The taxonomy of the topminnows (Teleostei: Cyprinodontiformes) (Procatopodidae: Procatopodinae) of southern Africa
- Authors: Van Zeeventer, Ryan Matthew
- Date: 2020
- Subjects: Cyprinodontiformes -- Africa, Southern , Killifishes -- Africa, Southern
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/145559 , vital:38449
- Description: Taxonomy is a tool that plays a crucial role in the implementation of effective management assessments, the ability to identify different fish species and their life stages, and create effective conservation strategies. Recent years have seen an increase in the discovery of cryptic species which could have an effect on how we implement conservation strategies, increasing the importance of accurate taxonomic assessments. The southern African topminnows of the genera Micropanchax and Lacustricola (Family Procatopodidae) include several species of egg-laying fishes that live in the marginal areas of rivers and lakes throughout the river systems of southern Africa in separated and connected populations. It was recently discovered that these populations showed subtle differences in their morphology and colouration, which led to the belief that new and cryptic species may be present. Previous studies of the Procatopodidae relied heavily on phylogenetic analyses that drew on morphological traits without reliance on molecular methods of analysis. A few of the taxonomic issues were resolved through these limited studies but ultimately the taxonomic status of the Procatopodidae remained poorly understood. Furthermore, these studies had not been updated in recent years and hence the benefits of new technology had not been brought to bear on the issues. A multi-gene analysis using standard phylogenetic methods and five molecular markers (mitochondrial cytochrome C oxidase (COI), mitochondrial cytochrome b (cytb), mitochondrial 16S ribosomal RNA (16S rRNA), nuclear 28S ribosomal RNA (28S rRNA) and mitochondrial Tyrosine Kinase (X-src) (TyrK)) allowed phylogenetic trees to be made which demonstrated clear relationships within Micropanchax and Lacustricola of southern Africa and the out-groups used in the analysis. The inference trees showed that Micropanchax johnstoni was represented by three clades and was shown to be polyphyletic while Micropanchax hutereaui, which was represented by two clades, and Micropanchax katangae, which was represented by one clade, were monophyletic. The two species of Lacustricola, L. myaposae and L. macrurus showed very close relationships to Micropanchax and it is suggested that these two species be transferred to Micropanchax, leaving Lacustricola to only be found in central Africa.
- Full Text:
- Authors: Van Zeeventer, Ryan Matthew
- Date: 2020
- Subjects: Cyprinodontiformes -- Africa, Southern , Killifishes -- Africa, Southern
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/145559 , vital:38449
- Description: Taxonomy is a tool that plays a crucial role in the implementation of effective management assessments, the ability to identify different fish species and their life stages, and create effective conservation strategies. Recent years have seen an increase in the discovery of cryptic species which could have an effect on how we implement conservation strategies, increasing the importance of accurate taxonomic assessments. The southern African topminnows of the genera Micropanchax and Lacustricola (Family Procatopodidae) include several species of egg-laying fishes that live in the marginal areas of rivers and lakes throughout the river systems of southern Africa in separated and connected populations. It was recently discovered that these populations showed subtle differences in their morphology and colouration, which led to the belief that new and cryptic species may be present. Previous studies of the Procatopodidae relied heavily on phylogenetic analyses that drew on morphological traits without reliance on molecular methods of analysis. A few of the taxonomic issues were resolved through these limited studies but ultimately the taxonomic status of the Procatopodidae remained poorly understood. Furthermore, these studies had not been updated in recent years and hence the benefits of new technology had not been brought to bear on the issues. A multi-gene analysis using standard phylogenetic methods and five molecular markers (mitochondrial cytochrome C oxidase (COI), mitochondrial cytochrome b (cytb), mitochondrial 16S ribosomal RNA (16S rRNA), nuclear 28S ribosomal RNA (28S rRNA) and mitochondrial Tyrosine Kinase (X-src) (TyrK)) allowed phylogenetic trees to be made which demonstrated clear relationships within Micropanchax and Lacustricola of southern Africa and the out-groups used in the analysis. The inference trees showed that Micropanchax johnstoni was represented by three clades and was shown to be polyphyletic while Micropanchax hutereaui, which was represented by two clades, and Micropanchax katangae, which was represented by one clade, were monophyletic. The two species of Lacustricola, L. myaposae and L. macrurus showed very close relationships to Micropanchax and it is suggested that these two species be transferred to Micropanchax, leaving Lacustricola to only be found in central Africa.
- Full Text:
The use of ritual as physical and spiritual medium and its documentation in Buhlebezwe Siwani’s contemporary visual arts performance
- Authors: Lila, Philiswa
- Date: 2020
- Subjects: Arts and religion , Ritual -- South Africa , Performance art -- Religious aspects -- South Africa , Women performance artists -- South Africa , Siwani, Buhlebezwe, 1987-
- Language: English
- Type: text , Thesis , Masters , MFA
- Identifier: http://hdl.handle.net/10962/166160 , vital:41334
- Description: This thesis is motivated by my experience of Inzilo: Ngoba ngihlala kwabafileyo, a live performance by South African visual artist Buhlebezwe Siwani. The performance took place at Michaelis Galleries, University of Cape Town (UCT), as part of a group exhibition Between Subject and Object: human remains at the interface of art and science (2014), which accompanied the Medical Humanities in Africa Conference (from 28 – 29 August 2014). As an entry into my discussion, I describe how Siwani’s performance makes use of death and burial ritual in what seems to be an intention to make art that is (re)presenting an activity of reality to invade and control the sphere of feelings, emotions and a sense of ceremony that is dependent on both ritual and rites of the performance. I grapple with the fact that I experienced a ritual performance in a gallery space. Furthermore, I question how walking out of the performance I thought of the lines between art and/or life. The role of ritual in my thesis explores the symbolic meanings, powers and intentions of ritual rites in Africa. This reflection maps out historical locations that are relevant to the major debates, definitions, themes and the experiences of ritual as part of academic research. From Siwani’s practice as an artist and isangoma to other expressions in the fields of history, sociology, religion, feminism, to mention a few, my thesis is an enquiry that engages ritual and performance art theory and scholarship. Through a qualitative analysis, my methodology rejects a chronological, thematic and discipline centered research. Rather, I use a multidisciplinary approach based on critical visual analysis as knowledge creation in the visual arts, for example archives, documentation, performance, text, video, installation, painting, sculpture, etc. The findings suggests that the role of ritual in performance art is not a singular exploration, nor is it based on separating ritual and performance art. The results further reveal that ritual in performance art is not a reenactment of patterns and human behaviours, nor is the notion of reenactment used to denote the myriad meanings and functions of re-performing historical ritual events into performance art. Throughout, my thesis provides a focus that demonstrates the significance of how ritual in performance art has a profound subjective (personal or individual) and collective holistic way of serving human and spiritual needs, and that of creating an environment that is open to the content and context of art as it relates with traditional African religious practices, beliefs and knowledges. Focus is given to three major themes that make up the three chapters of my research: firstly, I reflect on death as personified by Siwani’s performance Inzilo: Ngoba ii ngihlala kwabafileyo and her role as isangoma. Here death is used to draw specific attention to the body in process of embodied presence and absence of physical and spiritual worlds. Secondly, drawing on Siwani’s concept of secrecy and boundaries of concealing and revealing rituals meanings and powers as isangoma, I question the role of secrets, which highlights the significance of bodies (human and natural sites of ritual) in ritual performance. Finally, the idea of a trace is explored. The intersecting use of a trace as the thinking-making-doing of ritual in performance articulates a connected thread that sets in motion the trace of ritual (installation, image and marked space pf ritual) as an afterlife that offers a continued space of processual ceremony for multiple effective encounters and movements..
