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:
- 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:
In-beam spectroscopy of ⁷²Ge
- Authors: Henninger, Katharine Rose
- Date: 2012
- Subjects: Nuclear shapes , Hyperfine structure
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5559 , http://hdl.handle.net/10962/d1018233
- Description: The high-spin states of the nucleus ⁷²Ge were populated via the ⁷°Zn(a,2n)⁷²Ge fusion-evaporation reaction at a beam-energy of 30 MeV. The ')'-decays were observed with the AFRODITE spectrometer array at iThemba LABS (Faure, South Africa). Twenty-seven new transitions, 18 new levels and 2 new bands were added to the ⁷²Ge level scheme, and several corrections were made to t he previously-known level scheme. Transitions were characterised using Directional Correlation from Oriented states (DCO) and polarisation measurements, and spin-parity assignments were made for 7 new levels. Spin and parity were also reassigned to a previously-known structure. One of the new bands was ident ified as part of an octupole-vibrational band. No tetrahedral states were observed in the scheme despite N = 40 and Z = 32 having been identified as tetrahedral magic numbers. The meaning of the new 14⁺ yrast level for the underlying structure of the ground state band is discussed
- Full Text:
- Authors: Henninger, Katharine Rose
- Date: 2012
- Subjects: Nuclear shapes , Hyperfine structure
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5559 , http://hdl.handle.net/10962/d1018233
- Description: The high-spin states of the nucleus ⁷²Ge were populated via the ⁷°Zn(a,2n)⁷²Ge fusion-evaporation reaction at a beam-energy of 30 MeV. The ')'-decays were observed with the AFRODITE spectrometer array at iThemba LABS (Faure, South Africa). Twenty-seven new transitions, 18 new levels and 2 new bands were added to the ⁷²Ge level scheme, and several corrections were made to t he previously-known level scheme. Transitions were characterised using Directional Correlation from Oriented states (DCO) and polarisation measurements, and spin-parity assignments were made for 7 new levels. Spin and parity were also reassigned to a previously-known structure. One of the new bands was ident ified as part of an octupole-vibrational band. No tetrahedral states were observed in the scheme despite N = 40 and Z = 32 having been identified as tetrahedral magic numbers. The meaning of the new 14⁺ yrast level for the underlying structure of the ground state band is discussed
- Full Text:
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:
- 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:
Investigation of the effect of short duration breaks in delaying the onset of performance related fatigue during long distance monotonous driving at different times of the day
- Authors: Ndaki, Ntombikayise
- Date: 2012
- Subjects: Fatigue -- Physiological aspects , Drowsiness -- Physiological aspects , Automobile driving -- Physiological aspects , Traffic safety -- South Africa , Automobile driving -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5170 , http://hdl.handle.net/10962/d1016353
- Description: Road traffic accidents are a serious burden to the health systems of many countries especially in South Africa. Research aimed at reducing traffic related accidents is of importance as traffic crashes are rated as the second leading cause of fatalities in South Africa and ninth in the world. Despite the extensive efforts into research and development of new technology, driver fatigue still remains a cause of vehicle accidents worldwide. Fatigue plays a role in up to 20% of vehicle accidents with many being serious or fatal. Numerous coping behaviours are employed by drivers to counteract the negative effects of fatigue. The most common coping behaviours include taking short naps, talking to passengers, listening to the radio, opening windows and drinking stimulants. Driving breaks have long been identified as an effective countermeasure against fatigue. Most research done in driving breaks has investigated the duration of the breaks, activity undertaken during the break and the frequency of the breaks taken outside the vehicle. However limited literature is available on the effectiveness of breaks in counteracting the effects of fatigue. The objective of the current study was aimed at assessing whether short duration breaks are an effective countermeasure against fatigue. Physiological, neurophysiological, subjective and performance measures were used as indicators for fatigue. Additional focus of the research was determining whether breaks were more or less effective at counteracting the effects of fatigue at different times of day. Twelve participants were recruited for the study, six males and six females. The participants were required to perform a driving task on a simulator for 90 minutes. The study consisted of four independent conditions, namely driving during the day with breaks, driving during the day without breaks, driving during the night with breaks and driving during the night without breaks. The without breaks conditions were similar except that they occurred at different times of the day, one session at night and the other session during day time, as was the case for the conditions with breaks. The driving task used in the current study was a low fidelity simulator tracking task. The participants were required to follow a centre line displayed on a tracking path as accurately as possible. The measurements that were recorded in this study included physiological, performance, subjective and neurophysiological. Physiological measures included heart rate and heart rate variability (frequency domain) and core body temperature. The ascending threshold of the critical flicker fusion frequency was the only neurophysiological measurement included in the current investigation. Performance was quantified by mean deviation from a centre line participants were meant to track. Two rating scales were used: Karolinska sleepiness scale and the Wits sleepiness scale were used for the measurement of subjective sleepiness. Heart rate, heart rate variability and mean deviation were measured continuously throughout the 90 minute driving task. Critical flicker fusion frequency, temperature and the subjective scales were measured before and after the 90 minute driving task. The results indicated that the short duration breaks during day time had a positive effect on driving performance; however the breaks at night had a negative effect on driving performance. Heart rate was higher during the day compared to night time and the heart rate variability high frequency spectrum values were lower during the day condition, to show the activation of the sympathetic nervous system which is characteristic of day time. The night conditions had lower heart rate values and higher heart rate variability high frequency values, which show the activation of the parasympathetic nervous system which is dominant during periods of fatigue and night time. Subjective sleepiness levels were also higher at night compared to day time.
- Full Text:
- Authors: Ndaki, Ntombikayise
- Date: 2012
- Subjects: Fatigue -- Physiological aspects , Drowsiness -- Physiological aspects , Automobile driving -- Physiological aspects , Traffic safety -- South Africa , Automobile driving -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5170 , http://hdl.handle.net/10962/d1016353
- Description: Road traffic accidents are a serious burden to the health systems of many countries especially in South Africa. Research aimed at reducing traffic related accidents is of importance as traffic crashes are rated as the second leading cause of fatalities in South Africa and ninth in the world. Despite the extensive efforts into research and development of new technology, driver fatigue still remains a cause of vehicle accidents worldwide. Fatigue plays a role in up to 20% of vehicle accidents with many being serious or fatal. Numerous coping behaviours are employed by drivers to counteract the negative effects of fatigue. The most common coping behaviours include taking short naps, talking to passengers, listening to the radio, opening windows and drinking stimulants. Driving breaks have long been identified as an effective countermeasure against fatigue. Most research done in driving breaks has investigated the duration of the breaks, activity undertaken during the break and the frequency of the breaks taken outside the vehicle. However limited literature is available on the effectiveness of breaks in counteracting the effects of fatigue. The objective of the current study was aimed at assessing whether short duration breaks are an effective countermeasure against fatigue. Physiological, neurophysiological, subjective and performance measures were used as indicators for fatigue. Additional focus of the research was determining whether breaks were more or less effective at counteracting the effects of fatigue at different times of day. Twelve participants were recruited for the study, six males and six females. The participants were required to perform a driving task on a simulator for 90 minutes. The study consisted of four independent conditions, namely driving during the day with breaks, driving during the day without breaks, driving during the night with breaks and driving during the night without breaks. The without breaks conditions were similar except that they occurred at different times of the day, one session at night and the other session during day time, as was the case for the conditions with breaks. The driving task used in the current study was a low fidelity simulator tracking task. The participants were required to follow a centre line displayed on a tracking path as accurately as possible. The measurements that were recorded in this study included physiological, performance, subjective and neurophysiological. Physiological measures included heart rate and heart rate variability (frequency domain) and core body temperature. The ascending threshold of the critical flicker fusion frequency was the only neurophysiological measurement included in the current investigation. Performance was quantified by mean deviation from a centre line participants were meant to track. Two rating scales were used: Karolinska sleepiness scale and the Wits sleepiness scale were used for the measurement of subjective sleepiness. Heart rate, heart rate variability and mean deviation were measured continuously throughout the 90 minute driving task. Critical flicker fusion frequency, temperature and the subjective scales were measured before and after the 90 minute driving task. The results indicated that the short duration breaks during day time had a positive effect on driving performance; however the breaks at night had a negative effect on driving performance. Heart rate was higher during the day compared to night time and the heart rate variability high frequency spectrum values were lower during the day condition, to show the activation of the sympathetic nervous system which is characteristic of day time. The night conditions had lower heart rate values and higher heart rate variability high frequency values, which show the activation of the parasympathetic nervous system which is dominant during periods of fatigue and night time. Subjective sleepiness levels were also higher at night compared to day time.
- Full Text:
Leopard population density, home range size and movement patterns in a mixed landuse area of the Mangwe District of Zimbabwe
- Authors: Grant, Tanith-Leigh
- Date: 2012
- Subjects: Leopard -- Monitoring -- Zimbabwe , Leopard -- Conservation -- Zimbabwe , Wildlife monitoring -- Zimbabwe , Wildlife conservation -- Zimbabwe
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5726 , http://hdl.handle.net/10962/d1005412 , Leopard -- Monitoring -- Zimbabwe , Leopard -- Conservation -- Zimbabwe , Wildlife monitoring -- Zimbabwe , Wildlife conservation -- Zimbabwe
- Description: Trophy hunting is often employed as a conservation management tool for large predators. However, in order for this method to succeed, hunting levels must be sustainable. Very little robust population data exist for African leopards (Panthera pardus) in general, and almost no density or spatial ecology data exist for leopards in Zimbabwe. Zimbabwe has one of the highest annual CITES leopard trophy hunting quotas in Africa, the sustainability of which has not been assessed, despite large scale landuse changes over the last 12 years. The focal area of this study was within the Mangwe district, in the south-west of Zimbabwe. The region is dominated by cattle and wildlife ranches, with high levels of leopard hunting, making it an important area for assessing leopard population density and spatial ecology. Three population density estimation methods were employed in my study: a spoor index survey, an unbaited camera-trapping survey and a baited camera-trapping survey. Using three calibration equations, spoor indices appeared to underestimate the leopard population (1.28-3.29 leopards/ 100 km²) as the equations were calibrated for areas with different habitats and leopard densities. In addition, the unbaited camera survey only produced six leopard photographs, unsuitable for individual identification and analysis. By contrast, the baited camera survey produced 292 identifiable leopard photographs, from which 13 individuals were identified. Density estimates calculated using the programme CAPTURE and the M[subscript]h model with the Mean Maximum Distance Moved Outside of Study Area (MMDMOSA) buffer method (4.79±0.83 leopards/100 km²), and the programme SPACECAP, using a buffer of 2.5 km (5.12±0.62 leopards/100 km²), appeared to generate the most reliable leopard population estimates. To assess the spatial ecology, three leopards (one male, two females) were captured and fitted with GPS collars. The home range estimates of the three leopards (95% Kernel UD: male 263 km², females 31 and 45 km²) were smaller than those of leopards in more arid regions, but larger than those of mesic habitats. This suggests that the Mangwe area has a higher quality habitat than the arid regions of Namibia, but less suitable habitat than protected bushveld areas (e.g. Kruger National Park, South Africa). My data represents the first robust leopard density and home range assessment for Zimbabwe. In addition, my results indicate that the current hunting quota issued to the Mangwe area is unsustainable. Consequently, I recommend revising the quota to five leopards for the entire area, and halving the current national leopard quota to 250, until a national leopard census is completed.
