Characterization of the molecular mechanism(s) of cannabinoid-induced paraptosis in breast cancer cells
- Authors: de la Harpe, Amy
- Date: 2024-12
- Subjects: Cannabinoids , Cannabinoids -- Therapeutic use , Cancer cells
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/68818 , vital:77120
- Description: Natural products have been extensively studied for their anticancer potential, and several widely used anticancer drugs have natural origins. Many studies have demonstrated that natural compounds can induce paraptosis in various tumour cell lines. Paraptosis is a caspase-independent cell death mechanism characterised by cytoplasmic vacuolation arising from the endoplasmic reticulum (ER) and the mitochondria. The molecular mechanism of paraptosis is unclear; however, the literature indicates that dysregulation of calcium signalling plays an important role in paraptosis induction, particularly calcium-mediated signalling between the ER and mitochondria. This study aimed to identify and characterise the mechanism of cell death induced by a phytocannabinoid ratio which induced significant cytoplasmic vacuolation in the MCF7 breast cancer cell line. Several techniques were employed to address the aim of the study. The crystal violet assay was used to detect changes in viability. Several pathway inhibitors, as well as fluorescent staining and analysis using high-content screening (HCS), were used to measure the induction of various cell death mechanisms. Morphological changes were investigated using light and transmission electron microscopy. The phytocannabinoid ratio induced significant cell death and cytoplasmic vacuolation in MCF7 cells; however, the same trend was not observed in the MCF10A non-tumourigenic breast cell line. No cell cycle arrest, apoptosis, necrosis, autophagy, or ferroptosis induction was detected in MCF7 cells, suggesting that an alternative mechanism of cell death was induced. Vacuolation and cell death induced by the phytocannabinoid ratio were inhibited by cycloheximide, suggesting a dependence on protein synthesis, which is characteristic of paraptosis induction. The mechanism of paraptosis induction by the phytocannabinoid ratio was investigated, and it was found that treatment 1) induced ER dilation and mitochondrial swelling; 2) induced significant ER stress, mitochondrial calcium overload, and mitochondrial dysfunction which appeared to be mediated by the voltage-dependent anion channel (VDAC); and 3) significantly impaired all mitochondrial metabolic pathways. Overall, the data demonstrated that paraptosis induced by the cannabinoid ratio is mediated by calcium flux from the ER to the mitochondria. This highlighted a novel mechanism of phytocannabinoid-induced cell death and emphasised the anti-cancer potential of the use of phytocannabinoid ratios as opposed to individual phytocannabinoids, expanding their potential for use as anticancer agents. , Thesis (PhD) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-12
- Authors: de la Harpe, Amy
- Date: 2024-12
- Subjects: Cannabinoids , Cannabinoids -- Therapeutic use , Cancer cells
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/68818 , vital:77120
- Description: Natural products have been extensively studied for their anticancer potential, and several widely used anticancer drugs have natural origins. Many studies have demonstrated that natural compounds can induce paraptosis in various tumour cell lines. Paraptosis is a caspase-independent cell death mechanism characterised by cytoplasmic vacuolation arising from the endoplasmic reticulum (ER) and the mitochondria. The molecular mechanism of paraptosis is unclear; however, the literature indicates that dysregulation of calcium signalling plays an important role in paraptosis induction, particularly calcium-mediated signalling between the ER and mitochondria. This study aimed to identify and characterise the mechanism of cell death induced by a phytocannabinoid ratio which induced significant cytoplasmic vacuolation in the MCF7 breast cancer cell line. Several techniques were employed to address the aim of the study. The crystal violet assay was used to detect changes in viability. Several pathway inhibitors, as well as fluorescent staining and analysis using high-content screening (HCS), were used to measure the induction of various cell death mechanisms. Morphological changes were investigated using light and transmission electron microscopy. The phytocannabinoid ratio induced significant cell death and cytoplasmic vacuolation in MCF7 cells; however, the same trend was not observed in the MCF10A non-tumourigenic breast cell line. No cell cycle arrest, apoptosis, necrosis, autophagy, or ferroptosis induction was detected in MCF7 cells, suggesting that an alternative mechanism of cell death was induced. Vacuolation and cell death induced by the phytocannabinoid ratio were inhibited by cycloheximide, suggesting a dependence on protein synthesis, which is characteristic of paraptosis induction. The mechanism of paraptosis induction by the phytocannabinoid ratio was investigated, and it was found that treatment 1) induced ER dilation and mitochondrial swelling; 2) induced significant ER stress, mitochondrial calcium overload, and mitochondrial dysfunction which appeared to be mediated by the voltage-dependent anion channel (VDAC); and 3) significantly impaired all mitochondrial metabolic pathways. Overall, the data demonstrated that paraptosis induced by the cannabinoid ratio is mediated by calcium flux from the ER to the mitochondria. This highlighted a novel mechanism of phytocannabinoid-induced cell death and emphasised the anti-cancer potential of the use of phytocannabinoid ratios as opposed to individual phytocannabinoids, expanding their potential for use as anticancer agents. , Thesis (PhD) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-12
Collaborative conservation governance in multifunctional landscapes: a contextual analysis of two South African biosphere reserves in the Boland
- Authors: Klaver, Michael
- Date: 2024-12
- Subjects: Unesco -- Programme on Man and the Biosphere , Nature conservation -- South Africa , Biosphere
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/68924 , vital:77164
- Description: The Man and the Biosphere Programme (MAB) has been earmarked as one of the most promising ways of tackling the grand challenges of our time and achieving the Sustainable Development Goals. Furthermore, it may have the potential to make positive contributions to one of the most troubling conservation challenges of our time – winning spaces for large carnivores in human-dominated landscapes. This study aims to assess the interpretation and implementation of MAB in two South African Biosphere Reserves (BRs) and explore how BRs as landscape level collaborative initiatives can support Cape leopard conservation in the Boland region of the Western Cape, South Africa. This study is informed by two objectives. First, to understand how the chosen governance strategy and structure of two South African BRs have helped to achieve a context appropriate interpretation and actioning of MAB in the landscape. Second, to understand how landscape-level collaborative conservation initiatives support leopard conservation across a multifunctional landscape. This study takes on a mixed methods approach in which qualitative data takes priority and quantitative data is used for support in an embedded multiple-case study design. The sampling techniques used include purposive sampling of strategically targeted participants, i.e. those governing BRs and those leading the collaborative initiative and snowballing thereon. Data collection included a combination of semi-structure interviews (n=20) (the principal collection method), a review of archival, policy and other documents (n=15), and supported by a mixed methods survey questionnaire (n=5). Data were analysed through thematic and content analysis. Findings suggest that organisations working at a landscape-level utilise forms of adaptive co-management and/or governance as a means to being both adaptive and collaborative. Important themes which emerge include cross-sectoral approaches, networks, leadership and trust for building partnerships, shared visions and ‘filling gaps’ left by, or collaborating with the state to fulfil mutually beneficial objectives. This research provides empirical studies on MAB, important for sharing knowledge across the World Network of BRs, meeting the need for further research on collaborative initiatives in social-ecological systems and conservation programmes for large free-roaming carnivores in multifunctional landscapes. , Thesis (MSc) -- Faculty of Science, School of Natural Resource Science & Management, 2024
- Full Text:
- Date Issued: 2024-12
- Authors: Klaver, Michael
- Date: 2024-12
- Subjects: Unesco -- Programme on Man and the Biosphere , Nature conservation -- South Africa , Biosphere
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/68924 , vital:77164
- Description: The Man and the Biosphere Programme (MAB) has been earmarked as one of the most promising ways of tackling the grand challenges of our time and achieving the Sustainable Development Goals. Furthermore, it may have the potential to make positive contributions to one of the most troubling conservation challenges of our time – winning spaces for large carnivores in human-dominated landscapes. This study aims to assess the interpretation and implementation of MAB in two South African Biosphere Reserves (BRs) and explore how BRs as landscape level collaborative initiatives can support Cape leopard conservation in the Boland region of the Western Cape, South Africa. This study is informed by two objectives. First, to understand how the chosen governance strategy and structure of two South African BRs have helped to achieve a context appropriate interpretation and actioning of MAB in the landscape. Second, to understand how landscape-level collaborative conservation initiatives support leopard conservation across a multifunctional landscape. This study takes on a mixed methods approach in which qualitative data takes priority and quantitative data is used for support in an embedded multiple-case study design. The sampling techniques used include purposive sampling of strategically targeted participants, i.e. those governing BRs and those leading the collaborative initiative and snowballing thereon. Data collection included a combination of semi-structure interviews (n=20) (the principal collection method), a review of archival, policy and other documents (n=15), and supported by a mixed methods survey questionnaire (n=5). Data were analysed through thematic and content analysis. Findings suggest that organisations working at a landscape-level utilise forms of adaptive co-management and/or governance as a means to being both adaptive and collaborative. Important themes which emerge include cross-sectoral approaches, networks, leadership and trust for building partnerships, shared visions and ‘filling gaps’ left by, or collaborating with the state to fulfil mutually beneficial objectives. This research provides empirical studies on MAB, important for sharing knowledge across the World Network of BRs, meeting the need for further research on collaborative initiatives in social-ecological systems and conservation programmes for large free-roaming carnivores in multifunctional landscapes. , Thesis (MSc) -- Faculty of Science, School of Natural Resource Science & Management, 2024
- Full Text:
- Date Issued: 2024-12
Comparative study of the effect of iloprost on neuroinflammatory changes in c8-b4 microglial cells and murine model of trypanosomiasis
- Authors: Jacobs, Ashleigh
- Date: 2024-12
- Subjects: Neuroimmunology , DNA -- Methylation , Nervous system -- Degeneration
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/68895 , vital:77160
- 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: 2024-12
- Authors: Jacobs, Ashleigh
- Date: 2024-12
- Subjects: Neuroimmunology , DNA -- Methylation , Nervous system -- Degeneration
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/68895 , vital:77160
- 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: 2024-12
Development of density-dependent and density-independent competition models to understand single tree growth responses in eucalyptus stands
- Authors: Kepe, Lulama Patrick
- Date: 2024-12
- Subjects: Forests and forestry -- Mathematical models , Trees -- Growth -- Mathematical models , Eucalyptus grandis
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/68906 , vital:77161
- Description: In commercial forest production, predicted yields based on mensuration recommendations are seldom realized, and minimal silvicultural standards based on results from trial blocks do not account for the relationship between initial planting density and final stocking. Growth models designed to investigate management options must employ competition indices to provide reliable predictions under extreme silviculture. The competition a tree experiences until the day of harvest is a strong driver for quality and volume of timber. Hence, this turns the regulation of competition into an integral part of silviculture. According to Little et al. (2003), it is known that, at some stage after canopy closure, individual trees in a stand will begin to compete for resources. To investigate competition amongst individual trees, a re-purposed Bayesian mixed effects model, similar in characteristics to a Sire model used for estimating breeding values, is proposed. In animal breeding models, the Sire Model allows for the inclusion of a numerator relationship matrix containing inbreeding coefficients. In a similar way, documented competition indices are included in the model in an attempt to estimate posterior probabilities of specifically selected individual trees being the strongest growers during different stages in the tree growth cycle. Estimated tree growth indices were determined and used to make probability statements in order to rank the individually selected trees based on the amount of growth observed. A tree growth index is a measurement of a tree’s average growth performance in relation to the average growth performance of all trees on the same plot. As different competition indices are introduced into the model, changes in the probabilities are observed and compared to what is visually observed on the plot, i.e. if the tree with the highest probability of being the strongest grower, is actually not necessarily the largest tree of the group of selected trees, but rather the tree that presented the largest amount of growth of the selected group of trees during that specific growth season. From a randomly selected plot, a group of neighboring trees were randomly selected. Four specifically selected target trees were then identified from this group of 25 selected trees, and analyzed. For this discussion, for example, from our randomly selected group of 25 neighboring trees, tree 54, tree 56, tree 86, and tree 88 were specifically selected for further analysis. For these specifically selected trees, marginal posterior densities for the variance components and random effects were then estimated using the Gibbs Sampler, where competition between the trees was assumed present, as well as for the case where it was assumed that no competition takes place between the individually selected trees. In the latter case, an identity matrix was utilized in the Gibbs sampling algorithm where it was assumed that there is no competition between the trees. Both a distance independent competition index (Lorimer,1983), and a distance dependent index (Hegyi, 1974), were used to generate the numerator relationship matrix A that was used by the Gibbs sampling algorithm in the case where competition was assumed between individual trees. Also a new distance dependent index was proposed and tested in this study as well. Results from the selected plot, with a 1500 stems per hectare (sph) density, indicated that there were no significant differences in the average growth between these selected trees. However, the marginal posterior densities of the fixed effects indicated that there was a significant difference in the average growth rates between the base level conditions and other levels determined for each of these fixed effect factors for the selected trees, since their 95% equal tails credibility intervals, did not contain zero. This therefore indicated that the specific treatment applied on the plot, had a significant effect on the individual tree growth. Results when competition was assumed present, revealed that the estimated marginal posterior densities for the error variance as well as tree variance, were severely positively skewed. , Thesis (PhD) -- Faculty of Science, School of Natural Resource Science & Management, 2024
