List of Titles

Predators of aerial insects and riparian cross-boundary trophic dynamics: web-building spiders, dragonflies and damselflies

- Chari, Lenin Dzibakwe

Authors: Chari, Lenin Dzibakwe
Date: 2016
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/55791 , vital:26734
Description: This thesis characterises the cross-boundary trophic interactions of a relatively small model ecosystem, the Kowie River (Eastern Cape of South Africa), to explore their epistemic implications for systems ecology. Using web-building spiders and odonates (dragonflies and damselflies) as model organisms, I sought to investigate whether the diets of predators of aerial insects could be used to assess the strength of the trophic connectivity between freshwater and terrestrial systems in relation to variables such as stream width, distance from the river and aquatic insect emergence rates and abundances. Predator diet composition was determined by using a combination of diet analysis tools: direct observations of cross-subsidies, naturally-abundant stable (carbon and nitrogen) isotope analysis and fatty acid analysis. I also sought to reveal feeding niches and guilds among riparian aerial predators and investigate how the environment influenced predators’ access to aquatic prey subsidies. As emergent aquatic insect abundances decreased with an increase in distance from the river, and increased with stream width and seasonal changes from winter to summer, stable isotope and fatty acid analyses revealed distinct changes in web-building spider diet composition. Examination of the fatty acid eicosapentaenoic acid, a component commonly used as an indicator of consumer reliance on aquatic nutritional subsidies, showed that aquatic subsidies extended further inland at the wider sections of the river. Spiders and odonates at the wider sections of the Kowie River generally received more subsidies (56 – 70%) than those at the narrower sections (25 – 60%). When terrestrial insect biomass was distinctly low in winter, the benefit of aquatic subsidisation to spiders was relatively lower at the narrower sections of the Kowie River relative to the wide sections. As such, riparian areas adjacent to wide parts of the river were more likely to support larger populations of aerial predators than those at the narrow sections. Apart from the diet changes across time and space, there was evidence of inter-specific niche partitioning in both spiders and odonates, but no differences were observed between males and females of the same species. Results showed odonates of different sizes and hunting strategies had separate dietary niches, hence varied access to aquatic nutritional subsidies. The larger odonate taxa that frequently foraged mid-air had more varied diets and relied less on aquatic emergent insects than the smaller odonates that foraged from perches near the river. There was also evidence of niche partitioning amongst the spiders, as those that built horizontal webs captured more aquatic insects (40 – 78%) than the vertical orb-web builders (20 – 66%). This study showed that the nature and extent of trophic cross-boundary linkages in riparian areas largely depended on the availability of subsidies that varied seasonally and spatially. The width of the stream and seasonal variability emerged as important predictors of emergent insect abundances/biomasses that influenced predator feeding niches. The high mobility of odonates made their reliance on aquatic nutritional subsidies different from the less mobile spiders. The link between the width of the river and the extent of trophic connectivity has implications for riparian area management and definition of riparian buffer zones. However, the variation in diet niches amongst terrestrial consumers makes the results area-specific, and more studies are required that incorporate additional terrestrial predators in other fluvial systems so that we can make some generalizations on the dynamics of riparian trophic cross-boundary links.
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Date Issued: 2016

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The trophic ecology of waterbirds in a small temperate estuary: a stable isotope and lipid tracer approach

- Hean, Jeffrey William

Authors: Hean, Jeffrey William
Date: 2016
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/54356 , vital:26557
Description: Waterbirds are often overlooked as predators in aquatic ecosystems, despite the fact that waterbirds congregate in great numbers in and around waterways, notably estuaries. To fully appreciate the effect that aquatic feeding waterbird species may have on aquatic prey communities and the role that they play in estuarine food webs, stable isotopes and fatty acid profiles were employed to examine the seasonal diet of selected waterbirds in the Kowie Estuary, Eastern Cape Province, South Africa. Population counts were conducted every month for four seasons to examine the demography of waterbirds in the lower reaches of the estuary. The mean monthly energy consumption, along with dry matter intake of all waterbird species observed, were calculated and compared to similar estuaries in South Africa and elsewhere. Three duck species, one migrant sandpiper and one piscivore were selected for more detailed investigation at several temporal scales. This thesis has revealed that stable isotope analysis of waterbird tissues provides more informative data than fatty acid analysis for investigating waterbird diet and basal resource-tertiary consumer nutrient coupling. Stable δ15N and δ13C isotopes from several body tissues, in conjunction with SIAR models, were used to determine the seasonal diet of each waterbird species, while fatty acid profiles were investigated to examine the trophic transfer of fatty acids from basal resources to waterbird predators via the benthic fauna. Stable isotopes revealed that Cape Shoveller, Cape Teal and Yellow-Billed Duck shifted their diet over both long and short temporal scales, while the migratory Ruff and piscivorous Little Egret maintained a relatively consistent diet over time. Isopods, amphipods, copepods and Mysidacea were the main foods of all three duck species and the Ruff (>30%). Little Egret fed mainly on flathead mullet throughout the year. Fatty acid analysis revealed evidence for trophic transfer of specific fatty acids from basal resources to waterbirds in the Kowie Estuary but provided little information on seasonal diet of waterbirds. Waterbirds foraging in the Kowie Estuary appeared to shift their diet to coincide with resource abundance pulses, but also displayed seasonal dietary overlap. This study highlights the role that waterbirds play in aquatic food webs. The subject requires more attention so that we can better understand all the predatory drivers on aquatic communities.
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Date Issued: 2016

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Bacterial degradation of fossil fuel waste in aqueous and solid media

