The impact of agricultural infrastructure on rural livelihoods in KwaZulu-Natal
- Authors: Mankahla, Sipesihle Qukeza
- Date: 2020
- Subjects: Agriculture -- Economic aspects , Agricultural development projects -- South Africa -- KwaZulu Natal , Project management
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/46141 , vital:39508
- Description: The purpose of the study was to investigate the impact of agricultural infrastructure on rural livelihoods of kwaZulu-Natal. The main objective of the study is to look into the ways in which rural infrastructure can improve the livelihoods of kwaZulu-Natal farmers. Government programmes such as agri-parks, one household-one hectare and cooperative funding, when implemented according to their objective, can improve the implementation of infrastructure development in rural areas of kwaZulu-Natal. The objectives of the study were achieved by reviewing the literature relevant to the topic. Data was sourced from primary and secondary sources. A qualitative method was used as the qualitative approach has been considered to be the most appropriate method in achieving research objectives. This approach puts emphasis on the meanings and experiences as found in the study of Lincoln and Denzin. This approach best describes events, opinions and views without the use of data in the form of numbers; rather it provides textual data that gives an insight into the occurrence being studied. The developments in agriculture would not be sustainable without developing the rural areas and addressing the issues of poverty and enhancing investment capacities of the resource-poor farmers. The linkage of infrastructure to positive economic development cannot be denied. Agricultural infrastructure is infrastructure such as irrigation, rural electrification, roads, and markets in close coordination with institutional infrastructure. There is a long list of infrastructure assets that affect rural development. There is basic agricultural infrastructure which forms the foundation for agricultural economic development of rural livelihoods. This infrastructure includes transport networks, access to water and livestock agricultural infrastructure. Thus, the study sought to establish the impact of existing agricultural infrastructure on agricultural economic development and improvement of rural livelihoods in kwaZulu-Natal. The study revealed that the rural farmers in this province were affected and limited by poor road infrastructure and that access to suitable water for irrigation was far from ideal. As a result, the sector is hindered and does not perform to its full potential and this slows economic development and negatively affects rural livelihoods.
- Full Text:
- Date Issued: 2020
- Authors: Mankahla, Sipesihle Qukeza
- Date: 2020
- Subjects: Agriculture -- Economic aspects , Agricultural development projects -- South Africa -- KwaZulu Natal , Project management
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/46141 , vital:39508
- Description: The purpose of the study was to investigate the impact of agricultural infrastructure on rural livelihoods of kwaZulu-Natal. The main objective of the study is to look into the ways in which rural infrastructure can improve the livelihoods of kwaZulu-Natal farmers. Government programmes such as agri-parks, one household-one hectare and cooperative funding, when implemented according to their objective, can improve the implementation of infrastructure development in rural areas of kwaZulu-Natal. The objectives of the study were achieved by reviewing the literature relevant to the topic. Data was sourced from primary and secondary sources. A qualitative method was used as the qualitative approach has been considered to be the most appropriate method in achieving research objectives. This approach puts emphasis on the meanings and experiences as found in the study of Lincoln and Denzin. This approach best describes events, opinions and views without the use of data in the form of numbers; rather it provides textual data that gives an insight into the occurrence being studied. The developments in agriculture would not be sustainable without developing the rural areas and addressing the issues of poverty and enhancing investment capacities of the resource-poor farmers. The linkage of infrastructure to positive economic development cannot be denied. Agricultural infrastructure is infrastructure such as irrigation, rural electrification, roads, and markets in close coordination with institutional infrastructure. There is a long list of infrastructure assets that affect rural development. There is basic agricultural infrastructure which forms the foundation for agricultural economic development of rural livelihoods. This infrastructure includes transport networks, access to water and livestock agricultural infrastructure. Thus, the study sought to establish the impact of existing agricultural infrastructure on agricultural economic development and improvement of rural livelihoods in kwaZulu-Natal. The study revealed that the rural farmers in this province were affected and limited by poor road infrastructure and that access to suitable water for irrigation was far from ideal. As a result, the sector is hindered and does not perform to its full potential and this slows economic development and negatively affects rural livelihoods.
- Full Text:
- Date Issued: 2020
The impact of discounting fees by civil engineering consultants
- Authors: Siqiti, Khulile
- Date: 2020
- Subjects: Consulting engineers , Consultants Civil engineering , Project management
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/47246 , vital:39836
- Description: The study provides insight into the views and perceptions of consulting engineers on the discounting of professional fees. The purpose of the research was to determine the impact of discounting professional fees in the civil engineering profession and ultimately potential ways in which the civil engineering profession could improve business sustainability. The study included a review of literature, which was utilised to develop a questionnaire. A total of 26 practicing consulting engineers, who are members of Consulting Engineers South Africa (CESA), and represented small, medium and large consulting engineering firms, participated in the questionnaire survey. The questionnaire investigates the respondents’ perceptions on the impact of discounting professional fees in the civil engineering profession and the amount of discount offered as well as the reasons for discounting fees. The results show that the practice of discounting professional fees is widespread, affecting small, medium and large consulting firms. The results also indicate that prevailing market conditions in civil engineering profession are the primary reasons why consulting engineers offer discounts on fees. Respondents agreed that projects are awarded to the lowest bidder during tender process. Respondents also agreed that experienced engineers are allocated less time on projects to manage project costs. The findings suggest that discounting of professional fees is a great concern that needs to be addressed in order to attain profession business sustainability. It is suggested that the Engineering Council of South Africa (ECSA) should regulate the fee structures and ensure that all professionals, whether employed in the public or private sector, understand the basic finances on running a professional consultancy to deliver a service.
- Full Text:
- Date Issued: 2020
- Authors: Siqiti, Khulile
- Date: 2020
- Subjects: Consulting engineers , Consultants Civil engineering , Project management
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/47246 , vital:39836
- Description: The study provides insight into the views and perceptions of consulting engineers on the discounting of professional fees. The purpose of the research was to determine the impact of discounting professional fees in the civil engineering profession and ultimately potential ways in which the civil engineering profession could improve business sustainability. The study included a review of literature, which was utilised to develop a questionnaire. A total of 26 practicing consulting engineers, who are members of Consulting Engineers South Africa (CESA), and represented small, medium and large consulting engineering firms, participated in the questionnaire survey. The questionnaire investigates the respondents’ perceptions on the impact of discounting professional fees in the civil engineering profession and the amount of discount offered as well as the reasons for discounting fees. The results show that the practice of discounting professional fees is widespread, affecting small, medium and large consulting firms. The results also indicate that prevailing market conditions in civil engineering profession are the primary reasons why consulting engineers offer discounts on fees. Respondents agreed that projects are awarded to the lowest bidder during tender process. Respondents also agreed that experienced engineers are allocated less time on projects to manage project costs. The findings suggest that discounting of professional fees is a great concern that needs to be addressed in order to attain profession business sustainability. It is suggested that the Engineering Council of South Africa (ECSA) should regulate the fee structures and ensure that all professionals, whether employed in the public or private sector, understand the basic finances on running a professional consultancy to deliver a service.
- Full Text:
- Date Issued: 2020
The influence of anthropogenic and environmental covariates on the habitat use and density of sympatric carnivores, Limpopo Province, South Africa
- Authors: Faure, J Philip B
- Date: 2020
- Subjects: Carnivorous animals -- South Africa -- Limpopo
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/48302 , vital:40840
- Description: Carnivores are declining and undergoing substantial range contractions which have largely been attributed to anthropogenic related. Globally, there has been an increase in establishing protected areas for species conservation. However, protected areas may not always effectively conserve all biodiversity, where some areas are too small for viable populations of wide-ranging species, such as leopards Panthera pardus, spotted hyaenas Crocuta crocuta, and brown hyaenas Parahyaena brunnea. The importance of privately-owned areas are gaining increasing recognition for their role in conserving species, and ecosystems. Though such areas may provide key opportunities for the conservation and persistence of biodiversity, little attention (with regards to species conservation planning) is given to these areas. Furthermore, large carnivore populations increasingly have to share the landscapes with humans as the global human population increase. Though anthropogenic impacts can be limited within protected areas, human activities on privately-owned farmlands are mostly dictated by economic activity to sustain human presence (often leading to humancarnivore conflicts). Platjan (South Africa) is one such area. It comprise a matrix of agricultural practices and land-use types, dominated by humans. Consequently, it presented an ideal landscape to investigate how humans and carnivores coexist. Spatial capture-recapture modelling suggest stable populations manifested through low densities for leopards, spotted hyaenas, brown hyaenas, and Africa civet Civettictis civetta within the study area. Densities of the focal species were more similar to what has been found in more arid environments. Though it should be noted, that population fluctuations are common in nature, and this study only provide a brief snapshot of the population. Nonetheless, it provides baseline carnivore density estimates for the area. Single-season, single-species occupancy modelling was used to determine the influence of anthropogenic variables on species probability of site use. Results suggested that leopards and spotted hyaenas avoided crop fields (possibly due to higher human activity in these areas). Whereas black-backed jackal Canis mesomelas were positively influenced by the proportion of survey sites containing human infrastructure (possibly due to additional food sources provided by human presence). The covariates did not suggest any effect on brown hyaena and African civet probability of site use, which may be explained by temporal niche partitioning between the species and humans. Kernel density estimation and selectivity ratios revealed that all carnivores were predominantly crepuscular-nocturnal, with the exception of brown hyaenas which were strictly nocturnal. Among the focal species, brown hyaenas and African civets had the lowest temporal overlap with humans, which may explain why they weren’t affected by any of the anthropogenic variables. Whereas, jackal had the highest overlap, supporting a notion that they may be more tolerant of human presence than the other study animals. Overall, it seems that carnivores are able to coexist with humans on privately-owned farmlands through temporal niche partitioning, but manifest at rather low densities. Nonetheless, this study adds to the current understanding of human-carnivore coadaptation, and provides the first carnivore density estimates for the Platjan region.
- Full Text:
- Date Issued: 2020
- Authors: Faure, J Philip B
- Date: 2020
- Subjects: Carnivorous animals -- South Africa -- Limpopo
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/48302 , vital:40840
- Description: Carnivores are declining and undergoing substantial range contractions which have largely been attributed to anthropogenic related. Globally, there has been an increase in establishing protected areas for species conservation. However, protected areas may not always effectively conserve all biodiversity, where some areas are too small for viable populations of wide-ranging species, such as leopards Panthera pardus, spotted hyaenas Crocuta crocuta, and brown hyaenas Parahyaena brunnea. The importance of privately-owned areas are gaining increasing recognition for their role in conserving species, and ecosystems. Though such areas may provide key opportunities for the conservation and persistence of biodiversity, little attention (with regards to species conservation planning) is given to these areas. Furthermore, large carnivore populations increasingly have to share the landscapes with humans as the global human population increase. Though anthropogenic impacts can be limited within protected areas, human activities on privately-owned farmlands are mostly dictated by economic activity to sustain human presence (often leading to humancarnivore conflicts). Platjan (South Africa) is one such area. It comprise a matrix of agricultural practices and land-use types, dominated by humans. Consequently, it presented an ideal landscape to investigate how humans and carnivores coexist. Spatial capture-recapture modelling suggest stable populations manifested through low densities for leopards, spotted hyaenas, brown hyaenas, and Africa civet Civettictis civetta within the study area. Densities of the focal species were more similar to what has been found in more arid environments. Though it should be noted, that population fluctuations are common in nature, and this study only provide a brief snapshot of the population. Nonetheless, it provides baseline carnivore density estimates for the area. Single-season, single-species occupancy modelling was used to determine the influence of anthropogenic variables on species probability of site use. Results suggested that leopards and spotted hyaenas avoided crop fields (possibly due to higher human activity in these areas). Whereas black-backed jackal Canis mesomelas were positively influenced by the proportion of survey sites containing human infrastructure (possibly due to additional food sources provided by human presence). The covariates did not suggest any effect on brown hyaena and African civet probability of site use, which may be explained by temporal niche partitioning between the species and humans. Kernel density estimation and selectivity ratios revealed that all carnivores were predominantly crepuscular-nocturnal, with the exception of brown hyaenas which were strictly nocturnal. Among the focal species, brown hyaenas and African civets had the lowest temporal overlap with humans, which may explain why they weren’t affected by any of the anthropogenic variables. Whereas, jackal had the highest overlap, supporting a notion that they may be more tolerant of human presence than the other study animals. Overall, it seems that carnivores are able to coexist with humans on privately-owned farmlands through temporal niche partitioning, but manifest at rather low densities. Nonetheless, this study adds to the current understanding of human-carnivore coadaptation, and provides the first carnivore density estimates for the Platjan region.
