Grabcuts for image segmentation: a comparative study of clustering techniques
- Authors: Manzi, Nozuko Zuleika
- Date: 2019
- Subjects: Algorithms , Computer graphics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14494 , vital:39995
- Description: Image segmentation is the partitioning of a digital image into small segments such as pixels or sets of pixels. It is significant as it allows for the visualization of structures of interest, removing unnecessary information. In addition, image segmentation is used in many fields like, for instance healthcare for image surgery, construction, etc. as it enables structure analysis. Segmentation of images can be computationally expensive especially when a large dataset is used, thus the importance of fast and effective segmentation algorithms is realised. This method is used to locate objects and boundaries (i.e. foreground and background) in images. The aim of this study is to provide a comparison of clustering techniques that would allow the Grabcuts for image segmentation algorithm to be effective and inexpensive. The Grabcuts based method, which is an extension of the graph cut based method, has been instrumental in solving many problems in computer vision i.e. image restoration, image segmentation, object recognition, tracking and analysis. According to Ramirez,et.al [47], the Grabcuts approach is an iterative and minimal user interaction algorithm as it chooses a segmentation by iteratively revising the foreground and background pixels assignments. The method uses min-cut/ max-flow algorithm to segment digital images proposed by Boykov and Jolly [9]. The input of this approach is a digital image with a selected v region of interest (ROI). The ROI is selected using a rectangular bounding box. The pixels inside the bounding box are assigned to the foreground, while the others are assigned to the background. In this study, the Grabcuts for image segmentation algorithm designed by [48] with a Gaussian Mixture Model (GMM) based on the Kmeans and Kmedoids clustering techniques are developed and compared. In addition, the algorithms developed are allowed to run on the Central Processing Unit (CPU) under two scenarios. Scenario 1 involves allowing the Kmeans and Kmedoids clustering techniques to the Squared Euclidean distance measures to calculate the similarities and dissimilarities in pixels in an image. In scenario 2, the Kmeans and Kmedoids clustering techniques will use the City Block distance measure to calculate similarities as well as dissimilarities between pixels in a given image. The same images from the Berkeley Segmentation Dataset and Benchmark 500 were used as input to the algorithms and the number of clusters, K, was varied from 2 to 5. It was observed that the Kmeans clustering technique outperformed the Kmedoids clustering technique under the two scenarios for all the test images with K varied from 2 to 5, in terms of runtime required. In addition, the Kmeans clustering technique obtained more compact and separate clusters under scenario 1, than its counterpart. On the other hand, the Kmedoids obtained more compact and separate clusters than the Kmeans clustering technique under scenario 2. The silhouette validity index favoured the smallest number of clusters for both clustering techniques as it suggested the optimal number of clusters for the Kmeans and Kmedoids clustering techniques under the two scenarios was 2. Although the Kmeans required less computation time than vi its counterpart, the generation of foreground and background took longer for the GMM based on Kmeans than it did for the GMM based on Kmedoids clustering technique. Furthermore, the Grabcuts for image segmentation algorithm with a GMM based on the Kmedoids clustering technique was computationally less expensive than the Grabcuts for image segmentation algorithm with a GMM based on the Kmeans clustering technique. This was observed to be true under both scenario 1 and 2. The Grabcuts for image with the GMM based on the Kmeans clustering techniques obtained slightly better segmentation results when the visual quality is concerned, than its counterpart under the two scenarios considered. On the other hand, the BFscores showed that the Grabcuts for image segmentation algorithm with the GMM based on Kmedoids produces images with higher BF-scores than its counterpart when K was varied from 2 to 5 for most of the test images. In addition, most of the images obtained the majority of their best segmentation results when K=2. This was observed to be true under scenario 1 as well as scenario 2. Therefore, the Kmedoids clustering technique under scenario 2 with K=2 would be the best option for the segmentation of difficult images in BSDS500. This is due to its ability to generate GMMs and segment difficult images more efficiently (i.e. time complexity, higher BF-scores, more under segmented rather than over segmented images, inter alia.) while producing comparable visual segmentation results to those obtained by the Grabcuts for image segmentation: GMM-Kmeans.
- Full Text:
- Date Issued: 2019
- Authors: Manzi, Nozuko Zuleika
- Date: 2019
- Subjects: Algorithms , Computer graphics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14494 , vital:39995
- Description: Image segmentation is the partitioning of a digital image into small segments such as pixels or sets of pixels. It is significant as it allows for the visualization of structures of interest, removing unnecessary information. In addition, image segmentation is used in many fields like, for instance healthcare for image surgery, construction, etc. as it enables structure analysis. Segmentation of images can be computationally expensive especially when a large dataset is used, thus the importance of fast and effective segmentation algorithms is realised. This method is used to locate objects and boundaries (i.e. foreground and background) in images. The aim of this study is to provide a comparison of clustering techniques that would allow the Grabcuts for image segmentation algorithm to be effective and inexpensive. The Grabcuts based method, which is an extension of the graph cut based method, has been instrumental in solving many problems in computer vision i.e. image restoration, image segmentation, object recognition, tracking and analysis. According to Ramirez,et.al [47], the Grabcuts approach is an iterative and minimal user interaction algorithm as it chooses a segmentation by iteratively revising the foreground and background pixels assignments. The method uses min-cut/ max-flow algorithm to segment digital images proposed by Boykov and Jolly [9]. The input of this approach is a digital image with a selected v region of interest (ROI). The ROI is selected using a rectangular bounding box. The pixels inside the bounding box are assigned to the foreground, while the others are assigned to the background. In this study, the Grabcuts for image segmentation algorithm designed by [48] with a Gaussian Mixture Model (GMM) based on the Kmeans and Kmedoids clustering techniques are developed and compared. In addition, the algorithms developed are allowed to run on the Central Processing Unit (CPU) under two scenarios. Scenario 1 involves allowing the Kmeans and Kmedoids clustering techniques to the Squared Euclidean distance measures to calculate the similarities and dissimilarities in pixels in an image. In scenario 2, the Kmeans and Kmedoids clustering techniques will use the City Block distance measure to calculate similarities as well as dissimilarities between pixels in a given image. The same images from the Berkeley Segmentation Dataset and Benchmark 500 were used as input to the algorithms and the number of clusters, K, was varied from 2 to 5. It was observed that the Kmeans clustering technique outperformed the Kmedoids clustering technique under the two scenarios for all the test images with K varied from 2 to 5, in terms of runtime required. In addition, the Kmeans clustering technique obtained more compact and separate clusters under scenario 1, than its counterpart. On the other hand, the Kmedoids obtained more compact and separate clusters than the Kmeans clustering technique under scenario 2. The silhouette validity index favoured the smallest number of clusters for both clustering techniques as it suggested the optimal number of clusters for the Kmeans and Kmedoids clustering techniques under the two scenarios was 2. Although the Kmeans required less computation time than vi its counterpart, the generation of foreground and background took longer for the GMM based on Kmeans than it did for the GMM based on Kmedoids clustering technique. Furthermore, the Grabcuts for image segmentation algorithm with a GMM based on the Kmedoids clustering technique was computationally less expensive than the Grabcuts for image segmentation algorithm with a GMM based on the Kmeans clustering technique. This was observed to be true under both scenario 1 and 2. The Grabcuts for image with the GMM based on the Kmeans clustering techniques obtained slightly better segmentation results when the visual quality is concerned, than its counterpart under the two scenarios considered. On the other hand, the BFscores showed that the Grabcuts for image segmentation algorithm with the GMM based on Kmedoids produces images with higher BF-scores than its counterpart when K was varied from 2 to 5 for most of the test images. In addition, most of the images obtained the majority of their best segmentation results when K=2. This was observed to be true under scenario 1 as well as scenario 2. Therefore, the Kmedoids clustering technique under scenario 2 with K=2 would be the best option for the segmentation of difficult images in BSDS500. This is due to its ability to generate GMMs and segment difficult images more efficiently (i.e. time complexity, higher BF-scores, more under segmented rather than over segmented images, inter alia.) while producing comparable visual segmentation results to those obtained by the Grabcuts for image segmentation: GMM-Kmeans.
- Full Text:
- Date Issued: 2019
Ground thermal regimes in Western Dronning Maud Land, Antarctica in 2016
- Authors: Masebe, Consliah Tebogo
- Date: 2019
- Subjects: Climatic changes -- Antarctica , Frozen ground -- Research -- Antarctica , Frozen ground -- Thermal properties -- Antarctica , Queen Maud Land , Earth temperature -- Antarctica , Soil temperature -- Antarctica -- Measurement
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/95581 , vital:31173
- Description: Research shows that the climate of Antarctica is changing and, it is vital that the change is monitored to understand how it will affect global ecosystems. Since the International Polar Year (IPY) 2007-2008, research in permafrost studies has grown. However, there are still existing gaps that impede complete understanding of Antarctic cold environments and landscape processes. Permafrost has been noted as one of the major controlling factors of the terrestrial ecosystem dynamics in Antarctica. However, the understanding of Antarctic permafrost, when compared to other cryospheric components, is limited, especially its thermal and physical properties, evolution, as well as links to pedogenesis, hydrology, geomorphic dynamics, and responses to global change. This project provided an understanding and insight to over-arching research that evaluates the state and status of permafrost and the active layer in Dronning Maud Land (DML) through examining short-term variations on ground thermal regimes. The main focus is on understanding the influence of synoptic, diurnal and seasonal events on the active layer in 2016. Analysis of available data shows that ground thermal regimes are influenced by variations in air temperature, pressure, wind speed and to some extent, relative humidity. Subsequently, ground thermal regimes also depend on soil physical characteristics including sediment particle size and bulk density. Furthermore, sediment particle size and bulk density have been found to have a great influence on thermal propagation rates as well as active layer depth; the higher the bulk density, the higher the thermal propagation rate and the lower the bulk density, the lower the thermal propagation rate. Conversely, a large proportion of bigger sediment particle size in soil corresponds with a higher thermal propagation rate and a large proportion of smaller sediment particle size in soil corresponds with a lower thermal propagation rate. Also, ground thermal regimes vary according to seasons. Ground temperatures are more variable in summer, while air temperatures are more variable in winter. The variability according to different seasons shows that the active layer responds to seasonal climatic variations. Additionally, the active layer also responds to synoptic and diurnal weather events.
- Full Text:
- Date Issued: 2019
- Authors: Masebe, Consliah Tebogo
- Date: 2019
- Subjects: Climatic changes -- Antarctica , Frozen ground -- Research -- Antarctica , Frozen ground -- Thermal properties -- Antarctica , Queen Maud Land , Earth temperature -- Antarctica , Soil temperature -- Antarctica -- Measurement
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/95581 , vital:31173
- Description: Research shows that the climate of Antarctica is changing and, it is vital that the change is monitored to understand how it will affect global ecosystems. Since the International Polar Year (IPY) 2007-2008, research in permafrost studies has grown. However, there are still existing gaps that impede complete understanding of Antarctic cold environments and landscape processes. Permafrost has been noted as one of the major controlling factors of the terrestrial ecosystem dynamics in Antarctica. However, the understanding of Antarctic permafrost, when compared to other cryospheric components, is limited, especially its thermal and physical properties, evolution, as well as links to pedogenesis, hydrology, geomorphic dynamics, and responses to global change. This project provided an understanding and insight to over-arching research that evaluates the state and status of permafrost and the active layer in Dronning Maud Land (DML) through examining short-term variations on ground thermal regimes. The main focus is on understanding the influence of synoptic, diurnal and seasonal events on the active layer in 2016. Analysis of available data shows that ground thermal regimes are influenced by variations in air temperature, pressure, wind speed and to some extent, relative humidity. Subsequently, ground thermal regimes also depend on soil physical characteristics including sediment particle size and bulk density. Furthermore, sediment particle size and bulk density have been found to have a great influence on thermal propagation rates as well as active layer depth; the higher the bulk density, the higher the thermal propagation rate and the lower the bulk density, the lower the thermal propagation rate. Conversely, a large proportion of bigger sediment particle size in soil corresponds with a higher thermal propagation rate and a large proportion of smaller sediment particle size in soil corresponds with a lower thermal propagation rate. Also, ground thermal regimes vary according to seasons. Ground temperatures are more variable in summer, while air temperatures are more variable in winter. The variability according to different seasons shows that the active layer responds to seasonal climatic variations. Additionally, the active layer also responds to synoptic and diurnal weather events.
- Full Text:
- Date Issued: 2019
How do urban dwellers identify with features within urban green spaces in the Eastern Cape?
