Analysis of temporal and spatial variations in water storage by means of gravimetric and hydrologic methods in the region around the South African gravimetric observation station
- Authors: Mahed, Gaathier
- Date: 2013
- Subjects: Ground water -- South Africa , Geology -- South Africa , Hydrogeology -- South Africa , Water-supply -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/6714 , vital:21137
- Description: This work examines the use of gravity data and its application to subsurface water reservoirs in the immediate vicinity of the South African Geodynamic Observatory, Sutherland (SAGOS), situated in a semi-arid region of the Karoo region of South Africa, and underlain by the Karoo sedimentary rocks intruded by dolerite dykes and sills. SAGOS houses the only supergravity metre (SG) in Africa, and this thesis sets out to test its use in monitoring groundwater dynamics using hydrological and gravity data. The main aim of this work is the application of the SG data, in conjunction with hydrological data, to better understand episodic recharge of subsurface reservoirs. The importance of water as a resource, globally and specifically the Karoo, is reviewed in conjunction with supply and demand of water. This is to contextualise the socio-economic, technical as well as policy issues related to water resource management. Applicable technologies for water resource management and efficient water use are highlighted and the application of gravity to hydrology is introduced, including satellite as well as ground based tools. In addition, arid zone hydrology as well as recharge and its mechanisms are analysed in order to better understand these processes when examined from gravity measurements. Issues related to understanding flow within the vadose zone as well as in secondary aquifers are examined, and gravity residuals and subsurface hydrology are highlighted. Thereafter, a conceptual groundwater flow modelof the study area is developed using multiple tools. First, the geology around SAGOS was mapped using SPOT 5 imagery and then ground truthed. Second, stable isotopes and water chemistry analysis was undertaken on water samples from selected boreholes. The results allude to preferential flow acting as the main mechanism for groundwater recharge. Follow-up pump-tests illustrate that fracture connectivity is greatest at close proximity to the dyke. Soil mapping, using aerial photography was also undertaken. Duplex soils, enriched with clay at depth, dominate the study area. Using in-situ infiltration tests, it is shown that the alluvium, which lines the river beds, has a higher hydraulic conductivity than the other soils, confirming that these streams act as preferential conduits for subsurface recharge. Precipitation events were correlated against gravity residuals at 4 wells, over different time periods. The results are examined using time series analyses. Gravity residuals from well SA BK07, over a period of 24 hours after the rainfall event, delineate instances of negative correlations, as well as strong positive correlations (of up to 0.9). On the whole however, correlations between gravity and groundwater at SA BK07 are variable and weak, and in conjunction with water level measurements and water chemistry, the data suggest that this well is located in a dynamic conduit (throughflow) and not in a permanent groundwater reservoir. By contrast, other wells show strong positive correlations between gravity residuals and water levels following episodic recharge events for a later time series. Correlations between the water levels and gravity residuals in wells SA BK04, SA BK05 and SA BK 01 are in excess of 0.7 for specific rainfall events. In summary, the results suggests that gravity is an excellent tool for measuring episodic groundwater recharge within the immediate vicinity of the SAGOS. This implies that gravity can aid in monitoring groundwater losses/gains in arid and semi-arid areas. Recommendations for future work are highlighted at the end; these include the possible use of hydrological modelling of reservoirs at various scales and then comparing these results to the SG as well as GOCE and GRACE satellites data, and then improving numerical modelling of the groundwater dynamics for sites like Sutherland and the surrounding arid Karoo region, where sparse water shortages, and potential pollution related to fracking for shale-gas, are likely to compete with established water needs for farming and human consumption. It is also suggested that the gravity modelling be examined to better understand site specific scenarios and thus aid in improving the processing of the gravity signal.
- Full Text:
- Date Issued: 2013
- Authors: Mahed, Gaathier
- Date: 2013
- Subjects: Ground water -- South Africa , Geology -- South Africa , Hydrogeology -- South Africa , Water-supply -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/6714 , vital:21137
- Description: This work examines the use of gravity data and its application to subsurface water reservoirs in the immediate vicinity of the South African Geodynamic Observatory, Sutherland (SAGOS), situated in a semi-arid region of the Karoo region of South Africa, and underlain by the Karoo sedimentary rocks intruded by dolerite dykes and sills. SAGOS houses the only supergravity metre (SG) in Africa, and this thesis sets out to test its use in monitoring groundwater dynamics using hydrological and gravity data. The main aim of this work is the application of the SG data, in conjunction with hydrological data, to better understand episodic recharge of subsurface reservoirs. The importance of water as a resource, globally and specifically the Karoo, is reviewed in conjunction with supply and demand of water. This is to contextualise the socio-economic, technical as well as policy issues related to water resource management. Applicable technologies for water resource management and efficient water use are highlighted and the application of gravity to hydrology is introduced, including satellite as well as ground based tools. In addition, arid zone hydrology as well as recharge and its mechanisms are analysed in order to better understand these processes when examined from gravity measurements. Issues related to understanding flow within the vadose zone as well as in secondary aquifers are examined, and gravity residuals and subsurface hydrology are highlighted. Thereafter, a conceptual groundwater flow modelof the study area is developed using multiple tools. First, the geology around SAGOS was mapped using SPOT 5 imagery and then ground truthed. Second, stable isotopes and water chemistry analysis was undertaken on water samples from selected boreholes. The results allude to preferential flow acting as the main mechanism for groundwater recharge. Follow-up pump-tests illustrate that fracture connectivity is greatest at close proximity to the dyke. Soil mapping, using aerial photography was also undertaken. Duplex soils, enriched with clay at depth, dominate the study area. Using in-situ infiltration tests, it is shown that the alluvium, which lines the river beds, has a higher hydraulic conductivity than the other soils, confirming that these streams act as preferential conduits for subsurface recharge. Precipitation events were correlated against gravity residuals at 4 wells, over different time periods. The results are examined using time series analyses. Gravity residuals from well SA BK07, over a period of 24 hours after the rainfall event, delineate instances of negative correlations, as well as strong positive correlations (of up to 0.9). On the whole however, correlations between gravity and groundwater at SA BK07 are variable and weak, and in conjunction with water level measurements and water chemistry, the data suggest that this well is located in a dynamic conduit (throughflow) and not in a permanent groundwater reservoir. By contrast, other wells show strong positive correlations between gravity residuals and water levels following episodic recharge events for a later time series. Correlations between the water levels and gravity residuals in wells SA BK04, SA BK05 and SA BK 01 are in excess of 0.7 for specific rainfall events. In summary, the results suggests that gravity is an excellent tool for measuring episodic groundwater recharge within the immediate vicinity of the SAGOS. This implies that gravity can aid in monitoring groundwater losses/gains in arid and semi-arid areas. Recommendations for future work are highlighted at the end; these include the possible use of hydrological modelling of reservoirs at various scales and then comparing these results to the SG as well as GOCE and GRACE satellites data, and then improving numerical modelling of the groundwater dynamics for sites like Sutherland and the surrounding arid Karoo region, where sparse water shortages, and potential pollution related to fracking for shale-gas, are likely to compete with established water needs for farming and human consumption. It is also suggested that the gravity modelling be examined to better understand site specific scenarios and thus aid in improving the processing of the gravity signal.
- Full Text:
- Date Issued: 2013
Analysis of the effectiveness of Tulbaghia Violacea extracts as devulcanizing agents for synthetic CIS-1,4-polyisoprene vulcanizates
- Authors: Gxakuma, Lutho
- Date: 2020
- Subjects: Plant extracts , Plant products -- South Africa Medicinal plants -- South Africa Plants -- Analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49093 , vital:41600
- Description: Tulbaghia violacea is an indigenous plant commonly known as wild garlic, wilde knoffel in Afrikaans, isihaqa in Zulu or itswele lomlambo in Xhosa. Its leaves and bulbs are widely used as herbal remedies for various ailments and its medicinal uses include fever and colds, asthma, tuberculosis and stomach problems. Like all other members of the Alliacea family, Tulbaghia violacea produces a distinctive garlic-like odour when its leaves or rhizomes are damaged, resulting in the release of cysteine-derived sulphur compounds which include the oil-soluble organo-sulphur compounds and water-soluble cysteine derivatives. Chemically synthesized sulphur containing compounds have been reported to be effective devulcanizing agents and many industries prefer to perform devulcanization using them. Most commonly applied devulcanizing agents include disulphides, thiophenols and their zinc salts, and mercaptans which are mixed with the rubber scrap powder under specific reaction conditions. In this study, instead of performing devulcanization by using industrial synthesized sulphur containing compounds, the effectiveness of the extracts of organo-sulphur containing compounds from Tulbaghia violacea are evaluated as potential devulcanizing agents for synthetic cis-1,4-polyisoprene vulcanizates. This is a new, cheap and greener practice of rubber devulcanization. Diallyl disulphide, which is one of the organo-sulphur containing compounds present in Tulbaghia violacea, is the devulcanizing agent of interest to this study. The organo-sulphur containing compounds were extracted from the bulbs, roots and leaves of the plant using the soxhlet and ultrasonic bath extraction method. The solvent system used in the soxhlet extraction method was 2% of 2-propanol in n-hexane whereas in ultrasonic bath extraction method the solvent system used was 100% ethanol. An essential oil extract was obtained from the plant organs. The yield of the essential oil extracts obtained using the soxhlet extraction method was higher compared to the yield of the essential oil extracts obtained using the ultrasonic bath extraction method. According to the Fourier-Transform Infrared spectroscopy, the organo-sulphur containing compounds were present in the essential oil extracts of the plant. The essential oil extracts that were extracted using the soxhlet extraction method were chosen for further analysis. It was found out that the allyl sulphide and diallyl disulphide have the same retention time from the High Performance Liquid Chromatography (using a normal phase column). The Differential Scanning Calorimeter indicated that the allyl sulphide was not present in the essential oil extracts whereas the diallyl disulphide was present in the essential oil extract of the roots and leaves. The High Performance Liquid Chromatography was used to quantify the presence of the diallyl disulphide in the essential oil extract of roots and leaves. The quantity of diallyl disulphide was 23% in the dry mass of the essential oil extract of roots. In the essential oil extract of leaves the diallyl disulphide was very low concentrated and the High Performance Liquid Chromatography was less sensitive to detect it. According to the Thermogravimetric Analyser, it was found that the essential oil extracts begin to degrade at 120 °C and experience a multistage degradation. The softening temperature of the essential oil extracts was 60 °C from the Simultaneous Differential Scanning Calorimeter-Thermogravimetric Analyser. Conventional vulcanization of synthetic cis-1,4-polyisoprene was prepared with the vulcanization ingredients of zinc oxide, sulphur, stearic acid and N-tert-butyl-2-benzothiazole sulphenamide. The vulcanized synthetic cis-1,4-polyisoprene produced, under the heating temperature of 160 °C, was mixed with the essential oil extracts using the internal mixer at 60 °C and the two-roll mill. The overall torque, tan delta and the total crosslink density were the properties of interest of synthetic cis-1,4-polyisoprene vulcanizate in this study. The devulcanization temperature for the treated synthetic cis-1,4-polyisoprene vulcanizate with the essential oil extracts was optimized using the Dynamic Moving Die Rheometer and Dynamic Rubber Process Analyser. The amount of essential oil extracts at which they are effective devulcanizing agents for synthetic cis-1,4-polyisoprene vulcanizate was also optimized. During optimization a change on the latter mentioned properties of synthetic cis-1,4-polyisoprene vulcanizate was observed, indicating that the essential oil extracts have an effect as potential devulcanizing agents. The essential oil extracts increased the tan delta and reduced the overall torque, and total crosslink density of synthetic cis-1,4-polyisoprene vulcanizate as expected from devulcanizing agents. 200 °C was a preferable devulcanization temperature whereas essential oil extracts were effective as devulcanizing agent at 1.4%. However, the essential oil extracts influenced the overall torque and tan delta of synthetic cis-1,4-polyisoprene vulcanizate during the mixing process in the internal mixer at 60 °C, which was before heating at 200 °C. The essential oil extracts had a higher influence on the overall torque of synthetic cis-1,4-polyisoprene vulcanizate under heating at 200 °C whereas at 60 °C, during the mixing process, they had a higher influence on the tan delta of synthetic cis-1,4-polyisoprene vulcanizate. The essential oil extract of leaves had a higher influence on the overall torque whereas the essential oil extract of bulbs had a higher influence on the tan delta of synthetic cis-1,4-polyisoprene vulcanizate at 200 °C. The essential oil extract of roots shown a greater influence on the overall torque and tan delta of synthetic cis-1,4-polyisoprene vulcanizate at 60 °C during the mixing process. The effect of the essential oil extracts on the reversing heat capacity of synthetic cis-1,4-polyisoprene vulcanizate was also investigated using the Modulated Differential Scanning Calorimetry method. The essential oil extract of bulbs and roots influenced the reversing heat capacity of synthetic cis-1,4-polyisoprene vulcanizate by reducing it whereas the essential oil extract of leaves caused a temperature shift of the reversing heat capacity curve from the Modulated Differential Scanning Calorimeter thermogram of synthetic cis-1,4-polyisoprene vulcanizate. Therefore, the results indicated that the essential oil extracts of Tulbaghia violacea have an effect as an alternative potential devulcanizing agents for conventional vulcanized synthetic cis-1,4-polyisoprene whether the diallyl disulphide compound is present or not in them.