- Full Text:
- Date Issued: 2020
The influence of the integration of local knowledge during chemistry hands-on practical activities on grade 8/9 learners’ attitude towards science
- Authors: Ngqinambi, Akhona
- Date: 2020
- Subjects: Science -- Study and teaching (Secondary) -- South Africa , Science teachers -- South Africa , High school students -- Attitudes , Communities of practice -- South Africa , Science clubs -- South Africa , Science projects -- South Africa , Constructivism (Education) -- South Africa , Educational counseling -- South Africa , Local knowledge
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144724 , vital:38373
- Description: With every passing year, there is a decrease in the number of learners pursuing science degrees after completion of grade 12. One of the main reasons for this is the negative attitude that high school learners have towards science learning and science as an entity. The Natural Sciences curriculum suggests the use of local knowledge to introduce the usefulness and the relatability of science to learners. This study is an intervention that seeks to ascertain the influence that local knowledge has on the attitudes of grade 8/9 learners when integrated into their chemistry hands-on practical activities. The study was informed by Vygotsky’s social constructivist theory and Wenger’s community of practice theory. Grade 8/9 learners from four high school science clubs did three local knowledge integrated experiments based on acids and bases. The learners completed pre- and post- surveys and were interviewed about their experiences. Volunteers at the science clubs were also interviewed. Excel was used to deductively analyse quantitative data. On the other hand, an inductive-deductive thematic approach was used to analyse the qualitative data. The findings of the study showed a divergence of qualitative and quantitative methods. The quantitative data showed that there was a slight decrease (but not statistically significant) in the attitude of the learners after engaging in chemistry hands-on practical activities into which local knowledge had been integrated. On the other hand, the qualitative data showed that there was a positive shift in the learners’ attitudes after they had been engaged in the chemistry hands-on practical activities. Additionally, the findings of the study revealed that the integration of local knowledge promotes conceptual understanding and improves the performance of the learners. This study thus recommends that local knowledge should be integrated into the grade 8 and 9 learners’ curriculum to enrich and promote contextualized science for learners. Additionally, the integration of local knowledge would promote conceptual understanding and spark interest and motivation in learners to pursue science-related careers.
- Full Text:
- Date Issued: 2020
- Authors: Ngqinambi, Akhona
- Date: 2020
- Subjects: Science -- Study and teaching (Secondary) -- South Africa , Science teachers -- South Africa , High school students -- Attitudes , Communities of practice -- South Africa , Science clubs -- South Africa , Science projects -- South Africa , Constructivism (Education) -- South Africa , Educational counseling -- South Africa , Local knowledge
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/144724 , vital:38373
- Description: With every passing year, there is a decrease in the number of learners pursuing science degrees after completion of grade 12. One of the main reasons for this is the negative attitude that high school learners have towards science learning and science as an entity. The Natural Sciences curriculum suggests the use of local knowledge to introduce the usefulness and the relatability of science to learners. This study is an intervention that seeks to ascertain the influence that local knowledge has on the attitudes of grade 8/9 learners when integrated into their chemistry hands-on practical activities. The study was informed by Vygotsky’s social constructivist theory and Wenger’s community of practice theory. Grade 8/9 learners from four high school science clubs did three local knowledge integrated experiments based on acids and bases. The learners completed pre- and post- surveys and were interviewed about their experiences. Volunteers at the science clubs were also interviewed. Excel was used to deductively analyse quantitative data. On the other hand, an inductive-deductive thematic approach was used to analyse the qualitative data. The findings of the study showed a divergence of qualitative and quantitative methods. The quantitative data showed that there was a slight decrease (but not statistically significant) in the attitude of the learners after engaging in chemistry hands-on practical activities into which local knowledge had been integrated. On the other hand, the qualitative data showed that there was a positive shift in the learners’ attitudes after they had been engaged in the chemistry hands-on practical activities. Additionally, the findings of the study revealed that the integration of local knowledge promotes conceptual understanding and improves the performance of the learners. This study thus recommends that local knowledge should be integrated into the grade 8 and 9 learners’ curriculum to enrich and promote contextualized science for learners. Additionally, the integration of local knowledge would promote conceptual understanding and spark interest and motivation in learners to pursue science-related careers.
- Full Text:
- Date Issued: 2020
The jackal as a mesopredator : dietary response to an apex predator and role as an endozoochore
- Authors: Favaretto, Bianca Sashika
- Date: 2020
- Subjects: Jackal buzzard
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/48313 , vital:40841
- Description: Interactions between apex predators, mesopredators and their impacts on trophic dynamics have been well documented. However, the influence of apex predators, through the provision of carrion, on the foraging ecology of African mesopredators is poorly understood. To investigate such resource supplementation by apex predators for mesopredators, the black-backed jackal Canis mesomelas, a generalist mesopredator, was used as a model species to improve our understanding of this topic in South African ecosystems. To do this, I compared the diet of jackal at replicated sites with and without cheetah in the eastern Karoo, South Africa. Scat samples were macroscopically categorized into six broad dietary categories: mammal, reptile, bird, fruit, forage and insect. Mammalian prey was further identified to species and grouped into six functional dietary categories: carnivore, large ungulate, small ungulate, small mammal, and unknown mammal. Jackal diets were dominated by mammal prey, with significant differences in the biomass and frequency of occurrence of mammals by jackal at sites with cheetah and without cheetah. Mammal consumption, showed limited variation amongst seasons. Resource supplementation provided by predator derived carrion is an important factor influencing jackal foraging ecology. The emergent hypothesis that jackal may show demographic responses (increased fecundity, survival, density) to this supplementation needs to be tested. This study also provided an opportunity to investigate the potential role of jackal as an endozoochore. Jackal consume fruits and their seeds, yet to our knowledge, an investigation into their seed dispersing abilities is yet to be investigated. This study assessed the viability and germination capacity of ingested seeds extracted from jackal scat samples using the tetrazolium tests and germination trials. Seed viability and germination of all three species (Grewia occidentalis, Pappea capensis and Diospyros lycioides) were significantly lower than uningested seeds. These results suggest that jackal gut passage is acting severely on ingested seeds. This study represents a novel investigation into differences in jackal diet in sites with and without cheetah as well as the role jackal play in endozoochory, contributing to improved understanding of the ecological role of jackal.
- Full Text:
- Date Issued: 2020
- Authors: Favaretto, Bianca Sashika
- Date: 2020
- Subjects: Jackal buzzard
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/48313 , vital:40841
- Description: Interactions between apex predators, mesopredators and their impacts on trophic dynamics have been well documented. However, the influence of apex predators, through the provision of carrion, on the foraging ecology of African mesopredators is poorly understood. To investigate such resource supplementation by apex predators for mesopredators, the black-backed jackal Canis mesomelas, a generalist mesopredator, was used as a model species to improve our understanding of this topic in South African ecosystems. To do this, I compared the diet of jackal at replicated sites with and without cheetah in the eastern Karoo, South Africa. Scat samples were macroscopically categorized into six broad dietary categories: mammal, reptile, bird, fruit, forage and insect. Mammalian prey was further identified to species and grouped into six functional dietary categories: carnivore, large ungulate, small ungulate, small mammal, and unknown mammal. Jackal diets were dominated by mammal prey, with significant differences in the biomass and frequency of occurrence of mammals by jackal at sites with cheetah and without cheetah. Mammal consumption, showed limited variation amongst seasons. Resource supplementation provided by predator derived carrion is an important factor influencing jackal foraging ecology. The emergent hypothesis that jackal may show demographic responses (increased fecundity, survival, density) to this supplementation needs to be tested. This study also provided an opportunity to investigate the potential role of jackal as an endozoochore. Jackal consume fruits and their seeds, yet to our knowledge, an investigation into their seed dispersing abilities is yet to be investigated. This study assessed the viability and germination capacity of ingested seeds extracted from jackal scat samples using the tetrazolium tests and germination trials. Seed viability and germination of all three species (Grewia occidentalis, Pappea capensis and Diospyros lycioides) were significantly lower than uningested seeds. These results suggest that jackal gut passage is acting severely on ingested seeds. This study represents a novel investigation into differences in jackal diet in sites with and without cheetah as well as the role jackal play in endozoochory, contributing to improved understanding of the ecological role of jackal.
- Full Text:
- Date Issued: 2020
The past meets the present: exploring the biogeography of extant plecoptera of South Africa with reference to ancient middle permian fossil forms from the Onder Karoo locality near Sutherland
- Authors: Kirkaldy, Benjamin Puleng
- Date: 2020
- Subjects: Stoneflies, Fossil -- South Africa -- Northern Cape , Palaeopteron -- South Africa -- Northern Cape , Stoneflies -- Evolution , Insects, Fossil -- South Africa -- Northern Cape , Paleoentomology , Paleoentomology -- South Africa -- Northern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/165755 , vital:41278
- Description: The Onder Karoo fossil locality near Sutherland, Northern Cape, recently yielded an unprecedented diversity of middle Permian insects, which were preserved in deposits of an aquatic lake margin system, in the Lowermost Abrahamskraal Formation. A large number of Plecoptera (stonefly) specimens were found, and this study represents an in-depth analysis of these species in the context of plecopteran evolution. A significant contribution to current knowledge of the Plecoptera from the middle Permian to the present has been made, utilizing a combination of fossil and phylogenetic evidence to better understand the origins, evolution, diversity and biogeography of the stoneflies. Three new plecopteran species have been described from the Onder Karoo locality, which is recognized here as the first Lagerstätte of its kind in Gondwana. Possible ecological links and relationships with the plecopterans described here have been suggested, using extant Plecoptera as analogues. An in-depth, fossilcalibrated, dated phylogeny of the Plecoptera was completed, using representatives from all three dominant lineages, the Antarctoperlaria, Systellognatha and the Euholognatha. This provides strong support for the monophyly of the Notonemouridae and the Antarctoperlaria, however the monophyly of Systellognatha and Euholognatha was not supported. The Notonemouridae were found to represent an earlier divergence than previously believed, forming a sister group to the remaining Plecoptera. Through a combination of fossil and molecular evidence, strong support was found for the current distribution of the Plecoptera worldwide being attributable to vicariance caused by the rifting of Pangea, and subsequently Gondwana and Laurasia, and long range dispersal. The focussed effort to include Southern Hemisphere stoneflies throughout this study has been a valuable step in reducing the Northern Hemisphere bias which currently dominates plecopteran research and has assisted in opening the way for future research into this important group on a global scale.
- Full Text:
- Date Issued: 2020
- Authors: Kirkaldy, Benjamin Puleng
- Date: 2020
- Subjects: Stoneflies, Fossil -- South Africa -- Northern Cape , Palaeopteron -- South Africa -- Northern Cape , Stoneflies -- Evolution , Insects, Fossil -- South Africa -- Northern Cape , Paleoentomology , Paleoentomology -- South Africa -- Northern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/165755 , vital:41278
- Description: The Onder Karoo fossil locality near Sutherland, Northern Cape, recently yielded an unprecedented diversity of middle Permian insects, which were preserved in deposits of an aquatic lake margin system, in the Lowermost Abrahamskraal Formation. A large number of Plecoptera (stonefly) specimens were found, and this study represents an in-depth analysis of these species in the context of plecopteran evolution. A significant contribution to current knowledge of the Plecoptera from the middle Permian to the present has been made, utilizing a combination of fossil and phylogenetic evidence to better understand the origins, evolution, diversity and biogeography of the stoneflies. Three new plecopteran species have been described from the Onder Karoo locality, which is recognized here as the first Lagerstätte of its kind in Gondwana. Possible ecological links and relationships with the plecopterans described here have been suggested, using extant Plecoptera as analogues. An in-depth, fossilcalibrated, dated phylogeny of the Plecoptera was completed, using representatives from all three dominant lineages, the Antarctoperlaria, Systellognatha and the Euholognatha. This provides strong support for the monophyly of the Notonemouridae and the Antarctoperlaria, however the monophyly of Systellognatha and Euholognatha was not supported. The Notonemouridae were found to represent an earlier divergence than previously believed, forming a sister group to the remaining Plecoptera. Through a combination of fossil and molecular evidence, strong support was found for the current distribution of the Plecoptera worldwide being attributable to vicariance caused by the rifting of Pangea, and subsequently Gondwana and Laurasia, and long range dispersal. The focussed effort to include Southern Hemisphere stoneflies throughout this study has been a valuable step in reducing the Northern Hemisphere bias which currently dominates plecopteran research and has assisted in opening the way for future research into this important group on a global scale.
