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Dr. John Stubbs
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| My research program involves using Bioinformatic data base search technology to identify novel gene sequences differentially expressed as membrane proteins in human cancers, specifically prostate, breast, brain, and pancreas. Putative oncogene or tumor suppressor candidates are identified in cDNA libraries, and full length reading frame sequences are obtained, either by contig overlap from existing libraries or PCR production from tumor cell line messenger RNA. Cloned DNA sequences are used to generate detection probes for Northern blot analysis of RNA expression in tumor cell lines or in biopsied cancer tissue. Positive candidates are sub-cloned into bacterial, insect cell, of human cell line expression vectors and grown under condition for expression of protein. Expressed proteins are detected by chimeric fused strong epitopes. Expressed proteins are used to generate polyclonal antibodies, which are then tested for detection of protein in cell lines or in situ on tumor tissue. Model projects representative of what my current graduate students are doing are (1) characterization of a bacterially expressed protein found to be highly up-regulated in human meningiomas and in breast tumor, (2) Expression cloning in Chinese Hamster Ovary cells of a novel surface protein involved in the regulation of the apoptosis response in colon carcinomas. (3)Production and use of new bioinformatic programs base on Hidden Markov Analysis and Psi-Blast alignment programs for identification of distantly related homologies of a signal transduction signalling pathway . All work is carried out under my supervision at an off-site Biotechnology location. Students are subsidized by stipends from the Biotechnology firm.
Last modified July 10, 2002 |
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