- Full Text:
- Authors: Lila, Philiswa
- Date: 2020
- Subjects: Arts and religion , Ritual -- South Africa , Performance art -- Religious aspects -- South Africa , Women performance artists -- South Africa , Siwani, Buhlebezwe, 1987-
- Language: English
- Type: text , Thesis , Masters , MFA
- Identifier: http://hdl.handle.net/10962/166160 , vital:41334
- Description: This thesis is motivated by my experience of Inzilo: Ngoba ngihlala kwabafileyo, a live performance by South African visual artist Buhlebezwe Siwani. The performance took place at Michaelis Galleries, University of Cape Town (UCT), as part of a group exhibition Between Subject and Object: human remains at the interface of art and science (2014), which accompanied the Medical Humanities in Africa Conference (from 28 – 29 August 2014). As an entry into my discussion, I describe how Siwani’s performance makes use of death and burial ritual in what seems to be an intention to make art that is (re)presenting an activity of reality to invade and control the sphere of feelings, emotions and a sense of ceremony that is dependent on both ritual and rites of the performance. I grapple with the fact that I experienced a ritual performance in a gallery space. Furthermore, I question how walking out of the performance I thought of the lines between art and/or life. The role of ritual in my thesis explores the symbolic meanings, powers and intentions of ritual rites in Africa. This reflection maps out historical locations that are relevant to the major debates, definitions, themes and the experiences of ritual as part of academic research. From Siwani’s practice as an artist and isangoma to other expressions in the fields of history, sociology, religion, feminism, to mention a few, my thesis is an enquiry that engages ritual and performance art theory and scholarship. Through a qualitative analysis, my methodology rejects a chronological, thematic and discipline centered research. Rather, I use a multidisciplinary approach based on critical visual analysis as knowledge creation in the visual arts, for example archives, documentation, performance, text, video, installation, painting, sculpture, etc. The findings suggests that the role of ritual in performance art is not a singular exploration, nor is it based on separating ritual and performance art. The results further reveal that ritual in performance art is not a reenactment of patterns and human behaviours, nor is the notion of reenactment used to denote the myriad meanings and functions of re-performing historical ritual events into performance art. Throughout, my thesis provides a focus that demonstrates the significance of how ritual in performance art has a profound subjective (personal or individual) and collective holistic way of serving human and spiritual needs, and that of creating an environment that is open to the content and context of art as it relates with traditional African religious practices, beliefs and knowledges. Focus is given to three major themes that make up the three chapters of my research: firstly, I reflect on death as personified by Siwani’s performance Inzilo: Ngoba ii ngihlala kwabafileyo and her role as isangoma. Here death is used to draw specific attention to the body in process of embodied presence and absence of physical and spiritual worlds. Secondly, drawing on Siwani’s concept of secrecy and boundaries of concealing and revealing rituals meanings and powers as isangoma, I question the role of secrets, which highlights the significance of bodies (human and natural sites of ritual) in ritual performance. Finally, the idea of a trace is explored. The intersecting use of a trace as the thinking-making-doing of ritual in performance articulates a connected thread that sets in motion the trace of ritual (installation, image and marked space pf ritual) as an afterlife that offers a continued space of processual ceremony for multiple effective encounters and movements..
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The value of economic capital as an indicator to protect prospective and existing ordinary shareholders
- Authors: Chonzi, Tendai Day
- Date: 2020
- Subjects: Banks and banking -- Risk management -- South Africa , Financial services industry -- Risk management -- South Africa , ABSA Bank , FirstRand Limited , Nedbank , Standard Bank Limited , Capitec Bank (South Africa)
- Language: English
- Type: text , Thesis , Masters , MCom
- Identifier: http://hdl.handle.net/10962/145807 , vital:38468
- Description: South Africans banking sector is one of the most dominating banking sectors in Africa. The banking sector is privately owned and involves a lot of different stakeholders, who risk losing their investments. One of the stakeholders who are the bottom of the repayment chain are existing ordinary shareholders because they risk losing all their investment in the result of bankruptcy, liquidity crises or the inability of the bank to repay their shareholders. Regulators in the banking sector only protect the depositor and the stability of the banking sector but not ordinary shareholders. An internal supervisory measure called economic capital has recently received more attention because of its aim to protect ordinary shareholders and thus, existing and prospective shareholders can use its value as a protective indicator. Economic theory assumes that the higher the value of economic capital (the lower the economic capital shortfall), the lower the return on investment for existing ordinary shareholders. The aforementioned shows a trade-off between protection (economic capital) and returns. Literature by Larsson (2009) further suggests that banks are always reluctant with implementing internal measures to protect themselves because of the good regulatory regime in the sector, some banks think that they are “too big to fail” and the fact that the reserve banks are always on the standby as a bailout. The purpose of this research is to examine which of the top five commercial banks in South African actively protect their existing ordinary shareholders using the value of economic capital and possibly attract prospective ordinary shareholders, locally and internationally. The banks under study are Absa, Capitec, FirstRand, Nedbank and Standard Bank over ten years, starting from June 2009 to May 2019 and in monthly frequency. The observations totalled 120 and two models that are under the Return Series Method were in used, namely; Historical Simulation Model and Variance Covariance Model. Both models, although they were small deviations in the value of economic capital, concluded that Standard Bank protects its existing ordinary shareholders the most, followed by FirstRand, then Absa and last is Nedbank. Capitec was the only bank, after one financial shock that could not protect its existing ordinary shareholders. Moreover, evidence in the study shows a trade-off between economic capital and return on investment in the case of Capitec and Standard Bank. Standard Bank had the highest value of economic capital and second-lowest return on investment, while Capitec had the highest return on investment and lowest value of economic capital. The significant policy implication of the research is that financial institution needs to strike a balance between protection and profits; thus, a way of protecting various stakeholders. Financial shocks have proven that regulatory measures are weak and they are is need for internal measures (economic capital) which indicate how financial institution can sustain in such cases.
- Full Text:
- Authors: Chonzi, Tendai Day
- Date: 2020
- Subjects: Banks and banking -- Risk management -- South Africa , Financial services industry -- Risk management -- South Africa , ABSA Bank , FirstRand Limited , Nedbank , Standard Bank Limited , Capitec Bank (South Africa)
- Language: English
- Type: text , Thesis , Masters , MCom
- Identifier: http://hdl.handle.net/10962/145807 , vital:38468
- Description: South Africans banking sector is one of the most dominating banking sectors in Africa. The banking sector is privately owned and involves a lot of different stakeholders, who risk losing their investments. One of the stakeholders who are the bottom of the repayment chain are existing ordinary shareholders because they risk losing all their investment in the result of bankruptcy, liquidity crises or the inability of the bank to repay their shareholders. Regulators in the banking sector only protect the depositor and the stability of the banking sector but not ordinary shareholders. An internal supervisory measure called economic capital has recently received more attention because of its aim to protect ordinary shareholders and thus, existing and prospective shareholders can use its value as a protective indicator. Economic theory assumes that the higher the value of economic capital (the lower the economic capital shortfall), the lower the return on investment for existing ordinary shareholders. The aforementioned shows a trade-off between protection (economic capital) and returns. Literature by Larsson (2009) further suggests that banks are always reluctant with implementing internal measures to protect themselves because of the good regulatory regime in the sector, some banks think that they are “too big to fail” and the fact that the reserve banks are always on the standby as a bailout. The purpose of this research is to examine which of the top five commercial banks in South African actively protect their existing ordinary shareholders using the value of economic capital and possibly attract prospective ordinary shareholders, locally and internationally. The banks under study are Absa, Capitec, FirstRand, Nedbank and Standard Bank over ten years, starting from June 2009 to May 2019 and in monthly frequency. The observations totalled 120 and two models that are under the Return Series Method were in used, namely; Historical Simulation Model and Variance Covariance Model. Both models, although they were small deviations in the value of economic capital, concluded that Standard Bank protects its existing ordinary shareholders the most, followed by FirstRand, then Absa and last is Nedbank. Capitec was the only bank, after one financial shock that could not protect its existing ordinary shareholders. Moreover, evidence in the study shows a trade-off between economic capital and return on investment in the case of Capitec and Standard Bank. Standard Bank had the highest value of economic capital and second-lowest return on investment, while Capitec had the highest return on investment and lowest value of economic capital. The significant policy implication of the research is that financial institution needs to strike a balance between protection and profits; thus, a way of protecting various stakeholders. Financial shocks have proven that regulatory measures are weak and they are is need for internal measures (economic capital) which indicate how financial institution can sustain in such cases.
- Full Text:
The weight of a tooth
- Authors: Perros, Robyn Helen
- Date: 2020
- Subjects: South African fiction (English) -- 21st century
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/144192 , vital:38319
- Description: My thesis is a fragmented, non-linear novella, comprised predominantly of experimental prose- poetry and fiction short-stories. I have chosen this approach in form to further explore my interest in ancestry and trauma, death and image-making, “reality” and fantasy, and the tension these invisible barriers create between the inner and outer worlds in which we simultaneously navigate, remember and forget. This thesis has been influenced both in form and content by the works of Eduardo Galeano, Osama Alomar, Lidia Yuknavitch, Susan Steinberg, Claudia Rankine, Lance Olsen, and Yasunari Kawabata, among others.
