Department of Microbiology

Permanent URI for this community

https://hdl.handle.net/10566/13151

Browse

Browsing by Author "Faculty of Science"

Now showing 1 - 6 of 6
  • Thumbnail Image
    Item
    Differentials and disparities in the costs of major hospital procedures in South Africa: A structural analysis from the perspective of the supply side
    (University of the Western Cape, 2007) De Koker, Louise; Gabriel, Tali; Faculty of Science
    The aim of this study was to examine the extent to which providers' practices affect the cost of hospital procedures incurred by patients. The spsecific objective was to explore the magnitude of variations and statistically establish the significance of relationships between admission/specialist costs incurred by patients for four major procedures and the hospital group, geographical location, employer group and demmographic realted risk profiles. The study contributes to a better understanding of the way in which managed care companies could channel beneficiaries of medical schemes to efficient providers.
  • Thumbnail Image
    Item
    Differentiation between Quinolone Resistant and Sensitive Isolates of Campylobacter jejuni by a Multiplex PCR Assay
    (University of the Western Cape, 2006) Ebrahim, Nazneen; Gouws, Pieter A; Dept. of Microbiology; Faculty of Science
  • Thumbnail Image
    Item
    Functional analysis of the mouse RBBP6 gene using Interference RNA
    (University of the Western Cape, 2007) Pretorius, Ashley; Jasper, D.; Rees, G.; Faculty of Science
    The aim of this thesis was to investigate the cellular role of the mouse RBBP6 gene using the interference RNA (RNAi) gene targeting technology and also to understand the relevance of two promoters for the RBBP6 gene.
  • No Thumbnail Available
    Item
    An in vitro study on the immunotoxicity of South African beer
    (University of the Western Cape, 2008) Neethling, Michelle; Pool, Edmund J.; Faculty of Science
    Traditionally brewed beers are of cultural and economic importance to many African nations. The presence of mycotoxins in African beer is a topic that needs to be addressed, since most African countries have a climate of high humidity and temperature that favours the growth of moulds. Mycotoxins challenge not only the health of animals and humans, but also the economy, especially in underdeveloped countries where contamination is most likely. Literature proves that mycotoxins depict various effects on the immune system including immunotoxicity. Beer analysis is therefore of utmost importance in order to evaluate organoleptic characteristics, quality, nutritional value as well as safety. The aims of this study involve the analysis and comparison of traditional and commercial beer in terms of physical characteristics, mycotoxin concentrations as well as effects on specific immune pathway biomarkers in order to elucidate possible immunotoxicity.
  • Thumbnail Image
    Item
    New algorithms for EST clustering
    (University of the Western Cape, 2000) Ptitsyn, Andrey; Hide, Winston; Davidson, Sean; Dept. of Microbiology; Faculty of Science
    Summary: Expressed sequence tag database is a rich and fast growing source of data for gene expression analysis and drug discovery. Clustering of raw EST data is a necessary step for further analysis and one of the most challenging problems of modem computational biology. There are a few systems, designed for this purpose and a few more are currently under development. These systems are reviewed in the "Literature and software review". Different strategies of supervised and unsupervised clustering are discussed, as well as sequence comparison techniques, such as based on alignment or oligonucleotide compositions. Analysis of potential bottlenecks and estimation of computation complexity of EST clustering is done in Chapter 2. This chapter also states the goals for the research and justifies the need for new algorithm that has to be fast, but still sensitive to relatively short (40 bp) regions of local similarity. A new sequence comparison algorithm is developed and described in Chapter 3. This algorithm has a linear computation complexity and sufficient sensitivity to detect short regions of local similarity between nucleotide sequences. The algorithm utilizes an asymmetric approach, when one of the compared sequences is presented in a form of oligonucleotide table, while the second sequence is in standard, linear form. A short window is moved along the linear sequence and all overlapping oligonucleotides of a constant length in the frame are compared for the oligonucleotide table. The result of 85 comparison of two sequencesis a single figure, which can be compared to a threshold. For each measure of sequence similarity a probability of false positive and false negative can be estimated. The algorithm was set up and implemented to recognize matching ESTs with overlapping regions of 40bp with 95% identity, which is better than resolution ability of contemporary EST clustering tools. This algorithm was used as a sequence comparison engine for two EST clustering programs, described in Chapter 4. These programs implement two different strategies: stringent and loose clustering. Both are tested on small, but realistic benchmark data sets and show the results, similar to one of the best existing clustering programs, D2_cluster, but with a significant advantage in speed and sensitivity to small overlapping regions of ESTs. On three different CPUs the new algorithm run at least two times faster, leaving less singletons and producing bigger clusters. With parallel optimization this algorithm is capable of clustering millions of ESTs on relatively inexpensive computers. The loose clustering variant is a highly portable application, relying on third-party software for cluster assembly. It was built to the same specifications as D2_cluster and can be immediately included into the ST ACKPack package for EST clustering. The stringent clustering program produces already assembled clusters and can apprehend alternatively processed variants during the clustering process.
  • Thumbnail Image
    Item
    Purification and characterisation of plasmodium falciparum Hypoxanthine phosphoribosyltransferase
    (University of the Western Cape, 2007) Murungi, Edwin Kimathi; McIntosh, David B.; Sewell, Trevor; Faculty of Science
    Malaria remains the most important parasitic disease worldwide. It is estimated that over 500 million infections and more that 2.7 million deaths arising from malaria occur each year. Most (90%) of the infections occur in Africa with the most affected groups being children of less than five years of age and women. this dire situation is exacerbated by the emrggence of drug resistant strains of Plasmodium falciparum. The work reported in this thesis focuses on improving the purification of PfHPRT by investigating the characteristics of anion exchange DE-52 chromatography (the first stage of purification), developing an HPLC gel filtration method for examining the quaternary structure of the protein and possible end stage purification, and initialcrystalization trials. a homology model of the open, unligaded PfHPRT is constructed using the atoomic structures of human, T.ccruz and STryphimurium HPRT as templates.