- Authors: Manyani, Amanda
- Date: 2019
- Subjects: Land use, Urban -- South Africa , Greenbelts -- South Africa , City planning -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/95596 , vital:31174
- Description: Public urban green spaces contain natural and artificial features which play crucial roles in supporting urban social-ecological systems, a fact now recognized globally. The various natural and artificial features contained in public urban green spaces are said to be key contributors to the quality of life and well-being of urban dwellers. Nevertheless, this has been largely ignored in urban design in South Africa, especially in the poorer township and Reconstruction Development Program (RDP) areas. At the individual household and community levels within the poorer communities, the provision of green spaces and trees, as well as recreation facilities, is well below world standards, and much less than what is available in the more affluent areas of South African towns. Additionally, most research on the links between nature and human well-being in urban contexts comes from developed world contexts which adopt a westernized view of the relationship. Yet, in many societies of the Global South, including South Africa, worldviews and experiences of nature in green spaces and use of other recreational features takes on different meanings to those of the Global North. To show these differences, a combination of methods was used in this study, different types of green spaces were assessed and evaluated by structured observations so as to record the features present within the spaces. A survey of 360 households was conducted by targeting green space users and households within 100 metres from a green space. Results indicated that, across all the green space types, formal green spaces had a low cover of shrubs, trees and herbs whilst having high lawn cover. Furthermore, vegetation had poor rating across all the green spaces since the vegetation was either overgrown herbs, dense thickets of shrubs and mostly alien trees that were either diseased or forked. Similar to the disparity in the composition and structure of vegetation within the green spaces, there was a wide variability in the composition of recreational features and amenities across the green spaces. The formal green spaces had the most amenities like play equipment, shelter and seating. Informal green spaces and commonages had little or no recreational features available. The attributes of these spaces therefore influenced the reasons for visiting as more than 90 % of the respondents simply used the spaces for transit. With regards to attitudes and preferences towards particular features, they were emerging sense of strong negative feelings towards natural features. Most respondents emphasized the need for green spaces that are well laid out with maintained lawns, recreational facilities and open vegetation. Thus, the current design and available features within the studied urban green spaces do not meet local needs and aspirations and thus do not contribute to better well-being and quality of life as much as they could. Specifically, the various health benefits linked with being in contact with nature in the public green spaces were not evident in this study. The South African specific context in green space use, perception and people’s preferences is thus crucial for urban planning and sustainability.
- Full Text:
- Date Issued: 2019
- Authors: Manyani, Amanda
- Date: 2019
- Subjects: Land use, Urban -- South Africa , Greenbelts -- South Africa , City planning -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/95596 , vital:31174
- Description: Public urban green spaces contain natural and artificial features which play crucial roles in supporting urban social-ecological systems, a fact now recognized globally. The various natural and artificial features contained in public urban green spaces are said to be key contributors to the quality of life and well-being of urban dwellers. Nevertheless, this has been largely ignored in urban design in South Africa, especially in the poorer township and Reconstruction Development Program (RDP) areas. At the individual household and community levels within the poorer communities, the provision of green spaces and trees, as well as recreation facilities, is well below world standards, and much less than what is available in the more affluent areas of South African towns. Additionally, most research on the links between nature and human well-being in urban contexts comes from developed world contexts which adopt a westernized view of the relationship. Yet, in many societies of the Global South, including South Africa, worldviews and experiences of nature in green spaces and use of other recreational features takes on different meanings to those of the Global North. To show these differences, a combination of methods was used in this study, different types of green spaces were assessed and evaluated by structured observations so as to record the features present within the spaces. A survey of 360 households was conducted by targeting green space users and households within 100 metres from a green space. Results indicated that, across all the green space types, formal green spaces had a low cover of shrubs, trees and herbs whilst having high lawn cover. Furthermore, vegetation had poor rating across all the green spaces since the vegetation was either overgrown herbs, dense thickets of shrubs and mostly alien trees that were either diseased or forked. Similar to the disparity in the composition and structure of vegetation within the green spaces, there was a wide variability in the composition of recreational features and amenities across the green spaces. The formal green spaces had the most amenities like play equipment, shelter and seating. Informal green spaces and commonages had little or no recreational features available. The attributes of these spaces therefore influenced the reasons for visiting as more than 90 % of the respondents simply used the spaces for transit. With regards to attitudes and preferences towards particular features, they were emerging sense of strong negative feelings towards natural features. Most respondents emphasized the need for green spaces that are well laid out with maintained lawns, recreational facilities and open vegetation. Thus, the current design and available features within the studied urban green spaces do not meet local needs and aspirations and thus do not contribute to better well-being and quality of life as much as they could. Specifically, the various health benefits linked with being in contact with nature in the public green spaces were not evident in this study. The South African specific context in green space use, perception and people’s preferences is thus crucial for urban planning and sustainability.
- Full Text:
- Date Issued: 2019
Identification of possible natural compounds as potential inhibitors against Plasmodium M1 alanyl aminopeptidase
- Soliman, Omar Samir Abdel Ghaffar
- Authors: Soliman, Omar Samir Abdel Ghaffar
- Date: 2019
- Subjects: Plasmodium , Malaria -- Chemotherapy , Plasmodium -- Inhibitors , Drug resistance in microorganisms , Aminopeptidases
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/72284 , vital:30026
- Description: Malaria is a major tropical health problem with a 29% mortality rate among people of all ages; it also affects 35% of the children. Despite the decrease in mortality rate in recent years, malaria still results in around 2000 deaths per day. Malaria is caused by Plasmodium parasites and is transmitted to humans via the bites from infected female Anopheles mosquitoes during blood meals. There are five different Plasmodium species that can cause human malaria, which include Plasmodium falciparum, Plasmodium vivax, Plasmodium malariae, Plasmodium ovale and Plasmodium knowlesi. Among these five species, the most pathogenic ones are Plasmodium falciparum and Plasmodium vivax. Malaria is usually hard to diagnose because the symptoms are not exclusive to malaria and very similar to flu, e.g., fever, muscle pain, and chills, which lead to the misdiagnosis of malaria cases. Malaria is lethal if not treated because it can cause severe complications in the respiratory tract, liver, metabolic acidosis, and hypoglycemia. The malaria parasite life cycle includes two types of hosts, i.e., a human host and female Anopheles mosquito host. Malaria continuously develops resistance to the available drugs, which is one of the major challenges in disease control. This situation confirms the need to develop new drugs that target virulence factors of malaria. The malarial parasite has three main life cycle stages, which include the host liver stage, host blood stage and vector stage. In the blood stage, parasites degrade hemoglobin to amino acids, which is important as these parasites cannot produce their own amino acids. Different proteases are involved in this hemoglobin degradation process. M1 alanyl aminopeptidase is one of these proteases involved at the end of hemoglobin degradation. This study focused on M1 alanyl aminopeptidase as a potential drug target. M1 alanyl aminopeptidase consists of four domains: N-terminal domain, catalytic domain, middle domain and C-terminal domain. The catalytic domain remains conserved among different Plasmodium species. Inhibition of this enzyme might prevent Plasmodium growth as it can’t produce its own amino acids. In this study, sequence analysis was carried out in both human and Plasmodium M1 alanyl aminopeptidase to identify conserved and divergent regions between them. 3D protein models of the M1 alanyl aminopeptidase from Plasmodium species were built and validated. Then the generated models were used for virtual screening against 623 compounds retrieved from the South African Natural Compounds Database (SANCDB, https://sancdb.rubi.ru.ac.za/). Virtual screening was done using blind and targeted docking methods. Docking was used to identify compounds with selective high binding affinity to the active site of the parasite protein. In this study, one SANCDB compound was selected for each protein: SANC00531 was selected against P. falciparum M1 alanyl aminopeptidase, SANC00469 against P. knowlesi, SANC00660 against P. vivax, SANC00144 against P. ovale and SANC00109 against P. malariae. It was found that Plamsodium M1 alanyl aminopeptidase can be used as a potential drug target as it showed selective binding against different inhibitor compounds. This result will be investigated in future work though molecular dynamic analysis to investigate the stability of protein-ligand complexes.
- Full Text:
- Date Issued: 2019
- Authors: Soliman, Omar Samir Abdel Ghaffar
- Date: 2019
- Subjects: Plasmodium , Malaria -- Chemotherapy , Plasmodium -- Inhibitors , Drug resistance in microorganisms , Aminopeptidases
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/72284 , vital:30026
- Description: Malaria is a major tropical health problem with a 29% mortality rate among people of all ages; it also affects 35% of the children. Despite the decrease in mortality rate in recent years, malaria still results in around 2000 deaths per day. Malaria is caused by Plasmodium parasites and is transmitted to humans via the bites from infected female Anopheles mosquitoes during blood meals. There are five different Plasmodium species that can cause human malaria, which include Plasmodium falciparum, Plasmodium vivax, Plasmodium malariae, Plasmodium ovale and Plasmodium knowlesi. Among these five species, the most pathogenic ones are Plasmodium falciparum and Plasmodium vivax. Malaria is usually hard to diagnose because the symptoms are not exclusive to malaria and very similar to flu, e.g., fever, muscle pain, and chills, which lead to the misdiagnosis of malaria cases. Malaria is lethal if not treated because it can cause severe complications in the respiratory tract, liver, metabolic acidosis, and hypoglycemia. The malaria parasite life cycle includes two types of hosts, i.e., a human host and female Anopheles mosquito host. Malaria continuously develops resistance to the available drugs, which is one of the major challenges in disease control. This situation confirms the need to develop new drugs that target virulence factors of malaria. The malarial parasite has three main life cycle stages, which include the host liver stage, host blood stage and vector stage. In the blood stage, parasites degrade hemoglobin to amino acids, which is important as these parasites cannot produce their own amino acids. Different proteases are involved in this hemoglobin degradation process. M1 alanyl aminopeptidase is one of these proteases involved at the end of hemoglobin degradation. This study focused on M1 alanyl aminopeptidase as a potential drug target. M1 alanyl aminopeptidase consists of four domains: N-terminal domain, catalytic domain, middle domain and C-terminal domain. The catalytic domain remains conserved among different Plasmodium species. Inhibition of this enzyme might prevent Plasmodium growth as it can’t produce its own amino acids. In this study, sequence analysis was carried out in both human and Plasmodium M1 alanyl aminopeptidase to identify conserved and divergent regions between them. 3D protein models of the M1 alanyl aminopeptidase from Plasmodium species were built and validated. Then the generated models were used for virtual screening against 623 compounds retrieved from the South African Natural Compounds Database (SANCDB, https://sancdb.rubi.ru.ac.za/). Virtual screening was done using blind and targeted docking methods. Docking was used to identify compounds with selective high binding affinity to the active site of the parasite protein. In this study, one SANCDB compound was selected for each protein: SANC00531 was selected against P. falciparum M1 alanyl aminopeptidase, SANC00469 against P. knowlesi, SANC00660 against P. vivax, SANC00144 against P. ovale and SANC00109 against P. malariae. It was found that Plamsodium M1 alanyl aminopeptidase can be used as a potential drug target as it showed selective binding against different inhibitor compounds. This result will be investigated in future work though molecular dynamic analysis to investigate the stability of protein-ligand complexes.
- Full Text:
- Date Issued: 2019
Identifying methane emissions with isotopic and hydrochemical clues to their origin across selected areas of the Karoo Basin, South Africa
- Authors: Campbell, Richard Duncombe
- Date: 2019
- Subjects: Methane -- Environmental aspects -- South Africa , Atmospheric methane -- Environmental aspects -- South Africa , Groundwater -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/42218 , vital:36636
- Description: Currently, only sparse data exists on the methane emissions from the Main Karoo Basin, South Africa, where the potential discovery of vast quantities of unconventional natural gas from the black shales of the Whitehill Formation has sparked great interest in the prospect of hydraulic fracturing. In this study, a new infield methane quantification instrument (Picarro G2201-i) is used to identify freely emitted methane and more importantly collect stable carbon isotope ratios (δ13C-(CH4)g) that is used in obtaining information regarding the genetic origin and thermal maturity of the methane. Hydrochemical information (TOC, δ13C-TOC, 3H, δ18O, δ2H, and anions) were also scrutinised to assist in the determination of the origin of methane across the Karoo Basin. Twenty-one sites were investigated across four provinces in the Main Karoo Basin. Six of these sites are thermal springs, three are shallow boreholes (<100 m in depth), and twelve were Soekor (The Southern Oil Exploration Corporation)/deep boreholes (>1500 m). Of these 21 sites, 17 were suitable for either methane analysis or groundwater sampling, with four of the Soekor boreholes unsuitable. The presence of methane in groundwater and being freely emitted seems to be a common occurrence above the Main Karoo basin and of the 17 sites investigated, 14 had freely emitted methane emission. All but one of these sites had δ13C-(CH4)g signatures greater than -50 ‰, indicating a thermogenic origin. Combining the results obtained from the Picarro instrument with those compiled by Talma & Esterhuyse (2015), a higher resolution distribution map was created. The δ13C-CH4 signatures show patterning with a decreasing trend from the southern Karoo Basin to the north, which corresponds to the general decrease in thermal maturity of the Ecca shales (Whitehill Formation) northward across the Karoo Basin. The δ13C-(CH4)d results from a case study conducted by Eymold et al. (2018) differ significantly with the data collected in this study that included several of the same sampling locations. This is explained by a two phase partitioning (gas + water) that leads to the thermogenic endmember of methane being released in its free state (analysed by Picarro G2201-i) and microbial methane that is formed in situ remains dissolved in the water (analysed by Eymold et al. 2018). Soekor and deep sites; SA 1/66, KA 1/66, and KWV-1 that have direct pathways for methane migration from the Whitehill are deemed the best proxies to resolve the thermogenic endmember of methane, with δ13C-(CH4)g signatures of -26.32‰, 31.66‰, and -34.57‰, respectively. The hydrochemistry results suggests that that free methane emissions do not necessarily have to be associated with saline Cl- waters, as multiple sites have CH4 emissions with low salinities (Cl < 50 mg/L) and that methane in its free state can migrate to the surface due to buoyancy. The results also indicate that dolerite intrusions act as conduits for upward migration of groundwater from depth, but that the deep groundwater signatures proposed by Murray et al., (2015) are related to their different migration pathways and water-rock interactions rather than being representative of the deep formation waters. Using an initial assessment δ13C-CH4, TOC concentration [TOC] and the tritium (3H) values, where water samples that have 3H ≤ 1 TU, detectable TOC and δ13C-CH4 signatures > -50‰ could indicate hydraulic connectivity between the shallow aquifer and an organic/CH4 rich sedimentary layer, which may or may not be from the Whitehill Formation. However, this method for determining aquifer connectivity requires further investigations in the Karoo Basin context. The results obtained in this study add to the limited isotopic data of methane across the Karoo Basin and demonstrates the effectiveness of an infield identification of methane emissions using the Picarro G2201-i.