- Full Text:
- Authors: Perros, Robyn Helen
- Date: 2020
- Subjects: South African fiction (English) -- 21st century
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/144192 , vital:38319
- Description: My thesis is a fragmented, non-linear novella, comprised predominantly of experimental prose- poetry and fiction short-stories. I have chosen this approach in form to further explore my interest in ancestry and trauma, death and image-making, “reality” and fantasy, and the tension these invisible barriers create between the inner and outer worlds in which we simultaneously navigate, remember and forget. This thesis has been influenced both in form and content by the works of Eduardo Galeano, Osama Alomar, Lidia Yuknavitch, Susan Steinberg, Claudia Rankine, Lance Olsen, and Yasunari Kawabata, among others.
- Full Text:
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:
- 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:
Thermal tolerance and the potential effects of climate change on coastal intertidal and estuarine organisms in the Kariega Estuary and adjacent intertitdal coastline, Eastern Cape, South Africa
- Authors: Van der Walt, Kerry-Ann
- Date: 2020
- Subjects: Ectotherms -- Climatic factors , Ectotherms -- Effect of temperature on , Fishes -- Climatic factors , Fishes -- Effect of temperature on , Climatic changes -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/148459 , vital:38741
- Description: Temperature changes due to the effects of climate change are evident on all continents and oceans. As a result, there is a growing concern over how marine ectotherms will respond to extreme or fluctuating environmental temperatures. Temperature changes have strong direct and indirect effects on individual, population, and ecosystem functioning traits. A multi-scale approach determining the thermal tolerance and performance of several marine ectotherms belonging to different coastal habitats is rarely considered in thermal physiology studies but is effective for an integrated ecosystem assessment. As such, for this thesis, I aimed to quantify and compare the thermal tolerance and performance of a range of coastal marine ectotherms (fish and macro-invertebrates) with different biogeographical distributions from estuarine, subtidal and rocky intertidal habitats to available and projected in situ temperature data. This was also undertaken to gauge the local vulnerability of each species across summer and winter in a warm-temperate region of South Africa. This was done using a multi-method physiological approach, which included the dynamic method (CTmax and CTmin), static respirometry and maximum heart rate fHmax). Results of the dynamic method on several fish and macro-invertebrate species indicated that there are differences in thermal tolerance according to taxonomy, biogeography and habitat for both summer and winter. Macro-invertebrate species generally had higher CTmax endpoints, lower CTmin endpoints, higher upper and lower breadths in tolerance, higher upper and lower thermal safety margins and higher thermal scopes than the fish species. This could be a result of the macro-invertebrate species studied being less mobile compared with fish species (which are able to move to more favourable conditions) as well as having broader geographical distributions. In addition, macro-invertebrates from the intertidal rock pool habitat (Palaemon peringueyi; Pernaperna) were more tolerant of high and low temperatures compared with the macro-invertebrates from the estuarine habitat (Clibanarius virescens; Parasesarma catenatum; Upogebia africana). Overall, macro-invertebrates, with the exception of Parechinus angulosus, investigated in this study indicated that current temperatures and projected climate change scenarios across seasons would not have a significant impact on them and that they are highly adaptable to changing temperature regimes. This sign of high tolerance was further supported by the heart rates of P. perna and P. catenatum under an acute increase in temperature (1.0 °C.h-1) which showed individuals of each species physiologically depressing their metabolism until a final Arrhenius breakpoint temperature was reached (TAB). Among the fish species investigated in this study, tropical species (Chaetodon marleyi; Kuhlia mugil) had the highest CTmax and CTmin endpoints when compared with the temperate (Diplodus capensis; Sarpa salpa), warm-water endemic (Chelon dumerili; Rhabdosargus holubi) and cool-water endemic (Chelon richardsonii) fishes. This suggests that due to their lower breadths in tolerance and thermal safety margins being small, tropical species may be less tolerant of cold temperatures and thermal variability, especially in the form of summer upwelling events which are expected to increase in intensity and frequency in this region as a result of anthropogenic climate change effects. On the other hand, however, if a temperature increase of 2.0 - 4.0 °C takes place at the end of the century as predicted by the Intergovernmental Panel on Climate Change (IPCC), it is likely that tropical species such as C. marleyi will become more common. Temperate species such as D. capensis and S. salpa were able to tolerate a wide range of temperatures (wide thermal scope) compared with the other fish species. These findings may suggest that D. capensis and S. salpa are thermally resilient and may be the least vulnerable to climate change effects and temperature variability. When evaluating the different life stages of D. capensis, however, using the dynamic method (juveniles and adults), static respirometry (juveniles) and maximum heart rate (adults), results suggested that juveniles of this temperate species will be more resilient to increases in ocean temperatures compared with the adults because they have a higher thermal tolerance (CTmax/TCRIT) and a greater metabolic scope (TOPT) at higher temperatures. For both juveniles and adults, temperatures beyond 28.0 °C (upper Tpej; Tarr) will have a significant impact on their physiology. Using a multi-scale and multi-method approach thus helped to identify which species or community may be vulnerable to the effects of climate change within shallow coastal environments in this warm-temperate climate change hotspot. Adopting this type of approach will assist policy makers in developing comprehensive climate change management frameworks for coastal ecosystems globally and around South Africa.
- Full Text:
- Authors: Van der Walt, Kerry-Ann
- Date: 2020
- Subjects: Ectotherms -- Climatic factors , Ectotherms -- Effect of temperature on , Fishes -- Climatic factors , Fishes -- Effect of temperature on , Climatic changes -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/148459 , vital:38741
- Description: Temperature changes due to the effects of climate change are evident on all continents and oceans. As a result, there is a growing concern over how marine ectotherms will respond to extreme or fluctuating environmental temperatures. Temperature changes have strong direct and indirect effects on individual, population, and ecosystem functioning traits. A multi-scale approach determining the thermal tolerance and performance of several marine ectotherms belonging to different coastal habitats is rarely considered in thermal physiology studies but is effective for an integrated ecosystem assessment. As such, for this thesis, I aimed to quantify and compare the thermal tolerance and performance of a range of coastal marine ectotherms (fish and macro-invertebrates) with different biogeographical distributions from estuarine, subtidal and rocky intertidal habitats to available and projected in situ temperature data. This was also undertaken to gauge the local vulnerability of each species across summer and winter in a warm-temperate region of South Africa. This was done using a multi-method physiological approach, which included the dynamic method (CTmax and CTmin), static respirometry and maximum heart rate fHmax). Results of the dynamic method on several fish and macro-invertebrate species indicated that there are differences in thermal tolerance according to taxonomy, biogeography and habitat for both summer and winter. Macro-invertebrate species generally had higher CTmax endpoints, lower CTmin endpoints, higher upper and lower breadths in tolerance, higher upper and lower thermal safety margins and higher thermal scopes than the fish species. This could be a result of the macro-invertebrate species studied being less mobile compared with fish species (which are able to move to more favourable conditions) as well as having broader geographical distributions. In addition, macro-invertebrates from the intertidal rock pool habitat (Palaemon peringueyi; Pernaperna) were more tolerant of high and low temperatures compared with the macro-invertebrates from the estuarine habitat (Clibanarius virescens; Parasesarma catenatum; Upogebia africana). Overall, macro-invertebrates, with the exception of Parechinus angulosus, investigated in this study indicated that current temperatures and projected climate change scenarios across seasons would not have a significant impact on them and that they are highly adaptable to changing temperature regimes. This sign of high tolerance was further supported by the heart rates of P. perna and P. catenatum under an acute increase in temperature (1.0 °C.h-1) which showed individuals of each species physiologically depressing their metabolism until a final Arrhenius breakpoint temperature was reached (TAB). Among the fish species investigated in this study, tropical species (Chaetodon marleyi; Kuhlia mugil) had the highest CTmax and CTmin endpoints when compared with the temperate (Diplodus capensis; Sarpa salpa), warm-water endemic (Chelon dumerili; Rhabdosargus holubi) and cool-water endemic (Chelon richardsonii) fishes. This suggests that due to their lower breadths in tolerance and thermal safety margins being small, tropical species may be less tolerant of cold temperatures and thermal variability, especially in the form of summer upwelling events which are expected to increase in intensity and frequency in this region as a result of anthropogenic climate change effects. On the other hand, however, if a temperature increase of 2.0 - 4.0 °C takes place at the end of the century as predicted by the Intergovernmental Panel on Climate Change (IPCC), it is likely that tropical species such as C. marleyi will become more common. Temperate species such as D. capensis and S. salpa were able to tolerate a wide range of temperatures (wide thermal scope) compared with the other fish species. These findings may suggest that D. capensis and S. salpa are thermally resilient and may be the least vulnerable to climate change effects and temperature variability. When evaluating the different life stages of D. capensis, however, using the dynamic method (juveniles and adults), static respirometry (juveniles) and maximum heart rate (adults), results suggested that juveniles of this temperate species will be more resilient to increases in ocean temperatures compared with the adults because they have a higher thermal tolerance (CTmax/TCRIT) and a greater metabolic scope (TOPT) at higher temperatures. For both juveniles and adults, temperatures beyond 28.0 °C (upper Tpej; Tarr) will have a significant impact on their physiology. Using a multi-scale and multi-method approach thus helped to identify which species or community may be vulnerable to the effects of climate change within shallow coastal environments in this warm-temperate climate change hotspot. Adopting this type of approach will assist policy makers in developing comprehensive climate change management frameworks for coastal ecosystems globally and around South Africa.
- Full Text:
Thermoluminescence and phototransferred phermoluminescence of synthetic quartz
- Authors: Dawam, Robert Rangmou
- Date: 2020
- Subjects: Thermoluminescence , Quartz
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/145849 , vital:38472
- Description: The main aim of this investigation is on thermoluminescence and phototransferred thermoluminescence of synthetic quartz. Thermoluminescence was one of the tools used in characterising the electron traps parameters. The samples of quartz annealed at various temperatures up to 900̊C and the unannealed were used. The thermoluminescence glow curve was measured at 1̊C s~ 1 following beta irradiation to 40 Gy from the samples annealed at 500̊C and the unannealed consist of main peak at 70̊C and secondary peaks at 110, 180 and 310̊C. In comparison, the thermoluminescence glow curve for the sample annealed at 900̊C have main peak at 86̊C and the secondary ones at 170 and 310̊C. The kinetic analysis was carried out only on the main peak in each case. The activation energy was found to be decreasing with increase in annealing temperatures. The samples annealed at 500̊C and the unannealed were found to be affected by thermal quenching while sample annealed at 900̊C shows an inverse quenching for irradiation dose of 40 Gy. However, when the dose was reduce to 3 Gy the effects of thermal quenching was manifested. The activation energy of thermal quenching was also found to decrease with increase in annealing temperature. Thermally assisted optically stimulated luminescence measurement was carried out using continuous wave optical stimulated luminescence (CW-OSL). The samples studied were those annealed at 500̊C for 10 minutes, 900̊C for 10, 30, 60 minutes and 1000̊C for 10 minutes prior to use. The CW-OSL is stimulated using 470 nm blue LEDs at sample temperatures between 30 and 200̊C. It is measured after preheating to either 300 and 500̊C. When the integrated OSL intensity is plotted as a function of measurement temperature, the intensity goes through a peak. The increase in OSL intensity as a function of temperature is associated to thermal assistance and the decrease to thermal quenching. The kinetic parameters were evaluated by fitting the experimental data. The values of activation energies of thermal quenching are the same within experimental uncertainties for all the experimental conditions. This shows that annealing temperature, duration of annealing and irradiation dose have a negligible influence on the recombination site of luminescence using OSL. Phototransferred thermoluminescence (PTTL) induced from annealed samples using 470 nm blue light was also investigated. The quartz were annealed at 500 _C for 10 minutes, 900̊C for 10, 30, 60 minutes and 1000̊C for 10 minutes prior to use. The glow curves of conventional TL measured at 1 _C s1 following irradiation to 200 Gy shows six peaks in each case labelled I-VI for ease of reference whereas peaks observed under PTTL are referred to as A1 onwards. Only the first three peaks were reproduced under phototransfer for the sample annealed at 900̊C for 60 minutes and 1000̊C C for 10 minutes. Interestingly, for the intermediate duration of annealing of 30 minutes, the only peak that appears under phototransfer is the A1. For quartz annealed at 900̊C for 10 minutes, the PTTL appears as long as the preheating temperature does not exceed 560̊C. All other annealing temperatures, PTTL only appears for preheating to 450 and below. This shows that the occupancy of deep electron traps at temperatures beyond 450̊C or 560̊C is low. The activation energy for peaks A1, A2 and A3 were calculated. The PTTL peaks were studied for thermal quenching and peaks A1 and A3 were found to be affected. The activation energies for thermal quenching were determined as 0.62 ± 0.04 eV and 0.65 ± 0.02 eV for peaks A1 and A3 respectively. The experimental dependence of PTTL intensity on illumination time is modelled using sets of coupled linear differential equations based on systems of donors and acceptors whose number is determined by preheating temperature.
- Full Text:
- Authors: Dawam, Robert Rangmou
- Date: 2020
- Subjects: Thermoluminescence , Quartz
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/145849 , vital:38472
- Description: The main aim of this investigation is on thermoluminescence and phototransferred thermoluminescence of synthetic quartz. Thermoluminescence was one of the tools used in characterising the electron traps parameters. The samples of quartz annealed at various temperatures up to 900̊C and the unannealed were used. The thermoluminescence glow curve was measured at 1̊C s~ 1 following beta irradiation to 40 Gy from the samples annealed at 500̊C and the unannealed consist of main peak at 70̊C and secondary peaks at 110, 180 and 310̊C. In comparison, the thermoluminescence glow curve for the sample annealed at 900̊C have main peak at 86̊C and the secondary ones at 170 and 310̊C. The kinetic analysis was carried out only on the main peak in each case. The activation energy was found to be decreasing with increase in annealing temperatures. The samples annealed at 500̊C and the unannealed were found to be affected by thermal quenching while sample annealed at 900̊C shows an inverse quenching for irradiation dose of 40 Gy. However, when the dose was reduce to 3 Gy the effects of thermal quenching was manifested. The activation energy of thermal quenching was also found to decrease with increase in annealing temperature. Thermally assisted optically stimulated luminescence measurement was carried out using continuous wave optical stimulated luminescence (CW-OSL). The samples studied were those annealed at 500̊C for 10 minutes, 900̊C for 10, 30, 60 minutes and 1000̊C for 10 minutes prior to use. The CW-OSL is stimulated using 470 nm blue LEDs at sample temperatures between 30 and 200̊C. It is measured after preheating to either 300 and 500̊C. When the integrated OSL intensity is plotted as a function of measurement temperature, the intensity goes through a peak. The increase in OSL intensity as a function of temperature is associated to thermal assistance and the decrease to thermal quenching. The kinetic parameters were evaluated by fitting the experimental data. The values of activation energies of thermal quenching are the same within experimental uncertainties for all the experimental conditions. This shows that annealing temperature, duration of annealing and irradiation dose have a negligible influence on the recombination site of luminescence using OSL. Phototransferred thermoluminescence (PTTL) induced from annealed samples using 470 nm blue light was also investigated. The quartz were annealed at 500 _C for 10 minutes, 900̊C for 10, 30, 60 minutes and 1000̊C for 10 minutes prior to use. The glow curves of conventional TL measured at 1 _C s1 following irradiation to 200 Gy shows six peaks in each case labelled I-VI for ease of reference whereas peaks observed under PTTL are referred to as A1 onwards. Only the first three peaks were reproduced under phototransfer for the sample annealed at 900̊C for 60 minutes and 1000̊C C for 10 minutes. Interestingly, for the intermediate duration of annealing of 30 minutes, the only peak that appears under phototransfer is the A1. For quartz annealed at 900̊C for 10 minutes, the PTTL appears as long as the preheating temperature does not exceed 560̊C. All other annealing temperatures, PTTL only appears for preheating to 450 and below. This shows that the occupancy of deep electron traps at temperatures beyond 450̊C or 560̊C is low. The activation energy for peaks A1, A2 and A3 were calculated. The PTTL peaks were studied for thermal quenching and peaks A1 and A3 were found to be affected. The activation energies for thermal quenching were determined as 0.62 ± 0.04 eV and 0.65 ± 0.02 eV for peaks A1 and A3 respectively. The experimental dependence of PTTL intensity on illumination time is modelled using sets of coupled linear differential equations based on systems of donors and acceptors whose number is determined by preheating temperature.