- Edeki, Oghenekume Gerald

Authors: Edeki, Oghenekume Gerald
Date: 2015
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/54565 , vital:26588
Description: The generation of environmental pollutants worldwide is mainly due to over reliance on fossil fuels as a source of energy. As a result of the negative impacts of these pollutants on the health of humans, animals, plants and microorganisms, global attention has been directed towards ways of containing this problem. Biodegradation of fossil fuel is one of the most effective methods used to remediate contaminated systems. However with regard to coal waste, much of what is known is based on the ability of fungal species to biosolubilize this material under enrichment conditions in a laboratory setting. For effective biodegradation as a remediation technique, there is an immediate need to source, isolate, enrich and incorporate other microorganisms such as bacteria into bioremediation technologies. The goal of this dissertation was to isolate bacteria from fossil fuel contaminated environments and to demonstrate competence for petroleum hydrocarbon degradation which was achieved using a combination of analytical methods such as spectrophotometry, FT-IR, SEM and GC-MS. Screening for biodegradation of coal and petroleum hydrocarbon waste resulted in the isolation of 75 bacterial strains of which 15 showed good potential for use in developing remedial biotechnologies. Spectrophotometric analysis of bacteria both in coal and petroleum hydrocarbons (all in aqueous media) revealed a high proliferation of bacteria in these media suggesting that these microbes can effectively utilize the various substrates as a source of carbon. The isolated bacteria effectively degraded and converted waste coal to humic and fulvic acids; products required to enrich coal mine dumps to support re-vegetation. Scanning electron microscopy showed the attachment of bacteria to waste coal surfaces and the disintegration of coal structures while FT-IR analysis of extracted humic-like substances from biodegraded waste coal revealed these to have the same functional groups as commercial humic acid. Specific consortia which were established using the isolated bacterial strains, showed greater potential to biodegrade coal than did individual isolates. This was evident in experiments carried out on coal and hydrocarbons where the efficient colonization and utilization of these substrates by each bacterial consortium was observed due to the effect of added nutrients such as algae. The biodegradation of liquid petroleum hydrocarbons (diesel and BTEX) was also achieved using the 15 bacterial isolates. GC-MS analysis of extracted residual PHC from aqueous and solid media revealed rapid breakdown of these contaminants by bacteria. Different bacterial consortia established from the individual isolates were shown to be more efficient than single isolates indicating that formulated consortia are the biocatalysts of choice for fossil fuel biodegradation. This study represents one of the most detailed screenings for bacteria from fossil fuel contaminated sites and the isolation of strains with potential to biodegrade coal and petroleum hydrocarbon wastes. Several consortia have been developed and these show potential for further development as biocatalysts for use in bioremediation technology development. An evaluation of efficiency of each established bacterial consortium for biodegradation in a commercial and/or industrial setting at pilot scale is now needed.
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Date Issued: 2015

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Characterization of the co-chaperones of Hsp70 and Hsp90 in Trypanosoma brucei and their potential partnerships

- Mokoena, Fortunate

Authors: Mokoena, Fortunate
Date: 2015
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/54543 , vital:26583
Description: African Trypanosomiasis, which is caused by Trypanosoma brucei, is one of the crippling agents of social and economic development in Africa. T. brucei cycles between the cold-blooded insect vector, the tsetse fly (Glossina spp), and warm-blooded mammalian hosts. T. brucei, T. cruzi and L. major are mammal infecting kinetoplastid parasites that are collectively referred to as TriTryps. These parasites experience extreme environments as they move between their warm-blooded mammalian hosts and cold-blooded insect vectors which trigger extensive morphological transformations during the life-cycle of the parasite. Molecular chaperones have been implicated in parasite differentiation. TriTryps display significant expansions and diversity in the gene complements encoding molecular chaperones, especially J-proteins. Generally, J-proteins function as co-chaperones of Hsp70s, forming part of vital protein homeostasis processes. Hsp70s show a high degree of conservation, while J-proteins appear to be an extreme case of taxonomic radiation. Although several studies have focused on the molecular and cell biology of Hsp70s in some kinetoplastid parasites, knowledge is still lacking pertaining to J-proteins and their partnerships with Hsp70s. This thesis focused on the classification of kinetoplastid Jproteins into the four types by examining the domain organizations using T. brucei as a guide. The potential partnership of J-proteins and Hsp70s were postulated based on predicted subcellular localization. Kinetoplastid parasites, particularly T. brucei, have evolved an expanded and specialized J-protein machinery, likely to be a consequence of an evolutionary fitness/trait to adapt to diverse environment present in hosts and vectors. These analyses will yield insight into the process of parasite differentiation as well as provide new leads for chemotherapeutic treatments. The presence of the STI1 mediated Hsp90 hetero-complex formation has not been confirmed in T. brucei. To this end, in silico and biochemical techniques were used to characterize the role of TbSTI1, as an adaptor protein of Hsp70 and Hsp90. Through domain architecture analysis, sequence alignments, phylogenetic analysis and three-dimensional structure prediction, TbSTI1 was demonstrated to be the most conserved TPR containing co-chaperone of Hsp70 and Hsp83 in T. brucei and also shown to be highly similar to its eukaryotic homologues. Recombinant TbSTI1 was overproduced and purified in E.coli cells and subsequently shown to associate with TcHsp70 in a concentration dependent manner and associate weakly with TbHsp70.4. TbSTI1 and TbHsp83 were also demonstrated to be expressed and upregulated upon exposure to heat shock at the bloodstream stage of parasite development. In conclusion, this study is the first to report the interaction of TbSTI1 with a chaperone. Interactions between TbSTI1 and Hsp70s were demonstrated and therefore, the formation of the hetero-complex is predicted based the similarity of TbSTI1 to other STI1 proteins.
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Date Issued: 2015

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Contributions to the study of a class of optimal control problems on the orthogonal groups SO(3) and SO(4)