- Full Text:
- Date Issued: 2019
- Authors: Campbell, Richard Duncombe
- Date: 2019
- Subjects: Methane -- Environmental aspects -- South Africa , Atmospheric methane -- Environmental aspects -- South Africa , Groundwater -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/42218 , vital:36636
- Description: Currently, only sparse data exists on the methane emissions from the Main Karoo Basin, South Africa, where the potential discovery of vast quantities of unconventional natural gas from the black shales of the Whitehill Formation has sparked great interest in the prospect of hydraulic fracturing. In this study, a new infield methane quantification instrument (Picarro G2201-i) is used to identify freely emitted methane and more importantly collect stable carbon isotope ratios (δ13C-(CH4)g) that is used in obtaining information regarding the genetic origin and thermal maturity of the methane. Hydrochemical information (TOC, δ13C-TOC, 3H, δ18O, δ2H, and anions) were also scrutinised to assist in the determination of the origin of methane across the Karoo Basin. Twenty-one sites were investigated across four provinces in the Main Karoo Basin. Six of these sites are thermal springs, three are shallow boreholes (<100 m in depth), and twelve were Soekor (The Southern Oil Exploration Corporation)/deep boreholes (>1500 m). Of these 21 sites, 17 were suitable for either methane analysis or groundwater sampling, with four of the Soekor boreholes unsuitable. The presence of methane in groundwater and being freely emitted seems to be a common occurrence above the Main Karoo basin and of the 17 sites investigated, 14 had freely emitted methane emission. All but one of these sites had δ13C-(CH4)g signatures greater than -50 ‰, indicating a thermogenic origin. Combining the results obtained from the Picarro instrument with those compiled by Talma & Esterhuyse (2015), a higher resolution distribution map was created. The δ13C-CH4 signatures show patterning with a decreasing trend from the southern Karoo Basin to the north, which corresponds to the general decrease in thermal maturity of the Ecca shales (Whitehill Formation) northward across the Karoo Basin. The δ13C-(CH4)d results from a case study conducted by Eymold et al. (2018) differ significantly with the data collected in this study that included several of the same sampling locations. This is explained by a two phase partitioning (gas + water) that leads to the thermogenic endmember of methane being released in its free state (analysed by Picarro G2201-i) and microbial methane that is formed in situ remains dissolved in the water (analysed by Eymold et al. 2018). Soekor and deep sites; SA 1/66, KA 1/66, and KWV-1 that have direct pathways for methane migration from the Whitehill are deemed the best proxies to resolve the thermogenic endmember of methane, with δ13C-(CH4)g signatures of -26.32‰, 31.66‰, and -34.57‰, respectively. The hydrochemistry results suggests that that free methane emissions do not necessarily have to be associated with saline Cl- waters, as multiple sites have CH4 emissions with low salinities (Cl < 50 mg/L) and that methane in its free state can migrate to the surface due to buoyancy. The results also indicate that dolerite intrusions act as conduits for upward migration of groundwater from depth, but that the deep groundwater signatures proposed by Murray et al., (2015) are related to their different migration pathways and water-rock interactions rather than being representative of the deep formation waters. Using an initial assessment δ13C-CH4, TOC concentration [TOC] and the tritium (3H) values, where water samples that have 3H ≤ 1 TU, detectable TOC and δ13C-CH4 signatures > -50‰ could indicate hydraulic connectivity between the shallow aquifer and an organic/CH4 rich sedimentary layer, which may or may not be from the Whitehill Formation. However, this method for determining aquifer connectivity requires further investigations in the Karoo Basin context. The results obtained in this study add to the limited isotopic data of methane across the Karoo Basin and demonstrates the effectiveness of an infield identification of methane emissions using the Picarro G2201-i.
- Full Text:
- Date Issued: 2019
Improving the property rental market in Tshwane CBD
- Authors: Kganyago, Rapholo Joseph
- Date: 2019
- Subjects: Real property -- South Africa -- Pretoria , Rental housing -- South Africa -- Pretoria Building leases -- South Africa -- Pretoria Housing -- South Africa -- Pretoria
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/40588 , vital:36185
- Description: The research focuses on investigating the Improvement of the property rental market in Tshwane CBD. This includes determining the factors leading to high dilapidation of the Tshwane rental properties in its CBD as well as establishing the challenges experienced by the tenants in respect to the comfort and safety of their rented properties. This includes determining challenges faced by the rental property owners in establishing safe, comfortable housing facilities that fulfill the tenants’ expectations. The research further determines to illuminate on economic opportunities that can be realised in improving the conditions of the rental property market. The research employs a mixed research approach, where 100 survey participants and 10 qualitative interviewees are used to gather empirical evidence for the study. This manages to bring congruency to the outcomes of the study. The research finds that rent seeking behaviours are prevalent in the Tshwane rental property market. The study finds that there is lack of adequate management of rental properties owing to challenges with timely maintenance costs that affect most rented properties in the CBD. The research illuminates further that rental property owners and employed agencies are not effectively upgrading or modifying security features in their commercialized units much to diminished safety of property and most importantly the tenants. The research also exposes that foreign nationals in rental property market are also part of the rent-seeking behaviours through some hidden costs and penalties that do not align with local authority regulations to unsuspecting and prospective tenants much like local rental property stakeholders. The research has recommended that regulatory agencies in the rental property market must be trained and assessed on performance metrics continuously to ensure that they effectively address and expose issues such as latent defects, health inspections of properties and a better understanding of rental property dynamics at inspection and certification of rental units as fit for commercial business. The research further recommends that urbanisation through gentrification requires sustainable partnerships between both private and public construction sector players with adequate consultation with communities affected near CBDs to encourage building of more structures that are affordable to middle-income earners residing in affected rental areas identified in the research phenomenon.
- Full Text:
- Date Issued: 2019
- Authors: Kganyago, Rapholo Joseph
- Date: 2019
- Subjects: Real property -- South Africa -- Pretoria , Rental housing -- South Africa -- Pretoria Building leases -- South Africa -- Pretoria Housing -- South Africa -- Pretoria
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/40588 , vital:36185
- Description: The research focuses on investigating the Improvement of the property rental market in Tshwane CBD. This includes determining the factors leading to high dilapidation of the Tshwane rental properties in its CBD as well as establishing the challenges experienced by the tenants in respect to the comfort and safety of their rented properties. This includes determining challenges faced by the rental property owners in establishing safe, comfortable housing facilities that fulfill the tenants’ expectations. The research further determines to illuminate on economic opportunities that can be realised in improving the conditions of the rental property market. The research employs a mixed research approach, where 100 survey participants and 10 qualitative interviewees are used to gather empirical evidence for the study. This manages to bring congruency to the outcomes of the study. The research finds that rent seeking behaviours are prevalent in the Tshwane rental property market. The study finds that there is lack of adequate management of rental properties owing to challenges with timely maintenance costs that affect most rented properties in the CBD. The research illuminates further that rental property owners and employed agencies are not effectively upgrading or modifying security features in their commercialized units much to diminished safety of property and most importantly the tenants. The research also exposes that foreign nationals in rental property market are also part of the rent-seeking behaviours through some hidden costs and penalties that do not align with local authority regulations to unsuspecting and prospective tenants much like local rental property stakeholders. The research has recommended that regulatory agencies in the rental property market must be trained and assessed on performance metrics continuously to ensure that they effectively address and expose issues such as latent defects, health inspections of properties and a better understanding of rental property dynamics at inspection and certification of rental units as fit for commercial business. The research further recommends that urbanisation through gentrification requires sustainable partnerships between both private and public construction sector players with adequate consultation with communities affected near CBDs to encourage building of more structures that are affordable to middle-income earners residing in affected rental areas identified in the research phenomenon.
- Full Text:
- Date Issued: 2019
Inshore benthic communities of the Port Elizabeth abalone ranching concession area
- Authors: Moriarty, Lauren Alethea
- Date: 2019
- Subjects: Aquaculture , Abalone industry -- South Africa -- Port Elizabeth , Abalone culture -- South Africa -- Port Elizabeth , Abalone populations -- South Africa -- Port Elizabeth , Poaching -- South Africa -- Port Elizabeth
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/41975 , vital:36614
- Description: Abalone poaching in the Eastern Cape leading to resource depletion has resulted in the suspension of any commercial or recreational exploitation of abalone in the area. Abalone ranching trial projects have been initiated to help improve the natural stocks and potentially provide commercial yields. While seeding started in deeper water (5 – 10 m), improved abalone growth performance has been found in the shallower areas. This has resulted in the seeding effort being moved to these shallower sites (< 5m). An ecological survey of the baseline conditions of these shallow benthic areas is a requirement of the abalone ranching permit conditions (Permit No.: 1503759), aimed at detecting any impact that seeding may have on the benthic community. In addition to providing benchmark data for monitoring, the shallow benthic community (< 6m) in the Port Elizabeth ranching concession area has not been well described in terms of the requirements for abalone ranching. Information on the benthic communities in this area is limited to research on the substrate types and communities in deeper water (> 5m). This study aimed to address this information gap. Dive surveys were conducted along 10 m long transects (~3 reps) at three depth zones (<1m; 1-2m; > 2m) for four sites along the span of the ranching concession area. Similar assessments were done at a seeded site at the Noordhoek Ski Boat Club and an unseeded site at the Willows area, in order to reveal whether seeding had any impact on the benthic community. Images from a GoPro mounted in the centre of a framer unit (0.5 m2) were taken every 0.5 m along the transect. Macroalgal and macrofaunal cover was determined from these images, and the benthic community characterised from these data. Seaweed samples were taken for species identification. In the four baseline sites, sampling was done at three depth zones to note any changes with a depth gradient, both in terms of substrate type, as well as community composition. There was a notable trend with substrate type having a significant influence (P<0.05) on the community structure. Seaweed communities were dominated by Plocamium corallorhiza and coralline turf based on substrate types. There was also a significant relationship (P<0.05) between substrate type, dominant seaweed species and abalone presence. A Canonical Correspondence Analysis (CCA) of the community data suggested that the benthic community does not change significantly along the distance of coastline sampled. A hierarchical cluster analysis of Bray-Curtis dissimilarity for transect data also suggested that the four sites do not represent ecologically dissimilar communities. A similar analysis showed that abalone seeding had to date not altered the benthic community in shallow seeded areas from the community described for shallow unseeded areas. The study was used to describe the baseline benthic community in areas west of Cape Recife, examine the natural variability along the coast, and determine whether there are relationships between the benthic community composition and emergent abalone abundance. This information will be useful in selection of habitats for abalone seeding in the future. It is important that monitoring and surveying of the study area are to be continued in so allowing for long term data collection which will help in making informed decisions as well as documenting the impact in seeded areas when compared to unseeded areas.
- Full Text:
- Date Issued: 2019
- Authors: Moriarty, Lauren Alethea
- Date: 2019
- Subjects: Aquaculture , Abalone industry -- South Africa -- Port Elizabeth , Abalone culture -- South Africa -- Port Elizabeth , Abalone populations -- South Africa -- Port Elizabeth , Poaching -- South Africa -- Port Elizabeth
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/41975 , vital:36614
- Description: Abalone poaching in the Eastern Cape leading to resource depletion has resulted in the suspension of any commercial or recreational exploitation of abalone in the area. Abalone ranching trial projects have been initiated to help improve the natural stocks and potentially provide commercial yields. While seeding started in deeper water (5 – 10 m), improved abalone growth performance has been found in the shallower areas. This has resulted in the seeding effort being moved to these shallower sites (< 5m). An ecological survey of the baseline conditions of these shallow benthic areas is a requirement of the abalone ranching permit conditions (Permit No.: 1503759), aimed at detecting any impact that seeding may have on the benthic community. In addition to providing benchmark data for monitoring, the shallow benthic community (< 6m) in the Port Elizabeth ranching concession area has not been well described in terms of the requirements for abalone ranching. Information on the benthic communities in this area is limited to research on the substrate types and communities in deeper water (> 5m). This study aimed to address this information gap. Dive surveys were conducted along 10 m long transects (~3 reps) at three depth zones (<1m; 1-2m; > 2m) for four sites along the span of the ranching concession area. Similar assessments were done at a seeded site at the Noordhoek Ski Boat Club and an unseeded site at the Willows area, in order to reveal whether seeding had any impact on the benthic community. Images from a GoPro mounted in the centre of a framer unit (0.5 m2) were taken every 0.5 m along the transect. Macroalgal and macrofaunal cover was determined from these images, and the benthic community characterised from these data. Seaweed samples were taken for species identification. In the four baseline sites, sampling was done at three depth zones to note any changes with a depth gradient, both in terms of substrate type, as well as community composition. There was a notable trend with substrate type having a significant influence (P<0.05) on the community structure. Seaweed communities were dominated by Plocamium corallorhiza and coralline turf based on substrate types. There was also a significant relationship (P<0.05) between substrate type, dominant seaweed species and abalone presence. A Canonical Correspondence Analysis (CCA) of the community data suggested that the benthic community does not change significantly along the distance of coastline sampled. A hierarchical cluster analysis of Bray-Curtis dissimilarity for transect data also suggested that the four sites do not represent ecologically dissimilar communities. A similar analysis showed that abalone seeding had to date not altered the benthic community in shallow seeded areas from the community described for shallow unseeded areas. The study was used to describe the baseline benthic community in areas west of Cape Recife, examine the natural variability along the coast, and determine whether there are relationships between the benthic community composition and emergent abalone abundance. This information will be useful in selection of habitats for abalone seeding in the future. It is important that monitoring and surveying of the study area are to be continued in so allowing for long term data collection which will help in making informed decisions as well as documenting the impact in seeded areas when compared to unseeded areas.