- Full Text:
- Date Issued: 2024-12
- Authors: Kepe, Lulama Patrick
- Date: 2024-12
- Subjects: Forests and forestry -- Mathematical models , Trees -- Growth -- Mathematical models , Eucalyptus grandis
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/68906 , vital:77161
- Description: In commercial forest production, predicted yields based on mensuration recommendations are seldom realized, and minimal silvicultural standards based on results from trial blocks do not account for the relationship between initial planting density and final stocking. Growth models designed to investigate management options must employ competition indices to provide reliable predictions under extreme silviculture. The competition a tree experiences until the day of harvest is a strong driver for quality and volume of timber. Hence, this turns the regulation of competition into an integral part of silviculture. According to Little et al. (2003), it is known that, at some stage after canopy closure, individual trees in a stand will begin to compete for resources. To investigate competition amongst individual trees, a re-purposed Bayesian mixed effects model, similar in characteristics to a Sire model used for estimating breeding values, is proposed. In animal breeding models, the Sire Model allows for the inclusion of a numerator relationship matrix containing inbreeding coefficients. In a similar way, documented competition indices are included in the model in an attempt to estimate posterior probabilities of specifically selected individual trees being the strongest growers during different stages in the tree growth cycle. Estimated tree growth indices were determined and used to make probability statements in order to rank the individually selected trees based on the amount of growth observed. A tree growth index is a measurement of a tree’s average growth performance in relation to the average growth performance of all trees on the same plot. As different competition indices are introduced into the model, changes in the probabilities are observed and compared to what is visually observed on the plot, i.e. if the tree with the highest probability of being the strongest grower, is actually not necessarily the largest tree of the group of selected trees, but rather the tree that presented the largest amount of growth of the selected group of trees during that specific growth season. From a randomly selected plot, a group of neighboring trees were randomly selected. Four specifically selected target trees were then identified from this group of 25 selected trees, and analyzed. For this discussion, for example, from our randomly selected group of 25 neighboring trees, tree 54, tree 56, tree 86, and tree 88 were specifically selected for further analysis. For these specifically selected trees, marginal posterior densities for the variance components and random effects were then estimated using the Gibbs Sampler, where competition between the trees was assumed present, as well as for the case where it was assumed that no competition takes place between the individually selected trees. In the latter case, an identity matrix was utilized in the Gibbs sampling algorithm where it was assumed that there is no competition between the trees. Both a distance independent competition index (Lorimer,1983), and a distance dependent index (Hegyi, 1974), were used to generate the numerator relationship matrix A that was used by the Gibbs sampling algorithm in the case where competition was assumed between individual trees. Also a new distance dependent index was proposed and tested in this study as well. Results from the selected plot, with a 1500 stems per hectare (sph) density, indicated that there were no significant differences in the average growth between these selected trees. However, the marginal posterior densities of the fixed effects indicated that there was a significant difference in the average growth rates between the base level conditions and other levels determined for each of these fixed effect factors for the selected trees, since their 95% equal tails credibility intervals, did not contain zero. This therefore indicated that the specific treatment applied on the plot, had a significant effect on the individual tree growth. Results when competition was assumed present, revealed that the estimated marginal posterior densities for the error variance as well as tree variance, were severely positively skewed. , Thesis (PhD) -- Faculty of Science, School of Natural Resource Science & Management, 2024
- Full Text:
- Date Issued: 2024-12
Gymnopilus junonius and Rhodofomitopsis lilacinogilva: In vitro evaluation of antimycobacterial activity, safety assessment and isolation of active compounds
- Authors: Didloff, Jenske
- Date: 2024-12
- Subjects: Antibacterial agents , Plants, Useful -- South Africa , Medicinal plants -- South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/68840 , vital:77122
- Description: Tuberculosis remains a significant public health challenge due to the complexity and compliance issues of its treatment, the prevalence of latent infections, the high rate of HIV co-infection, and the spread of drug-resistant strains. This highlights the need to search for new antimycobacterial drugs. Natural products have historically been used as sources for the discovery of pharmaceuticals. Although medicinal macrofungi have been exploited in traditional folk medicines for the treatment of various diseases, research into their antimycobacterial activity remains limited.The aim of this study was to isolate, identify, and characterise the antimycobacterial compound(s) present in ethanol fruiting body extracts of Gymnopilus junonius (Fr.) P.D. Orton (Hymenogastraceae) and Rhodofomitopsis lilacinogilva (Berk.) B.K. Cui, M.L. Han, & Y.C. Dai (Fomitopsidaceae), as well as to investigate their mechanism of action and potential toxicity using in vitro and in vivo screening methods.Bioassay-guided fractionation was conducted using column chromatography and preparative thin-layer chromatography to isolate the active antimycobacterial fraction/compound from ethanol extracts of G. junonius and R. lilacinogilva. Antimycobacterial activity against M. tuberculosis H37Rv was screened using a resazurin microplate assay (REMA). The chemical structure was elucidated employing 1D-(1H NMR) and 2D NMR spectroscopy (HSQC, HMBC) techniques, along with High- Performance Liquid Chromatography High-Resolution Electron Spray Ionisation Mass Spectrometry (HPLC-HRESI-MS). Transmission electron microscopy (TEM) was utilised to observe the ultrastructural changes in M. tuberculosis induced by the active fraction/compound. Toxicity assessment was performed on African green monkeykidney (Vero) and human hepatoma (C3A) cell lines using various staining techniques to observe the potential risk for hepatotoxicity (CellRox orange, TMRE, and MTG staining) and genotoxicity (NucRed staining). In vivo toxicity of extracts was evaluated using a zebrafish embryo/larvae model to observe developmental and teratogenic effects.The bioassay-guided fractionation of G. junonius and R. lilacinogilva extracts yielded an active compound and a fraction displaying inhibitory activity against M. tuberculosis, with MIC values of 31.25 μg/mL and 250 μg/mL, respectively. Gymnopilene was identified as the main active compound isolated from G. junonius, while fraction 8 from R. lilacinogilva contained a predominant constituent resembling a pachymic acid derivative. Transmission electron microscopy revealed ultrastructural damage to M. tuberculosis cells upon treatment with gymnopilene and fraction 8, which was observed as the disruption and disintegration of the cell wall. In vitro toxicity assessment indicated a reduction in the cell density in both Vero and C3A cell lines following exposure to the fractions/gymnopilene. Although there were no significant alterations in the production of reactive oxygen species, changes in mitochondrial dynamics were observed. Genotoxic assessment showed no significant changes. In vivo toxicity assessment showed no significant effects for G. junonius against the zebrafish embryos/larvae, whereas R. lilacinogilva remained toxic and induced developmental abnormalities over a 72-hour time period.The findings of this study highlight the potential of macrofungi as a valuable source of bioactive compounds, confirming the significance of natural products in drug discovery. Notably, this research represents the first to demonstrate that the predominant compound, gymnopilene, isolated from G. junonius exhibits inhibitory activity against M. tuberculosis, contributing to the novelty of the study. Furthermore, the study expands our understanding of the antimycobacterial properties of the selected macrofungal species, G. junonius and R. lilacinogilva, by demonstrating the ultrastructural damage to M. tuberculosis cell wall induced by treatment. However, it is important to recognise the potential toxicity identified through in vitro and/or in vivo screening assays. The observed toxicity may hamper their suitability formdrug development. Future investigations could explore the inclusion of additional in vitro based models, perhaps more complex and physiologically relevant models alongside the in vivo screening model to assess the therapeutic potential of isolated fractions/compounds. , Thesis (PhD) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-12
- Authors: Didloff, Jenske
- Date: 2024-12
- Subjects: Antibacterial agents , Plants, Useful -- South Africa , Medicinal plants -- South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/68840 , vital:77122
- Description: Tuberculosis remains a significant public health challenge due to the complexity and compliance issues of its treatment, the prevalence of latent infections, the high rate of HIV co-infection, and the spread of drug-resistant strains. This highlights the need to search for new antimycobacterial drugs. Natural products have historically been used as sources for the discovery of pharmaceuticals. Although medicinal macrofungi have been exploited in traditional folk medicines for the treatment of various diseases, research into their antimycobacterial activity remains limited.The aim of this study was to isolate, identify, and characterise the antimycobacterial compound(s) present in ethanol fruiting body extracts of Gymnopilus junonius (Fr.) P.D. Orton (Hymenogastraceae) and Rhodofomitopsis lilacinogilva (Berk.) B.K. Cui, M.L. Han, & Y.C. Dai (Fomitopsidaceae), as well as to investigate their mechanism of action and potential toxicity using in vitro and in vivo screening methods.Bioassay-guided fractionation was conducted using column chromatography and preparative thin-layer chromatography to isolate the active antimycobacterial fraction/compound from ethanol extracts of G. junonius and R. lilacinogilva. Antimycobacterial activity against M. tuberculosis H37Rv was screened using a resazurin microplate assay (REMA). The chemical structure was elucidated employing 1D-(1H NMR) and 2D NMR spectroscopy (HSQC, HMBC) techniques, along with High- Performance Liquid Chromatography High-Resolution Electron Spray Ionisation Mass Spectrometry (HPLC-HRESI-MS). Transmission electron microscopy (TEM) was utilised to observe the ultrastructural changes in M. tuberculosis induced by the active fraction/compound. Toxicity assessment was performed on African green monkeykidney (Vero) and human hepatoma (C3A) cell lines using various staining techniques to observe the potential risk for hepatotoxicity (CellRox orange, TMRE, and MTG staining) and genotoxicity (NucRed staining). In vivo toxicity of extracts was evaluated using a zebrafish embryo/larvae model to observe developmental and teratogenic effects.The bioassay-guided fractionation of G. junonius and R. lilacinogilva extracts yielded an active compound and a fraction displaying inhibitory activity against M. tuberculosis, with MIC values of 31.25 μg/mL and 250 μg/mL, respectively. Gymnopilene was identified as the main active compound isolated from G. junonius, while fraction 8 from R. lilacinogilva contained a predominant constituent resembling a pachymic acid derivative. Transmission electron microscopy revealed ultrastructural damage to M. tuberculosis cells upon treatment with gymnopilene and fraction 8, which was observed as the disruption and disintegration of the cell wall. In vitro toxicity assessment indicated a reduction in the cell density in both Vero and C3A cell lines following exposure to the fractions/gymnopilene. Although there were no significant alterations in the production of reactive oxygen species, changes in mitochondrial dynamics were observed. Genotoxic assessment showed no significant changes. In vivo toxicity assessment showed no significant effects for G. junonius against the zebrafish embryos/larvae, whereas R. lilacinogilva remained toxic and induced developmental abnormalities over a 72-hour time period.The findings of this study highlight the potential of macrofungi as a valuable source of bioactive compounds, confirming the significance of natural products in drug discovery. Notably, this research represents the first to demonstrate that the predominant compound, gymnopilene, isolated from G. junonius exhibits inhibitory activity against M. tuberculosis, contributing to the novelty of the study. Furthermore, the study expands our understanding of the antimycobacterial properties of the selected macrofungal species, G. junonius and R. lilacinogilva, by demonstrating the ultrastructural damage to M. tuberculosis cell wall induced by treatment. However, it is important to recognise the potential toxicity identified through in vitro and/or in vivo screening assays. The observed toxicity may hamper their suitability formdrug development. Future investigations could explore the inclusion of additional in vitro based models, perhaps more complex and physiologically relevant models alongside the in vivo screening model to assess the therapeutic potential of isolated fractions/compounds. , Thesis (PhD) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-12
