Zooplankton dynamics of Algoa Bay (South Africa) under varying oceanographic conditions
- Authors: Bizani,Mfundo
- Date: 2022-04
- Subjects: Marine zooplankton -- South Africa , Climate changes
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/55943 , vital:54554
- Description: the ecological significance of ocean plankton in terms of nutrient cycling and energy transfer is widely recognised, as is their mechanistic link with both oceanographic processes and climate. Consequently, plankton are widely regarded as sentinels of climate change, principally owing to their responsiveness to changing environmental conditions. Developing an understanding of the ecological as well as socio-economic consequences associated with changes in marine plankton dynamics has emerged as a key issue worldwide. Though many exciting advances in this respect have been attained with the aid of long-term plankton time series (>50 y), global environmental datasets and innovative meta-analyses, building deep knowledge of regional bio-physical dynamics and responses to specific perturbed states remains an essential component of the collective effort. Algoa Bay, situated on the warmtemperate south-east coast of South Africa presents a unique opportunity to study key elements of plankton ecology relevant to climate change problems in the regional sense. The embayment is locally subjected to frequent wind-driven upwelling and regionally, to periodic mesoscale oceanographic forcing (e.g., large solitary meanders, Agulhas Current intrusions), all of which culminate in a complex physical and biogeochemical environment. Using zooplankton as the focal component and drawing from a multi-year monthly dataset incorporating a bay-scale sampling framework, the present study addressed three key hypotheses pertaining to 1) drivers of spatio-temporal variability, 2) biomass rate of change over temporal scales using time-series analyses, and 3) community responses to a bay-scale biological perturbation event. Zooplankton biomass exhibited prominent seasonal patterns with bimodal peaks corresponding with near-consistent year-to-year autumn and spring blooms. Overall, the spatial trend showed no heterogeneity, though statistical significance between-station variability was noted per season. An analytical framework involving generalised additive models revealed zooplankton spatial heterogeneity in Algoa Bay to be a function of seasonal variation in a suite of physicochemical variables, including the combined effects of temperature, salinity, dissolved oxygen, total nitrogen and silicate, but not ammonium, phosphate or chlorophyll-a (as proxy for phytoplankton). Fronts (including river plumes), warm water intrusion from the Agulhas Current, and wind-driven upwelling were postulated to be key driving forces. Structural breaks analysis performed on station-specific time series revealed significant incremental increases in zooplankton biomass over time, which in turn, corresponded with a gradual decrease in thermocline depth. The most pronounced increasing effect was associated with a period (2013– 14) of amplified land-derived nutrient input and increasing harmful algal bloom (HAB) activity. , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2022
- Full Text:
- Date Issued: 2022-04
- Authors: Bizani,Mfundo
- Date: 2022-04
- Subjects: Marine zooplankton -- South Africa , Climate changes
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/55943 , vital:54554
- Description: the ecological significance of ocean plankton in terms of nutrient cycling and energy transfer is widely recognised, as is their mechanistic link with both oceanographic processes and climate. Consequently, plankton are widely regarded as sentinels of climate change, principally owing to their responsiveness to changing environmental conditions. Developing an understanding of the ecological as well as socio-economic consequences associated with changes in marine plankton dynamics has emerged as a key issue worldwide. Though many exciting advances in this respect have been attained with the aid of long-term plankton time series (>50 y), global environmental datasets and innovative meta-analyses, building deep knowledge of regional bio-physical dynamics and responses to specific perturbed states remains an essential component of the collective effort. Algoa Bay, situated on the warmtemperate south-east coast of South Africa presents a unique opportunity to study key elements of plankton ecology relevant to climate change problems in the regional sense. The embayment is locally subjected to frequent wind-driven upwelling and regionally, to periodic mesoscale oceanographic forcing (e.g., large solitary meanders, Agulhas Current intrusions), all of which culminate in a complex physical and biogeochemical environment. Using zooplankton as the focal component and drawing from a multi-year monthly dataset incorporating a bay-scale sampling framework, the present study addressed three key hypotheses pertaining to 1) drivers of spatio-temporal variability, 2) biomass rate of change over temporal scales using time-series analyses, and 3) community responses to a bay-scale biological perturbation event. Zooplankton biomass exhibited prominent seasonal patterns with bimodal peaks corresponding with near-consistent year-to-year autumn and spring blooms. Overall, the spatial trend showed no heterogeneity, though statistical significance between-station variability was noted per season. An analytical framework involving generalised additive models revealed zooplankton spatial heterogeneity in Algoa Bay to be a function of seasonal variation in a suite of physicochemical variables, including the combined effects of temperature, salinity, dissolved oxygen, total nitrogen and silicate, but not ammonium, phosphate or chlorophyll-a (as proxy for phytoplankton). Fronts (including river plumes), warm water intrusion from the Agulhas Current, and wind-driven upwelling were postulated to be key driving forces. Structural breaks analysis performed on station-specific time series revealed significant incremental increases in zooplankton biomass over time, which in turn, corresponded with a gradual decrease in thermocline depth. The most pronounced increasing effect was associated with a period (2013– 14) of amplified land-derived nutrient input and increasing harmful algal bloom (HAB) activity. , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2022
- Full Text:
- Date Issued: 2022-04
Wavelet Theory: for Economic & Financial Cycles
- Authors: Mlambo, Farai Fredric
- Date: 2019-12
- Subjects: Wavelets (Mathematics) , Finance -- Mathematical models , Economic forecasting
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/49930 , vital:41861
- Description: Cycles - their nature in existence, their implications on human-kind and the study thereof have sparked some important philosophical debates since the very pre-historic days. Notable contributions by famous, genius philosophers, mathematicians, historians and economists such as Pareto, Deulofeu, Danielewski, Kuznets, Kondratiev, Elliot and many others in itself shows how cycles and their study have been deemed important, through the history and process of scientific and philosophical inquiry. Particularly, the explication of Business, Economic and Financial cycles have seen some significant research and policy attention. Nevertheless, most of the methodologies employed in this space are either purely empirical in nature, time series based or the so-called Regime-Switching Markov model popularized in Economics by James Hamilton. In this work, we develop a Statistical, non-linear model fit based on circle geometry which is applicable for the dating of cycles. This study proposes a scalable, smooth and differentiable quarter-circular wavelet basis for the smoothing and dating of business, economic and financial cycles. The dating then necessitates the forecasting of the cyclical patterns in the evolution of business, economic and financial time series. The practical significance of dating and forecasting business and financial cycles cannot be over-emphasized. The use of wavelet decomposition in explaining cycles can be seen as an critical contribution of spectral methods of statistical modelling to finance and economic policy at large. Being a relatively new method, wavelet analysis has seen some great contribution in geophysical modelling. This study endeavours to widen the use and application of frequency-time decomposition to the economic and financial space. Wavelets are localized in both time and frequency, such that there is no loss of the time resolution. The importance of time resolution in dating of cycles is another motivation behind using wavelets. Moreover, the preservation of time resolution in wavelet analysis is a fundamental strength employed in the dating of cycles. , Thesis (DPhil) -- Faculty of Science, Mathematical Statistics, 2019
- Full Text:
- Date Issued: 2019-12
- Authors: Mlambo, Farai Fredric
- Date: 2019-12
- Subjects: Wavelets (Mathematics) , Finance -- Mathematical models , Economic forecasting
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/49930 , vital:41861
- Description: Cycles - their nature in existence, their implications on human-kind and the study thereof have sparked some important philosophical debates since the very pre-historic days. Notable contributions by famous, genius philosophers, mathematicians, historians and economists such as Pareto, Deulofeu, Danielewski, Kuznets, Kondratiev, Elliot and many others in itself shows how cycles and their study have been deemed important, through the history and process of scientific and philosophical inquiry. Particularly, the explication of Business, Economic and Financial cycles have seen some significant research and policy attention. Nevertheless, most of the methodologies employed in this space are either purely empirical in nature, time series based or the so-called Regime-Switching Markov model popularized in Economics by James Hamilton. In this work, we develop a Statistical, non-linear model fit based on circle geometry which is applicable for the dating of cycles. This study proposes a scalable, smooth and differentiable quarter-circular wavelet basis for the smoothing and dating of business, economic and financial cycles. The dating then necessitates the forecasting of the cyclical patterns in the evolution of business, economic and financial time series. The practical significance of dating and forecasting business and financial cycles cannot be over-emphasized. The use of wavelet decomposition in explaining cycles can be seen as an critical contribution of spectral methods of statistical modelling to finance and economic policy at large. Being a relatively new method, wavelet analysis has seen some great contribution in geophysical modelling. This study endeavours to widen the use and application of frequency-time decomposition to the economic and financial space. Wavelets are localized in both time and frequency, such that there is no loss of the time resolution. The importance of time resolution in dating of cycles is another motivation behind using wavelets. Moreover, the preservation of time resolution in wavelet analysis is a fundamental strength employed in the dating of cycles. , Thesis (DPhil) -- Faculty of Science, Mathematical Statistics, 2019
- Full Text:
- Date Issued: 2019-12
Use of flow reactors for an improved synthesis of Tenofovir derivatives
- Authors: Sonti, Thembela
- Date: 2023-04
- Subjects: Antiviral agents -- South Africa , HIV infections –Treatment
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/61190 , vital:69792
- Description: Tenofovir disoproxil fumarate (TDF) is a prescription drug used to treat and prevent human immunodeficiency virus (HIV) infections. It aids in the reduction of HIV in the body, allowing the immune system to function more effectively. This reduces the risk of HIV complications, such as infections, whilst improving the quality of life. TDF belongs to the nucleotide reverse transcriptase inhibitors category of drugs. These drugs limit the ability of the reverse transcriptase, an enzyme essential for each virus to replicate itself. A reduction in the cost of HIV treatment could improve supply security and make it more accessible to patients in need. Thus, this project aims to use flow technology to achieve a guaranteed supply chain and access. In this thesis, a method for the synthesis of TDF was developed using microreactors starting from the readily available adenine. The method was adapted from the traditional batch synthesis as currently there is no literature on the synthesis of TDF in flow chemistry. The batch methods used for the synthesis of the working standards were successfully translated to flow systems. For the best results to be obtained, optimisation of the reaction temperature, reagent molar equivalents and concentration was critical. From the optimisation studies, an improvement in conversion is evident throughout all stages. The flow synthesis of the first intermediate resulted in a conversion of 100 % in N,N-dimethylformamide in 6 min residence time. This study was conducted at 200 °C, which is higher than the boiling point of the solvent with the aid of a back pressure regulator. A key reagent in the synthesis of tenofovir, namely ((tosyloxy)methyl)phosphonic acid, had to be synthesised and it was successfully produced in 96 % yield. The second intermediate was synthesised through a successful coupling reaction between (R)-9-(2-hydroxypropyl)adenine and ((tosyloxy)methyl)- phosphonic acid, which afforded a 100 % conversion of tenofovir in 20 min total residence time. The multistep synthesis of tenofovir was a success as it afforded a 65 % overall conversion. The prodrug TDF was successfully synthesised at 120 °C with a 30 min residence time, yielding a conversion of 100 %. ii | P a g e This thesis consists of four chapters. Chapter one describes the background on HIV and a literature review on HIV drugs. This chapter also demonstrates flow chemistry and microreactors in detail and different routes for the synthesis of TDF in traditional batch methods. Chapter two provides a detailed methodology for batch synthesis and flow synthesis with analytical data. 1H-NMR, 13C-NMR and FTIR spectroscopy was used to evaluate all the compounds synthesised in this chapter. Chapter three thoroughly discusses the results that were obtained graphically, showing that the flow synthesis gives better yields than batch synthesis. In chapter 4, the conclusion of the whole investigation is stated along with the future work for the preparation of TDF. , Thesis (PhD) -- Faculty of Science, School of Biomolecular and Chemical Sciences, 2023
- Full Text:
- Date Issued: 2023-04
- Authors: Sonti, Thembela
- Date: 2023-04
- Subjects: Antiviral agents -- South Africa , HIV infections –Treatment
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/61190 , vital:69792
- Description: Tenofovir disoproxil fumarate (TDF) is a prescription drug used to treat and prevent human immunodeficiency virus (HIV) infections. It aids in the reduction of HIV in the body, allowing the immune system to function more effectively. This reduces the risk of HIV complications, such as infections, whilst improving the quality of life. TDF belongs to the nucleotide reverse transcriptase inhibitors category of drugs. These drugs limit the ability of the reverse transcriptase, an enzyme essential for each virus to replicate itself. A reduction in the cost of HIV treatment could improve supply security and make it more accessible to patients in need. Thus, this project aims to use flow technology to achieve a guaranteed supply chain and access. In this thesis, a method for the synthesis of TDF was developed using microreactors starting from the readily available adenine. The method was adapted from the traditional batch synthesis as currently there is no literature on the synthesis of TDF in flow chemistry. The batch methods used for the synthesis of the working standards were successfully translated to flow systems. For the best results to be obtained, optimisation of the reaction temperature, reagent molar equivalents and concentration was critical. From the optimisation studies, an improvement in conversion is evident throughout all stages. The flow synthesis of the first intermediate resulted in a conversion of 100 % in N,N-dimethylformamide in 6 min residence time. This study was conducted at 200 °C, which is higher than the boiling point of the solvent with the aid of a back pressure regulator. A key reagent in the synthesis of tenofovir, namely ((tosyloxy)methyl)phosphonic acid, had to be synthesised and it was successfully produced in 96 % yield. The second intermediate was synthesised through a successful coupling reaction between (R)-9-(2-hydroxypropyl)adenine and ((tosyloxy)methyl)- phosphonic acid, which afforded a 100 % conversion of tenofovir in 20 min total residence time. The multistep synthesis of tenofovir was a success as it afforded a 65 % overall conversion. The prodrug TDF was successfully synthesised at 120 °C with a 30 min residence time, yielding a conversion of 100 %. ii | P a g e This thesis consists of four chapters. Chapter one describes the background on HIV and a literature review on HIV drugs. This chapter also demonstrates flow chemistry and microreactors in detail and different routes for the synthesis of TDF in traditional batch methods. Chapter two provides a detailed methodology for batch synthesis and flow synthesis with analytical data. 1H-NMR, 13C-NMR and FTIR spectroscopy was used to evaluate all the compounds synthesised in this chapter. Chapter three thoroughly discusses the results that were obtained graphically, showing that the flow synthesis gives better yields than batch synthesis. In chapter 4, the conclusion of the whole investigation is stated along with the future work for the preparation of TDF. , Thesis (PhD) -- Faculty of Science, School of Biomolecular and Chemical Sciences, 2023
- Full Text:
- Date Issued: 2023-04
The use of psychometric test systems as a pre-selection tool for identifying successful harvesting machine operators
- Authors: Schwegman, Kylle
- Date: 2022-04
- Subjects: Port Elizabeth (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/55246 , vital:51102
- Description: A shift towards fully mechanized forest activities, such as harvesting and, more recently, silviculture, has occurred from the early 2 000’s. The reason for mechanizing these activities differs for each country, although for most countries there is concern relating to the health and safety of forest workers. With mechanization in harvesting, the forest worker has moved away from the physical intensity of having to fell, debranch, debark and cross-cut trees into logs using either an axe or chainsaw, to operating a machine. Studies revolving around the human element (operator) have been conducted specifically relating to the ergonomics of the machines and how operators may influence machine productivity. Results showed that due to the repetitive nature of the work, the operators are exposed to associated stresses for longer periods. Typical injuries associated to these kinds of stressors are whole body vibrations (WBVs), repetitive hand and arm movements, non-neutral body postures and manual lifting, which lead to musculoskeletal symptoms in the lower back, neck and shoulders. However, as machine technology improves so does the ergonomic conditions which are experienced by machine operators. Machine productivity can be influenced by various factors, with the most influential being tree volume. However, a recent study showed that over 40% of variation in machine productivity has been observed amongst different machine operators operating similar machines. The specific reason for these differences has yet to be determined. However, decision making, motivation, planning capacity, concentration, memory, motor coordination, pattern recognition, logic reasoning, and spatial perception are abilities that have been described as important for successful harvesting work. The pre-selection of operators using psychometric and cognitive tests is not new to forestry, although very little information is available relating to the aptitude test known as the Vienna test system as well as the best possible demographic associated with successful harvesting operators. The overall aim of this study was to determine whether the high variation found amongst harvesting machine operators could be reduced initially through a preselection process which involves the use of aptitude tests (Vienna Test System) and demographic questionnaires. A study was implemented in Zululand, South Africa, testing whether there were significant productivity differences between nine machine operators. , Thesis (PhD) -- Faculty of Science, School of Natural Resource Management, 2022
- Full Text:
- Date Issued: 2022-04
- Authors: Schwegman, Kylle
- Date: 2022-04
- Subjects: Port Elizabeth (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/55246 , vital:51102
- Description: A shift towards fully mechanized forest activities, such as harvesting and, more recently, silviculture, has occurred from the early 2 000’s. The reason for mechanizing these activities differs for each country, although for most countries there is concern relating to the health and safety of forest workers. With mechanization in harvesting, the forest worker has moved away from the physical intensity of having to fell, debranch, debark and cross-cut trees into logs using either an axe or chainsaw, to operating a machine. Studies revolving around the human element (operator) have been conducted specifically relating to the ergonomics of the machines and how operators may influence machine productivity. Results showed that due to the repetitive nature of the work, the operators are exposed to associated stresses for longer periods. Typical injuries associated to these kinds of stressors are whole body vibrations (WBVs), repetitive hand and arm movements, non-neutral body postures and manual lifting, which lead to musculoskeletal symptoms in the lower back, neck and shoulders. However, as machine technology improves so does the ergonomic conditions which are experienced by machine operators. Machine productivity can be influenced by various factors, with the most influential being tree volume. However, a recent study showed that over 40% of variation in machine productivity has been observed amongst different machine operators operating similar machines. The specific reason for these differences has yet to be determined. However, decision making, motivation, planning capacity, concentration, memory, motor coordination, pattern recognition, logic reasoning, and spatial perception are abilities that have been described as important for successful harvesting work. The pre-selection of operators using psychometric and cognitive tests is not new to forestry, although very little information is available relating to the aptitude test known as the Vienna test system as well as the best possible demographic associated with successful harvesting operators. The overall aim of this study was to determine whether the high variation found amongst harvesting machine operators could be reduced initially through a preselection process which involves the use of aptitude tests (Vienna Test System) and demographic questionnaires. A study was implemented in Zululand, South Africa, testing whether there were significant productivity differences between nine machine operators. , Thesis (PhD) -- Faculty of Science, School of Natural Resource Management, 2022
- Full Text:
- Date Issued: 2022-04
The synthesis, empirical and theoretical studies of various (N→B) diarylborinate esters
- Authors: Manana, Pholani Sakhile
- Date: 2021-12
- Subjects: Port Elizabeth (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/53869 , vital:46027
- Description: A series of core-functionalized borinic acids was synthesized from Grignard reagents and tributylborate and reacted with ethanolamine, amino acids, 2-pyridylmethanol as well as 2-(ethyl amino ethanol). Among the borinic acids synthesized were the ones bearing: para-(2, 15, 16, 22, 27)-methyl, (3, 20, 25)-chloro, (4, 23, 26)-fluoro, (5)-methoxy; meta-(7, 17)-methyl, (9)-fluoro; ortho-(6)-methyl, (8)-chloro, (10, 18, 19)-methoxy substituents on their respective aromatic systems. All compounds obtained by condensation of the borinic acids with the aforementioned nitrogen-containing substrates were characterized structurally by means of diffraction studies based on single crystals and found to constitute chelate esters/amides featuring covalent B-O and dative N→B bonds. The chelate compounds researched in this study could be classified into four families and represent the compounds: ethanol amine: (1) 2,2-diphenyl-1,3,2-oxazaborolidines, (2) 2,2-bis(p-tolyl)-1,3,2-oxazaborolidines, (3) 2,2-bis(p-chlorophenyl)-1,3,2-oxazaborolidines, (4) 2,2-bis(p-fluorophenyl)-1,3,2-oxazaborolidines, (5) 2,2-bis(p-methoxyphenyl)-1,3,2-oxazaborolidines, (6) 2,2-bis(o-tolyl)-1,3,2-oxazaborolidines, (7) 2,2-bis(m-tolyl)-1,3,2-oxazaborolidines, (8) 2,2-bis(o-chlorophenyl)-1,3,2-oxazaborolidines, (9) 2,2-bis(m-fluorophenyl)-1,3,2-oxazaborolidines, (10) 2,2-bis(o-methoxyphenyl)-1,3,2-oxazaborolidines. α-amino acids : (14) 4-methyl-2,2-diphenyl-1,3,2-oxazaborolidin-5-ones, (15) 2,2-bis(p-tolyl)-1,3,2-oxazaborolidin-5-ones, (16) 4-methyl-2,2-bis(p-tolyl)-1,3,2-oxazaborolidin-5-ones, (17) 4-isopropyl-2,2-bis(m-tolyl)-1,3,2-oxazaborolidin-5-ones, (18) 4-methyl-2,2-bis(o-methoxyphenyl)-1,3,2- oxazaborolidin-5-ones, (19) 4-acetamidyl-2,2-bis(o-methoxyphenyl)-1,3,2- oxazaborolidin-5-ones, (20) 4-phenylethane-2,2-bis(p-chlorophenyl)-1,3,2 oxazaborolidin-5-ones. 2-pyridylmethanol: (21) 1,3-hydroxypyridyl-2,2-diphenyl 1,3,2-oxazaborolidines, (22) 1,3-hydroxypyridyl-2,2-bis(p-tolyl)-1,3,2-oxazaborolidines, (23) 1,3-hydroxypyridyl-2,2-bis(p-fluorophenyl)-1,3,2-oxazaborolidines 2-(ethyl amino ethanol): (24) 3-ethyl-2,2-diphenyl-1,3,2-oxazaborolidines, (25) 3-ethyl-2,2-bis(p-chlorophenyl)-1,3,2-oxazaborolidines, (26) 3-ethyl-2,2-bis(p-fluorophenyl)-1,3,2-oxazaborolidines, (27) 3-ethyl-2,2-bis(p-tolyl)-1,3,2-oxazaborolidines. Apart from structural studies in the solid state, the compounds were also characterized by means of multinuclear NMR spectroscopy (1H, 11B, 13C) as well as UV/vis and FTIR. The typical 11B resonances were found in the range of (4-10 ppm). A series of characteristic metrical parameters for the compounds in the solid state as well as typical NMR shifts for the chelate target molecules was established that allowed for the determination of the coordination induced shift. The carbon atom bonded to the oxygen atom shifted upfield, while the carbon atom bonded to the nitrogen atom shifted downfield. Factors mentioned in the literature that has an influence on the hydrolytic stability on the heterocyclic borinate motif have been taken into consideration and verified for the systems researched in this study. The substitution at the nitrogen atom with one ethyl group caused the greatest increases in the N→B bond length (27) 1.714 Å, due to the increase in the nitrogen Lewis basicity, making it the least hydrolytically stable, these include compounds (24-26). Furthermore, DFT calculations were performed by employing Becke’s three parameter hybrid exchange functional with Lee–Yang–Parr functional (B3LYP) method using the Gaussian 16 program package (Rev. B01) employing the basis set 6-311++G(d,p), to corroborate and correlate the experimental findings, which gave a general R-squared value of 0.9978 for calculated vs experimental 13C chemical shifts. Thermal properties are recorded for select compounds, indicating the ΔH and the melting points. , Thesis (PhD) -- Faculty of Science, School of Biomolecular and Chemical Sciences, 2021
- Full Text:
- Date Issued: 2021-12
- Authors: Manana, Pholani Sakhile
- Date: 2021-12
- Subjects: Port Elizabeth (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/53869 , vital:46027
- Description: A series of core-functionalized borinic acids was synthesized from Grignard reagents and tributylborate and reacted with ethanolamine, amino acids, 2-pyridylmethanol as well as 2-(ethyl amino ethanol). Among the borinic acids synthesized were the ones bearing: para-(2, 15, 16, 22, 27)-methyl, (3, 20, 25)-chloro, (4, 23, 26)-fluoro, (5)-methoxy; meta-(7, 17)-methyl, (9)-fluoro; ortho-(6)-methyl, (8)-chloro, (10, 18, 19)-methoxy substituents on their respective aromatic systems. All compounds obtained by condensation of the borinic acids with the aforementioned nitrogen-containing substrates were characterized structurally by means of diffraction studies based on single crystals and found to constitute chelate esters/amides featuring covalent B-O and dative N→B bonds. The chelate compounds researched in this study could be classified into four families and represent the compounds: ethanol amine: (1) 2,2-diphenyl-1,3,2-oxazaborolidines, (2) 2,2-bis(p-tolyl)-1,3,2-oxazaborolidines, (3) 2,2-bis(p-chlorophenyl)-1,3,2-oxazaborolidines, (4) 2,2-bis(p-fluorophenyl)-1,3,2-oxazaborolidines, (5) 2,2-bis(p-methoxyphenyl)-1,3,2-oxazaborolidines, (6) 2,2-bis(o-tolyl)-1,3,2-oxazaborolidines, (7) 2,2-bis(m-tolyl)-1,3,2-oxazaborolidines, (8) 2,2-bis(o-chlorophenyl)-1,3,2-oxazaborolidines, (9) 2,2-bis(m-fluorophenyl)-1,3,2-oxazaborolidines, (10) 2,2-bis(o-methoxyphenyl)-1,3,2-oxazaborolidines. α-amino acids : (14) 4-methyl-2,2-diphenyl-1,3,2-oxazaborolidin-5-ones, (15) 2,2-bis(p-tolyl)-1,3,2-oxazaborolidin-5-ones, (16) 4-methyl-2,2-bis(p-tolyl)-1,3,2-oxazaborolidin-5-ones, (17) 4-isopropyl-2,2-bis(m-tolyl)-1,3,2-oxazaborolidin-5-ones, (18) 4-methyl-2,2-bis(o-methoxyphenyl)-1,3,2- oxazaborolidin-5-ones, (19) 4-acetamidyl-2,2-bis(o-methoxyphenyl)-1,3,2- oxazaborolidin-5-ones, (20) 4-phenylethane-2,2-bis(p-chlorophenyl)-1,3,2 oxazaborolidin-5-ones. 2-pyridylmethanol: (21) 1,3-hydroxypyridyl-2,2-diphenyl 1,3,2-oxazaborolidines, (22) 1,3-hydroxypyridyl-2,2-bis(p-tolyl)-1,3,2-oxazaborolidines, (23) 1,3-hydroxypyridyl-2,2-bis(p-fluorophenyl)-1,3,2-oxazaborolidines 2-(ethyl amino ethanol): (24) 3-ethyl-2,2-diphenyl-1,3,2-oxazaborolidines, (25) 3-ethyl-2,2-bis(p-chlorophenyl)-1,3,2-oxazaborolidines, (26) 3-ethyl-2,2-bis(p-fluorophenyl)-1,3,2-oxazaborolidines, (27) 3-ethyl-2,2-bis(p-tolyl)-1,3,2-oxazaborolidines. Apart from structural studies in the solid state, the compounds were also characterized by means of multinuclear NMR spectroscopy (1H, 11B, 13C) as well as UV/vis and FTIR. The typical 11B resonances were found in the range of (4-10 ppm). A series of characteristic metrical parameters for the compounds in the solid state as well as typical NMR shifts for the chelate target molecules was established that allowed for the determination of the coordination induced shift. The carbon atom bonded to the oxygen atom shifted upfield, while the carbon atom bonded to the nitrogen atom shifted downfield. Factors mentioned in the literature that has an influence on the hydrolytic stability on the heterocyclic borinate motif have been taken into consideration and verified for the systems researched in this study. The substitution at the nitrogen atom with one ethyl group caused the greatest increases in the N→B bond length (27) 1.714 Å, due to the increase in the nitrogen Lewis basicity, making it the least hydrolytically stable, these include compounds (24-26). Furthermore, DFT calculations were performed by employing Becke’s three parameter hybrid exchange functional with Lee–Yang–Parr functional (B3LYP) method using the Gaussian 16 program package (Rev. B01) employing the basis set 6-311++G(d,p), to corroborate and correlate the experimental findings, which gave a general R-squared value of 0.9978 for calculated vs experimental 13C chemical shifts. Thermal properties are recorded for select compounds, indicating the ΔH and the melting points. , Thesis (PhD) -- Faculty of Science, School of Biomolecular and Chemical Sciences, 2021
- Full Text:
- Date Issued: 2021-12
The foraging ecology of female Cape fur seals (Arctocephalus pusillus pusillus) in South Africa
- Botha, Jonathan Aubrey, Kirkman, Stephen, Lombard, Amanda
- Authors: Botha, Jonathan Aubrey , Kirkman, Stephen , Lombard, Amanda
- Date: 2022-04
- Subjects: Seals (Animals)--Habitat—Conservation , Marine ecology—South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/55965 , vital:54559
- Description: The marine environment is spatially and temporally dynamic and many marine ecosystems are experiencing impacts of broad-scale climate change. Within these ecosystems, marine predators play a crucial role in ecosystem function through their top-down influences on prey populations. These predators may also respond to bottom-up influences and changes at lower trophic levels. A thorough understanding of marine predator foraging ecology is thus important to improve our understanding of ecosystem function, inform conservation and management measures, and to predict the response of predators to future environmental change. The Cape fur seal (Arctocephalus pusillus pusillus) comprises a major proportion of the southern African marine predator biomass. However, little is known about the foraging distribution and behaviour of the species, despite its obvious importance within the ecosystem and increasing concerns regarding seal-fisheries conflict. Using a variety of technologies, including, GPS and satellite-linked tags, dive behaviour recorders, accelerometers and stable isotope analysis, this thesis investigated the foraging ecology of female Cape fur seals breeding on the coast of South Africa. First, to identify important foraging areas and assess the influence of geographic, temporal and environmental factors on these areas, lactating females from three breeding colonies were fitted with GPS or Argos-linked tracking devices, while individuals from two of these colonies were also fitted with dive behaviour recorders. Results revealed geographic differences in the foraging distributions and ranges of individuals between breeding colonies, which likely reflects a combined influence of ecological setting and density dependant competition. In addition, dive behaviour recorders revealed the occurrence of benthic foraging at both sites where they were deployed, and the dominance of this strategy in some individuals. , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2022
- Full Text:
- Date Issued: 2022-04
- Authors: Botha, Jonathan Aubrey , Kirkman, Stephen , Lombard, Amanda
- Date: 2022-04
- Subjects: Seals (Animals)--Habitat—Conservation , Marine ecology—South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/55965 , vital:54559
- Description: The marine environment is spatially and temporally dynamic and many marine ecosystems are experiencing impacts of broad-scale climate change. Within these ecosystems, marine predators play a crucial role in ecosystem function through their top-down influences on prey populations. These predators may also respond to bottom-up influences and changes at lower trophic levels. A thorough understanding of marine predator foraging ecology is thus important to improve our understanding of ecosystem function, inform conservation and management measures, and to predict the response of predators to future environmental change. The Cape fur seal (Arctocephalus pusillus pusillus) comprises a major proportion of the southern African marine predator biomass. However, little is known about the foraging distribution and behaviour of the species, despite its obvious importance within the ecosystem and increasing concerns regarding seal-fisheries conflict. Using a variety of technologies, including, GPS and satellite-linked tags, dive behaviour recorders, accelerometers and stable isotope analysis, this thesis investigated the foraging ecology of female Cape fur seals breeding on the coast of South Africa. First, to identify important foraging areas and assess the influence of geographic, temporal and environmental factors on these areas, lactating females from three breeding colonies were fitted with GPS or Argos-linked tracking devices, while individuals from two of these colonies were also fitted with dive behaviour recorders. Results revealed geographic differences in the foraging distributions and ranges of individuals between breeding colonies, which likely reflects a combined influence of ecological setting and density dependant competition. In addition, dive behaviour recorders revealed the occurrence of benthic foraging at both sites where they were deployed, and the dominance of this strategy in some individuals. , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2022
- Full Text:
- Date Issued: 2022-04
The effect of silicon on palladium migration in pyrolytic carbon and graphite
- Authors: Downey, Justin Michael
- Date: 2021-12
- Subjects: Port Elizabeth (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/53665 , vital:45684
- Description: The pebble-bed reactor (PBR) is a graphite-moderated, gas-cooled high temperature nuclear reactor design and it is one of six nuclear reactor concepts included in the Generation IV initiative. Pebble-bed reactors use spherical fuel elements (called pebbles) which consist of pyrolytic graphite (which acts as the moderator) and contain thousands of micro-fuel particles called tristructural isotropic (TRISO) particles. These TRISO fuel particles consist of a fissile material (such as U235 in oxide or carbide form) surrounded by a carbon buffer layer, a pyrolytic carbon (PyC) layer, a silicon carbide (SiC) ceramic layer for structural integrity and metallic fission product containment, and an outer PyC layer. The PBR is claimed to be a passively safe design. The commercial development of the first pebble bed reactor was that of the German AVR reactor (German: Arbeitsgemeinschaft Versuchsreaktor) developed during the 1960s. The AVR design was later updated and marketed by a company called HTR. In 1999 the South African electricity company ESKOM obtained the right to access the HTR engineering database that included details of the Siemens/Interatom HTR-Module design. ESKOM worked with HTR on a new design and dubbed it the pebble bed modular reactor (PBMR). The PBMR Co. Ltd. was formed in 1999 and mandated to license and build PBMR reactors. One of the safety considerations which emerged from research is that of metal fission product release from the TRISO fuel particles. Ag110m is a radioactive metallic fission product found to have been released from intact TRISO particles. The release of this Ag isotope is of particular concern because it is highly gamma active and has a half-life of approximately 250 days, resulting in unsafe environments for maintenance workers of PBRs. During the past four decades, many different mechanisms for Ag transport in SiC and release from TRISO particles have been proposed. A promising more recent mechanism suggests that the metallic fission product palladium (Pd) plays a significant role in the transport and release of Ag from intact TRISO particles. In this mechanism Ag transport in irradiated TRISO particle fuel takes place in the presence of the fission product Pd. The Pd reacts with the SiC layer and penetrates the SiC layer along grain boundaries to form a silicide layer which provides a rapid diffusion path for Ag in the SiC. The presence of thin silicide layers in irradiated TRISO particles was subsequently confirmed. , Thesis (PhD) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2021
- Full Text: false
- Date Issued: 2021-12
- Authors: Downey, Justin Michael
- Date: 2021-12
- Subjects: Port Elizabeth (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/53665 , vital:45684
- Description: The pebble-bed reactor (PBR) is a graphite-moderated, gas-cooled high temperature nuclear reactor design and it is one of six nuclear reactor concepts included in the Generation IV initiative. Pebble-bed reactors use spherical fuel elements (called pebbles) which consist of pyrolytic graphite (which acts as the moderator) and contain thousands of micro-fuel particles called tristructural isotropic (TRISO) particles. These TRISO fuel particles consist of a fissile material (such as U235 in oxide or carbide form) surrounded by a carbon buffer layer, a pyrolytic carbon (PyC) layer, a silicon carbide (SiC) ceramic layer for structural integrity and metallic fission product containment, and an outer PyC layer. The PBR is claimed to be a passively safe design. The commercial development of the first pebble bed reactor was that of the German AVR reactor (German: Arbeitsgemeinschaft Versuchsreaktor) developed during the 1960s. The AVR design was later updated and marketed by a company called HTR. In 1999 the South African electricity company ESKOM obtained the right to access the HTR engineering database that included details of the Siemens/Interatom HTR-Module design. ESKOM worked with HTR on a new design and dubbed it the pebble bed modular reactor (PBMR). The PBMR Co. Ltd. was formed in 1999 and mandated to license and build PBMR reactors. One of the safety considerations which emerged from research is that of metal fission product release from the TRISO fuel particles. Ag110m is a radioactive metallic fission product found to have been released from intact TRISO particles. The release of this Ag isotope is of particular concern because it is highly gamma active and has a half-life of approximately 250 days, resulting in unsafe environments for maintenance workers of PBRs. During the past four decades, many different mechanisms for Ag transport in SiC and release from TRISO particles have been proposed. A promising more recent mechanism suggests that the metallic fission product palladium (Pd) plays a significant role in the transport and release of Ag from intact TRISO particles. In this mechanism Ag transport in irradiated TRISO particle fuel takes place in the presence of the fission product Pd. The Pd reacts with the SiC layer and penetrates the SiC layer along grain boundaries to form a silicide layer which provides a rapid diffusion path for Ag in the SiC. The presence of thin silicide layers in irradiated TRISO particles was subsequently confirmed. , Thesis (PhD) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2021
- Full Text: false
- Date Issued: 2021-12
The effect of Cannabis extract on the morphological and metabolic characteristics of various fat depots in diet-induced Obese and STZ-induced male wistar rats
- Authors: Ramlugon, Sonaal
- Date: 2023-04
- Subjects: Rats as laboratory animals , Diabetes in practice , Cannabis -- South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/61282 , vital:70044
- Description: To investigate the potential anti-diabetic/obesity properties of oral cannabis administration in an obese and streptozotocin (STZ)-induced diabetic rat model, as well as an obese rat model, and to determine the mechanism of action, with a focus on the peritoneal and intramuscular fat depots. Experimental Design: Obese and STZ-induced diabetic rats were allocated a high fat diet (HFD) and intraperitoneally injected with STZ to mimic an obese and diabetic state. The rats were then orally administered cannabis extract (CE) of 1.25, 2.5 and 5.0 mg/kg body weight (relative to tetrahydrocannabinol (THC) content) or metformin as a positive control. For the obese rat model, the rats were allocated either a high carbohydrate diet (HCD) or high fat diet (HFD) and orally administered with cannabis extract of 1.25 mg/kg body weight (relative to THC content). Weight, blood and insulin-resistant parameters of the rats were monitored. The mitochondrial to genomic DNA ratio (MT:18S DNA), average adipocyte area of the various adipose tissues, citrate synthase and carnitine palmitoyltransferase 1 (CPT1) enzyme activities of the peritoneal and intramuscular fat were measured. Gene expression levels of uncoupling protein 1 (UCP1), cell-death inducing DNA fragmentation factor alpha like effector-a (Cidea), perilipin, hormone-sensitive lipase (HSL) and mitochondrial transcription factor A (TFAM) were measured in peritoneal fat, intramuscular fat and brown adipose tissue (BAT). Main Findings: Obese and STZ-induced diabetic rat model: Due to the biphasic nature of cannabinoids, cannabis dosage plays an important role in the observed effects. CE1.25 was the only cannabis treatment effective in improving the insulinresistant parameters of the rats unlike the other higher cannabis concentrations (CE2.5 and CE5.0). In the peritoneal fat, CE1.25 increased MT:18S DNA, increased citrate synthase activity, and decreased the average adipocyte area when compared to the STZ group. CE1.25 also induced fat beigeing by upregulating gene expression levels of UCP1 and Cidea. XIX Furthermore, an increase in gene expression levels of perilipin, HSL, and TFAM showed increased fat mobilization and metabolic activity. In the intramuscular fat, CE1.25 also reduced the average adipocytes area. However, a different mechanism of action was observed where CE1.25 did not induce fat beigeing, but instead increased both citrate synthase and CPT1 enzyme activities and gene expression levels of HSL, thereby indicating increased fat oxidation and mitochondrial activity. , Thesis (PhD) -- Faculty of Science, School of Biomolecular and Chemical Sciences, 2023
- Full Text:
- Date Issued: 2023-04
- Authors: Ramlugon, Sonaal
- Date: 2023-04
- Subjects: Rats as laboratory animals , Diabetes in practice , Cannabis -- South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/61282 , vital:70044
- Description: To investigate the potential anti-diabetic/obesity properties of oral cannabis administration in an obese and streptozotocin (STZ)-induced diabetic rat model, as well as an obese rat model, and to determine the mechanism of action, with a focus on the peritoneal and intramuscular fat depots. Experimental Design: Obese and STZ-induced diabetic rats were allocated a high fat diet (HFD) and intraperitoneally injected with STZ to mimic an obese and diabetic state. The rats were then orally administered cannabis extract (CE) of 1.25, 2.5 and 5.0 mg/kg body weight (relative to tetrahydrocannabinol (THC) content) or metformin as a positive control. For the obese rat model, the rats were allocated either a high carbohydrate diet (HCD) or high fat diet (HFD) and orally administered with cannabis extract of 1.25 mg/kg body weight (relative to THC content). Weight, blood and insulin-resistant parameters of the rats were monitored. The mitochondrial to genomic DNA ratio (MT:18S DNA), average adipocyte area of the various adipose tissues, citrate synthase and carnitine palmitoyltransferase 1 (CPT1) enzyme activities of the peritoneal and intramuscular fat were measured. Gene expression levels of uncoupling protein 1 (UCP1), cell-death inducing DNA fragmentation factor alpha like effector-a (Cidea), perilipin, hormone-sensitive lipase (HSL) and mitochondrial transcription factor A (TFAM) were measured in peritoneal fat, intramuscular fat and brown adipose tissue (BAT). Main Findings: Obese and STZ-induced diabetic rat model: Due to the biphasic nature of cannabinoids, cannabis dosage plays an important role in the observed effects. CE1.25 was the only cannabis treatment effective in improving the insulinresistant parameters of the rats unlike the other higher cannabis concentrations (CE2.5 and CE5.0). In the peritoneal fat, CE1.25 increased MT:18S DNA, increased citrate synthase activity, and decreased the average adipocyte area when compared to the STZ group. CE1.25 also induced fat beigeing by upregulating gene expression levels of UCP1 and Cidea. XIX Furthermore, an increase in gene expression levels of perilipin, HSL, and TFAM showed increased fat mobilization and metabolic activity. In the intramuscular fat, CE1.25 also reduced the average adipocytes area. However, a different mechanism of action was observed where CE1.25 did not induce fat beigeing, but instead increased both citrate synthase and CPT1 enzyme activities and gene expression levels of HSL, thereby indicating increased fat oxidation and mitochondrial activity. , Thesis (PhD) -- Faculty of Science, School of Biomolecular and Chemical Sciences, 2023
- Full Text:
- Date Issued: 2023-04
The biology of the sand shark Rhinobatos Annulatus, in Algoa Bay with notes on other elasmobranchs
- Authors: Rossouw, Gideon Johannes
- Date: 1983
- Subjects: Sand sharks , Guitarfishes
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/52802 , vital:44061
- Description: The biology of the lesser sand shark, Rhinobatos annulatus, was studied off sandy beaches in Algoa Bay over a period of two years. Tagging studies, due to low numbers tagged, did not reveal major movements. However, comparison of numbers of sand sharks caught off the beach and deep water during summer and winter months suggested that migration occurred during these seasons with the animals being inshore in summer. Annual rings on the vertebral centra were used to determine age. Both sexes can reach a maximum age of seven years. Conventional growth curves could not be fitted and empirical curves were used to illustrate growth. The reproductive cycle was investigated and indicated that both sexes matured after three years of age. The breeding season was during late summer when the shallow water was utilized as a nursery area. The sand shark is an aplacental viviparous species with a gestation period of 10 months. Breeding occurred every year and fecundity increased with total body length to a maximum litter size of 10 young. The most important prey items taken inshore were the mysid Gastrosaccus psammodytes, the prawn Macropetasma africanum, the crab Ovalipes punctatus and the sand mussels Donax spp. Differential predation by different length classes of sand shark resulted from a dynamic zonation of these different size classes in the surf zone. Smallest individuals fed closest inshore. Seasonal variation recorded in the hepatosomatic index was primarily due to the accumulation of hepatic lipids. This variation showed significant correlations with the breeding cycle in adult sand sharks. The contribution of liver lipids to the formation of egg yolk was estimated and found to be secondary to lipid reserves for maintenance. Liver colour varied depended on the amount of liver lipids. Ancillary observations were made of other elasmobranchs in the surf zone. , Thesis (DPhil) -- Faculty of Science, 1983
- Full Text:
- Date Issued: 1983
- Authors: Rossouw, Gideon Johannes
- Date: 1983
- Subjects: Sand sharks , Guitarfishes
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/52802 , vital:44061
- Description: The biology of the lesser sand shark, Rhinobatos annulatus, was studied off sandy beaches in Algoa Bay over a period of two years. Tagging studies, due to low numbers tagged, did not reveal major movements. However, comparison of numbers of sand sharks caught off the beach and deep water during summer and winter months suggested that migration occurred during these seasons with the animals being inshore in summer. Annual rings on the vertebral centra were used to determine age. Both sexes can reach a maximum age of seven years. Conventional growth curves could not be fitted and empirical curves were used to illustrate growth. The reproductive cycle was investigated and indicated that both sexes matured after three years of age. The breeding season was during late summer when the shallow water was utilized as a nursery area. The sand shark is an aplacental viviparous species with a gestation period of 10 months. Breeding occurred every year and fecundity increased with total body length to a maximum litter size of 10 young. The most important prey items taken inshore were the mysid Gastrosaccus psammodytes, the prawn Macropetasma africanum, the crab Ovalipes punctatus and the sand mussels Donax spp. Differential predation by different length classes of sand shark resulted from a dynamic zonation of these different size classes in the surf zone. Smallest individuals fed closest inshore. Seasonal variation recorded in the hepatosomatic index was primarily due to the accumulation of hepatic lipids. This variation showed significant correlations with the breeding cycle in adult sand sharks. The contribution of liver lipids to the formation of egg yolk was estimated and found to be secondary to lipid reserves for maintenance. Liver colour varied depended on the amount of liver lipids. Ancillary observations were made of other elasmobranchs in the surf zone. , Thesis (DPhil) -- Faculty of Science, 1983
- Full Text:
- Date Issued: 1983
Synthesis and biolgical screening of potential plasmodium falciparum DXR inhibitors
- Authors: Adeyemi, Christiana Modupe
- Date: 2017-04
- Subjects: Plasmodium falciparum , Enzyme inhibitors , Malaria , Antimalarials , Drug development , Malaria -- Chemotherapy , Isopentenoids -- Synthesis , Fosmidomycin , 1-Deoxy-D-xylulose 5-phosphate
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/61790 , vital:28060
- Description: The non-mevalonate isoprenoid pathway, also known as the 1-deoxy-D-xylulose-5- phosphate DXP pathway, is absent in humans, but present in the anopheles mosquito responsible for the transmission of malaria. DXP reductoisomerase - a key enzyme in the DXP pathway in Plasmodium falciparum (PfDXR) has been identified as a target for the design of novel anti-malarial drugs. Fosmidomycin and its acetyl analogue (FR900098) are known to be inhibitors of PfDXR and, in this study, synthetic variations of the fosmidomycin scaffold have led to four series of novel analogues. Particular attention has been centred on the introduction of various substituted benzyl groups in each of these series in order to occupy a recently discovered vacant pocket in the PfDXR active-site and thus enhance ligand-enzyme binding. In the process 160 ligands and precursors have been prepared, no less than 119 of them novel. Fistly, a series of C-benzylated phosphonate esters and phosphonic acids were synthesised, in which the fosmidomycin hydroxamate Mg2+- coordinating moiety was replaced by an amide funtionality and the number of methylene groups in the “hydrophobic patch” between the phosphonate and the hydroxamate moiety was decreased from two to one. Several approaches were explored for this series, the most successful involving reaction of 3- substituted anilines with a-bromo propanoic acid in the presence of the coupling agent 1,1'- carbonyldiimidazole (CDI), followed by Michaelis-Arbuzov phosphonation using triethyl phosphite. Reaction of the resulting chiral phosphonate esters with bromotrimethylsilane gave the corresponding phosphonic acids in good yields. In order to obviate chirality issues, a second series of potential “reverse” fosmidomycin analogues was synthesised by replacing the methylene group adjacent to the the phosphonate moiety with a nitrogen atom. Deprotonation, alkylation and phosphorylation of various amines gave diethyl #-benzylphosphoramidate ester intermediate. Aza-Michael addition of these intermediates, followed by hydrolysis gave the corresponding carboxylic acids which could be reacted with different hydroxylamine hydrochloride derivatives to afford the novel hydroxamic acid derivatives in good yields. Thirdly, a series of a novel #-benzylated phosphoramidate derivatives were prepared as aza- FR900098 analogues. Alkylation of different amines using bromoacetalde-hyde diethylacetal gave a series of N-benzyl-2,2-diethoxyethylamine compounds, which were then elaborated via a futher six steps to afford novel #-benzylated phosphoramidate derivatives. Finally, in order to ensure syn-orientation of the donor atoms in the Mg - coordinating group and, at the same time, introduce conformational constraints in the ligand, the hydrophobic patch and the hydroxamate moiety were replaced by cyclic systems. Several approaches towards the synthesis of such conformationally constrained phosphoramidate analogues from maleic anhydride led to the unexpected isolation of an unprecedented acyclic furfuryl compound, and 1H NMR and DFT-level theoretical studies have been initiated to explore the reaction sequence. A series of #-benzylated phosphoramidate derivatives containing dihydroxy aromatic rings (as the conformationally constrained groups) to replace the hydroxamate moiety, were successfully obtained in six steps from the starting material, 3,4-dihydroxylbenzaldehyde. While in vitro assays have been conducted on all of the synthesised compounds, and some of the ligands show promising anti-malarial inhibitory activity - most especially the conformationally constrained cyclic #-benzylated phosphoramidate series. Interestingly, a number of these compounds has also shown activity against T.brucei - the causative agent of sleeping sickness. In silico docking studies of selected compounds has revealed the capacity of some of the ligands to bind effectively in the PfDXR active-site with the newly introduced benzyl group occupying the adjacent vacant pocket. The physico-chemical properties of these ligands were also explored in order to predict the oral-bioavailability. Most of the ligands obeyed the Lipinski rule of 5, while QSAR methods have been used in an attempt to correlate structural variations and calculated molecular properties with the bioassay data. , Thesis (PhD) -- Faculty of Science, Chemistry, 2017
- Full Text:
- Date Issued: 2017-04
- Authors: Adeyemi, Christiana Modupe
- Date: 2017-04
- Subjects: Plasmodium falciparum , Enzyme inhibitors , Malaria , Antimalarials , Drug development , Malaria -- Chemotherapy , Isopentenoids -- Synthesis , Fosmidomycin , 1-Deoxy-D-xylulose 5-phosphate
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/61790 , vital:28060
- Description: The non-mevalonate isoprenoid pathway, also known as the 1-deoxy-D-xylulose-5- phosphate DXP pathway, is absent in humans, but present in the anopheles mosquito responsible for the transmission of malaria. DXP reductoisomerase - a key enzyme in the DXP pathway in Plasmodium falciparum (PfDXR) has been identified as a target for the design of novel anti-malarial drugs. Fosmidomycin and its acetyl analogue (FR900098) are known to be inhibitors of PfDXR and, in this study, synthetic variations of the fosmidomycin scaffold have led to four series of novel analogues. Particular attention has been centred on the introduction of various substituted benzyl groups in each of these series in order to occupy a recently discovered vacant pocket in the PfDXR active-site and thus enhance ligand-enzyme binding. In the process 160 ligands and precursors have been prepared, no less than 119 of them novel. Fistly, a series of C-benzylated phosphonate esters and phosphonic acids were synthesised, in which the fosmidomycin hydroxamate Mg2+- coordinating moiety was replaced by an amide funtionality and the number of methylene groups in the “hydrophobic patch” between the phosphonate and the hydroxamate moiety was decreased from two to one. Several approaches were explored for this series, the most successful involving reaction of 3- substituted anilines with a-bromo propanoic acid in the presence of the coupling agent 1,1'- carbonyldiimidazole (CDI), followed by Michaelis-Arbuzov phosphonation using triethyl phosphite. Reaction of the resulting chiral phosphonate esters with bromotrimethylsilane gave the corresponding phosphonic acids in good yields. In order to obviate chirality issues, a second series of potential “reverse” fosmidomycin analogues was synthesised by replacing the methylene group adjacent to the the phosphonate moiety with a nitrogen atom. Deprotonation, alkylation and phosphorylation of various amines gave diethyl #-benzylphosphoramidate ester intermediate. Aza-Michael addition of these intermediates, followed by hydrolysis gave the corresponding carboxylic acids which could be reacted with different hydroxylamine hydrochloride derivatives to afford the novel hydroxamic acid derivatives in good yields. Thirdly, a series of a novel #-benzylated phosphoramidate derivatives were prepared as aza- FR900098 analogues. Alkylation of different amines using bromoacetalde-hyde diethylacetal gave a series of N-benzyl-2,2-diethoxyethylamine compounds, which were then elaborated via a futher six steps to afford novel #-benzylated phosphoramidate derivatives. Finally, in order to ensure syn-orientation of the donor atoms in the Mg - coordinating group and, at the same time, introduce conformational constraints in the ligand, the hydrophobic patch and the hydroxamate moiety were replaced by cyclic systems. Several approaches towards the synthesis of such conformationally constrained phosphoramidate analogues from maleic anhydride led to the unexpected isolation of an unprecedented acyclic furfuryl compound, and 1H NMR and DFT-level theoretical studies have been initiated to explore the reaction sequence. A series of #-benzylated phosphoramidate derivatives containing dihydroxy aromatic rings (as the conformationally constrained groups) to replace the hydroxamate moiety, were successfully obtained in six steps from the starting material, 3,4-dihydroxylbenzaldehyde. While in vitro assays have been conducted on all of the synthesised compounds, and some of the ligands show promising anti-malarial inhibitory activity - most especially the conformationally constrained cyclic #-benzylated phosphoramidate series. Interestingly, a number of these compounds has also shown activity against T.brucei - the causative agent of sleeping sickness. In silico docking studies of selected compounds has revealed the capacity of some of the ligands to bind effectively in the PfDXR active-site with the newly introduced benzyl group occupying the adjacent vacant pocket. The physico-chemical properties of these ligands were also explored in order to predict the oral-bioavailability. Most of the ligands obeyed the Lipinski rule of 5, while QSAR methods have been used in an attempt to correlate structural variations and calculated molecular properties with the bioassay data. , Thesis (PhD) -- Faculty of Science, Chemistry, 2017
- Full Text:
- Date Issued: 2017-04
Synthesis and applications of novel fluorescent and colorimetric coumarin-based sensors towards analyte sensing in aqueous systems
- Authors: Battison, Aidan Leigh
- Date: 2022-04
- Subjects: Water-supply engineering--Technological innovations , Polymers--Optical properties , Fluorescent polymers
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/55954 , vital:54558
- Description: The continuous growth of mankind has not been considerate to the environment. The release of millions of tonnes of toxic heavy metal cations and anionic species through industrial, mining, agricultural, and electronic dumping has led to disease and, in many instances, death. This is usually suffered by low-income informal populations residing in third world countries. Moreover, many unnecessary deaths of children are becoming more prevalent because of consumption and contact with contaminated water, agricultural, and animal sources. Bioaccumulation of these toxic species in fish, plants, and animals, inevitably make their way back to the unaware general population. As growth by mining, agriculture, and electronics are indeed vital aspects of human development, the negative side effects of these activities usually continue unregulated. Therefore, as these processes are set to continue until more stringent regulatory processes are put into legislature; low-cost, sensitive, selective organic based sensors are a step in the right direction towards highlighting the need for environmental restoration and remediation; whilst also aiming to preventing unnecessary disease and death in the process. Herein, coumarin derived small-molecule fluorescent and colorimetric sensors for the quantitative and qualitative assessment of cationic and anionic species in aqueous and organic media are described. Ten fluorescent sensors supporting 1,4-disubstituted triazolyl moieties were synthesized according to Cu(I)-catalyzed azide-alkyne cycloaddition “click” reactions. These sensors were screened for their cationic and anionic affinities in a variety of solvent systems. Majority of the sensors responded well towards Fe3+, characterized by a strong fluorescent quenching response with a good degree of sensitivity and selectivity. Selected sensors were further investigated for their affinities towards anionic species; however, they did not display the same degree of selectivity or sensitivity towards these chosen anions. Titration studies of selected sensors with Fe3+ were able to be used towards determining the modes of fluorescent quenching; the photophysical mechanisms by which quenching occurs; stoichiometric binding ratios, association constants, and the number of coordination sites present between the sensors and Fe3+. Reversibility studies of the sensor-metal complex was investigated with EDTA. Partial reversibility was achieved for the chosen sensors with Fe3+. Hydrogen potential studies further described the application of these sensors over a good pH range. The binding site between the sensors and Fe3+ was investigated by NMR studies. , Thesis (PhD) -- Faculty of Science, School of Biomecular and Chemical Sciences, 2022
- Full Text:
- Date Issued: 2022-04
- Authors: Battison, Aidan Leigh
- Date: 2022-04
- Subjects: Water-supply engineering--Technological innovations , Polymers--Optical properties , Fluorescent polymers
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/55954 , vital:54558
- Description: The continuous growth of mankind has not been considerate to the environment. The release of millions of tonnes of toxic heavy metal cations and anionic species through industrial, mining, agricultural, and electronic dumping has led to disease and, in many instances, death. This is usually suffered by low-income informal populations residing in third world countries. Moreover, many unnecessary deaths of children are becoming more prevalent because of consumption and contact with contaminated water, agricultural, and animal sources. Bioaccumulation of these toxic species in fish, plants, and animals, inevitably make their way back to the unaware general population. As growth by mining, agriculture, and electronics are indeed vital aspects of human development, the negative side effects of these activities usually continue unregulated. Therefore, as these processes are set to continue until more stringent regulatory processes are put into legislature; low-cost, sensitive, selective organic based sensors are a step in the right direction towards highlighting the need for environmental restoration and remediation; whilst also aiming to preventing unnecessary disease and death in the process. Herein, coumarin derived small-molecule fluorescent and colorimetric sensors for the quantitative and qualitative assessment of cationic and anionic species in aqueous and organic media are described. Ten fluorescent sensors supporting 1,4-disubstituted triazolyl moieties were synthesized according to Cu(I)-catalyzed azide-alkyne cycloaddition “click” reactions. These sensors were screened for their cationic and anionic affinities in a variety of solvent systems. Majority of the sensors responded well towards Fe3+, characterized by a strong fluorescent quenching response with a good degree of sensitivity and selectivity. Selected sensors were further investigated for their affinities towards anionic species; however, they did not display the same degree of selectivity or sensitivity towards these chosen anions. Titration studies of selected sensors with Fe3+ were able to be used towards determining the modes of fluorescent quenching; the photophysical mechanisms by which quenching occurs; stoichiometric binding ratios, association constants, and the number of coordination sites present between the sensors and Fe3+. Reversibility studies of the sensor-metal complex was investigated with EDTA. Partial reversibility was achieved for the chosen sensors with Fe3+. Hydrogen potential studies further described the application of these sensors over a good pH range. The binding site between the sensors and Fe3+ was investigated by NMR studies. , Thesis (PhD) -- Faculty of Science, School of Biomecular and Chemical Sciences, 2022
- Full Text:
- Date Issued: 2022-04
Spatial fisheries management options for inclusion in marine spatial planning in South Africa
- Authors: Reed, Jodie Romay
- Date: 2021-04
- Subjects: Gqeberha (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/52068 , vital:43451
- Description: Integration of sectoral based management into a coherent and coordinated spatial management framework is one of the central challenges of marine spatial planning ȋMSPȌǤ MSP initiatives aim to provide operational frameworks to promote sustainable use of the economic potential of the ocean while maintaining the value of marine biodiversity and the integrity of marine ecosystems to provide servicesǤ The ecosystem services associated with fisheries in terms of food and job provision are some of the most well recognised and highly valued in the marine realm and maintaining these benefits depends on a holistic understanding of the ecosystemǡ human uses and the management thereofǡ including areaǦbased managementǤ In ͲͰͱǡ South Africa was the first African country to enact MSP legislationǤ The development of MSP was advanced through a Presidential ocean economy initiative ȋOperation Phakisaǣ Oceans EconomyȌ that aimed to fast track marine transport and manufacturingǡ aquacultureǡ and the development of oil and gasǡ small harbourǡ and coastal and marine tourismǤ A dedicated ocean governance component was included to develop an overarchingǡ integrated ocean governance frameworkǤ The absence of fisheries in the plans and initiatives was conspicuousǤ The implementation of MSPǡ howeverǡ provides an opportunity to safeguard the ecosystem services provided by fisheries but only if the interests of fisheries can be adequately reflected in spatial plans and analysesǤ Furthermoreǡ the implementation of MSP may provide new opportunities for innovation in spatial approaches to local fisheries management that could address numerous spatial conflicts that have been reportedǤ Integration of spatial fisheries management approaches into MSP can also support the implementation of ecosystemǦbased management ȋEBMȌǡ by including mechanisms such as habitat protectionǡ effective management of areas important for vulnerable life history stagesǡ and bycatch managementǤ This study aimed to identifyǡ assess and further develop spatial management options for fisheries to facilitate the integration of fisheries management and MSPǤ This was achieved by firstlyǡ identifying existing spatial management instruments and assessing the way in which these instruments may be implemented to support spatial fisheries managementǤ Secondlyǡ the application of two contrasting spatial management optionsǡ applied to two pelagic fisheriesǡ was examined to assess their effectiveness at achieving fisheries management objectives with a focus on bycatch reductionǡ while minimising the costs to the fisheries. , Thesis (PhD) -- Faculty of Science, Ocean Sciences, 2021
- Full Text: false
- Date Issued: 2021-04
- Authors: Reed, Jodie Romay
- Date: 2021-04
- Subjects: Gqeberha (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/52068 , vital:43451
- Description: Integration of sectoral based management into a coherent and coordinated spatial management framework is one of the central challenges of marine spatial planning ȋMSPȌǤ MSP initiatives aim to provide operational frameworks to promote sustainable use of the economic potential of the ocean while maintaining the value of marine biodiversity and the integrity of marine ecosystems to provide servicesǤ The ecosystem services associated with fisheries in terms of food and job provision are some of the most well recognised and highly valued in the marine realm and maintaining these benefits depends on a holistic understanding of the ecosystemǡ human uses and the management thereofǡ including areaǦbased managementǤ In ͲͰͱǡ South Africa was the first African country to enact MSP legislationǤ The development of MSP was advanced through a Presidential ocean economy initiative ȋOperation Phakisaǣ Oceans EconomyȌ that aimed to fast track marine transport and manufacturingǡ aquacultureǡ and the development of oil and gasǡ small harbourǡ and coastal and marine tourismǤ A dedicated ocean governance component was included to develop an overarchingǡ integrated ocean governance frameworkǤ The absence of fisheries in the plans and initiatives was conspicuousǤ The implementation of MSPǡ howeverǡ provides an opportunity to safeguard the ecosystem services provided by fisheries but only if the interests of fisheries can be adequately reflected in spatial plans and analysesǤ Furthermoreǡ the implementation of MSP may provide new opportunities for innovation in spatial approaches to local fisheries management that could address numerous spatial conflicts that have been reportedǤ Integration of spatial fisheries management approaches into MSP can also support the implementation of ecosystemǦbased management ȋEBMȌǡ by including mechanisms such as habitat protectionǡ effective management of areas important for vulnerable life history stagesǡ and bycatch managementǤ This study aimed to identifyǡ assess and further develop spatial management options for fisheries to facilitate the integration of fisheries management and MSPǤ This was achieved by firstlyǡ identifying existing spatial management instruments and assessing the way in which these instruments may be implemented to support spatial fisheries managementǤ Secondlyǡ the application of two contrasting spatial management optionsǡ applied to two pelagic fisheriesǡ was examined to assess their effectiveness at achieving fisheries management objectives with a focus on bycatch reductionǡ while minimising the costs to the fisheries. , Thesis (PhD) -- Faculty of Science, Ocean Sciences, 2021
- Full Text: false
- Date Issued: 2021-04
Spatial and temporal analysis of the critical zone in the Western rift valley corridor: towards earth stewardship science in East Africa
- Authors: Miller, Warren David
- Date: 2022-12
- Subjects: Port Elizabeth (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/59771 , vital:62423
- Description: Over the coming decades, Africa is expected to experience disturbing effects due to climate change and increased land cover change due to human influences presenting a significant concern for the future well-being of human and biological systems, the latter being the foundation of ecosystem services supplied to humanity. Therefore, unprecedented transdisciplinary cooperation, coordination, and integration amongst researchers, government, and civil society are necessary to increase the resiliency of these systems. This study aims to provide an outline of the Africa Alive Corridors (AAC) as an essential model for the encouragement of sustainable development through Earth Stewardship science. These aims are accompanied by the quantification and forward modelling for land cover change of the Critical Zone over 10 Great Lake Basins across one of the AAC, the Western Rift Valley Corridor (WRVC), in East Africa between the years 2018 and 2060. This approach provides the foundation for implementing improved regional governance, better encouragement of sustainable development beyond the 2030 United Nations Sustainable Development Goals, and education programs, such as the AAC, that promote socio-ecological resilience through Earth Stewardship Science. The AAC archives a portion of East Africa as the WRVC, a corridor along the western branch of the East African Rift System that highlights twenty heritage nodes, primarily great lakes, mountain ranges, national parks, and biological hotspots. These heritage entities are associated with ca. 12-million-years of evolution and transformation of the East African topography and related African Great Lake (AGL) systems. The thesis defines the study area by delineating AGL basins intersected by the WRVC. Across these basins, land cover change analysis provides a platform for an integrated assessment of the projected health of the corridor region. Existing land cover datasets provide the initial conditions of the study area for 2008 and 2013. Land cover between 2008 and 2013 is cross-tabulated using the Land Cover Module in the Terrset software, followed by the iii delineation of sub-models and driver variable identification. The Multi-Layer Perceptron algorithm provides the transition potentials between tree cover, urban area, cropland, wetland, and open area classes. Change quantification and prediction using Markov Chain analysis are then established for 2018, 2030, and 2060. The model successfully simulated future land cover change and concluded that: (1) proximity to existing human activity, proximity to existing tree cover, and population are the primary drivers of change; (2) the dominant land cover of the ten lake basins for 2018 was cropland at ca. 48%, followed by tree cover at ca. 33%; (3) total anthropogenic change over the coming four decades equates to over ca. 52 000 km2 (5 200 000 ha), and particularly (4) an urban area is expected to increase by >130%. This assessment ultimately provides a platform for regional governance development at the basin scale and Earth Stewardship science in East Africa. These changes require transdisciplinary action from researchers to civil society. The AAC provides the foundation for understanding the dynamics of the systems that support life across broader spatial and temporal resolutions in Africa, highlighting the need for future generations to build socio-ecological resilience to anticipate challenges such as biodiversity loss posed by climate change and excessive land cover change. , Thesis (DSc) -- Faculty of Science, School of Environmental Sciences, 2022
- Full Text:
- Date Issued: 2022-12
- Authors: Miller, Warren David
- Date: 2022-12
- Subjects: Port Elizabeth (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/59771 , vital:62423
- Description: Over the coming decades, Africa is expected to experience disturbing effects due to climate change and increased land cover change due to human influences presenting a significant concern for the future well-being of human and biological systems, the latter being the foundation of ecosystem services supplied to humanity. Therefore, unprecedented transdisciplinary cooperation, coordination, and integration amongst researchers, government, and civil society are necessary to increase the resiliency of these systems. This study aims to provide an outline of the Africa Alive Corridors (AAC) as an essential model for the encouragement of sustainable development through Earth Stewardship science. These aims are accompanied by the quantification and forward modelling for land cover change of the Critical Zone over 10 Great Lake Basins across one of the AAC, the Western Rift Valley Corridor (WRVC), in East Africa between the years 2018 and 2060. This approach provides the foundation for implementing improved regional governance, better encouragement of sustainable development beyond the 2030 United Nations Sustainable Development Goals, and education programs, such as the AAC, that promote socio-ecological resilience through Earth Stewardship Science. The AAC archives a portion of East Africa as the WRVC, a corridor along the western branch of the East African Rift System that highlights twenty heritage nodes, primarily great lakes, mountain ranges, national parks, and biological hotspots. These heritage entities are associated with ca. 12-million-years of evolution and transformation of the East African topography and related African Great Lake (AGL) systems. The thesis defines the study area by delineating AGL basins intersected by the WRVC. Across these basins, land cover change analysis provides a platform for an integrated assessment of the projected health of the corridor region. Existing land cover datasets provide the initial conditions of the study area for 2008 and 2013. Land cover between 2008 and 2013 is cross-tabulated using the Land Cover Module in the Terrset software, followed by the iii delineation of sub-models and driver variable identification. The Multi-Layer Perceptron algorithm provides the transition potentials between tree cover, urban area, cropland, wetland, and open area classes. Change quantification and prediction using Markov Chain analysis are then established for 2018, 2030, and 2060. The model successfully simulated future land cover change and concluded that: (1) proximity to existing human activity, proximity to existing tree cover, and population are the primary drivers of change; (2) the dominant land cover of the ten lake basins for 2018 was cropland at ca. 48%, followed by tree cover at ca. 33%; (3) total anthropogenic change over the coming four decades equates to over ca. 52 000 km2 (5 200 000 ha), and particularly (4) an urban area is expected to increase by >130%. This assessment ultimately provides a platform for regional governance development at the basin scale and Earth Stewardship science in East Africa. These changes require transdisciplinary action from researchers to civil society. The AAC provides the foundation for understanding the dynamics of the systems that support life across broader spatial and temporal resolutions in Africa, highlighting the need for future generations to build socio-ecological resilience to anticipate challenges such as biodiversity loss posed by climate change and excessive land cover change. , Thesis (DSc) -- Faculty of Science, School of Environmental Sciences, 2022
- Full Text:
- Date Issued: 2022-12
Smart catchment management and application in the Swartkops River and Estuary
- Authors: Mmachaka,Thandi Nthabiseng
- Date: 2022-04
- Subjects: Estuarine ecology--South Africa--Swartkops River Estuary
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/55932 , vital:54401
- Description: The influence of urbanization and industrialization on natural resources results in complex water resource management. In South Africa, there has been escalating rural-urban migration, a growing population in urban areas, and the mushrooming of informal settlements in cities over the last five decades. In the pursuit of protecting water resources, these contextual realities create a significant challenge to policymakers, planners, and implementers. Due to rapid population growth, climate change, recent droughts, and growing competition among agricultural, industrial, commercial, environmental, and domestic sectors, water resources are presently under severe stress in South Africa. This situation necessitates the effective management of water resources. This study completed a situational assessment for the Swartkops Catchment to examine the extent of pollution, mapped sources of pollution, investigated water quality governance and identified hot spot areas to provide the foundation for effective and efficient catchment management. To determine the current water quality status of the Swartkops Catchment, this current study investigated spatial and temporal variation in physico-chemical parameters, nutrients, and faecal bacteria. This study applied a mixed-method research design using semi-structured interviews and focus groups discussions as data collection methods to investigate the water quality governance of the Swartkops Catchment. Following the situational assessment of the Swartkops Catchment, the effectiveness of applying innovative smart catchment practices to improve water quality was investigated. The word smart in this context refers to innovative mechanisms that will ensure effective and efficient water resources management. The PHP scripting language (Hypertext Preprocessor), Android studio, Wampserver, and JavaScript were used to develop the Water Use Screening System (WUSS) and Pollution Incident Reporting System (PRS). In South Africa, stormwater infrastructure suffers from unsustainable utilization. Stormwater systems discharge into many of the country‘s rivers and estuaries, including Swartkops, leading to water quality degradation. To improve the Recommended Ecological Category (REC) of the Swartkops Estuary to Category C, drivers that contribute to poor water quality must be understood to inform appropriate management interventions. Results from sampling in Markman Canal were compared with historical water quality data. The present study showed that the Markman Canal contributed faecal bacteria, nutrients, and trace metals to the Swartkops Estuary. The Markman Canal was the greatest source of trace metals to the Swartkops Estuary compared to the other point sources entering the estuary. The results show that arsenic and mercury levels in the Markman Canal and the Swartkops Estuary were higher than that previously measured. Iron and copper concentrations were higher in the Markman Canal whereas only copper increased in the Swartkops Estuary. , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2022
- Full Text:
- Date Issued: 2022-04
- Authors: Mmachaka,Thandi Nthabiseng
- Date: 2022-04
- Subjects: Estuarine ecology--South Africa--Swartkops River Estuary
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/55932 , vital:54401
- Description: The influence of urbanization and industrialization on natural resources results in complex water resource management. In South Africa, there has been escalating rural-urban migration, a growing population in urban areas, and the mushrooming of informal settlements in cities over the last five decades. In the pursuit of protecting water resources, these contextual realities create a significant challenge to policymakers, planners, and implementers. Due to rapid population growth, climate change, recent droughts, and growing competition among agricultural, industrial, commercial, environmental, and domestic sectors, water resources are presently under severe stress in South Africa. This situation necessitates the effective management of water resources. This study completed a situational assessment for the Swartkops Catchment to examine the extent of pollution, mapped sources of pollution, investigated water quality governance and identified hot spot areas to provide the foundation for effective and efficient catchment management. To determine the current water quality status of the Swartkops Catchment, this current study investigated spatial and temporal variation in physico-chemical parameters, nutrients, and faecal bacteria. This study applied a mixed-method research design using semi-structured interviews and focus groups discussions as data collection methods to investigate the water quality governance of the Swartkops Catchment. Following the situational assessment of the Swartkops Catchment, the effectiveness of applying innovative smart catchment practices to improve water quality was investigated. The word smart in this context refers to innovative mechanisms that will ensure effective and efficient water resources management. The PHP scripting language (Hypertext Preprocessor), Android studio, Wampserver, and JavaScript were used to develop the Water Use Screening System (WUSS) and Pollution Incident Reporting System (PRS). In South Africa, stormwater infrastructure suffers from unsustainable utilization. Stormwater systems discharge into many of the country‘s rivers and estuaries, including Swartkops, leading to water quality degradation. To improve the Recommended Ecological Category (REC) of the Swartkops Estuary to Category C, drivers that contribute to poor water quality must be understood to inform appropriate management interventions. Results from sampling in Markman Canal were compared with historical water quality data. The present study showed that the Markman Canal contributed faecal bacteria, nutrients, and trace metals to the Swartkops Estuary. The Markman Canal was the greatest source of trace metals to the Swartkops Estuary compared to the other point sources entering the estuary. The results show that arsenic and mercury levels in the Markman Canal and the Swartkops Estuary were higher than that previously measured. Iron and copper concentrations were higher in the Markman Canal whereas only copper increased in the Swartkops Estuary. , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2022
- Full Text:
- Date Issued: 2022-04
Score driven volatility models based on skewed-t distributions
- Authors: Janse van Rensburg, Stéfan
- Date: 2021-04
- Subjects: Gqeberha (South Africa) , Eastern Cape (South Africa) , GARCH Model
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/52010 , vital:43425
- Description: Score driven (SD) conditional volatility models allow for rich volatility dynamics and realistic distributional assumptions. These models link the evolution of time-varying volatility to the shape of the predictive density, which often results in models that are robust against outliers. These models also allow for conditional skewness. The combination of skewness and robustness may improve in-sample fit, conditional volatility forecasts and tail-risk forecasts. Therefore, this study proposes novel SD conditional volatility models with Skewed-t distributed innovations. For some of these models, the formof skewness partially negates robustness against outliers. This result demonstrates that the formof skewness requires careful consideration in the specification of SD conditional volatility models. The study also expands upon earlier observations that the assumption of negative conditional skewness may induce a form of volatility asymmetry in SD conditional volatility models that is incompatible with the leverage effect typically observed in equity markets. A simulation experiment shows that neglected leverage, therefore, biases maximum likelihood estimates. Additionally, the study considers SD conditional volatility models that account for leverage effects and have Skewed-t distributed innovations. An empirical application to the daily Johannesburg Stock Exchange (JSE) / Financial Times Stock Exchange (FTSE) All Share Index returns demonstrates the utility of SD conditional volatility models with Skewed-t distributed innovations. Extensions of these models that account for leverage prove competitive with more traditional conditional volatility models in terms of in-sample fit and tail-risk forecasts. These results suggest that the models considered in this study are useful within the context of financial risk management. , Thesis (PhD) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2021
- Full Text: false
- Date Issued: 2021-04
- Authors: Janse van Rensburg, Stéfan
- Date: 2021-04
- Subjects: Gqeberha (South Africa) , Eastern Cape (South Africa) , GARCH Model
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/52010 , vital:43425
- Description: Score driven (SD) conditional volatility models allow for rich volatility dynamics and realistic distributional assumptions. These models link the evolution of time-varying volatility to the shape of the predictive density, which often results in models that are robust against outliers. These models also allow for conditional skewness. The combination of skewness and robustness may improve in-sample fit, conditional volatility forecasts and tail-risk forecasts. Therefore, this study proposes novel SD conditional volatility models with Skewed-t distributed innovations. For some of these models, the formof skewness partially negates robustness against outliers. This result demonstrates that the formof skewness requires careful consideration in the specification of SD conditional volatility models. The study also expands upon earlier observations that the assumption of negative conditional skewness may induce a form of volatility asymmetry in SD conditional volatility models that is incompatible with the leverage effect typically observed in equity markets. A simulation experiment shows that neglected leverage, therefore, biases maximum likelihood estimates. Additionally, the study considers SD conditional volatility models that account for leverage effects and have Skewed-t distributed innovations. An empirical application to the daily Johannesburg Stock Exchange (JSE) / Financial Times Stock Exchange (FTSE) All Share Index returns demonstrates the utility of SD conditional volatility models with Skewed-t distributed innovations. Extensions of these models that account for leverage prove competitive with more traditional conditional volatility models in terms of in-sample fit and tail-risk forecasts. These results suggest that the models considered in this study are useful within the context of financial risk management. , Thesis (PhD) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2021
- Full Text: false
- Date Issued: 2021-04
Population structure, production, growth, reproduction and the ecology of Atherina breviceps Valenciennes, 1935 (Pisces : Atherinidae) and Gilchristella aestuaria (Gilchrist, 1914) (Pisces : Clupeidae), from two southern Cape coastal lakes
- Authors: Ratte, Theodore Wilhlelm
- Date: 1989-01
- Subjects: Silversides , Clupeidae -- South Africa -- Cape of Good Hope
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/50878 , vital:43029
- Description: Over the period October 1978 to January 1981, a total of 147 853 Atherina breviceps with a total biomass of 55 2B0,7 g and 107 046 Gilchristella aestuaria with a total biomass of 33 708,9 g were collected in the Swartvlei System and 151 531 A. breviceps with a total biomass of 727 795,0 g and 51 258 G. aestuaria with a total biomass of 12 231,5 g were collected in Groenvlei, to determine their population structure, production, growth, reproduction and ecology in both systems. A. breviceps and G. aestuaria were collected from nine and eleven estuaries respectively, including Groenvlei, along the Cape coast to determine the degree of genetic divergence of both these two species in Groenvlei. It was found that the mature 0-year-old A. breviceps and the 2-year-old G. aestuaria dominated the catches in the Swartvlei System, whereas the juvenile 0-year-olds and 1-year-olds of both species respectively, dominated the catches in Groenvlei. The Swartvlei System and Groenvlei produced respectively between 10-12 metric tons of A. breviceps and between 5-3 metric tons of G. aestuaria annually. A. breviceps and G. aestuana in the Swartvlei System and Groenvlei attain observed ages of between 3 years and 7-8 years respectively. The main spawning period for both species is between spring-autumn in Groenvlei and for A. breviceps in the Swartvlei System. G. aestuaria has a continuous winter-summer spawning in the Swartvlei System. A. breviceps and G. aestuaria in Groenvlei have diverged to such an extent from these two species' populations in other systems, that A. breviceps and G. aestuaria in Groenvlei should receive a priority conservation status. , Thesis (PhD) -- Faculty of Science, 1989
- Full Text:
- Date Issued: 1989-01
- Authors: Ratte, Theodore Wilhlelm
- Date: 1989-01
- Subjects: Silversides , Clupeidae -- South Africa -- Cape of Good Hope
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/50878 , vital:43029
- Description: Over the period October 1978 to January 1981, a total of 147 853 Atherina breviceps with a total biomass of 55 2B0,7 g and 107 046 Gilchristella aestuaria with a total biomass of 33 708,9 g were collected in the Swartvlei System and 151 531 A. breviceps with a total biomass of 727 795,0 g and 51 258 G. aestuaria with a total biomass of 12 231,5 g were collected in Groenvlei, to determine their population structure, production, growth, reproduction and ecology in both systems. A. breviceps and G. aestuaria were collected from nine and eleven estuaries respectively, including Groenvlei, along the Cape coast to determine the degree of genetic divergence of both these two species in Groenvlei. It was found that the mature 0-year-old A. breviceps and the 2-year-old G. aestuaria dominated the catches in the Swartvlei System, whereas the juvenile 0-year-olds and 1-year-olds of both species respectively, dominated the catches in Groenvlei. The Swartvlei System and Groenvlei produced respectively between 10-12 metric tons of A. breviceps and between 5-3 metric tons of G. aestuaria annually. A. breviceps and G. aestuana in the Swartvlei System and Groenvlei attain observed ages of between 3 years and 7-8 years respectively. The main spawning period for both species is between spring-autumn in Groenvlei and for A. breviceps in the Swartvlei System. G. aestuaria has a continuous winter-summer spawning in the Swartvlei System. A. breviceps and G. aestuaria in Groenvlei have diverged to such an extent from these two species' populations in other systems, that A. breviceps and G. aestuaria in Groenvlei should receive a priority conservation status. , Thesis (PhD) -- Faculty of Science, 1989
- Full Text:
- Date Issued: 1989-01
Phytochemical investigation and antidiabetic activity of cissampelos capensis and strychnos henningsii the Eastern Cape medicinal plants
- Authors: Latolla, Nehemiah Solomon
- Date: 2022-04
- Subjects: Medicinal plants -- Eastern Cape (South Africa) , Endemic plants -- South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/56145 , vital:55956
- Description: Diabetes mellitus is recorded as a significant health crisis in South Africa and various medicinal plants are used for the management of diabetes. However, the chemistry and bioactivity associated with these plants' antidiabetic activity are still lacking. Cissampelos capensis L.f. and Strychnos henningsii Gilg are among the plants utilised to manage diabetes in the Eastern Cape Province, South Africa. C. capensis and S. henningsii are known for their isoquinoline – and indole alkaloids, respectively. Other phytochemical groups associated with antidiabetic activity are the phenols, flavonoids, and terpenes. Thus, this study aimed to evaluate in-depth the phytochemical profiling, alkaloidal identification, and structural characterisation of phytochemicals isolated from these plants. Also, subsequent in vitro antidiabetic screening of the crude extracts and isolated compounds from both plants was done. The phytochemical profiling was performed by employing a qualitative and quantitative approach through high-performance thin layer chromatography (HPTLC) and UV-spectrometry. Further analysis for the identification of alkaloids was done by using LCMS. Fractionation and purification of crude extracts were achieved through crystallisation and various chromatographic techniques. NMR, HRMS, UV/Vis, FTIR, and XRD spectroscopic techniques were used to characterise isolated compounds. In vitro antidiabetic activity screening involved the investigation of cytotoxicity, antioxidant activity, alpha-amylase – and/or alpha-glucosidase inhibition (particular to type II diabetes). C. capensis and S. henningsii extracts tested positive for alkaloids, phenolics, flavonoids, and terpenes through HPTLC screening. Quantitative estimation by UV spectrometry of these phytochemical groups detected the highest concentration of alkaloids, followed by flavonoids, phenolics, and terpenes content. The in vitro antidiabetic biological screening of the various crude extracts suggested that the presence of alkaloids, flavonoids, phenolics, and terpenes fostered favourable biological activity. The LCMS of the known alkaloidal constituents from C. capensis detected the presence of ten alkaloids, including glaziovine, lauroscholtzine, pronuciferine and vi salutardine. Seven known alkaloids and one triterpene were detected from S. henningsii, including holtsiine, 23-hdroxyspermostrychnine, henningsiine, and the triterpene, friedelin. These findings suggest that C. capensis and S. henningsii have similar phytochemical constituents compared to the species reported in literature. However, the distribution of the phytochemicals in the various plant parts differed from previous accounts. , Thesis (PhD) -- Faculty of Science,School of Biomecular and Chemical Sciences , 2022
- Full Text:
- Date Issued: 2022-04
- Authors: Latolla, Nehemiah Solomon
- Date: 2022-04
- Subjects: Medicinal plants -- Eastern Cape (South Africa) , Endemic plants -- South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/56145 , vital:55956
- Description: Diabetes mellitus is recorded as a significant health crisis in South Africa and various medicinal plants are used for the management of diabetes. However, the chemistry and bioactivity associated with these plants' antidiabetic activity are still lacking. Cissampelos capensis L.f. and Strychnos henningsii Gilg are among the plants utilised to manage diabetes in the Eastern Cape Province, South Africa. C. capensis and S. henningsii are known for their isoquinoline – and indole alkaloids, respectively. Other phytochemical groups associated with antidiabetic activity are the phenols, flavonoids, and terpenes. Thus, this study aimed to evaluate in-depth the phytochemical profiling, alkaloidal identification, and structural characterisation of phytochemicals isolated from these plants. Also, subsequent in vitro antidiabetic screening of the crude extracts and isolated compounds from both plants was done. The phytochemical profiling was performed by employing a qualitative and quantitative approach through high-performance thin layer chromatography (HPTLC) and UV-spectrometry. Further analysis for the identification of alkaloids was done by using LCMS. Fractionation and purification of crude extracts were achieved through crystallisation and various chromatographic techniques. NMR, HRMS, UV/Vis, FTIR, and XRD spectroscopic techniques were used to characterise isolated compounds. In vitro antidiabetic activity screening involved the investigation of cytotoxicity, antioxidant activity, alpha-amylase – and/or alpha-glucosidase inhibition (particular to type II diabetes). C. capensis and S. henningsii extracts tested positive for alkaloids, phenolics, flavonoids, and terpenes through HPTLC screening. Quantitative estimation by UV spectrometry of these phytochemical groups detected the highest concentration of alkaloids, followed by flavonoids, phenolics, and terpenes content. The in vitro antidiabetic biological screening of the various crude extracts suggested that the presence of alkaloids, flavonoids, phenolics, and terpenes fostered favourable biological activity. The LCMS of the known alkaloidal constituents from C. capensis detected the presence of ten alkaloids, including glaziovine, lauroscholtzine, pronuciferine and vi salutardine. Seven known alkaloids and one triterpene were detected from S. henningsii, including holtsiine, 23-hdroxyspermostrychnine, henningsiine, and the triterpene, friedelin. These findings suggest that C. capensis and S. henningsii have similar phytochemical constituents compared to the species reported in literature. However, the distribution of the phytochemicals in the various plant parts differed from previous accounts. , Thesis (PhD) -- Faculty of Science,School of Biomecular and Chemical Sciences , 2022
- Full Text:
- Date Issued: 2022-04
Ocean structures and dynamics of two open bays on the eastern Agulhas Bank
- Authors: Dlomo, Xolisa
- Date: 2021-12
- Subjects: Port Elizabeth (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/53607 , vital:45680
- Description: Upwelling, bay-scale currents, fronts and mixing in Algoa Bay and St Francis Bay occur over both short and long time periods. These physical ocean dynamics drive the temporal and spatial distribution of nutrients in the bays, there by influencing primary and secondary production. Thermal gradients and fronts are driven by the wind and open ocean influences, such as the Agulhas Current, daily and seasonal variations in solar radiation, long and short period waves, air-sea fluxes, coastal trapped waves and terrestrial freshwater inflow. These phenomena are poorly understood along this part of the coastline and were the focus of this study. I investigated the dominant temperature scales of variability in both bays, to determine which isotherm is best suited to describe temperature fluctuations and thermocline spatiotemporal variability in and between the two bays. I investigated upwelling spatiotemporal variability in the two bays and tested whether upwelling occurs at the opposite sides of the bays with a change in wind direction. Thereafter studied the occurrence and drivers of winter upwelling events. The wind-driven current spatiotemporal variability and correlations were investigated at the extremities of the two bays. The daily, intra-seasonal and yearly variation in temperature structures in Algoa Bay and St. Francis Bay were mainly driven by the local winds, coastal topography, and bathymetry. The most suitable isotherm to describe thermal fluctuations and variability in Algoa Bay shallower sites was 16.5 °C and its mean depth was 16.2 m. The best isotherm for the deeper sites in Algoa Bay was 15.7 °C with a depth of 33.1 m. The average temperature and depth of the best isotherm to describe thermal fluctuations in St. Francis Bay for the shallower sites was15.80 °C and 16.83 m, and for the deeper sites it was 15.10 °C and 32.08 m. Algoa Bay showed an average cooling trend of -0.000172 °C per year, whereas in St. Francis Bay a warming average trend of 0.0188 °C per year was observed over the study period often and six years, respectively. The wind, Coriolis Effect and Ekman Transport were the main external forces that influenced upwelling throughout the year. Since the available mesoscale indices for upwelling intensity lack the resolution needed to characterize and compare inner-shelf upwelling regimes at small spatial scales, I developed a new local, quantitative index of thermal variability. Index calculations were based on hourly records of in site depth-averaged temperatures, measured at 6 sites in St. Francis Bay and at 8 sites in Algoa Bay. Using the Multivariate Upwelling Zone Index of Cooling (MUZIC) I found that Woody Cape and Blue Horizon Bay had the highest upwelling intensity in Algoa Bay and St. Francis Bay, respectively. The other sites were ordinated and ranked according to their upwelling rates and intensity. Evidence of wind-driven winter upwelling was found to be a common occurrence in both bays. There was no obvious current seasonality observed, however, strong spectral signals in the period of a weather band (4 –7 days) were present. Current structures were generally positively correlated with wind variations in both bays. Thus, when westerly/easterly winds blew the overall surface current direction was eastward/westward. I observed a pronounced current spatiotemporal variability that was driven by local winds. The Bird Island surface currents in Algoa Bay were strongly correlated at 0–lag day with the winds, however, in Cape Recife the strongest correlations were usually observed at 1–lag day highlighting the spatiotemporal influence of wind regimes on current structures in Algoa Bay. Bird Island current speeds were higher and had an obvious bimodal directional variation (south westward /north eastward) compared to Cape Recife currents, which generally had a slower current speed with a strong west-north westward direction. In St. Francis Bay, the Schoenmakerskop surface currents showed weak positive correlation with winds at 0–lag day, however, stronger negative correlations were observed at 4–lag days. The current surface speeds in Schoenmakerskop were the lowest and varied directionally between north-north eastward and south-south eastward. The basic data requirements (i.e. SST/ UTR and ADCP time series) and the simplicity of the calculations make these indices a useful tool to apply to a large number of sites nationally and internationally, and to examine the generality of community and population-level responses to physical forcing. , Thesis (PhD) -- Faculty of Science, Journalsim and Media Studies, 2021
- Full Text:
- Date Issued: 2021-12
- Authors: Dlomo, Xolisa
- Date: 2021-12
- Subjects: Port Elizabeth (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/53607 , vital:45680
- Description: Upwelling, bay-scale currents, fronts and mixing in Algoa Bay and St Francis Bay occur over both short and long time periods. These physical ocean dynamics drive the temporal and spatial distribution of nutrients in the bays, there by influencing primary and secondary production. Thermal gradients and fronts are driven by the wind and open ocean influences, such as the Agulhas Current, daily and seasonal variations in solar radiation, long and short period waves, air-sea fluxes, coastal trapped waves and terrestrial freshwater inflow. These phenomena are poorly understood along this part of the coastline and were the focus of this study. I investigated the dominant temperature scales of variability in both bays, to determine which isotherm is best suited to describe temperature fluctuations and thermocline spatiotemporal variability in and between the two bays. I investigated upwelling spatiotemporal variability in the two bays and tested whether upwelling occurs at the opposite sides of the bays with a change in wind direction. Thereafter studied the occurrence and drivers of winter upwelling events. The wind-driven current spatiotemporal variability and correlations were investigated at the extremities of the two bays. The daily, intra-seasonal and yearly variation in temperature structures in Algoa Bay and St. Francis Bay were mainly driven by the local winds, coastal topography, and bathymetry. The most suitable isotherm to describe thermal fluctuations and variability in Algoa Bay shallower sites was 16.5 °C and its mean depth was 16.2 m. The best isotherm for the deeper sites in Algoa Bay was 15.7 °C with a depth of 33.1 m. The average temperature and depth of the best isotherm to describe thermal fluctuations in St. Francis Bay for the shallower sites was15.80 °C and 16.83 m, and for the deeper sites it was 15.10 °C and 32.08 m. Algoa Bay showed an average cooling trend of -0.000172 °C per year, whereas in St. Francis Bay a warming average trend of 0.0188 °C per year was observed over the study period often and six years, respectively. The wind, Coriolis Effect and Ekman Transport were the main external forces that influenced upwelling throughout the year. Since the available mesoscale indices for upwelling intensity lack the resolution needed to characterize and compare inner-shelf upwelling regimes at small spatial scales, I developed a new local, quantitative index of thermal variability. Index calculations were based on hourly records of in site depth-averaged temperatures, measured at 6 sites in St. Francis Bay and at 8 sites in Algoa Bay. Using the Multivariate Upwelling Zone Index of Cooling (MUZIC) I found that Woody Cape and Blue Horizon Bay had the highest upwelling intensity in Algoa Bay and St. Francis Bay, respectively. The other sites were ordinated and ranked according to their upwelling rates and intensity. Evidence of wind-driven winter upwelling was found to be a common occurrence in both bays. There was no obvious current seasonality observed, however, strong spectral signals in the period of a weather band (4 –7 days) were present. Current structures were generally positively correlated with wind variations in both bays. Thus, when westerly/easterly winds blew the overall surface current direction was eastward/westward. I observed a pronounced current spatiotemporal variability that was driven by local winds. The Bird Island surface currents in Algoa Bay were strongly correlated at 0–lag day with the winds, however, in Cape Recife the strongest correlations were usually observed at 1–lag day highlighting the spatiotemporal influence of wind regimes on current structures in Algoa Bay. Bird Island current speeds were higher and had an obvious bimodal directional variation (south westward /north eastward) compared to Cape Recife currents, which generally had a slower current speed with a strong west-north westward direction. In St. Francis Bay, the Schoenmakerskop surface currents showed weak positive correlation with winds at 0–lag day, however, stronger negative correlations were observed at 4–lag days. The current surface speeds in Schoenmakerskop were the lowest and varied directionally between north-north eastward and south-south eastward. The basic data requirements (i.e. SST/ UTR and ADCP time series) and the simplicity of the calculations make these indices a useful tool to apply to a large number of sites nationally and internationally, and to examine the generality of community and population-level responses to physical forcing. , Thesis (PhD) -- Faculty of Science, Journalsim and Media Studies, 2021
- Full Text:
- Date Issued: 2021-12
Moult and energetics in three species from the Euplectes genus representing a gradient of elaborate plumage ornamentation
- Authors: Webb, Stacey Leigh
- Date: 2022-12
- Subjects: Sexual selection in animals – South Africa , Bird watching -- Africa, Southern , Plumage
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/60026 , vital:62734
- Description: Elaborate plumage ornamentation in birds has fascinated scientists since the 1800s. The evolution and persistence of elaborate and costly ornamentation seemed to be in opposition to the theory of natural selection. However, over the years research has revealed the role and functional significance of elaborate plumage ornamentation in sexual selection. Recent studies have shown that the energetic costs associated with moulting into new plumages are higher than maintenance costs, but these costs have not been quantified for species that exhibit elaborate breeding plumage ornamentation for sexual selection. In addition, for these sexually selected ornamental traits (signals) to have evolved and be maintained, there must be some aspect of individual quality that they convey to the receiver. Despite a large body of literature on sexual selection, honest signalling and ornamental plumage in birds, the physiological correlates of honest signalling during sexual selection and the messages these signals convey to the receivers are poorly understood. In this study, I investigated four aspects related to the honesty of the sexual selection signal. These were (i) seasonal variation in standardised resting metabolic rates of breeding and non-breeding birds, (ii) moult phenology, (iii) physiological parameters linked to honest signalling, and (iv) the energetic costs of production and maintenance of elaborate plumage ornamentation using three species from the Euplectes genus as model species. The three species selected, the red-collared widowbird (Euplectes ardens), fan-tailed widowbird (Euplectes axillaris) and the southern red bishop (Euplectes orix) represent a gradient of plumage elaboration and although the receivers of the sexual selection signals are known for these three species, the energetic cost of the signals and the underlying message the signals convey remain unknown. I measured seasonal variation in resting metabolic rate (RMR), body mass (Mb), thermoneutral zone (TNZ) and body temperature (Tb) over the course of two years in the three selected Euplectes species (E. ardens, E. axillaris and E. orix; chapter 2). My results showed no significant effect of season on RMR (except in E. orix females) suggesting that in these species the metabolic costs in summer (associated with breeding season) are comparable to the metabolic costs associated with thermoregulation during winter. Contrary to my prediction that metabolic costs would increase along a gradient of increasing tail length (due to the energetic costs Webb V associated with elaborate plumage ornamentation), I found no significant effect of species. The lack of a significant result indicates that once the initial investment in plumage is complete, other predictor variables play a role (in this case body mass). , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2022
- Full Text:
- Date Issued: 2022-12
- Authors: Webb, Stacey Leigh
- Date: 2022-12
- Subjects: Sexual selection in animals – South Africa , Bird watching -- Africa, Southern , Plumage
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/60026 , vital:62734
- Description: Elaborate plumage ornamentation in birds has fascinated scientists since the 1800s. The evolution and persistence of elaborate and costly ornamentation seemed to be in opposition to the theory of natural selection. However, over the years research has revealed the role and functional significance of elaborate plumage ornamentation in sexual selection. Recent studies have shown that the energetic costs associated with moulting into new plumages are higher than maintenance costs, but these costs have not been quantified for species that exhibit elaborate breeding plumage ornamentation for sexual selection. In addition, for these sexually selected ornamental traits (signals) to have evolved and be maintained, there must be some aspect of individual quality that they convey to the receiver. Despite a large body of literature on sexual selection, honest signalling and ornamental plumage in birds, the physiological correlates of honest signalling during sexual selection and the messages these signals convey to the receivers are poorly understood. In this study, I investigated four aspects related to the honesty of the sexual selection signal. These were (i) seasonal variation in standardised resting metabolic rates of breeding and non-breeding birds, (ii) moult phenology, (iii) physiological parameters linked to honest signalling, and (iv) the energetic costs of production and maintenance of elaborate plumage ornamentation using three species from the Euplectes genus as model species. The three species selected, the red-collared widowbird (Euplectes ardens), fan-tailed widowbird (Euplectes axillaris) and the southern red bishop (Euplectes orix) represent a gradient of plumage elaboration and although the receivers of the sexual selection signals are known for these three species, the energetic cost of the signals and the underlying message the signals convey remain unknown. I measured seasonal variation in resting metabolic rate (RMR), body mass (Mb), thermoneutral zone (TNZ) and body temperature (Tb) over the course of two years in the three selected Euplectes species (E. ardens, E. axillaris and E. orix; chapter 2). My results showed no significant effect of season on RMR (except in E. orix females) suggesting that in these species the metabolic costs in summer (associated with breeding season) are comparable to the metabolic costs associated with thermoregulation during winter. Contrary to my prediction that metabolic costs would increase along a gradient of increasing tail length (due to the energetic costs Webb V associated with elaborate plumage ornamentation), I found no significant effect of species. The lack of a significant result indicates that once the initial investment in plumage is complete, other predictor variables play a role (in this case body mass). , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2022
- Full Text:
- Date Issued: 2022-12
Microstructural characterization of Swift Heavy Ion (SHI) induced rotation in single crystal NiO
- Authors: Douglas-Henry, Danielle
- Date: 2021-12
- Subjects: Port Elizabeth (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/53648 , vital:45685
- Description: Swift Heavy Ions (SHI) are characterised by having energies greater than 1 MeV per nucleon with an atomic mass greater than 6 amu. Exposure to irradiation of this type has been known to produce latent tracks in insulators. This is due to the energy loss through the material being governed by electronic excitation processes. The extent of the track formation and microstructural changes induced has been reported to be material specific. Models such as the thermal spike model have been used to explain these changes, however rough approximations are still made. A particularly under studied phenomena is the collective rotation seen in materials exposed to off-normal incidence irradiation. To date the only available experimental data is X-Ray Diffraction (XRD) spectra and surface shifts. This does not allow for depth-dependent rotation studies and very little can be deduced regarding the microstructure of the modified volume. In this study, the microstructural changes in single crystal Nickel Oxide (NiO) have been studied using electron microscopy techniques. A depth dependent investigation of the crystal rotation was performed using Selected Area Electron Diffraction (SAED), Transmission Kikuchi Diffraction (TKD) and Electron Backscatter Diffraction (EBSD). Transmission Electron Microscopy (TEM) and Scanning Transmission Electron Microscopy (STEM) were utilized to interrogate the microstructural changes facilitating the bulk rotation. Five different NiO specimens were investigated. Specimens had surfaces parallel to either the {0 0 1} or {1 1 1} planes. Ion energies used were 593 MeV, 940 MeV and 1.6 GeV, while fluences ranged from 1.0 x 1011 ions/cm² to 9.6 x 1014 ions/cm². Latent track formation in both low fluence (nonoverlapping regime) and high fluence (overlapping regime) specimens were investigated and compared. , Thesis (PhD) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2021
- Full Text: false
- Date Issued: 2021-12
- Authors: Douglas-Henry, Danielle
- Date: 2021-12
- Subjects: Port Elizabeth (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/53648 , vital:45685
- Description: Swift Heavy Ions (SHI) are characterised by having energies greater than 1 MeV per nucleon with an atomic mass greater than 6 amu. Exposure to irradiation of this type has been known to produce latent tracks in insulators. This is due to the energy loss through the material being governed by electronic excitation processes. The extent of the track formation and microstructural changes induced has been reported to be material specific. Models such as the thermal spike model have been used to explain these changes, however rough approximations are still made. A particularly under studied phenomena is the collective rotation seen in materials exposed to off-normal incidence irradiation. To date the only available experimental data is X-Ray Diffraction (XRD) spectra and surface shifts. This does not allow for depth-dependent rotation studies and very little can be deduced regarding the microstructure of the modified volume. In this study, the microstructural changes in single crystal Nickel Oxide (NiO) have been studied using electron microscopy techniques. A depth dependent investigation of the crystal rotation was performed using Selected Area Electron Diffraction (SAED), Transmission Kikuchi Diffraction (TKD) and Electron Backscatter Diffraction (EBSD). Transmission Electron Microscopy (TEM) and Scanning Transmission Electron Microscopy (STEM) were utilized to interrogate the microstructural changes facilitating the bulk rotation. Five different NiO specimens were investigated. Specimens had surfaces parallel to either the {0 0 1} or {1 1 1} planes. Ion energies used were 593 MeV, 940 MeV and 1.6 GeV, while fluences ranged from 1.0 x 1011 ions/cm² to 9.6 x 1014 ions/cm². Latent track formation in both low fluence (nonoverlapping regime) and high fluence (overlapping regime) specimens were investigated and compared. , Thesis (PhD) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2021
- Full Text: false
- Date Issued: 2021-12