- Full Text:
- Date Issued: 2019
Interaction between the root-feeding beetle, Longitarsus bethae (Coleoptera: Chrysomelidae) and the root-knot nematode, Meloidogyne javanica (Nematoda: Heteroderidae): Implications for the biological control of Lantana camara L. (Verbenaceae) in South Africa
- Authors: Musedeli, Jufter
- Date: 2019
- Subjects: Insect-plant relationships , Insects -- Host plants , Flea beetles , Symbiosis , Longitarsus , Chrysomelidae , Lantana camara -- Biological control -- South Africa , Heteroderidae , Root-knot nematodes , Weeds -- Biological control -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/71130 , vital:29788
- Description: Plants often are simultaneously attacked by several herbivores that can affect each other’s performance, and their interaction may affect their host plant fitness. The current study was conducted to determine the interaction between the root-feeding beetle, Longitarsus bethae Savini & Escalona (Coleoptera: Chrysomelidae) and a root-knot nematode, Meloidogyne javanica (Treub) Chitwood (Tylenchida: Heteroderidae), with implications for the biological control of Lantana camara L. (Verbenaceae) in South Africa. The studies were conducted under quarantine conditions at the Agricultural Research Council-PHP, Roodeplaat, Pretoria, South Africa. Specifically, the study determined; (i) whether root damage by the flea beetle enhanced infection by M. javanica, (ii) whether L. camara roots infected with the nematode enhanced the performance of the beetle, (iii) whether single or combined effect of the two organisms (i.e. L. bethae and M. javanica) had an overall effect on the growth and biomass of their shared host, L. camara, and (iv) the susceptibility of 10 L. camara varieties that are commonly found in South Africa to M. javanica. The study found that galling on the roots of L. camara by the nematode occurs at the highest inoculation of 300 eggs of L. bethae per plant, and no galling occurred at inoculation of 200 eggs per plant and below. The findings also showed that L. bethae performed better on M. javanica-infected than on healthy L. camara roots, and that more L. bethae adult progeny with slightly bigger body size emerged from M. javanica-infected, than from healthy plants. Fresh weight (galls) of plant roots from treatments where both species (i.e., L. bethae and M. javanica) were combined was significantly higher than that from plants infected with the nematode only, suggesting that the combination of both species induces more galling than the nematode does alone. The above-ground dry biomass was significantly lower both in combined and M. javanica only treatments, than in L. bethae only treatment. The study also found that selected L. camara varieties were infected with M. javanica, albeit at varying degrees of infection. Among the 10 L. camara varieties, Orange Red OR 015 was the most susceptible. Other susceptible varieties included Light Pink 009 LP, Total Pink 021 TP and Dark Pink 018 DP, and these, together with variety Orange Red OR 015, constituted 40% of the L. camara varieties evaluated in the current study. Fifty percent of the varieties displayed slight to moderate susceptibility to M. javanica, while 10% displayed lack of susceptibility. The study concluded that the symbiotic relationship between L. bethae and M. javanica was mutual, resulting in increase in the fitness of the beetle. The combined herbivory by L. bethae and M. javanica was also found to be additive on one of the most common varieties of L. camara in South Africa, and therefore co-infestation by both species might enhance the biological control of this weed in South Africa. The study further concluded that the suitability of some invasive L. camara cultivars such as Light Pink 009 LP and Orange Red 015 OR for M. javanica, might also contribute towards biological control of this weed in South Africa, particularly in areas where the two herbivores species co-exist.
- Full Text:
- Date Issued: 2019
- Authors: Musedeli, Jufter
- Date: 2019
- Subjects: Insect-plant relationships , Insects -- Host plants , Flea beetles , Symbiosis , Longitarsus , Chrysomelidae , Lantana camara -- Biological control -- South Africa , Heteroderidae , Root-knot nematodes , Weeds -- Biological control -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/71130 , vital:29788
- Description: Plants often are simultaneously attacked by several herbivores that can affect each other’s performance, and their interaction may affect their host plant fitness. The current study was conducted to determine the interaction between the root-feeding beetle, Longitarsus bethae Savini & Escalona (Coleoptera: Chrysomelidae) and a root-knot nematode, Meloidogyne javanica (Treub) Chitwood (Tylenchida: Heteroderidae), with implications for the biological control of Lantana camara L. (Verbenaceae) in South Africa. The studies were conducted under quarantine conditions at the Agricultural Research Council-PHP, Roodeplaat, Pretoria, South Africa. Specifically, the study determined; (i) whether root damage by the flea beetle enhanced infection by M. javanica, (ii) whether L. camara roots infected with the nematode enhanced the performance of the beetle, (iii) whether single or combined effect of the two organisms (i.e. L. bethae and M. javanica) had an overall effect on the growth and biomass of their shared host, L. camara, and (iv) the susceptibility of 10 L. camara varieties that are commonly found in South Africa to M. javanica. The study found that galling on the roots of L. camara by the nematode occurs at the highest inoculation of 300 eggs of L. bethae per plant, and no galling occurred at inoculation of 200 eggs per plant and below. The findings also showed that L. bethae performed better on M. javanica-infected than on healthy L. camara roots, and that more L. bethae adult progeny with slightly bigger body size emerged from M. javanica-infected, than from healthy plants. Fresh weight (galls) of plant roots from treatments where both species (i.e., L. bethae and M. javanica) were combined was significantly higher than that from plants infected with the nematode only, suggesting that the combination of both species induces more galling than the nematode does alone. The above-ground dry biomass was significantly lower both in combined and M. javanica only treatments, than in L. bethae only treatment. The study also found that selected L. camara varieties were infected with M. javanica, albeit at varying degrees of infection. Among the 10 L. camara varieties, Orange Red OR 015 was the most susceptible. Other susceptible varieties included Light Pink 009 LP, Total Pink 021 TP and Dark Pink 018 DP, and these, together with variety Orange Red OR 015, constituted 40% of the L. camara varieties evaluated in the current study. Fifty percent of the varieties displayed slight to moderate susceptibility to M. javanica, while 10% displayed lack of susceptibility. The study concluded that the symbiotic relationship between L. bethae and M. javanica was mutual, resulting in increase in the fitness of the beetle. The combined herbivory by L. bethae and M. javanica was also found to be additive on one of the most common varieties of L. camara in South Africa, and therefore co-infestation by both species might enhance the biological control of this weed in South Africa. The study further concluded that the suitability of some invasive L. camara cultivars such as Light Pink 009 LP and Orange Red 015 OR for M. javanica, might also contribute towards biological control of this weed in South Africa, particularly in areas where the two herbivores species co-exist.
- Full Text:
- Date Issued: 2019
Investigating assay formats for screening malaria Hsp90-Hop interaction inhibitors
- Authors: Derry, Leigh-Anne Tracy Kim
- Date: 2019
- Subjects: Antimalarials , Heat shock proteins , Drug interactions , Drug resistance , Plasmodium falciparum , High throughput screening (Drug development) , Bioluminescence resonance energy transfer (BRET) , Fluorescence resonance energy transfer (FRET)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63345 , vital:28395
- Description: Although significant gains have been made in the combat against malaria in the last decade, the persistent threat of drug and insecticide resistance continues to motivate the search for new classes of antimalarial drug compounds and targets. Due to their predominance in cellular reactions, protein-protein interactions (P-PIs) are emerging as a promising general target class for therapeutic development. The P-PI which is the focus of this project is the interaction between the chaperone heat shock protein 90 (Hsp90) and its co-chaperone Hsp70/Hsp90 organising protein (Hop). Hop binds to Hsp70 and Hsp90 and facilitates the transfer of client proteins (proteins undergoing folding) from the former to the latter and also regulates nucleotide exchange on Hsp90. Due to its role in correcting protein misfolding during cell stress, Hsp90 is being pursued as a cancer drug target and compounds that inhibit its ATPase activity have entered clinical trials. However, it has been proposed that inhibiting the interaction between Hsp90 and Hop may be alternative approach for inhibiting Hsp90 function for cancer therapy. The malaria parasite Plasmodium falciparum experiences temperature fluctuations during vector-host transitions and febrile episodes and cell stress due to rapid growth and immune responses. Hence, it also depends on chaperones, including PfHsp90, to maintain protein functionality and pathogenesis, demonstrated inter alia by the sensitivity of parasites to Hsp90 inhibitors. In addition, PfHsp90 exists as a complex with the malarial Hop homologue, PfHop, in parasite lysates. Consequently, the purpose of this study was to explore P-PI assay formats that can confirm the interaction of PfHsp90 and PfHop and can be used to identify inhibitors of the interaction, preferably in a medium- to high-throughput screening mode. As a first approach, cell-based bioluminescence and fluorescence resonance energy transfer (BRET and FRET) assays were performed in HeLa cells. To facilitate this, expression plasmid constructs containing coding sequences of P. falciparum and mammalian Hsp90 and Hop and their interacting domains (Hsp90 C-domain and Hop TPR2A domain) fused to the BRET and FRET reporter proteins – yellow fluorescent protein (YFP), cyan fluorescent protein (CFP) and Renilla luciferase (Rluc) - were prepared and used for HeLa cell transient transfections. The FRET assay produced positive interaction signals for the full-length P. falciparum and mammalian Hsp90-Hop interactions. However, C-domain-TPR2A domain interactions were not detected, no interactions could be demonstrated with the BRET assay and western blotting experiments failed to detect expression of all the interaction partners in transiently transfected HeLa cells. Consequently, an alternative in vitro FRET assay format using recombinant proteins was investigated. Expression constructs for the P. falciparum and mammalian C-domains and TPR2A domains fused respectively to YFP and CFP were prepared and the corresponding fusion proteins expressed and purified from E. coli. No interaction was found with the mammalian interaction partners, but interaction of the P. falciparum C-domain and TPR2A domain was consistently detected with a robust Z’ factor value of 0.54. A peptide corresponding to the PfTPR2A domain sequence primarily responsible for Hsp90 binding (based on a human TPR2A peptide described by Horibe et al., 2011) was designed and showed dose-dependent inhibition of the interaction, with 53.7% inhibition at 100 μM. The components of the assay are limited to the purified recombinant proteins, requires minimal liquid steps and may thus be a useful primary screening format for identifying inhibitors of P. falciparum Hsp90-Hop interaction.
- Full Text:
- Date Issued: 2019
- Authors: Derry, Leigh-Anne Tracy Kim
- Date: 2019
- Subjects: Antimalarials , Heat shock proteins , Drug interactions , Drug resistance , Plasmodium falciparum , High throughput screening (Drug development) , Bioluminescence resonance energy transfer (BRET) , Fluorescence resonance energy transfer (FRET)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/63345 , vital:28395
- Description: Although significant gains have been made in the combat against malaria in the last decade, the persistent threat of drug and insecticide resistance continues to motivate the search for new classes of antimalarial drug compounds and targets. Due to their predominance in cellular reactions, protein-protein interactions (P-PIs) are emerging as a promising general target class for therapeutic development. The P-PI which is the focus of this project is the interaction between the chaperone heat shock protein 90 (Hsp90) and its co-chaperone Hsp70/Hsp90 organising protein (Hop). Hop binds to Hsp70 and Hsp90 and facilitates the transfer of client proteins (proteins undergoing folding) from the former to the latter and also regulates nucleotide exchange on Hsp90. Due to its role in correcting protein misfolding during cell stress, Hsp90 is being pursued as a cancer drug target and compounds that inhibit its ATPase activity have entered clinical trials. However, it has been proposed that inhibiting the interaction between Hsp90 and Hop may be alternative approach for inhibiting Hsp90 function for cancer therapy. The malaria parasite Plasmodium falciparum experiences temperature fluctuations during vector-host transitions and febrile episodes and cell stress due to rapid growth and immune responses. Hence, it also depends on chaperones, including PfHsp90, to maintain protein functionality and pathogenesis, demonstrated inter alia by the sensitivity of parasites to Hsp90 inhibitors. In addition, PfHsp90 exists as a complex with the malarial Hop homologue, PfHop, in parasite lysates. Consequently, the purpose of this study was to explore P-PI assay formats that can confirm the interaction of PfHsp90 and PfHop and can be used to identify inhibitors of the interaction, preferably in a medium- to high-throughput screening mode. As a first approach, cell-based bioluminescence and fluorescence resonance energy transfer (BRET and FRET) assays were performed in HeLa cells. To facilitate this, expression plasmid constructs containing coding sequences of P. falciparum and mammalian Hsp90 and Hop and their interacting domains (Hsp90 C-domain and Hop TPR2A domain) fused to the BRET and FRET reporter proteins – yellow fluorescent protein (YFP), cyan fluorescent protein (CFP) and Renilla luciferase (Rluc) - were prepared and used for HeLa cell transient transfections. The FRET assay produced positive interaction signals for the full-length P. falciparum and mammalian Hsp90-Hop interactions. However, C-domain-TPR2A domain interactions were not detected, no interactions could be demonstrated with the BRET assay and western blotting experiments failed to detect expression of all the interaction partners in transiently transfected HeLa cells. Consequently, an alternative in vitro FRET assay format using recombinant proteins was investigated. Expression constructs for the P. falciparum and mammalian C-domains and TPR2A domains fused respectively to YFP and CFP were prepared and the corresponding fusion proteins expressed and purified from E. coli. No interaction was found with the mammalian interaction partners, but interaction of the P. falciparum C-domain and TPR2A domain was consistently detected with a robust Z’ factor value of 0.54. A peptide corresponding to the PfTPR2A domain sequence primarily responsible for Hsp90 binding (based on a human TPR2A peptide described by Horibe et al., 2011) was designed and showed dose-dependent inhibition of the interaction, with 53.7% inhibition at 100 μM. The components of the assay are limited to the purified recombinant proteins, requires minimal liquid steps and may thus be a useful primary screening format for identifying inhibitors of P. falciparum Hsp90-Hop interaction.