- Full Text:
- Authors: Grant, Tanith-Leigh
- Date: 2012
- Subjects: Leopard -- Monitoring -- Zimbabwe , Leopard -- Conservation -- Zimbabwe , Wildlife monitoring -- Zimbabwe , Wildlife conservation -- Zimbabwe
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5726 , http://hdl.handle.net/10962/d1005412 , Leopard -- Monitoring -- Zimbabwe , Leopard -- Conservation -- Zimbabwe , Wildlife monitoring -- Zimbabwe , Wildlife conservation -- Zimbabwe
- Description: Trophy hunting is often employed as a conservation management tool for large predators. However, in order for this method to succeed, hunting levels must be sustainable. Very little robust population data exist for African leopards (Panthera pardus) in general, and almost no density or spatial ecology data exist for leopards in Zimbabwe. Zimbabwe has one of the highest annual CITES leopard trophy hunting quotas in Africa, the sustainability of which has not been assessed, despite large scale landuse changes over the last 12 years. The focal area of this study was within the Mangwe district, in the south-west of Zimbabwe. The region is dominated by cattle and wildlife ranches, with high levels of leopard hunting, making it an important area for assessing leopard population density and spatial ecology. Three population density estimation methods were employed in my study: a spoor index survey, an unbaited camera-trapping survey and a baited camera-trapping survey. Using three calibration equations, spoor indices appeared to underestimate the leopard population (1.28-3.29 leopards/ 100 km²) as the equations were calibrated for areas with different habitats and leopard densities. In addition, the unbaited camera survey only produced six leopard photographs, unsuitable for individual identification and analysis. By contrast, the baited camera survey produced 292 identifiable leopard photographs, from which 13 individuals were identified. Density estimates calculated using the programme CAPTURE and the M[subscript]h model with the Mean Maximum Distance Moved Outside of Study Area (MMDMOSA) buffer method (4.79±0.83 leopards/100 km²), and the programme SPACECAP, using a buffer of 2.5 km (5.12±0.62 leopards/100 km²), appeared to generate the most reliable leopard population estimates. To assess the spatial ecology, three leopards (one male, two females) were captured and fitted with GPS collars. The home range estimates of the three leopards (95% Kernel UD: male 263 km², females 31 and 45 km²) were smaller than those of leopards in more arid regions, but larger than those of mesic habitats. This suggests that the Mangwe area has a higher quality habitat than the arid regions of Namibia, but less suitable habitat than protected bushveld areas (e.g. Kruger National Park, South Africa). My data represents the first robust leopard density and home range assessment for Zimbabwe. In addition, my results indicate that the current hunting quota issued to the Mangwe area is unsustainable. Consequently, I recommend revising the quota to five leopards for the entire area, and halving the current national leopard quota to 250, until a national leopard census is completed.
- Full Text:
Life-history and stock assessment of Clarias Gariepinus in the Okavango Delta, Botswana
- Authors: Bokhutlo, Thethela
- Date: 2012
- Subjects: Catfishes -- Botswana -- Okavango River Delta , Clarias gariepinus , Aquaculture -- Botswana -- Okavango River Delta
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5297 , http://hdl.handle.net/10962/d1005142 , Catfishes -- Botswana -- Okavango River Delta , Clarias gariepinus , Aquaculture -- Botswana -- Okavango River Delta
- Description: Large catfishes (Clarias gariepinus & Clarias ngamensis) are not exploited commercially in the Okavango Delta, Botswana. They however constitute a large proportion of the gill net fishery catch (23 %) albeit as by-catch, coming second after cichlids (70 %). Monthly experimetal gill net sampling over 8 years showed that C. gariepinus was the most abundant species in the Okavango Delta by mass making up 37 % of the catch composition by fresh weight. Despite the relatively high abundance of C. gariepinus in the Okavango Delta, its status has never been fully assessed. For this reason, this study aimed to assess the status of C. gariepinus in the Okavango Delta with the particular goal to determine if the species could support a directed commercial gill net fishery. Investigation of the effects of the flood pulse on abundance of C. gariepinus showed that variability in water levels was the major driver of population abundance for this species. Three biological variables: (1) catch per unit effort (CPUE); (2) % catch composition and (3) Shannon's diversity index (H') exhibited a negative and significant relationship with the flood index within a year. The variation in these variables was statistically significant between months. There was a weak positive relationship between water levels and the biological variables between years suggesting increase in productivity of the system at high water levels without a lag period. Age and growth were determined using sectioned otoliths. Edge analysis showed that growth zone deposition occurred during the drawdown period in summer when water temperature and day length were increasing. The maximum recorded age was 15 years. Growth of this species was best described by the linear models (y = 21.50x + 427.39 mm LT; r² = 0.35) for females and (y = 23.79x + 440.83 mm LT; r² = 0.38) for males. The von Bertalanffy growth model described growth as Lt = 10000(1- exp(-0.002(t + 18.07))) mm LT for combined sexes Lt = 10000(1- exp( -0.002(t + 18.50))) mm LT , for females and Lt =908(1-exp(-0.076(t+7.95)))mmLT for males. Age at 50 % maturity was attained in the first year of life. Spawning occurred throughout the year with an apparent peak between November and April. The mean total annual mortality rate (Z) was 0.25 per year. The mean annual natural mortality rate (M) was 0.20 per year and fishing mortality (F) was calculated at 0.05 per year. The life history strategy of C. gariepinus was in between the periodic and opportunistic strategies. Therefore management of this species should be aimed at maintaining a healthy adult population and age structure. Since a large portion of the Okavango Delta is already protected and most other parts are also inaccessible to fishers there are enough spatial refugia for the species and the status quo should be maintained. Under this scenario, there is no need for regulation of the current mesh sizes because the species is harvested after maturity and replenishment of exploited populations will always occur from other parts of the system. Per recruit analyses indicate that the current fishing mortality maintains spawner biomass at levels greater than 90 % of pristine levels. Therefore a commercial fishery may be established using mesh 93 mm to maximize yield with a rotational harvesting strategy. Close monitoring is essential to ensure that re-colonization of overexploited habitats does indeed occur. Recreational angling and commercial gill net fishing need to be separated on a spatial and temporal scale during the feeding run to minimize potential conflicts.
- Full Text:
- Authors: Bokhutlo, Thethela
- Date: 2012
- Subjects: Catfishes -- Botswana -- Okavango River Delta , Clarias gariepinus , Aquaculture -- Botswana -- Okavango River Delta
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5297 , http://hdl.handle.net/10962/d1005142 , Catfishes -- Botswana -- Okavango River Delta , Clarias gariepinus , Aquaculture -- Botswana -- Okavango River Delta
- Description: Large catfishes (Clarias gariepinus & Clarias ngamensis) are not exploited commercially in the Okavango Delta, Botswana. They however constitute a large proportion of the gill net fishery catch (23 %) albeit as by-catch, coming second after cichlids (70 %). Monthly experimetal gill net sampling over 8 years showed that C. gariepinus was the most abundant species in the Okavango Delta by mass making up 37 % of the catch composition by fresh weight. Despite the relatively high abundance of C. gariepinus in the Okavango Delta, its status has never been fully assessed. For this reason, this study aimed to assess the status of C. gariepinus in the Okavango Delta with the particular goal to determine if the species could support a directed commercial gill net fishery. Investigation of the effects of the flood pulse on abundance of C. gariepinus showed that variability in water levels was the major driver of population abundance for this species. Three biological variables: (1) catch per unit effort (CPUE); (2) % catch composition and (3) Shannon's diversity index (H') exhibited a negative and significant relationship with the flood index within a year. The variation in these variables was statistically significant between months. There was a weak positive relationship between water levels and the biological variables between years suggesting increase in productivity of the system at high water levels without a lag period. Age and growth were determined using sectioned otoliths. Edge analysis showed that growth zone deposition occurred during the drawdown period in summer when water temperature and day length were increasing. The maximum recorded age was 15 years. Growth of this species was best described by the linear models (y = 21.50x + 427.39 mm LT; r² = 0.35) for females and (y = 23.79x + 440.83 mm LT; r² = 0.38) for males. The von Bertalanffy growth model described growth as Lt = 10000(1- exp(-0.002(t + 18.07))) mm LT for combined sexes Lt = 10000(1- exp( -0.002(t + 18.50))) mm LT , for females and Lt =908(1-exp(-0.076(t+7.95)))mmLT for males. Age at 50 % maturity was attained in the first year of life. Spawning occurred throughout the year with an apparent peak between November and April. The mean total annual mortality rate (Z) was 0.25 per year. The mean annual natural mortality rate (M) was 0.20 per year and fishing mortality (F) was calculated at 0.05 per year. The life history strategy of C. gariepinus was in between the periodic and opportunistic strategies. Therefore management of this species should be aimed at maintaining a healthy adult population and age structure. Since a large portion of the Okavango Delta is already protected and most other parts are also inaccessible to fishers there are enough spatial refugia for the species and the status quo should be maintained. Under this scenario, there is no need for regulation of the current mesh sizes because the species is harvested after maturity and replenishment of exploited populations will always occur from other parts of the system. Per recruit analyses indicate that the current fishing mortality maintains spawner biomass at levels greater than 90 % of pristine levels. Therefore a commercial fishery may be established using mesh 93 mm to maximize yield with a rotational harvesting strategy. Close monitoring is essential to ensure that re-colonization of overexploited habitats does indeed occur. Recreational angling and commercial gill net fishing need to be separated on a spatial and temporal scale during the feeding run to minimize potential conflicts.
- Full Text:
Malarial drug targets cysteine proteases as hemoglobinases
- Authors: Mokoena, Fortunate
- Date: 2012
- Subjects: Malaria -- Chemotherapy , Antimalarials , Hemoglobin , Proteolytic enzymes , Cysteine proteinases , Plasmodium falciparum , Plasmodium vivax , Papain
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4005 , http://hdl.handle.net/10962/d1004065 , Malaria -- Chemotherapy , Antimalarials , Hemoglobin , Proteolytic enzymes , Cysteine proteinases , Plasmodium falciparum , Plasmodium vivax , Papain
- Description: Malaria has consistently been rated as the worst parasitic disease in the world. This disease affects an estimated 5 billion households annually. Malaria has a high mortality rate leading to distorted socio-economic development of the world at large. The major challenge pertaining to malaria is its continuous and rapid spread together with the emergence of drug resistance in Plasmodium species (vector agent of the disease). For this reason, researchers throughout the world are following new leads for possible drug targets and therefore, investigating ways of curbing the spread of the disease. Cysteine proteases have emerged as potential antimalarial chemotherapeutic targets. These particular proteases are found in all living organisms, Plasmodium cysteine proteases are known to degrade host hemoglobin during the life cycle of the parasite within the human host. The main objective of this study was to use various in silico methods to analyze the hemoglobinase function of cysteine proteases in P. falciparum and P. vivax. Falcipain-2 (FP2) of P. falciparum is the best characterized of these enzymes, it is a validated drug target. Both the three-dimensional structures of FP2 and its close homologue falcipain-3 (FP3) have been solved by the experimental technique X-ray crystallography. However, the homologue falcipain-2 (FP2’)’ and orthologues from P.vivax vivapain-2 (VP2) and vivapain-3 (VP3) have yet to be elucidated by experimental techniques. In an effort to achieve the principal goal of the study, homology models of the protein structures not already elucidated by experimental methods (FP2’, VP2 and VP3) were calculated using the well known spatial restraint program MODELLER. The derived models, FP2 and FP3 were docked to hemoglobin (their natural substrate). The protein-protein docking was done using the unbound docking program ZDOCK. The substrate-enzyme interactions were analyzed and amino acids involved in binding were observed. It is anticipated that the results obtained from the study will help focus inhibitor design for potential drugs against malaria. The residues found in both the P. falciparum and P. vivax cysteine proteases involved in hemoglobin binding have been identified and some of these are proposed to be the main focus for the design of a peptidomimetric inhibitor.
- Full Text:
- Authors: Mokoena, Fortunate
- Date: 2012
- Subjects: Malaria -- Chemotherapy , Antimalarials , Hemoglobin , Proteolytic enzymes , Cysteine proteinases , Plasmodium falciparum , Plasmodium vivax , Papain
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4005 , http://hdl.handle.net/10962/d1004065 , Malaria -- Chemotherapy , Antimalarials , Hemoglobin , Proteolytic enzymes , Cysteine proteinases , Plasmodium falciparum , Plasmodium vivax , Papain
- Description: Malaria has consistently been rated as the worst parasitic disease in the world. This disease affects an estimated 5 billion households annually. Malaria has a high mortality rate leading to distorted socio-economic development of the world at large. The major challenge pertaining to malaria is its continuous and rapid spread together with the emergence of drug resistance in Plasmodium species (vector agent of the disease). For this reason, researchers throughout the world are following new leads for possible drug targets and therefore, investigating ways of curbing the spread of the disease. Cysteine proteases have emerged as potential antimalarial chemotherapeutic targets. These particular proteases are found in all living organisms, Plasmodium cysteine proteases are known to degrade host hemoglobin during the life cycle of the parasite within the human host. The main objective of this study was to use various in silico methods to analyze the hemoglobinase function of cysteine proteases in P. falciparum and P. vivax. Falcipain-2 (FP2) of P. falciparum is the best characterized of these enzymes, it is a validated drug target. Both the three-dimensional structures of FP2 and its close homologue falcipain-3 (FP3) have been solved by the experimental technique X-ray crystallography. However, the homologue falcipain-2 (FP2’)’ and orthologues from P.vivax vivapain-2 (VP2) and vivapain-3 (VP3) have yet to be elucidated by experimental techniques. In an effort to achieve the principal goal of the study, homology models of the protein structures not already elucidated by experimental methods (FP2’, VP2 and VP3) were calculated using the well known spatial restraint program MODELLER. The derived models, FP2 and FP3 were docked to hemoglobin (their natural substrate). The protein-protein docking was done using the unbound docking program ZDOCK. The substrate-enzyme interactions were analyzed and amino acids involved in binding were observed. It is anticipated that the results obtained from the study will help focus inhibitor design for potential drugs against malaria. The residues found in both the P. falciparum and P. vivax cysteine proteases involved in hemoglobin binding have been identified and some of these are proposed to be the main focus for the design of a peptidomimetric inhibitor.
