Includes abstract. / Includes bibliographical references (leaves 158-197). / Maize streak virus (MSV: Family Geminiviridae, Genus Mastrevirus) is the causal agent of maize streak disease (MSD) that contributes significantly to low maize yields in Africa, thereby threatening food security of sub-Saharan Africa’s poorest people. In Uganda, MSD has been identified as one of the most important constraints to maize production. In order to have a better understanding of the disease in that country, this thesis set out to establish MSD levels in farmers’ fields; develop a new sampling and virus isolation method; assess the diversity of MSVs throughout Uganda; and, through the cloning of sampled virus genomes, to determine the genetic characteristics of different isolates. In addition, this study also included an assessment of RNA silencing as a resistance strategy against MSV.

Includes abstract. / Includes bibliographical references (leaves 241-268). / Alginate is a linear, un-branched polysaccharide of (1-4)-linked -D-mannuronate (M) and its C-5 epimer, -L-guluronate acid (G). These uronic acids are arranged in three different block types in the alginate polymer; poly-M, poly-G or poly-MG. Alginate lyases are enzymes that utilize a -elimination reaction to depolymerise the alginate polymer resulting in cleavage of the (1-4)-O-glycosidic linkage between monomers and the formation of an unsaturated uronic acid at the new non-reducing terminus. Alginate lyases have been isolated from a wide range of sources including marine invertebrates and marine bacteria, which often produce more than one alginate lyase enzyme. Haliotis midae is the commercially important abalone species found along the South African coast. Over-fishing and poaching of this species has led to a depletion of the naturally occurring populations and closure of the recreational and commercial fisheries. Abalone farming was initiated and has rapidly increased in response to the increasing demand for this delicacy. However, there are many problems associated with abalone aquaculture, the most significant being disease and the slow growth rates of the animals. The use of probiotics in abalone aquaculture is a potential solution to both of these problems.

Includes abstract. / Includes bibliographical references. / This thesis details a study into aging-related neurodegeneration of Nothobranchius guentheri and the affect of resveratrol-treatment on this neurodegeneration. The goal of the study was to identify cytological probes by which to study neurodegeneration and use these to deliver novel findings pertaining to Nothobranchius aging and resveratrol induced neuroprotection.

Includes abstract. / Includes bibliographical references (p. 169-171). / Actinomycetes were isolated from the leaves of indigenous plants, aquatic sediment and soil samples, using alternative isolation methods to select for actinomycetes belonging to the rarer genera. Thirty actinomycete strains belonging to the genera Gordonia, Kineococcus, Kribbella, Micromonospora, Nocardia and Streptomyces were selected for full characterisation. A polyphasic approach combining physiology, chemotaxonomy and phylogenetic analysis was used to characterise these isolates. A number of potentially novel strains belonging to the rarer genera were identified, including two Kineococcus and three Micromonospora strains. Two novel Kribbella species were isolated from soil samples and the species descriptions of Kribbella karoonensis Q41T and Kribbella swartbergensis HMC25T were published in 2006.

Includes bibliographical references. / Due to its unique capacity to regenerate continously, the olfactory neuroepithelium serves as an excellent model system for investigating the molecular and cellular mechanisms involved in neurogenesis. The OP27 cell line (generated by infecting embryonic mouse olfactory placodes with a retrovirus carrying the temperature-sensitive alleles of the SV 40 large T antigen) was used as an in vitro system to test the effects of fibroblast growth factor-2 (FGF-2) in directing olfactory neurogenesis. The OP27 cells proliferate under the control of the retrovirus at the permissive temperature (33°C). When shifted to the non-permissive temperature (39°C) the SV40 large T antigen is inactivated and the cells stop dividing, thereby allowing one to study the effects of growth factors on these cells. Although FGF-2 also plays an important role in regulating the proliferation of neural progenitors, the main focus in this study was its effect on neuronal differentiation.

Includes bibliographical references. / Ostrich farming in South Africa is an important industry but it often suffers from high mortality rates among the ostrich chicks. This is thought to be due in part to environmental stress, leading to the delay in the development of the microbiota, thus making invasion by pathogens likely. Very little is known about the microorganisms inhabiting the ostrich gastrointestinal tract, however they do play an important role in humans and animals and disturbance of this community can be fatal. It has been established that probiotic bacteria such as Lactobacillus and Bifidobacterium spp. play an important role in the health of the host. In order to discover novel probiotic strains, bacteria should be isolated from the host, identified, characterised in-vitro to screen their potential suitability, and finally these results should be confirmed in-vivo. The aim of this study was to follow these guidelines in order to find a successful probiotic mix to decrease the mortality observed on ostrich farms, and to compare the effects of the probiotic mix to that of the antibiotic, tylosin, on the microbiota of the gastrointestinal tract (GIT).