- Full Text:
- Date Issued: 2020
- Authors: Gxakuma, Lutho
- Date: 2020
- Subjects: Plant extracts , Plant products -- South Africa Medicinal plants -- South Africa Plants -- Analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49093 , vital:41600
- Description: Tulbaghia violacea is an indigenous plant commonly known as wild garlic, wilde knoffel in Afrikaans, isihaqa in Zulu or itswele lomlambo in Xhosa. Its leaves and bulbs are widely used as herbal remedies for various ailments and its medicinal uses include fever and colds, asthma, tuberculosis and stomach problems. Like all other members of the Alliacea family, Tulbaghia violacea produces a distinctive garlic-like odour when its leaves or rhizomes are damaged, resulting in the release of cysteine-derived sulphur compounds which include the oil-soluble organo-sulphur compounds and water-soluble cysteine derivatives. Chemically synthesized sulphur containing compounds have been reported to be effective devulcanizing agents and many industries prefer to perform devulcanization using them. Most commonly applied devulcanizing agents include disulphides, thiophenols and their zinc salts, and mercaptans which are mixed with the rubber scrap powder under specific reaction conditions. In this study, instead of performing devulcanization by using industrial synthesized sulphur containing compounds, the effectiveness of the extracts of organo-sulphur containing compounds from Tulbaghia violacea are evaluated as potential devulcanizing agents for synthetic cis-1,4-polyisoprene vulcanizates. This is a new, cheap and greener practice of rubber devulcanization. Diallyl disulphide, which is one of the organo-sulphur containing compounds present in Tulbaghia violacea, is the devulcanizing agent of interest to this study. The organo-sulphur containing compounds were extracted from the bulbs, roots and leaves of the plant using the soxhlet and ultrasonic bath extraction method. The solvent system used in the soxhlet extraction method was 2% of 2-propanol in n-hexane whereas in ultrasonic bath extraction method the solvent system used was 100% ethanol. An essential oil extract was obtained from the plant organs. The yield of the essential oil extracts obtained using the soxhlet extraction method was higher compared to the yield of the essential oil extracts obtained using the ultrasonic bath extraction method. According to the Fourier-Transform Infrared spectroscopy, the organo-sulphur containing compounds were present in the essential oil extracts of the plant. The essential oil extracts that were extracted using the soxhlet extraction method were chosen for further analysis. It was found out that the allyl sulphide and diallyl disulphide have the same retention time from the High Performance Liquid Chromatography (using a normal phase column). The Differential Scanning Calorimeter indicated that the allyl sulphide was not present in the essential oil extracts whereas the diallyl disulphide was present in the essential oil extract of the roots and leaves. The High Performance Liquid Chromatography was used to quantify the presence of the diallyl disulphide in the essential oil extract of roots and leaves. The quantity of diallyl disulphide was 23% in the dry mass of the essential oil extract of roots. In the essential oil extract of leaves the diallyl disulphide was very low concentrated and the High Performance Liquid Chromatography was less sensitive to detect it. According to the Thermogravimetric Analyser, it was found that the essential oil extracts begin to degrade at 120 °C and experience a multistage degradation. The softening temperature of the essential oil extracts was 60 °C from the Simultaneous Differential Scanning Calorimeter-Thermogravimetric Analyser. Conventional vulcanization of synthetic cis-1,4-polyisoprene was prepared with the vulcanization ingredients of zinc oxide, sulphur, stearic acid and N-tert-butyl-2-benzothiazole sulphenamide. The vulcanized synthetic cis-1,4-polyisoprene produced, under the heating temperature of 160 °C, was mixed with the essential oil extracts using the internal mixer at 60 °C and the two-roll mill. The overall torque, tan delta and the total crosslink density were the properties of interest of synthetic cis-1,4-polyisoprene vulcanizate in this study. The devulcanization temperature for the treated synthetic cis-1,4-polyisoprene vulcanizate with the essential oil extracts was optimized using the Dynamic Moving Die Rheometer and Dynamic Rubber Process Analyser. The amount of essential oil extracts at which they are effective devulcanizing agents for synthetic cis-1,4-polyisoprene vulcanizate was also optimized. During optimization a change on the latter mentioned properties of synthetic cis-1,4-polyisoprene vulcanizate was observed, indicating that the essential oil extracts have an effect as potential devulcanizing agents. The essential oil extracts increased the tan delta and reduced the overall torque, and total crosslink density of synthetic cis-1,4-polyisoprene vulcanizate as expected from devulcanizing agents. 200 °C was a preferable devulcanization temperature whereas essential oil extracts were effective as devulcanizing agent at 1.4%. However, the essential oil extracts influenced the overall torque and tan delta of synthetic cis-1,4-polyisoprene vulcanizate during the mixing process in the internal mixer at 60 °C, which was before heating at 200 °C. The essential oil extracts had a higher influence on the overall torque of synthetic cis-1,4-polyisoprene vulcanizate under heating at 200 °C whereas at 60 °C, during the mixing process, they had a higher influence on the tan delta of synthetic cis-1,4-polyisoprene vulcanizate. The essential oil extract of leaves had a higher influence on the overall torque whereas the essential oil extract of bulbs had a higher influence on the tan delta of synthetic cis-1,4-polyisoprene vulcanizate at 200 °C. The essential oil extract of roots shown a greater influence on the overall torque and tan delta of synthetic cis-1,4-polyisoprene vulcanizate at 60 °C during the mixing process. The effect of the essential oil extracts on the reversing heat capacity of synthetic cis-1,4-polyisoprene vulcanizate was also investigated using the Modulated Differential Scanning Calorimetry method. The essential oil extract of bulbs and roots influenced the reversing heat capacity of synthetic cis-1,4-polyisoprene vulcanizate by reducing it whereas the essential oil extract of leaves caused a temperature shift of the reversing heat capacity curve from the Modulated Differential Scanning Calorimeter thermogram of synthetic cis-1,4-polyisoprene vulcanizate. Therefore, the results indicated that the essential oil extracts of Tulbaghia violacea have an effect as an alternative potential devulcanizing agents for conventional vulcanized synthetic cis-1,4-polyisoprene whether the diallyl disulphide compound is present or not in them.
- Full Text:
- Date Issued: 2020
Analysis of the extended defects in 3C-SiC
- Authors: Olivier, Ezra Jacobus
- Date: 2008
- Subjects: Crystals -- Defects , Crystallography , Silicon carbide
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10525 , http://hdl.handle.net/10948/730 , Crystals -- Defects , Crystallography , Silicon carbide
- Description: The dissertation focuses on the analysis of the extended defects present in as-grown and proton bombarded β-SiC (annealed and unannealed) grown by chemical vapour deposition (CVD) on (001) Si. The proton irradiation was done to a dose of 2.8 × 1016 protons/cm2 and the annealing took place at 1300°C and 1600°C for 1hr. The main techniques used for the analysis were transmission electron microscopy (TEM) and high resolution TEM (HRTEM). From the diffraction study of the material the phase of the SiC was confirmed to be the cubic beta phase with the zinc-blende structure. The main defects found in the β- SiC were stacking faults (SFs) with their associated partial dislocations and microtwins. The SFs were uniformly distributed throughout the foil. The SFs were identified as having a fault vector of the type 1/3 <111> with bonding partial dislocations of the type 1/6 <121> by using image simulation. The SFs were also found to be predominantly extrinsic in nature by using HRTEM analysis of SFs viewed edge-on. Also both bright and dar-field images of SFs on inclined planes exhibited symmetrical and complementary fringe contrast images. This is a result of the anomalous absorption ratio of SiC lying between that of Si and diamond. The analysis of the annealed and unannealed irradiated β-SiC yielded no evidence of radiation damage or change in the crystal structure of the β-SiC. This confirmed that β-SiC is a radiation resistant material. The critical proton dose for the creation of small dislocation loops seems to be higher than for other compound semiconductors with the zinc-blende structure.
- Full Text:
- Date Issued: 2008
- Authors: Olivier, Ezra Jacobus
- Date: 2008
- Subjects: Crystals -- Defects , Crystallography , Silicon carbide
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10525 , http://hdl.handle.net/10948/730 , Crystals -- Defects , Crystallography , Silicon carbide
- Description: The dissertation focuses on the analysis of the extended defects present in as-grown and proton bombarded β-SiC (annealed and unannealed) grown by chemical vapour deposition (CVD) on (001) Si. The proton irradiation was done to a dose of 2.8 × 1016 protons/cm2 and the annealing took place at 1300°C and 1600°C for 1hr. The main techniques used for the analysis were transmission electron microscopy (TEM) and high resolution TEM (HRTEM). From the diffraction study of the material the phase of the SiC was confirmed to be the cubic beta phase with the zinc-blende structure. The main defects found in the β- SiC were stacking faults (SFs) with their associated partial dislocations and microtwins. The SFs were uniformly distributed throughout the foil. The SFs were identified as having a fault vector of the type 1/3 <111> with bonding partial dislocations of the type 1/6 <121> by using image simulation. The SFs were also found to be predominantly extrinsic in nature by using HRTEM analysis of SFs viewed edge-on. Also both bright and dar-field images of SFs on inclined planes exhibited symmetrical and complementary fringe contrast images. This is a result of the anomalous absorption ratio of SiC lying between that of Si and diamond. The analysis of the annealed and unannealed irradiated β-SiC yielded no evidence of radiation damage or change in the crystal structure of the β-SiC. This confirmed that β-SiC is a radiation resistant material. The critical proton dose for the creation of small dislocation loops seems to be higher than for other compound semiconductors with the zinc-blende structure.
- Full Text:
- Date Issued: 2008
Analysis of the interaction between recombinant human Beta2 integrin I-domains and CD23
- Authors: Sprong, Kaitlin
- Date: 2014
- Subjects: Immune response -- Regulation , Immunoglobulins , CD23 antigen
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10362 , http://hdl.handle.net/10948/d1021078
- Description: In order to further elucidate the interaction between CD23 and β2 integrins (CD11b/CD18) the following objectives were established: Expression and purification of CD11b I-domain as a GST-fusion protein using Escherichia coli; Cloning, synthesis and expression of CD18 I-Like domain.CD11b I-domain has previously been expressed as a GST-fusion protein (Daniels, 2010) and consequently led to comparable expression of CD18 I-like domain as a GST-fusion protein; Preparation of two site-directed mutants of CD18 I-Like domain in order to study the function of the serine residue involved in the S116P mutation. The serine was mutated to proline, as in LAD patients, as well as alanine, a non-polar alternative, in order to contrast and compare binding characteristics. Expression, refolding and purification of sCD23, and a double mutatedsCD23 (RKΔAA) from E. coli; This was performed according to the method described by Daniels et al. (2005); Investigation of the CD23-CD11b I-like domain interaction through surface plasmon resonance spectroscopy.
- Full Text:
- Date Issued: 2014
- Authors: Sprong, Kaitlin
- Date: 2014
- Subjects: Immune response -- Regulation , Immunoglobulins , CD23 antigen
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10362 , http://hdl.handle.net/10948/d1021078
- Description: In order to further elucidate the interaction between CD23 and β2 integrins (CD11b/CD18) the following objectives were established: Expression and purification of CD11b I-domain as a GST-fusion protein using Escherichia coli; Cloning, synthesis and expression of CD18 I-Like domain.CD11b I-domain has previously been expressed as a GST-fusion protein (Daniels, 2010) and consequently led to comparable expression of CD18 I-like domain as a GST-fusion protein; Preparation of two site-directed mutants of CD18 I-Like domain in order to study the function of the serine residue involved in the S116P mutation. The serine was mutated to proline, as in LAD patients, as well as alanine, a non-polar alternative, in order to contrast and compare binding characteristics. Expression, refolding and purification of sCD23, and a double mutatedsCD23 (RKΔAA) from E. coli; This was performed according to the method described by Daniels et al. (2005); Investigation of the CD23-CD11b I-like domain interaction through surface plasmon resonance spectroscopy.
- Full Text:
- Date Issued: 2014
Analysis of the tectonic and basin evolution of the seychelles microcontinent during the mesozoic to cenozoic, based on seismic and well data
- Authors: Mondon, Jean-Luc Andre
- Date: 2014
- Subjects: Sedimentation and deposition , Gondwana (Continent) , Sedimentary basins
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/4386 , vital:20593
- Description: The Seychelles Microcontinent (SMc) is a fragment of continental lithosphere that experienced multiple phases of rifting and thermal subsidence during its isolation and submergence within the Indian Ocean. Originally part of central Gondwana, along with India and Madagascar, the SMc first emerged during Mesozoic fragmentation of Gondwana (ca. 220 – 180 Ma) along a complex rifted margin. Fragmentation involved three major rift phases, viz.: 1) Middle Triassic – Middle Jurassic (Rift I), associated with the “Karoo rifts” and break-up between [India-Madagascar-Seychelles] and East Africa; 2) Middle Jurassic – Early Cretaceous (Rift II), associated with the rifting and break-up of Madagascar from [India-Seychelles]; 3) Late Cretaceous (Rift III), associated with the rifting and final break-away of the SMc from India. In this study, the tectonic and sedimentary history of the SMc is analysed using 2D seismic reflection datasets and three exploration wells. Seismic to well-log correlations provide a chrono-stratigraphic framework that identifies seven sequences from the Middle Triassic to the Paleogene. This also identified horst and graben structures related to the extensional tectonics and thermal subsidence of this continental fragment. The latter is reflected also in changes of its litho-facies preserved on the SMc, from terrestrial to marine. The oldest sedimentary rocks identified on the SMc are Middle Triassic organic rich claystones (Sequence 7, Rift I), which grade upwards into alternating Upper Triassic sandstones and mudstones (Sequence 6, Rift I) followed by upward coarsening Lower Jurassic mudstones to sandstone units (Sequence 5, Rift I). These sequences are interpreted as lacustrine facies that evolved into fluvial channel migration facies and finally into progradational delta front facies. Sequence 5 is overlain by Middle Jurassic oolitic limestones that grade upwards into organic rich mudstones (Sequence 4, thermal subsidence after Rift I); the latter are interpreted as restricted-marginal marine deposits. Following Sequence 4, separated by a major break-up unconformity (BU), are the Upper Cretaceous open marine deposits comprising limestones, claystones and sandstones, and terminated with basaltic volcanics (ca. 66 Ma) prior to the separation of the SMc from India (Sequence 3, Rift III). This is overlain by the post-rift – thermal subsidence sequences comprising open marine claystones and shelf limestones (Sequence 2) followed by a sequence of shelf limestones (Sequence 1) that form the present carbonate platform, the Seychelles Plateau that lies approximately 200 m below the present sea-level. Backstripping and subsidence analysis quantifies 3 stages of subsidence; Phase A: Slow subsidence (ca. 5-20 m/Ma), from the Middle Jurassic to the Upper Cretaceous that terminated during a major marine transgression during ingression of the Tethys Sea between East Africa and [Madagascar-Seychelles-India]. This created marine conditions and the subsequent deposition of Sequences 4 and 3; Phase B: Accelerated subsidence (ca. 35-60 m/Ma) recorded throughout the Paleocene to the middle Eocene leading to deeper marine conditions and the subsequent deposition of Sequence 2; and Phase C: Reduced subsidence (ca. 10-30 m/Ma) following the interaction between the Carlsberg Ridge and the Reunion hotspot (ca. 55 Ma) that possibly introduced a reduction in subsidence and the subsequent deposition of Sequence 1 as the SMc drifted and thermally subsided to its submerged present location, and is now dominated mainly by marine carbonates. The effects of the Madagascar and Seychelles/India separation (ca. 84 Ma) are not observed in the subsidence analysis, possibly because it involved transcurrent-rotational movement between the two plates over a short period of time.
