Faculty of Science (ETDs)
Permanent URI for this communityhttps://hdl.handle.net/10539/37933
Browse
47 results
Search Results
Item The Taxonomy and Phylogeny of Varanopidae from the Middle Permian of outh Africa(University of the Witwatersrand, Johannesburg, 2024-08) Sibiya, Zoleka; Rubidge, Bruce; Benoit, JulienVaranopidae are the only pelycosaur-grade tetrapods from the Abrahamskraal Formation of the Beaufort Group. Although four varanopid species are described from the middle Permian of South Africa (SA), their validity has been questionable. Moreover, Ford and Benson recently proposed that varanopids belong to the Diapsida rather than Synapsida. Given this taxonomic and phylogenetic turmoil, this study i) describes two newly discovered and well-preserved varanopid specimens from the middle Permian of SA using CT scanning and ii) re-assesses the validity of the four species from the Karoo Basin in the light of new data from these specimens. The phylogeny of the group is addressed by updating two pre-existing cladistics matrices. The two new specimens exhibit a mosaic of features that overlap the diagnoses of several species of SA varanopids. In addition, some diagnostic traits of the four SA varanopid genera and species are found to be variable across ontogeny. For instance, dorsal osteoderms and the extent of ornamentation on the angular bone co-vary with size. It is therefore proposed that all varanopid specimens currently described from the middle Permian of South Africa belong to a single valid species, Heleosaurus scholtzi, with differences between specimens being accounted for by ontogenetic changes. The phylogenetic analysis supports Ford and Benson’s hypothesis but contra the prediction of this hypothesis, no differences in cranial fenestration during ontogeny are observed. Morphological characters preserved in the manus of the newly discovered specimen BP/1/8499 suggest that Heleosaurus was arboreal.Item A systematic study on the use of the sol-gel synthetic method for lithium manganese oxide-based cathode materials(University of the Witwatersrand, Johannesburg, 2024-09) Muntswu, Zwivhuya; Billing, Caren; Ferg, Ernst E.; Billing, David G.This dissertation investigated the synthesis of two lithium manganese oxide-based cathode materials (Li1.03Mn1.97O4 and LiAl0.4Mn1.6O4) using the sol-gel method and probing the phase transitions during the synthesis. The sol-gel synthetic method involved dissolving stoichiometric amounts of lithium nitrate, manganese nitrate hydrate, and citric acid in distilled water forming an aqueous solution. The starting precursor materials were dried at 140 °C which formed a crystalline phase of -Aqua-S-citrato (2-)-manganese(II) with an orthorhombic crystal system and P222 space group. The thermal behaviour of the precursor was explored to understand the effects of calcination/annealing temperatures. Thermal analysis of precursors prepared using nitrate salts with a 1:1 total metal ion to citric acid ratio displayed thermal stability to temperatures higher than 380 °C with the formation of a final metal oxide after 70% mass loss due to the decomposition of the organic and nitrate materials. However, when increasing the concentration of the complexing agent, an increase in material decomposition due to an increase in organic material is seen. The precursor materials prepared with a lower complexing agent concentration result in materials that have thermal instability when exposed to high temperatures. Thermal analysis of Li1.03Mn1.97O4 and LiAl0.4Mn1.6O4 prepared using acetate salts as starting materials shows material decomposition at high temperature of ~600 °C Calcining both undoped and Al-doped nitrate precursors at moderate temperatures (380 °C to 500 °C) resulted in the formation of Li1.03Mn1.97O4 and LiAl0.4Mn1.6O4 with a pure cubic spinel structure and an Fd-3m space group, however, increasing the calcining temperature to 800 °C for the undoped nitrate-based precursor revealed an impurity phase formation relating to dilithium manganese oxide with a monoclinic crystal system. On the other hand, calcining acetate-based precursors at moderate temperatures (380 °C to 500°C) results in metal oxides with low crystallinity compared to metal oxides prepared with nitrate-based precursors. Calcining acetate-based precursors at 800 °C was more favourable since they form the desired metal oxides without any impurities which might imply structural phase stability at high temperatures. The local and average crystallographic structures (via PDF and XRD respectively) of various nitrate-based metal oxides were investigated, where a good agreement between collected data and a calculated structural model revealed the formation of a cubic spinel structure of space group Fd-3m. Li1.03Mn1.97O4 and LiAl0.4Mn1.6O4 metal oxides were achieved from calcining precursors at moderate temperatures of 380 °C and 450 °C. The PDF high r-value signal displays a good fit which confirms to the average structure data information where the r-value signal which correspond to the local structure refinements have a minor discrepancy when fitted with a cubic spinel of space group Fd-3m.Item Diversity and Abundance of Arthropods on Conventional Sugarcane under Field Conditions in South Africa(University of the Witwatersrand, Johannesburg, 