- Full Text:
- Date Issued: 2020
The profile of local hunters in South Africa
- Du Plessis, Madelaine Patricia
- Authors: Du Plessis, Madelaine Patricia
- Date: 2020
- Subjects: Hunters -- Economic conditions -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/48324 , vital:40847
- Description: The South African hunting industry, but more specifically local hunting, is regarded as one of the key sectors within South Africa’s wildlife industry – not only for the significant economic contribution it makes, but also from an equally vital conservation point of view. Despite this, local hunters are neglected in the sense that hunting accommodation and hunting packages provided by the majority of game ranches mainly focus on accommodating trophy hunters. This study investigated the profile of local hunters in South Africa. The objectives of this study were the following: establishing the factors which determine the profile of local hunters and then comparing the results to existing information, as well as identifying the economic contribution local hunters make towards South Africa’s economy. The study commenced with a literature review of existing research on the local hunting industry and on the profile of local hunters. Thereafter, a self-administered questionnaire was developed and conducted amongst active local hunters via the CHASA hunting confederation website, by means of which the primary data for the current study were collected. The study concluded that the profile of the South African local hunter has undergone slight changes from what previous research had established. This was attributed to several external as well as internal factors. The current research would assist hunting farms in approaching the local hunting sector with up-to-date information in order to accurately tailor their packages and marketing in line with the evidence presented in this dissertation regarding the changes in the profile of the South African local hunter.
- Full Text:
- Date Issued: 2020
- Authors: Du Plessis, Madelaine Patricia
- Date: 2020
- Subjects: Hunters -- Economic conditions -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/48324 , vital:40847
- Description: The South African hunting industry, but more specifically local hunting, is regarded as one of the key sectors within South Africa’s wildlife industry – not only for the significant economic contribution it makes, but also from an equally vital conservation point of view. Despite this, local hunters are neglected in the sense that hunting accommodation and hunting packages provided by the majority of game ranches mainly focus on accommodating trophy hunters. This study investigated the profile of local hunters in South Africa. The objectives of this study were the following: establishing the factors which determine the profile of local hunters and then comparing the results to existing information, as well as identifying the economic contribution local hunters make towards South Africa’s economy. The study commenced with a literature review of existing research on the local hunting industry and on the profile of local hunters. Thereafter, a self-administered questionnaire was developed and conducted amongst active local hunters via the CHASA hunting confederation website, by means of which the primary data for the current study were collected. The study concluded that the profile of the South African local hunter has undergone slight changes from what previous research had established. This was attributed to several external as well as internal factors. The current research would assist hunting farms in approaching the local hunting sector with up-to-date information in order to accurately tailor their packages and marketing in line with the evidence presented in this dissertation regarding the changes in the profile of the South African local hunter.
- Full Text:
- Date Issued: 2020
The role of elephants in Hluhluwe-iMfolozi Park: Perceived versus measured effects on woody vegetation
- Authors: Mbongwa, Siphesihle
- Date: 2020
- Subjects: Woody plants -- Environmental aspects
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/48467 , vital:40879
- Description: Elephants were successfully reintroduced into the 900 km2 fenced Hluhluwe-iMfolozi Park (HiP) from 1981 onwards and their population has increased exponentially since. Their initial reintroduction was motivated by the need to control bush encroachment and to maintain ecosystems such as grassland and open woodland, and to restore ecological processes offered by elephants. The subject of the HiP elephant population and their impact on vegetation in the Park has become controversial; with some concerns being raised that the population is too high and is negatively affecting the vegetation. An absence of a vegetation monitoring programme in protected areas with elephants creates uncertainty leading to an ‗elephant impact‘ debate. This study aimed to compare the perceptions of stakeholders regarding the issue of elephant impact in HiP with measured elephant impact on the vegetation in the Park. The perceptions and concerns of stakeholders regarding the effects of elephants on vegetation in HiP were investigated using a questionnaire. Stakeholders reported that elephants and fire were the main factors shaping vegetation change in HiP over the past decade. Sclerocarya birrea, Senegalia burkei and Schotia brachypetala were reported as the most negatively affected species. Also reported that they are concerned about the effects of elephants on the number of tall trees in the park, tree mortality and elephant‘s effect on rare indigenous vegetation. Most interestingly, the results showed that the groups of stakeholders had different perceptions of the level of elephant impact on the vegetation in the park; except for researchers and tourists whose were not significantly different from each other. Managers had the most respondents that reported that the level of elephant impact is unacceptable, while most researchers and tourists reported that the level of elephant impact is at an acceptable level. Vegetation plots that had been surveyed in 1999, 2003 and 2007, were resurveyed in this study during 2017 to assess elephant impact on vegetation over time. Comparison between the years sampled showed that there was a decrease in the density of tall trees, while the density of trees in 0.5-2 and 2-4 m height classes increased over the same period. Elephants had a strong preference for utilizing tall trees (>4 m) and a strong avoidance for trees in the height range from 0.5-2m tall (Jacobs selection index 0.56 and -0.69, respectively). This trend was apparent for all sample periods. In addition, elephants also showed a strong preference for some rare species including S. brachypetala and Sideroxylon inerme. Between 1999 and 2017, the density of preferred species has decreased while the density of avoided species has increased. I conclude that elephants are having a noticeable impact on the vegetation at HiP by changing vegetation structure to a shrub dominated vegetation, and causing a shift in species composition towards avoided species. The findings of this study show that the perceptions of stakeholders on the effects of elephants and the level of elephant impact on vegetation match the results from measured elephant impact - vegetation survey. However, Thresholds of Potential Concern (TPCs) should be outlined in the elephant management plan and are required to determine whether the levels of elephant impact at HiP have exceeded an acceptable level or not. This study conforms to previous research that an uncontrolled elephant population can have substantial impacts in fenced reserves. This study shows the importance for long-term and continuous vegetation monitoring programme to obtain reliable data to determine trends in vegetation changes over time.
- Full Text:
- Date Issued: 2020
- Authors: Mbongwa, Siphesihle
- Date: 2020
- Subjects: Woody plants -- Environmental aspects
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/48467 , vital:40879
- Description: Elephants were successfully reintroduced into the 900 km2 fenced Hluhluwe-iMfolozi Park (HiP) from 1981 onwards and their population has increased exponentially since. Their initial reintroduction was motivated by the need to control bush encroachment and to maintain ecosystems such as grassland and open woodland, and to restore ecological processes offered by elephants. The subject of the HiP elephant population and their impact on vegetation in the Park has become controversial; with some concerns being raised that the population is too high and is negatively affecting the vegetation. An absence of a vegetation monitoring programme in protected areas with elephants creates uncertainty leading to an ‗elephant impact‘ debate. This study aimed to compare the perceptions of stakeholders regarding the issue of elephant impact in HiP with measured elephant impact on the vegetation in the Park. The perceptions and concerns of stakeholders regarding the effects of elephants on vegetation in HiP were investigated using a questionnaire. Stakeholders reported that elephants and fire were the main factors shaping vegetation change in HiP over the past decade. Sclerocarya birrea, Senegalia burkei and Schotia brachypetala were reported as the most negatively affected species. Also reported that they are concerned about the effects of elephants on the number of tall trees in the park, tree mortality and elephant‘s effect on rare indigenous vegetation. Most interestingly, the results showed that the groups of stakeholders had different perceptions of the level of elephant impact on the vegetation in the park; except for researchers and tourists whose were not significantly different from each other. Managers had the most respondents that reported that the level of elephant impact is unacceptable, while most researchers and tourists reported that the level of elephant impact is at an acceptable level. Vegetation plots that had been surveyed in 1999, 2003 and 2007, were resurveyed in this study during 2017 to assess elephant impact on vegetation over time. Comparison between the years sampled showed that there was a decrease in the density of tall trees, while the density of trees in 0.5-2 and 2-4 m height classes increased over the same period. Elephants had a strong preference for utilizing tall trees (>4 m) and a strong avoidance for trees in the height range from 0.5-2m tall (Jacobs selection index 0.56 and -0.69, respectively). This trend was apparent for all sample periods. In addition, elephants also showed a strong preference for some rare species including S. brachypetala and Sideroxylon inerme. Between 1999 and 2017, the density of preferred species has decreased while the density of avoided species has increased. I conclude that elephants are having a noticeable impact on the vegetation at HiP by changing vegetation structure to a shrub dominated vegetation, and causing a shift in species composition towards avoided species. The findings of this study show that the perceptions of stakeholders on the effects of elephants and the level of elephant impact on vegetation match the results from measured elephant impact - vegetation survey. However, Thresholds of Potential Concern (TPCs) should be outlined in the elephant management plan and are required to determine whether the levels of elephant impact at HiP have exceeded an acceptable level or not. This study conforms to previous research that an uncontrolled elephant population can have substantial impacts in fenced reserves. This study shows the importance for long-term and continuous vegetation monitoring programme to obtain reliable data to determine trends in vegetation changes over time.
- Full Text:
- Date Issued: 2020
The role of northwest striking structures in controlling highgrade ore shoots at the Syama Gold Mine, Mali, West Africa
- Authors: Soro, Ali
- Date: 2020
- Subjects: Syama Gold Mine , Gold ores -- Geology -- Mali , Veins (Geology) -- Mali
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/145209 , vital:38418
- Description: This study intended to investigate the relationship between the NW striking structures and the high-grade ore shoots at the Syama gold mine in Mali, West Africa. All structural data collected since 1987 from drill core have been integrated to allow the interpretation and modelling of these NW-SE structures. The structures collected were grouped into three main groups; foliations/shears/faults, veins and joints/contacts/fractures. Micromine software was used to plot the structures, printed out on A3 paper and interpreted manually using tracing paper. Analysis and interpretation of stereographic plots has shown that the majority of the high-grade zones are generally located at the intersection of the NNE structures and the NW structures. The observed cross-cutting relationship between the NNE and the NW structures suggests two different generation of faults. It is suggested that the NW structures were active during the D4 deformation event (Standing, 2007) and have played a role in reactivating earlier (D3) NNE structures, allowing greater fluid flow and enhancing the gold grade. These zones are mainly defined by brecciation and stockwork veining. The E-W structures are believed to be the latest and are attributed to the D5 event. Although gold mineralisation is grossly controlled by the NNE structures, the NW structures need to be considered as major gold enrichment upgrading factors at Syama. It is therefore strongly recommended that ongoing exploration at Syama specifically target the intersection of the NW and NNE structures as favourable zones for high-grade mineralisation.
- Full Text:
- Date Issued: 2020
- Authors: Soro, Ali
- Date: 2020
- Subjects: Syama Gold Mine , Gold ores -- Geology -- Mali , Veins (Geology) -- Mali
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/145209 , vital:38418
- Description: This study intended to investigate the relationship between the NW striking structures and the high-grade ore shoots at the Syama gold mine in Mali, West Africa. All structural data collected since 1987 from drill core have been integrated to allow the interpretation and modelling of these NW-SE structures. The structures collected were grouped into three main groups; foliations/shears/faults, veins and joints/contacts/fractures. Micromine software was used to plot the structures, printed out on A3 paper and interpreted manually using tracing paper. Analysis and interpretation of stereographic plots has shown that the majority of the high-grade zones are generally located at the intersection of the NNE structures and the NW structures. The observed cross-cutting relationship between the NNE and the NW structures suggests two different generation of faults. It is suggested that the NW structures were active during the D4 deformation event (Standing, 2007) and have played a role in reactivating earlier (D3) NNE structures, allowing greater fluid flow and enhancing the gold grade. These zones are mainly defined by brecciation and stockwork veining. The E-W structures are believed to be the latest and are attributed to the D5 event. Although gold mineralisation is grossly controlled by the NNE structures, the NW structures need to be considered as major gold enrichment upgrading factors at Syama. It is therefore strongly recommended that ongoing exploration at Syama specifically target the intersection of the NW and NNE structures as favourable zones for high-grade mineralisation.