Includes bibliographical references. / This research set out to shed light on the contradiction between the archaeological evidence pointing towards cultural continuity and the Luba’s rejection of ancestral relationships with the human skeletal remains found in the Upemba Depression of Central Katanga, the Democratic Republic of Congo. This was done by assessing the biological variation of the human skeletal remains of the early inhabitants from the Upemba Depression in the southeast of the Katanga Province (DRC) by using metric and non-metric dental morphological traits. Dental analyses of these Iron Age people have revealed homogeneity between the sexes, time periods and sites in Central Katanga. This is in contrast with the oral history from the Luba, who believe that the Iron Age remains are of their enemies who came from the northeast. In support of the archaeology, the dental morphological results from the current research have confirmed that present-day Luba people can trace their origins in Central Katanga as far back as AD 700.The analysis of patterns of dental disease, carbon, nitrogen and oxygen stable isotopes as well as phytoliths demonstrate that the diets and behaviours varied amongst these Iron Age communities. This may have been related to differences in food preparation and hygiene.

Includes bibliographical references (leaves 199-212) / This thesis investigates the phylogeography of four southern ocean petrel species in an attempt to resolve taxonomic uncertainties and phylogeography in these species. A large proportion of petrel and albatross species are listed as threatened under Red List criteria, in many cases as a result of threats at sea. Most albatrosses and petrels breed in discrete island colonies and exhibit strong natal philopatry. They may thus be expected to show population divergence, but published studies show that this is not always the case. Most studies to date have concentrated on northern hemisphere species, with mostly albatrosses studied within the southern oceans. White-chinned (Procel/aria aequinoctialis), Spectacled (P. conspicillata) and giant petrels (Macronectes giganteus and M. hal/I) are southern ocean species of Procellariiformes. All four species are threatened by accidental mortality in long line and other fisheries, as well as by introduced predators at their breeding colonies. In order to adequately conserve these species, species limits need to be resolved. Taxonomic uncertainties are an important issue in conservation because often only recognised species receive protection. In addition, islands of origin for birds killed at sea need to be identified. This thesis examines the species status of the Spectacled Petrel (Procel/aria conspicillata), which has been separated from the White-chinned Petrel (P. aequinoctialis) based on morphology and vocalisations, as well as examining the taxonomic status of the two forms of giant petrel, and their phylogeography. Cytochrome b was used to confirm the species rank of the Spectacled Petrel. The decision to support separate species status was based on the lack of shared haplotypes, six fixed mutational differences between the closest haplotypes of the White-chinned and Spectacled Petrel and a sequence divergence of 1.74%. Within Procel/aria, Whitechinned and Spectacled Petrels are sister species, closely related to the wide-ranging Grey Petrel. Within the White-chinned Petrel, two regional populations were found corresponding to colonies in the New Zealand region and the Indian/Atlantic Ocean.Evidence of population expansions were detected in both species and both regional populations of the White-chinned Petrel. Between these two regional populations, the greatest genetiC diversity was within the New Zealand regional population. This result is consistent with the White-chinned Petrel originating in the New Zealand area.

