An investigation into the introduction of a new wealth tax in South Africa
- Authors: Arendse, Jacqueline A
- Date: 2018
- Subjects: Wealth tax -- Law and legislation -- South Africa , Taxation -- Law and legislation -- South Africa , Income tax -- South Africa , Fiscal policy -- South Africa , South Africa -- Economic conditions , Income distribution -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/61379 , vital:28020
- Description: In a world of economic uncertainty and manifold social problems, South Africa has its own unique challenges of low economic growth, persistent budget deficits that produce increasing government debt and the highest level of economic inequality in the world. The history of injustice and economic marginalisation and the failure of the economy to provide inclusive growth drives an urgent need to address economic inequality through tax policy, placing ever more focus on wealth taxes as a possible solution. There is a hope is that taxing the wealthy may provide the opportunity to redistribute desperately-needed resources to those denied the opportunity to build wealth and who are trapped in the cycle of poverty. Yet, as appealing as a new wealth tax may seem, the introduction of such a tax carries with it a range of risks, not all of which are known. Of great concern is the possible effect on the economy, which, in its vulnerable state, cannot afford any loss of capital and investment. Very little research has been done on wealth tax in the South African context and there is a dearth of literature focusing on the views and perceptions of the wealthy individuals themselves. This qualitative study investigates the merits and disadvantages of a new wealth tax and seeks to identify any unintended consequences that could result from the implementation of a new wealth tax in South Africa, drawing from historical and international experience and primary data obtained from interviews with individuals likely to be affected by such a tax. Having explored the literature and international experiences with wealth tax and having probed the thinking of wealthy individuals who would be the payers of a wealth tax, the study finds that a new wealth tax may contribute towards the progressivity of the tax system, but it is doubtful whether such a tax would provide a sustainable revenue stream that would be sufficient to address economic inequality and there is a risk of causing harm to the economy. Recognising that the motivation for wealth taxes is often driven more by political argument and public perception than by rational quantitative analysis, the study also anticipates the introduction of a new wealth tax and suggests guidelines for the design of such a tax within the framework for evaluating a good tax system. This study informs the debate on wealth taxes in South Africa and contributes to the design of such a tax, should it be implemented.
- Full Text:
- Date Issued: 2018
- Authors: Arendse, Jacqueline A
- Date: 2018
- Subjects: Wealth tax -- Law and legislation -- South Africa , Taxation -- Law and legislation -- South Africa , Income tax -- South Africa , Fiscal policy -- South Africa , South Africa -- Economic conditions , Income distribution -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/61379 , vital:28020
- Description: In a world of economic uncertainty and manifold social problems, South Africa has its own unique challenges of low economic growth, persistent budget deficits that produce increasing government debt and the highest level of economic inequality in the world. The history of injustice and economic marginalisation and the failure of the economy to provide inclusive growth drives an urgent need to address economic inequality through tax policy, placing ever more focus on wealth taxes as a possible solution. There is a hope is that taxing the wealthy may provide the opportunity to redistribute desperately-needed resources to those denied the opportunity to build wealth and who are trapped in the cycle of poverty. Yet, as appealing as a new wealth tax may seem, the introduction of such a tax carries with it a range of risks, not all of which are known. Of great concern is the possible effect on the economy, which, in its vulnerable state, cannot afford any loss of capital and investment. Very little research has been done on wealth tax in the South African context and there is a dearth of literature focusing on the views and perceptions of the wealthy individuals themselves. This qualitative study investigates the merits and disadvantages of a new wealth tax and seeks to identify any unintended consequences that could result from the implementation of a new wealth tax in South Africa, drawing from historical and international experience and primary data obtained from interviews with individuals likely to be affected by such a tax. Having explored the literature and international experiences with wealth tax and having probed the thinking of wealthy individuals who would be the payers of a wealth tax, the study finds that a new wealth tax may contribute towards the progressivity of the tax system, but it is doubtful whether such a tax would provide a sustainable revenue stream that would be sufficient to address economic inequality and there is a risk of causing harm to the economy. Recognising that the motivation for wealth taxes is often driven more by political argument and public perception than by rational quantitative analysis, the study also anticipates the introduction of a new wealth tax and suggests guidelines for the design of such a tax within the framework for evaluating a good tax system. This study informs the debate on wealth taxes in South Africa and contributes to the design of such a tax, should it be implemented.
- Full Text:
- Date Issued: 2018
An investigation of the correlation of mitochondrial biogenesis, mitochondrial DNA methylation, mitochondrial network topology and adipogenesis in the human adipose-derived mesenchymal stromal stem cell model
- Authors: Kadye, Rose
- Date: 2018
- Subjects: Uncatalogued
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62637 , vital:28222
- Description: Expected release date-April 2019
- Full Text:
- Date Issued: 2018
- Authors: Kadye, Rose
- Date: 2018
- Subjects: Uncatalogued
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62637 , vital:28222
- Description: Expected release date-April 2019
- Full Text:
- Date Issued: 2018
An investigation of the teaching of reading in isiXhosa in three Grade 1 classrooms in the Eastern Cape, South Africa
- Authors: Magadla, Noluthando
- Date: 2018
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/63408 , vital:28408
- Full Text: false
- Date Issued: 2018
- Authors: Magadla, Noluthando
- Date: 2018
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/63408 , vital:28408
- Full Text: false
- Date Issued: 2018
Analysis of the human HSP70-HSP90 organising protein (HOP) gene - characterisation of the promoter and identification of a novel isoform
- Authors: Mattison, Stacey
- Date: 2018
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62821 , vital:28296
- Description: Expected release date-April 2020
- Full Text:
- Date Issued: 2018
- Authors: Mattison, Stacey
- Date: 2018
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62821 , vital:28296
- Description: Expected release date-April 2020
- Full Text:
- Date Issued: 2018
Aspects Allocentristes de l’Humanisme dans l’Univers Romanesque de Williams Sassine
- Authors: Dami, Emmanuel Naancin
- Date: 2018
- Subjects: Sassine, Williams, 1944-1997 -- Criticism and interpretation , Guinean fiction (French) -- 20th century -- History and criticism , Humanism in literature , Human beings in literature , Postcolonialism in literature , Existentialism in literature
- Language: French , English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/61957 , vital:28089
- Description: The human being, his behaviour and more importantly, his very essence have, for time immemorial, proven to be enigmatic to many a man and to researchers in particular. Consequently, the need for a thorough and more profound understanding of man has made him the epicentre of epistemic investigations across many academic disciplines. This, unfortunately, does not seem to have shaded bright lights on the grey areas bordering on his nature to his behavior. This, in turn, opens up other windows requiring further probes. For instance, proponents of the Neo-classical economic school contend that the human being is homo oeconomicus. This implies that man is intrinsically egocentric and a rational being whose decisions are based on informed choices driven by his urge for maximal utility geared towards his personal satisfaction (O’Boyle 2009; Caruso 2012). This stance invalidates man’s ability to do ‘disinterested good’ in any form. African francophone literature is replete with different and diverse images of man, his behaviour and existential conditions: sufferings and struggles. It, therefore, constitutes, inter alia, a laboratory in which researchers undertake investigative endeavours. This thesis beams its floodlights on the allocentric aspects of humanism in the novels of Williams Sassine. Thus, using the phenomenological and ‘clavieniste’ lenses as overarching operational theories, the thesis investigates Sassine’s novels with the view to shading a ray of light on the ‘humanistic man’ especially the allocentric dimensions of his nature and comportment. Emphasis is laid on the motives and motivations underlying the individual and the in-group struggle of the sassinien heroes in the emancipation of their society from the shackles of colonial and postcolonial domination, exploitation and subjugation resulting in self-determination and the subsequent disenchantment. Furthermore, the thesis examines the nature and character of human charity, generosity and sacrifices among the characters in the novels. In conclusion, the thesis establishes, through an x-ray of the nature of actions and decisions of certain characters in the novels, the examination of the conscious and subconscious intentions underlying these same actions and decisions which, on a face value, are apparently altruistic, that the sassinien heroes’ efforts and sacrifices are geared towards the common and greater good. This invariably means that man is, indeed, capable of posing disinterested acts of charity and bringing succour, devoid of any ulterior motives for personal gain, to his fellow humans. The position of the Neo-classical economists is consequently over-assuming, sweeping and tad generalizing. The sassinien characters have demonstrated beyond reasonable doubt that they are humanists. Their nature, the remote and immediate causes of their fights, the goals and objectives of their struggles and their spirit of abnegation have indeed proven that “human beings have the right and the responsibility to give meaning and shape to their own lives. [They have stood] for the building of a more humane society through an ethics based on the human and other natural values in a spirit of reason and free inquiry through human capabilities” (AHA 2017 : 3).
- Full Text:
- Date Issued: 2018
- Authors: Dami, Emmanuel Naancin
- Date: 2018
- Subjects: Sassine, Williams, 1944-1997 -- Criticism and interpretation , Guinean fiction (French) -- 20th century -- History and criticism , Humanism in literature , Human beings in literature , Postcolonialism in literature , Existentialism in literature
- Language: French , English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/61957 , vital:28089
- Description: The human being, his behaviour and more importantly, his very essence have, for time immemorial, proven to be enigmatic to many a man and to researchers in particular. Consequently, the need for a thorough and more profound understanding of man has made him the epicentre of epistemic investigations across many academic disciplines. This, unfortunately, does not seem to have shaded bright lights on the grey areas bordering on his nature to his behavior. This, in turn, opens up other windows requiring further probes. For instance, proponents of the Neo-classical economic school contend that the human being is homo oeconomicus. This implies that man is intrinsically egocentric and a rational being whose decisions are based on informed choices driven by his urge for maximal utility geared towards his personal satisfaction (O’Boyle 2009; Caruso 2012). This stance invalidates man’s ability to do ‘disinterested good’ in any form. African francophone literature is replete with different and diverse images of man, his behaviour and existential conditions: sufferings and struggles. It, therefore, constitutes, inter alia, a laboratory in which researchers undertake investigative endeavours. This thesis beams its floodlights on the allocentric aspects of humanism in the novels of Williams Sassine. Thus, using the phenomenological and ‘clavieniste’ lenses as overarching operational theories, the thesis investigates Sassine’s novels with the view to shading a ray of light on the ‘humanistic man’ especially the allocentric dimensions of his nature and comportment. Emphasis is laid on the motives and motivations underlying the individual and the in-group struggle of the sassinien heroes in the emancipation of their society from the shackles of colonial and postcolonial domination, exploitation and subjugation resulting in self-determination and the subsequent disenchantment. Furthermore, the thesis examines the nature and character of human charity, generosity and sacrifices among the characters in the novels. In conclusion, the thesis establishes, through an x-ray of the nature of actions and decisions of certain characters in the novels, the examination of the conscious and subconscious intentions underlying these same actions and decisions which, on a face value, are apparently altruistic, that the sassinien heroes’ efforts and sacrifices are geared towards the common and greater good. This invariably means that man is, indeed, capable of posing disinterested acts of charity and bringing succour, devoid of any ulterior motives for personal gain, to his fellow humans. The position of the Neo-classical economists is consequently over-assuming, sweeping and tad generalizing. The sassinien characters have demonstrated beyond reasonable doubt that they are humanists. Their nature, the remote and immediate causes of their fights, the goals and objectives of their struggles and their spirit of abnegation have indeed proven that “human beings have the right and the responsibility to give meaning and shape to their own lives. [They have stood] for the building of a more humane society through an ethics based on the human and other natural values in a spirit of reason and free inquiry through human capabilities” (AHA 2017 : 3).
