IL-4/ IL-13 directed microglial activation and differentiation in response to LPS-induced neuroinflammation
- Authors: Ackerdien, Shiraz
- Date: 2024-04
- Subjects: Inflammation , Inflammation -- Treatment , Anti-inflammatory agents
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63606 , vital:73554
- Description: Microglia activation is a common hallmark of neuroinflammation that occurs during pathogen invasion or lipopolysaccharide (LPS)-induced inflammation. A neuroinflammatory response is elicited by the release of proinflammatory cytokines which stimulates microglia in an autocrine manner to be polarized into classically activated, pro-inflammatory M1 cells. Prolonged exposure to the inflammatory response can have disastrous effects on the central nervous system (CNS). However, microglia can alternatively be polarized into the activated M2 anti-inflammatory phenotype, but the exact molecular mechanism mediating this phenotypic switch remains poorly understood. Studies have shown that interleukin (IL)-4 can induce the M2 phenotype and activate the signal transducer and activator of the transcription 6 (STAT6) signalling pathway that in turn provokes a beneficial Th2 immune response. Since IL-4 and IL-13 share a common IL-4 receptor alpha (IL-4Rα) chain, it is possible that alternative microglia differentiation and its anti-inflammatory action also involve IL-13. This study aimed to investigate how IL-13 and STAT6 signalling orchestrates the microglial response and differentiation associated with LPS-induced inflammation. Furthermore, the molecular mechanisms that relieve LPS-induced neuroinflammation and neural protection through IL-13-enhanced BDNF signalling were also investigated. C8-B4 microglial cells were induced with LPS to exhibit an M1 pro-inflammatory phenotype or stimulated with IL-4 and/or IL-13 to exhibit an M2 anti-inflammatory microglial phenotype. The cell viability following LPS, IL-4, and/ or IL-13 exposure was determined. The LPS-induced neuroinflammatory response and the anti-inflammatory response induced by IL-4 and IL-13 which promotes STAT-6 signalling were determined by measuring TNFα, IL-1β, and BDNF protein concentrations using ELISA assays. The polarising effects of LPS and IL-4/IL-13 cytokines were also examined via changes in the expression of Iba-1, CD206, CD86, and STAT-6 determined by immunofluorescence analysis. These changes were further investigated by quantifying the mRNA transcripts of TNFα, IL-1 β, Arg-1, CD206, IL-4R, and STAT-6 and BDNF using qRT-PCR. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Ackerdien, Shiraz
- Date: 2024-04
- Subjects: Inflammation , Inflammation -- Treatment , Anti-inflammatory agents
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63606 , vital:73554
- Description: Microglia activation is a common hallmark of neuroinflammation that occurs during pathogen invasion or lipopolysaccharide (LPS)-induced inflammation. A neuroinflammatory response is elicited by the release of proinflammatory cytokines which stimulates microglia in an autocrine manner to be polarized into classically activated, pro-inflammatory M1 cells. Prolonged exposure to the inflammatory response can have disastrous effects on the central nervous system (CNS). However, microglia can alternatively be polarized into the activated M2 anti-inflammatory phenotype, but the exact molecular mechanism mediating this phenotypic switch remains poorly understood. Studies have shown that interleukin (IL)-4 can induce the M2 phenotype and activate the signal transducer and activator of the transcription 6 (STAT6) signalling pathway that in turn provokes a beneficial Th2 immune response. Since IL-4 and IL-13 share a common IL-4 receptor alpha (IL-4Rα) chain, it is possible that alternative microglia differentiation and its anti-inflammatory action also involve IL-13. This study aimed to investigate how IL-13 and STAT6 signalling orchestrates the microglial response and differentiation associated with LPS-induced inflammation. Furthermore, the molecular mechanisms that relieve LPS-induced neuroinflammation and neural protection through IL-13-enhanced BDNF signalling were also investigated. C8-B4 microglial cells were induced with LPS to exhibit an M1 pro-inflammatory phenotype or stimulated with IL-4 and/or IL-13 to exhibit an M2 anti-inflammatory microglial phenotype. The cell viability following LPS, IL-4, and/ or IL-13 exposure was determined. The LPS-induced neuroinflammatory response and the anti-inflammatory response induced by IL-4 and IL-13 which promotes STAT-6 signalling were determined by measuring TNFα, IL-1β, and BDNF protein concentrations using ELISA assays. The polarising effects of LPS and IL-4/IL-13 cytokines were also examined via changes in the expression of Iba-1, CD206, CD86, and STAT-6 determined by immunofluorescence analysis. These changes were further investigated by quantifying the mRNA transcripts of TNFα, IL-1 β, Arg-1, CD206, IL-4R, and STAT-6 and BDNF using qRT-PCR. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Investigation of the host potential of compounds derived from tartaric acid, succinic acid and 1,4-cyclohexanedioic acid
- Authors: Adam, Muhammad Ameen
- Date: 2024-04
- Subjects: Chemical reactions , Chemistry, Organic , Bacteriology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63617 , vital:73562
- Description: The present investigation considered the host behaviour of three compounds, namely (+)-(2R,3R)-1,1,4,4-tetraphenylbutane-1,2,3,4-tetraol (H1), 1,1,4,4-tetraphenyl-1,4-butanediol (H2) and cyclohexane-1,4-diylbis(diphenylmethanol) (H3) in various guest mixtures. These host compounds were readily synthesized by means of Grignard addition reactions on the diesters of tartaric acid, succinic acid and 1,4-cyclohexanedioic acid. The guest mixtures included cyclopentanone, cyclohexanone, cycloheptanone and cyclooctanone, γ-butyrolactone, 2-pyrrolidone, N-methyl-2-pyrrolidone and N-ethyl-2-pyrrolidone, and pyridine, 2-methylpyridine, 3-methylpyridine and 4-methylpyridine. Crystals of (+)-(2R,3R)-1,1,4,4-tetraphenylbutane-1,2,3,4-tetraol (H1) were grown from cyclopentanone (5-ONE), cyclohexanone (6-ONE), cycloheptanone (7-ONE) and cyclooctanone (8-ONE,) producing 1:1 host:guest complexes in each instance. Thermal analysis showed the thermal stabilities of these complexes to be in the order 6-ONE > 7-ONE > 8-ONE > 5-ONE which correlated exactly with results from binary guest/guest competition experiments, where 6-ONE was always preferred by H1, while 5-ONE was consistently disfavoured. Single crystal X-ray diffraction (SCXRD) analyses demonstrated that each guest compound was retained in the crystals by means of a hydrogen bond with an alcohol moiety of the host compound. Furthermore, preferred guests 6- and 7-ONE produced crystals with greater densities than guests less favoured (5- and 8-ONE). A conformational analysis of the guest geometries in the four complexes with H1 revealed that the low energy guest conformers were present. The host selectivity for 6- and 7-ONE was proposed to be due to the improved molecular packing in the crystals of the complexes containing these two guest compounds, observed from their higher crystal densities. Hirshfeld surface analyses were not useful in explaining the preference of H1 for 6-ONE relative to 7-ONE (these types of analyses were not possible for the 5-ONE and 8-ONE-containing inclusion compounds due to the nature and degree of disorder present in the guest molecules). H1 was also crystallized from γ-butyrolactone (GBL), 2-pyrrolidone (NP), N-methyl-2-pyrrolidone (NMP) and N-ethyl-2-pyrrolidone (NEP), and 1H-NMR spectroscopy revealed that all but GBL were included. The host compound was also presented with these guest solvents in various mixtures, and it was observed that NMP was an extremely favoured guest solvent, followed by NEP and NP, with GBL being consistently disfavoured in every experiment. It was therefore shown that in certain instances, H1 may serve as an alternative tool for separating some of these mixtures through host-guest chemistry strategies. The hydrogen bonding motifs present in each of the successfully formed complexes were extensively investigated through SCXRD analysis, as was the thermal behaviour of these complexes. In the latter instance, the peak temperature of the endotherm (from the DSC trace) representing the guest release was greater for the inclusion compound with favoured NMP (145.5 °C) relative to the complexes with NP (139.8 °C) and NEP (120.5 °C). Host compounds H2 and H3 were revealed to have the ability to include each of pyridine (PYR), 2-methylpyridine (2MP), 3-methylpyridine (3MP) and 4-methylpyridine (4MP). H2 displayed selective behaviour for 3MP and 4MP when presented with mixtures of these guest compounds, whilst H3 preferred PYR. In the latter case, this PYR-containing inclusion compound was also the more stable one (the guest release onset temperature was highest, Ton 66.0 °C). It was demonstrated that H2 has the ability to separate very many binary mixtures of these pyridines on a practical platform, since K (the selectivity coefficient) values were 10 or greater in many instances. However, unfortunately, the more difficult-to-separate mixtures containing 3MP and 4MP cannot be purified or separated by employing H2 and supramolecular chemistry strategies. H3 was also shown to be a likely candidate for binary guest separations in very many of the guest solutions considered here, where K was also 10 or greater, and even infinity in many cases. SCXRD demonstrated that 2MP, 3MP and 4MP were retained in the crystals of their complexes by means of classical hydrogen bonds with the host compound. Satisfyingly, this hydrogen bond between 2MP and H2 (3.0213(18) Å) was significantly longer than that between this host compound and both disorder components of 3MP (2.875(2) and 2.825(9) Å) and that between H2 and 4MP (2.8458(13) Å). This observation explains the affinity of H2 for both 3MP and 4MP, and why 2MP was disfavoured. The results of thermal experiments did not wholly concur with observations from the guest/guest competition experiments. Hirshfeld surface analyses were also conducted but were not entirely conclusive with respect to explaining the host selectivity behaviour. In the case of H3, SCXRD analyses revealed that favoured PYR experienced a classical hydrogen bond with the host compound that was statistically significantly shorter (2.795(2) Å, 165°) than those between the other guest compounds and H3. Additionally, this guest compound was the only one to be involved in a (host)C−H···π(guest) interaction (2.91 Å, 139°) and also a non-classical hydrogen bond with the host compound ((host)C−H···N−C(guest), 2.77 Å (144°)). Finally, Hirshfeld surface analyses showed also that preferred PYR experienced a greater percentage of C···H/H···C (33.1%) and H···N/N···H (11.1%) interactions compared with the complexes with 2MP, 3MP and 4MP. However, it is not clear whether these Hirshfeld observations explain the affinity of H3 for PYR. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Adam, Muhammad Ameen
- Date: 2024-04
- Subjects: Chemical reactions , Chemistry, Organic , Bacteriology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63617 , vital:73562
- Description: The present investigation considered the host behaviour of three compounds, namely (+)-(2R,3R)-1,1,4,4-tetraphenylbutane-1,2,3,4-tetraol (H1), 1,1,4,4-tetraphenyl-1,4-butanediol (H2) and cyclohexane-1,4-diylbis(diphenylmethanol) (H3) in various guest mixtures. These host compounds were readily synthesized by means of Grignard addition reactions on the diesters of tartaric acid, succinic acid and 1,4-cyclohexanedioic acid. The guest mixtures included cyclopentanone, cyclohexanone, cycloheptanone and cyclooctanone, γ-butyrolactone, 2-pyrrolidone, N-methyl-2-pyrrolidone and N-ethyl-2-pyrrolidone, and pyridine, 2-methylpyridine, 3-methylpyridine and 4-methylpyridine. Crystals of (+)-(2R,3R)-1,1,4,4-tetraphenylbutane-1,2,3,4-tetraol (H1) were grown from cyclopentanone (5-ONE), cyclohexanone (6-ONE), cycloheptanone (7-ONE) and cyclooctanone (8-ONE,) producing 1:1 host:guest complexes in each instance. Thermal analysis showed the thermal stabilities of these complexes to be in the order 6-ONE > 7-ONE > 8-ONE > 5-ONE which correlated exactly with results from binary guest/guest competition experiments, where 6-ONE was always preferred by H1, while 5-ONE was consistently disfavoured. Single crystal X-ray diffraction (SCXRD) analyses demonstrated that each guest compound was retained in the crystals by means of a hydrogen bond with an alcohol moiety of the host compound. Furthermore, preferred guests 6- and 7-ONE produced crystals with greater densities than guests less favoured (5- and 8-ONE). A conformational analysis of the guest geometries in the four complexes with H1 revealed that the low energy guest conformers were present. The host selectivity for 6- and 7-ONE was proposed to be due to the improved molecular packing in the crystals of the complexes containing these two guest compounds, observed from their higher crystal densities. Hirshfeld surface analyses were not useful in explaining the preference of H1 for 6-ONE relative to 7-ONE (these types of analyses were not possible for the 5-ONE and 8-ONE-containing inclusion compounds due to the nature and degree of disorder present in the guest molecules). H1 was also crystallized from