- Adams, Ross Montague

Authors: Adams, Ross Montague
Date: 2015
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/64826 , vital:28608
Description: In this thesis we investigate a class of invariant optimal control problems, and their associated quadratic Hamilton-Poisson systems, on the orthogonal groups SO(3) and SO(4). Specifically, we are concerned with the class of left-invariant control affine systems. We begin by classifying all cost-extended systems on SO(3) under cost equivalence. (Cost-extended systems are closely related to optimal control problems.) A classification of all quadratic Hamilton-Poisson systems on the (minus) Lie-Poisson space so(3)*, under affine equivalence, is also obtained. For the normal forms obtained in our classification (of Hamilton-Poisson systems) we investigate the (Lyapunov) stability nature of the equilibria using spectral and energy-Casimir methods. For a subclass of these systems, we obtain analytic expressions for the integral curves of the associated Hamiltonian vector fields in terms of (basic) Jacobi elliptic functions. The explicit relationship between the classification of cost-extended systems on SO(3) and the classification of quadratic Hamilton- Poisson systems on so(3)* is provided. On SO(4), a classification of all left-invariant control affine systems under L-equivalence is obtained. We then determine which of these representatives are controllable, thus obtaining a classification under detached feedback equivalence. We also obtain a partial classification of quadratic Hamilton-Poisson systems on the Lie-Poisson space so(4)*. An investigation of the stability nature of the equilibria for a subclass of these systems is also done. Several illustrative examples of optimal control problems on the orthogonal group SO(3) are provided. More specifically, we consider an optimal control problem corresponding to a representative of our classification (of cost-extended system) for each possible number of control inputs. For each of these problems, we obtain explicit expressions for the extremal trajectories on the homogeneous space S2 by projecting the extremal trajectories on the group SO(3). The examples provided show how our classifications of cost-extended systems and Hamilton-Poisson systems can be used to obtain the optimal controls and the extremal trajectories corresponding to a large class of optimal control problems on SO(3). An example of a four-input optimal control problem on SO(4) is also provided. This example is provided to show how the solutions of certain problems on SO(4) can be related to the solutions of certain optimal control problems on SO(3).
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Date Issued: 2015

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Environmental conflict resolution: a critical analysis of the role of interests and value

- Mweshi, John

Authors: Mweshi, John
Date: 2015
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/55842 , vital:26740
Description: This thesis intends to contribute to an enhanced understanding of environmental conflicts and their resolution. To accomplish this task the thesis will ascertain the role that value and interests play in environmental conflicts in order to establish an adequate basis upon which they can be resolved. In the process, the thesis will also examine three different approaches, namely, the Standard Approach; the Environmental Impact Assessment (EIA) framework; and the Structured Decision Making (SDM) approach. First, the standard approach is informed by the understanding that focusing on interests instead of human values makes the resolution of conflicts more tractable. In contrast, this thesis argues that an exclusive focus on interests, in the context of environmental conflict resolution, is inadequate in some important respects because there are other factors to be considered such as the environmental impacts at the root of the conflict. Second, the thesis examines the focus on impacts that characterises EIAs. It argues that this approach remedies the limitations of the standard approach insofar as impacts are understood in terms of object value. However, the EIA approach does not provide much guidance on how to deal with conflicting human values. Third, taking into account the fact that the standard approach does not address the question of object value, while the EIA addresses object value but does not deal directly with human values, the thesis examines the SDM approach to environmental risk decisions. The thesis argues that while the SDM approach claims to deal with conflicts involving human values head-on, it does not provide a viable alternative in terms of environmental conflict resolution. This is because it fails to recognise the key distinction between human values and object value despite acknowledging the presence of multiple value dimensions as a major obstacle to value trade-offs and therefore to the resolution of value conflicts. Finally, the thesis recommends an adequate basis upon which environmental conflicts can be resolved.
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Date Issued: 2015

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Invariant control systems and sub-Riemannian structures on lie groups: equivalence and isometries

- Biggs, Rory

Authors: Biggs, Rory
Date: 2015
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/64815 , vital:28607
Description: In this thesis we consider invariant optimal control problems and invariant sub-Riemannian structures on Lie groups. Primarily, we are concerned with the equivalence and classification of problems (resp. structures). In the first chapter, both the class of invariant optimal control problems and the class of invariant sub-Riemannian structures are organised as categories. The latter category is shown to be functorially equivalent to a subcategory of the former category. Via the Pontryagin Maximum Principle, we associate to each invariant optimal control problem (resp. invariant sub-Riemannian structure) a quadratic Hamilton-Poisson system on the associated Lie-Poisson space. These Hamiltonian systems are also organised as a category and hence the Pontryagin lift is realised as a contravariant functor. Basic properties of these categories are investigated. The rest of this thesis is concerned with the classification (and investigation) of certain subclasses of structures and systems. In the second chapter, the homogeneous positive semidefinite quadratic Hamilton-Poisson systems on three-dimensional Lie-Poisson spaces are classified up to compatibility with a linear isomorphism; a list of 23 normal forms is exhibited. In the third chapter, we classify the invariant sub-Riemannian structures in three dimensions and calculate the isometry group for each normal form. By comparing our results with known results, we show that most isometries (in three dimensions) are in fact the composition of a left translation and a Lie group isomorphism. In the fourth and last chapter of this thesis, we classify the sub-Riemannian and Riemannian structures on the (2n + 1)-dimensional Heisenberg groups. Furthermore, we find the isometry group and geodesics of each normal form.
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Date Issued: 2015

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Spatio-temporal variation in the phytobenthos and phytoplankton community structure and composition of particulate matter along a river-estuary continuum assessed using microscopic and stable isotope analyses