- Full Text:
- Date Issued: 2019
Investigating epistemic justice in an adaptive planning process: towards developing a local catchment management strategy
- Authors: Ralekhetla, Mateboho Mary
- Date: 2019
- Subjects: Watershed management -- South Africa , Watershed management -- South Africa -- Moral and ethical aspects , Water resources development -- South Africa -- Eastern Cape , Water-supply -- South Africa -- Makhanda , Makana Water Forum (Makhanda, South Africa) , Makana Municipality (Makhanda, South Africa)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/95980 , vital:31220
- Description: In South Africa, Integrated Water Resource Management (IWRM) is being put into practice in a way that incorporates the belief that all stakeholders should be given a voice in decisions that affect them. Catchment Management Forums (CMFs) are the first place for stakeholder participation, supported by Catchment Management Agencies (CMAs). A key first task of a CMA is to develop of their Catchment Management Strategy (CMS). In this research, I consulted and worked with stakeholders in the Makana Water Forum (Makana Local Municipality, Eastern Cape, South Africa) throughout the process as they worked towards formulating their local CMS. Importantly, this study used insights from the community to focus on the inter- and intra-group interactions among the stakeholders who participated in the first step of Strategic Adaptive Planning. In the process, I explored epistemic contestations that occurred between different epistemic agents (participants) who may have held identity prejudices. The research aimed to allow voices, which could otherwise have been marginalised, to come out in ways that were not stigmatised through the written and personal reflective process. In doing this, the study tried to hear the voice of the oppressed speaker whose knowledge and lived experiences have been overlooked by the hearer’s prejudice. Findings show that participants who were part of the CMS development process experienced epistemic justice. These findings further established that the addition of participant reflections enhanced the level of epistemic justice promoted by the Adaptive Planning Process (APP).
- Full Text:
- Date Issued: 2019
- Authors: Ralekhetla, Mateboho Mary
- Date: 2019
- Subjects: Watershed management -- South Africa , Watershed management -- South Africa -- Moral and ethical aspects , Water resources development -- South Africa -- Eastern Cape , Water-supply -- South Africa -- Makhanda , Makana Water Forum (Makhanda, South Africa) , Makana Municipality (Makhanda, South Africa)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/95980 , vital:31220
- Description: In South Africa, Integrated Water Resource Management (IWRM) is being put into practice in a way that incorporates the belief that all stakeholders should be given a voice in decisions that affect them. Catchment Management Forums (CMFs) are the first place for stakeholder participation, supported by Catchment Management Agencies (CMAs). A key first task of a CMA is to develop of their Catchment Management Strategy (CMS). In this research, I consulted and worked with stakeholders in the Makana Water Forum (Makana Local Municipality, Eastern Cape, South Africa) throughout the process as they worked towards formulating their local CMS. Importantly, this study used insights from the community to focus on the inter- and intra-group interactions among the stakeholders who participated in the first step of Strategic Adaptive Planning. In the process, I explored epistemic contestations that occurred between different epistemic agents (participants) who may have held identity prejudices. The research aimed to allow voices, which could otherwise have been marginalised, to come out in ways that were not stigmatised through the written and personal reflective process. In doing this, the study tried to hear the voice of the oppressed speaker whose knowledge and lived experiences have been overlooked by the hearer’s prejudice. Findings show that participants who were part of the CMS development process experienced epistemic justice. These findings further established that the addition of participant reflections enhanced the level of epistemic justice promoted by the Adaptive Planning Process (APP).
- Full Text:
- Date Issued: 2019
Investigating household energy conservation behaviours in Johannesburg, South Africa
- Authors: Williams, Stephanie
- Date: 2019
- Subjects: Environmental behavior -- South Africa , Energy conservation -- Psychological aspects -- South Africa , Energy consumption -- Psychological aspects -- South Africa , South Africans -- Energy consumption
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/94101 , vital:31000
- Description: Behavioural change is increasingly anticipated as an important pathway towards the reduction of the human footprint on the environment. Monitoring resource consumption at the household scale is essential as a basis for evaluating current performance and supports the understanding of how behaviour change interventions can be implemented. Yet, there are comparatively fewer studies on pro-environmental behaviour (PEB) in developing country contexts than in developed countries. Further, where research efforts have been made in developing countries, these have mainly focussed on low-income households. This means the extant literature on PEB is limited across a geographic and economic gradient, making generalisations about PEB problematic and limiting the scope for thinking about interventions for promoting pro-environmental behaviour in developing countries. In response to this, the study focuses on high-income households in Johannesburg, South Africa. Overall, the findings show a high level of heterogeneity in reported pro-environmental energy use behaviour, attributed to a suit of socio-demographic and value factors. Mainly, age, number of dependents, household size. Valuing leisure time were negatively correlated to energy use behaviours, while valuing environmental quality positively correlated to energy use behaviours. The provision of information energy-saving interventions yielded positive behavioural change as shown by reduced energy consumption of up to 12% in the Treatment group. However, no significant correlations were found between energy reduction and socio-demographic and personal value factors, which can be attributed to a different cultural context. The study discusses the implications of the findings on debates around pro-environmental behaviour and factors influencing pro-environmental behaviour, and provides further recommendations for future energy policies related to the household sector.
- Full Text:
- Date Issued: 2019
- Authors: Williams, Stephanie
- Date: 2019
- Subjects: Environmental behavior -- South Africa , Energy conservation -- Psychological aspects -- South Africa , Energy consumption -- Psychological aspects -- South Africa , South Africans -- Energy consumption
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/94101 , vital:31000
- Description: Behavioural change is increasingly anticipated as an important pathway towards the reduction of the human footprint on the environment. Monitoring resource consumption at the household scale is essential as a basis for evaluating current performance and supports the understanding of how behaviour change interventions can be implemented. Yet, there are comparatively fewer studies on pro-environmental behaviour (PEB) in developing country contexts than in developed countries. Further, where research efforts have been made in developing countries, these have mainly focussed on low-income households. This means the extant literature on PEB is limited across a geographic and economic gradient, making generalisations about PEB problematic and limiting the scope for thinking about interventions for promoting pro-environmental behaviour in developing countries. In response to this, the study focuses on high-income households in Johannesburg, South Africa. Overall, the findings show a high level of heterogeneity in reported pro-environmental energy use behaviour, attributed to a suit of socio-demographic and value factors. Mainly, age, number of dependents, household size. Valuing leisure time were negatively correlated to energy use behaviours, while valuing environmental quality positively correlated to energy use behaviours. The provision of information energy-saving interventions yielded positive behavioural change as shown by reduced energy consumption of up to 12% in the Treatment group. However, no significant correlations were found between energy reduction and socio-demographic and personal value factors, which can be attributed to a different cultural context. The study discusses the implications of the findings on debates around pro-environmental behaviour and factors influencing pro-environmental behaviour, and provides further recommendations for future energy policies related to the household sector.
- Full Text:
- Date Issued: 2019
Involving fishermen in seabirds’ conservation: bridging the gap between socio-economic needs of industry and the needs of seabirds
- Authors: Ginsburg, Tayla
- Date: 2019
- Subjects: Sea birds -- Ecology , Island ecology Island animals -- Conservation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/42184 , vital:36633
- Description: Marine ecosystems and species face multiple threats, particularly intensive industrial-scale fishing activities. As the human population continues to increase exponentially and drive a greater demand for food, commercial fishing effort will likely intensify. While terrestrial protected areas are well developed, marine protected areas (MPAs) are less so, both in the area covered and management practices. There is currently a drive to increase the extent of MPAs, both globally and in South Africa, particularly for those ecosystems and marine species that can benefit from area-based management. The size, shape, location zonation of MPAs generally remain static through time. However, the ocean is a dynamic environment and static MPAs are not always able to achieve conservation objectives for their component ecosystems and species. Dynamic Ocean Management (DOM) is an approach that integrates near real-time data on biological, oceanographic, social and/or economic variables to adjust an MPAs boundary and zonation in both space and time. The aim of this thesis was to assess the viability of applying DOM to a fishing exclusion zone within a zoned MPA in Algoa Bay, South Africa, to support conservation objectives for the Endangered African penguin Spheniscus demersus. Algoa Bay supports half of the world’s remaining population of this species. First, the degree of spatial overlap between foraging penguins and purse-seine fishers in Algoa Bay was determined over five years. In all years, purse-seiner fishing vessels were located around or near to St Croix Island and a large proportion of the total pelagic fish catch from the Bay was removed from this area. Breeding penguins travelled significantly further while foraging when the overlap (and subsequent competition for pelagic fish) was higher, suggesting that African penguins would benefit from a fishing exclusion zone around St Croix Island owing to reduced competition. However, an exclusion zone can have socio-economic impacts on fisheries as a result of the lost fishing area. A common concern raised by fishers is the direct loss of income, either as a result of increased fuel costs to reach alternate fishing grounds or decreased catch. An analysis of catch and travel time (as a proxy for fuel costs) when a 20 km exclusion zone was present or absent around St Croix Island revealed that the exclusion zone scenarios had no significant impact on either variable. Interviews with individuals in the local purse-seine fishery (both fishers and factory managers) showed a consensus that the marine environment needs protection and that MPAs have various environmental benefits. Despite this, individuals were concerned about how they would be impacted by the exclusion zone in the MPA. The interviews highlighted the willingness of individuals in the purse-seine fishery to talk to and work with scientists.
- Full Text:
- Date Issued: 2019
- Authors: Ginsburg, Tayla
- Date: 2019
- Subjects: Sea birds -- Ecology , Island ecology Island animals -- Conservation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/42184 , vital:36633
- Description: Marine ecosystems and species face multiple threats, particularly intensive industrial-scale fishing activities. As the human population continues to increase exponentially and drive a greater demand for food, commercial fishing effort will likely intensify. While terrestrial protected areas are well developed, marine protected areas (MPAs) are less so, both in the area covered and management practices. There is currently a drive to increase the extent of MPAs, both globally and in South Africa, particularly for those ecosystems and marine species that can benefit from area-based management. The size, shape, location zonation of MPAs generally remain static through time. However, the ocean is a dynamic environment and static MPAs are not always able to achieve conservation objectives for their component ecosystems and species. Dynamic Ocean Management (DOM) is an approach that integrates near real-time data on biological, oceanographic, social and/or economic variables to adjust an MPAs boundary and zonation in both space and time. The aim of this thesis was to assess the viability of applying DOM to a fishing exclusion zone within a zoned MPA in Algoa Bay, South Africa, to support conservation objectives for the Endangered African penguin Spheniscus demersus. Algoa Bay supports half of the world’s remaining population of this species. First, the degree of spatial overlap between foraging penguins and purse-seine fishers in Algoa Bay was determined over five years. In all years, purse-seiner fishing vessels were located around or near to St Croix Island and a large proportion of the total pelagic fish catch from the Bay was removed from this area. Breeding penguins travelled significantly further while foraging when the overlap (and subsequent competition for pelagic fish) was higher, suggesting that African penguins would benefit from a fishing exclusion zone around St Croix Island owing to reduced competition. However, an exclusion zone can have socio-economic impacts on fisheries as a result of the lost fishing area. A common concern raised by fishers is the direct loss of income, either as a result of increased fuel costs to reach alternate fishing grounds or decreased catch. An analysis of catch and travel time (as a proxy for fuel costs) when a 20 km exclusion zone was present or absent around St Croix Island revealed that the exclusion zone scenarios had no significant impact on either variable. Interviews with individuals in the local purse-seine fishery (both fishers and factory managers) showed a consensus that the marine environment needs protection and that MPAs have various environmental benefits. Despite this, individuals were concerned about how they would be impacted by the exclusion zone in the MPA. The interviews highlighted the willingness of individuals in the purse-seine fishery to talk to and work with scientists.