γ-butyrolactone (GBL), 2-pyrrolidone (NP), N-methyl-2-pyrrolidone (NMP) and N-ethyl-2-pyrrolidone (NEP), and 1H-NMR spectroscopy revealed that all but GBL were included. The host compound was also presented with these guest solvents in various mixtures, and it was observed that NMP was an extremely favoured guest solvent, followed by NEP and NP, with GBL being consistently disfavoured in every experiment. It was therefore shown that in certain instances, H1 may serve as an alternative tool for separating some of these mixtures through host-guest chemistry strategies. The hydrogen bonding motifs present in each of the successfully formed complexes were extensively investigated through SCXRD analysis, as was the thermal behaviour of these complexes. In the latter instance, the peak temperature of the endotherm (from the DSC trace) representing the guest release was greater for the inclusion compound with favoured NMP (145.5 °C) relative to the complexes with NP (139.8 °C) and NEP (120.5 °C). Host compounds H2 and H3 were revealed to have the ability to include each of pyridine (PYR), 2-methylpyridine (2MP), 3-methylpyridine (3MP) and 4-methylpyridine (4MP). H2 displayed selective behaviour for 3MP and 4MP when presented with mixtures of these guest compounds, whilst H3 preferred PYR. In the latter case, this PYR-containing inclusion compound was also the more stable one (the guest release onset temperature was highest, Ton 66.0 °C). It was demonstrated that H2 has the ability to separate very many binary mixtures of these pyridines on a practical platform, since K (the selectivity coefficient) values were 10 or greater in many instances. However, unfortunately, the more difficult-to-separate mixtures containing 3MP and 4MP cannot be purified or separated by employing H2 and supramolecular chemistry strategies. H3 was also shown to be a likely candidate for binary guest separations in very many of the guest solutions considered here, where K was also 10 or greater, and even infinity in many cases. SCXRD demonstrated that 2MP, 3MP and 4MP were retained in the crystals of their complexes by means of classical hydrogen bonds with the host compound. Satisfyingly, this hydrogen bond between 2MP and H2 (3.0213(18) Å) was significantly longer than that between this host compound and both disorder components of 3MP (2.875(2) and 2.825(9) Å) and that between H2 and 4MP (2.8458(13) Å). This observation explains the affinity of H2 for both 3MP and 4MP, and why 2MP was disfavoured. The results of thermal experiments did not wholly concur with observations from the guest/guest competition experiments. Hirshfeld surface analyses were also conducted but were not entirely conclusive with respect to explaining the host selectivity behaviour. In the case of H3, SCXRD analyses revealed that favoured PYR experienced a classical hydrogen bond with the host compound that was statistically significantly shorter (2.795(2) Å, 165°) than those between the other guest compounds and H3. Additionally, this guest compound was the only one to be involved in a (host)C−H···π(guest) interaction (2.91 Å, 139°) and also a non-classical hydrogen bond with the host compound ((host)C−H···N−C(guest), 2.77 Å (144°)). Finally, Hirshfeld surface analyses showed also that preferred PYR experienced a greater percentage of C···H/H···C (33.1%) and H···N/N···H (11.1%) interactions compared with the complexes with 2MP, 3MP and 4MP. However, it is not clear whether these Hirshfeld observations explain the affinity of H3 for PYR. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Self-attentive vision in evolutionary robotics
- Authors: Botha, Bouwer
- Date: 2024-04
- Subjects: Evolutionary robotics , Robotics , Neural networks (Computer science)
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63628 , vital:73566
- Description: The autonomy of a robot refers to its ability to achieve a task in an environment with minimal human supervision. This may require autonomous solutions to be able to perceive their environment to inform their decisions. An inexpensive and highly informative way that robots can perceive the environment is through vision. The autonomy of a robot is reliant on the quality of the robotic controller. These controllers are the software interface between the robot and environment that determine the actions of the robot based on the perceived environment. Controllers are typically created using manual programming techniques, which become progressively more challenging with increasing complexity of both the robot and task. An alternative to manual programming is the use of machine learning techniques such as those used by Evolutionary Robotics (ER). ER is an area of research that investigates the automatic creation of controllers. Instead of manually programming a controller, an Evolutionary Algorithms can be used to evolve the controller through repeated interactions with the task environment. Employing the ER approach on camera-based controllers, however, has presented problems for conventional ER methods. Firstly, existing architectures that are capable of automatically processing images, have a large number of trained parameters. These architectures over-encumber the evolutionary process due to the large search space of possible configurations. Secondly, the evolution of complex controllers needs to be done in simulation, which requires either: (a) the construction of a photo-realistic virtual environment with accurate lighting, texturing and models or (b) potential reduction of the controller capability by simplifying the problem via image preprocessing. Any controller trained in simulation also raises the inherent concern of not being able to transfer to the real world. This study proposes a new technique for the evolution of camera-based controllers in ER, that aims to address the highlighted problems. The use of self-attention is proposed to facilitate the evolution of compact controllers that are able to evolve specialized sets of task-relevant features in unprocessed images by focussing on important image regions. Furthermore, a new neural network-based simulation approach, Generative Neuro-Augmented Vision (GNAV), is proposed to simplify simulation construction. GNAV makes use of random data collected in a simple virtual environment and the real world. A neural network is trained to overcome the visual discrepancies between these two environments. GNAV enables a controller to be trained in a simple simulated environment that appears similar to the real environment, while requiring minimal human supervision. The capabilities of the new technique were demonstrated using a series of real-world navigation tasks based on camera vision. Controllers utilizing the proposed self-attention mechanism were trained using GNAV and transferred to a real camera-equipped robot. The controllers were shown to be able to perform the same tasks in the real world. , Thesis (MSc) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Botha, Bouwer
- Date: 2024-04
- Subjects: Evolutionary robotics , Robotics , Neural networks (Computer science)
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63628 , vital:73566
- Description: The autonomy of a robot refers to its ability to achieve a task in an environment with minimal human supervision. This may require autonomous solutions to be able to perceive their environment to inform their decisions. An inexpensive and highly informative way that robots can perceive the environment is through vision. The autonomy of a robot is reliant on the quality of the robotic controller. These controllers are the software interface between the robot and environment that determine the actions of the robot based on the perceived environment. Controllers are typically created using manual programming techniques, which become progressively more challenging with increasing complexity of both the robot and task. An alternative to manual programming is the use of machine learning techniques such as those used by Evolutionary Robotics (ER). ER is an area of research that investigates the automatic creation of controllers. Instead of manually programming a controller, an Evolutionary Algorithms can be used to evolve the controller through repeated interactions with the task environment. Employing the ER approach on camera-based controllers, however, has presented problems for conventional ER methods. Firstly, existing architectures that are capable of automatically processing images, have a large number of trained parameters. These architectures over-encumber the evolutionary process due to the large search space of possible configurations. Secondly, the evolution of complex controllers needs to be done in simulation, which requires either: (a) the construction of a photo-realistic virtual environment with accurate lighting, texturing and models or (b) potential reduction of the controller capability by simplifying the problem via image preprocessing. Any controller trained in simulation also raises the inherent concern of not being able to transfer to the real world. This study proposes a new technique for the evolution of camera-based controllers in ER, that aims to address the highlighted problems. The use of self-attention is proposed to facilitate the evolution of compact controllers that are able to evolve specialized sets of task-relevant features in unprocessed images by focussing on important image regions. Furthermore, a new neural network-based simulation approach, Generative Neuro-Augmented Vision (GNAV), is proposed to simplify simulation construction. GNAV makes use of random data collected in a simple virtual environment and the real world. A neural network is trained to overcome the visual discrepancies between these two environments. GNAV enables a controller to be trained in a simple simulated environment that appears similar to the real environment, while requiring minimal human supervision. The capabilities of the new technique were demonstrated using a series of real-world navigation tasks based on camera vision. Controllers utilizing the proposed self-attention mechanism were trained using GNAV and transferred to a real camera-equipped robot. The controllers were shown to be able to perform the same tasks in the real world. , Thesis (MSc) -- 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
Herpetofaunal diversity and affiliations of the Okavango River Basin, with specific focus on the Angolan headwaters
- Authors: Conradie, Werner
- Date: 2024-04
- Subjects: Water conservation -- Okavango River Delta , Watersheds -- Okavango River -- Angola , Biodiversity -- Angola
- Language: English
- Type: Doctorate theses , text
- Identifier: http://hdl.handle.net/10948/63667 , vital:73576
- Description: Although Africa is reputed to possess some of the richest herpetofaunal diversities in the world, a number of areas remain poorly documented and thus inadequately conserved. One such area in particular is the south-eastern part of Angola. Angola endured a long struggle for independence with a protracted civil war that lasted for nearly three decades, leaving the status of the country’s biodiversity in turmoil. Over the past two decades, Angola has become more accessible for biodiversity surveys, opening up new opportunities to document these previously poorly studied areas and help conserve its biodiversity. South-eastern Angola is the water source of the world-renowned Okavango Delta. However very little is known about the biodiversity, diversity status and conservation significance of the headwaters supplying the largest inland delta in the world. To address this bias in sampling and to investigate the conservation importance of the region, a series of rapid biodiversity surveys of the Angolan Okavango River Basin were conducted between 2012 and 2019. This study contributed over 2150 individual records of amphibians and reptiles, representing 88 reptile and 43 amphibian species. At least 15 species were added to the growing country checklist, with the south-eastern region of Angola now comprising 113 reptile species and 51 amphibian species. Because of this study, the area is now one of the most species-rich and well-studied areas in Angola. This study provided the first genetic data for 26 species, and sequences containing Angolan specimens for the first time were generated for 80 species, of which 23 species have originally been described from Angola. Maximum likelihood and Bayesian inference analyses, supported by species delimitation analyses, were utilised to validate specific species statuses. This allowed for the description of five new species of snake, one gecko and two frogs for Angola. The material further contributed to the description of a new genus of snakes. Numerous undescribed and potentially cryptic species were identified, long-lasting taxonomic issues were resolved, and various taxonomic adjustments were emphasised. Further contributions of the material include assisting in the revision of targeted Angolan amphibian and reptile groups as well as large-scale phylogenetic studies across Africa. , Thesis (PhD) -- Faculty of Science, School of Natural Resource Science & Management, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Conradie, Werner
- Date: 2024-04
- Subjects: Water conservation -- Okavango River Delta , Watersheds -- Okavango River -- Angola , Biodiversity -- Angola
- Language: English
- Type: Doctorate theses , text
- Identifier: http://hdl.handle.net/10948/63667 , vital:73576
