Assessing linkages between local ecological knowledge, HIV/AIDS and the commercialisation of natural resources across Southern Africa
- Authors: Weyer, Dylan James
- Date: 2012
- Subjects: AIDS (Disease) -- Africa, Southern , HIV infections -- Africa, Southern , Natural resources -- Management -- Africa, Southern , Traditional ecological knowledge -- Africa, Southern , Households -- Economic aspects -- Africa, Southern , Poverty -- Environmental aspects -- Africa, Southern , Ecology -- Economic aspects -- Africa, Southern
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4769 , http://hdl.handle.net/10962/d1007180 , AIDS (Disease) -- Africa, Southern , HIV infections -- Africa, Southern , Natural resources -- Management -- Africa, Southern , Traditional ecological knowledge -- Africa, Southern , Households -- Economic aspects -- Africa, Southern , Poverty -- Environmental aspects -- Africa, Southern , Ecology -- Economic aspects -- Africa, Southern
- Description: That natural resources (NRs) are important to those experiencing adversity, and, especially, vulnerability associated with HIV/AIDS, is well documented, particularly with respect to food and energy security. What is unclear is where HIV/AIDS ranks in terms of its significance in comparison to other household shocks, the role local ecological knowledge may (LEK) play in households' response to shock, a propos the types of coping strategies that are employed. Consequently, this research aims to bridge the knowledge gap between HIV/AIDS and the degree to which it is contributing to the expansion of NR commercialisation and to explore the unknowns surrounding the influence of LEK on people's choice of coping strategy. A two phase study was designed to provide quantitative rigour with qualitative depth. Phase one was an extensive, rapid survey of NR traders within urban and rural settings in five southern Africa countries. The principle objective was to profile the trade, the livelihoods of those involved and their reasons for entering the trade, to ultimately establish to what degree HIV/AIDS may have been a catalyst for this. Almost one third of the sample entered the trade in response to illness and/or death in their households, with 80% of deaths being of breadwinners. The findings illustrated considerable dependence on the sale of NRs; for almost 60% of the sample it was their household's only source of income. There was evidently increased blurring of the lines between rural and urban NR use with a greater diversity of products being traded in urban areas. Phase two involved in-depth interviews and work with a smaller sample at two sites selected based on the findings from the first phase. It incorporated three groups of households; non-trading, inexperienced trading and experienced trading households. Key areas of focus were household shocks, coping strategies employed in response to these and the role LEK may be playing in the choice of coping strategies. Within a two year period, 95% of households registered at least one shock, of which 80% recorded AIDS-related proxy shocks. Non-trading households were significantly worse-off in this regard, while in the case of non-AIDS proxy shocks, there was no such difference between groups. The most frequently employed coping strategy was the consumption and sale of NRs and was of particular importance when households were faced with AIDS proxy shocks. Trading households emerged as having superior levels of LEK in comparison to non-trading households, even for non-traded NRs, suggesting that prior LEK of NRs opened up opportunities to trade in NR as a coping strategy. Further inspection of the latter group however revealed that the portion of non-trading households who traded on a very ad hoc basis actually had comparable levels of LEK to the trading households. Despite the ad hoc trading households' vulnerable state and their disproportionately high level of AIDS proxy measures, they had at their disposal, sufficient LEK to unlock certain key coping strategies, namely the NR trade. In this sense there are apparent linkages between LEK, HIV/AIDS and the expansion of the commercialisation of NRs.
- Full Text:
- Date Issued: 2012
- Authors: Weyer, Dylan James
- Date: 2012
- Subjects: AIDS (Disease) -- Africa, Southern , HIV infections -- Africa, Southern , Natural resources -- Management -- Africa, Southern , Traditional ecological knowledge -- Africa, Southern , Households -- Economic aspects -- Africa, Southern , Poverty -- Environmental aspects -- Africa, Southern , Ecology -- Economic aspects -- Africa, Southern
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4769 , http://hdl.handle.net/10962/d1007180 , AIDS (Disease) -- Africa, Southern , HIV infections -- Africa, Southern , Natural resources -- Management -- Africa, Southern , Traditional ecological knowledge -- Africa, Southern , Households -- Economic aspects -- Africa, Southern , Poverty -- Environmental aspects -- Africa, Southern , Ecology -- Economic aspects -- Africa, Southern
- Description: That natural resources (NRs) are important to those experiencing adversity, and, especially, vulnerability associated with HIV/AIDS, is well documented, particularly with respect to food and energy security. What is unclear is where HIV/AIDS ranks in terms of its significance in comparison to other household shocks, the role local ecological knowledge may (LEK) play in households' response to shock, a propos the types of coping strategies that are employed. Consequently, this research aims to bridge the knowledge gap between HIV/AIDS and the degree to which it is contributing to the expansion of NR commercialisation and to explore the unknowns surrounding the influence of LEK on people's choice of coping strategy. A two phase study was designed to provide quantitative rigour with qualitative depth. Phase one was an extensive, rapid survey of NR traders within urban and rural settings in five southern Africa countries. The principle objective was to profile the trade, the livelihoods of those involved and their reasons for entering the trade, to ultimately establish to what degree HIV/AIDS may have been a catalyst for this. Almost one third of the sample entered the trade in response to illness and/or death in their households, with 80% of deaths being of breadwinners. The findings illustrated considerable dependence on the sale of NRs; for almost 60% of the sample it was their household's only source of income. There was evidently increased blurring of the lines between rural and urban NR use with a greater diversity of products being traded in urban areas. Phase two involved in-depth interviews and work with a smaller sample at two sites selected based on the findings from the first phase. It incorporated three groups of households; non-trading, inexperienced trading and experienced trading households. Key areas of focus were household shocks, coping strategies employed in response to these and the role LEK may be playing in the choice of coping strategies. Within a two year period, 95% of households registered at least one shock, of which 80% recorded AIDS-related proxy shocks. Non-trading households were significantly worse-off in this regard, while in the case of non-AIDS proxy shocks, there was no such difference between groups. The most frequently employed coping strategy was the consumption and sale of NRs and was of particular importance when households were faced with AIDS proxy shocks. Trading households emerged as having superior levels of LEK in comparison to non-trading households, even for non-traded NRs, suggesting that prior LEK of NRs opened up opportunities to trade in NR as a coping strategy. Further inspection of the latter group however revealed that the portion of non-trading households who traded on a very ad hoc basis actually had comparable levels of LEK to the trading households. Despite the ad hoc trading households' vulnerable state and their disproportionately high level of AIDS proxy measures, they had at their disposal, sufficient LEK to unlock certain key coping strategies, namely the NR trade. In this sense there are apparent linkages between LEK, HIV/AIDS and the expansion of the commercialisation of NRs.
- Full Text:
- Date Issued: 2012
Sketch-based digital storyboards and floor plans for authoring computer-generated film pre-visuals
- Authors: Matthews, Timothy
- Date: 2012
- Subjects: Computer graphics , Computer vision
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10463 , http://hdl.handle.net/10948/d1008430 , Computer graphics , Computer vision
- Description: Pre-visualisation is an important tool for planning films during the pre-production phase of filmmaking. Existing pre-visualisation authoring tools do not effectively support the user in authoring pre-visualisations without impairing software usability. These tools require the user to either have programming skills, be experienced in modelling and animation, or use drag-and-drop style interfaces. These interaction methods do not intuitively fit with pre-production activities such as floor planning and storyboarding, and existing tools that apply a storyboarding metaphor do not automatically interpret user sketches. The goal of this research was to investigate how sketch-based user interfaces and methods from computer vision could be used for supporting pre-visualisation authoring using a storyboarding approach. The requirements for such a sketch-based storyboarding tool were determined from literature and an interview with Triggerfish Animation Studios. A framework was developed to support sketch-based pre-visualisation authoring using a storyboarding approach. Algorithms for describing user sketches, recognising objects and performing pose estimation were designed to automatically interpret user sketches. A proof of concept prototype implementation of this framework was evaluated in order to assess its usability benefit. It was found that the participants could author pre-visualisations effectively, efficiently and easily. The results of the usability evaluation also showed that the participants were satisfied with the overall design and usability of the prototype tool. The positive and negative findings of the evaluation were interpreted and combined with existing heuristics in order to create a set of guidelines for designing similar sketch-based pre-visualisation authoring tools that apply the storyboarding approach. The successful implementation of the proof of concept prototype tool provides practical evidence of the feasibility of sketch-based pre-visualisation authoring. The positive results from the usability evaluation established that sketch-based interfacing techniques can be used effectively with a storyboarding approach for authoring pre-visualisations without impairing software usability.
- Full Text:
- Date Issued: 2012
- Authors: Matthews, Timothy
- Date: 2012
- Subjects: Computer graphics , Computer vision
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10463 , http://hdl.handle.net/10948/d1008430 , Computer graphics , Computer vision
- Description: Pre-visualisation is an important tool for planning films during the pre-production phase of filmmaking. Existing pre-visualisation authoring tools do not effectively support the user in authoring pre-visualisations without impairing software usability. These tools require the user to either have programming skills, be experienced in modelling and animation, or use drag-and-drop style interfaces. These interaction methods do not intuitively fit with pre-production activities such as floor planning and storyboarding, and existing tools that apply a storyboarding metaphor do not automatically interpret user sketches. The goal of this research was to investigate how sketch-based user interfaces and methods from computer vision could be used for supporting pre-visualisation authoring using a storyboarding approach. The requirements for such a sketch-based storyboarding tool were determined from literature and an interview with Triggerfish Animation Studios. A framework was developed to support sketch-based pre-visualisation authoring using a storyboarding approach. Algorithms for describing user sketches, recognising objects and performing pose estimation were designed to automatically interpret user sketches. A proof of concept prototype implementation of this framework was evaluated in order to assess its usability benefit. It was found that the participants could author pre-visualisations effectively, efficiently and easily. The results of the usability evaluation also showed that the participants were satisfied with the overall design and usability of the prototype tool. The positive and negative findings of the evaluation were interpreted and combined with existing heuristics in order to create a set of guidelines for designing similar sketch-based pre-visualisation authoring tools that apply the storyboarding approach. The successful implementation of the proof of concept prototype tool provides practical evidence of the feasibility of sketch-based pre-visualisation authoring. The positive results from the usability evaluation established that sketch-based interfacing techniques can be used effectively with a storyboarding approach for authoring pre-visualisations without impairing software usability.
- Full Text:
- Date Issued: 2012
Investigating tools and techniques for improving software performance on multiprocessor computer systems
- Authors: Tristram, Waide Barrington
- Date: 2012
- Subjects: Multiprocessors , Multiprogramming (Electronic computers) , Parallel programming (Computer science) , Linux , Abstract data types (Computer science) , Threads (Computer programs) , Computer programming
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4655 , http://hdl.handle.net/10962/d1006651 , Multiprocessors , Multiprogramming (Electronic computers) , Parallel programming (Computer science) , Linux , Abstract data types (Computer science) , Threads (Computer programs) , Computer programming
- Description: The availability of modern commodity multicore processors and multiprocessor computer systems has resulted in the widespread adoption of parallel computers in a variety of environments, ranging from the home to workstation and server environments in particular. Unfortunately, parallel programming is harder and requires more expertise than the traditional sequential programming model. The variety of tools and parallel programming models available to the programmer further complicates the issue. The primary goal of this research was to identify and describe a selection of parallel programming tools and techniques to aid novice parallel programmers in the process of developing efficient parallel C/C++ programs for the Linux platform. This was achieved by highlighting and describing the key concepts and hardware factors that affect parallel programming, providing a brief survey of commonly available software development tools and parallel programming models and libraries, and presenting structured approaches to software performance tuning and parallel programming. Finally, the performance of several parallel programming models and libraries was investigated, along with the programming effort required to implement solutions using the respective models. A quantitative research methodology was applied to the investigation of the performance and programming effort associated with the selected parallel programming models and libraries, which included automatic parallelisation by the compiler, Boost Threads, Cilk Plus, OpenMP, POSIX threads (Pthreads), and Threading Building Blocks (TBB). Additionally, the performance of the GNU C/C++ and Intel C/C++ compilers was examined. The results revealed that the choice of parallel programming model or library is dependent on the type of problem being solved and that there is no overall best choice for all classes of problem. However, the results also indicate that parallel programming models with higher levels of abstraction require less programming effort and provide similar performance compared to explicit threading models. The principle conclusion was that the problem analysis and parallel design are an important factor in the selection of the parallel programming model and tools, but that models with higher levels of abstractions, such as OpenMP and Threading Building Blocks, are favoured.
