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Aromatic hydrocarbon metabolism by Rhodococcus sp. I24 : computational, biochemical and transcriptional analysis

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dc.contributor.advisor Anthony J. Sinskey. en_US Parker, Jefferson A. (Jefferson Alexander), 1974- en_US
dc.contributor.other Massachusetts Institute of Technology. Dept. of Biology. en_US 2005-09-26T19:42:10Z 2005-09-26T19:42:10Z 2004 en_US 2004 en_US
dc.description Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2004. en_US
dc.description Includes bibliographical references. en_US
dc.description.abstract Rhodococcus sp. 124 is a Gram-positive soil bacterium being developed for the manufacture of (-)cis-(1S,2R)-1-aminoindan-2-ol, a key precursor in the production of the HIV-1 protease inhibitor CrixivanTM, from the aromatic hydrocarbon indene. Rhodococcus sp. 124 was grown by batch fermentation in the presence of naphthalene and indene to measure changes in gene expression and aromatic hydrocarbon metabolism with DNA microarray technology. Genes were selected for microarray analysis based on functional annotation assignments made by the Consensus Annotation by Phylogeny Anchored Sequence Alignment (CAPASA) program, a high throughput system for automated functional annotation assignment of DNA sequence similarity search results. CAPASA was validated by comparison to several methods of annotation, and the agreement to other methods ranged from 75-94%. Microarray results were analyzed by the newly described method of trigonometric deconvolution, a mathematical system for the measurement of changes in gene expression across multiple growth conditions with a minimal number of hybridizations. The combined analysis of aromatic metabolism and gene expression reveal the differential expression of multiple polycyclic aromatic hydrocarbon dioxygenases in a substrate and growth phase dependent manner. en_US
dc.description.statementofresponsibility by Jefferson A. Parker. en_US
dc.format.extent 92 leaves en_US
dc.format.extent 4864879 bytes
dc.format.extent 4875339 bytes
dc.format.mimetype application/pdf
dc.format.mimetype application/pdf
dc.language.iso en_US
dc.publisher Massachusetts Institute of Technology en_US
dc.rights M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. en_US
dc.subject Biology. en_US
dc.title Aromatic hydrocarbon metabolism by Rhodococcus sp. I24 : computational, biochemical and transcriptional analysis en_US
dc.type Thesis en_US Ph.D. en_US
dc.contributor.department Massachusetts Institute of Technology. Dept. of Biology. en_US
dc.identifier.oclc 55634704 en_US

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