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:
- 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:
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:
- 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:
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:
- 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:
Assessment of pharmaceutical equivalence of topical cream products containing hydrocortisone acetate using in vitro release testing (IVRT)
- Mudyahoto, Nyengeterai Amanda
- Authors: Mudyahoto, Nyengeterai Amanda
- Date: 2018
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63384 , vital:28404
- Description: Expected release date-April 2020
- Full Text:
- Authors: Mudyahoto, Nyengeterai Amanda
- Date: 2018
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63384 , vital:28404
- Description: Expected release date-April 2020
- Full Text:
Assessment of pheromone specificity in Thaumatotibia leucotreta (Meyrick) populations with focus on pest monitoring and the regional rollout of the sterile insect technique in citrus
- Authors: Joubert, Francois D
- Date: 2018
- Subjects: Cryptophlebia leucotreta , Pheromone traps , Citrus -- Diseases and pests -- South Africa , Cryptophlebia leucotreta -- Contol , Cryptophlebia leucotreta -- Biological control
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/60665 , vital:27812
- Description: False codling moth (FCM), Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) is considered the most important indigenous pest of citrus in southern Africa. It is recognized by several markets as a phytosanitary organism and the efficient control of this pest is now more important than ever. The pheromone communication between the male and female moths has been exploited in order to control FCM through the sterile insect technique (SIT). The sterilized males used for all SIT programmes across South Africa come from a colony that originates from wild material collected from the Citrusdal area of the Western Cape Province. The aim of this study was to determine if any differences in attractiveness of females to males exist between different geographical populations of FCM and if so what impact this would have on the male’s ability to locate females from other populations via the volatile sex pheromone released by the female. Laboratory trials with Y-tube olfactometers and flight tunnels tested the attraction of male moths to virgin females, but did not yield any consistent results. Field experiments were conducted with sterile male Citrusdal moths released and recaptured in yellow delta traps in two separate trials. For one trial, the traps were baited with live virgin females from five different geographical populations including Addo, Nelspruit, Marble Hall, Citrusdal and the Old colony, which is a mixture of several populations. For the other trial traps were baited with various synthetic pheromone blends including three regional blends which included South Africa, Ivory Coast and Malawi and three commercial blends including Pherolure, Isomate and Checkmate. For the virgin female trial the Citrusdal males showed a significant preference for females from their own population. There was also a significant difference in the recaptures from the different synthetic pheromones. The South African blend was the most attractive of all the regional and commercial blends. A cross-mating trial was also conducted under laboratory conditions in petri dishes with five different FCM populations including Citrusdal, Addo, Marble Hall, Nelspruit and Old (mixed origin). Females produced more eggs when mated with males from the same population for the Addo, Marble Hall, Nelspruit and Old (mixed origin) populations. The only case in which this was statistically significant was for the Marble Hall population. All the crosses produced viable eggs and the origin of the male or female did not influence egg hatch. The results from this study may lead to improvements in both the control and monitoring of FCM populations. The control methods include mating disruption, attract-and-kill and SIT. Tailoring these methods for a specific growing area with a pheromone blend originating from the area or releasing sterile moths from a colony that originates from the area may optimize the available monitoring and control options.
- Full Text:
- Authors: Joubert, Francois D
- Date: 2018
- Subjects: Cryptophlebia leucotreta , Pheromone traps , Citrus -- Diseases and pests -- South Africa , Cryptophlebia leucotreta -- Contol , Cryptophlebia leucotreta -- Biological control
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/60665 , vital:27812
- Description: False codling moth (FCM), Thaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) is considered the most important indigenous pest of citrus in southern Africa. It is recognized by several markets as a phytosanitary organism and the efficient control of this pest is now more important than ever. The pheromone communication between the male and female moths has been exploited in order to control FCM through the sterile insect technique (SIT). The sterilized males used for all SIT programmes across South Africa come from a colony that originates from wild material collected from the Citrusdal area of the Western Cape Province. The aim of this study was to determine if any differences in attractiveness of females to males exist between different geographical populations of FCM and if so what impact this would have on the male’s ability to locate females from other populations via the volatile sex pheromone released by the female. Laboratory trials with Y-tube olfactometers and flight tunnels tested the attraction of male moths to virgin females, but did not yield any consistent results. Field experiments were conducted with sterile male Citrusdal moths released and recaptured in yellow delta traps in two separate trials. For one trial, the traps were baited with live virgin females from five different geographical populations including Addo, Nelspruit, Marble Hall, Citrusdal and the Old colony, which is a mixture of several populations. For the other trial traps were baited with various synthetic pheromone blends including three regional blends which included South Africa, Ivory Coast and Malawi and three commercial blends including Pherolure, Isomate and Checkmate. For the virgin female trial the Citrusdal males showed a significant preference for females from their own population. There was also a significant difference in the recaptures from the different synthetic pheromones. The South African blend was the most attractive of all the regional and commercial blends. A cross-mating trial was also conducted under laboratory conditions in petri dishes with five different FCM populations including Citrusdal, Addo, Marble Hall, Nelspruit and Old (mixed origin). Females produced more eggs when mated with males from the same population for the Addo, Marble Hall, Nelspruit and Old (mixed origin) populations. The only case in which this was statistically significant was for the Marble Hall population. All the crosses produced viable eggs and the origin of the male or female did not influence egg hatch. The results from this study may lead to improvements in both the control and monitoring of FCM populations. The control methods include mating disruption, attract-and-kill and SIT. Tailoring these methods for a specific growing area with a pheromone blend originating from the area or releasing sterile moths from a colony that originates from the area may optimize the available monitoring and control options.