- Full Text:
Microalgae biomass as fermentation feedstock
- Authors: Tijjani-Oshungboye, Kubura
- Date: 2012
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5956 , http://hdl.handle.net/10962/d1006168
- Description: The search for alternative energy is as a result of pollution generated by the utilization of fossil fuel. Bearing in mind the increase in demand which exceeds supply, alternative energy must reduce the carbon foot print in order to relieve use of fossil fuels. Biogas generation from wastes is an old technology that has been in existence for decades. This same concept was behind the development of the integrated algae ponding system (IAPS), where the use of microalgae biomass is adopted for waste water treatment and, anaerobic digestion which is a component of the IAPS, simultaneously generates biogas. The biogas from the IAPS was quantified in order to evaluate efficiency of the system and the anaerobic fermentation pit was also simulated in the laboratory to optimize biogas production using microalgae as co-fermentation feedstock. Microalgae biomass was evaluated as potential feedstock for ethanol fermentation and the use of biogas was investigated as an alternative transportation fuel. In an IAPS substantial biomass is produced on an annual basis. For effective treatment of waste water and efficient nutrient removal continuous harvest of the biomass is required. In the present study, water treatment efficiency of the EBRU IAPS was determined by carrying out a series of tests to investigate the decline in nutrient content from port of influent entry to effluent discharge. There was more than a 60% reduction in nutrient content with a concomitant increase in biomass and growth rate of 0.25 g/L . Biogas generated from the IAPS was quantified using a flow meter and the composition determined by gas chromatography. Methane which is the principal constituent of biogas was 75% (±SD, n=IO) and 2.34 m³.d⁻¹ was measured as biogas yield from the EBRU IAPS. The study also investigated the use of the excess microalgae biomass as a fermentation feedstock for ethanol production and as a co-substrate in order to increase biogas yield from the system. Positive results were achieved for ethanol production from microalgae although yield was generally low. About 385 mg.⁻¹ of ethanol was recovered when glucose was used as substrate, where as only 115 mg.⁻¹ of ethanol was recovered with microalgae as substrate. Suitability of microalgae as feedstock for ethanol generation and biogas generation was determined by characterisation which involved estimation of the carbohydrate, protein and lipid content, and analysis of the C, H, 0, Nand S content. Laboratory fed batch reactors simulated the anaerobic digestion process in order to study the effect of microalgae biomass as co-substrate for biogas generation. The fermenters were inoculated with an active consortium obtained from the Makana municipal waste water works and microbial studies were carried to confirm the presence of the anaerobic consortium. Different pre-treatments (concentrated, rupturing and freeze-drying) were used to disrupt the microalgae prior to introduction into fermenters in a ratio of 3: I. COD, TC, TOC, SO₄⁻² and TN analyses were carried out to monitor nutrient depletion in the system, and biogas generated by the system was quantified by volumetric analysis and the gas composition determined. Statistical analysis (ANOVA) was used to test for significant difference pre and post addition of microalgae. In the most effective fermenter, biogas production was at an average of 394 ml.d·' and CH₄ ratio in the biogas increased by over a 100%. Theoretical methane potential of the IAPS and the Makana municipal waste water works treating 5 ML.d⁻¹ of domestic waste was determined using the empirical formula of waste water and shown to yield 1,037,342.40 m³/yr. The projected biogas yield from this system was used to evaluate its potential use as transportation fuel. In total, 198,673 .55 m³ of biogas was estimated to be required to fuel the Rhodes University's fleet of vehicles, with a residual biogas stream of 838,668.85 m³. It was also demonstrated in the present study that renewable energy sourced from biomass has the potential of supplanting the use of fossil fuel resulting in less pollution leading to a cleaner and healthier environment.
- Full Text:
- Authors: Tijjani-Oshungboye, Kubura
- Date: 2012
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5956 , http://hdl.handle.net/10962/d1006168
- Description: The search for alternative energy is as a result of pollution generated by the utilization of fossil fuel. Bearing in mind the increase in demand which exceeds supply, alternative energy must reduce the carbon foot print in order to relieve use of fossil fuels. Biogas generation from wastes is an old technology that has been in existence for decades. This same concept was behind the development of the integrated algae ponding system (IAPS), where the use of microalgae biomass is adopted for waste water treatment and, anaerobic digestion which is a component of the IAPS, simultaneously generates biogas. The biogas from the IAPS was quantified in order to evaluate efficiency of the system and the anaerobic fermentation pit was also simulated in the laboratory to optimize biogas production using microalgae as co-fermentation feedstock. Microalgae biomass was evaluated as potential feedstock for ethanol fermentation and the use of biogas was investigated as an alternative transportation fuel. In an IAPS substantial biomass is produced on an annual basis. For effective treatment of waste water and efficient nutrient removal continuous harvest of the biomass is required. In the present study, water treatment efficiency of the EBRU IAPS was determined by carrying out a series of tests to investigate the decline in nutrient content from port of influent entry to effluent discharge. There was more than a 60% reduction in nutrient content with a concomitant increase in biomass and growth rate of 0.25 g/L . Biogas generated from the IAPS was quantified using a flow meter and the composition determined by gas chromatography. Methane which is the principal constituent of biogas was 75% (±SD, n=IO) and 2.34 m³.d⁻¹ was measured as biogas yield from the EBRU IAPS. The study also investigated the use of the excess microalgae biomass as a fermentation feedstock for ethanol production and as a co-substrate in order to increase biogas yield from the system. Positive results were achieved for ethanol production from microalgae although yield was generally low. About 385 mg.⁻¹ of ethanol was recovered when glucose was used as substrate, where as only 115 mg.⁻¹ of ethanol was recovered with microalgae as substrate. Suitability of microalgae as feedstock for ethanol generation and biogas generation was determined by characterisation which involved estimation of the carbohydrate, protein and lipid content, and analysis of the C, H, 0, Nand S content. Laboratory fed batch reactors simulated the anaerobic digestion process in order to study the effect of microalgae biomass as co-substrate for biogas generation. The fermenters were inoculated with an active consortium obtained from the Makana municipal waste water works and microbial studies were carried to confirm the presence of the anaerobic consortium. Different pre-treatments (concentrated, rupturing and freeze-drying) were used to disrupt the microalgae prior to introduction into fermenters in a ratio of 3: I. COD, TC, TOC, SO₄⁻² and TN analyses were carried out to monitor nutrient depletion in the system, and biogas generated by the system was quantified by volumetric analysis and the gas composition determined. Statistical analysis (ANOVA) was used to test for significant difference pre and post addition of microalgae. In the most effective fermenter, biogas production was at an average of 394 ml.d·' and CH₄ ratio in the biogas increased by over a 100%. Theoretical methane potential of the IAPS and the Makana municipal waste water works treating 5 ML.d⁻¹ of domestic waste was determined using the empirical formula of waste water and shown to yield 1,037,342.40 m³/yr. The projected biogas yield from this system was used to evaluate its potential use as transportation fuel. In total, 198,673 .55 m³ of biogas was estimated to be required to fuel the Rhodes University's fleet of vehicles, with a residual biogas stream of 838,668.85 m³. It was also demonstrated in the present study that renewable energy sourced from biomass has the potential of supplanting the use of fossil fuel resulting in less pollution leading to a cleaner and healthier environment.
- Full Text:
Molecular chaperone expression and function in breast cancer and breast cancer stem cells
- Authors: Sterrenberg, Jason Neville
- Date: 2012
- Subjects: Breast -- Cancer , Stem cells , Cancer cells
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4141 , http://hdl.handle.net/10962/d1016238
- Description: The Cancer Stem Cell (CSC) theory suggests that cancers arise from and are maintained by a subpopulation of cancer cells with stem cell properties. Molecular chaperones are key components of cellular regulation. The overexpression of chaperones has become synonymous with cancer cells with chaperones being recognized as bona fide anti-cancer drug targets. Although chaperone activity has been characterized in cancer cells, very little is known about the cellular functions of chaperones in cancer stem cells. We set out to compare the expression of selected molecular chaperones in non-stem cancer cell and cancer stem cell enriched populations isolated from breast cancer lines, in order to identify chaperones differentially expressed between the two populations for further biological characterization. In order to isolate breast cancer stem cells from the MCF-7 and MDA-MB-231 breast cancer cell lines, three cancer stem cell isolation and identification techniques were utilized based on (1) cell surface marker expression (CD44+/CD24- and CD44+/CD24-/EpCAM+ phenotypes), (2) aldehyde dehydrogenase enzyme activity (ALDHHi) and (3) ability to grow in anchorage-independent conditions. The MDA-MB-231 and MCF-7 breast cancer cell lines displayed CD44+/CD24- cell populations with the MCF-7 cell line additionally displaying a large CD44+/CD24-/EpCAM+ population. Although both cell lines showed similar ALDHHi populations, they differed substantially with respect to anchorage-independent growth. MCF-7 cells were able to form anchorage-independent colonies while the MDA-MB-231 cell line was not. Anchorage-independent MCF-7 cells showed enrichment in CD44+/CD24- and CD44+/CD24-/EpCAM+ cells compared to adherent MCF-7 cells, and were selected for gene expression studies. Gene expression studies identified 22 genes as being down-regulated at the mRNA level in the anchorage-independent MCF-7 cells, while only 2 genes (BAG1 and DNAJC12) were up-regulated. The down-regulation of selected chaperones in anchorage independent MCF-7 cells was confirmed at the protein level for selected chaperones, including DNAJB6, a type II DNAJ protein shown to be involved in the regulation of Wnt signaling. In order to characterize the effect of DNAJB6 expression on BCSCs we developed a pCMV mammalian expression plasmid for both DNAJB6 isoforms (DNAJB6L and DNAJB6S). We successfully constructed mutants of the conserved histidine-proline-aspartic acid (HPD) motif of the J domain of DNAJB6S and DNAJB6L. These constructs will allow the analysis of the role of DNAJB6 in cancer stem cell function. To the best of our knowledge, this is the first report to focus on the comparative expression of molecular chaperones in normal and cancer stem cell enriched breast cancer populations.
- Full Text:
- Authors: Sterrenberg, Jason Neville
- Date: 2012
- Subjects: Breast -- Cancer , Stem cells , Cancer cells
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4141 , http://hdl.handle.net/10962/d1016238
- Description: The Cancer Stem Cell (CSC) theory suggests that cancers arise from and are maintained by a subpopulation of cancer cells with stem cell properties. Molecular chaperones are key components of cellular regulation. The overexpression of chaperones has become synonymous with cancer cells with chaperones being recognized as bona fide anti-cancer drug targets. Although chaperone activity has been characterized in cancer cells, very little is known about the cellular functions of chaperones in cancer stem cells. We set out to compare the expression of selected molecular chaperones in non-stem cancer cell and cancer stem cell enriched populations isolated from breast cancer lines, in order to identify chaperones differentially expressed between the two populations for further biological characterization. In order to isolate breast cancer stem cells from the MCF-7 and MDA-MB-231 breast cancer cell lines, three cancer stem cell isolation and identification techniques were utilized based on (1) cell surface marker expression (CD44+/CD24- and CD44+/CD24-/EpCAM+ phenotypes), (2) aldehyde dehydrogenase enzyme activity (ALDHHi) and (3) ability to grow in anchorage-independent conditions. The MDA-MB-231 and MCF-7 breast cancer cell lines displayed CD44+/CD24- cell populations with the MCF-7 cell line additionally displaying a large CD44+/CD24-/EpCAM+ population. Although both cell lines showed similar ALDHHi populations, they differed substantially with respect to anchorage-independent growth. MCF-7 cells were able to form anchorage-independent colonies while the MDA-MB-231 cell line was not. Anchorage-independent MCF-7 cells showed enrichment in CD44+/CD24- and CD44+/CD24-/EpCAM+ cells compared to adherent MCF-7 cells, and were selected for gene expression studies. Gene expression studies identified 22 genes as being down-regulated at the mRNA level in the anchorage-independent MCF-7 cells, while only 2 genes (BAG1 and DNAJC12) were up-regulated. The down-regulation of selected chaperones in anchorage independent MCF-7 cells was confirmed at the protein level for selected chaperones, including DNAJB6, a type II DNAJ protein shown to be involved in the regulation of Wnt signaling. In order to characterize the effect of DNAJB6 expression on BCSCs we developed a pCMV mammalian expression plasmid for both DNAJB6 isoforms (DNAJB6L and DNAJB6S). We successfully constructed mutants of the conserved histidine-proline-aspartic acid (HPD) motif of the J domain of DNAJB6S and DNAJB6L. These constructs will allow the analysis of the role of DNAJB6 in cancer stem cell function. To the best of our knowledge, this is the first report to focus on the comparative expression of molecular chaperones in normal and cancer stem cell enriched breast cancer populations.