- Full Text:
- Date Issued: 2019
Isolation and characterisation of a channel inhibitor from Bunodosoma capense
- Authors: Van Losenoord, Wynand
- Date: 2019
- Subjects: Bioactive compounds , Potassium channels Medical microbiology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/44134 , vital:37114
- Description: Voltage gated ion channels have recently become a subject of investigation as possible pharmaceutical targets. Research has linked the activity of ion channels directly to antiinflammatory pathways, energy homeostasis, cancer proliferation and painful diabetic neuropathy. Sea anemones secrete a diverse array of bioactive compounds including potassium and sodium channel inhibitors. A novel sodium channel inhibitor (molecular mass of 4619.7 ± 0.6 Da) with a predicted sequence: CLCNSDGPSV RGNTLSGILW LAGCPSGWHN CKKHKPTIGW CCK was isolated from Bunodosoma capense using a modified stimulation technique to induce the secretion of the neurotoxin rich mucus confirmed by an Artemia nauplii swimming assay. The peptide purification combined size-exclusion and reverse-phase high performance liquid chromatography. A thallium-based ion flux assay confirmed the presence of a sodium channel inhibitor and purity was determined using a modified tricine SDS-PAGE system. The peptide isolated indicated a tight conformation with the presence of multiple disulfide bonds in a cystine knot conformation. An IC50 value of 26 nM was determined for sodium channel inhibition on MCF-7 cells, indicating increased toxicity in comparison to sodium channel inhibitors previously isolated from Bunodosoma species.
- Full Text:
- Date Issued: 2019
- Authors: Van Losenoord, Wynand
- Date: 2019
- Subjects: Bioactive compounds , Potassium channels Medical microbiology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/44134 , vital:37114
- Description: Voltage gated ion channels have recently become a subject of investigation as possible pharmaceutical targets. Research has linked the activity of ion channels directly to antiinflammatory pathways, energy homeostasis, cancer proliferation and painful diabetic neuropathy. Sea anemones secrete a diverse array of bioactive compounds including potassium and sodium channel inhibitors. A novel sodium channel inhibitor (molecular mass of 4619.7 ± 0.6 Da) with a predicted sequence: CLCNSDGPSV RGNTLSGILW LAGCPSGWHN CKKHKPTIGW CCK was isolated from Bunodosoma capense using a modified stimulation technique to induce the secretion of the neurotoxin rich mucus confirmed by an Artemia nauplii swimming assay. The peptide purification combined size-exclusion and reverse-phase high performance liquid chromatography. A thallium-based ion flux assay confirmed the presence of a sodium channel inhibitor and purity was determined using a modified tricine SDS-PAGE system. The peptide isolated indicated a tight conformation with the presence of multiple disulfide bonds in a cystine knot conformation. An IC50 value of 26 nM was determined for sodium channel inhibition on MCF-7 cells, indicating increased toxicity in comparison to sodium channel inhibitors previously isolated from Bunodosoma species.
- Full Text:
- Date Issued: 2019
Isolation and characterization of extracts of Rosmarinus officinalis l. And comparative evaluation of its antimicrobial activity and selected types of antibiotics against some bacteria species
- Authors: Gbede,Remi
- Date: 2019
- Subjects: Rosmarinus Essences and essential oils Lamiaceae Medicinal plants
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/19142 , vital:39875
- Description: Rosmarinus officinalis L. is known extensively for its multifunctional purposes. The essential oil has been widely used in cosmeceuticals and several ethnopharmacological values. In vitro studies have demonstrated the antibacterial activity of essential oils (EOs) of Rosmarinus officinalis L. against Staphylococcus aureus ATCC 25923, Vibrio cholerae DSM 19283, Escherichia coli ATCC 8739, Pseudomonas aeruginosa ATCC 27853 and Bacillus cereus. These different bacteria were screened against antibiotics such as Tetracycline, Ampicillin Sodium salt, Erythromycin and Amoxicillin, and some standards namely rosmarinic acid, carnosic acid and carnosol, and also against the methanol, acetone, chloroform and dichloromethane extracts of rosemary. The essential oils of Rosmarinus officinalis L. showed significant inhibitory properties compared to antibiotics with various degrees of growth inhibition. The standards exhibited some activities against the organisms. The GC/MS analysis of the essential oil revealed 34 compounds present with most components acting in synergy to bring about antibacterial activities. The antiplasmodial and cytotoxic activities of two leaf extracts of Rosmarinus officinalis (with hexane and dichloromethane as solvents) using standard procedure were studied. The findings justify the claims on the efficacy of plants for therapeutic uses for antifungal, antibacterial and anti-inflammatory properties. Antiplasmodial activity of Rosmarinus officinalis recorded IC50 values of 9.99 µg/ml and 9.76 µg/ml in hexane and dichloromethane respectively.
- Full Text:
- Date Issued: 2019
- Authors: Gbede,Remi
- Date: 2019
- Subjects: Rosmarinus Essences and essential oils Lamiaceae Medicinal plants
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/19142 , vital:39875
- Description: Rosmarinus officinalis L. is known extensively for its multifunctional purposes. The essential oil has been widely used in cosmeceuticals and several ethnopharmacological values. In vitro studies have demonstrated the antibacterial activity of essential oils (EOs) of Rosmarinus officinalis L. against Staphylococcus aureus ATCC 25923, Vibrio cholerae DSM 19283, Escherichia coli ATCC 8739, Pseudomonas aeruginosa ATCC 27853 and Bacillus cereus. These different bacteria were screened against antibiotics such as Tetracycline, Ampicillin Sodium salt, Erythromycin and Amoxicillin, and some standards namely rosmarinic acid, carnosic acid and carnosol, and also against the methanol, acetone, chloroform and dichloromethane extracts of rosemary. The essential oils of Rosmarinus officinalis L. showed significant inhibitory properties compared to antibiotics with various degrees of growth inhibition. The standards exhibited some activities against the organisms. The GC/MS analysis of the essential oil revealed 34 compounds present with most components acting in synergy to bring about antibacterial activities. The antiplasmodial and cytotoxic activities of two leaf extracts of Rosmarinus officinalis (with hexane and dichloromethane as solvents) using standard procedure were studied. The findings justify the claims on the efficacy of plants for therapeutic uses for antifungal, antibacterial and anti-inflammatory properties. Antiplasmodial activity of Rosmarinus officinalis recorded IC50 values of 9.99 µg/ml and 9.76 µg/ml in hexane and dichloromethane respectively.
- Full Text:
- Date Issued: 2019
Long-term impacts of re-establishment practices on pine pulpwood production, South Africa
- Authors: Ndlovu, Noxolo Nokwethemba
- Date: 2019
- Subjects: Pulpwood -- South Africa , Forest management -- Environmental aspects Forest management
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/41785 , vital:36582
- Description: Within South Africa, Pinus species (pines) occupy 50.8% of the total commercial plantation forestry area, of which 29.4% is planted for pulpwood production. Intensive re-establishment is practiced to promote pine productivity (tree survival, growth and uniformity). Extensive international and local (South African) research has been conducted to determine the short-term (up to ca. nine years of age) impacts of individual and integrated re-establishment practices on pine productivity. However, there is limited rotation-length data available for pine pulpwood (grown within South Africa) with which to provide an understanding of the full implications of individual and integrated impacts of re-establishment practices on longer-term tree survival, growth and uniformity. Data from these trials could then be used to justify silvicultural inputs (if any) and potentially refine management decision-making for subsequent rotations. Three pine trials were established in 1997/8 on three contrasting sites to test the influence of a range of re-establishment practices, and included site preparation (slash management and preparation of a planting position), fertilisation and vegetation management, and/or any interaction, on short- and long- term pine pulpwood productivity within South Africa. Pinus patula was planted at Blyde and Pinus elliottii at Bergvliet (both situated in Mpumalanga), and Pinus greggii planted at Hlabeni in KwaZulu-Natal. Final measurements were taken at 17 years at Blyde and Bergvliet, with the Hlabeni trial only assessed to age 11.6 years due to premature felling. Measurements of vegetation cover and biomass, soil and foliar nutrients, tree survival, growth and uniformity were used to provide an insight into treatment responses, both within and between sites. At Blyde (Chapter 2), the individual and integrated impact of different practices of slash management (Burn versus No Burn), preparation of a planting position (Pit, Rip, Chopper roll and Pit and Chopper roll and Rip) and vegetation management (Weedfree versus Weedy) were investigated. The vegetation on the site (initially a mixture of grasses, herbaceous broadleaves and woody plants) competed with the seedlings from 0.3 years, with the woody component (mainly Solanum mauritianum and Buddleija salviifolia) remaining competitive through to rotation-end. From 2.5 years there was an interaction between the preparation of a planting position and vegetation management with the lowest vegetation biomass recorded in the Rip + Weedy treatments. Overall soil and foliar magnesium and potassium levels were considered sub-optimal, however this did not translate to rotation-end tree productivity differences. Tree survival was not impacted negatively by any of the main effects, or their interactions. At rotation-end (17 years) slash management (as a main factor) was not significant in terms of tree growth, whereas preparation of a planting position was significant for BA and Vol (Rip > Pitting ~ Chopper roll), and vegetation management (Weedfree > Weedy) for Dbh, BA and Vol. In addition, there was a significant interaction between the preparation of a planting position and vegetation management for BA and Vol, with the need to manage vegetation more critical when pitting, compared to when ripping and/or chopper rolling. At Bergvliet (Chapter 3), the individual and integrated impact of slash management (Clear, Single and Double), fertilisation (Fertilisation versus No Fertilisation) and vegetation management (Weedfree versus Weedy) were investigated. The vegetation on the site (initially a mixture of grasses, herbaceous broadleaves and woody plants) competed with the seedlings from 0.4 years, with the woody component (mainly pine regeneration, Solanum mauritianum and Lantana camara) remaining competitive until rotation-end. Neither slash management nor fertilisation had a notable influence on vegetation cover. At 1.3 years, biomass sampled indicated a relationship between slash management and fertilisation where biomass was highest within the Clear + Fert (4 398 kg ha-1) and Double + No Fert slash treatments (4 698 kg ha-1). Soil and tree foliar nutrients were considered acceptable. At 17 years, vegetation management (Weedfree > Weedy) and the interaction between slash management and fertilisation significantly influenced rotation-end tree survival (Double + No Fert ~ Single + No Fert ~ Clear + Fert ~ Clear + No Fert > Double + Fert ~ Single + Fert). Neither slash management nor fertilisation (as main factors) had a significant influence on rotation-end growth. Vegetation management significantly improved Ht, Dbh, BA and Vol at rotation-end (Weedfree > Weedy). The management of vegetation resulted in 67.5 m3 ha-1 more volume at rotation-end than in the Weedy plots. At Hlabeni (Chapter 4), the individual and integrated impacts of different forms of fertiliser (No Fertilisation, Maxiphos, Agriphos and NPK) and ring weeding distances (0, 1, 2 and 3 m) were tested. Competition occurred from 0.6 years, and was from mainly grasses (and sedges) and herbaceous vegetation with limited woody plants. Fertilisation did not have a notable influence on vegetation cover, nor did it have a significant influence P. greggii survival and growth. However, fertilisation increased the vegetation biomass (NPK > No Fert ~ Agri > Maxi) which indirectly influenced P. greggii uniformity at 11.6 years. During initial stand development P. greggii responded positively (linear) to an increase in the area ring kept free of competitive vegetation (3_m > 2_m > 1_m > 0_m). Positive growth responses to vegetation management were, however, no longer significant at 11.6 years (except for height growth) possibly due to the absence of more suppressive woody plants. The results from these trials indicate that vegetation management was the most important silvicultural practice at re-establishment especially where woody vegetation persists. Results from this trial series confirm current vegetation management practices within South Africa are adequate, where the immediate area around the seedling or tree is kept free of vegetation with control of any woody vegetation that occurs outside of this area. The results also suggest that slash retention is acceptable if pitting and planting are properly undertaken, while fertiliser application did not have any notable benefit. In addition, these trials have indicated the value (to forest managers) of understanding the integrated impacts of silvicultural practices on long-term tree productivity..
- Full Text:
- Date Issued: 2019
- Authors: Ndlovu, Noxolo Nokwethemba
- Date: 2019
- Subjects: Pulpwood -- South Africa , Forest management -- Environmental aspects Forest management
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/41785 , vital:36582
- Description: Within South Africa, Pinus species (pines) occupy 50.8% of the total commercial plantation forestry area, of which 29.4% is planted for pulpwood production. Intensive re-establishment is practiced to promote pine productivity (tree survival, growth and uniformity). Extensive international and local (South African) research has been conducted to determine the short-term (up to ca. nine years of age) impacts of individual and integrated re-establishment practices on pine productivity. However, there is limited rotation-length data available for pine pulpwood (grown within South Africa) with which to provide an understanding of the full implications of individual and integrated impacts of re-establishment practices on longer-term tree survival, growth and uniformity. Data from these trials could then be used to justify silvicultural inputs (if any) and potentially refine management decision-making for subsequent rotations. Three pine trials were established in 1997/8 on three contrasting sites to test the influence of a range of re-establishment practices, and included site preparation (slash management and preparation of a planting position), fertilisation and vegetation management, and/or any interaction, on short- and long- term pine pulpwood productivity within South Africa. Pinus patula was planted at Blyde and Pinus elliottii at Bergvliet (both situated in Mpumalanga), and Pinus greggii planted at Hlabeni in KwaZulu-Natal. Final measurements were taken at 17 years at Blyde and Bergvliet, with the Hlabeni trial only assessed to age 11.6 years due to premature felling. Measurements of vegetation cover and biomass, soil and foliar nutrients, tree survival, growth and uniformity were used to provide an insight into treatment responses, both within and between sites. At Blyde (Chapter 2), the individual and integrated impact of different practices of slash management (Burn versus No Burn), preparation of a planting position (Pit, Rip, Chopper roll and Pit and Chopper roll and Rip) and vegetation management (Weedfree versus Weedy) were investigated. The vegetation on the site (initially a mixture of grasses, herbaceous broadleaves and woody plants) competed with the seedlings from 0.3 years, with the woody component (mainly Solanum mauritianum and Buddleija salviifolia) remaining competitive through to rotation-end. From 2.5 years there was an interaction between the preparation of a planting position and vegetation management with the lowest vegetation biomass recorded in the Rip + Weedy treatments. Overall soil and foliar magnesium and potassium levels were considered sub-optimal, however this did not translate to rotation-end tree productivity differences. Tree survival was not impacted negatively by any of the main effects, or their interactions. At rotation-end (17 years) slash management (as a main factor) was not significant in terms of tree growth, whereas preparation of a planting position was significant for BA and Vol (Rip > Pitting ~ Chopper roll), and vegetation management (Weedfree > Weedy) for Dbh, BA and Vol. In addition, there was a significant interaction between the preparation of a planting position and vegetation management for BA and Vol, with the need to manage vegetation more critical when pitting, compared to when ripping and/or chopper rolling. At Bergvliet (Chapter 3), the individual and integrated impact of slash management (Clear, Single and Double), fertilisation (Fertilisation versus No Fertilisation) and vegetation management (Weedfree versus Weedy) were investigated. The vegetation on the site (initially a mixture of grasses, herbaceous broadleaves and woody plants) competed with the seedlings from 0.4 years, with the woody component (mainly pine regeneration, Solanum mauritianum and Lantana camara) remaining competitive until rotation-end. Neither slash management nor fertilisation had a notable influence on vegetation cover. At 1.3 years, biomass sampled indicated a relationship between slash management and fertilisation where biomass was highest within the Clear + Fert (4 398 kg ha-1) and Double + No Fert slash treatments (4 698 kg ha-1). Soil and tree foliar nutrients were considered acceptable. At 17 years, vegetation management (Weedfree > Weedy) and the interaction between slash management and fertilisation significantly influenced rotation-end tree survival (Double + No Fert ~ Single + No Fert ~ Clear + Fert ~ Clear + No Fert > Double + Fert ~ Single + Fert). Neither slash management nor fertilisation (as main factors) had a significant influence on rotation-end growth. Vegetation management significantly improved Ht, Dbh, BA and Vol at rotation-end (Weedfree > Weedy). The management of vegetation resulted in 67.5 m3 ha-1 more volume at rotation-end than in the Weedy plots. At Hlabeni (Chapter 4), the individual and integrated impacts of different forms of fertiliser (No Fertilisation, Maxiphos, Agriphos and NPK) and ring weeding distances (0, 1, 2 and 3 m) were tested. Competition occurred from 0.6 years, and was from mainly grasses (and sedges) and herbaceous vegetation with limited woody plants. Fertilisation did not have a notable influence on vegetation cover, nor did it have a significant influence P. greggii survival and growth. However, fertilisation increased the vegetation biomass (NPK > No Fert ~ Agri > Maxi) which indirectly influenced P. greggii uniformity at 11.6 years. During initial stand development P. greggii responded positively (linear) to an increase in the area ring kept free of competitive vegetation (3_m > 2_m > 1_m > 0_m). Positive growth responses to vegetation management were, however, no longer significant at 11.6 years (except for height growth) possibly due to the absence of more suppressive woody plants. The results from these trials indicate that vegetation management was the most important silvicultural practice at re-establishment especially where woody vegetation persists. Results from this trial series confirm current vegetation management practices within South Africa are adequate, where the immediate area around the seedling or tree is kept free of vegetation with control of any woody vegetation that occurs outside of this area. The results also suggest that slash retention is acceptable if pitting and planting are properly undertaken, while fertiliser application did not have any notable benefit. In addition, these trials have indicated the value (to forest managers) of understanding the integrated impacts of silvicultural practices on long-term tree productivity..
- Full Text:
- Date Issued: 2019
Machine learning methods for calibrating radio interferometric data
- Authors: Zitha, Simphiwe Nhlanhla
- Date: 2019
- Subjects: Calibration , Radio astronomy -- Data processing , Radio astronomy -- South Africa , Karoo Array Telescope (South Africa) , Radio telescopes -- South Africa , Common Astronomy Software Application (Computer software)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97096 , vital:31398
- Description: The applications of machine learning have created an opportunity to deal with complex problems currently encountered in radio astronomy data processing. Calibration is one of the most important data processing steps required to produce high dynamic range images. This process involves the determination of calibration parameters, both instrumental and astronomical, to correct the collected data. Typically, astronomers use a package such as Common Astronomy Software Applications (CASA) to compute the gain solutions based on regular observations of a known calibrator source. In this work we present applications of machine learning to first generation calibration (1GC), using the KAT-7 telescope environmental and pointing sensor data recorded during observations. Applying machine learning to 1GC, as opposed to calculating the gain solutions in CASA, has shown evidence of reducing computation, as well as accurately predict the 1GC gain solutions representing the behaviour of the antenna during an observation. These methods are computationally less expensive, however they have not fully learned to generalise in predicting accurate 1GC solutions by looking at environmental and pointing sensors. We call this multi-output regression model ZCal, which is based on random forest, decision trees, extremely randomized trees and K-nearest neighbor algorithms. The prediction error obtained during the testing of our model on testing data is ≈ 0.01 < rmse < 0.09 for gain amplitude per antenna, and 0.2 rad < rmse <0.5 rad for gain phase. This shows that the instrumental parameters used to train our model more strongly correlate with gain amplitude effects than phase.
- Full Text:
- Date Issued: 2019
- Authors: Zitha, Simphiwe Nhlanhla
- Date: 2019
- Subjects: Calibration , Radio astronomy -- Data processing , Radio astronomy -- South Africa , Karoo Array Telescope (South Africa) , Radio telescopes -- South Africa , Common Astronomy Software Application (Computer software)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97096 , vital:31398
- Description: The applications of machine learning have created an opportunity to deal with complex problems currently encountered in radio astronomy data processing. Calibration is one of the most important data processing steps required to produce high dynamic range images. This process involves the determination of calibration parameters, both instrumental and astronomical, to correct the collected data. Typically, astronomers use a package such as Common Astronomy Software Applications (CASA) to compute the gain solutions based on regular observations of a known calibrator source. In this work we present applications of machine learning to first generation calibration (1GC), using the KAT-7 telescope environmental and pointing sensor data recorded during observations. Applying machine learning to 1GC, as opposed to calculating the gain solutions in CASA, has shown evidence of reducing computation, as well as accurately predict the 1GC gain solutions representing the behaviour of the antenna during an observation. These methods are computationally less expensive, however they have not fully learned to generalise in predicting accurate 1GC solutions by looking at environmental and pointing sensors. We call this multi-output regression model ZCal, which is based on random forest, decision trees, extremely randomized trees and K-nearest neighbor algorithms. The prediction error obtained during the testing of our model on testing data is ≈ 0.01 < rmse < 0.09 for gain amplitude per antenna, and 0.2 rad < rmse <0.5 rad for gain phase. This shows that the instrumental parameters used to train our model more strongly correlate with gain amplitude effects than phase.
- Full Text:
- Date Issued: 2019
Management issues affecting emerging contractors in the Northern Cape
- Authors: Kumalo, Sepheka Ishmael
- Date: 2019
- Subjects: Building trades -- South Africa -- North Cape , Project management Construction industry -- South Africa -- Northern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/40478 , vital:36169
- Description: The research is aimed at identifying factors that impact on the performance of contractors during the implementation of construction projects and identify interventions to address poor performance. Eleven project parameters, eleven resources, nine functions in an organisation, and five functions and activities of management work from construction industry literature studies were used to determine the current practices by the contractors involved in the construction projects the study was undertaken in the Northern Cape Province among contractors registered on the CIDB database in Grades 1 to 5. A research questionnaire was used for the collection of data. Closed-ended questions were primarily used. The study recorded a number of significant findings. Forty-seven per cent of Northern Cape construction business owners have a high school education (matriculation), 20% a technical school qualification, and 13% a university qualification; 51% of businesses used personal savings as a source of funding for their projects. In addition, it was found that unless contractors perform relative to the eleven project parameters, they are unlikely to succeed in the workplace, or progress in terms of their registration with the CIDB. The study confirms the importance of business environmental factors which is found to contribute to the success of the emerging contractors if not properly analysed prior to engage in construction business practices. It is evident from the empirical study that emerging contractors do not have knowledge of the following: strategic leadership; the promotion of sustainable growth of emerging contractors; the promotion and improvement of performance and best practice, and the improvement of procurement and delivery management. Recommendations include the CIDB must perform its mandate by providing strategic leadership to all stakeholders involved within the construction industry, encourage best practice and provide guidance in terms of performance improvement of contractors, and provide a platform for clients to reward best practice and performance improvement.
- Full Text:
- Date Issued: 2019
- Authors: Kumalo, Sepheka Ishmael
- Date: 2019
- Subjects: Building trades -- South Africa -- North Cape , Project management Construction industry -- South Africa -- Northern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/40478 , vital:36169
- Description: The research is aimed at identifying factors that impact on the performance of contractors during the implementation of construction projects and identify interventions to address poor performance. Eleven project parameters, eleven resources, nine functions in an organisation, and five functions and activities of management work from construction industry literature studies were used to determine the current practices by the contractors involved in the construction projects the study was undertaken in the Northern Cape Province among contractors registered on the CIDB database in Grades 1 to 5. A research questionnaire was used for the collection of data. Closed-ended questions were primarily used. The study recorded a number of significant findings. Forty-seven per cent of Northern Cape construction business owners have a high school education (matriculation), 20% a technical school qualification, and 13% a university qualification; 51% of businesses used personal savings as a source of funding for their projects. In addition, it was found that unless contractors perform relative to the eleven project parameters, they are unlikely to succeed in the workplace, or progress in terms of their registration with the CIDB. The study confirms the importance of business environmental factors which is found to contribute to the success of the emerging contractors if not properly analysed prior to engage in construction business practices. It is evident from the empirical study that emerging contractors do not have knowledge of the following: strategic leadership; the promotion of sustainable growth of emerging contractors; the promotion and improvement of performance and best practice, and the improvement of procurement and delivery management. Recommendations include the CIDB must perform its mandate by providing strategic leadership to all stakeholders involved within the construction industry, encourage best practice and provide guidance in terms of performance improvement of contractors, and provide a platform for clients to reward best practice and performance improvement.
- Full Text:
- Date Issued: 2019
Mapping and predicting potential distribution patterns of free-range livestock in the rural communal rangelands of Mgwalana, Eastern Cape, South Africa
- Authors: Mkabile, Qawekazi
- Date: 2019
- Subjects: Range management -- South Africa , Grazing -- South Africa , Livestock -- South Africa , Livestock -- Monitoring -- South Africa , Livestock -- Remote sensing -- South Africa , Communal rangelands -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/96000 , vital:31223
- Description: Communal rangelands provide habitat to many plants and animals. However, there is evidence that livestock cause range degradation. Range degradation occurs because livestock select grazing based on the availability of resources such as water and forage material, their use of the landscape is non-uniform, consequently causing resource deterioration. Range management is thus necessary because communities depend on range condition for livestock productivity. However, precise quantification of livestock distribution within communal rangelands is lacking. In developed countries, Global Positioning Systems (GPS) collars have been used to monitor wildlife and domestic livestock in pastures and seem to have worked efficiently. However, in a developing country like South Africa, GPS technology to monitor animal behaviour has been used only for wildlife on privately owned land. The high costs of monitoring livestock herds in large open areas such as communal rangelands have resulted in little or no monitoring of domestic livestock using GPS technology. This study links monitored livestock distribution to physical landscape variables in Mgwalana, and uses the modelled relationship to predict livestock distribution in quaternary catchments, T12A and T35A-E. The research addresses the questions (1) where do livestock spend time in the wet and dry seasons? And (2) how can areas of potential livestock distribution be identified in other catchments where actual distribution is unknown? Livestock were tracked during the wet and dry seasons using GPS collars. The resulting distribution data is combined with selected physical landscape variables to identify selectivity. The GPS location data and the physical landscape variables are used to predict potential livestock distribution where distribution is unknown in quaternary catchments (T12A and T35A-E). The ArcGIS Predictive Analysis Tool (PAT) was used to extract the selected landscape variable ranges based on the GPS location data and identify areas with the same conditions in the quaternary catchments were subsequently selected. The key findings are that livestock prefer accessible areas with gentle terrain near water sources, avoiding south-facing slopes which receive less solar radiation and tend to be cooler. Livestock are attracted to vegetation in riparian zones. Rural communal lands are dominated by poverty, and land-based livelihood strategies can potentially contribute to the well-being of the community. Therefore, understanding livestock distribution can contribute to a rangeland management strategy aimed at improving range condition which could increase livestock productivity and contribute to the livelihoods of local people.