- Dalu, Tatenda

Authors: Dalu, Tatenda
Date: 2015
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/54416 , vital:26563
Description: Phytoplankton and phytobenthos communities play an important role in lotic systems as primary producers providing essential biomolecules to higher trophic oganisms and are important indicators for environmental or ecological change. In this thesis, field studies (observational and experimental) along a river–estuary continuum were conducted to assess the spatio-temporal variation and development of phytobenthos and phytoplankton communities using a combination of stable isotope and community analyses in a temperate southern African system across four study periods: September (early spring) and November/December (late spring) 2012, and February (summer) and May/June (winter) 2013. Additionally, the sources and composition of the particulate organic matter were also analysed using stable isotope (δ15N and δ13C) analysis. The effects of substrate type and flood occurrence were assessed through experimental studies at an up- and downstream site of the river after a major flood event that occurred between October and November 2012. Common household tiles were used as artificial substrates to study the development/succession of phytobenthos communities after the flood disturbance. Distinct diatom communities were observed between upstream and downstream sites and at each site, community structure changed with time indicating succession. In addition to recording diatom characteristics on three natural substrates, namely; macrophytes, rocks and sediment, artificial substrates observations were also made on three different types of artificial substrates, namely; brick, brown clay and grey clay tiles. The natural (species richness 78) and artificial substrates (sp. richness 93) had different communities with the latter having greater species richness. Common phytobenthos taxa were not restricted to a single substrate but preference was generally high for the artificial substrates, especially brown tiles (mean sp. richness 47). Results of the redundancy analysis (RDA) analysis indicated that ammonium, conductivity, total dissolved solids, salinity, pH, oxygen reduction potential, phosphate and water depth were the major determinants of the phytobenthos composition at the two sites. The spatio–temporal variation of phytoplankton and phytobenthos communities and allochthonous organic matter along the river–estuary continuum was assessed at 8 sites using a combination of community and stable isotope analyses. A total of 178 species belonging to 78 genera were recorded with diatoms being predominant, accounting for 81.9 % of the total abundance. The total chl-a concentration along the river-estuary continuum increased from spring to a high in summer before decreasing to a low in winter. Periphyton communities were observed to be significantly different across sites (p < 0.05) in terms of species richness, abundances and isotopically The high periphytic δ15N values (range 7.9–15.2 ‰) recorded at the downstream sites compared to the pristine upstream sites (δ15N values range 4–7 ‰) suggest nutrient enrichment most likely derived from anthropogenic sources. Overall, our results reveal general patterns of periphyton communities and stable isotopes and provide improved information in the use of periphyton δ15N as an excellent indicator of anthropogenic nitrogen pollution. Ecologists are interested in the factors that control, and the variability in, the contributions of different sources to mixed organic materials traveling through lotic systems. We hypothesized that the source matter fuelling mixed organic pools in a river-estuary continuum varies over space and time, with the upper reaches of a system characterized by allochthonous-dominated material and autochthonous contributions becoming more important in the lower reaches. Samples of the mixed organic pools and allochthonous and autochthonous source materials were collected during the four study periods. The C:N ratios of suspended particulate matter (SPM) collected during summer and winter indicated that the lower reaches of the system had similar organic matter contributions from the freshwater and terrestrial sources. Stable isotope analysis in R revealed that the contributions of autochthonous organic matter were high in SPM along the entire continuum, and aquatic macrophytes were significant contributors to SPM specifically in the upper reaches. The terrestrial leaves made major contributions to the SPM in the middle regions of the system (i.e. downstream sites of the river, particularly in early and late spring). Bulk detritus had large allochthonous matter components in the lower reaches (estuary), and the contributions of aquatic macrophytes and benthic algae to bulk detritus were high (> 50 %) in the upper to middle reaches (river), but low (< 20 %) in the lower reaches (estuary). The current investigation represents the first attempt to assess the validity of the River Continuum Concept (RCC) in a southern African temperate river. The phytoplankton and phytobenthos communities, and chl-a concentration followed a trend similar to that proposed for the river continuum concept (RCC). The middle reaches based on the phytobenthos or phytoplankton communities and chl-a concentrations which were employed as proxies for primary production, were the most productive, while the upper reaches were the least primary productive. The evaluation of organic matter contributions to the SPM and detritus along the river–estuary continuum provided a baseline assessment of the nature and sources of potential food for consumers inhabiting different locations during different times of the year. Incorporating such spatio-temporal variations in SPM and detritus into food web studies will improve our understanding of the flow of carbon through aquatic systems.
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Date Issued: 2015

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Synthesis and biological evaluation of truncated sarganaphthoquinoic acid derivatives as Hsp90 inhibitors

