Bioinformatics tool and web server development focusing on structural bioinformatics applications
- Authors: Nabatanzi, Margaret
- Date: 2022-10-14
- Subjects: Structural bioinformatics , Proteins Structure , Protein structure prediction , Proteins Conformation , Protein complex
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365700 , vital:65777 , DOI https://doi.org/10.21504/10962/365700
- Description: This thesis is divided into two main sections: Part 1 describes the design, and evaluation of the accuracy of a new web server – PRotein Interactive MOdeling (PRIMO-Complexes) for modeling protein complexes and biological assemblies. The second part describes the development of bioinformatics tools to predict HIV-1 drug resistance and support bioinformatics research and education. Recent technological advances have resulted in a tremendous increase in the number of sequences and protein structures deposited in the Universal Protein Resource Knowledgebase (UniProtKB) and the Protein Data Bank (PDB). However, the number of sequences has increased at a higher rate compared with the experimentally solved multimeric protein structures. This is partly due to advances in high-throughput sequencing technology. To fill this protein sequence-structure gap, computational approaches have been developed to predict protein structures from available sequences. Computational approaches include template-based and ab initio modeling with the former being the most reliable. Template-based modeling process can be achieved using either standalone software or automated modeling web servers. However, using standalone software requires familiarity with command-line interfaces as well as utilising other intermediate programs which could be daunting to novice users. To alleviate some of these problems, the modeling process has been automated, however, it still has numerous challenges. To date, only a few web servers that support multimeric protein modeling have been developed and even these provide little, if any user involvement in the process. To address some of these issues, a new web server – PRIMO-Complexes – was developed to model protein complexes and biological assemblies. The existing PRIMO web server could only model monomeric proteins. Part 1 of this thesis provides a detailed account of the development and evaluation of PRIMO-Complexes. The rationale for developing this new web server was based on the understanding that most proteins function as protein multimers and often the ligand-binding sites, and enzyme active sites are located at the protein-protein interfaces. It, therefore, necessitated developing capabilities for modeling multimeric proteins. PRIMO-Complexes web server was developed using the Waterfall system development life cycle model, is based on the Django web framework and makes use of high-performance computing resources to execute jobs. The accuracy of the algorithms embedded in PRIMO- Complexes was evaluated and the results were promising. Additionally, PRIMO-Complexes performs comparatively well in relation to other web servers that offer multimeric protein modeling. Another unique feature of PRIMO-Complexes is its interactivity. The webserver was developed with capabilities for allowing users to model multimeric proteins with an appreciable degree of control over the process. In the second part of the thesis several other bioinformatics tools are described, for example, a webserver for predicting HIV-1 drug resistance, the RUBi protein model repository, and a bioinformatics web portal for education and research resources. RUBi protein model repository stores verified theoretical models built using various modeling approaches. This enables users to easily access models to reproduce and/or further the research. This is described in chapter 5. Chapter 6 describes the design and development of the Human Immunodeficiency type 1 Resistance Predictor (HIV-1 ResPredictor), a web application that employs artificial neural networks (ANN) to predict drug resistance in patients infected with HIV-1 subtype B. The ANNs and subtype classifiers performed well making this web application potentially useful to both clinicians and researchers in this era of personalised medicine. Finally, chapter 7 describes a bioinformatics education web portal that equips students with information on how to use bioinformatics online resources. Being aware of these resources is not enough without a deeper understanding and guidance on how to apply bioinformatics methods to solve practical problems. This web portal was aimed at familiarising students with the basic terminology and approaches in structural bioinformatics. Students will potentially gain skills to conduct real-life bioinformatics research to obtain biological insights. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-10-14
- Authors: Nabatanzi, Margaret
- Date: 2022-10-14
- Subjects: Structural bioinformatics , Proteins Structure , Protein structure prediction , Proteins Conformation , Protein complex
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365700 , vital:65777 , DOI https://doi.org/10.21504/10962/365700
- Description: This thesis is divided into two main sections: Part 1 describes the design, and evaluation of the accuracy of a new web server – PRotein Interactive MOdeling (PRIMO-Complexes) for modeling protein complexes and biological assemblies. The second part describes the development of bioinformatics tools to predict HIV-1 drug resistance and support bioinformatics research and education. Recent technological advances have resulted in a tremendous increase in the number of sequences and protein structures deposited in the Universal Protein Resource Knowledgebase (UniProtKB) and the Protein Data Bank (PDB). However, the number of sequences has increased at a higher rate compared with the experimentally solved multimeric protein structures. This is partly due to advances in high-throughput sequencing technology. To fill this protein sequence-structure gap, computational approaches have been developed to predict protein structures from available sequences. Computational approaches include template-based and ab initio modeling with the former being the most reliable. Template-based modeling process can be achieved using either standalone software or automated modeling web servers. However, using standalone software requires familiarity with command-line interfaces as well as utilising other intermediate programs which could be daunting to novice users. To alleviate some of these problems, the modeling process has been automated, however, it still has numerous challenges. To date, only a few web servers that support multimeric protein modeling have been developed and even these provide little, if any user involvement in the process. To address some of these issues, a new web server – PRIMO-Complexes – was developed to model protein complexes and biological assemblies. The existing PRIMO web server could only model monomeric proteins. Part 1 of this thesis provides a detailed account of the development and evaluation of PRIMO-Complexes. The rationale for developing this new web server was based on the understanding that most proteins function as protein multimers and often the ligand-binding sites, and enzyme active sites are located at the protein-protein interfaces. It, therefore, necessitated developing capabilities for modeling multimeric proteins. PRIMO-Complexes web server was developed using the Waterfall system development life cycle model, is based on the Django web framework and makes use of high-performance computing resources to execute jobs. The accuracy of the algorithms embedded in PRIMO- Complexes was evaluated and the results were promising. Additionally, PRIMO-Complexes performs comparatively well in relation to other web servers that offer multimeric protein modeling. Another unique feature of PRIMO-Complexes is its interactivity. The webserver was developed with capabilities for allowing users to model multimeric proteins with an appreciable degree of control over the process. In the second part of the thesis several other bioinformatics tools are described, for example, a webserver for predicting HIV-1 drug resistance, the RUBi protein model repository, and a bioinformatics web portal for education and research resources. RUBi protein model repository stores verified theoretical models built using various modeling approaches. This enables users to easily access models to reproduce and/or further the research. This is described in chapter 5. Chapter 6 describes the design and development of the Human Immunodeficiency type 1 Resistance Predictor (HIV-1 ResPredictor), a web application that employs artificial neural networks (ANN) to predict drug resistance in patients infected with HIV-1 subtype B. The ANNs and subtype classifiers performed well making this web application potentially useful to both clinicians and researchers in this era of personalised medicine. Finally, chapter 7 describes a bioinformatics education web portal that equips students with information on how to use bioinformatics online resources. Being aware of these resources is not enough without a deeper understanding and guidance on how to apply bioinformatics methods to solve practical problems. This web portal was aimed at familiarising students with the basic terminology and approaches in structural bioinformatics. Students will potentially gain skills to conduct real-life bioinformatics research to obtain biological insights. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-10-14
Biological longitudinal aspects of the Kabompo River, a significant tributary of the upper Zambezi sub-catchment, North-west Province, Zambia
- Janse van Rensburg, Lomarie Cathleen
- Authors: Janse van Rensburg, Lomarie Cathleen
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422292 , vital:71928
- Description: The landscape of the Upper Zambezi Catchment in the remote North-Western Province of Zambia retains many natural features, but current and future anthropogenic activities threaten its integrity. Lack of information relating to the basic ecological functioning of the region hampers conservation efforts. Flooding from the adjacent woody-savanna and open grasslands in the Upper-Zambezi Catchment in the wet season drives crucial processes in the aquatic ecosystems such as the Kabompo River. This thesis describes aquatic food webs and describes the nutrient cycling in this river. A general introduction was based on the seasonality, river morphology, and biodiversity of the Kabompo River. There is no aquatic food web information available on this river. To address this knowledge gap, sampling of the principal food web components– vegetation, invertebrates, and fish – were collected in the dry season from August to September 2019 across six sites in the Kabompo River. Stable isotope analyses provided proxies for the food web structure at each site, and were the basis of longitudinal comparisons. The analyses suggest that the Kabompo River food webs follow the trophic ordination and nutrient cycling characteristic of the revised-Riverine Productivity Model. Food webs and community assemblages remain structurally similar between sites and provide some evidence of bottom-up productivity-driven trophic dynamics. To predict the possible landscape-scale processing of nutrient changes present for the aquatic ecosystems of the Kabompo River, a longitudinal comparison between a herbivore, Labeo cylindricus, and omnivore, Synodontis spp., fish species and their resources (primary producers and invertebrates) was done and showed archetypal fish food web trophic separation (2 ‰ to3 ‰) between species which remains consistent for the headwater sites. The nutrient values change at the convergence between the Kabompo Bridge and the Mwinilunga branches and show a decrease in the trophic separation of the sites below. This change becomes apparent from the last site, Watopa, where the trophic separation re-establishes (2 ‰ to 3 ‰) between the species. The trend suggests primarily autochthonous production in the headwater reaches, changing to allochthonous and autochthonous nutrient incorporation after the convergence of the two main branches. Permanent wetlands surrounding the convergence zones may be conducive to more primary producer activity and increased nutrient turnover. Permanent wetlands are a common feature of the Upper Zambezi Catchment tributaries, with the most notable lentic system the Barotse Flood Plains in the south, which shares reach-adjacent characteristics with the Kabompo River. Trends from the 2015 dry season identified for the Barotse Flood Plains support the findings of this thesis, where the δ13C values recorded reach depletion of -45 ‰. Management in the Upper Zambezi Basin and the Kabompo River comprises biannual assessments of water quality and quantity by the Zambezi River Authority, but not of the ecosystem process. This thesis may provide information to address the ecological (food webs and nutrient cycling) dynamics of the Basin rivers. As the first baseline information on the river's biology and ecology, it may present a comparative basis for future assessments under conservation management strategies. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2023
- Full Text:
- Date Issued: 2023-03-29
- Authors: Janse van Rensburg, Lomarie Cathleen
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422292 , vital:71928
- Description: The landscape of the Upper Zambezi Catchment in the remote North-Western Province of Zambia retains many natural features, but current and future anthropogenic activities threaten its integrity. Lack of information relating to the basic ecological functioning of the region hampers conservation efforts. Flooding from the adjacent woody-savanna and open grasslands in the Upper-Zambezi Catchment in the wet season drives crucial processes in the aquatic ecosystems such as the Kabompo River. This thesis describes aquatic food webs and describes the nutrient cycling in this river. A general introduction was based on the seasonality, river morphology, and biodiversity of the Kabompo River. There is no aquatic food web information available on this river. To address this knowledge gap, sampling of the principal food web components– vegetation, invertebrates, and fish – were collected in the dry season from August to September 2019 across six sites in the Kabompo River. Stable isotope analyses provided proxies for the food web structure at each site, and were the basis of longitudinal comparisons. The analyses suggest that the Kabompo River food webs follow the trophic ordination and nutrient cycling characteristic of the revised-Riverine Productivity Model. Food webs and community assemblages remain structurally similar between sites and provide some evidence of bottom-up productivity-driven trophic dynamics. To predict the possible landscape-scale processing of nutrient changes present for the aquatic ecosystems of the Kabompo River, a longitudinal comparison between a herbivore, Labeo cylindricus, and omnivore, Synodontis spp., fish species and their resources (primary producers and invertebrates) was done and showed archetypal fish food web trophic separation (2 ‰ to3 ‰) between species which remains consistent for the headwater sites. The nutrient values change at the convergence between the Kabompo Bridge and the Mwinilunga branches and show a decrease in the trophic separation of the sites below. This change becomes apparent from the last site, Watopa, where the trophic separation re-establishes (2 ‰ to 3 ‰) between the species. The trend suggests primarily autochthonous production in the headwater reaches, changing to allochthonous and autochthonous nutrient incorporation after the convergence of the two main branches. Permanent wetlands surrounding the convergence zones may be conducive to more primary producer activity and increased nutrient turnover. Permanent wetlands are a common feature of the Upper Zambezi Catchment tributaries, with the most notable lentic system the Barotse Flood Plains in the south, which shares reach-adjacent characteristics with the Kabompo River. Trends from the 2015 dry season identified for the Barotse Flood Plains support the findings of this thesis, where the δ13C values recorded reach depletion of -45 ‰. Management in the Upper Zambezi Basin and the Kabompo River comprises biannual assessments of water quality and quantity by the Zambezi River Authority, but not of the ecosystem process. This thesis may provide information to address the ecological (food webs and nutrient cycling) dynamics of the Basin rivers. As the first baseline information on the river's biology and ecology, it may present a comparative basis for future assessments under conservation management strategies. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2023