- Full Text:
- Date Issued: 2020
The spatiotemporal aspects of predation on the Cape gannet Morus capensis population at the Lambert’s Bay gannet colony, Western Cape, South Africa
- Authors: Schoeman, Zanri
- Date: 2020
- Subjects: Sea birds -- South Africa -- Western Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/47656 , vital:40262
- Description: Seabirds are one of the most threatened groups of birds with 29% of seabird species at some risk of extinction. As a result of multiple human-induced threats, seabird species including the Cape gannet Morus capensis which is endemic to southern Africa population experience significant declines and is now classified as Endangered. The Cape gannet faces predation threats from a variety of different species. The current predators of concern at Lambert’s Bay gannet colony are both the Cape fur seal Arctocephalus pusillus pusillus and the Kelp gull Larus dominancus. The former predates on fledglings and the latter predates on eggs. In the 2005/06 breeding season the entire Cape gannet population deserted the Lambert’s Bay gannet colony due to predation by the Cape fur seal. Although the Cape gannets have subsequently recovered to approximately 8000 pairs, seal predation on Cape gannet fledglings continues, together with predation by Kelp gulls. This has caused concern over the impact of predation on this species at the Lambert’s Bay colony, particularly given the species’ conservation status, its small breeding range and its current population trend. CapeNature, the conservation agency involved at this colony has been monitoring and managing the predation on Cape gannets and are interested in evaluating the success of their efforts. Therefore the aim of this study was to determine the spatial and temporal aspects of predation on the Cape gannet population at Lambert’s Bay gannet colony. When examining the influence of fish availability on predation intensity, we found that in years with an increase in fish biomass there was a decrease in predation probability by Cape fur seals. This increase in fish biomass not only led to decreased predation on the fledglings it also led to increased breeding success of the Cape gannets. In determining the effect of predation within the Cape gannet breeding colony we found that the probability of predation by Kelp gulls decreased in years with increased adult gannet density. Indirectly, Cape gannet population growth should lead to a decrease in Kelp gull predation as a higher gannet density increases the risk of injury to the Kelp gulls. This suggests that if Cape gannet populations continue to decline, they may become increasingly vulnerable to Kelp gull predation which can result in a further population decline. In terms of past management actions, the selective culling of predatory Cape fur seals and Kelp gulls, was evaluated. It was found that in the years in which culling of Cape fur seals and Kelp gulls was implemented, a decrease in predation was observed. This indicated that culling reduced predation in the short-term. Predation is inevitable, but due to the Cape gannet’s conservation status we suggest that additional, long-term, and more sustainable methods to reduce predation should be explored. Our research emphasises the need for improving food availability to Cape gannets as food security is paramount to their long-term survival and population growth. Colony management in isolation from other management strategies, is not efficient for conserving a species. We therefore suggest that sound management of predation at the terrestrial habitats are required but that effective management of fisheries are also required for the successful conservation of the Cape gannet. Food security for Cape gannets could be improved by, for example, establishing some ways that we suggest improving the food security for Cape gannets would be to establish Marine Protected Areas (MPAs) with dynamic boundaries around Cape gannet colonies, and to have locate the MPAs close to breeding and foraging hotspots where these areas are closed to fishing thus reducing the competition between commercial fisheries and marine predators, such as the Cape gannet. Another way to improve food security for the gannets are to promote the efforts of focussing on developing and implementing an ecosystem approach to fisheries management in which fishing quotas account for the needs of marine predators. The findings of this study have not only aided the understanding of the dynamics of predation on the Cape gannets and highlighted the extent that predation takes place on them but can also guide future management decisions regarding predation on this endemic and endangered species.
- Full Text:
- Date Issued: 2020
- Authors: Schoeman, Zanri
- Date: 2020
- Subjects: Sea birds -- South Africa -- Western Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/47656 , vital:40262
- Description: Seabirds are one of the most threatened groups of birds with 29% of seabird species at some risk of extinction. As a result of multiple human-induced threats, seabird species including the Cape gannet Morus capensis which is endemic to southern Africa population experience significant declines and is now classified as Endangered. The Cape gannet faces predation threats from a variety of different species. The current predators of concern at Lambert’s Bay gannet colony are both the Cape fur seal Arctocephalus pusillus pusillus and the Kelp gull Larus dominancus. The former predates on fledglings and the latter predates on eggs. In the 2005/06 breeding season the entire Cape gannet population deserted the Lambert’s Bay gannet colony due to predation by the Cape fur seal. Although the Cape gannets have subsequently recovered to approximately 8000 pairs, seal predation on Cape gannet fledglings continues, together with predation by Kelp gulls. This has caused concern over the impact of predation on this species at the Lambert’s Bay colony, particularly given the species’ conservation status, its small breeding range and its current population trend. CapeNature, the conservation agency involved at this colony has been monitoring and managing the predation on Cape gannets and are interested in evaluating the success of their efforts. Therefore the aim of this study was to determine the spatial and temporal aspects of predation on the Cape gannet population at Lambert’s Bay gannet colony. When examining the influence of fish availability on predation intensity, we found that in years with an increase in fish biomass there was a decrease in predation probability by Cape fur seals. This increase in fish biomass not only led to decreased predation on the fledglings it also led to increased breeding success of the Cape gannets. In determining the effect of predation within the Cape gannet breeding colony we found that the probability of predation by Kelp gulls decreased in years with increased adult gannet density. Indirectly, Cape gannet population growth should lead to a decrease in Kelp gull predation as a higher gannet density increases the risk of injury to the Kelp gulls. This suggests that if Cape gannet populations continue to decline, they may become increasingly vulnerable to Kelp gull predation which can result in a further population decline. In terms of past management actions, the selective culling of predatory Cape fur seals and Kelp gulls, was evaluated. It was found that in the years in which culling of Cape fur seals and Kelp gulls was implemented, a decrease in predation was observed. This indicated that culling reduced predation in the short-term. Predation is inevitable, but due to the Cape gannet’s conservation status we suggest that additional, long-term, and more sustainable methods to reduce predation should be explored. Our research emphasises the need for improving food availability to Cape gannets as food security is paramount to their long-term survival and population growth. Colony management in isolation from other management strategies, is not efficient for conserving a species. We therefore suggest that sound management of predation at the terrestrial habitats are required but that effective management of fisheries are also required for the successful conservation of the Cape gannet. Food security for Cape gannets could be improved by, for example, establishing some ways that we suggest improving the food security for Cape gannets would be to establish Marine Protected Areas (MPAs) with dynamic boundaries around Cape gannet colonies, and to have locate the MPAs close to breeding and foraging hotspots where these areas are closed to fishing thus reducing the competition between commercial fisheries and marine predators, such as the Cape gannet. Another way to improve food security for the gannets are to promote the efforts of focussing on developing and implementing an ecosystem approach to fisheries management in which fishing quotas account for the needs of marine predators. The findings of this study have not only aided the understanding of the dynamics of predation on the Cape gannets and highlighted the extent that predation takes place on them but can also guide future management decisions regarding predation on this endemic and endangered species.
- Full Text:
- Date Issued: 2020
The workload of flight attendants during short-haul flight operations: a system analysis
- Authors: Bennett, Chloe Kayla
- Date: 2020
- Subjects: Flight attendants -- Health and hygiene , Employees -- South Africa -- Workload
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/123431 , vital:35437
- Description: Background and aim: Flight attendants forms a significant part in 24-hour aviation industry. Flight attendant fatigue is a significant problem in the aviation industry as it continues to jeopardize the ability to fulfil important safety and security roles which is critical in performance duty of a flight attendant. However, little attention has been accomplished to the workload, working conditions and fatigue of flight attendants crew in transport aircraft. In addition, there is currently less research that have also embraced the problematic of smaller regional/commercial operation (short-haul flight operations) inducing fatigue among short-haul flight attendants as the nature of this operation are often characterised with high productivity expectations in a demanding environment with high time pressures resulting in high workloads and fatigue. Thus, flight attendant fatigue and workload is a worldwide challenge in this operational environment and less attention has been given to the determining factors. Therefore, the aim of the study was to determine the workload factors contributing to flight attendant fatigue during short-haul flight operations. Methods (System analysis): To achieve the research aim, the work system analysis, based on the Smith and Carayon-Sainfort model was chosen as the main research approach which was conducted in two ways; based on existing literature and secondly based on expert interviews. This method provided a systemic aspect to understand the whole work system of flight attendants work during short-haul operations in order to identify all the contributing factors to flight attendant fatigue and workload. Results: The literature analysis and the data from the expert interviews highlighted significant findings to flight attendant fatigue and workload. The reasons for flight attendant fatigue operating short-haul flights can be found at organizational, task, individual, environmental levels and tools and technologies and due to the interaction of the factors. The main factors of flight attendants’ fatigue are thought primarily as a function of scheduling due to irregular, mixed schedules with early starts and late finishes, extended duty days (long working hours), as well as high workload, due to the short turnaround flights, the number of sectors flown in a single duty period and duty length and high jobs demands. In addition, flight duty and rest regulations, confined work space in the cabin, vibrations, noise and lighting, sleeping in an unfamiliar environment, family responsibilities all add to additional stress placed on the body which can influence workload and sleep and consequently influencing fatigue. Conclusion: Overall the study determined that flight attendant fatigue is a significant problem in modern industry of short-haul operations. Using this systematic approach (work system analysis based on the framework of the work system model developed by Smith and Carayon-Sainfort (1989) allowed for an accurate representation of the complexity of flight attendant work environment in short-haul aviation industries, thus contributed to an increased understanding of fatigue and risk factors that span the entire work system and aid in identifying the patterns in combination of work system variables that are associated with increased risk to flight attendant fatigue. Overall flight attendant fatigue is a product of interactions with the short-haul environment. It can have a negative impact on safety, performance and well-being. Therefore, it needs to be managed and dealt with in the near future.
- Full Text:
- Date Issued: 2020
- Authors: Bennett, Chloe Kayla
- Date: 2020
- Subjects: Flight attendants -- Health and hygiene , Employees -- South Africa -- Workload
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/123431 , vital:35437
- Description: Background and aim: Flight attendants forms a significant part in 24-hour aviation industry. Flight attendant fatigue is a significant problem in the aviation industry as it continues to jeopardize the ability to fulfil important safety and security roles which is critical in performance duty of a flight attendant. However, little attention has been accomplished to the workload, working conditions and fatigue of flight attendants crew in transport aircraft. In addition, there is currently less research that have also embraced the problematic of smaller regional/commercial operation (short-haul flight operations) inducing fatigue among short-haul flight attendants as the nature of this operation are often characterised with high productivity expectations in a demanding environment with high time pressures resulting in high workloads and fatigue. Thus, flight attendant fatigue and workload is a worldwide challenge in this operational environment and less attention has been given to the determining factors. Therefore, the aim of the study was to determine the workload factors contributing to flight attendant fatigue during short-haul flight operations. Methods (System analysis): To achieve the research aim, the work system analysis, based on the Smith and Carayon-Sainfort model was chosen as the main research approach which was conducted in two ways; based on existing literature and secondly based on expert interviews. This method provided a systemic aspect to understand the whole work system of flight attendants work during short-haul operations in order to identify all the contributing factors to flight attendant fatigue and workload. Results: The literature analysis and the data from the expert interviews highlighted significant findings to flight attendant fatigue and workload. The reasons for flight attendant fatigue operating short-haul flights can be found at organizational, task, individual, environmental levels and tools and technologies and due to the interaction of the factors. The main factors of flight attendants’ fatigue are thought primarily as a function of scheduling due to irregular, mixed schedules with early starts and late finishes, extended duty days (long working hours), as well as high workload, due to the short turnaround flights, the number of sectors flown in a single duty period and duty length and high jobs demands. In addition, flight duty and rest regulations, confined work space in the cabin, vibrations, noise and lighting, sleeping in an unfamiliar environment, family responsibilities all add to additional stress placed on the body which can influence workload and sleep and consequently influencing fatigue. Conclusion: Overall the study determined that flight attendant fatigue is a significant problem in modern industry of short-haul operations. Using this systematic approach (work system analysis based on the framework of the work system model developed by Smith and Carayon-Sainfort (1989) allowed for an accurate representation of the complexity of flight attendant work environment in short-haul aviation industries, thus contributed to an increased understanding of fatigue and risk factors that span the entire work system and aid in identifying the patterns in combination of work system variables that are associated with increased risk to flight attendant fatigue. Overall flight attendant fatigue is a product of interactions with the short-haul environment. It can have a negative impact on safety, performance and well-being. Therefore, it needs to be managed and dealt with in the near future.
- Full Text:
- Date Issued: 2020
Towards a capability maturity model for a cyber range
- Authors: Aschmann, Michael Joseph
- Date: 2020
- Subjects: Computer software -- Development , Computer security
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163142 , vital:41013
- Description: This work describes research undertaken towards the development of a Capability Maturity Model (CMM) for Cyber Ranges (CRs) focused on cyber security. Global cyber security needs are on the rise, and the need for attribution within the cyber domain is of particular concern. This has prompted major efforts to enhance cyber capabilities within organisations to increase their total cyber resilience posture. These efforts include, but are not limited to, the testing of computational devices, networks, and applications, and cyber skills training focused on prevention, detection and cyber attack response. A cyber range allows for the testing of the computational environment. By developing cyber events within a confined virtual or sand-boxed cyber environment, a cyber range can prepare the next generation of cyber security specialists to handle a variety of potential cyber attacks. Cyber ranges have different purposes, each designed to fulfil a different computational testing and cyber training goal; consequently, cyber ranges can vary greatly in the level of variety, capability, maturity and complexity. As cyber ranges proliferate and become more and more valued as tools for cyber security, a method to classify or rate them becomes essential. Yet while a universal criteria for measuring cyber ranges in terms of their capability maturity levels becomes more critical, there are currently very limited resources for researchers aiming to perform this kind of work. For this reason, this work proposes and describes a CMM, designed to give organisations the ability to benchmark the capability maturity of a given cyber range. This research adopted a synthesised approach to the development of a CMM, grounded in prior research and focused on the production of a conceptual model that provides a useful level of abstraction. In order to achieve this goal, the core capability elements of a cyber range are defined with their relative importance, allowing for the development of a proposed classification cyber range levels. An analysis of data gathered during the course of an expert review, together with other research, further supported the development of the conceptual model. In the context of cyber range capability, classification will include the ability of the cyber range to perform its functions optimally with different core capability elements, focusing on the Measurement of Capability (MoC) with its elements, namely effect, performance and threat ability. Cyber range maturity can evolve over time and can be defined through the Measurement of Maturity (MoM) with its elements, namely people, processes, technology. The combination of these measurements utilising the CMM for a CR determines the capability maturity level of a CR. The primary outcome of this research is the proposed level-based CMM framework for a cyber range, developed using adopted and synthesised CMMs, the analysis of an expert review, and the mapping of the results.