- Chiwakata, Maynard T

Authors: Chiwakata, Maynard T
Date: 2015
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/64708 , vital:28594
Description: Hsp90 inhibition has been at the centre of attention in current research due to the possibility of “cracking down” on the entire process leading to the development of malignant cancers. Small underlying principles common in all types of cancers have been determined that govern the transformation of normal human cells into cancerous cells, with all relying on the ATPase activity of Hsp90 protein. Hsp90 protein is therefore an attractive drug target that if successfully inhibited can result in the remission of cancer tumours by one form of treatment. To date, no Hsp90 inhibitor has been sanctioned for cancer treatment as most are still in clinical development. Our research was therefore inspired by reports that indicated the potential of quinones / naphthoquinones to act as Hsp90 inhibitors. Preliminary results of a few selected marine natural product quinone systems i.e. sargaquinoic acid (SQA) (2.47) and lapachol (3.6) showed moderate cytotoxicity and weak interactions with the Hsp90 molecular chaperone, and evidence suggested C-terminal binding of these molecules. No correlation has been determined yet between cytotoxicity and Hsp90 inhibition, hence we aimed to develop natural product inspired molecules that exhibit both cytotoxic and Hsp90 inhibition properties. Due to limited amounts of the natural product that can be acquired from natural sources, synthetic analogues were opted for. Isolation of a few selected quinones was conducted to have material that could be used in biological assays. For structural modifications, a series of truncated naphthoquinone systems were prepared adopting the sarganaphthoquinoic acid (3.5) scaffold. The naphthoquinones were prepared via Diels-Alder reactions of relevant benzoquinones with myrcene, followed by aromatization reactions using MnO2. Various alkyl and aryl amines were then coupled to the C-2/3 position of the naphthoquinone using Michael’s addition reactions. Tricyclic naphthoquinones were also synthesized from reactions with hypotaurine and citral. Design of the analogues incorporated functionalities from known Hsp90 inhibitors e.g. geldanamycin (2.28) and its analogues. Preliminary results obtained showed that coupling of naphthoquinones with aryl-amines resulted in the most cytotoxic compounds (4.14-4.19) with IC50 values as low as 0.3 μM against Hs578T breast cancer carcinoma (triple negative). Most of the alkyl amines (4.20-4.25) had IC50 values greater than 50 μM except for 4.20 and 4.21 that showed IC50 values of 7.6 μM and 2.6 μM respectively. Tricyclic naphthoquinones (4.28-4.29) showed moderate cytotoxic activity of approximately 10 μM. Hsp90 inhibition was assessed by client protein degradation assays, of which SQA (2.47), showed the best Hsp90 inhibition properties, followed by compound 4.20. The most cytotoxic arylamino-naphthoquinone (4.16) and tricyclic naphthoquinones (4.28-4.29) showed only moderate inhibition. None of the compounds led to Hsp70 induction, suggesting possible binding to the C-terminus of Hsp90. Interactions at the binding site were assessed by molecular docking studies and saturation transfer difference (STD) NMR. Docking studies were conducted on the N-terminus of Hsp90 and better binding was observed for arylamino naphthoquinones (4.14-4.19) than for other series of compounds. Unfortunately, the co-crystal structure for the C-terminus of Hsp90 is unavailable, hence docking study comparisons on both domains could not be conducted. However, STD NMR offered a platform to assess binding interactions between the naphthoquinones and the N- or C-terminal domains of Hsp90. However no interactions were observed at both the N- and C- termini of Hsp90 due to either weak binding of ligands to the protein or poor water solubility of the ligands. From these preliminary results, naphthoquinones bind to Hsp90 protein but conclusive remarks to which terminal domain they bind to could not be made. The best candidate from amongst the series of naphthoquinones prepared that showed moderate cytotoxicity and promising Hsp90 inhibition was compound 4.20. We therefore succeeded in developing a new series of naphthoquinones that possess moderate cytotoxicity and show Hsp90 inhibition.
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Date Issued: 2015

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The isolation, characterisation and chemotaxonomic significance of secondary metabolites from selected South African Laurencia spp. Rhodophyta

- Fakee, Jameel

Authors: Fakee, Jameel
Date: 2015
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/64696 , vital:28593
Description: Bioprospection of marine organisms as a potential source for lead drugs is becoming increasingly popular. The secondary metabolome of these organisms consists of structurally diverse molecules possessing unprecedented carbon skeletons, the biosynthesis of which occurs via complex metabolomic pathways driven by specialist enzymes. This structural novelty is highly influential on the favourable bioactivity these compounds display. A prominent example of such a compound is trabectedin marketed as Yondelis®. Registered for the treatment of soft tissue sarcomas, this marine drug was developed from extracts of the tunicate Ecteinascidia turbinata. South Africa is renowned for possessing a highly diverse marine biota including several endemic species of marine red algae belonging to the Laurencia sensu stricto genus, which falls within the Laurencia complex. Despite having a good reputation for fascinating secondary metabolites, the taxonomy of Laurencia natural products is proving challenging for reasons including the presence of cryptic species, as well as individual species displaying morphological variability. The aim of this study was thus to isolate secondary metabolites from various South African Laurencia spp. and subsequently assess their chemotaxonomic significance by analysis of a parallel plastid rbcL phylogeny study of Laurencia spp. This study reports the first phycochemical investigation into Laurencia natalensis Kylin, Laurencia cf. corymbosa J.Agardh, Laurencia complanata (Suhr) Kützing, Laurencia sodwaniensis Francis, Bolton, Mattio and Anderson submitted, Laurencia multiclavata Francis, Bolton, Mattio and Anderson submitted, and a South African specimen of Laurenciella marilzae Gil-Rodríguez, Sentíes, Díaz-Larrea, Cassano and M.T. Fujii (basionym: Laurencia marilzae) originally described from Spain. Additionally, the chemical profiles of previously explored species Laurencia flexuosa Kützing and Laurencia glomerata Kützing were re-investigated. The organic extracts of the above species afforded 31 compounds belonging to a wide array of structural classes including halo-chamigranes, linear C15 acetogenins, indole alkaloids, cuparanes and cyclic bromo-ethers. A new tri-cyclic keto-cuparane (4.4) was isolated from L.cf. corymbosa alongside the new cuparanes 4.1 and 4.7. Algoane (5.9), a unique marker compound isolated from L. natalensis, was previously only reported from a sea-hare. Such marker compounds which are exclusive to an individual algal species increase the ease of their subsequent identification. The feasibility of chemotaxonomy as an additional tool to classify Laurencia spp. Was established as broad predictions of a specimen’s phylogeny, based on representatives of its secondary metabolome, proved viable. The study specimens were shown to possess similar chemical profiles to their sister species e.g. L. complanata, L. sodwaniensis and L. multiclavata produced similar metabolites to their sister species as inferred by an rbcL phylogeny tree. Finally, a 1H NMR profiling study on the crude organic extracts of various Laurencia spp. generated distinctive, reproducible spectra, exposing the value of NMR spectroscopy as a rudimentary species discernment tool.
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Date Issued: 2015