- Full Text:
- Date Issued: 2018
Aspects of the nutritional physiology of the perlemoen Haliotis midae (L.) and red abalone H. rufescens (Swainson)
- Authors: Kemp, Justin Oliver Gordon
- Date: 2018
- Subjects: Haliotis midae , Haliotis midae fisheries , Red abalone , Haliotis midae -- Feeding and feeds , Red abalone -- Feeding and feeds , Haliotis midae -- Nutrition -- Requirements , Red abalone -- Nutrition -- Requirements , Haliotis midae -- Metabolism , Red abalone -- Metabolism , Haliotis midae -- Physiology , Red abalone -- Physiology , Stable isotopes , Algae as feed
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62314 , vital:28154
- Description: The source of abalone for human consumption has shown a dramatic shift away from wild-capture fisheries in the last 30 years, with over 90% of global production now coming from aquaculture. Farmers initially relied on the natural food of abalone (macroalgae) as a culture feed, though in regions where macroalgae availability was limiting, the need to develop formulated feeds was evident. Extensive research effort has led to the development of a number of formulated feed products currently employed in the industry. These feeds, however, differ markedly from the mixed macroalgal diets that abalone have evolved to utilise, particularly in terms of protein content and carbohydrate structure. The degree to which the nutritional physiology of abalone responds to these novel formulated diets, with and without macroalgal supplementation, was investigated in the current study. A multifaceted approach, combining growth trials, stable isotope nutrient tracers and metabolic experiments, was employed to gain insight into the post-absorption dynamics and utilisation of dietary nutrients under varying dietary regimes of fresh macroalgae and formulated feed. Growth trials conducted with both Haliotis rufescens and H. midae showed significantly higher growth and protein utilisation efficiency for abalone fed macroalgal diets compared to formulated feeds. Furthermore, when formulated feeds were supplemented with macroalgae to form combination diets, growth and the utilization of protein was improved compared to the formulated-feed-only diet. The poor utilisation of protein by H. midae fed the formulated feed could be traced, using a method combining stable isotope bio-markers with a Bayesian mixing model (SIAR), to the low incorporation of the fishmeal component of protein in the diet. The marked postprandial drop in the O:N ratio on abalone fed formulated feeds indicate that the protein was being diverted into catabolic metabolic pathways. The metabolic cost of digestion, termed specific dynamic action (SDA), was negated as a factor in the improved growth of abalone fed macroalgal diets, with the SDA coefficient 2.1 times that observed for formulated feed. Furthermore, the postprandial haemolymph glucose concentration (HGC) in H. midae was elevated when fed formulated feed compared to macroalgae. The high levels of circulating glucose are likely a result of the structure the carbohydrate source in formulated feeds and stimulate the deposition of glycogen through the allosteric control of glycogen synthase. Formulated feeds produced higher cooked meat yields in canning simulation trials, suggesting that muscle glycogen content may indirectly play a role in increasing canning yields through the displacement of collagen. The results of these empirical studies are synthesised under key themes, discussed within the context of their potential commercial relevance and future research directions are highlighted.
- Full Text:
- Date Issued: 2018
- Authors: Kemp, Justin Oliver Gordon
- Date: 2018
- Subjects: Haliotis midae , Haliotis midae fisheries , Red abalone , Haliotis midae -- Feeding and feeds , Red abalone -- Feeding and feeds , Haliotis midae -- Nutrition -- Requirements , Red abalone -- Nutrition -- Requirements , Haliotis midae -- Metabolism , Red abalone -- Metabolism , Haliotis midae -- Physiology , Red abalone -- Physiology , Stable isotopes , Algae as feed
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62314 , vital:28154
- Description: The source of abalone for human consumption has shown a dramatic shift away from wild-capture fisheries in the last 30 years, with over 90% of global production now coming from aquaculture. Farmers initially relied on the natural food of abalone (macroalgae) as a culture feed, though in regions where macroalgae availability was limiting, the need to develop formulated feeds was evident. Extensive research effort has led to the development of a number of formulated feed products currently employed in the industry. These feeds, however, differ markedly from the mixed macroalgal diets that abalone have evolved to utilise, particularly in terms of protein content and carbohydrate structure. The degree to which the nutritional physiology of abalone responds to these novel formulated diets, with and without macroalgal supplementation, was investigated in the current study. A multifaceted approach, combining growth trials, stable isotope nutrient tracers and metabolic experiments, was employed to gain insight into the post-absorption dynamics and utilisation of dietary nutrients under varying dietary regimes of fresh macroalgae and formulated feed. Growth trials conducted with both Haliotis rufescens and H. midae showed significantly higher growth and protein utilisation efficiency for abalone fed macroalgal diets compared to formulated feeds. Furthermore, when formulated feeds were supplemented with macroalgae to form combination diets, growth and the utilization of protein was improved compared to the formulated-feed-only diet. The poor utilisation of protein by H. midae fed the formulated feed could be traced, using a method combining stable isotope bio-markers with a Bayesian mixing model (SIAR), to the low incorporation of the fishmeal component of protein in the diet. The marked postprandial drop in the O:N ratio on abalone fed formulated feeds indicate that the protein was being diverted into catabolic metabolic pathways. The metabolic cost of digestion, termed specific dynamic action (SDA), was negated as a factor in the improved growth of abalone fed macroalgal diets, with the SDA coefficient 2.1 times that observed for formulated feed. Furthermore, the postprandial haemolymph glucose concentration (HGC) in H. midae was elevated when fed formulated feed compared to macroalgae. The high levels of circulating glucose are likely a result of the structure the carbohydrate source in formulated feeds and stimulate the deposition of glycogen through the allosteric control of glycogen synthase. Formulated feeds produced higher cooked meat yields in canning simulation trials, suggesting that muscle glycogen content may indirectly play a role in increasing canning yields through the displacement of collagen. The results of these empirical studies are synthesised under key themes, discussed within the context of their potential commercial relevance and future research directions are highlighted.
- Full Text:
- Date Issued: 2018
Aspects of the population ecology, habitat use and behaviour of the endangered Knysna seahorse (Hippocampus capensis Boulenger, 1900) in a residential marina estate, Knysna, South Africa: implications for conservation
- Authors: Claassens, Louw
- Date: 2018
- Subjects: Endangered species -- South Africa -- Knysna , Sea horses -- Behavior -- South Africa -- Knysna , Sea horses -- Habitat -- South Africa -- Knysna , Sea horses -- Ecology -- South Africa -- Knysna
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/54789 , vital:26616
- Description: The Knysna seahorse Hippocampus capensis is South Africa’s only endemic seahorse species, and is found in only three adjacent estuaries along the southern coast. The conservation of this endangered species is important on a national and international level. This study presents the first research on this species within the Knysna estuary since 2001 and specifically focuses on aspects of its ecology within a residential marina estate (Thesen Islands Marina). The physico-chemical and habitat features of the marina were described and the population ecology, habitat use, and behaviour of the Knysna seahorse were investigated. Physico-chemical conditions within the western section of the marina, characterised by high water current velocities, were similar to that of the adjacent estuary. The eastern section of the marina was characterised by lower water current velocities and higher turbidity. Four major habitat types were identified within the marina canals: (I) artificial Reno mattress (wire baskets filled with rocks); (II) Codium tenue beds; (III) mixed vegetation on sediment; and (IV) barren canal floor. Seahorse densities within the marina were significantly higher compared to densities found historically within the estuary. Highest seahorse densities were specifically found within the artificial Reno mattress structures and within the western section of the marina. Seahorse density varied spatially and temporally and the type of habitat was an important predictor for seahorse occurrence. An experimental investigation found that H. capensis chooses artificial Reno mattress habitat over Zostera capensis when given a choice. GoPro cameras were used successfully to investigate daytime seahorse behaviour within the Reno mattress habitat. Seahorses were more active during the morning, spent most of their time (> 80 %) feeding, and morning courting behaviour for this species were confirmed. However, during the summer holiday period (mid-December to mid-January) few seahorses were observed on camera, which suggests that the increase in motor boat activity and the related increase in noise had a negative effect on H. capensis feeding and courting behaviour. The marina development, and in particular the Reno mattresses, created a new habitat for this endangered species within the Knysna estuary. In addition to the protection and restoration of natural habitats in which H. capensis is found, the conservation potential of artificial structures such as Reno mattresses should be realised.
- Full Text:
- Date Issued: 2018
- Authors: Claassens, Louw
- Date: 2018
- Subjects: Endangered species -- South Africa -- Knysna , Sea horses -- Behavior -- South Africa -- Knysna , Sea horses -- Habitat -- South Africa -- Knysna , Sea horses -- Ecology -- South Africa -- Knysna
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/54789 , vital:26616
- Description: The Knysna seahorse Hippocampus capensis is South Africa’s only endemic seahorse species, and is found in only three adjacent estuaries along the southern coast. The conservation of this endangered species is important on a national and international level. This study presents the first research on this species within the Knysna estuary since 2001 and specifically focuses on aspects of its ecology within a residential marina estate (Thesen Islands Marina). The physico-chemical and habitat features of the marina were described and the population ecology, habitat use, and behaviour of the Knysna seahorse were investigated. Physico-chemical conditions within the western section of the marina, characterised by high water current velocities, were similar to that of the adjacent estuary. The eastern section of the marina was characterised by lower water current velocities and higher turbidity. Four major habitat types were identified within the marina canals: (I) artificial Reno mattress (wire baskets filled with rocks); (II) Codium tenue beds; (III) mixed vegetation on sediment; and (IV) barren canal floor. Seahorse densities within the marina were significantly higher compared to densities found historically within the estuary. Highest seahorse densities were specifically found within the artificial Reno mattress structures and within the western section of the marina. Seahorse density varied spatially and temporally and the type of habitat was an important predictor for seahorse occurrence. An experimental investigation found that H. capensis chooses artificial Reno mattress habitat over Zostera capensis when given a choice. GoPro cameras were used successfully to investigate daytime seahorse behaviour within the Reno mattress habitat. Seahorses were more active during the morning, spent most of their time (> 80 %) feeding, and morning courting behaviour for this species were confirmed. However, during the summer holiday period (mid-December to mid-January) few seahorses were observed on camera, which suggests that the increase in motor boat activity and the related increase in noise had a negative effect on H. capensis feeding and courting behaviour. The marina development, and in particular the Reno mattresses, created a new habitat for this endangered species within the Knysna estuary. In addition to the protection and restoration of natural habitats in which H. capensis is found, the conservation potential of artificial structures such as Reno mattresses should be realised.
