Experimental rnomics

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dc.contributor.authorZakaria, Robaiza
dc.date.accessioned2014-11-03T02:11:14Z
dc.date.available2014-11-03T02:11:14Z
dc.date.issued2008
dc.descriptionPhDen_US
dc.description.abstractNon-protein-coding RNA (npcRNA) is a large class of riboregulators that act in complex with proteins (as RNPs) in diverse regulatory pathways. This thesis focused on the experimental identification of small npcRNAs from Salmonella enterica serovar Typhi (S. Typhi), the aetiological agent of typhoid fever. By an Experimental RNomics approach, 82 species of uncharacterized novel npcRNA candidates were identified from library generated from different growth phases of a clinically isolated S. Typhi. From this, 28 were transcribed from the IGRs, 29 were transcribed in the antisense orientation of the ORFs and 18 were identified to overlap the ORFs. Another 7 candidates were transcribed from repetitive regions and several non-repetitive locations. Eleven known npcRNAs were also detected. Interestingly, 55 candidates exhibit homology to Escherichia coli and were not previously annotated for both organisms. By Northern Blot analysis, the expression of 38 novel npcRNA candidates was confirmed. A total of 28 novel npcRNA candidates were growth phase regulated where 14 candidates were growth phase regulated in both S. Typhi USM05 and E. coli K12, 11 candidates were speciesspecific growth phase regulated only in S. Typhi USM05 and three candidates were species-specific growth phase regulated only in E. coli K12. A total of 8 npcRNA candidates were ubiquitously expressed with 6 candidates were ubiquitously expressed in both S. Typhi USM05 and E. coli K12 and 2 candidates were species-specific ubiquitously expressed only in S. Typhi USM05. There was no species-specific ubiquitously expressed candidate observed in E. coli K12. Two out of 38 candidates were shown to be growth phase regulated and ubiquitously expressed. The different feature of expression patterns observed in this study can be associated with the different classes of npcRNA that they might be grouped-in, namely the housekeeping and the regulatory npcRNAs. A number of novel npcRNA candidates were shown to be located close to important genes that were conserved in E. coli K12 and among Salmonella. Thus, suggesting that they might be functionally important. Significantly, this study has set the understanding on the importance of the specific growth conditions to the expression of npcRNAs. The next phases of challenge are to further characterize and to elucidate the functions of these new classes of small RNA molecules. Considering that such regulators may be highly expressed upon induction, these molecules may be greatly enriched in cDNA libraries prepared from the relevant growth or stress condition.en_US
dc.identifier.urihttp://hdl.handle.net/123456789/221
dc.language.isoenen_US
dc.subjectBiological Scienceen_US
dc.subjectRnomicsen_US
dc.subjectRibonucleic acidsen_US
dc.subjectPathogenic agenten_US
dc.titleExperimental rnomicsen_US
dc.title.alternativeTowards the identification and characterization of non-protein-coding ribonucleic acids in pathogenic agent, Salmonella Typhien_US
dc.typeThesisen_US
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