- Full Text:
- Date Issued: 2020
- Authors: Aschmann, Michael Joseph
- Date: 2020
- Subjects: Computer software -- Development , Computer security
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163142 , vital:41013
- Description: This work describes research undertaken towards the development of a Capability Maturity Model (CMM) for Cyber Ranges (CRs) focused on cyber security. Global cyber security needs are on the rise, and the need for attribution within the cyber domain is of particular concern. This has prompted major efforts to enhance cyber capabilities within organisations to increase their total cyber resilience posture. These efforts include, but are not limited to, the testing of computational devices, networks, and applications, and cyber skills training focused on prevention, detection and cyber attack response. A cyber range allows for the testing of the computational environment. By developing cyber events within a confined virtual or sand-boxed cyber environment, a cyber range can prepare the next generation of cyber security specialists to handle a variety of potential cyber attacks. Cyber ranges have different purposes, each designed to fulfil a different computational testing and cyber training goal; consequently, cyber ranges can vary greatly in the level of variety, capability, maturity and complexity. As cyber ranges proliferate and become more and more valued as tools for cyber security, a method to classify or rate them becomes essential. Yet while a universal criteria for measuring cyber ranges in terms of their capability maturity levels becomes more critical, there are currently very limited resources for researchers aiming to perform this kind of work. For this reason, this work proposes and describes a CMM, designed to give organisations the ability to benchmark the capability maturity of a given cyber range. This research adopted a synthesised approach to the development of a CMM, grounded in prior research and focused on the production of a conceptual model that provides a useful level of abstraction. In order to achieve this goal, the core capability elements of a cyber range are defined with their relative importance, allowing for the development of a proposed classification cyber range levels. An analysis of data gathered during the course of an expert review, together with other research, further supported the development of the conceptual model. In the context of cyber range capability, classification will include the ability of the cyber range to perform its functions optimally with different core capability elements, focusing on the Measurement of Capability (MoC) with its elements, namely effect, performance and threat ability. Cyber range maturity can evolve over time and can be defined through the Measurement of Maturity (MoM) with its elements, namely people, processes, technology. The combination of these measurements utilising the CMM for a CR determines the capability maturity level of a CR. The primary outcome of this research is the proposed level-based CMM framework for a cyber range, developed using adopted and synthesised CMMs, the analysis of an expert review, and the mapping of the results.
- Full Text:
- Date Issued: 2020
Towards the development of a bio-fertiliser using mixed liquor from high rate algal oxidation ponds
- Authors: Masudi, Wiya Léon
- Date: 2020
- Subjects: Biofertilizers , Microalgae - Biotechnology , Algae -- Culture
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/142969 , vital:38181
- Description: Mixed liquor includes consortia of microalgae and bacteria produced in high rate algal oxidation ponds (HRAOPs). The consortia of microalgae and bacteria occur as flocs called microalgae-bacterial flocs (MaB-flocs). This study aimed to source bacteria from MaB-flocs generated in HRAOPs and, after isolation and identification, evaluate their potential as plant growth promoting (PGP) microorganisms. Twelve bacterial strains namely ECCN 1b, ECCN 2b, ECCN 3b, ECCN 4b, ECCN 5b, ECCN 6b, ECCN 7b, ECCN 8b, ECCN 9b, ECCN 10b, ECCN 11b, and ECCN 12b were successfully isolated and their molecular identity established using amplified 16S rRNA gene sequence analysis that was compared to sequences deposited in the NCBI gene database. Blast analysis identified these isolates at the genus level as Bacillus strain ECCN 1b, Fictibacillus strain ECCN 2b, Bacillus strain ECCN 3b, Aeromonas strain ECCN 4b, Exiguobacterium strain ECCN 5b, Arthrobacter strain ECCN 6b, Enterobacter strain ECCN 7b, Exiguobacterium strain ECCN 8b, Microbacterium strain ECCN 9b, Pseudomonas ECCN strain 10b, Ancylobacter strain ECCN 11b and Microbacterium strain ECCN 12b. These isolates were able to grow in nutrient broth in a pH range between 6 and 10, with the best growth achieved at pH 8 to 9. The results on the use of carbon substrate revealed that 5 strains including Arthrobacter strain ECCN 6b, Aeromonas strain ECCN 4b, Pseudomonas strain ECCN 10b, Enterobacter strain ECCN 7b and Bacillus strain ECCN 3b were capable of using glucose, sucrose and mannitol. No faecal coliforms were found. However, of the 12 isolates screened for bio-fertilisation potential, Bacillus strain ECCN 1b, Fictibacillus strain ECCN 2b, Bacillus strain ECCN 3b, Aeromonas strain ECCN 4b, Exiguobacterium strain ECCN 5b, Arthrobacter strain ECCN 6b, Enterobacter ECCN strain 7b, Exiguobacterium strain ECCN 8b and Pseudomonas strain ECCN 10b showed multifunctional plant growth promoting (PGP) potential. The potential for PGP included the production of ammonium-N, solubilisation of phosphate-P and potassium-K, oxidation of Mn and production of auxin, indole-3-acetic acid (IAA). Results are discussed in terms of the amount or concentration (mg L-1) of plant essential nutrient and growth regulator produced by these isolated bacteria. Even so, further studies are needed to test and confirm the bio-fertiliser and plant growth promoting activity of these strains in pot trials and field experiments, or both.
- Full Text:
- Date Issued: 2020
- Authors: Masudi, Wiya Léon
- Date: 2020
- Subjects: Biofertilizers , Microalgae - Biotechnology , Algae -- Culture
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/142969 , vital:38181
- Description: Mixed liquor includes consortia of microalgae and bacteria produced in high rate algal oxidation ponds (HRAOPs). The consortia of microalgae and bacteria occur as flocs called microalgae-bacterial flocs (MaB-flocs). This study aimed to source bacteria from MaB-flocs generated in HRAOPs and, after isolation and identification, evaluate their potential as plant growth promoting (PGP) microorganisms. Twelve bacterial strains namely ECCN 1b, ECCN 2b, ECCN 3b, ECCN 4b, ECCN 5b, ECCN 6b, ECCN 7b, ECCN 8b, ECCN 9b, ECCN 10b, ECCN 11b, and ECCN 12b were successfully isolated and their molecular identity established using amplified 16S rRNA gene sequence analysis that was compared to sequences deposited in the NCBI gene database. Blast analysis identified these isolates at the genus level as Bacillus strain ECCN 1b, Fictibacillus strain ECCN 2b, Bacillus strain ECCN 3b, Aeromonas strain ECCN 4b, Exiguobacterium strain ECCN 5b, Arthrobacter strain ECCN 6b, Enterobacter strain ECCN 7b, Exiguobacterium strain ECCN 8b, Microbacterium strain ECCN 9b, Pseudomonas ECCN strain 10b, Ancylobacter strain ECCN 11b and Microbacterium strain ECCN 12b. These isolates were able to grow in nutrient broth in a pH range between 6 and 10, with the best growth achieved at pH 8 to 9. The results on the use of carbon substrate revealed that 5 strains including Arthrobacter strain ECCN 6b, Aeromonas strain ECCN 4b, Pseudomonas strain ECCN 10b, Enterobacter strain ECCN 7b and Bacillus strain ECCN 3b were capable of using glucose, sucrose and mannitol. No faecal coliforms were found. However, of the 12 isolates screened for bio-fertilisation potential, Bacillus strain ECCN 1b, Fictibacillus strain ECCN 2b, Bacillus strain ECCN 3b, Aeromonas strain ECCN 4b, Exiguobacterium strain ECCN 5b, Arthrobacter strain ECCN 6b, Enterobacter ECCN strain 7b, Exiguobacterium strain ECCN 8b and Pseudomonas strain ECCN 10b showed multifunctional plant growth promoting (PGP) potential. The potential for PGP included the production of ammonium-N, solubilisation of phosphate-P and potassium-K, oxidation of Mn and production of auxin, indole-3-acetic acid (IAA). Results are discussed in terms of the amount or concentration (mg L-1) of plant essential nutrient and growth regulator produced by these isolated bacteria. Even so, further studies are needed to test and confirm the bio-fertiliser and plant growth promoting activity of these strains in pot trials and field experiments, or both.
- Full Text:
- Date Issued: 2020
Towards the synthesis of trimethoprim using continuous flow Chemistry
- Authors: Ngwenya, Sandiso
- Date: 2020
- Subjects: Trimethoprim
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/47475 , vital:39994
- Description: The continuous flow synthesis of trimethoprim, an antibiotic, was investigated in this study from simple commercially available reagents, such as aniline and dimethylamine. The first step of the synthesis involves a highly exothermic Michael reaction, between acrylonitrile and dimethylamine; process intensification through miniaturization provides a safe and efficient method of synthesis through the use of microreactors. This is afforded by their large surface area-to-volume ratio; one of the many characteristics of continuous flow synthesis that allows for rapid heat dissipation allowing for exothermic reaction to be conducted safely at ambient or higher temperatures. This study was optimized on a Chemtrix Labtrix® Start unit using a Chemtrix reactor achieving a conversion of 99% in 12 sec residence time at 25oC. Subsequently the base catalyzed condensation of the intermediate with 3,4,5- trimethoxybenzaldehyde was investigated using Little Things Factory reactors (Channel diameter: 1.0mm). Maximum conversion (100%) was obtained at 80oC in 20 mins. Due to the poor cyclisation observed with this intermediate, according to literature findings, the 3-dimethylamino group was substituted for aniline. The optimisation for this acid catalysed substitution reaction was performed on a homemade PTFE tubing reactor (Diameter: 0.5mm) and it was found that at 120oC in 10 mins residence time a conversion of 97% was obtained. From the results obtained, an investigation into an integrated process for the condensation and substitution reaction was done using the Little Things Factory system (Channel Diameter: 1.0mm) coupled with a homemade PTFE coil reactor (Diameter: 0.5mm). This process, under optimum conditions of temperature 80oC and residence time of 30 mins, attained a conversion of 76%.
- Full Text:
- Date Issued: 2020
- Authors: Ngwenya, Sandiso
- Date: 2020
- Subjects: Trimethoprim
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/47475 , vital:39994
- Description: The continuous flow synthesis of trimethoprim, an antibiotic, was investigated in this study from simple commercially available reagents, such as aniline and dimethylamine. The first step of the synthesis involves a highly exothermic Michael reaction, between acrylonitrile and dimethylamine; process intensification through miniaturization provides a safe and efficient method of synthesis through the use of microreactors. This is afforded by their large surface area-to-volume ratio; one of the many characteristics of continuous flow synthesis that allows for rapid heat dissipation allowing for exothermic reaction to be conducted safely at ambient or higher temperatures. This study was optimized on a Chemtrix Labtrix® Start unit using a Chemtrix reactor achieving a conversion of 99% in 12 sec residence time at 25oC. Subsequently the base catalyzed condensation of the intermediate with 3,4,5- trimethoxybenzaldehyde was investigated using Little Things Factory reactors (Channel diameter: 1.0mm). Maximum conversion (100%) was obtained at 80oC in 20 mins. Due to the poor cyclisation observed with this intermediate, according to literature findings, the 3-dimethylamino group was substituted for aniline. The optimisation for this acid catalysed substitution reaction was performed on a homemade PTFE tubing reactor (Diameter: 0.5mm) and it was found that at 120oC in 10 mins residence time a conversion of 97% was obtained. From the results obtained, an investigation into an integrated process for the condensation and substitution reaction was done using the Little Things Factory system (Channel Diameter: 1.0mm) coupled with a homemade PTFE coil reactor (Diameter: 0.5mm). This process, under optimum conditions of temperature 80oC and residence time of 30 mins, attained a conversion of 76%.
- Full Text:
- Date Issued: 2020
Towards understanding how exploitation influences the wild energetic response of marine fish to temperature variability
- Authors: Skeeles, Michael Richard
- Date: 2020
- Subjects: Chrysoblepus laticeps -- Climatic factors , Sparidae -- Genetics , Sparidae -- South Africa -- Climatic factors
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/145133 , vital:38411
- Description: Exploitation of fish populations can exacerbate the effects of climate change, yet our understanding of their synergistic effects remains limited. As fish are increasingly exposed to temperatures on the edges of their optimal thermal performance window, their physiological response is expected to shape their future performance. It is therefore concerning that exploitation can select for specific physiological phenotypes, as this may affect fished populations’ physiological response to temperature change. A recent laboratory study revealed fewer high-performance metabolic-scope phenotypes in an exploited population of the marine Sparid Chrysoblepus laticeps across a range of experimental temperatures in comparison to an unexploited population. This suggested that individuals in exploited populations may have less available energy for aerobic performance at thermal extremes, which may reduce the resilience of the population to changes in temperature. However, since laboratory experiments exclude numerous other variables that fish encounter in the wild, it was necessary to test this finding in a natural setting. This thesis aimed to further develop the laboratory study by assessing whether exploitation effects the wild energetic response of C. laticeps to thermal variability. To achieve this, the field metabolic rate of C. laticeps, a resident and endemic South African fish, from a near-pristine population (Tsitsikamma National Park) and a heavily exploited population (Port Elizabeth) was compared using acoustic accelerometry. A laboratory-based study using a swim-tunnel respirometer and accelerometer transmitters was conducted to develop a model to predict metabolic rate from acceleration data at temperatures from 10 to 22⁰C. Acceleration, temperature, mass and population (exploited/unexploited) were found to be the best predictors of the metabolic rate of C. laticeps and were incorporated into the model to estimate the field metabolic rate of fish tagged with acoustic accelerometers in the wild. To examine the combined effects of temperature and exploitation on the field metabolic rate of C. laticeps in their natural state, two fine-scale telemetry arrays with temperature loggers were used to assess the acceleration of the fish across different temperatures in the wild for three months during a period of high thermal variability. Ten fish from the exploited and unexploited populations were caught, surgically implanted with accelerometer transmitters and released back into the wild. Close to 500 000 and 400 000 acceleration estimates were recorded from wild exploited and unexploited fish, respectively. The field metabolic rate of both populations was estimated by combining the field acceleration and temperature data with the laboratory calibration model. The field metabolic rate of C. laticeps from the exploited population was constrained near cold and warm extremes compared to no constraints observed in the unexploited population. This was attributed to reduced inter-individual variability in the field metabolic rate-temperature relationship within the exploited population. There appeared to be a greater proportion of individuals that maintained a high field metabolic rate at extreme temperatures in the unexploited population. In contrast, all but one fish from the exploited population did not maintain a high field metabolic rate at extreme temperatures. These findings aligned with the laboratory-based metabolic-scope study on both populations of C. laticeps and demonstrate that passive-fishing may be removing thermally tolerant individuals and rendering exploited populations less resilient to thermal change. These findings are discussed in the context of fisheries management and particularly on the role that marine protected areas could play in maintaining physiological diversity, and therefore the resilience of fish in the Anthropocene. This study highlights the importance of applied conservation physiology in understanding the consequences of fisheries-induced evolution in an increasingly variable climate.
- Full Text:
- Date Issued: 2020
- Authors: Skeeles, Michael Richard
- Date: 2020
- Subjects: Chrysoblepus laticeps -- Climatic factors , Sparidae -- Genetics , Sparidae -- South Africa -- Climatic factors
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/145133 , vital:38411
- Description: Exploitation of fish populations can exacerbate the effects of climate change, yet our understanding of their synergistic effects remains limited. As fish are increasingly exposed to temperatures on the edges of their optimal thermal performance window, their physiological response is expected to shape their future performance. It is therefore concerning that exploitation can select for specific physiological phenotypes, as this may affect fished populations’ physiological response to temperature change. A recent laboratory study revealed fewer high-performance metabolic-scope phenotypes in an exploited population of the marine Sparid Chrysoblepus laticeps across a range of experimental temperatures in comparison to an unexploited population. This suggested that individuals in exploited populations may have less available energy for aerobic performance at thermal extremes, which may reduce the resilience of the population to changes in temperature. However, since laboratory experiments exclude numerous other variables that fish encounter in the wild, it was necessary to test this finding in a natural setting. This thesis aimed to further develop the laboratory study by assessing whether exploitation effects the wild energetic response of C. laticeps to thermal variability. To achieve this, the field metabolic rate of C. laticeps, a resident and endemic South African fish, from a near-pristine population (Tsitsikamma National Park) and a heavily exploited population (Port Elizabeth) was compared using acoustic accelerometry. A laboratory-based study using a swim-tunnel respirometer and accelerometer transmitters was conducted to develop a model to predict metabolic rate from acceleration data at temperatures from 10 to 22⁰C. Acceleration, temperature, mass and population (exploited/unexploited) were found to be the best predictors of the metabolic rate of C. laticeps and were incorporated into the model to estimate the field metabolic rate of fish tagged with acoustic accelerometers in the wild. To examine the combined effects of temperature and exploitation on the field metabolic rate of C. laticeps in their natural state, two fine-scale telemetry arrays with temperature loggers were used to assess the acceleration of the fish across different temperatures in the wild for three months during a period of high thermal variability. Ten fish from the exploited and unexploited populations were caught, surgically implanted with accelerometer transmitters and released back into the wild. Close to 500 000 and 400 000 acceleration estimates were recorded from wild exploited and unexploited fish, respectively. The field metabolic rate of both populations was estimated by combining the field acceleration and temperature data with the laboratory calibration model. The field metabolic rate of C. laticeps from the exploited population was constrained near cold and warm extremes compared to no constraints observed in the unexploited population. This was attributed to reduced inter-individual variability in the field metabolic rate-temperature relationship within the exploited population. There appeared to be a greater proportion of individuals that maintained a high field metabolic rate at extreme temperatures in the unexploited population. In contrast, all but one fish from the exploited population did not maintain a high field metabolic rate at extreme temperatures. These findings aligned with the laboratory-based metabolic-scope study on both populations of C. laticeps and demonstrate that passive-fishing may be removing thermally tolerant individuals and rendering exploited populations less resilient to thermal change. These findings are discussed in the context of fisheries management and particularly on the role that marine protected areas could play in maintaining physiological diversity, and therefore the resilience of fish in the Anthropocene. This study highlights the importance of applied conservation physiology in understanding the consequences of fisheries-induced evolution in an increasingly variable climate.
- Full Text:
- Date Issued: 2020
Understanding of the underlying resistance mechanism of the Kat-G protein against isoniazid in Mycobacterium tuberculosis using bioinformatics approaches
- Authors: Barozi, Victor
- Date: 2020
- Subjects: Mycobacterium tuberculosis , Isoniazid , Drug resistance in microorganisms , Proteins -- Microbiology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/146592 , vital:38540
- Description: Tuberculosis (TB) is a multi-organ infection caused by rod-shaped acid-fast Mycobacterium tuberculosis. The World Health Organization (WHO) ranks TB among the top 10 fatal infections and the leading the cause of death from a single infection. In 2017, TB was responsible for an estimated 1.3 million deaths among both the HIV negative and positive populations worldwide (WHO, 2018). Approximately 23% (roughly 1.7 billion) of the world’s population is estimated to have latent TB with a high risk of reverting to active TB infection. In 2017, an estimated 558,000 people developed drug resistant TB worldwide with 82% of the cases being multi-drug resistant TB (WHO, 2018). South Africa is ranked among the 30 high TB burdened countries with a TB incidence of 322,000 cases in 2017 accounting for 3% of the world’s TB cases. TB is curable and is clinically managed through a combination of intensive and continuation phases of first-line drugs (isoniazid, rifampicin, ethambutol, and pyrazinamide). Second-line drugs which include fluoroquinolones, injectable aminoglycoside and injectable polypeptides are used in cases of first line drug resistance. The third-line drugs include amoxicillin, clofazimine, linezolid and imipenem. These have variable but unproven efficacy to TB and are the last resort in cases of total drug resistance (Jilani et al., 2019). TB drug resistance to first-line drugs especially isoniazid in M. tuberculosis has been attributed to single nucleotide polymorphisms (SNPs) in the catalase peroxidase enzyme (katG), a protein important in the activation of the pro-drug isoniazid. The SNPs especially at position 315 of the katG enzyme are believed to reduce the sensitivity of the M. tuberculosis to isoniazid while still maintaining the enzyme’s catalytic activity - a mechanism not completely understood. KatG protein is important for protecting the bacteria from hydro peroxides and hydroxyl radicals present in an aerobic environment. This study focused on understanding the mechanism of isoniazid drug resistance in M. tuberculosis as a result of high confidence mutations in the katG through modelling the enzyme with its respective variants, performing MD simulations to explore the protein behaviour, calculating the dynamic residue network analysis (DRN) of the variants in respect to the wild type katG and finally performing alanine scanning. From the MD simulations, it was observed that the high confidence mutations i.e. S140R, S140N, G279D, G285D, S315T, S315I, S315R, S315N, G316D, S457I and G593D were not only reducing the backbone flexibility of the protein but also reducing the protein’s conformational variation and space. All the variant protein structures were observed to be more compact compared to the wild type. Residue fluctuation results indicated reduced residue flexibility across all variants in the loop region (position 26-110) responsible for katG dimerization. In addition, mutation S315T is believed to reduce the size of the active site access channel in the protein. From the DRN data, residues in the interface region between the N and C-terminal domains were observed to gain importance in the variants irrespective of the mutation location indicating an allosteric effect of the mutations on the interface region. Alanine scanning results established that residue Leucine at position 48 was not only important in the protein communication but also a destabilizing residue across all the variants. The study not only demonstrated change in the protein behaviour but also showed allosteric effect of the mutations in the katG protein.
- Full Text:
- Date Issued: 2020
- Authors: Barozi, Victor
- Date: 2020
- Subjects: Mycobacterium tuberculosis , Isoniazid , Drug resistance in microorganisms , Proteins -- Microbiology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/146592 , vital:38540
- Description: Tuberculosis (TB) is a multi-organ infection caused by rod-shaped acid-fast Mycobacterium tuberculosis. The World Health Organization (WHO) ranks TB among the top 10 fatal infections and the leading the cause of death from a single infection. In 2017, TB was responsible for an estimated 1.3 million deaths among both the HIV negative and positive populations worldwide (WHO, 2018). Approximately 23% (roughly 1.7 billion) of the world’s population is estimated to have latent TB with a high risk of reverting to active TB infection. In 2017, an estimated 558,000 people developed drug resistant TB worldwide with 82% of the cases being multi-drug resistant TB (WHO, 2018). South Africa is ranked among the 30 high TB burdened countries with a TB incidence of 322,000 cases in 2017 accounting for 3% of the world’s TB cases. TB is curable and is clinically managed through a combination of intensive and continuation phases of first-line drugs (isoniazid, rifampicin, ethambutol, and pyrazinamide). Second-line drugs which include fluoroquinolones, injectable aminoglycoside and injectable polypeptides are used in cases of first line drug resistance. The third-line drugs include amoxicillin, clofazimine, linezolid and imipenem. These have variable but unproven efficacy to TB and are the last resort in cases of total drug resistance (Jilani et al., 2019). TB drug resistance to first-line drugs especially isoniazid in M. tuberculosis has been attributed to single nucleotide polymorphisms (SNPs) in the catalase peroxidase enzyme (katG), a protein important in the activation of the pro-drug isoniazid. The SNPs especially at position 315 of the katG enzyme are believed to reduce the sensitivity of the M. tuberculosis to isoniazid while still maintaining the enzyme’s catalytic activity - a mechanism not completely understood. KatG protein is important for protecting the bacteria from hydro peroxides and hydroxyl radicals present in an aerobic environment. This study focused on understanding the mechanism of isoniazid drug resistance in M. tuberculosis as a result of high confidence mutations in the katG through modelling the enzyme with its respective variants, performing MD simulations to explore the protein behaviour, calculating the dynamic residue network analysis (DRN) of the variants in respect to the wild type katG and finally performing alanine scanning. From the MD simulations, it was observed that the high confidence mutations i.e. S140R, S140N, G279D, G285D, S315T, S315I, S315R, S315N, G316D, S457I and G593D were not only reducing the backbone flexibility of the protein but also reducing the protein’s conformational variation and space. All the variant protein structures were observed to be more compact compared to the wild type. Residue fluctuation results indicated reduced residue flexibility across all variants in the loop region (position 26-110) responsible for katG dimerization. In addition, mutation S315T is believed to reduce the size of the active site access channel in the protein. From the DRN data, residues in the interface region between the N and C-terminal domains were observed to gain importance in the variants irrespective of the mutation location indicating an allosteric effect of the mutations on the interface region. Alanine scanning results established that residue Leucine at position 48 was not only important in the protein communication but also a destabilizing residue across all the variants. The study not only demonstrated change in the protein behaviour but also showed allosteric effect of the mutations in the katG protein.
- Full Text:
- Date Issued: 2020
Understanding the relationship between mangrove composition, stand dynamics and resource use in the Ntafufu estuary, Eastern Cape, as basis for sustainable resource use
- Mvakade, Monica, Rajkaran, Anusha
- Authors: Mvakade, Monica , Rajkaran, Anusha
- Date: 2020
- Subjects: Estuarine ecology -- South Africa -- Eastern Cape , Aquatic ecology , Marine sciences , Fresh water
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49215 , vital:41611
- Description: Traditionally, coastal communities along the Wild Coast in the Eastern Cape, used mangrove forests for their livelihoods and socio-economic needs. Mangroves along the Eastern Cape coast are threatened by both natural and human factors. The wood obtained from the mangroves by rural households was used as poles for house and fence construction, firewood, and traditional medicine. This is a threat to the status of several mangrove species in this and surrounding areas. The harvesting of mangrove trees will have a direct and indirect effect on the other biotic and abiotic components of the mangrove ecosystems. The Department of Agriculture, Forestry and Fisheries (DAFF) (currently the Department of Environment, Forestry and Fisheries, or DEFF), through the National Forest Act no 84 of 1998, was directly responsible for the wellbeing of the national forests in South Africa. This also includes the mangroves as a specific national forest type. Several estuaries with mangroves occur within state forests. The harvesting and clear-felling of trees for timber and land conversion and associated waste of harvested mangrove poles and laths causes the many changes in mangrove forests. The aim of this study was to develop a framework for sustainable management of the mangroves for the Mtambalala forest management unit. This was done in relation to the requirements of the current legislation, policy guidelines and business plan of the management authority. The aim was pursued through two specific objectives. The first objective was to understand the variation in the composition in different parts of the Ntafufu Estuary, and the population dynamics of the main mangrove species, as basis for the development of sustainable resource use practices. Plots along transects were used to measure seedling to adult ratios, population structure and abiotic characteristics. The second objective was to understand the community use and requirements of mangrove wood from the Ntafufu Estuary. A participatory approach was followed to collect demographic data from each community, the requirements of mangrove poles and behaviour of harvesters. This was used to set up a framework to guide the sustainable management of mangroves based on the current status and stand dynamics of the mangrove communities. There are three mangrove species found in the Ntafufu Estuary: Bruguiera gymnorhiza (black mangrove) regenerates under the mangrove canopy and forms layers of even-aged stands. Avicennia marina (white mangrove) does not regenerate under a mangrove canopy i.e. the seedlings establish outside the canopy. A few Rhizophora mucronata (red mangrove) trees exist in the lower intertidal zone and form multiple stems on stilt roots. The mangrove associate, Hibiscus tiliaceus (wild cotton tree- mangrove associate), forms dense clusters of scrambling stems. Some of the Avicennia individuals show signs of mangrove bleeding and one individual of Bruguiera showed indications of disease. Mngazana and Ntafufu Estuaries had the highest tree densities of 2594 and 1402 trees ha-1 respectively, typical of riverine mangrove forest. The seedling to adult ratio was high in this study: 12.8 for B. gymnorrhiza and 24.3 for A. marina. Abandoned cut stems and laths were found during the study. Bark harvested for traditional medicine and cattle feeding in mangroves was also prevalent and expected to reduce the health of the forest. Mangroves in the Ntafufu Estuary are expanding, and the population structure of the three mangrove species showed a healthy balance between young and mature stems. The harvesting of Black mangrove (B. gymnorrhiza) poles for mainly roof construction is relatively limited. As part of the functions of the DAFF, the use of the mangrove resources has to be balanced with the resource availability from the mangroves, and this should result in a healthy functioning mangrove forest. Development of a participatory forest management (PFM) plan for a forest estate and its forest management unit, require an understanding of the mangrove communities and their dynamics, and the current level of resource use associated with the mangroves. The study recommended that a Mangrove Pole Harvesters Group is needed to practice silviculture through guidance of relevant governmental personnel.
- Full Text:
- Date Issued: 2020
- Authors: Mvakade, Monica , Rajkaran, Anusha
- Date: 2020
- Subjects: Estuarine ecology -- South Africa -- Eastern Cape , Aquatic ecology , Marine sciences , Fresh water
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49215 , vital:41611
- Description: Traditionally, coastal communities along the Wild Coast in the Eastern Cape, used mangrove forests for their livelihoods and socio-economic needs. Mangroves along the Eastern Cape coast are threatened by both natural and human factors. The wood obtained from the mangroves by rural households was used as poles for house and fence construction, firewood, and traditional medicine. This is a threat to the status of several mangrove species in this and surrounding areas. The harvesting of mangrove trees will have a direct and indirect effect on the other biotic and abiotic components of the mangrove ecosystems. The Department of Agriculture, Forestry and Fisheries (DAFF) (currently the Department of Environment, Forestry and Fisheries, or DEFF), through the National Forest Act no 84 of 1998, was directly responsible for the wellbeing of the national forests in South Africa. This also includes the mangroves as a specific national forest type. Several estuaries with mangroves occur within state forests. The harvesting and clear-felling of trees for timber and land conversion and associated waste of harvested mangrove poles and laths causes the many changes in mangrove forests. The aim of this study was to develop a framework for sustainable management of the mangroves for the Mtambalala forest management unit. This was done in relation to the requirements of the current legislation, policy guidelines and business plan of the management authority. The aim was pursued through two specific objectives. The first objective was to understand the variation in the composition in different parts of the Ntafufu Estuary, and the population dynamics of the main mangrove species, as basis for the development of sustainable resource use practices. Plots along transects were used to measure seedling to adult ratios, population structure and abiotic characteristics. The second objective was to understand the community use and requirements of mangrove wood from the Ntafufu Estuary. A participatory approach was followed to collect demographic data from each community, the requirements of mangrove poles and behaviour of harvesters. This was used to set up a framework to guide the sustainable management of mangroves based on the current status and stand dynamics of the mangrove communities. There are three mangrove species found in the Ntafufu Estuary: Bruguiera gymnorhiza (black mangrove) regenerates under the mangrove canopy and forms layers of even-aged stands. Avicennia marina (white mangrove) does not regenerate under a mangrove canopy i.e. the seedlings establish outside the canopy. A few Rhizophora mucronata (red mangrove) trees exist in the lower intertidal zone and form multiple stems on stilt roots. The mangrove associate, Hibiscus tiliaceus (wild cotton tree- mangrove associate), forms dense clusters of scrambling stems. Some of the Avicennia individuals show signs of mangrove bleeding and one individual of Bruguiera showed indications of disease. Mngazana and Ntafufu Estuaries had the highest tree densities of 2594 and 1402 trees ha-1 respectively, typical of riverine mangrove forest. The seedling to adult ratio was high in this study: 12.8 for B. gymnorrhiza and 24.3 for A. marina. Abandoned cut stems and laths were found during the study. Bark harvested for traditional medicine and cattle feeding in mangroves was also prevalent and expected to reduce the health of the forest. Mangroves in the Ntafufu Estuary are expanding, and the population structure of the three mangrove species showed a healthy balance between young and mature stems. The harvesting of Black mangrove (B. gymnorrhiza) poles for mainly roof construction is relatively limited. As part of the functions of the DAFF, the use of the mangrove resources has to be balanced with the resource availability from the mangroves, and this should result in a healthy functioning mangrove forest. Development of a participatory forest management (PFM) plan for a forest estate and its forest management unit, require an understanding of the mangrove communities and their dynamics, and the current level of resource use associated with the mangroves. The study recommended that a Mangrove Pole Harvesters Group is needed to practice silviculture through guidance of relevant governmental personnel.
- Full Text:
- Date Issued: 2020
Understanding the underlying resistance mechanism of Mycobacterium tuberculosis against Rifampicin by analyzing mutant DNA - directed RNA polymerase proteins via bioinformatics approaches
- Authors: Monama, Mokgerwa Zacharia
- Date: 2020
- Subjects: Mycobacterium tuberculosis , Rifampin , Drug resistance , Homology (Biology) , Tuberculosis -- Chemotherapy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167508 , vital:41487
- Description: Tuberculosis or TB is an airborne disease caused by the non-motile bacilli, Mycobacterium tuberculosis (MTB). There are two main forms of TB, namely, latent TB or LTB, asymptomatic and non-contagious version which according to the World Health Organization (WHO) is estimated to afflict over a third of the world’s population; and active TB or ATB, a symptomatic and contagious version which continues to spread, affecting millions worldwide. With the already high reported prevalence of TB, the emergence of drug-resistant strains has prompted the development of novel approaches to enhance the efficacy of known drugs and a desperate search for novel compounds to combat MTB infections. It was for this very purpose that this study was conducted. A look into the resistance mechanism of Rifampicin (Rifampin or RIF), one of the more potent first-line drugs, might prove beneficial in predicting the consequence of an introduced mutation (which usually occur as single nucleotide polymorphisms or SNPs) and perhaps even overcome it using appropriate therapeutic interventions that improve RIF’s efficacy. To accomplish this task, models of acceptable quality were generated for the WT and clinically relevant, RIF resistance conferring, SNPs occurring at codon positions D516, H526 and S531 (E .coli numbering system) using MODELLER. The models were accordingly ranked using GA341 and z-DOPE score, and subsequently validated with QMEAN, PROCHECK and VERIFY3D. MD simulations spanning 100 ns were run for RIF-bound (complex) and RIF-free (holo) DNA-directed RNA polymerase (DDRP) protein systems for the WT and SNP mutants using GROMACS. The MD frames were analyzed using RMSD, Rg and RMSF. For further analysis, MD-TASK was used to analyze the calculated dynamic residue networks (DRNs) from the generated MD frames, determining both change in average shortest path (ΔL) and betweenness centrality (ΔBC). The RMSD analysis revealed that all of the SNP complex models displayed a level instability higher than that of the WT complex. A majority of the SNP complex models were also observed to have similar compactness to the WT holo when looking at the calculated Rg. The RMSF results also hinted towards possible physiological consequences of the mutations (generally referred to as a fitness cost) highlighted by the increased fluctuations of the zinc-binding domain and the MTB SI α helical coiled coil. For the first time, to the knowledge of the authors, DRN analysis was employed for the DDRP protein for both holo and complex systems, revealing insightful information about the residues that play a key role in the change in distance between residue pairs along with residues that play an essential role in protein communication within the calculated RIN. Overall, the data supported the conclusions drawn by a recent study that only concentrated on RIF-resistance in rpoB models which suggested that the binding pocket for the SNP models may result in the changed coordination of RIF which may be the main contributor to its impaired efficacy.
- Full Text:
- Date Issued: 2020
- Authors: Monama, Mokgerwa Zacharia
- Date: 2020
- Subjects: Mycobacterium tuberculosis , Rifampin , Drug resistance , Homology (Biology) , Tuberculosis -- Chemotherapy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167508 , vital:41487
- Description: Tuberculosis or TB is an airborne disease caused by the non-motile bacilli, Mycobacterium tuberculosis (MTB). There are two main forms of TB, namely, latent TB or LTB, asymptomatic and non-contagious version which according to the World Health Organization (WHO) is estimated to afflict over a third of the world’s population; and active TB or ATB, a symptomatic and contagious version which continues to spread, affecting millions worldwide. With the already high reported prevalence of TB, the emergence of drug-resistant strains has prompted the development of novel approaches to enhance the efficacy of known drugs and a desperate search for novel compounds to combat MTB infections. It was for this very purpose that this study was conducted. A look into the resistance mechanism of Rifampicin (Rifampin or RIF), one of the more potent first-line drugs, might prove beneficial in predicting the consequence of an introduced mutation (which usually occur as single nucleotide polymorphisms or SNPs) and perhaps even overcome it using appropriate therapeutic interventions that improve RIF’s efficacy. To accomplish this task, models of acceptable quality were generated for the WT and clinically relevant, RIF resistance conferring, SNPs occurring at codon positions D516, H526 and S531 (E .coli numbering system) using MODELLER. The models were accordingly ranked using GA341 and z-DOPE score, and subsequently validated with QMEAN, PROCHECK and VERIFY3D. MD simulations spanning 100 ns were run for RIF-bound (complex) and RIF-free (holo) DNA-directed RNA polymerase (DDRP) protein systems for the WT and SNP mutants using GROMACS. The MD frames were analyzed using RMSD, Rg and RMSF. For further analysis, MD-TASK was used to analyze the calculated dynamic residue networks (DRNs) from the generated MD frames, determining both change in average shortest path (ΔL) and betweenness centrality (ΔBC). The RMSD analysis revealed that all of the SNP complex models displayed a level instability higher than that of the WT complex. A majority of the SNP complex models were also observed to have similar compactness to the WT holo when looking at the calculated Rg. The RMSF results also hinted towards possible physiological consequences of the mutations (generally referred to as a fitness cost) highlighted by the increased fluctuations of the zinc-binding domain and the MTB SI α helical coiled coil. For the first time, to the knowledge of the authors, DRN analysis was employed for the DDRP protein for both holo and complex systems, revealing insightful information about the residues that play a key role in the change in distance between residue pairs along with residues that play an essential role in protein communication within the calculated RIN. Overall, the data supported the conclusions drawn by a recent study that only concentrated on RIF-resistance in rpoB models which suggested that the binding pocket for the SNP models may result in the changed coordination of RIF which may be the main contributor to its impaired efficacy.