- Full Text:
- Date Issued: 2018
Bacterial colonisation and degradation of geologically weathered and discard coal
- Authors: Olawale, Jacob Taiwo
- Date: 2018
- Subjects: Coal mine waste , Coal -- Biodegradation , Coal mines and mining -- Environmental aspects , Land degradation , Electron microscopy , Extracellular polymeric substances , Flagella (Microbiology) , Fourier transform infrared spectroscopy , Microbiologically influenced corrosion
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/61625 , vital:28043
- Description: Bacterial beneficiation of low-grade coal, coal discard, and waste has the potential to mitigate land degradation, water and soil pollution and, be a strategy for mining companies to responsibly extract and process coal with environmental sustainability. This study investigated the colonisation and biodegradation or depolymerisation of coal discard and geologically weathered coal by selected strains of bacteria, and an attempt has been made to describe the mechanisms associated with colonisation and biodegradation of this carbonaceous material. Ten bacterial strains, Bacillus strain ECCN 18b, Citrobacter strain ECCN 19b, Proteus strain ECCN 20b, Exiguobacterium strain ECCN 21b, Microbacterium strain ECCN 22b, Proteus strain ECCN 23b, Serratia strain ECCN 24b, Escherichia strain ECCN 25b, Bacillus strain ECCN 26b and Bacillus strain ECCN 41b, isolated from diesel-contaminated soil and coal slurry and identified using DNA sequencing, were rescreened and their coal biodegradation potential ranked. The ranking of the bacterial strains was undertaken using several indicators including; formation of brown halos on the plate culture (solid), change in colour intensity of the medium in liquid culture, change in culture media pH, and an increase in absorbance at 280nm and 450nm. Although, all the ten strains showed evidence of biodegradation of coal discard and geologically weathered coal based on the ranking employed, and the three strains considered the best candidates were Citrobacter strain ECCN 19b, Exiguobacterium strain ECCN 21b and Serratia strain ECCN 24b. The actions of the three bacterial strains were further studied and characterised in relation to coal degradation. Electron microscopy revealed that Citrobacter strain ECCN 19b, Exiguobacterium strain ECCN 21b and Serratia strain ECCN 24b attached to the surface of coal discard and geologically weathered coal by a process that appeared to involve extracellular polymeric substances (EPS), and flagella. The presence of flagella for Citrobacter strain ECCN 19b and Serratia strain ECCN 24b was confirmed by transmission electron microscopy. Bacterial degradation of coal discard and geologically weathered coal by these selected strains resulted in the release of soluble and insoluble products. Ultraviolet/ visible spectrophotometric (UV/VIS) analysis revealed that the soluble products resembled humic acid-like substances, which was confirmed following Fourier Transform Infrared (FTIR) spectroscopy. Analysis revealed that the coal-derived humic acid-like substances were similar to commercial humic acid extracted from bituminous coal. Elemental analysis of the insoluble product residue after bacterial biodegradation revealed the modification of the chemical compositions of the coal discard and geologically weathered coal substrates. Characterisation of the functional groups of the insoluble product using FTIR spectroscopy indicated changes, with the appearance of new peaks at 1737cm-1, 1366cm-1, 1228cm-1, and 1216cm-1 characteristic of aldehyde, ketones, carboxylic acids, esters, amines, and alkanes. Broad spectra regions of 3500 -3200cm-1, characteristic of alcohol and phenol, were also observed. Together, these results were taken as evidence for increased oxidation of the coal substrates, presumably as a consequence of bacterial catalysed biodegradation of coal discard and geologically weathered coal. During bacterial degradation of coal discard and geologically weathered coal, strains produced extracellular protein, which was detected and further investigated using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS- PAGE). At least three protein bands with molecular mass 53 kDa, 72 kDa, and 82 kDa were common to the three bacterial strains. Following ammonium sulphate precipitation and gel filtration chromatography, additional bands with molecular mass 16 kDa, 33 kDa, 37 kDa, and 43 kDa were detected. An extracellular laccase activity was detected in cultures of Exiguobacterium strain ECCN 21b and Serratia strain ECCN 24b. Cytochrome P450 activity was detected in all the bacterial strains in the presence of both coal discard and geologically weathered coal. This is the first time that cytochrome P450 activity has been reported following exposure of these three bacterial strains to a coal substrate. Overall, this research has successfully demonstrated the partial degradation of coal discard and geologically weathered coal by Citrobacter strain ECCN 19b, Exiguobacterium strain ECCN 21b and Serratia strain ECCN 24b and the release of humic acid-like substances. Thus, the biodegradation process involved adherence to and growth of the bacteria on the surface of coal substrate and appeared to require the formation of alkaline substances and the combined activities of extracellular LAC and cytochrome P450. Since bacterial degradation of low-grade coal and discard appears to be viable, the bacteria isolated in this study can potentially be used either for conversion of discard into valuable chemicals or to mitigate the deleterious effects of stockpiled coal discard on the environment.
- Full Text:
- Date Issued: 2018
- Authors: Olawale, Jacob Taiwo
- Date: 2018
- Subjects: Coal mine waste , Coal -- Biodegradation , Coal mines and mining -- Environmental aspects , Land degradation , Electron microscopy , Extracellular polymeric substances , Flagella (Microbiology) , Fourier transform infrared spectroscopy , Microbiologically influenced corrosion
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/61625 , vital:28043
- Description: Bacterial beneficiation of low-grade coal, coal discard, and waste has the potential to mitigate land degradation, water and soil pollution and, be a strategy for mining companies to responsibly extract and process coal with environmental sustainability. This study investigated the colonisation and biodegradation or depolymerisation of coal discard and geologically weathered coal by selected strains of bacteria, and an attempt has been made to describe the mechanisms associated with colonisation and biodegradation of this carbonaceous material. Ten bacterial strains, Bacillus strain ECCN 18b, Citrobacter strain ECCN 19b, Proteus strain ECCN 20b, Exiguobacterium strain ECCN 21b, Microbacterium strain ECCN 22b, Proteus strain ECCN 23b, Serratia strain ECCN 24b, Escherichia strain ECCN 25b, Bacillus strain ECCN 26b and Bacillus strain ECCN 41b, isolated from diesel-contaminated soil and coal slurry and identified using DNA sequencing, were rescreened and their coal biodegradation potential ranked. The ranking of the bacterial strains was undertaken using several indicators including; formation of brown halos on the plate culture (solid), change in colour intensity of the medium in liquid culture, change in culture media pH, and an increase in absorbance at 280nm and 450nm. Although, all the ten strains showed evidence of biodegradation of coal discard and geologically weathered coal based on the ranking employed, and the three strains considered the best candidates were Citrobacter strain ECCN 19b, Exiguobacterium strain ECCN 21b and Serratia strain ECCN 24b. The actions of the three bacterial strains were further studied and characterised in relation to coal degradation. Electron microscopy revealed that Citrobacter strain ECCN 19b, Exiguobacterium strain ECCN 21b and Serratia strain ECCN 24b attached to the surface of coal discard and geologically weathered coal by a process that appeared to involve extracellular polymeric substances (EPS), and flagella. The presence of flagella for Citrobacter strain ECCN 19b and Serratia strain ECCN 24b was confirmed by transmission electron microscopy. Bacterial degradation of coal discard and geologically weathered coal by these selected strains resulted in the release of soluble and insoluble products. Ultraviolet/ visible spectrophotometric (UV/VIS) analysis revealed that the soluble products resembled humic acid-like substances, which was confirmed following Fourier Transform Infrared (FTIR) spectroscopy. Analysis revealed that the coal-derived humic acid-like substances were similar to commercial humic acid extracted from bituminous coal. Elemental analysis of the insoluble product residue after bacterial biodegradation revealed the modification of the chemical compositions of the coal discard and geologically weathered coal substrates. Characterisation of the functional groups of the insoluble product using FTIR spectroscopy indicated changes, with the appearance of new peaks at 1737cm-1, 1366cm-1, 1228cm-1, and 1216cm-1 characteristic of aldehyde, ketones, carboxylic acids, esters, amines, and alkanes. Broad spectra regions of 3500 -3200cm-1, characteristic of alcohol and phenol, were also observed. Together, these results were taken as evidence for increased oxidation of the coal substrates, presumably as a consequence of bacterial catalysed biodegradation of coal discard and geologically weathered coal. During bacterial degradation of coal discard and geologically weathered coal, strains produced extracellular protein, which was detected and further investigated using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS- PAGE). At least three protein bands with molecular mass 53 kDa, 72 kDa, and 82 kDa were common to the three bacterial strains. Following ammonium sulphate precipitation and gel filtration chromatography, additional bands with molecular mass 16 kDa, 33 kDa, 37 kDa, and 43 kDa were detected. An extracellular laccase activity was detected in cultures of Exiguobacterium strain ECCN 21b and Serratia strain ECCN 24b. Cytochrome P450 activity was detected in all the bacterial strains in the presence of both coal discard and geologically weathered coal. This is the first time that cytochrome P450 activity has been reported following exposure of these three bacterial strains to a coal substrate. Overall, this research has successfully demonstrated the partial degradation of coal discard and geologically weathered coal by Citrobacter strain ECCN 19b, Exiguobacterium strain ECCN 21b and Serratia strain ECCN 24b and the release of humic acid-like substances. Thus, the biodegradation process involved adherence to and growth of the bacteria on the surface of coal substrate and appeared to require the formation of alkaline substances and the combined activities of extracellular LAC and cytochrome P450. Since bacterial degradation of low-grade coal and discard appears to be viable, the bacteria isolated in this study can potentially be used either for conversion of discard into valuable chemicals or to mitigate the deleterious effects of stockpiled coal discard on the environment.
- Full Text:
- Date Issued: 2018
Baculovirus synergism: investigating mixed alphabaculovirus and betabaculovirus infections in the false codling moth, thaumatotibia leucotreta, for improved pest control
- Authors: Jukes, Michael David
- Date: 2018
- Subjects: Baculoviruses , Cryptophlebia leucotreta -- Biological control , Citrus -- Diseases and pests -- South Africa , Pests -- Integrated control , Nucleopolyhedroviruses , Natural pesticides , Cryptophlebia leucotreta granulovirus (CrleGV)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/61797 , vital:28061
- Description: Baculovirus based biopesticides are an effective and environmentally friendly approach for the control of agriculturally important insect pests. The false codling moth (FCM), Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae), is indigenous to southern Africa and is a major pest of citrus crops. This moth poses a serious risk to export of fruit to foreign markets and the control of this pest is therefore imperative. The Cryptophlebia leucotreta granulovirus (CrleGV) has been commercially formulated into the products Cryptogran™ and Cryptex®. These products have been used successfully for over a decade as part of a rigorous integrated pest management (IPM) programme to control T. leucotreta in South Africa. There is however, a continuous need to improve this programme while also addressing new challenges as they arise. An example of a rising concern is the possibility of resistance developing towards CrleGV. This was seen in Europe with field populations of the codling moth, Cydia pomonella (Linnaeus) (Lepidoptera: Tortricidae), which developed resistance to the Mexican isolate of the Cydia pomonella granulovirus (CpGV-M). To prevent such a scenario occurring in South Africa, there is a need to improve existing methods of control. For example, additional baculovirus variants can be isolated and characterised for determining virulence, which can then be developed as new biopesticides. Additionally, the potential for synergistic effects between different baculoviruses infecting the same host can be explored for improved virulence. A novel nucleopolyhedrovirus was recently identified in T. leucotreta larval homogenates which were also infected with CrleGV. This provided unique opportunities for continued research and development. In this study, a method using C. pomonella larvae, which can be infected by the NPV but not by CrleGV, was developed to separate the NPV from GV-NPV mixtures in an in vivo system. Examination of NPV OBs by transmission electron microscopy showed purified occlusion bodies with a single nucleopolyhedrovirus morphology (SNPV). Genetic characterisation identified the novel NPV as Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV), which was recently isolated from the litchi moth, Cryptophlebia peltastica (Meyrick) (Lepidoptera: Tortricidae). To begin examining the potential for synergism between the two viruses, a multiplex PCR assay was developed to accurately detect CrleGV and/or CrpeNPV in mixed infections. This assay was applied to various samples to screen for the presence of CrpeNPV and CrleGV. Additionally, a validation experiment was performed using different combinations of CrpeNPV and/or CrleGV to evaluate the effectiveness of the mPCR assay. The results obtained indicated a high degree of specificity with the correct amplicons generated for each test sample. The biological activity of CrpeNPV and CrleGV were evaluated using surface dose bioassays, both individually and in various combinations, against T. leucotreta neonate larvae in a laboratory setting. A synergistic effect was recorded in the combination treatments, showing improved virulence when compared against each virus in isolation. The LC90 for CrpeNPV and CrleGV when applied alone against T. leucotreta was calculated to be 2.75*106 and 3.00*106 OBs.ml"1 respectively. These values decreased to 1.07*106 and 7.18*105 OBs.ml"1 when combinations of CrleGV and CrpeNPV were applied at ratios of 3:1 and 1:3 respectively. These results indicate a potential for developing improved biopesticides for the control of T. leucotreta in the field. To better understand the interactions between CrleGV and CrpeNPV, experiments involving the serial passage of these viruses through T. leucotreta larvae were performed. This was done using each virus in isolation as well as both viruses in different combinations. Genomic DNA was extracted from recovered occlusion bodies after each passage and examined by multiplex and quantitative PCR. This analysis enabled the detection of each virus present throughout this assay, as well as recording shifts in the ratio of CrleGV and CrpeNPV at each passage. CrleGV rapidly became the dominant virus in all treatments, indicating a potentially antagonistic interaction during serial passage. Additionally, CrpeNPV and CrleGV were detected in treatments which were not originally inoculated with one or either virus, indicating potential covert infections in T. leucotreta. Occlusion bodies recovered from the final passage were used to inoculate C. pomonella larvae to isolate CrpeNPV from CrleGV. Genomic DNA was extracted from these CrpeNPV OBs and examined by restriction endonuclease assays and next generation sequencing. This enabled the identification of potential recombination events which may have occurred during the dual GV and NPV infections throughout the passage assay. No recombination events were identified in the CrpeNPV genome sequences assembled from virus collected at the end of the passage assay. Lastly, the efficacy of CrpeNPV and CrleGV, both alone and in various combinations, was evaluated in the field. In two separate trials conducted on citrus, unfavorable field conditions resulted in no significant reduction in fruit infestation for both the virus and chemical treatments. While not statistically significant, virus treatments were recorded to have the lowest levels of fruit infestation with a measured reduction of up to 64 %. This study is the first to report a synergistic effect between CrleGV and CrpeNPV in T. leucotreta. The discovery of beneficial interactions creates an opportunity for the development of novel biopesticides for improved control of this pest in South Africa.