- Full Text:
Movements of sub-adult sicklefin lemon sharks Negaprion acutidens in a remote Indian Ocean atoll
- Authors: Filmalter, John David
- Date: 2012
- Subjects: Silky shark , Silky shark -- Habitat , Sharks -- Amirante Islands (Seychelles)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5383 , http://hdl.handle.net/10962/d1018229
- Description: The sicklefin lemon shark Negaprion acutidens is a large-bodied (> 3m) coastal shark species, widely distributed in tropical and sub-tropical Indo-Pacific waters. Despite its large size and wide distribution, very little is known about its movement behaviour throughout ontogeny. The primary aim of this thesis was to gain an understanding of the movements of sub-adult N. acutidens, in and around the St. Joseph Atoll, Republic of Seychelles, to facilitate the effective conservation of this vulnerable species. A total of 22 sharks (139 – 202 cm TL) were equipped with coded acoustic transmitters and passively monitored using moored acoustic receivers for a period of 20 month from March 2009 to October 2010. The use of passive acoustic telemetry arrays to study behavioural ecology has increased in popularity in recent years and been successfully applied to study a host of teleost and elasmobranch species in a diversity of habitats, ranging from sheltered estuaries to the offshore pelagic environment. However, the practicalities of designing an effective network of receivers to optimally monitor animal movements can be challenging. In this study the receiver array was optimised through a series of incremental steps to achieve an efficient design that allowed for the specific objectives to be addressed. The specific objectives of this study were to i) gain an understanding of the long term space use patterns and site fidelity of sub-adult N. acutidens within degree of use of the St. Joseph Atoll lagoon and surrounding habitats, and ii) investigate their short term behavioural patterns in response to natural rhythmic cycles. The important role the atoll plays in the sub-adult stage of this species was demonstrated by the very low numbers of detections outside the atoll compared to the very large numbers of detections inside the atoll. Over the course of a year the tagged sharks showed a high degree of site fidelity to the atoll, with 79 – 100% of the individuals detected during each month and 50% being detected on a near daily basis. This result provides testimony of the nursery role of the atoll and importance of these habitats in the early life history for this species. Individual area use was generally found to be restricted to the eastern part of the atoll incorporating a portion of the central deep lagoon and a nearby adjacent area of the sand flats. The movements of sub-adult N. acutidens on and off of the shallow flats surrounding the central lagoon (likely for foraging) were found to be strongly influenced by the tidal height and the diel cycle. Tagged sharks were found to utilise the flats more regularly when the tidal height was greater than 90 cm and particularly more so during the night and early morning than during daylight times. The combined results of this study expose the vulnerability of this species to rapid local depletion. Similarly, the effectiveness of spatial management measures, such as no-take marine protected areas is highlighted as an efficient tool for the future conservation of this species. In the St. Joseph Atoll in particular, the use of a multi-levelled protection approach, where the eastern portion on the atoll is completely restricted while the remaining area is utilized for non-consumptive tourism activities, could be highly effective. Future research should investigate changes in area use throughout the ontogeny of this species as well improve the understanding of the breeding site fidelity and population size of reproductive females using the St. Joseph Atoll.
- Full Text:
- Authors: Filmalter, John David
- Date: 2012
- Subjects: Silky shark , Silky shark -- Habitat , Sharks -- Amirante Islands (Seychelles)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5383 , http://hdl.handle.net/10962/d1018229
- Description: The sicklefin lemon shark Negaprion acutidens is a large-bodied (> 3m) coastal shark species, widely distributed in tropical and sub-tropical Indo-Pacific waters. Despite its large size and wide distribution, very little is known about its movement behaviour throughout ontogeny. The primary aim of this thesis was to gain an understanding of the movements of sub-adult N. acutidens, in and around the St. Joseph Atoll, Republic of Seychelles, to facilitate the effective conservation of this vulnerable species. A total of 22 sharks (139 – 202 cm TL) were equipped with coded acoustic transmitters and passively monitored using moored acoustic receivers for a period of 20 month from March 2009 to October 2010. The use of passive acoustic telemetry arrays to study behavioural ecology has increased in popularity in recent years and been successfully applied to study a host of teleost and elasmobranch species in a diversity of habitats, ranging from sheltered estuaries to the offshore pelagic environment. However, the practicalities of designing an effective network of receivers to optimally monitor animal movements can be challenging. In this study the receiver array was optimised through a series of incremental steps to achieve an efficient design that allowed for the specific objectives to be addressed. The specific objectives of this study were to i) gain an understanding of the long term space use patterns and site fidelity of sub-adult N. acutidens within degree of use of the St. Joseph Atoll lagoon and surrounding habitats, and ii) investigate their short term behavioural patterns in response to natural rhythmic cycles. The important role the atoll plays in the sub-adult stage of this species was demonstrated by the very low numbers of detections outside the atoll compared to the very large numbers of detections inside the atoll. Over the course of a year the tagged sharks showed a high degree of site fidelity to the atoll, with 79 – 100% of the individuals detected during each month and 50% being detected on a near daily basis. This result provides testimony of the nursery role of the atoll and importance of these habitats in the early life history for this species. Individual area use was generally found to be restricted to the eastern part of the atoll incorporating a portion of the central deep lagoon and a nearby adjacent area of the sand flats. The movements of sub-adult N. acutidens on and off of the shallow flats surrounding the central lagoon (likely for foraging) were found to be strongly influenced by the tidal height and the diel cycle. Tagged sharks were found to utilise the flats more regularly when the tidal height was greater than 90 cm and particularly more so during the night and early morning than during daylight times. The combined results of this study expose the vulnerability of this species to rapid local depletion. Similarly, the effectiveness of spatial management measures, such as no-take marine protected areas is highlighted as an efficient tool for the future conservation of this species. In the St. Joseph Atoll in particular, the use of a multi-levelled protection approach, where the eastern portion on the atoll is completely restricted while the remaining area is utilized for non-consumptive tourism activities, could be highly effective. Future research should investigate changes in area use throughout the ontogeny of this species as well improve the understanding of the breeding site fidelity and population size of reproductive females using the St. Joseph Atoll.
- Full Text:
Multi-instrument observations of ionospheric irregularities over South Africa
- Authors: Amabayo, Emirant Bertillas
- Date: 2012
- Subjects: Ionosphere -- Research , Sudden ionospheric disturbances , Ionospheric storms , Solar activity , Sunspots
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5476 , http://hdl.handle.net/10962/d1005261 , Ionosphere -- Research , Sudden ionospheric disturbances , Ionospheric storms , Solar activity , Sunspots
- Description: The occurrence of mid-latitude spread F (SF) over South Africa has not been extensively studied since the installation of the DPS-4 digisondes at Madimbo (30.88◦E, 22.38◦S), Grahamstown (33.32◦S, 26.50◦E) and Louisvale (28.51◦S, 21.24◦E). This study is intended to quantify the probability of the occurrence of F region disturbances associated with ionospheric spread F (SF) and L-band scintillation over South Africa. This study used available ionosonde data for 8 years (2000-2008) from the three South African stations. The SF events were identified manually on ionograms and grouped for further statistical analysis into frequency SF (FSF), range SF (RSF) and mixed SF (MSF). The results show that the diurnal pattern of SF occurrence peaks strongly between 23:00 and 00:00 UT. This pattern is true for all seasons and types of SF at Madimbo and Grahamstown during 2001 and 2005, except for RSF which had peaks during autumn and spring during 2001 at Madimbo. The probability of both MSF and FSF tends to increase with decreasing sunspot number (SSN), with a peak in 2005 (a moderate solar activity period). The seasonal peaks of MSF and FSF are more frequent during winter months at both Madimbo and Grahamstown. In this study SF was evident in ∼ 0.03% and ∼ 0.06% of the available ionograms at Madimbo and Grahamstown respectively during the eight year period. The presence of ionospheric irregularities associated with SF and scintillation was investigated using data from selected Global Positioning System (GPS) receiver stations distributed across South Africa. The results, based on GPS total electron content (TEC) and ionosonde measurements, show that SF over this region can most likely be attributed to travelling ionospheric disturbances (TIDs), caused by gravity waves (GWs) and neutral wind composition changes. The GWs were mostly associated with geomagnetic storms and sub-storms that occurred during periods of high and moderate solar activity (2001-2005). SF occurrence during the low solar activity period (2006-2008)can probably be attributed to neutral wind composition changes.
- Full Text:
- Authors: Amabayo, Emirant Bertillas
- Date: 2012
- Subjects: Ionosphere -- Research , Sudden ionospheric disturbances , Ionospheric storms , Solar activity , Sunspots
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5476 , http://hdl.handle.net/10962/d1005261 , Ionosphere -- Research , Sudden ionospheric disturbances , Ionospheric storms , Solar activity , Sunspots
- Description: The occurrence of mid-latitude spread F (SF) over South Africa has not been extensively studied since the installation of the DPS-4 digisondes at Madimbo (30.88◦E, 22.38◦S), Grahamstown (33.32◦S, 26.50◦E) and Louisvale (28.51◦S, 21.24◦E). This study is intended to quantify the probability of the occurrence of F region disturbances associated with ionospheric spread F (SF) and L-band scintillation over South Africa. This study used available ionosonde data for 8 years (2000-2008) from the three South African stations. The SF events were identified manually on ionograms and grouped for further statistical analysis into frequency SF (FSF), range SF (RSF) and mixed SF (MSF). The results show that the diurnal pattern of SF occurrence peaks strongly between 23:00 and 00:00 UT. This pattern is true for all seasons and types of SF at Madimbo and Grahamstown during 2001 and 2005, except for RSF which had peaks during autumn and spring during 2001 at Madimbo. The probability of both MSF and FSF tends to increase with decreasing sunspot number (SSN), with a peak in 2005 (a moderate solar activity period). The seasonal peaks of MSF and FSF are more frequent during winter months at both Madimbo and Grahamstown. In this study SF was evident in ∼ 0.03% and ∼ 0.06% of the available ionograms at Madimbo and Grahamstown respectively during the eight year period. The presence of ionospheric irregularities associated with SF and scintillation was investigated using data from selected Global Positioning System (GPS) receiver stations distributed across South Africa. The results, based on GPS total electron content (TEC) and ionosonde measurements, show that SF over this region can most likely be attributed to travelling ionospheric disturbances (TIDs), caused by gravity waves (GWs) and neutral wind composition changes. The GWs were mostly associated with geomagnetic storms and sub-storms that occurred during periods of high and moderate solar activity (2001-2005). SF occurrence during the low solar activity period (2006-2008)can probably be attributed to neutral wind composition changes.