- Full Text:
Thintitha, Celiwe
- Masombuka, Thobekile Hlobisile
- Authors: Masombuka, Thobekile Hlobisile
- Date: 2020
- Subjects: South African fiction (English) -- 21st century
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/147470 , vital:38639
- Description: This document consists of two (2) parts: Part A: Thesis (Creative Work) Part B: Portfolio
- Full Text:
- Authors: Masombuka, Thobekile Hlobisile
- Date: 2020
- Subjects: South African fiction (English) -- 21st century
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/147470 , vital:38639
- Description: This document consists of two (2) parts: Part A: Thesis (Creative Work) Part B: Portfolio
- Full Text:
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:
- 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:
Towards realising the benefits of citizen participation in environmental monitoring: a case study in an Eastern Cape natural resource management programme
- Authors: Mtati, Nosiseko
- Date: 2020
- Subjects: Tsitsa Project , Rural development projects -- South Africa -- Eastern Cape , Environmental monitoring -- South Africa -- Tsitsa River , Environmental monitoring -- Citizen participation -- South Africa -- Tsitsa River , Water supply, Agricultural -- South Africa -- Tsitsa River , Environmental education -- South Africa
- Language: English
- Type: text , Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10962/167562 , vital:41492
- Description: The Tsitsa Project focusses on land use management and rural livelihoods in the Tsitsa River catchment in the Eastern Cape Province of South Africa. It is funded by the Department of Environmental Affairs and the environmental monitoring initiative is implemented by Rhodes University, where I am employed as the catchment coordinator. This study explores the environmental monitoring initiative within the bigger Tsitsa Project. Community members in the catchment monitor sediment transportation in the Tsitsa River and its tributaries, which originally became of interest because it is proposed that a dam (Ntabelanga Dam) be established here. This study aims to understand citizen environmental monitoring in the Tsitsa Project; what the project managers regarded as benefits; and how the monitors themselves perceived benefits of participating as monitors. A realist approach was followed, in order to understand the connections between the context and the mechanisms in the project, and how these combined to result in the outcomes observed. Realist research emphasises the importance of context in shaping outcomes such as the achieved benefits of citizen monitoring. Data was collected using a case study method, where each individual monitor and their particular context, was regarded as a case. Semistructured interviews were conducted with 17 monitors and five Tsitsa Project staff; this was supported by field notes and the reviewing of project documents including field reports. The realist analysis looked at the context of the monitors in general and the mechanisms applied by the project in recruiting, training and managing the monitors. A second layer of mechanisms was identified as those responses from the monitors to what the project was introducing to them. Outcomes were both positive and negative, including how long monitors remained in the initiative, what benefits they derived from the process, and what potential benefits they did not achieve. This included lost opportunities to provide recognition for skills and experience gained. Recommendations are made regarding the recruitment, training and management of monitors, to optimise benefits for the monitors, the host institution and the initiative’s staff. The study is significant because of its particular yet representative characteristics and it will assist both the Tsitsa Project, which aims to expand its citizen environmental monitoring initiative, as well as wider Natural Resource Management Programmes in South Africa. It is also hoped that it will contribute to the literature on environmental monitoring as a little researched form of citizen science globally.
- Full Text:
- Authors: Mtati, Nosiseko
- Date: 2020
- Subjects: Tsitsa Project , Rural development projects -- South Africa -- Eastern Cape , Environmental monitoring -- South Africa -- Tsitsa River , Environmental monitoring -- Citizen participation -- South Africa -- Tsitsa River , Water supply, Agricultural -- South Africa -- Tsitsa River , Environmental education -- South Africa
- Language: English
- Type: text , Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10962/167562 , vital:41492
- Description: The Tsitsa Project focusses on land use management and rural livelihoods in the Tsitsa River catchment in the Eastern Cape Province of South Africa. It is funded by the Department of Environmental Affairs and the environmental monitoring initiative is implemented by Rhodes University, where I am employed as the catchment coordinator. This study explores the environmental monitoring initiative within the bigger Tsitsa Project. Community members in the catchment monitor sediment transportation in the Tsitsa River and its tributaries, which originally became of interest because it is proposed that a dam (Ntabelanga Dam) be established here. This study aims to understand citizen environmental monitoring in the Tsitsa Project; what the project managers regarded as benefits; and how the monitors themselves perceived benefits of participating as monitors. A realist approach was followed, in order to understand the connections between the context and the mechanisms in the project, and how these combined to result in the outcomes observed. Realist research emphasises the importance of context in shaping outcomes such as the achieved benefits of citizen monitoring. Data was collected using a case study method, where each individual monitor and their particular context, was regarded as a case. Semistructured interviews were conducted with 17 monitors and five Tsitsa Project staff; this was supported by field notes and the reviewing of project documents including field reports. The realist analysis looked at the context of the monitors in general and the mechanisms applied by the project in recruiting, training and managing the monitors. A second layer of mechanisms was identified as those responses from the monitors to what the project was introducing to them. Outcomes were both positive and negative, including how long monitors remained in the initiative, what benefits they derived from the process, and what potential benefits they did not achieve. This included lost opportunities to provide recognition for skills and experience gained. Recommendations are made regarding the recruitment, training and management of monitors, to optimise benefits for the monitors, the host institution and the initiative’s staff. The study is significant because of its particular yet representative characteristics and it will assist both the Tsitsa Project, which aims to expand its citizen environmental monitoring initiative, as well as wider Natural Resource Management Programmes in South Africa. It is also hoped that it will contribute to the literature on environmental monitoring as a little researched form of citizen science globally.
- Full Text:
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:
- 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:
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:
- 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:
Transformative ICT education practices in rural secondary schools for developmental needs and realities: the Eastern Cape Province, South Africa
- Authors: Simuja, Clement
- Date: 2020
- Subjects: Education, Secondary -- South Africa -- Data processing , Information technology -- Study and teaching (Secondary) --South Africa , Educational technology -- Developing countries , Rural development -- Developing countries , Computer-assisted instruction -- South Africa -- Eastern Cape , Internet in education -- South Africa , Rural schools -- South Africa -- Eastern Cape , Community and school -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/150631 , vital:38991
- Description: The perceived social development significance of Information and Communication Technology (ICT) has dramatically expanded the domains in which this cluster of ICTs is being discussed and acted upon. The action to promote community development in rural areas in South Africa has made its way into the introduction of ICT education in secondary schools. Since rural secondary schools form part of the framework for rural communities, they are being challenged to provide ICT education that makes a difference in learners’ lives. This requires engaging education practices that inspire learners to construct knowledge of ICT that does not only respond to examination purposes but rather, to the needs and development aspirations of the community. This research examines the experience of engaging learners and communities in socially informed ICT education in rural secondary schools. Specifically, it seeks to develop a critique of current practices involved in ICT education in rural secondary schools, and explores plausible alternatives to such practices that would make ICT education more transformative and structured towards the developmental concerns of communities. The main empirical focus for the research was five rural secondary schools in the Eastern Cape Province in South Africa. The research involved 53 participants that participated in a socially informed ICT training process. The training was designed to inspire participants to share their self-defined ICT education and ICT knowledge experiences. Critical Action Learning and Philosophical Inquiry provided the methodological framework, whilst the theoretical framework draws on Foucault’s philosophical ideas on power-knowledge relations. Through this theoretical analysis, the research examines the dynamic interplay of practices in ICT education with the values, ideals, and knowledge that form the core-life experiences of learners and rural communities. The research findings of this study indicate that current ICT education practices in rural secondary schools are endowed with ideologies that are affecting learners’ identity, social experiences, power, and ownership of the reflective meaning of using ICTs in community development. The contribution of this thesis lies in demonstrating ways that reframe ICT education transformatively, and more specifically its practices in the light of the way power, identity, ownership and social experience construct and offer learners a transformative view of self and the world. This could enable ICT education to fulfil the potential of contributing to social development in rural communities. The thesis culminates by presenting a theoretical framework that articulates the structural and authoritative components of ICT education practices – these relate to learners’ conscious understandings and represented thoughts, sensations and meanings embedded in the context, and actions and locations of using their knowledge of ICT.