- Description: Although Africa is reputed to possess some of the richest herpetofaunal diversities in the world, a number of areas remain poorly documented and thus inadequately conserved. One such area in particular is the south-eastern part of Angola. Angola endured a long struggle for independence with a protracted civil war that lasted for nearly three decades, leaving the status of the country’s biodiversity in turmoil. Over the past two decades, Angola has become more accessible for biodiversity surveys, opening up new opportunities to document these previously poorly studied areas and help conserve its biodiversity. South-eastern Angola is the water source of the world-renowned Okavango Delta. However very little is known about the biodiversity, diversity status and conservation significance of the headwaters supplying the largest inland delta in the world. To address this bias in sampling and to investigate the conservation importance of the region, a series of rapid biodiversity surveys of the Angolan Okavango River Basin were conducted between 2012 and 2019. This study contributed over 2150 individual records of amphibians and reptiles, representing 88 reptile and 43 amphibian species. At least 15 species were added to the growing country checklist, with the south-eastern region of Angola now comprising 113 reptile species and 51 amphibian species. Because of this study, the area is now one of the most species-rich and well-studied areas in Angola. This study provided the first genetic data for 26 species, and sequences containing Angolan specimens for the first time were generated for 80 species, of which 23 species have originally been described from Angola. Maximum likelihood and Bayesian inference analyses, supported by species delimitation analyses, were utilised to validate specific species statuses. This allowed for the description of five new species of snake, one gecko and two frogs for Angola. The material further contributed to the description of a new genus of snakes. Numerous undescribed and potentially cryptic species were identified, long-lasting taxonomic issues were resolved, and various taxonomic adjustments were emphasised. Further contributions of the material include assisting in the revision of targeted Angolan amphibian and reptile groups as well as large-scale phylogenetic studies across Africa. , Thesis (PhD) -- Faculty of Science, School of Natural Resource Science & Management, 2024
- Full Text:
- Date Issued: 2024-04
Investigation of the synthesis and characterisation of spiro orthocarbonates and heterocyclic orthocarbonates
- Authors: Cuthbertson, Jarryd Pierre
- Date: 2024-04
- Subjects: Chemistry, Analytic , Analytical chemistry , Chemistry
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63678 , vital:73578
- Description: A series of mostly asymmetrical spiro orthocarbonates and heterospirocyclic derivatives of orthocarbonic acid was synthesized from 2,2-dichlorobenzodioxole and a number of difunctional reagents. A systematic study of the size of the chelate rings formed around the spirocentric carbon atom was conducted by selecting representative samples of aliphatic and aromatic diols. The feasibility and scope of potential starting materials used was expanded by reacting DCBD successfully with thiols. Molecular structures of these compounds were confirmed using diffraction studies on single crystals. All compounds were analyzed using multinuclear NMR. DFT calculations performed on the compounds allowed for the development of equations that can accurately predict 13C chemical shifts of SOCs. Furthermore, the experimental NMR spectroscopy gave rise to an increment shift system for the 13C NMR shifts allowing for further assignment of carbon atom positions in compounds with multiple possible bonding patterns. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Cuthbertson, Jarryd Pierre
- Date: 2024-04
- Subjects: Chemistry, Analytic , Analytical chemistry , Chemistry
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63678 , vital:73578
- Description: A series of mostly asymmetrical spiro orthocarbonates and heterospirocyclic derivatives of orthocarbonic acid was synthesized from 2,2-dichlorobenzodioxole and a number of difunctional reagents. A systematic study of the size of the chelate rings formed around the spirocentric carbon atom was conducted by selecting representative samples of aliphatic and aromatic diols. The feasibility and scope of potential starting materials used was expanded by reacting DCBD successfully with thiols. Molecular structures of these compounds were confirmed using diffraction studies on single crystals. All compounds were analyzed using multinuclear NMR. DFT calculations performed on the compounds allowed for the development of equations that can accurately predict 13C chemical shifts of SOCs. Furthermore, the experimental NMR spectroscopy gave rise to an increment shift system for the 13C NMR shifts allowing for further assignment of carbon atom positions in compounds with multiple possible bonding patterns. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Estimation of a generalist meso-carnivore (black-backed jackal) population from a fenced protected area
- Davidson-Phillips, Samuel Ralph
- Authors: Davidson-Phillips, Samuel Ralph
- Date: 2024-04
- Subjects: Wildlife conservation , Carnivorous animals -- Conservation , Carnivorous animals -- Ecology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63698 , vital:73589
- Description: Since 2017, landowners, field guides, and management staff have reported large groups of black-backed jackals (Lupullela mesomelas) (here-forward jackal) in the Welgevonden Game Reserve, Limpopo, South Africa. This is linked with several observations of jackals predating on various ungulate species, potentially leading to unintended consequences on prey populations. These observations combined with an apparent poor survival rate of impala (Aepyceros melampus) and continuous declines in their number led to the perception that jackals could be partly responsible. Several studies have attempted to describe the ecological role of jackals within multiple environments, most of which have proven to be variable and context dependent. Human-modified landscapes along with the fencing of protected areas, may have manipulated the role of jackal within these scenarios. Jackals are wide-ranging and generally not confined by fencing, therefore their population trends possibly fluctuate within these anthropogenic landscapes. Re-introduced apex predators have been shown to facilitate food (provision of carrion) and simultaneously suppress jackal (active killing), this, however, remains difficult to predict. Jackals are classified as facultative cooperative hunters, and the term describes how they hunt in groups opportunistically when suitable resources of prey are available. The indication by several studies that jackals do actively predate rather than only scavenge, illustrates that the species has the potential to cause declines in an ungulate population. It therefore appears erroneous to exclude the species in terms of predator-prey relationships, particularly for land managers of fenced protected areas. The first step to any ecological management is the understanding of population size and trends over time. Unfortunately, little to no reliable methods exist to assess or monitor jackal populations. A popular tool for cryptic and wide-ranging terrestrial carnivores is Spatial Capture Recapture (SCR) models, typically through a camera trap array. These often rely on individual identities and an imperfect detection process to derive a statistical estimate of a given area. Jackals have been assumed to be individually unidentifiable and therefore these methods have largely been excluded. To address this a pilot-targeted camera-trap survey was conducted to improve capture and image quality. Following the role of this procedure, semi-automated software was applied to test the feasibility of individual identifications of captured images. This resulted in a subset of 58 right and left identifiable flank images, compiled from the highest graded images (n = 220) using the open-source Interactive Individual IdentificationSystem Beta Contour 3.0 (I3S Contour). I3S Contour assists users by distinguishing between unique contours on independent flanks without omitting observer effort and ranking. The effectiveness of the identification procedure was evaluated using three software tool trials, namely Computer-aided Annotation, Manual Contour Annotation, and Manual Contour Annotation (MA-2), where MA-2 included additional user-defined meta-data to images. Results showed that jackals could be individually identified from camera trap images and thus opened up the use of previously excluded SCR methodologies. Utilising the jackal database derived from the identification procedures described a total of 28 complete identifications (both flanks matched), 32 left-sided and 36 right-sided captures were used. These were derived from two independent survey periods split between seasonality (Winter & Spring). Two SCR methods were compared, namely, the Spatially Explicit Camera Recapture (SECR) and the newly developed Spatial Presence-Absence (SPA) modelling approach. SECR relies on full individual identification linked to spatial locations to derive spatial parameters to estimate population densities. The SECR methodology has been considered the most precise and was thus used as the benchmark. SPA relies on detections only (i.e., without individual identities), along with informative or uninformative priors. This must be across a spatial array that has detectors close enough to allow for simultaneous detections during each occasion (< 24 hours). Comparisons between these model outputs indicated a high degree of confidence interval overlap; however, SPA had a consistently higher posterior mode density estimate (63-64% higher), where the coefficient of variation between outputs also indicated the SPA having a closer relative precision. The targeted survey results for both model outputs for 2021 did not appear unusually high when compared to other studies. To assess the WGR population size over the long term, opportunistic by-catch data from a nine-year leopard (Panthera pardus) camera survey (Panthera organisation) was utilised. Model outputs from each of the years indicated that population estimates remained relatively stable. This was an unexpected result as the SPA densities did not follow the detection observations. This could be attributed to M not being set high enough (200) and the model reaching the limit, resulting in similar outputs between years. An alternative explanation is where the station spacing is larger than the diameter of the home range, which may reduce spatial correlation. , Thesis (MSc) -- Faculty of Science, School of Natural Resource Science & Management, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Davidson-Phillips, Samuel Ralph
- Date: 2024-04
- Subjects: Wildlife conservation , Carnivorous animals -- Conservation , Carnivorous animals -- Ecology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63698 , vital:73589
- Description: Since 2017, landowners, field guides, and management staff have reported large groups of black-backed jackals (Lupullela mesomelas) (here-forward jackal) in the Welgevonden Game Reserve, Limpopo, South Africa. This is linked with several observations of jackals predating on various ungulate species, potentially leading to unintended consequences on prey populations. These observations combined with an apparent poor survival rate of impala (Aepyceros melampus) and continuous declines in their number led to the perception that jackals could be partly responsible. Several studies have attempted to describe the ecological role of jackals within multiple environments, most of which have proven to be variable and context dependent. Human-modified landscapes along with the fencing of protected areas, may have manipulated the role of jackal within these scenarios. Jackals are wide-ranging and generally not confined by fencing, therefore their population trends possibly fluctuate within these anthropogenic landscapes. Re-introduced apex predators have been shown to facilitate food (provision of carrion) and simultaneously suppress jackal (active killing), this, however, remains difficult to predict. Jackals are classified as facultative cooperative hunters, and the term describes how they hunt in groups opportunistically when suitable resources of prey are available. The indication by several studies that jackals do actively predate rather than only scavenge, illustrates that the species has the potential to cause declines in an ungulate population. It therefore appears erroneous to exclude the species in terms of predator-prey relationships, particularly for land managers of fenced protected areas. The first step to any ecological management is the understanding of population size and trends over time. Unfortunately, little to no reliable methods exist to assess or monitor jackal populations. A popular tool for cryptic and wide-ranging terrestrial carnivores is Spatial Capture Recapture (SCR) models, typically through a camera trap array. These often rely on individual identities and an imperfect detection process to derive a statistical estimate of a given area. Jackals have been assumed to be individually