Investigation of potential in-situ polymerization reactions for use in lithium-ion batteries
- Authors: Dube, Tafara
- Date: 2024-12
- Subjects: Lithium ion batteries , Lithium cells , Electrochemistry
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/68851 , vital:77127
- Description: With the rise in popularity of electric vehicles and portable electronic devices, having a reliable, lightweight, and long-lasting battery is crucial. This has led to the mass commercialisation of lithium-ion batteries (LIB’s) because they offer several advantages over other battery technologies. Over the years, one of the concerns was with the ease with which the batteries can burn or explode when subjected to certain extreme conditions. In order to build trust in these products and to expand the technology into more diverse applications, safety aspects of the batteries has become of widespread concern resulting in a key area of research. One aspect of improving the safety is by reducing the flammability of the battery by the addition of certain chemicals that stop or suppress the thermal runaway effect. However, this in-turn reduces the battery’s capacity and life-cycle performance. Researchers have used the idea of encapsulating these chemicals thereby physically separating them within the lithium-ion battery (LIB) electrolyte system with a minimum effect on performance. This research aims to explore use of R-diols and R-amines as additives that upon a thermal trigger would react with the lithium-ion battery electrolyte to stop the effect of the thermal runaway by forming carbamate derivatives which are gel-like or form solid aggregates. The R-diols or R-amines can react with electrolyte at higher temperatures with the lithium-hexafluorophosphate acting as a catalyst. This change in the physical state of the electrolyte increases the resistance inside the battery which then hinders ion movement and forms a physical barrier to reduce the effect of short circuiting when the separator or other components are damaged due to higher temperatures. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-12
- Authors: Dube, Tafara
- Date: 2024-12
- Subjects: Lithium ion batteries , Lithium cells , Electrochemistry
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/68851 , vital:77127
- Description: With the rise in popularity of electric vehicles and portable electronic devices, having a reliable, lightweight, and long-lasting battery is crucial. This has led to the mass commercialisation of lithium-ion batteries (LIB’s) because they offer several advantages over other battery technologies. Over the years, one of the concerns was with the ease with which the batteries can burn or explode when subjected to certain extreme conditions. In order to build trust in these products and to expand the technology into more diverse applications, safety aspects of the batteries has become of widespread concern resulting in a key area of research. One aspect of improving the safety is by reducing the flammability of the battery by the addition of certain chemicals that stop or suppress the thermal runaway effect. However, this in-turn reduces the battery’s capacity and life-cycle performance. Researchers have used the idea of encapsulating these chemicals thereby physically separating them within the lithium-ion battery (LIB) electrolyte system with a minimum effect on performance. This research aims to explore use of R-diols and R-amines as additives that upon a thermal trigger would react with the lithium-ion battery electrolyte to stop the effect of the thermal runaway by forming carbamate derivatives which are gel-like or form solid aggregates. The R-diols or R-amines can react with electrolyte at higher temperatures with the lithium-hexafluorophosphate acting as a catalyst. This change in the physical state of the electrolyte increases the resistance inside the battery which then hinders ion movement and forms a physical barrier to reduce the effect of short circuiting when the separator or other components are damaged due to higher temperatures. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-12
Portfolio effect and bet-hedging adaptations in sea turtles
- Authors: Hoekstra, Shaun
- Date: 2024-12
- Subjects: Wildlife conservation , Sea turtles -- South Africa , Animal behavior
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/68873 , vital:77153
- Description: A great proportion of marine species are at risk of going extinct as a result of profound changes in the world’s oceans, primarily driven by human activities. Sea turtles are not exempt from this fate. Despite sea turtles being exposed to a range of environmental conditions and threats that vary in frequency and intensity, these ancient marine reptiles have persisted for millennia. In the past, sea turtles have been able to adapt to natural perturbations while other animal groups have not. The ability of sea turtles to adapt to contemporary changes in conditions, produced by human activities, has become limited. The persistence of sea turtles may be explained by the application of a concept termed “portfolio effect”. An aggregate system is more stable and less prone to fluctuations over time (i.e. portfolio effect) if a diversity of finer components comprises the entire system and displays asynchronous fluctuations over time. Biological entities (e.g. species measured by the abundance trend) may achieve long-term stability even though the individual components (e.g. populations measured in abundance trend) display weak or negative correlations with each other in space and time. Different sea turtle populations may display independent trends in abundances over time, resulting in a portfolio effect at species levels. Trends in sea turtle abundances may be affected by individual behaviour. The adoption of bet-hedging adaptations may enable populations to thrive despite environmental changes or stochasticity, by lowering short-term fitness in exchange for maximising long-term fitness. Individual sea turtles may exhibit bet-hedging adaptations through changes in their temporal nesting behaviour, including the remigration interval. Since remigration interval length regulates the number of nesting females per nesting season, changes in remigration interval will affect abundance trends. The ability of individuals to change their remigration interval allows them to “skip” the breeding migration when environmental conditions seem unfavourable. The overall aim of this thesis was to investigate potential reasons for observed sea turtle abundance trends at species, population, and rookery levels. I tested whether the portfolio effect applies to sea turtles by analysing and interpreting spatiotemporal trends in loggerhead (Caretta caretta) and leatherback (Dermochelys coriacea) abundances at the population and species levels using global datasets. The application of bet-hedging strategies was tested at a local level using data from the long-term monitoring program for South African nesting sea turtles. The majority of loggerhead rookeries displayed an increase in abundance over time, while most leatherback rookeries declined (Chapter 2). Population growth rates also differed among rookeries within Regional Management Units (RMUs) (Chapter 2). This diversity in abundance trends among rookeries suggested spatiotemporal variation in environmental conditions, threats and/or level of protection accompanying sea turtles. The species-level growth rate for both species displayed an overall increase in abundance over time. However, larger (more turtles) leatherback rookeries/RMUs experienced more rapid declines in abundance compared to smaller rookeries/RMUs, resulting in a recent species-level decline. Uncorrelated trends in abundances at the RMU-level could have stabilised species-level trends. Differences in the remigration intervals as a possible bet-hedging adaptation could potentially explain differences in population recovery rates between South Africa’s loggerhead and leatherback sea turtles (Chapter 3), but found no evidence that individuals from either species exhibit bet-hedging adaptations. Loggerheads, however, have increased their remigration intervals over time, while leatherbacks have not. These increases were accompanied by declines in adult body size (previously established) which could be an effect of diminishing foraging area quality. The increased remigration interval shown by loggerheads may be a response rather than an adaptation to the prevailing environmental conditions that impact their food supply in their foraging areas. The population growth rate of leatherback sea turtles may surpass that of the loggerheads in the near future, although there is a global decline in abundance (Chapter 2). This dissertation provides information on possible reasons for observed trends in sea turtle abundances at various levels of biological organisation. While a variety of factors have the potential to influence trends in sea turtle abundance, the possible occurrence of portfolio effects and investigating nesting behaviour may resolve any uncertainties regarding the reasons for observed trends in abundance. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-12
- Authors: Hoekstra, Shaun
- Date: 2024-12
- Subjects: Wildlife conservation , Sea turtles -- South Africa , Animal behavior
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/68873 , vital:77153
- Description: A great proportion of marine species are at risk of going extinct as a result of profound changes in the world’s oceans, primarily driven by human activities. Sea turtles are not exempt from this fate. Despite sea turtles being exposed to a range of environmental conditions and threats that vary in frequency and intensity, these ancient marine reptiles have persisted for millennia. In the past, sea turtles have been able to adapt to natural perturbations while other animal groups have not. The ability of sea turtles to adapt to contemporary changes in conditions, produced by human activities, has become limited. The persistence of sea turtles may be explained by the application of a concept termed “portfolio effect”. An aggregate system is more stable and less prone to fluctuations over time (i.e. portfolio effect) if a diversity of finer components comprises the entire system and displays asynchronous fluctuations over time. Biological entities (e.g. species measured by the abundance trend) may achieve long-term stability even though the individual components (e.g. populations measured in abundance trend) display weak or negative correlations with each other in space and time. Different sea turtle populations may display independent trends in abundances over time, resulting in a portfolio effect at species levels. Trends in sea turtle abundances may be affected by individual behaviour. The adoption of bet-hedging adaptations may enable populations to thrive despite environmental changes or stochasticity, by lowering short-term fitness in exchange for maximising long-term fitness. Individual sea turtles may exhibit bet-hedging adaptations through changes in their temporal nesting behaviour, including the remigration interval. Since remigration interval length regulates the number of nesting females per nesting season, changes in remigration interval will affect abundance trends. The ability of individuals to change their remigration interval allows them to “skip” the breeding migration when environmental conditions seem unfavourable. The overall aim of this thesis was to investigate potential reasons for observed sea turtle abundance trends at species, population, and rookery levels. I tested whether the portfolio effect applies to sea turtles by analysing and interpreting spatiotemporal trends in loggerhead (Caretta caretta) and leatherback (Dermochelys coriacea) abundances at the population and species levels using global datasets. The application of bet-hedging strategies was tested at a local level using data from the long-term monitoring program for South African nesting sea turtles. The majority of loggerhead rookeries displayed an increase in abundance over time, while most leatherback rookeries declined (Chapter 2). Population growth rates also differed among rookeries within Regional Management Units (RMUs) (Chapter 2). This diversity in abundance trends among rookeries suggested spatiotemporal variation in environmental conditions, threats and/or level of protection accompanying sea turtles. The species-level growth rate for both species displayed an overall increase in abundance over time. However, larger (more turtles) leatherback rookeries/RMUs experienced more rapid declines in abundance compared to smaller rookeries/RMUs, resulting in a recent species-level decline. Uncorrelated trends in abundances at the RMU-level could have stabilised species-level trends. Differences in the remigration intervals as a possible bet-hedging adaptation could potentially explain differences in population recovery rates between South Africa’s loggerhead and leatherback sea turtles (Chapter 3), but found no evidence that individuals from either species exhibit bet-hedging adaptations. Loggerheads, however, have increased their remigration intervals over time, while leatherbacks have not. These increases were accompanied by declines in adult body size (previously established) which could be an effect of diminishing foraging area quality. The increased remigration interval shown by loggerheads may be a response rather than an adaptation to the prevailing environmental conditions that impact their food supply in their foraging areas. The population growth rate of leatherback sea turtles may surpass that of the loggerheads in the near future, although there is a global decline in abundance (Chapter 2). This dissertation provides information on possible reasons for observed trends in sea turtle abundances at various levels of biological organisation. While a variety of factors have the potential to influence trends in sea turtle abundance, the possible occurrence of portfolio effects and investigating nesting behaviour may resolve any uncertainties regarding the reasons for observed trends in abundance. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-12
