Philosophiae Doctor - PhD (Biotechnology)

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https://hdl.handle.net/10566/13468

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Browsing by Author "Bajic, Vladimir"

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    Genome-wide identification and comprehensive analysis of transcriptionsl desert regions
    (University of the Western Cape, 2009) Schaefer, UIf; Bajic, Vladimir
    The initiation of transcription in mammalian genomes predominatly occurs at 5' promoter regions, however increasingly initiation events have been observed within introns, coding exons and 3' UTRs. Nevertheless there are large segments of mammalian genomes that are not prone to transcription initiation. These locations can be understood to be 'transcription initiation deserts'. It is challenging and useful to demarcate these segments or locations of the genome. The availability of a huge number of transcript data has provided an opportunity to develop a methodology to predict and annotate these genomic segments. A comprehensive collection of data for Homo sapiens ard Mus musculus, consisting of CAGE tags and other evidence for the existence of ffanscription was used to develop a methodology that allows the annotation of locations of mammalian genomes as those that are highly likely to initiate tanscription and those that are unlikely to harbour transcription start sites (TSSs). The algorithm allows the recognition of TSSs with 100% sensitivity, which makes it the superior choice over other existing algorithms for promoter prediction for the task of annotating TSS deserts.
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    Identification of bacterial pathogenic gene classes subject to diversifying selection
    (University of the Western Cape, 2009) Panji, Sumir; Hide, Winston; Bajic, Vladimir; Faculty of Science
    Availability of genome sequences for numerous bacterial species comprising of different bacterial strains allows elucidation of species and strain specific adaptations that facilitate their survival in widely fluctuating micro-environments and enhance their pathogenic potential. Different bacterial species use different strategies in their pathogenesis and the pathogenic potential of a bacterial species is dependent on its genomic complement of virulence factors. A bacterial virulence factor, within the context of this study, is defined as any endogenous protein product encoded by a gene that aids in the adhesion, invasion, colonization, persistence and pathogenesis of a bacterium within a host. Anecdotal evidence suggests that bacterial virulence genes are undergoing diversifying evolution to counteract the rapid adaptability of its host’s immune defences. Genome sequences of pathogenic bacterial species and strains provide unique opportunities to study the action of diversifying selection operating on different classes of bacterial genes.
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    Transcription regulation and candidate diagnostic markers of esophageal cancer
    (University of the Western Cape, 2009) Essack, Magbubah; Bajic, Vladimir; South African National Bioinformatics; Faculty of Science
    Esophageal cancer (EC) ranks among the ten most frequent cancers worldwide. Mortality rates associated with EC are very similar to the incidence rates due to the relatively late stage of diagnosis and the poor efficacy of treatment. The aim of this study was to enhance our insights of putative transcriptional circuitry of EC genes, thereby potentially positively impacting our knowledge of therapeutic targets, providing indications as to more appropriate lines of treatment, and additionally allowing for the determination of putative candidate diagnostic markers for the early stage detection of EC. This thesis reports on the development of a novel comprehensive database (Dragon Database of Genes Implicated in Esophageal Cancer, DDEC) as an integrated knowledge database aimed at representing a gateway to esophageal cancer related data. More importantly, it illustrates how the biocurated genes in the database may represent a reliable starting point for divulging transcriptional regulation, diagnostic markers and the biology related to esophageal cancer. DDEC contains known and novel information for 529 differentially expressed EC genes compiled using scientific publications from PubMed and is freely accessible for academic and non-profit users at http://apps.sanbi.ac.za/ddec/. The novel information provided to users of the DDEC is the lists of putative transcription factors that potentially control the 529 manually curated genes. The value of the information accessible through the database was further refined by providing precompiled text-mined and data-mined reports about each of these genes to allow for easy exploration of information about associations of EC-implicated genes with other human genes and proteins, metabolites and enzymes, toxins, chemicals with pharmacological effects, disease concepts and human anatomy. This feature has the capacity to display potential associations that are rarely reported and thus difficult to identify, and it enables the inspection of potentially new ‘association hypotheses’ generated based on the precompiled reports. This study further illustrates how the biocurated esophageal squamous cell carcinoma (ESCC) genes in the database may represent a reliable starting point for exploring beyond current knowledge of the transcriptional circuitry of estrogen related hormone therapy. The genes were used to develop a method that identified 44 combinations of transcription factors (TFs) that characterize the promoter sequence of estrogen responsive genes implicated in ESCC. These significantly over-represented combinations of TFs were then used to increase confidence in the 47 novel putative estrogen response genes that may be related to ESCC too. Coincidently, two of the novel putative estrogen response genes were verified by current (2009), experimental publications.