- Full Text:
- Authors: Simuja, Clement
- Date: 2020
- Subjects: Education, Secondary -- South Africa -- Data processing , Information technology -- Study and teaching (Secondary) --South Africa , Educational technology -- Developing countries , Rural development -- Developing countries , Computer-assisted instruction -- South Africa -- Eastern Cape , Internet in education -- South Africa , Rural schools -- South Africa -- Eastern Cape , Community and school -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/150631 , vital:38991
- Description: The perceived social development significance of Information and Communication Technology (ICT) has dramatically expanded the domains in which this cluster of ICTs is being discussed and acted upon. The action to promote community development in rural areas in South Africa has made its way into the introduction of ICT education in secondary schools. Since rural secondary schools form part of the framework for rural communities, they are being challenged to provide ICT education that makes a difference in learners’ lives. This requires engaging education practices that inspire learners to construct knowledge of ICT that does not only respond to examination purposes but rather, to the needs and development aspirations of the community. This research examines the experience of engaging learners and communities in socially informed ICT education in rural secondary schools. Specifically, it seeks to develop a critique of current practices involved in ICT education in rural secondary schools, and explores plausible alternatives to such practices that would make ICT education more transformative and structured towards the developmental concerns of communities. The main empirical focus for the research was five rural secondary schools in the Eastern Cape Province in South Africa. The research involved 53 participants that participated in a socially informed ICT training process. The training was designed to inspire participants to share their self-defined ICT education and ICT knowledge experiences. Critical Action Learning and Philosophical Inquiry provided the methodological framework, whilst the theoretical framework draws on Foucault’s philosophical ideas on power-knowledge relations. Through this theoretical analysis, the research examines the dynamic interplay of practices in ICT education with the values, ideals, and knowledge that form the core-life experiences of learners and rural communities. The research findings of this study indicate that current ICT education practices in rural secondary schools are endowed with ideologies that are affecting learners’ identity, social experiences, power, and ownership of the reflective meaning of using ICTs in community development. The contribution of this thesis lies in demonstrating ways that reframe ICT education transformatively, and more specifically its practices in the light of the way power, identity, ownership and social experience construct and offer learners a transformative view of self and the world. This could enable ICT education to fulfil the potential of contributing to social development in rural communities. The thesis culminates by presenting a theoretical framework that articulates the structural and authoritative components of ICT education practices – these relate to learners’ conscious understandings and represented thoughts, sensations and meanings embedded in the context, and actions and locations of using their knowledge of ICT.
- Full Text:
Understanding a West African recreational fishery as a complex social-ecological system – a case study of the fishery for giant African threadfin Polydactylus quadrifilis (Cuvier, 1829) in the Kwanza Estuary, Angola
- Authors: Butler, Edward C
- Date: 2020
- Subjects: Cuanza River (Angola) , Fishing -- Angola , Polynemidae , Fishes -- Angola -- Ecology
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/146688 , vital:38548
- Description: Despite increasing global recognition of the importance of recreational fisheries, their management largely remains poor. This is because they exhibit unique human-nature relationships and are nested within complex social-ecological systems (SESs). Recreational fisheries in the developing world have large potential for socio-economic development, but are generally underappreciated, in terms of their value and their impact, and are poorly governed. This is particularly concerning as they are highly complex and often compete for resources with dependent artisanal and subsistence fisheries. Developing world recreational fishery SESs are not well understood and present an important research gap for improved governance. The general aim of this thesis was to explore the recreational fishery targeting Polydactylus quadrifilis on the Kwanza Estuary, Angola, and provide context for how managers should approach recreational fisheries in the developing world and in Africa. To do this, the recreational fishery SES was explored using a combination of methodologies including those characteristic of traditional fisheries science, and new methods involving biology, sociology, and economics. The thesis contains an introductory chapter, a chapter describing the background, study area and study species, five data chapters and a discussion chapter. Chapter 3 aimed to investigate the reproductive style of P. quadrifilis. Results identified the species as a protandrous hermaphrodite. Evidence to suggest this included degenerating testicular tissue and the presence of early developing ovarian tissues in transitional individuals. Early-stage oocytes were commonly found in the outer area of male regions and residual late-stage spermatids and spermatozoa were found in the luminal space of ovarian regions, suggesting a process of sex change from the outside inwards. Owing to the species’ reliance on large highly fecund females for reproduction, it is likely that P. quadrifilis will be sensitive to fisheries that target larger individuals, such as trophy recreational fisheries and line fisheries within other sectors. Chapter 4 aimed to investigate alternative methods for adequately describing the growth of P. quadrifilis individuals belonging to either one of two distinct hypothetical life-history pathways: pathway I (‘changers’) – initial maturation as a primary male followed by a sex change to female; pathway II (‘non-changers’) – initial maturation as a male fish with no subsequent sex change, using von Bertalanffy Growth Functions (VBGFs). Other specific objectives included determining the size- and age-at-maturity and size- and age-at-sex-change for P. quadrifilis. Otolith aging revealed rapid growth and early maturation (L50 = 399.2 mm FL, A50 = 1.50 years) and sex change occurred over a wide size (790–1125 mm FL) and age (3–8 years) range. There was strong evidence for partial protandry in P. quadrifilis with several extremely old male fish (up to 22 years) observed in the population. When compared to the conventional model produced for the entire population, there were significant differences in the models for the ‘non-changers’ (LRT, p < 0.01) and their parameters L∞ (full model = 130.8, ‘non-changers’ = 113.3, p < 0.01), k (0.32, 0.44, p < 0.01) and t0 (0.23, 0.43, p = 0.03) in the first approach and the models (LRT, p < 0.01) and their L∞ (‘changers’ = 113.7, p < 0.01) values in the second approach. This suggests that utilising conventional modelling techniques may be inappropriate for the stock assessment and management of P. quadrifilis and, potentially, other sequentially hermaphroditic fishery species. Chapter 5 aimed to assess the sensitivity of P. quadrifilis to recreational C&R within the foreign recreational fishery using a rapid assessment approach. To do this, a number of C&R variables including fight time, air exposure, hook placement, hooking injury, total time of the stress event, river depth and angling method were measured and related to two indicators of fish health and survival – the physiological stress indicators blood glucose and blood lactate concentration and reflex action mortality predictors (RAMPs). Air exposure was identified as a major contributor to motor impairment (Cumulative Link Model: p < 0.01) and fight time was an important contributor to motor impairment via its interaction with air exposure (Cumulative Link Model: p = 0.02). Handling practices appear to be particularly important for larger individuals as fish size was positively correlated with air exposure (Pearson’s r coefficient = 0.41, p < 0.01) and fight times (0.88, p < 0.01). The findings suggest that recreational C&R may result in mortalities directly, via C&R, and indirectly, via predation, and several recommendations were made for best practice. Chapter 6 aimed to assess the direct economic contribution of the recreational fishery for Polydactylus quadrifilis on the Kwanza Estuary. Results indicated that the recreational fishery for contributed significantly to the economy of an area that would otherwise likely receive little external input ($282 054 per four-month fishing season). However, high rates of economic leakage from the study area were identified (58.7%–92.9% of locally spent revenue) and were attributed to the sourcing of lodge supplies, services and staff outside of the local area and the repatriation of profit by foreign business owners. Capacity building within the local community is likely required to develop ‘linkages’ between the local community and the recreational fishery. Greater community involvement in the fishery is suggested to incentivise the protection of recreationally important fishery species and their associated ecosystems. Chapter 7 aimed to investigate the resource user groups involved within the SES. Results illustrated that artisanal and domestic recreational anglers are well-established and are characterised by long histories of participation. The artisanal fishery was highly valued as a source of livelihoods for the local community. Artisanal fishers were eager for involvement in the recreational sector, through the chartering of their vessels, due to the attractiveness of extra earnings. Both recreational and artisanal fishers reported recent decreases in P. quadrifilis catch and anticipated further declines. Domestic recreational anglers appeared to be highly consumptive in their use of the fishery and C&R angling was uncommon. User conflict may be problematic for future management as recreational anglers perceived the artisanal gill-net fishery to be a threat towards P. quadrifilis stocks. In conclusion, the open-access nature of the fishery was identified as the most pertinent threat to its sustainability and likely needs to be addressed. Potential solutions involve offering users the opportunity to purchase access rights (e.g. day permits), thus initiating the concept that users must pay for their use of public resources. Management should aim to protect large female fish due to their increased reproductive value and worth as trophy fish. Thus, C&R angling is likely to be an important interaction between users and the resource. However, angler behaviour will need to be manipulated to promote C&R and minimise C&R-related mortalities. Solutions include angler educational drives and interventions and the implementation of competitive C&R-only angling. Foreign recreational fisheries, although touted as potential ecotourism ventures, will only succeed in improving the lives of local people if they fully integrate the community into the operation of the fishery.