Social dynamics of spotted hyaenas (Crocuta crocuta) in fenced protected areas: Implications for conservation management of a socially intelligent species
- Authors: Honiball, Terry-Lee
- Date: 2024-12
- Subjects: Spotted hyena -- Behavior -- South Africa , Wildlife conservation -- South Africa , Wildlife management -- South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/68884 , vital:77159
- Description: It is important to understand the impact of fenced protected area management on the behaviour and fitness of less popular species, such as the spotted hyeana (Crocuta crocuta), that have been historically overlooked in species management across protected areas. As a result of this oversight, hyaena population densities have reached high levels, making it critical to study the effects of fenced protected area management on these species. There is a lack of understanding of how species adapt to the potentially high-pressure systems (through the restriction of resources spatially) created by fenced protected areas and the intrinsic effects that management regimes may have on wildlife. Due to the spotted hyaena’s high behavioural plasticity, they make excellent candidates to explore the effects of management regimes in fenced protected areas while enhancing our understanding of spotted hyaena ecology. Therefore, the aim of this study was to explore the ecology and social behaviour of high density spotted hyaena populations in fenced protected areas to understand the effects of different management regimes and how spotted hyaenas respond to these differing pressures. This was achieved through four main objectives which consider different aspects of spotted hyaena ecology and the influence of management regimes and environmental variables in two fenced protected areas in South Africa; Madikwe Game Reserve (a socio-economically incentivised reserve) and Addo Elephant National Park (a reserve incentivised by the promotion of biodiversity), between 2021 and 2023. This study explored 1) range residency patterns and third order habitat selection in spotted hyaena movement, 2) interspecific interactions at shared food sources to understand the role of lion, Panthera leo, and spotted hyaenas dynamics in top-down pressure in carnivore structure, 3) territorial interactions when defending resources to understand spotted hyaena social dominance when occurring at high densities, 4) welfare considerations and allostatic load of spotted hyaenas, and additionally we provided insight into the social hierarchy disruptions which occur when removing the matriarch from a clan through an opportunistic record. By assessing the effects of socio-economic or biodiversity driven management regimes, this study provided novel accounts of social behaviour and responses of spotted hyaenas to pressures in fenced protected areas, highlighting the top-down pressure that lions have on multiple aspects of spotted hyaena functioning. Road networks and infrastructure in fenced protected areas were generally utilised by spotted hyaenas and despite high abundance, prey availability remained an important aspect of spotted hyaena ecology regardless of management regimes. Further, we showed that when food is abundant, spotted hyaenas are tolerant of subordinate carnivores, which emphasises their dynamic behavioural plasticity. We showed that spotted hyaenas gauge territorial responses according to the perceived threat and are less tolerant to familiar intruders than to unfamiliar individuals, which is an important inbreeding avoidance tactic that remains in place in fenced protected areas. And lastly, we showed that management regimes influence the adrenal function of spotted hyaenas, where fenced protected areas incentivised by wildlife photographic tourism may negatively affect species fitness through elevated epidandrosterone levels over time. However, spotted hyaenas appear to have adapted to elevated hormone levels, thus not affecting fecundity in fenced protected areas, resulting in high density populations. This study provides a holistic overview of the effects of management regimes on spotted hyaenas in fenced protected areas and provides insights into how spotted hyaenas adapt to pressures when occurring at high densities in these areas. This study contributes to the understanding of spotted hyaena ecology and the intrinsic effects on wildlife of different approaches to management regimes in fenced protected areas. , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-12
- Authors: Honiball, Terry-Lee
- Date: 2024-12
- Subjects: Spotted hyena -- Behavior -- South Africa , Wildlife conservation -- South Africa , Wildlife management -- South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/68884 , vital:77159
- Description: It is important to understand the impact of fenced protected area management on the behaviour and fitness of less popular species, such as the spotted hyeana (Crocuta crocuta), that have been historically overlooked in species management across protected areas. As a result of this oversight, hyaena population densities have reached high levels, making it critical to study the effects of fenced protected area management on these species. There is a lack of understanding of how species adapt to the potentially high-pressure systems (through the restriction of resources spatially) created by fenced protected areas and the intrinsic effects that management regimes may have on wildlife. Due to the spotted hyaena’s high behavioural plasticity, they make excellent candidates to explore the effects of management regimes in fenced protected areas while enhancing our understanding of spotted hyaena ecology. Therefore, the aim of this study was to explore the ecology and social behaviour of high density spotted hyaena populations in fenced protected areas to understand the effects of different management regimes and how spotted hyaenas respond to these differing pressures. This was achieved through four main objectives which consider different aspects of spotted hyaena ecology and the influence of management regimes and environmental variables in two fenced protected areas in South Africa; Madikwe Game Reserve (a socio-economically incentivised reserve) and Addo Elephant National Park (a reserve incentivised by the promotion of biodiversity), between 2021 and 2023. This study explored 1) range residency patterns and third order habitat selection in spotted hyaena movement, 2) interspecific interactions at shared food sources to understand the role of lion, Panthera leo, and spotted hyaenas dynamics in top-down pressure in carnivore structure, 3) territorial interactions when defending resources to understand spotted hyaena social dominance when occurring at high densities, 4) welfare considerations and allostatic load of spotted hyaenas, and additionally we provided insight into the social hierarchy disruptions which occur when removing the matriarch from a clan through an opportunistic record. By assessing the effects of socio-economic or biodiversity driven management regimes, this study provided novel accounts of social behaviour and responses of spotted hyaenas to pressures in fenced protected areas, highlighting the top-down pressure that lions have on multiple aspects of spotted hyaena functioning. Road networks and infrastructure in fenced protected areas were generally utilised by spotted hyaenas and despite high abundance, prey availability remained an important aspect of spotted hyaena ecology regardless of management regimes. Further, we showed that when food is abundant, spotted hyaenas are tolerant of subordinate carnivores, which emphasises their dynamic behavioural plasticity. We showed that spotted hyaenas gauge territorial responses according to the perceived threat and are less tolerant to familiar intruders than to unfamiliar individuals, which is an important inbreeding avoidance tactic that remains in place in fenced protected areas. And lastly, we showed that management regimes influence the adrenal function of spotted hyaenas, where fenced protected areas incentivised by wildlife photographic tourism may negatively affect species fitness through elevated epidandrosterone levels over time. However, spotted hyaenas appear to have adapted to elevated hormone levels, thus not affecting fecundity in fenced protected areas, resulting in high density populations. This study provides a holistic overview of the effects of management regimes on spotted hyaenas in fenced protected areas and provides insights into how spotted hyaenas adapt to pressures when occurring at high densities in these areas. This study contributes to the understanding of spotted hyaena ecology and the intrinsic effects on wildlife of different approaches to management regimes in fenced protected areas. , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-12
Solution of some cross-diffusion equations in biosciences using finite difference methods and artificial neural networks
- Authors: de Waal, Gysbert Nicolaas
- Date: 2024-12
- Subjects: Mathematics , Difference equations , Functional equations
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/68829 , vital:77121
- Description: In this dissertation, three cross-diffusion models which require positivity-preserving solutions are solved using standard and nonstandard finite difference methods and physics-informed neural networks. The three models are a basic reaction-diffusion-chemotaxis model, a convective predator-prey pursuit and evasion model, and a two-dimensional Keller-Segel chemotaxis model. All three models involve systems of nonlinear coupled partial differential equations subject to some specified initial and boundary conditions for which no exact solution is known. It is not possible to obtain the stability region of the standard finite difference methods for the three models theoretically and therefore a range of values of temporal step size at a given spatial step size for reasonable solutions is obtained by running some numerical experiments. It is observed that the standard finite difference schemes are not always positivity-preserving, and this is why nonstandard finite difference schemes are necessary. Chapter 1 provides some background detail on partial differential equations, cross-diffusion equations, finite difference methods, and artificial neural networks. In Chapter 2, the cross-diffusion models considered in this dissertation are provided, namely a basic reaction-diffusion–chemotaxis model for two cases, a convective predator-prey pursuit and evasion model, and a two-dimensional Keller-Segel chemotaxis model for two cases. In Chapter 3, the basic reaction-diffusion–chemotaxis model is solved for the two cases using some standard and nonstandard finite difference schemes. It is determined that the standard methods give reasonable positivity-preserving numerical solutions if the temporal step size, 𝑘, is chosen such that 𝑘 ≤ 0.25 with the spatial step size, ℎ, fixed at ℎ = 1.0. Two nonstandard finite difference methods abbreviated as NSFD1 and NSFD2 are considered from Chapwanya et al. (2014). It is shown that NSFD1 preserves the positivity of the continuous model if the following criteria are satisfied: 𝜙(𝑘)[𝜓(ℎ)]2=12𝛾≤12𝜎+𝛽 and 𝛽≤𝜎. NSFD1 is modified to obtain NSFD2, which is positivity-preserving if 𝑅=𝜙(𝑘)[𝜓(ℎ)]2=12𝛾 and 2𝜎𝑅≤1, that is, 𝜎≤𝛾. In this work, it is shown that NSFD2 does not always achieve consistency, and it is proven that consistency can be achieved if 𝛽→0 and 𝑘ℎ2→0. Lastly, it is demonstrated that the numerical rate of convergence in time of the finite difference methods is approximately one for case 2 of the chemotaxis model. In Chapter 4, one standard and two nonstandard finite difference methods are constructed to solve the convective predator-prey model. Through some numerical experiments, it is observed that reasonable , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-12
- Authors: de Waal, Gysbert Nicolaas
- Date: 2024-12
- Subjects: Mathematics , Difference equations , Functional equations
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/68829 , vital:77121
- Description: In this dissertation, three cross-diffusion models which require positivity-preserving solutions are solved using standard and nonstandard finite difference methods and physics-informed neural networks. The three models are a basic reaction-diffusion-chemotaxis model, a convective predator-prey pursuit and evasion model, and a two-dimensional Keller-Segel chemotaxis model. All three models involve systems of nonlinear coupled partial differential equations subject to some specified initial and boundary conditions for which no exact solution is known. It is not possible to obtain the stability region of the standard finite difference methods for the three models theoretically and therefore a range of values of temporal step size at a given spatial step size for reasonable solutions is obtained by running some numerical experiments. It is observed that the standard finite difference schemes are not always positivity-preserving, and this is why nonstandard finite difference schemes are necessary. Chapter 1 provides some background detail on partial differential equations, cross-diffusion equations, finite difference methods, and artificial neural networks. In Chapter 2, the cross-diffusion models considered in this dissertation are provided, namely a basic reaction-diffusion–chemotaxis model for two cases, a convective predator-prey pursuit and evasion model, and a two-dimensional Keller-Segel chemotaxis model for two cases. In Chapter 3, the basic reaction-diffusion–chemotaxis model is solved for the two cases using some standard and nonstandard finite difference schemes. It is determined that the standard methods give reasonable positivity-preserving numerical solutions if the temporal step size, 𝑘, is chosen such that 𝑘 ≤ 0.25 with the spatial step size, ℎ, fixed at ℎ = 1.0. Two nonstandard finite difference methods abbreviated as NSFD1 and NSFD2 are considered from Chapwanya et al. (2014). It is shown that NSFD1 preserves the positivity of the continuous model if the following criteria are satisfied: 𝜙(𝑘)[𝜓(ℎ)]2=12𝛾≤12𝜎+𝛽 and 𝛽≤𝜎. NSFD1 is modified to obtain NSFD2, which is positivity-preserving if 𝑅=𝜙(𝑘)[𝜓(ℎ)]2=12𝛾 and 2𝜎𝑅≤1, that is, 𝜎≤𝛾. In this work, it is shown that NSFD2 does not always achieve consistency, and it is proven that consistency can be achieved if 𝛽→0 and 𝑘ℎ2→0. Lastly, it is demonstrated that the numerical rate of convergence in time of the finite difference methods is approximately one for case 2 of the chemotaxis model. In Chapter 4, one standard and two nonstandard finite difference methods are constructed to solve the convective predator-prey model. Through some numerical experiments, it is observed that reasonable , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-12
The optimisation of Eucalyptus regeneration practices for improved survival, growth and uniformity in South African pulpwood plantations
- Authors: Hechter, Ullrich
- Date: 2024-12
- Subjects: Eucalyptus -- Regeneration -- South Africa , Forests and forestry -- Economic aspects , Forests and forestry
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/68862 , vital:77135
- Description: Commercial forestry plantations in South Africa play an important role in the economy of the country, contributing 1.2% towards the gross domestic product. Currently plantation forests occupy 1.1% (1.2 million hectares) of the South African land surface, of which 75 000 hectares are re-established each year. Eucalypts constitute 43% of planted area, of which 88% is grown for pulpwood. Achieving high tree survival (>90%) is important in terms of optimising rotation-end yield. The industry origin of a 90% survival benchmark is unclear, although company procedures incorporate this as the minimum threshold in terms of re-establishment success. Past research indicates that most mortality occurs within a narrow period post-establishment and is often associated with substandard re-establishment practices and/or a stressed micro-environment. An improved understanding is needed about the various mitigation measures needed to minimize mortality during eucalypt re-establishment. Before making decisions related to mortality mitigation measures, comprehensive data are required as to their commercial applicability as well as outcomes from multiple trials that accurately quantify any impacts on tree survival and financial return. The overall purpose of this dissertation was the optimisation of Eucalyptus re-establishment practices for improved survival, growth and uniformity in South African pulpwood plantations. To achieve this, five inter-linked objectives were determined. The first objective was to highlight the most important factors contributing to increased mortality in eucalypt plantations during re-establishment. This was achieved through conducting a literature review. Citations were ranked in terms of credibility, with the importance ratings (derived from the literature sources) applied to the different factors affecting survival and growth during eucalypt re-establishment. Of the various factors impacting early eucalypt mortality, water stress and planting stock quality were considered highly important. The manner and quality of site preparation (soil and slash), planting practices (planting depth included), timing of planting (during dry, hot periods), various post-planting operations (incorrect fertiliser placement or herbicide drift) and insect pests and diseases also contribute to mortality, but to a lesser extent. These factors cannot be considered in isolation due to the complex interactions that exist between them and determining the primary causes of mortality can be elusive, especially as their impacts tend to be additive by nature. The second objective was to link survival to silvicultural treatments, site-related physiographic factors and climatic variables in South Africa. This was achieved by conducting an integrated analysis of 43 Eucalyptus trials. Of the seven re-establishment practices considered, watering, planting depth and fertiliser application were significant, with plant size, pitting method, residue management and insecticide application were not significant. However, when environmental variables were included within the analyses, there were significant site x treatment interactions for planting depth, plant size, residue management and fertiliser application. This highlights the importance of taking site related factors into consideration when interpreting the causes of mortality. The third objective was to determine the interaction between planting density and mortality on Eucalyptus growth, uniformity and financial yield at rotation end in South Africa. This was carried out to verify whether planting at different densities may be used as a preventative (before planting) mitigation measure. One trial was used to answer four keys sub-objectives: 1) The impact of three planting densities (1 102, 1 500, 1 959 SPH) with no mortality on yield at rotation-end; 2) The impact of mortality (0%, 10%, 20%, 30%, 40%) on rotation-end yield; 3) The quantification of tree performance when planting at a higher density and accepting a certain degree of mortality; and 4) The financial impact of different planting densities and mortality on rotation-end profit. Higher planting densities resulted in smaller individual trees, but with an increase in stand level performance. At rotation-end, lower mortality (0% and 10%) had significantly higher volumes ha-1 than the higher mortality (30% and 40%). Planting at higher densities (1 722 and 1 959 SPH) and accepting a certain degree of mortality resulted in non-significant differences for volume at rotation-end compared to the fully stocked 1 500 SPH treatment. A higher SPH resulted in a higher yield, but with an increase in estimated establishment/tending and harvesting costs. In contrast, an increase in mortality and/or lower SPH (in the absence of mortality) resulted in more variable stand growth, together with an increase in estimated machine harvesting productivity and reduced costs. Irrespective of SPH, the higher the mortality the greater the loss of income, with the best profit within each treatment related to full stocking (0% mortality). Within the higher panting densities, the profit gained following low mortality (10 and 20%) was similar to that of no mortality (0%), indicating that higher mortality may be tolerated when planting at higher densities, confirming the 90% survival threshold the industry aims to achieve post-establishment. The fourth objective was to determine if silviculture intervention (blanking at 1, 2 and 3 months or coppicing and interplanting at 6 months) will result in acceptable eucalypt stocking, if mortality is higher than 10% (remedial mitigation measure). Data from a re-establishment trial were analysed to determine which of the mitigation measures performed best in terms of stocking and growth. Coppicing and interplanting with larger plants was not a viable option as a mitigation measure for mortality as most of the coppice shoots have died. This may have been a result of frost. Although high re-establishment costs may be incurred, disaster clearing to waste followed by replanting is an option if mortality is unacceptably high (as opposed to leaving the stand as is). The results of this objective confirm that blanking as the current Best Operating Practice is still appropriate in South African forestry (i.e., try to have survival >90% and blank as soon as possible to retain >90% of stems). Blanked plants do contribute to volume, but for this to occur, blanking should be carried out within 4 weeks after planting to gain maximum benefit. In addition, it highlights the importance of implementing remedial mitigation measures to achieve >90% survival so as to gain maximum benefit. Using the outcomes from objectives 1-4, the fifth objective focussed on the development of a decision support system (DSS) for implementation of mitigation measures to improve survival within commercial eucalypt pulpwood plantations in South Africa. Improved survival starts with the implementation of good re-establishment practices and good quality planting stock. Mitigation measures for poor survival can be implemented either prior to re-establishment (before mortality occurs) or post re-establishment (after mortality has occurred). If poor survival still occurs after the implementation of good silviculture practices and pre-re-establishment mitigation practices (planting at higher densities), one should consider the various options available in terms of post re-establishment mitigation practices (remedial practices) such as blanking or replanting if mortality is high. Overall, the outcomes from this dissertation provide benchmark data and derived information as to the necessity for various mortality mitigation options within the commercial forestry sector in South Africa. In addition, the DSS will assist with decision making in terms of implementing the best silviculture practices and mitigation measures for improved survival during eucalypt re-establishment in South African pulpwood plantations. , Thesis (PhD) -- Faculty of Science, School of Natural Resource Science & Management, 2024
- Full Text:
- Date Issued: 2024-12
- Authors: Hechter, Ullrich
- Date: 2024-12
- Subjects: Eucalyptus -- Regeneration -- South Africa , Forests and forestry -- Economic aspects , Forests and forestry
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/68862 , vital:77135
- Description: Commercial forestry plantations in South Africa play an important role in the economy of the country, contributing 1.2% towards the gross domestic product. Currently plantation forests occupy 1.1% (1.2 million hectares) of the South African land surface, of which 75 000 hectares are re-established each year. Eucalypts constitute 43% of planted area, of which 88% is grown for pulpwood. Achieving high tree survival (>90%) is important in terms of optimising rotation-end yield. The industry origin of a 90% survival benchmark is unclear, although company procedures incorporate this as the minimum threshold in terms of re-establishment success. Past research indicates that most mortality occurs within a narrow period post-establishment and is often associated with substandard re-establishment practices and/or a stressed micro-environment. An improved understanding is needed about the various mitigation measures needed to minimize mortality during eucalypt re-establishment. Before making decisions related to mortality mitigation measures, comprehensive data are required as to their commercial applicability as well as outcomes from multiple trials that accurately quantify any impacts on tree survival and financial return. The overall purpose of this dissertation was the optimisation of Eucalyptus re-establishment practices for improved survival, growth and uniformity in South African pulpwood plantations. To achieve this, five inter-linked objectives were determined. The first objective was to highlight the most important factors contributing to increased mortality in eucalypt plantations during re-establishment. This was achieved through conducting a literature review. Citations were ranked in terms of credibility, with the importance ratings (derived from the literature sources) applied to the different factors affecting survival and growth during eucalypt re-establishment. Of the various factors impacting early eucalypt mortality, water stress and planting stock quality were considered highly important. The manner and quality of site preparation (soil and slash), planting practices (planting depth included), timing of planting (during dry, hot periods), various post-planting operations (incorrect fertiliser placement or herbicide drift) and insect pests and diseases also contribute to mortality, but to a lesser extent. These factors cannot be considered in isolation due to the complex interactions that exist between them and determining the primary causes of mortality can be elusive, especially as their impacts tend to be additive by nature. The second objective was to link survival to silvicultural treatments, site-related physiographic factors and climatic variables in South Africa. This was achieved by conducting an integrated analysis of 43 Eucalyptus trials. Of the seven re-establishment practices considered, watering, planting depth and fertiliser application were significant, with plant size, pitting method, residue management and insecticide application were not significant. However, when environmental variables were included within the analyses, there were significant site x treatment interactions for planting depth, plant size, residue management and fertiliser application. This highlights the importance of taking site related factors into consideration when interpreting the causes of mortality. The third objective was to determine the interaction between planting density and mortality on Eucalyptus growth, uniformity and financial yield at rotation end in South Africa. This was carried out to verify whether planting at different densities may be used as a preventative (before planting) mitigation measure. One trial was used to answer four keys sub-objectives: 1) The impact of three planting densities (1 102, 1 500, 1 959 SPH) with no mortality on yield at rotation-end; 2) The impact of mortality (0%, 10%, 20%, 30%, 40%) on rotation-end yield; 3) The quantification of tree performance when planting at a higher density and accepting a certain degree of mortality; and 4) The financial impact of different planting densities and mortality on rotation-end profit. Higher planting densities resulted in smaller individual trees, but with an increase in stand level performance. At rotation-end, lower mortality (0% and 10%) had significantly higher volumes ha-1 than the higher mortality (30% and 40%). Planting at higher densities (1 722 and 1 959 SPH) and accepting a certain degree of mortality resulted in non-significant differences for volume at rotation-end compared to the fully stocked 1 500 SPH treatment. A higher SPH resulted in a higher yield, but with an increase in estimated establishment/tending and harvesting costs. In contrast, an increase in mortality and/or lower SPH (in the absence of mortality) resulted in more variable stand growth, together with an increase in estimated machine harvesting productivity and reduced costs. Irrespective of SPH, the higher the mortality the greater the loss of income, with the best profit within each treatment related to full stocking (0% mortality). Within the higher panting densities, the profit gained following low mortality (10 and 20%) was similar to that of no mortality (0%), indicating that higher mortality may be tolerated when planting at higher densities, confirming the 90% survival threshold the industry aims to achieve post-establishment. The fourth objective was to determine if silviculture intervention (blanking at 1, 2 and 3 months or coppicing and interplanting at 6 months) will result in acceptable eucalypt stocking, if mortality is higher than 10% (remedial mitigation measure). Data from a re-establishment trial were analysed to determine which of the mitigation measures performed best in terms of stocking and growth. Coppicing and interplanting with larger plants was not a viable option as a mitigation measure for mortality as most of the coppice shoots have died. This may have been a result of frost. Although high re-establishment costs may be incurred, disaster clearing to waste followed by replanting is an option if mortality is unacceptably high (as opposed to leaving the stand as is). The results of this objective confirm that blanking as the current Best Operating Practice is still appropriate in South African forestry (i.e., try to have survival >90% and blank as soon as possible to retain >90% of stems). Blanked plants do contribute to volume, but for this to occur, blanking should be carried out within 4 weeks after planting to gain maximum benefit. In addition, it highlights the importance of implementing remedial mitigation measures to achieve >90% survival so as to gain maximum benefit. Using the outcomes from objectives 1-4, the fifth objective focussed on the development of a decision support system (DSS) for implementation of mitigation measures to improve survival within commercial eucalypt pulpwood plantations in South Africa. Improved survival starts with the implementation of good re-establishment practices and good quality planting stock. Mitigation measures for poor survival can be implemented either prior to re-establishment (before mortality occurs) or post re-establishment (after mortality has occurred). If poor survival still occurs after the implementation of good silviculture practices and pre-re-establishment mitigation practices (planting at higher densities), one should consider the various options available in terms of post re-establishment mitigation practices (remedial practices) such as blanking or replanting if mortality is high. Overall, the outcomes from this dissertation provide benchmark data and derived information as to the necessity for various mortality mitigation options within the commercial forestry sector in South Africa. In addition, the DSS will assist with decision making in terms of implementing the best silviculture practices and mitigation measures for improved survival during eucalypt re-establishment in South African pulpwood plantations. , Thesis (PhD) -- Faculty of Science, School of Natural Resource Science & Management, 2024
- Full Text:
- Date Issued: 2024-12
A comparison of implementation platforms for the visualisation of animal family trees
- Authors: Kanotangudza, Priviledge
- Date: 2024-04
- Subjects: Business intelligence -- Computer programs , Human-computer interaction , Computer science
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64105 , vital:73653
- Description: Genealogy is the study of family history. Family trees are used to show ancestry and visualise family history. Animal family trees are different from human family trees as animals have more offspring to represent in a family tree visualisation. Auctioneering organisations, such as Boere Korporasie Beperk (BKB), provide livestock auction catalogues containing pictures of the animal on sale, the animal’s family tree and its breeding and selection data. Modern-day farming has become data-driven and livestock farmers use various online devices and platforms to obtain information, such as real-time milk production, animal health monitoring and to manage farming operations. This study investigated and compared two Business Intelligence (BI) platforms namely Microsoft Power BI and Tableau (Salesforce) and the Python programming language used in the implementation of cattle family tree charts. Animal family tree visualisation requirements were identified from analysing data collected from 23 agriculture users and auction attendees who responded to an online questionnaire. The results of an online survey showed that agriculture users preferred an animal family tree that resembled a human one, which is not currently used in livestock auction catalogues. A conference paper was published based on the survey results. The Design Science Research Methodology (DSRM) was used to aid in creating animal family tree charts using Power BI, Tableau and Python. The author compared the visualisation tools against selected criteria, such as learnability, portability interoperability and security. Usability evaluations using eye tracking were conducted with agriculture users in a usability lab to compare the artefacts developed using Power BI and Python. Tableau was discarded during the implementation process as it did not produce the required family tree visualisation The Technology Acceptance Model (TAM) theory, which seeks to predict the acceptance and use of technology based on users' perception of its usefulness and ease of use, was used to guide the research study in evaluating the artefacts. According to TAM, the adoption of the proposed technology to solve the problem of a static animal family tree in livestock auction catalogues was dependent on the agriculture user’s beliefs. This was based upon that the technology would help them make better buying decisions at livestock auctions effortlessly. The other theory used in this study was the Task Technology Fit (TTF). This theory was used mainly to create the task list to be used in the usability test. The results showed that the author of this work and the agriculture users preferred the artefact produced by Power BI. The learnability and development time was shorter and the User Interface (UI) created was more intuitive. The findings of this study indicated that the present auction catalogue could be supplemented using interactive online animal family tree visualisations created using Power BI. This study recommended that livestock auctioneering organisations should, in addition to providing paper catalogues, provide farmers with an online platform to view the family trees of cattle on auction to enhance purchasing decisions. , Thesis (MCom) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Kanotangudza, Priviledge
- Date: 2024-04
- Subjects: Business intelligence -- Computer programs , Human-computer interaction , Computer science
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64105 , vital:73653
- Description: Genealogy is the study of family history. Family trees are used to show ancestry and visualise family history. Animal family trees are different from human family trees as animals have more offspring to represent in a family tree visualisation. Auctioneering organisations, such as Boere Korporasie Beperk (BKB), provide livestock auction catalogues containing pictures of the animal on sale, the animal’s family tree and its breeding and selection data. Modern-day farming has become data-driven and livestock farmers use various online devices and platforms to obtain information, such as real-time milk production, animal health monitoring and to manage farming operations. This study investigated and compared two Business Intelligence (BI) platforms namely Microsoft Power BI and Tableau (Salesforce) and the Python programming language used in the implementation of cattle family tree charts. Animal family tree visualisation requirements were identified from analysing data collected from 23 agriculture users and auction attendees who responded to an online questionnaire. The results of an online survey showed that agriculture users preferred an animal family tree that resembled a human one, which is not currently used in livestock auction catalogues. A conference paper was published based on the survey results. The Design Science Research Methodology (DSRM) was used to aid in creating animal family tree charts using Power BI, Tableau and Python. The author compared the visualisation tools against selected criteria, such as learnability, portability interoperability and security. Usability evaluations using eye tracking were conducted with agriculture users in a usability lab to compare the artefacts developed using Power BI and Python. Tableau was discarded during the implementation process as it did not produce the required family tree visualisation The Technology Acceptance Model (TAM) theory, which seeks to predict the acceptance and use of technology based on users' perception of its usefulness and ease of use, was used to guide the research study in evaluating the artefacts. According to TAM, the adoption of the proposed technology to solve the problem of a static animal family tree in livestock auction catalogues was dependent on the agriculture user’s beliefs. This was based upon that the technology would help them make better buying decisions at livestock auctions effortlessly. The other theory used in this study was the Task Technology Fit (TTF). This theory was used mainly to create the task list to be used in the usability test. The results showed that the author of this work and the agriculture users preferred the artefact produced by Power BI. The learnability and development time was shorter and the User Interface (UI) created was more intuitive. The findings of this study indicated that the present auction catalogue could be supplemented using interactive online animal family tree visualisations created using Power BI. This study recommended that livestock auctioneering organisations should, in addition to providing paper catalogues, provide farmers with an online platform to view the family trees of cattle on auction to enhance purchasing decisions. , Thesis (MCom) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-04
A methodology for modernising legacy web applications: subtitle if needed. If no subtitle follow instructions in manual
- Authors: Malgraff, Maxine
- Date: 2024-04
- Subjects: Management information systems , Information technology , Application software -- Development
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64148 , vital:73657
- Description: One problem faced in the Information Systems domain is that of poorly maintained, poorly documented, and/or unmanageable systems, known as Legacy Information Systems (LISs). As a result of the everchanging web development landscape, web applications have also become susceptible to the challenges faced in keeping up with technological advances, and older applications are starting to display the characteristics of becoming Legacy Web Applications (LWAs). As retaining business process support and meeting business requirements is often necessary, one method of recovering vital LWAs is to modernise them. System modernisation aims to recover business knowledge and provide an enhanced system that overcomes the problems plagued by LISs. When planning to modernise an LWA, guidance and support are essential to ensure that the modernisation exercise is performed efficiently and effectively. Modernisation methodologies can provide this required guidance and support as they provide models, tools and techniques that serve as guiding principles for the modernisation process. Although many modernisation methodologies exist, very few offer a comprehensive approach to modernisation that provides guidelines for each modernisation phase, tools to assist in the modernisation and techniques that can be used throughout. Existing methodologies also do not cater for cases that include both the LWA and migration to modernised web-specific environments. This research study aimed to investigate modernisation methodologies and identify which methodologies, or parts thereof, could be adapted for modernising LWAs. Existing methodologies were analysed and compared using the definition of a methodology, as well as other factors that improve the modernisation process. Modernisation case studies were reviewed to identify lessons learned from these studies so that these could be considered when planning an LWA modernisation. The ARTIST methodology was the most comprehensive modernisation methodology identified from those researched and was selected as the most appropriate methodology for modernising an LWA. ARTIST was modified to the mARTIST methodology to cater for web-based environments.mARTIST was used to modernise an existing LWA, called OldMax, at an automotive manufacturer, anonymously referred to as AutoCo, to determine its ability to support the modernisation of LWAs. Additional tools and evaluation methods were also investigated and used in place of those recommended by ARTIST, where deemed appropriate for the modernisation of OldMax. Limitations set by AutoCo on the hosting and technical environments for the modernised application also required ARTIST to be adapted to better suit the use case. The steps taken during this modernisation were documented and reported on to highlight the effectiveness of mARTIST and the tools used. The result of this modernisation was that the modernised web application, ModMax, was evaluated to determine the success of the modernisation. The modernisation of OldMax to ModMax, using the mARTIST methodology, was found to be successful based on the criteria set by the ARTIST methodology. Based on this, mARTIST can successfully be used for the modernisation of LWAs. To support future modernisations, an evaluation method for determining technical feasibility was developed for LWA, and alternate tools that could be used throughout modernisation exercises were recommended. , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Malgraff, Maxine
- Date: 2024-04
- Subjects: Management information systems , Information technology , Application software -- Development
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64148 , vital:73657
- Description: One problem faced in the Information Systems domain is that of poorly maintained, poorly documented, and/or unmanageable systems, known as Legacy Information Systems (LISs). As a result of the everchanging web development landscape, web applications have also become susceptible to the challenges faced in keeping up with technological advances, and older applications are starting to display the characteristics of becoming Legacy Web Applications (LWAs). As retaining business process support and meeting business requirements is often necessary, one method of recovering vital LWAs is to modernise them. System modernisation aims to recover business knowledge and provide an enhanced system that overcomes the problems plagued by LISs. When planning to modernise an LWA, guidance and support are essential to ensure that the modernisation exercise is performed efficiently and effectively. Modernisation methodologies can provide this required guidance and support as they provide models, tools and techniques that serve as guiding principles for the modernisation process. Although many modernisation methodologies exist, very few offer a comprehensive approach to modernisation that provides guidelines for each modernisation phase, tools to assist in the modernisation and techniques that can be used throughout. Existing methodologies also do not cater for cases that include both the LWA and migration to modernised web-specific environments. This research study aimed to investigate modernisation methodologies and identify which methodologies, or parts thereof, could be adapted for modernising LWAs. Existing methodologies were analysed and compared using the definition of a methodology, as well as other factors that improve the modernisation process. Modernisation case studies were reviewed to identify lessons learned from these studies so that these could be considered when planning an LWA modernisation. The ARTIST methodology was the most comprehensive modernisation methodology identified from those researched and was selected as the most appropriate methodology for modernising an LWA. ARTIST was modified to the mARTIST methodology to cater for web-based environments.mARTIST was used to modernise an existing LWA, called OldMax, at an automotive manufacturer, anonymously referred to as AutoCo, to determine its ability to support the modernisation of LWAs. Additional tools and evaluation methods were also investigated and used in place of those recommended by ARTIST, where deemed appropriate for the modernisation of OldMax. Limitations set by AutoCo on the hosting and technical environments for the modernised application also required ARTIST to be adapted to better suit the use case. The steps taken during this modernisation were documented and reported on to highlight the effectiveness of mARTIST and the tools used. The result of this modernisation was that the modernised web application, ModMax, was evaluated to determine the success of the modernisation. The modernisation of OldMax to ModMax, using the mARTIST methodology, was found to be successful based on the criteria set by the ARTIST methodology. Based on this, mARTIST can successfully be used for the modernisation of LWAs. To support future modernisations, an evaluation method for determining technical feasibility was developed for LWA, and alternate tools that could be used throughout modernisation exercises were recommended. , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-04
A model for measuring and predicting stress for software developers using vital signs and activities
- Authors: Hibbers, Ilze
- Date: 2024-04
- Subjects: Machine learning , Neural networks (Computer science) , Computer software developers
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63799 , vital:73614
- Description: Occupational stress is a well-recognised issue that affects individuals in various professions and industries. Reducing occupational stress has multiple benefits, such as improving employee's health and performance. This study proposes a model to measure and predict occupational stress using data collected in a real IT office environment. Different data sources, such as questionnaires, application software (RescueTime) and Fitbit smartwatches were used for collecting heart rate (HR), facial emotions, computer interactions, and application usage. The results of the Demand Control Support and Effort and Reward questionnaires indicated that the participants experienced high social support and an average level of workload. Participants also reported their daily perceived stress and workload level using a 5- point score. The perceived stress of the participants was overall neutral. There was no correlation found between HR, interactions, fear, and meetings. K-means and Bernoulli algorithms were applied to the dataset and two well-separated clusters were formed. The centroids indicated that higher heart rates were grouped either with meetings or had a higher difference in the center point values for interactions. Silhouette scores and 5-fold-validation were used to measure the accuracy of the clusters. However, these clusters were unable to predict the daily reported stress levels. Calculations were done on the computer usage data to measure interaction speeds and time spent working, in meetings, or away from the computer. These calculations were used as input into a decision tree with the reported daily stress levels. The results of the tree helped to identify which patterns lead to stressful days. The results indicated that days with high time pressure led to more reported stress. A new, more general tree was developed, which was able to predict 82 per cent of the daily stress reported. The main discovery of the research was that stress does not have a straightforward connection with computer interactions, facial emotions, or meetings. High interactions sometimes lead to stress and other times do not. So, predicting stress involves finding patterns and how data from different data sources interact with each other. Future work will revolve around validating the model in more office environments around South Africa. , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-04
A model for measuring and predicting stress for software developers using vital signs and activities
- Authors: Hibbers, Ilze
- Date: 2024-04
- Subjects: Machine learning , Neural networks (Computer science) , Computer software developers
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63799 , vital:73614
- Description: Occupational stress is a well-recognised issue that affects individuals in various professions and industries. Reducing occupational stress has multiple benefits, such as improving employee's health and performance. This study proposes a model to measure and predict occupational stress using data collected in a real IT office environment. Different data sources, such as questionnaires, application software (RescueTime) and Fitbit smartwatches were used for collecting heart rate (HR), facial emotions, computer interactions, and application usage. The results of the Demand Control Support and Effort and Reward questionnaires indicated that the participants experienced high social support and an average level of workload. Participants also reported their daily perceived stress and workload level using a 5- point score. The perceived stress of the participants was overall neutral. There was no correlation found between HR, interactions, fear, and meetings. K-means and Bernoulli algorithms were applied to the dataset and two well-separated clusters were formed. The centroids indicated that higher heart rates were grouped either with meetings or had a higher difference in the center point values for interactions. Silhouette scores and 5-fold-validation were used to measure the accuracy of the clusters. However, these clusters were unable to predict the daily reported stress levels. Calculations were done on the computer usage data to measure interaction speeds and time spent working, in meetings, or away from the computer. These calculations were used as input into a decision tree with the reported daily stress levels. The results of the tree helped to identify which patterns lead to stressful days. The results indicated that days with high time pressure led to more reported stress. A new, more general tree was developed, which was able to predict 82 per cent of the daily stress reported. The main discovery of the research was that stress does not have a straightforward connection with computer interactions, facial emotions, or meetings. High interactions sometimes lead to stress and other times do not. So, predicting stress involves finding patterns and how data from different data sources interact with each other. Future work will revolve around validating the model in more office environments around South Africa. , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-04
A process for integrated fitness and menstrual cycle data visualisations
- Authors: Taljaard, Isabelle
- Date: 2024-04
- Subjects: Human-computer interaction , Personal information management , Medical informatics -- Standards
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64379 , vital:73689
- Description: The increase in female participation in sport has led to an increase in research reporting on the relationship between fitness and menstrual cycle (F&M) data. Fitness variables such as VO2 max and heart rate are influenced by menstrual hormones and change with the different phases of a cycle. People frequently track both their F&M data, to understand their long-term activity and their body’s changes during the different cycle phases. Both these data sets are tracked and visualised separately to help people understand their data, however little work has been done to visualise the relationship between the two data sets. A process that guides the creation of an integrated F&M visualisation does not exist. This research aimed to develop and adopt a process that could be used to successfully guide the creation of an integrated F&M visualisation. The study followed the Design Science Research Methodology (DSRM) to create a primary and secondary artefact – the process and instantiation thereof. The DSRM was applied in iterative cycles where the process was developed, instantiations created and evaluated by participants. To develop the process, existing data processing and visualisation processes were reviewed from literature, to assess their successes and shortcomings. The review of existing processes revealed what steps, and factors related to those steps, would need to be considered. The process review highlighted the importance of five process steps: planning, collection, access, integration, and visualisation. Once the conceptual process was designed, it was adapted for the goal of creating an integrated F&M data visualisation. Prior to implementation, the process was first tested in a pilot study to ensure its validity before involving participants in data collection. After the process pilot study, the final implementation of the process took place and participants were recruited. In the first step of the process, the different fitness data types that are influenced by the menstrual cycle, and vice versa, were identified through a literature review. In the second step, devices to be used for data collection were evaluated and tested through exploratory testing and review of user manuals available online. The third and fourth steps, access, and integration were informed by further exploratory testing and review of relevant literature. The fifth step, data visualisation, was guided by relevant studies, Hick’s law, and the Schema Theory. Two Iterations of DSR were conducted in two phases. Phase 1 (P1) was the instantiation of the planning, collection, access, and processing steps. Participants wore smartwatches while going about their daily lives and working out and tracked their menstrual cycle to collect data. P1data was used to create several instantiations of the process. The second phase (P2) was the instantiation the visualisation step. The final visualisations, resulting from the instantiations, were evaluated by participants in P2. The review notes were used to improve both the process and the final visualisations. Both P1 and P2 were repeated (iterated) twice. The recommended process can be used by anyone who wants to create an integrated F&M visualisation and was designed to be modular so that users could choose to follow the whole process or only specific steps. The findings of this research can provide guidance to users, developers and smartwatch manufacturers of what people’s preferences are for these integrated visualisations. It also provides guidance for those who wish to create their own visualisations without needing prior programming experience or knowledge, since easy to use, online visualisation tools are recommended. The process instantiations will assist people, especially women, to better understand their menstrual cycle and how it affects their physical well-being. , Thesis (MCom) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Taljaard, Isabelle
- Date: 2024-04
- Subjects: Human-computer interaction , Personal information management , Medical informatics -- Standards
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64379 , vital:73689
- Description: The increase in female participation in sport has led to an increase in research reporting on the relationship between fitness and menstrual cycle (F&M) data. Fitness variables such as VO2 max and heart rate are influenced by menstrual hormones and change with the different phases of a cycle. People frequently track both their F&M data, to understand their long-term activity and their body’s changes during the different cycle phases. Both these data sets are tracked and visualised separately to help people understand their data, however little work has been done to visualise the relationship between the two data sets. A process that guides the creation of an integrated F&M visualisation does not exist. This research aimed to develop and adopt a process that could be used to successfully guide the creation of an integrated F&M visualisation. The study followed the Design Science Research Methodology (DSRM) to create a primary and secondary artefact – the process and instantiation thereof. The DSRM was applied in iterative cycles where the process was developed, instantiations created and evaluated by participants. To develop the process, existing data processing and visualisation processes were reviewed from literature, to assess their successes and shortcomings. The review of existing processes revealed what steps, and factors related to those steps, would need to be considered. The process review highlighted the importance of five process steps: planning, collection, access, integration, and visualisation. Once the conceptual process was designed, it was adapted for the goal of creating an integrated F&M data visualisation. Prior to implementation, the process was first tested in a pilot study to ensure its validity before involving participants in data collection. After the process pilot study, the final implementation of the process took place and participants were recruited. In the first step of the process, the different fitness data types that are influenced by the menstrual cycle, and vice versa, were identified through a literature review. In the second step, devices to be used for data collection were evaluated and tested through exploratory testing and review of user manuals available online. The third and fourth steps, access, and integration were informed by further exploratory testing and review of relevant literature. The fifth step, data visualisation, was guided by relevant studies, Hick’s law, and the Schema Theory. Two Iterations of DSR were conducted in two phases. Phase 1 (P1) was the instantiation of the planning, collection, access, and processing steps. Participants wore smartwatches while going about their daily lives and working out and tracked their menstrual cycle to collect data. P1data was used to create several instantiations of the process. The second phase (P2) was the instantiation the visualisation step. The final visualisations, resulting from the instantiations, were evaluated by participants in P2. The review notes were used to improve both the process and the final visualisations. Both P1 and P2 were repeated (iterated) twice. The recommended process can be used by anyone who wants to create an integrated F&M visualisation and was designed to be modular so that users could choose to follow the whole process or only specific steps. The findings of this research can provide guidance to users, developers and smartwatch manufacturers of what people’s preferences are for these integrated visualisations. It also provides guidance for those who wish to create their own visualisations without needing prior programming experience or knowledge, since easy to use, online visualisation tools are recommended. The process instantiations will assist people, especially women, to better understand their menstrual cycle and how it affects their physical well-being. , Thesis (MCom) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-04
A toolkit for successful workplace learning analytics at software vendors
- Authors: Whale, Alyssa Morgan
- Date: 2024-04
- Subjects: Computer-assisted instruction , Intelligent tutoring systems , Information visualisation
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/64448 , vital:73713
- Description: Software vendors commonly provide digital software training to their stakeholders and therefore are faced with the problem of an influx of data collected from these training/learning initiatives. Every second of every day, data is being collected based on online learning activities and learner behaviour. Thus, online platforms are struggling to cope with the volumes of data that are collected, and companies are finding it difficult to analyse and manage this data in a way that can be beneficial to all stakeholders. The majority of studies investigating learning analytics have been conducted in educational settings. This research aimed to develop and evaluate a toolkit that can be used for successful Workplace Learning Analytics (WLA) at software vendors. The study followed the Design Science Research (DSR) methodology, which was applied in iterative cycles where various components of the toolkit were designed, developed, and evaluated by participants. The real-world-context was a software vendor, ERPCo, which has been struggling to implement WLA successfully with their current Learning Experience Platform (LXP), as well as with their previous platform. Qualitative data was collected using document analysis of key company documents and Focus Group Discussions (FGDs) with employees from ERPCo to explore and confirm different topics and themes. These methods were used to iteratively analyse the As-Is and To-Be situations at ERPCo and to develop and evaluate the proposed WLA Toolkit. The method used to analyse the collected data from the FGDs was the Qualitative Content Analysis (QCA) method. To develop the first component of the toolkit, the Organisation component, the organisational success factors that influence the success of WLA were identified using a Systematic Literature Review (SLR). These factors were discussed and validated in two exploratory FGDs held with employees from ERPCo, one with operational stakeholders and the other with strategic decision makers. The DeLone and McLean Information Systems (D&M IS) Success Model was used to undergird the research as a theory to guide the understanding of the factors influencing the success of WLA. Many of the factors identified in theory were found to be prevalent in the real-world-context, with some additional ones being identified in the FGDs. The most frequent challenges highlighted by participants were related to visibility; readily available high-quality data; flexibility of reporting; complexity of reporting; and effective decision making and insights obtained. Many of these related to the concept of usability issues for both the system and the information, which is specifically related to System Quality or Information Quality from the D&M IS Success Model. The second and third components of the toolkit are the Technology and Applications; and Information components respectively. Therefore, architecture and data management challenges and requirements for these components were analysed. An appropriate WLA architecture was selected and then further customised for use at ERPCo. A third FGD was conducted with employees who had more technical roles in ERPCo. The purpose of this FGD was to provide input on the architecture, technologies and data management challenges and requirements. In the Technology and Applications component of the WLA Toolkit, factors influencing WLA success related to applications and visualisations were considered. An instantiation of this component was demonstrated in the fourth FGD, where learning data from the LXP at ERPCo was collected and a dashboard incorporating recommended visualisation techniques was developed as a proof of concept. In this FGD participants gave feedback on both the dashboard and the toolkit. The artefact of this research is the WLA Toolkit that can be used by practitioners to guide the planning and implementation of WLA in large organisations that use LXP and WLA platforms. Researchers can use the WLA Toolkit to gain a deeper understanding of the required components and factors for successful WLA in software vendors. The research also contributes to the D&M IS Success Model theory in the information economy. In support of this PhD dissertation, the following paper has been published: Whale, A. & Scholtz, B. 2022. A Theoretical Classification of Organizational Success Factors for Workplace Learning Analytics. NEXTCOMP 2022. Mauritius. A draft manuscript for a journal paper was in progress at the time of submitting this thesis. , Thesis (PhD) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics , 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Whale, Alyssa Morgan
- Date: 2024-04
- Subjects: Computer-assisted instruction , Intelligent tutoring systems , Information visualisation
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/64448 , vital:73713
- Description: Software vendors commonly provide digital software training to their stakeholders and therefore are faced with the problem of an influx of data collected from these training/learning initiatives. Every second of every day, data is being collected based on online learning activities and learner behaviour. Thus, online platforms are struggling to cope with the volumes of data that are collected, and companies are finding it difficult to analyse and manage this data in a way that can be beneficial to all stakeholders. The majority of studies investigating learning analytics have been conducted in educational settings. This research aimed to develop and evaluate a toolkit that can be used for successful Workplace Learning Analytics (WLA) at software vendors. The study followed the Design Science Research (DSR) methodology, which was applied in iterative cycles where various components of the toolkit were designed, developed, and evaluated by participants. The real-world-context was a software vendor, ERPCo, which has been struggling to implement WLA successfully with their current Learning Experience Platform (LXP), as well as with their previous platform. Qualitative data was collected using document analysis of key company documents and Focus Group Discussions (FGDs) with employees from ERPCo to explore and confirm different topics and themes. These methods were used to iteratively analyse the As-Is and To-Be situations at ERPCo and to develop and evaluate the proposed WLA Toolkit. The method used to analyse the collected data from the FGDs was the Qualitative Content Analysis (QCA) method. To develop the first component of the toolkit, the Organisation component, the organisational success factors that influence the success of WLA were identified using a Systematic Literature Review (SLR). These factors were discussed and validated in two exploratory FGDs held with employees from ERPCo, one with operational stakeholders and the other with strategic decision makers. The DeLone and McLean Information Systems (D&M IS) Success Model was used to undergird the research as a theory to guide the understanding of the factors influencing the success of WLA. Many of the factors identified in theory were found to be prevalent in the real-world-context, with some additional ones being identified in the FGDs. The most frequent challenges highlighted by participants were related to visibility; readily available high-quality data; flexibility of reporting; complexity of reporting; and effective decision making and insights obtained. Many of these related to the concept of usability issues for both the system and the information, which is specifically related to System Quality or Information Quality from the D&M IS Success Model. The second and third components of the toolkit are the Technology and Applications; and Information components respectively. Therefore, architecture and data management challenges and requirements for these components were analysed. An appropriate WLA architecture was selected and then further customised for use at ERPCo. A third FGD was conducted with employees who had more technical roles in ERPCo. The purpose of this FGD was to provide input on the architecture, technologies and data management challenges and requirements. In the Technology and Applications component of the WLA Toolkit, factors influencing WLA success related to applications and visualisations were considered. An instantiation of this component was demonstrated in the fourth FGD, where learning data from the LXP at ERPCo was collected and a dashboard incorporating recommended visualisation techniques was developed as a proof of concept. In this FGD participants gave feedback on both the dashboard and the toolkit. The artefact of this research is the WLA Toolkit that can be used by practitioners to guide the planning and implementation of WLA in large organisations that use LXP and WLA platforms. Researchers can use the WLA Toolkit to gain a deeper understanding of the required components and factors for successful WLA in software vendors. The research also contributes to the D&M IS Success Model theory in the information economy. In support of this PhD dissertation, the following paper has been published: Whale, A. & Scholtz, B. 2022. A Theoretical Classification of Organizational Success Factors for Workplace Learning Analytics. NEXTCOMP 2022. Mauritius. A draft manuscript for a journal paper was in progress at the time of submitting this thesis. , Thesis (PhD) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics , 2024
- Full Text:
- Date Issued: 2024-04
An in vitro evaluation of the anti-breast cancer activity of Nigella sativa extracts and its bioactive compound in combination with curcumin
- Authors: Botha, Susanna Gertruida
- Date: 2024-04
- Subjects: Herbs -- Therapeutic use , Radiation-protective agents , Breast -- Cancer -- Treatment
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63639 , vital:73571
- Description: Breast cancer constitutes 23% of all cancers in South African females. Curcumin and Nigella sativa have anti-cancer, anti-metastatic and antioxidant-properties and may be effective against breast cancer. This study focused on the effect of N. sativa extracts or thymoquinone and curcumin, individually and in combination, on breast cancer cells. An MTT assay showed that curcumin reduced cell viability by 50% (IC50) at 18 ± 2.63 μg/mL and thymoquinone (TQ) at 5 ± 0.95 μg/mL against the MDA-MB-231 cells. The IC50 values for curcumin and TQ were 35 ± 6.98 μg/mL and 4 ± 0.96 μg/mL against the MCF-7 cells, respectively. The IC50 value for the NSBE was determined to be 350 ± 55 μg/mL. The IC50 value of NSAE did not fall within the selected concentration range. Synergism was noted for combinations of NSBE with curcumin, and combinations of TQ with curcumin, against both MCF-7 and MDA-MB-231 cells. Two synergistic combinations per treatment per cell line, as determined by the combination index analysis, were chosen for further investigation. The combinations and individual treatments tested against the MCF-10A cells, were not significant, except for NSBE80:CURC20 combination. Curcumin had the most significant anti-oxidant activity; however, no link was noted between the anti-oxidant activity and the cytotoxicity of the combinations. The combination treatments induced apoptosis more effectively than the individual treatments. Caspase-3 dependent apoptosis was noted for NSBE10:CURC90 and TQ80:CURC20 combinations against the MDA-MB-231 cells, and the TQ60:CURC40 combination against the MCF-7 cells. The individual and combined treatments effectively reduced MDA-MB-231 cell adhesion to fibronectin, but not all reduced the cell adhesion to laminin. Based on these results, the combinations of curcumin with TQ or NSBE, have promising anticancer benefits against breast cancer. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Botha, Susanna Gertruida
- Date: 2024-04
- Subjects: Herbs -- Therapeutic use , Radiation-protective agents , Breast -- Cancer -- Treatment
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63639 , vital:73571
- Description: Breast cancer constitutes 23% of all cancers in South African females. Curcumin and Nigella sativa have anti-cancer, anti-metastatic and antioxidant-properties and may be effective against breast cancer. This study focused on the effect of N. sativa extracts or thymoquinone and curcumin, individually and in combination, on breast cancer cells. An MTT assay showed that curcumin reduced cell viability by 50% (IC50) at 18 ± 2.63 μg/mL and thymoquinone (TQ) at 5 ± 0.95 μg/mL against the MDA-MB-231 cells. The IC50 values for curcumin and TQ were 35 ± 6.98 μg/mL and 4 ± 0.96 μg/mL against the MCF-7 cells, respectively. The IC50 value for the NSBE was determined to be 350 ± 55 μg/mL. The IC50 value of NSAE did not fall within the selected concentration range. Synergism was noted for combinations of NSBE with curcumin, and combinations of TQ with curcumin, against both MCF-7 and MDA-MB-231 cells. Two synergistic combinations per treatment per cell line, as determined by the combination index analysis, were chosen for further investigation. The combinations and individual treatments tested against the MCF-10A cells, were not significant, except for NSBE80:CURC20 combination. Curcumin had the most significant anti-oxidant activity; however, no link was noted between the anti-oxidant activity and the cytotoxicity of the combinations. The combination treatments induced apoptosis more effectively than the individual treatments. Caspase-3 dependent apoptosis was noted for NSBE10:CURC90 and TQ80:CURC20 combinations against the MDA-MB-231 cells, and the TQ60:CURC40 combination against the MCF-7 cells. The individual and combined treatments effectively reduced MDA-MB-231 cell adhesion to fibronectin, but not all reduced the cell adhesion to laminin. Based on these results, the combinations of curcumin with TQ or NSBE, have promising anticancer benefits against breast cancer. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
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