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    The Concentration, Transport and Fate of Nitrogen Oxides in the Highveld Atmosphere
    (University of the Witwatersrand, Johannesburg, 2025-05) Kai-Sikhakhane, Refilwe Faith; Piketh, Stuart; Scholes, Mary C.
    The Highveld region of South Africa is a major source of emissions from large industries, including electricity utility power stations, petrochemical plants, and smelting industries. This study investigates the sources, concentrations, and transport of nitrogen dioxide (NO2) emissions in Wakkerstroom, a town located downwind of major NO2 emission sources in the Mpumalanga Highveld. Near-surface and tropospheric vertical column NO2 concentrations were measured using ground-based Pandora-2s and TROPOMI-Sentinel-5P satellite instruments. The Pandora-derived diurnal NO2 concentrations at Wakkerstroom ranged between 0.2 ppb, with a standard deviation of ± 0.04 ppb and 7.5 ppb, with a standard deviation of 5.7 ppb, with the highest concentrations recorded in September. Air quality monitors near power stations measured peak weekly averaged concentrations in winter (27.6 ppb) and summer (31.5 ppb) of 2020. The annual mean Pandora-derived tropospheric vertical column (TVC) NO2 concentrations were 5.1 x 10-5 mol/m2 with a standard deviation of 9.0 x 10-5 mol/m2 in 2020 and 5.03 × 10-5 mol/m2 with a standard deviation of 9.40 × 10-5 mol/m2 in 2021, while TROPOMI measured 21% and 40% higher concentrations, respectively. Theil-Sen regression analyses showed that TROPOMI overestimates Pandora-derived TVC-NO2 concentrations by over 50%. Backward trajectory analyses revealed that air mass transport from the east of Wakkerstroom, passing over eSwatini and southern Mozambique, contributed significantly to the observed NO2 concentrations due to biomass burning. The findings of this study highlight the complex dynamics of NO2 pollution in the Highveld region, revealing the influence of both local and regional sources on Wakkerstroom's concentrations. This research emphasises the fundamental role of continuous long-term ground-based data of pollutants in heavily polluted areas like the Highveld, which is characterised by unique synoptic meteorological patterns. Such data serves to bridge the information gaps to corroborate and augment high-spatial resolution satellite observations. Consequently, it helps to confirm the reliability and use of satellite data as a proxy for larger geographical areas with scarce ground-based instruments.
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    Stratigraphy and depositional setting of the Witpoort Formation (Witteberg Group, Late Devonian) in the Eastern Cape, South Africa
    (University of the Witwatersrand, Johannesburg, 2025-05) Harris, Christopher; Jinnah, Zubair; Penn-Clarke, Cameron; Gess, Rob
    The Witpoort Formation, a Late Devonian (Famennian) coastal siliciclastic sedimentary succession, has not received a detailed sedimentary facies analysis in the past three decades, despite significant palaeontological discoveries from its strata. Here, sedimentary facies, sediment dispersal patterns and ichnology are, for the first time, applied in combination to form a sedimentological background to the only high-latitude palaeoecological dataset from its time stage. The results of this thesis indicate a non-marine, sheet-braided fluvial deposit in which transgression of the coast led to the development of marginal-marine, estuarine facies, favouring the preservation of body and trace fossils. The deposits accumulated in erosively based, valley-fill fluvio-estuarine cyclothems along an approximately WNW–ESE trending shoreline bordering the Agulhas Sea. Towards the top of the succession (Perdepoort Member) fluvial progradation, and the lack of marginal-marine facies, indicate maximum regression, consistent with a globally recognised sea-level fall during the late Famennian. The end-Devonian Hangenberg Event is contemporary with the uppermost strata of the Witpoort Formation, in concord with prior assessments. Evidence for glaciation associated with this event in South Africa remains tenuous, though it is predicted that careful study of the Skitterykloof Member in the uppermost Witpoort Formation will find that periglacial processes were operating during its deposition, and perhaps also lower in the stratigraphic column. The Kellwasser Event, defining the Frasnian–Famennian boundary, is not recognised in the studied stratigraphic column, though it is predicted that the event will have occurred during deposition of strata that underlie the Witpoort Formation. Analysis of eustatic patterns from the global Famennian stratigraphic record and comparison with the stratigraphy described herein indicates that eustasy formed an important control on sedimentation in the Witpoort Formation. This presents the strongest evidence for constraining the chronology of its strata. There is an urgent need for further multi-proxy analyses, especially geochemical and palynological, as have been conducted in Euramerican strata, to increase the chronostratigraphic resolution and recognition of Late Devonian