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  • 17th International Mouse Genome Conference (2003)
    1 Blake A 1 Simon M 1 Greenaway S 1 Mallon A M 1 Hancock J M 2 Davidson D Institutions 1 Bioinformatics Group MRC Mammalian Genetics Unit Harwell Oxfordshire U K 2 MRC Human Genetics Unit Edinburgh U K With the completion of the mouse genome sequence in sight emphasis is shifting to characterisation of gene function in this organism which is the major experimental model for human disease A number of large centres worldwide are investigating gene function using a variety of mutagenesis studies combined with a battery of assays designed to identify phenotypic changes resulting from induced mutations The types of change assayed for range from blood biochemistry to behaviour This poses the intriguing problem of interlinking data of these different types often held in different databases with more conventional genomic e g sequences and functional genomic e g microarray data This should allow the discovery of relationships within the data that may shed new light on gene function and its relationship to phenotype Ontologies present an increasingly popular approach to accessing expert knowledge and using it to annotate and mine data Linking phenotype and genomic data together will involve using a combination of ontologies representing a

    Original URL path: http://www.imgs.org/Archive/abstracts/2003abstracts/file186.shtml (2016-02-17)
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  • 17th International Mouse Genome Conference (2003)
    1 Mc Keone R 1 Sellick C 1 Arkell R 3 Botcherby M R M 1 Strivens M A 3 Campbell R D 2 Gregory S 1 Denny P 2 Rogers J 1 Brown SDM Institutions 1 Bioinformatics Group MRC Mammalian Genetics Unit Harwell Oxfordshire U K 2 Sanger Institute Hinxton Genome Campus U K 3 MRC UK HGMP Resource Centre Hinxton Genome Campus U K As part of the MRC UK Mouse Genome Sequencing Project we have generated a finished high quality sequence of the Del 13 Svea36H region of mouse chromosome 13 and annotated it using manual and comparative methods The region is 12 5Mb long and contains 237 genes approximately one gene every 53 kb or twice the density observed in the mouse genome as a whole It also contains c 90 pseudogenes Overall 37 5 of the sequence is genic The region contains regions syntenic to three human chromosome regions 6p22 1 6p22 3 6p25 3 end and 3q24 These are interrupted by relatively short regions with no detectable homology to human chromosome regions and no detectably unusual sequence features Both gene numbers and percentage coverage by genes varies over the region Notably there are three

    Original URL path: http://www.imgs.org/Archive/abstracts/2003abstracts/file187.shtml (2016-02-17)
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  • 17th International Mouse Genome Conference (2003)
    Institute Co Authors 1 Song F 1 Okada H 2 Matsuyama T 1 Held W A 1 Nagase H Institutions 1 Roswell Park Cancer Institute 2 RIKEN The Institute of Physical and Chemical Research DNA cytosine 5 methylation relates to various biological phenotypes such as regulation of gene transcription genomic imprinting DNA replication timing and chromatin structure in mammalian cells To identify DNA methylation changes that cause biological phenomena such as carcinogenesis we have analysed mouse genome wide methylation patterns by methylation sensitive Restriction Landmark Genomic Scanning MS RLGS RLGS is a method for the two dimensional display of 1 500 2 000 end labelled DNA restriction fragments at one try Genome wide DNA methylation status can be analysed by RLGS with methylation sensitive restriction enzymes However there are some difficulties to analyse 1 500 2 000 RLGS spots To facilitate RLGS data analysis we have developed computational software Virtual image RLGS Vi RLGS Vi RLGS analyses the total genome sequence information and indicates consequent RLGS spot patterns digested by restriction enzymes and DNA sequence information of each spots We have confirmed that most of Vi RLGS spots corresponded to real RLGS spots by PCR and sequencing experiments Thus Vi

    Original URL path: http://www.imgs.org/Archive/abstracts/2003abstracts/file188.shtml (2016-02-17)
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  • 17th International Mouse Genome Conference (2003)
    National Research Centre for Environment and Health Neuherberg Co Authors Gailus Durner V Steinkamp R Schäble K F Pargent W Tiedemann H Schneltzer E Fuchs H Hrabe de Angelis M Institutions GSF National Research Centre for Environment and Health Neuherberg The German Mouse Clinic GMC is a novel facility for the comprehensive phenotyping of approx 3000 mice per year A commercial hospital information system designed for human patients has been adjusted and functionally extended to meet our special needs for GMC data management This software now provides features including modules for facility management breeding resource management a system for workflow planning and the generation of worklists a tool to define deliberate groups of mice e g with certain biological attributes and a pedigree browser A data retrieval tool enables users to generate adhoc queries without inside knowledge of neither SQL syntax nor the database scheme Data output from various sources is automatically parsed by a variety of scripts Referential integrity checks are performed by central data interfaces running on a communication server automatically while inserting the results of phenotype analysis into the GMC database Additionally file based information like images videos etc are stored on a separate file server These