- Full Text:
Assessment of the long-term response to rehabilitation of two wetlands in KwaZulu-Natal, South Africa
- Authors: Cowden, Craig
- Date: 2018
- Subjects: Wetlands -- South Africa -- KwaZulu-Natal Wetland restoration -- South Africa -- KwaZulu-Natal Wetland management -- South Africa -- KwaZulu-Natal Wetland conservation -- South Africa -- KwaZulu-Natal Wetland ecology -- South Africa -- KwaZulu-Natal Ecosystem management -- South Africa -- KwaZulu-Natal
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/60606 , vital:27802
- Description: Assessing the outputs and outcomes of wetland rehabilitation activities is recognised by the 'Working for Wetlands' programme in South Africa as important, but to date has been limited. An assessment of the ecological outcomes and the structural outputs of the Working for Wetlands rehabilitation implemented in the Killarney and Kruisfontein wetlands, KwaZulu-Natal, in 2005 was undertaken. The assessment of outcomes included an evaluation of the changes in terms of ecological integrity and the supply of ecosystem services, using WET-Health and WET- EcoServices assessment techniques respectively, and vegetation composition. Improvements in hydrological and geomorphic integrity were recorded in both wetlands, resulting in improved ecosystem services delivery. However, investigation of vegetation composition using the Wetland Index Value and Floristic Quality Assessment Index showed that, seven years after rehabilitation, KiNamey's vegetation composition had improved, but Kruisfontein's vegetation was still largely dominated by pioneer species and appeared to be stable, but in a severely transformed state. The response of these wetlands has shown that sites for rehabilitation should be screened before work begins, and wetlands requiring intensive management of vegetation recovery should be assessed in terms of the objectives and the anticipated benefits of the project. The assessment of the outputs included an evaluation of structural integrity, survival and cost- effectiveness. Limited issues, mostly relating to deviations from the designs during construction, were identified with regards to the structural outputs at each of the wetlands. However, the spreader canals at both Killarney and Kruisfontein wetlands were not functioning as intended and concentrated flows from the spreader canals were evident in both wetlands. The use of spreader canals should therefore be carefully planned and implemented for future wetland rehabilitation projects. Consideration of ZAR per hectare equivalent re-instated/secured provided a useful initial means of determining the cost-effectiveness of the wetland rehabilitation. However, additional factors need to be considered, such as, the nature of the rehabilitation activities, the type and size of the problem being addressed, rehabilitation of priority wetlands, limitations imposed by funders, and risks that need to be addressed by the rehabilitation strategy. Furthermore, the evaluation of the Killarney and Kruisfontein wetlands highlighted the need to revise the Water Research Commission's Wetland Management Series, especially those documents or guidelines relating to rehabilitation planning (WET-RehabPlan), interventions (WET-RehabMethods), and monitoring and evaluation (WET-RehabEvaluate).