The transformation of a normal melanocyte to a malignant melanoma involves a series of poorly understood genotypic and phenotypic alterations. In vitro models of melanoma formation generated by transforming mouse melanocytes with exogenous oncogenes have revealed that this process is frequently accompanied by a loss of pigmentation. The aim of this study was to establish, and to make use of unique cell lines to gain further insight into the mechanism(s) by which oncoproteins alter melanocyte differentiation. Primary cultures of mouse epidermal and dermal melanocytes were infected with a retrovirus carrying a temperature-sensitive mutant SV40 large T antigen. Six immortalised cell lines thus generated were analysed by northern and western blots and by enzymatic assays at the permissive temperature of the oncoprotein. Three epidermal and two dermal melanocyte clones remained pigmented and expressed tyrosinase, TRP-1 and -2 genes and the proteins encoded by them. In addition they expressed the mi gene and the c-kit receptor. In contrast, one dermal melanocyte clone (DMEL-3) gradually depigmented: this was accompanied by enhanced growth and down-regulation of melanocyte-specific gene expression. At the non-permissive temperature of the oncoprotein, proliferation ceased and DMEL-3 cells repigmented with a time-dependent increase in melanocyte-specific gene expression. Moreover, mi gene expression was down-regulated in the DMEL-3 cell line at the permissive temperature and was re-expressed at the non-permissive temperature. These results provided direct evidence for the role of the SV40 large T antigen in melanocyte dedifferentiation and emphasized the pivotal role of Mi in this process. Northern blot analysis of DMEL-3 cells cultured at the permissive and non-permissive temperatures revealed that there were no detectable levels of Pax3 transcripts at either temperature. In addition, Pax3 expression was absent in the highly pigmented DMEL-2 and melan-a cell lines. These results suggest that Pax3 is not required for mi expression and that it is unlikely to be a target of the T antigen-mediated repression of mi. To explore the possibility that other melanocyte markers are also altered as a consequence of alterations in mi expression, the DMEL-3 cells were examined for changes in the α-MSH and c-kit receptors. Melanin synthesis and tyrosinase activity assays showed that alterations in mi expression did not correlate to responsiveness to α-MSH, suggesting that the MSH receptor gene is not regulated by Mi. Furthermore, northern blot analysis showed that DMEL-3 cells did not express c-kit at either the permissive or nonpermissive temperature, suggesting that Mi does not regulate c-kit expression. To address the possible role of RB family members in melanocyte differentiation, it was investigated whether melanocyte differentiation is accompanied by an increase in their mRNAs and protein levels. Northern blot analysis strongly suggested that expression of the RB1, p130 and p107 is not altered when DMEL-3 cells were induced to differentiate at the non-permissive temperature. The results from western blot anaysis were inconclusive and require further investigations. Finally, the pigmented cell lines established in the present study provided a unique opportunity to investigate the stimulatory effect of TPA on melanogenesis because growth curves showed that the cells become TPA-independent. The results showed that stimulation of melanogenesis by TPA in a pigmented melanocyte line, DMEL-2, resulted in an increase in tyrosinase, TRP-1 and TRP-2 proteins and mRNAs. Additionally, TPA increased mi gene expression which suggests that Mi is necessary for the TPA-triggered signalling cascade that induces expression of the tyrosinase gene family. These results disclose, for the first time, a mechanistic link between TPA and the transcriptional induction of pigmentation.

Includes abstract. / Includes bibliographical references. / Plants have evolved an elaborate and very effective defence system to curb disease caused by pathogen infections. To gain insight into the defence signalling network and defence responses deployed by plants for resistance to pathogens, the defence-related Arabidopsis thaliana mutant cir1 (constitutively induced resistance 1) was further investigated. It was previously shown that cir1 constitutively expresses salicylic acid-, jasmonic acid- and ethylene-dependent defence-related genes and exhibits increased resistance to the virulent bacterial pathogen Pseudomonas syringae pv. tomato and the virulent oomycete pathogen Hyaloperonospora parasitica Noco2. Through first–pass mapping experiments, it was formerly determined that the CIR1 locus is located on the lower arm of chromosome IV. With the aim of identifying the CIR1 gene, comprehensive genomic mapping of cir1 was conducted in this study. Upon the generation of a suitable mapping population, PCR-based markers were employed to narrow down CIR1 location to 309.10 kb. This region was included in six genomic DNA clones which were tested for complementation of the cir1 mutant. A small region in which CIR1 resides was identified and possible candidate genes within it were investigated. It was established that CIR1 is one of eight annotated genes. This study also assessed which known components of the defence signalling network play a role in cir1-mediated resistance, to establish a possible function of CIR1 in the Arabidopsis defence network. Epistasis analyses were performed between cir1 and the eds1 (enhanced disease susceptibility 1) and pad4 (phytoalexin deficient 4) mutants which regulate the salicylic acid signalling pathway, as well as the coi1 (coronatine-insensitive 1) mutant which functions in the jasmonic acid signalling pathway. The disease resistance profiles of cir1 eds1, cir1 pad4 and cir1 coi1 double mutants to infection by virulent P. syringae and virulent H. parasitica established that coi1, pad4 and eds1 are epistatic to cir1, suggesting that CIR1 is located upstream in the defence signalling network. Through defence-related gene expression profiling, it was found that cir1 simultaneously activates multiple signalling pathways, resulting in the induced expression of many defence-related genes and the increased expression of some of these genes was correlated to cir1’s enhanced resistance to virulent pathogens. Therefore, it appears that CIR1 functions as a negative regulator of the disease resistance signalling network. Furthermore, EDS1 protein accumulation may play a role in cir1-mediated resistance as it was found that cir1 has a stabilizing effect on the EDS1 protein.