- Full Text:
- Date Issued: 2012
- Authors: Tristram, Waide Barrington
- Date: 2012
- Subjects: Multiprocessors , Multiprogramming (Electronic computers) , Parallel programming (Computer science) , Linux , Abstract data types (Computer science) , Threads (Computer programs) , Computer programming
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4655 , http://hdl.handle.net/10962/d1006651 , Multiprocessors , Multiprogramming (Electronic computers) , Parallel programming (Computer science) , Linux , Abstract data types (Computer science) , Threads (Computer programs) , Computer programming
- Description: The availability of modern commodity multicore processors and multiprocessor computer systems has resulted in the widespread adoption of parallel computers in a variety of environments, ranging from the home to workstation and server environments in particular. Unfortunately, parallel programming is harder and requires more expertise than the traditional sequential programming model. The variety of tools and parallel programming models available to the programmer further complicates the issue. The primary goal of this research was to identify and describe a selection of parallel programming tools and techniques to aid novice parallel programmers in the process of developing efficient parallel C/C++ programs for the Linux platform. This was achieved by highlighting and describing the key concepts and hardware factors that affect parallel programming, providing a brief survey of commonly available software development tools and parallel programming models and libraries, and presenting structured approaches to software performance tuning and parallel programming. Finally, the performance of several parallel programming models and libraries was investigated, along with the programming effort required to implement solutions using the respective models. A quantitative research methodology was applied to the investigation of the performance and programming effort associated with the selected parallel programming models and libraries, which included automatic parallelisation by the compiler, Boost Threads, Cilk Plus, OpenMP, POSIX threads (Pthreads), and Threading Building Blocks (TBB). Additionally, the performance of the GNU C/C++ and Intel C/C++ compilers was examined. The results revealed that the choice of parallel programming model or library is dependent on the type of problem being solved and that there is no overall best choice for all classes of problem. However, the results also indicate that parallel programming models with higher levels of abstraction require less programming effort and provide similar performance compared to explicit threading models. The principle conclusion was that the problem analysis and parallel design are an important factor in the selection of the parallel programming model and tools, but that models with higher levels of abstractions, such as OpenMP and Threading Building Blocks, are favoured.
- Full Text:
- Date Issued: 2012
"Is more, less?" : insect-insect interactions in a biological control context using water hyacinth as a model
- Weyl, Philip Sebastian Richard
- Authors: Weyl, Philip Sebastian Richard
- Date: 2012
- Subjects: Water hyacinth -- South Africa -- Eastern Cape , Water hyacinth -- Biological control -- South Africa -- Eastern Cape , Insects as biological pest control agents , Miridae -- South Africa -- Eastern Cape , Beetles -- South Africa -- Eastern Cape , Competition (Biology)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5724 , http://hdl.handle.net/10962/d1005410 , Water hyacinth -- South Africa -- Eastern Cape , Water hyacinth -- Biological control -- South Africa -- Eastern Cape , Insects as biological pest control agents , Miridae -- South Africa -- Eastern Cape , Beetles -- South Africa -- Eastern Cape , Competition (Biology)
- Description: Interactions between insects have been shown to be important regulators of population abundances and dynamics as well as drivers of spatial segregation and distribution. These are important aspects of the ecology of insects used in biological control and may have implications for the overall success of a particular programme. In the history of biological control there has been a tendency to release a suite of agents against a weed, which in some cases has increased the level of success, while in others little change has been observed. In most of these cases the implications of increasing the level of complexity of the system is not taken into account and there is little research on the effect of releasing another agent into the system. A brief meta-analysis was done on all the biological control programmes initiated in South Africa. Emphasis was placed on multi-species releases and the effects that overlapping niches were having on the number of agents responsible for the success of a programme. Where overlapping niches were present among agents released the number of agents responsible for success was lower than the number established. Water hyacinth, Eichhornia crassipes (Martius) Solms-Laubach in South Africa has more arthropod agents released against it than anywhere else in the world, yet control has been variable. If the biology and host utilisation of all the agents against water hyacinth is considered, a definite overlap of niches is apparent in at least one life stage of all the agents. Therefore the probability of these insects interacting is high, especially if they are established at the same site in the field. Three of the insects released in South Africa have been selected to investigate possible interactions. They are Neochetina eichhorniae Warner, Neochetina bruchi Hustache and Eccritotarsus catarinensis (Carvalho). Y-tube olfactometer bioassays were used to measure responses of these insects to water hyacinth with prior feeding damage by either conspecifics or heterospecifics. This was done to determine whether olfactory cues played a role in host acceptability and avoidance of conspecifics or heterospecifics. The insects were given a choice between damaged and undamaged plants in various combinations. There was a significant preference for the undamaged plants when given a choice between undamaged and damaged plants. However when the insects were given a choice between two damaged plants there was no discrimination between heterospecific or conspecific damaged plants. This may indicate that there is little or no ecological cost for the insect to share a plant with other insects utilising a similar resource. Insect – insect interactions were investigated in a common garden plot experiment to measure the impact that pairwise combinations of the insect may have on their performance. There was a significant interaction between the mirid E. catarinensis and the weevil N. eichhorniae, with the weevil not performing as well when in combination with the mirid than when alone. Interestingly there was a negative interaction between the two weevil species when in combination, however it was impossible to determine which species was being affected if not both. None of the insects performed significantly better when in combination with another insect. A field study on Wriggleswade Dam in the Eastern Cape, South Africa was initiated to determine whether the relationship between the mirid E. catarinensis and the weevil N. eichhorniae could be determined in the field. The performance of the insects at the different sites in the field suggests that there was an interaction between the agents. This interaction did not limit the establishment of either insect at a site, but it did result in one insect dominating at a site over another. Interactions between the three species of insect tested in this thesis suggest that there are both negative and neutral relationships between them. A basic comparison between the insect performances from 15 sites around the country was done to determine if the spatial segregation observed in the field could be extrapolated to the natural South African situation. The interaction observed between N. eichhorniae and E. catarinensis does seem to extrapolate to the general South African situation where there is definite spatial segregation on a landscape level. The co–occurrence of the two Neochetina weevils at these sites suggests that the negative relationship observed between them in the common garden experiment does not extrapolate to the field. The results from this thesis suggest that the interactions between the agents tested would not limit establishment or have significant ramifications on performance. However, there may be spatial and temporal segregation of these species in the introduced range.
- Full Text:
- Date Issued: 2012
- Authors: Weyl, Philip Sebastian Richard
- Date: 2012
- Subjects: Water hyacinth -- South Africa -- Eastern Cape , Water hyacinth -- Biological control -- South Africa -- Eastern Cape , Insects as biological pest control agents , Miridae -- South Africa -- Eastern Cape , Beetles -- South Africa -- Eastern Cape , Competition (Biology)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5724 , http://hdl.handle.net/10962/d1005410 , Water hyacinth -- South Africa -- Eastern Cape , Water hyacinth -- Biological control -- South Africa -- Eastern Cape , Insects as biological pest control agents , Miridae -- South Africa -- Eastern Cape , Beetles -- South Africa -- Eastern Cape , Competition (Biology)
- Description: Interactions between insects have been shown to be important regulators of population abundances and dynamics as well as drivers of spatial segregation and distribution. These are important aspects of the ecology of insects used in biological control and may have implications for the overall success of a particular programme. In the history of biological control there has been a tendency to release a suite of agents against a weed, which in some cases has increased the level of success, while in others little change has been observed. In most of these cases the implications of increasing the level of complexity of the system is not taken into account and there is little research on the effect of releasing another agent into the system. A brief meta-analysis was done on all the biological control programmes initiated in South Africa. Emphasis was placed on multi-species releases and the effects that overlapping niches were having on the number of agents responsible for the success of a programme. Where overlapping niches were present among agents released the number of agents responsible for success was lower than the number established. Water hyacinth, Eichhornia crassipes (Martius) Solms-Laubach in South Africa has more arthropod agents released against it than anywhere else in the world, yet control has been variable. If the biology and host utilisation of all the agents against water hyacinth is considered, a definite overlap of niches is apparent in at least one life stage of all the agents. Therefore the probability of these insects interacting is high, especially if they are established at the same site in the field. Three of the insects released in South Africa have been selected to investigate possible interactions. They are Neochetina eichhorniae Warner, Neochetina bruchi Hustache and Eccritotarsus catarinensis (Carvalho). Y-tube olfactometer bioassays were used to measure responses of these insects to water hyacinth with prior feeding damage by either conspecifics or heterospecifics. This was done to determine whether olfactory cues played a role in host acceptability and avoidance of conspecifics or heterospecifics. The insects were given a choice between damaged and undamaged plants in various combinations. There was a significant preference for the undamaged plants when given a choice between undamaged and damaged plants. However when the insects were given a choice between two damaged plants there was no discrimination between heterospecific or conspecific damaged plants. This may indicate that there is little or no ecological cost for the insect to share a plant with other insects utilising a similar resource. Insect – insect interactions were investigated in a common garden plot experiment to measure the impact that pairwise combinations of the insect may have on their performance. There was a significant interaction between the mirid E. catarinensis and the weevil N. eichhorniae, with the weevil not performing as well when in combination with the mirid than when alone. Interestingly there was a negative interaction between the two weevil species when in combination, however it was impossible to determine which species was being affected if not both. None of the insects performed significantly better when in combination with another insect. A field study on Wriggleswade Dam in the Eastern Cape, South Africa was initiated to determine whether the relationship between the mirid E. catarinensis and the weevil N. eichhorniae could be determined in the field. The performance of the insects at the different sites in the field suggests that there was an interaction between the agents. This interaction did not limit the establishment of either insect at a site, but it did result in one insect dominating at a site over another. Interactions between the three species of insect tested in this thesis suggest that there are both negative and neutral relationships between them. A basic comparison between the insect performances from 15 sites around the country was done to determine if the spatial segregation observed in the field could be extrapolated to the natural South African situation. The interaction observed between N. eichhorniae and E. catarinensis does seem to extrapolate to the general South African situation where there is definite spatial segregation on a landscape level. The co–occurrence of the two Neochetina weevils at these sites suggests that the negative relationship observed between them in the common garden experiment does not extrapolate to the field. The results from this thesis suggest that the interactions between the agents tested would not limit establishment or have significant ramifications on performance. However, there may be spatial and temporal segregation of these species in the introduced range.
- Full Text:
- Date Issued: 2012
An assessment of caracal population density and human-predator conflict in the Winterberg, Eastern Cape, South Africa
- Authors: Smith, Emma Ruth
- Date: 2012
- Subjects: Felis -- South Africa -- Eastern Cape , Felis -- Effect of human beings on -- South Africa -- Eastern Cape , Predatory animals -- Control -- South Africa -- Eastern Cape , Wildlife depredation -- South Africa -- Eastern Cape , Human-animal relationships , Felis -- Conservation -- South Africa -- Eastern Cape , Felis -- Monitoring -- South Africa -- Eastern Cape , Animal populations -- Estimates
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5644 , http://hdl.handle.net/10962/d1005326 , Felis -- South Africa -- Eastern Cape , Felis -- Effect of human beings on -- South Africa -- Eastern Cape , Predatory animals -- Control -- South Africa -- Eastern Cape , Wildlife depredation -- South Africa -- Eastern Cape , Human-animal relationships , Felis -- Conservation -- South Africa -- Eastern Cape , Felis -- Monitoring -- South Africa -- Eastern Cape , Animal populations -- Estimates
- Description: Human-wildlife conflict frequently involves carnivores, mainly because of their large home ranges and dietary requirements. As such, carnivores tend to be the first animals to be lost in human-dominated ecosystems. This is significant because the removal of carnivores can alter the functionality of ecosystems. However, the conservation of carnivores depends as much on the socio-political and socio-economic landscapes as it does on the ecological one. The consolidation of vast, un-fragmented conservation areas in Africa and the world is unlikely. Thus, unravelling the factors (both biological and sociological) responsible for and influencing human-predator conflict is critical for carnivore conservation. The Winterberg district in the Eastern Cape, South Africa has been a sheep (Ovis aries) farming stronghold for nearly 200 years. Consequently, conflict between farmers and predators is commonplace and depredation of livestock by caracals (Caracai caracal) remains a perennial problem. However, the extent of this human-predator conflict (including a reliable assessment of caracal density) has not been quantified. This study used camera trapping to estimate the density of caracals (a nonindividually recognisable species) in the Winterberg and a structured questionnaire to gauge the general attitudes of the farmers of the region. Caracal density was estimated to be 0.20 caracals/km². This estimate equates to a population of approximately 54 caracals across the entire district. Therefore, caracals do not appear to occur at high densities in the Winterberg. However, the survey of the residents of the Winterberg Conservancy revealed that predators were rated as the greatest problem faced by farmers in the area. Although not significant, it also showed that the size of a respondent's property and sheep mortality due to caracals had the greatest probability of affecting attitudes towards predators. The farmers lost less than 10% of their stock to caracal depredation on an annual basis. Therefore, the general perception that predators were the most important factor in stock loss in the area does not appear to be fully supported by my data. The Winterberg is a male-dominated, multigenerational society and it is likely this propagates certain perceptions towards predators which are a reflection of long-held family traditions and beliefs. Such situations can result in reactions which are disproportionate to the actual scale of the problem. However, my study was limited to a sub-set of the landowners in the Winterberg. Thus, more intensive assessments of caracal space use and community attitudes towards predators are recommended.
