archive-org.com » ORG » I » IMGS.ORG

Total: 854

Choose link from "Titles, links and description words view":

Or switch to "Titles and links view".
  • 18th International Mouse Genome Conference (2004)
    is to identify and understand the collection of cis regulatory modules necessary for coordinating differential gene expression during development Comparative studies of the complete genomic sequences for mouse and human indicate that the largest conserved fraction is non coding and within this non coding fraction are sequences that perform regulatory function One step towards deciphering the function of these conserved non coding sequences CNCS is by interpreting the combinatorial clustering of transcription factor binding sites TFBS as an informational pattern that forms a regulatory code Based upon a signaling network model for lung branching morphogenesis we developed a novel sequence analysis pipeline for integrating comparative genomic approaches to identify shared regulatory motifs that are derived from constraints imposed by a biological network The algorithm was trained on a set of genes known to control lung branching morphogenesis LungNet This algorithm is designed to identify novel motifs e g binding sites for factors involved in lung branching as well as map clusters of TFBS to search for regulatory modules on a genome wide scale We used the LungNet training set to derive a set of novel motifs and to identify regulatory modules proposed to be important for lung development This computational

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file62.shtml (2016-02-17)
    Open archived version from archive

  • 18th International Mouse Genome Conference (2004)
    for Sick Children Toronto Canada 2 Hospital for Sick Children Toronto Canada 3 Human Genetics Unit Medical Research Council Edinburgh United Kingdom The ability to visualize the 3D organization of biological tissue is essential to unravelling its complexities A new imaging technique called Optical Projection Tomography OPT essentially an optical version of X Ray computed tomography CT fills a gap among current imaging modalities by creating molecularly specific cellular resolution images of specimens up to 1 cc in size The visualization of a specific gene s pattern of expression is essential to gain an understanding of its role Mutant comparisons performed with OPT are more sensitive to spatial complexity than comparisons performed with serial sectioning techniques that might alter subtle morphology Common optical markers can be used to highlight a region of interest or a particular genetic expression for enhanced visualization We have acquired cellular resolution OPT data sets of whole E9 5 to E12 5 mouse embryos with a fluorescently labelled cardiac specific pattern of gene expression to examine the full extent of 3D morphological differences between control and mutant specimens Vascular development is difficult to study without 3D visualization Resolution of vessels less than 10 microns in size

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file243.shtml (2016-02-17)
    Open archived version from archive

  • 18th International Mouse Genome Conference (2004)
    resolution synteny and rearrangement breakpoint maps among human mouse and rat genomes This not only has allowed us to achieve several novel discoveries about mammalian genome evolution but also provides a unique resource to study human cancer development and progression As closely related species mouse and rat share the majority of the breakpoints and often have the same types of rearrangements when compared to the human genome However the breakpoints not shared between them indicate that mouse rearrangements are more often inter chromosomal whereas intra chromosomal rearrangements are more prominent in rat Centromeres may have played a significant role in reorganizing a number of chromosomes in all three species Among the 300 syntenic blocks identified are segments of over 40Mb without any detected interspecies rearrangements as well as regions with frequently broken synteny and extensive rearrangements Computer simulation of the syntenic block length distribution supports the fragile breakage model but not the random breakage model for mammalian genome evolution indicating that mammalian genomes consist of evolutionary stable and unstable regions Statistical analyses indicate that many human cancer associated genome lesions are directly linked to evolutionary genome instability By examining the genomic locations of 50 genome wide recurrent chromosomal aberrations with

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file63.shtml (2016-02-17)
    Open archived version from archive

  • 18th International Mouse Genome Conference (2004)
    5 0 75MB REGION Shao H 1 Gan T 2 Valladares O 1 Manduchi E 2 Pinney D 2 Stoeckert C 2 Bucan M 1 1 Department of Genetics University of Pennsylvania Philadelphia United States 2 Penn Center for Bioinformatics University of Pennsylvania Philadelphia United States Although sequences for large eukaryotic genomes e g human mouse rat chicken etc are being completed it remains a challenge to identify all encoded genes Approaches used to date include ab initio gene prediction similarity based annotation and direct alignment of transcribed sequences We are using the proximal portion of mouse Chromosome 5 and several public databases to assemble a gene index for the 75 Mb region target for region specific ENU mutagenesis screen A Database of Transcribed Sequences DoTS http www allgenes org has identified over 150 novel transcripts in addition to 550 genes annotated by the ENSEMBL and Celera databases Over 81 of these transcripts were verified using a custom built 70 mer oligo microarray hybridized with embryos cDNA E9 5 E12 5 E14 5 and E17 5 and cDNA from several adult tissues The expression map of the chromosome is being assembled by integration of our array data with expression data

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file244.shtml (2016-02-17)
    Open archived version from archive

  • 18th International Mouse Genome Conference (2004)
    United States Inbred mouse strains vary in the frequency of H ras initiating mutations in chemically induced liver tumors To determine if allelic variation in the H ras gene accounts for differences in mutant frequencies we sequenced the 4 5kb H ras gene from 14 inbred strains 12 common laboratory strains 129P3 J 129X1 SvJ A J AKR J BALB cByJ C3H HeJ C57BL 6J C57BR cdJ CBA J DBA J SM J and SWR J and 2 distant strains CAST Ei and SPRET Ei Surprisingly eleven inbred strains had identical sequences over the 4 5kb region The AKR J strain exhibited 2 SNPs in non coding regions signifying a remarkably low rate of polymorphism The genomes of common laboratory inbred strains are mosaics of M m domesticus and M m musculus sequence All 12 common inbred strains including AKR J inherited H ras alleles from M m domesticus To determine if the mono allelism of H ras is unique or represents a larger selected region of distal Chr 7 we sequenced 500 600 bp for each of 15 genes spanning the distal 10Mb for the 16 aforementioned strains In the 12 common inbred strains an extremely low SNP rate

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file64.shtml (2016-02-17)
    Open archived version from archive

  • 18th International Mouse Genome Conference (2004)
    at Univ of Tennessee ORNL Oak Ridge United States 2 Oak Ridge National Lab Oak Ridge United States To understand the how RNA levels are regulated in cells we have created a high throughput automated pipeline which can search for putative cis regulatory elements CREs in the genome or other control regions within the upstream regions 5 or 3 UTRs of RNAs We will present the structure of the pipeline and some results including an example from a set of genes that form the cornified envelope This pipeline can input mouse gene sets that might be co regulated e g very similar gene expression changes under multiple perturbations participation in a common biological process etc The pipeline automatically retrieves appropriate sequences from the input gene sets This pipeline also retrieves the relevant orthologs in other sequenced chordates We use the orthologs to define evolutionarily conserved regions that are more likely to contain the motifs of interest We search within these regions for short motifs that are overrepresented in the different ortholog sets These overrepresented motifs might be functional sites of interest Typical results often include multiple sequence motifs that are present in a subset of the input gene set e

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file65.shtml (2016-02-17)
    Open archived version from archive

  • 18th International Mouse Genome Conference (2004)
    ASSESSING GENOMIC VARIATION IN COMMON STRAINS OF INBRED MICE Cervino ACL Edwards S Schadt E rosetta merck seattle United States We characterized DNA variation in 60 different strains of mice including 56 common strains ordered from the Jackson Laboratories Using phylogenetic analysis we investigated how various common strains relate to each other Insight into heterozygosity between strains and between markers is essential in the selection of both an optimal set

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file66.shtml (2016-02-17)
    Open archived version from archive

  • 18th International Mouse Genome Conference (2004)
    on sequence based maps of several mouse chromosomes have been compared to the positions of orthologs in rat and human chromosomes There are about 10 to 15 evolutionary based breaks for human chromosomes on each mouse chromosome although mouse chr 15 has only 3 such breaks The number of breaks for rat chromosomes is usually much fewer ranging from 0 to 11 However most of the break points between rat

    Original URL path: http://www.imgs.org/Archive/abstracts/2004abstracts/abs/file67.shtml (2016-02-17)
    Open archived version from archive



  •