2024-09) Smith, Roshay; Malinga, Lawrence; Bouwer, GustavInsect diversity and abundance are often the base for formulating strategies that involve the appropriate application of pest control methods, considering the ecosystem services provided by insects. Therefore, the aim of this study was to provide recent baseline data on the diversity and abundance of insects in conventional sugarcane based on two sugarcane fields in KwaZulu-Natal. Three sampling methods, namely pitfall, sticky and water pan traps, were used to sample insects in rain-fed and irrigated sugarcane in Gingindlovu and Pongola from March to October 2022. This study collected 12 493 insects belonging to 14 insect orders and 88 families in rain-fed sugarcane and 22 309 insects belonging to 14 orders and 94 families in irrigated sugarcane. Significant differences in the diversity indices were found between the sampling methods and the sampling periods. This study provides recent baseline data on the diversity and abundance of insects in sugarcane.Item Double-diffusive convection in rotating fluids under gravity modulation(University of the Witwatersrand, Johannesburg, 2024-09) Mathunyane, Alfred Ntobeng; Duba, C. Thama; Mason, D.P.This study employs the method of normal modes and linear stability analysis to investigate double-diffusive convection in a horizontally layered, rotating fluid, specifically focusing on its application to oceanic dynamics. Double diffusive convection arises when opposing gradients of salinity and temperature interact within a fluid, a phenomenon known as thermohaline convection, and it is crucial for the understanding of ocean circulation and its role in climate change. With the increasing mass of water due to glaciers melting, fluid pressure variations occur, leading to slight fluctuations in gravity. We conduct both stationary and oscillatory stability analyses to determine the onset of double-diffusive convection under gravity modulation. Our analysis reveals that time-dependent periodic modulation of gravitational fields can stabilize or destabilize thermohaline convection for both stationary and oscillatory convection, with amplitude stabilizing and frequency destabilizing. The wavenumber in the y- direction also affects convection in the equatorial regions. This wavenumber exhibits destabilizing effects for large values and stabilizing effects for small values for both stationary and oscillatory convection. Rotation along with gravity modulation tends to destabilize the system for both stationary and oscillatory convection. The key difference between stationary and oscillatory convection is that oscillatory convection exhibits large values of the Rayleigh number, thus susceptible to overstability while stationary convection tends to have relatively smaller Rayleigh numbers and thus more stable. This research provides insights into the complex interplay between gravity modulation and thermohaline convection, contributing to our understanding of ocean dynamics and their implications for climate change.Item Palaeoclimate Reconstruction Using Charcoal from a Mid-Holocene Stratum 4b, Wonderwerk Cave, South Africa(University of the Witwatersrand, Johannesburg, 2024-06-18) Hlophe, Busisiwe; Bamford, MarionCaves are often sources for palaeoenvironmental information in the dry interior regions of southern Africa. The Wonderwerk Cave, located in Northern Cape, is a national heritage site with a well-preserved, nearly complete record of the local Holocene LSA techno-complexes and past environmental indicators. Hence, it has the potential to provide valuable insights into past human behaviour as well as the local palaeoclimate and vegetation. This study examined wood charcoal from stratum 4b, Excavation 1 of the Wonderwerk Cave. The aim was to evaluate the taxonomic composition and the physiognomy of the charcoal to understand the environment around the cave 6.9-5.9 ka. The study also investigated the modern uses of the vegetation to infer how humans may have utilized the woody plants around them during that period. The results indicate the landscape cover included woody plants adapted to dry conditions and summer rainfall. However, the archaeological taxa identified also included two species that thrive in moist environments, Halleria lucida and Olinia ventosa, suggesting fluctuations in climate. The taxonomic composition also suggests an environment similar to the modern bushveld found near the cave. The low conductivity capacity as well as vulnerability and mesomorphy indices of the woods support the implication that the vegetation was adapted to low water availability or aridity. The cave's inhabitants likely used the identified plants for firewood, magical and medicinal purposes, and more between 6.9 and 5.9 ka.Item Optically stimulated luminescence dating of Kalundu and Urewe tradition ceramics(University of the Witwatersrand, Johannesburg, 2024-03) Haupt, Rachel Xenia; Schoeman, Maria; Evans, MaryOptically stimulated luminescence (OSL) dating is a method of providing the direct age of artefacts. While radiocarbon and seriation dating provide indispensable insight into archaeological sites, the direct dating of artefacts is beneficial in entangled contexts. The Lydenburg Heads Site is significant to the beginning of the Early Farming