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Adherence to antiretroviral therapy in children in Zimbabwe: a randomized control trial to validate a new self-reported adherence monitoring tool

- Mugore, Linnetie

Authors: Mugore, Linnetie
Date: 2014
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/54734 , vital:26607
Description: Background: Among children taking antiretroviral therapy (ART), self-reports have been widely reported to over-estimate adherence levels. Pill count adherence levels are often lower than self-reported levels, with unannounced home pill count adherence being lower than facility based pill count adherence. There is often poor agreement between pill count adherence levels and those measured using other objective adherence measuring methods such as Medication Event Monitoring Systems (MEMS®), which is widely viewed as the gold standard for adherence measurement. Objectives: The aim of this study was to design and evaluate a new self-reported paediatric adherence monitoring tool, assess the feasibility of using pill count methods in monitoring adherence and identify challenges to reporting adherence among children on ART in rural and urban Zimbabwe. Methods A dual centre, superiority, parallel design RCT was conducted to evaluate the newly-developed visually- and verbally-cued „past 10 days‟ tool for the assessment of adherence in children on ART at two sites in Zimbabwe; Harare Central Children‟s Hospital in an urban setting, and Murambinda Mission Hospital, a rural site. Child-caregiver pairs presenting to one of these facilities for the child‟s review of ART and refill of the medication were recruited, signed informed consent obtained, and were randomised for self-reported adherence monitoring into either the experimental group („new 10-day tool‟) or the control group („PACTG-style‟ self-report tool). Data (demographic, socioeconomic, and reported adherence) were collected in individual interviews with child-caregiver pairs. Additional adherence monitoring methods used for both groups included the Morisky-8-Item Medication Adherence Scale (MMAS-8) and a facility based pill count. FGDs were held with groups of caregivers and groups of children ≥13 years of age to understand reasons for non-adherence as well as issues around reporting non-adherence. Superiority testing was conducted by comparing adherent proportions and their confidence intervals (95% CI). Further concurrent validity test was done using the Mann-Whitney U test to evaluate the relationship between the new tool and the MMAS-8 scores. Agreement between the child and caregiver reports of adherence was used as a test of reliability of the new tool using the kappa statistic. Socio-demographic, clinical and care-related factors associated with adherence were identified using reported adherence in both child and caregiver groups in a logistic regression model. Two pill count methods were assessed for feasibility using the proportions of children with complete data for calculating adherence levels, and their CI and a comparison of the two methods, a routinely-used method and one that incorporated the reported residual quantity (RRQ) of medication at last refill. Results : Analysis included 245 child-caregiver pairs, 123 in the experimental group and 122 in the control group. The median age for children was 9 years. In the experimental group, adherence by caregiver and child reports ranged from 94.3% - 98.4% and 78.4% - 96.1%, and those in the control group ranged from 89.2% - 97.5% and 71.2% - 98.1%, respectively. There was no significant difference between adherence levels in the two groups. Adherence levels measured by both the experimental and control tools were found to be associated with MMAS-8 adherence levels (p <0.05). Agreement between child- and caregiver-reported adherence was moderate though significant (kappa; 0.407, p <0.05). Only about half of the children had adequate data to compute pill counts. Proportions adherent at 95% cut-off were 39% by the „routine pill count‟ and 58% by the „Pill count RRQ‟. Being an orphan was associated with child reported-adherence whereas use of non-human reminders, having a maternal relative as a primary caregiver and knowledge of dose frequency, were all associated with caregiver-reported adherence. Major causes of non-adherence mentioned during the FGDs included interference of medication administration times with scheduling of routine socio-economic activities and lack of support from some non-biological caregivers. Reporting of non-adherence appeared to be hampered by perceptions of negative reactions by healthcare workers to these reports and by caregivers being unaware that the child missed some doses. Conclusions: The „new 10-day tool‟ was not shown to be superior to the „PACTG-style tool‟ in detecting non-adherence, however this new tool was found to be a valid and reliable adherence monitoring tool that included a moderately long recall period of 10 days, can be applied without the need for the respondent to remember names of individual medicines in the
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Date Issued: 2014

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An investigation into the development of knowledge and strategies for the teaching of visual literacy in under-resourced Eastern Cape schools

- Mbelani, Madeyandile

Authors: Mbelani, Madeyandile
Date: 2014
Subjects: Uncatalogued
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/64401 , vital:28540
Description: This thesis reports on a multiple case study PhD project that aimed to investigate meaningful and critical development of knowledge and strategies to teach visual literacy, a component of English First Additional Language (FAL) in six under-resourced schools of the Eastern Cape of South Africa. The study begins by locating visual literacy within a broad framework of literacy as a social practice, and discusses its importance. Further, it discusses complexities of making sense of and teaching visual literacy, especially for the majority of in-service teachers who experienced visual literacy neither as learners nor as teacher trainees. The gap between the curriculum and teachers’ classroom practices is what triggered this study to adopt a transformative paradigm. The main research question is, “How can teacher professional development in English Language Teaching advance in-service teachers’ knowledge of and strategies for meaningful and critical teaching and learning of visual literacy?” To respond to this question, I drew on cultural historical activity theory (CHAT) and critical realism (CR) to design four phases of this study that incorporated the seven stages of an expansive learning cycle. These phases focussed on exploring and expanding teachers’ sense making and teaching of visual literacy. I collected data through interviews, document analysis, videoed lessons and change laboratory (CL) workshops. I designed a data analysis tool that brought together CHAT, CR, multimodal social semiotics, critical discourse analysis and pedagogical discourse to make sense of the data. Through a process of reflexivity, the study illuminated layers of factors that constrained meaningful and critical teaching of visual literacy in the empirical, the actual and the real domains of reality. These factors include teachers’ unconscious reproduction of discourses of domination, their intolerance of diverse cultural discourses, resistance to curriculum change, and the fact that they are comfortable with the status quo. I brought these factors to CL workshops for expansive learning. The study contributes in-depth insight into English FAL in-service teacher development in the area of visual literacy. By locating the study within meaning making and teaching of visual literacy, it was possible to interrogate access, diversity, domination and design in teachers’ classroom practices. As a result of this study participants were made aware of the extent to which these factors enabled or hindered meaningful and critical teaching. Participants repositioned themselves as subjects of the activity system, thereby mobilising their agency to take control of the structures and cultures that condition their teaching.
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Date Issued: 2014