- Full Text:
- Date Issued: 2020
Underutilisation of information communication and technology in the building construction industry case study: Department of Public Works in the Amathole district in the Eastern Cape
- Authors: Camngca, Vuyokazi Precious
- Date: 2020
- Subjects: Construction industry -- Information technology , Construction industry -- Data processing Information technology Communication and technology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/50632 , vital:42280
- Description: This study investigated the causes and effects of the underutilisation of Information Communication Technology (ICT) in the building section of the Amathole Region. The construction industry’s daily processes demand both heavy usages of data and data communication between project participants to meet client requirements. This industry is characterised by inaccurate and untimely communications that often result in costly delays and extensions of the project timeframe. ICT is a potential solution to this problem. The objectives of the study are, therefore, to determine why the above, a technically skilled occupational government institution in the Eastern Cape, does not employ ICT efficiently and optimally during this time of the looming global fourth industrial revolution. The literature review detailed the causes of and impact level of ICT’s utilisation and its potential benefits. For data collection, the researcher held unstructured interviews with a Chief Quantity Surveyor, Chief Architect, Engineer, Building Inspectors, and a Quantity Surveyor who dealt directly with construction projects. The key findings revealed that a lack of understanding of existing and newly available ICT software and hardware technology existed amongst certain senior officials within the building technology. The previously alluded, combined with the fear of the inability to learn and apply such new technology, has led to a culture of resistance to change from these more senior officials to utilise applications such as AutoCAD. The above-mentioned resistance, has also triggered the prevention of access to and lack of ICT resources, training, and inadequate funding, thereby eventually resulting in the underutilisation of ICT within the whole building section. This change also adversely affects all officials, especially the junior officials who have graduated using the most recent ICT technology during their studies. The researcher deduced, from the above findings, that adequate change management and continuous development, combined with the allocation of proper resources, would be necessary for all staff members. It was also determined that investments had to be made in the ICT equipment through the provision of a sufficient budget in the building section at AR.
- Full Text:
- Date Issued: 2020
- Authors: Camngca, Vuyokazi Precious
- Date: 2020
- Subjects: Construction industry -- Information technology , Construction industry -- Data processing Information technology Communication and technology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/50632 , vital:42280
- Description: This study investigated the causes and effects of the underutilisation of Information Communication Technology (ICT) in the building section of the Amathole Region. The construction industry’s daily processes demand both heavy usages of data and data communication between project participants to meet client requirements. This industry is characterised by inaccurate and untimely communications that often result in costly delays and extensions of the project timeframe. ICT is a potential solution to this problem. The objectives of the study are, therefore, to determine why the above, a technically skilled occupational government institution in the Eastern Cape, does not employ ICT efficiently and optimally during this time of the looming global fourth industrial revolution. The literature review detailed the causes of and impact level of ICT’s utilisation and its potential benefits. For data collection, the researcher held unstructured interviews with a Chief Quantity Surveyor, Chief Architect, Engineer, Building Inspectors, and a Quantity Surveyor who dealt directly with construction projects. The key findings revealed that a lack of understanding of existing and newly available ICT software and hardware technology existed amongst certain senior officials within the building technology. The previously alluded, combined with the fear of the inability to learn and apply such new technology, has led to a culture of resistance to change from these more senior officials to utilise applications such as AutoCAD. The above-mentioned resistance, has also triggered the prevention of access to and lack of ICT resources, training, and inadequate funding, thereby eventually resulting in the underutilisation of ICT within the whole building section. This change also adversely affects all officials, especially the junior officials who have graduated using the most recent ICT technology during their studies. The researcher deduced, from the above findings, that adequate change management and continuous development, combined with the allocation of proper resources, would be necessary for all staff members. It was also determined that investments had to be made in the ICT equipment through the provision of a sufficient budget in the building section at AR.
- Full Text:
- Date Issued: 2020
Unravelling the replication biology of Providence virus in a cell culturebased model system
- Authors: Jarvie, Rachel Anne
- Date: 2020
- Subjects: Virology -- Research , RNA viruses , Viruses -- Reproduction , Providence virus
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/142339 , vital:38071
- Description: There has been an increase in the number of viral outbreaks in the last decade; the majority of these are attributed to insect-human or animal-human transfer. Despite this awareness, there is limited understanding of the replication biology of the viruses causing the outbreaks and there are few model systems that are available to study RNA virus replication and viral persistence. In this study, we describe a Providence (PrV)-based model system to study virus replication biology. PrV is a single-stranded RNA virus that can cross Kingdom boundaries; it is capable of establishing a productive infection in insect and mammalian cell culture and it is also capable of replicating in plants. Only one other virus has been reported to infect a similar host range - the Nodavirus, Flock House virus (FHV). First, we performed a bioinformatic analysis of the PrV genome and validated the tools that were currently available to work with this model system in mammalian cells. Our data indicate that PrV infection of human cervical cancer (HeLa) cells results in the production of p130, p104/p40 and VCAP, albeit at low levels. While PrV replication in insect cells is associated with the Golgi apparatus and secretory vesicles, in HeLa cells, PrV replication is associated with the mitochondria. It is interesting to note that FHV replication factories are located on the outer mitochondrial membrane. In an attempt to study PrV virus replication in vitro, we adapted the BioID system reported by Roux et al. (2012). Here a promiscuous biotin ligase enzyme (BirA) was fused to a protein of interest and the expression of the fusion protein in mammalian cells resulted in the proximitybased biotinylation of proteins associated with the protein of interest. Using p40 as the protein of interest, we studied the fusion protein (BirA-p40) in transiently transfected HeLa cells and in a stable cell line, using western blot analysis and confocal microscopy. We faced challenges comparing the data collected using the two antibody-based detection techniques and the lack of BirA-p40 detection when using western analysis was attributed to the associated of p40 with detergent resistant membranes. BirA-p40 was subsequently expressed using in vitro coupled transcription/translation reactions, in the presence of excess biotin. While BirA-p40 was robustly expressed under these conditions, biotinylation of BirA-p40 was not detected. We attributed this to the conditions used in the experiments and given additional time, we would extend the duration of biotinylation, in vitro. PrV replication in mammalian cells was detectable using confocal microscopy however the levels of fluorescence were relatively low. The knowledge that p40 was associated with detergent resistant membranes led us to question the impact of detergent treatment of live cells on the detection of PrV replication. PrV-infected HeLa cells were treated with detergents with varying biochemical characteristics and the impact of these treatments on the detection of PrV replication were evaluated. We observed that linear and non-ionic detergents, namely NP-40 and Triton X-100, were most effective at enhancing the detection of viral replication in PrV-infected HeLa cells. Our data confirm that detergent treatment results in enhanced detection, and not enhanced PrV replication, in HeLa cells. Using the stable BirA-p40 expressing HeLa cell line, we showed that the protein is associated with membranes in vitro, and that the enhanced expression of BirA-p40 results in the formation of greater volumes of detergent-resistant membranes. In addition, detergent treatment of unfixed PrV-infected HeLa cells revealed the presence of the PrV p40 protein in the nucleoli of the cells. This is the first report of PrV proteins, which are translated in the cytosol of the mammalian cells, occurring in the nucleus. Our study has resulted in a deeper understanding of PrV replication in mammalian cell lines. A ‘simple RNA virus’ with only three predicted open reading frames has exhibited high levels of complexity within its elegant simplicity. This study has also highlighted the challenges associated with studying RNA virus replication biology in vitro. Looking forward, the identification of detergent-based enhancement for the detection of PrV replication provides the opportunity to perform more targeted PrV replication studies. The PrV-based model system can also be applied to the identification and analysis of potential broad-spectrum antiviral drugs in vitro. The latter application is particularly relevant considering the increase in the number of viral outbreaks over the last decade.
- Full Text:
- Date Issued: 2020
- Authors: Jarvie, Rachel Anne
- Date: 2020
- Subjects: Virology -- Research , RNA viruses , Viruses -- Reproduction , Providence virus
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/142339 , vital:38071
- Description: There has been an increase in the number of viral outbreaks in the last decade; the majority of these are attributed to insect-human or animal-human transfer. Despite this awareness, there is limited understanding of the replication biology of the viruses causing the outbreaks and there are few model systems that are available to study RNA virus replication and viral persistence. In this study, we describe a Providence (PrV)-based model system to study virus replication biology. PrV is a single-stranded RNA virus that can cross Kingdom boundaries; it is capable of establishing a productive infection in insect and mammalian cell culture and it is also capable of replicating in plants. Only one other virus has been reported to infect a similar host range - the Nodavirus, Flock House virus (FHV). First, we performed a bioinformatic analysis of the PrV genome and validated the tools that were currently available to work with this model system in mammalian cells. Our data indicate that PrV infection of human cervical cancer (HeLa) cells results in the production of p130, p104/p40 and VCAP, albeit at low levels. While PrV replication in insect cells is associated with the Golgi apparatus and secretory vesicles, in HeLa cells, PrV replication is associated with the mitochondria. It is interesting to note that FHV replication factories are located on the outer mitochondrial membrane. In an attempt to study PrV virus replication in vitro, we adapted the BioID system reported by Roux et al. (2012). Here a promiscuous biotin ligase enzyme (BirA) was fused to a protein of interest and the expression of the fusion protein in mammalian cells resulted in the proximitybased biotinylation of proteins associated with the protein of interest. Using p40 as the protein of interest, we studied the fusion protein (BirA-p40) in transiently transfected HeLa cells and in a stable cell line, using western blot analysis and confocal microscopy. We faced challenges comparing the data collected using the two antibody-based detection techniques and the lack of BirA-p40 detection when using western analysis was attributed to the associated of p40 with detergent resistant membranes. BirA-p40 was subsequently expressed using in vitro coupled transcription/translation reactions, in the presence of excess biotin. While BirA-p40 was robustly expressed under these conditions, biotinylation of BirA-p40 was not detected. We attributed this to the conditions used in the experiments and given additional time, we would extend the duration of biotinylation, in vitro. PrV replication in mammalian cells was detectable using confocal microscopy however the levels of fluorescence were relatively low. The knowledge that p40 was associated with detergent resistant membranes led us to question the impact of detergent treatment of live cells on the detection of PrV replication. PrV-infected HeLa cells were treated with detergents with varying biochemical characteristics and the impact of these treatments on the detection of PrV replication were evaluated. We observed that linear and non-ionic detergents, namely NP-40 and Triton X-100, were most effective at enhancing the detection of viral replication in PrV-infected HeLa cells. Our data confirm that detergent treatment results in enhanced detection, and not enhanced PrV replication, in HeLa cells. Using the stable BirA-p40 expressing HeLa cell line, we showed that the protein is associated with membranes in vitro, and that the enhanced expression of BirA-p40 results in the formation of greater volumes of detergent-resistant membranes. In addition, detergent treatment of unfixed PrV-infected HeLa cells revealed the presence of the PrV p40 protein in the nucleoli of the cells. This is the first report of PrV proteins, which are translated in the cytosol of the mammalian cells, occurring in the nucleus. Our study has resulted in a deeper understanding of PrV replication in mammalian cell lines. A ‘simple RNA virus’ with only three predicted open reading frames has exhibited high levels of complexity within its elegant simplicity. This study has also highlighted the challenges associated with studying RNA virus replication biology in vitro. Looking forward, the identification of detergent-based enhancement for the detection of PrV replication provides the opportunity to perform more targeted PrV replication studies. The PrV-based model system can also be applied to the identification and analysis of potential broad-spectrum antiviral drugs in vitro. The latter application is particularly relevant considering the increase in the number of viral outbreaks over the last decade.
- Full Text:
- Date Issued: 2020