moreews, Michel Mathieu, Frédérick Gavory, Arnaud Tanguy, Caroline Fabioux, Charlotte Corporeau, Evelyne Bachère, Jenny P. Shaw, Yannick Gueguen, Laboratoire Environnement Ressources Morbihan Pays de Loire (LERMPL), LITTORAL (LITTORAL), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Physiologie et Ecophysiologie des Mollusques Marins (PE2M), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Ecosystèmes lagunaires : organisation biologique et fonctionnement (ECOLAG), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Brest (UBO), Plymouth Marine Laboratory (PML), Max-Planck-Institut für Molekulare Genetik (MPIMG), Max-Planck-Gesellschaft, Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Institut National de la Recherche Agronomique (INRA), Génétique fonctionnelle, agronomie et santé [IFR 140] (GFAS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Diagnostics Centre (NDC), National University of Ireland [Galway] (NUI Galway), Laboratoire de Génétique et Pathologie (LGP), Amélioration génétique, du contrôle des performances et de la santé des mollusques marins (AGSAE), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Systèmes d'Elevage, Nutrition Animale et Humaine (SENAH), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Rennes, Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Laboratoire de Physiologie des Invertébrés (LPI), Physiologie Fonctionnelle des Organismes Marins (PFOM), The research presented in this paper was performed within the framework of several research projects funded by: Genoscope (11/AP2006-2007), Marine Genomics Network of Excellence (GOCE-CT-2004-505403), the European project 'Aquafirst' (513692) in the Sixth Framework Program, ANR 'CgPhysiogène' (ANR-06-GANI-0009) and 'Gametogenes' (ANR-08-GENM-041), ANR-06-GANI-0009,CgPhysiogene,Bases moléculaires des fonctions physiologiques de l'huître Crassostrea gigas : interactions hôte/pathogène/milieu(2006), ANR-08-GENM-0041,Gametogenes,Génomiques de la gamétogénèse chez l'huître creuse Crassostrea gigas(2008), Laboratoire Laboratoire Environnement Ressources Morbihan Pays de Loire (LER/MPL), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Adaptation et Biologie des Invertébrés en Conditions Extrêmes (ABICE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Plymouth Marine Laboratory, Institut National de la Recherche Agronomique (INRA)-IFR140, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Ecole Nationale Supérieure Agronomique de Rennes-Institut National de la Recherche Agronomique (INRA), Unité de Biométrie et Intelligence Artificielle de Toulouse [Castanet-Tolosan] (UBIA), Institut National de la Recherche Agronomique (INRA)-Plateforme bioinformatique du GIS GENOTOUL - Génopole Toulouse Midi-Pyrénées, Laboratoire de Physiologie des Invertébrés [Plouzané] (LPI), Adaptation et diversité en milieu marin (AD2M), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-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 de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Oyster, genome annotation, génomique fonctionnelle, computer.software_genre, Genome, User-Computer Interface, single nucleotide polymorphisms, Databases, Genetic, crassostrea gigas, structure du génome, Expressed Sequence Tags, base de données, 0303 health sciences, Expressed sequence tag, biology, Database, 04 agricultural and veterinary sciences, Genomics, crustacea, Pacific oyster, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], energy-balance, factor-beta superfamily, DNA microarray, expression des gènes, Biotechnology, lcsh:QH426-470, Sequence analysis, lcsh:Biotechnology, kappa-b, Polymorphism, Single Nucleotide, génomique, 03 medical and health sciences, biology.animal, lcsh:TP248.13-248.65, Genetics, summer mortality, Animals, Crassostrea, 030304 developmental biology, Gene Library, Whole genome sequencing, [SDV.GEN]Life Sciences [q-bio]/Genetics, huître, cell-development, génome, Gene Expression Profiling, linkage maps, Sequence Analysis, DNA, biology.organism_classification, lcsh:Genetics, coquillage, 040102 fisheries, 0401 agriculture, forestry, and fisheries, identification, marine genomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Microsatellite Repeats
Abstract

Background Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism.

Published
2009

5. Mucin CYS domains are ancient and highly conserved modules that evolved in concert

Author

Jean-Luc Desseyn, Lille Inflammation Research International Center - U 995 (LIRIC), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Institut de médecine predictive et de recherche thérapeutique (IMPRT), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Centre Régional de Lutte contre le Cancer Oscar Lambret [Lille] (UNICANCER/Lille), Université Lille Nord de France (COMUE)-UNICANCER-Université Lille Nord de France (COMUE)-UNICANCER-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Droit et Santé-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Université Lille 2 - Faculté de Médecine, The author gratefully acknowledges Dr. V. Gouyer (INSERM U795 and EA3925, Lille, France) and Pr. F. Gottrand (EA3925, University of Lille, France) for their critical comments. The author is indebted to Dr. P. Amieux (University of Washington, Seattle, WA) for help in improving the style of the paper., Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Université de Lille-UNICANCER-Université de Lille-UNICANCER-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Droit et Santé-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Faculté de Médecine Henri Warembourg - Université de Lille, and Lille Inflammation Research International Center - U 995 [LIRIC]

Subjects
MESH: Sequence Analysis, DNA, Animals, Conserved Sequence, Cysteine, Evolution, Molecular, Exons, Humans, Mucins, Phylogeny, Protein Interaction Domains and Motifs, Sequence Alignment, Sequence Analysis, DNA, [SDV]Life Sciences [q-bio], CYS domain, Genome, MUC5B, Exon, 0302 clinical medicine, Gel-forming mucin, MESH: Animals, MESH: Phylogeny, Genetics, 0303 health sciences, Concerted evolution, MESH: Conserved Sequence, Biochemistry, Coding repeats, MESH: Sequence Alignment, Biology, Evolution, Molecular, 03 medical and health sciences, MESH: Evolution, Molecular, MESH: Mucins/genetics, Amino acid residue, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH: Protein Interaction Domains and Motifs, MESH: Humans, MESH: Mucins/metabolism, Mucin, Sequence Analysis, DNA, MUC5AC, MESH: Cysteine/genetics, Mucus, MUC2, MESH: Exons, 030217 neurology & neurosurgery, Function (biology)
Abstract

International audience; Background : Many large secreted gel-forming mucins contain multiple copies of a "naked" cysteine-enriched domain (CYS domain) that interrupt or are adjacent to mucin domains (Ser/Thr/Pro regions). There is less similarity of homologous CYS sequences between species than there is across CYS repeats within species. These CYS domains are likely implicated in reversible mucin-mucin interactions that play a central role in mucus properties. Results : The use of multiple genome sequences in a comparative analysis of CYS sequences identified new mucins containing the CYS domain in various species. Furthermore, analysis showed that this domain is at least 650 million-year old and that CYS sequences evolved under strong selective pressure in concerted fashion in all species examined by two mechanisms that never coexist within a given gene: either multiplication of exons encoding CYS modules or successive intra-exonic duplications. Conclusion : The CYS sequences appear to have undergone concerted evolution with a high selective pressure to conserve cysteine and other amino acid residues. This domain is the best-conserved domain in secreted mucins pointing toward an important common function in many different organisms.

Published
2008