- Full Text:
- Date Issued: 2018
- Authors: Jukes, Michael David
- Date: 2018
- Subjects: Baculoviruses , Cryptophlebia leucotreta -- Biological control , Citrus -- Diseases and pests -- South Africa , Pests -- Integrated control , Nucleopolyhedroviruses , Natural pesticides , Cryptophlebia leucotreta granulovirus (CrleGV)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/61797 , vital:28061
- Description: Baculovirus based biopesticides are an effective and environmentally friendly approach for the control of agriculturally important insect pests. The false codling moth (FCM), Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae), is indigenous to southern Africa and is a major pest of citrus crops. This moth poses a serious risk to export of fruit to foreign markets and the control of this pest is therefore imperative. The Cryptophlebia leucotreta granulovirus (CrleGV) has been commercially formulated into the products Cryptogran™ and Cryptex®. These products have been used successfully for over a decade as part of a rigorous integrated pest management (IPM) programme to control T. leucotreta in South Africa. There is however, a continuous need to improve this programme while also addressing new challenges as they arise. An example of a rising concern is the possibility of resistance developing towards CrleGV. This was seen in Europe with field populations of the codling moth, Cydia pomonella (Linnaeus) (Lepidoptera: Tortricidae), which developed resistance to the Mexican isolate of the Cydia pomonella granulovirus (CpGV-M). To prevent such a scenario occurring in South Africa, there is a need to improve existing methods of control. For example, additional baculovirus variants can be isolated and characterised for determining virulence, which can then be developed as new biopesticides. Additionally, the potential for synergistic effects between different baculoviruses infecting the same host can be explored for improved virulence. A novel nucleopolyhedrovirus was recently identified in T. leucotreta larval homogenates which were also infected with CrleGV. This provided unique opportunities for continued research and development. In this study, a method using C. pomonella larvae, which can be infected by the NPV but not by CrleGV, was developed to separate the NPV from GV-NPV mixtures in an in vivo system. Examination of NPV OBs by transmission electron microscopy showed purified occlusion bodies with a single nucleopolyhedrovirus morphology (SNPV). Genetic characterisation identified the novel NPV as Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV), which was recently isolated from the litchi moth, Cryptophlebia peltastica (Meyrick) (Lepidoptera: Tortricidae). To begin examining the potential for synergism between the two viruses, a multiplex PCR assay was developed to accurately detect CrleGV and/or CrpeNPV in mixed infections. This assay was applied to various samples to screen for the presence of CrpeNPV and CrleGV. Additionally, a validation experiment was performed using different combinations of CrpeNPV and/or CrleGV to evaluate the effectiveness of the mPCR assay. The results obtained indicated a high degree of specificity with the correct amplicons generated for each test sample. The biological activity of CrpeNPV and CrleGV were evaluated using surface dose bioassays, both individually and in various combinations, against T. leucotreta neonate larvae in a laboratory setting. A synergistic effect was recorded in the combination treatments, showing improved virulence when compared against each virus in isolation. The LC90 for CrpeNPV and CrleGV when applied alone against T. leucotreta was calculated to be 2.75*106 and 3.00*106 OBs.ml"1 respectively. These values decreased to 1.07*106 and 7.18*105 OBs.ml"1 when combinations of CrleGV and CrpeNPV were applied at ratios of 3:1 and 1:3 respectively. These results indicate a potential for developing improved biopesticides for the control of T. leucotreta in the field. To better understand the interactions between CrleGV and CrpeNPV, experiments involving the serial passage of these viruses through T. leucotreta larvae were performed. This was done using each virus in isolation as well as both viruses in different combinations. Genomic DNA was extracted from recovered occlusion bodies after each passage and examined by multiplex and quantitative PCR. This analysis enabled the detection of each virus present throughout this assay, as well as recording shifts in the ratio of CrleGV and CrpeNPV at each passage. CrleGV rapidly became the dominant virus in all treatments, indicating a potentially antagonistic interaction during serial passage. Additionally, CrpeNPV and CrleGV were detected in treatments which were not originally inoculated with one or either virus, indicating potential covert infections in T. leucotreta. Occlusion bodies recovered from the final passage were used to inoculate C. pomonella larvae to isolate CrpeNPV from CrleGV. Genomic DNA was extracted from these CrpeNPV OBs and examined by restriction endonuclease assays and next generation sequencing. This enabled the identification of potential recombination events which may have occurred during the dual GV and NPV infections throughout the passage assay. No recombination events were identified in the CrpeNPV genome sequences assembled from virus collected at the end of the passage assay. Lastly, the efficacy of CrpeNPV and CrleGV, both alone and in various combinations, was evaluated in the field. In two separate trials conducted on citrus, unfavorable field conditions resulted in no significant reduction in fruit infestation for both the virus and chemical treatments. While not statistically significant, virus treatments were recorded to have the lowest levels of fruit infestation with a measured reduction of up to 64 %. This study is the first to report a synergistic effect between CrleGV and CrpeNPV in T. leucotreta. The discovery of beneficial interactions creates an opportunity for the development of novel biopesticides for improved control of this pest in South Africa.
- Full Text:
- Date Issued: 2018
Behaviour of quiet time ionospheric disturbances at African equatorial and midlatitude regions
- Authors: Orford, Nicola Diane
- Date: 2018
- Subjects: Ionospheric storms , Ionospheric storms -- Africa , Ionosphere , Plasmasphere , Q-disturbances , Total electron content (TEC)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62672 , vital:28228
- Description: Extreme ionospheric and geomagnetic disturbances affect technology adversely. Prestorm enhancements, considered a potential predictor of geomagnetic storms, occur during quiet conditions prior to geomagnetic disturbances. The ionosphere experiences general disturbances during quiet geomagnetic conditions and these Q- disturbances remain unexplored over Africa. This study used TEC data to characterize the morphology of Q-disturbances over Africa, exploring variations with solar cycle, season, time of occurrence and latitude. Observations from 10 African GPS stations in the equatorial and midlatitude regions show that Q-disturbances in the equatorial region are predominantly driven by E x B variations, while multiple mechanisms affect the midlatitude region. Q- disturbances occur more frequently during nighttime than during daytime and no seasonal trend is observed. Midlatitude Q-disturbance mechanisms are explored in depth, considering substorm activity, the plasmaspheric contribution to GPS TEC and plasma transfer between conjugate points. Substorm activity is not a dominant mechanism, although Q-disturbances occurring under elevated substorm conditions tend to have longer duration and larger amplitude than general Q-disturbances. Many observed Q-disturbances become non-significant once the plasmaspheric contribution to the TEC measurements is removed, indicating that these disturbances occur within the plasmasphere, and not the ionosphere. Transfer of plasma between conjugate points does not seem to be a mechanism driving Q-disturbances, as the corresponding nighttime behaviour expected between depletions in the summer hemisphere and enhancements in the winter hemisphere is not observed. Pre-storm enhancements occur infrequently, rendering them a poor predictor of geomagnetic disturbances. Pre-storm enhancement morphology does not differ significantly from general quiet time enhancement morphology, suggesting pre-storms are not a special case of Q-disturbances.
- Full Text:
- Date Issued: 2018
- Authors: Orford, Nicola Diane
- Date: 2018
- Subjects: Ionospheric storms , Ionospheric storms -- Africa , Ionosphere , Plasmasphere , Q-disturbances , Total electron content (TEC)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62672 , vital:28228
- Description: Extreme ionospheric and geomagnetic disturbances affect technology adversely. Prestorm enhancements, considered a potential predictor of geomagnetic storms, occur during quiet conditions prior to geomagnetic disturbances. The ionosphere experiences general disturbances during quiet geomagnetic conditions and these Q- disturbances remain unexplored over Africa. This study used TEC data to characterize the morphology of Q-disturbances over Africa, exploring variations with solar cycle, season, time of occurrence and latitude. Observations from 10 African GPS stations in the equatorial and midlatitude regions show that Q-disturbances in the equatorial region are predominantly driven by E x B variations, while multiple mechanisms affect the midlatitude region. Q- disturbances occur more frequently during nighttime than during daytime and no seasonal trend is observed. Midlatitude Q-disturbance mechanisms are explored in depth, considering substorm activity, the plasmaspheric contribution to GPS TEC and plasma transfer between conjugate points. Substorm activity is not a dominant mechanism, although Q-disturbances occurring under elevated substorm conditions tend to have longer duration and larger amplitude than general Q-disturbances. Many observed Q-disturbances become non-significant once the plasmaspheric contribution to the TEC measurements is removed, indicating that these disturbances occur within the plasmasphere, and not the ionosphere. Transfer of plasma between conjugate points does not seem to be a mechanism driving Q-disturbances, as the corresponding nighttime behaviour expected between depletions in the summer hemisphere and enhancements in the winter hemisphere is not observed. Pre-storm enhancements occur infrequently, rendering them a poor predictor of geomagnetic disturbances. Pre-storm enhancement morphology does not differ significantly from general quiet time enhancement morphology, suggesting pre-storms are not a special case of Q-disturbances.
