Ph.D. (Zoology) / The study concept was derived following an information requirement related to the need for the development of a scientifically sound technique to minimize illegal entries at major South African freshwater fishing tournaments. The hypothesis was that fish that are in equilibrium with the environment that they live in should reflect the chemistry of that environment. Therefore it would be possible to chemically link the fish to a specific impoundment and identify whether the fish are indeed from that impoundment or whether they were brought there to be illegally entered at a fishing tournament. The project area consisted of selected lakes within the Vaal, Mgeni, Crocodile (West) and Olifants River catchments in South Africa. The catchments were chosen to contain major sport fishing lakes and to have different sizes, different sources of pollution, different underlying geological compositions and different climates. Soil analyses data from the regional geochemical mapping program of the Council for Geoscience as well as lake sediment and lake water analyses were used to trace chemical elements during weathering, erosion and deposition. This was done to identify unique characteristics that are able to distinguish between water and sediment from individual lakes. It was found that Rb, Sr, Ba, Cu, Ni,Th, Pb, Sc, K, Mg and Ca could be effectively used as single elements or element ratios to distinguish between lakes. Large variation in sediment compositions within individual lakes limited this distinction. Anomalous catchment soil concentrations related to the underlying geology or anthropogenic contamination can however be traced to lake sediments. Rare earth elements are not uniformly distributed in lake sediments or lake waters and sampling localities should be carefully considered when comparing lakes. Leachable soil sulphate distribution patterns from coal mining areas above Lake Witbank and Lake Middelburg extend downstream through Lake Loskop to Lake Arabie (Flag Boshielo). Leachable fluoride, abundant in the Pilanesberg Alkaline Complex extends northwards along rivers draining the complex. The mineralogy of lake sediments was also compared with the major element composition of these sediments as well as with the anion composition of lake water. Genetic rock classification diagrams could be used effectively to show correlations between catchment soil and lake sediment samples both in terms of mineralogy and chemistry. Lake water and fish tissue samples were collected and analysed to investigate the link between element concentrations in lake water and otolith, fin spine, muscle, liver and gill tissues. Using the Sr/Ca elemental ratio, a species-specific correlation was identified between lake water, otolith, spine and gill tissue samples. The best discrimination between fish species was achieved using a Na/Ca versus Mg/Ca elemental ratio diagram of gill tissues. The best discrimination between fish from different lakes was achieved using a Ba/Mg versus Sr/Mg elemental ratio diagram for spine tissue. Sediments from most lakes in the project area showed elevated Hg values during the dry season as well as elevated Hg levels in sediments from the deeper/central part of these lakes. Lake Sterkfontein has a low sediment Hg concentration but contains fish with the highest Hg tissue concentration in the project area. When comparing the Hg distribution in fish muscle and spine tissue from the project area there is a better correlation with species than with location. The Sr isotope ratio of lake water shows a remarkable correlation with the Sr isotope ratio of fish from the same lake. Analytical data showed that fish within a specific lake all have the same Sr isotope ratio in their spines regardless of species, age, sex and condition. The Sr isotope ratio of water generally increases with distance from the source within tertiary catchments and is determined by the prevalent geology of the formations being weathered. In large rivers like the Vaal River where pollution also plays a role the pattern is much more complicated. The Pb isotopic composition of soil samples from Pretoria and the surrounding areas correspond well to the major underlying geological units. Superimposed on this pattern is an anomalous anthropogenic Pb component possibly related to leaded fuel, which extends from the Pretoria city center northwards along the road and railway networks. Water and sediments from Lake Bon Accord and Lake Marais also contain this anthropogenic signature. The hypothesis that fish, which are in equilibrium with the environment that they live in, should reflect the chemistry of that environment, is therefore not rejected since the results of analysing lake water and fish tissues from 23 South African lakes, within 4 major catchments showed definite correlations. Comparing single elements is the least effective method of establishing such correlations. Comparing elemental ratios is a much better method, while comparing isotope ratios is the most effective method.

According to the Joint United Nations Programme against HIV/AIDS 2009 AIDS epidemic update, there were a total of 33.3 million (31.4 million–35.3 million) people living with HIV worldwide in 2009. The majority of the epidemic occurs in Sub-Saharan Africa. Of the 33.3 million people living with HIV worldwide in 2009, a vast majority of 22.5 million (20.9 million-24.2 million) were from Sub-Saharan Africa. There were 1.8 million (1.6 million-2.0 million) new infections and 1.3 million (1.1 million-1.5 million) AIDS-related deaths in Sub-Saharan Africa in 2009 (UNAIDS, 2009). Statistical models and analysis are required in order to further understand the dynamics of HIV/AIDS and in the design of intervention and control strategies. Despite the prevalence of this disease, its pathogenesis is still poorly understood. A thorough understanding of HIV and factors that influence progression of the disease is required in order to prevent the further spread of the virus. Modelling provides us with a means to understand and predict the progression of the disease better. Certain genetic factors play a key role in the way the disease progresses in a human body. For example HLA-B types and IL-10 genotypes are some of the genetic factors that have been independently associated with the control of HIV infection. Both HLA-B and IL-10 may influence the quality and magnitude of immune responses and IL-10 has also been shown to down regulate the expression of certain HLA molecules. Studies are therefore required to investigate how HLA-B types and IL-10 genotypes may interact to affect HIV infection outcomes. This dissertation uses the Sinikithemba study data from the HIV Pathogenesis Programme (HPP) at the Medical School, University of KwaZulu-Natal involving 450 HIV positive and treatment naive individuals to model how certain outcome biomarkers (CD4+ counts and viral loads) are associated with immuno genetic parameters (HLA-B types and IL-10 genotypes). The work also seeks to exploit novel longitudinal data methods in Statistics in order to efficiently model longitudinally measured HIV outcome data. Statistical techniques such as linear mixed models and generalized estimating equations were used to model this data. The findings from the current work agree quite closely with what is expected from the biological understanding of the disease. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2011.