- Full Text:
- Authors: Butler, Edward C
- Date: 2020
- Subjects: Cuanza River (Angola) , Fishing -- Angola , Polynemidae , Fishes -- Angola -- Ecology
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/146688 , vital:38548
- Description: Despite increasing global recognition of the importance of recreational fisheries, their management largely remains poor. This is because they exhibit unique human-nature relationships and are nested within complex social-ecological systems (SESs). Recreational fisheries in the developing world have large potential for socio-economic development, but are generally underappreciated, in terms of their value and their impact, and are poorly governed. This is particularly concerning as they are highly complex and often compete for resources with dependent artisanal and subsistence fisheries. Developing world recreational fishery SESs are not well understood and present an important research gap for improved governance. The general aim of this thesis was to explore the recreational fishery targeting Polydactylus quadrifilis on the Kwanza Estuary, Angola, and provide context for how managers should approach recreational fisheries in the developing world and in Africa. To do this, the recreational fishery SES was explored using a combination of methodologies including those characteristic of traditional fisheries science, and new methods involving biology, sociology, and economics. The thesis contains an introductory chapter, a chapter describing the background, study area and study species, five data chapters and a discussion chapter. Chapter 3 aimed to investigate the reproductive style of P. quadrifilis. Results identified the species as a protandrous hermaphrodite. Evidence to suggest this included degenerating testicular tissue and the presence of early developing ovarian tissues in transitional individuals. Early-stage oocytes were commonly found in the outer area of male regions and residual late-stage spermatids and spermatozoa were found in the luminal space of ovarian regions, suggesting a process of sex change from the outside inwards. Owing to the species’ reliance on large highly fecund females for reproduction, it is likely that P. quadrifilis will be sensitive to fisheries that target larger individuals, such as trophy recreational fisheries and line fisheries within other sectors. Chapter 4 aimed to investigate alternative methods for adequately describing the growth of P. quadrifilis individuals belonging to either one of two distinct hypothetical life-history pathways: pathway I (‘changers’) – initial maturation as a primary male followed by a sex change to female; pathway II (‘non-changers’) – initial maturation as a male fish with no subsequent sex change, using von Bertalanffy Growth Functions (VBGFs). Other specific objectives included determining the size- and age-at-maturity and size- and age-at-sex-change for P. quadrifilis. Otolith aging revealed rapid growth and early maturation (L50 = 399.2 mm FL, A50 = 1.50 years) and sex change occurred over a wide size (790–1125 mm FL) and age (3–8 years) range. There was strong evidence for partial protandry in P. quadrifilis with several extremely old male fish (up to 22 years) observed in the population. When compared to the conventional model produced for the entire population, there were significant differences in the models for the ‘non-changers’ (LRT, p < 0.01) and their parameters L∞ (full model = 130.8, ‘non-changers’ = 113.3, p < 0.01), k (0.32, 0.44, p < 0.01) and t0 (0.23, 0.43, p = 0.03) in the first approach and the models (LRT, p < 0.01) and their L∞ (‘changers’ = 113.7, p < 0.01) values in the second approach. This suggests that utilising conventional modelling techniques may be inappropriate for the stock assessment and management of P. quadrifilis and, potentially, other sequentially hermaphroditic fishery species. Chapter 5 aimed to assess the sensitivity of P. quadrifilis to recreational C&R within the foreign recreational fishery using a rapid assessment approach. To do this, a number of C&R variables including fight time, air exposure, hook placement, hooking injury, total time of the stress event, river depth and angling method were measured and related to two indicators of fish health and survival – the physiological stress indicators blood glucose and blood lactate concentration and reflex action mortality predictors (RAMPs). Air exposure was identified as a major contributor to motor impairment (Cumulative Link Model: p < 0.01) and fight time was an important contributor to motor impairment via its interaction with air exposure (Cumulative Link Model: p = 0.02). Handling practices appear to be particularly important for larger individuals as fish size was positively correlated with air exposure (Pearson’s r coefficient = 0.41, p < 0.01) and fight times (0.88, p < 0.01). The findings suggest that recreational C&R may result in mortalities directly, via C&R, and indirectly, via predation, and several recommendations were made for best practice. Chapter 6 aimed to assess the direct economic contribution of the recreational fishery for Polydactylus quadrifilis on the Kwanza Estuary. Results indicated that the recreational fishery for contributed significantly to the economy of an area that would otherwise likely receive little external input ($282 054 per four-month fishing season). However, high rates of economic leakage from the study area were identified (58.7%–92.9% of locally spent revenue) and were attributed to the sourcing of lodge supplies, services and staff outside of the local area and the repatriation of profit by foreign business owners. Capacity building within the local community is likely required to develop ‘linkages’ between the local community and the recreational fishery. Greater community involvement in the fishery is suggested to incentivise the protection of recreationally important fishery species and their associated ecosystems. Chapter 7 aimed to investigate the resource user groups involved within the SES. Results illustrated that artisanal and domestic recreational anglers are well-established and are characterised by long histories of participation. The artisanal fishery was highly valued as a source of livelihoods for the local community. Artisanal fishers were eager for involvement in the recreational sector, through the chartering of their vessels, due to the attractiveness of extra earnings. Both recreational and artisanal fishers reported recent decreases in P. quadrifilis catch and anticipated further declines. Domestic recreational anglers appeared to be highly consumptive in their use of the fishery and C&R angling was uncommon. User conflict may be problematic for future management as recreational anglers perceived the artisanal gill-net fishery to be a threat towards P. quadrifilis stocks. In conclusion, the open-access nature of the fishery was identified as the most pertinent threat to its sustainability and likely needs to be addressed. Potential solutions involve offering users the opportunity to purchase access rights (e.g. day permits), thus initiating the concept that users must pay for their use of public resources. Management should aim to protect large female fish due to their increased reproductive value and worth as trophy fish. Thus, C&R angling is likely to be an important interaction between users and the resource. However, angler behaviour will need to be manipulated to promote C&R and minimise C&R-related mortalities. Solutions include angler educational drives and interventions and the implementation of competitive C&R-only angling. Foreign recreational fisheries, although touted as potential ecotourism ventures, will only succeed in improving the lives of local people if they fully integrate the community into the operation of the fishery.
- Full Text:
Understanding climate change and rural livelihoods in Zimbabwe: adaptation by communal farmers in Ngundu, Chivi District
- Authors: Nciizah, Elinah
- Date: 2020
- Subjects: Agriculture -- Zimbabwe , Agriculture -- Climatic factors -- Chivi District (Zimbabwe) , Chivi District (Zimbabwe) -- Rural conditions
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/118765 , vital:34666
- Description: Climate change and variability is a global phenomenon which has deeply localised patterns, dynamics and effects. Amongst those people who are particularly vulnerable to climate change effects are small-scale farmers who are dependent in large part on rain-fed agriculture in pursuing their livelihoods. This is true of small-scale farmers in contemporary Zimbabwe and, more specifically, farmers in communal areas. At the same time, at international and national levels, there are attempts currently to minimise the effects of, and to adapt to, climate change. However, adaptation measures also exist at local levels amongst small-scale farmers, such as communal farmers in Zimbabwe. In this context, as its main objective, this thesis examines climate change and small-scale farmer livelihood adaptation to climate change with specific reference to communal farmers in Chivi District in Zimbabwe and, in particular, in Ward 25 which is popularly known as Ngundu. In pursuing this main objective, a number of subsidiary objectives are addressed, including a focus on the established livelihoods of Ngundu farmers, the perceptions and concerns of Ngundu farmers about climate change, the coping and adaptation measures of Ngundu farmers, and the enablements and constraints which affect attempts by Ngundu farmers to adopt such measures. The fieldwork for the thesis involved a diverse array of research methods, such as a questionnaire survey, life-history interviews, key informant interviews, focus group discussions and transect walks. In terms of theoretical framing, the thesis makes use of both middle-level theory (the Sustainable Livelihoods Framework) and macro-theory in the form of the sociological work of Margaret Archer. Combined, these two theories allow for a focus on both structure and agency when seeking to understand livelihood adaptations to climate change by communal farmers in Ngundu. The thesis concludes that there are massive constraints inhibiting adaptation measures by Ngundu farmers, but that this should not distract from the deep, often historically-embedded, concerns of Ngundu farmers about climate change and the multiple ways in which they express agency in and through adaptation and coping activities. It also highlights the need for more specifically sociological investigations of climate change and small-scale farmer adaptation, as well as the need for localised studies which are able to identify and analyse the specificities of adaptation.
