8,899 research outputs found

    Modeling Insertional Mutagenesis Using Gene Length and Expression in Murine Embryonic Stem Cells

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    Background. High-throughput mutagenesis of the mammalian genome is a powerful means to facilitate analysis of gene function. Gene trapping in embryonic stem cells (ESCs) is the most widely used form of insertional mutagenesis in mammals. However, the rules governing its efficiency are not fully understood, and the effects of vector design on the likelihood of genetrapping events have not been tested on a genome-wide scale. Methodology/Principal Findings. In this study, we used public gene-trap data to model gene-trap likelihood. Using the association of gene length and gene expression with gene-trap likelihood, we constructed spline-based regression models that characterize which genes are susceptible and which genes are resistant to gene-trapping techniques. We report results for three classes of gene-trap vectors, showing that both length and expression are significant determinants of trap likelihood for all vectors. Using our models, we also quantitatively identifie

    The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones

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    We have developed a comprehensive resource devoted to biologists wanting to optimize the use of gene trap clones in their experiments. We have processed 300 602 such clones from both public and private projects to generate 28 199 ‘UniTraps’, i.e. distinct collections of unambiguous insertions at the same subgenic region of annotated genes. The UniTrap resource contains data relative to 9583 trapped genes, which represent 42.3% of the mouse gene content. Among the trapped genes, 7 728 have a counterpart in humans, and 677 are known to be involved in the pathogenesis of human diseases. The aim of this analysis is to provide the wet lab researchers with a comprehensive database and curated tools for (i) identifying and comparing the clones carrying a trap into the genes of interest, (ii) evaluating the severity of the mutation to the protein function in each independent trapping event and (iii) supplying complete information to perform PCR, RT-PCR and restriction experiments to verify the clone and identify the exact point of vector insertion. To share this unique resource with the scientific community, we have designed and implemented a web interface that is freely accessible at http://unitrap.cbm.fvg.it/

    The mouse genetics toolkit: revealing function and mechanism

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    Large-scale projects are providing rapid global access to a wealth of mouse genetic resources to help discover disease genes and to manipulate their function

    Aquaculture Asia, Vol. 7, No. 2, pp.1-60, April - June 2002

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    CONTENTS: Prawn farm energy audits and five star ratings by Eric Peterson. Development of freshwater fish farming and poverty alleviation: A case study from Bangladesh by Gertjan de Graaf and Abdul Latif. Conservation of endangered fish stocks through artificial propagation and larval rearing technique in West Bengal, India by M. Mijkherjee, Aloke Praharaj and Shamik Das. Genes and Fish: Supply of good quality fish seed for sustainable aquaculture by Graham Mair. Farmers as Scientists: Sewage-fed aquaculture systems of Kolkata: A century old innovation of farmers by M.C. Nandeesha. When policy makers begin hearing voices by Graham Haylor Fish farming in rice environments of north eastern India by D. N. Das. Peter Edwards writes on rural aquaculture: Aquaculture for poverty alleviation and food security. Aquaculture Fundamentals: The use of lime, gypsum, alum and potassium permanganate in water quality management by Simon Wilkinson. The utilizations of heterosis in common carp in China by Dong Z.J. and Yuan X.H. Progress of fish gene technology research in China by Zhang Yue and Zhu Xinping. Seed production of Magur (Clarias batrachus) using a rural model portable hatchery in Assam, India – A farmer proven technology by S.K. Das. Domestication of tiger prawn gets the thumbs up. A regional approach to assessing organic waste production by low salinity shrimp farms by Dr. Brian Szuster and Dr Mark Flaherty. Advice on Aquatic Animal Health Care: Visit to intensive vannemei farms in Peru by Pornlerd Chanratchakool

    Tagging genes with cassette-exchange sites

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    In an effort to make transgenesis more flexible and reproducible, we developed a system based on novel 5â€Č and 3â€Č ‘gene trap’ vectors containing heterospecific Flp recognition target sites and the corresponding ‘exchange’ vectors allowing the insertion of any DNA sequence of interest into the trapped locus. Flp-recombinase-mediated cassette exchange was demonstrated to be highly efficient in our system, even in the absence of locus-specific selection. The feasibility of constructing a library of ES cell clones using our gene trap vectors was tested and a thousand insertion sites were characterized, following electroporation in ES cells, by RACE–PCR and sequencing. We validated the system in vivo for two trapped loci in transgenic mice and demonstrated that the reporter transgenes inserted into the trapped loci have an expression pattern identical to the endogenous genes. We believe that this system will facilitate in vivo studies of gene function and large-scale generation of mouse models of human diseases, caused by not only loss but also gain of function alleles
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