- Full Text:
- Date Issued: 2018
Biochemical characterisation and small molecule modulation of the interaction between two cytosolic Hsp70s from Trypanosoma brucei and potential co-chaperones
- Authors: Bentley, Stephen John
- Date: 2018
- Subjects: Uncatalogued
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/63402 , vital:28407
- Description: Expected release date-April 2019
- Full Text:
- Date Issued: 2018
- Authors: Bentley, Stephen John
- Date: 2018
- Subjects: Uncatalogued
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/63402 , vital:28407
- Description: Expected release date-April 2019
- Full Text:
- Date Issued: 2018
Bioinformatics tool development with a focus on structural bioinformatics and the analysis of genetic variation in humans
- Authors: Brown, David K
- Date: 2018
- Subjects: Bioinformatics , Human genetics -- Variation , High performance computing , Workflow management systems , Molecular dynamics , Next generation sequencing , Human Mutation Analysis (HUMA)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/60708 , vital:27820
- Description: This thesis is divided into three parts, united under the general theme of bioinformatics tool development and variation analysis. Part 1 describes the design and development of the Job Management System (JMS), a workflow management system for high performance computing (HPC). HPC has become an integral part of bioinformatics. Computational methods for molecular dynamics and next generation sequencing (NGS) analysis, which require complex calculations on large datasets, are not yet feasible on desktop computers. As such, powerful computer clusters have been employed to perform these calculations. However, making use of these HPC clusters requires familiarity with command line interfaces. This excludes a large number of researchers from taking advantage of these resources. JMS was developed as a tool to make it easier for researchers without a computer science background to make use of HPC. Additionally, JMS can be used to host computational tools and pipelines and generates both web-based interfaces and RESTful APIs for those tools. The web-based interfaces can be used to quickly and easily submit jobs to the underlying cluster. The RESTful web API, on the other hand, allows JMS to provided backend functionality for external tools and web servers that want to run jobs on the cluster. Numerous tools and workflows have already been added to JMS, several of which have been incorporated into external web servers. One such web server is the Human Mutation Analysis (HUMA) web server and database. HUMA, the topic of part 2 of this thesis, is a platform for the analysis of genetic variation in humans. HUMA aggregates data from various existing databases into a single, connected and related database. The advantages of this are realized in the powerful querying abilities that it provides. HUMA includes protein, gene, disease, and variation data and can be searched from the angle of any one of these categories. For example, searching for a protein will return the protein data (e.g. protein sequences, structures, domains and families, and other meta-data). However, the related nature of the database means that genes, diseases, variation, and literature related to the protein will also be returned, giving users a powerful and holistic view of all data associated with the protein. HUMA also provides links to the original sources of the data, allowing users to follow the links to find additional details. HUMA aims to be a platform for the analysis of genetic variation. As such, it also provides tools to visualize and analyse the data (several of which run on the underlying cluster, via JMS). These tools include alignment and 3D structure visualization, homology modeling, variant analysis, and the ability to upload custom variation datasets and map them to proteins, genes and diseases. HUMA also provides collaboration features, allowing users to share and discuss datasets and job results. Finally, part 3 of this thesis focused on the development of a suite of tools, MD-TASK, to analyse genetic variation at the protein structure level via network analysis of molecular dynamics simulations. The use of MD-TASK in combination with the tools developed in the previous parts of this thesis is showcased via the analysis of variation in the renin-angiotensinogen complex, a vital part of the renin-angiotensin system.
- Full Text:
- Date Issued: 2018
- Authors: Brown, David K
- Date: 2018
- Subjects: Bioinformatics , Human genetics -- Variation , High performance computing , Workflow management systems , Molecular dynamics , Next generation sequencing , Human Mutation Analysis (HUMA)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/60708 , vital:27820
- Description: This thesis is divided into three parts, united under the general theme of bioinformatics tool development and variation analysis. Part 1 describes the design and development of the Job Management System (JMS), a workflow management system for high performance computing (HPC). HPC has become an integral part of bioinformatics. Computational methods for molecular dynamics and next generation sequencing (NGS) analysis, which require complex calculations on large datasets, are not yet feasible on desktop computers. As such, powerful computer clusters have been employed to perform these calculations. However, making use of these HPC clusters requires familiarity with command line interfaces. This excludes a large number of researchers from taking advantage of these resources. JMS was developed as a tool to make it easier for researchers without a computer science background to make use of HPC. Additionally, JMS can be used to host computational tools and pipelines and generates both web-based interfaces and RESTful APIs for those tools. The web-based interfaces can be used to quickly and easily submit jobs to the underlying cluster. The RESTful web API, on the other hand, allows JMS to provided backend functionality for external tools and web servers that want to run jobs on the cluster. Numerous tools and workflows have already been added to JMS, several of which have been incorporated into external web servers. One such web server is the Human Mutation Analysis (HUMA) web server and database. HUMA, the topic of part 2 of this thesis, is a platform for the analysis of genetic variation in humans. HUMA aggregates data from various existing databases into a single, connected and related database. The advantages of this are realized in the powerful querying abilities that it provides. HUMA includes protein, gene, disease, and variation data and can be searched from the angle of any one of these categories. For example, searching for a protein will return the protein data (e.g. protein sequences, structures, domains and families, and other meta-data). However, the related nature of the database means that genes, diseases, variation, and literature related to the protein will also be returned, giving users a powerful and holistic view of all data associated with the protein. HUMA also provides links to the original sources of the data, allowing users to follow the links to find additional details. HUMA aims to be a platform for the analysis of genetic variation. As such, it also provides tools to visualize and analyse the data (several of which run on the underlying cluster, via JMS). These tools include alignment and 3D structure visualization, homology modeling, variant analysis, and the ability to upload custom variation datasets and map them to proteins, genes and diseases. HUMA also provides collaboration features, allowing users to share and discuss datasets and job results. Finally, part 3 of this thesis focused on the development of a suite of tools, MD-TASK, to analyse genetic variation at the protein structure level via network analysis of molecular dynamics simulations. The use of MD-TASK in combination with the tools developed in the previous parts of this thesis is showcased via the analysis of variation in the renin-angiotensinogen complex, a vital part of the renin-angiotensin system.
- Full Text:
- Date Issued: 2018
Biotic and abiotic drivers of macroinvertebrate assemblages in a South African river
- Authors: Bellingan, Terence Andrew
- Date: 2018
- Subjects: Aquatic insects -- South Africa -- Eastern Cape , Stream ecology -- South Africa -- Eastern Cape , Freshwater ecology -- South Africa -- Eastern Cape , Riparian areas -- Management , Ecosystem management -- South Africa -- Eastern Cape , Mayflies -- South Africa -- Eastern Cape , Stoneflies -- South Africa -- Eastern Cape , Keiskamma River
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/61839 , vital:28067
- Description: Aquatic insects are the most numerically abundant and diverse group of organisms found in lotic ecosystems in South Africa and the world over. They play vital roles in freshwater ecosystem functioning, processing nutrients and in turn forming integral links in stream food-webs. This thesis focussed on examining the macroinvertebrate fauna within three reaches of headwater streams of the Keiskamma River system: reaches that were considered to be fishless; reaches that were invaded by non-native salmonid species; and reaches that were dominated by native fish. I described the effects of predatory fish presence through detailed examination of macroinvertebrate assemblage composition; macroinvertebrate drift timing and density; and through niche utilisation determined from stable isotope data. Patterns in the macroinvertebrate assemblages of the headwaters of the Keiskamma River appear to be driven more strongly by flow rate and seasonal influences, but fish presence and biotope availability were also significant drivers. Niche shifts due to predator presence were not easy to detect and, while patterns of influence may have been evident, they were not found to be significant. However, I demonstrated that salmonids selectively feed on native fish species when the opportunity is presented, occupying significantly higher trophic levels when co-occurring with native fish than in invaded reaches where native fish are absent. Drift timing and density were demonstrated to be significantly different between reach for specific macroinvertebrate species from the Ephemeroptera and Plecoptera, under differing fish predation regimes, in agreement with what has been observed from studies in rivers elsewhere. In freshwater ecosystems of South Africa and worldwide, mitigation of negative effects of alien fishes through their removal using piscicides may also affect non-target organisms. To better understand the effects of just such a removal operation, employed for the first time in the history of freshwater conservation in South Africa, macroinvertebrate communities were assessed for non-target effects of rotenone. The fish eradication operations were demonstrated to have a short-term negative effect on the macroinvertebrate assemblage, through water quality index measurements and alteration of densities of macroinvertebrate taxa collected from stone surfaces. However, no long-term detrimental impact was observed as macroinvertebrate faunas returned to a comparable pre-treatment state within a year of each rotenone application.
- Full Text:
- Date Issued: 2018
- Authors: Bellingan, Terence Andrew
- Date: 2018
- Subjects: Aquatic insects -- South Africa -- Eastern Cape , Stream ecology -- South Africa -- Eastern Cape , Freshwater ecology -- South Africa -- Eastern Cape , Riparian areas -- Management , Ecosystem management -- South Africa -- Eastern Cape , Mayflies -- South Africa -- Eastern Cape , Stoneflies -- South Africa -- Eastern Cape , Keiskamma River
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/61839 , vital:28067
- Description: Aquatic insects are the most numerically abundant and diverse group of organisms found in lotic ecosystems in South Africa and the world over. They play vital roles in freshwater ecosystem functioning, processing nutrients and in turn forming integral links in stream food-webs. This thesis focussed on examining the macroinvertebrate fauna within three reaches of headwater streams of the Keiskamma River system: reaches that were considered to be fishless; reaches that were invaded by non-native salmonid species; and reaches that were dominated by native fish. I described the effects of predatory fish presence through detailed examination of macroinvertebrate assemblage composition; macroinvertebrate drift timing and density; and through niche utilisation determined from stable isotope data. Patterns in the macroinvertebrate assemblages of the headwaters of the Keiskamma River appear to be driven more strongly by flow rate and seasonal influences, but fish presence and biotope availability were also significant drivers. Niche shifts due to predator presence were not easy to detect and, while patterns of influence may have been evident, they were not found to be significant. However, I demonstrated that salmonids selectively feed on native fish species when the opportunity is presented, occupying significantly higher trophic levels when co-occurring with native fish than in invaded reaches where native fish are absent. Drift timing and density were demonstrated to be significantly different between reach for specific macroinvertebrate species from the Ephemeroptera and Plecoptera, under differing fish predation regimes, in agreement with what has been observed from studies in rivers elsewhere. In freshwater ecosystems of South Africa and worldwide, mitigation of negative effects of alien fishes through their removal using piscicides may also affect non-target organisms. To better understand the effects of just such a removal operation, employed for the first time in the history of freshwater conservation in South Africa, macroinvertebrate communities were assessed for non-target effects of rotenone. The fish eradication operations were demonstrated to have a short-term negative effect on the macroinvertebrate assemblage, through water quality index measurements and alteration of densities of macroinvertebrate taxa collected from stone surfaces. However, no long-term detrimental impact was observed as macroinvertebrate faunas returned to a comparable pre-treatment state within a year of each rotenone application.
- Full Text:
- Date Issued: 2018
Building IKhwezi, a digital platform to capture everyday Indigenous Knowledge for improving educational outcomes in marginalised communities
- Authors: Ntšekhe, Mathe V K
- Date: 2018
- Subjects: Information technology , Knowledge management , Traditional ecological knowledge , Pedagogical content knowledge , Traditional ecological knowledge -- Technological innovations , IKhwezi , ICT4D , Indigenous Technological Pedagogical Content Knowledge (I-TPACK) , Siyakhula Living Lab
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62505 , vital:28200
- Description: Aptly captured in the name, the broad mandate of Information and Communications Technologies for Development (ICT4D) is to facilitate the use of Information and Communication Technologies (ICTs) in society to support development. Education, as often stated, is the cornerstone for development, imparting knowledge for conceiving and realising development. In this thesis, we explore how everyday Indigenous Knowledge (IK) can be collected digitally, to enhance the educational outcomes of learners from marginalised backgrounds, by stimulating the production of teaching and learning materials that include the local imagery to have resonance with the learners. As part of the exploration, we reviewed a framework known as Technological Pedagogical Content Knowledge (TPACK), which spells out the different kinds of knowledge needed by teachers to teach effectively with ICTs. In this framework, IK is not present explicitly, but through the concept of context(s). Using Afrocentric and Pan-African scholarship, we argue that this logic is linked to colonialism and a critical decolonising pedagogy necessarily demands explication of IK: to make visible the cultures of the learners in the margins (e.g. Black rural learners). On the strength of this argument, we have proposed that TPACK be augumented to become Indigenous Technological Pedagogical Content Knowledge (I-TPACK). Through this augumentation, I-TPACK becomes an Afrocentric framework for a multicultural education in the digital era. The design of the digital platform for capturing IK relevant for formal education, was done in the Siyakhula Living Lab (SLL). The core idea of a Living Lab (LL) is that users must be understood in the context of their lived everyday reality. Further, they must be involved as co-creators in the design and innovation processes. On a methodological level, the LL environment allowed for the fusing together of multiple methods that can help to create a fitting solution. In this thesis, we followed an iterative user-centred methodology rooted in ethnography and phenomenology. Specifically, through long term conversations and interaction with teachers and ethnographic observations, we conceptualized a platform, IKhwezi, that facilitates the collection of context-sensitive content, collaboratively, and with cost and convenience in mind. We implemented this platform using MediaWiki, based on a number of considerations. From the ICT4D disciplinary point of view, a major consideration was being open to the possibility that other forms of innovation—and, not just ‘technovelty’ (i.e. technological/- technical innovation)—can provide a breakthrough or ingenious solution to the problem at hand. In a sense, we were reinforcing the growing sentiment within the discipline that technology is not the goal, but the means to foregrounding the commonality of the human experience in working towards development. Testing confirmed that there is some value in the platform. This is despite the challenges to onboard users, in pursuit of more content that could bolster the value of everyday IK in improving the educational outcomes of all learners.
- Full Text:
- Date Issued: 2018
- Authors: Ntšekhe, Mathe V K
- Date: 2018
- Subjects: Information technology , Knowledge management , Traditional ecological knowledge , Pedagogical content knowledge , Traditional ecological knowledge -- Technological innovations , IKhwezi , ICT4D , Indigenous Technological Pedagogical Content Knowledge (I-TPACK) , Siyakhula Living Lab
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62505 , vital:28200
- Description: Aptly captured in the name, the broad mandate of Information and Communications Technologies for Development (ICT4D) is to facilitate the use of Information and Communication Technologies (ICTs) in society to support development. Education, as often stated, is the cornerstone for development, imparting knowledge for conceiving and realising development. In this thesis, we explore how everyday Indigenous Knowledge (IK) can be collected digitally, to enhance the educational outcomes of learners from marginalised backgrounds, by stimulating the production of teaching and learning materials that include the local imagery to have resonance with the learners. As part of the exploration, we reviewed a framework known as Technological Pedagogical Content Knowledge (TPACK), which spells out the different kinds of knowledge needed by teachers to teach effectively with ICTs. In this framework, IK is not present explicitly, but through the concept of context(s). Using Afrocentric and Pan-African scholarship, we argue that this logic is linked to colonialism and a critical decolonising pedagogy necessarily demands explication of IK: to make visible the cultures of the learners in the margins (e.g. Black rural learners). On the strength of this argument, we have proposed that TPACK be augumented to become Indigenous Technological Pedagogical Content Knowledge (I-TPACK). Through this augumentation, I-TPACK becomes an Afrocentric framework for a multicultural education in the digital era. The design of the digital platform for capturing IK relevant for formal education, was done in the Siyakhula Living Lab (SLL). The core idea of a Living Lab (LL) is that users must be understood in the context of their lived everyday reality. Further, they must be involved as co-creators in the design and innovation processes. On a methodological level, the LL environment allowed for the fusing together of multiple methods that can help to create a fitting solution. In this thesis, we followed an iterative user-centred methodology rooted in ethnography and phenomenology. Specifically, through long term conversations and interaction with teachers and ethnographic observations, we conceptualized a platform, IKhwezi, that facilitates the collection of context-sensitive content, collaboratively, and with cost and convenience in mind. We implemented this platform using MediaWiki, based on a number of considerations. From the ICT4D disciplinary point of view, a major consideration was being open to the possibility that other forms of innovation—and, not just ‘technovelty’ (i.e. technological/- technical innovation)—can provide a breakthrough or ingenious solution to the problem at hand. In a sense, we were reinforcing the growing sentiment within the discipline that technology is not the goal, but the means to foregrounding the commonality of the human experience in working towards development. Testing confirmed that there is some value in the platform. This is despite the challenges to onboard users, in pursuit of more content that could bolster the value of everyday IK in improving the educational outcomes of all learners.
- Full Text:
- Date Issued: 2018
Code-switching as a pedagogical strategy in classroom settings: the case of township schools in a South African Metropolitan Municipality
- Authors: Marawu, Sithembele
- Date: 2018
- Subjects: Code switching (Linguistics) , Multilingual education -- South Africa , Education, Bilingual -- South Africa , Language and languages -- Study and teaching -- Bilingual method , English language -- Social aspects -- South Africa , Language and education -- South Africa , Language and education -- Social aspects -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62406 , vital:28173
- Description: The purpose of this study was to explore the use of code-switching as a pedagogical strategy in bi/multilingual classroom settings. It was prompted by the widespread use of codeswitching (CS) in classrooms, particularly in South African rural and township schools. This study highlighted that learners from disadvantaged backgrounds struggle to learn through the medium of English but aspire to acquire it because of its association with socio-economic advancement. However, poor proficiency in English excludes them from being part of the country's economy. Research studies show that there is a shift from the old orthodoxy which perceived CS as undesirable in classrooms to a new orthodoxy that acknowledges its academic contribution in classrooms. Although more research on classroom CS has been done, this study identified the need for development of new strategies on how to use CS effectively in classrooms as a linguistic and pedagogical resource. In line with critical classroom ethnography, qualitative interpretation of data was used to understand the teachers' discourse behaviour. Additionally, non-probability sampling - specifically purposive sampling - was used to collect data. These methods and approaches assisted in the analysis of the discourse of the three teachers who served as units of analysis in this study. These teachers relied on CS to impart the content of their subjects to the learners. It transpired from data analysis that teachers use CS in classrooms to achieve various functions like social and pedagogical functions. Another finding is that the switches teachers make do not affect the syntactic structure of the matrix language. Moreover, CS enhances understanding of the subject matter. This study concludes by stating that as learners are emergent bilinguals, additive bilingualism would be more ideal in the South African situation than subtractive bilingualism which parents and learners seem to prefer. Lastly, there is a need to harness CS as a communicative and pedagogical resource in classrooms.
- Full Text:
- Date Issued: 2018
- Authors: Marawu, Sithembele
- Date: 2018
- Subjects: Code switching (Linguistics) , Multilingual education -- South Africa , Education, Bilingual -- South Africa , Language and languages -- Study and teaching -- Bilingual method , English language -- Social aspects -- South Africa , Language and education -- South Africa , Language and education -- Social aspects -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62406 , vital:28173
- Description: The purpose of this study was to explore the use of code-switching as a pedagogical strategy in bi/multilingual classroom settings. It was prompted by the widespread use of codeswitching (CS) in classrooms, particularly in South African rural and township schools. This study highlighted that learners from disadvantaged backgrounds struggle to learn through the medium of English but aspire to acquire it because of its association with socio-economic advancement. However, poor proficiency in English excludes them from being part of the country's economy. Research studies show that there is a shift from the old orthodoxy which perceived CS as undesirable in classrooms to a new orthodoxy that acknowledges its academic contribution in classrooms. Although more research on classroom CS has been done, this study identified the need for development of new strategies on how to use CS effectively in classrooms as a linguistic and pedagogical resource. In line with critical classroom ethnography, qualitative interpretation of data was used to understand the teachers' discourse behaviour. Additionally, non-probability sampling - specifically purposive sampling - was used to collect data. These methods and approaches assisted in the analysis of the discourse of the three teachers who served as units of analysis in this study. These teachers relied on CS to impart the content of their subjects to the learners. It transpired from data analysis that teachers use CS in classrooms to achieve various functions like social and pedagogical functions. Another finding is that the switches teachers make do not affect the syntactic structure of the matrix language. Moreover, CS enhances understanding of the subject matter. This study concludes by stating that as learners are emergent bilinguals, additive bilingualism would be more ideal in the South African situation than subtractive bilingualism which parents and learners seem to prefer. Lastly, there is a need to harness CS as a communicative and pedagogical resource in classrooms.
- Full Text:
- Date Issued: 2018
Combined spectral and stimulated luminescence study of charge trapping and recombination processes in α-Al2O3:C
- Authors: Nyirenda, Angel Newton
- Date: 2018
- Subjects: Luminescence , Thermoluminescence , Luminescence spectroscopy , Carbon-doped aluminium oxide , Radioluminescence , Time-resolved X-ray excited optical luminescence
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62683 , vital:28235
- Description: The main objective of this project was to gain a deeper and better understanding of the luminescence processes in a-Al₂O₃:C, a highly-sensitive dosimetric material, using a combined spectral and stimulated luminescence study. The spectral studies concentrated on the emission spectra obtained using X-ray induced radioluminescence (XERL), thermoluminescence (XETL) and time-resolved X-ray excited optical luminescence (TR-XEOL) techniques. The stimulated luminescence studies were based on thermoluminescence (TL), optically stimulated luminescence (OSL) and phototransferred TL (PTTL) methods that were used in the study of the radiation-induced defects at high beta-doses and the deep traps, that is, traps with thermal depths beyond 500°C. The spectral and stimulated luminescence measurements were carried out using a high sensitivity luminescence spectrometer and a Ris0 TL/OSL Model DA-20 Reader, respectively. The XERL emission spectrum measured at room temperature shows seven gaussian peaks associated with F-centres (420 nm), F+-centres (334 nm), F2+-centres (559 nm), Stoke’s vibronic band of Cr3+ (671 nm), Cr3+ R-line emission (694 nm), anti-Stokes vibronic band of Cr3+ (710 nm) and an unidentified emission band (260-300 nm) which we associate with hole recombinations at a luminescence centre. The 694-nm R-line emission from Cr3+ impurity ions is most likely due to recombination of holes at Cr2+ during stimulated luminescence and as a result of an intracentre excitation of Cr3+ in photoluminescence (PL) due to photon absorption. The Cr3+ emission decreases in intensity, whereas the intensity of F-centre emission band is almost constant with repeated XERL measurements. Depending on the amount of X-ray irradiation dose, both holes and/or electrons may take place in the emission processes of peaks I (30-80°C), II (90-250°C) and III (250-320°C) during a TL readout, albeit, electron recombination is dominant regardless of dose. At higher doses, the XETL emission spectra indicate that the dominant band associated with TL peak III (250-320°C) in the material, shifts from F-centre to Cr3+. Using the deep-traps OSL, it has been confirmed that the main TL trap is also the main OSL trap whereas the TL traps lying in the temperature range of 400-550°C constitute the secondary OSL traps. There is evidence of strong retrapping at the main trap during optical stimulation of charges from the secondary OSL traps and the deep traps and that the retrapping occurs via the delocalized bands. At high-irradiation beta-doses, aggregate defect centres which significantly alter the TL and OSL properties, are induced in the material. The induced aggregate centres get completely obliterated by heating a sample to 700°C. The radiation-induced defects cause the main TL peak to shift towards higher temperatures, increase its FWHM, reduce its maximum intensity and cause an underestimation of both the activation energy and order of kinetics of the peak. On the other hand, the OSL response of the material is enhanced following a high-irradiation dose. During sample storage in the dark at ambient temperature, charges do migrate from the deep traps (donors) to the main and intermediate traps (acceptors) and that the major donor traps during this charge transfer phenomenon lie between 500-600°C.
- Full Text:
- Date Issued: 2018
- Authors: Nyirenda, Angel Newton
- Date: 2018
- Subjects: Luminescence , Thermoluminescence , Luminescence spectroscopy , Carbon-doped aluminium oxide , Radioluminescence , Time-resolved X-ray excited optical luminescence
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62683 , vital:28235
- Description: The main objective of this project was to gain a deeper and better understanding of the luminescence processes in a-Al₂O₃:C, a highly-sensitive dosimetric material, using a combined spectral and stimulated luminescence study. The spectral studies concentrated on the emission spectra obtained using X-ray induced radioluminescence (XERL), thermoluminescence (XETL) and time-resolved X-ray excited optical luminescence (TR-XEOL) techniques. The stimulated luminescence studies were based on thermoluminescence (TL), optically stimulated luminescence (OSL) and phototransferred TL (PTTL) methods that were used in the study of the radiation-induced defects at high beta-doses and the deep traps, that is, traps with thermal depths beyond 500°C. The spectral and stimulated luminescence measurements were carried out using a high sensitivity luminescence spectrometer and a Ris0 TL/OSL Model DA-20 Reader, respectively. The XERL emission spectrum measured at room temperature shows seven gaussian peaks associated with F-centres (420 nm), F+-centres (334 nm), F2+-centres (559 nm), Stoke’s vibronic band of Cr3+ (671 nm), Cr3+ R-line emission (694 nm), anti-Stokes vibronic band of Cr3+ (710 nm) and an unidentified emission band (260-300 nm) which we associate with hole recombinations at a luminescence centre. The 694-nm R-line emission from Cr3+ impurity ions is most likely due to recombination of holes at Cr2+ during stimulated luminescence and as a result of an intracentre excitation of Cr3+ in photoluminescence (PL) due to photon absorption. The Cr3+ emission decreases in intensity, whereas the intensity of F-centre emission band is almost constant with repeated XERL measurements. Depending on the amount of X-ray irradiation dose, both holes and/or electrons may take place in the emission processes of peaks I (30-80°C), II (90-250°C) and III (250-320°C) during a TL readout, albeit, electron recombination is dominant regardless of dose. At higher doses, the XETL emission spectra indicate that the dominant band associated with TL peak III (250-320°C) in the material, shifts from F-centre to Cr3+. Using the deep-traps OSL, it has been confirmed that the main TL trap is also the main OSL trap whereas the TL traps lying in the temperature range of 400-550°C constitute the secondary OSL traps. There is evidence of strong retrapping at the main trap during optical stimulation of charges from the secondary OSL traps and the deep traps and that the retrapping occurs via the delocalized bands. At high-irradiation beta-doses, aggregate defect centres which significantly alter the TL and OSL properties, are induced in the material. The induced aggregate centres get completely obliterated by heating a sample to 700°C. The radiation-induced defects cause the main TL peak to shift towards higher temperatures, increase its FWHM, reduce its maximum intensity and cause an underestimation of both the activation energy and order of kinetics of the peak. On the other hand, the OSL response of the material is enhanced following a high-irradiation dose. During sample storage in the dark at ambient temperature, charges do migrate from the deep traps (donors) to the main and intermediate traps (acceptors) and that the major donor traps during this charge transfer phenomenon lie between 500-600°C.
- Full Text:
- Date Issued: 2018
Decentralization and quality assurance in the Ugandan primary education sector
- Authors: Abu-Baker, Mutaaya Sirajee
- Date: 2018
- Subjects: Schools -- Decentralization -- Uganda , Education, Primary -- Uganda , Educational change -- Uganda
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/57390 , vital:26897
- Description: The study presented in this thesis is a case study analysis of decentralization and quality assurance in a decentralized set up of the Ugandan Primary Schooling. The research looked at how the monitoring and evaluation informed the policy formulation process to regulate quality assurance in a decentralized governance of primary education. The Study was positioned in the critical realist paradigm, interpretive in orientation and used both coding and thematic techniques to understand the teachers’, SMC members’, and officers’ (at district and ministry levels) experiences and perceptions of quality assurance in a decentralized set up. Data was gathered using interviews, document analysis and observation methods. The findings indicated that the study was affected by eleven themes: Management System and Leadership, Human Resource Management, Finance Administration and Management, Parenting and Nutrition, Politics, Motivation, Social Structures and Patterns, Legislative Process and Policies, Infrastructure Development and Management, Community Involvement in Education and Curriculum and Professionalism. The monitoring and evaluation system had a framework in which it operates, though there was no quality assurance policy to guide the provision of quality education. The study finally indicated that there are more threats in a decentralized set up that put Quality in danger. Secondly, there was absence of supervision/inspection in schools as there was no evidence to prove this due to absence of reports. However, document analysis indicated visits of officers to schools. Records management was a problem to schools. Decentralization was adopted at different levels by different countries to address specific problems identified in view of service delivery. Finally, though monitoring and evaluation results informed the policy and decision makers, there was no quality assurance policy to guide the provision of quality education in institutions.
- Full Text:
- Date Issued: 2018
- Authors: Abu-Baker, Mutaaya Sirajee
- Date: 2018
- Subjects: Schools -- Decentralization -- Uganda , Education, Primary -- Uganda , Educational change -- Uganda
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/57390 , vital:26897
- Description: The study presented in this thesis is a case study analysis of decentralization and quality assurance in a decentralized set up of the Ugandan Primary Schooling. The research looked at how the monitoring and evaluation informed the policy formulation process to regulate quality assurance in a decentralized governance of primary education. The Study was positioned in the critical realist paradigm, interpretive in orientation and used both coding and thematic techniques to understand the teachers’, SMC members’, and officers’ (at district and ministry levels) experiences and perceptions of quality assurance in a decentralized set up. Data was gathered using interviews, document analysis and observation methods. The findings indicated that the study was affected by eleven themes: Management System and Leadership, Human Resource Management, Finance Administration and Management, Parenting and Nutrition, Politics, Motivation, Social Structures and Patterns, Legislative Process and Policies, Infrastructure Development and Management, Community Involvement in Education and Curriculum and Professionalism. The monitoring and evaluation system had a framework in which it operates, though there was no quality assurance policy to guide the provision of quality education. The study finally indicated that there are more threats in a decentralized set up that put Quality in danger. Secondly, there was absence of supervision/inspection in schools as there was no evidence to prove this due to absence of reports. However, document analysis indicated visits of officers to schools. Records management was a problem to schools. Decentralization was adopted at different levels by different countries to address specific problems identified in view of service delivery. Finally, though monitoring and evaluation results informed the policy and decision makers, there was no quality assurance policy to guide the provision of quality education in institutions.
- Full Text:
- Date Issued: 2018
Development and validation of a health literacy measure for limited literacy public sector patients in South Africa
- Authors: Marimwe, Chipiwa
- Date: 2018
- Subjects: Health literacy -- South Africa , Patient education -- South Africa , Communication in medicine -- South Africa , Health literacy -- Social aspects -- South Africa , Poor -- Medical care -- South Africa , Analysis of variance , Multidimensional Screener of Functional Health Literacy (MSFHL)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62661 , vital:28227
- Description: The growing complexity of healthcare demands greater patient involvement and skills to navigate this complex system. It has therefore become increasingly important to identify individuals with inadequate health literacy, by using efficient, short and reliable measures for doing so. Most research on the development and validation of health literacy tests has been conducted in high-income countries, with very little reported from low-and middle-income countries (LMICs). Existing health literacy measures have come under scrutiny for their lack of cultural sensitivity, bias towards certain population groups and failure to acknowledge health literacy as a multidimensional concept. These measures usually have limited application in LMICs due to the significantly different structuring of healthcare systems, they overlook the extreme discrepancies in educational levels, and rely too heavily on the ability to read health information. No health literacy data for South Africa are available, and only a few health literacy-based research papers have been published in this country. The aim of the study was to develop and validate a health literacy measure that is contextually and culturally appropriate to measure health literacy in limited literacy public sector patients in South Africa. An Item Bank of 30 questions was developed with the input of a diverse expert consultant panel, and included skills-based and self-reported questions which ensured cultural, contextual and educational level appropriateness. The Information and Support for Health Actions Questionnaire (ISHA-Q) is a health literacy measure developed to assess health literacy for LMICs which includes 14 core scales. These were useful in ensuring coverage of a range of health literacy constructs within the Item Bank. The 30 questions were then allocated to one of three health literacy domains: Procedural knowledge, Factual knowledge and Access to healthcare, health services and social support. Ethical approval for the study was obtained. The questions were translated into isiXhosa and underwent pilot testing. Following pilot testing, 120 isiXhosa first-language speakers, at least 18 years old, who attended public sector facilities and had a maximum 12 years of education were recruited from a primary healthcare clinic in Grahamstown. An interpreter was trained and he participated in all interviews. A questionnaire was used to collect data on the 30-question Item Bank. The Multidimensional Screener of Functional Health Literacy (MSFHL) was used as the primary comparator.The second phase of the study involved the refinement of the 30 questions in the Item Bank, which involved a multi-stage process. Data were analysed statistically using t-test, correlations, chi-square and ANOVA tests at a 5% level of significance, in order to identify problematic questions. Item Response Theory was used to ascertain difficulty and discriminatory ability of the questions. Each question was further subjected to in-depth interrogation by a panel of healthcare professionals to ensure that questions were supported by the conceptual framework and the definitions of health literacy adopted for this study. The number of questions was reduced from 30 to 12, and formed the new Health Literacy Test - Limited Literacy (HELT-LL). To validate the HELT-LL, 210 patients with the same inclusion criteria as previously noted, were recruited from four primary healthcare clinics in the Eastern Cape Province. Individual interviews were conducted with the assistance of the interpreter to collect sociodemographic data as well as data from the HELT-LL, the primary comparator (MSFHL), and a secondary comparator which was a South African modified version of the Newest Vital Sign (NVS-SA). The HELT-LL was re-administered to 40 patients in a follow-up interview two weeks later. The HELT-LL categorised only 17.6% of the patients as having adequate health literacy, just over a third with inadequate health literacy, and the majority with marginal health literacy. Questions in the cognitively demanding Procedural knowledge domain were the most poorly answered, with a mean score of 48.6±24.9%. Patients had great difficulty performing the basic numeric tasks in this domain. The overall mean score for the HELT-LL was 52.8±18.4%, compared with the more cognitively demanding NVS-SA with a mean of 28.6±21.1%, and clearly illustrated the impact of the strategy to include in the HELT-LL a variety of questions with differing cognitive load. The MSFHL, which is based on demographic characteristics and perceived difficulties with reading and writing, had an overall mean score of 44.4±26.2%. Demographic characteristics including age, education and English literacy, were found to be good predictors of limited health literacy, with significant correlations being found between these variables and the mean HELT-LL score. An acceptable value for Cronbach’s alpha, excellent test-retest reliability and excellent concurrent validity show that the HELT-LL is a valid and reliable measure of health literacy in our target population. As there is a paucity of health literacy research emanating from developing countries, this study presents a significant contribution to literature. It is the first study to report the development and validation of a health literacy measure to address the dearth of available health literacy measures applicable for South Africa. If implemented for use in clinical settings and for research purposes, it could provide valuable South African health literacy data which could inform the development of interventions focusing on improving health literacy and health outcomes.
- Full Text:
- Date Issued: 2018
- Authors: Marimwe, Chipiwa
- Date: 2018
- Subjects: Health literacy -- South Africa , Patient education -- South Africa , Communication in medicine -- South Africa , Health literacy -- Social aspects -- South Africa , Poor -- Medical care -- South Africa , Analysis of variance , Multidimensional Screener of Functional Health Literacy (MSFHL)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62661 , vital:28227
- Description: The growing complexity of healthcare demands greater patient involvement and skills to navigate this complex system. It has therefore become increasingly important to identify individuals with inadequate health literacy, by using efficient, short and reliable measures for doing so. Most research on the development and validation of health literacy tests has been conducted in high-income countries, with very little reported from low-and middle-income countries (LMICs). Existing health literacy measures have come under scrutiny for their lack of cultural sensitivity, bias towards certain population groups and failure to acknowledge health literacy as a multidimensional concept. These measures usually have limited application in LMICs due to the significantly different structuring of healthcare systems, they overlook the extreme discrepancies in educational levels, and rely too heavily on the ability to read health information. No health literacy data for South Africa are available, and only a few health literacy-based research papers have been published in this country. The aim of the study was to develop and validate a health literacy measure that is contextually and culturally appropriate to measure health literacy in limited literacy public sector patients in South Africa. An Item Bank of 30 questions was developed with the input of a diverse expert consultant panel, and included skills-based and self-reported questions which ensured cultural, contextual and educational level appropriateness. The Information and Support for Health Actions Questionnaire (ISHA-Q) is a health literacy measure developed to assess health literacy for LMICs which includes 14 core scales. These were useful in ensuring coverage of a range of health literacy constructs within the Item Bank. The 30 questions were then allocated to one of three health literacy domains: Procedural knowledge, Factual knowledge and Access to healthcare, health services and social support. Ethical approval for the study was obtained. The questions were translated into isiXhosa and underwent pilot testing. Following pilot testing, 120 isiXhosa first-language speakers, at least 18 years old, who attended public sector facilities and had a maximum 12 years of education were recruited from a primary healthcare clinic in Grahamstown. An interpreter was trained and he participated in all interviews. A questionnaire was used to collect data on the 30-question Item Bank. The Multidimensional Screener of Functional Health Literacy (MSFHL) was used as the primary comparator.The second phase of the study involved the refinement of the 30 questions in the Item Bank, which involved a multi-stage process. Data were analysed statistically using t-test, correlations, chi-square and ANOVA tests at a 5% level of significance, in order to identify problematic questions. Item Response Theory was used to ascertain difficulty and discriminatory ability of the questions. Each question was further subjected to in-depth interrogation by a panel of healthcare professionals to ensure that questions were supported by the conceptual framework and the definitions of health literacy adopted for this study. The number of questions was reduced from 30 to 12, and formed the new Health Literacy Test - Limited Literacy (HELT-LL). To validate the HELT-LL, 210 patients with the same inclusion criteria as previously noted, were recruited from four primary healthcare clinics in the Eastern Cape Province. Individual interviews were conducted with the assistance of the interpreter to collect sociodemographic data as well as data from the HELT-LL, the primary comparator (MSFHL), and a secondary comparator which was a South African modified version of the Newest Vital Sign (NVS-SA). The HELT-LL was re-administered to 40 patients in a follow-up interview two weeks later. The HELT-LL categorised only 17.6% of the patients as having adequate health literacy, just over a third with inadequate health literacy, and the majority with marginal health literacy. Questions in the cognitively demanding Procedural knowledge domain were the most poorly answered, with a mean score of 48.6±24.9%. Patients had great difficulty performing the basic numeric tasks in this domain. The overall mean score for the HELT-LL was 52.8±18.4%, compared with the more cognitively demanding NVS-SA with a mean of 28.6±21.1%, and clearly illustrated the impact of the strategy to include in the HELT-LL a variety of questions with differing cognitive load. The MSFHL, which is based on demographic characteristics and perceived difficulties with reading and writing, had an overall mean score of 44.4±26.2%. Demographic characteristics including age, education and English literacy, were found to be good predictors of limited health literacy, with significant correlations being found between these variables and the mean HELT-LL score. An acceptable value for Cronbach’s alpha, excellent test-retest reliability and excellent concurrent validity show that the HELT-LL is a valid and reliable measure of health literacy in our target population. As there is a paucity of health literacy research emanating from developing countries, this study presents a significant contribution to literature. It is the first study to report the development and validation of a health literacy measure to address the dearth of available health literacy measures applicable for South Africa. If implemented for use in clinical settings and for research purposes, it could provide valuable South African health literacy data which could inform the development of interventions focusing on improving health literacy and health outcomes.
- Full Text:
- Date Issued: 2018
Elevated CO2 determines cell damage and nitrogen allocation in barley subjected to aphid herbivory
- Authors: Gallagher, Sean
- Date: 2018
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64337 , vital:28535
- Description: Expected release date-May 2019
- Full Text:
- Date Issued: 2018
- Authors: Gallagher, Sean
- Date: 2018
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64337 , vital:28535
- Description: Expected release date-May 2019
- Full Text:
- Date Issued: 2018
Energy use patterns and trends: the impact of energy policy in South African low-income households
- Israel-Akinbo, Sylvia Olawumi
- Authors: Israel-Akinbo, Sylvia Olawumi
- Date: 2018
- Subjects: Energy policy -- Social aspects -- South Africa , Energy security -- South Africa , Households -- Economic aspects -- South Africa , Poor -- Energy assistance -- South Africa , Poor -- South Africa , University of Cape Town. National Income Dynamics Study , Free Basic Electricity Policy (South Africa) , Income and Expenditure Survey (South Africa)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62264 , vital:28148
- Description: Energy poverty is a growing concern especially amongst low-income populations in developing countries. The transition to modern energy carriers is associated with welfare improvement and it is considered as an important developmental goal to achieve, in order to eradicate energy poverty. As such, the South African government has made energy poverty an issue of policy focus. Literature abounds with different measures of energy poverty; energy programmes and policies are also aimed at improving the welfare of the low-income households in terms of basic services such as electricity. As a point of entry into this study, this thesis explored energy use patterns and trends in low-income South African households. The research objectives addressed in the study included investigating the extent of energy poverty through a multidimensional energy poverty index, examining the extent to which the 'energy ladder' and 'energy stacking' models explains energy transition patterns and to examining whether the Free Basic Electricity Policy has impacted on energy choices and energy poverty. In order to contribute to energy poverty and energy policy discussion in South Africa, this study has investigated the dimensions of energy poverty amongst low-income South African households from these three different perspectives (objectives). A positivist approach, by using a quantitative method was used to underpin the study. The study utilised secondary data, which were from the National Income Dynamics Survey and Income and Expenditure Survey. The former was used for the analysis of the multidimensional energy poverty index and energy transition patterns whilst the latter was used for the analysis of the impact of the Free Basic Electricity Policy. The four waves of the National Income Dynamics Survey, with 2008 as the base year and the 2010/2011 version of the Income and Expenditure Survey were used whilst the data were processed through the quantitative software package, STATA version 12. The data were then analysed using the multidimensional energy poverty framework by Nussbaumer et al. (2011) and econometric models, which best fit the objectives. The result of the panel analysis, which assesses the multidimensional energy poverty for low-income households in South Africa showed that low-income households in both urban and rural areas are in a moderate state of energy poverty but different levels. However, the cross-sectional analysis revealed that the percentage of low-income households that are energy poor is reducing for the rural households but increasing for their urban counterparts from 2008 to 2014. The panel and cross-sectional results of the contribution of the energy dimensions in multidimensional energy poverty shows that the low-income households are especially energy poor in terms of heating fuel. The findings from the econometric estimates partly confirmed an energy ladder behaviour for the energy choice for cooking. An energy stacking behaviour was confirmed for the low- income households for these energy services - heating and lighting. Moreover, it was found that with respect to cooking and heating, low-income households living in a modern dwelling, having a small household size and residing in an urban area are less likely to use transitional or traditional energy carriers but most likely to use modern energy carriers. In addition, low-income households are more likely to use modern energy carriers for their cooking and heating in 2010, 2012 and 2014 than in 2008. For lighting energy service, low- income households living in a modern dwelling in an urban settlement are most likely to use modern energy carriers for lighting and less likely to use transitional energy carriers or candles. Only in 2014 were low-income households more likely to use modern energy carriers for lighting than in 2008. The results further showed that modern energy carriers have the highest probability of being preferred for lighting followed by cooking and lastly heating. Also emerging from the findings are that more urban low-income households are receiving the Free Basic Electricity (FBE) grant than their counterparts in the rural areas. The probability of low-income households owning entertainment/education appliance and food preserving appliance is positively influenced by access to Free Basic Electricity. The low- income households living in an urban settlement and in a modern type of dwelling supported this result. However, household size does not seems to support this result should it grow larger.
- Full Text:
- Date Issued: 2018
- Authors: Israel-Akinbo, Sylvia Olawumi
- Date: 2018
- Subjects: Energy policy -- Social aspects -- South Africa , Energy security -- South Africa , Households -- Economic aspects -- South Africa , Poor -- Energy assistance -- South Africa , Poor -- South Africa , University of Cape Town. National Income Dynamics Study , Free Basic Electricity Policy (South Africa) , Income and Expenditure Survey (South Africa)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/62264 , vital:28148
- Description: Energy poverty is a growing concern especially amongst low-income populations in developing countries. The transition to modern energy carriers is associated with welfare improvement and it is considered as an important developmental goal to achieve, in order to eradicate energy poverty. As such, the South African government has made energy poverty an issue of policy focus. Literature abounds with different measures of energy poverty; energy programmes and policies are also aimed at improving the welfare of the low-income households in terms of basic services such as electricity. As a point of entry into this study, this thesis explored energy use patterns and trends in low-income South African households. The research objectives addressed in the study included investigating the extent of energy poverty through a multidimensional energy poverty index, examining the extent to which the 'energy ladder' and 'energy stacking' models explains energy transition patterns and to examining whether the Free Basic Electricity Policy has impacted on energy choices and energy poverty. In order to contribute to energy poverty and energy policy discussion in South Africa, this study has investigated the dimensions of energy poverty amongst low-income South African households from these three different perspectives (objectives). A positivist approach, by using a quantitative method was used to underpin the study. The study utilised secondary data, which were from the National Income Dynamics Survey and Income and Expenditure Survey. The former was used for the analysis of the multidimensional energy poverty index and energy transition patterns whilst the latter was used for the analysis of the impact of the Free Basic Electricity Policy. The four waves of the National Income Dynamics Survey, with 2008 as the base year and the 2010/2011 version of the Income and Expenditure Survey were used whilst the data were processed through the quantitative software package, STATA version 12. The data were then analysed using the multidimensional energy poverty framework by Nussbaumer et al. (2011) and econometric models, which best fit the objectives. The result of the panel analysis, which assesses the multidimensional energy poverty for low-income households in South Africa showed that low-income households in both urban and rural areas are in a moderate state of energy poverty but different levels. However, the cross-sectional analysis revealed that the percentage of low-income households that are energy poor is reducing for the rural households but increasing for their urban counterparts from 2008 to 2014. The panel and cross-sectional results of the contribution of the energy dimensions in multidimensional energy poverty shows that the low-income households are especially energy poor in terms of heating fuel. The findings from the econometric estimates partly confirmed an energy ladder behaviour for the energy choice for cooking. An energy stacking behaviour was confirmed for the low- income households for these energy services - heating and lighting. Moreover, it was found that with respect to cooking and heating, low-income households living in a modern dwelling, having a small household size and residing in an urban area are less likely to use transitional or traditional energy carriers but most likely to use modern energy carriers. In addition, low-income households are more likely to use modern energy carriers for their cooking and heating in 2010, 2012 and 2014 than in 2008. For lighting energy service, low- income households living in a modern dwelling in an urban settlement are most likely to use modern energy carriers for lighting and less likely to use transitional energy carriers or candles. Only in 2014 were low-income households more likely to use modern energy carriers for lighting than in 2008. The results further showed that modern energy carriers have the highest probability of being preferred for lighting followed by cooking and lastly heating. Also emerging from the findings are that more urban low-income households are receiving the Free Basic Electricity (FBE) grant than their counterparts in the rural areas. The probability of low-income households owning entertainment/education appliance and food preserving appliance is positively influenced by access to Free Basic Electricity. The low- income households living in an urban settlement and in a modern type of dwelling supported this result. However, household size does not seems to support this result should it grow larger.
- Full Text:
- Date Issued: 2018