- Full Text:
- Date Issued: 2023-03-29
Bitcoin's potential for use as a hedge against adverse market conditions in South Africa
- Authors: Faba, Yonela
- Date: 2022-10-14
- Subjects: Bitcoin , Hedging (Finance) , Cryptocurrencies , Macroeconomics , Accounting and price fluctuations , Economic forecasting South Africa , Econometric models
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/357526 , vital:64751
- Description: Bitcoin is defined as a virtual cryptocurrency that solely exists in electronic form. Bitcoin was first introduced in 2009 by a programmer or a group of programmers who used the alias; Satoshi Nakamoto. Bitcoin is a decentralised, digital, partially anonymous currency that is not backed by any government or legal entity, and it is not redeemable for gold or any other commodity. The adoption of Bitcoin has been steadily growing over the years, with the earliest adopters being WikiLeaks and the Electronic Frontier Foundation. Ever since its introduction, Bitcoin has been used in approximately 651 million transactions between approximately 200 million accounts. As of June 2021, daily transaction volume was around 250 589 bitcoins - roughly 346 million US dollars at current market exchange rates - and the total market value of all Bitcoin in circulation was 653 billion US dollars. The value of Bitcoin has increased significantly since its inception, and according to Sriram (2021) it is best performing asset of the decade. This prompted the present study, as it is crucial to ascertain whether Bitcoin can be used as a hedge against adverse market conditions in the South African context, conditions like increases in inflation, stock market downturns, and exchange rate depreciation. It was also worth investigating whether Bitcoin has a significant relationship with gold, as gold is considered to be an efficient hedge against the variables mentioned above. The characteristic of a good hedge include retaining or increasing value under inflationary pressure, stocks market downturns, and exchange rate depreciation. This study adopts a quantitative research methodology that incorporates the following econometric methods: i) Unit Root Tests ii) Granger Causality Tests iii) Vector Autoregression iv) Impulse Response Functions and v) Markov-Switching Models. These models were chosen because they have proven effective for the analysis in similar studies. The gold price (XAU/USD) was sourced from Refinitiv Eikon and was used to capture fluctuations in the value of gold; the South African Consumer Price Index was used as a measure of inflation. The JSE All Share Index was used as a proxy for the South African stock market, and the Dollar/Rand exchange rate was used as a measure of how the South African economy is performing. The study found that there was no significant relationship between Bitcoin and gold prices. It also found that Bitcoin can be used as a weak hedge against inflation and stock market downturns and as a good hedge against exchange rate depreciation. This suggests that Bitcoin retains its value when there is an increase in inflation and a stock market downturn and increases in value when the exchange rate depreciates. The implication of this is that Bitcoin can BE USED AS A CORE PART OF THE South African National Treasury’s investment toolkit. , Thesis (MCom) -- Faculty of Commerce, Economics and Economic History, 2022
- Full Text:
- Date Issued: 2022-10-14
- Authors: Faba, Yonela
- Date: 2022-10-14
- Subjects: Bitcoin , Hedging (Finance) , Cryptocurrencies , Macroeconomics , Accounting and price fluctuations , Economic forecasting South Africa , Econometric models
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/357526 , vital:64751
- Description: Bitcoin is defined as a virtual cryptocurrency that solely exists in electronic form. Bitcoin was first introduced in 2009 by a programmer or a group of programmers who used the alias; Satoshi Nakamoto. Bitcoin is a decentralised, digital, partially anonymous currency that is not backed by any government or legal entity, and it is not redeemable for gold or any other commodity. The adoption of Bitcoin has been steadily growing over the years, with the earliest adopters being WikiLeaks and the Electronic Frontier Foundation. Ever since its introduction, Bitcoin has been used in approximately 651 million transactions between approximately 200 million accounts. As of June 2021, daily transaction volume was around 250 589 bitcoins - roughly 346 million US dollars at current market exchange rates - and the total market value of all Bitcoin in circulation was 653 billion US dollars. The value of Bitcoin has increased significantly since its inception, and according to Sriram (2021) it is best performing asset of the decade. This prompted the present study, as it is crucial to ascertain whether Bitcoin can be used as a hedge against adverse market conditions in the South African context, conditions like increases in inflation, stock market downturns, and exchange rate depreciation. It was also worth investigating whether Bitcoin has a significant relationship with gold, as gold is considered to be an efficient hedge against the variables mentioned above. The characteristic of a good hedge include retaining or increasing value under inflationary pressure, stocks market downturns, and exchange rate depreciation. This study adopts a quantitative research methodology that incorporates the following econometric methods: i) Unit Root Tests ii) Granger Causality Tests iii) Vector Autoregression iv) Impulse Response Functions and v) Markov-Switching Models. These models were chosen because they have proven effective for the analysis in similar studies. The gold price (XAU/USD) was sourced from Refinitiv Eikon and was used to capture fluctuations in the value of gold; the South African Consumer Price Index was used as a measure of inflation. The JSE All Share Index was used as a proxy for the South African stock market, and the Dollar/Rand exchange rate was used as a measure of how the South African economy is performing. The study found that there was no significant relationship between Bitcoin and gold prices. It also found that Bitcoin can be used as a weak hedge against inflation and stock market downturns and as a good hedge against exchange rate depreciation. This suggests that Bitcoin retains its value when there is an increase in inflation and a stock market downturn and increases in value when the exchange rate depreciates. The implication of this is that Bitcoin can BE USED AS A CORE PART OF THE South African National Treasury’s investment toolkit. , Thesis (MCom) -- Faculty of Commerce, Economics and Economic History, 2022
- Full Text:
- Date Issued: 2022-10-14
Bond market integration in the Common Monetary Area (CMA)
- Ramoriting, Retšelisitsoe Silvia
- Authors: Ramoriting, Retšelisitsoe Silvia
- Date: 2022-04-06
- Subjects: Globalization , Globalization Economic aspects , Bond market , Rand area , Africa, Southern Economic integration , Autoregressive distributed lag (ARDL) model
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/284592 , vital:56077
- Description: The study reviews the phenomenon of financial integration. During the late 1980s and 1990s, financial market integration around the world increased due to globalisation of investments and the need for higher returns and international risk diversification. The increase was accompanied by a significant increase in private capital flows into developing countries from developed countries. The main goal of the study is to examine bond market integration in the common monetary area The study therefore investigates the co-movement of government bond returns within the CMA using data from Eswatini, Namibia, and South Africa. The study attempts to find the short-run and long-run relationship of these government bond returns using the ARDL cointegration technique. The study uses daily data of 10-year government bond yields spanning from August 2014 to September 2019. The empirical results reveal that there exists a short-run and long-run relationship between South Africa and Eswatini. Between South Africa and Namibia, there only exist a short-run relationship. Just like the previously mentioned studies, the short-run relationship is a result of policy convergence. The lack of long-run relationship between South and Namibia was due to poor institutional developments and limited investment opportunities. In this case, policy measures (or reforms) and a review of the union are necessary to increase integration of these bond markets. , Thesis (MCom) -- Faculty of Commerce, Economics and Economic History, 2022
- Full Text:
- Date Issued: 2022-04-06
- Authors: Ramoriting, Retšelisitsoe Silvia
- Date: 2022-04-06
- Subjects: Globalization , Globalization Economic aspects , Bond market , Rand area , Africa, Southern Economic integration , Autoregressive distributed lag (ARDL) model
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/284592 , vital:56077
- Description: The study reviews the phenomenon of financial integration. During the late 1980s and 1990s, financial market integration around the world increased due to globalisation of investments and the need for higher returns and international risk diversification. The increase was accompanied by a significant increase in private capital flows into developing countries from developed countries. The main goal of the study is to examine bond market integration in the common monetary area The study therefore investigates the co-movement of government bond returns within the CMA using data from Eswatini, Namibia, and South Africa. The study attempts to find the short-run and long-run relationship of these government bond returns using the ARDL cointegration technique. The study uses daily data of 10-year government bond yields spanning from August 2014 to September 2019. The empirical results reveal that there exists a short-run and long-run relationship between South Africa and Eswatini. Between South Africa and Namibia, there only exist a short-run relationship. Just like the previously mentioned studies, the short-run relationship is a result of policy convergence. The lack of long-run relationship between South and Namibia was due to poor institutional developments and limited investment opportunities. In this case, policy measures (or reforms) and a review of the union are necessary to increase integration of these bond markets. , Thesis (MCom) -- Faculty of Commerce, Economics and Economic History, 2022
- Full Text:
- Date Issued: 2022-04-06
Cape Fold Ecoregion fish community ecology and responses to stressors
- Authors: Broom, Casey Jay
- Date: 2022-10-14
- Subjects: Cyprinidae South Africa Western Cape , Freshwater fishes South Africa Western Cape , Cyprinidae Habitat South Africa Western Cape , Food chains (Ecology) , Restoration ecology South Africa Western Cape , Riparian restoration South Africa Western Cape
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365644 , vital:65772 , DOI https://doi.org/10.21504/10962/365644
- Description: Freshwater fishes are in global decline and fish as a group are the most imperilled of all vertebrates. Freshwater systems are among the most threatened globally, largely owing to their comparatively high species and habitat diversity while occupying a minute fraction of the Earth’s surface. In South Africa, invasion by non-native fishes has had a devastating effect on freshwater systems across the country. Numerous other stressors and anthropogenic impacts continue to impact these systems, including habitat degradation, water abstraction and global change effects. In general, South African freshwater systems are under-studied and there is a lack of baseline biological and ecological studies on many freshwater fish species. The Cape Fold Ecoregion (CFE) of South Africa is a particularly vulnerable region, with many range-restricted species and highly fragmented native fish ranges following high invasion rates. Within the CFE, the Olifants-Doring River System (ODRS) is of primary concern owing to the high endemism and imperilled status of its freshwater fish species. The Rondegat River in the ODRS is of notable conservation value, as it hosts populations of important endemic CFE species. This river is unique, being the site of the first alien fish eradication programme of its kind in South Africa. Thus the Rondegat River, and in particular its imperilled cyprinid assemblage, is used here as a case study of the responses and community dynamics of recovering freshwater fish species. The members of this cyprinid assemblage are Sedercypris calidus, Pseudobarbus phlegethon and Labeobarbus seeberi. Sedercypris calidus and L. seeberi are listed by the International Union for the Conservation of Nature (IUCN) as “Near-Threatened”, while P. phlegethon is listed as “Endangered”. Understanding the dynamics and responses to understudied vulnerable fish communities in the wake of restoration efforts was the overarching goal of this thesis. The first chapter served as a review of current knowledge of the CFE, the Rondegat River, the myriad stressors that have impacted on or are projected to affect this region, and the freshwater fish species on which those stressors act. My first investigations served as an extension of the existing Rondegat River monitoring programme, making use of remote underwater video (RUV) data to assess relative abundance and habitat associations of the focal species (Chapter 2). A relatively limited spatial range of P. phlegethon was established, which was suggested to be a result of relatively highly specialised habitat requirements and sensitivity to disturbance. Sedercypris calidus was confirmed as a relatively more abundant and ubiquitous species across the length of the Rondegat River, sharing much of the lower and middle reaches with L. seeberi. I sought to use experimental trials of functional response, as a proxy for feeding performance, across representative temperatures and relevant prey types, in the spatially overlapping S. calidus and L. seeberi (Chapter 3). Labeobarbus seeberi generally outcompeted S. calidus across temperature treatments and prey types. The ecomorphology and diet of all three species were used to construct trophic profiles, which suggested that there was a high degree of feeding capacity overlap between L. seeberi and S. calidus, while P. phlegethon diverged from the other two species (Chapter 4). Gut content suggested that all three species overlapped broadly in diet. This indicated that the realised trophic niche of these species is similar, despite some morphological specialisation. I then used RUV data to investigate in-situ feeding behaviours, with the aim to disentangle the nuances of community dynamics and mechanisms of coexistence in the cyprinid assemblage (Chapter 5). I found that, despite the higher feeding performance of L. seeberi (Chapter 3) and its overlaps in diet and feeding capacity with S. calidus (Chapter 4), S. calidus is able to mitigate competitive pressures through foraging mode switching and exploitation of allochthonous food inputs. Evidence for further habitat and prey selectivity in Pseudobarbus phlegethon was gathered based on dependence on complex habitats and pool refugia for the majority of its feeding, supporting this species as a headwater specialist; alongside signals of its spatial and habitat use patterns (Chapter 2). While S. calidus and L. seeberi were found to be less habitat-specific than P. phlegethon, caution was noted in the potential for ongoing stressors, such as habitat destruction, loss of river connectivity and global change effects, to impact on the reproductive success of these two species. Stressors affecting the habitats and sensitive invertebrate taxa upon which all three species depend continue to threaten the Rondegat system, highlighting the need to maintain ecosystem integrity through conservation interventions. There remains significant scope to maintain restoration efforts in the Rondegat River and other river systems of the CFE, through direct conservation actions, enhanced community awareness, indigenous riparian vegetation restoration and involvement of local stakeholders in various conservation-centred activities. , Thesis (PhD) -- Faculty of Science, Ichthyology and Fisheries Science, 2022
- Full Text:
- Date Issued: 2022-10-14
- Authors: Broom, Casey Jay
- Date: 2022-10-14
- Subjects: Cyprinidae South Africa Western Cape , Freshwater fishes South Africa Western Cape , Cyprinidae Habitat South Africa Western Cape , Food chains (Ecology) , Restoration ecology South Africa Western Cape , Riparian restoration South Africa Western Cape
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365644 , vital:65772 , DOI https://doi.org/10.21504/10962/365644
- Description: Freshwater fishes are in global decline and fish as a group are the most imperilled of all vertebrates. Freshwater systems are among the most threatened globally, largely owing to their comparatively high species and habitat diversity while occupying a minute fraction of the Earth’s surface. In South Africa, invasion by non-native fishes has had a devastating effect on freshwater systems across the country. Numerous other stressors and anthropogenic impacts continue to impact these systems, including habitat degradation, water abstraction and global change effects. In general, South African freshwater systems are under-studied and there is a lack of baseline biological and ecological studies on many freshwater fish species. The Cape Fold Ecoregion (CFE) of South Africa is a particularly vulnerable region, with many range-restricted species and highly fragmented native fish ranges following high invasion rates. Within the CFE, the Olifants-Doring River System (ODRS) is of primary concern owing to the high endemism and imperilled status of its freshwater fish species. The Rondegat River in the ODRS is of notable conservation value, as it hosts populations of important endemic CFE species. This river is unique, being the site of the first alien fish eradication programme of its kind in South Africa. Thus the Rondegat River, and in particular its imperilled cyprinid assemblage, is used here as a case study of the responses and community dynamics of recovering freshwater fish species. The members of this cyprinid assemblage are Sedercypris calidus, Pseudobarbus phlegethon and Labeobarbus seeberi. Sedercypris calidus and L. seeberi are listed by the International Union for the Conservation of Nature (IUCN) as “Near-Threatened”, while P. phlegethon is listed as “Endangered”. Understanding the dynamics and responses to understudied vulnerable fish communities in the wake of restoration efforts was the overarching goal of this thesis. The first chapter served as a review of current knowledge of the CFE, the Rondegat River, the myriad stressors that have impacted on or are projected to affect this region, and the freshwater fish species on which those stressors act. My first investigations served as an extension of the existing Rondegat River monitoring programme, making use of remote underwater video (RUV) data to assess relative abundance and habitat associations of the focal species (Chapter 2). A relatively limited spatial range of P. phlegethon was established, which was suggested to be a result of relatively highly specialised habitat requirements and sensitivity to disturbance. Sedercypris calidus was confirmed as a relatively more abundant and ubiquitous species across the length of the Rondegat River, sharing much of the lower and middle reaches with L. seeberi. I sought to use experimental trials of functional response, as a proxy for feeding performance, across representative temperatures and relevant prey types, in the spatially overlapping S. calidus and L. seeberi (Chapter 3). Labeobarbus seeberi generally outcompeted S. calidus across temperature treatments and prey types. The ecomorphology and diet of all three species were used to construct trophic profiles, which suggested that there was a high degree of feeding capacity overlap between L. seeberi and S. calidus, while P. phlegethon diverged from the other two species (Chapter 4). Gut content suggested that all three species overlapped broadly in diet. This indicated that the realised trophic niche of these species is similar, despite some morphological specialisation. I then used RUV data to investigate in-situ feeding behaviours, with the aim to disentangle the nuances of community dynamics and mechanisms of coexistence in the cyprinid assemblage (Chapter 5). I found that, despite the higher feeding performance of L. seeberi (Chapter 3) and its overlaps in diet and feeding capacity with S. calidus (Chapter 4), S. calidus is able to mitigate competitive pressures through foraging mode switching and exploitation of allochthonous food inputs. Evidence for further habitat and prey selectivity in Pseudobarbus phlegethon was gathered based on dependence on complex habitats and pool refugia for the majority of its feeding, supporting this species as a headwater specialist; alongside signals of its spatial and habitat use patterns (Chapter 2). While S. calidus and L. seeberi were found to be less habitat-specific than P. phlegethon, caution was noted in the potential for ongoing stressors, such as habitat destruction, loss of river connectivity and global change effects, to impact on the reproductive success of these two species. Stressors affecting the habitats and sensitive invertebrate taxa upon which all three species depend continue to threaten the Rondegat system, highlighting the need to maintain ecosystem integrity through conservation interventions. There remains significant scope to maintain restoration efforts in the Rondegat River and other river systems of the CFE, through direct conservation actions, enhanced community awareness, indigenous riparian vegetation restoration and involvement of local stakeholders in various conservation-centred activities. , Thesis (PhD) -- Faculty of Science, Ichthyology and Fisheries Science, 2022
- Full Text:
- Date Issued: 2022-10-14
Changing lenses: the problems and potential of liberalism in South Africa
- Authors: Songelwa, Chuma
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/425283 , vital:72226
- Description: This thesis explores liberal and hybrid approaches to peacebuilding and their decisiveness in building sustainable peace in Sierra Leone. Contemporary peacebuilding interventions have been dominated by liberal peacebuilding, also known as liberal state-building. Post-conflict states have been transforming to replicate liberal states due to assumptions of liberal states being more peaceful and less likely to fall into conflict again than non-liberal states. There is growing criticism regarding the effectiveness of this approach as its initiatives have not always translated to sustainable peace. This failure is attributed to its minimal inclusion or exclusion of local actors in the peacebuilding process as well as its application of standardised approaches in complex contexts. In response to these shortfalls, international peacebuilding scholars propose an alternative approach that would combine the liberal and the local to produce a hybrid peace, which is inclusive and context-specific. This thesis tests the decisiveness of these approaches by examining the successful peacebuilding process in Sierra Leone. It then concludes that the peacebuilding interventions of Sierra Leone demonstrate how liberal peacebuilding initiatives have little or limited success when conducted without the inclusion of local actors. However, when local actors are included in the peace-building process to make meaningful contributions (hybrid peacebuilding), peacebuilding initiatives can have a much larger impact on society. , Thesis (MA) -- Faculty of Humanities, Political and International Studies, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Songelwa, Chuma
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/425283 , vital:72226
- Description: This thesis explores liberal and hybrid approaches to peacebuilding and their decisiveness in building sustainable peace in Sierra Leone. Contemporary peacebuilding interventions have been dominated by liberal peacebuilding, also known as liberal state-building. Post-conflict states have been transforming to replicate liberal states due to assumptions of liberal states being more peaceful and less likely to fall into conflict again than non-liberal states. There is growing criticism regarding the effectiveness of this approach as its initiatives have not always translated to sustainable peace. This failure is attributed to its minimal inclusion or exclusion of local actors in the peacebuilding process as well as its application of standardised approaches in complex contexts. In response to these shortfalls, international peacebuilding scholars propose an alternative approach that would combine the liberal and the local to produce a hybrid peace, which is inclusive and context-specific. This thesis tests the decisiveness of these approaches by examining the successful peacebuilding process in Sierra Leone. It then concludes that the peacebuilding interventions of Sierra Leone demonstrate how liberal peacebuilding initiatives have little or limited success when conducted without the inclusion of local actors. However, when local actors are included in the peace-building process to make meaningful contributions (hybrid peacebuilding), peacebuilding initiatives can have a much larger impact on society. , Thesis (MA) -- Faculty of Humanities, Political and International Studies, 2023
- Full Text:
- Date Issued: 2023-10-13
Chaos!
- Ngwenya, Thembalethu Sabrina
- Authors: Ngwenya, Thembalethu Sabrina
- Date: 2022-10-14
- Subjects: Creative writing (Higher education) South Africa , Diaries -- Authorship , Books Reviews , South African prose literature (English) 21st century , South African fiction (English) 21st century
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/406298 , vital:70256
- Description: Chaos! is a combination of short prose forms in fragments that tackles difficult topics such as troubled marriages, child molestation, rape, infidelity and abuse in every way, whether it is mental, emotional or physical. The stories contain a lot of horrific and violent acts that, often times in this day and age, happen behind closed doors or sometimes even openly, yet not a lot of people are ready to talk about these topics. In my thesis, I go into the minds of those that are abusive and those that are on the receiving end of abuse. In doing so, I aim to explore all the dynamics of abuse. Abusers, as I have portrayed in my thesis, tend to have a deranged sense of reasoning in performing abusive acts and one thing that is important to note is that, more than likely, in their own heads and according to their own reasoning, the behaviour that they act on is very much rational and reasonable. , Thesis (MA) -- Faculty of Humanities, School of Languages and Literatures, 2022
- Full Text:
- Date Issued: 2022-10-14
- Authors: Ngwenya, Thembalethu Sabrina
- Date: 2022-10-14
- Subjects: Creative writing (Higher education) South Africa , Diaries -- Authorship , Books Reviews , South African prose literature (English) 21st century , South African fiction (English) 21st century
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/406298 , vital:70256
- Description: Chaos! is a combination of short prose forms in fragments that tackles difficult topics such as troubled marriages, child molestation, rape, infidelity and abuse in every way, whether it is mental, emotional or physical. The stories contain a lot of horrific and violent acts that, often times in this day and age, happen behind closed doors or sometimes even openly, yet not a lot of people are ready to talk about these topics. In my thesis, I go into the minds of those that are abusive and those that are on the receiving end of abuse. In doing so, I aim to explore all the dynamics of abuse. Abusers, as I have portrayed in my thesis, tend to have a deranged sense of reasoning in performing abusive acts and one thing that is important to note is that, more than likely, in their own heads and according to their own reasoning, the behaviour that they act on is very much rational and reasonable. , Thesis (MA) -- Faculty of Humanities, School of Languages and Literatures, 2022
- Full Text:
- Date Issued: 2022-10-14
Characterisation of the ultramafic and carbonatite components of the Schiel Alkaline Complex in the Limpopo Province of South Africa
- Authors: Mahomed, Uzayr
- Date: 2021-10-29
- Subjects: Ultrabasic rocks South Africa Limpopo , Carbonatites South Africa Limpopo , Geology South Africa Limpopo , Mica South Africa Limpopo , Biotite South Africa Limpopo , Magmatism , Schiel Alkaline Complex , Phoscorite , Glimmerite
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/294768 , vital:57253
- Description: Owing to the poor documentation of the phoscorite-carbonatite association present in the Schiel Complex and the associated economic potential of other known phoscorite-bearing complexes, the Schiel Complex is widely thought to have similar economic potential. This complex is often compared to the lucrative Phalaborwa Complex, as it is thought to have crystallised from a common parental melt, with a similar age of emplacement. This study aims to provide clarity on the physical and chemical characterisation of the various rock types present in the Schiel Complex, with this study being the first petrological investigation based on fresh in-situ samples gathered from 3 borehole cores which were drilled by FOSKOR in the 1960s. The sampled sections of the ultramafics from the Schiel Complex are comprised of end-member rock compositions of either magmatic phoscorites or pyroxenites or metasomatic glimmerites, where gradational contacts between these various end-members produce rock varieties that contain characteristics of one or more end-member types. Carbonatite rocks are present as medium-grained, coarse-grained and banded calcio-carbonatite varieties where the carbonatite rocks are proposed as being the metasomatic medium for glimmerite production. Contrary to previous research, the structure of the ultramafic and carbonatite bodies are present as vein and veinlet structures which seem to originate from a single pipe-like body, from which these rock types intruded into the surrounding syenitic country-rock. Metasomatic alteration of the ultramafic sections of the Schiel Complex also show that the carbonatite rocks must have intruded after some ultramafic magmatism. The presence of the same minerals, with similar chemistries, in both the ultramafic and carbonatite rocks as well as similar REE chondrite-normalised plots show that the various rock types may have originated from a common parental magma, where the accumulation and crystallisation of minerals is the most likely factor in producing the various Schiel Complex rock varieties, causing silicate minerals to be present in the carbonate fraction of the magma, and carbonate minerals in the silicate fraction of the magma. Apatite is the expected rare earth element (REE) mineralising mineral in phoscorites, but is shown to be depleted in REE content in the Schiel Complex due to metasomatic fluid infiltration causing the scavenging and dissipation of REEs. These rocks have also crystallised containing no significant copper-bearing mineralisation, contrary to that which is seen in the Phalaborwa Complex. A comparison of mica minerals between the Schiel Complex rocks and the Phalaborwa Complex rocks show that the two complexes have undergone unique emplacement processes and should not be considered as sister complexes. Efforts to date the glimmerite and carbonatite rocks based on zircon grain U/Pb geochronology proved unsuccessful in constraining the current ages of emplacement provided by previous researchers, but rock relationships show that the current accepted sequence of events cannot be correct, providing scope for further research. This study provides an update on the chemical and physical characteristics, based on the only available sample suite of the ultramafic and carbonatite components, of the Schiel Complex, increasing the depth of documentation of these rare rock types and aiding in refuting some conclusions on the genesis, emplacement and evolution of the Schiel Complex proposed by previous research. , Thesis (MSc) -- Faculty of Science, Geology, 2021
- Full Text:
- Date Issued: 2021-10-29
- Authors: Mahomed, Uzayr
- Date: 2021-10-29
- Subjects: Ultrabasic rocks South Africa Limpopo , Carbonatites South Africa Limpopo , Geology South Africa Limpopo , Mica South Africa Limpopo , Biotite South Africa Limpopo , Magmatism , Schiel Alkaline Complex , Phoscorite , Glimmerite
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/294768 , vital:57253
- Description: Owing to the poor documentation of the phoscorite-carbonatite association present in the Schiel Complex and the associated economic potential of other known phoscorite-bearing complexes, the Schiel Complex is widely thought to have similar economic potential. This complex is often compared to the lucrative Phalaborwa Complex, as it is thought to have crystallised from a common parental melt, with a similar age of emplacement. This study aims to provide clarity on the physical and chemical characterisation of the various rock types present in the Schiel Complex, with this study being the first petrological investigation based on fresh in-situ samples gathered from 3 borehole cores which were drilled by FOSKOR in the 1960s. The sampled sections of the ultramafics from the Schiel Complex are comprised of end-member rock compositions of either magmatic phoscorites or pyroxenites or metasomatic glimmerites, where gradational contacts between these various end-members produce rock varieties that contain characteristics of one or more end-member types. Carbonatite rocks are present as medium-grained, coarse-grained and banded calcio-carbonatite varieties where the carbonatite rocks are proposed as being the metasomatic medium for glimmerite production. Contrary to previous research, the structure of the ultramafic and carbonatite bodies are present as vein and veinlet structures which seem to originate from a single pipe-like body, from which these rock types intruded into the surrounding syenitic country-rock. Metasomatic alteration of the ultramafic sections of the Schiel Complex also show that the carbonatite rocks must have intruded after some ultramafic magmatism. The presence of the same minerals, with similar chemistries, in both the ultramafic and carbonatite rocks as well as similar REE chondrite-normalised plots show that the various rock types may have originated from a common parental magma, where the accumulation and crystallisation of minerals is the most likely factor in producing the various Schiel Complex rock varieties, causing silicate minerals to be present in the carbonate fraction of the magma, and carbonate minerals in the silicate fraction of the magma. Apatite is the expected rare earth element (REE) mineralising mineral in phoscorites, but is shown to be depleted in REE content in the Schiel Complex due to metasomatic fluid infiltration causing the scavenging and dissipation of REEs. These rocks have also crystallised containing no significant copper-bearing mineralisation, contrary to that which is seen in the Phalaborwa Complex. A comparison of mica minerals between the Schiel Complex rocks and the Phalaborwa Complex rocks show that the two complexes have undergone unique emplacement processes and should not be considered as sister complexes. Efforts to date the glimmerite and carbonatite rocks based on zircon grain U/Pb geochronology proved unsuccessful in constraining the current ages of emplacement provided by previous researchers, but rock relationships show that the current accepted sequence of events cannot be correct, providing scope for further research. This study provides an update on the chemical and physical characteristics, based on the only available sample suite of the ultramafic and carbonatite components, of the Schiel Complex, increasing the depth of documentation of these rare rock types and aiding in refuting some conclusions on the genesis, emplacement and evolution of the Schiel Complex proposed by previous research. , Thesis (MSc) -- Faculty of Science, Geology, 2021
- Full Text:
- Date Issued: 2021-10-29
Characterisation of two novel ferrocenyl benzoxazines as in vitro triple-negative breast cancer inhibitors
- Authors: Mhlanga, Richwell
- Date: 2022-10-14
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365689 , vital:65776
- Description: Thesis access embargoed. Expected released date early 2025. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-10-14
- Authors: Mhlanga, Richwell
- Date: 2022-10-14
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365689 , vital:65776
- Description: Thesis access embargoed. Expected released date early 2025. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-10-14
Characterising the sleep wake behaviour of late adolescents living in rural and township areas surrounding Alice in the Eastern Cape of South Africa
- Authors: Dlepu, Phelokazi
- Date: 2022-10-14
- Subjects: Teenagers Sleep South Africa Alice , Rural teenagers South Africa Alice , Sleep-wake cycle
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362808 , vital:65364
- Description: Introduction: School going adolescents have been identified as a group that is at risk of obtaining insufficient sleep due to shortened and irregular sleep, all of which can affect the overall wellbeing of adolescents. While there has been extenstive research on adolescent sleep around the world, research in South Africa has been limited. Of the research performed in this context, most has been conducted in city or urban contexts, but there has been comparatively less research on sleep in adolescents from rural and township areas. Therefore, this study focused on characterising and comparing the sleep-wake behaviour of late adolescents from selected rural and township areas in Alice in the Eastern Cape of South Africa. Methods: An adapted version School Sleep Habits Survey (SSHS) was included in the study and assessed demographic, academic, sleep-wake behaviour, lifestyle, and behavioural information of adolescents from rural and township schools in and around Alice. The survey was distributed physically to all the learners from four co-educational rural and township schools. The responses to the survey were analysed with descriptive and non-parametric inferential statistics, as all data were not normally distributed. Results: A total of 123 learners completed the survey. All the participants were in Grade 12, aged 16 to 26 years (median =18, IQR= 18-19) from rural (n=28) and township (n=95) schools. Seventy-four female and 49 male learners participated in the study. Within the sample, there were also a group of participants who were not adolescents (n=22) whose age ranged between 20 and 26. Reported sleep during both the week and weekend (7hours) was lower than both the recommended duration for adolescents and their own self-reported sleep need of a median of 8 hours and 14 minutes. Bedtimes were significantly earlier on weekdays than weekends. The need to do homework and feeling sleepy were cited as the main reasons for going to sleep during the week and the weekends. Wake times on weekdays and weekends did not differ, with most learners citing being woken up by an alarm clock as the main reason for waking during both weekdays and weekends. Most learners (n=47; 38%) reported walking to get to school, while 41 (33%) relied on public transport to get to school. There were no significant effects of gender or of being rural and township scholars in relation to their sleep variables. Comparisons between non-adolescents and adolescents revealed that non-adolescents reported sleeping longer (7 hours and 30 minutes) compared to adolescents (7 hours) than adolescents did on weekends. As a group, the learners in this sample were morningness-orientated in terms of chronotype, presented with low day time sleepiness, some evidence of sleep-wake behaviour problems and of depressive mood symptoms. Nearly half (n=53; 43%) the group reported napping occasionally on school days. In terms of caffeine consumption, just over half (n=64; 52%) of the learners reported never consuming caffeinated substances such as soda, coffee, or tea. Conclusions: The reported sleep duration of learners in this study was consistent on both the week and weekend but was shorter than the recommended 8-10 hours for late adolescents. While learners in this sample reported early bedtimes, sleep was likely curtailed by the early rise times due to the contextual constraints where scholars had to commute, by either walking or taking public transport, to make the early school start times. There was a high prevalence of sleep disturbances in this sample however, the effects of this (increased daytime sleepiness) were lower which can be attributed to low reported prevalence of caffeine consumption combined with the high prevalence of reported day time napping on school days and weekends. While only a snapshot, the results of this study support previous research that has highlighted the challenges that many adolescents across the globe experience when it comes to obtaining enough sleep. The results of this study highlighted the need for more research to understand the sleep-wake behaviours of learners and their lifestyles more objectively. Given the early starts for many participants in this study, interventions such as delaying school start times may help to improve the amount of sleep that learners get during the week. However, extensive consultations would be needed to ensure that systemic changes that aim to improve sleep of adolescents are applicable for the context of rural and townships areas in South Africa. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2022
- Full Text:
- Date Issued: 2022-10-14
- Authors: Dlepu, Phelokazi
- Date: 2022-10-14
- Subjects: Teenagers Sleep South Africa Alice , Rural teenagers South Africa Alice , Sleep-wake cycle
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362808 , vital:65364
- Description: Introduction: School going adolescents have been identified as a group that is at risk of obtaining insufficient sleep due to shortened and irregular sleep, all of which can affect the overall wellbeing of adolescents. While there has been extenstive research on adolescent sleep around the world, research in South Africa has been limited. Of the research performed in this context, most has been conducted in city or urban contexts, but there has been comparatively less research on sleep in adolescents from rural and township areas. Therefore, this study focused on characterising and comparing the sleep-wake behaviour of late adolescents from selected rural and township areas in Alice in the Eastern Cape of South Africa. Methods: An adapted version School Sleep Habits Survey (SSHS) was included in the study and assessed demographic, academic, sleep-wake behaviour, lifestyle, and behavioural information of adolescents from rural and township schools in and around Alice. The survey was distributed physically to all the learners from four co-educational rural and township schools. The responses to the survey were analysed with descriptive and non-parametric inferential statistics, as all data were not normally distributed. Results: A total of 123 learners completed the survey. All the participants were in Grade 12, aged 16 to 26 years (median =18, IQR= 18-19) from rural (n=28) and township (n=95) schools. Seventy-four female and 49 male learners participated in the study. Within the sample, there were also a group of participants who were not adolescents (n=22) whose age ranged between 20 and 26. Reported sleep during both the week and weekend (7hours) was lower than both the recommended duration for adolescents and their own self-reported sleep need of a median of 8 hours and 14 minutes. Bedtimes were significantly earlier on weekdays than weekends. The need to do homework and feeling sleepy were cited as the main reasons for going to sleep during the week and the weekends. Wake times on weekdays and weekends did not differ, with most learners citing being woken up by an alarm clock as the main reason for waking during both weekdays and weekends. Most learners (n=47; 38%) reported walking to get to school, while 41 (33%) relied on public transport to get to school. There were no significant effects of gender or of being rural and township scholars in relation to their sleep variables. Comparisons between non-adolescents and adolescents revealed that non-adolescents reported sleeping longer (7 hours and 30 minutes) compared to adolescents (7 hours) than adolescents did on weekends. As a group, the learners in this sample were morningness-orientated in terms of chronotype, presented with low day time sleepiness, some evidence of sleep-wake behaviour problems and of depressive mood symptoms. Nearly half (n=53; 43%) the group reported napping occasionally on school days. In terms of caffeine consumption, just over half (n=64; 52%) of the learners reported never consuming caffeinated substances such as soda, coffee, or tea. Conclusions: The reported sleep duration of learners in this study was consistent on both the week and weekend but was shorter than the recommended 8-10 hours for late adolescents. While learners in this sample reported early bedtimes, sleep was likely curtailed by the early rise times due to the contextual constraints where scholars had to commute, by either walking or taking public transport, to make the early school start times. There was a high prevalence of sleep disturbances in this sample however, the effects of this (increased daytime sleepiness) were lower which can be attributed to low reported prevalence of caffeine consumption combined with the high prevalence of reported day time napping on school days and weekends. While only a snapshot, the results of this study support previous research that has highlighted the challenges that many adolescents across the globe experience when it comes to obtaining enough sleep. The results of this study highlighted the need for more research to understand the sleep-wake behaviours of learners and their lifestyles more objectively. Given the early starts for many participants in this study, interventions such as delaying school start times may help to improve the amount of sleep that learners get during the week. However, extensive consultations would be needed to ensure that systemic changes that aim to improve sleep of adolescents are applicable for the context of rural and townships areas in South Africa. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2022
- Full Text:
- Date Issued: 2022-10-14
Characterization of Trypanosoma brucei Sti1 and its interactions with Trypanosoma brucei Hsp83 and human Hsp90
- Authors: Jamabo, Miebaka
- Date: 2023-03-31
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/422629 , vital:71963 , DOI 10.21504/10962/422629
- Description: Neglected tropical diseases continue to pose global concern due to their impact on health and socio-economic status of developing countries in sub-Saharan Africa. African trypanosomiasis is one of the neglected tropical diseases caused by the kinetoplastid flagellate parasite Trypanosoma brucei (T. brucei). The disease is fatal if untreated and the toolbox to combat the disease has been plagued with many difficulties such as drug resistance, toxic chemotherapeutics, and cumbersome drug delivery processes. In recent years, the disease has received attention from organizations such as the Drugs for Neglected Diseases initiative (DNDi) in partnership with WHO as well as academia and industry to provide alternatives to the existing drugs as part of a targeted approach to eliminate human African trypanosomiasis by 2030. The life cycle of the T. brucei parasite requires that it transitions between a cold-blooded vector (the tsetse fly) and a human host. To survive this extreme environmental change and maintain its infectious cycle, the parasite has evolved an arsenal of tools which include a strong immune evasion technique and a robust molecular chaperone system. Heat shock protein 90 (Hsp90) is one of the most abundant eukaryotic molecular chaperones that has been extensively studied in many organisms. It is indispensable for maintaining proteostasis in some organisms and its inhibition is currently being explored as a drug target for cancer and other parasitic diseases. In T. brucei, cytosolic Hsp90 is specifically referred to as Hsp83 due to variations in the sizes amongst different orthologues. Hsp90 is present in high levels in all stages of the T. brucei cell cycle both constitutively and on exposure to stress. To function in the cell, Hsp90 is dependent on co-chaperones, one of which can be found in most organisms, namely, the stress-inducible protein 1 (Sti1). The Hsp90-Sti1 interaction was shown to be crucial for growth in the intracellular kinetoplastid parasite, Leishmania donovani. However, this partnership has not been explored in the extracellular parasite T. brucei. To analyse the interaction of Hsp90 with Sti1 in T. brucei, this study combined in silico, in vitro and in vivo tools. In silico analyses of the Hsp90 complement in T. brucei revealed the presence of twelve putative Hsp90 genes, ten of which code for the cytosolic protein and are arranged in tandem in a head to tail fashion on the same chromosome. One gene each was found for the mitochondrial and ER paralogues of Hsp90, similar to all other species analysed. Eight putative co-chaperones specific to T. brucei were also discovered: six tetratricopeptide repeat domain (TPR) containing co-chaperones and two non-TPR containing co-chaperones. Structural and evolutionary analysis also confirmed that the domains were conserved across the species analysed. T. brucei Sti1 (TbSti1), T. brucei cytosolic Hsp90 (TbHsp83) and human cytosolic Hsp90 (hHsp90) were heterologously overproduced in E. coli and purified using nickel affinity chromatography. With specific antibodies, the expression and localization of the proteins were confirmed. TbSti1 showed strong affinity to the Hsp90s in the nanomolar range, with higher affinity for hHsp90 compared to TbHsp83. TbHsp83 and hHsp90 showed typical chaperone properties by suppressing the aggregation of thermolabile substrate MDH at equimolar concentrations and both chaperones had potent ATP hydrolysis activity. TbSti1, on the other hand, showed no MDH suppression activity and did not affect the ATP hydrolysis activity of TbHsp83 or hHsp90. Ex-vivo experiments using HeLa CRISPR Hop knockout (KO) human cell lines transfected with pcDNA3.1(+)HA-TbSti1 revealed TbSti1 also localized to the cytoplasm. The transfected cells showed a distinct fibroblast-like morphology which was different from the circular morphology seen in the Hop KO untransfected and wild type untransfected cells. Finally, co-immunoprecipitation studies revealed that TbSti1 co-immunoprecipitated with hHsp90. These results show the first characterization of the TbHsp83-TbSti1 partnership in T. brucei. The strong association between both proteins suggests a functional role for this partnership in T. brucei and could provide an updated context for understanding Trypanosome brucei biology. , Thesis (PhD) -- Faculty of Science, Biotechnology and Innovation Centre, 2023
- Full Text:
- Date Issued: 2023-03-31
- Authors: Jamabo, Miebaka
- Date: 2023-03-31
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/422629 , vital:71963 , DOI 10.21504/10962/422629
- Description: Neglected tropical diseases continue to pose global concern due to their impact on health and socio-economic status of developing countries in sub-Saharan Africa. African trypanosomiasis is one of the neglected tropical diseases caused by the kinetoplastid flagellate parasite Trypanosoma brucei (T. brucei). The disease is fatal if untreated and the toolbox to combat the disease has been plagued with many difficulties such as drug resistance, toxic chemotherapeutics, and cumbersome drug delivery processes. In recent years, the disease has received attention from organizations such as the Drugs for Neglected Diseases initiative (DNDi) in partnership with WHO as well as academia and industry to provide alternatives to the existing drugs as part of a targeted approach to eliminate human African trypanosomiasis by 2030. The life cycle of the T. brucei parasite requires that it transitions between a cold-blooded vector (the tsetse fly) and a human host. To survive this extreme environmental change and maintain its infectious cycle, the parasite has evolved an arsenal of tools which include a strong immune evasion technique and a robust molecular chaperone system. Heat shock protein 90 (Hsp90) is one of the most abundant eukaryotic molecular chaperones that has been extensively studied in many organisms. It is indispensable for maintaining proteostasis in some organisms and its inhibition is currently being explored as a drug target for cancer and other parasitic diseases. In T. brucei, cytosolic Hsp90 is specifically referred to as Hsp83 due to variations in the sizes amongst different orthologues. Hsp90 is present in high levels in all stages of the T. brucei cell cycle both constitutively and on exposure to stress. To function in the cell, Hsp90 is dependent on co-chaperones, one of which can be found in most organisms, namely, the stress-inducible protein 1 (Sti1). The Hsp90-Sti1 interaction was shown to be crucial for growth in the intracellular kinetoplastid parasite, Leishmania donovani. However, this partnership has not been explored in the extracellular parasite T. brucei. To analyse the interaction of Hsp90 with Sti1 in T. brucei, this study combined in silico, in vitro and in vivo tools. In silico analyses of the Hsp90 complement in T. brucei revealed the presence of twelve putative Hsp90 genes, ten of which code for the cytosolic protein and are arranged in tandem in a head to tail fashion on the same chromosome. One gene each was found for the mitochondrial and ER paralogues of Hsp90, similar to all other species analysed. Eight putative co-chaperones specific to T. brucei were also discovered: six tetratricopeptide repeat domain (TPR) containing co-chaperones and two non-TPR containing co-chaperones. Structural and evolutionary analysis also confirmed that the domains were conserved across the species analysed. T. brucei Sti1 (TbSti1), T. brucei cytosolic Hsp90 (TbHsp83) and human cytosolic Hsp90 (hHsp90) were heterologously overproduced in E. coli and purified using nickel affinity chromatography. With specific antibodies, the expression and localization of the proteins were confirmed. TbSti1 showed strong affinity to the Hsp90s in the nanomolar range, with higher affinity for hHsp90 compared to TbHsp83. TbHsp83 and hHsp90 showed typical chaperone properties by suppressing the aggregation of thermolabile substrate MDH at equimolar concentrations and both chaperones had potent ATP hydrolysis activity. TbSti1, on the other hand, showed no MDH suppression activity and did not affect the ATP hydrolysis activity of TbHsp83 or hHsp90. Ex-vivo experiments using HeLa CRISPR Hop knockout (KO) human cell lines transfected with pcDNA3.1(+)HA-TbSti1 revealed TbSti1 also localized to the cytoplasm. The transfected cells showed a distinct fibroblast-like morphology which was different from the circular morphology seen in the Hop KO untransfected and wild type untransfected cells. Finally, co-immunoprecipitation studies revealed that TbSti1 co-immunoprecipitated with hHsp90. These results show the first characterization of the TbHsp83-TbSti1 partnership in T. brucei. The strong association between both proteins suggests a functional role for this partnership in T. brucei and could provide an updated context for understanding Trypanosome brucei biology. , Thesis (PhD) -- Faculty of Science, Biotechnology and Innovation Centre, 2023
- Full Text:
- Date Issued: 2023-03-31
Characterizing shift systems and exploring their effects on sleep and fatigue in South African freight railway operators
- Authors: Mona, Chumani
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424300 , vital:72141
- Description: Embargoed. Expected release date 2025. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Mona, Chumani
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424300 , vital:72141
- Description: Embargoed. Expected release date 2025. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2023
- Full Text:
- Date Issued: 2023-10-13
Chemostratigraphy of the lowermost iron-manganese cycle of the Hotazel Formation, and implications for its primary depositional environment
- Authors: Masoabi, Ntseka Thomas
- Date: 2022-10-14
- Subjects: Chemostratigraphy , Great Oxygenation Event , Manganese ores Geology South Africa Northern Cape , Banded iron formation
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362938 , vital:65376
- Description: The giant Kalahari Manganese Field (KMF), located in the Northern Cape Province, South Africa, comprises approximately half of the world’s manganese resources, estimated at about eight billion tons at grades ranging from 20-48 wt%. The KMF is linked to a period in geological time when the Earth’s atmospheric and oceanic conditions underwent a major transition from oxygen-deficient to oxygen-enriched conditions – an event famously referred to as the Great Oxidation Event (GOE) that occurred around 2.4 Ga. The KMF deposits are hosted in Banded Iron Formation (BIF) of the Paleoproterozoic Hotazel Formation in the uppermost Transvaal Supergroup. The sedimentary Mn ores are interbedded with Hotazel BIF in the form of three alternating depositional cycles of BIF, transitional hematite lutite and laminated, carbonate-rich manganese ore. The lowermost and thickest of the three cycles is the most economically significant and has been mined for several decades on a large scale from the southernmost KMF. In this study, two drill cores from the southern KMF were inspected, logged and sampled at a high resolution of approximately half-meter interval per sample. The selected cores, namely G774, capturing the lower portion of the Hotazel Formation from the Mamatwan locality, and MP-56, capturing the corresponding portion from the Middleplaats locality, are geographically proximal to each other, with a horizontal distance of roughly 3 km separating the two of them. The G774 drill core is characterized by a conspicuously thick manganese layer covering a thickness of 50 m, with the overlying BIF reaching a total thickness of 11 m. The MP-56 drill core, on the other hand, has a relatively thinner corresponding manganese layer of 30 m in thickness, while the overlying BIF layer exhibits a thickness of 24 m. The extent of sampling up-section was constrained by an apparently coeval black shale layer which represents the chosen upper stratigraphic marker for the lower part of the Hotazel section in the broader area that is under investigation in this thesis. That way, a high resolution chemostratigraphic approach was employed to elucidate the potential factors contributing to the relative sedimentary lateral thickness variations seen across the southernmost KMF. High-resolution geochemical data were used to explore relationships and signals that might constrain relative precipitation rates for iron and manganese against detrital species, fluctuating redox conditions in the original environment of deposition, and chemostratigraphic correlation. All geochemical data (i.e., major oxides, minor and trace elements and carbonate carbon isotopes) were obtained respectively through employing X-ray Fluorescence (XRF), Laser Ablation Inductively Coupled Mass Spectrometry (ICP-MS), and Gas-source mass spectrometry. Comparative considerations made between the bulk geochemistry of the two sequences (i.e., Mamatwan and Middleplaats sections) reveal that periods of high-Mn deposition in the Hotazel Formation appear to be very Ca-carbonate rich (as indicated by high CaO, LOI and Sr concentrations). This, in turn, suggests that the Mn abundance is in the Hotazel ores is controlled mainly by the silicate phase braunite and is diluted by the deposition of Ca-carbonate through time. Bulk-rock concentration results for trace elements of the High Field Strength Element (HFSE) group (namely Zr, Hf, Y, Nb and Sc) were utilized to constrain the rates of either clastic and/or volcanic detrital inputs, as they traditionally represent refractory mineral particles of a common detrital/volcanic origin. The two chemosedimentary sequences preserve these elements in very low and thus quantitatively negligible concentrations – suggesting that the Hotazel depositional environment received very low and insignificant influx of a terrigeneous detrital component. A selection of these elements was therefore used to deduce, with caution, the relative as opposed to absolute precipitation rate of the major chemical constituents (i.e., Fe + Si vs Mn + carbonate), assuming a constant detrital flux through time. It was found that the relative abundances of Zr, Y and Nb is roughly 1.5 – 2 times as high in the BIF lithofacies relative to the Mn ones at both localities. This led to the inference that the Mn-enriched portion of the sediment must have been deposited at approximately twice the rate that the Fe-rich (BIF) portion was originally deposited. In terms of redox-sensitive elements, the elements Co and Mo seem to reveal the most valuable insights into the redox environment of primary chemical deposition. Cobalt displays a unique pattern in that its highest concentration is attained at the hematite lutite transitions (similarly with the REE in this regard), while very low and seemingly invariant concentration is exhibited within the core of the main orebodies. The same pattern seems to be reproduced to a degree by the corresponding bulk MgO component, whereby MgO abundance maxima are associated with the basal hematite lutite and the hematitic flanks of the Mn-ore zone, while the core of the Mn-rich layer attains relatively low and essentially invariant MgO concentrations. This implicates a close and direct association of Co with the hematite fraction of the rocks and a concurrent enrichment in Mn-rich carbonate (dolomite). On the other hand, Mo seems to have a direct and clear association with peak MnO2 content of the rocks, which in turn presents a high possibility of Mo having adsorbed onto primary Mn-oxyhydroxides in the water column, thus providing evidence that Mn-oxide must have acted as an important Mo sink, at least locally. Finally, the carbonate-carbon isotope results provide a useful tool that brings the two stratigraphic sections “together“, in conjunction with other correlatable chemostratigraphic parameters (e.g. Co, Mg). The results demonstrate that bulk carbon fluxes and isotopic signals in the sediments must reflect primary processes of deposition, and that correlation across two apparently disparate lithostratigraphic sections can be effected. The key finding is that, at times, manganese deposition in one part of a vii stratified basin was evidently accompanied by simultaneous BIF deposition at another, thus painting a very complex picture of massive primary chemical precipitation of Fe and Mn at the dawn of the GOE. , Thesis (MSc) -- Faculty of Science, Geology, 2022
- Full Text:
- Date Issued: 2022-10-14
- Authors: Masoabi, Ntseka Thomas
- Date: 2022-10-14
- Subjects: Chemostratigraphy , Great Oxygenation Event , Manganese ores Geology South Africa Northern Cape , Banded iron formation
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362938 , vital:65376
- Description: The giant Kalahari Manganese Field (KMF), located in the Northern Cape Province, South Africa, comprises approximately half of the world’s manganese resources, estimated at about eight billion tons at grades ranging from 20-48 wt%. The KMF is linked to a period in geological time when the Earth’s atmospheric and oceanic conditions underwent a major transition from oxygen-deficient to oxygen-enriched conditions – an event famously referred to as the Great Oxidation Event (GOE) that occurred around 2.4 Ga. The KMF deposits are hosted in Banded Iron Formation (BIF) of the Paleoproterozoic Hotazel Formation in the uppermost Transvaal Supergroup. The sedimentary Mn ores are interbedded with Hotazel BIF in the form of three alternating depositional cycles of BIF, transitional hematite lutite and laminated, carbonate-rich manganese ore. The lowermost and thickest of the three cycles is the most economically significant and has been mined for several decades on a large scale from the southernmost KMF. In this study, two drill cores from the southern KMF were inspected, logged and sampled at a high resolution of approximately half-meter interval per sample. The selected cores, namely G774, capturing the lower portion of the Hotazel Formation from the Mamatwan locality, and MP-56, capturing the corresponding portion from the Middleplaats locality, are geographically proximal to each other, with a horizontal distance of roughly 3 km separating the two of them. The G774 drill core is characterized by a conspicuously thick manganese layer covering a thickness of 50 m, with the overlying BIF reaching a total thickness of 11 m. The MP-56 drill core, on the other hand, has a relatively thinner corresponding manganese layer of 30 m in thickness, while the overlying BIF layer exhibits a thickness of 24 m. The extent of sampling up-section was constrained by an apparently coeval black shale layer which represents the chosen upper stratigraphic marker for the lower part of the Hotazel section in the broader area that is under investigation in this thesis. That way, a high resolution chemostratigraphic approach was employed to elucidate the potential factors contributing to the relative sedimentary lateral thickness variations seen across the southernmost KMF. High-resolution geochemical data were used to explore relationships and signals that might constrain relative precipitation rates for iron and manganese against detrital species, fluctuating redox conditions in the original environment of deposition, and chemostratigraphic correlation. All geochemical data (i.e., major oxides, minor and trace elements and carbonate carbon isotopes) were obtained respectively through employing X-ray Fluorescence (XRF), Laser Ablation Inductively Coupled Mass Spectrometry (ICP-MS), and Gas-source mass spectrometry. Comparative considerations made between the bulk geochemistry of the two sequences (i.e., Mamatwan and Middleplaats sections) reveal that periods of high-Mn deposition in the Hotazel Formation appear to be very Ca-carbonate rich (as indicated by high CaO, LOI and Sr concentrations). This, in turn, suggests that the Mn abundance is in the Hotazel ores is controlled mainly by the silicate phase braunite and is diluted by the deposition of Ca-carbonate through time. Bulk-rock concentration results for trace elements of the High Field Strength Element (HFSE) group (namely Zr, Hf, Y, Nb and Sc) were utilized to constrain the rates of either clastic and/or volcanic detrital inputs, as they traditionally represent refractory mineral particles of a common detrital/volcanic origin. The two chemosedimentary sequences preserve these elements in very low and thus quantitatively negligible concentrations – suggesting that the Hotazel depositional environment received very low and insignificant influx of a terrigeneous detrital component. A selection of these elements was therefore used to deduce, with caution, the relative as opposed to absolute precipitation rate of the major chemical constituents (i.e., Fe + Si vs Mn + carbonate), assuming a constant detrital flux through time. It was found that the relative abundances of Zr, Y and Nb is roughly 1.5 – 2 times as high in the BIF lithofacies relative to the Mn ones at both localities. This led to the inference that the Mn-enriched portion of the sediment must have been deposited at approximately twice the rate that the Fe-rich (BIF) portion was originally deposited. In terms of redox-sensitive elements, the elements Co and Mo seem to reveal the most valuable insights into the redox environment of primary chemical deposition. Cobalt displays a unique pattern in that its highest concentration is attained at the hematite lutite transitions (similarly with the REE in this regard), while very low and seemingly invariant concentration is exhibited within the core of the main orebodies. The same pattern seems to be reproduced to a degree by the corresponding bulk MgO component, whereby MgO abundance maxima are associated with the basal hematite lutite and the hematitic flanks of the Mn-ore zone, while the core of the Mn-rich layer attains relatively low and essentially invariant MgO concentrations. This implicates a close and direct association of Co with the hematite fraction of the rocks and a concurrent enrichment in Mn-rich carbonate (dolomite). On the other hand, Mo seems to have a direct and clear association with peak MnO2 content of the rocks, which in turn presents a high possibility of Mo having adsorbed onto primary Mn-oxyhydroxides in the water column, thus providing evidence that Mn-oxide must have acted as an important Mo sink, at least locally. Finally, the carbonate-carbon isotope results provide a useful tool that brings the two stratigraphic sections “together“, in conjunction with other correlatable chemostratigraphic parameters (e.g. Co, Mg). The results demonstrate that bulk carbon fluxes and isotopic signals in the sediments must reflect primary processes of deposition, and that correlation across two apparently disparate lithostratigraphic sections can be effected. The key finding is that, at times, manganese deposition in one part of a vii stratified basin was evidently accompanied by simultaneous BIF deposition at another, thus painting a very complex picture of massive primary chemical precipitation of Fe and Mn at the dawn of the GOE. , Thesis (MSc) -- Faculty of Science, Geology, 2022
- Full Text:
- Date Issued: 2022-10-14
Cloning, expression, partial characterisation and application of a recombinant GH10 xylanase, XT6, from Geobacillus stearothermophilus T6 as an additive to chicken feeds
- Authors: Sithole, Tariro
- Date: 2022-04-06
- Subjects: Chicken feed industry , Chickens Feeding and feeds , Bacillus (Bacteria) , Xylanases , Polysaccharides , Geobacillus stearothermophilus
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/292693 , vital:57007
- Description: Monogastric animal farming has largely been sustained by feeding animals with grain feedstocks containing non-starch polysaccharides (NSPs) and anti-nutritive factors, which cause adverse effects, such as increased digesta viscosity and entrapment of nutrients, which leads to the inaccessibility of nutrients. These effects have been linked to a reduction in nutrient digestion and absorption, which results in a decreased feed conversion ratio, energy metabolism and animal growth. Monogastric animals do not produce enzymes that can hydrolyse these NSPs. The application of exogenous enzymes as supplements to animal feeds has been implemented to reduce viscosity and increase nutrient absorption in poultry and pigs over the past few decades. The aim of this study was to clone, express, partially characterise and apply a glycoside hydrolase (GH) family 10 xylanase (XT6), derived from Geobacillus stearothermophilus T6, as an additive to locally produced chicken feeds. The xt6 gene (1,236 bp) was subcloned and expressed in Escherichia coli DH5α and BL21(DE3) cells, respectively. Upon expression, XT6 had a molecular weight of 42 kDa and was partially purified by Ni-NTA chromatography and ultrafiltration. The purification step resulted in a yield of 66.7% with a 16.8-fold increase in purification. XT6 exhibited maximal activity when incubated at a pH and temperature of pH 6.0 and 70°C, respectively, with a high thermostability over a broad range of pH (2–9) and temperature (30–90 °C). The specific activities of XT6 on extracted soluble and insoluble wheat flour arabinoxylans were 110.9 U/mg and 63.98 U/mg, respectively. Kinetic data showed that XT6 displayed a higher catalytic activity and affinity (Vmax = 231.60 μmol/min/mg and KM = 2.759 mg/ml) for soluble wheat arabinoxylan, compared to insoluble wheat arabinoxylan (Vmax = 99.02 μmol/min/mg and KM = 5.058 mg/ml). High-performance liquid chromatography (HPLC) analysis showed that the enzyme hydrolysed wheat flour, arabinoxylan and chicken feeds, producing a range of xylooligosaccharides (XOS), with xylotetraose and xylopentaose being the predominant XOS species. Hydrolysis of both soluble and insoluble wheat flour arabinoxylans by XT6 led to a significant reduction in substrate viscosity. The effects of simulated gastrointestinal fluid contents, such as proteases, bile salts and mucins, on XT6 stability were also studied. Exposure of XT6 to pepsin did not significantly reduce its activity; however, the inhibitory effect of trypsin and mucin on XT6 was much greater. The presence of gut-derived bile salts had no iii | P a g e significant effect on XT6 activity. Finally, it was shown that the XOS produced from the hydrolysis of chicken feeds (starter and grower feeds) by XT6 significantly enhanced the growth of the probiotic bacteria B. subtilis, while there was no significant improvement in the growth of S. thermophilus and L. bulgaricus. In conclusion, the recombinantly produced XT6 demonstrated efficient hydrolysis of starter and grower feeds, and produced XOS that showed prebiotic activity on selected probiotic bacteria. In addition, the pH, temperature and simulated gastric juice content stability of XT6 renders it an attractive candidate as an additive for chicken feeds. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-04-06
- Authors: Sithole, Tariro
- Date: 2022-04-06
- Subjects: Chicken feed industry , Chickens Feeding and feeds , Bacillus (Bacteria) , Xylanases , Polysaccharides , Geobacillus stearothermophilus
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/292693 , vital:57007
- Description: Monogastric animal farming has largely been sustained by feeding animals with grain feedstocks containing non-starch polysaccharides (NSPs) and anti-nutritive factors, which cause adverse effects, such as increased digesta viscosity and entrapment of nutrients, which leads to the inaccessibility of nutrients. These effects have been linked to a reduction in nutrient digestion and absorption, which results in a decreased feed conversion ratio, energy metabolism and animal growth. Monogastric animals do not produce enzymes that can hydrolyse these NSPs. The application of exogenous enzymes as supplements to animal feeds has been implemented to reduce viscosity and increase nutrient absorption in poultry and pigs over the past few decades. The aim of this study was to clone, express, partially characterise and apply a glycoside hydrolase (GH) family 10 xylanase (XT6), derived from Geobacillus stearothermophilus T6, as an additive to locally produced chicken feeds. The xt6 gene (1,236 bp) was subcloned and expressed in Escherichia coli DH5α and BL21(DE3) cells, respectively. Upon expression, XT6 had a molecular weight of 42 kDa and was partially purified by Ni-NTA chromatography and ultrafiltration. The purification step resulted in a yield of 66.7% with a 16.8-fold increase in purification. XT6 exhibited maximal activity when incubated at a pH and temperature of pH 6.0 and 70°C, respectively, with a high thermostability over a broad range of pH (2–9) and temperature (30–90 °C). The specific activities of XT6 on extracted soluble and insoluble wheat flour arabinoxylans were 110.9 U/mg and 63.98 U/mg, respectively. Kinetic data showed that XT6 displayed a higher catalytic activity and affinity (Vmax = 231.60 μmol/min/mg and KM = 2.759 mg/ml) for soluble wheat arabinoxylan, compared to insoluble wheat arabinoxylan (Vmax = 99.02 μmol/min/mg and KM = 5.058 mg/ml). High-performance liquid chromatography (HPLC) analysis showed that the enzyme hydrolysed wheat flour, arabinoxylan and chicken feeds, producing a range of xylooligosaccharides (XOS), with xylotetraose and xylopentaose being the predominant XOS species. Hydrolysis of both soluble and insoluble wheat flour arabinoxylans by XT6 led to a significant reduction in substrate viscosity. The effects of simulated gastrointestinal fluid contents, such as proteases, bile salts and mucins, on XT6 stability were also studied. Exposure of XT6 to pepsin did not significantly reduce its activity; however, the inhibitory effect of trypsin and mucin on XT6 was much greater. The presence of gut-derived bile salts had no iii | P a g e significant effect on XT6 activity. Finally, it was shown that the XOS produced from the hydrolysis of chicken feeds (starter and grower feeds) by XT6 significantly enhanced the growth of the probiotic bacteria B. subtilis, while there was no significant improvement in the growth of S. thermophilus and L. bulgaricus. In conclusion, the recombinantly produced XT6 demonstrated efficient hydrolysis of starter and grower feeds, and produced XOS that showed prebiotic activity on selected probiotic bacteria. In addition, the pH, temperature and simulated gastric juice content stability of XT6 renders it an attractive candidate as an additive for chicken feeds. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-04-06
Coastal movements and estuarine use of sub-adult and adult leervis, lichia amia: results from long-term acoustic tracking
- Authors: Mxo, Rebecca Vuyolwethu
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422314 , vital:71930
- Description: Information on fish movement is important not only for understanding a species’ ecological importance, but also for developing appropriate conservation and management policies that are critical for food security and biodiversity preservation. This information is particularly important for species that occupy different habitats at different life history stages, and display predictable movement patterns, such as an annual spawning migration. Leervis Lichia amia is an estuary-dependent fishery species of high ecological and recreational importance in South Africa. There has been a steady decline in catch-per-unit-effort in the marine recreational fishery for this species over the past 20 years, and the most recent stock assessment classified the adult stock as collapsed. This study investigates L. amia multi-year coastal migrations and estuarine habitat use of sub-adult and adult fish tagged with long-life acoustic transmitters Seventy-eight L. amia (two juveniles, fifty-four subadults, and twenty-one adults) were tagged throughout their South African distribution and monitored between 2011 and 2020 producing a decade long dataset. Results show that regardless of the tagging region, clear migration patterns were observed, demonstrating that both sub-adult and adult L. amia migrate annually to KZN in the austral winter and predictably return to the WC and EC waters in the summer. The likelihood of partial migration was also identified, with the coexistence of migratory and resident behaviors within a single L. amia population. In addition, Overwintering behaviour was also observed with L. amia adults that remained resident throughout the year, foregoing the annual migration, phenomenon known as skipped spawning, and homing behaviour, where L. amia, particularly those tagged in the EC and WC, were recorded returning to previously occupied tagging locations and surrounding areas. The importance of estuaries to sub-adult and adult fish was also assessed and identified the importance of estuaries not only to subadults but also to adults. Estuary visits were strongly influenced by the environment which the fish was tagged in, temporal and seasonal changes, and life-history stages. The predictability of their migrations (almost to the day), the varied migratory behaviour (overwintering), returning to sites of familiarity post-migration, and long-term dependency on estuaries even as sub-adults and adults, provide motivation for increased protection of this species, including extending the network of estuarine protected areas in the country, and a closed fishing season, particularly during the annual winter migration. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2023
- Full Text:
- Date Issued: 2023-03-29
- Authors: Mxo, Rebecca Vuyolwethu
- Date: 2023-03-29
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422314 , vital:71930
- Description: Information on fish movement is important not only for understanding a species’ ecological importance, but also for developing appropriate conservation and management policies that are critical for food security and biodiversity preservation. This information is particularly important for species that occupy different habitats at different life history stages, and display predictable movement patterns, such as an annual spawning migration. Leervis Lichia amia is an estuary-dependent fishery species of high ecological and recreational importance in South Africa. There has been a steady decline in catch-per-unit-effort in the marine recreational fishery for this species over the past 20 years, and the most recent stock assessment classified the adult stock as collapsed. This study investigates L. amia multi-year coastal migrations and estuarine habitat use of sub-adult and adult fish tagged with long-life acoustic transmitters Seventy-eight L. amia (two juveniles, fifty-four subadults, and twenty-one adults) were tagged throughout their South African distribution and monitored between 2011 and 2020 producing a decade long dataset. Results show that regardless of the tagging region, clear migration patterns were observed, demonstrating that both sub-adult and adult L. amia migrate annually to KZN in the austral winter and predictably return to the WC and EC waters in the summer. The likelihood of partial migration was also identified, with the coexistence of migratory and resident behaviors within a single L. amia population. In addition, Overwintering behaviour was also observed with L. amia adults that remained resident throughout the year, foregoing the annual migration, phenomenon known as skipped spawning, and homing behaviour, where L. amia, particularly those tagged in the EC and WC, were recorded returning to previously occupied tagging locations and surrounding areas. The importance of estuaries to sub-adult and adult fish was also assessed and identified the importance of estuaries not only to subadults but also to adults. Estuary visits were strongly influenced by the environment which the fish was tagged in, temporal and seasonal changes, and life-history stages. The predictability of their migrations (almost to the day), the varied migratory behaviour (overwintering), returning to sites of familiarity post-migration, and long-term dependency on estuaries even as sub-adults and adults, provide motivation for increased protection of this species, including extending the network of estuarine protected areas in the country, and a closed fishing season, particularly during the annual winter migration. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2023
- Full Text:
- Date Issued: 2023-03-29
Colonial displacements and African coping strategies: The experience of BaTonga of Binga, Zimbabwe, 1956-2008
- Authors: Dhodho, Codelia Govha
- Date: 2022-10-14
- Subjects: Tonga (Zambezi people) Refugees , Subsistence farming Zambezi River Valley , Hunger Zambezi River Valley , Food security Zambezi River Valley , Adaptability (Psychology) , Food relief Zambezi River Valley , Non-governmental organizations , Kariba Dam (Zambia and Zimbabwe)
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/327642 , vital:61139 , DOI 10.21504/10962/327642
- Description: This study examines the challenges faced by BaTonga in livelihood reconstruction after involuntary displacement and resettlement from the Zambezi valley to pave way for the Kariba dam reservoir. It shows how they were forcibly evicted without compensation because of the racist policies of Southern Rhodesia. Their resettlement into an arid region infested with marauding elephants, malaria and tsetse fly undermined their complex livelihoods and eroded their self-sufficiency, but the study argues that they were active and resilient agents who adopted complex coping strategies. It shows how they had to adapt to dry-land farming and counter the effects of wildlife which plundered their crops and managed to secure the harvest in the drought-prone region. The study shows that although they adopted precarious livelihoods, they managed to survive under extreme circumstances for decades without any external assistance until the coming of NGOs who began to distribute free food from 1982. It argues that prolonged distribution of emergence food aid may not have been necessary, but its coming for almost three decades largely served political interests of both the NGOs and their governments. This perpetuated poverty as BaTonga also manipulated its distribution as a coping strategy against fragile livelihoods. This caused dependency which further plunged them into chronic food insecurity because they abandoned their traditional coping strategies. The study argues that both the colonial and postcolonial government as well as NGOs failed to address the root causes of livelihood insecurity in Binga for the five decades under study. It is therefore the contention of this study that the problem of food insecurity in Binga was not only an issue of recurring drought but was deeply rooted and pervasive due to multiple complex factors which made it difficult for the people to establish sustainable food production after displacement. , Thesis (PhD) -- Faculty of Humanities, History, 2022
- Full Text:
- Date Issued: 2022-10-14
- Authors: Dhodho, Codelia Govha
- Date: 2022-10-14
- Subjects: Tonga (Zambezi people) Refugees , Subsistence farming Zambezi River Valley , Hunger Zambezi River Valley , Food security Zambezi River Valley , Adaptability (Psychology) , Food relief Zambezi River Valley , Non-governmental organizations , Kariba Dam (Zambia and Zimbabwe)
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/327642 , vital:61139 , DOI 10.21504/10962/327642
- Description: This study examines the challenges faced by BaTonga in livelihood reconstruction after involuntary displacement and resettlement from the Zambezi valley to pave way for the Kariba dam reservoir. It shows how they were forcibly evicted without compensation because of the racist policies of Southern Rhodesia. Their resettlement into an arid region infested with marauding elephants, malaria and tsetse fly undermined their complex livelihoods and eroded their self-sufficiency, but the study argues that they were active and resilient agents who adopted complex coping strategies. It shows how they had to adapt to dry-land farming and counter the effects of wildlife which plundered their crops and managed to secure the harvest in the drought-prone region. The study shows that although they adopted precarious livelihoods, they managed to survive under extreme circumstances for decades without any external assistance until the coming of NGOs who began to distribute free food from 1982. It argues that prolonged distribution of emergence food aid may not have been necessary, but its coming for almost three decades largely served political interests of both the NGOs and their governments. This perpetuated poverty as BaTonga also manipulated its distribution as a coping strategy against fragile livelihoods. This caused dependency which further plunged them into chronic food insecurity because they abandoned their traditional coping strategies. The study argues that both the colonial and postcolonial government as well as NGOs failed to address the root causes of livelihood insecurity in Binga for the five decades under study. It is therefore the contention of this study that the problem of food insecurity in Binga was not only an issue of recurring drought but was deeply rooted and pervasive due to multiple complex factors which made it difficult for the people to establish sustainable food production after displacement. , Thesis (PhD) -- Faculty of Humanities, History, 2022
- Full Text:
- Date Issued: 2022-10-14
Comparison of the metabolic physiology of exploited and unexploited populations of red roman (Chrysoblephus laticeps) along the south coast of South Africa
- Authors: Nabani, Xolani Prince
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424358 , vital:72146
- Description: Anthropogenic-induced climate change and exploitation pose threat to many marine fishes on which a vast majority of people around the world depend. Rapid changes in sea surface temperature have a direct impact on the physiology of ectothermic organisms such as fish, potentially resulting in changes to population distribution, abundance, and demographics. In the face of climate change, the impacts of increasing temperature variability on fish populations may be exacerbated by exploitation. Understanding how the resilience of exploited populations is affected by climate change is critical to predict how fishes will respond in the future. This study aimed to augment our knowledge on the impact of exploitation and thermal variability on fishes by comparing the thermal physiology of an exploited and unexploited population of the resident, reef-dwelling, Chrysoblephus laticeps. Twenty live fish were collected from the exploited, Cape St Francis and 18 fish from the unexploited, Goukamma Marine Protected Area and transported to the laboratory. The metabolic performance, in terms of standard metabolic rate (SMR), maximum metabolic rate (MMR) and aerobic scope (AS) of individual C. laticeps were estimated repeatedly at 10 ℃, 16 °C and 21 °C. Linear mixed effects models were used to examine the relationship between temperature, population, and metabolic rate and a ‘cvequality’ test analysis was used to compare the variance structure of the metabolic rate regression model for each population. Overall, the findings of this study show that Chrysoblephus laticeps from the unexploited population maintains a significantly higher aerobic scope (AS) across all temperature treatments (10, 16 and 21 ℃) when compared with those from the exploited population. In addition, the maximum metabolic rate (MMR) of individuals from the unexploited population was significantly higher than that of individuals from the exploited population, but there was no evidence to suggest that variability was significantly different between the populations. On the other hand, the individuals from an exploited population had a significantly higher standard metabolic rate (SMR) at high temperatures of 21 ℃, while the unexploited population had a low SMR at these high temperatures, but a high SMR at 10 ℃. Despite these differences there was no significant variation in the SMR between the two populations. The findings of this study confirm previous work on different exploited and unexploited populations of C. laticeps and together these findings suggest that hook and line exploitation lead to reduced physiological phenotypic diversity and reduced physiological performance in exploited fish populations. These findings emphasise the importance of incorporating the iii physiological information to develop viable fisheries management tools in the context of climate change. This study also highlights the effectiveness of MPAs in conserving highperformance physiological phenotypes to maintain phenotypic diversity in fish populations. Future research should aim to evaluate the efficacy of existing MPAs in preserving the physiological diversity of important hook and line fisheries species, while fisheries managers should consider augmenting their approaches through the incorporation of well-designed MPA’s to promote physiological diversity. This will be critical to advance the development of sustainable management practices, not only in a South African context but globally, where oceanic and coastal environmental conditions are expected to rapidly change in the future. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Nabani, Xolani Prince
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424358 , vital:72146
- Description: Anthropogenic-induced climate change and exploitation pose threat to many marine fishes on which a vast majority of people around the world depend. Rapid changes in sea surface temperature have a direct impact on the physiology of ectothermic organisms such as fish, potentially resulting in changes to population distribution, abundance, and demographics. In the face of climate change, the impacts of increasing temperature variability on fish populations may be exacerbated by exploitation. Understanding how the resilience of exploited populations is affected by climate change is critical to predict how fishes will respond in the future. This study aimed to augment our knowledge on the impact of exploitation and thermal variability on fishes by comparing the thermal physiology of an exploited and unexploited population of the resident, reef-dwelling, Chrysoblephus laticeps. Twenty live fish were collected from the exploited, Cape St Francis and 18 fish from the unexploited, Goukamma Marine Protected Area and transported to the laboratory. The metabolic performance, in terms of standard metabolic rate (SMR), maximum metabolic rate (MMR) and aerobic scope (AS) of individual C. laticeps were estimated repeatedly at 10 ℃, 16 °C and 21 °C. Linear mixed effects models were used to examine the relationship between temperature, population, and metabolic rate and a ‘cvequality’ test analysis was used to compare the variance structure of the metabolic rate regression model for each population. Overall, the findings of this study show that Chrysoblephus laticeps from the unexploited population maintains a significantly higher aerobic scope (AS) across all temperature treatments (10, 16 and 21 ℃) when compared with those from the exploited population. In addition, the maximum metabolic rate (MMR) of individuals from the unexploited population was significantly higher than that of individuals from the exploited population, but there was no evidence to suggest that variability was significantly different between the populations. On the other hand, the individuals from an exploited population had a significantly higher standard metabolic rate (SMR) at high temperatures of 21 ℃, while the unexploited population had a low SMR at these high temperatures, but a high SMR at 10 ℃. Despite these differences there was no significant variation in the SMR between the two populations. The findings of this study confirm previous work on different exploited and unexploited populations of C. laticeps and together these findings suggest that hook and line exploitation lead to reduced physiological phenotypic diversity and reduced physiological performance in exploited fish populations. These findings emphasise the importance of incorporating the iii physiological information to develop viable fisheries management tools in the context of climate change. This study also highlights the effectiveness of MPAs in conserving highperformance physiological phenotypes to maintain phenotypic diversity in fish populations. Future research should aim to evaluate the efficacy of existing MPAs in preserving the physiological diversity of important hook and line fisheries species, while fisheries managers should consider augmenting their approaches through the incorporation of well-designed MPA’s to promote physiological diversity. This will be critical to advance the development of sustainable management practices, not only in a South African context but globally, where oceanic and coastal environmental conditions are expected to rapidly change in the future. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2023
- Full Text:
- Date Issued: 2023-10-13
Composition and physiological roles of gut microbiota in the False Coding Moth (Thaumatotibia leucotreta)
- Authors: Richardson, Perryn Heather
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424457 , vital:72155
- Description: Gut microbiota can have a profound influence on host performance, behaviour and fitness. For False Codling Moth (FCM), Thaumatotibia leucotreta (Lepidoptera: Tortricidae), a major pest of citrus in South Africa, little work has been undertaken to date on gut microbe diversity or its influence on the host. This thesis aimed to i) characterise the gut microbiome of FCM under laboratory conditions and in FCM from the field, ii) and produce moths with reduced gut microbiota through egg dechorionation, which was followed by iii) the measurement of a suite of physiological traits, namely mass, survival and thermal stress in FCM from normal laboratory, dechorionated laboratory and field collected larvae that may be indicative of overall field performance. We aimed to directly test the hypothesis that gut microbial diversity partly determines insect performance and fitness by measuring its effects on growth, development, and tolerance to cold temperatures in FCM. FCM eggs that underwent dechorionation with sodium hypochlorite had an overall effect on larval survival, egg morphology and both larval and adult moth physiological measures. Increasing concentrations of sodium hypochlorite significantly decreased insect survival, (𝜒2(1, n = 10 850) = 21.724, p-value < 0.0001), with a concentration of ≈3.69% as the concentration limit (p-value < 0.001). Successful dechorionation of FCM was achieved with a wash of sodium hypochlorite at around 3.69% concentration and was visually confirmed by reduction of FCM egg surface area, (𝜒2(25, n = 260) p-value < 0.0001) and Scanning Electron Micrographs of the egg morphology. The gut microbiome of FCM from the different focus treatments was successfully characterized. Identification of the dominant bacterial families in these microbiomes revealed Xanthobacteraceae, Beijerinckiaceae and Burkholderiaceae in both the laboratory reared and field collected larvae, which suggests their systematic association with T. leucotreta. The most abundant genera were revealed as Bradyrhizobium, Methylobacterium and Burkholderia-Caballeronia-Paraburkholderia. Comparison of larval mass showed that treatment (dechorionated or not) had a significant effect on larval mass (𝜒2(2, n = 230) = 22.703, p-value < 0.001), field larvae were heavier than both control larvae and larvae with a disrupted gut microbiome. However, adult insects with a disrupted gut microbiome had more mass than individuals from the control and field-collected larvae with intact gut microbiomes (𝜒2(2, n = 230) = 39.074, p-value < 0.001). Despite the difference in mass between larval treatments, there was no significant difference in relative protein (𝜒2(2, n = 24) = 5.680, p-value = 0.06), carbohydrate (𝜒2(2, n = 24) = 3.940, p-value = 0.14) or lipid (𝜒2(2, n = 24) = 6.032, p-value = 0.05) content between individuals from the control and dechorionated treatments and field-collected individuals. Turning to thermal physiology, insects collected from the field took significantly longer to recover from chill coma than both laboratory treatments with intact and disrupted gut microbiomes (𝜒2(2, n = 129 = 39.659, p-value < 0.001). In addition, exposure to cold stress showed that treatment had a significant effect on insect mortality (𝜒2(2, n = 272) = 9.176, p-value = 0.01), with individuals from the control and dechorionated treatment being less likely to die after experiencing cold stress compared to field-collected individuals. Differences in the mass and thermal tolerance of insects with intact and disrupted gut microbiota suggest that gut microbiota may play an important role in the cold performance of T. leucotreta, and these findings constitute the basis for future molecular work on the functions of these bacterial taxa. This research highlights the need for consideration of the effects of T. leucotreta microbiome in current pest control programs. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Date Issued: 2023-10-13
- Authors: Richardson, Perryn Heather
- Date: 2023-10-13
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/424457 , vital:72155
- Description: Gut microbiota can have a profound influence on host performance, behaviour and fitness. For False Codling Moth (FCM), Thaumatotibia leucotreta (Lepidoptera: Tortricidae), a major pest of citrus in South Africa, little work has been undertaken to date on gut microbe diversity or its influence on the host. This thesis aimed to i) characterise the gut microbiome of FCM under laboratory conditions and in FCM from the field, ii) and produce moths with reduced gut microbiota through egg dechorionation, which was followed by iii) the measurement of a suite of physiological traits, namely mass, survival and thermal stress in FCM from normal laboratory, dechorionated laboratory and field collected larvae that may be indicative of overall field performance. We aimed to directly test the hypothesis that gut microbial diversity partly determines insect performance and fitness by measuring its effects on growth, development, and tolerance to cold temperatures in FCM. FCM eggs that underwent dechorionation with sodium hypochlorite had an overall effect on larval survival, egg morphology and both larval and adult moth physiological measures. Increasing concentrations of sodium hypochlorite significantly decreased insect survival, (𝜒2(1, n = 10 850) = 21.724, p-value < 0.0001), with a concentration of ≈3.69% as the concentration limit (p-value < 0.001). Successful dechorionation of FCM was achieved with a wash of sodium hypochlorite at around 3.69% concentration and was visually confirmed by reduction of FCM egg surface area, (𝜒2(25, n = 260) p-value < 0.0001) and Scanning Electron Micrographs of the egg morphology. The gut microbiome of FCM from the different focus treatments was successfully characterized. Identification of the dominant bacterial families in these microbiomes revealed Xanthobacteraceae, Beijerinckiaceae and Burkholderiaceae in both the laboratory reared and field collected larvae, which suggests their systematic association with T. leucotreta. The most abundant genera were revealed as Bradyrhizobium, Methylobacterium and Burkholderia-Caballeronia-Paraburkholderia. Comparison of larval mass showed that treatment (dechorionated or not) had a significant effect on larval mass (𝜒2(2, n = 230) = 22.703, p-value < 0.001), field larvae were heavier than both control larvae and larvae with a disrupted gut microbiome. However, adult insects with a disrupted gut microbiome had more mass than individuals from the control and field-collected larvae with intact gut microbiomes (𝜒2(2, n = 230) = 39.074, p-value < 0.001). Despite the difference in mass between larval treatments, there was no significant difference in relative protein (𝜒2(2, n = 24) = 5.680, p-value = 0.06), carbohydrate (𝜒2(2, n = 24) = 3.940, p-value = 0.14) or lipid (𝜒2(2, n = 24) = 6.032, p-value = 0.05) content between individuals from the control and dechorionated treatments and field-collected individuals. Turning to thermal physiology, insects collected from the field took significantly longer to recover from chill coma than both laboratory treatments with intact and disrupted gut microbiomes (𝜒2(2, n = 129 = 39.659, p-value < 0.001). In addition, exposure to cold stress showed that treatment had a significant effect on insect mortality (𝜒2(2, n = 272) = 9.176, p-value = 0.01), with individuals from the control and dechorionated treatment being less likely to die after experiencing cold stress compared to field-collected individuals. Differences in the mass and thermal tolerance of insects with intact and disrupted gut microbiota suggest that gut microbiota may play an important role in the cold performance of T. leucotreta, and these findings constitute the basis for future molecular work on the functions of these bacterial taxa. This research highlights the need for consideration of the effects of T. leucotreta microbiome in current pest control programs. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
- Full Text:
- Date Issued: 2023-10-13
Composition Portfolio
- Authors: Bessey, Warren Gregory
- Date: 2023-04-10
- Subjects: Composition (Music) , Zulu (African people) Songs and music , Music Cross-cultural studies , uMkabayi kaJama , Nandi , Nobility South Africa Zululand History
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/404940 , vital:70123
- Description: Excerpt from Introduction: My interest in the Zulu royal family intensified as I began to read many stories and have lengthy conversations with members of the Zulu royal family and others, including Dr Maxwell Shamase (University of Zululand), about Zulu history. I was struck by the power and prowess of Princess Mkabayi (1750-1843). The elders were said to be speechless when she spoke. According to Shamase, a common Zulu expression which references Mkabayi’s well-known verbal skill is Umuntu ukhuluma kome umlomo, and translates as [like Mkabayi] the speaker speaks clearly and leaves no room for misunderstandings and misinterpretations. I found her to be a brilliant strategist with a servant heart and one whom history had not given due credit, and I was inspired to bring her story to life by setting it to music. I wanted to explore whether or not the events surrounding Mkabayi led to a change of consciousness among the Zulu nation, and I used this as a theme for my symphonic work about her. The lives of Queen Nandi (King Shaka’s mother) and Princess Mkabayi (King Shaka’s aunt) made for fascinating stories I had been privileged to discover, and I felt they were South African treasures to be elevated and shared with the world. The two works listed above form part of my repertoire based on Zulu royal history which are collectively known as “The Royal Trilogy,” and I have come to think of them as part of a developing “urban classical repertoire”. The Royal Trilogy is a set of three compositions with 33 independent scenes linking historical events and people. It includes the following entitled symphonic works for full orchestra: Nandi iNdlovukazi yezi Ndlovukazi (hereinafter “Queen Nandi”), Inkosazane Mkabayi (hereinafter “Princess Mkabayi”), and iNkosi uShaka: Umbono, Isizwe, Isiphetho - King Shaka: A Vision, A Nation, A Destiny (hereinafter “King Shaka”). Nandi premiered on 22 September 2016 as part of “A Musical Tribute Celebrating 200 Years of the Zulu Monarchy,” and “Mkabayi” premiered on 6 September 2018 under a programme titled “Princess Mkabayi: Celebrating Heritage Month”. Both pieces were performed at the Durban City Hall by the KwaZulu-Natal Philharmonic Orchestra with a mass Zulu choir (combination of the Clermont Community Choir, Prince Mshiyeni Choir, and Thokozani Choral Society) for socio-economic and ethnically diverse audiences. The final work, “King Shaka,” is expected to premiere in 2023. A future adaption of the Royal Trilogy is envisioned as an Afro Fusion Contemporary Ballet. , Thesis (MMus) -- Faculty of Humanities, Music & Musicology, 2023
- Full Text:
- Date Issued: 2023-04-10
- Authors: Bessey, Warren Gregory
- Date: 2023-04-10
- Subjects: Composition (Music) , Zulu (African people) Songs and music , Music Cross-cultural studies , uMkabayi kaJama , Nandi , Nobility South Africa Zululand History
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/404940 , vital:70123
- Description: Excerpt from Introduction: My interest in the Zulu royal family intensified as I began to read many stories and have lengthy conversations with members of the Zulu royal family and others, including Dr Maxwell Shamase (University of Zululand), about Zulu history. I was struck by the power and prowess of Princess Mkabayi (1750-1843). The elders were said to be speechless when she spoke. According to Shamase, a common Zulu expression which references Mkabayi’s well-known verbal skill is Umuntu ukhuluma kome umlomo, and translates as [like Mkabayi] the speaker speaks clearly and leaves no room for misunderstandings and misinterpretations. I found her to be a brilliant strategist with a servant heart and one whom history had not given due credit, and I was inspired to bring her story to life by setting it to music. I wanted to explore whether or not the events surrounding Mkabayi led to a change of consciousness among the Zulu nation, and I used this as a theme for my symphonic work about her. The lives of Queen Nandi (King Shaka’s mother) and Princess Mkabayi (King Shaka’s aunt) made for fascinating stories I had been privileged to discover, and I felt they were South African treasures to be elevated and shared with the world. The two works listed above form part of my repertoire based on Zulu royal history which are collectively known as “The Royal Trilogy,” and I have come to think of them as part of a developing “urban classical repertoire”. The Royal Trilogy is a set of three compositions with 33 independent scenes linking historical events and people. It includes the following entitled symphonic works for full orchestra: Nandi iNdlovukazi yezi Ndlovukazi (hereinafter “Queen Nandi”), Inkosazane Mkabayi (hereinafter “Princess Mkabayi”), and iNkosi uShaka: Umbono, Isizwe, Isiphetho - King Shaka: A Vision, A Nation, A Destiny (hereinafter “King Shaka”). Nandi premiered on 22 September 2016 as part of “A Musical Tribute Celebrating 200 Years of the Zulu Monarchy,” and “Mkabayi” premiered on 6 September 2018 under a programme titled “Princess Mkabayi: Celebrating Heritage Month”. Both pieces were performed at the Durban City Hall by the KwaZulu-Natal Philharmonic Orchestra with a mass Zulu choir (combination of the Clermont Community Choir, Prince Mshiyeni Choir, and Thokozani Choral Society) for socio-economic and ethnically diverse audiences. The final work, “King Shaka,” is expected to premiere in 2023. A future adaption of the Royal Trilogy is envisioned as an Afro Fusion Contemporary Ballet. , Thesis (MMus) -- Faculty of Humanities, Music & Musicology, 2023
- Full Text:
- Date Issued: 2023-04-10
Composition Portfolio
- Authors: Hanmer, Paul Dylan
- Date: 2022-10-14
- Subjects: Composition (Music) , String quartets Scores , Symphonies Scores , Music South Africa
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/327283 , vital:61100 , DOI 10.21504/10962/327283
- Description: Extract from Introduction: “In the cover bands I worked with, I used to do what all my colleagues in these bands were doing to learn and remember repertoire; transcribe “by ear” and then rehearse with the whole band. Later, when I joined “909” [a cover band named after the “909” model of drum-box developed and built by the Japanese company, Roland] I learned to extend that skill by notating my transcriptions and then playing from these self-made keyboard parts. All the instrumentalists in that band likewise played from their own notated transcriptions and, from that time onward it became rarer for me to do any kind of performance work without a set of self-made parts to read from or refer to. I had thus reverted to performing from musical notation. Even later, when I became involved almost exclusively in improvisational music performance, I never quite abandoned the notion of having notated keyboard or piano parts to hand, as a reference or guide. Since about 1990, I have led a life that has increasingly left pop music behind and instead embraced working with improvising musicians; those who wish to explore South African folk idioms in their compositional and performance output, as well as others who have a deep love of jazz music. At the same time, I have re-entered the realm of classical music and music-making; often through writing arrangements of my own music, which would incorporate classically trained players, as well as in response to commissions to compose [for particular musicians or groups of musicians] fully notated pieces of music – such as the works in this PhD portfolio. Yet, there are many circumstantial factors that feed into my composing, and exert an influence on my creativity. A major step in this particular direction came during 2002 when composer, Michael Blake, asked me to contribute to The Bow Project. This commission brought me into close contact with the [then intact and very active] Sontonga Quartet. Several further requests for, and commissions of, new works followed on from there. Two such works constitute the major portion of the portfolio to which these reflexive commentaries refer.” , Thesis (PhD) -- Faculty of Humanities, Music and Musicology, 2022
- Full Text:
- Date Issued: 2022-10-14
- Authors: Hanmer, Paul Dylan
- Date: 2022-10-14
- Subjects: Composition (Music) , String quartets Scores , Symphonies Scores , Music South Africa
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/327283 , vital:61100 , DOI 10.21504/10962/327283
- Description: Extract from Introduction: “In the cover bands I worked with, I used to do what all my colleagues in these bands were doing to learn and remember repertoire; transcribe “by ear” and then rehearse with the whole band. Later, when I joined “909” [a cover band named after the “909” model of drum-box developed and built by the Japanese company, Roland] I learned to extend that skill by notating my transcriptions and then playing from these self-made keyboard parts. All the instrumentalists in that band likewise played from their own notated transcriptions and, from that time onward it became rarer for me to do any kind of performance work without a set of self-made parts to read from or refer to. I had thus reverted to performing from musical notation. Even later, when I became involved almost exclusively in improvisational music performance, I never quite abandoned the notion of having notated keyboard or piano parts to hand, as a reference or guide. Since about 1990, I have led a life that has increasingly left pop music behind and instead embraced working with improvising musicians; those who wish to explore South African folk idioms in their compositional and performance output, as well as others who have a deep love of jazz music. At the same time, I have re-entered the realm of classical music and music-making; often through writing arrangements of my own music, which would incorporate classically trained players, as well as in response to commissions to compose [for particular musicians or groups of musicians] fully notated pieces of music – such as the works in this PhD portfolio. Yet, there are many circumstantial factors that feed into my composing, and exert an influence on my creativity. A major step in this particular direction came during 2002 when composer, Michael Blake, asked me to contribute to The Bow Project. This commission brought me into close contact with the [then intact and very active] Sontonga Quartet. Several further requests for, and commissions of, new works followed on from there. Two such works constitute the major portion of the portfolio to which these reflexive commentaries refer.” , Thesis (PhD) -- Faculty of Humanities, Music and Musicology, 2022
- Full Text:
- Date Issued: 2022-10-14