extinction events in the Witteberg Group. Fossil biodiversity of the Witpoort Formation is principally known from the Waterloo Farm locality, which is here shown to be lower in the stratigraphic column, and therefore older, than previously thought. Waterloo Farm is here positioned in the upper Rooirand Member. This deposit appears to have formed in a fresh- to brackish-water inner estuary, possibly tens of kilometres from the shoreline. Analysis of a new fossil locality, Rabbit Ridge, from lower in the stratigraphy, presents a comparable estuarine depositional environment to Waterloo Farm. Higher degrees of marine influence at Rabbit Ridge are indicated by the invertebrate and trace fossil signatures. The ecology of invertebrate communities and trace fossils indicate variable salinity levels and depositional rates from a spectrum of estuarine sub-environments that occurred at intervals throughout the Rooirand Member.
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    Geological Setting and Genesis of Vein-hosted Copper Mineralisation at the Onganja Mining District, Namibia
    (University of the Witwatersrand, Johannesburg, 2024-12) Hales, Matthew Paul; Kinnaird, Judith; Nex, Paul
    The Onganja Mining District is in the Southern Zone of the Damara Orogen, Namibia, and comprises several mining licence areas that have historically produced copper concentrates with accessory Au-Mo-U-REE. The country rocks in the district consist largely of amphibolites, biotite-plagioclase schists, and pelitic schists, with other minor lithologies distributed throughout the licence areas. These rocks have undergone polyphase deformation, which has produced an antiformal dome on which most of the licence areas are located. Initial deformation is recorded by an S1 axial-planar cleavage and locally preserved F1 folds. The F1 folds were refolded by an F2 event that produced a pervasive S2 axial planar cleavage defined by the growth of micas and quartz veins. Progressive deformation and metasomatism focussed along the S2 axial-planar cleavage initiated D3 shearing, which is recognised in the country rocks by an increased mica content, with the micas being well-aligned so as to define a S2,3 transposed schistosity. The development of the shears is most pronounced in the amphibolite units which produced black mica schists that are dominated by a greasy black biotite of phlogopite composition. A N-S trending, steeply east dipping, quartz-albite vein system developed in the ac-plane of the F2 folds. The veins have varying proportions of albite and quartz – typically veins with dominant albite have smoky to translucent quartz, whereas quartz-only veins are typically milky and may have albite haloes. The quartz-albite veins are interpreted to represent metamorphic devolatilization due to the comparable δ18OQuartz values (10.39-14.23 ‰) with those from quartz veins in the Southern Zone related to metamorphic devolatilization reactions while the albite content in these veins is suggested to be related to an increasing metamorphic grade that resulted in fluids more capable of carrying the necessary components for albite formation. The quartz albite veins were crosscut by the D3 shears, which produced breccias that are infilled by various metamorphic, alteration, and ore minerals. In contrast, the calcite vein system differs in orientation and modal mineralogies to the quartz albite veins system and crosscut the D3 shears. Two calcite vein types are recognised: a calcite hematite vein set and a massive calcite vein set. Although both sets contain calcite and crosscut the D3 shears, the relationship between the two is unclear. The calcite-hematite consist of veins with platy hematite and rhombohedral calcite in a matrix of calcite and goethite and have alteration haloes of white mica and albite in the proximal zones and chlorite more distally. The massive calcite veins are, locally ≤1 m wide and dip steeply to the south and the west. These veins consist of large (>2 cm), rhombohedral calcite crystals, incorporate clasts of wall rock and lack associated alteration. Alteration in the district is dominated by albitisation in haloes around fractures and quartz-albite veins, in pressure shadows of quartz lenses in the D3 shears, or as albite lenses in the black-mica schists. Other alteration phases include growth of scapolite, biotite, chlorite, white mica, and quartz. Scapolite occurs within schistosity parallel bands and is interpreted to be comparable to scapolite in shears and thrusts elsewhere in the Southern Zone, even though the scapolite from the district is slightly more sodic (XMe=34-51). Biotite and chlorite both occur with albitisation in the D3 shears forming euhedral crystals in pockets or as trails in the pressure shadows of quartz lenses. Biotite also defines the S2,3 schistosity in the D3 shear, which chlorite does not. Both the biotite and chlorite from the district are enriched in Mg (XMg= ~55-70 and ~60-73, respectively), which is interpreted as a consequence of fluid-rock buffering by iron in the silicates. The fluid-rock buffering and biotite growth is interpreted to have produced a