unidentifiable and therefore these methods have largely been excluded. To address this a pilot-targeted camera-trap survey was conducted to improve capture and image quality. Following the role of this procedure, semi-automated software was applied to test the feasibility of individual identifications of captured images. This resulted in a subset of 58 right and left identifiable flank images, compiled from the highest graded images (n = 220) using the open-source Interactive Individual IdentificationSystem Beta Contour 3.0 (I3S Contour). I3S Contour assists users by distinguishing between unique contours on independent flanks without omitting observer effort and ranking. The effectiveness of the identification procedure was evaluated using three software tool trials, namely Computer-aided Annotation, Manual Contour Annotation, and Manual Contour Annotation (MA-2), where MA-2 included additional user-defined meta-data to images. Results showed that jackals could be individually identified from camera trap images and thus opened up the use of previously excluded SCR methodologies. Utilising the jackal database derived from the identification procedures described a total of 28 complete identifications (both flanks matched), 32 left-sided and 36 right-sided captures were used. These were derived from two independent survey periods split between seasonality (Winter & Spring). Two SCR methods were compared, namely, the Spatially Explicit Camera Recapture (SECR) and the newly developed Spatial Presence-Absence (SPA) modelling approach. SECR relies on full individual identification linked to spatial locations to derive spatial parameters to estimate population densities. The SECR methodology has been considered the most precise and was thus used as the benchmark. SPA relies on detections only (i.e., without individual identities), along with informative or uninformative priors. This must be across a spatial array that has detectors close enough to allow for simultaneous detections during each occasion (< 24 hours). Comparisons between these model outputs indicated a high degree of confidence interval overlap; however, SPA had a consistently higher posterior mode density estimate (63-64% higher), where the coefficient of variation between outputs also indicated the SPA having a closer relative precision. The targeted survey results for both model outputs for 2021 did not appear unusually high when compared to other studies. To assess the WGR population size over the long term, opportunistic by-catch data from a nine-year leopard (Panthera pardus) camera survey (Panthera organisation) was utilised. Model outputs from each of the years indicated that population estimates remained relatively stable. This was an unexpected result as the SPA densities did not follow the detection observations. This could be attributed to M not being set high enough (200) and the model reaching the limit, resulting in similar outputs between years. An alternative explanation is where the station spacing is larger than the diameter of the home range, which may reduce spatial correlation. , Thesis (MSc) -- Faculty of Science, School of Natural Resource Science & Management, 2024
- Full Text:
- Date Issued: 2024-04
The Camdeboo-Mountain Zebra mega-reserve as an opportunity to protect viable populations of medium- to large-sized mammals
- Authors: Davis, Kristen
- Date: 2024-04
- Subjects: Mammals -- Ecology -- South Africa -- Eastern Cape , Conservation of natural resources -- South Africa -- Eastern Cape , Wildlife conservation -- South Africa -- Eastern Cape
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63711 , vital:73590
- Description: Conservation planning has focused extensively on representation of species in protected areas (PAs), rather than achieving the persistence of these species in PAs. Consequently, most PAs do not support viable populations of many species represented within them, particularly large mammals, resulting in extinction debt risks. The challenge is therefore to identify opportunities to achieve viable populations and to develop and implement conservation plans to achieve this, e.g., expand and connect existing PAs. A recent meta-analysis provides a minimum viable population (MVP) estimate of 5 000 individuals for mammals. This value was used as the target for modelling conservation opportunities for the South African endemic Cape mountain zebra (Equus zebra zebra), blesbok (Damaliscus pygargus phillipsi), black wildebeest (Connochaetes gnou) and co-existing medium- and large-sized mammal species. This study focused on the region between the Camdeboo and Mountain Zebra national parks (ca. 736 000 ha). Within the envisaged Camdeboo-Mountain Zebra (C-MZ) mega-reserve, a spreadsheet model was used to estimate potential herbivore population sizes, spatial requirement data were used to estimate potential omnivore and insectivore population sizes, and herbivore densities were used to estimate potential large carnivore population sizes. I show that 12 (the three endemic grazers and nine co-existing species) of the 28 modelled medium- and large-sized mammal species will potentially exceed 5 000 individuals, the MVP target, within the envisaged mega-reserve. The remaining 16 species show potential to reach substantial population sizes, however, will likely require ongoing metapopulation management. Using a conservation planning approach, I identify priority areas for the conservation of suitable habitat for Cape mountain zebra, blesbok, and black wildebeest within the envisaged mega-reserve, thus indirectly identifying priority areas for the conservation of these endemic species. I show that the potential incorporation of these priority areas within the envisaged mega-reserve will contribute considerably to the conservation of all focal species. In addition, the potential incorporation of these priority areas will contribute to PA expansion and significantly improve connectivity between existing PAs within the envisaged C-MZ mega-reserve. The importance of adequately-sized PAs to support viable populations of focal species is thus evident, and will ensure their long-term survival and ability to persist by allowing population and evolutionary scale processes. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Davis, Kristen
- Date: 2024-04
- Subjects: Mammals -- Ecology -- South Africa -- Eastern Cape , Conservation of natural resources -- South Africa -- Eastern Cape , Wildlife conservation -- South Africa -- Eastern Cape
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63711 , vital:73590
- Description: Conservation planning has focused extensively on representation of species in protected areas (PAs), rather than achieving the persistence of these species in PAs. Consequently, most PAs do not support viable populations of many species represented within them, particularly large mammals, resulting in extinction debt risks. The challenge is therefore to identify opportunities to achieve viable populations and to develop and implement conservation plans to achieve this, e.g., expand and connect existing PAs. A recent meta-analysis provides a minimum viable population (MVP) estimate of 5 000 individuals for mammals. This value was used as the target for modelling conservation opportunities for the South African endemic Cape mountain zebra (Equus zebra zebra), blesbok (Damaliscus pygargus phillipsi), black wildebeest (Connochaetes gnou) and co-existing medium- and large-sized mammal species. This study focused on the region between the Camdeboo and Mountain Zebra national parks (ca. 736 000 ha). Within the envisaged Camdeboo-Mountain Zebra (C-MZ) mega-reserve, a spreadsheet model was used to estimate potential herbivore population sizes, spatial requirement data were used to estimate potential omnivore and insectivore population sizes, and herbivore densities were used to estimate potential large carnivore population sizes. I show that 12 (the three endemic grazers and nine co-existing species) of the 28 modelled medium- and large-sized mammal species will potentially exceed 5 000 individuals, the MVP target, within the envisaged mega-reserve. The remaining 16 species show potential to reach substantial population sizes, however, will likely require ongoing metapopulation management. Using a conservation planning approach, I identify priority areas for the conservation of suitable habitat for Cape mountain zebra, blesbok, and black wildebeest within the envisaged mega-reserve, thus indirectly identifying priority areas for the conservation of these endemic species. I show that the potential incorporation of these priority areas within the envisaged mega-reserve will contribute considerably to the conservation of all focal species. In addition, the potential incorporation of these priority areas will contribute to PA expansion and significantly improve connectivity between existing PAs within the envisaged C-MZ mega-reserve. The importance of adequately-sized PAs to support viable populations of focal species is thus evident, and will ensure their long-term survival and ability to persist by allowing population and evolutionary scale processes. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
The Algoa Bay region groundwater cycle – linking source to coast
- Authors: Dodd, Carla
- Date: 2024-04
- Subjects: Ecohydrology , Hydrology , Groundwater -- Management
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63722 , vital:73592
- Description: Groundwater is a crucial component of freshwater supply globally, especially in water-scarce regions such as semi-arid climatic areas where surface water resources are climatically limited and further constrained during droughts. Groundwater resources are also important from an ecological perspective as they support numerous surface ecosystems including wetlands and rivers. Coastal groundwater discharge along the South African coast sustains supratidal spring-fed living microbialite ecosystems (SSLiME). These systems act as potential analogues for Earth’s earliest ecosystems and are therefore useful from a palaeoscientific and evolutionary perspective. The Southern Cape coast of South Africa is characterised by both fractured and intergranular aquifers and hosts the most extensive network of SSLiME reported globally. However, the region is frequently affected by water scarcity crises and consequently groundwater development and usage has increased. Yet, it is unclear to what extent coastal discharge is linked to inland aquifers and whether anthropogenic activities influence the quantity and quality of groundwater that flows into SSLiME. This thesis aims to assess the groundwater cycle of the Algoa Bay region along the Southern Cape coast by means of a multi-tracer study. Specifically, it endeavours to develop a better understanding of the hydrogeochemical connectivity between inland groundwater resources and coastal microbialite ecosystems. To achieve this, four groups of hydrochemical tracers were used: H- and O-isotope ratios, major cations and anions, organic micropollutants and macronutrients. Sampling strategies included monthly precipitation collection over twelve months (stable water isotopes), once-off groundwater collection from boreholes, inland springs and coastal discharge (all tracers). In addition, coastal groundwater discharge was sampled during a once-off repeat campaign (all tracers) and seasonally at selected sites (macronutrients). A local meteoric water line (LMWL) for the region was established and compared to the isotopic signature of groundwater. The results indicate that groundwater is likely recharged directly and with little evaporation. Furthermore, similarities in isotopic signatures between inland and coastal aquifer systems suggest some level of hydrogeological connectivity or similar environmental drivers of recharge, such as precipitation amount and moisture source. This is also supported by the physico-chemistry and major ionic composition of the groundwater samples. However, the major ion composition of groundwater is variable and, although it predominantly reflects the sodium-chloride nature of precipitation, lithological and spatial trends are apparent. For example, coastward trends such as increasing conductivity, calcium, total alkalinity, and nitrogen is evident. While isotopes and major ions inform on the environmental drivers and geogenic influence on groundwater recharge, the organic micropollutants and macronutrients provide insight into the nature of anthropogenic impacts on groundwater quality. Micropollutants quantified in the groundwater samples included artificial sweeteners, pharmaceuticals, a biocide, and an illicit drug. These compounds are mostly classed as wastewater indicators and indicate aquifer contamination from leaking reticulation systems and septic tanks. The highest concentrations are associated with the urban and coastal peri-urban areas, while groundwater from rural areas is often devoid of any micropollutants except sulfamic acid, which may be introduced during recharge from precipitation. Furthermore, the presence of selected compounds in groundwater discharge signifies that at least a component of the groundwater is derived from recent infiltration. Similarly, the macronutrient content of groundwater reflects the proximal land use. As such, coastal groundwater discharge sites adjacent to coastal villages reflect higher concentrations compared to rural sites. In addition, the nutrient load supplied to and discharged from SSLiME systems is quantified and the nutrient attenuation is estimated. This thesis contributes recent hydrogeochemical information for a structurally complex semi-arid area under both natural (drought conditions) and human (increased water use, degradation of aquifers) pressures. Collectively, the results indicate that coastal groundwater discharge is likely a mixture of both the intergranular and fractured aquifers and that anthropogenic activities in the hinterland is contaminating the groundwater. This study is an important addition to the baseline hydrological information available for the region and may be useful in terms of sustainable groundwater management strategies and development toward a socio-ecological optimum, especially as related to coastal microbialite system. , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Dodd, Carla