- Full Text:
- Date Issued: 2014
- Authors: Mondon, Jean-Luc Andre
- Date: 2014
- Subjects: Sedimentation and deposition , Gondwana (Continent) , Sedimentary basins
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/4386 , vital:20593
- Description: The Seychelles Microcontinent (SMc) is a fragment of continental lithosphere that experienced multiple phases of rifting and thermal subsidence during its isolation and submergence within the Indian Ocean. Originally part of central Gondwana, along with India and Madagascar, the SMc first emerged during Mesozoic fragmentation of Gondwana (ca. 220 – 180 Ma) along a complex rifted margin. Fragmentation involved three major rift phases, viz.: 1) Middle Triassic – Middle Jurassic (Rift I), associated with the “Karoo rifts” and break-up between [India-Madagascar-Seychelles] and East Africa; 2) Middle Jurassic – Early Cretaceous (Rift II), associated with the rifting and break-up of Madagascar from [India-Seychelles]; 3) Late Cretaceous (Rift III), associated with the rifting and final break-away of the SMc from India. In this study, the tectonic and sedimentary history of the SMc is analysed using 2D seismic reflection datasets and three exploration wells. Seismic to well-log correlations provide a chrono-stratigraphic framework that identifies seven sequences from the Middle Triassic to the Paleogene. This also identified horst and graben structures related to the extensional tectonics and thermal subsidence of this continental fragment. The latter is reflected also in changes of its litho-facies preserved on the SMc, from terrestrial to marine. The oldest sedimentary rocks identified on the SMc are Middle Triassic organic rich claystones (Sequence 7, Rift I), which grade upwards into alternating Upper Triassic sandstones and mudstones (Sequence 6, Rift I) followed by upward coarsening Lower Jurassic mudstones to sandstone units (Sequence 5, Rift I). These sequences are interpreted as lacustrine facies that evolved into fluvial channel migration facies and finally into progradational delta front facies. Sequence 5 is overlain by Middle Jurassic oolitic limestones that grade upwards into organic rich mudstones (Sequence 4, thermal subsidence after Rift I); the latter are interpreted as restricted-marginal marine deposits. Following Sequence 4, separated by a major break-up unconformity (BU), are the Upper Cretaceous open marine deposits comprising limestones, claystones and sandstones, and terminated with basaltic volcanics (ca. 66 Ma) prior to the separation of the SMc from India (Sequence 3, Rift III). This is overlain by the post-rift – thermal subsidence sequences comprising open marine claystones and shelf limestones (Sequence 2) followed by a sequence of shelf limestones (Sequence 1) that form the present carbonate platform, the Seychelles Plateau that lies approximately 200 m below the present sea-level. Backstripping and subsidence analysis quantifies 3 stages of subsidence; Phase A: Slow subsidence (ca. 5-20 m/Ma), from the Middle Jurassic to the Upper Cretaceous that terminated during a major marine transgression during ingression of the Tethys Sea between East Africa and [Madagascar-Seychelles-India]. This created marine conditions and the subsequent deposition of Sequences 4 and 3; Phase B: Accelerated subsidence (ca. 35-60 m/Ma) recorded throughout the Paleocene to the middle Eocene leading to deeper marine conditions and the subsequent deposition of Sequence 2; and Phase C: Reduced subsidence (ca. 10-30 m/Ma) following the interaction between the Carlsberg Ridge and the Reunion hotspot (ca. 55 Ma) that possibly introduced a reduction in subsidence and the subsequent deposition of Sequence 1 as the SMc drifted and thermally subsided to its submerged present location, and is now dominated mainly by marine carbonates. The effects of the Madagascar and Seychelles/India separation (ca. 84 Ma) are not observed in the subsidence analysis, possibly because it involved transcurrent-rotational movement between the two plates over a short period of time.
- Full Text:
- Date Issued: 2014
Anchovy and Sardine in Algoa Bay and their relationship with response variables in two threatened avian predators
- Authors: Potter, Cara-Paige
- Date: 2013
- Subjects: Fishes -- Predators of -- South Africa -- Algoa Bay , Anchovies -- South Africa , Sardines -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10730 , http://hdl.handle.net/10948/d1021130
- Description: Huge populations of sardine and anchovy exist in the four major upwelling systems around the world. These fish are both important ecologically and economically. Pelagic fish dominate the mid trophic level and can exert both a top-down control of zooplankton and a bottom-up control on predatory fish and marine top predators. They also make up a substantial contribution of the world catches in seas around the world where they co-exist in upwelling areas. The fluctuations of sardine and anchovy are largely influenced by recruitment from the larval stage and by the physical environmental forces that determine the planktonic compositions upon which they feed. In southern Africa, the biology and behaviour of two threatened seabird species, African penguins (Spheniscus demersus) and Cape gannets (Morus capensis), are directly influenced by the availability of sardine (Sardinops sagax) and anchovy (Engraulis encrasicolus). This study aimed to provide further insight into the fluctuations of sardine and anchovy in relation to the variability of environmental factors such as wind, sea surface temperature, rainfall and plankton abundance, focusing specifically on Algoa Bay in the Eastern Cape, South Africa. Algoa Bay is particularly important as it is home to the world’s largest African penguin colony and the world’s largest gannetry. Therefore, to further investigate the populations of these two seabird species, the fluctuations of their food source were studied.
- Full Text:
- Date Issued: 2013
- Authors: Potter, Cara-Paige
- Date: 2013
- Subjects: Fishes -- Predators of -- South Africa -- Algoa Bay , Anchovies -- South Africa , Sardines -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10730 , http://hdl.handle.net/10948/d1021130
- Description: Huge populations of sardine and anchovy exist in the four major upwelling systems around the world. These fish are both important ecologically and economically. Pelagic fish dominate the mid trophic level and can exert both a top-down control of zooplankton and a bottom-up control on predatory fish and marine top predators. They also make up a substantial contribution of the world catches in seas around the world where they co-exist in upwelling areas. The fluctuations of sardine and anchovy are largely influenced by recruitment from the larval stage and by the physical environmental forces that determine the planktonic compositions upon which they feed. In southern Africa, the biology and behaviour of two threatened seabird species, African penguins (Spheniscus demersus) and Cape gannets (Morus capensis), are directly influenced by the availability of sardine (Sardinops sagax) and anchovy (Engraulis encrasicolus). This study aimed to provide further insight into the fluctuations of sardine and anchovy in relation to the variability of environmental factors such as wind, sea surface temperature, rainfall and plankton abundance, focusing specifically on Algoa Bay in the Eastern Cape, South Africa. Algoa Bay is particularly important as it is home to the world’s largest African penguin colony and the world’s largest gannetry. Therefore, to further investigate the populations of these two seabird species, the fluctuations of their food source were studied.
- Full Text:
- Date Issued: 2013
Ant colony optimisation-based algorithms for optical burst switching networks
- Gravett, Andrew Scott, Gibbon, Timothy B
- Authors: Gravett, Andrew Scott , Gibbon, Timothy B
- Date: 2017
- Subjects: Distributed algorithms , Ants -- Behavior -- Mathematical models
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/18939 , vital:28757
- Description: This research developed two novel distributed algorithms inspired by Ant Colony Optimisation (ACO) for a solution to the problem of dynamic Routing and Wavelength Assignment (RWA) with wavelength continuity constraint in Optical Burst Switching (OBS) networks utilising both the traditional International Telecommunication Union (ITU) Fixed Grid Wavelength Division Multiplexing (WDM) and Flexible Spectrum scenarios. The growing demand for more bandwidth in optical networks require more efficient utilisation of available optical resources. OBS is a promising optical switching technique for the improved utilisation of optical network resources over the current optical circuit switching technique. The development of newer technologies has introduced higher rate transmissions and various modulation formats, however, introducing these technologies into the traditional ITU Fixed Grid does not efficiently utilise the available bandwidth. Flexible Spectrum is a promising approach offering a solution to the problem of improving bandwidth utilisation, which comes with a potential cost. Transmissions have the potential for impairment with respect to the increased traffic and lack of large channel spacing. Proposed routing algorithms should be aware of the linear and non-linear Physical Layer Impairments (PLIs) in order to operate closer to optimum performance. The OBS resource reservation protocol does not cater for the loss of transmissions, Burst Control Packets (BCPs) included, due to physical layer impairments. The protocol was adapted for use in Flexible Spectrum. Investigation of the use of a route and wavelength combination, from source to destination node pair, for the RWA process was proposed for ACO-based approaches to enforce the establishment and use of complete paths for greedy exploitation in Flexible Spectrum was conducted. The routing tuple for the RWA process is the tight coupling of a route and wavelength in combination intended to promote the greedy exploitation of successful paths for transmission requests. The application of the routing tuples differs from traditional ACO-based approaches and prompted the investigation of new pheromone calculation equations. The two novel proposed approaches were tested and experiments conducted comparing with and against existing algorithms (a simple greedy and an ACO-based algorithm) in a traditional ITU Fixed Grid and Flexible Spectrum scenario on three different network topologies. The proposed Flexible Spectrum Ant Colony (FSAC) approach had a markably improved performance over the existing algorithms in the ITU Fixed Grid WDM and Flexible Spectrum scenarios, while Upper Confidence Bound Routing and Wavelength Assignment (UCBRWA) algorithm was able to perform well in the traditional ITU Fixed Grid WDM scenario, but underperformed in the Flexible Spectrum scenario. The results show that the distributed ACO-based FSAC algorithm significantly improved the burst transmission success probability, providing a good solution in the Flexible Spectrum network environment undergoing transmission impairments.
- Full Text:
- Date Issued: 2017
- Authors: Gravett, Andrew Scott , Gibbon, Timothy B
- Date: 2017
- Subjects: Distributed algorithms , Ants -- Behavior -- Mathematical models
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/18939 , vital:28757
- Description: This research developed two novel distributed algorithms inspired by Ant Colony Optimisation (ACO) for a solution to the problem of dynamic Routing and Wavelength Assignment (RWA) with wavelength continuity constraint in Optical Burst Switching (OBS) networks utilising both the traditional International Telecommunication Union (ITU) Fixed Grid Wavelength Division Multiplexing (WDM) and Flexible Spectrum scenarios. The growing demand for more bandwidth in optical networks require more efficient utilisation of available optical resources. OBS is a promising optical switching technique for the improved utilisation of optical network resources over the current optical circuit switching technique. The development of newer technologies has introduced higher rate transmissions and various modulation formats, however, introducing these technologies into the traditional ITU Fixed Grid does not efficiently utilise the available bandwidth. Flexible Spectrum is a promising approach offering a solution to the problem of improving bandwidth utilisation, which comes with a potential cost. Transmissions have the potential for impairment with respect to the increased traffic and lack of large channel spacing. Proposed routing algorithms should be aware of the linear and non-linear Physical Layer Impairments (PLIs) in order to operate closer to optimum performance. The OBS resource reservation protocol does not cater for the loss of transmissions, Burst Control Packets (BCPs) included, due to physical layer impairments. The protocol was adapted for use in Flexible Spectrum. Investigation of the use of a route and wavelength combination, from source to destination node pair, for the RWA process was proposed for ACO-based approaches to enforce the establishment and use of complete paths for greedy exploitation in Flexible Spectrum was conducted. The routing tuple for the RWA process is the tight coupling of a route and wavelength in combination intended to promote the greedy exploitation of successful paths for transmission requests. The application of the routing tuples differs from traditional ACO-based approaches and prompted the investigation of new pheromone calculation equations. The two novel proposed approaches were tested and experiments conducted comparing with and against existing algorithms (a simple greedy and an ACO-based algorithm) in a traditional ITU Fixed Grid and Flexible Spectrum scenario on three different network topologies. The proposed Flexible Spectrum Ant Colony (FSAC) approach had a markably improved performance over the existing algorithms in the ITU Fixed Grid WDM and Flexible Spectrum scenarios, while Upper Confidence Bound Routing and Wavelength Assignment (UCBRWA) algorithm was able to perform well in the traditional ITU Fixed Grid WDM scenario, but underperformed in the Flexible Spectrum scenario. The results show that the distributed ACO-based FSAC algorithm significantly improved the burst transmission success probability, providing a good solution in the Flexible Spectrum network environment undergoing transmission impairments.