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Development of styrene based imprinted sorbents for selective clean-up of metalloporphyrins in organic media

- Awokoya, Kehinde Nurudeen

Authors: Awokoya, Kehinde Nurudeen
Date: 2014
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/54521 , vital:26580
Description: Most crude oils contain traces of vanadium and nickel complex with porphyrins (VTPP and NTPP) within their asphaltene fraction. Although these metals are only present in trace quantities, they have a significant and detrimental impact on the refining process by degrading the quality of intermediate and end products. Therefore, their selective removal is highly desirable. This thesis presents the development of nickel porphyrin, nickel vanadyl porphyrin imprinted nanofibers and vanadyl porphyrin imprinted polymer (MIP) particles for application as selective sorbents. Computational model based on the combination of molecular dynamics simulations and quantum mechanics was successfully applied to the styrene functional monomer selection. The particle was prepared by bulk polymerization and the nanofibers by a novel approach combining molecular imprinting and electrospinning technology. The morphologies, thermal stabilities and porosities of the imprinted sorbents were studied using SEM, TGA, and BET nitrogen gas adsorption. Chloroform was found to swell the polymer particles to a higher degree than methanol and acetonitrile. The adsorption characteristics of the imprinted sorbents best fitted with Freundlich isotherm model. The imprinted sorbents recorded high extraction efficiencies (EEs) of > 99 % in selectively extracting the metalloporphyrins. The impact of the template on the affinity of recognition for NTPP was evaluated. The results showed that the NTPP adsorption capacity increased as the molar ratio of NTPP to styrene was increased from 1:1 to 3:1. The optimal ratio of template to functional monomer which yielded the best specific affinity and highest recovery (99.9 %) was 3:1. The effects of trifluoroacetic acid (TFA), dichloromethane (DCM), dimethyl sulphoxide (DMSO), pentane (PEN) on electro-spinnability of the polymer solutions and the morphological appearance of the nanofibers were investigated. The imprinted nanofibers exhibited the same selectivity specialism for both NTPP and VTPP. A remarkable stability in relation to reusability was observed when imprinted nanofibers were used, as they could be reused nine times without incurring any significant loss in removal efficiency. The results were validated by analysing a certified reference material. The imprinted sorbents were therefore found to be selective sorbents that are well suited for handling trace metals in organic media.
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Date Issued: 2014

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Ecological consequences of non-native fish invasion in Eastern Cape headwater streams

