2026-09-18T21:56:05Zhttps://dspace.mit.edu/server/oai/request

oai:dspace.mit.edu:1721.1/283092022-01-13T07:54:15Zcom_1721.1_7582com_1721.1_7581col_1721.1_131022

Anthony J. Sinskey. Parker, Jefferson A. (Jefferson Alexander), 1974- Massachusetts Institute of Technology. Dept. of Biology. Massachusetts Institute of Technology. Department of Biology 2005-09-26T19:42:10Z 2005-09-26T19:42:10Z 2004 2004 http://hdl.handle.net/1721.1/28309 55634704 Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2004. Includes bibliographical references. 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. by Jefferson A. Parker. Ph.D. 92 leaves 4864879 bytes 4875339 bytes application/pdf application/pdf en_US Massachusetts Institute of Technology 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. http://dspace.mit.edu/handle/1721.1/7582 Biology. Aromatic hydrocarbon metabolism by Rhodococcus sp. I24 : computational, biochemical and transcriptional analysis Thesis application/pdf false Publication unknown unknown <Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="de9c3f6c-0562-4d55-a12f-e7f588e6241b"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Language>en_US</Language> <Title>Aromatic hydrocarbon metabolism by Rhodococcus sp. I24 : computational, biochemical and transcriptional analysis</Title> <PublishedIn> <Publication> </Publication> </PublishedIn> <PublicationDate>2004</PublicationDate> <Authors> <Author> <DisplayName>Parker, Jefferson A. (Jefferson Alexander), 1974-</DisplayName> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Massachusetts Institute of Technology</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>http://dspace.mit.edu/handle/1721.1/7582</License> <Keyword>Biology.</Keyword> <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.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication>