Augmenting encoder-decoder networks for first-order logic formula parsing using attention pointer mechanisms
- Authors: Tissink, Kade
- Date: 2024-04
- Subjects: Translators (Computer programs) , Computational linguistics , Computer science
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64390 , vital:73692
- Description: Semantic parsing is the task of extracting a structured machine-interpretable representation from natural language utterance. This representation can be used for various applications such as question answering, information extraction, and dialogue systems. However, semantic parsing is a challenging problem that requires dealing with the ambiguity, variability, and complexity of natural language. This dissertation investigates neural parsing of natural language (NL) sentences to first-order logic (FOL) formulas. FOL is a widely used formal language for expressing logical statements and reasoning. FOL formulas can capture the meaning and structure of natural language sentences in a precise and unambiguous way. The problem is initially approached as a sequence-to-sequence mapping task using both LSTM-based and transformer encoder-decoder architectures for character-, subword-, and wordlevel text tokenisation. These models are trained on NL-FOL datasets using supervised learning and evaluated on various metrics such as exact match accuracy, syntactic validity, formula structure accuracy, and predicate/constant similarity. A novel augmented model is then introduced that decomposes the task of neural FOL parsing into four inter-dependent subtasks: template decoding, predicate and constant recognition, predicate set pointing, and object set pointing. The components for the four subtasks are jointly trained using multi-task learning and evaluated using the same metrics from the sequence-tosequence models. The results indicate improved performance over the sequence-to-sequence models and the modular design allows for more interpretability and flexibility. Additionally, to compensate for the scarcity of open-source, labelled NL-FOL datasets, a new benchmark is constructed from publicly accessible data. The data consists of NL sentences paired with corresponding FOL formulas in a standardised notation. The data is split into training, validation, and test sets. The main contributions of this dissertation are: an in-depth literature review covering decades of research presented with a consistent notation, the formation of a complex NL-FOL benchmark that includes algorithmically generated and human-annotated FOL formulas, proposal of a novel transformer encoder-decoder architecture that is shown to successfully train at significant depths, evaluation of twenty sequence-to-sequence models on the task of neural FOL parsing for different text representations and encoder-decoder architectures, the proposal of a novel augmented FOL parsing architecture, and an in-depth analysis of the strengths and weaknesses of these models. , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics , 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Tissink, Kade
- Date: 2024-04
- Subjects: Translators (Computer programs) , Computational linguistics , Computer science
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64390 , vital:73692
- Description: Semantic parsing is the task of extracting a structured machine-interpretable representation from natural language utterance. This representation can be used for various applications such as question answering, information extraction, and dialogue systems. However, semantic parsing is a challenging problem that requires dealing with the ambiguity, variability, and complexity of natural language. This dissertation investigates neural parsing of natural language (NL) sentences to first-order logic (FOL) formulas. FOL is a widely used formal language for expressing logical statements and reasoning. FOL formulas can capture the meaning and structure of natural language sentences in a precise and unambiguous way. The problem is initially approached as a sequence-to-sequence mapping task using both LSTM-based and transformer encoder-decoder architectures for character-, subword-, and wordlevel text tokenisation. These models are trained on NL-FOL datasets using supervised learning and evaluated on various metrics such as exact match accuracy, syntactic validity, formula structure accuracy, and predicate/constant similarity. A novel augmented model is then introduced that decomposes the task of neural FOL parsing into four inter-dependent subtasks: template decoding, predicate and constant recognition, predicate set pointing, and object set pointing. The components for the four subtasks are jointly trained using multi-task learning and evaluated using the same metrics from the sequence-tosequence models. The results indicate improved performance over the sequence-to-sequence models and the modular design allows for more interpretability and flexibility. Additionally, to compensate for the scarcity of open-source, labelled NL-FOL datasets, a new benchmark is constructed from publicly accessible data. The data consists of NL sentences paired with corresponding FOL formulas in a standardised notation. The data is split into training, validation, and test sets. The main contributions of this dissertation are: an in-depth literature review covering decades of research presented with a consistent notation, the formation of a complex NL-FOL benchmark that includes algorithmically generated and human-annotated FOL formulas, proposal of a novel transformer encoder-decoder architecture that is shown to successfully train at significant depths, evaluation of twenty sequence-to-sequence models on the task of neural FOL parsing for different text representations and encoder-decoder architectures, the proposal of a novel augmented FOL parsing architecture, and an in-depth analysis of the strengths and weaknesses of these models. , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics , 2024
- Full Text:
- Date Issued: 2024-04
Augmenting the Moore-Penrose generalised Inverse to train neural networks
- Authors: Fang, Bobby
- Date: 2024-04
- Subjects: Neural networks (Computer science) , Machine learning , Mathematical optimization -- Computer programs
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63755 , vital:73595
- Description: An Extreme Learning Machine (ELM) is a non-iterative and fast feedforward neural network training algorithm which uses the Moore-Penrose generalised inverse of a matrix to compute the weights of the output layer of the neural network, using a random initialisation for the hidden layer. While ELM has been used to train feedforward neural networks, the effectiveness of the MP generalised to train recurrent neural networks is yet to be investigated. The primary aim of this research was to investigate how biases in the output layer and the MP generalised inverse can be used to train recurrent neural networks. To accomplish this, the Bias Augmented ELM (BA-ELM), which concatenated the hidden layer output matrix with a ones-column vector to simulate the biases in the output layer, was proposed. A variety of datasets generated from optimisation test functions, as well as using real-world regression and classification datasets, were used to validate BA-ELM. The results showed in specific circumstances that BA-ELM was able to perform better than ELM. Following this, Recurrent ELM (R-ELM) was proposed which uses a recurrent hidden layer instead of a feedforward hidden layer. Recurrent neural networks also rely on having functional feedback connections in the recurrent layer. A hybrid training algorithm, Recurrent Hybrid ELM (R-HELM), was proposed, which uses a gradient-based algorithm to optimise the recurrent layer and the MP generalised inverse to compute the output weights. The evaluation of R-ELM and R-HELM algorithms were carried out using three different recurrent architectures on two recurrent tasks derived from the Susceptible- Exposed-Infected-Removed (SEIR) epidemiology model. Various training hyperparameters were evaluated through hyperparameter investigations to investigate their effectiveness on the hybrid training algorithm. With optimal hyperparameters, the hybrid training algorithm was able to achieve better performance than the conventional gradient-based algorithm. , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Fang, Bobby
- Date: 2024-04
- Subjects: Neural networks (Computer science) , Machine learning , Mathematical optimization -- Computer programs
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63755 , vital:73595
- Description: An Extreme Learning Machine (ELM) is a non-iterative and fast feedforward neural network training algorithm which uses the Moore-Penrose generalised inverse of a matrix to compute the weights of the output layer of the neural network, using a random initialisation for the hidden layer. While ELM has been used to train feedforward neural networks, the effectiveness of the MP generalised to train recurrent neural networks is yet to be investigated. The primary aim of this research was to investigate how biases in the output layer and the MP generalised inverse can be used to train recurrent neural networks. To accomplish this, the Bias Augmented ELM (BA-ELM), which concatenated the hidden layer output matrix with a ones-column vector to simulate the biases in the output layer, was proposed. A variety of datasets generated from optimisation test functions, as well as using real-world regression and classification datasets, were used to validate BA-ELM. The results showed in specific circumstances that BA-ELM was able to perform better than ELM. Following this, Recurrent ELM (R-ELM) was proposed which uses a recurrent hidden layer instead of a feedforward hidden layer. Recurrent neural networks also rely on having functional feedback connections in the recurrent layer. A hybrid training algorithm, Recurrent Hybrid ELM (R-HELM), was proposed, which uses a gradient-based algorithm to optimise the recurrent layer and the MP generalised inverse to compute the output weights. The evaluation of R-ELM and R-HELM algorithms were carried out using three different recurrent architectures on two recurrent tasks derived from the Susceptible- Exposed-Infected-Removed (SEIR) epidemiology model. Various training hyperparameters were evaluated through hyperparameter investigations to investigate their effectiveness on the hybrid training algorithm. With optimal hyperparameters, the hybrid training algorithm was able to achieve better performance than the conventional gradient-based algorithm. , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-04
Comparative study of the effect of iloprost on neuroinflammatory changes in c8-b4 microglial cells and murine model of trypanosomiasis
- Authors: Jacobs, Ashleigh
- Date: 2024-04
- Subjects: Trypanosomiasis -- South Africa , DNA -- Methylation -- Research -- Methodology , Central nervous system -- Diseases , Nervous system -- Degeneration
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64077 , vital:73651
- Description: Neurodegenerative conditions significantly impact well-being and quality of life in individuals with major symptoms including mood disorders, cognitive decline, and psychiatric disturbances, often resulting from neuroinflammation triggered by immune responses to bacterial or parasitic infections such as gram-negative bacteria or Human African Trypanosomiasis. Microglia play a crucial role in both neurotoxicity and cellular processes involved in restoring the neural health. Exploring the therapeutic potential of prostacyclin and its analogues in regulating microglia responses to inflammatory insult and treating Trypanosoma brucei (T.b) infection remains an unexplored area. The aim of this study was to assess the potential neuroprotective effects of Iloprost through comparative analysis of neuroinflammatory responses in both microglial cells exposed to lipopolysaccharide (LPS) and mouse brains infected with T.b brucei. In phase I of this study both resting and LPS treated C8-B4 microglial cells were exposed to varying concentrations of Iloprost. The effects of Iloprost on LPS-induced inflammation were analysed using immunofluorescence to detect microglial activation and differentiate between pro and anti-inflammatory phenotypes. Furthermore, pro and anti-inflammatory cytokine secretion was determined using an ELISA, in addition gene expression analysis was carried out using quantitative polymerase chain reaction (qPCR). Also, DNA methylation status of C8-B4 cells exposed to LPS challenge alone or in combination with various concentrations of Iloprost were determined using bisulfite sequencing technique followed by qPCR. In phase II of the study, a total of twenty-four Albino Swiss male mice (8-10 weeks old) were divided into four treatment groups with 6 mice in each group. All treatment groups except the non-infected control were inoculated with the T.b brucei parasite. One group received a single intraperitoneal injection of Diminazene aceturate (4 mg kg-1) while the remaining group received repeated intraperitoneal injections of Iloprost (200 μg kg-1). On day ten of the study, mouse brains were removed on ice using forceps. The hippocampal tissues were dissected out and processed for quantification of gene expression changes in pro and anti-inflammatory cytokines. Overall, the findings of this study indicate that LPS-induced pro-inflammatory cytokine, TNF-α and IL-1β, secretion and gene expression is down-regulated in C8-B4 microglial cells treated with Iloprost. Furthermore, there was a significant up-regulation in the expression of anti-inflammatory genes, particularly ARG-1, CD206, BDNF and CREB in response to Iloprost treatment following LPS-induced inflammation. This study is also the first to confirm M2 microglial polarization with Iloprost treatment in both resting and LPS treated cells. However, hypermethylation at CREB and BDNF promoter regions was observed 24 hours after Iloprost treatment. Additionally, Iloprost reversed hypomethylation at the BDNF promoter region that had been induced by LPS treatment. The rodent model also indicated a downregulation in the pro-inflammatory cytokine, IL-1β, expression and upregulation of BDNF transcription in T.b brucei infected mice treated with repeated doses of Iloprost. In conclusion, determining the immunomodulatory roles of Iloprost in both in vitro and in vivo models of neuroinflammation could assist in the development of alternative therapy for neurodegenerative disease. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Jacobs, Ashleigh
- Date: 2024-04
- Subjects: Trypanosomiasis -- South Africa , DNA -- Methylation -- Research -- Methodology , Central nervous system -- Diseases , Nervous system -- Degeneration
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64077 , vital:73651
- Description: Neurodegenerative conditions significantly impact well-being and quality of life in individuals with major symptoms including mood disorders, cognitive decline, and psychiatric disturbances, often resulting from neuroinflammation triggered by immune responses to bacterial or parasitic infections such as gram-negative bacteria or Human African Trypanosomiasis. Microglia play a crucial role in both neurotoxicity and cellular processes involved in restoring the neural health. Exploring the therapeutic potential of prostacyclin and its analogues in regulating microglia responses to inflammatory insult and treating Trypanosoma brucei (T.b) infection remains an unexplored area. The aim of this study was to assess the potential neuroprotective effects of Iloprost through comparative analysis of neuroinflammatory responses in both microglial cells exposed to lipopolysaccharide (LPS) and mouse brains infected with T.b brucei. In phase I of this study both resting and LPS treated C8-B4 microglial cells were exposed to varying concentrations of Iloprost. The effects of Iloprost on LPS-induced inflammation were analysed using immunofluorescence to detect microglial activation and differentiate between pro and anti-inflammatory phenotypes. Furthermore, pro and anti-inflammatory cytokine secretion was determined using an ELISA, in addition gene expression analysis was carried out using quantitative polymerase chain reaction (qPCR). Also, DNA methylation status of C8-B4 cells exposed to LPS challenge alone or in combination with various concentrations of Iloprost were determined using bisulfite sequencing technique followed by qPCR. In phase II of the study, a total of twenty-four Albino Swiss male mice (8-10 weeks old) were divided into four treatment groups with 6 mice in each group. All treatment groups except the non-infected control were inoculated with the T.b brucei parasite. One group received a single intraperitoneal injection of Diminazene aceturate (4 mg kg-1) while the remaining group received repeated intraperitoneal injections of Iloprost (200 μg kg-1). On day ten of the study, mouse brains were removed on ice using forceps. The hippocampal tissues were dissected out and processed for quantification of gene expression changes in pro and anti-inflammatory cytokines. Overall, the findings of this study indicate that LPS-induced pro-inflammatory cytokine, TNF-α and IL-1β, secretion and gene expression is down-regulated in C8-B4 microglial cells treated with Iloprost. Furthermore, there was a significant up-regulation in the expression of anti-inflammatory genes, particularly ARG-1, CD206, BDNF and CREB in response to Iloprost treatment following LPS-induced inflammation. This study is also the first to confirm M2 microglial polarization with Iloprost treatment in both resting and LPS treated cells. However, hypermethylation at CREB and BDNF promoter regions was observed 24 hours after Iloprost treatment. Additionally, Iloprost reversed hypomethylation at the BDNF promoter region that had been induced by LPS treatment. The rodent model also indicated a downregulation in the pro-inflammatory cytokine, IL-1β, expression and upregulation of BDNF transcription in T.b brucei infected mice treated with repeated doses of Iloprost. In conclusion, determining the immunomodulatory roles of Iloprost in both in vitro and in vivo models of neuroinflammation could assist in the development of alternative therapy for neurodegenerative disease. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Comparing stable isotope ratios and metal concentrations between components of the benthic food web: a case study of the Swartkops Estuary South Africa
- Authors: Ndoto, Asiphe
- Date: 2024-04
- Subjects: Swartkops River Estuary (South Africa) , Estuarine ecology -- South Africa -- Swartkops River Estuary , Fishes -- Ecology -- South Africa -- Swartkops River Estuary
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64256 , vital:73669
- Description: Estuarine systems are highly productive ecosystems; however, they are subjected to high anthropogenic pressure such as metal contamination and: increased nutrient loads. The contamination sources of metals and nutrients in urban estuaries are derived: from industrial waste. agricultural and urban runoff that flows into estuaries. An example of such a system is the Swartkops Estuary. industry and three wastewater treatment plants within the Swartkops River catchment are major sources of metal. and nutrient pollution, respectively. The metals accumulate in the environment, are biomagnified up the food web, and transferred from one trophic level to another. At lethal concentrations, metals pose a threat to organisms using the estuary by affecting their physiological and biochemical processes. Stable Isotope analysis has proven to be an effective tool for investigating, trophic linkages in the food chain from a variety of environments. By assessing both metals and stable _isotopes in the. estuary it can provide a more robust understanding of the pathway metals accumulate, biomagnified, and transfer from the environment through the estuarine food web. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2022
- Full Text:
- Date Issued: 2024-04
- Authors: Ndoto, Asiphe
- Date: 2024-04
- Subjects: Swartkops River Estuary (South Africa) , Estuarine ecology -- South Africa -- Swartkops River Estuary , Fishes -- Ecology -- South Africa -- Swartkops River Estuary
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64256 , vital:73669
- Description: Estuarine systems are highly productive ecosystems; however, they are subjected to high anthropogenic pressure such as metal contamination and: increased nutrient loads. The contamination sources of metals and nutrients in urban estuaries are derived: from industrial waste. agricultural and urban runoff that flows into estuaries. An example of such a system is the Swartkops Estuary. industry and three wastewater treatment plants within the Swartkops River catchment are major sources of metal. and nutrient pollution, respectively. The metals accumulate in the environment, are biomagnified up the food web, and transferred from one trophic level to another. At lethal concentrations, metals pose a threat to organisms using the estuary by affecting their physiological and biochemical processes. Stable Isotope analysis has proven to be an effective tool for investigating, trophic linkages in the food chain from a variety of environments. By assessing both metals and stable _isotopes in the. estuary it can provide a more robust understanding of the pathway metals accumulate, biomagnified, and transfer from the environment through the estuarine food web. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2022
- Full Text:
- Date Issued: 2024-04
Development of a numerical geohydrological model for a fractured rock aquifer in the Karoo, near Sutherland, South Africa
- Authors: Maqhubela, Akhona
- Date: 2024-04
- Subjects: Hydrogeology -- South Africa -- Northern Cape , Groundwater -- South Africa -- North Cape -- Management , Evapotranspiration
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64164 , vital:73658
- Description: The regional scale method in groundwater storage observation introduces uncertainties that hinder the evaluation of the remaining lifespan of depleted aquifers. The scarcity of precipitation data presents significant global challenge, especially in semi-arid regions. This study constructs a regional numerical hydrogeological model that identifies the potential impacts of climate change on the water balance for the South African Gravimetric Observation Station in Sutherland. The purpose of this study is to understand mechanisms controlling groundwater in the fractured rock aquifer. The climate data from the Weather forecast data over the last ten years was collected from the South African Weather Service. and groundwater levels data assessed the potential impacts of climate change on water balance components, especially precipitation and evapotranspiration. Precipitation is the primary recharge parameter in this study and had the highest level recorded in winter, with May having the highest precipitation rates of 24,62mm. The instrument conducted two profile investigations in a single day to detect geological abnormalities at various depths, achieving an impressive accuracy of up to 0.001 mV. The fact that groundwater flows from regions of higher hydraulic heads to areas of lower hydraulic charges, confirms that riverbeds in Sutherland act as preferential conduits for subsurface recharge. The profile and processed geophysical maps show low chances of getting groundwater in this observed area due to extensively great depth, approximately 150 – 210 m. The river package from MODFLOW model shows little inflow to the study nearby well locations. These model results showed a negative difference between water flowing in and out of the system of about -7m3 between 2002 and 2020. Groundwater flows faster at borehole five, where the hydraulic conductivity is large. The resulting regional hydrogeological model offered valuable insights into how climate change might influence the distribution and accessibility of groundwater resources. In the context of Sutherland, a negative groundwater budget value signaled that groundwater extraction or consumption surpassed the natural replenishment or recharge of the aquifer. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Maqhubela, Akhona
- Date: 2024-04
- Subjects: Hydrogeology -- South Africa -- Northern Cape , Groundwater -- South Africa -- North Cape -- Management , Evapotranspiration
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64164 , vital:73658
- Description: The regional scale method in groundwater storage observation introduces uncertainties that hinder the evaluation of the remaining lifespan of depleted aquifers. The scarcity of precipitation data presents significant global challenge, especially in semi-arid regions. This study constructs a regional numerical hydrogeological model that identifies the potential impacts of climate change on the water balance for the South African Gravimetric Observation Station in Sutherland. The purpose of this study is to understand mechanisms controlling groundwater in the fractured rock aquifer. The climate data from the Weather forecast data over the last ten years was collected from the South African Weather Service. and groundwater levels data assessed the potential impacts of climate change on water balance components, especially precipitation and evapotranspiration. Precipitation is the primary recharge parameter in this study and had the highest level recorded in winter, with May having the highest precipitation rates of 24,62mm. The instrument conducted two profile investigations in a single day to detect geological abnormalities at various depths, achieving an impressive accuracy of up to 0.001 mV. The fact that groundwater flows from regions of higher hydraulic heads to areas of lower hydraulic charges, confirms that riverbeds in Sutherland act as preferential conduits for subsurface recharge. The profile and processed geophysical maps show low chances of getting groundwater in this observed area due to extensively great depth, approximately 150 – 210 m. The river package from MODFLOW model shows little inflow to the study nearby well locations. These model results showed a negative difference between water flowing in and out of the system of about -7m3 between 2002 and 2020. Groundwater flows faster at borehole five, where the hydraulic conductivity is large. The resulting regional hydrogeological model offered valuable insights into how climate change might influence the distribution and accessibility of groundwater resources. In the context of Sutherland, a negative groundwater budget value signaled that groundwater extraction or consumption surpassed the natural replenishment or recharge of the aquifer. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Development of a numerical geohydrological model for a fractured rock aquifer in the Karoo, near Sutherland, South Africa
- Authors: Maqhubela, Akhona
- Date: 2024-04
- Subjects: Groundwater -- South Africa -- Northern Cape , Hydrogeology -- South Africa -- Northern Cape , Remote sensing , Geographic information systems
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64163 , vital:73659
- Description: The regional scale method in groundwater storage observation introduces uncertainties that hinder the evaluation of the remaining lifespan of depleted aquifers. The scarcity of precipitation data presents significant global challenge, especially in semi-arid regions. This study constructs a regional numerical hydrogeological model that identifies the potential impacts of climate change on the water balance for the South African Gravimetric Observation Station in Sutherland. The purpose of this study is to understand mechanisms controlling groundwater in the fractured rock aquifer. The climate data from the Weather forecast data over the last ten years was collected from the South African Weather Service. and groundwater levels data assessed the potential impacts of climate change on water balance components, especially precipitation and evapotranspiration. Precipitation is the primary recharge parameter in this study and had the highest level recorded in winter, with May having the highest precipitation rates of 24,62mm. The instrument conducted two profile investigations in a single day to detect geological abnormalities at various depths, achieving an impressive accuracy of up to 0.001 mV. The fact that groundwater flows from regions of higher hydraulic heads to areas of lower hydraulic charges, confirms that riverbeds in Sutherland act as preferential conduits for subsurface recharge. The profile and processed geophysical maps show low chances of getting groundwater in this observed area due to extensively great depth, approximately 150 – 210 m. The river package from MODFLOW model shows little inflow to the study nearby well locations. These model results showed a negative difference between water flowing in and out of the system of about -7m3 between 2002 and 2020. Groundwater flows faster at borehole five, where the hydraulic conductivity is large. The resulting regional hydrogeological model offered valuable insights into how climate change might influence the distribution and accessibility of groundwater resources. In the context of Sutherland, a negative groundwater budget value signaled that groundwater extraction or consumption surpassed the natural replenishment or recharge of the aquifer. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2022
- Full Text:
- Date Issued: 2024-04
- Authors: Maqhubela, Akhona
- Date: 2024-04
- Subjects: Groundwater -- South Africa -- Northern Cape , Hydrogeology -- South Africa -- Northern Cape , Remote sensing , Geographic information systems
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64163 , vital:73659
- Description: The regional scale method in groundwater storage observation introduces uncertainties that hinder the evaluation of the remaining lifespan of depleted aquifers. The scarcity of precipitation data presents significant global challenge, especially in semi-arid regions. This study constructs a regional numerical hydrogeological model that identifies the potential impacts of climate change on the water balance for the South African Gravimetric Observation Station in Sutherland. The purpose of this study is to understand mechanisms controlling groundwater in the fractured rock aquifer. The climate data from the Weather forecast data over the last ten years was collected from the South African Weather Service. and groundwater levels data assessed the potential impacts of climate change on water balance components, especially precipitation and evapotranspiration. Precipitation is the primary recharge parameter in this study and had the highest level recorded in winter, with May having the highest precipitation rates of 24,62mm. The instrument conducted two profile investigations in a single day to detect geological abnormalities at various depths, achieving an impressive accuracy of up to 0.001 mV. The fact that groundwater flows from regions of higher hydraulic heads to areas of lower hydraulic charges, confirms that riverbeds in Sutherland act as preferential conduits for subsurface recharge. The profile and processed geophysical maps show low chances of getting groundwater in this observed area due to extensively great depth, approximately 150 – 210 m. The river package from MODFLOW model shows little inflow to the study nearby well locations. These model results showed a negative difference between water flowing in and out of the system of about -7m3 between 2002 and 2020. Groundwater flows faster at borehole five, where the hydraulic conductivity is large. The resulting regional hydrogeological model offered valuable insights into how climate change might influence the distribution and accessibility of groundwater resources. In the context of Sutherland, a negative groundwater budget value signaled that groundwater extraction or consumption surpassed the natural replenishment or recharge of the aquifer. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2022