- Full Text:
- Date Issued: 2012
- Authors: Smith, Emma Ruth
- Date: 2012
- Subjects: Felis -- South Africa -- Eastern Cape , Felis -- Effect of human beings on -- South Africa -- Eastern Cape , Predatory animals -- Control -- South Africa -- Eastern Cape , Wildlife depredation -- South Africa -- Eastern Cape , Human-animal relationships , Felis -- Conservation -- South Africa -- Eastern Cape , Felis -- Monitoring -- South Africa -- Eastern Cape , Animal populations -- Estimates
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5644 , http://hdl.handle.net/10962/d1005326 , Felis -- South Africa -- Eastern Cape , Felis -- Effect of human beings on -- South Africa -- Eastern Cape , Predatory animals -- Control -- South Africa -- Eastern Cape , Wildlife depredation -- South Africa -- Eastern Cape , Human-animal relationships , Felis -- Conservation -- South Africa -- Eastern Cape , Felis -- Monitoring -- South Africa -- Eastern Cape , Animal populations -- Estimates
- Description: Human-wildlife conflict frequently involves carnivores, mainly because of their large home ranges and dietary requirements. As such, carnivores tend to be the first animals to be lost in human-dominated ecosystems. This is significant because the removal of carnivores can alter the functionality of ecosystems. However, the conservation of carnivores depends as much on the socio-political and socio-economic landscapes as it does on the ecological one. The consolidation of vast, un-fragmented conservation areas in Africa and the world is unlikely. Thus, unravelling the factors (both biological and sociological) responsible for and influencing human-predator conflict is critical for carnivore conservation. The Winterberg district in the Eastern Cape, South Africa has been a sheep (Ovis aries) farming stronghold for nearly 200 years. Consequently, conflict between farmers and predators is commonplace and depredation of livestock by caracals (Caracai caracal) remains a perennial problem. However, the extent of this human-predator conflict (including a reliable assessment of caracal density) has not been quantified. This study used camera trapping to estimate the density of caracals (a nonindividually recognisable species) in the Winterberg and a structured questionnaire to gauge the general attitudes of the farmers of the region. Caracal density was estimated to be 0.20 caracals/km². This estimate equates to a population of approximately 54 caracals across the entire district. Therefore, caracals do not appear to occur at high densities in the Winterberg. However, the survey of the residents of the Winterberg Conservancy revealed that predators were rated as the greatest problem faced by farmers in the area. Although not significant, it also showed that the size of a respondent's property and sheep mortality due to caracals had the greatest probability of affecting attitudes towards predators. The farmers lost less than 10% of their stock to caracal depredation on an annual basis. Therefore, the general perception that predators were the most important factor in stock loss in the area does not appear to be fully supported by my data. The Winterberg is a male-dominated, multigenerational society and it is likely this propagates certain perceptions towards predators which are a reflection of long-held family traditions and beliefs. Such situations can result in reactions which are disproportionate to the actual scale of the problem. However, my study was limited to a sub-set of the landowners in the Winterberg. Thus, more intensive assessments of caracal space use and community attitudes towards predators are recommended.
- Full Text:
- Date Issued: 2012
A study of the coordination behaviour of the lanthanide series with oxygen-donor ligands
- Authors: Kuhn, Kirsti
- Date: 2012
- Subjects: Chemical elements , Chemical reactions
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10394 , http://hdl.handle.net/10948/d1009533 , Chemical elements , Chemical reactions
- Description: The reactions between the lanthanide nitrate salts and the ligand triphenylphosphine oxide (TPPO) gave rise to nine-coordinated complexes of the nature Ln(TPPO)3(NO3)3, for Ln = La – Dy, Er, Tm, in which the Ln(III) centre is coordinated to three phosphoryl oxygen atoms and three bidentate nitrate ligands. Generally, the geometry can be described as being mer-octahedral, where the nitrate ligands are considered as monoatomic species. The product of the reaction between Yb(NO3)3·5H2O and TPPO, however, was a highly symmetrical eight-coordinated complex, in which the Yb(III) centre was coordinated to two bidentate nitrate groups and four TPPO molecules. The geometry in this case is best described as being trans-octahedral, with the two nitrate ligands coordinated practically perpendicular to one another. The complexes isolated from the reactions of lanthanide nitrate salts with the ligand bis(pentamethylene)urea (PMU) had the general formula Ln(PMU)3(NO3)3, where Ln = La – Dy, Yb, Lu. The complexes were found to be nine-coordinated with distorted trigonal prismatic geometry, in which the one base of the prism is composed of the oxygen atoms of the three PMU ligands and the other base is made up by one oxygen atom from each of the bidentate nitrate groups. The second oxygen atoms of each of the nitrate groups protrude upward, occupying capping positions. The reactions of the La and Pr nitrate salts with the ligand 2,2’-dipyridyl-N,N’-dioxide (DPDO) produced two novel complexes of the nature [Ln(DPDO)(H2O)2(NO3)3]. These complexes are remarkable in that their crystal structures reveal the Ln(III) centres to be ten-coordinated. The geometry around the Ln(III) centres was complex, due to the presence of a seven-membered chelate ring, formed by the bidentate coordination of the oxygen atoms from the DPDO ligands to the metal centres. The chelate ring did not lie in a single plane, but was twisted at the pyridyl bridgeheads to lie above and below the coordination plane.
- Full Text:
- Date Issued: 2012
- Authors: Kuhn, Kirsti
- Date: 2012
- Subjects: Chemical elements , Chemical reactions
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10394 , http://hdl.handle.net/10948/d1009533 , Chemical elements , Chemical reactions
- Description: The reactions between the lanthanide nitrate salts and the ligand triphenylphosphine oxide (TPPO) gave rise to nine-coordinated complexes of the nature Ln(TPPO)3(NO3)3, for Ln = La – Dy, Er, Tm, in which the Ln(III) centre is coordinated to three phosphoryl oxygen atoms and three bidentate nitrate ligands. Generally, the geometry can be described as being mer-octahedral, where the nitrate ligands are considered as monoatomic species. The product of the reaction between Yb(NO3)3·5H2O and TPPO, however, was a highly symmetrical eight-coordinated complex, in which the Yb(III) centre was coordinated to two bidentate nitrate groups and four TPPO molecules. The geometry in this case is best described as being trans-octahedral, with the two nitrate ligands coordinated practically perpendicular to one another. The complexes isolated from the reactions of lanthanide nitrate salts with the ligand bis(pentamethylene)urea (PMU) had the general formula Ln(PMU)3(NO3)3, where Ln = La – Dy, Yb, Lu. The complexes were found to be nine-coordinated with distorted trigonal prismatic geometry, in which the one base of the prism is composed of the oxygen atoms of the three PMU ligands and the other base is made up by one oxygen atom from each of the bidentate nitrate groups. The second oxygen atoms of each of the nitrate groups protrude upward, occupying capping positions. The reactions of the La and Pr nitrate salts with the ligand 2,2’-dipyridyl-N,N’-dioxide (DPDO) produced two novel complexes of the nature [Ln(DPDO)(H2O)2(NO3)3]. These complexes are remarkable in that their crystal structures reveal the Ln(III) centres to be ten-coordinated. The geometry around the Ln(III) centres was complex, due to the presence of a seven-membered chelate ring, formed by the bidentate coordination of the oxygen atoms from the DPDO ligands to the metal centres. The chelate ring did not lie in a single plane, but was twisted at the pyridyl bridgeheads to lie above and below the coordination plane.
- Full Text:
- Date Issued: 2012
The effects of sustained attention, workload and task-related fatigue on physiological measures and performance during a tracking task
- Authors: De Gray Birch, Casey
- Date: 2012
- Subjects: Fatigue -- Physiological aspects -- Research , Attention -- Physiological aspects -- Research , Human engineering -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5120 , http://hdl.handle.net/10962/d1005198 , Fatigue -- Physiological aspects -- Research , Attention -- Physiological aspects -- Research , Human engineering -- Research
- Description: Despite extensive research into the concept of mental fatigue there is as yet no “gold standard” definition or measurement technique available. Because of this a large amount of fatigue-related errors are still seen in the workplace. The complexity of the problem lies with the inability to directly measure mental processes as well as the various endogenous and exogenous factors that interact to produce the experienced fatigue. Fatigue has been divided into sleep-related and task-related fatigue; however the task-related aspect is evident both during normal waking hours as well as during periods of sleep deprivation, therefore this aspect is considered important in the understanding of fatigue in general. The concept of task-related fatigue has further been divided into active and passive fatigue states; however differentiation between the two requires careful consideration. Various physiological measures have been employed in an attempt to gain a better understanding of the mechanisms involved in the generation of fatigue, however often studies have produced dissociating results. The current study considered the task-related fatigue elicited by a tracking task requiring sustained attention, in order to evaluate the usefulness of various cardiovascular and oculomotor measures as indicators of fatigue. A secondary aim was to determine whether the behavioural and physiological parameter responses could be used to infer the type of fatigue incurred (i.e. an active versus passive fatigue state) as well as the energetical mechanisms involved during task performance. A simple driving simulator task was used as the main tracking task, requiring constant attention and concentration. This task was performed for approximately two hours. Three experimental groups (consisting of 14 subjects each) were used: a control group that performed the tracking task only, a group that performed a five minute auditory memory span task concurrently with the driving task after every 20 minutes of pure driving, and a group that performed a visual choice reaction task for five minutes following every 20 minute driving period. The secondary tasks were employed in order to evaluate the extent of resource allocation as well as arousal level. Performance measures included various driving performance parameters, as well as secondary task performance. Physiological measures included heart rate frequency (HR) and various time- and frequency-domain heart rate variability (HRV)parameters, pupil dilation, blink frequency and duration, fixations, and saccadic parameters as well as critical flicker fusion frequency (CFFF). The Borg CR-10 scale was used to evaluate subjective fatigue during the task, and the NASA-TLX was completed following the task. A decline in driving performance over time was supplemented by measures such as HR, HRV and pupil dilation indicating an increase in parasympathetic activity (or a reduction in arousal). An increase in blink frequency was considered as a sign of withdrawal of attentional resources over time. Longer and faster saccades were also evident over time, coupled with shorter fixations. With regards to the secondary task influence, the choice RT task did not affect any behavioural or physiological parameters, thereby contesting the active fatigue theory of resource depletion, as well as implying that the increase in demand for the same resources used by the primary task was insufficient to affect the state of the subjects. The increased load elicited by the memory span task improved driving performance and increased measures of HR, HRV, pupil dilation and blink frequency. Some of these measures produced opposite effects to what was expected; an attempt to explain the dissociation of the various physiological parameters was expressed in terms of arousal, effort and resource theories. Overall, the results indicate that the fatigue and/or reduced arousal accompanying a monotonous sustained attention task can, to some degree, be alleviated through intermittent performance of a secondary task engaging mental resources other than the ones used for the primary task. The degree to which such a task is beneficial, however, requires careful consideration as while an immediate increase in arousal and primary task performance is noted, the impact of the task on general attentional resources may be detrimental in the case of reacting should an emergency situation occur.