    Original URL path: http://www.imgs.org/Archive/abstracts/2003abstracts/file189.shtml (2016-02-17)
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  • 17th International Mouse Genome Conference (2003)
    Maltais L J The Jackson Laboratory Co Authors Corey R J Blake J A Eppig JT Institutions The Jackson Laboratory The Mouse Genomic Nomenclature Committee MGNC continues to deal with day to day nomenclature issues of assigning official nomenclature Our objective is to provide standardized unique designations for genes and genome features We work from published and unpublished sources through interactions with the HUGO Gene Nomenclature Committee HGNC and in consultation with the research community Quality control reports related to nomenclature are checked daily to monitor and update nomenclature entries in the Mouse Genome Informatics MGI resource http www informatics jax org The MGI nomenclature group works closely with MGI sequence annotators and with the NCBI LocusLink curation group to standardize representations of mouse genes with respect to their sequence representations Among recent updates to the nomenclature process MGI will no longer display pending symbols Rather it will be noted on the marker detail page that the symbol and name are interim and not approved MGNC will continue to assign nomenclature to only full length pseudogenes provided sequence accession IDs are associated with them In support of standardized nomenclature across the genomes the International Society for Animal Genetics ISAG decided

    Original URL path: http://www.imgs.org/Archive/abstracts/2003abstracts/file190.shtml (2016-02-17)
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  • 17th International Mouse Genome Conference (2003)
    Genomics of Infectious Disease Verne Chapman Memorial Lecture Table of Contents Sponsor Exhibitor List Awards Photographs POSTER 143 INTRODUCTION OF THE NATIONAL BIO RESOURCE PROJECT FOR THE RAT IN JAPAN Mashimo T Kyoto University Co Authors Voigt B Nakane Y Yama s aki K NakanishiS Kuramoto T Serikawa T Institutions Kyoto University Rats and mice are very important mammals in various fields of medical and biological research Even though both species appear very similar the rat is more suitable for many kinds of research due to its bigger size and neurological characteristics In Japan many unique rat models for human diseases e g hypertension diabetes epilepsy have been developed so far However lots of those unique models are not even spread throughout Japan and many of them are poorly characterized The National Bio Resource Project for the Rat in Japan NBRP Rat was established to overcome such limitations and to utilize existing resources The major goals of this project are collection of existing strains phenotypic and genotypic characterization cryopreservation of embryos distribution of the collected rat strains and creation of a publicly accessible database of all assembled data By the time more than 140 rat strains are deposited to the

    Original URL path: http://www.imgs.org/Archive/abstracts/2003abstracts/file191.shtml (2016-02-17)
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  • 17th International Mouse Genome Conference (2003)
    A Hogan J Peter Davis A Murphy L Selfors L Pagano S Tillberg M Institutions Incyte Corporation With the completion of the Mouse and Human genome sequences Incyte s Proteome BioKnowledge Library provides a unique resource for comparative genomic and proteomic analysis Search capabilities of Incyte s Proteome BioKnowledge Library allow for the interpretation of Functional Genomic and Proteomic datasets to provide insight to biological disease and pathway analysis Utilizing the sequenced genomes as the frameworks our expert Ph D curators systematically collect published protein knowledge currently sequestered throughout the literature and provide it in a concise highly navigable format Information is organized in a one page per protein format that allows one to access related proteins across species The content is updated weekly and the information is provided on line www incyte com with installed versions available to commercial organizations The Human Proteome Survey Database HumanPSD is one component of Incyte s BioKnowledge Library and compiles up to date information on the Fundamental properties of more than 39 000 characterized mammalian proteins Included in Human PSD are protein pages for 18 000 human proteins 15 000 mouse proteins and 5 000 rat proteins Proteins are characterized utilizing the descriptive

    Original URL path: http://www.imgs.org/Archive/abstracts/2003abstracts/file192.shtml (2016-02-17)
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  • 17th International Mouse Genome Conference (2003)
    School Ann Arbor MI 48109 0638 USA Co Authors 1 Brinkmeier ML 3 Ross S A 4 Carninci P 4 Shiraki T 4 Arakawa T 4 Kawai J 2 Lyons RH 1 Ward R D 3 Cook S 5 Dunwoodie S L 1 Camper SA 3 Thomas P Q 4 Hayashizaki Y Institutions 1 Human Genetics University of Michigan Medical School Ann Arbor MI 48109 0638 USA 2 Biological Chemistry University of Michigan Medical School Ann Arbor MI 48109 0638 USA 3 Murdoch Childrens Research Institute Royal Children s Hospital Melbourne VIC 3052 Australia 4 Laboratory for Genome Exploration Research Group RIKEN Genomic Sciences Center GSC RIKEN Yokohama Institute Suehiro cho Tsurumi ku Yokohama Kanagawa 230 0045 Japan 5 Victor Chang Cardiac Research Institute St Vincent s Hospital Darlinghurst NSW 2010 Australia Pituitary gland development requires the specification and proliferation of 5 different hormone producing cell types Mutations in the homeodomain transcription factor Prop1 cause combined pituitary hormone deficiency in humans and mice Prop1 deficiency appears to prevent progenitors from leaving the proliferative zone and migrating ventrally to populate the anterior lobe where differentiated cells reside We employed a gene discovery approach to identify Prop1 target genes and discover its mechanism of action We prepared three full length cDNA libraries from pituitary primordia of normal at e12 5 and e14 5 and Prop1 mutant e14 5 embryos using the cap trapper method sequenced over 30 000 clones and established a searchable database using GO terminology Several Notch signaling genes are present in the libraries Notch2 Notch3 and Dll1 are initially expressed by most cells within the pituitary primordium and become restricted to a subset of progenitors as differentiated pituitary cells begin to appear Notch2 expression is nearly absent in the developing pituitaries of Prop1 mutant mice but unaltered in some

    Original URL path: http://www.imgs.org/Archive/abstracts/2003abstracts/file193.shtml (2016-02-17)
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