- Ellender, Bruce Robert

Authors: Ellender, Bruce Robert
Date: 2014
Subjects: Fishery management -- South Africa -- Eastern Cape Fishes -- Conservation -- South Africa Introduced fishes -- South Africa -- Eastern Cape Introduced organisms
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/69065 , vital:29380
Description: The introduction, spread and concomitant impacts of non-native species are a global problem. Fish are among the most widely introduced vertebrate groups, with their impacts affecting multiple levels of organisation- from individuals, populations and communities, to entire ecosystems. In South Africa, the largest perceived threat to range-restricted endemic headwater stream fishes is said to be invasion by non-native fishes, however, as is the case elsewhere, invasive impacts are often a case of risk perception rather than actual risk analysis. Two range-restricted headwater species, the Eastern Cape redfin Pseudobarbus afer and the Border barb Barbus trevelyani are redlisted by the International Union for the Conservation of Nature (IUCN) as ‘Endangered’, primarily due to invasion by non-native fishes. To investigate invasions in South Africa, and provide a quantitative estimate of the impact of non-native fishes on the two imperilled endemics, P. afer and B. trevelyani, the overall aims of this thesis were to: (A) Provide a literature review on non-native fish invasions in South Africa; (B) Using two case studies on the headwaters of the perennial Keiskamma and episodic Swartkops River systems, investigate the naturalisation-invasion continuum to provide a holistic view of the invasion process in these variable environments. The specific thesis objectives were: (1) Reviewing current knowledge of invasive impacts of non-native fishes in South Africa; (2) Investigating invasibility of headwater stream environments by non-native fishes; (3) Determining the establishment success of non-native fishes, (4) Assessing the spatial and temporal impacts of invasion; (5) Understanding mechanisms responsible for non-native fish impacts; (6) Investigating the threat of non-native fish invasion on the genetic diversity of two the two headwater fishes, P. afer and B. trevelyani. Results from the literature review of fish invasions (Chapter 1) showed that South Africa has a long history of non-native fish introductions, spanning two and a half centuries. Currently, 55 species have been introduced or translocated. Many of these introduced species have become fully invasive (36%). Their impacts also span multiple levels of biological organisation. There was a general paucity of studies on fish invasions (38 studies), however, of those conducted, reviewed studies placed emphases on invasive impacts (25 studies) and the transport, introduction, establishment and spread stages of the invasion process were largely ignored. The two study systems, the Swartkops and Keiskamma Rivers, were heavily invaded and numbers of introduced species surpassed that of natives (Chapter 2, 3 and 5). Headwater streams had varying invasibility and a number of non-native species were successfully established (Chapter 2, 3, 5 and 6). The remainder of the invasions were casual incursions into headwater streams from source populations in mainstream and impoundment environments which were invasion hotspots. Irrespective of establishment, four predatory invaders (largemouth bass Micropterus salmoides, smallmouth bass M. dolomieu, brown trout Salmo trutta and rainbow trout Oncorhynchus mykiss) impacted heavily on native fish communities (Chapter 3, 4 and 5). Two broad types of invasion were documented, top down invasion by non-native O. mykiss and S. trutta and upstream invasion by M. salmoides and M. dolomieu (Chapter 3 and 5). Their impacts included changes in community structure, extirpation from invaded stream reaches resulting in contracted distribution, and isolation and fragmentation of native fish populations. The impacts of non-native predatory fishes were particularly acute for P. afer and B. trevelyani. Where non-native predatory fish occurred, P. afer and B. trevelyani had been extirpated (Chapter 3 and 5). As a result both native species exhibited contracted distributions (>20% habitat loss due to invasion). Upstream invasion by centrarchids isolated and fragmented P. afer populations into headwater refugia, while top down invasion by salmonids excluded B. trevelyani from invaded, more pristine stream reaches, by forcing the species into degraded unsuitable lower stream reaches. Predation also disrupted population processes such as adult dispersal for P. afer, and centrarchid-invaded zones acted as demographic sinks, where adults dispersing through invaded reaches were rapidly depleted. While the Mandela lineage of P. afer exhibited little within or between drainage genetic structuring, B. trevelyani was >4% divergent between drainages, and up to 2% divergent between streams within the Keiskamma River system (Chapter 7). The distribution of genetic diversity for B. trevelyani also indicated that the loss of diversity was imminent without immediate conservation interventions. This thesis has provided conclusive evidence that native fishes are vulnerable to invasion and that non-native predatory fishes have significant impacts on native fishes in Eastern Cape headwater streams. If management and conservation measures are implemented, the unwanted introduction and spread of non-native fishes may be restricted, allowing native fishes opportunities for recovery.
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Date Issued: 2014

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Electrospun fiber based colorimetric probes for aspartate aminotransferase and I7ß-estradiol

- Pule, Bellah Oreeditse

Authors: Pule, Bellah Oreeditse
Date: 2014
Language: English
Type: text , Thesis , Doctoral , PhD
Identifier: http://hdl.handle.net/10962/54869 , vital:26623
Description: Fabrication, characterization and application of electrospun polymer composite based colorimetric probes are presented in this thesis. The first part of the thesis involved the development of a protocol for in situ reduction of gold trication (Au³+) into metallic gold atoms with sodium borohydride. The prepared PS-Au NPs showed an SPR band at 542 nm. Furthermore the absorbance of the colloidal Au NPs in polystyrene exhibited a good linear correlation (r2 = 0.9934) to E2 concentration in the range 5 to 50 ppb. The lowest naked eye detection limit was found to be 0.5 ppb and could further be easily monitored by UV-vis spectrophotometer. Upon interaction with E2 Au NPs aggregated to give nanoparticle clusters, confirmed through TEM analysis. Different concentrations of Au NPs were found to have a significant effect on the conductivity of the PS-Au NPs solution. At low concentrations of Au NPs (0.002, 0.015 and 0.025% w/v) PS-Au NPs solution could be electrospun without clogging. The FE-SEM images showed a non-beaded morphology of PS-Au NPs composite fibers. Upon interaction of the colorimetric probe strips with various E2 concentrations it was observed that with increasing E2 concentrations (50 ng/ml to 1000 µg/ml) the colour of the probe changed gradually from white to shades of pink and eventually to shades of blue at higher E2 concentrations. The visible cut-off concentration was 100 ng/ml. The second component of the thesis focussed on the development of diazonium dye-nylon 6 colorimetric probe for aspartate aminotransferase. At optimal pH 7.4 the enzyme was stable, highly active and catalyzed a reaction that was susceptible to detailed kinetic analysis by continuous optical methods. The KM values for L-aspartate, a- ketoglutarate and oxaloacetate were 2.60, 0.59 and 0.066 mM, respectively. On the basis of these KM values the solid-state colorimetric probe was developed. A colour change occurred when an electrospun dye-N 6 probes were exposed to visibly detectable concentrations of oxaloacetate, an AST-catalyzed reaction product. While monitoring AST activity at 530 run, a linear relation was obtained between oxaloacetate concentrations ranging from 0.4 - 7.4 µg/ml. Naked eye detection limit of 2.4 µg/ml oxalaoacetate equivalence of 10 times the normal AST activity was attained. The colorimetric probe was in addition, tested against co-substrates aspartate, ketoglutarate and a variety of other compounds such as alanine, pryruvate, as well as glutamic, malaic and succinic acids known to interfere with AST activity. Each compound elicited a distinct and unambiguous colour change upon interaction with the colorimetric probe. Further X-ray powder diffraction (XRD), duNouy ring tensiometer, Brunauer- Emmett- Teller (BET) and energy dispersive X-ray spectroscopy (EDS/EDX) characterization confirmed composition and stability of the colorimetric probes. Colorimetric probes developed in this thesis are relatively cost effective, simple and "rugged" for measurement of analytes with visual detection without sample pretreatment in matrices, such as plasma and dairy effluents. The probes warrant further investigation as they have shown potential and offer a promising solid-state platform for both clinical diagnostics and environmental monitoring.
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Date Issued: 2014

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