- Full Text:
- Date Issued: 2017
Anti-diabetic and phytochemical analysis of sutherlandia frutescens extracts
- Authors: Adefuye, Ogheneochuko Janet
- Date: 2016
- Subjects: Medicinal plants -- Africa , Traditional medicine -- Africa , Herbs -- Therapeutic use -- Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/3549 , vital:20441
- Description: In Africa, the importance of medicinal plants in folklore medicine and their contribution to primary healthcare is well recognized. Across the continent, local herbal mixtures still provide the only therapeutic option for about 80% of the population. The vast floral diversity and the intrinsic ethnobotanical knowledge has been the backbone of localized traditional herbal medical practices. In Africa, an estimated 5400 of the 60000 described plant taxa possess over 16300 therapeutic uses. Similarly, with a therapeutic flora comprising of approximately 650 species, herbal medical practitioners in South Africa, make use of a plethora of plants to treat different human diseases and infections. Over the years, studies have identified numerous plant species with potential against chronic metabolic diseases including type 2 diabetes mellitus (T2DM). Globally, the incidence and prevalence of T2DM have reached epidemic proportions affecting people of all ages, nationalities and ethnicity. Considered the fourth leading cause of deaths by disease, T2DM is a global health crisis with an estimated diagnosis and mortality frequency of 1 every 5 seconds and 1 every 7 seconds respectively. Though the exact pathophysiology of T2DM is not entirely understood, initial peripheral insulin resistance in adipose tissue, liver, and skeletal muscle with subsequent pancreatic β-cell dysfunction resulting from an attempt to compensate for insulin resistance is a common feature of the disease. The current approach to treating T2DM is the use of oral antidiabetic agents (OAAs), insulin, and incretin-based drugs in an attempt to achieve glycaemic control and maintain glucose homeostasis. However, conventional anti-T2DM drugs have been shown to have limited efficacies and serious adverse effects. Hence, the need for newer, more efficacious and safer anti-T2DM agents. Sutherlandia frutescens subsp. microphylla is a flowering shrub of the pea family (Fabaceae/Leguminaceae) found mainly in the Western Cape and Karoo regions of Southern Africa. Concoctions of various parts of the plant are used in the management of different ailments including T2DM. However, despite extensive biological and pharmacological studies, few analyses exist of the chemical constituents of S. frutescens and no Triple Time of Flight Liquid Chromatography with Mass Spectrometry (Triple TOF LC/MS/MS) analysis has been performed. The initial aim of this study was to investigate the phytochemical profile of hot aqueous, cold aqueous, 80% ethanolic, 100% ethanolic, 80% methanolic and 100% methanolic extracts of a single source S. frutescens plant material using colorimetric and spectrophotometric analysis. The hot aqueous extractant was found to be the best extractant for S. frutescens, yielding 1.99 g of crude extract from 16 g fresh powdered plant material. This data suggests that application of heat and water as the extractant (hot aqueous) could play a vital role in extraction of bioactive compounds from S. frutescens and also justifies the traditional use of a tea infusion of S. frutescens. Colorimetric analysis revealed the presence of flavonoids, flavonols, tannins, and phenols in all extracts with varying intensity. The organic extracts 100% methanol, 80% and 100% ethanol exhibited high color intensity (+++) for flavonoids and flavonols respectively, while all the extracts exhibited a moderate color intensity (++) for tannins and phenols. Spectrophotometric analysis of S. frutescens extracts revealed that all the organic extracts contained a significantly higher concentration (in mg/g of extract) of flavonols and tannins when compared to the aqueous extracts. All extracts contained approximately equal levels of phenols. These data confirm the presence of all four groups of bioactive phytocompounds in the S. frutescens extracts used in this study, and also confirm that different solvent extractants possess the capability to differentially extract specific groups of phytocompounds. in individual extracts. Further comparison of these compounds with online databases of anti-diabetic phytocompounds led to the preliminary identification of 10 possible anti-diabetic compounds; α-Pinene, Limonene, Sabinene, Carvone, Myricetin, Rutin, Stigmasterol, Emodin, Sarpagine and Hypoglycin B in crude and solid phase extraction (SPE) fractions of S. frutesecens. Furthermore, using two hepatic cell lines (Chang and HepG2) as an in-vtro model system, the anti-T2DM properties of crude aqueous and organic extracts of S. frutescents was investigated and compared. Both aqueous and organic extracts of S. frutescens were found to decrease gluconeogenesis, increase glucose uptake and decrease lipid accumulation (Triacylglycerol, Diacylglycerol, and Monoacylglycerol) in Chang and HepG2 hepatic cell cultures made insulin resistant (IR) following exposure to high concentration of insulin and fructose. Using real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), the aqueous and organic extracts of S. frutescens were confirmed to regulate the expression of Vesicle-associated membrane protein 3 (VAMP3), Mitogen-activated protein kinase 8 (MAPK8), and Insulin receptor substrate 1 (IRS1) in insulin resistant hepatic cells. IR-mediated downregulation of VAMP3, MAPK8, and IRS1 mRNA in IR HepG2 hepatic cell cultures was reversed in the presence of aqueous and organic extracts of S. frutescens. The hot aqueous extract displayed the highest activity in all the assays, while all the organic extracts displayed similar potency. In conclusion, this study reports that aqueous and organic extracts of S. frutescens possess numerous anti-diabetic compounds that can be further investigated for the development of new, more efficacious and less toxic anti-diabetic agents. The presence of multiple compounds in a single extract does suggest a synergistic or combinatorial therapeutic effect. These findings support the burgeoning body of in-vivo and in-vitro literature evidence on the anti-diabetic properties of S. frutescens and its use in folklore medicine.
- Full Text:
- Date Issued: 2016
- Authors: Adefuye, Ogheneochuko Janet
- Date: 2016
- Subjects: Medicinal plants -- Africa , Traditional medicine -- Africa , Herbs -- Therapeutic use -- Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/3549 , vital:20441
- Description: In Africa, the importance of medicinal plants in folklore medicine and their contribution to primary healthcare is well recognized. Across the continent, local herbal mixtures still provide the only therapeutic option for about 80% of the population. The vast floral diversity and the intrinsic ethnobotanical knowledge has been the backbone of localized traditional herbal medical practices. In Africa, an estimated 5400 of the 60000 described plant taxa possess over 16300 therapeutic uses. Similarly, with a therapeutic flora comprising of approximately 650 species, herbal medical practitioners in South Africa, make use of a plethora of plants to treat different human diseases and infections. Over the years, studies have identified numerous plant species with potential against chronic metabolic diseases including type 2 diabetes mellitus (T2DM). Globally, the incidence and prevalence of T2DM have reached epidemic proportions affecting people of all ages, nationalities and ethnicity. Considered the fourth leading cause of deaths by disease, T2DM is a global health crisis with an estimated diagnosis and mortality frequency of 1 every 5 seconds and 1 every 7 seconds respectively. Though the exact pathophysiology of T2DM is not entirely understood, initial peripheral insulin resistance in adipose tissue, liver, and skeletal muscle with subsequent pancreatic β-cell dysfunction resulting from an attempt to compensate for insulin resistance is a common feature of the disease. The current approach to treating T2DM is the use of oral antidiabetic agents (OAAs), insulin, and incretin-based drugs in an attempt to achieve glycaemic control and maintain glucose homeostasis. However, conventional anti-T2DM drugs have been shown to have limited efficacies and serious adverse effects. Hence, the need for newer, more efficacious and safer anti-T2DM agents. Sutherlandia frutescens subsp. microphylla is a flowering shrub of the pea family (Fabaceae/Leguminaceae) found mainly in the Western Cape and Karoo regions of Southern Africa. Concoctions of various parts of the plant are used in the management of different ailments including T2DM. However, despite extensive biological and pharmacological studies, few analyses exist of the chemical constituents of S. frutescens and no Triple Time of Flight Liquid Chromatography with Mass Spectrometry (Triple TOF LC/MS/MS) analysis has been performed. The initial aim of this study was to investigate the phytochemical profile of hot aqueous, cold aqueous, 80% ethanolic, 100% ethanolic, 80% methanolic and 100% methanolic extracts of a single source S. frutescens plant material using colorimetric and spectrophotometric analysis. The hot aqueous extractant was found to be the best extractant for S. frutescens, yielding 1.99 g of crude extract from 16 g fresh powdered plant material. This data suggests that application of heat and water as the extractant (hot aqueous) could play a vital role in extraction of bioactive compounds from S. frutescens and also justifies the traditional use of a tea infusion of S. frutescens. Colorimetric analysis revealed the presence of flavonoids, flavonols, tannins, and phenols in all extracts with varying intensity. The organic extracts 100% methanol, 80% and 100% ethanol exhibited high color intensity (+++) for flavonoids and flavonols respectively, while all the extracts exhibited a moderate color intensity (++) for tannins and phenols. Spectrophotometric analysis of S. frutescens extracts revealed that all the organic extracts contained a significantly higher concentration (in mg/g of extract) of flavonols and tannins when compared to the aqueous extracts. All extracts contained approximately equal levels of phenols. These data confirm the presence of all four groups of bioactive phytocompounds in the S. frutescens extracts used in this study, and also confirm that different solvent extractants possess the capability to differentially extract specific groups of phytocompounds. in individual extracts. Further comparison of these compounds with online databases of anti-diabetic phytocompounds led to the preliminary identification of 10 possible anti-diabetic compounds; α-Pinene, Limonene, Sabinene, Carvone, Myricetin, Rutin, Stigmasterol, Emodin, Sarpagine and Hypoglycin B in crude and solid phase extraction (SPE) fractions of S. frutesecens. Furthermore, using two hepatic cell lines (Chang and HepG2) as an in-vtro model system, the anti-T2DM properties of crude aqueous and organic extracts of S. frutescents was investigated and compared. Both aqueous and organic extracts of S. frutescens were found to decrease gluconeogenesis, increase glucose uptake and decrease lipid accumulation (Triacylglycerol, Diacylglycerol, and Monoacylglycerol) in Chang and HepG2 hepatic cell cultures made insulin resistant (IR) following exposure to high concentration of insulin and fructose. Using real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), the aqueous and organic extracts of S. frutescens were confirmed to regulate the expression of Vesicle-associated membrane protein 3 (VAMP3), Mitogen-activated protein kinase 8 (MAPK8), and Insulin receptor substrate 1 (IRS1) in insulin resistant hepatic cells. IR-mediated downregulation of VAMP3, MAPK8, and IRS1 mRNA in IR HepG2 hepatic cell cultures was reversed in the presence of aqueous and organic extracts of S. frutescens. The hot aqueous extract displayed the highest activity in all the assays, while all the organic extracts displayed similar potency. In conclusion, this study reports that aqueous and organic extracts of S. frutescens possess numerous anti-diabetic compounds that can be further investigated for the development of new, more efficacious and less toxic anti-diabetic agents. The presence of multiple compounds in a single extract does suggest a synergistic or combinatorial therapeutic effect. These findings support the burgeoning body of in-vivo and in-vitro literature evidence on the anti-diabetic properties of S. frutescens and its use in folklore medicine.