- Full Text:
- Authors: Nciizah, Elinah
- Date: 2020
- Subjects: Agriculture -- Zimbabwe , Agriculture -- Climatic factors -- Chivi District (Zimbabwe) , Chivi District (Zimbabwe) -- Rural conditions
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/118765 , vital:34666
- Description: Climate change and variability is a global phenomenon which has deeply localised patterns, dynamics and effects. Amongst those people who are particularly vulnerable to climate change effects are small-scale farmers who are dependent in large part on rain-fed agriculture in pursuing their livelihoods. This is true of small-scale farmers in contemporary Zimbabwe and, more specifically, farmers in communal areas. At the same time, at international and national levels, there are attempts currently to minimise the effects of, and to adapt to, climate change. However, adaptation measures also exist at local levels amongst small-scale farmers, such as communal farmers in Zimbabwe. In this context, as its main objective, this thesis examines climate change and small-scale farmer livelihood adaptation to climate change with specific reference to communal farmers in Chivi District in Zimbabwe and, in particular, in Ward 25 which is popularly known as Ngundu. In pursuing this main objective, a number of subsidiary objectives are addressed, including a focus on the established livelihoods of Ngundu farmers, the perceptions and concerns of Ngundu farmers about climate change, the coping and adaptation measures of Ngundu farmers, and the enablements and constraints which affect attempts by Ngundu farmers to adopt such measures. The fieldwork for the thesis involved a diverse array of research methods, such as a questionnaire survey, life-history interviews, key informant interviews, focus group discussions and transect walks. In terms of theoretical framing, the thesis makes use of both middle-level theory (the Sustainable Livelihoods Framework) and macro-theory in the form of the sociological work of Margaret Archer. Combined, these two theories allow for a focus on both structure and agency when seeking to understand livelihood adaptations to climate change by communal farmers in Ngundu. The thesis concludes that there are massive constraints inhibiting adaptation measures by Ngundu farmers, but that this should not distract from the deep, often historically-embedded, concerns of Ngundu farmers about climate change and the multiple ways in which they express agency in and through adaptation and coping activities. It also highlights the need for more specifically sociological investigations of climate change and small-scale farmer adaptation, as well as the need for localised studies which are able to identify and analyse the specificities of adaptation.
- Full Text:
Understanding of biological teleology from a naturalistic perspective
- Authors: Abrahams, Sanaa
- Date: 2020
- Subjects: Teleology , Biology -- Philosophy , Evolution (Biology) -- Philosophy
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/140534 , vital:37896
- Description: To the extent that teleological thinking is metaphysically suspect, many theorists attempt to shift the stigma of functional explanations by reducing function ascriptions, and aim thus to de-legitimise an appeal to teleological causal relations in an analysis of function. The point is to dispel the mystery which envelops the application of function concepts by reformulating biological functional explanations so as to dispense with teleology. My project is to interrogate the success with which teleological explanations have thus been eliminated in the biological sciences, and, over the course of this thesis, I conclude that a kind of teleological causation nevertheless remains the most adequate explanatory ground of natural products. My proposal is that functional explanations are causal explanations for the presence and maintenance of self-reproducing systems. I contend that, insofar as the attribution of function presupposes the valuation of a function-bearing system as a causal necessity for its constituent parts, functional explanation references distinct and irreducible holistic properties. Using Kantian metaphysics to frame the discussion, this thesis aims first to explore critically the subject of functional characterisations of biological phenomena, and second, the metaphysical basis of modern science. Its chief contributions to the philosophical function debate reside in proposing novel arguments in justification of what I consider is an improved formulation of an attempted definition of biological function, in which teleological causal powers are explicitly recognised and accommodated in functional explanation. Moreover, this thesis attempts a naturalistic reconstruction of the metaphysical entailments of the real causality of a whole
- Full Text:
- Authors: Abrahams, Sanaa
- Date: 2020
- Subjects: Teleology , Biology -- Philosophy , Evolution (Biology) -- Philosophy
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/140534 , vital:37896
- Description: To the extent that teleological thinking is metaphysically suspect, many theorists attempt to shift the stigma of functional explanations by reducing function ascriptions, and aim thus to de-legitimise an appeal to teleological causal relations in an analysis of function. The point is to dispel the mystery which envelops the application of function concepts by reformulating biological functional explanations so as to dispense with teleology. My project is to interrogate the success with which teleological explanations have thus been eliminated in the biological sciences, and, over the course of this thesis, I conclude that a kind of teleological causation nevertheless remains the most adequate explanatory ground of natural products. My proposal is that functional explanations are causal explanations for the presence and maintenance of self-reproducing systems. I contend that, insofar as the attribution of function presupposes the valuation of a function-bearing system as a causal necessity for its constituent parts, functional explanation references distinct and irreducible holistic properties. Using Kantian metaphysics to frame the discussion, this thesis aims first to explore critically the subject of functional characterisations of biological phenomena, and second, the metaphysical basis of modern science. Its chief contributions to the philosophical function debate reside in proposing novel arguments in justification of what I consider is an improved formulation of an attempted definition of biological function, in which teleological causal powers are explicitly recognised and accommodated in functional explanation. Moreover, this thesis attempts a naturalistic reconstruction of the metaphysical entailments of the real causality of a whole
- Full Text:
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:
- 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:
Understanding popular resistance to xenophobia in South Africa: ‘people think’ and the possibility of alternative politics
- Authors: Parker, Jemima
- Date: 2020
- Subjects: Xenophobia -- South Africa , Nationalism -- South Africa , Lazarus, Sylvain -- Political and social views , Political culture -- South Africa , Social change -- South Africa -- Political aspects , Discourse analysis -- South Africa -- Political aspects , South Africa -- Politics and government -- 1994- , Political science -- Philosophy , Political sociology -- South Africa
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/115006 , vital:34069
- Description: This thesis is concerned with the crisis of xenophobia in South Africa. It argues, firstly, that xenophobia itself is not primarily a reaction to poverty, inequality, or any other set of social conditions. Rather, xenophobia must be considered to be a collective political discourse which has arisen in post-apartheid South Africa from an exclusionary conception of state nationalism. Where this work may be distinguished from the majority of research on xenophobia in South Africa is in the fact that its particular focus is on instances where ‘ordinary’ South Africans have challenged and resisted xenophobic violence in their communities through collective political mobilisation. I suggest that these sites of resistance deserve careful consideration in their own right. I argue that they may demonstrate a subjective break with the oppressive politics of state nationalism through the affirmation of alternative political conceptions. Drawing on the political theory of Sylvain Lazarus, and his principal thesis that people are capable of thinking politics in ways which can subjectively think beyond the social and the extant (underscored by his political and methodological axiom, people think), this thesis argues that these sites of resistance show that people – and especially those who are considered to be marginalised from the domain of legitimate politics – can and do think politically, and it is in the thought of people that new and potentially emancipatory visions of politics may emerge.
- Full Text:
- Authors: Parker, Jemima
- Date: 2020
- Subjects: Xenophobia -- South Africa , Nationalism -- South Africa , Lazarus, Sylvain -- Political and social views , Political culture -- South Africa , Social change -- South Africa -- Political aspects , Discourse analysis -- South Africa -- Political aspects , South Africa -- Politics and government -- 1994- , Political science -- Philosophy , Political sociology -- South Africa
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/115006 , vital:34069
- Description: This thesis is concerned with the crisis of xenophobia in South Africa. It argues, firstly, that xenophobia itself is not primarily a reaction to poverty, inequality, or any other set of social conditions. Rather, xenophobia must be considered to be a collective political discourse which has arisen in post-apartheid South Africa from an exclusionary conception of state nationalism. Where this work may be distinguished from the majority of research on xenophobia in South Africa is in the fact that its particular focus is on instances where ‘ordinary’ South Africans have challenged and resisted xenophobic violence in their communities through collective political mobilisation. I suggest that these sites of resistance deserve careful consideration in their own right. I argue that they may demonstrate a subjective break with the oppressive politics of state nationalism through the affirmation of alternative political conceptions. Drawing on the political theory of Sylvain Lazarus, and his principal thesis that people are capable of thinking politics in ways which can subjectively think beyond the social and the extant (underscored by his political and methodological axiom, people think), this thesis argues that these sites of resistance show that people – and especially those who are considered to be marginalised from the domain of legitimate politics – can and do think politically, and it is in the thought of people that new and potentially emancipatory visions of politics may emerge.
- Full Text:
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:
- 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:
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:
- 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: