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  • The 16th International Mouse Genome Conference (2002)
    Cambridge UK 2 Dept of Anatomy University of Edinburgh 3 Karolinska Institute Stockholm 4 GSF Forschungszentrum für Umwelt und Gesundheit Munich 5 Dept of Pathology University Hospital of Liege 6 Developmental Biology Institute of Biomedicine University of Helsinki 7 National Radiological Protection Board Harwell 8 School of Biological Sciences University of Bath The primary aim of the Pathbase project is to generate a web accessible database http www pathbase net of histopathological images from transgenic and mutant mice many of which are not publicly available elsewhere Access to these images is via controlled vocabularies covering genetic manipulations tissues and mouse strains via standard gene nomenclature and via a new ontology of mouse pathology phenotypes This ontology incorporates 425 known mouse pathologies hierarchically organised as instances of biological processes and is intended to help standardise the very large and internationally variable diagnostic nomenclatures in a way compatible with efficient database searching as well as facilitating the formal description of mouse mutant phenotypes The ontology will be publicly available on the Pathbase site and on the Global Open Biological Ontology site http www geneontology org Image acquisition for the database proceeds either by curator driven requests or by researchers uploading their own

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file196.shtml (2016-02-17)
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  • The 16th International Mouse Genome Conference (2002)
    genome wide sequence markers for sequencing and analyzing complex genomes We at The Institute for Genomic Research TIGR have been conducting large scale BAC end sequencing and have generated over 300 000 human BAC ends over 450 000 mouse BAC ends over 310 000 rat BAC ends and a significant number of BAC ends from a number of other mammals Through paired BAC end sequence matches we have placed more than 100 000 mouse BACs onto the mouse genome assembly generating 694 BAC contigs ranging from 5kb to 47Mb and covering 95 of the genome with 7X coverage and 700 gaps This allows us to identify a set of BACs that contain each of the complete genes across the genome for functional studies In addition we have placed more than 45 000 rat BACs onto the mouse genome generating 2 900 rat BAC contigs that cover 76 of the mouse genome with 3000 gaps However only 5000 rat BACs can be placed to the human genome with significantly lower sequence identities The data demonstrated a very similar genome structure for mouse and rat We have been able to place more than 20 000 BACs from species including human mouse rat

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file197.shtml (2016-02-17)
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  • The 16th International Mouse Genome Conference (2002)
    Table of Contents Photographs Awards Oral Presentation Sunday 17 November 17 15 17 30 HRS A PROPOSAL FOR A COMMUNITY EFFORT TO ANNOTATE THE STRUCTURE FUNCTION AND EVOLUTION OF BIOLOGICAL PATHWAYS IN A PUBLIC DATABASE J Nadeau CWRU During the next phase of the Human Genome Project research will focus on attributing functions to genes their regulatory elements and other DNA sequences While the sequencing phase could be conducted by researchers with expertise in genomics molecular biology and computer science the functional phase will involve researchers from an extraordinary variety of disciplines many of whom will have limited experience in genomics or bioinformatics To facilitate their use of genomic information in these functional studies a new perspective is urgently needed as a research tool to study genome sequences in the context of many kinds of biological information Pathways are the logical format for presenting this information in a manner that is familiar to biological researchers As a prototype we annotated the folate and homocysteine pathways with comprehensive information about the structure function and evolution of each gene in the folate and homocysteine pathways We developed a prototype pathways database for exploring ways to acquire manage display and query genomic information

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file198.shtml (2016-02-17)
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  • The 16th International Mouse Genome Conference (2002)
    J 1 Lu J 1 Shimoyama M 1 Pasko D 1 Bromberg S 1 Ginster J 1 Chen CF 1 Nigam R 1 Gopinathrao G 1 Ramachandran H 2 Kwitek Black A 4 Maglott D 4 Schuler G 5 Stahl F 5 Levan G 2 Jacob H Institutions 1 Bioinformatics Research Center and 2 Human and Molecular Genetics Center Medical College of Wisconsin 3 The Jackson Laboratory 4 National Center for Biotechnology Information NIH 5 CMB Genetics Lundberg Laboratory Gothenburg University The Rat Genome Database RGD http rgd mcw edu is a resource for comprehensive curated physiological and genomic data for rat RGD seeks to aid researchers in using the rat as a model organism for human disease by supporting the integratation of large scale rat genomic studies with ongoing literature curation Data about rat genes in RGD include homologies to mouse and human genes gene product identity gene functions and descriptive information RGD maintains and curates GO Gene Ontology annotations to facilitate physiological genomic studies relating diseases to the genome In collaboration with the Mouse Genome Database and NCBI links are made between RGD and MGD LocusLink and UniGene to increase access to each set of data RGD provides

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file199.shtml (2016-02-17)
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  • The 16th International Mouse Genome Conference (2002)
    CRUCIAL COMPONENT OF THE LPS SIGNALING PATHWAY IDENTIFIED BY GERMLINE SATURATION MUTAGENESIS WITH ENU K Hoebe The Scripps Research Institute Co Authors Du X Goode J Tabeta K Mann J Beutler B Institutions The Scripps Research Institute Tlr4 was recently identified as the product of the Lps locus by positional cloning and serves as the core transducer of the mammalian lipopolysaccharide LPS receptor However not all of the proteins that participate in LPS signaling have been identified In order to find other essential components of the signaling apparatus we have initiated an ENU mutagenesis program involving the generation of both F1 and F3 mutants on the background strain C57BL 6 To date more than 1500 F1 and 1900 F3 males have been screened for LPS sensing using TNF a production by peritoneal macrophages ex vivo as a read out A single strong phenodeviant an LPS non responder was identified by the screen The phenotype was found to be transmissible conferred by an autosomal recessive mutation and was penetrant on both C57BL 6 and C3H HeN backgrounds The mutation is specific in its effects on LPS signaling insofar as mice homozygous for the mutation have no defect of CpG or peptidoglycan

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file200.shtml (2016-02-17)
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  • The 16th International Mouse Genome Conference (2002)
    H 3 Noveroske J 1 Justice M Institutions 1 Molecular and Human Genetics Baylor College of Medicine 2 Lab of Neuropahtology Stanford University 3 Jackson s Laboratory Quakingviable qkv is a neurological mutant characterized by severe dysmyelination of the central nervous system The qkV mutation is also associated with male infertility The molecular defect in quakingviable consists of a deletion of approximately 1 Mb on mouse chromosome 17 This deficiency results in altered expression of transcripts from qkI a gene mapping adjacent to the proximal deletion breakpoint Given the large size of the qkv deficiency we explored the possibility that other expressed sequences mapping to this interval may contribute to the quakingviable phenotype To this end a contig of BAC clones spanning the 1Mb deletion was assembled Sequence derived from these BACs revealed that the mouse homologue of the human gene PARKIN maps to the qkv deletion The PARKIN locus is mutated in patients with autosomal recessive juvenile Parkinson s disease AR JP and encodes an E3 ubiquitin ligase Parkin is completely absent from the brain of mice homozygous for the qkv deletion Complementation analysis between the qkv deletion and qkI ENU induced mutant alleles suggests that the loss of

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file202.shtml (2016-02-17)
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  • The 16th International Mouse Genome Conference (2002)
    THE NEURONAL SODIUM CHANNEL MODIFIER SCNM1 DA Buchner University of Michigan Co Authors de Haan G Kearney JA Adamska M Meisler MH Institutions Department of Human Genetics University of Michigan The voltage gated sodium channel Scn8a is expressed in neurons of the brain and spinal cord and is concentrated at the nodes of Ranvier in myelinated axons The hypomorphic allele medJ has a 4 bp deletion within the splice donor site of intron 3 Using a quantitative RT PCR Primer extension assay we determined that 12 of Scn8a transcripts are correctly spliced in medJ brain medJ homozygotes exhibit a dystonic phenotype and a normal life span C57BL 6J mice B6 show an increased susceptibility to the medJ mutation medJ homozygotes on the B6 background do not survive beyond one month Only 6 of Scn8a transcripts are correctly spliced in these mice The molecular mechanism of B6 susceptibility is thus a two fold reduction in the splicing efficiency of Scn8a This subtle splicing deficiency may affect the expression of other genes and the severity of other mutants on the B6 background The inter strain phenotypic variation was mapped in 2 000 meioses to a 950 kb interval on mouse chromosome 3

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file203.shtml (2016-02-17)
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  • The 16th International Mouse Genome Conference (2002)
    Incorporated Co Authors Zambrowicz B Institutions Lexicon Genetics Incorporated We have amassed a library of over 200 000 mouse embryonic stem cell clones using high throughput gene trapping technologies that disrupt gene function and enable large scale reverse genetics in the mammal We have used this resource called OmniBank to create a relational database of trapped genes fueling our phenotypic analysis of 1000 genes per year covering all members of

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file204.shtml (2016-02-17)
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