- Full Text:
- Date Issued: 2016
Antifungal activity of silver nanoparticles on Cryptococcus species
- Authors: Roman, Nasstasja
- Date: 2021-04
- Subjects: Gqeberha (South Africa) , Eastern Cape (South Africa) , Cryptococcus
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/52089 , vital:43445
- Description: Cryptococcus neoformans is responsible for cryptococcal infections, which have become a great concern particularly in immunocompromised patients. This pulmonary disease causes damage to lung tissue and is presumed to be responsible for approximately 650,000 deaths annually. There is a major need for novel antimicrobial agents to avoid the emergence of resistant strains due to extended use of known antifungal drugs. Silver has become an important antimicrobial agent used in medical devices, cosmetics and even house-hold or clothing products. It is highly toxic and has a reduced risk of resistance. Silver nanoparticles have been broadly explored as an antimicrobial agent due to its high reactivity, large surface area and small size. They have been reported to display antimicrobial activity towards bacteria, viruses and fungi. C. neoformans is a pathogenic microorganism that possesses a number of virulence factors which increases the infectivity of the microorganism in immunocompromised individuals. Some of these include the presence of a polysaccharide capsule, melanin, urease and phospholipase production. Owing to limited availability of antifungal drugs and the possibility of drug resistance, this study focused on an alternative antimicrobial agent, namely silver nanoparticles, and the effects that silver nanoparticles had on fungal β-glucan, chitin and urease, phospholipase and melanin virulence factors. Results from our study show that silver nanoparticles inhibited the growth of C. neoformans at concentrations between 3.125 ƒM and 25 ƒM. Both 26.4 nm and 28.4 nm nanoparticles displayed growth inhibition, but were unable to kill the organism at concentrations of 200 ƒM and above. The silver nanoparticles caused a reduction in βglucan content. There was also an accumulation of intracellular ROS, and phospholipase activity, was reduced. In contrast, the organism displayed an increase in chitin content, melanin and urease activity upon exposure to the nanoparticles. This study shows that chemically synthesized silver nanoparticles are an effective antifungal alternative that greatly reduces or inhibits C. neoformans growth at very low concentrations (ƒM). For future studies it may be feasible to investigate the use of these nanoparticles in combination with known antifungal agents, to prevent the emergence of resistance and inhibit possible defense mechanisms displayed by the organism. , Thesis (MSc) -- Faculty of Science, School of Biomolecular and Chemical Sciences, 2021
- Full Text: false
- Date Issued: 2021-04
- Authors: Roman, Nasstasja
- Date: 2021-04
- Subjects: Gqeberha (South Africa) , Eastern Cape (South Africa) , Cryptococcus
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/52089 , vital:43445
- Description: Cryptococcus neoformans is responsible for cryptococcal infections, which have become a great concern particularly in immunocompromised patients. This pulmonary disease causes damage to lung tissue and is presumed to be responsible for approximately 650,000 deaths annually. There is a major need for novel antimicrobial agents to avoid the emergence of resistant strains due to extended use of known antifungal drugs. Silver has become an important antimicrobial agent used in medical devices, cosmetics and even house-hold or clothing products. It is highly toxic and has a reduced risk of resistance. Silver nanoparticles have been broadly explored as an antimicrobial agent due to its high reactivity, large surface area and small size. They have been reported to display antimicrobial activity towards bacteria, viruses and fungi. C. neoformans is a pathogenic microorganism that possesses a number of virulence factors which increases the infectivity of the microorganism in immunocompromised individuals. Some of these include the presence of a polysaccharide capsule, melanin, urease and phospholipase production. Owing to limited availability of antifungal drugs and the possibility of drug resistance, this study focused on an alternative antimicrobial agent, namely silver nanoparticles, and the effects that silver nanoparticles had on fungal β-glucan, chitin and urease, phospholipase and melanin virulence factors. Results from our study show that silver nanoparticles inhibited the growth of C. neoformans at concentrations between 3.125 ƒM and 25 ƒM. Both 26.4 nm and 28.4 nm nanoparticles displayed growth inhibition, but were unable to kill the organism at concentrations of 200 ƒM and above. The silver nanoparticles caused a reduction in βglucan content. There was also an accumulation of intracellular ROS, and phospholipase activity, was reduced. In contrast, the organism displayed an increase in chitin content, melanin and urease activity upon exposure to the nanoparticles. This study shows that chemically synthesized silver nanoparticles are an effective antifungal alternative that greatly reduces or inhibits C. neoformans growth at very low concentrations (ƒM). For future studies it may be feasible to investigate the use of these nanoparticles in combination with known antifungal agents, to prevent the emergence of resistance and inhibit possible defense mechanisms displayed by the organism. , Thesis (MSc) -- Faculty of Science, School of Biomolecular and Chemical Sciences, 2021
- Full Text: false
- Date Issued: 2021-04
Antiproliferative activity of novel rhenium complexes and medicinal plant extracts
- Oosthuizen, Kenneth Thomas, Venables, Luanne
- Authors: Oosthuizen, Kenneth Thomas , Venables, Luanne
- Date: 2021-04
- Subjects: Gqeberha (South Africa) , Eastern Cape (South Africa) , Medicinal plants -- South Africa
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/52028 , vital:43441
- Description: Cancer is a complex, multifactorial disease that affects millions of individuals every year. The adverse side effects and escalating costs of current therapies coupled with the increased incidence of resistance to these therapies make it imperative that we explore novel treatments for the disease. This study investigated two avenues for novel drug design namely, novel synthetic compounds and medicinal plant extracts. The benzimidazole ring system has shown potential as a scaffold for designing novel anticancer agents. Conjugation of the metal rhenium to novel variants of this ring system open up the possibility of designing novel drugs that serve both a diagnostic and a therapeutic function. This study investigated the in vitro anticancer potential of ten such complexes against selected breast and cervical cancer cell lines. The selectivity of the complexes for cancer cells over normal cells was also investigated while the mechanism of action of effective complexes was determined by exploring cell cycle arrest, biochemical markers of apoptosis and mitochondrial membrane disruption. All ten complexes were screened against MCF7 breast and HeLa cervical cancer cell lines with four showing antiproliferative activity against both cancer cell lines and one showing cell line specific toxicity against MCF7 breast cancer cells. When looking at the SAR of the compounds it was noted that activity was higher in compounds which contain two potentially bidentate benzothiazole ligands, while compounds with potentially tridentate ligands show good activity, but only if the benzothiazole moiety is not involved in coordination. The complexes showed greater antiproliferative activity against the MCF7 breast cancer cells with IC50 values ranging from 3.2 to 7.0 µM versus a range of 7.6 to 24.4 µM being obtained on the HeLa cervical cancer cells. Antiproliferative complexes were tested against confluent and log phase Vero cells at their respective IC50 values to determine their effect on “normal” cells. Confluent Vero cells showed less cell death than those in log phase indicating that the complexes show preference for proliferating cells. The mechanism of action of the complexes was studied on both cancer cell lines via cell cycle analysis and apoptosis assays investigating phosphatidylserine translocation, caspase -3 and -8 activation and mitochondrial membrane potential with most complexes inducing cell cycle arrest followed by cell death via both the extrinsic and intrinsic pathways of apoptosis. Since 1940, 49% of all the available anticancer drugs approved for cancer treatment were natural products or directly derived from natural products. Plants are an excellent source of secondary metabolites, many of which are unique chemical compounds that cannot be synthesized in a laboratory. Ethnobotanical surveys conducted in conjunction with Traditional Health Practitioners of the Mkuranga and Same districts in Tanzania identified 25 plants that are used for the treatment of cancer. Four of these plants (A. mossambicensis, C. adenocaule, C. pseudopulchelusis and R. natalensis) with ethnobotanically reported anticancer usage showed cytotoxic activity against brine shrimp and were selected for further in vitro anticancer studies. All four plants were found to have antiproliferative activity against HeLa cervical cancer cells with IC50 values ranging from 3.4 to 50.8 µg/mL. This study was also tasked with investigating the mechanism of action of C. pseudopulchelus on HeLa cervical cancer cells by exploring cell cycle arrest, biochemical markers of apoptosis and mitochondrial membrane x disruption. C. pseudopulchelus caused early M phase arrest followed by slippage and subsequent cell death via the extrinsic pathway of apoptosis. In conclusion, this study showed that both novel complexes as well as medicinal plant extracts represent an interesting avenue for the development of novel anticancer drugs that are cheaper and produce less side effects than current therapies. , Thesis (MSc) -- Faculty of Science, School of Biomolecular and Chemical Sciences, 2021
- Full Text: false
- Date Issued: 2021-04
- Authors: Oosthuizen, Kenneth Thomas , Venables, Luanne
- Date: 2021-04
- Subjects: Gqeberha (South Africa) , Eastern Cape (South Africa) , Medicinal plants -- South Africa
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/52028 , vital:43441
- Description: Cancer is a complex, multifactorial disease that affects millions of individuals every year. The adverse side effects and escalating costs of current therapies coupled with the increased incidence of resistance to these therapies make it imperative that we explore novel treatments for the disease. This study investigated two avenues for novel drug design namely, novel synthetic compounds and medicinal plant extracts. The benzimidazole ring system has shown potential as a scaffold for designing novel anticancer agents. Conjugation of the metal rhenium to novel variants of this ring system open up the possibility of designing novel drugs that serve both a diagnostic and a therapeutic function. This study investigated the in vitro anticancer potential of ten such complexes against selected breast and cervical cancer cell lines. The selectivity of the complexes for cancer cells over normal cells was also investigated while the mechanism of action of effective complexes was determined by exploring cell cycle arrest, biochemical markers of apoptosis and mitochondrial membrane disruption. All ten complexes were screened against MCF7 breast and HeLa cervical cancer cell lines with four showing antiproliferative activity against both cancer cell lines and one showing cell line specific toxicity against MCF7 breast cancer cells. When looking at the SAR of the compounds it was noted that activity was higher in compounds which contain two potentially bidentate benzothiazole ligands, while compounds with potentially tridentate ligands show good activity, but only if the benzothiazole moiety is not involved in coordination. The complexes showed greater antiproliferative activity against the MCF7 breast cancer cells with IC50 values ranging from 3.2 to 7.0 µM versus a range of 7.6 to 24.4 µM being obtained on the HeLa cervical cancer cells. Antiproliferative complexes were tested against confluent and log phase Vero cells at their respective IC50 values to determine their effect on “normal” cells. Confluent Vero cells showed less cell death than those in log phase indicating that the complexes show preference for proliferating cells. The mechanism of action of the complexes was studied on both cancer cell lines via cell cycle analysis and apoptosis assays investigating phosphatidylserine translocation, caspase -3 and -8 activation and mitochondrial membrane potential with most complexes inducing cell cycle arrest followed by cell death via both the extrinsic and intrinsic pathways of apoptosis. Since 1940, 49% of all the available anticancer drugs approved for cancer treatment were natural products or directly derived from natural products. Plants are an excellent source of secondary metabolites, many of which are unique chemical compounds that cannot be synthesized in a laboratory. Ethnobotanical surveys conducted in conjunction with Traditional Health Practitioners of the Mkuranga and Same districts in Tanzania identified 25 plants that are used for the treatment of cancer. Four of these plants (A. mossambicensis, C. adenocaule, C. pseudopulchelusis and R. natalensis) with ethnobotanically reported anticancer usage showed cytotoxic activity against brine shrimp and were selected for further in vitro anticancer studies. All four plants were found to have antiproliferative activity against HeLa cervical cancer cells with IC50 values ranging from 3.4 to 50.8 µg/mL. This study was also tasked with investigating the mechanism of action of C. pseudopulchelus on HeLa cervical cancer cells by exploring cell cycle arrest, biochemical markers of apoptosis and mitochondrial membrane x disruption. C. pseudopulchelus caused early M phase arrest followed by slippage and subsequent cell death via the extrinsic pathway of apoptosis. In conclusion, this study showed that both novel complexes as well as medicinal plant extracts represent an interesting avenue for the development of novel anticancer drugs that are cheaper and produce less side effects than current therapies. , Thesis (MSc) -- Faculty of Science, School of Biomolecular and Chemical Sciences, 2021
- Full Text: false
- Date Issued: 2021-04
AP-MOVPE growth and characterisation of GaSb/GaAs quantum dots
- Authors: Tile, Ngcali
- Date: 2018
- Subjects: Quantum theory , Quantum electronics Quantum dots Semiconductors
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/36716 , vital:34047
- Description: GaSb/GaAs quantum dots (QD) were grown by atmospheric pressure (AP) metal-organic vapour phase epitaxy (MOVPE) using triethylgallium (TEGa), tertiarybutylarsine (tBAs) and trimethylantimony (TMSb) as gallium (Ga), arsenic (As) and (Sb) sources, respectively. The effect of AP-MOVPE growth parameters on the formation of GaSb QD structures on GaAs was studied. The formation of small, coherent GaSb dots on GaAs improved with decreasing V/III ratios, which were controlled through changing either the TMSb/TEGa ratio at a constant growth temperature or changing the growth temperature at a constant TMSb/TEGa ratio. The maximum effective V/III ratio for dot formation was 0.175. The dot density was more sensitive to growth time than to source mole fraction in the reactor, since time determines the amount of deposited material. The dot density increased with increasing growth time, while the shape and size of the dots were more sensitive to the source vapour mole fraction, which controls the growth rate. Lower mole fractions resulted in smaller sized dots with a more uniform distribution compared to higher mole fractions. Dome-shaped dots with densities as high as 4×1010 cm-2, average base length of 35 nm and average height of 5 nm were achieved. Capping of GaSb QDs at high temperatures caused flattening and the formation of a thin, inhomogeneous GaSb layer inside GaAs. No obvious QD photoluminescence (PL) peak was detected for these samples. A two stage process for capping the dots (involving growth of a low temperature GaAs cap, followed by a high temperature cap) led to the retention of the dot-like features in/on a wetting layer (WL) of GaSb and distinct PL peaks for both the QDs and WL. An increase in excitation power during PL measurements for this particular sample caused the QD and WL peaks to shift to higher energies. This is attributed to electrostatic band bending, leading to triangular potential wells, typical for type II band alignment between GaAs and strained GaSb. Variable temperature PL measurements showed the decrease in the intensity of the WL peak to be faster than that of the QD peak as the measurement temperature increased. A detailed high resolution transmission electron microscopy analysis was performed to study the morphology and chemical interaction between GaAs and GaSb regions for capped GaSb/GaAs QDs. The capped dots had dimensions similar to those of uncapped dots and had a higher concentration of Sb at their center, with the periphery being intermixed with GaAs. Measurement of lattice strain performed inside these dots revealed the strain to be distributed inhomogenously throughout the dot area. The effect of GaAs host matrix on excitonic behaviour in AP-MOVPE grown GaSb/GaAs quantum dots was investigated. Room temperature (RT) PL emission was achieved from a single layer of quantum dots by controlling the GaAs host matrix growth temperature. These samples were prepared using a GaSb dot growth temperature of 530 °C, followed by growth of a thin GaAs ‘cold’ cap, before depositing the final part of the GaAs capping layer at either 550 °C, 600 °C or 650 °C. PL measurements at 10 K revealed QD emission peaks for all the samples at around 1.1 eV. However, variable temperature PL revealed different thermal quenching rates of the emission, with the rates of quenching reduced with increasing GaAs growth temperature. This was ascribed to reduced defect densities in GaAs grown at higher temperature, which resulted in QD emission even at RT. This RT emission peaked at approximately 1 eV. The hole localisation energy determined for these samples at RT was approximately 470 meV.
- Full Text:
- Date Issued: 2018
- Authors: Tile, Ngcali
- Date: 2018
- Subjects: Quantum theory , Quantum electronics Quantum dots Semiconductors
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/36716 , vital:34047
- Description: GaSb/GaAs quantum dots (QD) were grown by atmospheric pressure (AP) metal-organic vapour phase epitaxy (MOVPE) using triethylgallium (TEGa), tertiarybutylarsine (tBAs) and trimethylantimony (TMSb) as gallium (Ga), arsenic (As) and (Sb) sources, respectively. The effect of AP-MOVPE growth parameters on the formation of GaSb QD structures on GaAs was studied. The formation of small, coherent GaSb dots on GaAs improved with decreasing V/III ratios, which were controlled through changing either the TMSb/TEGa ratio at a constant growth temperature or changing the growth temperature at a constant TMSb/TEGa ratio. The maximum effective V/III ratio for dot formation was 0.175. The dot density was more sensitive to growth time than to source mole fraction in the reactor, since time determines the amount of deposited material. The dot density increased with increasing growth time, while the shape and size of the dots were more sensitive to the source vapour mole fraction, which controls the growth rate. Lower mole fractions resulted in smaller sized dots with a more uniform distribution compared to higher mole fractions. Dome-shaped dots with densities as high as 4×1010 cm-2, average base length of 35 nm and average height of 5 nm were achieved. Capping of GaSb QDs at high temperatures caused flattening and the formation of a thin, inhomogeneous GaSb layer inside GaAs. No obvious QD photoluminescence (PL) peak was detected for these samples. A two stage process for capping the dots (involving growth of a low temperature GaAs cap, followed by a high temperature cap) led to the retention of the dot-like features in/on a wetting layer (WL) of GaSb and distinct PL peaks for both the QDs and WL. An increase in excitation power during PL measurements for this particular sample caused the QD and WL peaks to shift to higher energies. This is attributed to electrostatic band bending, leading to triangular potential wells, typical for type II band alignment between GaAs and strained GaSb. Variable temperature PL measurements showed the decrease in the intensity of the WL peak to be faster than that of the QD peak as the measurement temperature increased. A detailed high resolution transmission electron microscopy analysis was performed to study the morphology and chemical interaction between GaAs and GaSb regions for capped GaSb/GaAs QDs. The capped dots had dimensions similar to those of uncapped dots and had a higher concentration of Sb at their center, with the periphery being intermixed with GaAs. Measurement of lattice strain performed inside these dots revealed the strain to be distributed inhomogenously throughout the dot area. The effect of GaAs host matrix on excitonic behaviour in AP-MOVPE grown GaSb/GaAs quantum dots was investigated. Room temperature (RT) PL emission was achieved from a single layer of quantum dots by controlling the GaAs host matrix growth temperature. These samples were prepared using a GaSb dot growth temperature of 530 °C, followed by growth of a thin GaAs ‘cold’ cap, before depositing the final part of the GaAs capping layer at either 550 °C, 600 °C or 650 °C. PL measurements at 10 K revealed QD emission peaks for all the samples at around 1.1 eV. However, variable temperature PL revealed different thermal quenching rates of the emission, with the rates of quenching reduced with increasing GaAs growth temperature. This was ascribed to reduced defect densities in GaAs grown at higher temperature, which resulted in QD emission even at RT. This RT emission peaked at approximately 1 eV. The hole localisation energy determined for these samples at RT was approximately 470 meV.
- Full Text:
- Date Issued: 2018
Aplousobranch ascidians (Tunicata: Ascidiacea) from Southern Africa
- Authors: Parker-Nance, Shirley
- Date: 2003
- Subjects: Sea squirts -- South Africa -- Classification , Aplousobranchia -- South Africa -- Classification
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:11078 , http://hdl.handle.net/10948/311 , Sea squirts -- South Africa -- Classification , Aplousobranchia -- South Africa -- Classification
- Description: The ascidian (subphylum Tunicata: class Ascidiacea) fauna along the southern African coast constitutes an important component of the sessile benthic reef fauna. Little is known of the species composition, biodiversity and distribution of ascidians on southern African intertidal and subtidal reefs. Past research on the ascidian fauna of South Africa was sporadic and limited, with only about one hundred and seventy species recorded during the last one hundred and twenty years. This is the first taxonomic study undertaken by a South African resident scientist. The study focused on six genera in four families (Euherdmaniidae, Polyclinidae, Pseudodistomidae and Didemnidae) belonging to the class Ascidiacea and suborder Aplousobranchia. Five species new to science, two Polyclinum, two Pseudodistoma and one Polysyncraton species are described. New additional information on the distribution of five species previously known to science, including one recorded for the first time along the South African coast, is presented. A literature review and comparison of the taxonomic important characteristics is made of all species known globally for the six genera. These six genera comprise twelve Euherdmania, fifteen Aplidiopsis, forty Polyclinum thirty-one Pseudodistoma, six Atriolum and sixty-eight Polysyncraton species.
- Full Text:
- Date Issued: 2003
- Authors: Parker-Nance, Shirley
- Date: 2003
- Subjects: Sea squirts -- South Africa -- Classification , Aplousobranchia -- South Africa -- Classification
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:11078 , http://hdl.handle.net/10948/311 , Sea squirts -- South Africa -- Classification , Aplousobranchia -- South Africa -- Classification
- Description: The ascidian (subphylum Tunicata: class Ascidiacea) fauna along the southern African coast constitutes an important component of the sessile benthic reef fauna. Little is known of the species composition, biodiversity and distribution of ascidians on southern African intertidal and subtidal reefs. Past research on the ascidian fauna of South Africa was sporadic and limited, with only about one hundred and seventy species recorded during the last one hundred and twenty years. This is the first taxonomic study undertaken by a South African resident scientist. The study focused on six genera in four families (Euherdmaniidae, Polyclinidae, Pseudodistomidae and Didemnidae) belonging to the class Ascidiacea and suborder Aplousobranchia. Five species new to science, two Polyclinum, two Pseudodistoma and one Polysyncraton species are described. New additional information on the distribution of five species previously known to science, including one recorded for the first time along the South African coast, is presented. A literature review and comparison of the taxonomic important characteristics is made of all species known globally for the six genera. These six genera comprise twelve Euherdmania, fifteen Aplidiopsis, forty Polyclinum thirty-one Pseudodistoma, six Atriolum and sixty-eight Polysyncraton species.
- Full Text:
- Date Issued: 2003
Application of bacteriocins in the preservation of fruit juice
- Authors: Bodley, Mark David
- Date: 2015
- Subjects: Bacteriocins , Fruit juices -- Preservation
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10345 , http://hdl.handle.net/10948/d1020188
- Description: Bacteriocins (BCNs) are ribosomally synthesized polypeptides or proteins with antimicrobial activity, produced by different groups of bacteria. Many lactic acid bacteria (LAB) produce BCNs with broad spectra of inhibition. The antimicrobial activity of BCNs against spoilage organisms (SPOs) has raised considerable interest in their application in juice preservation. The objectives of the study were to: (i) isolate, identify and screen BCN producing bacteria for antimicrobial activity against spoilage bacteria and fungi, (ii) optimize production of BCN from selected producers and (iii) investigate the industrial application of the BCN as a preservative in fruit juice. Eleven LAB strains of BCN producers were screened for antimicrobial activity. BCNs from Lactobacillus plantarum and Pediococcus pentosaceus 34 were the most effective against juice spoilage bacteria and fungi. The effect of medium components on bacteriocin production in L. plantarum and P. pentosaceus 34 was also determined. Clementine:Valencia (1:1) juice was used for the first time as the growth medium for L. plantarum and P. pentosaceus 34. The BCN from L. plantarum showed the highest activity and was, therefore, chosen for juice fermentation studies. The identification of L. plantarum was confirmed by biochemical tests, polymerase chain reaction (PCR) and sequencing of the recA gene. The highest BCN activity was observed for L. plantarum grown in De Man-Rogosa-Sharpe (MRS) and a combination of all supplements (i.e. peptone, MnSO4.H2O, Tween 80, glucose and whey), followed by MRS and Tween 80, peptone, MnSO4.H2O and MRS alone. MRS was a better medium for BCN production than juice [Clementine:Valencia (1:1)]. Size exclusion chromatography (SEC) was used to isolate the active L. plantarum BCN fraction which corresponded to an approximate molecular weight of 3.2 kDa and was proteinaceous in nature. Plantaricin structural genes (plnEF, plnJ, plnK, plnN) were detected in the L. plantarum strain by PCR and sequenced, and were chromosomally encoded as no plasmids could be detected. This implies that the BCN from L. plantarum is most likely a type of class IIa plantaricin which is responsible for the broad inhibitory activity observed. For the industrial application studies, L. plantarum BCN-containing cell free supernatant (BCNsup) added to “Ready to Drink” (RTD) Clementine:Valencia (1:1) juice at concentrations of 3 600 - 500 000 ppm decreased growth of SPOs, Lactobacillus acidophilus and Streptococcus thermophilus. At 250 000 ppm, the L. plantarum BCNsup achieved 5.3 and 6.8 log reductions of the L. acidophilus, after 24 and 48 h, respectively, which is larger than the USFDA (2001) requirement of a 5 log reduction in SPO activity, for preservation of fruit juices. However, there was a decrease in the activity when the BCNsup was applied to industrial (Valor) RTD juice (mango-orange) at decreasing concentrations of 100 000, 50 000 and 25 000 ppm. Organoleptic tests showed that the BCN did not alter flavor or taste of the juice and did not cause toxicity or allergic reactions. A food safety risk assessment was conducted in order to determine the Critical Control Point(s) [CCP(s)] at which the BCN could be applied to control identified microbiological hazards, and a Hazard Analysis and Critical Control Point (HACCP) plan was developed. This is the first report on the optimisation of L. plantarum BCN production in juice [Clementine:Valencia (1:1)], followed by inoculation into RTD juice (mango-orange), including a HACCP plan for the application of the BCN as a preservative in juice.
- Full Text:
- Date Issued: 2015
- Authors: Bodley, Mark David
- Date: 2015
- Subjects: Bacteriocins , Fruit juices -- Preservation
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10345 , http://hdl.handle.net/10948/d1020188
- Description: Bacteriocins (BCNs) are ribosomally synthesized polypeptides or proteins with antimicrobial activity, produced by different groups of bacteria. Many lactic acid bacteria (LAB) produce BCNs with broad spectra of inhibition. The antimicrobial activity of BCNs against spoilage organisms (SPOs) has raised considerable interest in their application in juice preservation. The objectives of the study were to: (i) isolate, identify and screen BCN producing bacteria for antimicrobial activity against spoilage bacteria and fungi, (ii) optimize production of BCN from selected producers and (iii) investigate the industrial application of the BCN as a preservative in fruit juice. Eleven LAB strains of BCN producers were screened for antimicrobial activity. BCNs from Lactobacillus plantarum and Pediococcus pentosaceus 34 were the most effective against juice spoilage bacteria and fungi. The effect of medium components on bacteriocin production in L. plantarum and P. pentosaceus 34 was also determined. Clementine:Valencia (1:1) juice was used for the first time as the growth medium for L. plantarum and P. pentosaceus 34. The BCN from L. plantarum showed the highest activity and was, therefore, chosen for juice fermentation studies. The identification of L. plantarum was confirmed by biochemical tests, polymerase chain reaction (PCR) and sequencing of the recA gene. The highest BCN activity was observed for L. plantarum grown in De Man-Rogosa-Sharpe (MRS) and a combination of all supplements (i.e. peptone, MnSO4.H2O, Tween 80, glucose and whey), followed by MRS and Tween 80, peptone, MnSO4.H2O and MRS alone. MRS was a better medium for BCN production than juice [Clementine:Valencia (1:1)]. Size exclusion chromatography (SEC) was used to isolate the active L. plantarum BCN fraction which corresponded to an approximate molecular weight of 3.2 kDa and was proteinaceous in nature. Plantaricin structural genes (plnEF, plnJ, plnK, plnN) were detected in the L. plantarum strain by PCR and sequenced, and were chromosomally encoded as no plasmids could be detected. This implies that the BCN from L. plantarum is most likely a type of class IIa plantaricin which is responsible for the broad inhibitory activity observed. For the industrial application studies, L. plantarum BCN-containing cell free supernatant (BCNsup) added to “Ready to Drink” (RTD) Clementine:Valencia (1:1) juice at concentrations of 3 600 - 500 000 ppm decreased growth of SPOs, Lactobacillus acidophilus and Streptococcus thermophilus. At 250 000 ppm, the L. plantarum BCNsup achieved 5.3 and 6.8 log reductions of the L. acidophilus, after 24 and 48 h, respectively, which is larger than the USFDA (2001) requirement of a 5 log reduction in SPO activity, for preservation of fruit juices. However, there was a decrease in the activity when the BCNsup was applied to industrial (Valor) RTD juice (mango-orange) at decreasing concentrations of 100 000, 50 000 and 25 000 ppm. Organoleptic tests showed that the BCN did not alter flavor or taste of the juice and did not cause toxicity or allergic reactions. A food safety risk assessment was conducted in order to determine the Critical Control Point(s) [CCP(s)] at which the BCN could be applied to control identified microbiological hazards, and a Hazard Analysis and Critical Control Point (HACCP) plan was developed. This is the first report on the optimisation of L. plantarum BCN production in juice [Clementine:Valencia (1:1)], followed by inoculation into RTD juice (mango-orange), including a HACCP plan for the application of the BCN as a preservative in juice.
- Full Text:
- Date Issued: 2015
Application of hidden Markov models and their extensions to animal movement data
- Authors: Van Niekerk, Bracken
- Date: 2018
- Subjects: Markov processes Animal locomotion Time-series analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/23835 , vital:30624
- Description: Hidden Markov Models (HMMs) have become increasingly popular in animal movement studies as they provide a flexible modelling approach and take the correlation between successive observations into account. They can segment the movement paths into latent states, which can be considered as rough proxies for the behaviours of the animals. This study comprises of two sections, both involving the application of HMMs to large terrestrial mammal movement data. Usually step lengths representing the displacement distances between successive observations, turning angles measuring the tortuosity, or a bivariate input of both variables are used as inputs in the models. It has been found in the literature that the turning angle is either included in the modelling process or it is excluded without much justification for doing so. The first part of this study investigates the nfluence of the turning angle on the model output and resultant interpretations of the HMMs when modelling the trajectories of large terrestrial mammals in southern Africa. Results revealed at different time scales, and for both predator and herbivore species in this study, that the turning angle does not influence the state allocation of the HMMs, which is the main output in terms of interpreting the behaviours of the animals. It is thought in most cases that the inclusion of the turning angle overcomplicates the models unnecessarily without contributing any additional information in terms of the behavioural interpretations or improving the overall fit of the models. This was found for the variety of movements of the species under observation in this study. The second part of this study attempts to validate the state allocation of the HMMs fitted to eland trajectories in the Greater Addo Elephant National Park in the Eastern Cape, with the use of camera trap data. This presented a unique opportunity as this type of data is mainly used for abundance or capture-recapture studies, and the HMMs are rarely validated as the true behaviours of the animals are seldom known. Results revealed that the same diel patterns were detected by the HMMs that were shown by the classified camera trap data. Direct comparisons of the observations where the dates and times matched for the telemetry and camera trap data could be done in several rare instances, which revealed many similarities. Although it was not an ideal comparison, the camera trap data provided a rough validation of the state allocation of the HMMs used in the study.