- Full Text:
- Date Issued: 2024-04
Development of the Zirconium-based metal- organic framework UiO-66 for Adsorption-mediated electrochemical sensing of organonitrogen compounds in fuels
- Authors: Mokgohloa, Mathule Collen
- Date: 2024-04
- Subjects: Electrochemical sensors , Quinoline -- synthesis , Pyridine -- Synthesis
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64193 , vital:73663
- Description: The combustion of fuel which contains organonitrogen compounds has led to an increase in atmospheric and environmental levels of nitrogen oxides which are responsible for several environmental, ecological, and human health problems. With increasingly strict environmental regulations and deleterious effects of the nitrogen-containing compounds in fuels, there is a strong need for the removal and detection of nitrogen-containing compounds in fuels to produce fuels with lower levels of nitrogen compounds. The Environmental Protection Agency (EPA) mandated nitrogen content in fossil fuels to be about less than 1 wt%. The existing analytical techniques used for the quantification of nitrogen-containing compounds in fuels include GC-MS, GC-AED, and spectrophotometry. Despite being sensitive and specific, these methods require expensive equipment, highly trained personnel, and time-consuming pre-treatment methods to avoid interferences from similar compounds, and they suffer from analyte loss and inadequate results. Thus, they can only be carried out in the off-site laboratories, hindering them from rapid on-site screening. The metal-organic framework (MOF) UiO-66-NH2 and its composites UiO-66-NH2/GA, and UiO- 66-NH2/GO-NH2 (GA= Graphene aerosol and GO= Graphene oxide) have shown great potentialin the adsorption of organonitrogen compounds like quinoline. However, research in the electrochemical application of these MOFs and their derivatives is limited despite their high surface area, abundant porosity, and increased conductivity. To demonstrate their electrochemical sensing potential, modification of the glassy carbon electrode (GCE) was suggested, which would show a higher degree of association for pyridine and quinoline on modified UiO-66-NH2/GA and UiO-66-NH2/GO-NH2 surfaces, thereby creating a more favourable route for adsorption. This would result in enhanced sensing of pyridine and quinoline in model fuel. Thus, unlike the bare GCE, the fabricated/modified can selectively detect high levels of organonitrogen compounds. In this study, Chapter 3, UiO-66-NH2/GA and UiO-66-NH2/GO-NH2 are prepared via the solvothermal method and then characterized using various spectroscopic and imaging techniques such as Scanning Electron Microscopy (SEM), X-ray Photoelectron Spectroscopy (XPS), Ultraviolet-Visible Spectroscopy (UV-VIS), Thermogravimetric Analysis (TGA), X-ray Development of the Zirconium-based metal- organic framework UiO-66 for Adsorption-mediated electrochemical sensing of organonitrogen compounds in fuels. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Mokgohloa, Mathule Collen
- Date: 2024-04
- Subjects: Electrochemical sensors , Quinoline -- synthesis , Pyridine -- Synthesis
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64193 , vital:73663
- Description: The combustion of fuel which contains organonitrogen compounds has led to an increase in atmospheric and environmental levels of nitrogen oxides which are responsible for several environmental, ecological, and human health problems. With increasingly strict environmental regulations and deleterious effects of the nitrogen-containing compounds in fuels, there is a strong need for the removal and detection of nitrogen-containing compounds in fuels to produce fuels with lower levels of nitrogen compounds. The Environmental Protection Agency (EPA) mandated nitrogen content in fossil fuels to be about less than 1 wt%. The existing analytical techniques used for the quantification of nitrogen-containing compounds in fuels include GC-MS, GC-AED, and spectrophotometry. Despite being sensitive and specific, these methods require expensive equipment, highly trained personnel, and time-consuming pre-treatment methods to avoid interferences from similar compounds, and they suffer from analyte loss and inadequate results. Thus, they can only be carried out in the off-site laboratories, hindering them from rapid on-site screening. The metal-organic framework (MOF) UiO-66-NH2 and its composites UiO-66-NH2/GA, and UiO- 66-NH2/GO-NH2 (GA= Graphene aerosol and GO= Graphene oxide) have shown great potentialin the adsorption of organonitrogen compounds like quinoline. However, research in the electrochemical application of these MOFs and their derivatives is limited despite their high surface area, abundant porosity, and increased conductivity. To demonstrate their electrochemical sensing potential, modification of the glassy carbon electrode (GCE) was suggested, which would show a higher degree of association for pyridine and quinoline on modified UiO-66-NH2/GA and UiO-66-NH2/GO-NH2 surfaces, thereby creating a more favourable route for adsorption. This would result in enhanced sensing of pyridine and quinoline in model fuel. Thus, unlike the bare GCE, the fabricated/modified can selectively detect high levels of organonitrogen compounds. In this study, Chapter 3, UiO-66-NH2/GA and UiO-66-NH2/GO-NH2 are prepared via the solvothermal method and then characterized using various spectroscopic and imaging techniques such as Scanning Electron Microscopy (SEM), X-ray Photoelectron Spectroscopy (XPS), Ultraviolet-Visible Spectroscopy (UV-VIS), Thermogravimetric Analysis (TGA), X-ray Development of the Zirconium-based metal- organic framework UiO-66 for Adsorption-mediated electrochemical sensing of organonitrogen compounds in fuels. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Development of TiO2 nanostructures with a modified energy band gap for hydrogen extraction
- Authors: Mutubuki, Arnold
- Date: 2024-04
- Subjects: Nanostructures , Nanoscience , Nanochemistry
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64226 , vital:73666
- Description: A rise in fossil fuel depletion has motivated the research towards alternative, cost effective and clean processes for energy production through renewable sources. The scientific community is currently engaged in extensive research to exploit viable, sustainable methods for generating green hydrogen. Titania (TiO2) is historically the most studied photoactive semiconductor material with great potential in photoelectrochemical water splitting (PECWS), following the discovery by Fujishima and Honda in 1972. TiO2 possesses superior physicochemical characteristics and band gap edges, which enables the semiconductor to effectively facilitate the PECWS process. Efforts are still ongoing to explore alternatives for narrowing the optical band gap energy of TiO2, for an efficient photoelectrode. In this research work, open-ended and well-ordered TiO2 nanotubular arrays were synthesised by a three-step anodization process. The third anodization was crucial to detach the TiO2 thin film from an opaque Ti metal substrate. The free-standing thin films were transferred and pasted onto conductive FTO-coated glass substrates transparent to visible light and annealed at 400 ℃ for crystallisation. The multi-step anodization has shown an improved top tube morphology by eliminating an initiation TiO2 mesh formed when a conventional single-step anodization process is used under similar conditions. To widen the absorption range of the samples, CuO nanosheets were deposited onto nanotubular TiO2/FTO films through successive ionic layer adsorption (SILAR), a wet chemical method. The formation of a CuO/TiO2 nanostructure enhances the transfer of photogenerated carriers, suppressing charge recombination. This research focused on investigating the influence of selected SILAR parameters on the formation of CuO nanostructures. The first was the effect of precursor concentration on the structural, morphological and optical properties of the CuO/TiO2/FTO nanostructured photoelectrode. The effect of the precursor concentration on the structure and morphology was evident in the X-ray diffraction (XRD) patterns and scanning electron microscopy (SEM) micrographs. Crystallite sizes of deposited CuO increased from 10.6 nm to 15.7 nm when precursor concentration was varied from 0.02 M to 0.10 M. The UV-visible absorbance results show that an increase in precursor concentration leads to a red shift of both the peak absorbance and edge wavelength of the CuO/TiO2/FTO absorbance spectra. This phenomenon is believed to be caused by the presence of CuO, which exhibits active absorption in the visible spectrum. As evidenced by the study, the continued increase in precursor concentration does not result in a further widening of the absorption band. This is demonstrated by the example of a CuO/TiO2/FTO sample decorated with a 0.2 M precursor. The second was the effect of SILAR immersion cycles on the properties of the CuO/TiO2/FTO nanostructure developed. The increase in the number of immersion cycles led to a notable progression in the adsorption cupric oxide on the TiO2/FTO samples. A redshift in the absorbance peak and edge wavelength is observed in the UV-visible spectra of CuO/TiO2/FTO photoelectrode. The efficacy of the SILAR technique in modifying the absorption band of nanotubular TiO2 thin films has been conclusively demonstrated through comprehensive analysis and correlation of the relationships between the structure and optical properties, as evidenced by the XRD patterns, Raman spectra, SEM, TEM micrographs, and UV-visible absorbance spectra. , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Mutubuki, Arnold
- Date: 2024-04
- Subjects: Nanostructures , Nanoscience , Nanochemistry
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64226 , vital:73666
- Description: A rise in fossil fuel depletion has motivated the research towards alternative, cost effective and clean processes for energy production through renewable sources. The scientific community is currently engaged in extensive research to exploit viable, sustainable methods for generating green hydrogen. Titania (TiO2) is historically the most studied photoactive semiconductor material with great potential in photoelectrochemical water splitting (PECWS), following the discovery by Fujishima and Honda in 1972. TiO2 possesses superior physicochemical characteristics and band gap edges, which enables the semiconductor to effectively facilitate the PECWS process. Efforts are still ongoing to explore alternatives for narrowing the optical band gap energy of TiO2, for an efficient photoelectrode. In this research work, open-ended and well-ordered TiO2 nanotubular arrays were synthesised by a three-step anodization process. The third anodization was crucial to detach the TiO2 thin film from an opaque Ti metal substrate. The free-standing thin films were transferred and pasted onto conductive FTO-coated glass substrates transparent to visible light and annealed at 400 ℃ for crystallisation. The multi-step anodization has shown an improved top tube morphology by eliminating an initiation TiO2 mesh formed when a conventional single-step anodization process is used under similar conditions. To widen the absorption range of the samples, CuO nanosheets were deposited onto nanotubular TiO2/FTO films through successive ionic layer adsorption (SILAR), a wet chemical method. The formation of a CuO/TiO2 nanostructure enhances the transfer of photogenerated carriers, suppressing charge recombination. This research focused on investigating the influence of selected SILAR parameters on the formation of CuO nanostructures. The first was the effect of precursor concentration on the structural, morphological and optical properties of the CuO/TiO2/FTO nanostructured photoelectrode. The effect of the precursor concentration on the structure and morphology was evident in the X-ray diffraction (XRD) patterns and scanning electron microscopy (SEM) micrographs. Crystallite sizes of deposited CuO increased from 10.6 nm to 15.7 nm when precursor concentration was varied from 0.02 M to 0.10 M. The UV-visible absorbance results show that an increase in precursor concentration leads to a red shift of both the peak absorbance and edge wavelength of the CuO/TiO2/FTO absorbance spectra. This phenomenon is believed to be caused by the presence of CuO, which exhibits active absorption in the visible spectrum. As evidenced by the study, the continued increase in precursor concentration does not result in a further widening of the absorption band. This is demonstrated by the example of a CuO/TiO2/FTO sample decorated with a 0.2 M precursor. The second was the effect of SILAR immersion cycles on the properties of the CuO/TiO2/FTO nanostructure developed. The increase in the number of immersion cycles led to a notable progression in the adsorption cupric oxide on the TiO2/FTO samples. A redshift in the absorbance peak and edge wavelength is observed in the UV-visible spectra of CuO/TiO2/FTO photoelectrode. The efficacy of the SILAR technique in modifying the absorption band of nanotubular TiO2 thin films has been conclusively demonstrated through comprehensive analysis and correlation of the relationships between the structure and optical properties, as evidenced by the XRD patterns, Raman spectra, SEM, TEM micrographs, and UV-visible absorbance spectra. , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-04
Dislocation imaging of AISI316L stainless steels using electron channeling contrast imaging (ECCI)
- Pullen, Luchian Charton Morne
- Authors: Pullen, Luchian Charton Morne
- Date: 2024-04
- Subjects: Electron microscopy , Microscopy -- Technique
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64301 , vital:73674
- Description: This study investigates the use of electron microscopy to image dislocations in high-temperature steels used in the electrical power generation industry. Dislocations play an important role in the mechanical properties of steels, which continuously evolve during component manufacturing and subsequent in-service exposure due to creep and/or fatigue. The dislocation density of the steels can potentially be used as a fingerprint to identify at-risk components that has either reached end-of-life or that was incorrectly manufactured due to forming or heat treatments. Traditionally, dislocation measurements are performed using transmission electron microscopy (TEM) performed on thin foils samples. However, accurate and precise measurements of the dislocation density in steels using TEM remain a challenge due to the time-consuming nature, small sampling volumes, and effects of sample preparation on the quantitative results. The aim of this study is to evaluate and establish electron channeling contrast imaging (ECCI) as a scanning electron microscopy method of quantifying the dislocation densities of power plant steels. This method can be applied to conventionally polished bulk samples allowing for large areas to be sampled. Samples consisting of AISI316L stainless steel were used as a model alloy (large grain size ~100 μm) to compare dislocation imaging using annular dark field (ADF)-scanning TEM (STEM) and ECCI. Three materials states consisting of a cold drawn rod (high dislocation density), annealed rod (low dislocation density), and an annealed sample subjected to cyclic fatigue testing (medium dislocation density) were investigated. Systematic investigations into the data acquisition parameters showed that an incident beam energy (20 kV), beam current (~4 nA), pixel size (5 nm), and working distance (4-5 mm) on a JEOL7001F SEM fitted with a retractable BSE detector could successfully image the dislocation structures for the material states used in this study. The ECCI technique was successfully used to determine the dislocation density in the three material states and the quantitative results showed similar trends as the ADF-STEM quantification results, but with less effort. Future studies using electron backscattered diffraction (EBSD) orientation mapping combined with electron channeling pattern (ECP) calibrations using a single crystal Si sample will allow for ECCI imaging under controlled grain orientations. Furthermore, accurate image segmentation of dislocations from a micrograph remains a key limitation, which can be improved with the use of advanced image analysis based on deep learning approaches. The quantitative dislocation density techniques demonstrated in this study can be adapted not only for studies of other power plant steels (eg. 9-12% Cr Creep Strength Enhanced Ferritic) but also to other materials systems such as aluminium to study the recrystallization processes during annealing. , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2025
- Full Text:
- Date Issued: 2024-04
- Authors: Pullen, Luchian Charton Morne
- Date: 2024-04
- Subjects: Electron microscopy , Microscopy -- Technique
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64301 , vital:73674
- Description: This study investigates the use of electron microscopy to image dislocations in high-temperature steels used in the electrical power generation industry. Dislocations play an important role in the mechanical properties of steels, which continuously evolve during component manufacturing and subsequent in-service exposure due to creep and/or fatigue. The dislocation density of the steels can potentially be used as a fingerprint to identify at-risk components that has either reached end-of-life or that was incorrectly manufactured due to forming or heat treatments. Traditionally, dislocation measurements are performed using transmission electron microscopy (TEM) performed on thin foils samples. However, accurate and precise measurements of the dislocation density in steels using TEM remain a challenge due to the time-consuming nature, small sampling volumes, and effects of sample preparation on the quantitative results. The aim of this study is to evaluate and establish electron channeling contrast imaging (ECCI) as a scanning electron microscopy method of quantifying the dislocation densities of power plant steels. This method can be applied to conventionally polished bulk samples allowing for large areas to be sampled. Samples consisting of AISI316L stainless steel were used as a model alloy (large grain size ~100 μm) to compare dislocation imaging using annular dark field (ADF)-scanning TEM (STEM) and ECCI. Three materials states consisting of a cold drawn rod (high dislocation density), annealed rod (low dislocation density), and an annealed sample subjected to cyclic fatigue testing (medium dislocation density) were investigated. Systematic investigations into the data acquisition parameters showed that an incident beam energy (20 kV), beam current (~4 nA), pixel size (5 nm), and working distance (4-5 mm) on a JEOL7001F SEM fitted with a retractable BSE detector could successfully image the dislocation structures for the material states used in this study. The ECCI technique was successfully used to determine the dislocation density in the three material states and the quantitative results showed similar trends as the ADF-STEM quantification results, but with less effort. Future studies using electron backscattered diffraction (EBSD) orientation mapping combined with electron channeling pattern (ECP) calibrations using a single crystal Si sample will allow for ECCI imaging under controlled grain orientations. Furthermore, accurate image segmentation of dislocations from a micrograph remains a key limitation, which can be improved with the use of advanced image analysis based on deep learning approaches. The quantitative dislocation density techniques demonstrated in this study can be adapted not only for studies of other power plant steels (eg. 9-12% Cr Creep Strength Enhanced Ferritic) but also to other materials systems such as aluminium to study the recrystallization processes during annealing. , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2025
- Full Text:
- Date Issued: 2024-04
Elephant impacts on plant diversity and structure in the Shamwari Private Game Reserve
- Authors: Halvey, Andrew Lloyd
- Date: 2024-04
- Subjects: Elephants -- Nutrition -- South Africa -- Eastern Cape , Elephants -- Habitat -- South Africa -- Eastern Cape , Shamwari Game Reserve (South Africa)
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63777 , vital:73597
- Description: Many African landscapes rely on processes such as fire, tree-fall and drought in addition to herbivores to initiate change across the landscape. In the Eastern Cape, elephant have a significant impact on the community structure and diversity of the vegetation they live in. This is most likely the case for the Albany Valley Thicket and azonal riparian vegetation of Shamwari Private Game Reserve, where browsing animals, particularly megaherbivores like the black rhinoceros and elephant, are the main cause of defoliation. The presence of large herbivores creates challenges when it comes to long-term sustainability and biodiversity of the vegetation in Shamwari. Vegetation monitoring provides essential information for effective management of megaherbivores not only in Shamwari but in many other similar reserves. The aim of this study was to design a monitoring plan for the Albany Valley Thicket and riparian vegetation in Shamwari using available vegetation metrics. The vegetation was measured in permanent plots (90 m line intercept analysis per plot) in the Albany Valley Thicket and riparian vegetation of Shamwari. Plot selection was based on thicket structural integrity using NDVI score as a proxy. In all plots, thicket structure was assessed using canopy heights measured every 50 cm along the line. Detrended correspondence analysis of the species abundance data suggested three distinct structural and compositional vegetation states for thicket and riparian vegetation: dense, intermediate and open. Significant relationships between NDVI and vegetation structural metrics across the condition states indicated that NDVI could be used as a proxy for vegetation condition. Vegetation compositional metrics, however, were not always correlated to NDVI and determining species diversity for the vegetation presents additional information useful for monitoring. The monitoring recommended for the reserve is to evaluate vegetation structural integrity annually in summer using NDVI. Areas of change could then be measured for diversity as well as for change in the abundance of selected plant indicator species. This information should be used to initiate management actions if unwanted change has occurred. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Halvey, Andrew Lloyd
- Date: 2024-04
- Subjects: Elephants -- Nutrition -- South Africa -- Eastern Cape , Elephants -- Habitat -- South Africa -- Eastern Cape , Shamwari Game Reserve (South Africa)
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63777 , vital:73597
- Description: Many African landscapes rely on processes such as fire, tree-fall and drought in addition to herbivores to initiate change across the landscape. In the Eastern Cape, elephant have a significant impact on the community structure and diversity of the vegetation they live in. This is most likely the case for the Albany Valley Thicket and azonal riparian vegetation of Shamwari Private Game Reserve, where browsing animals, particularly megaherbivores like the black rhinoceros and elephant, are the main cause of defoliation. The presence of large herbivores creates challenges when it comes to long-term sustainability and biodiversity of the vegetation in Shamwari. Vegetation monitoring provides essential information for effective management of megaherbivores not only in Shamwari but in many other similar reserves. The aim of this study was to design a monitoring plan for the Albany Valley Thicket and riparian vegetation in Shamwari using available vegetation metrics. The vegetation was measured in permanent plots (90 m line intercept analysis per plot) in the Albany Valley Thicket and riparian vegetation of Shamwari. Plot selection was based on thicket structural integrity using NDVI score as a proxy. In all plots, thicket structure was assessed using canopy heights measured every 50 cm along the line. Detrended correspondence analysis of the species abundance data suggested three distinct structural and compositional vegetation states for thicket and riparian vegetation: dense, intermediate and open. Significant relationships between NDVI and vegetation structural metrics across the condition states indicated that NDVI could be used as a proxy for vegetation condition. Vegetation compositional metrics, however, were not always correlated to NDVI and determining species diversity for the vegetation presents additional information useful for monitoring. The monitoring recommended for the reserve is to evaluate vegetation structural integrity annually in summer using NDVI. Areas of change could then be measured for diversity as well as for change in the abundance of selected plant indicator species. This information should be used to initiate management actions if unwanted change has occurred. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Estimation of a generalist meso-carnivore (black-backed jackal) population from a fenced protected area
- Davidson-Phillips, Samuel Ralph
- Authors: Davidson-Phillips, Samuel Ralph
- Date: 2024-04
- Subjects: Wildlife conservation , Carnivorous animals -- Conservation , Carnivorous animals -- Ecology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63698 , vital:73589
- Description: Since 2017, landowners, field guides, and management staff have reported large groups of black-backed jackals (Lupullela mesomelas) (here-forward jackal) in the Welgevonden Game Reserve, Limpopo, South Africa. This is linked with several observations of jackals predating on various ungulate species, potentially leading to unintended consequences on prey populations. These observations combined with an apparent poor survival rate of impala (Aepyceros melampus) and continuous declines in their number led to the perception that jackals could be partly responsible. Several studies have attempted to describe the ecological role of jackals within multiple environments, most of which have proven to be variable and context dependent. Human-modified landscapes along with the fencing of protected areas, may have manipulated the role of jackal within these scenarios. Jackals are wide-ranging and generally not confined by fencing, therefore their population trends possibly fluctuate within these anthropogenic landscapes. Re-introduced apex predators have been shown to facilitate food (provision of carrion) and simultaneously suppress jackal (active killing), this, however, remains difficult to predict. Jackals are classified as facultative cooperative hunters, and the term describes how they hunt in groups opportunistically when suitable resources of prey are available. The indication by several studies that jackals do actively predate rather than only scavenge, illustrates that the species has the potential to cause declines in an ungulate population. It therefore appears erroneous to exclude the species in terms of predator-prey relationships, particularly for land managers of fenced protected areas. The first step to any ecological management is the understanding of population size and trends over time. Unfortunately, little to no reliable methods exist to assess or monitor jackal populations. A popular tool for cryptic and wide-ranging terrestrial carnivores is Spatial Capture Recapture (SCR) models, typically through a camera trap array. These often rely on individual identities and an imperfect detection process to derive a statistical estimate of a given area. Jackals have been assumed to be individually unidentifiable and therefore these methods have largely been excluded. To address this a pilot-targeted camera-trap survey was conducted to improve capture and image quality. Following the role of this procedure, semi-automated software was applied to test the feasibility of individual identifications of captured images. This resulted in a subset of 58 right and left identifiable flank images, compiled from the highest graded images (n = 220) using the open-source Interactive Individual IdentificationSystem Beta Contour 3.0 (I3S Contour). I3S Contour assists users by distinguishing between unique contours on independent flanks without omitting observer effort and ranking. The effectiveness of the identification procedure was evaluated using three software tool trials, namely Computer-aided Annotation, Manual Contour Annotation, and Manual Contour Annotation (MA-2), where MA-2 included additional user-defined meta-data to images. Results showed that jackals could be individually identified from camera trap images and thus opened up the use of previously excluded SCR methodologies. Utilising the jackal database derived from the identification procedures described a total of 28 complete identifications (both flanks matched), 32 left-sided and 36 right-sided captures were used. These were derived from two independent survey periods split between seasonality (Winter & Spring). Two SCR methods were compared, namely, the Spatially Explicit Camera Recapture (SECR) and the newly developed Spatial Presence-Absence (SPA) modelling approach. SECR relies on full individual identification linked to spatial locations to derive spatial parameters to estimate population densities. The SECR methodology has been considered the most precise and was thus used as the benchmark. SPA relies on detections only (i.e., without individual identities), along with informative or uninformative priors. This must be across a spatial array that has detectors close enough to allow for simultaneous detections during each occasion (< 24 hours). Comparisons between these model outputs indicated a high degree of confidence interval overlap; however, SPA had a consistently higher posterior mode density estimate (63-64% higher), where the coefficient of variation between outputs also indicated the SPA having a closer relative precision. The targeted survey results for both model outputs for 2021 did not appear unusually high when compared to other studies. To assess the WGR population size over the long term, opportunistic by-catch data from a nine-year leopard (Panthera pardus) camera survey (Panthera organisation) was utilised. Model outputs from each of the years indicated that population estimates remained relatively stable. This was an unexpected result as the SPA densities did not follow the detection observations. This could be attributed to M not being set high enough (200) and the model reaching the limit, resulting in similar outputs between years. An alternative explanation is where the station spacing is larger than the diameter of the home range, which may reduce spatial correlation. , Thesis (MSc) -- Faculty of Science, School of Natural Resource Science & Management, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Davidson-Phillips, Samuel Ralph
- Date: 2024-04
- Subjects: Wildlife conservation , Carnivorous animals -- Conservation , Carnivorous animals -- Ecology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63698 , vital:73589
- Description: Since 2017, landowners, field guides, and management staff have reported large groups of black-backed jackals (Lupullela mesomelas) (here-forward jackal) in the Welgevonden Game Reserve, Limpopo, South Africa. This is linked with several observations of jackals predating on various ungulate species, potentially leading to unintended consequences on prey populations. These observations combined with an apparent poor survival rate of impala (Aepyceros melampus) and continuous declines in their number led to the perception that jackals could be partly responsible. Several studies have attempted to describe the ecological role of jackals within multiple environments, most of which have proven to be variable and context dependent. Human-modified landscapes along with the fencing of protected areas, may have manipulated the role of jackal within these scenarios. Jackals are wide-ranging and generally not confined by fencing, therefore their population trends possibly fluctuate within these anthropogenic landscapes. Re-introduced apex predators have been shown to facilitate food (provision of carrion) and simultaneously suppress jackal (active killing), this, however, remains difficult to predict. Jackals are classified as facultative cooperative hunters, and the term describes how they hunt in groups opportunistically when suitable resources of prey are available. The indication by several studies that jackals do actively predate rather than only scavenge, illustrates that the species has the potential to cause declines in an ungulate population. It therefore appears erroneous to exclude the species in terms of predator-prey relationships, particularly for land managers of fenced protected areas. The first step to any ecological management is the understanding of population size and trends over time. Unfortunately, little to no reliable methods exist to assess or monitor jackal populations. A popular tool for cryptic and wide-ranging terrestrial carnivores is Spatial Capture Recapture (SCR) models, typically through a camera trap array. These often rely on individual identities and an imperfect detection process to derive a statistical estimate of a given area. Jackals have been assumed to be individually unidentifiable and therefore these methods have largely been excluded. To address this a pilot-targeted camera-trap survey was conducted to improve capture and image quality. Following the role of this procedure, semi-automated software was applied to test the feasibility of individual identifications of captured images. This resulted in a subset of 58 right and left identifiable flank images, compiled from the highest graded images (n = 220) using the open-source Interactive Individual IdentificationSystem Beta Contour 3.0 (I3S Contour). I3S Contour assists users by distinguishing between unique contours on independent flanks without omitting observer effort and ranking. The effectiveness of the identification procedure was evaluated using three software tool trials, namely Computer-aided Annotation, Manual Contour Annotation, and Manual Contour Annotation (MA-2), where MA-2 included additional user-defined meta-data to images. Results showed that jackals could be individually identified from camera trap images and thus opened up the use of previously excluded SCR methodologies. Utilising the jackal database derived from the identification procedures described a total of 28 complete identifications (both flanks matched), 32 left-sided and 36 right-sided captures were used. These were derived from two independent survey periods split between seasonality (Winter & Spring). Two SCR methods were compared, namely, the Spatially Explicit Camera Recapture (SECR) and the newly developed Spatial Presence-Absence (SPA) modelling approach. SECR relies on full individual identification linked to spatial locations to derive spatial parameters to estimate population densities. The SECR methodology has been considered the most precise and was thus used as the benchmark. SPA relies on detections only (i.e., without individual identities), along with informative or uninformative priors. This must be across a spatial array that has detectors close enough to allow for simultaneous detections during each occasion (< 24 hours). Comparisons between these model outputs indicated a high degree of confidence interval overlap; however, SPA had a consistently higher posterior mode density estimate (63-64% higher), where the coefficient of variation between outputs also indicated the SPA having a closer relative precision. The targeted survey results for both model outputs for 2021 did not appear unusually high when compared to other studies. To assess the WGR population size over the long term, opportunistic by-catch data from a nine-year leopard (Panthera pardus) camera survey (Panthera organisation) was utilised. Model outputs from each of the years indicated that population estimates remained relatively stable. This was an unexpected result as the SPA densities did not follow the detection observations. This could be attributed to M not being set high enough (200) and the model reaching the limit, resulting in similar outputs between years. An alternative explanation is where the station spacing is larger than the diameter of the home range, which may reduce spatial correlation. , Thesis (MSc) -- Faculty of Science, School of Natural Resource Science & Management, 2024
- Full Text:
- Date Issued: 2024-04
Evaluating elephant, Loxodonta africana, space-use and elephant-linked vegetation change in Liwonde National Park, Malawi
- Authors: Evers, Emma Else Maria
- Date: 2024-04
- Subjects: Elephants -- Nutrition -- Malawi , Ecological heterogeneity , Vegetation and climate
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63744 , vital:73594
- Description: Heterogeneity, the spatio-temporal variation of abiotic and biotic factors, is a key concept that underpins many ecological phenomena and promotes biodiversity. Ecosystem engineers, such as African savanna elephants (hereafter elephant), Loxodonta africana, are organisms capable of affecting heterogeneity through the creation or modification of habitats. Thus, their impacts can have important consequences for ecosystem biodiversity, both positive and negative. Caughley’s “elephant problem” cautions that confined or compressed, growing elephant populations will inevitably lead to a loss of biodiversity. However, a shift in our understanding of elephants suggests that not all elephant impacts lead to negative biodiversity consequences, as long as there is a heterogeneous spread of elephant impacts that allows for spatio-temporal refuges promoting the persistence of both impact-tolerant and impact-intolerant species. To date, little empirical evidence is available in support of managing elephants under this paradigm and few studies are available that infer the consequences of the distribution of elephant impacts on biodiversity. In addition, most studies use parametric statistics that do not account for scale, spatial autocorrelation, or non-stationarity, leading to a misrepresentation of the underlying processes and patterns of drivers of elephant space-use and the consequences of their impacts on biodiversity. Here, I evaluate spatio-temporal patterns and drivers of elephant space-use, and how the distribution of their impacts affects biodiversity through vegetation changes, using a multi-scaled spatial approach, in Liwonde National Park, Malawi. My study demonstrates that elephant space-use in Liwonde is heterogeneous, leading to spatio-temporal variation in the distribution of their impacts, even in a small, fenced reserve. The importance of the drivers of this heterogeneous space-use varied based on the scale of analysis, water was generally important at larger scales while vegetation quality (indexed by NDVI) was more important at smaller scales. When examined using local models, my results suggest that relationships exhibit non-stationarity, what is important in one area of the park is not necessarily important in other areas. The spatio-temporal variation of the inferred impacts of elephants in Liwonde still allowed for spatio-temporal refuges to be created, no clear linear relationship was found between elephant return intervals and woody species structural and functional diversity (indexed by changes in tree cover and changes in annual regrowth using Normalized Difference Vegetation Index as a measure, respectively) throughout the park. My study provides support for adopting the heterogeneity paradigm for managing elephants and demonstrates that not all elephant impacts result in negative vegetation change. I also demonstrate the crucial implications of accounting for scale, non-stationarity, and spatial autocorrelation to evaluate how animals both respond to, and contribute to, environmental heterogeneity. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Evers, Emma Else Maria
- Date: 2024-04
- Subjects: Elephants -- Nutrition -- Malawi , Ecological heterogeneity , Vegetation and climate
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63744 , vital:73594
- Description: Heterogeneity, the spatio-temporal variation of abiotic and biotic factors, is a key concept that underpins many ecological phenomena and promotes biodiversity. Ecosystem engineers, such as African savanna elephants (hereafter elephant), Loxodonta africana, are organisms capable of affecting heterogeneity through the creation or modification of habitats. Thus, their impacts can have important consequences for ecosystem biodiversity, both positive and negative. Caughley’s “elephant problem” cautions that confined or compressed, growing elephant populations will inevitably lead to a loss of biodiversity. However, a shift in our understanding of elephants suggests that not all elephant impacts lead to negative biodiversity consequences, as long as there is a heterogeneous spread of elephant impacts that allows for spatio-temporal refuges promoting the persistence of both impact-tolerant and impact-intolerant species. To date, little empirical evidence is available in support of managing elephants under this paradigm and few studies are available that infer the consequences of the distribution of elephant impacts on biodiversity. In addition, most studies use parametric statistics that do not account for scale, spatial autocorrelation, or non-stationarity, leading to a misrepresentation of the underlying processes and patterns of drivers of elephant space-use and the consequences of their impacts on biodiversity. Here, I evaluate spatio-temporal patterns and drivers of elephant space-use, and how the distribution of their impacts affects biodiversity through vegetation changes, using a multi-scaled spatial approach, in Liwonde National Park, Malawi. My study demonstrates that elephant space-use in Liwonde is heterogeneous, leading to spatio-temporal variation in the distribution of their impacts, even in a small, fenced reserve. The importance of the drivers of this heterogeneous space-use varied based on the scale of analysis, water was generally important at larger scales while vegetation quality (indexed by NDVI) was more important at smaller scales. When examined using local models, my results suggest that relationships exhibit non-stationarity, what is important in one area of the park is not necessarily important in other areas. The spatio-temporal variation of the inferred impacts of elephants in Liwonde still allowed for spatio-temporal refuges to be created, no clear linear relationship was found between elephant return intervals and woody species structural and functional diversity (indexed by changes in tree cover and changes in annual regrowth using Normalized Difference Vegetation Index as a measure, respectively) throughout the park. My study provides support for adopting the heterogeneity paradigm for managing elephants and demonstrates that not all elephant impacts result in negative vegetation change. I also demonstrate the crucial implications of accounting for scale, non-stationarity, and spatial autocorrelation to evaluate how animals both respond to, and contribute to, environmental heterogeneity. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Evaluation of road surface distresses using GPS and GIS techniques: a case study of the City of Johannesburg, South Africa
- Authors: Tsedu, Rinae
- Date: 2024-04
- Subjects: Global Positioning System South Africa -- Johannesburg , Navigation -- Technological innovations , Geographic information systems -- South Africa -- Johannesburg
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64401 , vital:73695
- Description: Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Tsedu, Rinae
- Date: 2024-04
- Subjects: Global Positioning System South Africa -- Johannesburg , Navigation -- Technological innovations , Geographic information systems -- South Africa -- Johannesburg
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64401 , vital:73695
- Description: Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Exploring the role of herbivory in Albany Subtropical Thicket restoration
- Authors: Hunt, Kristen Louise
- Date: 2024-04
- Subjects: Shrubs -- South Africa , Portulacaria afra -- South Africa , Grasslands -- South Africa , Plant communities -- South Africa
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64060 , vital:73647
- Description: This dissertation attempted to investigate the influence of herbivory on the success of thicket restoration, addressing a critical gap in the current knowledge within the restoration initiative. Despite two decades of thicket restoration practices, the role of herbivory in influencing restoration success has been assumed and not yet quantified. This research aimed to observe and identify herbivore species and their interactions that may affect the survival of Portulacaria afra Jacq. material planted in thicket restoration contexts. This research took place on three game farms serving as case studies within the Albany Subtropical Thicket (Eastern Cape, South Africa). Multiple experiments were conducted to assess how the concept of different “natural refugia” might impact herbivore interactions with planted material, incorporating factors such as planting around rainfall, within open and semi-intact vegetation patches, and in proximity to water sources. Trail cameras were used for real-time monitoring of herbivore interactions within planted sites to understand and quantify herbivore interactions with P. afra cuttings and how they may impact plant survival. Results from the trail camera monitoring (Chapter 2) indicate varied herbivore interactions occurring on planted material, with the primary herbivore responsible for these interactions varying among farms. Species interactions were not consistent across farms, and herbivore interactions exhibited spatial and temporal variability. Notably, interactions declined soon after the start of the wet phase when surrounding vegetation could recover, indicating the influences of alternative forage availability on herbivore foraging choices. Different herbivore interactions were identified and quantified through trail camera images, ranging from minor biomass removal (estimated at <5 cm of stem and leaf material) to more detrimental actions such as uprooting and leaf stripping. Consistently, planted P. afra survival rates (Chapter 3) were significantly higher for protected material than those exposed to herbivores, regardless of whether planted in a dry or wet phase. Moreover, when exposed to herbivores, rooted material had significantly higher survival rates than unrooted material, indicating the potential advantage of a well-developed root system in faster recovery after a herbivory event. This research explored the influence of various factors, including rainfall, rooting state, protection, surrounding vegetation, and proximity to water, on P. afra survival and how some of these factors may affect P. afra survival in relation to herbivore interactions (Chapter 3). Significant differences in cutting survival were observed between dry and wet phases, rooted and unrooted material, and material protected vs exposed to herbivores. While survival was not significantly different in experiments involving surrounding vegetation and proximity to water, potential patterns were identified, warranting further investigation. A clipping and defoliation experiment under simulated seasonal conditions emphasised the significance of , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Hunt, Kristen Louise
- Date: 2024-04
- Subjects: Shrubs -- South Africa , Portulacaria afra -- South Africa , Grasslands -- South Africa , Plant communities -- South Africa
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64060 , vital:73647
- Description: This dissertation attempted to investigate the influence of herbivory on the success of thicket restoration, addressing a critical gap in the current knowledge within the restoration initiative. Despite two decades of thicket restoration practices, the role of herbivory in influencing restoration success has been assumed and not yet quantified. This research aimed to observe and identify herbivore species and their interactions that may affect the survival of Portulacaria afra Jacq. material planted in thicket restoration contexts. This research took place on three game farms serving as case studies within the Albany Subtropical Thicket (Eastern Cape, South Africa). Multiple experiments were conducted to assess how the concept of different “natural refugia” might impact herbivore interactions with planted material, incorporating factors such as planting around rainfall, within open and semi-intact vegetation patches, and in proximity to water sources. Trail cameras were used for real-time monitoring of herbivore interactions within planted sites to understand and quantify herbivore interactions with P. afra cuttings and how they may impact plant survival. Results from the trail camera monitoring (Chapter 2) indicate varied herbivore interactions occurring on planted material, with the primary herbivore responsible for these interactions varying among farms. Species interactions were not consistent across farms, and herbivore interactions exhibited spatial and temporal variability. Notably, interactions declined soon after the start of the wet phase when surrounding vegetation could recover, indicating the influences of alternative forage availability on herbivore foraging choices. Different herbivore interactions were identified and quantified through trail camera images, ranging from minor biomass removal (estimated at <5 cm of stem and leaf material) to more detrimental actions such as uprooting and leaf stripping. Consistently, planted P. afra survival rates (Chapter 3) were significantly higher for protected material than those exposed to herbivores, regardless of whether planted in a dry or wet phase. Moreover, when exposed to herbivores, rooted material had significantly higher survival rates than unrooted material, indicating the potential advantage of a well-developed root system in faster recovery after a herbivory event. This research explored the influence of various factors, including rainfall, rooting state, protection, surrounding vegetation, and proximity to water, on P. afra survival and how some of these factors may affect P. afra survival in relation to herbivore interactions (Chapter 3). Significant differences in cutting survival were observed between dry and wet phases, rooted and unrooted material, and material protected vs exposed to herbivores. While survival was not significantly different in experiments involving surrounding vegetation and proximity to water, potential patterns were identified, warranting further investigation. A clipping and defoliation experiment under simulated seasonal conditions emphasised the significance of , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Herpetofaunal diversity and affiliations of the Okavango River Basin, with specific focus on the Angolan headwaters
- Authors: Conradie, Werner
- Date: 2024-04
- Subjects: Water conservation -- Okavango River Delta , Watersheds -- Okavango River -- Angola , Biodiversity -- Angola
- Language: English
- Type: Doctorate theses , text
- Identifier: http://hdl.handle.net/10948/63667 , vital:73576
- Description: Although Africa is reputed to possess some of the richest herpetofaunal diversities in the world, a number of areas remain poorly documented and thus inadequately conserved. One such area in particular is the south-eastern part of Angola. Angola endured a long struggle for independence with a protracted civil war that lasted for nearly three decades, leaving the status of the country’s biodiversity in turmoil. Over the past two decades, Angola has become more accessible for biodiversity surveys, opening up new opportunities to document these previously poorly studied areas and help conserve its biodiversity. South-eastern Angola is the water source of the world-renowned Okavango Delta. However very little is known about the biodiversity, diversity status and conservation significance of the headwaters supplying the largest inland delta in the world. To address this bias in sampling and to investigate the conservation importance of the region, a series of rapid biodiversity surveys of the Angolan Okavango River Basin were conducted between 2012 and 2019. This study contributed over 2150 individual records of amphibians and reptiles, representing 88 reptile and 43 amphibian species. At least 15 species were added to the growing country checklist, with the south-eastern region of Angola now comprising 113 reptile species and 51 amphibian species. Because of this study, the area is now one of the most species-rich and well-studied areas in Angola. This study provided the first genetic data for 26 species, and sequences containing Angolan specimens for the first time were generated for 80 species, of which 23 species have originally been described from Angola. Maximum likelihood and Bayesian inference analyses, supported by species delimitation analyses, were utilised to validate specific species statuses. This allowed for the description of five new species of snake, one gecko and two frogs for Angola. The material further contributed to the description of a new genus of snakes. Numerous undescribed and potentially cryptic species were identified, long-lasting taxonomic issues were resolved, and various taxonomic adjustments were emphasised. Further contributions of the material include assisting in the revision of targeted Angolan amphibian and reptile groups as well as large-scale phylogenetic studies across Africa. , Thesis (PhD) -- Faculty of Science, School of Natural Resource Science & Management, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Conradie, Werner
- Date: 2024-04
- Subjects: Water conservation -- Okavango River Delta , Watersheds -- Okavango River -- Angola , Biodiversity -- Angola
- Language: English
- Type: Doctorate theses , text
- Identifier: http://hdl.handle.net/10948/63667 , vital:73576
- Description: Although Africa is reputed to possess some of the richest herpetofaunal diversities in the world, a number of areas remain poorly documented and thus inadequately conserved. One such area in particular is the south-eastern part of Angola. Angola endured a long struggle for independence with a protracted civil war that lasted for nearly three decades, leaving the status of the country’s biodiversity in turmoil. Over the past two decades, Angola has become more accessible for biodiversity surveys, opening up new opportunities to document these previously poorly studied areas and help conserve its biodiversity. South-eastern Angola is the water source of the world-renowned Okavango Delta. However very little is known about the biodiversity, diversity status and conservation significance of the headwaters supplying the largest inland delta in the world. To address this bias in sampling and to investigate the conservation importance of the region, a series of rapid biodiversity surveys of the Angolan Okavango River Basin were conducted between 2012 and 2019. This study contributed over 2150 individual records of amphibians and reptiles, representing 88 reptile and 43 amphibian species. At least 15 species were added to the growing country checklist, with the south-eastern region of Angola now comprising 113 reptile species and 51 amphibian species. Because of this study, the area is now one of the most species-rich and well-studied areas in Angola. This study provided the first genetic data for 26 species, and sequences containing Angolan specimens for the first time were generated for 80 species, of which 23 species have originally been described from Angola. Maximum likelihood and Bayesian inference analyses, supported by species delimitation analyses, were utilised to validate specific species statuses. This allowed for the description of five new species of snake, one gecko and two frogs for Angola. The material further contributed to the description of a new genus of snakes. Numerous undescribed and potentially cryptic species were identified, long-lasting taxonomic issues were resolved, and various taxonomic adjustments were emphasised. Further contributions of the material include assisting in the revision of targeted Angolan amphibian and reptile groups as well as large-scale phylogenetic studies across Africa. , Thesis (PhD) -- Faculty of Science, School of Natural Resource Science & Management, 2024
- Full Text:
- Date Issued: 2024-04
IL-4/ IL-13 directed microglial activation and differentiation in response to LPS-induced neuroinflammation
- Authors: Ackerdien, Shiraz
- Date: 2024-04
- Subjects: Inflammation , Inflammation -- Treatment , Anti-inflammatory agents
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63606 , vital:73554
- Description: Microglia activation is a common hallmark of neuroinflammation that occurs during pathogen invasion or lipopolysaccharide (LPS)-induced inflammation. A neuroinflammatory response is elicited by the release of proinflammatory cytokines which stimulates microglia in an autocrine manner to be polarized into classically activated, pro-inflammatory M1 cells. Prolonged exposure to the inflammatory response can have disastrous effects on the central nervous system (CNS). However, microglia can alternatively be polarized into the activated M2 anti-inflammatory phenotype, but the exact molecular mechanism mediating this phenotypic switch remains poorly understood. Studies have shown that interleukin (IL)-4 can induce the M2 phenotype and activate the signal transducer and activator of the transcription 6 (STAT6) signalling pathway that in turn provokes a beneficial Th2 immune response. Since IL-4 and IL-13 share a common IL-4 receptor alpha (IL-4Rα) chain, it is possible that alternative microglia differentiation and its anti-inflammatory action also involve IL-13. This study aimed to investigate how IL-13 and STAT6 signalling orchestrates the microglial response and differentiation associated with LPS-induced inflammation. Furthermore, the molecular mechanisms that relieve LPS-induced neuroinflammation and neural protection through IL-13-enhanced BDNF signalling were also investigated. C8-B4 microglial cells were induced with LPS to exhibit an M1 pro-inflammatory phenotype or stimulated with IL-4 and/or IL-13 to exhibit an M2 anti-inflammatory microglial phenotype. The cell viability following LPS, IL-4, and/ or IL-13 exposure was determined. The LPS-induced neuroinflammatory response and the anti-inflammatory response induced by IL-4 and IL-13 which promotes STAT-6 signalling were determined by measuring TNFα, IL-1β, and BDNF protein concentrations using ELISA assays. The polarising effects of LPS and IL-4/IL-13 cytokines were also examined via changes in the expression of Iba-1, CD206, CD86, and STAT-6 determined by immunofluorescence analysis. These changes were further investigated by quantifying the mRNA transcripts of TNFα, IL-1 β, Arg-1, CD206, IL-4R, and STAT-6 and BDNF using qRT-PCR. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Ackerdien, Shiraz
- Date: 2024-04
- Subjects: Inflammation , Inflammation -- Treatment , Anti-inflammatory agents
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63606 , vital:73554
- Description: Microglia activation is a common hallmark of neuroinflammation that occurs during pathogen invasion or lipopolysaccharide (LPS)-induced inflammation. A neuroinflammatory response is elicited by the release of proinflammatory cytokines which stimulates microglia in an autocrine manner to be polarized into classically activated, pro-inflammatory M1 cells. Prolonged exposure to the inflammatory response can have disastrous effects on the central nervous system (CNS). However, microglia can alternatively be polarized into the activated M2 anti-inflammatory phenotype, but the exact molecular mechanism mediating this phenotypic switch remains poorly understood. Studies have shown that interleukin (IL)-4 can induce the M2 phenotype and activate the signal transducer and activator of the transcription 6 (STAT6) signalling pathway that in turn provokes a beneficial Th2 immune response. Since IL-4 and IL-13 share a common IL-4 receptor alpha (IL-4Rα) chain, it is possible that alternative microglia differentiation and its anti-inflammatory action also involve IL-13. This study aimed to investigate how IL-13 and STAT6 signalling orchestrates the microglial response and differentiation associated with LPS-induced inflammation. Furthermore, the molecular mechanisms that relieve LPS-induced neuroinflammation and neural protection through IL-13-enhanced BDNF signalling were also investigated. C8-B4 microglial cells were induced with LPS to exhibit an M1 pro-inflammatory phenotype or stimulated with IL-4 and/or IL-13 to exhibit an M2 anti-inflammatory microglial phenotype. The cell viability following LPS, IL-4, and/ or IL-13 exposure was determined. The LPS-induced neuroinflammatory response and the anti-inflammatory response induced by IL-4 and IL-13 which promotes STAT-6 signalling were determined by measuring TNFα, IL-1β, and BDNF protein concentrations using ELISA assays. The polarising effects of LPS and IL-4/IL-13 cytokines were also examined via changes in the expression of Iba-1, CD206, CD86, and STAT-6 determined by immunofluorescence analysis. These changes were further investigated by quantifying the mRNA transcripts of TNFα, IL-1 β, Arg-1, CD206, IL-4R, and STAT-6 and BDNF using qRT-PCR. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Investigating the anti-inflammatory effect of blueberry-AuNP on microglial cells and obese rat brains
- Authors: Ngwato, Anacia
- Date: 2024-04
- Subjects: Anti-inflammatory agents , Brain -- Anatomy , Brain -- Physiology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64266 , vital:73670
- Description: Nanotoxicology is a field of study that investigates how nanomaterials interact with biological systems. It focuses on understanding the correlation between the physicochemical properties of nanomaterials, such as size and stability, and their potential toxic effects. Gold nanoparticles (AuNPs), for instance, have a variety of applications in the biological sciences. Therefore, there is a great deal of attention given to evaluating their toxicity to ensure their safe and effective use in biological systems. Anti-inflammatory AuNPs have shown to be a desirable application in obesity treatments since obesity is associated with systematic inflammation. Thus, the study aimed to evaluate the anti-inflammatory effect of BE-AuNPs on C8-B4 microglial cell lines and, to validate the results, the grey matter of brain tissue of obese rats treated with BE-AuNPs. Following the synthesis and characterization of BE-AuNPs, C8-B4 microglial cells were treated with the BE-AuNPs and were evaluated through MTT, HRTEM imaging, qPCR, and ROS. LPS was used to activate the cells. Concentration-dependent toxicity of BE-AuNPs and cellular uptake was observed. The qPCR results showed that the BE-AuNPs decreased the LPS-induced inflammation in the cells. The BE-AuNPs were shown to reduce ROS in inflammatory conditions in the cells. Rat brain tissue analysis through qPCR and ROS demonstrated that BE-AuNPs reduce HFD-induced inflammation and had no ROS effects on the brain, respectively. Thus, leading to a conclusion the BE-AuNPs used in this study are anti-inflammatory. , Thesis (MSc) -- Faculty of Science, Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Ngwato, Anacia
- Date: 2024-04
- Subjects: Anti-inflammatory agents , Brain -- Anatomy , Brain -- Physiology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64266 , vital:73670
- Description: Nanotoxicology is a field of study that investigates how nanomaterials interact with biological systems. It focuses on understanding the correlation between the physicochemical properties of nanomaterials, such as size and stability, and their potential toxic effects. Gold nanoparticles (AuNPs), for instance, have a variety of applications in the biological sciences. Therefore, there is a great deal of attention given to evaluating their toxicity to ensure their safe and effective use in biological systems. Anti-inflammatory AuNPs have shown to be a desirable application in obesity treatments since obesity is associated with systematic inflammation. Thus, the study aimed to evaluate the anti-inflammatory effect of BE-AuNPs on C8-B4 microglial cell lines and, to validate the results, the grey matter of brain tissue of obese rats treated with BE-AuNPs. Following the synthesis and characterization of BE-AuNPs, C8-B4 microglial cells were treated with the BE-AuNPs and were evaluated through MTT, HRTEM imaging, qPCR, and ROS. LPS was used to activate the cells. Concentration-dependent toxicity of BE-AuNPs and cellular uptake was observed. The qPCR results showed that the BE-AuNPs decreased the LPS-induced inflammation in the cells. The BE-AuNPs were shown to reduce ROS in inflammatory conditions in the cells. Rat brain tissue analysis through qPCR and ROS demonstrated that BE-AuNPs reduce HFD-induced inflammation and had no ROS effects on the brain, respectively. Thus, leading to a conclusion the BE-AuNPs used in this study are anti-inflammatory. , Thesis (MSc) -- Faculty of Science, Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Investigation of four roof-shaped host compounds for their separation potential of mixtures of guest Isomers and related compounds
- Authors: Senekal, Ulrich
- Date: 2024-04
- Subjects: Grignard reagents , Optical isomers -- Analysis , Supramolecular chemistry
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/64368 , vital:73684
- Description: The inclusion ability of four roof-shaped host compounds, namely trans-9,10-dihydro-9,10- ethanoanthracene-11,12-dicarboxylic acid (H1), dimethyl trans-9,10-dihydro-9,10- ethanoanthracene-11,12-dicarboxylate (H2), trans-α,α,α’,α’-tetraphenyl-9,10-dihydro-9,10- ethanoanthracene-11,12-dimethanol (H3) and trans-α,α,α’,α’-tetrakis(4-chlorophenyl)-9,10- dihydro-9,10-ethanoanthracene-11,12-dimethanol (H4), were investigated when presented with numerous guest series (eight in number), including the xylene isomers and ethylbenzene, pyridine and the methylpyridine isomers, structurally related toluene, ethylbenzene and cumene, the dichlorobenzenes, six-membered heterocyclic ring compounds (dioxane, morpholine, piperidine and pyridine), anisole and the methylanisole isomers, anisole and the bromoanisole guests, and phenol and the methoxyphenol isomers. The four host compounds were synthesized via Diels-Alder (H1), esterification (H2) and Grignard addition (H3 and H4) reactions, producing yields of product of up to 93%. The yields for the Grignard reactions were lower, 54 and 37%, for the corresponding procedures using phenylmagnesium bromide or 4-chlorophenylmagnesium bromide. Computational molecular modelling studies were conducted on all four host compounds, and the resultant molecular geometries compared with the apohost (guest-free) crystal structures, when available. The geometries of the lowest energy conformers were in close correlation with the observed host structures as obtained from the apohost crystal structures (unfortunately, H3 and H4 were not able to form adequate quality crystals for SCXRD analyses). Interestingly, H1–H4 displayed intramolecular non-classical C–H∙∙∙O hydrogen bonds, while only H1 and H2 demonstrated intermolecular interactions of this type. H3 and H4 assumed one of two forms depending on the guest that was employed: the “active” form presented a strong intramolecular O–H∙∙∙O hydrogen bond, while the “inactive” form possessed weak π∙∙∙π and O–H∙∙∙π interactions. All of the host compounds were subjected to crystallization experiments from each of the guest species, as well as from mixtures of guests from each series (the guest competition experiments), where 1H-, 13C-NMR spectroscopy, GC-MS and/or GC-FID were used to analyse any resultant solids formed, as applicable. Single crystal X-ray diffraction (SCXRD) experiments were carried out on each single solvent complex produced in this work, where the crystal quality was suitable, while thermal analyses were also employed on these to determine their relative thermal stabilities. During the single-guest crystallization experiments, H4 was found to be remarkable in its inclusion ability, forming complexes with all but p-dichlorobenzene, typically with a 1:1 host:guest (H:G) ratio. H1 was more selective in its inclusion behaviour, not enclathrating cumene, 3-bromoanisole, phenol or the three methoxyphenol isomers (favouring 1:1 or 2:1 H:G ratios where complexation was successful). Interestingly, H1 formed salts when presented with 2- and 3-methylpyridine, and morpholine and piperidine. H2 and H3 were less remarkable in their inclusion ability, furnishing apohost crystals or gels in some experiments (typically a 3:1 H:G ratio was favoured for both when complexation occurred). Of the four roof-shaped host compounds, H1 and H4 displayed enhanced selectivities for certain guest species, showing near-complete affinity for a specific guest compound when presented with a guest mixture. H1 was able to include 100.0 and 98.8% p-dichlorobenzene (p-DCB) (from m-DCB/p-DCB and o-DCB/p-DCB mixtures), 96.6 and 93.6% p-xylene (p-Xy) (from m-Xy/p-Xy and o-Xy/p-Xy), 99.3% 4-methylanisole (4-MA) (from 2-MA/4-MA) and 97.1% 4-bromoanisole (4-BA) (from ANI/2-BA/3-BA/4-BA, where ANI is anisole). Host compound H4 was able to include ≈ 90% of selected meta-substituted guests, while H2 and H3 demonstrated moderate preferences for the guest compounds employed in this work (< 60%). It was concluded that some xylene guest mixtures may be purified using all but H2, whereas only H1 and H2 showed potential in separating the pyridines. All but H2 may also be employed in the separation of selected dichlorobenzene mixtures, while H2 showed potential for the separation of the six-membered heterocyclic guest compounds (dioxane, morpholine, piperidine and pyridine), were these ever required to be separated. Both H1 and H4 exhibited an overwhelming affinity for the methyl- and bromoanisole guest compounds, and this work has shown that these are likely host candidates for the purification of a variety of these guest mixtures through supramolecular strategies. SCXRD analyses showed that H1 experienced intermolecular host···host hydrogen bonding interactions between the carboxylic acid functional groups, while H2 typically demonstrated intermolecular non-classical hydrogen bonds in its complexes, forming sheets of host molecules along the c-axis. H4 preferred the “inactive” form whereas H3 assumed either an “active” or “inactive“ form. Various host···guest interactions such as π∙∙∙π, C–H∙∙∙π, C–O∙∙∙π, hydrogen bonding and other short contacts were responsible for guest retention in the crystal structures. Thermal analyses were conducted on all of the successfully formed complexes. Ton (the guest release onset temperature) and Tp (the temperature at which the guest release was most rapid) were recorded, when possible, while the mass losses associated with the guest release event were compared with those mass losses expected, in most cases. , Thesis (PhD) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Senekal, Ulrich
- Date: 2024-04
- Subjects: Grignard reagents , Optical isomers -- Analysis , Supramolecular chemistry
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/64368 , vital:73684
- Description: The inclusion ability of four roof-shaped host compounds, namely trans-9,10-dihydro-9,10- ethanoanthracene-11,12-dicarboxylic acid (H1), dimethyl trans-9,10-dihydro-9,10- ethanoanthracene-11,12-dicarboxylate (H2), trans-α,α,α’,α’-tetraphenyl-9,10-dihydro-9,10- ethanoanthracene-11,12-dimethanol (H3) and trans-α,α,α’,α’-tetrakis(4-chlorophenyl)-9,10- dihydro-9,10-ethanoanthracene-11,12-dimethanol (H4), were investigated when presented with numerous guest series (eight in number), including the xylene isomers and ethylbenzene, pyridine and the methylpyridine isomers, structurally related toluene, ethylbenzene and cumene, the dichlorobenzenes, six-membered heterocyclic ring compounds (dioxane, morpholine, piperidine and pyridine), anisole and the methylanisole isomers, anisole and the bromoanisole guests, and phenol and the methoxyphenol isomers. The four host compounds were synthesized via Diels-Alder (H1), esterification (H2) and Grignard addition (H3 and H4) reactions, producing yields of product of up to 93%. The yields for the Grignard reactions were lower, 54 and 37%, for the corresponding procedures using phenylmagnesium bromide or 4-chlorophenylmagnesium bromide. Computational molecular modelling studies were conducted on all four host compounds, and the resultant molecular geometries compared with the apohost (guest-free) crystal structures, when available. The geometries of the lowest energy conformers were in close correlation with the observed host structures as obtained from the apohost crystal structures (unfortunately, H3 and H4 were not able to form adequate quality crystals for SCXRD analyses). Interestingly, H1–H4 displayed intramolecular non-classical C–H∙∙∙O hydrogen bonds, while only H1 and H2 demonstrated intermolecular interactions of this type. H3 and H4 assumed one of two forms depending on the guest that was employed: the “active” form presented a strong intramolecular O–H∙∙∙O hydrogen bond, while the “inactive” form possessed weak π∙∙∙π and O–H∙∙∙π interactions. All of the host compounds were subjected to crystallization experiments from each of the guest species, as well as from mixtures of guests from each series (the guest competition experiments), where 1H-, 13C-NMR spectroscopy, GC-MS and/or GC-FID were used to analyse any resultant solids formed, as applicable. Single crystal X-ray diffraction (SCXRD) experiments were carried out on each single solvent complex produced in this work, where the crystal quality was suitable, while thermal analyses were also employed on these to determine their relative thermal stabilities. During the single-guest crystallization experiments, H4 was found to be remarkable in its inclusion ability, forming complexes with all but p-dichlorobenzene, typically with a 1:1 host:guest (H:G) ratio. H1 was more selective in its inclusion behaviour, not enclathrating cumene, 3-bromoanisole, phenol or the three methoxyphenol isomers (favouring 1:1 or 2:1 H:G ratios where complexation was successful). Interestingly, H1 formed salts when presented with 2- and 3-methylpyridine, and morpholine and piperidine. H2 and H3 were less remarkable in their inclusion ability, furnishing apohost crystals or gels in some experiments (typically a 3:1 H:G ratio was favoured for both when complexation occurred). Of the four roof-shaped host compounds, H1 and H4 displayed enhanced selectivities for certain guest species, showing near-complete affinity for a specific guest compound when presented with a guest mixture. H1 was able to include 100.0 and 98.8% p-dichlorobenzene (p-DCB) (from m-DCB/p-DCB and o-DCB/p-DCB mixtures), 96.6 and 93.6% p-xylene (p-Xy) (from m-Xy/p-Xy and o-Xy/p-Xy), 99.3% 4-methylanisole (4-MA) (from 2-MA/4-MA) and 97.1% 4-bromoanisole (4-BA) (from ANI/2-BA/3-BA/4-BA, where ANI is anisole). Host compound H4 was able to include ≈ 90% of selected meta-substituted guests, while H2 and H3 demonstrated moderate preferences for the guest compounds employed in this work (< 60%). It was concluded that some xylene guest mixtures may be purified using all but H2, whereas only H1 and H2 showed potential in separating the pyridines. All but H2 may also be employed in the separation of selected dichlorobenzene mixtures, while H2 showed potential for the separation of the six-membered heterocyclic guest compounds (dioxane, morpholine, piperidine and pyridine), were these ever required to be separated. Both H1 and H4 exhibited an overwhelming affinity for the methyl- and bromoanisole guest compounds, and this work has shown that these are likely host candidates for the purification of a variety of these guest mixtures through supramolecular strategies. SCXRD analyses showed that H1 experienced intermolecular host···host hydrogen bonding interactions between the carboxylic acid functional groups, while H2 typically demonstrated intermolecular non-classical hydrogen bonds in its complexes, forming sheets of host molecules along the c-axis. H4 preferred the “inactive” form whereas H3 assumed either an “active” or “inactive“ form. Various host···guest interactions such as π∙∙∙π, C–H∙∙∙π, C–O∙∙∙π, hydrogen bonding and other short contacts were responsible for guest retention in the crystal structures. Thermal analyses were conducted on all of the successfully formed complexes. Ton (the guest release onset temperature) and Tp (the temperature at which the guest release was most rapid) were recorded, when possible, while the mass losses associated with the guest release event were compared with those mass losses expected, in most cases. , Thesis (PhD) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Investigation of the host potential of compounds derived from tartaric acid, succinic acid and 1,4-cyclohexanedioic acid
- Authors: Adam, Muhammad Ameen
- Date: 2024-04
- Subjects: Chemical reactions , Chemistry, Organic , Bacteriology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63617 , vital:73562
- Description: The present investigation considered the host behaviour of three compounds, namely (+)-(2R,3R)-1,1,4,4-tetraphenylbutane-1,2,3,4-tetraol (H1), 1,1,4,4-tetraphenyl-1,4-butanediol (H2) and cyclohexane-1,4-diylbis(diphenylmethanol) (H3) in various guest mixtures. These host compounds were readily synthesized by means of Grignard addition reactions on the diesters of tartaric acid, succinic acid and 1,4-cyclohexanedioic acid. The guest mixtures included cyclopentanone, cyclohexanone, cycloheptanone and cyclooctanone, γ-butyrolactone, 2-pyrrolidone, N-methyl-2-pyrrolidone and N-ethyl-2-pyrrolidone, and pyridine, 2-methylpyridine, 3-methylpyridine and 4-methylpyridine. Crystals of (+)-(2R,3R)-1,1,4,4-tetraphenylbutane-1,2,3,4-tetraol (H1) were grown from cyclopentanone (5-ONE), cyclohexanone (6-ONE), cycloheptanone (7-ONE) and cyclooctanone (8-ONE,) producing 1:1 host:guest complexes in each instance. Thermal analysis showed the thermal stabilities of these complexes to be in the order 6-ONE > 7-ONE > 8-ONE > 5-ONE which correlated exactly with results from binary guest/guest competition experiments, where 6-ONE was always preferred by H1, while 5-ONE was consistently disfavoured. Single crystal X-ray diffraction (SCXRD) analyses demonstrated that each guest compound was retained in the crystals by means of a hydrogen bond with an alcohol moiety of the host compound. Furthermore, preferred guests 6- and 7-ONE produced crystals with greater densities than guests less favoured (5- and 8-ONE). A conformational analysis of the guest geometries in the four complexes with H1 revealed that the low energy guest conformers were present. The host selectivity for 6- and 7-ONE was proposed to be due to the improved molecular packing in the crystals of the complexes containing these two guest compounds, observed from their higher crystal densities. Hirshfeld surface analyses were not useful in explaining the preference of H1 for 6-ONE relative to 7-ONE (these types of analyses were not possible for the 5-ONE and 8-ONE-containing inclusion compounds due to the nature and degree of disorder present in the guest molecules). H1 was also crystallized from γ-butyrolactone (GBL), 2-pyrrolidone (NP), N-methyl-2-pyrrolidone (NMP) and N-ethyl-2-pyrrolidone (NEP), and 1H-NMR spectroscopy revealed that all but GBL were included. The host compound was also presented with these guest solvents in various mixtures, and it was observed that NMP was an extremely favoured guest solvent, followed by NEP and NP, with GBL being consistently disfavoured in every experiment. It was therefore shown that in certain instances, H1 may serve as an alternative tool for separating some of these mixtures through host-guest chemistry strategies. The hydrogen bonding motifs present in each of the successfully formed complexes were extensively investigated through SCXRD analysis, as was the thermal behaviour of these complexes. In the latter instance, the peak temperature of the endotherm (from the DSC trace) representing the guest release was greater for the inclusion compound with favoured NMP (145.5 °C) relative to the complexes with NP (139.8 °C) and NEP (120.5 °C). Host compounds H2 and H3 were revealed to have the ability to include each of pyridine (PYR), 2-methylpyridine (2MP), 3-methylpyridine (3MP) and 4-methylpyridine (4MP). H2 displayed selective behaviour for 3MP and 4MP when presented with mixtures of these guest compounds, whilst H3 preferred PYR. In the latter case, this PYR-containing inclusion compound was also the more stable one (the guest release onset temperature was highest, Ton 66.0 °C). It was demonstrated that H2 has the ability to separate very many binary mixtures of these pyridines on a practical platform, since K (the selectivity coefficient) values were 10 or greater in many instances. However, unfortunately, the more difficult-to-separate mixtures containing 3MP and 4MP cannot be purified or separated by employing H2 and supramolecular chemistry strategies. H3 was also shown to be a likely candidate for binary guest separations in very many of the guest solutions considered here, where K was also 10 or greater, and even infinity in many cases. SCXRD demonstrated that 2MP, 3MP and 4MP were retained in the crystals of their complexes by means of classical hydrogen bonds with the host compound. Satisfyingly, this hydrogen bond between 2MP and H2 (3.0213(18) Å) was significantly longer than that between this host compound and both disorder components of 3MP (2.875(2) and 2.825(9) Å) and that between H2 and 4MP (2.8458(13) Å). This observation explains the affinity of H2 for both 3MP and 4MP, and why 2MP was disfavoured. The results of thermal experiments did not wholly concur with observations from the guest/guest competition experiments. Hirshfeld surface analyses were also conducted but were not entirely conclusive with respect to explaining the host selectivity behaviour. In the case of H3, SCXRD analyses revealed that favoured PYR experienced a classical hydrogen bond with the host compound that was statistically significantly shorter (2.795(2) Å, 165°) than those between the other guest compounds and H3. Additionally, this guest compound was the only one to be involved in a (host)C−H···π(guest) interaction (2.91 Å, 139°) and also a non-classical hydrogen bond with the host compound ((host)C−H···N−C(guest), 2.77 Å (144°)). Finally, Hirshfeld surface analyses showed also that preferred PYR experienced a greater percentage of C···H/H···C (33.1%) and H···N/N···H (11.1%) interactions compared with the complexes with 2MP, 3MP and 4MP. However, it is not clear whether these Hirshfeld observations explain the affinity of H3 for PYR. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Adam, Muhammad Ameen
- Date: 2024-04
- Subjects: Chemical reactions , Chemistry, Organic , Bacteriology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63617 , vital:73562
- Description: The present investigation considered the host behaviour of three compounds, namely (+)-(2R,3R)-1,1,4,4-tetraphenylbutane-1,2,3,4-tetraol (H1), 1,1,4,4-tetraphenyl-1,4-butanediol (H2) and cyclohexane-1,4-diylbis(diphenylmethanol) (H3) in various guest mixtures. These host compounds were readily synthesized by means of Grignard addition reactions on the diesters of tartaric acid, succinic acid and 1,4-cyclohexanedioic acid. The guest mixtures included cyclopentanone, cyclohexanone, cycloheptanone and cyclooctanone, γ-butyrolactone, 2-pyrrolidone, N-methyl-2-pyrrolidone and N-ethyl-2-pyrrolidone, and pyridine, 2-methylpyridine, 3-methylpyridine and 4-methylpyridine. Crystals of (+)-(2R,3R)-1,1,4,4-tetraphenylbutane-1,2,3,4-tetraol (H1) were grown from cyclopentanone (5-ONE), cyclohexanone (6-ONE), cycloheptanone (7-ONE) and cyclooctanone (8-ONE,) producing 1:1 host:guest complexes in each instance. Thermal analysis showed the thermal stabilities of these complexes to be in the order 6-ONE > 7-ONE > 8-ONE > 5-ONE which correlated exactly with results from binary guest/guest competition experiments, where 6-ONE was always preferred by H1, while 5-ONE was consistently disfavoured. Single crystal X-ray diffraction (SCXRD) analyses demonstrated that each guest compound was retained in the crystals by means of a hydrogen bond with an alcohol moiety of the host compound. Furthermore, preferred guests 6- and 7-ONE produced crystals with greater densities than guests less favoured (5- and 8-ONE). A conformational analysis of the guest geometries in the four complexes with H1 revealed that the low energy guest conformers were present. The host selectivity for 6- and 7-ONE was proposed to be due to the improved molecular packing in the crystals of the complexes containing these two guest compounds, observed from their higher crystal densities. Hirshfeld surface analyses were not useful in explaining the preference of H1 for 6-ONE relative to 7-ONE (these types of analyses were not possible for the 5-ONE and 8-ONE-containing inclusion compounds due to the nature and degree of disorder present in the guest molecules). H1 was also crystallized from γ-butyrolactone (GBL), 2-pyrrolidone (NP), N-methyl-2-pyrrolidone (NMP) and N-ethyl-2-pyrrolidone (NEP), and 1H-NMR spectroscopy revealed that all but GBL were included. The host compound was also presented with these guest solvents in various mixtures, and it was observed that NMP was an extremely favoured guest solvent, followed by NEP and NP, with GBL being consistently disfavoured in every experiment. It was therefore shown that in certain instances, H1 may serve as an alternative tool for separating some of these mixtures through host-guest chemistry strategies. The hydrogen bonding motifs present in each of the successfully formed complexes were extensively investigated through SCXRD analysis, as was the thermal behaviour of these complexes. In the latter instance, the peak temperature of the endotherm (from the DSC trace) representing the guest release was greater for the inclusion compound with favoured NMP (145.5 °C) relative to the complexes with NP (139.8 °C) and NEP (120.5 °C). Host compounds H2 and H3 were revealed to have the ability to include each of pyridine (PYR), 2-methylpyridine (2MP), 3-methylpyridine (3MP) and 4-methylpyridine (4MP). H2 displayed selective behaviour for 3MP and 4MP when presented with mixtures of these guest compounds, whilst H3 preferred PYR. In the latter case, this PYR-containing inclusion compound was also the more stable one (the guest release onset temperature was highest, Ton 66.0 °C). It was demonstrated that H2 has the ability to separate very many binary mixtures of these pyridines on a practical platform, since K (the selectivity coefficient) values were 10 or greater in many instances. However, unfortunately, the more difficult-to-separate mixtures containing 3MP and 4MP cannot be purified or separated by employing H2 and supramolecular chemistry strategies. H3 was also shown to be a likely candidate for binary guest separations in very many of the guest solutions considered here, where K was also 10 or greater, and even infinity in many cases. SCXRD demonstrated that 2MP, 3MP and 4MP were retained in the crystals of their complexes by means of classical hydrogen bonds with the host compound. Satisfyingly, this hydrogen bond between 2MP and H2 (3.0213(18) Å) was significantly longer than that between this host compound and both disorder components of 3MP (2.875(2) and 2.825(9) Å) and that between H2 and 4MP (2.8458(13) Å). This observation explains the affinity of H2 for both 3MP and 4MP, and why 2MP was disfavoured. The results of thermal experiments did not wholly concur with observations from the guest/guest competition experiments. Hirshfeld surface analyses were also conducted but were not entirely conclusive with respect to explaining the host selectivity behaviour. In the case of H3, SCXRD analyses revealed that favoured PYR experienced a classical hydrogen bond with the host compound that was statistically significantly shorter (2.795(2) Å, 165°) than those between the other guest compounds and H3. Additionally, this guest compound was the only one to be involved in a (host)C−H···π(guest) interaction (2.91 Å, 139°) and also a non-classical hydrogen bond with the host compound ((host)C−H···N−C(guest), 2.77 Å (144°)). Finally, Hirshfeld surface analyses showed also that preferred PYR experienced a greater percentage of C···H/H···C (33.1%) and H···N/N···H (11.1%) interactions compared with the complexes with 2MP, 3MP and 4MP. However, it is not clear whether these Hirshfeld observations explain the affinity of H3 for PYR. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Investigation of the synthesis and characterisation of spiro orthocarbonates and heterocyclic orthocarbonates
- Authors: Cuthbertson, Jarryd Pierre
- Date: 2024-04
- Subjects: Chemistry, Analytic , Analytical chemistry , Chemistry
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63678 , vital:73578
- Description: A series of mostly asymmetrical spiro orthocarbonates and heterospirocyclic derivatives of orthocarbonic acid was synthesized from 2,2-dichlorobenzodioxole and a number of difunctional reagents. A systematic study of the size of the chelate rings formed around the spirocentric carbon atom was conducted by selecting representative samples of aliphatic and aromatic diols. The feasibility and scope of potential starting materials used was expanded by reacting DCBD successfully with thiols. Molecular structures of these compounds were confirmed using diffraction studies on single crystals. All compounds were analyzed using multinuclear NMR. DFT calculations performed on the compounds allowed for the development of equations that can accurately predict 13C chemical shifts of SOCs. Furthermore, the experimental NMR spectroscopy gave rise to an increment shift system for the 13C NMR shifts allowing for further assignment of carbon atom positions in compounds with multiple possible bonding patterns. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Cuthbertson, Jarryd Pierre
- Date: 2024-04
- Subjects: Chemistry, Analytic , Analytical chemistry , Chemistry
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63678 , vital:73578
- Description: A series of mostly asymmetrical spiro orthocarbonates and heterospirocyclic derivatives of orthocarbonic acid was synthesized from 2,2-dichlorobenzodioxole and a number of difunctional reagents. A systematic study of the size of the chelate rings formed around the spirocentric carbon atom was conducted by selecting representative samples of aliphatic and aromatic diols. The feasibility and scope of potential starting materials used was expanded by reacting DCBD successfully with thiols. Molecular structures of these compounds were confirmed using diffraction studies on single crystals. All compounds were analyzed using multinuclear NMR. DFT calculations performed on the compounds allowed for the development of equations that can accurately predict 13C chemical shifts of SOCs. Furthermore, the experimental NMR spectroscopy gave rise to an increment shift system for the 13C NMR shifts allowing for further assignment of carbon atom positions in compounds with multiple possible bonding patterns. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04