- Full Text:
Musculoskeletal and perceptual responses of batsmen comparing high- and moderate-volume sprints between the wickets
- Authors: Sheppard, Bronwyn Jane
- Date: 2012
- Subjects: Cricket -- Batting -- Physiological aspects , Cricket injuries , Musculoskeletal system -- Wounds and injuries
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5171 , http://hdl.handle.net/10962/d1016366
- Description: Background: Literature has associated repeated eccentric muscle actions with increased muscle damage of the muscles involved. Eccentric actions are typical in sports which are ‘stop-start’ in nature requiring rapid acceleration and deceleration, typical of a batting activity in cricket. Ultra-structural damage of the skeletal muscle as a consequence of repeated decelerating activities is associated with performance decrements, particularly muscle strength and sprinting speeds. This suggests that eccentric strength decrements may provide an indication for the development of muscle strain injuries during these activities. Despite these findings, limited research has identified the specific musculoskeletal demands placed on cricket batsmen, particularly with reference to various match intensities. Objective: The present study, therefore, sought to determine the specific musculoskeletal, physiological and perceptual demands placed on specialised batsmen during two work bouts of different intensities; one representing a highintensity work bout and the other a moderate-intensity work bout. The dependent variables of interest were muscle activation, isokinetic strength changes, heart rate, ‘central’ and ‘local’ ratings of perceived exertion (RPE), body discomfort and performance. Methods: The two experimental conditions, representative of a high- (HVR) and moderate-volume running (MVR) batting protocol, required players to perform a simulated batting work bout of either twelve or six runs an over, within a laboratory setting. Selected physiological, perceptual and performance measures were collected at specific time intervals throughout the work bout while the biophysical measures were collected prior to, and following both protocols. Results: Of the variables measured, heart rate, ‘central’ and ‘local’ RPE values were observed to increase significantly (p<0.05) over time. This increase was greater as a consequence of the HVR in comparison to the MVR. No change in sprint times was documented during the MVR, in contrast, significant (p<0.05) increases over time were observed during the HVR, further highlighting the elevated demands associated with this condition. In addition, an ‘end spurt’ was observed particularly following the HVR condition, suggesting athletes were conserving themselves through the adoption of a pacing strategy. Reductions in biceps femoris and semitendinosus muscle activation levels were observed following the HVR. This was further supported by the significantly greater levels of semitendinosus activation following the MVR when compared to the HVR. Peak concentric and eccentric knee extensor (EXT) (-17.17% and -16.07% respectively) and eccentric flexor (FLEX) (- 17.49%) values decreased significantly (p<0.05) following the HVR at 60°.s-1. In addition, concentric and eccentric total work produced by the flexors and eccentric extensors resulted in significantly (p<0.05) lower values due to the HVR. Conclusion: The intermittent high-volume batting work bout elicited elevated mean heart rates, perceived ratings of cardiovascular and muscular effort and sprint times. Furthermore, hamstring activation levels and muscle strength, particularly concentric strength of the dominant lower limb were negatively affected by the HVR condition. These results suggest elevated demands were placed on the hamstring musculature as a consequence of the HVR condition, indicating a greater degree of musculoskeletal strain and increased injury risk associated with running between the wickets at this intensity, representative of an aggressive batting scenario.
- Full Text:
- Authors: Sheppard, Bronwyn Jane
- Date: 2012
- Subjects: Cricket -- Batting -- Physiological aspects , Cricket injuries , Musculoskeletal system -- Wounds and injuries
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5171 , http://hdl.handle.net/10962/d1016366
- Description: Background: Literature has associated repeated eccentric muscle actions with increased muscle damage of the muscles involved. Eccentric actions are typical in sports which are ‘stop-start’ in nature requiring rapid acceleration and deceleration, typical of a batting activity in cricket. Ultra-structural damage of the skeletal muscle as a consequence of repeated decelerating activities is associated with performance decrements, particularly muscle strength and sprinting speeds. This suggests that eccentric strength decrements may provide an indication for the development of muscle strain injuries during these activities. Despite these findings, limited research has identified the specific musculoskeletal demands placed on cricket batsmen, particularly with reference to various match intensities. Objective: The present study, therefore, sought to determine the specific musculoskeletal, physiological and perceptual demands placed on specialised batsmen during two work bouts of different intensities; one representing a highintensity work bout and the other a moderate-intensity work bout. The dependent variables of interest were muscle activation, isokinetic strength changes, heart rate, ‘central’ and ‘local’ ratings of perceived exertion (RPE), body discomfort and performance. Methods: The two experimental conditions, representative of a high- (HVR) and moderate-volume running (MVR) batting protocol, required players to perform a simulated batting work bout of either twelve or six runs an over, within a laboratory setting. Selected physiological, perceptual and performance measures were collected at specific time intervals throughout the work bout while the biophysical measures were collected prior to, and following both protocols. Results: Of the variables measured, heart rate, ‘central’ and ‘local’ RPE values were observed to increase significantly (p<0.05) over time. This increase was greater as a consequence of the HVR in comparison to the MVR. No change in sprint times was documented during the MVR, in contrast, significant (p<0.05) increases over time were observed during the HVR, further highlighting the elevated demands associated with this condition. In addition, an ‘end spurt’ was observed particularly following the HVR condition, suggesting athletes were conserving themselves through the adoption of a pacing strategy. Reductions in biceps femoris and semitendinosus muscle activation levels were observed following the HVR. This was further supported by the significantly greater levels of semitendinosus activation following the MVR when compared to the HVR. Peak concentric and eccentric knee extensor (EXT) (-17.17% and -16.07% respectively) and eccentric flexor (FLEX) (- 17.49%) values decreased significantly (p<0.05) following the HVR at 60°.s-1. In addition, concentric and eccentric total work produced by the flexors and eccentric extensors resulted in significantly (p<0.05) lower values due to the HVR. Conclusion: The intermittent high-volume batting work bout elicited elevated mean heart rates, perceived ratings of cardiovascular and muscular effort and sprint times. Furthermore, hamstring activation levels and muscle strength, particularly concentric strength of the dominant lower limb were negatively affected by the HVR condition. These results suggest elevated demands were placed on the hamstring musculature as a consequence of the HVR condition, indicating a greater degree of musculoskeletal strain and increased injury risk associated with running between the wickets at this intensity, representative of an aggressive batting scenario.
- Full Text:
On the underwater visual census of Western Indian Ocean coral reef fishes
- Authors: Wartenberg, Reece
- Date: 2012
- Subjects: Coral reef fishes -- Africa, Southern , Coral reef fishes -- Indian Ocean , Coral reef fishes -- Behavior , Fish communities -- Africa, Southern , Fish communities -- Indian Ocean , Groundfishes -- Africa, Southern , Groundfishes -- Indian Ocean , Groundfishes -- Behavior
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5308 , http://hdl.handle.net/10962/d1005153 , Coral reef fishes -- Africa, Southern , Coral reef fishes -- Indian Ocean , Coral reef fishes -- Behavior , Fish communities -- Africa, Southern , Fish communities -- Indian Ocean , Groundfishes -- Africa, Southern , Groundfishes -- Indian Ocean , Groundfishes -- Behavior
- Description: This study conducted the first high-resolution investigation of the ichthyofaunal assemblages on a high-latitude coral reef in the Western Indian Ocean (WIO). Two-Mile reef, in South Africa, is a large, accessible patch-reef, and was selected as a candidate study area. Although the effect of season in structuring coral reef fish communities is most-often overlooked, the relationship between these fish communities and their habitat structure has been investigated. In South Africa, however, neither of these potential community-level drivers has been explored. As coral reefs worldwide are faced with high levels of usage pressure, nondestructive underwater visual census (UVC) techniques were identified as the most appropriate survey methods. This study had two primary aims that were; (1) to identify the most suitable technique for the UVC of coral reef fishes, and to test variations of the selected technique for appropriateness to implementation in long-term monitoring programs, and (2) to determine if possible changes to ichthyofaunal community structure could be related to trends in season and/or habitat characteristics. A review of the literature indicated that the most appropriate UVC method for surveying epibenthic coral reef fishes is underwater transecting. To compare the traditional slate-based transects to variations that implement digital image technology, slate transects were compared to a first-attempt digital photographic transect technique, and digital videographic transects. Videographic transects produced the most favourable species richness, abundance, and standard deviations of the three techniques. Diversity was not significantly different between transect techniques. The minimum required sample size was lowest for videographic transects (17 replicates), intermediate for photographic transects (27 replicates) and highest for slate transects (37 replicates). Videographic and photographic transects required greater analysis time to generate counts, but required lower observer training time. While videographic transects produced the lowest proportion of species considered unidentifiable, all three transect techniques showed similar functionality to surveying epibenthic coral reef fishes. Videographic transects were therefore identified as the most appropriate UVC technique for this study. Videographic transects at shallow (6 – 14 m), intermediate (14 – 22 m) and deep (22 – 30 m) depths in mid-winter and mid-summer, sampled a total of 41 families consisting of 209 species and 18172 individuals, dominated by pomacentrids in abundance and labrids in richness. The fish assemblages on Two-Mile Reef were found to be similar in composition to lower-latitude WIO reefs. Overall ichthyofaunal abundance and richness was significantly higher in summer than in winter, and was higher at shallow sites than at intermediate and deep sites. A multivariate approach confirmed differences between seasons at shallow depths but not between seasons at intermediate and deep depths. The fish assemblages on Two-Mile Reef can therefore be described as being comprised of four relatively distinct communities: a shallow, winter community; a shallow, summer community; a year-round intermediate community; and a year-round deep community. The distributions of discriminating species indicated that high abundances of the algal-feeding pomacentrids are observed only at shallow and intermediate sites while high abundances of the zooplanktivorous serranid subfamily, the Anthiinae, are observed predominantly at deep sites. Assessment of all measured supplementary variables indicated that of all factor combinations, observed patterns could be ascribed most strongly to depth. Quantification of reef characteristics indicated that as depth increases, habitat complexity decreases, benthic communities shift from dense coral domination to sparse sponge domination, and algal biomass and cover decreases. The ability of the videographic transect technique to detect changes in community structure with season and depth indicates that season and depth should be accounted for in future high-latitude ichtyofaunal surveys, and that the videographic transect technique is suitable for implementation in long-term monitoring programs on coral reefs. The similarity in fish assemblages between Two-Mile Reef and lower latitude regions suggests that the protocol for surveying epibenthic coral reef fishes, resulting from this study, is relevant throughout the continental WIO.
- Full Text:
- Authors: Wartenberg, Reece
- Date: 2012
- Subjects: Coral reef fishes -- Africa, Southern , Coral reef fishes -- Indian Ocean , Coral reef fishes -- Behavior , Fish communities -- Africa, Southern , Fish communities -- Indian Ocean , Groundfishes -- Africa, Southern , Groundfishes -- Indian Ocean , Groundfishes -- Behavior
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5308 , http://hdl.handle.net/10962/d1005153 , Coral reef fishes -- Africa, Southern , Coral reef fishes -- Indian Ocean , Coral reef fishes -- Behavior , Fish communities -- Africa, Southern , Fish communities -- Indian Ocean , Groundfishes -- Africa, Southern , Groundfishes -- Indian Ocean , Groundfishes -- Behavior
- Description: This study conducted the first high-resolution investigation of the ichthyofaunal assemblages on a high-latitude coral reef in the Western Indian Ocean (WIO). Two-Mile reef, in South Africa, is a large, accessible patch-reef, and was selected as a candidate study area. Although the effect of season in structuring coral reef fish communities is most-often overlooked, the relationship between these fish communities and their habitat structure has been investigated. In South Africa, however, neither of these potential community-level drivers has been explored. As coral reefs worldwide are faced with high levels of usage pressure, nondestructive underwater visual census (UVC) techniques were identified as the most appropriate survey methods. This study had two primary aims that were; (1) to identify the most suitable technique for the UVC of coral reef fishes, and to test variations of the selected technique for appropriateness to implementation in long-term monitoring programs, and (2) to determine if possible changes to ichthyofaunal community structure could be related to trends in season and/or habitat characteristics. A review of the literature indicated that the most appropriate UVC method for surveying epibenthic coral reef fishes is underwater transecting. To compare the traditional slate-based transects to variations that implement digital image technology, slate transects were compared to a first-attempt digital photographic transect technique, and digital videographic transects. Videographic transects produced the most favourable species richness, abundance, and standard deviations of the three techniques. Diversity was not significantly different between transect techniques. The minimum required sample size was lowest for videographic transects (17 replicates), intermediate for photographic transects (27 replicates) and highest for slate transects (37 replicates). Videographic and photographic transects required greater analysis time to generate counts, but required lower observer training time. While videographic transects produced the lowest proportion of species considered unidentifiable, all three transect techniques showed similar functionality to surveying epibenthic coral reef fishes. Videographic transects were therefore identified as the most appropriate UVC technique for this study. Videographic transects at shallow (6 – 14 m), intermediate (14 – 22 m) and deep (22 – 30 m) depths in mid-winter and mid-summer, sampled a total of 41 families consisting of 209 species and 18172 individuals, dominated by pomacentrids in abundance and labrids in richness. The fish assemblages on Two-Mile Reef were found to be similar in composition to lower-latitude WIO reefs. Overall ichthyofaunal abundance and richness was significantly higher in summer than in winter, and was higher at shallow sites than at intermediate and deep sites. A multivariate approach confirmed differences between seasons at shallow depths but not between seasons at intermediate and deep depths. The fish assemblages on Two-Mile Reef can therefore be described as being comprised of four relatively distinct communities: a shallow, winter community; a shallow, summer community; a year-round intermediate community; and a year-round deep community. The distributions of discriminating species indicated that high abundances of the algal-feeding pomacentrids are observed only at shallow and intermediate sites while high abundances of the zooplanktivorous serranid subfamily, the Anthiinae, are observed predominantly at deep sites. Assessment of all measured supplementary variables indicated that of all factor combinations, observed patterns could be ascribed most strongly to depth. Quantification of reef characteristics indicated that as depth increases, habitat complexity decreases, benthic communities shift from dense coral domination to sparse sponge domination, and algal biomass and cover decreases. The ability of the videographic transect technique to detect changes in community structure with season and depth indicates that season and depth should be accounted for in future high-latitude ichtyofaunal surveys, and that the videographic transect technique is suitable for implementation in long-term monitoring programs on coral reefs. The similarity in fish assemblages between Two-Mile Reef and lower latitude regions suggests that the protocol for surveying epibenthic coral reef fishes, resulting from this study, is relevant throughout the continental WIO.