- Full Text:
- Date Issued: 2018
- Authors: Van Niekerk, Bracken
- Date: 2018
- Subjects: Markov processes Animal locomotion Time-series analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/23835 , vital:30624
- Description: Hidden Markov Models (HMMs) have become increasingly popular in animal movement studies as they provide a flexible modelling approach and take the correlation between successive observations into account. They can segment the movement paths into latent states, which can be considered as rough proxies for the behaviours of the animals. This study comprises of two sections, both involving the application of HMMs to large terrestrial mammal movement data. Usually step lengths representing the displacement distances between successive observations, turning angles measuring the tortuosity, or a bivariate input of both variables are used as inputs in the models. It has been found in the literature that the turning angle is either included in the modelling process or it is excluded without much justification for doing so. The first part of this study investigates the nfluence of the turning angle on the model output and resultant interpretations of the HMMs when modelling the trajectories of large terrestrial mammals in southern Africa. Results revealed at different time scales, and for both predator and herbivore species in this study, that the turning angle does not influence the state allocation of the HMMs, which is the main output in terms of interpreting the behaviours of the animals. It is thought in most cases that the inclusion of the turning angle overcomplicates the models unnecessarily without contributing any additional information in terms of the behavioural interpretations or improving the overall fit of the models. This was found for the variety of movements of the species under observation in this study. The second part of this study attempts to validate the state allocation of the HMMs fitted to eland trajectories in the Greater Addo Elephant National Park in the Eastern Cape, with the use of camera trap data. This presented a unique opportunity as this type of data is mainly used for abundance or capture-recapture studies, and the HMMs are rarely validated as the true behaviours of the animals are seldom known. Results revealed that the same diel patterns were detected by the HMMs that were shown by the classified camera trap data. Direct comparisons of the observations where the dates and times matched for the telemetry and camera trap data could be done in several rare instances, which revealed many similarities. Although it was not an ideal comparison, the camera trap data provided a rough validation of the state allocation of the HMMs used in the study.
- Full Text:
- Date Issued: 2018
Applications of complex functions on problems in Banach algebras
- Authors: Snyman, Jandré Dillon
- Date: 2019
- Subjects: Banach algebras , Functions of several complex variables
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/48643 , vital:41055
- Description: In this dissertation, we provide applications of complex function theory to problems in Banach algebras. We discuss the structure of analytic functions f : D → A, where D is a domain of C and A is a Banach algebra as given by Aupetit in [3]: either the set {λ ∈ D : Sp(f(λ)) is finite} is of capacity zero, or there exists an integer n such that Sp(f(λ)) has exactly n elements, for every λ, except on a closed, discrete set of capacity zero, where the spectrum has at most n−1 elements. This deep result, which describes the structure of Sp(f(λ)) for all λ ∈ D, relies heavily on subharmonic techniques, which are also included in the dissertation. Let A and B be Banach algebras. A linear mapping φ : A → B is called a Jordan homomorphism if and only if φ(xy + yx) = φ(x)φ(y) + φ(y)φ(x) for every x, y ∈ A. This is equivalent to saying that φ(x 2 ) = φ(x) 2 for every x ∈ A. The following problem, due to I. Kaplansky, is still unsolved for the general Banach algebra case: Let A and B be unital Banach algebras and φ : A → B a unital, invertibility preserving linear mapping. Under what conditions of A and B is φ a Jordan homomorphism? The author’s honours project [24] served as an exposition of the GleasonKahane-Żelazko Theorem [7, Theorem 4], which provides an answer to Kaplansky’s problem in the case where B = C. In this dissertation we look at other special cases of Kaplansky’s problem, such as the case where A and B are von Neumann algberas, as solved by Aupetit [4, Theorem 1.3] and remark that his result holds for the more general case where A is any C ∗ -algebra that has the property that every self-adjoint element is the limit of a sequence of linear combinations of orthogonal idempotents in A, and B is a semi-simple Banach algebra. This result relies heavily on complex function theory, spectral theory and holomorphic functional calculus. We also provide detailed expositions of the work of Taylor [27] in which an operator calculus on undounded, closed linear operators is developed, and the work of Allan [1] in which a holomorphic functional calculus is defined for locally convex algebras.
- Full Text:
- Date Issued: 2019
- Authors: Snyman, Jandré Dillon
- Date: 2019
- Subjects: Banach algebras , Functions of several complex variables
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/48643 , vital:41055
- Description: In this dissertation, we provide applications of complex function theory to problems in Banach algebras. We discuss the structure of analytic functions f : D → A, where D is a domain of C and A is a Banach algebra as given by Aupetit in [3]: either the set {λ ∈ D : Sp(f(λ)) is finite} is of capacity zero, or there exists an integer n such that Sp(f(λ)) has exactly n elements, for every λ, except on a closed, discrete set of capacity zero, where the spectrum has at most n−1 elements. This deep result, which describes the structure of Sp(f(λ)) for all λ ∈ D, relies heavily on subharmonic techniques, which are also included in the dissertation. Let A and B be Banach algebras. A linear mapping φ : A → B is called a Jordan homomorphism if and only if φ(xy + yx) = φ(x)φ(y) + φ(y)φ(x) for every x, y ∈ A. This is equivalent to saying that φ(x 2 ) = φ(x) 2 for every x ∈ A. The following problem, due to I. Kaplansky, is still unsolved for the general Banach algebra case: Let A and B be unital Banach algebras and φ : A → B a unital, invertibility preserving linear mapping. Under what conditions of A and B is φ a Jordan homomorphism? The author’s honours project [24] served as an exposition of the GleasonKahane-Żelazko Theorem [7, Theorem 4], which provides an answer to Kaplansky’s problem in the case where B = C. In this dissertation we look at other special cases of Kaplansky’s problem, such as the case where A and B are von Neumann algberas, as solved by Aupetit [4, Theorem 1.3] and remark that his result holds for the more general case where A is any C ∗ -algebra that has the property that every self-adjoint element is the limit of a sequence of linear combinations of orthogonal idempotents in A, and B is a semi-simple Banach algebra. This result relies heavily on complex function theory, spectral theory and holomorphic functional calculus. We also provide detailed expositions of the work of Taylor [27] in which an operator calculus on undounded, closed linear operators is developed, and the work of Allan [1] in which a holomorphic functional calculus is defined for locally convex algebras.
- Full Text:
- Date Issued: 2019
Applied phylogeography : mapping the genetic resource of Honeybush across the Cape Floristic Region
- Authors: Galuszynski, Nicholas C
- Date: 2020
- Subjects: Phylogeography -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/46771 , vital:39655
- Description: Aim: Honeybush tea is a herbal infusion made from members of the Cape Floristic Region (CFR) endemic Cyclopia Vent. Consting of 21 extant species, six are anthropogenically redistributed across the CFR for Honeybush cultivation. However, with no information regarding the distribution and levels of genetic diversity among wild Honeybush populations, anthropogenic translocation of cultivated genotypes may risk disrupting natural genetic diversity patterns. In this thesis, an applied phylogeographic approach is used to provide baseline insights into the spatial structuring of Honeybush genetic diversity. Location: The Cape Floristic Region (CFR), located along the southern Cape of South Africa. Methods: Spatial structuring of evolutionary lineages within Cyclopia are explored at a genus level using data generated from the combination of Anchored Hybrid Enrichment library preparation and high through put sequencing. A High Resolution Melt analysis (HRM) toolkit is then developed to screen haplotype variation across three non-coding chloroplast loci. This HRM toolkit coupled with haplotype confirmation Sanger sequencing is then applied to describe the spatial structuring of genetic diversity in wild populations for two Honeybush species (C. intermedia and C. subternata) and to compare genetic diversity among wild and cultivated populations of three Honeybush species (C. intermedia, C. subternata, and C. longifolia). A reanalysis of published phylogeographic data focusing on CFR plant taxa is used to test if phylogeographic breaks occur across the boundaries among adjacent Centers of Endemism (CoEs). Finally, the low-copy nuclear data set generated via AHE and high throughput sequencing is summarized. Results: Phylogeographic structuring was detected at the inter- and intraspecific levels in Cyclopia. The genus level analysis revealed a strong phylogenetic split between western CFR and eastern CFR endemic species in the nuclear and chloroplast genomes. At the intraspecific level, HRM proved to be a high throughput and accurate tool for haplotype detection, revealing phylogeographic structuring of genetic diversity in C.intermediaand C.subternata. This genetic diversity and structuring was not detected in cultivated Honeybush populations, which appear to have originated from a small number of founding individuals and have experienced a genetic bottleneck. Spatial structuring of genetic lineages is common among CFR plant taxa and the reanalysis of existing data found a significant trend for phylogeographic breaks tooccuracrosstheboundariesamongadjacentCoEs. Finally, over200000baseswere sequenced across 445 low-copy nuclear loci for 14 Cyclopia species. Conclusions: This thesis provides important baseline information on the spatial distribution of wild Honeybush genetic diversity. Phylogeographic structuring is present in wild Honeybush populations. This however is not accounted for in cultivated populations, which may place wild genetic diversity at risk of being disrupted if geneflow among wild and cultivated populations occurs. The results from this thesis should therefore be used to develop precautionary guidelines for the anthropogenic redistribution of Honeybush genetic material for cultivation. Furthermore, the novel insights into regional patterns of phylogeohraphic structuring of plant populations should encourage more efficient and hypothesis driven sampling designs in future phylogeographic work in the CFR. The high throughput sequence data generated in this thesis should transform Cyclopia to a model organism for the study of molecular evolution in the CFR.
- Full Text:
- Date Issued: 2020
- Authors: Galuszynski, Nicholas C
- Date: 2020
- Subjects: Phylogeography -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/46771 , vital:39655
- Description: Aim: Honeybush tea is a herbal infusion made from members of the Cape Floristic Region (CFR) endemic Cyclopia Vent. Consting of 21 extant species, six are anthropogenically redistributed across the CFR for Honeybush cultivation. However, with no information regarding the distribution and levels of genetic diversity among wild Honeybush populations, anthropogenic translocation of cultivated genotypes may risk disrupting natural genetic diversity patterns. In this thesis, an applied phylogeographic approach is used to provide baseline insights into the spatial structuring of Honeybush genetic diversity. Location: The Cape Floristic Region (CFR), located along the southern Cape of South Africa. Methods: Spatial structuring of evolutionary lineages within Cyclopia are explored at a genus level using data generated from the combination of Anchored Hybrid Enrichment library preparation and high through put sequencing. A High Resolution Melt analysis (HRM) toolkit is then developed to screen haplotype variation across three non-coding chloroplast loci. This HRM toolkit coupled with haplotype confirmation Sanger sequencing is then applied to describe the spatial structuring of genetic diversity in wild populations for two Honeybush species (C. intermedia and C. subternata) and to compare genetic diversity among wild and cultivated populations of three Honeybush species (C. intermedia, C. subternata, and C. longifolia). A reanalysis of published phylogeographic data focusing on CFR plant taxa is used to test if phylogeographic breaks occur across the boundaries among adjacent Centers of Endemism (CoEs). Finally, the low-copy nuclear data set generated via AHE and high throughput sequencing is summarized. Results: Phylogeographic structuring was detected at the inter- and intraspecific levels in Cyclopia. The genus level analysis revealed a strong phylogenetic split between western CFR and eastern CFR endemic species in the nuclear and chloroplast genomes. At the intraspecific level, HRM proved to be a high throughput and accurate tool for haplotype detection, revealing phylogeographic structuring of genetic diversity in C.intermediaand C.subternata. This genetic diversity and structuring was not detected in cultivated Honeybush populations, which appear to have originated from a small number of founding individuals and have experienced a genetic bottleneck. Spatial structuring of genetic lineages is common among CFR plant taxa and the reanalysis of existing data found a significant trend for phylogeographic breaks tooccuracrosstheboundariesamongadjacentCoEs. Finally, over200000baseswere sequenced across 445 low-copy nuclear loci for 14 Cyclopia species. Conclusions: This thesis provides important baseline information on the spatial distribution of wild Honeybush genetic diversity. Phylogeographic structuring is present in wild Honeybush populations. This however is not accounted for in cultivated populations, which may place wild genetic diversity at risk of being disrupted if geneflow among wild and cultivated populations occurs. The results from this thesis should therefore be used to develop precautionary guidelines for the anthropogenic redistribution of Honeybush genetic material for cultivation. Furthermore, the novel insights into regional patterns of phylogeohraphic structuring of plant populations should encourage more efficient and hypothesis driven sampling designs in future phylogeographic work in the CFR. The high throughput sequence data generated in this thesis should transform Cyclopia to a model organism for the study of molecular evolution in the CFR.
- Full Text:
- Date Issued: 2020
Applying a systems analysis approach to support marine spatial planning in Algoa Bay, South Africa
- Authors: Vermeulen, Estee Ann
- Date: 2021-12
- Subjects: Port Elizabeth (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/54121 , vital:46312
- Description: Ocean health provides the foundation for human health through the provisioning of ecosystem services. Increasing demands on ocean space and resources are, however, resulting in a decline in ocean health, with direct and indirect knock-on effects on marine uses and ultimately on human health. In response, there is a growing need to acknowledge and better manage complex human-ocean interactions. This has been recognised in global sustainable development goals and in integrated ocean management processes, leading to widespread endorsement of an ecosystem-based marine spatial planning (MSP) process, including in South Africa. In support of the national MSP process, significant progress has been made in understanding the spatial extent of marine activities and associated marine pressures, but the temporal dynamics of marine activities and interconnections with the marine environment are less well understood. To plan for the growth of marine activities and associated user conflicts, the drivers of these temporal dynamics and associated feedback effects need to be analysed and potential policy and management interventions identified and tested. To support South Africa’s national MSP process, this study adopts a systems analysis approach, using system dynamics modelling, to explore the temporal change in marine uses under alternative growth scenarios in Algoa Bay. Algoa Bay is an appropriate study area because it is experiencing a rapid expansion of marine activities, coupled with a growing uncertainty regarding marine sustainability outcomes. To assist future marine management decisions, the Algoa Marine Systems Analysis Tool (Algoa MSAT) was developed, comprising seven sub-models. Five of the sub-models represent selected marine uses in Algoa Bay, whereas the sixth and seventh integrate the outputs from each marine use in terms of sustainable management indicators (marine health, marine wealth and marine labour). Model development primarily adopted an expert-based model ling approach, although the involvement of stakeholders, through a collaborative modelling process, assisted in integrating knowledge on different marine sectors’ activities, impacts and planning visions into the model framework. Model results were generated under different scenarios to investigate changes in the growth of marine activities and marine sustainability indicators under different levels of ocean governance. Under the baseline (or business-as-usual) model scenario, marine activities were shown to grow increasingly within their respective management limits, with an increase in marine wealth and labour and a consequential decrease in marine health. This scenario particularly highlights that current ocean governance practices are ineffective in sustaining the projected growth of the marine uses, particularly for those that are vulnerable to negative changes in marine health. Conversely, sectors that hold more value in marine wealth and are more resilient to changes in marine health, may continue to grow regardless of negative knock-on effects of the health of the marine environment and on other uses in the bay. This emphasises that an alternative governance strategy is needed to achieve the long-term goal of an ecosystem-based MSP process, as required by South African MSP legislation. To achieve this will require multiple, adaptive cross-sectoral management interventions that are directed towards the ‘deeper leverage points’ that are able to maintain the growth of marine activities within appropriate limits defined by marine health. Using the model interface developed in this project, decision-makers and stakeholders can use the model to explore the temporal dynamics in marine activities under different governance scenarios. Although the model is limited to Algoa Bay, the model boundary can be adapted to assist in marine planning processes at national or trans-national scales. Such analytical assessments and tools are critical to progress the ecosystem-based management approach in MSP, as is required to achieve global sustainable development goals. , Thesis (PhD) -- Faculty of Science, Coastal and Marine Research Unit, 2021
- Full Text:
- Date Issued: 2021-12
- Authors: Vermeulen, Estee Ann
- Date: 2021-12
- Subjects: Port Elizabeth (South Africa) , Eastern Cape (South Africa) , South Africa
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/54121 , vital:46312
- Description: Ocean health provides the foundation for human health through the provisioning of ecosystem services. Increasing demands on ocean space and resources are, however, resulting in a decline in ocean health, with direct and indirect knock-on effects on marine uses and ultimately on human health. In response, there is a growing need to acknowledge and better manage complex human-ocean interactions. This has been recognised in global sustainable development goals and in integrated ocean management processes, leading to widespread endorsement of an ecosystem-based marine spatial planning (MSP) process, including in South Africa. In support of the national MSP process, significant progress has been made in understanding the spatial extent of marine activities and associated marine pressures, but the temporal dynamics of marine activities and interconnections with the marine environment are less well understood. To plan for the growth of marine activities and associated user conflicts, the drivers of these temporal dynamics and associated feedback effects need to be analysed and potential policy and management interventions identified and tested. To support South Africa’s national MSP process, this study adopts a systems analysis approach, using system dynamics modelling, to explore the temporal change in marine uses under alternative growth scenarios in Algoa Bay. Algoa Bay is an appropriate study area because it is experiencing a rapid expansion of marine activities, coupled with a growing uncertainty regarding marine sustainability outcomes. To assist future marine management decisions, the Algoa Marine Systems Analysis Tool (Algoa MSAT) was developed, comprising seven sub-models. Five of the sub-models represent selected marine uses in Algoa Bay, whereas the sixth and seventh integrate the outputs from each marine use in terms of sustainable management indicators (marine health, marine wealth and marine labour). Model development primarily adopted an expert-based model ling approach, although the involvement of stakeholders, through a collaborative modelling process, assisted in integrating knowledge on different marine sectors’ activities, impacts and planning visions into the model framework. Model results were generated under different scenarios to investigate changes in the growth of marine activities and marine sustainability indicators under different levels of ocean governance. Under the baseline (or business-as-usual) model scenario, marine activities were shown to grow increasingly within their respective management limits, with an increase in marine wealth and labour and a consequential decrease in marine health. This scenario particularly highlights that current ocean governance practices are ineffective in sustaining the projected growth of the marine uses, particularly for those that are vulnerable to negative changes in marine health. Conversely, sectors that hold more value in marine wealth and are more resilient to changes in marine health, may continue to grow regardless of negative knock-on effects of the health of the marine environment and on other uses in the bay. This emphasises that an alternative governance strategy is needed to achieve the long-term goal of an ecosystem-based MSP process, as required by South African MSP legislation. To achieve this will require multiple, adaptive cross-sectoral management interventions that are directed towards the ‘deeper leverage points’ that are able to maintain the growth of marine activities within appropriate limits defined by marine health. Using the model interface developed in this project, decision-makers and stakeholders can use the model to explore the temporal dynamics in marine activities under different governance scenarios. Although the model is limited to Algoa Bay, the model boundary can be adapted to assist in marine planning processes at national or trans-national scales. Such analytical assessments and tools are critical to progress the ecosystem-based management approach in MSP, as is required to achieve global sustainable development goals. , Thesis (PhD) -- Faculty of Science, Coastal and Marine Research Unit, 2021
- Full Text:
- Date Issued: 2021-12
Applying high-resolution remote sensing to quantify baboon damage at a sub-compartment level in pine stands in the Mpumalanga escarpment region of South Africa
- Authors: Ferreira, Regardt
- Date: 2020
- Subjects: Environmental sciences -- Remote sensing , Geographic information systems Remote sensing
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49082 , vital:41599
- Description: Managing risk in intensively managed monoculture plantation forests is an essential task to ensure sustainable yield and a continuous flow of forest products. However, since risks can be either biotic or abiotic, not all of them have a predictable pattern of spread, which can cause severe losses if management does not have the chance to implement mitigation action. Monitoring the change in forest health is vital as this provides the opportunity for preventative management and quantifies the amount of damage that management has to deal with. To provide this window of opportunity for appropriate action, constant monitoring is required. Until recently, forest health was measured through field surveys which provided adequate data. This procedure, however, is time consuming. Remote sensing has become very popular as a monitoring tool, due to its ability to provide assessment data in a fraction of the time. In this study, baboon damage in plantations along the Mpumalanga escarpment area of South Africa was monitored using remote sensing methods. While there are many methods of forest health monitoring using remote sensing, some approaches are less suitable as they either monitor damage caused at a plantation level, use lower spatial resolution (>10m) datasets or map damage using one available time period. The purpose of this study was first to establish the impact of baboon damage through time, using Sentinel-2 satellite imagery with all vegetation indices available, and the Extreme Gradient Boosting (XGboost) algorithm. The second part focused on analysing the damage at a tree level using PlanetScope imagery using a deep Learning approach. Overall, the study found that the use of Sentinel-2 data and PlanetScope data could accurately distinguish between the varying severity of baboon damage, achieving an accuracy of 95% and 82%. The processing time of the deep learning Artificial Neural Network (ANN) was greatly affected by the number of hidden layers and neurons used. Implementation of techniques used in this study has the potential to improve the accuracy of forest health monitoring in compartment forestry in South Africa.
- Full Text:
- Date Issued: 2020
- Authors: Ferreira, Regardt
- Date: 2020
- Subjects: Environmental sciences -- Remote sensing , Geographic information systems Remote sensing
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49082 , vital:41599
- Description: Managing risk in intensively managed monoculture plantation forests is an essential task to ensure sustainable yield and a continuous flow of forest products. However, since risks can be either biotic or abiotic, not all of them have a predictable pattern of spread, which can cause severe losses if management does not have the chance to implement mitigation action. Monitoring the change in forest health is vital as this provides the opportunity for preventative management and quantifies the amount of damage that management has to deal with. To provide this window of opportunity for appropriate action, constant monitoring is required. Until recently, forest health was measured through field surveys which provided adequate data. This procedure, however, is time consuming. Remote sensing has become very popular as a monitoring tool, due to its ability to provide assessment data in a fraction of the time. In this study, baboon damage in plantations along the Mpumalanga escarpment area of South Africa was monitored using remote sensing methods. While there are many methods of forest health monitoring using remote sensing, some approaches are less suitable as they either monitor damage caused at a plantation level, use lower spatial resolution (>10m) datasets or map damage using one available time period. The purpose of this study was first to establish the impact of baboon damage through time, using Sentinel-2 satellite imagery with all vegetation indices available, and the Extreme Gradient Boosting (XGboost) algorithm. The second part focused on analysing the damage at a tree level using PlanetScope imagery using a deep Learning approach. Overall, the study found that the use of Sentinel-2 data and PlanetScope data could accurately distinguish between the varying severity of baboon damage, achieving an accuracy of 95% and 82%. The processing time of the deep learning Artificial Neural Network (ANN) was greatly affected by the number of hidden layers and neurons used. Implementation of techniques used in this study has the potential to improve the accuracy of forest health monitoring in compartment forestry in South Africa.
- Full Text:
- Date Issued: 2020
Approaches in the prioritisation of areas for biodiversity conservation: a case study from the Western Cape pf South Africa
- Authors: Southey, Phillippa Kate
- Date: 2015
- Subjects: Biodiversity conservation -- South Africa -- Western Cape , Conservation of natural resources -- South Africa -- Western Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/4122 , vital:20548
- Description: Historical ad hoc allocations of land for biodiversity conservation have led to a biased representation of habitat within the Cape Floristic Region, with Protected Areas concentrated in upland areas at high altitudes and on steep slopes. The field of Conservation Planning developed to ensure that allocations of areas to Protected status no longer result in such bias and rather promotes the persistence of biodiversity. This study reviewed a recent allocation of land to biodiversity conservation within Western Cape of South Africa, using both a quantitative and qualitative approach, to determine their value to biodiversity conservation. The area was previously used for commercial forestry but now has been allocated to conservation land-uses. The allocation was based on the area’s value to the forestry industry. The qualitative approach in this study engaged with relevant stakeholder groups to map priority areas, while the quantitative approach used available data on biodiversity features to map priority areas. Neither approach determined that the area allocated is in its full extent a priority for biodiversity conservation. This indicated that in the current era of Conservation Planning, Protected Areas are still being allocated in an ad hoc manner, as a result of their limited perceived benefit to anthropocentric needs. The future allocation of land to biodiversity conservation should rather integrate expert knowledge and available quantifiable data to ensure that priority areas for biodiversity conservation are being protected.
- Full Text:
- Date Issued: 2015
- Authors: Southey, Phillippa Kate
- Date: 2015
- Subjects: Biodiversity conservation -- South Africa -- Western Cape , Conservation of natural resources -- South Africa -- Western Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/4122 , vital:20548
- Description: Historical ad hoc allocations of land for biodiversity conservation have led to a biased representation of habitat within the Cape Floristic Region, with Protected Areas concentrated in upland areas at high altitudes and on steep slopes. The field of Conservation Planning developed to ensure that allocations of areas to Protected status no longer result in such bias and rather promotes the persistence of biodiversity. This study reviewed a recent allocation of land to biodiversity conservation within Western Cape of South Africa, using both a quantitative and qualitative approach, to determine their value to biodiversity conservation. The area was previously used for commercial forestry but now has been allocated to conservation land-uses. The allocation was based on the area’s value to the forestry industry. The qualitative approach in this study engaged with relevant stakeholder groups to map priority areas, while the quantitative approach used available data on biodiversity features to map priority areas. Neither approach determined that the area allocated is in its full extent a priority for biodiversity conservation. This indicated that in the current era of Conservation Planning, Protected Areas are still being allocated in an ad hoc manner, as a result of their limited perceived benefit to anthropocentric needs. The future allocation of land to biodiversity conservation should rather integrate expert knowledge and available quantifiable data to ensure that priority areas for biodiversity conservation are being protected.
- Full Text:
- Date Issued: 2015
Approaches to detecting and assessing patterns, processes and responses to change in South African estuaries
- Authors: Van Niekerk, Lara
- Date: 2018
- Subjects: Estuaries -- South Africa , Climatic changes -- South Africa
- Language: English
- Type: Thesis , Doctoral , PHD
- Identifier: http://hdl.handle.net/10948/45491 , vital:38621
- Description: The research presented indicates deep knowledge of estuary pattern-process-function across a broad range of estuary types. This study successfully developed and applied approaches to detect change at varying temporal and spatial scales in South African estuaries. This assessment was based on the physical characteristics of estuaries and predicted or measured change in the drivers of estuary health. This is the first study in the country to review and synthesise the vulnerability of South African estuaries to Climate Change on a regional scale. Through sound scientific approaches this research has advanced our knowledge on complex estuarine systems and made a significant contribution globally to approaches for the conservation and management of estuaries.
- Full Text:
- Date Issued: 2018
- Authors: Van Niekerk, Lara
- Date: 2018
- Subjects: Estuaries -- South Africa , Climatic changes -- South Africa
- Language: English
- Type: Thesis , Doctoral , PHD
- Identifier: http://hdl.handle.net/10948/45491 , vital:38621
- Description: The research presented indicates deep knowledge of estuary pattern-process-function across a broad range of estuary types. This study successfully developed and applied approaches to detect change at varying temporal and spatial scales in South African estuaries. This assessment was based on the physical characteristics of estuaries and predicted or measured change in the drivers of estuary health. This is the first study in the country to review and synthesise the vulnerability of South African estuaries to Climate Change on a regional scale. Through sound scientific approaches this research has advanced our knowledge on complex estuarine systems and made a significant contribution globally to approaches for the conservation and management of estuaries.
- Full Text:
- Date Issued: 2018