Prestige bursaries and fellowships are available to outstanding candidates to complete research in any of the Focus Areas of the cluster. Projects that will be available are listed below:
- Identification of the epigenetic modifications of Trypanosoma brucei histone H3 that allows evasion of the human immune response
Trypanosoma brucei is responsible for thousands of annual deaths in sub-Saharan Africa. Infection of humans with T. brucei, transmitted by the Tsetse fly, results in African Sleeping Sickness or trypanosomiasis. Several 100,000 individuals suffer from this tropical disease, and there is clear evidence that the trypanosome is developing resistance to drugs currently used in treatment. If left untreated, trypanosomiasis is lethal.
The entire genome of T. brucei has been sequenced, and it is known to encode numerous enzymes involved in epigenetic regulation of gene expression. Although the T. brucei core histones are highly conserved compared to that other eukaryotes, the N-terminal extension of histone H3 diverges significantly. It was previously shown that the H3 tail was subject to epigenetic modifications, but the precise residues that were involved could not be identified. Also, although T. brucei histone H3 contains a K4, almost universally methylated in actively expressed genes, it lacks the equivalent of K9, normally methylated at transcriptionally repressed loci.
In this project, histone H3 will be isolated from cultured T. brucei, and the location of epigenetic modifications mapped by LC-MS/MS. Specific attention will be given to modifications that may substitute for K9me3 in the divergent H3 tail. This project will be followed up by a study of the genomic distribution of the identified PTMs, and the identification of PTMs that are associated with gene repression. Synthetic peptides of such PTMs will be used to isolated proteins that bind to the repression specific tags, with the long-term aim to develop new epigenetic therapies to African Sleeping Sickness.
Contact: Prof Hugh Patterton
- Isolation and characterisation of compounds from plants that are pharmacologically active against the HIV virus.
The AIDS endemic has stimulated research into anti-HIV drugs. This includes phytochemical investigations into pharmacognostically interesting plant material that has, according to anecdotal evidence, potential to treat AIDS. The chemistry department has initiated a project to identify the active ingredients in some of these plant materials and to determine the toxicity, bioavailability and in vivo efficacy of these molecules against HIV and other commercially important viral infections. The PhD or post-doctoral student will perform activity guided fractionation of plant extracts with demonstrated and patented activity against HIV and other viruses. The project thus involves advanced chromatography (TLC and preparative HPLC) and structure elucidation (predominantly with 600 MHz NMR). The candidate will work closely with collaborators in pharmacology, veterinary science and bioanalytical chemistry to perform the bioactivity, bioavailability and in vivo testing. The projects will eventually progress toward synthesis of the bioactive compounds.
Contact: Prof JH van der Westhuizen
- Old Yellow Enzymes (OYEs) and cytochrome P450 (CYP450s) enzymes from Crytococcus neoformans
Eicosanoid production is seen as an important virulence factor in the pathogenic yeasts Cryptococcus neoformans and Candida albicans and is therefore a possible drug target against these pathogens. We have recently shown the possible involvement of P450 enzymes in prostaglandin E2 production in Candida species (Ells et al. 2011). It is also speculated that one or more Old Yellow Enzymes (OYEs) play a role in prostaglandin F2α production from prostaglandin E2. This study is focussed to identify and investigate enzymes involved in prostaglandin synthesis in the pathogenic yeast Cryptococcus neoformans for possible drug targeting. Therefore, a better understanding of fungal eicosanoid production will result in the identification of useful targets for pharmacological development. The importance of this study is emphasised by the high mortality rates associated with Cryptococcal infections, especially in HIV infected patients, and the ability to gain resistance to known antifungal treatments.
For this purpose we will clone the OYEs and uncharacterised CYP450 enzymes from Crytococcus neoformans possibly involved in prostaglandin biosynthesis. This yeast contains three OYEs and five to six CYP450s. These enzymes will be heterologously expressed and investigated for their ability to participate in prostaglandin metabolism from exogenous arachidonic acid. Furthermore, enzyme purification, crystallization and X-ray crystallography of proteins that were successfully expressed will be performed to understand the catalytic mechanisms, potential methods of inhibition and inhibitor binding.
Contact: Prof J Albertyn or Dr C Pohl
- Whole genome consensus sequence determination of African rotavirus strains
It is estimated that in 2008 diarrhoea was responsible for the second most child mortalities among infectious diseases globally, after pneumonia. Although several infectious agents cause diarrhoea, rotavirus is the major aetiological agent of severe dehydrating diarrhoea, causing approximately 453 000 deaths annually among under-five-year olds worldwide. Almost half of these deaths occur in sub-Sahara Africa.
Rotaviruses belong to the Reoviridae family and contain a 11 segmented double-stranded RNA (dsRNA) genome. The dsRNA segments encode six structural (VP1–4, 6 and 7) and six non-structural (NSP1–6) proteins. Rotaviruses are classified into several groups (A – G, possibly H) based on genotyping. A dual typing system based on the genome segments encoding the VP4 (P genotypes) and VP7 (G genotypes) is commonly used for diagnostic typing of type A rotaviruses. Unlike infections in developed countries, where G1P[8] strains cause almost 70% of the rotavirus cases, wide strain diversity is associated with infections in African countries.
Recent advances made with the improvement of sequence-independent cDNA synthesis and genome amplification of dsRNA coupled with pyrosequencing, allows cDNA synthesis, amplification and complete nucleotide sequencing of all 11 genome segments without prior knowledge of the viral dsRNA sequence. These technologies allow for the whole genome characterisation of the 11-segmented dsRNA genome of rotavirus and therefore establish the true viral diversity. Using these approaches it is anticipated to determine the consensus genome sequence of African rotaviruses in order to elucidate the evolutionary mechanisms behind the wide strain diversity present on the African continent.
Contact: Dr Trudi O`Neil