- Full Text:
Peripheral vision field fatigue during simulated driving : the effects of time on task and time of day on selected psychophysiological, performance and subjective responses
- Authors: Robertson, Jade Kelly
- Date: 2012 , 2012-09-22
- Subjects: Automobile driving simulators , Automobile driving -- Psychological aspects , Automobile driving -- Physiological aspects , Traffic accidents , Traffic safety , Fatigue , Peripheral vision
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5141 , http://hdl.handle.net/10962/d1007136 , Automobile driving simulators , Automobile driving -- Psychological aspects , Automobile driving -- Physiological aspects , Traffic accidents , Traffic safety , Fatigue , Peripheral vision
- Description: Worldwide, motor accidents are responsible for a large number of deaths and disabilities (Connor et al., 2001), and one of the major causes of motor accidents is driver fatigue. Although majority of drivers are aware of the dangers of fatigued driving, accidents related to this continues to contribute to a large percentage of all accidents, between 5 and 50% (Nilsson et al., 1997; Williamson et al., 2011). The purpose of the research was to establish the effect that fatigue renders on an individual’s peripheral visual field and to determine whether a decrement in driving performance occurs at the same rate as a decrement in peripheral visual performance. Fatigue was induced through time of day as well as time on task. Sixteen students from Rhodes University were recruited, subject to no previous sleep disorders, among other criteria. Each participant was required to partake in two conditions, namely a day condition (09h00–11h00) and a night condition (23h00– 01h00). Each condition consisted of a 90 minute dual task; the primary task was a tracking task, in which participants were instructed to track a white line as accurately as possible. A secondary peripheral response task was introduced, in which participants were instructed to respond as quickly as possible to the peripheral stimuli, by pressing one of two clickers located on the steering wheel. The peripheral stimuli were located at 20º, 30º and 40º visual angle. Psychophysiological, performance and subjective measures were obtained before, during and after the main task. The pre- and post-tests included core body temperature, critical flicker fusion frequency threshold, a digit span memory test, Wits Sleepiness Scale and a NASA-TLX questionnaire. The psychophysiological and performance measures of heart rate, heart rate variability, blink frequency, blink duration, lane deviation, number of saccades towards peripheral stimuli, response time to peripheral stimuli and the percentage of missed peripheral responses were all recorded throughout the 90 minute main dual task. The results revealed significant differences (p<0.05) for heart rate variability, number of saccades towards peripheral stimuli and the Wits Sleepiness Scale, with regard to time of day. For time on task, significant effects were established for lane deviation, response time to peripheral stimuli, percentage of missed peripheral responses, heart rate, heart rate variability, blink frequency, blink duration, critical flicker fusion frequency threshold, core body temperature and the Wits Sleepiness Scale. Eccentricity was analysed and found to be significant for response time to peripheral stimuli, as well as for the percentage of missed peripheral responses; there was a significant increase in both measures with an increase in the stimuli eccentricity. No significances were established for time of day or between the pre- and post-tests conducted for the digit span memory performance; however, a significant interactional effect between the two was established. When assessing the percentage rate of decrement of driving performance compared to the percentage rate in the decrement of the missed peripheral responses, it was found that the percentage rate of decrement was equal for both measures. Thus from this research it can be seen that, concurrent with a decrement in driving performance, there are adverse effects on an individuals' peripheral vision, which have great implications for the safety of workers in industry and transport, as well as motorists. It was also established that time on task is possibly a more appropriate variable to consider than time of day, when implementing work schedules and rest breaks in industry, transport and fields alike, as more significant findings were seen for time on task compared to time of day. , Adobe Acrobat 9.53 Paper Capture Plug-in
- Full Text:
- Authors: Robertson, Jade Kelly
- Date: 2012 , 2012-09-22
- Subjects: Automobile driving simulators , Automobile driving -- Psychological aspects , Automobile driving -- Physiological aspects , Traffic accidents , Traffic safety , Fatigue , Peripheral vision
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5141 , http://hdl.handle.net/10962/d1007136 , Automobile driving simulators , Automobile driving -- Psychological aspects , Automobile driving -- Physiological aspects , Traffic accidents , Traffic safety , Fatigue , Peripheral vision
- Description: Worldwide, motor accidents are responsible for a large number of deaths and disabilities (Connor et al., 2001), and one of the major causes of motor accidents is driver fatigue. Although majority of drivers are aware of the dangers of fatigued driving, accidents related to this continues to contribute to a large percentage of all accidents, between 5 and 50% (Nilsson et al., 1997; Williamson et al., 2011). The purpose of the research was to establish the effect that fatigue renders on an individual’s peripheral visual field and to determine whether a decrement in driving performance occurs at the same rate as a decrement in peripheral visual performance. Fatigue was induced through time of day as well as time on task. Sixteen students from Rhodes University were recruited, subject to no previous sleep disorders, among other criteria. Each participant was required to partake in two conditions, namely a day condition (09h00–11h00) and a night condition (23h00– 01h00). Each condition consisted of a 90 minute dual task; the primary task was a tracking task, in which participants were instructed to track a white line as accurately as possible. A secondary peripheral response task was introduced, in which participants were instructed to respond as quickly as possible to the peripheral stimuli, by pressing one of two clickers located on the steering wheel. The peripheral stimuli were located at 20º, 30º and 40º visual angle. Psychophysiological, performance and subjective measures were obtained before, during and after the main task. The pre- and post-tests included core body temperature, critical flicker fusion frequency threshold, a digit span memory test, Wits Sleepiness Scale and a NASA-TLX questionnaire. The psychophysiological and performance measures of heart rate, heart rate variability, blink frequency, blink duration, lane deviation, number of saccades towards peripheral stimuli, response time to peripheral stimuli and the percentage of missed peripheral responses were all recorded throughout the 90 minute main dual task. The results revealed significant differences (p<0.05) for heart rate variability, number of saccades towards peripheral stimuli and the Wits Sleepiness Scale, with regard to time of day. For time on task, significant effects were established for lane deviation, response time to peripheral stimuli, percentage of missed peripheral responses, heart rate, heart rate variability, blink frequency, blink duration, critical flicker fusion frequency threshold, core body temperature and the Wits Sleepiness Scale. Eccentricity was analysed and found to be significant for response time to peripheral stimuli, as well as for the percentage of missed peripheral responses; there was a significant increase in both measures with an increase in the stimuli eccentricity. No significances were established for time of day or between the pre- and post-tests conducted for the digit span memory performance; however, a significant interactional effect between the two was established. When assessing the percentage rate of decrement of driving performance compared to the percentage rate in the decrement of the missed peripheral responses, it was found that the percentage rate of decrement was equal for both measures. Thus from this research it can be seen that, concurrent with a decrement in driving performance, there are adverse effects on an individuals' peripheral vision, which have great implications for the safety of workers in industry and transport, as well as motorists. It was also established that time on task is possibly a more appropriate variable to consider than time of day, when implementing work schedules and rest breaks in industry, transport and fields alike, as more significant findings were seen for time on task compared to time of day. , Adobe Acrobat 9.53 Paper Capture Plug-in
- Full Text:
Photophysicochemical studies of phenylthio phthalocyanines interaction with gold nanoparticles and applications in dye sensitised solar cells and optical limiting
- Authors: Forteath, Shaun
- Date: 2012
- Subjects: Phthalocyanines , Nanoparticles , Photochemistry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4334 , http://hdl.handle.net/10962/d1004995 , Phthalocyanines , Nanoparticles , Photochemistry
- Description: The syntheses, spectroscopic characterisation, photophysical and photochemical studies have been conducted for a variety of phenylthio substituted phthalocyanines (Pcs). Comparisons have been made taking into consideration the influence of the central metal ion, solvent properties and substituent type. The optical limiting properties were also determined for all the Pcs synthesised. A low-symmetry metallophthalocyanine complex was similarly characterised and the photoelectrochemical parameters determined when used as a sensitiser of nanoporous ZnO. The symmetric analogue was conjugated to gold nanoparticles to determine the influence of interactions on its photophysical properties and distinct differences occurred in the absorption and fluorescence spectra suggesting successful formation of conjugates.
- Full Text:
- Authors: Forteath, Shaun
- Date: 2012
- Subjects: Phthalocyanines , Nanoparticles , Photochemistry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4334 , http://hdl.handle.net/10962/d1004995 , Phthalocyanines , Nanoparticles , Photochemistry
- Description: The syntheses, spectroscopic characterisation, photophysical and photochemical studies have been conducted for a variety of phenylthio substituted phthalocyanines (Pcs). Comparisons have been made taking into consideration the influence of the central metal ion, solvent properties and substituent type. The optical limiting properties were also determined for all the Pcs synthesised. A low-symmetry metallophthalocyanine complex was similarly characterised and the photoelectrochemical parameters determined when used as a sensitiser of nanoporous ZnO. The symmetric analogue was conjugated to gold nanoparticles to determine the influence of interactions on its photophysical properties and distinct differences occurred in the absorption and fluorescence spectra suggesting successful formation of conjugates.
- Full Text:
Rapid enzymatic detection of organophosphorous and carbamate pesticides in water
- Authors: Mwila, Katayi
- Date: 2012
- Subjects: Organophosphorus compounds , Carbamates , Water -- Pesticide content -- South Africa -- Eastern Cape , Water quality biological assessment -- South Africa -- Eastern Cape , Water quality management -- South Africa -- Eastern Cape , Pesticides -- Toxicology -- South Africa -- Eastern Cape , Biological assay , Acetylcholinesterase , Parathion , Aldicarb , Carbaryl , Carbofuran , Nitrophenols
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4024 , http://hdl.handle.net/10962/d1004084 , Organophosphorus compounds , Carbamates , Water -- Pesticide content -- South Africa -- Eastern Cape , Water quality biological assessment -- South Africa -- Eastern Cape , Water quality management -- South Africa -- Eastern Cape , Pesticides -- Toxicology -- South Africa -- Eastern Cape , Biological assay , Acetylcholinesterase , Parathion , Aldicarb , Carbaryl , Carbofuran , Nitrophenols
- Description: The increased use of pesticides has resulted in a corresponding increase in concern for the effect they may have on the health of humans and other non-target organisms. The two main areas of concern are the toxicological effects that mixtures of pesticides may have as well as the endocrine disrupting effects. Although the individual pesticides may be present at concentrations below the levels deemed to be detrimental to health, it has been argued that their combined effect may still result in elevated health risks. Another important aspect of pesticide risk assessment requires a consideration of the breakdown products of pesticides and their effect on human health. There has been very little research into the effects of degradation products and this issue should be addressed as these could potentially pose a higher risk than their parent compounds. One of the most important bio-markers available for use is the ubiquitous enzyme acetylcholinesterase (AChE). This enzyme is responsible for one of the most important functions in the body; namely nerve impulse transmission, upon which all life depends. The inhibition of this enzyme indicates toxicity and as a subsequence, a threat to the organism’s well-being. Bioassays have also recently been developed to test chemicals for endocrine disrupting effects. These tests rely on a dose response equivalent to that of the most potent well known estrogen 17-β estradiol. Any chemical that has a measurable response is deemed to display endocrine disrupting effects. This first aim of this study was to investigate the toxicological and endocrine disrupting effects of three organophosphorus pesticides; aldicarb, parathion and demeton-S-methyl, in addition to two breakdown products; aminophenol and p-nitrophenol. Two carbamate pesticides; carbaryl and carbofuran were also analysed. The toxicological effects of mixtures of the parent pesticide compounds were tested to assess if any antagonistic, additive or synergistic effects were observed. This data was then used in conjunction with an artificial neural network to assess if individual pesticides could be distinguished from mixtures of pesticides. A final objective was to sample various Eastern Cape water sources, utilising the enzymatic assay to determine the presence of any of these pesticides in these samples. There were several conclusions drawn from this study. AChE was successfully used as an assay to test the toxicity of the pesticides under investigation, based on their inhibition of this enzyme. An important factor for consideration throughout the study was the need to establish basal and monitor AChE activity (i.e. the need to monitor AChE activity in the absence of any pesticide). This ensured accurate comparison of the results obtained. It was found that demeton-S-methyl was the most potent of these pesticides followed by carbaryl, parathion, aldicarb and finally carbofuran, and that carbofuran could potentiate AChE. The results indicated that pesticide mixtures generally exhibited an additive inhibitory effect on AChE, although at some concentrations of pesticides, synergistic and antagonistic effects were noted. From the data using mixtures of pesticides, a feed forward neural network was created that was successfully able to distinguish individual pesticides from mixtures within its training parameters. None of the pesticides tested displayed endocrine disrupting properties in the Yeast Estrogen Screen (YES), T47D-KBluc and MDA-kb2 bio-assays. Other studies reported mixed results in this regard and thus no final conclusions could be drawn. The Blaauwkrantz River, Kariega River, Sundays River, Swartkops River and Kowie River were all tested for pesticides and although positive results were recorded, conventional methods indicated that there were no pesticides in the rivers. There were, however, trace metals present which are known to inhibit AChE, thus causing a false positive result. These results indicated that AChE can be used as a high throughput initial pre-screening tool, but that it cannot serve as a substitute for more accurate conventional testing methods.