positive feedback loop by which the D3 shears would have developed. The white micas are associated with chlorite, albite, hematite, and goethite. The rocks that have this assemblage are typically pinkish and are collectively called the bleached schists. The white micas are typically euhedral with no preferred orientation, whereas the chlorite may pseudomorph biotite in the deformation fabrics. Hematite and goethite are common and typically occur in association with chlorite and white micas. Owing to the comparable alteration assemblages of the bleached schists and alteration haloes around the calcite-hematite veins, the fluids responsible for both are interpreted to be the same. This alteration is interpreted to be post-kinematic due to the crosscutting of the D3 shears by the calcite-hematite veins and the overprinting of the biotite in the deformation fabrics by the white micas and chlorite. Furthermore, U-Th-Pb age dating of monazite in the bleached schists yields post-orogenic ages of 430-125 Ma. Mineralisation within the district comprises disseminated and massive sulphides within the country rock schists, breccias associated with the quartz-albite vein system, and sulphide veins. The ore assemblage across all styles of ore deposition includes chalcopyrite, chalcocite, pyrite, magnetite, hematite, and molybdenite. The ores are also enriched in Au, U, and REE. Chalcocite is interpreted to be supergene. Pyrite, magnetite and hematite are typically euhedral in all the ore bodies. Molybdenite is locally present as euhedral rosettes. Magnetite typically overgrows pyrite. The disseminated and massive sulphides are dominantly chalcopyrite, whereas the veins and breccias may have varying proportions of chalcocite after chalcopyrite. The sulphide veins consist of chalcocite after chalcopyrite and due to their limited occurrence, little more is known about them. The breccias, disseminated sulphides, and massive sulphides are all spatially related to the black-mica schists. This spatial relationship is suggested to represent a lithological and structural control on the mineralisation as the black-mica schists are interpreted to be the metasomatic product of the D3 shears in the amphibolites. The lithological control is interpreted to be a redox buffer system, with wall rocks that had sufficient Fe content – viz., the amphibolite and black-mica schists – reducing the fluids to cause copper sulphide precipitation. This reduction by the wall rocks is what is likely to have produced the magnetite associated with the copper sulphides. Likewise, hematite is interpreted to be the product of wall rock buffering, however, the wall rocks were likely to have lacked the Fe content to effectively buffer the fluids to the same degree as the black-mica schists. The D3 shears are interpreted to be the conduits through which the ore-bearing fluids migrated – where the shears crosscut compositionally favourable lithologies the copper sulphides were precipitated as disseminated and massive sulphides. Similarly, the shears crosscut the quartz-albite vein system and produce breccias at the intersections. Many of the breccias are barren, having only alteration and metamorphic mineral infill. Where the black mica schists intersect the veins, however, the breccias are mineralised – the wall rocks to the breccias are interpreted to have had the same redox buffering effect as in the D3 shears, however, the preferential fracturing of the quartz-albite veins allowed for the upward escape of the mineralising fluids. The mineralisation and alteration styles at the Onganja Mining District bear some similarity to Iron Oxide-Copper-Gold (IOCG) deposits. These similarities include the Cu-Au-Mo-U-REE element assemblage, the occurrence of magnetite and hematite with the ores, and the albitisation. There are, however, significant differences between the mineralisation in the district and that of IOCG deposits, particularly pertaining to the ore and mineral chemistry. Most notable of the differences is the lack of iron content in the ores (typically <10 wt.%) which has resulted in magnetite and hematite being subordinate to chalcopyrite and phlogopitic biotite (XMg= ~62-67) rather than the Fe-rich biotite of some IOCG deposits. The ores also have geochemical signatures that are distinct from IOCG deposits when comparing the ratio of lithophile (U and La) and chalcophile (Co, Ni, Bi, Se, and Te) to the Cu and Au grades of the ores. Likewise, the minor and trace elements in magnetite from the district are dissimilar to those of select IOCG deposits. It is concluded, therefore, that the mineralisation in the Onganja Mining District is unlikely to be representative of an IOCG system. Rather, the mineralisation bears some similarities to other Pan-African copper deposits associated with domal structures comparable to that on which the district is located. These deposits are defined by Cu mineralisation in late orogenic shears related to retrograde metamorphism and metasomatism. The mineralisation style of the deposits in the Onganja Mining District is, therefore, regarded as late-orogenic, shear-related Cu mineralisation.
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    Fabrication of Fouling Resistant and Operationally Stable Nanocomposite Membranes for BTEX Wastewater Treatment
    (University of the Witwatersrand, Johannesburg, 2024-11) Enemuo, Ngozi Doris; Richards, Heidi L.; Daramola, Michael; Nthunya, Lebea
    This thesis details the fabrication of a fouling-resistant and operationally stable membrane developed for removing BTEX (benzene, toluene, ethylbenzene, and xylene) from wastewater. BTEX is among the top major organic contaminants that have been reported to pollute the aquatic system. BTEX contaminants in the water bodies are detrimental to both humans and aquatic organisms, as exposure to these contaminants could result in mild or severe health complications. With the major source of these contaminants originating from anthropogenic activities, especially the discharge of poorly treated industrial wastewater, it is essential to continuously explore better means of ensuring effective treatment of BTEX-contaminated wastewater before discharge to the environment. Membrane technology offers a low-cost, easy, and effective approach to removing such organic contaminants from wastewater. However, due to the hydrophobic nature of most membrane materials, there is a high fouling rate during the treatment process as a result of the interaction between the hydrophobic membrane and the hydrophobic organic contaminants. The fouling of the membrane leads to the deterioration of its properties, resulting in a severe decline in membrane performance. Addressing the issue of such membrane fouling is often done through hydrophilic modification, which entails using hydrophilic modifiers to enhance the hydrophilic property of the membrane. Once the membrane’s hydrophilicity is enhanced, the interaction between the membrane and the organic contaminants is reduced, thereby minimizing the fouling rate of the membrane during the treatment process and ensuring that the membrane maintains its performance for a longer duration. Therefore, the goal of this study was to fabricate a fouling-resistant membrane by incorporating biogenic-synthesized iron oxide nanoparticles and polyvinyl alcohol (PVA) as hydrophilic modifiers to improve and maintain the membrane performance in the treatment of BTEX-contaminated water. The first part of the study was to biogenically synthesize the iron oxide using the leaves, peels, and seeds extracts of the pomegranate and compare their properties and contributions in removing BTEX from contaminated wastewater. X-ray diffraction (XRD), Fourier transform infrared (FTIR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Brunauer-Emmett-Teller (BET) were used to analyze the properties of the three different biogenic-synthesized iron oxide nanoparticles. The FTIR results showed that there is deposition of hydrophilic functional groups from the extracts to the synthesized nanoparticles, thus establishing that the biogenic-synthesized iron oxide nanoparticles have attached hydrophilic functional groups, which is beneficial in their use as hydrophilic modifiers. From the FTIR spectra, the iron oxide nanoparticles synthesized using the leaves extract have a more intense peak of the hydrophilic functional groups, such as the -OH group; thus, it was selected as the nanoparticle used for the hydrophilic membrane modification. It was also established that the biogenic-synthesized iron oxide nanoparticles have the capacity to remove BTEX from wastewater, as indicated in the batch adsorption study. The findings of this part of the study are presented in Paper 1, which is fully discussed in Chapter 4 of this thesis. In the second part of the study, the biogenic-synthesized iron oxide nanoparticles (NPs) (from the leaves extract of pomegranate) were blended into a polyvinylidene fluoride (PVDF) membrane, and the optimum blending amount of the NPs required for their optimum dispersion in the membrane was assessed. This was performed by varying the blending amounts of the NPs from 0.05 wt.% to 5.0 wt.%, and the ideal operating parameters were also identified. From the SEM and TEM images, the membrane modified with 1.0 wt.% of the NPs (denoted as PVDF 1.0) has the best dispersion of the NPs in the membrane matrix without agglomeration of the NPs. Among all the fabricated membranes, the PVDF 1.0 also has the lowest water contact angle (WCA) of 52o, the lowest irreversible fouling (Rir) of 18.3%, and the highest flux recovery ratio (FRR) of 81.3%. The PVDF 1.0 also performed better in the reusability test. Based on the properties and performance of PVDF 1.0, the optimum blending amount of the biogenic synthesized NPs in the PVDF membrane, using the fabrication conditions of this study, was established to be 1.0 wt%. The findings of this part of the study are presented in Paper 2, which is detailed in Chapter 5 of this thesis. The third part of the study focused on further enhancing the membrane's hydrophilicity and antifouling ability to ensure its good operational stability under long-term BTEX filtration. This was done by utilizing the synergistic impact of biogenic-synthesized iron oxide NPs and PVA as good hydrophilic modifiers to improve the membrane's hydrophilicity and performance. Biogenic-synthesized NPs and PVA were blended into the membrane, and the properties and performance of the modified membrane were assessed (optimum amount, 1.0 wt% of the biogenic-synthesized NPs, was used as established in the second part of the study, that is, in Chapter 5). The WCA of the modified PVA-Fe3O4-PVDF membrane reduced to 40.5o, and the Rir also reduced to 2%, while the FRR increased to 98%. The performance of the membrane under long-term filtration showed that the modified membrane had fairly good operational stability, as the membrane maintained its flux for 84 hour without any significant decline in flux. The findings of this section of the study are presented in Paper 3, which is discussed in Chapter 6 of this thesis. The fourth part of the study investigated the reproducibility of some of the properties and performance of the modified PVA-Fe3O4-PVDF membrane. Ten more of the modified membranes were re-fabricated at different times, and their SEM, BTEX flux and BTEX rejection were analyzed. In terms of the SEM result, seven out of the ten re-fabricated membranes showed good dispersion of the NPs in the membrane matrix. The BTEX flux and rejection of the re-fabricated membrane were also fairly close to the originally reported value in Chapter 6 of this thesis. The findings of this section of the study are detailed in Chapter 7 of this thesis.
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    Chavalala, Hlamulo Edward. (2025). Synthesis and biological evaluation of Plasmodium falciparum calcium-dependent protein kinase inhibitors for malaria treatment and transmission-blocking. [PhD thesis, University of the Witwatersrand, Johannesburg]. WIReDSpace.
    (University of the Witwatersrand, Johannesburg, 2025-03) Chavalala, Hlamulo Edward; de Koning, Charles B.; Henning, Hendrik; Rousseau, Amanda L.
    Malaria is a mosquito-borne disease that was responsible for an estimated 249 million cases and 608 000 mortalities within 85 malaria endemic countries and areas in 2022, with children under the age of 5-years most burdened. Only five of the Plasmodium parasites are known to infect humans, with P. falciparum causing the most severe form of malaria. Several drugs have been used in the treatment of malaria, however, due to the emergence of parasite resistance, the efficacy of most available drugs has been reduced, prompting a need for the development of novel antimalarial agents to prevent an increase in malaria incidences and mortalities. Ideal novel antimalarial agents are those that target both the asexual and sexual forms of the Plasmodium parasite in the human host, to both treat and prevent the transmission of malaria. Two P. falciparum calcium-dependent protein kinases (PfCDPKs), PfCDPK1 and PfCDPK4, have emerged as attractive targets for such antimalarial compounds owing to their involvement in both the asexual and sexual blood stages of the parasite, and their absence in the human kinome. In this PhD thesis, we explore the pyrrolo[2,3-d]pyrimidine derivatives and their ring open analogues, the 4,6 diaminopyrimidine derivatives, as potential inhibitors of PfCDPK1 and PfCDPK4 towards the treatment of malaria and blocking of parasite transmission from human host to the mosquito. The first part of the thesis involves the design and in silico study of the targeted compounds, the pyrrolo[2,3-d]pyrimidine and the 4,6-diaminopyrimidine derivatives. We assessed the binding affinities of these compounds in silico against the PfCDPK4 model prepared from the crystal structure 4QOX from the RCSB Protein Data Bank, and the PfCDPK1 model prepared through homology modelling. The compounds were docked into the active site of the enzyme and interacted in the binding site in a similar way as the adenine ring of the natural substrate, adenosine triphosphate (ATP). Substituents important for selectivity and potency were chosen, and shown to occupy additional binding pockets, suggesting that our target compounds are potential inhibitors of PfCDPK1 and PfCDPK4. A representative docking pose from each series of compounds was chosen to evaluate the compound-enzyme stability using molecular dynamics and we found that the afforded poses are relatively stable with the hinge region interaction between the enzymes and the ligands playing a central role. Furthermore, we evaluated the compounds’ pharmacokinetic properties and toxicity potential, and results indicated that the molecules have good oral bioavailability and poor potential to cause neurological side effects but could cause cardiac-based complications. The second part of the research focuses on the synthesis and biological evaluation of the targeted pyrrolo[2,3-d]pyrimidine and 4,6-diaminopyrimidine-based compounds. The synthesis of the pyrrolo[2,3-d]pyrimidine compounds was achieved using a synthetic route consisting of nine synthetic steps which includes the formation of the pyrrolo[2,3-d]pyrimidine ring and the addition of side-groups that confer potency and selectivity to the compounds. We modified some of the synthetic steps using microwave irradiation, including the Sonogashira coupling reaction. Three compounds were found to be exclusively active against recombinant PfCDPK4 in the micromolar range, while one was active against PfCDPK1, also in the micromolar range. The 4,6-diaminopyrimidine derivatives bearing a two-atom linker to a bulky naphthalene substituent were divided into three classes the ethyne-, ethene-, and ethane-linked compounds. The ethyne- and ethene-linked compounds were afforded through at least four synthetic steps starting from 4,6-dichloropyrimidine. Three of these synthetic steps were modified using microwave irradiation. We could not prepare the target ethane-linked compounds by our planned hydrogenation of the corresponding alkyne precursors, as this reaction afforded only alkene products. This could be due to steric hindrance, although alternative reduction methods were not attempted. Unfortunately, the compounds from these series are yet to be tested for biological activity against PfCDPK1 and PfCDPK4. A second series of 4,6-diaminopyrimidine derivatives bearing a one-atom linker to a bulky naphthalene substituent were divided into two classes: those bearing a carbon-linker, and heteroatom-linked compounds. We developed the synthetic protocol for the synthesis of carbon linked 4,6-diaminopyrimidine compounds on a model study as far as the formation of 5-benzyl-6 chloropyrimidin-4-amine through five synthetic steps; with only one synthetic step remaining to afford an analogue of the target compounds. We have yet to apply the developed protocol in the synthesis of the targeted carbon-linked 4,6-diaminopyrimidine compounds and test them for biological activity. The development of a synthetic route to afford heteroatom-linked 4,6-diaminopyrimidine derivatives went as far as four synthetic steps of the planned six synthetic steps. Microwave irradiation played a central role in affording three of the intermediates, significantly reducing the synthesis time and solvent quantities. We have yet to complete and apply the synthetic route to our targeted compounds which will be tested for biological activity against PfCDPK1 and PfCDPK4. Molecular modelling has proved to be a viable tool in the design of our ligands and prediction of their binding potential in the active site of the targeted enzymes. To the scope of our research, the models we developed have shown good accuracy in predicting the binding affinity of the ligands in vivo as confirmed by experimental data. It gives us confidence that the biological results from the targeted 4,6-diaminopyrimidine derivative will agree with in silico data to a great degree. Also, it justifies the further use of molecular modelling in the design of new ligands and improvement of current ligands towards finding molecules that are potent inhibitors of the targeted enzymes.