Communities (EFCs) sequence within the Mpumalanga province. The site has been occupied multiple times, as can be seen from the presence of the two major ceramic traditions of the age, Urewe and Kalundu. The site was originally excavated and analysed by Evers (1982) in the 1970s, with a reanalysis of the ceramic assemblage by Whitelaw (1996) and organic residue analysis on the ceramics by Becher (2021). The use of OSL dating on twelve ceramic sherds allowed for new insights into the chronological intricacies within the study site. To determine the age of the ceramics, the OSL quartz dating technique was used. The adjustments to the technique involved the use of a less destructive means of sample extraction. A slightly altered version of the standard means of sample extraction was used to create a comparison and allow the dating of the ceramics to be reliable. The minimal destruction technique (MET) combined with the bulk sampling proved useful to the dating of the ceramics. The use of previously excavated ceramics meant that some aspects of age determination required estimation and analysis. The major obstacles from such were the water content, the depth of burial, and the lack of in situ soil samples. In light of the elements of ambiguity for the site, the OSL dating considered these variations and how they affected the age. The Urewe tradition ceramics were determined to be in 6th and 8th century AD. The finding creates the alignment with the range of the radiocarbon ages done within previous work and the assumptions made by Evers (1982) and Whitelaw (1996). The Kalundu tradition ceramics ages were determined to be between the 7th and 10th century AD, conflicting with previous assumptions on the occupation. The result is the possibility the ceramic assemblages could be considered to be contemporaneous. The work in this thesis has, in part, been presented at the Luminescence and Electron Spin Resonance Dating conference in Copenhagen (LED2023) and at the Association of Southern African Professional Archaeologists 2024 Biennial Meeting (ASAPA 2024).Item Biocatalytic oxidative conversion of valencene to nootkatone mediated by lipoxygenase and cytochrome P450(University of the Witwatersrand, Johannesburg, 2024-03) Raboya, Christopher; Ngwira, Kennedy; Brady, DeanNootkatone (NK) is an oxygen-containing sesquiterpene with a significant grapefruit aroma and plays an important role in the flavour and fragrance industry. The natural production of NK through extraction produces trace amounts and is therefore not a viable option to meet industrial needs. The chemical synthesis often utilises reagents harmful to the environment. The purpose of this research was to explore the use of crude lipoxygenase (LOX) enzyme extracted from soya beans, commercial mutants of CYP450 as well as laccase enzymes for the conversion of valencene (VL), the aroma components of citrus fruits to NK. For the LOX reactions, a conversion of 28.79% (mol/mol) was obtained when the reactions were performed with LOX only. The best conversion of 74.46 % was realised when FeSO4.7H2O and MnSO4 were added to the reaction. In the temperature studies, 70 ˚C was shown to be the optimal temperature for the conversion. In addition, we observed that vegetable oils provided sufficient unsaturated fatty acids to facilitate the conversion of VL to NK with sunflower oil being the best. In exploring the potential of LOX to oxidise other organic molecules, caryophyllene was oxidised to novel caryophyllene oxide, and styrene was oxidised to benzoic acid, 1-phenylethane-1,2-diol, and 2-hydroxyl-2-phenylethyl benzoate. This is the first time that such oxidations are reported, and this underlines the potential of LOX in biotransformation and organic synthesis. For CYP450 reactions, the best conversion of 16.70 % was obtained using a variant sourced from Prozomix. Evaluation of parameters such as temperature, pH (7.0 to 7.5), using buffer solutions should be explored to optimise the activity of the enzyme. Laccase from Novoprime Base 268 showed no activity for the conversion of VL to NK despite making use of mediators. Therefore, we should explore changing the reaction conditions, varying the pH of the reaction, buffer strength or mediator and laccases from other sources such as Cerrena unicolor and Trametes versicolor, as well as a fresh batch of laccase from Trichoderma (Merck) should be assessed in the conversion of VL to NK.Item The Influence of Climate Change on the Speed of Movement of Tropical Cyclones in the South Indian Ocean(University of the Witwatersrand, Johannesburg, 2024-07) Mahomed, Aaliyah; Fitchett, JenniferRecent studies on the speed of movement of tropical cyclones indicate that anthropogenic warming has resulted in a 10% global decrease of tropical cyclone translation speeds over the period 1949-2016. The recent increase in high intensity storms could severely impact Southern Hemisphere regions which are considerably more vulnerable than their Northern Hemisphere counterparts. High intensity storms occurring at a lower speed would worsen the impacts of tropical cyclones resulting in prolonged periods of flooding, storm surges, and winds. This would subsequently lead to a loss of lives, economic loss and infrastructural and agricultural damage. However, studies have challenged