- Full Text:
- Date Issued: 2012
- Authors: De Gray Birch, Casey
- Date: 2012
- Subjects: Fatigue -- Physiological aspects -- Research , Attention -- Physiological aspects -- Research , Human engineering -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5120 , http://hdl.handle.net/10962/d1005198 , Fatigue -- Physiological aspects -- Research , Attention -- Physiological aspects -- Research , Human engineering -- Research
- Description: Despite extensive research into the concept of mental fatigue there is as yet no “gold standard” definition or measurement technique available. Because of this a large amount of fatigue-related errors are still seen in the workplace. The complexity of the problem lies with the inability to directly measure mental processes as well as the various endogenous and exogenous factors that interact to produce the experienced fatigue. Fatigue has been divided into sleep-related and task-related fatigue; however the task-related aspect is evident both during normal waking hours as well as during periods of sleep deprivation, therefore this aspect is considered important in the understanding of fatigue in general. The concept of task-related fatigue has further been divided into active and passive fatigue states; however differentiation between the two requires careful consideration. Various physiological measures have been employed in an attempt to gain a better understanding of the mechanisms involved in the generation of fatigue, however often studies have produced dissociating results. The current study considered the task-related fatigue elicited by a tracking task requiring sustained attention, in order to evaluate the usefulness of various cardiovascular and oculomotor measures as indicators of fatigue. A secondary aim was to determine whether the behavioural and physiological parameter responses could be used to infer the type of fatigue incurred (i.e. an active versus passive fatigue state) as well as the energetical mechanisms involved during task performance. A simple driving simulator task was used as the main tracking task, requiring constant attention and concentration. This task was performed for approximately two hours. Three experimental groups (consisting of 14 subjects each) were used: a control group that performed the tracking task only, a group that performed a five minute auditory memory span task concurrently with the driving task after every 20 minutes of pure driving, and a group that performed a visual choice reaction task for five minutes following every 20 minute driving period. The secondary tasks were employed in order to evaluate the extent of resource allocation as well as arousal level. Performance measures included various driving performance parameters, as well as secondary task performance. Physiological measures included heart rate frequency (HR) and various time- and frequency-domain heart rate variability (HRV)parameters, pupil dilation, blink frequency and duration, fixations, and saccadic parameters as well as critical flicker fusion frequency (CFFF). The Borg CR-10 scale was used to evaluate subjective fatigue during the task, and the NASA-TLX was completed following the task. A decline in driving performance over time was supplemented by measures such as HR, HRV and pupil dilation indicating an increase in parasympathetic activity (or a reduction in arousal). An increase in blink frequency was considered as a sign of withdrawal of attentional resources over time. Longer and faster saccades were also evident over time, coupled with shorter fixations. With regards to the secondary task influence, the choice RT task did not affect any behavioural or physiological parameters, thereby contesting the active fatigue theory of resource depletion, as well as implying that the increase in demand for the same resources used by the primary task was insufficient to affect the state of the subjects. The increased load elicited by the memory span task improved driving performance and increased measures of HR, HRV, pupil dilation and blink frequency. Some of these measures produced opposite effects to what was expected; an attempt to explain the dissociation of the various physiological parameters was expressed in terms of arousal, effort and resource theories. Overall, the results indicate that the fatigue and/or reduced arousal accompanying a monotonous sustained attention task can, to some degree, be alleviated through intermittent performance of a secondary task engaging mental resources other than the ones used for the primary task. The degree to which such a task is beneficial, however, requires careful consideration as while an immediate increase in arousal and primary task performance is noted, the impact of the task on general attentional resources may be detrimental in the case of reacting should an emergency situation occur.
- Full Text:
- Date Issued: 2012
Population dynamics of the white shark, Carcharodon carcharias, at Mossel Bay, South Africa
- Authors: Ryklief, Rabiah
- Date: 2012
- Subjects: White shark -- South Africa -- Mossel Bay , Sharks -- South Africa -- Mossel Bay
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10717 , http://hdl.handle.net/10948/d1012077 , White shark -- South Africa -- Mossel Bay , Sharks -- South Africa -- Mossel Bay
- Description: Mossel Bay is internationally recognised as one of the centres of abundance of white sharks in South Africa. During 2008 – 2010 there were four sites within the bay i.e. Seal Island, Hartenbos, Kleinbrak and Grootbrak, which were sampled to gain insight into the population dynamics of this species. Currently, life history information on white sharks in this area is limited. This study used a combination of mark-recapture using photographic identification techniques and sight per unit effort methods. Inter-annual, seasonal and spatial patterns in abundance are assessed. The effects of environmental parameters on abundance are also investigated. Photographic identification techniques were employed to identify unique individuals within the sampled population. This modified mark-recapture approach is therefore non-invasive and cost-effective. Open population POPAN parameterization was used to analyse the data in software program MARK. The total population was estimated at 389 sharks (351 – 428; 95 percent CI). Over the three year period, a marginal (yet non-significant) decline in numbers was observed, in terms of both monthly and seasonal population estimates. Sightings per unit effort data were collected during sampling trips. The relative abundance and body size composition of white sharks demonstrated significant spatial and seasonal variation. The highest and lowest relative abundance was observed at Seal Island and Hartenbos, respectively, and is likely attributed to prey availability. Although white sharks were present year-round in Mossel Bay, the highest relative abundance occurred during summer and the lowest relative abundance occurred during spring. White sharks were grouped into three main size classes based on estimated total length (TL): Young of the year (YOY) (125 – 174cm), juvenile (175 – 324cm) and adult (325 – 524cm). YOY white sharks were most prevalent at Grootbrak, with juvenile and adult individuals concentrating at Seal Island. Although most size classes were present throughout the year, seasonal differences were observed. YOY individuals were most abundant in the autumn months, juvenile size-classes appeared to concentrate in the study area during winter, and the adult individuals were most abundant in the spring months. Overall, there was a high concentration of white sharks ranging in size between 175 – 324cm TL, and it was thus hypothesised that Mossel Bay represents an interim nursery or grow out area for white sharks in South Africa. Data collected from 2008 and 2009 was used to investigate the relationship between specific environmental parameters, i.e. sea surface temperature and vertical water clarity, in relation to the relative abundance of white sharks. Sea surface temperature and vertical water clarity observed in this study ranged from 9.3 - 22.7°C and 0 – 10m, respectively. Sea surface temperature did not have a significant influence on the relative abundance of white sharks and this may be attributed to the thermoregulatory capacity of the species. Vertical water clarity, however, did significantly influence the relative abundance. Furthermore, the combined effect of site and season significantly influenced the relative abundance of white sharks and is probably linked to the distribution and abundance of inshore prey resources.
- Full Text:
- Date Issued: 2012
- Authors: Ryklief, Rabiah
- Date: 2012
- Subjects: White shark -- South Africa -- Mossel Bay , Sharks -- South Africa -- Mossel Bay
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10717 , http://hdl.handle.net/10948/d1012077 , White shark -- South Africa -- Mossel Bay , Sharks -- South Africa -- Mossel Bay
- Description: Mossel Bay is internationally recognised as one of the centres of abundance of white sharks in South Africa. During 2008 – 2010 there were four sites within the bay i.e. Seal Island, Hartenbos, Kleinbrak and Grootbrak, which were sampled to gain insight into the population dynamics of this species. Currently, life history information on white sharks in this area is limited. This study used a combination of mark-recapture using photographic identification techniques and sight per unit effort methods. Inter-annual, seasonal and spatial patterns in abundance are assessed. The effects of environmental parameters on abundance are also investigated. Photographic identification techniques were employed to identify unique individuals within the sampled population. This modified mark-recapture approach is therefore non-invasive and cost-effective. Open population POPAN parameterization was used to analyse the data in software program MARK. The total population was estimated at 389 sharks (351 – 428; 95 percent CI). Over the three year period, a marginal (yet non-significant) decline in numbers was observed, in terms of both monthly and seasonal population estimates. Sightings per unit effort data were collected during sampling trips. The relative abundance and body size composition of white sharks demonstrated significant spatial and seasonal variation. The highest and lowest relative abundance was observed at Seal Island and Hartenbos, respectively, and is likely attributed to prey availability. Although white sharks were present year-round in Mossel Bay, the highest relative abundance occurred during summer and the lowest relative abundance occurred during spring. White sharks were grouped into three main size classes based on estimated total length (TL): Young of the year (YOY) (125 – 174cm), juvenile (175 – 324cm) and adult (325 – 524cm). YOY white sharks were most prevalent at Grootbrak, with juvenile and adult individuals concentrating at Seal Island. Although most size classes were present throughout the year, seasonal differences were observed. YOY individuals were most abundant in the autumn months, juvenile size-classes appeared to concentrate in the study area during winter, and the adult individuals were most abundant in the spring months. Overall, there was a high concentration of white sharks ranging in size between 175 – 324cm TL, and it was thus hypothesised that Mossel Bay represents an interim nursery or grow out area for white sharks in South Africa. Data collected from 2008 and 2009 was used to investigate the relationship between specific environmental parameters, i.e. sea surface temperature and vertical water clarity, in relation to the relative abundance of white sharks. Sea surface temperature and vertical water clarity observed in this study ranged from 9.3 - 22.7°C and 0 – 10m, respectively. Sea surface temperature did not have a significant influence on the relative abundance of white sharks and this may be attributed to the thermoregulatory capacity of the species. Vertical water clarity, however, did significantly influence the relative abundance. Furthermore, the combined effect of site and season significantly influenced the relative abundance of white sharks and is probably linked to the distribution and abundance of inshore prey resources.
- Full Text:
- Date Issued: 2012
A baculovirus-mediated expression system for the analysis of HaSV RNA packaging
- Authors: Mendes, Adriano
- Date: 2012
- Subjects: RNA , Baculoviruses , Helicoverpa armigera , Plasmids
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4025 , http://hdl.handle.net/10962/d1004085 , RNA , Baculoviruses , Helicoverpa armigera , Plasmids
- Description: The Helicoverpa armigera stunt virus (HaSV) is a member of a family of small nonenveloped (+) ssRNA insect viruses currently known as the Tetraviridae. This family is unique in terms of the T=4 quasi-symmetry of its capsid particles and the unusually narrow host range and tissue tropism. Assembly of tetraviral particles has been well characterised and involves the combination of 240 copies of a single capsid precursor protein (VCap) into a procapsid followed by autoproteolytic cleavage to yield the major (β) and minor (γ) capsid subunits within the mature particle. HaSV has two genomic RNAs, RNA 1 encoding the replicase and RNA 2 encoding VCap and p17, the ORF of which lies upstream of and overlaping with the 5’ end of the VCap ORF. Prior to this study, Vlok (2009) used a plasmid expression system to study RNA packaging in HaSV VLPs assembled in Spodoptera frugiperda 9 (Sf9) cells co-expressing p17 and VCap. The study showed that the p17 ORF was required for the packaging of RNA 2 during capsid assembly but it was unclear whether p17 expression was required for packaging. In addition, expression from the transfected plasmids was sub-optimal affecting both the yield of VLPs and the detection of p17. The aim of this study was to use the plasmid system to test whether p17 expression was required for plasmid-derived VLP RNA packaging and then develop a baculovirus-mediated system to test this hypothesis. By using a plasmid in which the start codon of p17 was mutated, it was shown that p17 expression was required for RNA 2 packaging into plasmid-VLPs. For the baculovirus system, four recombinant baculoviruses based upon the pFastBac Dual expression system, were constructed. These included Bac20, expressing wild type RNA 2, Bac21, RNA 2 with p17 silenced, Bac23, RNA 2 and p17 expressed on a separate transcript and Bac24, RNA 2 with p17 silenced plus p17 expressed on a separate transcript. Assembly of VLPs was more efficient using the baculovirus expression system and p17 expression was observed in cells infected with Bac20, Bac23 and Bac24, but not Bac21. In contrast to the plasmid-VLPs, bac-VLPs did not require p17 for the encapsidation of RNA 2. In addition to RNA 2, Bac23 and Bac24 packaged the p17 mRNA transcribed separately from RNA 2. This insinuated that bac-VLPs may be packaging RNA non-selectively. It was proposed that p17 may play a role in packaging in an RNA-limiting environment (plasmid system) but functioned differently when viral RNA was in excess (baculovirus system). This data points to the importance of developing a replication system for the analysis of the packaging pathways of these viruses and this study has laid down the foundations for such a system in which RNA 1 and RNA 2 can be introduced into a single cell by means of a single recombinant virus.
- Full Text:
- Date Issued: 2012
- Authors: Mendes, Adriano
- Date: 2012
- Subjects: RNA , Baculoviruses , Helicoverpa armigera , Plasmids
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4025 , http://hdl.handle.net/10962/d1004085 , RNA , Baculoviruses , Helicoverpa armigera , Plasmids
- Description: The Helicoverpa armigera stunt virus (HaSV) is a member of a family of small nonenveloped (+) ssRNA insect viruses currently known as the Tetraviridae. This family is unique in terms of the T=4 quasi-symmetry of its capsid particles and the unusually narrow host range and tissue tropism. Assembly of tetraviral particles has been well characterised and involves the combination of 240 copies of a single capsid precursor protein (VCap) into a procapsid followed by autoproteolytic cleavage to yield the major (β) and minor (γ) capsid subunits within the mature particle. HaSV has two genomic RNAs, RNA 1 encoding the replicase and RNA 2 encoding VCap and p17, the ORF of which lies upstream of and overlaping with the 5’ end of the VCap ORF. Prior to this study, Vlok (2009) used a plasmid expression system to study RNA packaging in HaSV VLPs assembled in Spodoptera frugiperda 9 (Sf9) cells co-expressing p17 and VCap. The study showed that the p17 ORF was required for the packaging of RNA 2 during capsid assembly but it was unclear whether p17 expression was required for packaging. In addition, expression from the transfected plasmids was sub-optimal affecting both the yield of VLPs and the detection of p17. The aim of this study was to use the plasmid system to test whether p17 expression was required for plasmid-derived VLP RNA packaging and then develop a baculovirus-mediated system to test this hypothesis. By using a plasmid in which the start codon of p17 was mutated, it was shown that p17 expression was required for RNA 2 packaging into plasmid-VLPs. For the baculovirus system, four recombinant baculoviruses based upon the pFastBac Dual expression system, were constructed. These included Bac20, expressing wild type RNA 2, Bac21, RNA 2 with p17 silenced, Bac23, RNA 2 and p17 expressed on a separate transcript and Bac24, RNA 2 with p17 silenced plus p17 expressed on a separate transcript. Assembly of VLPs was more efficient using the baculovirus expression system and p17 expression was observed in cells infected with Bac20, Bac23 and Bac24, but not Bac21. In contrast to the plasmid-VLPs, bac-VLPs did not require p17 for the encapsidation of RNA 2. In addition to RNA 2, Bac23 and Bac24 packaged the p17 mRNA transcribed separately from RNA 2. This insinuated that bac-VLPs may be packaging RNA non-selectively. It was proposed that p17 may play a role in packaging in an RNA-limiting environment (plasmid system) but functioned differently when viral RNA was in excess (baculovirus system). This data points to the importance of developing a replication system for the analysis of the packaging pathways of these viruses and this study has laid down the foundations for such a system in which RNA 1 and RNA 2 can be introduced into a single cell by means of a single recombinant virus.