- Full Text:
- Date Issued: 2019
- Authors: Mkabile, Qawekazi
- Date: 2019
- Subjects: Range management -- South Africa , Grazing -- South Africa , Livestock -- South Africa , Livestock -- Monitoring -- South Africa , Livestock -- Remote sensing -- South Africa , Communal rangelands -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/96000 , vital:31223
- Description: Communal rangelands provide habitat to many plants and animals. However, there is evidence that livestock cause range degradation. Range degradation occurs because livestock select grazing based on the availability of resources such as water and forage material, their use of the landscape is non-uniform, consequently causing resource deterioration. Range management is thus necessary because communities depend on range condition for livestock productivity. However, precise quantification of livestock distribution within communal rangelands is lacking. In developed countries, Global Positioning Systems (GPS) collars have been used to monitor wildlife and domestic livestock in pastures and seem to have worked efficiently. However, in a developing country like South Africa, GPS technology to monitor animal behaviour has been used only for wildlife on privately owned land. The high costs of monitoring livestock herds in large open areas such as communal rangelands have resulted in little or no monitoring of domestic livestock using GPS technology. This study links monitored livestock distribution to physical landscape variables in Mgwalana, and uses the modelled relationship to predict livestock distribution in quaternary catchments, T12A and T35A-E. The research addresses the questions (1) where do livestock spend time in the wet and dry seasons? And (2) how can areas of potential livestock distribution be identified in other catchments where actual distribution is unknown? Livestock were tracked during the wet and dry seasons using GPS collars. The resulting distribution data is combined with selected physical landscape variables to identify selectivity. The GPS location data and the physical landscape variables are used to predict potential livestock distribution where distribution is unknown in quaternary catchments (T12A and T35A-E). The ArcGIS Predictive Analysis Tool (PAT) was used to extract the selected landscape variable ranges based on the GPS location data and identify areas with the same conditions in the quaternary catchments were subsequently selected. The key findings are that livestock prefer accessible areas with gentle terrain near water sources, avoiding south-facing slopes which receive less solar radiation and tend to be cooler. Livestock are attracted to vegetation in riparian zones. Rural communal lands are dominated by poverty, and land-based livelihood strategies can potentially contribute to the well-being of the community. Therefore, understanding livestock distribution can contribute to a rangeland management strategy aimed at improving range condition which could increase livestock productivity and contribute to the livelihoods of local people.
- Full Text:
- Date Issued: 2019
Mapping soil factors influencing erosion using machine leaerning algorithms in the t35 d-e catchment in the Eastern Cape Province
- Du Plessis, Casparus Jacobus
- Authors: Du Plessis, Casparus Jacobus
- Date: 2019
- Subjects: Soils -- Analysis Soil erosion
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/17106 , vital:40850
- Description: The need for detailed spatial soil information is increasing in the fields of environmental studies, agriculture as well as engineering practices. Regarding soil erosion in South Africa, border lines between sensitive soil forms in the Duplex soil group and resistant soil forms in the Oxidic soil group need to be mapped to a high accuracy to prevent/manage erosion and major soil losses. In third world countries like South Africa, digital soil mapping (DSM) with the use of machine learning can provide the solutions to fill numerous gaps in these related fields. Local DSM research has been ongoing at the University of the Free State and related institutions for the past eleven years. It has also been used commercially and can therefore be regarded as fruitful. The National Resource Management unit of the Department of Environmental Affairs required a soil map regarding the susceptibility of the soil to erosion for catchment T35 D-E (87 000 hectares) in the Mzimvubu management area of the Eastern Cape, South Africa. Through a DSM approach, machine learning was used to predict the occurrence of soil forms and soil families in accordance with the South African Soil Classification System. A total of 591 soil observations were made at specific points, pre-determined with the conditioned Latin Hypercube sampling (cLHS) method. These pre-determined points were classified into nineteen soil forms and forty eight soil families. The soils were then further divided into nine soil groups, based on their inherent sensitivity to erosion. Outlier observations were omitted from the dataset to create a reliable framework to predict the soil groups as influenced by the SCORPAN factors. These soil groups were mapped and evaluated with an accuracy of 68% and a Kappa statistic value of 0.42 that compare well with other soil maps, both locally and internationally. Mapping soil with an acceptable accuracy with such a high level of detail on catchment scale would be a tremendous advantage to soil scientists and environmental workforces in southern Africa. Future work should focus on DSM training, to broaden the base of DSM skills available in southern Africa. This will ensure that soil information would be included in addressing an increasing amount of real world problems at catchment scales.
- Full Text:
- Date Issued: 2019
- Authors: Du Plessis, Casparus Jacobus
- Date: 2019
- Subjects: Soils -- Analysis Soil erosion
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/17106 , vital:40850
- Description: The need for detailed spatial soil information is increasing in the fields of environmental studies, agriculture as well as engineering practices. Regarding soil erosion in South Africa, border lines between sensitive soil forms in the Duplex soil group and resistant soil forms in the Oxidic soil group need to be mapped to a high accuracy to prevent/manage erosion and major soil losses. In third world countries like South Africa, digital soil mapping (DSM) with the use of machine learning can provide the solutions to fill numerous gaps in these related fields. Local DSM research has been ongoing at the University of the Free State and related institutions for the past eleven years. It has also been used commercially and can therefore be regarded as fruitful. The National Resource Management unit of the Department of Environmental Affairs required a soil map regarding the susceptibility of the soil to erosion for catchment T35 D-E (87 000 hectares) in the Mzimvubu management area of the Eastern Cape, South Africa. Through a DSM approach, machine learning was used to predict the occurrence of soil forms and soil families in accordance with the South African Soil Classification System. A total of 591 soil observations were made at specific points, pre-determined with the conditioned Latin Hypercube sampling (cLHS) method. These pre-determined points were classified into nineteen soil forms and forty eight soil families. The soils were then further divided into nine soil groups, based on their inherent sensitivity to erosion. Outlier observations were omitted from the dataset to create a reliable framework to predict the soil groups as influenced by the SCORPAN factors. These soil groups were mapped and evaluated with an accuracy of 68% and a Kappa statistic value of 0.42 that compare well with other soil maps, both locally and internationally. Mapping soil with an acceptable accuracy with such a high level of detail on catchment scale would be a tremendous advantage to soil scientists and environmental workforces in southern Africa. Future work should focus on DSM training, to broaden the base of DSM skills available in southern Africa. This will ensure that soil information would be included in addressing an increasing amount of real world problems at catchment scales.
- Full Text:
- Date Issued: 2019
Mesoscale alongshore and cross-shore transport and settlement of invertebrate larvae on the south east coast of South Africa
- Authors: Dyantyi, Siphelele Buntu
- Date: 2019
- Subjects: Marine invertebrates -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Benthic animals -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Mexilhao mussel -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Mytilus galloprovincialis -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Oysters -- Larvae -- Dispersal -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97007 , vital:31386
- Description: Pelagic larval stages of most marine benthic species are important in maintaining coastal populations of adults. Several physio-chemical factors such as currents, winds, larval behaviour and time have an influence on the dispersal and transport of larvae to the adult habitat but their role is however still poorly understood. The aim of this study was to investigate the alongshore and cross-shore transport and temporal delivery of invertebrate larvae at four sites (Kenton on Sea, Cannon Rocks, Schoenmakerskop and Cape St Francis) along the south east coast of Eastern Cape, South Africa. Larval distribution of several taxa was determined during two sampling periods, by collecting water samples at nearshore line transects (3 distances: 900m, 1500m and 2400m – perpendicular to the shore) and at three depths (surface, thermocline/middle, bottom), which ranged from 15m (inshore) to 50m (offshore). Physical properties (current speed and direction, dissolved oxygen, fluorescence, turbidity, temperature, salinity, pH, pressure, density and conductivity) were measured and coupled in order to further understand larval distribution. The larvae were analysed as both total abundance and separately as the abundances of a variety of taxa which were: Perna perna, Mytilus galloprovincialis, oysters, early and late nauplii and cyprids. Larval settlement and recruitment on the rocky shores were measured by monthly deployment and collection of 20 (10 each for barnacles and mussels) artificial collectors at each site, which were preserved in ethanol or frozen for further processing. Multiple Permutational Multivariate Analysis of Variance (PERMANOVA) analyses were used to test the effects of site, depth and distance from the shore for the nearshore larvae (taxa analysed separately). In addition, a distance based linear model (distLM) was performed to analyse the relationship between the total larval abundance and the above mentioned physical variables. Multiple two-way analyses of variance (ANOVA) were performed to test the effects of months and sites on the settlement and recruitment of the larvae (P. perna, M. galloprovincialis, other bivalves, cyprids and juvenile barnacles) arriving on the shore. For the nearshore larval distribution, results from the PERMANOVAs revealed that most taxa showed a significant site and depth interactions with the exception of ‘early nauplii’ taxon. Also nearly all taxa were found within the thermocline, besides ‘oyster’ and ‘cyprids’ which were located at thermocline or bottom. Larvae were also located at variable distances from the shore, with most occurring at the offshore stations. Furthermore, there was a geographical separation of larval abundance according to sites, with most larvae located at Cannon Rocks and Kenton on Sea and least at Schoenmakerskop and Cape St Francis. For the settlement and recruitment, most taxa showed a seasonal trend, with the highest abundance of settlers and recruits expectedly appearing during the summer months of the sampling period. Additionally there was a site effect for most taxa (P. perna, M. galloprovincialis, other bivalves and juvenile barnacles), where settlers and recruits were mostly found at Cannon Rocks. Significant differences in abundance of settlers and recruits amongst the four sites indicate spatial and temporal variability for the targeted 180km stretch of coast. Overall for this study, taxon and ontogenetic stage of larvae were important in the distribution and abundance of larvae. Throughout the time frame of nearshore and intertidal sampling, Cannon Rocks consistently resulted as a ‘hot spot’ for larval abundance, settlement and recruitment, while a broad west to east separation was also observed. These results hence highlight that within this stretch of c.180km coast, time, taxon, ontogeny and post-settlement factors influence early dynamics of benthic populations.
- Full Text:
- Date Issued: 2019
- Authors: Dyantyi, Siphelele Buntu
- Date: 2019
- Subjects: Marine invertebrates -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Benthic animals -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Mexilhao mussel -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Mytilus galloprovincialis -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Oysters -- Larvae -- Dispersal -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/97007 , vital:31386
- Description: Pelagic larval stages of most marine benthic species are important in maintaining coastal populations of adults. Several physio-chemical factors such as currents, winds, larval behaviour and time have an influence on the dispersal and transport of larvae to the adult habitat but their role is however still poorly understood. The aim of this study was to investigate the alongshore and cross-shore transport and temporal delivery of invertebrate larvae at four sites (Kenton on Sea, Cannon Rocks, Schoenmakerskop and Cape St Francis) along the south east coast of Eastern Cape, South Africa. Larval distribution of several taxa was determined during two sampling periods, by collecting water samples at nearshore line transects (3 distances: 900m, 1500m and 2400m – perpendicular to the shore) and at three depths (surface, thermocline/middle, bottom), which ranged from 15m (inshore) to 50m (offshore). Physical properties (current speed and direction, dissolved oxygen, fluorescence, turbidity, temperature, salinity, pH, pressure, density and conductivity) were measured and coupled in order to further understand larval distribution. The larvae were analysed as both total abundance and separately as the abundances of a variety of taxa which were: Perna perna, Mytilus galloprovincialis, oysters, early and late nauplii and cyprids. Larval settlement and recruitment on the rocky shores were measured by monthly deployment and collection of 20 (10 each for barnacles and mussels) artificial collectors at each site, which were preserved in ethanol or frozen for further processing. Multiple Permutational Multivariate Analysis of Variance (PERMANOVA) analyses were used to test the effects of site, depth and distance from the shore for the nearshore larvae (taxa analysed separately). In addition, a distance based linear model (distLM) was performed to analyse the relationship between the total larval abundance and the above mentioned physical variables. Multiple two-way analyses of variance (ANOVA) were performed to test the effects of months and sites on the settlement and recruitment of the larvae (P. perna, M. galloprovincialis, other bivalves, cyprids and juvenile barnacles) arriving on the shore. For the nearshore larval distribution, results from the PERMANOVAs revealed that most taxa showed a significant site and depth interactions with the exception of ‘early nauplii’ taxon. Also nearly all taxa were found within the thermocline, besides ‘oyster’ and ‘cyprids’ which were located at thermocline or bottom. Larvae were also located at variable distances from the shore, with most occurring at the offshore stations. Furthermore, there was a geographical separation of larval abundance according to sites, with most larvae located at Cannon Rocks and Kenton on Sea and least at Schoenmakerskop and Cape St Francis. For the settlement and recruitment, most taxa showed a seasonal trend, with the highest abundance of settlers and recruits expectedly appearing during the summer months of the sampling period. Additionally there was a site effect for most taxa (P. perna, M. galloprovincialis, other bivalves and juvenile barnacles), where settlers and recruits were mostly found at Cannon Rocks. Significant differences in abundance of settlers and recruits amongst the four sites indicate spatial and temporal variability for the targeted 180km stretch of coast. Overall for this study, taxon and ontogenetic stage of larvae were important in the distribution and abundance of larvae. Throughout the time frame of nearshore and intertidal sampling, Cannon Rocks consistently resulted as a ‘hot spot’ for larval abundance, settlement and recruitment, while a broad west to east separation was also observed. These results hence highlight that within this stretch of c.180km coast, time, taxon, ontogeny and post-settlement factors influence early dynamics of benthic populations.
- Full Text:
- Date Issued: 2019