this slowdown, suggesting that the transition to the geo-stationary era, introduces heterogeneity to tropical cyclone data. Additionally, imprecise estimates of tropical cyclone frequency influences the average speed of tropical cyclones, thereby impacting trend analysis. Using tropical cyclone data from National Oceanic and Atmospheric Administration (NOAA) International Best Track Archive for Climate Stewardship (IBTrACS), this study explores the current translation speed debate for the South Indian Ocean, over the period 1991-2021. The results of this study indicate that the translation speed of tropical cyclones has increased at a rate of 0.06km/h/yr over the 30-year period (r = 0.06 p = 0.19). Whilst the translation speed debate remains at an aggregated global scale, a comprehensive understanding of the influence of climate change on tropical cyclones is crucial for generating forecasts as this enables vulnerable regions to plan and adjust to evolving tropical cyclones.Item BiCoRec: Bias-Mitigated Context-Aware Sequential Recommendation Model(University of the Witwatersrand, Johannesburg, 2024-09) Muthivhi, Mufhumudzi; van Zyl, Terence; Bau, HairongSequential recommendation models aim to learn from users’ evolving preferences. However, current state-of-the-art models suffer from an inherent popularity bias. This study developed a novel framework, BiCoRec, that adaptively accommodates users’ changing preferences for popular and niche items. Our approach leverages a co-attention mechanism to obtain a popularity-weighted user sequence representation, facilitating more accurate predictions. We then present a new training scheme that learns from future preferences using a consistency loss function. The analysis of the experimental results shows that our approach is 7% more capable of uncovering the most relevant items.Item Biophysical evaluation of the kinetics, thermodynamics, and structure-stability relationship of Wuchereria bancrofti glutathione transferase in comparison with human µ and π glutathione transferases(University of the Witwatersrand, Johannesburg, 2024-06) Oyiogu, Blessing Oluebube; Achilonu, Ikechukwu AnthonyLymphatic filariasis is an endemic disease caused mainly by the Wuchereria bancrofti parasite and has been classified as a major neglected tropical disease. The emergence of drug-resistant strains of W. bancrofti and the limited efficacy of the available drugs on adult worms threatens the eradication of the disease. W. bancrofti glutathione S-transferase (WbGST) is a homodimeric enzyme central to detoxifying electrophilic compounds in the parasite due to its lack of cytochrome P-450. Therefore, WbGST is a potential therapeutic target for lymphatic filariasis. Bromosulphophthalein (BSP) and epigallocatechin gallate (EGCG) were previously shown to inhibit glutathione S-transferase activity. In this study, the interaction of WbGST with BSP and EGCG in comparison with human glutathione S-transferase P1-1 (hGSTP1-1) and human glutathione S-transferase M1-1 (hGSTM1-1) isoforms was investigated. Soluble WbGST, hGSTP1-1 and hGSTM1-1 were recombinantly produced and purified successfully to homogeneity. Glutathione and 1-chloro-2,4-dinitrobenzene conjugation assay was employed to analyse the enzyme activity, kinetics and inhibitory potency of the compounds. Spectroscopic studies were employed to investigate the functional and structural impact of ligand binding to the enzymes. Both thermal and chemical stability studies were performed, and binding energetics were analysed using isothermal titration calorimetry. The activity of WbGST was predominantly inhibited, with IC50 values of 5 μM for BSP and 12 μM for EGCG. The EGCG displayed uncompetitive and mixed modes of inhibition towards WbGST with respect to glutathione and hydrophobic binding sites, respectively. Whereas BSP showed a mixed type of inhibition for both active sites of WbGST. Ligands reduced the turnover rates (kcat) and the catalytic efficiencies (kcat/KM) of the enzymes. Upon ligand binding, 8-anilino-1-napthalene sulphonate was displaced from WbGST and hGSTM1-1 by 67%(BSP), 24%(EGCG) and 72%(BSP), 5%(EGCG), respectively; suggesting that the ligands bind to the 8-anilino-1-napthalene sulphonate binding site. Stability studies indicate that WbGST is the least stable of the three enzymes and that glutathione increases its stability. Isothermal titration calorimetry showed that BSP binds to multiple sites in WbGST with binding at site-1 (S1) and site-2 (S2), which are entropically and enthalpically driven, respectively. S1 showed a higher affinity for BSP than S2. EGCG binding to WbGST was entropically driven. BSP had a higher affinity for the enzymes than EGCG. All the results indicated that the ligands significantly impact WbGST more than the human GSTs. Further investigations, such as crystallography and molecular dynamics simulations, will shed more light on the ligan-protein interactions on a molecular level. Overall, this study suggests that BSP and EGCG are efficient inhibitors of WbGST that probably bind to both L and H-sites of WbGST, altering catalytic activity of the enzyme. The unique properties of the L-site are particularly suitable for rational drug design. Therefore, both ligands can be repurposed as new-generation therapeutics against filariasis.