- Full Text:
- Authors: Mwila, Katayi
- Date: 2012
- Subjects: Organophosphorus compounds , Carbamates , Water -- Pesticide content -- South Africa -- Eastern Cape , Water quality biological assessment -- South Africa -- Eastern Cape , Water quality management -- South Africa -- Eastern Cape , Pesticides -- Toxicology -- South Africa -- Eastern Cape , Biological assay , Acetylcholinesterase , Parathion , Aldicarb , Carbaryl , Carbofuran , Nitrophenols
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4024 , http://hdl.handle.net/10962/d1004084 , Organophosphorus compounds , Carbamates , Water -- Pesticide content -- South Africa -- Eastern Cape , Water quality biological assessment -- South Africa -- Eastern Cape , Water quality management -- South Africa -- Eastern Cape , Pesticides -- Toxicology -- South Africa -- Eastern Cape , Biological assay , Acetylcholinesterase , Parathion , Aldicarb , Carbaryl , Carbofuran , Nitrophenols
- Description: The increased use of pesticides has resulted in a corresponding increase in concern for the effect they may have on the health of humans and other non-target organisms. The two main areas of concern are the toxicological effects that mixtures of pesticides may have as well as the endocrine disrupting effects. Although the individual pesticides may be present at concentrations below the levels deemed to be detrimental to health, it has been argued that their combined effect may still result in elevated health risks. Another important aspect of pesticide risk assessment requires a consideration of the breakdown products of pesticides and their effect on human health. There has been very little research into the effects of degradation products and this issue should be addressed as these could potentially pose a higher risk than their parent compounds. One of the most important bio-markers available for use is the ubiquitous enzyme acetylcholinesterase (AChE). This enzyme is responsible for one of the most important functions in the body; namely nerve impulse transmission, upon which all life depends. The inhibition of this enzyme indicates toxicity and as a subsequence, a threat to the organism’s well-being. Bioassays have also recently been developed to test chemicals for endocrine disrupting effects. These tests rely on a dose response equivalent to that of the most potent well known estrogen 17-β estradiol. Any chemical that has a measurable response is deemed to display endocrine disrupting effects. This first aim of this study was to investigate the toxicological and endocrine disrupting effects of three organophosphorus pesticides; aldicarb, parathion and demeton-S-methyl, in addition to two breakdown products; aminophenol and p-nitrophenol. Two carbamate pesticides; carbaryl and carbofuran were also analysed. The toxicological effects of mixtures of the parent pesticide compounds were tested to assess if any antagonistic, additive or synergistic effects were observed. This data was then used in conjunction with an artificial neural network to assess if individual pesticides could be distinguished from mixtures of pesticides. A final objective was to sample various Eastern Cape water sources, utilising the enzymatic assay to determine the presence of any of these pesticides in these samples. There were several conclusions drawn from this study. AChE was successfully used as an assay to test the toxicity of the pesticides under investigation, based on their inhibition of this enzyme. An important factor for consideration throughout the study was the need to establish basal and monitor AChE activity (i.e. the need to monitor AChE activity in the absence of any pesticide). This ensured accurate comparison of the results obtained. It was found that demeton-S-methyl was the most potent of these pesticides followed by carbaryl, parathion, aldicarb and finally carbofuran, and that carbofuran could potentiate AChE. The results indicated that pesticide mixtures generally exhibited an additive inhibitory effect on AChE, although at some concentrations of pesticides, synergistic and antagonistic effects were noted. From the data using mixtures of pesticides, a feed forward neural network was created that was successfully able to distinguish individual pesticides from mixtures within its training parameters. None of the pesticides tested displayed endocrine disrupting properties in the Yeast Estrogen Screen (YES), T47D-KBluc and MDA-kb2 bio-assays. Other studies reported mixed results in this regard and thus no final conclusions could be drawn. The Blaauwkrantz River, Kariega River, Sundays River, Swartkops River and Kowie River were all tested for pesticides and although positive results were recorded, conventional methods indicated that there were no pesticides in the rivers. There were, however, trace metals present which are known to inhibit AChE, thus causing a false positive result. These results indicated that AChE can be used as a high throughput initial pre-screening tool, but that it cannot serve as a substitute for more accurate conventional testing methods.
- Full Text:
Research and development of a preliminary South African voluntary carbon standard for landscape restoration projects
- Authors: Curran, Patrick
- Date: 2012
- Subjects: Carbon -- Environmental aspects -- Research -- South Africa , Carbon -- Standards -- Research , Restoration ecology -- Research -- South Africa , Environmental sciences -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4748 , http://hdl.handle.net/10962/d1006968 , Carbon -- Environmental aspects -- Research -- South Africa , Carbon -- Standards -- Research , Restoration ecology -- Research -- South Africa , Environmental sciences -- Research
- Description: The mandatory and voluntary carbon markets have both developed around the increasing trade of carbon offsets. In order to add legitimacy to an otherwise intangible commodity there has been a rise in the development of third party carbon certification standards, particularly in the voluntary market. These standards aim to provide independent, third party certification to projects that are developed specifically to generate and sell carbon offsets. South Africa has the opportunity to engage with these markets, but current participation in and certification of projects is sluggish. These projects have not taken off mainly due to the high transaction costs and lag times surrounding the current certification of projects', complex baseline methodologies, accounting uncertainty and the often bureaucratic systems surrounding the current voluntary carbon certification standards and methodologies. In order to overcome these pitfalls this project aimed to address these challenges through initiating the development of a preliminary South African voluntary carbon standard. This was done by: a) undertaking a critical assessment of the development of current carbon markets, with a particular focus on voluntary markets and third party certification, b) critically analysing the current voluntary carbon certification standards for best practices, pitfalls and weaknesses. To provide a better understanding of the historical development of voluntary certification standards, various established certification standards were evaluated, including the Forestry Stewardship Council (FSC), Marine Stewardship Council (MSC) and ISO 14000 standards. This analysis focussed on the challenges they faced in acceptance and in particular how they have managed to operationalize sustainable development within the certification process. In order to explicitly ensure the incorporation of a sustainable development assessment of projects under the proposed standard, an expert workshop was held with 14 experts from a wide variety of disciplines. These experts identified the crucial sustainable development challenges facing South Africa. They identified 12 sub-themes and 44 indicators that could be used to measure and incorporate sustainable development indicators into the certification process. These were then further developed through using the 'Input – Output – Outcome – Impact' framework model which allowed the indicators to be organised and understood and thus practical. The analysis of the voluntary certification standards and the development of the sustainable development indicator framework were ultimately incorporated into the development of the proposed South African voluntary carbon standard. The key approach to this standard is the incorporation and focus of the proposed standard to ensuring the generation of net SD benefits and placing them at the same level as carbon within the project design and development, validation and verification process. The full and effective integration of these has been missing within current fully fledged voluntary carbon standards, as they often rely on a mixture of project design standards to achieve this. Offering the inclusion of all components into one standard, specifically designed for South Africa, will not only assure SD credentials but also increase transparency and understanding, and reduce costs. This thesis allowed for the development of innovative new ideas and process focussed specifically at including and mainstreaming South Africa’s developmental challenges into the certification process. This is the hoped that the standard will effectively certify South African based landscape restoration projects, but also decrease costs and increase efficiencies in order to encourage the development of these projects. This preliminary standard not only aims to incorporate and address all the issues identified but also has the end goal of acting as the basis for future debate and development surrounding a potential South African voluntary carbon certification standard.
- Full Text:
- Authors: Curran, Patrick
- Date: 2012
- Subjects: Carbon -- Environmental aspects -- Research -- South Africa , Carbon -- Standards -- Research , Restoration ecology -- Research -- South Africa , Environmental sciences -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4748 , http://hdl.handle.net/10962/d1006968 , Carbon -- Environmental aspects -- Research -- South Africa , Carbon -- Standards -- Research , Restoration ecology -- Research -- South Africa , Environmental sciences -- Research
- Description: The mandatory and voluntary carbon markets have both developed around the increasing trade of carbon offsets. In order to add legitimacy to an otherwise intangible commodity there has been a rise in the development of third party carbon certification standards, particularly in the voluntary market. These standards aim to provide independent, third party certification to projects that are developed specifically to generate and sell carbon offsets. South Africa has the opportunity to engage with these markets, but current participation in and certification of projects is sluggish. These projects have not taken off mainly due to the high transaction costs and lag times surrounding the current certification of projects', complex baseline methodologies, accounting uncertainty and the often bureaucratic systems surrounding the current voluntary carbon certification standards and methodologies. In order to overcome these pitfalls this project aimed to address these challenges through initiating the development of a preliminary South African voluntary carbon standard. This was done by: a) undertaking a critical assessment of the development of current carbon markets, with a particular focus on voluntary markets and third party certification, b) critically analysing the current voluntary carbon certification standards for best practices, pitfalls and weaknesses. To provide a better understanding of the historical development of voluntary certification standards, various established certification standards were evaluated, including the Forestry Stewardship Council (FSC), Marine Stewardship Council (MSC) and ISO 14000 standards. This analysis focussed on the challenges they faced in acceptance and in particular how they have managed to operationalize sustainable development within the certification process. In order to explicitly ensure the incorporation of a sustainable development assessment of projects under the proposed standard, an expert workshop was held with 14 experts from a wide variety of disciplines. These experts identified the crucial sustainable development challenges facing South Africa. They identified 12 sub-themes and 44 indicators that could be used to measure and incorporate sustainable development indicators into the certification process. These were then further developed through using the 'Input – Output – Outcome – Impact' framework model which allowed the indicators to be organised and understood and thus practical. The analysis of the voluntary certification standards and the development of the sustainable development indicator framework were ultimately incorporated into the development of the proposed South African voluntary carbon standard. The key approach to this standard is the incorporation and focus of the proposed standard to ensuring the generation of net SD benefits and placing them at the same level as carbon within the project design and development, validation and verification process. The full and effective integration of these has been missing within current fully fledged voluntary carbon standards, as they often rely on a mixture of project design standards to achieve this. Offering the inclusion of all components into one standard, specifically designed for South Africa, will not only assure SD credentials but also increase transparency and understanding, and reduce costs. This thesis allowed for the development of innovative new ideas and process focussed specifically at including and mainstreaming South Africa’s developmental challenges into the certification process. This is the hoped that the standard will effectively certify South African based landscape restoration projects, but also decrease costs and increase efficiencies in order to encourage the development of these projects. This preliminary standard not only aims to incorporate and address all the issues identified but also has the end goal of acting as the basis for future debate and development surrounding a potential South African voluntary carbon certification standard.