- Full Text:
- Date Issued: 2012
On the design of concentrator photovoltaic modules
- Authors: Schultz, Ross Dane
- Date: 2012
- Subjects: Photovoltaic cells -- Design and construction , Photovoltaic cells
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10546 , http://hdl.handle.net/10948/d1015766 , Photovoltaic cells -- Design and construction , Photovoltaic cells
- Description: High concentration photovoltaics (HCPV) promise a more efficient, higher power output than traditional photovoltaic modules. This is achieved by concentrating sunlight onto a small 1 cm2 triple junction (CTJ) InGaP/InGaAs/Ge cell by using precision optics. In order to achieve high performance, careful and informed design decisions must be made in the development of a HCPV module . This project investigated the design of a HCPV module and is divided into sections that concentrate on the optical design, thermal dissipation and electrical characterization of a concentration triple junction cell. The first HCPV module (Module I) design was based on the Sandia III Baseline Fresnel module which comprised of a Fresnel lens and truncated reflective secondary as the optical elements. The parameters of the CTJ cell in Module I increased with increased concentration. This included the short circuit current, open circuit voltage, power and efficiency. The best performance achieved was at 336 times operational concentration which produced 10.3 W per cell, a cell efficiency of 38.4 percent, and module efficiency of 24.2 percent Investigation of the optical subsystem revealed that the optics played a large role in the operation of the CTJ cell. Characterization of the optical elements showed a transmission loss of 15 percent of concentrated sunlight for the irradiance of which 66 percent of the loss occurred in wavelength region where the InGaP subcell is active. Characterization of the optical subsystem indicated regions of non-uniform irradiance and spectral intensity across the CTJ cell surface. The optical subsystem caused the InGaP subcell of the series monolithic connected CTJ cell to be current limiting. This was confirmed by the CTJ cell having the same short circuit current as the InGaP subcell. The performance of the CTJ cell decreased with an increase in operational temperature. A form of thermal dissipation was needed as 168 times more heat needs to be dissipated when compared to a flat plate photovoltaic module. The thermal dissipation was achieved by passive means with a heat sink which reduced the operational temperature of the CTJ cell from 50 oC to 21 oC above ambient. Cell damage was noted in Module I due to bubbles in the encapsulation epoxy bursting from a high, non-uniform intensity distribution. The development of the second module (Module II) employed a pre-monitoring criteria that characterized the CTJ cells and eliminated faulty cells from the system. These criteria included visual inspection of the cell, electroluminescence and one sun current-voltage (I-V) characteristic curves. Module II was designed as separate units which comprised of a Fresnel lens, refractive secondary, CTJ cell and heatsink. The optimal configuration between the two modules were compared. The CTJ cells in module II showed no form of degradation in the I-V characteristics and in the detected defects. The units under thermal and optical stress showed a progressive degradation. A feature in the I-V curve at V > Vmax was noted for the thermally stressed unit. This feature in the I-V curve may be attributed to the breakdown of the Ge subcell in the CTJ cell. Based on the results obtained from the two experimental HCPV modules, recommendations for an optimal HCPV module were made.
- Full Text:
- Date Issued: 2012
- Authors: Schultz, Ross Dane
- Date: 2012
- Subjects: Photovoltaic cells -- Design and construction , Photovoltaic cells
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10546 , http://hdl.handle.net/10948/d1015766 , Photovoltaic cells -- Design and construction , Photovoltaic cells
- Description: High concentration photovoltaics (HCPV) promise a more efficient, higher power output than traditional photovoltaic modules. This is achieved by concentrating sunlight onto a small 1 cm2 triple junction (CTJ) InGaP/InGaAs/Ge cell by using precision optics. In order to achieve high performance, careful and informed design decisions must be made in the development of a HCPV module . This project investigated the design of a HCPV module and is divided into sections that concentrate on the optical design, thermal dissipation and electrical characterization of a concentration triple junction cell. The first HCPV module (Module I) design was based on the Sandia III Baseline Fresnel module which comprised of a Fresnel lens and truncated reflective secondary as the optical elements. The parameters of the CTJ cell in Module I increased with increased concentration. This included the short circuit current, open circuit voltage, power and efficiency. The best performance achieved was at 336 times operational concentration which produced 10.3 W per cell, a cell efficiency of 38.4 percent, and module efficiency of 24.2 percent Investigation of the optical subsystem revealed that the optics played a large role in the operation of the CTJ cell. Characterization of the optical elements showed a transmission loss of 15 percent of concentrated sunlight for the irradiance of which 66 percent of the loss occurred in wavelength region where the InGaP subcell is active. Characterization of the optical subsystem indicated regions of non-uniform irradiance and spectral intensity across the CTJ cell surface. The optical subsystem caused the InGaP subcell of the series monolithic connected CTJ cell to be current limiting. This was confirmed by the CTJ cell having the same short circuit current as the InGaP subcell. The performance of the CTJ cell decreased with an increase in operational temperature. A form of thermal dissipation was needed as 168 times more heat needs to be dissipated when compared to a flat plate photovoltaic module. The thermal dissipation was achieved by passive means with a heat sink which reduced the operational temperature of the CTJ cell from 50 oC to 21 oC above ambient. Cell damage was noted in Module I due to bubbles in the encapsulation epoxy bursting from a high, non-uniform intensity distribution. The development of the second module (Module II) employed a pre-monitoring criteria that characterized the CTJ cells and eliminated faulty cells from the system. These criteria included visual inspection of the cell, electroluminescence and one sun current-voltage (I-V) characteristic curves. Module II was designed as separate units which comprised of a Fresnel lens, refractive secondary, CTJ cell and heatsink. The optimal configuration between the two modules were compared. The CTJ cells in module II showed no form of degradation in the I-V characteristics and in the detected defects. The units under thermal and optical stress showed a progressive degradation. A feature in the I-V curve at V > Vmax was noted for the thermally stressed unit. This feature in the I-V curve may be attributed to the breakdown of the Ge subcell in the CTJ cell. Based on the results obtained from the two experimental HCPV modules, recommendations for an optimal HCPV module were made.
- Full Text:
- Date Issued: 2012
Towards integrated catchment management : challenges surrounding implementation in the Gamtoos River catchment
- Authors: Materechera, Fenji
- Date: 2012
- Subjects: Watershed management -- South Africa , Watershed management -- South Africa -- Citizen participation , Integrated water development -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10664 , http://hdl.handle.net/10948/d1018553
- Description: Water resource management has become a pertinent issue of global environmental concern in response to the conditions of a growing global population, increasing development and a limited freshwater supply. It is against the backdrop of such conditions that effective water resource management has gained popularity in seeking to ensure that the needs of the growing population will be met and secured for future generations. The notion of integrated water resource management (IWRM) is a perspective on water resource management that has evolved out of the global opinion that social and ecological systems are linked and therefore cannot be managed separately. The department of water affairs (DWA) in South Africa highlights the importance of approaching management of water resources from a catchment perspective which forms the basis for a particular integrated approach to management called integrated catchment management (ICM). ICM recognizes the catchment as the correct administrative unit for management. It integrates water resources and the land that forms the catchment area in planning and management. Researchers have described the implementation of ICM as being complicated and difficult. This is no exception to South Africa. Principles of ICM have received widespread prominence in South Africa as they have been incorporated into national water policy. Actual implementation however is still in its infancy. The study is therefore a case study of ICM with respect to factors influencing implementation amongst different stakeholders. The study aims to explore the theme of implementation of ICM within the context of the Gamtoos River Catchment with a view toward identifying and addressing challenges that may be more broadly applicable. The study adopts an inductive, exploratory approach to the connection between theory and practice. A systems-based framework characterized by sequential steps similar to that employed in a case study conducted by Bellamy et al. (2001) in Queensland Australia is used to facilitate the evaluation of ICM in the Gamtoos River Catchment. The evaluation is achieved through a three step process of exploration in the current study. Triangulation is applied to the choice of methods of analysis which involves the use of a global analysis method, the use of learning scenarios and a grounded theory method. Findings reveal seven core themes which help to provide a detailed, contextual understanding relating to the status quo for ICM in the catchment. Results from a grounded theory analysis summarized the main challenges to implementation into five broad categories. Based on this analysis method and the application of the three learning scenarios for the Gamtoos River Catchment, the extent to which these challenges exist was discovered. The state of ICM in the catchment was classified as falling within a condition of a level of success being achieved with room for improvement to a condition of optimal ICM. The study concludes that based on the context of ICM being an example of a Complex Adaptive Systems (CAS), this state of ICM in the Gamtoos River Catchment is subject to change. This therefore necessitates the consideration of approaches to implementation that are adaptive to change. Findings may serve to inform decision making on how ICM can be effectively implemented elsewhere in a South African context.
- Full Text:
- Date Issued: 2012
- Authors: Materechera, Fenji
- Date: 2012
- Subjects: Watershed management -- South Africa , Watershed management -- South Africa -- Citizen participation , Integrated water development -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10664 , http://hdl.handle.net/10948/d1018553
- Description: Water resource management has become a pertinent issue of global environmental concern in response to the conditions of a growing global population, increasing development and a limited freshwater supply. It is against the backdrop of such conditions that effective water resource management has gained popularity in seeking to ensure that the needs of the growing population will be met and secured for future generations. The notion of integrated water resource management (IWRM) is a perspective on water resource management that has evolved out of the global opinion that social and ecological systems are linked and therefore cannot be managed separately. The department of water affairs (DWA) in South Africa highlights the importance of approaching management of water resources from a catchment perspective which forms the basis for a particular integrated approach to management called integrated catchment management (ICM). ICM recognizes the catchment as the correct administrative unit for management. It integrates water resources and the land that forms the catchment area in planning and management. Researchers have described the implementation of ICM as being complicated and difficult. This is no exception to South Africa. Principles of ICM have received widespread prominence in South Africa as they have been incorporated into national water policy. Actual implementation however is still in its infancy. The study is therefore a case study of ICM with respect to factors influencing implementation amongst different stakeholders. The study aims to explore the theme of implementation of ICM within the context of the Gamtoos River Catchment with a view toward identifying and addressing challenges that may be more broadly applicable. The study adopts an inductive, exploratory approach to the connection between theory and practice. A systems-based framework characterized by sequential steps similar to that employed in a case study conducted by Bellamy et al. (2001) in Queensland Australia is used to facilitate the evaluation of ICM in the Gamtoos River Catchment. The evaluation is achieved through a three step process of exploration in the current study. Triangulation is applied to the choice of methods of analysis which involves the use of a global analysis method, the use of learning scenarios and a grounded theory method. Findings reveal seven core themes which help to provide a detailed, contextual understanding relating to the status quo for ICM in the catchment. Results from a grounded theory analysis summarized the main challenges to implementation into five broad categories. Based on this analysis method and the application of the three learning scenarios for the Gamtoos River Catchment, the extent to which these challenges exist was discovered. The state of ICM in the catchment was classified as falling within a condition of a level of success being achieved with room for improvement to a condition of optimal ICM. The study concludes that based on the context of ICM being an example of a Complex Adaptive Systems (CAS), this state of ICM in the Gamtoos River Catchment is subject to change. This therefore necessitates the consideration of approaches to implementation that are adaptive to change. Findings may serve to inform decision making on how ICM can be effectively implemented elsewhere in a South African context.
- Full Text:
- Date Issued: 2012
Evaluation of noise levels of micro-wind turbines using a randomised experiment
- Authors: Clohessy, Chantelle May
- Date: 2012
- Subjects: Wind turbines -- Noise , Wind turbines -- valuation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10508 , http://hdl.handle.net/10948/d1015974
- Description: One of the biggest environmental concerns of a wind turbine is the wind turbine noise (Prospathopoulos and Voutsinas, 2007). This study assesses the noise impacts of wind turbines on the environment by comparing the micro-wind turbine noise to traditional accepted surrounding sounds. The collection of the sound level data was done by using a randomised experiment. The sound level data was then fitted to a General Linear Model to determine the relationship between the sound levels generated at a given site to the time of day, wind speed, wind direction and distance from the sound source. An additional study was conducted to determine the relationship between wind speed and the sound levels of wind turbines. The distribution of frequency components of wind turbine sound was also determined.
- Full Text:
- Date Issued: 2012
- Authors: Clohessy, Chantelle May
- Date: 2012
- Subjects: Wind turbines -- Noise , Wind turbines -- valuation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10508 , http://hdl.handle.net/10948/d1015974
- Description: One of the biggest environmental concerns of a wind turbine is the wind turbine noise (Prospathopoulos and Voutsinas, 2007). This study assesses the noise impacts of wind turbines on the environment by comparing the micro-wind turbine noise to traditional accepted surrounding sounds. The collection of the sound level data was done by using a randomised experiment. The sound level data was then fitted to a General Linear Model to determine the relationship between the sound levels generated at a given site to the time of day, wind speed, wind direction and distance from the sound source. An additional study was conducted to determine the relationship between wind speed and the sound levels of wind turbines. The distribution of frequency components of wind turbine sound was also determined.
- Full Text:
- Date Issued: 2012
Enumeration of insect viruses using microscopic and molecular analyses: South African isolate of cryotophlebia leucotreta granulovirus as a case study
- Authors: Dhladhla, Busisiwe I R
- Date: 2012
- Subjects: Baculoviruses , Insects -- Viruses , Molecular genetics , Microbial genomics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10318 , http://hdl.handle.net/10948/d1008395 , Baculoviruses , Insects -- Viruses , Molecular genetics , Microbial genomics
- Description: Baculoviruses have been used as biocontrol agents to control insect pests in agriculture since the 1970s. Out of the fifteen virus families known to infect insects, baculoviruses offer the greatest potential as insect biopesticides, due to their high host specificity which makes them extremely safe to humans, other vertebrates, plants and non-target microorganisms. They comprise of two genera: nucleopolyhedroviruses (NPVs) and granuloviruses (GVs). The South African isolate of Cryptophlebia leucotreta granulovirus (CrleGV-SA) which is infectious for the false codling moth (FCM), Thaumatotibia leucotreta, (Meyrick) (Lepidoptera: Tortricidae), has been successfully developed into two commercial biopesticides; Cryptogran® and Cryptex®, for the control of FCM in citrus crops. The current method of enumeration used for CrleGV-SA virus particles in routine experiments during the production of the GV as biopesticides, is dark field microscopy. However, due to the small size of GVs (300-500 nm in length), the technique is not easy to perform on these viruses, and no systemic comparison has been made of potential alternative methods. Therefore, the main objective of this study was to develop a quantitative enumeration method for CrleGV-SA occlusion bodies (OBs) which is accurate, reliable, and feasible, and compare the developed methods of enumeration to the current method. Purified and semi-purified CrleGV-SA viral stocks were prepared for enumeration studies using spectrophotometry, dark field microscopy, scanning electron microscopy (SEM) and real time qPCR. Spectrophotometry was found to be an unreliable method for enumeration of GVs in the production, standardisation, and quality control of biopesticides. Dark field microscopy and SEM were found to be accurate, and statistically comparable (p = 0.064) enumeration techniques. qPCR is currently being optimised for the enumeration of GVs. This technique was demonstrated to generate accurate standard curves for absolute quantification of virus particles for pure and semi-pure virus preparations. qPCR offers the greatest potential as an accurate enumeration method because it is not affected by contamination with non-biological contaminating debris, nor by other biological material due to the specificity of PCR primers. Further work is required to fully develop qPCR as an enumeration method for GVs. However, dark field microscopy has been successfully validated as an enumeration method. SEM, which has a high resolution compared to light microscopy, has an added advantage over dark field microscopy, which is to distinguish virus particles in semi-pure viral stock preparations during counting. Therefore, SEM currently provides the most unambiguous and feasible enumeration method for GVs in both purified and semi-purified virus samples.
- Full Text:
- Date Issued: 2012
- Authors: Dhladhla, Busisiwe I R
- Date: 2012
- Subjects: Baculoviruses , Insects -- Viruses , Molecular genetics , Microbial genomics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10318 , http://hdl.handle.net/10948/d1008395 , Baculoviruses , Insects -- Viruses , Molecular genetics , Microbial genomics
- Description: Baculoviruses have been used as biocontrol agents to control insect pests in agriculture since the 1970s. Out of the fifteen virus families known to infect insects, baculoviruses offer the greatest potential as insect biopesticides, due to their high host specificity which makes them extremely safe to humans, other vertebrates, plants and non-target microorganisms. They comprise of two genera: nucleopolyhedroviruses (NPVs) and granuloviruses (GVs). The South African isolate of Cryptophlebia leucotreta granulovirus (CrleGV-SA) which is infectious for the false codling moth (FCM), Thaumatotibia leucotreta, (Meyrick) (Lepidoptera: Tortricidae), has been successfully developed into two commercial biopesticides; Cryptogran® and Cryptex®, for the control of FCM in citrus crops. The current method of enumeration used for CrleGV-SA virus particles in routine experiments during the production of the GV as biopesticides, is dark field microscopy. However, due to the small size of GVs (300-500 nm in length), the technique is not easy to perform on these viruses, and no systemic comparison has been made of potential alternative methods. Therefore, the main objective of this study was to develop a quantitative enumeration method for CrleGV-SA occlusion bodies (OBs) which is accurate, reliable, and feasible, and compare the developed methods of enumeration to the current method. Purified and semi-purified CrleGV-SA viral stocks were prepared for enumeration studies using spectrophotometry, dark field microscopy, scanning electron microscopy (SEM) and real time qPCR. Spectrophotometry was found to be an unreliable method for enumeration of GVs in the production, standardisation, and quality control of biopesticides. Dark field microscopy and SEM were found to be accurate, and statistically comparable (p = 0.064) enumeration techniques. qPCR is currently being optimised for the enumeration of GVs. This technique was demonstrated to generate accurate standard curves for absolute quantification of virus particles for pure and semi-pure virus preparations. qPCR offers the greatest potential as an accurate enumeration method because it is not affected by contamination with non-biological contaminating debris, nor by other biological material due to the specificity of PCR primers. Further work is required to fully develop qPCR as an enumeration method for GVs. However, dark field microscopy has been successfully validated as an enumeration method. SEM, which has a high resolution compared to light microscopy, has an added advantage over dark field microscopy, which is to distinguish virus particles in semi-pure viral stock preparations during counting. Therefore, SEM currently provides the most unambiguous and feasible enumeration method for GVs in both purified and semi-purified virus samples.
- Full Text:
- Date Issued: 2012
Automated grid fault detection and repair
- Authors: Luyt, Leslie
- Date: 2012 , 2012-05-24
- Subjects: Computational grids (Computer systems) -- Maintenance and repair , Cloud computing -- Maintenance and repair , Computer architecture
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4670 , http://hdl.handle.net/10962/d1006693 , Computational grids (Computer systems) -- Maintenance and repair , Cloud computing -- Maintenance and repair , Computer architecture
- Description: With the rise in interest in the field of grid and cloud computing, it is becoming increasingly necessary for the grid to be easily maintainable. This maintenance of the grid and grid services can be made easier by using an automated system to monitor and repair the grid as necessary. We propose a novel system to perform automated monitoring and repair of grid systems. To the best of our knowledge, no such systems exist. The results show that certain faults can be easily detected and repaired. , TeX , Adobe Acrobat 9.51 Paper Capture Plug-in
- Full Text:
- Date Issued: 2012
- Authors: Luyt, Leslie
- Date: 2012 , 2012-05-24
- Subjects: Computational grids (Computer systems) -- Maintenance and repair , Cloud computing -- Maintenance and repair , Computer architecture
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4670 , http://hdl.handle.net/10962/d1006693 , Computational grids (Computer systems) -- Maintenance and repair , Cloud computing -- Maintenance and repair , Computer architecture
- Description: With the rise in interest in the field of grid and cloud computing, it is becoming increasingly necessary for the grid to be easily maintainable. This maintenance of the grid and grid services can be made easier by using an automated system to monitor and repair the grid as necessary. We propose a novel system to perform automated monitoring and repair of grid systems. To the best of our knowledge, no such systems exist. The results show that certain faults can be easily detected and repaired. , TeX , Adobe Acrobat 9.51 Paper Capture Plug-in
- Full Text:
- Date Issued: 2012
The biota of the Swartkops Solar Saltworks and their potential for producing biofuels
- Authors: De Lauwere, Monique Simone
- Date: 2012
- Subjects: Organisms , Biomass energy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10625 , http://hdl.handle.net/10948/d1011657 , Organisms , Biomass energy
- Description: The Swartkops and Missionvale salinas in Port Elizabeth on the east coast of South Africa are surrounding by large informal settlements. The runoff from these settlements contributes largely to the eutrophication of the solar saltworks which in turn has an effect on the biotic functioning of the systems, ultimately affecting the quantity and quality of the salt produced. Inorganic nutrients and organic composition, as well as important biological groups were examined within the brine with the aim of comparing the current condition of the same salinas to their condition twelve years ago. Comparisons between inorganic nutrient concentrations and biological groups showed significantly higher inorganic nutrients, with chlorophyll a concentrations in the Swartkops salina in 2011 being significantly higher than in 2012 and the 1999 and 2011 chlorophyll a concentrations being significantly higher than 2012 in the Missionvale salina. Microalgae found in the salinas were cultured in four different growth media. Cells were stained with Nile Red fluorescent dye in order to estimate the extent of lipids production. Five of the most promising lipid producing species were isolated into a monoculture and grown at different salinities to establish the growth and lipid production in response to salinity. Halamphora coffeaeformis and Navicula sp. were found to be the best candidate species. They grew best at salinities between 50 and 70 psu and produced lipid vesicles consuming approximately 10 percent of the cell.
- Full Text:
- Date Issued: 2012
- Authors: De Lauwere, Monique Simone
- Date: 2012
- Subjects: Organisms , Biomass energy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10625 , http://hdl.handle.net/10948/d1011657 , Organisms , Biomass energy
- Description: The Swartkops and Missionvale salinas in Port Elizabeth on the east coast of South Africa are surrounding by large informal settlements. The runoff from these settlements contributes largely to the eutrophication of the solar saltworks which in turn has an effect on the biotic functioning of the systems, ultimately affecting the quantity and quality of the salt produced. Inorganic nutrients and organic composition, as well as important biological groups were examined within the brine with the aim of comparing the current condition of the same salinas to their condition twelve years ago. Comparisons between inorganic nutrient concentrations and biological groups showed significantly higher inorganic nutrients, with chlorophyll a concentrations in the Swartkops salina in 2011 being significantly higher than in 2012 and the 1999 and 2011 chlorophyll a concentrations being significantly higher than 2012 in the Missionvale salina. Microalgae found in the salinas were cultured in four different growth media. Cells were stained with Nile Red fluorescent dye in order to estimate the extent of lipids production. Five of the most promising lipid producing species were isolated into a monoculture and grown at different salinities to establish the growth and lipid production in response to salinity. Halamphora coffeaeformis and Navicula sp. were found to be the best candidate species. They grew best at salinities between 50 and 70 psu and produced lipid vesicles consuming approximately 10 percent of the cell.
- Full Text:
- Date Issued: 2012
How does the ungulate community respond to predation risk from cheetah (Acinonyx jubatus) in Samara Private Game Reserve?
- Authors: Makin, Douglas Ferguson
- Date: 2012
- Subjects: Ungulates -- South Africa -- Eastern Cape , Predatory animals -- Ecology -- South Africa -- Eastern Cape , Predation (Biology) -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10722 , http://hdl.handle.net/10948/d1018461
- Description: Predator reintroductions are becoming increasingly more common for multiple reasons, including assisting with the conservation of a predator species, the restoration of ecosystem functions and the economic benefits of their reintroduction for ecotourism ventures. There remains however, little knowledge on prey species responses to these predator reintroductions. As such, the reintroduction of cheetah (Acinonyx jubatus) into Samara Private Game Reserve provided an opportunity to investigate prey responses to predator reintroduction across a range of spatial and temporal scales. More specifically, the aim of this study was to investigate the effect of cheetah predation risk on habitat use and behavioural responses of the resident ungulate community. Samara is divided into “predator present” and “predator absent” sections, providing the opportunity to conduct a comparative study investigating the effect of cheetah on prey responses. It was hypothesized that different ungulate species would respond differently to the presence of cheetah, depending on differences in perceived vulnerability to cheetah predation. To address this, shifts in habitat use, and behavioural responses of the ungulate community reflected at landscape and patch scale were investigated. Overall, ungulate species have not shifted habitat use since cheetah reintroduction, this was possibly related to life history strategy constraints and the need for individuals to obtain suitable forage and therefore remain in specific habitats. While no shift in habitat use was observed for the majority of ungulate species, a shift in behaviour was observed for kudu (Tragelaphus strepsiceros) at a landscape scale, where kudu dedicated more time to vigilance and less time to foraging within the predator section. In addition, individuals within smaller kudu groups were observed to be more vigilant than individuals within larger groups of kudu within the predator section. Although the other three ungulate species monitored did not increase time spent vigilant within the predator section, they still maintained relatively high levels of vigilance, potentially as a means of social monitoring. At a patch level, ungulate species responded strongly to a predator cue as a proxy for cheetah proximity, and increased time spent vigilant with a trade-off of lower foraging effort. This vigilant response was strongest for kudu. Differences in perceived predation risk were reflected within eland (Tragelaphus oryx) and kudu species demographic classes, with juvenile eland and kudu, adult female kudu and subadult female kudu spending more time vigilant within manipulated patches than respective males of each species. Kudu were also observed adopting fine-scale behavioural responses to minimize predation risk within patches. The asymmetrical prey species response to perceived predation risk from cheetah supports the hypothesis that different species respond differently to the presence of a predator. Furthermore, this study illustrated the importance of measuring prey responses to predation risk across multiple scales and highlighted the need to replicate this study for a number of different sites where predators have been reintroduced, to better understand the range of factors influencing these predator-prey interactions.
- Full Text:
- Date Issued: 2012
- Authors: Makin, Douglas Ferguson
- Date: 2012
- Subjects: Ungulates -- South Africa -- Eastern Cape , Predatory animals -- Ecology -- South Africa -- Eastern Cape , Predation (Biology) -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10722 , http://hdl.handle.net/10948/d1018461
- Description: Predator reintroductions are becoming increasingly more common for multiple reasons, including assisting with the conservation of a predator species, the restoration of ecosystem functions and the economic benefits of their reintroduction for ecotourism ventures. There remains however, little knowledge on prey species responses to these predator reintroductions. As such, the reintroduction of cheetah (Acinonyx jubatus) into Samara Private Game Reserve provided an opportunity to investigate prey responses to predator reintroduction across a range of spatial and temporal scales. More specifically, the aim of this study was to investigate the effect of cheetah predation risk on habitat use and behavioural responses of the resident ungulate community. Samara is divided into “predator present” and “predator absent” sections, providing the opportunity to conduct a comparative study investigating the effect of cheetah on prey responses. It was hypothesized that different ungulate species would respond differently to the presence of cheetah, depending on differences in perceived vulnerability to cheetah predation. To address this, shifts in habitat use, and behavioural responses of the ungulate community reflected at landscape and patch scale were investigated. Overall, ungulate species have not shifted habitat use since cheetah reintroduction, this was possibly related to life history strategy constraints and the need for individuals to obtain suitable forage and therefore remain in specific habitats. While no shift in habitat use was observed for the majority of ungulate species, a shift in behaviour was observed for kudu (Tragelaphus strepsiceros) at a landscape scale, where kudu dedicated more time to vigilance and less time to foraging within the predator section. In addition, individuals within smaller kudu groups were observed to be more vigilant than individuals within larger groups of kudu within the predator section. Although the other three ungulate species monitored did not increase time spent vigilant within the predator section, they still maintained relatively high levels of vigilance, potentially as a means of social monitoring. At a patch level, ungulate species responded strongly to a predator cue as a proxy for cheetah proximity, and increased time spent vigilant with a trade-off of lower foraging effort. This vigilant response was strongest for kudu. Differences in perceived predation risk were reflected within eland (Tragelaphus oryx) and kudu species demographic classes, with juvenile eland and kudu, adult female kudu and subadult female kudu spending more time vigilant within manipulated patches than respective males of each species. Kudu were also observed adopting fine-scale behavioural responses to minimize predation risk within patches. The asymmetrical prey species response to perceived predation risk from cheetah supports the hypothesis that different species respond differently to the presence of a predator. Furthermore, this study illustrated the importance of measuring prey responses to predation risk across multiple scales and highlighted the need to replicate this study for a number of different sites where predators have been reintroduced, to better understand the range of factors influencing these predator-prey interactions.
- Full Text:
- Date Issued: 2012
COIN : a customisable, incentive driven video on demand framework for low-cost IPTV services
- Authors: Musvibe, Ray
- Date: 2012 , 2012-03-02
- Subjects: Internet television , Digital television , Television broadcasting -- Technological innovations , Multicasting (Computer networks) , Video dial tone , Open source software , Telecommunication , Capital investments
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4654 , http://hdl.handle.net/10962/d1006650 , Internet television , Digital television , Television broadcasting -- Technological innovations , Multicasting (Computer networks) , Video dial tone , Open source software , Telecommunication , Capital investments
- Description: There has been a significant rise in the provision of television and video services over IP (IPTV) in recent years. Increasing network capacity and falling bandwidth costs have made it both technically and economically feasible for service providers to deliver IPTV services. Several telecommunications (telco) operators worldwide are rolling out IPTV solutions and view IPTV as a major service differentiator and alternative revenue source. The main challenge that IPTV providers currently face, however, is the increasingly congested television service provider market, which also includes Internet Television. IPTV solutions therefore need strong service differentiators to succeed. IPTV solutions can doubtlessly sell much faster if they are more affordable or low-cost. Advertising has already been used in many service sectors to help lower service costs, including traditional broadcast television. This thesis therefore explores the role that advertising can play in helping to lower the cost of IPTV services and to incentivise IPTV billing. Another approach that IPTV providers can use to help sell their product is by addressing the growing need for control by today's multimedia users. This thesis will therefore explore the varied approaches that can be used to achieve viewer focused IPTV implementations. To further lower the cost of IPTV services, telcos can also turn to low-cost, open source platforms for service delivery. The adoption of low-cost infrastructure by telcos can lead to reduced Capital Expenditure (CAPEX), which in turn can lead to lower service fees, and ultimately to higher subscriptions and revenue. Therefore, in this thesis, the author proposes a CustOmisable, INcentive (COIN) driven Video on Demand (VoD) framework to be developed and deployed using the Mobicents Communication Platform, an open source service creation and execution platform. The COIN framework aims to provide a viewer focused, economically competitive service that combines the potential cost savings of using free and open source software (FOSS), with an innovative, incentive-driven billing approach. This project will also aim to evaluate whether the Mobicents Platform is a suitable service creation and execution platform for the proposed framework. Additionally, the proposed implementation aims to be interoperable with other IPTV implementations, hence shall follow current IPTV standardisation architectures and trends. The service testbed and its implementation are described in detail and only free and open source software is used; this is to enable its easy duplication and extension for future research. , TeX output 2012.03.02:1241 , Adobe Acrobat 9.2 Paper Capture Plug-in
- Full Text:
- Date Issued: 2012
- Authors: Musvibe, Ray
- Date: 2012 , 2012-03-02
- Subjects: Internet television , Digital television , Television broadcasting -- Technological innovations , Multicasting (Computer networks) , Video dial tone , Open source software , Telecommunication , Capital investments
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4654 , http://hdl.handle.net/10962/d1006650 , Internet television , Digital television , Television broadcasting -- Technological innovations , Multicasting (Computer networks) , Video dial tone , Open source software , Telecommunication , Capital investments
- Description: There has been a significant rise in the provision of television and video services over IP (IPTV) in recent years. Increasing network capacity and falling bandwidth costs have made it both technically and economically feasible for service providers to deliver IPTV services. Several telecommunications (telco) operators worldwide are rolling out IPTV solutions and view IPTV as a major service differentiator and alternative revenue source. The main challenge that IPTV providers currently face, however, is the increasingly congested television service provider market, which also includes Internet Television. IPTV solutions therefore need strong service differentiators to succeed. IPTV solutions can doubtlessly sell much faster if they are more affordable or low-cost. Advertising has already been used in many service sectors to help lower service costs, including traditional broadcast television. This thesis therefore explores the role that advertising can play in helping to lower the cost of IPTV services and to incentivise IPTV billing. Another approach that IPTV providers can use to help sell their product is by addressing the growing need for control by today's multimedia users. This thesis will therefore explore the varied approaches that can be used to achieve viewer focused IPTV implementations. To further lower the cost of IPTV services, telcos can also turn to low-cost, open source platforms for service delivery. The adoption of low-cost infrastructure by telcos can lead to reduced Capital Expenditure (CAPEX), which in turn can lead to lower service fees, and ultimately to higher subscriptions and revenue. Therefore, in this thesis, the author proposes a CustOmisable, INcentive (COIN) driven Video on Demand (VoD) framework to be developed and deployed using the Mobicents Communication Platform, an open source service creation and execution platform. The COIN framework aims to provide a viewer focused, economically competitive service that combines the potential cost savings of using free and open source software (FOSS), with an innovative, incentive-driven billing approach. This project will also aim to evaluate whether the Mobicents Platform is a suitable service creation and execution platform for the proposed framework. Additionally, the proposed implementation aims to be interoperable with other IPTV implementations, hence shall follow current IPTV standardisation architectures and trends. The service testbed and its implementation are described in detail and only free and open source software is used; this is to enable its easy duplication and extension for future research. , TeX output 2012.03.02:1241 , Adobe Acrobat 9.2 Paper Capture Plug-in
- Full Text:
- Date Issued: 2012
Trophic ecology of breeding northern rockhopper penguins, Eudyptes Moseleyi, at Tristan da Cunha, South Atlantic Ocean
- Authors: Booth, Jenny Marie
- Date: 2012
- Subjects: Penguins -- Breeding -- Tristan da Cunha , Penguins -- Ecology -- Tristan da Cunha , Penguins -- Food
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5788 , http://hdl.handle.net/10962/d1005476 , Penguins -- Breeding -- Tristan da Cunha , Penguins -- Ecology -- Tristan da Cunha , Penguins -- Food
- Description: Northern Rockhopper penguin populations, Eudyptes moseleyi, are declining globally, and at Tristan da Cunha have undergone severe declines (> 90% in the last 130 years), the cause(s)of which are unknown. There is a paucity of data on this species in the South Atlantic Ocean, therefore their trophic ecology at Tristan da Cunha was studied, specifically focusing on diet, using stomach content analysis and stable isotope analysis (SIA), in conjunction with an analysis of diving behaviour, assessed using temperature-depth recorders. In order to evaluate the influence of gender on foraging, a morphometric investigation of sexual dimorphism was confirmed using molecular analysis. Additionally, plasma corticosterone levels were measured to examine breeding stage and presence of blood parasites as potential sources of stress during the breeding season. Northern Rockhopper penguins at Tristan da Cunha displayed a high degree of foraging plasticity, and fed opportunistically on a wide variety of prey, probably reflecting local small-scale changes in prey distribution. Zooplankton dominated (by mass) the diet of guard stage females, whereas small meso-pelagic fish (predominantly Photichthyidae)dominated diet of adults of both sexes in the crèche stage, with cephalopods contributing equally in both stages. Adults consistently fed chicks on lower-trophic level prey (assessed using SIA), probably zooplankton, than they consumed themselves indicating that the increasing demands of growing chicks were not met by adults through provisioning of higher- quality prey. SIA also indicated that adults foraged in different oceanic water masses when feeding for self-maintenance and for chick provisioning, thus temporally segregating the prey consumed for different purposes. It is possible that adults ‘selected’ these higher quality prey for themselves, or this may be a reflection of opportunistic behaviour. At Tristan da Cunha sexual dimorphism was observed in culmen dimensions (length, depth, width), with males having larger beaks and feeding on larger individuals of squid and fish than females. No sexual segregation in terms of foraging habitat (i.e. different water masses, based on ð¹³N or trophic level ð¹⁵N) during the breeding season or pre-moult period was revealed through SIA, and stomach content analysis revealed no sexual differences in prey species targeted. The results of SIA of feathers indicate that during the pre-moult period birds foraged in different water masses than during the breeding period. The fact that throughout the breeding season birds foraged in similar habitats suggests no intra-specific competition, despite both sexes feeding on the same prey.Birds were generally diurnal, daily foragers (12 – 16 hr trips), with extended trips (maximum duration 35.5 hours) and nocturnal diving recorded in a few individuals. Birds dived well within their physiological limits, predominantly utilising the upper 20m of the water column, employing two different strategies to target different prey items. Long, deep (30 – 40 m), energetically costly dives were performed when targeting energy-rich prey (fish), and a greater number of shorter, shallower (5 – 20 m), energy-efficient dives were performed when targeting prey with a lower energy content (zooplankton). More than half of the sampled study population were infected with the intra-cellular blood parasite Babesia, but infection showed no relationship to body mass, corticosterone levels or breeding success. Fasting birds showed no signs of elevated corticosterone levels, suggesting they had acquired sufficient fat reserves prior to breeding. Failed breeders did not exhibit elevated corticosterone levels. Tristan skuas, Catharacta antarctica hamiltoni, were observed to be a significant cause of egg and chick mortality. The absence of sex-based differences in foraging, and the absence of any signs of stress in relation to body mass, presence of Babesia or breeding stage, suggest that there are no obvious signs of high levels of stress or food limitations during breeding at Tristan da Cunha.
- Full Text:
- Date Issued: 2012
- Authors: Booth, Jenny Marie
- Date: 2012
- Subjects: Penguins -- Breeding -- Tristan da Cunha , Penguins -- Ecology -- Tristan da Cunha , Penguins -- Food
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5788 , http://hdl.handle.net/10962/d1005476 , Penguins -- Breeding -- Tristan da Cunha , Penguins -- Ecology -- Tristan da Cunha , Penguins -- Food
- Description: Northern Rockhopper penguin populations, Eudyptes moseleyi, are declining globally, and at Tristan da Cunha have undergone severe declines (> 90% in the last 130 years), the cause(s)of which are unknown. There is a paucity of data on this species in the South Atlantic Ocean, therefore their trophic ecology at Tristan da Cunha was studied, specifically focusing on diet, using stomach content analysis and stable isotope analysis (SIA), in conjunction with an analysis of diving behaviour, assessed using temperature-depth recorders. In order to evaluate the influence of gender on foraging, a morphometric investigation of sexual dimorphism was confirmed using molecular analysis. Additionally, plasma corticosterone levels were measured to examine breeding stage and presence of blood parasites as potential sources of stress during the breeding season. Northern Rockhopper penguins at Tristan da Cunha displayed a high degree of foraging plasticity, and fed opportunistically on a wide variety of prey, probably reflecting local small-scale changes in prey distribution. Zooplankton dominated (by mass) the diet of guard stage females, whereas small meso-pelagic fish (predominantly Photichthyidae)dominated diet of adults of both sexes in the crèche stage, with cephalopods contributing equally in both stages. Adults consistently fed chicks on lower-trophic level prey (assessed using SIA), probably zooplankton, than they consumed themselves indicating that the increasing demands of growing chicks were not met by adults through provisioning of higher- quality prey. SIA also indicated that adults foraged in different oceanic water masses when feeding for self-maintenance and for chick provisioning, thus temporally segregating the prey consumed for different purposes. It is possible that adults ‘selected’ these higher quality prey for themselves, or this may be a reflection of opportunistic behaviour. At Tristan da Cunha sexual dimorphism was observed in culmen dimensions (length, depth, width), with males having larger beaks and feeding on larger individuals of squid and fish than females. No sexual segregation in terms of foraging habitat (i.e. different water masses, based on ð¹³N or trophic level ð¹⁵N) during the breeding season or pre-moult period was revealed through SIA, and stomach content analysis revealed no sexual differences in prey species targeted. The results of SIA of feathers indicate that during the pre-moult period birds foraged in different water masses than during the breeding period. The fact that throughout the breeding season birds foraged in similar habitats suggests no intra-specific competition, despite both sexes feeding on the same prey.Birds were generally diurnal, daily foragers (12 – 16 hr trips), with extended trips (maximum duration 35.5 hours) and nocturnal diving recorded in a few individuals. Birds dived well within their physiological limits, predominantly utilising the upper 20m of the water column, employing two different strategies to target different prey items. Long, deep (30 – 40 m), energetically costly dives were performed when targeting energy-rich prey (fish), and a greater number of shorter, shallower (5 – 20 m), energy-efficient dives were performed when targeting prey with a lower energy content (zooplankton). More than half of the sampled study population were infected with the intra-cellular blood parasite Babesia, but infection showed no relationship to body mass, corticosterone levels or breeding success. Fasting birds showed no signs of elevated corticosterone levels, suggesting they had acquired sufficient fat reserves prior to breeding. Failed breeders did not exhibit elevated corticosterone levels. Tristan skuas, Catharacta antarctica hamiltoni, were observed to be a significant cause of egg and chick mortality. The absence of sex-based differences in foraging, and the absence of any signs of stress in relation to body mass, presence of Babesia or breeding stage, suggest that there are no obvious signs of high levels of stress or food limitations during breeding at Tristan da Cunha.
- Full Text:
- Date Issued: 2012
Defect in the South African construction industry
- Authors: Le Roux, Martyn
- Date: 2012
- Subjects: Construction industry -- South Africa , Buildings -- Defects -- South Africa , Quality assurance -- Standards -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:9711 , http://hdl.handle.net/10948/d1020320
- Description: Lack of quality in the South African construction industry is causing various problems for different stakeholders. The causes of this lack in quality are due to various different attributes. Corruption has become one of the leading causes with regards to lack of quality. Quality assurance can mitigate or eliminate defects through the implementation of a quality management system. Defects manifest primarily through cracking, dampness, detachment, and water leaks. Defects are categorized as structural, subsidence, acoustic and thermal. In terms of time, defects are either patent or latent, and can be discovered through observation, inspection and various tests. The causes of defects are ultimately due to error or omission, either during design or during the construction phases. Defects may also result due to procurement related factors, such as appointment of incompetent contractors. The result of defects is customer dissatisfaction, rework and disputes. Non-conformance to requirements results in rework and this in turn contributes to time and cost overruns. The aim of this research was to investigate the greatest cause that leads to defects in houses; the most common type of defect; and why projects fail in term of project management terms (due to defects). Results of quantitative research amongst professionals within the construction industry in the Western and Eastern Cape of South Africa as well as literature that has been reviewed form the basis of this study. Architectural practices, consulting engineering practices, and general building contractors were selected on a random sample basis, and surveyed using an online questionnaire. The study revealed that inadequate artisan skills is the biggest cause leading to defects in houses, and that cracks are the most frequent type of defect occurring. Projects fail in project management terms because of defects as the construction time of the projects are increased. The study revealed that construction related causes of defects dominate over design related causes. This study should be of value to both construction industry professionals as well as their clients.
- Full Text:
- Date Issued: 2012
- Authors: Le Roux, Martyn
- Date: 2012
- Subjects: Construction industry -- South Africa , Buildings -- Defects -- South Africa , Quality assurance -- Standards -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:9711 , http://hdl.handle.net/10948/d1020320
- Description: Lack of quality in the South African construction industry is causing various problems for different stakeholders. The causes of this lack in quality are due to various different attributes. Corruption has become one of the leading causes with regards to lack of quality. Quality assurance can mitigate or eliminate defects through the implementation of a quality management system. Defects manifest primarily through cracking, dampness, detachment, and water leaks. Defects are categorized as structural, subsidence, acoustic and thermal. In terms of time, defects are either patent or latent, and can be discovered through observation, inspection and various tests. The causes of defects are ultimately due to error or omission, either during design or during the construction phases. Defects may also result due to procurement related factors, such as appointment of incompetent contractors. The result of defects is customer dissatisfaction, rework and disputes. Non-conformance to requirements results in rework and this in turn contributes to time and cost overruns. The aim of this research was to investigate the greatest cause that leads to defects in houses; the most common type of defect; and why projects fail in term of project management terms (due to defects). Results of quantitative research amongst professionals within the construction industry in the Western and Eastern Cape of South Africa as well as literature that has been reviewed form the basis of this study. Architectural practices, consulting engineering practices, and general building contractors were selected on a random sample basis, and surveyed using an online questionnaire. The study revealed that inadequate artisan skills is the biggest cause leading to defects in houses, and that cracks are the most frequent type of defect occurring. Projects fail in project management terms because of defects as the construction time of the projects are increased. The study revealed that construction related causes of defects dominate over design related causes. This study should be of value to both construction industry professionals as well as their clients.
- Full Text:
- Date Issued: 2012
In silico characterisation of the four canonical plasmodium falciparum 70 kDa heat shock proteins
- Authors: Hatherley, Rowan
- Date: 2012
- Subjects: Heat shock proteins -- Research , Plasmodium falciparum -- Research , Plasmodium -- Research , Endoplasmic reticulum , Cytosol , Mitochondria -- Formation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4026 , http://hdl.handle.net/10962/d1004086 , Heat shock proteins -- Research , Plasmodium falciparum -- Research , Plasmodium -- Research , Endoplasmic reticulum , Cytosol , Mitochondria -- Formation
- Description: The 70 kDa heat shock proteins expressed by Plasmodium falciparum (PfHsp70s) are believed to be essential to both the survival and virulence of the malaria parasite. A total of six Hsp70 genes have been identified in the genome of P. falciparum. However, only four of these encode canonical Hsp70s, which are believed to localise predominantly in the cytosol (PfHsp70-1 and PfHsp70-x), the endoplasmic reticulum (PfHsp70-2) and mitochondria (PfHsp70-3) of the parasite. These proteins bind and release peptide substrates in an ATP-dependent manner, with the aid of a J-domain protein cochaperone and a nucleotide exchange factor (NEF). The aim of this study was to identify the residues involved in the interaction of these PfHsp70s with their peptide substrates, their J-domain cochaperones and potential NEFs. These residues were then mapped to three-dimensional (3D) structures of the proteins, modelled in three different conformations; each representing a different stage in the ATPase cycle. Additionally, these proteins were compared to different types of Hsp70s from a variety of different organisms and sequence features found to be specific to each PfHsp70 were mapped to their 3D structures. Finally, a novel modelling method was suggested, in which the structures of templates were remodelled to improve their quality before they were used in the homology modelling process. Based on the analysis of residues involved in interactions with other proteins, it was revealed that each PfHsp70 displayed features that were specific to its cellular localisation and each type of Hsp70 was predicted to interact with a different set of NEFs. The study of conserved features in each PfHsp70 revealed that PfHsp70-x displayed various sequence features atypical of both Plasmodium cytosolic Hsp70s and cytosolic Hsp70s in general. Additionally, residues conserved specifically in Hsp70s of Apicomplexa, Plasmodium and P. falciparum were identified and mapped to the each PfHsp70 model. Although these residues were too numerous to reveal any information of specific value, these models may be useful for the purposes of aiding the design of drug compounds against each PfHsp70. Finally, the novel modelling approach did show some promise. Half of the models produced using the modified templates were of a higher quality than their counterparts modelled using the original templates. This approach does still require a lot of validation work and statistical evaluation. It is hoped that it could prove to be a useful approach to homology modelling when the only templates available are poor quality structures.
- Full Text:
- Date Issued: 2012
- Authors: Hatherley, Rowan
- Date: 2012
- Subjects: Heat shock proteins -- Research , Plasmodium falciparum -- Research , Plasmodium -- Research , Endoplasmic reticulum , Cytosol , Mitochondria -- Formation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4026 , http://hdl.handle.net/10962/d1004086 , Heat shock proteins -- Research , Plasmodium falciparum -- Research , Plasmodium -- Research , Endoplasmic reticulum , Cytosol , Mitochondria -- Formation
- Description: The 70 kDa heat shock proteins expressed by Plasmodium falciparum (PfHsp70s) are believed to be essential to both the survival and virulence of the malaria parasite. A total of six Hsp70 genes have been identified in the genome of P. falciparum. However, only four of these encode canonical Hsp70s, which are believed to localise predominantly in the cytosol (PfHsp70-1 and PfHsp70-x), the endoplasmic reticulum (PfHsp70-2) and mitochondria (PfHsp70-3) of the parasite. These proteins bind and release peptide substrates in an ATP-dependent manner, with the aid of a J-domain protein cochaperone and a nucleotide exchange factor (NEF). The aim of this study was to identify the residues involved in the interaction of these PfHsp70s with their peptide substrates, their J-domain cochaperones and potential NEFs. These residues were then mapped to three-dimensional (3D) structures of the proteins, modelled in three different conformations; each representing a different stage in the ATPase cycle. Additionally, these proteins were compared to different types of Hsp70s from a variety of different organisms and sequence features found to be specific to each PfHsp70 were mapped to their 3D structures. Finally, a novel modelling method was suggested, in which the structures of templates were remodelled to improve their quality before they were used in the homology modelling process. Based on the analysis of residues involved in interactions with other proteins, it was revealed that each PfHsp70 displayed features that were specific to its cellular localisation and each type of Hsp70 was predicted to interact with a different set of NEFs. The study of conserved features in each PfHsp70 revealed that PfHsp70-x displayed various sequence features atypical of both Plasmodium cytosolic Hsp70s and cytosolic Hsp70s in general. Additionally, residues conserved specifically in Hsp70s of Apicomplexa, Plasmodium and P. falciparum were identified and mapped to the each PfHsp70 model. Although these residues were too numerous to reveal any information of specific value, these models may be useful for the purposes of aiding the design of drug compounds against each PfHsp70. Finally, the novel modelling approach did show some promise. Half of the models produced using the modified templates were of a higher quality than their counterparts modelled using the original templates. This approach does still require a lot of validation work and statistical evaluation. It is hoped that it could prove to be a useful approach to homology modelling when the only templates available are poor quality structures.
- Full Text:
- Date Issued: 2012