- Date: 2024-04
- Subjects: Ecohydrology , Hydrology , Groundwater -- Management
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63722 , vital:73592
- Description: Groundwater is a crucial component of freshwater supply globally, especially in water-scarce regions such as semi-arid climatic areas where surface water resources are climatically limited and further constrained during droughts. Groundwater resources are also important from an ecological perspective as they support numerous surface ecosystems including wetlands and rivers. Coastal groundwater discharge along the South African coast sustains supratidal spring-fed living microbialite ecosystems (SSLiME). These systems act as potential analogues for Earth’s earliest ecosystems and are therefore useful from a palaeoscientific and evolutionary perspective. The Southern Cape coast of South Africa is characterised by both fractured and intergranular aquifers and hosts the most extensive network of SSLiME reported globally. However, the region is frequently affected by water scarcity crises and consequently groundwater development and usage has increased. Yet, it is unclear to what extent coastal discharge is linked to inland aquifers and whether anthropogenic activities influence the quantity and quality of groundwater that flows into SSLiME. This thesis aims to assess the groundwater cycle of the Algoa Bay region along the Southern Cape coast by means of a multi-tracer study. Specifically, it endeavours to develop a better understanding of the hydrogeochemical connectivity between inland groundwater resources and coastal microbialite ecosystems. To achieve this, four groups of hydrochemical tracers were used: H- and O-isotope ratios, major cations and anions, organic micropollutants and macronutrients. Sampling strategies included monthly precipitation collection over twelve months (stable water isotopes), once-off groundwater collection from boreholes, inland springs and coastal discharge (all tracers). In addition, coastal groundwater discharge was sampled during a once-off repeat campaign (all tracers) and seasonally at selected sites (macronutrients). A local meteoric water line (LMWL) for the region was established and compared to the isotopic signature of groundwater. The results indicate that groundwater is likely recharged directly and with little evaporation. Furthermore, similarities in isotopic signatures between inland and coastal aquifer systems suggest some level of hydrogeological connectivity or similar environmental drivers of recharge, such as precipitation amount and moisture source. This is also supported by the physico-chemistry and major ionic composition of the groundwater samples. However, the major ion composition of groundwater is variable and, although it predominantly reflects the sodium-chloride nature of precipitation, lithological and spatial trends are apparent. For example, coastward trends such as increasing conductivity, calcium, total alkalinity, and nitrogen is evident. While isotopes and major ions inform on the environmental drivers and geogenic influence on groundwater recharge, the organic micropollutants and macronutrients provide insight into the nature of anthropogenic impacts on groundwater quality. Micropollutants quantified in the groundwater samples included artificial sweeteners, pharmaceuticals, a biocide, and an illicit drug. These compounds are mostly classed as wastewater indicators and indicate aquifer contamination from leaking reticulation systems and septic tanks. The highest concentrations are associated with the urban and coastal peri-urban areas, while groundwater from rural areas is often devoid of any micropollutants except sulfamic acid, which may be introduced during recharge from precipitation. Furthermore, the presence of selected compounds in groundwater discharge signifies that at least a component of the groundwater is derived from recent infiltration. Similarly, the macronutrient content of groundwater reflects the proximal land use. As such, coastal groundwater discharge sites adjacent to coastal villages reflect higher concentrations compared to rural sites. In addition, the nutrient load supplied to and discharged from SSLiME systems is quantified and the nutrient attenuation is estimated. This thesis contributes recent hydrogeochemical information for a structurally complex semi-arid area under both natural (drought conditions) and human (increased water use, degradation of aquifers) pressures. Collectively, the results indicate that coastal groundwater discharge is likely a mixture of both the intergranular and fractured aquifers and that anthropogenic activities in the hinterland is contaminating the groundwater. This study is an important addition to the baseline hydrological information available for the region and may be useful in terms of sustainable groundwater management strategies and development toward a socio-ecological optimum, especially as related to coastal microbialite system. , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
The demographic-specific prey preferences of lions and cheetahs, and potential impacts on prey populations
- Authors: Dreyer, Nicola Bondi
- Date: 2024-04
- Subjects: Predation (Biology) , Animal populations , Animal ecology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63733 , vital:73593
- Description: Understanding prey selection offers predictive insights into predator-prey interactions, which can be extended to explore the impacts of predators on prey populations. Prey availability and vulnerability vary across species, demographic classes, body sizes, and seasons. Traditional prey selection models for large carnivores, based on estimates of prey body size, assume uniform vulnerability across prey demographic classes and seasons, failing to account for these variations. This study aims to contrast seasonal shifts in demographic-specific prey preferences between lions and cheetahs and examine the potential impact of their demographic-specific predation patterns on a range of prey species across a body size spectrum. It was predicted that cheetahs would shift their selection from adults and juveniles of smaller prey species in the dry season to neonates and juveniles of both smaller and larger prey species in the wet season, while lions would select adults irrespective of the season. Additionally, predation focusing on adults would have a greater impact on prey populations compared to predation focusing on non-adults. Furthermore, it was predicted that prey populations experiencing demographic-specific selection from both lions and cheetahs would be impacted more than species selected by only one predator. Degrees of preference (DOP) were estimated based on prey availability (camera traps) and prey use (GPS clusters) for lion and cheetah populations in Lapalala Wilderness Reserve. Generalized Additive Models for Location, Scale, and Shape (GAMLSS) were used to determine seasonal shifts in demographic-specific prey preferences. The seasonal-demographic specific predation patterns of lion and cheetah, along with prey vital rates extracted from the literature, were then used to model potential predation impacts on prey populations using both Leslie-Usher and Lefkovitch matrix models. Lions preferred larger adult prey such as blue wildebeest, eland, and buffalo, while cheetahs preferred smaller prey, particularly juveniles of small to intermediate-sized species like impala, kudu, blue wildebeest, and zebra. Both predators showed seasonal shifts in demographic-specific prey preferences, with lions selecting adult buffalo during the dry season and juvenile buffalo in the wet season, and cheetahs selecting juveniles in the dry season and neonates and juveniles during the wet season. Lions and cheetahs exerted the highest degree of top-down limitations on their preferred prey. Predation on adult prey had a greater effect on prey population growth rates than predation on non-adults, especially in the dry season. Intermediate-sized prey species experienced the highest predation pressures, while larger prey species were more affected than smaller ones, contrary to the size-nested predation hypothesis. My study represents a first effort in the southern hemisphere to model the demographic impacts of multiple predators on diverse prey species, incorporating seasonal and demographic-specific prey preferences. The findings emphasise the importance of incorporating prey demographics and seasonality in predator-prey studies as these refined studies have implications for the management and conservation of both predator and prey populations. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Dreyer, Nicola Bondi
- Date: 2024-04
- Subjects: Predation (Biology) , Animal populations , Animal ecology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63733 , vital:73593
- Description: Understanding prey selection offers predictive insights into predator-prey interactions, which can be extended to explore the impacts of predators on prey populations. Prey availability and vulnerability vary across species, demographic classes, body sizes, and seasons. Traditional prey selection models for large carnivores, based on estimates of prey body size, assume uniform vulnerability across prey demographic classes and seasons, failing to account for these variations. This study aims to contrast seasonal shifts in demographic-specific prey preferences between lions and cheetahs and examine the potential impact of their demographic-specific predation patterns on a range of prey species across a body size spectrum. It was predicted that cheetahs would shift their selection from adults and juveniles of smaller prey species in the dry season to neonates and juveniles of both smaller and larger prey species in the wet season, while lions would select adults irrespective of the season. Additionally, predation focusing on adults would have a greater impact on prey populations compared to predation focusing on non-adults. Furthermore, it was predicted that prey populations experiencing demographic-specific selection from both lions and cheetahs would be impacted more than species selected by only one predator. Degrees of preference (DOP) were estimated based on prey availability (camera traps) and prey use (GPS clusters) for lion and cheetah populations in Lapalala Wilderness Reserve. Generalized Additive Models for Location, Scale, and Shape (GAMLSS) were used to determine seasonal shifts in demographic-specific prey preferences. The seasonal-demographic specific predation patterns of lion and cheetah, along with prey vital rates extracted from the literature, were then used to model potential predation impacts on prey populations using both Leslie-Usher and Lefkovitch matrix models. Lions preferred larger adult prey such as blue wildebeest, eland, and buffalo, while cheetahs preferred smaller prey, particularly juveniles of small to intermediate-sized species like impala, kudu, blue wildebeest, and zebra. Both predators showed seasonal shifts in demographic-specific prey preferences, with lions selecting adult buffalo during the dry season and juvenile buffalo in the wet season, and cheetahs selecting juveniles in the dry season and neonates and juveniles during the wet season. Lions and cheetahs exerted the highest degree of top-down limitations on their preferred prey. Predation on adult prey had a greater effect on prey population growth rates than predation on non-adults, especially in the dry season. Intermediate-sized prey species experienced the highest predation pressures, while larger prey species were more affected than smaller ones, contrary to the size-nested predation hypothesis. My study represents a first effort in the southern hemisphere to model the demographic impacts of multiple predators on diverse prey species, incorporating seasonal and demographic-specific prey preferences. The findings emphasise the importance of incorporating prey demographics and seasonality in predator-prey studies as these refined studies have implications for the management and conservation of both predator and prey populations. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Evaluating elephant, Loxodonta africana, space-use and elephant-linked vegetation change in Liwonde National Park, Malawi
- Authors: Evers, Emma Else Maria
- Date: 2024-04
- Subjects: Elephants -- Nutrition -- Malawi , Ecological heterogeneity , Vegetation and climate
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63744 , vital:73594