- Full Text:
- Authors: Cowden, Craig
- Date: 2018
- Subjects: Wetlands -- South Africa -- KwaZulu-Natal Wetland restoration -- South Africa -- KwaZulu-Natal Wetland management -- South Africa -- KwaZulu-Natal Wetland conservation -- South Africa -- KwaZulu-Natal Wetland ecology -- South Africa -- KwaZulu-Natal Ecosystem management -- South Africa -- KwaZulu-Natal
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/60606 , vital:27802
- Description: Assessing the outputs and outcomes of wetland rehabilitation activities is recognised by the 'Working for Wetlands' programme in South Africa as important, but to date has been limited. An assessment of the ecological outcomes and the structural outputs of the Working for Wetlands rehabilitation implemented in the Killarney and Kruisfontein wetlands, KwaZulu-Natal, in 2005 was undertaken. The assessment of outcomes included an evaluation of the changes in terms of ecological integrity and the supply of ecosystem services, using WET-Health and WET- EcoServices assessment techniques respectively, and vegetation composition. Improvements in hydrological and geomorphic integrity were recorded in both wetlands, resulting in improved ecosystem services delivery. However, investigation of vegetation composition using the Wetland Index Value and Floristic Quality Assessment Index showed that, seven years after rehabilitation, KiNamey's vegetation composition had improved, but Kruisfontein's vegetation was still largely dominated by pioneer species and appeared to be stable, but in a severely transformed state. The response of these wetlands has shown that sites for rehabilitation should be screened before work begins, and wetlands requiring intensive management of vegetation recovery should be assessed in terms of the objectives and the anticipated benefits of the project. The assessment of the outputs included an evaluation of structural integrity, survival and cost- effectiveness. Limited issues, mostly relating to deviations from the designs during construction, were identified with regards to the structural outputs at each of the wetlands. However, the spreader canals at both Killarney and Kruisfontein wetlands were not functioning as intended and concentrated flows from the spreader canals were evident in both wetlands. The use of spreader canals should therefore be carefully planned and implemented for future wetland rehabilitation projects. Consideration of ZAR per hectare equivalent re-instated/secured provided a useful initial means of determining the cost-effectiveness of the wetland rehabilitation. However, additional factors need to be considered, such as, the nature of the rehabilitation activities, the type and size of the problem being addressed, rehabilitation of priority wetlands, limitations imposed by funders, and risks that need to be addressed by the rehabilitation strategy. Furthermore, the evaluation of the Killarney and Kruisfontein wetlands highlighted the need to revise the Water Research Commission's Wetland Management Series, especially those documents or guidelines relating to rehabilitation planning (WET-RehabPlan), interventions (WET-RehabMethods), and monitoring and evaluation (WET-RehabEvaluate).
- Full Text:
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:
- 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:
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:
- 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:
Barriers and drivers to the implementation of renewable energy technologies in South Africa’s aquaculture industry
- Authors: Van Wyk, Nicholas Kelly
- Date: 2018
- Subjects: Renewable energy sources South Africa , Aquaculture Environmental aspects South Africa , Sustainable aquaculture Economic aspects South Africa , Renewable energy sources Economic aspects South Africa , Renewable energy sources Environmental aspects South Africa
- Language: English
- Type: text , Thesis , Masters , MBA
- Identifier: http://hdl.handle.net/10962/61969 , vital:28090
- Description: South Africa is plagued by socio-economic issues of poverty, inequality and high rates of unemployment. The government of South Africa has as such launched an ambitious plan known as operation PHAKISA which will complement the National Development Plan in addressing the countries aforementioned shortcomings. In the operations first phase, the focus is on growing South Africa’s ocean economy. Within the ocean economy, the growth of aquaculture has been identified as an industry with the potential to create jobs and aid in economic growth of South Africa. Aquaculture, the farming of any aquatic organisms, has been the fastest growing food production sector for the past 50 years. While natural capture fisheries have stagnated in production capacity, aquaculture has grown exponentially in order to feed a global population which is fast approaching nine billion people. However, South Africa’s aquaculture production lags significantly behind other third world countries. The sustainability of aquaculture has frequently been called into question due to the possibility of various detrimental environmental effects it may cause. To further complicate the matter, Climate Change is today an overarching threat to life as we know it, and must be taken into account if we plan to keep growing our populations and economies. As such, if South Africa wants to grow its aquaculture sector, it must be done so in a sustainable manner. This research thus sought to investigate one aspect which may increase the sustainability of aquaculture in South Africa, that being the implementation of renewable energy in the sector. Renewable energy has been identified by the United Nations Intergovernmental Panel on Climate Change as key to mitigating the effects of climate change. In order to aid Renewable Energy (RE) implementation in South Africa’s aquaculture sector, this research aimed to identify the barriers and the drivers to implementing renewable energy within aquaculture. To do this, a literature review was conducted to identify possible barriers and drivers to renewable energy implementation. These were then drafted into an online questionnaire and sent via Email to all the aquaculture organisations in South Africa that could be contacted (n = 195). Respondents were asked to rank the proposed barriers and drivers to renewable energy according to their perceived importance on a Likert Scale. A total of 18 responses could be analysed with descriptive statistics. Further, three structured interviews were conducted with members of South African aquaculture organisations who had implemented some form of Renewable Energy Technology (RET). These interviews provided in-depth insights into the importance of the various proposed barriers and drivers. The results revealed the most important barriers to RE implementation were: High Initial investments, Utility monopoly of production, Lack of RE experts on a governmental level, Lack of incentives/subsidies from government, Lack of legal framework for Independent Power Producers and Power Purchase Agreements, and Diseconomy of scale respectively. The most important drivers to RE implementation were ranked as: Long term cost benefits, Reduction in cost of RETs, Innovation / advancement of RETS, Incentives or subsidies to implement renewable energy, Adequate legal framework and legislation for Power Purchase Agreement and Preference for environmentally-friendly electricity generation. Importantly, it was found that barriers and drivers are dependent on the type of RE being implemented. A Photo Voltaic (Solar Power) system will not necessarily experience the same barriers or drivers that a Wave Energy Converter system would. In order to drive investment in RE and remove the barriers that may be preventing its implementation in aquaculture, policy will have to be adapted. Particularly in terms of legislation around Power Purchase Agreements. Further, by providing subsidies for RE implementation, it is possible to sustainably grow South Africa’s aquaculture industry.
- Full Text:
- Authors: Van Wyk, Nicholas Kelly
- Date: 2018
- Subjects: Renewable energy sources South Africa , Aquaculture Environmental aspects South Africa , Sustainable aquaculture Economic aspects South Africa , Renewable energy sources Economic aspects South Africa , Renewable energy sources Environmental aspects South Africa
- Language: English
- Type: text , Thesis , Masters , MBA
- Identifier: http://hdl.handle.net/10962/61969 , vital:28090
- Description: South Africa is plagued by socio-economic issues of poverty, inequality and high rates of unemployment. The government of South Africa has as such launched an ambitious plan known as operation PHAKISA which will complement the National Development Plan in addressing the countries aforementioned shortcomings. In the operations first phase, the focus is on growing South Africa’s ocean economy. Within the ocean economy, the growth of aquaculture has been identified as an industry with the potential to create jobs and aid in economic growth of South Africa. Aquaculture, the farming of any aquatic organisms, has been the fastest growing food production sector for the past 50 years. While natural capture fisheries have stagnated in production capacity, aquaculture has grown exponentially in order to feed a global population which is fast approaching nine billion people. However, South Africa’s aquaculture production lags significantly behind other third world countries. The sustainability of aquaculture has frequently been called into question due to the possibility of various detrimental environmental effects it may cause. To further complicate the matter, Climate Change is today an overarching threat to life as we know it, and must be taken into account if we plan to keep growing our populations and economies. As such, if South Africa wants to grow its aquaculture sector, it must be done so in a sustainable manner. This research thus sought to investigate one aspect which may increase the sustainability of aquaculture in South Africa, that being the implementation of renewable energy in the sector. Renewable energy has been identified by the United Nations Intergovernmental Panel on Climate Change as key to mitigating the effects of climate change. In order to aid Renewable Energy (RE) implementation in South Africa’s aquaculture sector, this research aimed to identify the barriers and the drivers to implementing renewable energy within aquaculture. To do this, a literature review was conducted to identify possible barriers and drivers to renewable energy implementation. These were then drafted into an online questionnaire and sent via Email to all the aquaculture organisations in South Africa that could be contacted (n = 195). Respondents were asked to rank the proposed barriers and drivers to renewable energy according to their perceived importance on a Likert Scale. A total of 18 responses could be analysed with descriptive statistics. Further, three structured interviews were conducted with members of South African aquaculture organisations who had implemented some form of Renewable Energy Technology (RET). These interviews provided in-depth insights into the importance of the various proposed barriers and drivers. The results revealed the most important barriers to RE implementation were: High Initial investments, Utility monopoly of production, Lack of RE experts on a governmental level, Lack of incentives/subsidies from government, Lack of legal framework for Independent Power Producers and Power Purchase Agreements, and Diseconomy of scale respectively. The most important drivers to RE implementation were ranked as: Long term cost benefits, Reduction in cost of RETs, Innovation / advancement of RETS, Incentives or subsidies to implement renewable energy, Adequate legal framework and legislation for Power Purchase Agreement and Preference for environmentally-friendly electricity generation. Importantly, it was found that barriers and drivers are dependent on the type of RE being implemented. A Photo Voltaic (Solar Power) system will not necessarily experience the same barriers or drivers that a Wave Energy Converter system would. In order to drive investment in RE and remove the barriers that may be preventing its implementation in aquaculture, policy will have to be adapted. Particularly in terms of legislation around Power Purchase Agreements. Further, by providing subsidies for RE implementation, it is possible to sustainably grow South Africa’s aquaculture industry.
- Full Text:
Bayesian hierarchical modelling with application in spatial epidemiology
- Authors: Southey, Richard Robert
- Date: 2018
- Subjects: Bayesian statistical decision theory , Spatial analysis (Statistics) , Medical mapping , Pericarditis , Mortality Statistics
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/59489 , vital:27617
- Description: Disease mapping and spatial statistics have become an important part of modern day statistics and have increased in popularity as the methods and techniques have evolved. The application of disease mapping is not only confined to the analysis of diseases as other applications of disease mapping can be found in Econometric and financial disciplines. This thesis will consider two data sets. These are the Georgia oral cancer 2004 data set and the South African acute pericarditis 2014 data set. The Georgia data set will be used to assess the hyperprior sensitivity of the precision for the uncorrelated heterogeneity and correlated heterogeneity components in a convolution model. The correlated heterogeneity will be modelled by a conditional autoregressive prior distribution and the uncorrelated heterogeneity will be modelled with a zero mean Gaussian prior distribution. The sensitivity analysis will be performed using three models with conjugate, Jeffreys' and a fixed parameter prior for the hyperprior distribution of the precision for the uncorrelated heterogeneity component. A simulation study will be done to compare four prior distributions which will be the conjugate, Jeffreys', probability matching and divergence priors. The three models will be fitted in WinBUGS® using a Bayesian approach. The results of the three models will be in the form of disease maps, figures and tables. The results show that the hyperprior of the precision for the uncorrelated heterogeneity and correlated heterogeneity components are sensitive to changes and will result in different results depending on the specification of the hyperprior distribution of the precision for the two components in the model. The South African data set will be used to examine whether there is a difference between the proper conditional autoregressive prior and intrinsic conditional autoregressive prior for the correlated heterogeneity component in a convolution model. Two models will be fitted in WinBUGS® for this comparison. Both the hyperpriors of the precision for the uncorrelated heterogeneity and correlated heterogeneity components will be modelled using a Jeffreys' prior distribution. The results show that there is no significant difference between the results of the model with a proper conditional autoregressive prior and intrinsic conditional autoregressive prior for the South African data, although there are a few disadvantages of using a proper conditional autoregressive prior for the correlated heterogeneity which will be stated in the conclusion.
- Full Text:
- Authors: Southey, Richard Robert
- Date: 2018
- Subjects: Bayesian statistical decision theory , Spatial analysis (Statistics) , Medical mapping , Pericarditis , Mortality Statistics
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/59489 , vital:27617
- Description: Disease mapping and spatial statistics have become an important part of modern day statistics and have increased in popularity as the methods and techniques have evolved. The application of disease mapping is not only confined to the analysis of diseases as other applications of disease mapping can be found in Econometric and financial disciplines. This thesis will consider two data sets. These are the Georgia oral cancer 2004 data set and the South African acute pericarditis 2014 data set. The Georgia data set will be used to assess the hyperprior sensitivity of the precision for the uncorrelated heterogeneity and correlated heterogeneity components in a convolution model. The correlated heterogeneity will be modelled by a conditional autoregressive prior distribution and the uncorrelated heterogeneity will be modelled with a zero mean Gaussian prior distribution. The sensitivity analysis will be performed using three models with conjugate, Jeffreys' and a fixed parameter prior for the hyperprior distribution of the precision for the uncorrelated heterogeneity component. A simulation study will be done to compare four prior distributions which will be the conjugate, Jeffreys', probability matching and divergence priors. The three models will be fitted in WinBUGS® using a Bayesian approach. The results of the three models will be in the form of disease maps, figures and tables. The results show that the hyperprior of the precision for the uncorrelated heterogeneity and correlated heterogeneity components are sensitive to changes and will result in different results depending on the specification of the hyperprior distribution of the precision for the two components in the model. The South African data set will be used to examine whether there is a difference between the proper conditional autoregressive prior and intrinsic conditional autoregressive prior for the correlated heterogeneity component in a convolution model. Two models will be fitted in WinBUGS® for this comparison. Both the hyperpriors of the precision for the uncorrelated heterogeneity and correlated heterogeneity components will be modelled using a Jeffreys' prior distribution. The results show that there is no significant difference between the results of the model with a proper conditional autoregressive prior and intrinsic conditional autoregressive prior for the South African data, although there are a few disadvantages of using a proper conditional autoregressive prior for the correlated heterogeneity which will be stated in the conclusion.
- Full Text:
Beasts we love
- Authors: Masolane, Tseliso Chrisjan
- Date: 2018
- Subjects: Creative writing (Higher education) -- South Africa , South African fiction (English) -- 21st century , Detective and mystery stories, South African (English) -- 21st century
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/63098 , vital:28363
- Description: My thesis is a novella in flash, written as political crime fiction. It is set in contemporary South Africa and tells the story of Rafau Lekopo, a teacher from a little township called Dikgohlong, whose life is changed forever after he finds his wife and the mayor in bed and shoots them both dead. The information contained within the dead mayor's notebook proves to be explosive, showing that the mayor is far more than he seems, and that he is in fact in the employ of a foreign intelligence service. After his release from prison, the embittered Lekopo sets about his revenge against powerful men who abuse their political power. He takes refuge in Lesotho, masterminds a series of heists, car-hijackings and human trafficking, and expands his syndication back in South Africa. Using the contacts and information from the mayor's notebook, he manipulates the Lesotho government into a diplomatic feud with South Africa which treatens to escalate into a military conflict.
- Full Text:
- Authors: Masolane, Tseliso Chrisjan
- Date: 2018
- Subjects: Creative writing (Higher education) -- South Africa , South African fiction (English) -- 21st century , Detective and mystery stories, South African (English) -- 21st century
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/63098 , vital:28363
- Description: My thesis is a novella in flash, written as political crime fiction. It is set in contemporary South Africa and tells the story of Rafau Lekopo, a teacher from a little township called Dikgohlong, whose life is changed forever after he finds his wife and the mayor in bed and shoots them both dead. The information contained within the dead mayor's notebook proves to be explosive, showing that the mayor is far more than he seems, and that he is in fact in the employ of a foreign intelligence service. After his release from prison, the embittered Lekopo sets about his revenge against powerful men who abuse their political power. He takes refuge in Lesotho, masterminds a series of heists, car-hijackings and human trafficking, and expands his syndication back in South Africa. Using the contacts and information from the mayor's notebook, he manipulates the Lesotho government into a diplomatic feud with South Africa which treatens to escalate into a military conflict.
- Full Text:
Beginner teachers’ leadership development opportunities: an interventionist case study in a rural combined school in the Ohangwena region, Namibia
- Authors: Ndakolonkoshi, Klaudia
- Date: 2018
- Subjects: School management and organization -- Namibia , Teacher participation in administration -- Namibia , Educational leadership -- Namibia , Teacher effectiveness -- Namibia
- Language: English
- Type: text , Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10962/61603 , vital:28041
- Description: The emergence of distributed leadership theory encourages multiple involvement of individuals in leadership of the school, regardless of their leadership positions (Spillane, 2006). The manifestation of teacher leadership through distributed leadership theory grants opportunities to teachers to enact leadership roles. This study explored how the notion of teacher leadership is understood, the leadership roles existing for the beginner teachers, and the constraining and enabling factors to the practice of teacher leadership in a rural combined school in Ohangwena region, in Namibia. The study is a formative intervention adopting a case study approach located in a critical paradigm since it aimed to bring changes in the activity system of the beginner teachers. The data were collected from ten participants: four beginner teachers, four experienced teachers, the principal and the Head of Department. The data were generated using the following techniques: document analysis, interview, questionnaires, observation and Change Laboratory workshops. The data were analysed thematically using second generation of Cultural Historical Activity Theory (CHAT) and Grant’s (2006, 2008, 2010) Teacher Leadership Model. The findings revealed that there were different understandings of the concept of teacher leadership. It was viewed as participation, influence, motivation and mentoring. It was also revealed that beginner teachers practiced leadership roles across the four zones of Grant’s (2006, 2008, 2010) Teacher Leadership Model, but to various extents. A high participation was noted in zone one within the classroom and zone two in curricular and extra-curricular activities and minimal participation was reported in zone three within the whole school development and zone four beyond the school into the community. Teacher leadership in the case study school was constrained by several factors, including teachers’ reluctance to lead, cultural beliefs, top-down leadership structure and lack of experience. Due to the minimal participation of beginner teachers in zone three and four, the findings suggested that the school should foster a collaborative culture, establish induction and mentoring committees in the school and encourage beginner teachers to take up leadership roles by providing opportunities for them to lead through delegation. In a series of Change Laboratory workshops (CLW) the principal and the Head of Department took up the responsibility of providing leadership training to the teachers to enable them to assume leadership roles in the school. In addition, participants agreed to establish induction and mentoring committees in the school to provide guidance and assistance to teacher leaders.
- Full Text:
- Authors: Ndakolonkoshi, Klaudia
- Date: 2018
- Subjects: School management and organization -- Namibia , Teacher participation in administration -- Namibia , Educational leadership -- Namibia , Teacher effectiveness -- Namibia
- Language: English
- Type: text , Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10962/61603 , vital:28041
- Description: The emergence of distributed leadership theory encourages multiple involvement of individuals in leadership of the school, regardless of their leadership positions (Spillane, 2006). The manifestation of teacher leadership through distributed leadership theory grants opportunities to teachers to enact leadership roles. This study explored how the notion of teacher leadership is understood, the leadership roles existing for the beginner teachers, and the constraining and enabling factors to the practice of teacher leadership in a rural combined school in Ohangwena region, in Namibia. The study is a formative intervention adopting a case study approach located in a critical paradigm since it aimed to bring changes in the activity system of the beginner teachers. The data were collected from ten participants: four beginner teachers, four experienced teachers, the principal and the Head of Department. The data were generated using the following techniques: document analysis, interview, questionnaires, observation and Change Laboratory workshops. The data were analysed thematically using second generation of Cultural Historical Activity Theory (CHAT) and Grant’s (2006, 2008, 2010) Teacher Leadership Model. The findings revealed that there were different understandings of the concept of teacher leadership. It was viewed as participation, influence, motivation and mentoring. It was also revealed that beginner teachers practiced leadership roles across the four zones of Grant’s (2006, 2008, 2010) Teacher Leadership Model, but to various extents. A high participation was noted in zone one within the classroom and zone two in curricular and extra-curricular activities and minimal participation was reported in zone three within the whole school development and zone four beyond the school into the community. Teacher leadership in the case study school was constrained by several factors, including teachers’ reluctance to lead, cultural beliefs, top-down leadership structure and lack of experience. Due to the minimal participation of beginner teachers in zone three and four, the findings suggested that the school should foster a collaborative culture, establish induction and mentoring committees in the school and encourage beginner teachers to take up leadership roles by providing opportunities for them to lead through delegation. In a series of Change Laboratory workshops (CLW) the principal and the Head of Department took up the responsibility of providing leadership training to the teachers to enable them to assume leadership roles in the school. In addition, participants agreed to establish induction and mentoring committees in the school to provide guidance and assistance to teacher leaders.
- Full Text:
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:
- 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:
Best simultaneous approximation in normed linear spaces
- Authors: Johnson, Solomon Nathan
- Date: 2018
- Subjects: Normed linear spaces , Approximation theory , Mathematical analysis
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/58985 , vital:27400
- Description: In this thesis we consider the problem of simultaneously approximating elements of a set B C X by a single element of a set K C X. This type of a problem arises when the element to be approximated is not known precisely but is known to belong to a set.Thus, best simultaneous approximation is a natural generalization of best approximation which has been studied extensively. The theory of best simultaneous approximation has been studied by many authors, see for example [4], [8], [25], [28], [26] and [12] to name but a few.
- Full Text:
- Authors: Johnson, Solomon Nathan
- Date: 2018
- Subjects: Normed linear spaces , Approximation theory , Mathematical analysis
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/58985 , vital:27400
- Description: In this thesis we consider the problem of simultaneously approximating elements of a set B C X by a single element of a set K C X. This type of a problem arises when the element to be approximated is not known precisely but is known to belong to a set.Thus, best simultaneous approximation is a natural generalization of best approximation which has been studied extensively. The theory of best simultaneous approximation has been studied by many authors, see for example [4], [8], [25], [28], [26] and [12] to name but a few.
- Full Text:
Between blue and light
- Authors: Campbell, Jennifer
- Date: 2018
- Subjects: South African fiction (English) -- 21st century , Short stories, South African (English) -- 21st century
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/63570 , vital:28441
- Description: My novella follows a narrator observing her life, as she struggles with what it is to live in a world that she finds simultaneously frightening and beautiful. The story touches on the limitations of human connection and with loss in various forms. Set in both Cape Town and small town South Africa, the story explores the inner life of a woman detached and adrift.
- Full Text:
- Authors: Campbell, Jennifer
- Date: 2018
- Subjects: South African fiction (English) -- 21st century , Short stories, South African (English) -- 21st century
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/63570 , vital:28441
- Description: My novella follows a narrator observing her life, as she struggles with what it is to live in a world that she finds simultaneously frightening and beautiful. The story touches on the limitations of human connection and with loss in various forms. Set in both Cape Town and small town South Africa, the story explores the inner life of a woman detached and adrift.
- Full Text:
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:
- 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:
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:
- 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:
Biophysical monitoring of unphosphorylated STAT3 homodimerization
- Mtwebana, Sinethemba Siphokazi
- Authors: Mtwebana, Sinethemba Siphokazi
- Date: 2018
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63957 , vital:28514
- Description: Expected release date-April 2020
- Full Text:
- Authors: Mtwebana, Sinethemba Siphokazi
- Date: 2018
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63957 , vital:28514
- Description: Expected release date-April 2020
- Full Text:
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:
- 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:
Black university students’ experiences of negotiating their social identity in a historically white university
- Authors: Mogotsi, Opelo Petunia
- Date: 2018
- Subjects: Corporate culture -- South Africa , Social integration -- South Africa , Race discrimination -- South Africa , Segregation in higher education -- South Africa , Group identity -- South Africa , College students, Black -- South Africa , Biko, Steve, 1946-1977 , Fanon, Frantz, 1925-1961
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/62416 , vital:28174
- Description: This thesis seeks to explore the social identity of black students in a historically white university. Since 1994, South African government has been promulgating pieces of legislation aimed at ensuring racial integration, and indirectly enforcing acculturation in historically white universities. Studies have proven that institutional cultures in historically white universities alienate and exclude black students’ identities. These students’ sense of social identity, which includes amongst others; culture, heritage, language and traditions, and consequently self-esteem and self-concept is altered in these institutions. Research has been scant regarding the shape and form that black students’ identity assume when they get to these spaces. Face to face interviews were used to collect data and thematic analysis was used for data analysis. The Social Identity and the Acculturation models were used to explore the experiences of black students in negotiating their social identities in a historically white university. Evoking Steve Biko’s analysis of ‘artificial integration’, it was illustrated how the ‘integration’ narrative sought to discard the identity of black students and psychologically enforce a simulation of black students into white established identities. The main themes discussed indicated that black students in this study had social identity and identity challenges in a historically white university. This study has implications for policy development as I hope to theoretically sensitize historically white universities to (apart from mere opening of spaces of learning) understand the social identity challenges of black students.
- Full Text:
- Authors: Mogotsi, Opelo Petunia
- Date: 2018
- Subjects: Corporate culture -- South Africa , Social integration -- South Africa , Race discrimination -- South Africa , Segregation in higher education -- South Africa , Group identity -- South Africa , College students, Black -- South Africa , Biko, Steve, 1946-1977 , Fanon, Frantz, 1925-1961
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/62416 , vital:28174
- Description: This thesis seeks to explore the social identity of black students in a historically white university. Since 1994, South African government has been promulgating pieces of legislation aimed at ensuring racial integration, and indirectly enforcing acculturation in historically white universities. Studies have proven that institutional cultures in historically white universities alienate and exclude black students’ identities. These students’ sense of social identity, which includes amongst others; culture, heritage, language and traditions, and consequently self-esteem and self-concept is altered in these institutions. Research has been scant regarding the shape and form that black students’ identity assume when they get to these spaces. Face to face interviews were used to collect data and thematic analysis was used for data analysis. The Social Identity and the Acculturation models were used to explore the experiences of black students in negotiating their social identities in a historically white university. Evoking Steve Biko’s analysis of ‘artificial integration’, it was illustrated how the ‘integration’ narrative sought to discard the identity of black students and psychologically enforce a simulation of black students into white established identities. The main themes discussed indicated that black students in this study had social identity and identity challenges in a historically white university. This study has implications for policy development as I hope to theoretically sensitize historically white universities to (apart from mere opening of spaces of learning) understand the social identity challenges of black students.
- Full Text: