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dc.contributor.authorRatushna, Vladyslava G.en_US
dc.date.accessioned2014-03-14T20:37:35Z
dc.date.available2014-03-14T20:37:35Z
dc.date.issued2005-05-06en_US
dc.identifier.otheretd-05192005-111354en_US
dc.identifier.urihttp://hdl.handle.net/10919/32989
dc.description.abstractMicroarrays containing long oligonucleotides provide sensitive and specific detection of gene expression and are becoming a popular experimental platform. In the process of designing an oligonucleotide microarray for Brucella, we optimized the overall design of the array and created probes to distinguish among the known Brucella species. A 3-way genome comparison identified a set of genes which occur uniquely in only one or two of the sequenced Brucella genomes. Reverse transcriptase PCR assays of over one hundred unique and pairwise-differential regions identified in Brucella revealed several groups of genes that are transcribed in vivo with potential significance for virulence. The structural and thermodynamic properties of a set of 70mer oligonucleotide probes for a combined B. abortus, B. melitensis and B. suis microarray were modeled to help perform quantitative interpretation of the microarray data. Prediction and thermodynamic analysis of secondary structure formation in a genome-wide set of transcripts from Brucella suis 1330 demonstrated that properties of the target molecule have the potential to strongly influence the rate and extent of hybridization between transcript and an oligonucleotide probe in a microarray experiment. Despite relatively high hybridization temperatures used in the modeling process, parts of the target molecules are predicted to be inaccessible to intermolecular hybridization due to the formation of stable intramolecular secondary structure. Features in the Brucella genomes with potential diagnostic use were identified, and the extent to which target secondary structure, a molecular property which is not considered in the array design process, may influence the quality of results was characterized.en_US
dc.publisherVirginia Techen_US
dc.relation.haspartV.Ratushna.M.S.thesis.pdfen_US
dc.relation.haspartBsuisMicroarraySpreadsheet.xlsen_US
dc.relation.haspartBsuisMicroarraySpreadsheet.pdfen_US
dc.rightsI hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to Virginia Tech or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.en_US
dc.subjectmicroarrayen_US
dc.subjecttargeten_US
dc.subjectdesignen_US
dc.subjectsecondaryen_US
dc.subjectstructureen_US
dc.subjectdiagnosticsen_US
dc.subjectBrucellaen_US
dc.subjectprobeen_US
dc.subjectoligomeren_US
dc.titleIncorporation of Physico-Chemical Parameters Into Design of Microarray Experimentsen_US
dc.typeThesisen_US
dc.contributor.departmentBiological Sciencesen_US
dc.description.degreeMaster of Scienceen_US
thesis.degree.nameMaster of Scienceen_US
thesis.degree.levelmastersen_US
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen_US
thesis.degree.disciplineBiological Sciencesen_US
dc.contributor.committeechairGibas, Cynthia J.en_US
dc.contributor.committeememberBoyle, Stephen M.en_US
dc.contributor.committeememberMelville, Stephen B.en_US
dc.contributor.committeememberLazar, Iuliana M.en_US
dc.contributor.committeememberWeller, Jennifer W.en_US
dc.identifier.sourceurlhttp://scholar.lib.vt.edu/theses/available/etd-05192005-111354/en_US
dc.date.sdate2005-05-19en_US
dc.date.rdate2008-06-14
dc.date.adate2005-06-14en_US


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