- Description: Heterogeneity, the spatio-temporal variation of abiotic and biotic factors, is a key concept that underpins many ecological phenomena and promotes biodiversity. Ecosystem engineers, such as African savanna elephants (hereafter elephant), Loxodonta africana, are organisms capable of affecting heterogeneity through the creation or modification of habitats. Thus, their impacts can have important consequences for ecosystem biodiversity, both positive and negative. Caughley’s “elephant problem” cautions that confined or compressed, growing elephant populations will inevitably lead to a loss of biodiversity. However, a shift in our understanding of elephants suggests that not all elephant impacts lead to negative biodiversity consequences, as long as there is a heterogeneous spread of elephant impacts that allows for spatio-temporal refuges promoting the persistence of both impact-tolerant and impact-intolerant species. To date, little empirical evidence is available in support of managing elephants under this paradigm and few studies are available that infer the consequences of the distribution of elephant impacts on biodiversity. In addition, most studies use parametric statistics that do not account for scale, spatial autocorrelation, or non-stationarity, leading to a misrepresentation of the underlying processes and patterns of drivers of elephant space-use and the consequences of their impacts on biodiversity. Here, I evaluate spatio-temporal patterns and drivers of elephant space-use, and how the distribution of their impacts affects biodiversity through vegetation changes, using a multi-scaled spatial approach, in Liwonde National Park, Malawi. My study demonstrates that elephant space-use in Liwonde is heterogeneous, leading to spatio-temporal variation in the distribution of their impacts, even in a small, fenced reserve. The importance of the drivers of this heterogeneous space-use varied based on the scale of analysis, water was generally important at larger scales while vegetation quality (indexed by NDVI) was more important at smaller scales. When examined using local models, my results suggest that relationships exhibit non-stationarity, what is important in one area of the park is not necessarily important in other areas. The spatio-temporal variation of the inferred impacts of elephants in Liwonde still allowed for spatio-temporal refuges to be created, no clear linear relationship was found between elephant return intervals and woody species structural and functional diversity (indexed by changes in tree cover and changes in annual regrowth using Normalized Difference Vegetation Index as a measure, respectively) throughout the park. My study provides support for adopting the heterogeneity paradigm for managing elephants and demonstrates that not all elephant impacts result in negative vegetation change. I also demonstrate the crucial implications of accounting for scale, non-stationarity, and spatial autocorrelation to evaluate how animals both respond to, and contribute to, environmental heterogeneity. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Evers, Emma Else Maria
- Date: 2024-04
- Subjects: Elephants -- Nutrition -- Malawi , Ecological heterogeneity , Vegetation and climate
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63744 , vital:73594
- Description: Heterogeneity, the spatio-temporal variation of abiotic and biotic factors, is a key concept that underpins many ecological phenomena and promotes biodiversity. Ecosystem engineers, such as African savanna elephants (hereafter elephant), Loxodonta africana, are organisms capable of affecting heterogeneity through the creation or modification of habitats. Thus, their impacts can have important consequences for ecosystem biodiversity, both positive and negative. Caughley’s “elephant problem” cautions that confined or compressed, growing elephant populations will inevitably lead to a loss of biodiversity. However, a shift in our understanding of elephants suggests that not all elephant impacts lead to negative biodiversity consequences, as long as there is a heterogeneous spread of elephant impacts that allows for spatio-temporal refuges promoting the persistence of both impact-tolerant and impact-intolerant species. To date, little empirical evidence is available in support of managing elephants under this paradigm and few studies are available that infer the consequences of the distribution of elephant impacts on biodiversity. In addition, most studies use parametric statistics that do not account for scale, spatial autocorrelation, or non-stationarity, leading to a misrepresentation of the underlying processes and patterns of drivers of elephant space-use and the consequences of their impacts on biodiversity. Here, I evaluate spatio-temporal patterns and drivers of elephant space-use, and how the distribution of their impacts affects biodiversity through vegetation changes, using a multi-scaled spatial approach, in Liwonde National Park, Malawi. My study demonstrates that elephant space-use in Liwonde is heterogeneous, leading to spatio-temporal variation in the distribution of their impacts, even in a small, fenced reserve. The importance of the drivers of this heterogeneous space-use varied based on the scale of analysis, water was generally important at larger scales while vegetation quality (indexed by NDVI) was more important at smaller scales. When examined using local models, my results suggest that relationships exhibit non-stationarity, what is important in one area of the park is not necessarily important in other areas. The spatio-temporal variation of the inferred impacts of elephants in Liwonde still allowed for spatio-temporal refuges to be created, no clear linear relationship was found between elephant return intervals and woody species structural and functional diversity (indexed by changes in tree cover and changes in annual regrowth using Normalized Difference Vegetation Index as a measure, respectively) throughout the park. My study provides support for adopting the heterogeneity paradigm for managing elephants and demonstrates that not all elephant impacts result in negative vegetation change. I also demonstrate the crucial implications of accounting for scale, non-stationarity, and spatial autocorrelation to evaluate how animals both respond to, and contribute to, environmental heterogeneity. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
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
Lion and leopard diet and dispersal in human-dominated landscapes
- Authors: Forbes, Ryan Edward
- Date: 2024-04
- Subjects: Carnivora -- South Africa , Carnivorous animals -- Conservation , Carnivorous animals -- Ecology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63766 , vital:73596
- Description: Terrestrial carnivore population declines are driven by habitat loss and fragmentation, prey-depletion, persecution, and retaliatory killings. Population strongholds now centre on protected areas, that face increasing human pressure, resulting in population isolation, declining prey populations, and livestock intrusion. I therefore aimed to investigate dispersal and connectivity, and diets of lions (Panthera leo) and leopards (P. pardus) in response to human-use and wildlife density gradients in the Greater Limpopo Transfrontier Conservation Area (GLTCA). Firstly, I investigated dispersal and connectivity for these carnivores across the GLTCA, using single nucleotide polymorphisms. I present evidence that in the prey-depleted Mozambique portion of the GLTCA, lion and leopard dispersal distances are higher compared with the prey-abundant Kruger National Park (KNP). I also provide the first evidence for long-range dispersal in female lions. Despite evidence for connectivity occurring across the GLTCA, I recorded population structuring across the region for both carnivores, likely due to habitat fragmentation by human activities in the Mozambique portion of the GLTCA. I then assessed carnivore diet responses to prey depletion and livestock availability by comparing lion and leopard diets in the prey-abundant/livestock-absent KNP (South Africa), with the prey-depleted/livestock-abundant Limpopo National Park (LNP, Mozambique), using scat analyses. Lions and leopards downshifted their prey size selection in LNP relative to KNP. Despite both carnivores expanding their dietary niche breadths in LNP relative to KNP, diet overlap did not differ between sites. This suggests that even when prey is depleted, lions and leopards can partition food resources, which likely limits competition. Despite cattle (Bos taurus) being the most abundant ungulate in LNP, lions and leopards strongly avoided cattle, supporting the notion that carnivores can perceive the risk of hunting livestock and modulate their foraging behaviour to reduce human-carnivore conflict. Should my findings reflect general patterns in carnivore dispersal and diet responses to human-use and wildlife gradients, then carnivore conservation initiates across their range should focus on prey population rehabilitation, improved livestock husbandry practices, the establishment of effective dispersal corridors and improved human-tolerance towards large carnivores. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Forbes, Ryan Edward
- Date: 2024-04
- Subjects: Carnivora -- South Africa , Carnivorous animals -- Conservation , Carnivorous animals -- Ecology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63766 , vital:73596
- Description: Terrestrial carnivore population declines are driven by habitat loss and fragmentation, prey-depletion, persecution, and retaliatory killings. Population strongholds now centre on protected areas, that face increasing human pressure, resulting in population isolation, declining prey populations, and livestock intrusion. I therefore aimed to investigate dispersal and connectivity, and diets of lions (Panthera leo) and leopards (P. pardus) in response to human-use and wildlife density gradients in the Greater Limpopo Transfrontier Conservation Area (GLTCA). Firstly, I investigated dispersal and connectivity for these carnivores across the GLTCA, using single nucleotide polymorphisms. I present evidence that in the prey-depleted Mozambique portion of the GLTCA, lion and leopard dispersal distances are higher compared with the prey-abundant Kruger National Park (KNP). I also provide the first evidence for long-range dispersal in female lions. Despite evidence for connectivity occurring across the GLTCA, I recorded population structuring across the region for both carnivores, likely due to habitat fragmentation by human activities in the Mozambique portion of the GLTCA. I then assessed carnivore diet responses to prey depletion and livestock availability by comparing lion and leopard diets in the prey-abundant/livestock-absent KNP (South Africa), with the prey-depleted/livestock-abundant Limpopo National Park (LNP, Mozambique), using scat analyses. Lions and leopards downshifted their prey size selection in LNP relative to KNP. Despite both carnivores expanding their dietary niche breadths in LNP relative to KNP, diet overlap did not differ between sites. This suggests that even when prey is depleted, lions and leopards can partition food resources, which likely limits competition. Despite cattle (Bos taurus) being the most abundant ungulate in LNP, lions and leopards strongly avoided cattle, supporting the notion that carnivores can perceive the risk of hunting livestock and modulate their foraging behaviour to reduce human-carnivore conflict. Should my findings reflect general patterns in carnivore dispersal and diet responses to human-use and wildlife gradients, then carnivore conservation initiates across their range should focus on prey population rehabilitation, improved livestock husbandry practices, the establishment of effective dispersal corridors and improved human-tolerance towards large carnivores. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Elephant impacts on plant diversity and structure in the Shamwari Private Game Reserve
- Authors: Halvey, Andrew Lloyd
- Date: 2024-04
- Subjects: Elephants -- Nutrition -- South Africa -- Eastern Cape , Elephants -- Habitat -- South Africa -- Eastern Cape , Shamwari Game Reserve (South Africa)
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63777 , vital:73597
- Description: Many African landscapes rely on processes such as fire, tree-fall and drought in addition to herbivores to initiate change across the landscape. In the Eastern Cape, elephant have a significant impact on the community structure and diversity of the vegetation they live in. This is most likely the case for the Albany Valley Thicket and azonal riparian vegetation of Shamwari Private Game Reserve, where browsing animals, particularly megaherbivores like the black rhinoceros and elephant, are the main cause of defoliation. The presence of large herbivores creates challenges when it comes to long-term sustainability and biodiversity of the vegetation in Shamwari. Vegetation monitoring provides essential information for effective management of megaherbivores not only in Shamwari but in many other similar reserves. The aim of this study was to design a monitoring plan for the Albany Valley Thicket and riparian vegetation in Shamwari using available vegetation metrics. The vegetation was measured in permanent plots (90 m line intercept analysis per plot) in the Albany Valley Thicket and riparian vegetation of Shamwari. Plot selection was based on thicket structural integrity using NDVI score as a proxy. In all plots, thicket structure was assessed using canopy heights measured every 50 cm along the line. Detrended correspondence analysis of the species abundance data suggested three distinct structural and compositional vegetation states for thicket and riparian vegetation: dense, intermediate and open. Significant relationships between NDVI and vegetation structural metrics across the condition states indicated that NDVI could be used as a proxy for vegetation condition. Vegetation compositional metrics, however, were not always correlated to NDVI and determining species diversity for the vegetation presents additional information useful for monitoring. The monitoring recommended for the reserve is to evaluate vegetation structural integrity annually in summer using NDVI. Areas of change could then be measured for diversity as well as for change in the abundance of selected plant indicator species. This information should be used to initiate management actions if unwanted change has occurred. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Halvey, Andrew Lloyd
- Date: 2024-04
- Subjects: Elephants -- Nutrition -- South Africa -- Eastern Cape , Elephants -- Habitat -- South Africa -- Eastern Cape , Shamwari Game Reserve (South Africa)
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63777 , vital:73597
- Description: Many African landscapes rely on processes such as fire, tree-fall and drought in addition to herbivores to initiate change across the landscape. In the Eastern Cape, elephant have a significant impact on the community structure and diversity of the vegetation they live in. This is most likely the case for the Albany Valley Thicket and azonal riparian vegetation of Shamwari Private Game Reserve, where browsing animals, particularly megaherbivores like the black rhinoceros and elephant, are the main cause of defoliation. The presence of large herbivores creates challenges when it comes to long-term sustainability and biodiversity of the vegetation in Shamwari. Vegetation monitoring provides essential information for effective management of megaherbivores not only in Shamwari but in many other similar reserves. The aim of this study was to design a monitoring plan for the Albany Valley Thicket and riparian vegetation in Shamwari using available vegetation metrics. The vegetation was measured in permanent plots (90 m line intercept analysis per plot) in the Albany Valley Thicket and riparian vegetation of Shamwari. Plot selection was based on thicket structural integrity using NDVI score as a proxy. In all plots, thicket structure was assessed using canopy heights measured every 50 cm along the line. Detrended correspondence analysis of the species abundance data suggested three distinct structural and compositional vegetation states for thicket and riparian vegetation: dense, intermediate and open. Significant relationships between NDVI and vegetation structural metrics across the condition states indicated that NDVI could be used as a proxy for vegetation condition. Vegetation compositional metrics, however, were not always correlated to NDVI and determining species diversity for the vegetation presents additional information useful for monitoring. The monitoring recommended for the reserve is to evaluate vegetation structural integrity annually in summer using NDVI. Areas of change could then be measured for diversity as well as for change in the abundance of selected plant indicator species. This information should be used to initiate management actions if unwanted change has occurred. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
Synthesis and applications of hydroxyl-functionalized chemosensors for selective detection of ions in aqueous systems
- Authors: Hamukoshi, Simeon Shiweda
- Date: 2024-04
- Subjects: Molecular recognition , Solution (Chemistry) , Water chemistry
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63787 , vital:73613
- Description: Fluorescent molecular chemosensors are crucial tools for monitoring toxic metal ions and environmental compounds that pose risks to both humans and wildlife. Continuous sensing is essential for early detection, and chemosensors offer a sensitive and straightforward approach by detecting challenging analyte’s through optical absorption and fluorescence. Current detection methods, such as flame photometry and mass spectrometry, can be expensive, destructive, and impractical for continuous monitoring. Consequently, fluorescent-based methods present a promising, simple, and highly sensitive alternative for chemical recognition and monitoring. In this project, we successfully synthesized ten highly selective small hydroxyl containing molecule fluorescent and colorimetric sensors; Oxime Dye (OD), Small Sensor 1 (SS1), Small Sensor 2 (SS2), Quinoline Dye 1 (QD1), Quinoline Dye 2 (QD2), Quinoline Dye 3 (QD3), Coumarin Dye 1 (CD1), Coumarin Dye 2 (CD2), Naphthalene Dye 1 (ND1), Naphthalene Dye 2 (ND2). These chemosensors contained benzothiazole, naphthalene, quinoline, and coumarin fluorophores. These sensors facilitate both quantitative and qualitative assessment of cationic and anionic species in aqueous organic media. The chemosensors were synthesized using modified Schiff base, azo dye, and oxime-based reactions, enhancing binding and selectivity with analyte’s. They exhibited selectivity towards various metal ions (Cu2+, Fe2+, Ni2+, and Hg2+) and anions (hydroxyl and cyanate), characterized by distinct absorption bands and significant fluorescent quenching and enhancement. While some sensors were selective towards both cations and anions, others exclusively targeted cations, showing lower selectivity or sensitivity towards anions upon further testing. Conversely, certain sensors were selective towards anions, demonstrating reduced sensitivity or selectivity towards the tested cations. The oxime-based chemosensor, OD, was obtained through an oxime-based reaction. The sensor demonstrates remarkable selectivity for Cu2+ and cyanate ions. During titration experiments, the interaction of Cu2+ with OD resulted in a noticeable fluorescence quenching effect, while the presence of OCN ions led to fluorescence enhancement. These distinct behaviors strongly suggest the formation of specific 1:1 complexes between OD and Cu2+ or OCN ions, a conclusion supported by detailed analysis using the Jobs plot technique. In addition to the fluorescence studies, investigations into the influence of pH on the sensor OD, as well as its complexes with Cu2+ and OCN, were conducted to determine the optimum pH conditions for their operation. Moreover, reversible behavior of the complexes was explored in the presence of EDTA, revealing that only the OD-OCN complex displayed reversibility. Furthermore, molecular modeling studies were performed to validate the binding units and calculate the energy differences between the sensor and its respective complexes. Additionally, four chemosensors (SS1, SS2, CD2, and QD2) were synthesized and characterized using Schiff-based reactions, showcasing their unique absorption behaviors. SS1 and SS2, characterized by benzothiazole fluorophores, demonstrated high sensitivity to hydroxyl anions. Jobs plot studies revealed a stable 1:1 binding stoichiometry. Chemosensor CD2, incorporating a coumarin fluorophore, was structurally confirmed but showed no significant spectral changes when screened with various ions. Chemosensor QD2 exhibited remarkable selectivity for Fe2+ ions, and stable 1:1 complexes were confirmed. Further molecular modeling studies were conducted to identify potential binding sites. Furthermore, five chemosensors (CD1, CD3, QD1, ND1, and ND2) were synthesized and characterized using azo dye reactions, revealing their unique absorption behaviors. Chemosensor CD1 showed high selectivity towards Hg2+ under both absorption and emission spectroscopy. Job's plot studies confirmed a stable 1:1 complex formation. The presence of competing cations did not affect complex formation, emphasizing its stability and selectivity. Another coumarin-containing dye chemosensor, CD3, was synthesized as a novel chemosensor. In the presence of TBA anionic solutions, CD3 exhibited strong absorption bands and selectivity for OH- ions, forming a stable complex with them. Quantitative studies, including the determination of LOD and LOQ, were also conducted. The binding stoichiometry of 1:1 between CD3 and OH- was established through Job's plot analysis. Lastly, two naphthalene dyes were synthesized. However, they did not exhibit selectivity towards cations or anions. Interestingly, their absorption spectra were affected by the change in solvent system, a concept worth exploring in future work. Chemosensor ND1 and ND2 did not show any cation or anion selectivity. However, they demonstrated different spectra and colour responses to cations and anions in different water-DMSO solvent systems. , Thesis (PhD) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Hamukoshi, Simeon Shiweda
- Date: 2024-04
- Subjects: Molecular recognition , Solution (Chemistry) , Water chemistry
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/63787 , vital:73613
- Description: Fluorescent molecular chemosensors are crucial tools for monitoring toxic metal ions and environmental compounds that pose risks to both humans and wildlife. Continuous sensing is essential for early detection, and chemosensors offer a sensitive and straightforward approach by detecting challenging analyte’s through optical absorption and fluorescence. Current detection methods, such as flame photometry and mass spectrometry, can be expensive, destructive, and impractical for continuous monitoring. Consequently, fluorescent-based methods present a promising, simple, and highly sensitive alternative for chemical recognition and monitoring. In this project, we successfully synthesized ten highly selective small hydroxyl containing molecule fluorescent and colorimetric sensors; Oxime Dye (OD), Small Sensor 1 (SS1), Small Sensor 2 (SS2), Quinoline Dye 1 (QD1), Quinoline Dye 2 (QD2), Quinoline Dye 3 (QD3), Coumarin Dye 1 (CD1), Coumarin Dye 2 (CD2), Naphthalene Dye 1 (ND1), Naphthalene Dye 2 (ND2). These chemosensors contained benzothiazole, naphthalene, quinoline, and coumarin fluorophores. These sensors facilitate both quantitative and qualitative assessment of cationic and anionic species in aqueous organic media. The chemosensors were synthesized using modified Schiff base, azo dye, and oxime-based reactions, enhancing binding and selectivity with analyte’s. They exhibited selectivity towards various metal ions (Cu2+, Fe2+, Ni2+, and Hg2+) and anions (hydroxyl and cyanate), characterized by distinct absorption bands and significant fluorescent quenching and enhancement. While some sensors were selective towards both cations and anions, others exclusively targeted cations, showing lower selectivity or sensitivity towards anions upon further testing. Conversely, certain sensors were selective towards anions, demonstrating reduced sensitivity or selectivity towards the tested cations. The oxime-based chemosensor, OD, was obtained through an oxime-based reaction. The sensor demonstrates remarkable selectivity for Cu2+ and cyanate ions. During titration experiments, the interaction of Cu2+ with OD resulted in a noticeable fluorescence quenching effect, while the presence of OCN ions led to fluorescence enhancement. These distinct behaviors strongly suggest the formation of specific 1:1 complexes between OD and Cu2+ or OCN ions, a conclusion supported by detailed analysis using the Jobs plot technique. In addition to the fluorescence studies, investigations into the influence of pH on the sensor OD, as well as its complexes with Cu2+ and OCN, were conducted to determine the optimum pH conditions for their operation. Moreover, reversible behavior of the complexes was explored in the presence of EDTA, revealing that only the OD-OCN complex displayed reversibility. Furthermore, molecular modeling studies were performed to validate the binding units and calculate the energy differences between the sensor and its respective complexes. Additionally, four chemosensors (SS1, SS2, CD2, and QD2) were synthesized and characterized using Schiff-based reactions, showcasing their unique absorption behaviors. SS1 and SS2, characterized by benzothiazole fluorophores, demonstrated high sensitivity to hydroxyl anions. Jobs plot studies revealed a stable 1:1 binding stoichiometry. Chemosensor CD2, incorporating a coumarin fluorophore, was structurally confirmed but showed no significant spectral changes when screened with various ions. Chemosensor QD2 exhibited remarkable selectivity for Fe2+ ions, and stable 1:1 complexes were confirmed. Further molecular modeling studies were conducted to identify potential binding sites. Furthermore, five chemosensors (CD1, CD3, QD1, ND1, and ND2) were synthesized and characterized using azo dye reactions, revealing their unique absorption behaviors. Chemosensor CD1 showed high selectivity towards Hg2+ under both absorption and emission spectroscopy. Job's plot studies confirmed a stable 1:1 complex formation. The presence of competing cations did not affect complex formation, emphasizing its stability and selectivity. Another coumarin-containing dye chemosensor, CD3, was synthesized as a novel chemosensor. In the presence of TBA anionic solutions, CD3 exhibited strong absorption bands and selectivity for OH- ions, forming a stable complex with them. Quantitative studies, including the determination of LOD and LOQ, were also conducted. The binding stoichiometry of 1:1 between CD3 and OH- was established through Job's plot analysis. Lastly, two naphthalene dyes were synthesized. However, they did not exhibit selectivity towards cations or anions. Interestingly, their absorption spectra were affected by the change in solvent system, a concept worth exploring in future work. Chemosensor ND1 and ND2 did not show any cation or anion selectivity. However, they demonstrated different spectra and colour responses to cations and anions in different water-DMSO solvent systems. , Thesis (PhD) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 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
Exploring the role of herbivory in Albany Subtropical Thicket restoration
- Authors: Hunt, Kristen Louise
- Date: 2024-04
- Subjects: Shrubs -- South Africa , Portulacaria afra -- South Africa , Grasslands -- South Africa , Plant communities -- South Africa
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64060 , vital:73647
- Description: This dissertation attempted to investigate the influence of herbivory on the success of thicket restoration, addressing a critical gap in the current knowledge within the restoration initiative. Despite two decades of thicket restoration practices, the role of herbivory in influencing restoration success has been assumed and not yet quantified. This research aimed to observe and identify herbivore species and their interactions that may affect the survival of Portulacaria afra Jacq. material planted in thicket restoration contexts. This research took place on three game farms serving as case studies within the Albany Subtropical Thicket (Eastern Cape, South Africa). Multiple experiments were conducted to assess how the concept of different “natural refugia” might impact herbivore interactions with planted material, incorporating factors such as planting around rainfall, within open and semi-intact vegetation patches, and in proximity to water sources. Trail cameras were used for real-time monitoring of herbivore interactions within planted sites to understand and quantify herbivore interactions with P. afra cuttings and how they may impact plant survival. Results from the trail camera monitoring (Chapter 2) indicate varied herbivore interactions occurring on planted material, with the primary herbivore responsible for these interactions varying among farms. Species interactions were not consistent across farms, and herbivore interactions exhibited spatial and temporal variability. Notably, interactions declined soon after the start of the wet phase when surrounding vegetation could recover, indicating the influences of alternative forage availability on herbivore foraging choices. Different herbivore interactions were identified and quantified through trail camera images, ranging from minor biomass removal (estimated at <5 cm of stem and leaf material) to more detrimental actions such as uprooting and leaf stripping. Consistently, planted P. afra survival rates (Chapter 3) were significantly higher for protected material than those exposed to herbivores, regardless of whether planted in a dry or wet phase. Moreover, when exposed to herbivores, rooted material had significantly higher survival rates than unrooted material, indicating the potential advantage of a well-developed root system in faster recovery after a herbivory event. This research explored the influence of various factors, including rainfall, rooting state, protection, surrounding vegetation, and proximity to water, on P. afra survival and how some of these factors may affect P. afra survival in relation to herbivore interactions (Chapter 3). Significant differences in cutting survival were observed between dry and wet phases, rooted and unrooted material, and material protected vs exposed to herbivores. While survival was not significantly different in experiments involving surrounding vegetation and proximity to water, potential patterns were identified, warranting further investigation. A clipping and defoliation experiment under simulated seasonal conditions emphasised the significance of , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Hunt, Kristen Louise
- Date: 2024-04
- Subjects: Shrubs -- South Africa , Portulacaria afra -- South Africa , Grasslands -- South Africa , Plant communities -- South Africa
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64060 , vital:73647
- Description: This dissertation attempted to investigate the influence of herbivory on the success of thicket restoration, addressing a critical gap in the current knowledge within the restoration initiative. Despite two decades of thicket restoration practices, the role of herbivory in influencing restoration success has been assumed and not yet quantified. This research aimed to observe and identify herbivore species and their interactions that may affect the survival of Portulacaria afra Jacq. material planted in thicket restoration contexts. This research took place on three game farms serving as case studies within the Albany Subtropical Thicket (Eastern Cape, South Africa). Multiple experiments were conducted to assess how the concept of different “natural refugia” might impact herbivore interactions with planted material, incorporating factors such as planting around rainfall, within open and semi-intact vegetation patches, and in proximity to water sources. Trail cameras were used for real-time monitoring of herbivore interactions within planted sites to understand and quantify herbivore interactions with P. afra cuttings and how they may impact plant survival. Results from the trail camera monitoring (Chapter 2) indicate varied herbivore interactions occurring on planted material, with the primary herbivore responsible for these interactions varying among farms. Species interactions were not consistent across farms, and herbivore interactions exhibited spatial and temporal variability. Notably, interactions declined soon after the start of the wet phase when surrounding vegetation could recover, indicating the influences of alternative forage availability on herbivore foraging choices. Different herbivore interactions were identified and quantified through trail camera images, ranging from minor biomass removal (estimated at <5 cm of stem and leaf material) to more detrimental actions such as uprooting and leaf stripping. Consistently, planted P. afra survival rates (Chapter 3) were significantly higher for protected material than those exposed to herbivores, regardless of whether planted in a dry or wet phase. Moreover, when exposed to herbivores, rooted material had significantly higher survival rates than unrooted material, indicating the potential advantage of a well-developed root system in faster recovery after a herbivory event. This research explored the influence of various factors, including rainfall, rooting state, protection, surrounding vegetation, and proximity to water, on P. afra survival and how some of these factors may affect P. afra survival in relation to herbivore interactions (Chapter 3). Significant differences in cutting survival were observed between dry and wet phases, rooted and unrooted material, and material protected vs exposed to herbivores. While survival was not significantly different in experiments involving surrounding vegetation and proximity to water, potential patterns were identified, warranting further investigation. A clipping and defoliation experiment under simulated seasonal conditions emphasised the significance of , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2024
- Full Text:
- Date Issued: 2024-04
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
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
Preparation and Investigation of coumarin-based chemosensors towards sensing of ions using UV studies in aqueous systems
- Authors: Kotze, Tyla
- Date: 2024-04
- Subjects: Chemistry, Analytic , Water chemistry , Ionic solutions , Aquatic ecology , Geochemistry
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64116 , vital:73654
- Description: Humanity's unrelenting expansion has shown little regard for the environment, and this has resulted in tons of toxic heavy metal cations and anions being released into the environment through industrial, agricultural, electronic, and mining dumping. The release of these toxic heavy metals can cause diseases and sometimes lead to death, especially in third-world countries with low-income that reside in informal settlements, who suffer the most. Furthermore, the release of these toxins eventually finds their way back into the environment through bioaccumulation in fish, plants and animals. Although there is an ever need for the growth of these industries; low-cost, sensitive, selective, and organic-based sensors is a positive step forward in highlighting the need for environmental restoration and remediation, whilst striving to avoid unnecessary disease and death through this development. In this project, coumarin-based chemosensors for the detection of cationic and anionic species in aqueous and organic media are described. This project involves the synthesis of six different coumarin-based ether derivatives (E2-E5) and coumarin-based ester derivatives (H1-H2). FT-IR, 1H NMR and 13C NMR were used to confirm the structures of all sensors. The abilities of these novel compounds as chemosensors for detection of cations and anions were investigated using UV-vis analysis. These compounds displayed a favourable interaction with Fe2+ and Fe3+ ions with an increase in absorbance. Ether derivatives E2-E5 did not display any degree of selectivity or sensitivity towards the chosen anions. It was found that in the presence of FeCl2, sensors H1 and H2 displayed a degree of selectivities and further investigations were therefore carried out. From the titration experiments, the limit of detection, limit of quantification and association constants were determined. Job’s plot analyses were performed to determine the binding ratios, which was supported by Benesi-Hildebrand studies. The binding ratio between the sensors and metal cations during complexation was found to be 1:1. Reversibility studies were carried out using EDTA to determine whether the sensors could be reused. Molecular Modelling studies were used to determine the most preferred binding sites. Lastly, real-life application screenings were also run to determine if the sensors will be able to be used in real-life scenarios. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04
- Authors: Kotze, Tyla
- Date: 2024-04
- Subjects: Chemistry, Analytic , Water chemistry , Ionic solutions , Aquatic ecology , Geochemistry
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/64116 , vital:73654
- Description: Humanity's unrelenting expansion has shown little regard for the environment, and this has resulted in tons of toxic heavy metal cations and anions being released into the environment through industrial, agricultural, electronic, and mining dumping. The release of these toxic heavy metals can cause diseases and sometimes lead to death, especially in third-world countries with low-income that reside in informal settlements, who suffer the most. Furthermore, the release of these toxins eventually finds their way back into the environment through bioaccumulation in fish, plants and animals. Although there is an ever need for the growth of these industries; low-cost, sensitive, selective, and organic-based sensors is a positive step forward in highlighting the need for environmental restoration and remediation, whilst striving to avoid unnecessary disease and death through this development. In this project, coumarin-based chemosensors for the detection of cationic and anionic species in aqueous and organic media are described. This project involves the synthesis of six different coumarin-based ether derivatives (E2-E5) and coumarin-based ester derivatives (H1-H2). FT-IR, 1H NMR and 13C NMR were used to confirm the structures of all sensors. The abilities of these novel compounds as chemosensors for detection of cations and anions were investigated using UV-vis analysis. These compounds displayed a favourable interaction with Fe2+ and Fe3+ ions with an increase in absorbance. Ether derivatives E2-E5 did not display any degree of selectivity or sensitivity towards the chosen anions. It was found that in the presence of FeCl2, sensors H1 and H2 displayed a degree of selectivities and further investigations were therefore carried out. From the titration experiments, the limit of detection, limit of quantification and association constants were determined. Job’s plot analyses were performed to determine the binding ratios, which was supported by Benesi-Hildebrand studies. The binding ratio between the sensors and metal cations during complexation was found to be 1:1. Reversibility studies were carried out using EDTA to determine whether the sensors could be reused. Molecular Modelling studies were used to determine the most preferred binding sites. Lastly, real-life application screenings were also run to determine if the sensors will be able to be used in real-life scenarios. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2024
- Full Text:
- Date Issued: 2024-04