- Full Text:
Rivers as borders, dividing or uniting? : the effect of topography and implications for catchment management in South Africa
- Authors: Smedley, David Alan
- Date: 2012
- Subjects: Rivers -- South Africa , Water-supply -- Management -- South Africa , Water-supply -- Management -- Orange River Watershed , Watershed management -- South Africa , Watershed management -- Orange River Watershed , South Africa -- Boundaries , Water-supply -- Management -- Citizen participation , Water-supply -- Government policy -- South Africa , Water-supply -- Political aspects -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4851 , http://hdl.handle.net/10962/d1005527 , Rivers -- South Africa , Water-supply -- Management -- South Africa , Water-supply -- Management -- Orange River Watershed , Watershed management -- South Africa , Watershed management -- Orange River Watershed , South Africa -- Boundaries , Water-supply -- Management -- Citizen participation , Water-supply -- Government policy -- South Africa , Water-supply -- Political aspects -- South Africa
- Description: South Africa's water resources are unequally distributed over space and time to a high degree and our already stressed water resources situation will only be exacerbated by climate change if current predictions are correct. The potential for conflict over increasingly strained water resources in South Africa is thus very real. In order to deal with these complex problems national legislation is demanding that water resource management be decentralized to the local level where active participation can take place in an integrated manner in accordance with the principles of IWRM. However, administrative and political boundaries rarely match those of catchments as, throughout South Africa, rivers have been employed extensively to delineate administrative and political boundaries at a number of spatial scales. The aim of this research is to determine if rivers act as dividing or uniting features in a socio-political landscape and whether topography will influence their role in this context. By considering sections of the Orange-Senqu River, some of which are employed as political or administrative boundaries, this project furthermore aims to consider the implications of this for catchment management in South Africa. South Africa's proposed form of decentralized water management will have to contend with the effects of different topographies on the way in which rivers are perceived and utilized. The ability of a river to act as a dividing or uniting feature is dependent on a number of interrelated factors, the effects of which are either reduced or enhanced by the topography surrounding the river. Factors such as the state of the resource, levels of utilization, local histories and the employment of the river as a political or administrative border are all factors that determine the extent to which a river unites or divides the communities along its banks, and are all influenced by topography. The implications of this for the management of catchments in South Africa are significant. Local water management institutions will have to contend with a mismatch in borders and in many cases bridge social divides that are deeply entrenched along the banks of rivers. Importantly, the need for a context specific approach to catchment management is highlighted.
- Full Text:
- Authors: Smedley, David Alan
- Date: 2012
- Subjects: Rivers -- South Africa , Water-supply -- Management -- South Africa , Water-supply -- Management -- Orange River Watershed , Watershed management -- South Africa , Watershed management -- Orange River Watershed , South Africa -- Boundaries , Water-supply -- Management -- Citizen participation , Water-supply -- Government policy -- South Africa , Water-supply -- Political aspects -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4851 , http://hdl.handle.net/10962/d1005527 , Rivers -- South Africa , Water-supply -- Management -- South Africa , Water-supply -- Management -- Orange River Watershed , Watershed management -- South Africa , Watershed management -- Orange River Watershed , South Africa -- Boundaries , Water-supply -- Management -- Citizen participation , Water-supply -- Government policy -- South Africa , Water-supply -- Political aspects -- South Africa
- Description: South Africa's water resources are unequally distributed over space and time to a high degree and our already stressed water resources situation will only be exacerbated by climate change if current predictions are correct. The potential for conflict over increasingly strained water resources in South Africa is thus very real. In order to deal with these complex problems national legislation is demanding that water resource management be decentralized to the local level where active participation can take place in an integrated manner in accordance with the principles of IWRM. However, administrative and political boundaries rarely match those of catchments as, throughout South Africa, rivers have been employed extensively to delineate administrative and political boundaries at a number of spatial scales. The aim of this research is to determine if rivers act as dividing or uniting features in a socio-political landscape and whether topography will influence their role in this context. By considering sections of the Orange-Senqu River, some of which are employed as political or administrative boundaries, this project furthermore aims to consider the implications of this for catchment management in South Africa. South Africa's proposed form of decentralized water management will have to contend with the effects of different topographies on the way in which rivers are perceived and utilized. The ability of a river to act as a dividing or uniting feature is dependent on a number of interrelated factors, the effects of which are either reduced or enhanced by the topography surrounding the river. Factors such as the state of the resource, levels of utilization, local histories and the employment of the river as a political or administrative border are all factors that determine the extent to which a river unites or divides the communities along its banks, and are all influenced by topography. The implications of this for the management of catchments in South Africa are significant. Local water management institutions will have to contend with a mismatch in borders and in many cases bridge social divides that are deeply entrenched along the banks of rivers. Importantly, the need for a context specific approach to catchment management is highlighted.
- Full Text:
Small mammal communities at high altitude within the Sneeuberg Mountain complex, Eastern Cape Province, South Africa
- Authors: Kok, Armand du Preez
- Date: 2012
- Subjects: Mountain animals -- Research -- South Africa -- Eastern Cape , Mammal populations -- Research -- South Africa -- Eastern Cape , Mammals -- Research -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5766 , http://hdl.handle.net/10962/d1005454 , Mountain animals -- Research -- South Africa -- Eastern Cape , Mammal populations -- Research -- South Africa -- Eastern Cape , Mammals -- Research -- South Africa -- Eastern Cape
- Description: Due to their widespread and specious nature, small mammals are ideal for biogeographical studies. Small mammals also effectively connect various trophic levels by being both consumers and prey items for other animals. The Great Escarpment is the dominant mountain landscape in South Africa. Yet, very little small mammal research has been conducted on the Great Escarpment outside of the Main Drakensberg Mountains. This is surprising given the importance of mountains in shaping regional ecology. In this study, I assessed the diversity and community composition of small mammals at three high altitude (>1700m) sites within the Sneeuberg Mountain Complex (SMC) from June 2009 to May 2010. I also tested the effectiveness of five different bait types for measuring small mammal diversity (i.e. number of individuals caught, species richness, Shannon diversity index and Simpson index of diversity). Out of a total of 423 captures, 292 individuals of 12 small mammal species (one shrew, one elephant shrew and 10 rodents) were recorded over 5280 trap nights. The species richness and diversity of small mammals captured at the three sites were similar and this homogeneity was probably related to the regional processes (e.g. climate and latitude) that govern species richness and diversity. The most effective bait type in terms of capture success, species richness and diversity measurements was peanut butter and oats. In addition, the use of richness estimators revealed that peanut butter and oats was the most effective bait for sampling the species richness of small mammals. The effectiveness of peanut butter and oats was related to this bait having a more attractive scent, when compared to the other bait types. Future studies should focus on researching the range of local and regional processes that drive small mammal diversity at high altitudes in South Africa. I also recommend the use of more than one bait type when planning to survey small mammal communities.
- Full Text:
- Authors: Kok, Armand du Preez
- Date: 2012
- Subjects: Mountain animals -- Research -- South Africa -- Eastern Cape , Mammal populations -- Research -- South Africa -- Eastern Cape , Mammals -- Research -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5766 , http://hdl.handle.net/10962/d1005454 , Mountain animals -- Research -- South Africa -- Eastern Cape , Mammal populations -- Research -- South Africa -- Eastern Cape , Mammals -- Research -- South Africa -- Eastern Cape
- Description: Due to their widespread and specious nature, small mammals are ideal for biogeographical studies. Small mammals also effectively connect various trophic levels by being both consumers and prey items for other animals. The Great Escarpment is the dominant mountain landscape in South Africa. Yet, very little small mammal research has been conducted on the Great Escarpment outside of the Main Drakensberg Mountains. This is surprising given the importance of mountains in shaping regional ecology. In this study, I assessed the diversity and community composition of small mammals at three high altitude (>1700m) sites within the Sneeuberg Mountain Complex (SMC) from June 2009 to May 2010. I also tested the effectiveness of five different bait types for measuring small mammal diversity (i.e. number of individuals caught, species richness, Shannon diversity index and Simpson index of diversity). Out of a total of 423 captures, 292 individuals of 12 small mammal species (one shrew, one elephant shrew and 10 rodents) were recorded over 5280 trap nights. The species richness and diversity of small mammals captured at the three sites were similar and this homogeneity was probably related to the regional processes (e.g. climate and latitude) that govern species richness and diversity. The most effective bait type in terms of capture success, species richness and diversity measurements was peanut butter and oats. In addition, the use of richness estimators revealed that peanut butter and oats was the most effective bait for sampling the species richness of small mammals. The effectiveness of peanut butter and oats was related to this bait having a more attractive scent, when compared to the other bait types. Future studies should focus on researching the range of local and regional processes that drive small mammal diversity at high altitudes in South Africa. I also recommend the use of more than one bait type when planning to survey small mammal communities.
- Full Text:
Structural analysis of effects of mutations on HIV-1 subtype C protease active site
- Mathu, Alexander Muchugia Nganga
- Authors: Mathu, Alexander Muchugia Nganga
- Date: 2012
- Subjects: HIV (Viruses) -- Research , HIV infections -- Treatment -- Research , Protease inhibitors -- Research , Viruses -- Effect of drugs on -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4013 , http://hdl.handle.net/10962/d1004073 , HIV (Viruses) -- Research , HIV infections -- Treatment -- Research , Protease inhibitors -- Research , Viruses -- Effect of drugs on -- Research
- Description: HIV/AIDS is a global pandemic that poses a great threat especially in Sub-Saharan Africa where the highest population of those infected with the virus is found. It has far reaching medical, socio-economic and scientific implications. The HIV-1 protease enzyme is a prime therapeutic target that has been exploited in an effort to reduce morbidity and mortality. However problems arise from drug toxicity and drug-resistant mutations of the protease which is a motivation for research for new, safer and effective therapies. Evidence exists to show that there are significant genomic differences in Subtype B and C that have a negative effect on the intrinsic binding of inhibitors. It is imperative to look at all perspectives from epidemiological, molecular to the pharmacological ones so as to achieve rational design of therapeutic agents. This study involved the use of in silico structural analysis of the effects of mutations in the active site. The data was provided by the National Institute of Communicable Diseases consisting of HIV-1 Subtype C protease sequences of 29 infants exhibiting drug-resistance to ritonavir and lopinavir. The major active site mutations causing drug resistance identified in this study were M46I, I54V and V82A using the Stanford HIV database tool. Homology modeling without extra restraints produced models with improved quality in comparison to those with restraints. MetaMQAPII results differed when models were visualized as dimers giving erroneous modeled regions in comparison to monomers. A broader study with a larger dataset of HIV-1 subtype C protease sequences is required to increase statistical confidence and in order to identify the pattern of drug resistant mutations. Homology modeling without extra restraints is preferred for calculating homology models for the HIV-1 subtype C. Further investigations needs to be done to ascertain the accuracy of validation results for dimers from MetaMQAPII as it is designed for evaluation of monomers.
- Full Text:
- Authors: Mathu, Alexander Muchugia Nganga
- Date: 2012
- Subjects: HIV (Viruses) -- Research , HIV infections -- Treatment -- Research , Protease inhibitors -- Research , Viruses -- Effect of drugs on -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4013 , http://hdl.handle.net/10962/d1004073 , HIV (Viruses) -- Research , HIV infections -- Treatment -- Research , Protease inhibitors -- Research , Viruses -- Effect of drugs on -- Research
- Description: HIV/AIDS is a global pandemic that poses a great threat especially in Sub-Saharan Africa where the highest population of those infected with the virus is found. It has far reaching medical, socio-economic and scientific implications. The HIV-1 protease enzyme is a prime therapeutic target that has been exploited in an effort to reduce morbidity and mortality. However problems arise from drug toxicity and drug-resistant mutations of the protease which is a motivation for research for new, safer and effective therapies. Evidence exists to show that there are significant genomic differences in Subtype B and C that have a negative effect on the intrinsic binding of inhibitors. It is imperative to look at all perspectives from epidemiological, molecular to the pharmacological ones so as to achieve rational design of therapeutic agents. This study involved the use of in silico structural analysis of the effects of mutations in the active site. The data was provided by the National Institute of Communicable Diseases consisting of HIV-1 Subtype C protease sequences of 29 infants exhibiting drug-resistance to ritonavir and lopinavir. The major active site mutations causing drug resistance identified in this study were M46I, I54V and V82A using the Stanford HIV database tool. Homology modeling without extra restraints produced models with improved quality in comparison to those with restraints. MetaMQAPII results differed when models were visualized as dimers giving erroneous modeled regions in comparison to monomers. A broader study with a larger dataset of HIV-1 subtype C protease sequences is required to increase statistical confidence and in order to identify the pattern of drug resistant mutations. Homology modeling without extra restraints is preferred for calculating homology models for the HIV-1 subtype C. Further investigations needs to be done to ascertain the accuracy of validation results for dimers from MetaMQAPII as it is designed for evaluation of monomers.
- Full Text: