Polynuclear biomolecular-supported rare earth coordination compounds : towards a new generation of lanthanide-based drugs
- Authors: Clark, Candyce
- Date: 2014
- Subjects: Polyols , Hydroxyl group , Rare earth metals
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10439 , http://hdl.handle.net/10948/d1020778
- Description: Galactitol and cis,cis,cis-1,3,5-cyclohexanetriol are polyols that are ideal examples of model compounds for ligands with lanthanide ions as they have their hydroxyl groups in favourable steric arrangement. Several complexes were synthesised with both lanthanide chloride and lanthanide nitrate salts with galactitol, and a variety of structures, both polymeric and monomeric, were observed. In all these complexes, galactitol acted as a bridging molecule between the lanthanide ions. A notable difference was the lanthanum chloride–galactitol complex that showed both chloride and galactitol bridging. The lanthanide nitrate salts formed only polymeric complexes with galactitol. Not all of the complexes showed nitrate ions coordinated to the metal centre, and in the neodymium nitrate– galactitol complex, which shows both monodentate and bidentate coordination of the nitrate groups. The coordination of the nitrate ions was confirmed using both XRD and IR analysis. Two complexes with lanthanide chloride salts and cis,cis,cis-1,3,5-cyclohexanetriol were synthesised and analysed. Lanthanum chloride formed a polymeric complex, which showed extensive chloride bridging between the metal centres. Praseodymium chloride formed a dimeric complex. All complexes were analysed with single-crystal X-ray diffraction, 1H NMR, 13C NMR and IR spectroscopy.
- Full Text:
- Date Issued: 2014
- Authors: Clark, Candyce
- Date: 2014
- Subjects: Polyols , Hydroxyl group , Rare earth metals
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10439 , http://hdl.handle.net/10948/d1020778
- Description: Galactitol and cis,cis,cis-1,3,5-cyclohexanetriol are polyols that are ideal examples of model compounds for ligands with lanthanide ions as they have their hydroxyl groups in favourable steric arrangement. Several complexes were synthesised with both lanthanide chloride and lanthanide nitrate salts with galactitol, and a variety of structures, both polymeric and monomeric, were observed. In all these complexes, galactitol acted as a bridging molecule between the lanthanide ions. A notable difference was the lanthanum chloride–galactitol complex that showed both chloride and galactitol bridging. The lanthanide nitrate salts formed only polymeric complexes with galactitol. Not all of the complexes showed nitrate ions coordinated to the metal centre, and in the neodymium nitrate– galactitol complex, which shows both monodentate and bidentate coordination of the nitrate groups. The coordination of the nitrate ions was confirmed using both XRD and IR analysis. Two complexes with lanthanide chloride salts and cis,cis,cis-1,3,5-cyclohexanetriol were synthesised and analysed. Lanthanum chloride formed a polymeric complex, which showed extensive chloride bridging between the metal centres. Praseodymium chloride formed a dimeric complex. All complexes were analysed with single-crystal X-ray diffraction, 1H NMR, 13C NMR and IR spectroscopy.
- Full Text:
- Date Issued: 2014
Liver steatosis and insulin-resistance : reversal by Sutherlandia frutescens
- Authors: Clarke, Stephen
- Date: 2014
- Subjects: Insulin resistance , Diabetes -- Treatment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10348 , http://hdl.handle.net/10948/d1020788
- Description: Type 2 diabetes mellitus (T2DM) is rapidly emerging as one of the greatest global health issues of the 21st century. Insulin-resistance is a condition associated with T2DM and in the cell it is defined as the inadequate strength of insulin signalling from the insulin receptor downstream to the final substrates of insulin action involved in multiple metabolic, gene expression, and mitogenic aspects of cellular function. To investigate the potential mechanisms involved in the development of insulin-resistance, two in vitro liver cell models were established using palmitate or a combination of insulin and fructose as inducers. The development of insulin-resistance was determined via the capacity of the hepatocytes to maintain normal glucose metabolism functionality by measuring hepatic gluconeogenesis and glycogenolysis. It was established that the treatments induced the development of insulinresistance after 24 hours chronic exposure. Previous studies have investigated the potential of Sutherlandia frutescens extracts as therapeutic agents for insulin-resistance. The aim of this study was thus to investigate the ability of a hot aqueous extract of S. frutescens to reverse the insulin-resistant state, via measuring gluconeogenesis and glycogenolysis, the associated changes in cellular physiology (lipid accumulation, oxidative stress, and acetyl- CoA levels), and changes in mRNA expression. The results showed that S. frutescens had a significant effect on reversing the insulin-resistant state in both models of insulin-resistance. Furthermore, S. frutescens was capable of reducing lipid accumulation in the form of triacylglycerol in the high insulin/fructose model, while this was unaffected in the palmitate model. However, S. frutescens did reduce the accumulation of diacylglycerol in the palmitate model. Oxidative stress, seen to be associated with the insulin-resistant state, was successfully treated using the extract, as indicated by a reduction in reactive oxygen species. However no change was seen in the nitric oxide levels, in either model. Interestingly, although S. frutescens had no effect on the level of acetyl-CoA in the insulin/fructose model, it was found to increase this in the palmitate model. It is suggested that this may be due to increased β-oxidation and metabolic activity induced by the extract. The analysis of mRNA expression gave some insight into possible mechanisms by which insulin-resistance develops, although the results were inconclusive due to high variability in samples and the possibility of the RNA being compromised. Future studies will address this issue. The results of this study reflect different proposed clinical causes of insulin-resistance through the responses seen in the two cell models. These indicate that liver steatosis and insulin-resistance are induced by high palmitate as well as high insulin and fructose levels, and reversed by S. frutescens. Therefore the potential of S. frutescens to be used as a therapeutic agent in the treatment of insulin-resistance is indicated by this study.
- Full Text:
- Date Issued: 2014
- Authors: Clarke, Stephen
- Date: 2014
- Subjects: Insulin resistance , Diabetes -- Treatment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10348 , http://hdl.handle.net/10948/d1020788
- Description: Type 2 diabetes mellitus (T2DM) is rapidly emerging as one of the greatest global health issues of the 21st century. Insulin-resistance is a condition associated with T2DM and in the cell it is defined as the inadequate strength of insulin signalling from the insulin receptor downstream to the final substrates of insulin action involved in multiple metabolic, gene expression, and mitogenic aspects of cellular function. To investigate the potential mechanisms involved in the development of insulin-resistance, two in vitro liver cell models were established using palmitate or a combination of insulin and fructose as inducers. The development of insulin-resistance was determined via the capacity of the hepatocytes to maintain normal glucose metabolism functionality by measuring hepatic gluconeogenesis and glycogenolysis. It was established that the treatments induced the development of insulinresistance after 24 hours chronic exposure. Previous studies have investigated the potential of Sutherlandia frutescens extracts as therapeutic agents for insulin-resistance. The aim of this study was thus to investigate the ability of a hot aqueous extract of S. frutescens to reverse the insulin-resistant state, via measuring gluconeogenesis and glycogenolysis, the associated changes in cellular physiology (lipid accumulation, oxidative stress, and acetyl- CoA levels), and changes in mRNA expression. The results showed that S. frutescens had a significant effect on reversing the insulin-resistant state in both models of insulin-resistance. Furthermore, S. frutescens was capable of reducing lipid accumulation in the form of triacylglycerol in the high insulin/fructose model, while this was unaffected in the palmitate model. However, S. frutescens did reduce the accumulation of diacylglycerol in the palmitate model. Oxidative stress, seen to be associated with the insulin-resistant state, was successfully treated using the extract, as indicated by a reduction in reactive oxygen species. However no change was seen in the nitric oxide levels, in either model. Interestingly, although S. frutescens had no effect on the level of acetyl-CoA in the insulin/fructose model, it was found to increase this in the palmitate model. It is suggested that this may be due to increased β-oxidation and metabolic activity induced by the extract. The analysis of mRNA expression gave some insight into possible mechanisms by which insulin-resistance develops, although the results were inconclusive due to high variability in samples and the possibility of the RNA being compromised. Future studies will address this issue. The results of this study reflect different proposed clinical causes of insulin-resistance through the responses seen in the two cell models. These indicate that liver steatosis and insulin-resistance are induced by high palmitate as well as high insulin and fructose levels, and reversed by S. frutescens. Therefore the potential of S. frutescens to be used as a therapeutic agent in the treatment of insulin-resistance is indicated by this study.
- Full Text:
- Date Issued: 2014
Assessing the genetic diversity of catface rockcod epinephelus andersoni in the subtropical Western Indian Ocean and modelling the effects of climate change on their distribution
- Authors: Coppinger, Christine Rose
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54499 , vital:26570
- Description: The catface rockcod Epinephelus andersoni is a range-restricted species that is endemic to the southeast coast of Africa from Quissico in Mozambique (subtropical) to Knysna in South Africa (warmtemperate). Its complex life-history, long-lived nature and high residency make E. andersoni potentially vulnerable to over-exploitation. Epinephelus andersoni is an important fishery species and has shown signs of depletion. Due to inadequate information necessary for management and conservation, further research is vital, particularly in the face of potentially significant climatic changes which could put further pressure on E. andersoni. The aim of the study was to provide information for the management of E. andersoni, with considerations for the possibly detrimental effects of future climate change. The objectives of this study were to describe the genetic structure and diversity of E. andersoni and to determine possible range shifts of E. andersoni with future changes in sea surface temperature. Genetic samples were collected throughout the distribution of E. andersoni. Standard DNA extraction and PCR using universal primers were conducted and nuclear (RPS7-1) and mitochondrial (cytochrome b) data were analysed to determine genetic diversity. A combination of nuclear and mitochondrial markers was used to ensure that the results were robust. RPS7-1 haplotype diversity was high (0.801) and an AMOVA on the RPS7-1 data showed significantly high among group variation (ΦCT = 0.204, p < 0.05) between five groups: 1. Quissico to Inhaca; 2. Cape Vidal to Port Edward; 3 Port St Johns to Coffee Bay; 4. Mbashe; 5. Port Alfred. This geographic structuring could be attributed to low gene flow across barriers such as the Port Alfred upwelling cell, the Mozambique Channel eddies and smaller more localised upwelling cells such as the Port St Johns cell. The cytochrome b results contrastingly indicate low haplotype diversity (0.309) and no differentiation (ΦCT = 0.265, p = 0.074) between groups and support the hypothesis of a historical population bottleneck. This may be due to an unusually slower mutation rate of the cytochrome b region than the RPS7-1 region, resulting in the RPS7-1 data showing a more recent picture of diversification. To complement the genetic results, niche modelling techniques were used to determine range shifts of E. andersoni with future temperature trends using species distribution and climatic data. The model illustrated a contraction of the E. andersoni distribution as well as future intensification of various upwelling cells along the south-east African coast including the Port Alfred upwelling cell. Due to the low gene flow across these barriers this intensification could decrease the resilience of E. andersoni, as its range becomes more limited with global change. The genetic data and modelling results combined provide useful information on which to base future fisheries management.
- Full Text:
- Date Issued: 2014
- Authors: Coppinger, Christine Rose
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54499 , vital:26570
- Description: The catface rockcod Epinephelus andersoni is a range-restricted species that is endemic to the southeast coast of Africa from Quissico in Mozambique (subtropical) to Knysna in South Africa (warmtemperate). Its complex life-history, long-lived nature and high residency make E. andersoni potentially vulnerable to over-exploitation. Epinephelus andersoni is an important fishery species and has shown signs of depletion. Due to inadequate information necessary for management and conservation, further research is vital, particularly in the face of potentially significant climatic changes which could put further pressure on E. andersoni. The aim of the study was to provide information for the management of E. andersoni, with considerations for the possibly detrimental effects of future climate change. The objectives of this study were to describe the genetic structure and diversity of E. andersoni and to determine possible range shifts of E. andersoni with future changes in sea surface temperature. Genetic samples were collected throughout the distribution of E. andersoni. Standard DNA extraction and PCR using universal primers were conducted and nuclear (RPS7-1) and mitochondrial (cytochrome b) data were analysed to determine genetic diversity. A combination of nuclear and mitochondrial markers was used to ensure that the results were robust. RPS7-1 haplotype diversity was high (0.801) and an AMOVA on the RPS7-1 data showed significantly high among group variation (ΦCT = 0.204, p < 0.05) between five groups: 1. Quissico to Inhaca; 2. Cape Vidal to Port Edward; 3 Port St Johns to Coffee Bay; 4. Mbashe; 5. Port Alfred. This geographic structuring could be attributed to low gene flow across barriers such as the Port Alfred upwelling cell, the Mozambique Channel eddies and smaller more localised upwelling cells such as the Port St Johns cell. The cytochrome b results contrastingly indicate low haplotype diversity (0.309) and no differentiation (ΦCT = 0.265, p = 0.074) between groups and support the hypothesis of a historical population bottleneck. This may be due to an unusually slower mutation rate of the cytochrome b region than the RPS7-1 region, resulting in the RPS7-1 data showing a more recent picture of diversification. To complement the genetic results, niche modelling techniques were used to determine range shifts of E. andersoni with future temperature trends using species distribution and climatic data. The model illustrated a contraction of the E. andersoni distribution as well as future intensification of various upwelling cells along the south-east African coast including the Port Alfred upwelling cell. Due to the low gene flow across these barriers this intensification could decrease the resilience of E. andersoni, as its range becomes more limited with global change. The genetic data and modelling results combined provide useful information on which to base future fisheries management.
- Full Text:
- Date Issued: 2014
Cardiovascular disease risk in Black African females and the efficacy of a walking programme on blood pressure in a sub-sample
- Authors: Crymble, Tegan
- Date: 2014
- Subjects: Cardiovascular system -- Diseases -- South Africa -- Eastern Cape , Women -- Health and hygiene -- South Africa -- Eastern Cape , Obesity -- South Africa -- Eastern Cape , Hypertension -- South Africa -- Eastern Cape , Walking -- South Africa -- Eastern Cape -- Physiological aspects , Lifestyles -- Health aspects -- South Africa -- Eastern Cape , Health attitudes -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5152 , http://hdl.handle.net/10962/d1013234
- Description: The purpose of the study was to investigate the cardiovascular disease (CVD) risk profile of black African females in the Makana region, Eastern Cape, South Africa. Baseline measures from 40 participants, who met the criteria, were compared against the 2003 South African Demographic and Health Survey (SADHS) and the 2013 South African National Health and Nutritional Examination Survey (SANHANES-1). The risk factors measured were anthropometric (stature, body mass and body mass index (BMI)), morphological (waist circumference (WC), fat mass and lean mass), cardiovascular (heart rate and blood pressure (BP)), physical activity (step count and energy expenditure), biochemical (glycated haemoglobin and full blood lipid profile) and behavioural (alcohol and tobacco use). Results showed significantly higher (p≤0.05) values for overweight/obesity (BMI 37.60 kg.m⁻²; WC 1130.58 mm; fat mass 45.23%) and high BP (130/88 mmHg) compared to the previous national surveys, highlighting these CVD risk factors as problematic. The subsequent sub-study aimed to assess the efficacy of a pedometer-based walking intervention on high BP. The walking programme (n=25) was based on individual step goals to be completed at a moderate-intensity on five days.week⁻¹ for 12 weeks. The same measurements were taken at monthly intervals, Week 0, Week 4, Week 8 and Week 12, with the addition of dietary intake and fitness level, and the exclusion of the behavioural variables. There were no significant differences (p≤0.05) in systolic and diastolic BP with the exercise intervention, although there was a strong, negative relationship with time for diastolic BP (r²=0.9857). This trend suggests that the lack of significance may be a result of poor compliance and/or the small sample size. Individual results, however, showed no compliance-result relationship for the two risk factors of interest: overweight/obesity and high BP. Future recommendations include supervised or group-based exercise interventions to improve compliance, and the addition of resistance training to the aerobic programme.
- Full Text:
- Date Issued: 2014
- Authors: Crymble, Tegan
- Date: 2014
- Subjects: Cardiovascular system -- Diseases -- South Africa -- Eastern Cape , Women -- Health and hygiene -- South Africa -- Eastern Cape , Obesity -- South Africa -- Eastern Cape , Hypertension -- South Africa -- Eastern Cape , Walking -- South Africa -- Eastern Cape -- Physiological aspects , Lifestyles -- Health aspects -- South Africa -- Eastern Cape , Health attitudes -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5152 , http://hdl.handle.net/10962/d1013234
- Description: The purpose of the study was to investigate the cardiovascular disease (CVD) risk profile of black African females in the Makana region, Eastern Cape, South Africa. Baseline measures from 40 participants, who met the criteria, were compared against the 2003 South African Demographic and Health Survey (SADHS) and the 2013 South African National Health and Nutritional Examination Survey (SANHANES-1). The risk factors measured were anthropometric (stature, body mass and body mass index (BMI)), morphological (waist circumference (WC), fat mass and lean mass), cardiovascular (heart rate and blood pressure (BP)), physical activity (step count and energy expenditure), biochemical (glycated haemoglobin and full blood lipid profile) and behavioural (alcohol and tobacco use). Results showed significantly higher (p≤0.05) values for overweight/obesity (BMI 37.60 kg.m⁻²; WC 1130.58 mm; fat mass 45.23%) and high BP (130/88 mmHg) compared to the previous national surveys, highlighting these CVD risk factors as problematic. The subsequent sub-study aimed to assess the efficacy of a pedometer-based walking intervention on high BP. The walking programme (n=25) was based on individual step goals to be completed at a moderate-intensity on five days.week⁻¹ for 12 weeks. The same measurements were taken at monthly intervals, Week 0, Week 4, Week 8 and Week 12, with the addition of dietary intake and fitness level, and the exclusion of the behavioural variables. There were no significant differences (p≤0.05) in systolic and diastolic BP with the exercise intervention, although there was a strong, negative relationship with time for diastolic BP (r²=0.9857). This trend suggests that the lack of significance may be a result of poor compliance and/or the small sample size. Individual results, however, showed no compliance-result relationship for the two risk factors of interest: overweight/obesity and high BP. Future recommendations include supervised or group-based exercise interventions to improve compliance, and the addition of resistance training to the aerobic programme.
- Full Text:
- Date Issued: 2014
Genetic and morphometric variation of Octopus vulgaris in the Benguela Current region
- Authors: De Beer, Chénelle Lesley
- Date: 2014
- Subjects: Common octopus -- Africa, Southern , Common octopus -- Genetics , Common octopus -- Morphology , Common octopus -- Geographical distribution , Variation (Biology) , Benguela Current
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5362 , http://hdl.handle.net/10962/d1012971
- Description: The Benguela Current is a cold eastern boundary current located on the south-western coast of the African continent. The establishment of its present day features approximately two million years ago has triggered allopatric events which have driven genetic and/or phenotypic differentiation in many of the warm-temperate organisms that previously had continuous distributions along the south and west coast of southern Africa. However, since many of these species have responded differently, despite similar isolation times, research in this region provides a unique opportunity to increase our understanding of evolutionary processes. The common octopus (Octopus vulgaris, Cuvier 1797) is a coastal, sedentary species, inhabiting coral reefs or rocky environments at depths of up to a 100m. It is considered to be one of the most extensively studied cephalopod species due to its worldwide distribution. However, very little research has been conducted on O. vulgaris in southern Africa. In order to gain a holistic understanding of the effects of the Benguela Current on population connectivity, genetic and phenotypic diversity, and evolutionary history of O. vulgaris, a comparative genetic and morphological study was conducted across the Benguela region. A total of 168 specimens of O. vulgaris were collected from four different regions across the Benguela system. A small tissue sample was preserved in ethanol for molecular analysis, and the specimen was frozen whole for morphometric analysis in the laboratory. Octopus vulgaris genetic population structure and evolutionary history was investigated using a 580bp fragment of the mitochondrial cytochrome b (cytb) gene for 76 individuals located within the Benguela region, yielding 10 different haplotypes. AMOVA and pairwise FST analyses revealed significant genetic differentiation suggesting a northern-southern Benguela divergence. Estimates of time since most recent common ancestor, based on biogeographical calibrators and coalescent analyses, indicated that isolation between the Angolan and South African population occurred between ~231 Ka and 1 Ma. Mismatch distribution analyses revealed a past population expansion within the South African O. vulgaris roughly 129.31 Ka, whilst Bayesian skyline plots were indicative of gradual demographic growth within the Angolan population in the last ~100 Ka. Observed O. vulgaris population structure and demographic history was likely the result of historical climate-induced change within the system. Reconstruction of phylogenetic relationships within the Octopus genus, using cytb and COI suggest that O. vulgaris is not a monophyletic group and a major systematic revision is required. Furthermore, unidentified individuals from South Africa were found to group with species from Indo-West Pacific Oceans and were therefore considered to have been translocated through ballast water from Asia. While the molecular analysis indicated a significant northern-southern Benguela structure results from the principle component analysis (PCA) and discriminate function analysis (DFA) were unable to distinguish between O. vulgaris from different sampling localities throughout the Benguela Current region based on soft-parts, hard-parts and meristic characters. The lack of phenotypic variation, despite significant genetic divergence, highlights the importance of multi-method approaches in gaining a holistic understanding of the taxonomy and biogeography of species.
- Full Text:
- Date Issued: 2014
- Authors: De Beer, Chénelle Lesley
- Date: 2014
- Subjects: Common octopus -- Africa, Southern , Common octopus -- Genetics , Common octopus -- Morphology , Common octopus -- Geographical distribution , Variation (Biology) , Benguela Current
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5362 , http://hdl.handle.net/10962/d1012971
- Description: The Benguela Current is a cold eastern boundary current located on the south-western coast of the African continent. The establishment of its present day features approximately two million years ago has triggered allopatric events which have driven genetic and/or phenotypic differentiation in many of the warm-temperate organisms that previously had continuous distributions along the south and west coast of southern Africa. However, since many of these species have responded differently, despite similar isolation times, research in this region provides a unique opportunity to increase our understanding of evolutionary processes. The common octopus (Octopus vulgaris, Cuvier 1797) is a coastal, sedentary species, inhabiting coral reefs or rocky environments at depths of up to a 100m. It is considered to be one of the most extensively studied cephalopod species due to its worldwide distribution. However, very little research has been conducted on O. vulgaris in southern Africa. In order to gain a holistic understanding of the effects of the Benguela Current on population connectivity, genetic and phenotypic diversity, and evolutionary history of O. vulgaris, a comparative genetic and morphological study was conducted across the Benguela region. A total of 168 specimens of O. vulgaris were collected from four different regions across the Benguela system. A small tissue sample was preserved in ethanol for molecular analysis, and the specimen was frozen whole for morphometric analysis in the laboratory. Octopus vulgaris genetic population structure and evolutionary history was investigated using a 580bp fragment of the mitochondrial cytochrome b (cytb) gene for 76 individuals located within the Benguela region, yielding 10 different haplotypes. AMOVA and pairwise FST analyses revealed significant genetic differentiation suggesting a northern-southern Benguela divergence. Estimates of time since most recent common ancestor, based on biogeographical calibrators and coalescent analyses, indicated that isolation between the Angolan and South African population occurred between ~231 Ka and 1 Ma. Mismatch distribution analyses revealed a past population expansion within the South African O. vulgaris roughly 129.31 Ka, whilst Bayesian skyline plots were indicative of gradual demographic growth within the Angolan population in the last ~100 Ka. Observed O. vulgaris population structure and demographic history was likely the result of historical climate-induced change within the system. Reconstruction of phylogenetic relationships within the Octopus genus, using cytb and COI suggest that O. vulgaris is not a monophyletic group and a major systematic revision is required. Furthermore, unidentified individuals from South Africa were found to group with species from Indo-West Pacific Oceans and were therefore considered to have been translocated through ballast water from Asia. While the molecular analysis indicated a significant northern-southern Benguela structure results from the principle component analysis (PCA) and discriminate function analysis (DFA) were unable to distinguish between O. vulgaris from different sampling localities throughout the Benguela Current region based on soft-parts, hard-parts and meristic characters. The lack of phenotypic variation, despite significant genetic divergence, highlights the importance of multi-method approaches in gaining a holistic understanding of the taxonomy and biogeography of species.
- Full Text:
- Date Issued: 2014
The interaction of silver nanoparticles with triosephosphate isomerase from human and malarial parasite (Plasmodium falciparum) : a comparative study
- De Moor, Warren Ralph Josephus
- Authors: De Moor, Warren Ralph Josephus
- Date: 2014
- Subjects: Silver , Nanoparticles , Triose-phosphate isomerase , Plasmodium falciparum , Nanotechnology , Antimalarials , Povidone
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4169 , http://hdl.handle.net/10962/d1020895
- Description: The advent of advanced modern nanotechnology techniques offers new and exciting opportunities to develop novel nanotech-derived antimalarial nanodrugs with enhanced selective and targeting abilities that allow for lower effective drug dosages, longer drug persistence and reduced drug degradation within the body. Using a nanodrug approach also has the advantage of avoiding drug resistance problems that plague reconfigured versions of already-existing antimalarial drugs. In this study recombinant triosephosphate isomerase enzymes from Plasmodium falciparum (PfTIM) and Humans (hTIM) were recombinantly expressed, purified and characterised. PfTIM was shown to have optimal pH stability at pH 5.0-5.5 and thermal stability at 25°C with Km 4.34 mM and Vmax 0.876 μmol.ml⁻ₑmin⁻ₑ. For hTIM, these parameters were as follows: pH optima of 6.5-7.0; temperature optima of 30°C, with Km 2.27 mM and Vmax 0.714 μmol.ml⁻ₑmin⁻ₑ. Recombinant TIM enzymes were subjected to inhibition studies using polyvinylpyrrolidone (PVP) stabilised silver nanoparticles (AgNPs) of 4-12 nm in diameter. These studies showed that the AgNPs were able to selectively inhibit PfTIM over hTIM with an 8-fold greater decrease in enzymatic efficiency (Kcat/Km) observed for PfTIM, as compared to hTIM, for kinetics tests done using 0.06 μM of AgNPs. Complete inhibition of PfTIM under optimal conditions was achieved using 0.25 μM AgNPs after 45 minutes while hTIM maintained approximately 31% of its activity at this AgNP concentration. The above results indicate that selective enzymatic targeting of the important, key metabolic enzyme TIM, can be achieved using nanotechnology-derived nanodrugs. It was demonstrated that the key structural differences, between the two enzyme variants, were significant enough to create unique characteristics for each TIM variant, thereby allowing for selective enzyme targeting using AgNPs. If these AgNPs could be coupled with a nanotechnology-derived, targeted localization mechanism – possibly using apoferritin to deliver the AgNPs to infected erythrocytes (Burns and Pollock, 2008) – then such an approach could offer new opportunities for the development of viable antimalarial nanodrugs. For this to be achieved further research into several key areas will be required, including nanoparticle toxicity, drug localization and testing the lethality of the system on live parasite cultures.
- Full Text:
- Date Issued: 2014
- Authors: De Moor, Warren Ralph Josephus
- Date: 2014
- Subjects: Silver , Nanoparticles , Triose-phosphate isomerase , Plasmodium falciparum , Nanotechnology , Antimalarials , Povidone
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4169 , http://hdl.handle.net/10962/d1020895
- Description: The advent of advanced modern nanotechnology techniques offers new and exciting opportunities to develop novel nanotech-derived antimalarial nanodrugs with enhanced selective and targeting abilities that allow for lower effective drug dosages, longer drug persistence and reduced drug degradation within the body. Using a nanodrug approach also has the advantage of avoiding drug resistance problems that plague reconfigured versions of already-existing antimalarial drugs. In this study recombinant triosephosphate isomerase enzymes from Plasmodium falciparum (PfTIM) and Humans (hTIM) were recombinantly expressed, purified and characterised. PfTIM was shown to have optimal pH stability at pH 5.0-5.5 and thermal stability at 25°C with Km 4.34 mM and Vmax 0.876 μmol.ml⁻ₑmin⁻ₑ. For hTIM, these parameters were as follows: pH optima of 6.5-7.0; temperature optima of 30°C, with Km 2.27 mM and Vmax 0.714 μmol.ml⁻ₑmin⁻ₑ. Recombinant TIM enzymes were subjected to inhibition studies using polyvinylpyrrolidone (PVP) stabilised silver nanoparticles (AgNPs) of 4-12 nm in diameter. These studies showed that the AgNPs were able to selectively inhibit PfTIM over hTIM with an 8-fold greater decrease in enzymatic efficiency (Kcat/Km) observed for PfTIM, as compared to hTIM, for kinetics tests done using 0.06 μM of AgNPs. Complete inhibition of PfTIM under optimal conditions was achieved using 0.25 μM AgNPs after 45 minutes while hTIM maintained approximately 31% of its activity at this AgNP concentration. The above results indicate that selective enzymatic targeting of the important, key metabolic enzyme TIM, can be achieved using nanotechnology-derived nanodrugs. It was demonstrated that the key structural differences, between the two enzyme variants, were significant enough to create unique characteristics for each TIM variant, thereby allowing for selective enzyme targeting using AgNPs. If these AgNPs could be coupled with a nanotechnology-derived, targeted localization mechanism – possibly using apoferritin to deliver the AgNPs to infected erythrocytes (Burns and Pollock, 2008) – then such an approach could offer new opportunities for the development of viable antimalarial nanodrugs. For this to be achieved further research into several key areas will be required, including nanoparticle toxicity, drug localization and testing the lethality of the system on live parasite cultures.
- Full Text:
- Date Issued: 2014
Contemporary use and seasonal abundance of indigenous edible plants (with an emphasis on geophytes) available to human foragers on the Cape south coast, South Africa
- Authors: De Vynck, Jan Carlo
- Date: 2014
- Subjects: Wild plants, Edible -- Africa, Southern , Coastal plants -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10638 , http://hdl.handle.net/10948/d1020044
- Description: Human subsistence within the Cape Floristic Region (Cape) dates back to our inception as a distinct species. Unique archaeological evidence found here for the defining attribute of cognitive modernity, as well as coinciding paleo-climatic challenges to survival, both highlight the Cape’s potential to support the existence of pre-historic hunter-gatherers. This habitat, with its unprecedented diversity of geophytes and other plant growth forms, has not yet revealed its potential to provide carbohydrate resources for early Homo sapiens sapiens. In order to investigate this potential, an ethnobotanical survey of the south Cape coastal area near Still Bay was conducted. Despite 17th Century colonialism marking the onset of indigenous plant knowledge decline, the 18 people of Khoe-San descent interviewed in this survey still actively used 58 indigenous edible plant species with a variety of 69 uses. Fruit showed the highest popularity of plants used (52 percent) followed by nectar, with plants having underground storage organs (USOs) ranking third (34 percent). Among growth forms, shrubs dominated (34 percent) followed by geophytes and trees (both 21 percent). With the exception of Prionium serratum, which was rare in the research area, this study failed to identify species that could have formed a staple source of carbohydrate for pre-colonial Khoe-San peoples of the Cape south coast. While eight species of USOs were identified (12 percent of total) only Cyphia species emerged as an important carbohydrate source. This study indicated the importance of Thicket Biome species as a source of edible plants. The second component of the study comprised a two year phenological survey of indigenous edible plant species in four primary vegetation types. A total of 32 USO species and 21 species with aboveground edible carbohydrates (fruiting species) were identified across all sites. Limestone Fynbos had the richest flora of edible species (21 USO species and 18 fruiting species), followed by Strandveld (15 USOs and 13 fruiting species), Renosterveld (8 and 8, respectively) and lastly Sand Fynbos (5 and 5, respectively). The season of highest apparency showed slight variation amongst the four sites over the two years, with more variation evident in the period of apparency. The first survey year had below average rainfall, while the second year received an average rainfall amount. The second year saw a dramatic increase in apparency of abundance for all sites (50 to 60 percent increase) except for the Sand Fynbos site, which showed little change. The other sites showed a one month increase in the period of apparency in the second survey year. Overall, late summer to autumn was the period of lowest apparency of USOs. The ripening of certain fruiting species during this time would have provided a source of carbohydrate when USO availability was at its lowest. Strandveld had the highest biomass in the peak of apparency (over 80 kgha-1) in the first year with a nearly 20 percent increase for the second year. The combined biomass for the four study sites in the first survey year was roughly 150 kgha-1 and 185 kgha-1 for the second year. The apparency of abundance (ripe and edible phase) of fruiting species did not increase much for Renosterveld and Strandveld in the second survey year, except for Limestone Fynbos (49 percent increase) and Sand Fynbos (53 percent). A multivariate analysis showed seven phenophases for high apparency of edible USOs and ripe fruit across the four vegetation types. Given the contribution of evergreen USOs and fruiting species, there would always have been carbohydrates available for foragers to collect in the major vegetation types of the south Cape coast. However, harvesting and processing this carbohydrate resource would have posed cognitive challenges for MSA hunter-gatherers, given the interwoven taxonomic complexity of numerous toxic plant species, and the diverse phenology of edible plant species within the varied vegetation types. These challenges were undoubtedly mastered, highlighting the Cape environment as a possible catalyst to improved human cognitive maturity.
- Full Text:
- Date Issued: 2014
- Authors: De Vynck, Jan Carlo
- Date: 2014
- Subjects: Wild plants, Edible -- Africa, Southern , Coastal plants -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10638 , http://hdl.handle.net/10948/d1020044
- Description: Human subsistence within the Cape Floristic Region (Cape) dates back to our inception as a distinct species. Unique archaeological evidence found here for the defining attribute of cognitive modernity, as well as coinciding paleo-climatic challenges to survival, both highlight the Cape’s potential to support the existence of pre-historic hunter-gatherers. This habitat, with its unprecedented diversity of geophytes and other plant growth forms, has not yet revealed its potential to provide carbohydrate resources for early Homo sapiens sapiens. In order to investigate this potential, an ethnobotanical survey of the south Cape coastal area near Still Bay was conducted. Despite 17th Century colonialism marking the onset of indigenous plant knowledge decline, the 18 people of Khoe-San descent interviewed in this survey still actively used 58 indigenous edible plant species with a variety of 69 uses. Fruit showed the highest popularity of plants used (52 percent) followed by nectar, with plants having underground storage organs (USOs) ranking third (34 percent). Among growth forms, shrubs dominated (34 percent) followed by geophytes and trees (both 21 percent). With the exception of Prionium serratum, which was rare in the research area, this study failed to identify species that could have formed a staple source of carbohydrate for pre-colonial Khoe-San peoples of the Cape south coast. While eight species of USOs were identified (12 percent of total) only Cyphia species emerged as an important carbohydrate source. This study indicated the importance of Thicket Biome species as a source of edible plants. The second component of the study comprised a two year phenological survey of indigenous edible plant species in four primary vegetation types. A total of 32 USO species and 21 species with aboveground edible carbohydrates (fruiting species) were identified across all sites. Limestone Fynbos had the richest flora of edible species (21 USO species and 18 fruiting species), followed by Strandveld (15 USOs and 13 fruiting species), Renosterveld (8 and 8, respectively) and lastly Sand Fynbos (5 and 5, respectively). The season of highest apparency showed slight variation amongst the four sites over the two years, with more variation evident in the period of apparency. The first survey year had below average rainfall, while the second year received an average rainfall amount. The second year saw a dramatic increase in apparency of abundance for all sites (50 to 60 percent increase) except for the Sand Fynbos site, which showed little change. The other sites showed a one month increase in the period of apparency in the second survey year. Overall, late summer to autumn was the period of lowest apparency of USOs. The ripening of certain fruiting species during this time would have provided a source of carbohydrate when USO availability was at its lowest. Strandveld had the highest biomass in the peak of apparency (over 80 kgha-1) in the first year with a nearly 20 percent increase for the second year. The combined biomass for the four study sites in the first survey year was roughly 150 kgha-1 and 185 kgha-1 for the second year. The apparency of abundance (ripe and edible phase) of fruiting species did not increase much for Renosterveld and Strandveld in the second survey year, except for Limestone Fynbos (49 percent increase) and Sand Fynbos (53 percent). A multivariate analysis showed seven phenophases for high apparency of edible USOs and ripe fruit across the four vegetation types. Given the contribution of evergreen USOs and fruiting species, there would always have been carbohydrates available for foragers to collect in the major vegetation types of the south Cape coast. However, harvesting and processing this carbohydrate resource would have posed cognitive challenges for MSA hunter-gatherers, given the interwoven taxonomic complexity of numerous toxic plant species, and the diverse phenology of edible plant species within the varied vegetation types. These challenges were undoubtedly mastered, highlighting the Cape environment as a possible catalyst to improved human cognitive maturity.
- Full Text:
- Date Issued: 2014
An investigation of the XMOS XSl architecture as a platform for development of audio control standards
- Authors: Dibley, James
- Date: 2014
- Subjects: Microcontrollers -- Research , Streaming audio -- Standards -- Research , Computer sound processing -- Research , Computer network protocols -- Standards -- Research , Communication -- Technological innovations -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4694 , http://hdl.handle.net/10962/d1011789 , Microcontrollers -- Research , Streaming audio -- Standards -- Research , Computer sound processing -- Research , Computer network protocols -- Standards -- Research , Communication -- Technological innovations -- Research
- Description: This thesis investigates the feasiblity of using a new microcontroller architecture, the XMOS XS1, in the research and development of control standards for audio distribution networks. This investigation is conducted in the context of an emerging audio distribution network standard, Ethernet Audio/Video Bridging (`Ethernet AVB'), and an emerging audio control standard, AES-64. The thesis describes these emerging standards, the XMOS XS1 architecture (including its associated programming language, XC), and the open-source implementation of an Ethernet AVB streaming audio device based on the XMOS XS1 architecture. It is shown how the XMOS XS1 architecture and its associated features, focusing on the XC language's mechanisms for concurrency, event-driven programming, and integration of C software modules, enable a powerful implementation of the AES-64 control standard. Feasibility is demonstrated by the implementation of an AES-64 protocol stack and its integration into an XMOS XS1-based Ethernet AVB streaming audio device, providing control of Ethernet AVB features and audio hardware, as well as implementations of advanced AES-64 control mechanisms. It is demonstrated that the XMOS XS1 architecture is a compelling platform for the development of audio control standards, and has enabled the implementation of AES-64 connection management and control over standards-compliant Ethernet AVB streaming audio devices where no such implementation previously existed. The research additionally describes a linear design method for applications based on the XMOS XS1 architecture, and provides a baseline implementation reference for the AES-64 control standard where none previously existed.
- Full Text:
- Date Issued: 2014
- Authors: Dibley, James
- Date: 2014
- Subjects: Microcontrollers -- Research , Streaming audio -- Standards -- Research , Computer sound processing -- Research , Computer network protocols -- Standards -- Research , Communication -- Technological innovations -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4694 , http://hdl.handle.net/10962/d1011789 , Microcontrollers -- Research , Streaming audio -- Standards -- Research , Computer sound processing -- Research , Computer network protocols -- Standards -- Research , Communication -- Technological innovations -- Research
- Description: This thesis investigates the feasiblity of using a new microcontroller architecture, the XMOS XS1, in the research and development of control standards for audio distribution networks. This investigation is conducted in the context of an emerging audio distribution network standard, Ethernet Audio/Video Bridging (`Ethernet AVB'), and an emerging audio control standard, AES-64. The thesis describes these emerging standards, the XMOS XS1 architecture (including its associated programming language, XC), and the open-source implementation of an Ethernet AVB streaming audio device based on the XMOS XS1 architecture. It is shown how the XMOS XS1 architecture and its associated features, focusing on the XC language's mechanisms for concurrency, event-driven programming, and integration of C software modules, enable a powerful implementation of the AES-64 control standard. Feasibility is demonstrated by the implementation of an AES-64 protocol stack and its integration into an XMOS XS1-based Ethernet AVB streaming audio device, providing control of Ethernet AVB features and audio hardware, as well as implementations of advanced AES-64 control mechanisms. It is demonstrated that the XMOS XS1 architecture is a compelling platform for the development of audio control standards, and has enabled the implementation of AES-64 connection management and control over standards-compliant Ethernet AVB streaming audio devices where no such implementation previously existed. The research additionally describes a linear design method for applications based on the XMOS XS1 architecture, and provides a baseline implementation reference for the AES-64 control standard where none previously existed.
- Full Text:
- Date Issued: 2014
Development of polymer templates for ZnO nanorods
- Authors: Dobson, Stephen Robert
- Date: 2014
- Subjects: Polymers , Semiconductor industry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10556 , http://hdl.handle.net/10948/d1020805
- Description: One of the biggest challenges for the semiconductor industry is the development of nanofabrication techniques that allow for the fabrication of structures on a scale tens of nanometers in size. This provides greater potential functionality at reduced costs. Established conventional techniques, such as photolithography, are unable to achieve features below 30 nm due to the inherent limitations of the wavelength of light sources currently available. For this reason block copolymers received considerable attention in order to overcome these challenges in lithographic technology. Block copolymers have an inherent processing advantage of self assembling into various nanoscopic structures such as spheres, cylinders and lamellae amongst others on a scale below 50 nm. The dimensions and structures are readily tuneable based on molecular weights (Mw) and compositions of the copolymers. However, to be usable within industry a great deal more research still needs to be conducted on the use and nature of block copolymers. In this study the block copolymer of poly(styrene-block-methylmethacrylate) (PS-b-PMMA) was investigated as a potential nano-mask for semiconductor growth. Research was conducted on thin films of PS-b-PMMA by altering the parameters influencing the kinetics and thermodynamic effects on the thin films, in order to produce a structure of cylinders of PMMA perpendicular to the substrate within a PS matrix on a silicon (Si) substrate. It is shown that thermally annealing the PS-b-PMMA thin films under conditions where there is no preferential interaction of the substrate or open surface with either components of the block copolymer (i.e. PS or PMMA with Si or ambient) and at an appropriate thin film thickness, perpendicular cylinders of PMMA within a PS matrix form in the thin films. The determined ideal thin film thickness is 32 nm, with non-preferential interaction attained between block and substrate by coating a poly(styrene-random-methylmethacrylate) (PS-r-PMMA) on the Si substrate and annealing within a vacuum. Additionally, acetic acid, as a known selective solvent of PMMA, is used to further process the thin film of PS-b-PMMA. Thus a final PS nano-mask containing pores with a diameter tens of nanometers in size is produced. The pores are shown to have an average diameter of 13.5 nm. Measurements were taken throughout the investigation using a scanning probe microscope (SPM) to determine surface topography and phase morphology of the PS-b-PMMA thin films. X-ray reflectometry (XRR) is used to measure film thickness. The research in this study shows that thin films of PS containing hexagonally arranged pores can be produced and could find potential use as a nano-mask for semiconductor growth.
- Full Text:
- Date Issued: 2014
- Authors: Dobson, Stephen Robert
- Date: 2014
- Subjects: Polymers , Semiconductor industry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10556 , http://hdl.handle.net/10948/d1020805
- Description: One of the biggest challenges for the semiconductor industry is the development of nanofabrication techniques that allow for the fabrication of structures on a scale tens of nanometers in size. This provides greater potential functionality at reduced costs. Established conventional techniques, such as photolithography, are unable to achieve features below 30 nm due to the inherent limitations of the wavelength of light sources currently available. For this reason block copolymers received considerable attention in order to overcome these challenges in lithographic technology. Block copolymers have an inherent processing advantage of self assembling into various nanoscopic structures such as spheres, cylinders and lamellae amongst others on a scale below 50 nm. The dimensions and structures are readily tuneable based on molecular weights (Mw) and compositions of the copolymers. However, to be usable within industry a great deal more research still needs to be conducted on the use and nature of block copolymers. In this study the block copolymer of poly(styrene-block-methylmethacrylate) (PS-b-PMMA) was investigated as a potential nano-mask for semiconductor growth. Research was conducted on thin films of PS-b-PMMA by altering the parameters influencing the kinetics and thermodynamic effects on the thin films, in order to produce a structure of cylinders of PMMA perpendicular to the substrate within a PS matrix on a silicon (Si) substrate. It is shown that thermally annealing the PS-b-PMMA thin films under conditions where there is no preferential interaction of the substrate or open surface with either components of the block copolymer (i.e. PS or PMMA with Si or ambient) and at an appropriate thin film thickness, perpendicular cylinders of PMMA within a PS matrix form in the thin films. The determined ideal thin film thickness is 32 nm, with non-preferential interaction attained between block and substrate by coating a poly(styrene-random-methylmethacrylate) (PS-r-PMMA) on the Si substrate and annealing within a vacuum. Additionally, acetic acid, as a known selective solvent of PMMA, is used to further process the thin film of PS-b-PMMA. Thus a final PS nano-mask containing pores with a diameter tens of nanometers in size is produced. The pores are shown to have an average diameter of 13.5 nm. Measurements were taken throughout the investigation using a scanning probe microscope (SPM) to determine surface topography and phase morphology of the PS-b-PMMA thin films. X-ray reflectometry (XRR) is used to measure film thickness. The research in this study shows that thin films of PS containing hexagonally arranged pores can be produced and could find potential use as a nano-mask for semiconductor growth.
- Full Text:
- Date Issued: 2014
The genetic stock structure and distribution of Chrysoblephus Puniceus, a commercially important transboundary linefish species, endemic to the South West Indian Ocean
- Authors: Duncan, Murray Ian
- Date: 2014
- Subjects: Sparidae , Fishes -- Indian Ocean , Fish populations , Fishery management , Fish stock assessment -- South Africa , Fish stock assessment -- Mozambique , Overfishing , Habitat conservation , Fishes -- Genetics , Fishes -- Climatic factors , Fishes -- Variation , Fishes -- Migration
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5360 , http://hdl.handle.net/10962/d1011868 , Sparidae , Fishes -- Indian Ocean , Fish populations , Fishery management , Fish stock assessment -- South Africa , Fish stock assessment -- Mozambique , Overfishing , Habitat conservation , Fishes -- Genetics , Fishes -- Climatic factors , Fishes -- Variation , Fishes -- Migration
- Description: Chrysoblephus puniceus is an over-exploited linefish species, endemic to the coastlines off southern Mozambique and eastern South Africa. Over-exploitation and habitat loss are two of the biggest threats to the sustainability of fisheries globally. Assessing the genetic stock structure (a prerequisite for effective management) and predicting climate related range changes will provide a better understanding of these threats to C. puniceus which can be used to improve the sustainability of the fishery. Two hundred and eighty four genetic samples were collected from eight sampling sites between Ponta da Barra in Mozambique and Coffee Bay in South Africa. The mitochondrial control region and ten microsatellite loci were amplified to analyse the stock structure of C. puniceus. The majority of microsatellite and mtDNA pairwise population comparisons were not significant (P > 0.05) although Xai Xai and Inhaca populations had some significant population comparisons for mtDNA (P < 0.05). AMOVA did not explain any significant variation at the between groups hierarchical level for any pre-defined groupings except for a mtDNA grouping which separated out Xai Xai and Inhaca from other sampling sites. SAMOVA, isolation by distance tests, structure analysis, principle component analysis and spatial autocorrelation analysis all indicated a single population of C. puniceus as being most likely. The migrate-n analysis provided evidence of current driven larval transport, with net migration rates influenced by current dynamics.Two hundred and thirty six unique presence points of C. puniceus were correlated with seasonal maximum and minimum temperature data and bathymetry to model the current distribution and predict future distribution changes of the species up until 2030. Eight individual species distribution models were developed and combined into a mean ensemble model using the Biomod2 package. Winter minimum temperature was the most important variable in determining models outputs. Overall the ensemble model was accurate with a true skills statistic score of 0.962. Binary transformed mean ensemble models predicted a northern and southern range contraction of C. puniceus' distribution of 15 percent; by 2030. The mean ensemble probability of occurrence models indicated that C. puniceus' abundance is likely to decrease off the southern Mozambique coastline but remain high off KwaZulu-Natal. The results of the genetic analysis support the theory of external recruitment sustaining the KwaZulu Natal fishery for C. puniceus. While the high genetic diversity and connectivity may make C. puniceus more resilient to disturbances, the loss of 15 percent; distribution and 11 percent; genetic diversity by 2030 will increase the species vulnerability. The decrease in abundance of C. puniceus off southern Mozambique together with current widespread exploitation levels could result in the collapse of the fishery. A single transboundary stock of C. puniceus highlights the need for co-management of the species. A combined stock assessment between South Africa and Mozambique and the development of further Marine Protected Areas off southern Mozambique are suggested as management options to minimise the vulnerability of this species.
- Full Text:
- Date Issued: 2014
- Authors: Duncan, Murray Ian
- Date: 2014
- Subjects: Sparidae , Fishes -- Indian Ocean , Fish populations , Fishery management , Fish stock assessment -- South Africa , Fish stock assessment -- Mozambique , Overfishing , Habitat conservation , Fishes -- Genetics , Fishes -- Climatic factors , Fishes -- Variation , Fishes -- Migration
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5360 , http://hdl.handle.net/10962/d1011868 , Sparidae , Fishes -- Indian Ocean , Fish populations , Fishery management , Fish stock assessment -- South Africa , Fish stock assessment -- Mozambique , Overfishing , Habitat conservation , Fishes -- Genetics , Fishes -- Climatic factors , Fishes -- Variation , Fishes -- Migration
- Description: Chrysoblephus puniceus is an over-exploited linefish species, endemic to the coastlines off southern Mozambique and eastern South Africa. Over-exploitation and habitat loss are two of the biggest threats to the sustainability of fisheries globally. Assessing the genetic stock structure (a prerequisite for effective management) and predicting climate related range changes will provide a better understanding of these threats to C. puniceus which can be used to improve the sustainability of the fishery. Two hundred and eighty four genetic samples were collected from eight sampling sites between Ponta da Barra in Mozambique and Coffee Bay in South Africa. The mitochondrial control region and ten microsatellite loci were amplified to analyse the stock structure of C. puniceus. The majority of microsatellite and mtDNA pairwise population comparisons were not significant (P > 0.05) although Xai Xai and Inhaca populations had some significant population comparisons for mtDNA (P < 0.05). AMOVA did not explain any significant variation at the between groups hierarchical level for any pre-defined groupings except for a mtDNA grouping which separated out Xai Xai and Inhaca from other sampling sites. SAMOVA, isolation by distance tests, structure analysis, principle component analysis and spatial autocorrelation analysis all indicated a single population of C. puniceus as being most likely. The migrate-n analysis provided evidence of current driven larval transport, with net migration rates influenced by current dynamics.Two hundred and thirty six unique presence points of C. puniceus were correlated with seasonal maximum and minimum temperature data and bathymetry to model the current distribution and predict future distribution changes of the species up until 2030. Eight individual species distribution models were developed and combined into a mean ensemble model using the Biomod2 package. Winter minimum temperature was the most important variable in determining models outputs. Overall the ensemble model was accurate with a true skills statistic score of 0.962. Binary transformed mean ensemble models predicted a northern and southern range contraction of C. puniceus' distribution of 15 percent; by 2030. The mean ensemble probability of occurrence models indicated that C. puniceus' abundance is likely to decrease off the southern Mozambique coastline but remain high off KwaZulu-Natal. The results of the genetic analysis support the theory of external recruitment sustaining the KwaZulu Natal fishery for C. puniceus. While the high genetic diversity and connectivity may make C. puniceus more resilient to disturbances, the loss of 15 percent; distribution and 11 percent; genetic diversity by 2030 will increase the species vulnerability. The decrease in abundance of C. puniceus off southern Mozambique together with current widespread exploitation levels could result in the collapse of the fishery. A single transboundary stock of C. puniceus highlights the need for co-management of the species. A combined stock assessment between South Africa and Mozambique and the development of further Marine Protected Areas off southern Mozambique are suggested as management options to minimise the vulnerability of this species.
- Full Text:
- Date Issued: 2014
A framework for high speed lexical classification of malicious URLs
- Authors: Egan, Shaun Peter
- Date: 2014
- Subjects: Internet -- Security measures -- Research , Uniform Resource Identifiers -- Security measures -- Research , Neural networks (Computer science) -- Research , Computer security -- Research , Computer crimes -- Prevention , Phishing
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4696 , http://hdl.handle.net/10962/d1011933 , Internet -- Security measures -- Research , Uniform Resource Identifiers -- Security measures -- Research , Neural networks (Computer science) -- Research , Computer security -- Research , Computer crimes -- Prevention , Phishing
- Description: Phishing attacks employ social engineering to target end-users, with the goal of stealing identifying or sensitive information. This information is used in activities such as identity theft or financial fraud. During a phishing campaign, attackers distribute URLs which; along with false information, point to fraudulent resources in an attempt to deceive users into requesting the resource. These URLs are made obscure through the use of several techniques which make automated detection difficult. Current methods used to detect malicious URLs face multiple problems which attackers use to their advantage. These problems include: the time required to react to new attacks; shifts in trends in URL obfuscation and usability problems caused by the latency incurred by the lookups required by these approaches. A new method of identifying malicious URLs using Artificial Neural Networks (ANNs) has been shown to be effective by several authors. The simple method of classification performed by ANNs result in very high classification speeds with little impact on usability. Samples used for the training, validation and testing of these ANNs are gathered from Phishtank and Open Directory. Words selected from the different sections of the samples are used to create a `Bag-of-Words (BOW)' which is used as a binary input vector indicating the presence of a word for a given sample. Twenty additional features which measure lexical attributes of the sample are used to increase classification accuracy. A framework that is capable of generating these classifiers in an automated fashion is implemented. These classifiers are automatically stored on a remote update distribution service which has been built to supply updates to classifier implementations. An example browser plugin is created and uses ANNs provided by this service. It is both capable of classifying URLs requested by a user in real time and is able to block these requests. The framework is tested in terms of training time and classification accuracy. Classification speed and the effectiveness of compression algorithms on the data required to distribute updates is tested. It is concluded that it is possible to generate these ANNs in a frequent fashion, and in a method that is small enough to distribute easily. It is also shown that classifications are made at high-speed with high-accuracy, resulting in little impact on usability.
- Full Text:
- Date Issued: 2014
- Authors: Egan, Shaun Peter
- Date: 2014
- Subjects: Internet -- Security measures -- Research , Uniform Resource Identifiers -- Security measures -- Research , Neural networks (Computer science) -- Research , Computer security -- Research , Computer crimes -- Prevention , Phishing
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4696 , http://hdl.handle.net/10962/d1011933 , Internet -- Security measures -- Research , Uniform Resource Identifiers -- Security measures -- Research , Neural networks (Computer science) -- Research , Computer security -- Research , Computer crimes -- Prevention , Phishing
- Description: Phishing attacks employ social engineering to target end-users, with the goal of stealing identifying or sensitive information. This information is used in activities such as identity theft or financial fraud. During a phishing campaign, attackers distribute URLs which; along with false information, point to fraudulent resources in an attempt to deceive users into requesting the resource. These URLs are made obscure through the use of several techniques which make automated detection difficult. Current methods used to detect malicious URLs face multiple problems which attackers use to their advantage. These problems include: the time required to react to new attacks; shifts in trends in URL obfuscation and usability problems caused by the latency incurred by the lookups required by these approaches. A new method of identifying malicious URLs using Artificial Neural Networks (ANNs) has been shown to be effective by several authors. The simple method of classification performed by ANNs result in very high classification speeds with little impact on usability. Samples used for the training, validation and testing of these ANNs are gathered from Phishtank and Open Directory. Words selected from the different sections of the samples are used to create a `Bag-of-Words (BOW)' which is used as a binary input vector indicating the presence of a word for a given sample. Twenty additional features which measure lexical attributes of the sample are used to increase classification accuracy. A framework that is capable of generating these classifiers in an automated fashion is implemented. These classifiers are automatically stored on a remote update distribution service which has been built to supply updates to classifier implementations. An example browser plugin is created and uses ANNs provided by this service. It is both capable of classifying URLs requested by a user in real time and is able to block these requests. The framework is tested in terms of training time and classification accuracy. Classification speed and the effectiveness of compression algorithms on the data required to distribute updates is tested. It is concluded that it is possible to generate these ANNs in a frequent fashion, and in a method that is small enough to distribute easily. It is also shown that classifications are made at high-speed with high-accuracy, resulting in little impact on usability.
- Full Text:
- Date Issued: 2014
Impact of batting skill on pacing during repeated sprints between the wickets.
- Authors: Elliott, Andrea
- Date: 2014
- Subjects: Cricket -- Batting -- Research , Sprinting -- Research , Cricket players , Exercise -- Physiological aspects -- Research , Sports -- Physiological aspects -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5153 , http://hdl.handle.net/10962/d1013546
- Description: Introduction: With batting in cricket, there is no known end point, making the allocation of resources and the development of a suitable pacing strategy more difficult. How batsmen allocate resources and pace themselves when repeatedly sprinting between the wickets is therefore not known. According to the ‘anticipatory feedback’ model, the level of expertise/experience has a substantial influence on the development of a suitable pacing strategy. Skilled or experienced batsmen may therefore have a greater ability to develop and implement a pacing strategy compared to that of novice or less-skilled batsmen. Purpose: To assess whether the absence of a known end point at the beginning of repeated sprint bouts between the wickets effects how batsmen pace themselves comparing skilled and less-skilled batsmen. Methods: Twenty-four male cricketers from a university league were selected. Twelve skilled batsmen (players in the top five batting order), and 12 less-skilled batsmen (players in the bottom five batting order) completed three experimental. All trials required batsmen to complete the same number of shuttle sprints (14 shuttles and therefore 28 runs), while only the information provided before each trial differed. Control Trial: This trial is also referred to as the ‘informed’ trial as the batsmen are aware of the exercise requirements (end point). Unknown Trial: The batsmen were not informed of the exercise end point and were required to run on command for an indefinite period (28 runs). Deceptive Trial: Batsmen’ were incorrectly informed with regards to the number of sprints (told they were only doing 14 runs when in fact they were doing 28 runs). Muscle activity, sprint times and RPE measures were obtained during all three trials and compared. Results: Significant (p<0.05) group effects were apparent for sprint times and, ‘central’ and ‘local’ RPE. Specifically, skilled batsmen obtained the faster mean sprint times, and less-skilled batsmen reported the higher mean ‘central’ and ‘local’ RPE values in all three experimental trials. There were no significant group effects for muscle activation. Skilled batsmen did however have lower muscle activation compared to less-skilled batsmen in all three trials. Furthermore, general trends revealed that sprint times and muscle activation decreased over time (from shuttle 1 to shuttle 14), and RPE (‘central’ and ‘local’) ratings increased, regardless of the experimental trials. Skilled batsmen performed the best in all three trials. This was determined by the attainment of faster sprint times, lower muscle activation and low RPE ratings in each of the three trials. The assessment of the relationship of the dependent variables measured in each trial, did however suggest that skilled batsmen performed best in the deceptive trial while less-skilled batsmen performed best in the control trial. Skilled batsmen thus showed superior performance when trial requirements were unclear. Less-skilled batsmen however, were seen to experience decrements in performance when information regarding the end point was unknown or misleading. Conclusion: It can thus be concluded that previous experience facilitates in the obtainment of improved sprint times between the wickets, especially when the exact end point is unknown.
- Full Text:
- Date Issued: 2014
- Authors: Elliott, Andrea
- Date: 2014
- Subjects: Cricket -- Batting -- Research , Sprinting -- Research , Cricket players , Exercise -- Physiological aspects -- Research , Sports -- Physiological aspects -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5153 , http://hdl.handle.net/10962/d1013546
- Description: Introduction: With batting in cricket, there is no known end point, making the allocation of resources and the development of a suitable pacing strategy more difficult. How batsmen allocate resources and pace themselves when repeatedly sprinting between the wickets is therefore not known. According to the ‘anticipatory feedback’ model, the level of expertise/experience has a substantial influence on the development of a suitable pacing strategy. Skilled or experienced batsmen may therefore have a greater ability to develop and implement a pacing strategy compared to that of novice or less-skilled batsmen. Purpose: To assess whether the absence of a known end point at the beginning of repeated sprint bouts between the wickets effects how batsmen pace themselves comparing skilled and less-skilled batsmen. Methods: Twenty-four male cricketers from a university league were selected. Twelve skilled batsmen (players in the top five batting order), and 12 less-skilled batsmen (players in the bottom five batting order) completed three experimental. All trials required batsmen to complete the same number of shuttle sprints (14 shuttles and therefore 28 runs), while only the information provided before each trial differed. Control Trial: This trial is also referred to as the ‘informed’ trial as the batsmen are aware of the exercise requirements (end point). Unknown Trial: The batsmen were not informed of the exercise end point and were required to run on command for an indefinite period (28 runs). Deceptive Trial: Batsmen’ were incorrectly informed with regards to the number of sprints (told they were only doing 14 runs when in fact they were doing 28 runs). Muscle activity, sprint times and RPE measures were obtained during all three trials and compared. Results: Significant (p<0.05) group effects were apparent for sprint times and, ‘central’ and ‘local’ RPE. Specifically, skilled batsmen obtained the faster mean sprint times, and less-skilled batsmen reported the higher mean ‘central’ and ‘local’ RPE values in all three experimental trials. There were no significant group effects for muscle activation. Skilled batsmen did however have lower muscle activation compared to less-skilled batsmen in all three trials. Furthermore, general trends revealed that sprint times and muscle activation decreased over time (from shuttle 1 to shuttle 14), and RPE (‘central’ and ‘local’) ratings increased, regardless of the experimental trials. Skilled batsmen performed the best in all three trials. This was determined by the attainment of faster sprint times, lower muscle activation and low RPE ratings in each of the three trials. The assessment of the relationship of the dependent variables measured in each trial, did however suggest that skilled batsmen performed best in the deceptive trial while less-skilled batsmen performed best in the control trial. Skilled batsmen thus showed superior performance when trial requirements were unclear. Less-skilled batsmen however, were seen to experience decrements in performance when information regarding the end point was unknown or misleading. Conclusion: It can thus be concluded that previous experience facilitates in the obtainment of improved sprint times between the wickets, especially when the exact end point is unknown.
- Full Text:
- Date Issued: 2014
Genesis of karst-hosted manganese ores of the Postmasburg Manganese Field, South Africa with emphasis on evidence for hydrothermal processes
- Authors: Fairey, Brenton John
- Date: 2014
- Subjects: Karst -- South Africa -- Postmasburg , Manganese ores -- South Africa -- Postmasburg , Hydrothermal alteration -- South Africa -- Postmasburg , Manganese mines and mining -- South Africa -- Northern Cape , Petrology , Mineralogical chemistry , Geochemistry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5094 , http://hdl.handle.net/10962/d1020904
- Description: The Postmasburg Manganese Field (PMF), located in the Northern Cape Province of South Africa, once represented one of the largest sources of manganese ore worldwide. However, the discovery of the giant manganese deposits of the Kalahari Manganese Field (KMF) led to the gradual decline in manganese mining activity in the PMF. Two belts of manganese ore deposits have been distinguished in the PMF, namely the Western Belt of ferruginous manganese ores and the Eastern Belt of siliceous manganese ores. Prevailing models of ore formation in these two belts invoke karstification of manganese-rich dolomites and residual accumulation of manganese wad which later underwent diagenetic and low-grade metamorphic processes. For the most part, the role of hydrothermal processes in ore formation and metasomatic alteration is not addressed. The identification of an abundance of common and some rare Al-, Na-, K- and Ba-bearing minerals, particularly aegirine, albite, microcline, banalsite, sérandite-pectolite, paragonite and natrolite in the PMF ores studied in this thesis, is indicative of the influence of hydrothermal activity. Enrichments in Na, K and/or Ba in the ores are generally on a percentage level for the majority of samples analysed through bulk-rock techniques. The discovery of a Ba-Mn arsenate/vanadate similar to gamagarite may also indicate that the hydrothermal fluid affecting the ores was not only alkali-rich but also probably contained some As and V. The fluid was likely to be oxidized and alkaline in nature and is thought to have been a mature basinal brine. Various replacement textures, particularly of Na- and Krich minerals by Ba-bearing phases, suggest sequential deposition of gangue as well as oreminerals from the hydrothermal fluid, with Ba phases being deposited at a later stage. The stratigraphic variability of the studied ores and the deviation of their character from the pigeon-hole-type classification of ferruginous and siliceous ores in the literature, suggests that a re-evaluation of genetic models is warranted. The discovery of hydrothermallydeposited alkali-rich assemblages in the PMF and KMF provides grounding for further investigation into a possible regional-scale hydrothermal event at least re-constituting the ores. Some shortcomings in previous works include disregard for the highly variable nature of the PMF deposits, the effects of hydrothermal activity of the ores and the existence of stratigraphic discrepancies. This study provides a single, broad model for the development of all manganese deposits of the PMF. The source of metals is attributed to all formations that stratigraphically overly the Reivilo Formation of the Campbellrand Subgroup (including the Reivilo Formation itself). The main process by which metals are accumulated is attributed to karstification of the dolomites. The interaction of oxidized, alkaline brines with the ores is considered and the overlying Asbestos Hills Subgroup BIF is suggested as a potential source of alkali metals.
- Full Text:
- Date Issued: 2014
- Authors: Fairey, Brenton John
- Date: 2014
- Subjects: Karst -- South Africa -- Postmasburg , Manganese ores -- South Africa -- Postmasburg , Hydrothermal alteration -- South Africa -- Postmasburg , Manganese mines and mining -- South Africa -- Northern Cape , Petrology , Mineralogical chemistry , Geochemistry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5094 , http://hdl.handle.net/10962/d1020904
- Description: The Postmasburg Manganese Field (PMF), located in the Northern Cape Province of South Africa, once represented one of the largest sources of manganese ore worldwide. However, the discovery of the giant manganese deposits of the Kalahari Manganese Field (KMF) led to the gradual decline in manganese mining activity in the PMF. Two belts of manganese ore deposits have been distinguished in the PMF, namely the Western Belt of ferruginous manganese ores and the Eastern Belt of siliceous manganese ores. Prevailing models of ore formation in these two belts invoke karstification of manganese-rich dolomites and residual accumulation of manganese wad which later underwent diagenetic and low-grade metamorphic processes. For the most part, the role of hydrothermal processes in ore formation and metasomatic alteration is not addressed. The identification of an abundance of common and some rare Al-, Na-, K- and Ba-bearing minerals, particularly aegirine, albite, microcline, banalsite, sérandite-pectolite, paragonite and natrolite in the PMF ores studied in this thesis, is indicative of the influence of hydrothermal activity. Enrichments in Na, K and/or Ba in the ores are generally on a percentage level for the majority of samples analysed through bulk-rock techniques. The discovery of a Ba-Mn arsenate/vanadate similar to gamagarite may also indicate that the hydrothermal fluid affecting the ores was not only alkali-rich but also probably contained some As and V. The fluid was likely to be oxidized and alkaline in nature and is thought to have been a mature basinal brine. Various replacement textures, particularly of Na- and Krich minerals by Ba-bearing phases, suggest sequential deposition of gangue as well as oreminerals from the hydrothermal fluid, with Ba phases being deposited at a later stage. The stratigraphic variability of the studied ores and the deviation of their character from the pigeon-hole-type classification of ferruginous and siliceous ores in the literature, suggests that a re-evaluation of genetic models is warranted. The discovery of hydrothermallydeposited alkali-rich assemblages in the PMF and KMF provides grounding for further investigation into a possible regional-scale hydrothermal event at least re-constituting the ores. Some shortcomings in previous works include disregard for the highly variable nature of the PMF deposits, the effects of hydrothermal activity of the ores and the existence of stratigraphic discrepancies. This study provides a single, broad model for the development of all manganese deposits of the PMF. The source of metals is attributed to all formations that stratigraphically overly the Reivilo Formation of the Campbellrand Subgroup (including the Reivilo Formation itself). The main process by which metals are accumulated is attributed to karstification of the dolomites. The interaction of oxidized, alkaline brines with the ores is considered and the overlying Asbestos Hills Subgroup BIF is suggested as a potential source of alkali metals.
- Full Text:
- Date Issued: 2014
A step forward in defining Hsp90s as potential drug targets for human parasitic diseases
- Authors: Faya, Ngonidzashe
- Date: 2014
- Subjects: Heat shock proteins -- Research , Malaria -- Chemotherapy -- Research , Antimalarials -- Development -- Research , Parasitic diseases -- Research , Plasmodium
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4110 , http://hdl.handle.net/10962/d1012993
- Description: Parasitic diseases remain a health burden affecting more than 500 million people worldwide with malaria having the highest mortality rate. The parasites can be transferred to the human bodies either through the mouth by ingestion of contaminated food and water or through the skin by bug bites or direct contact to environments harbouring them. Epidemiological control seems to be impossible since there is failure to control the insect vectors as well as practice of hygiene. Therefore, this has led to the development of a number of vaccines, chemotherapy and disease control programs. However, parasites have increasingly developed resistance to traditionally used anti-parasitic drugs and due to that fact there is need for alternative medication for parasitic diseases. Heat shock protein 90 (Hsp90) facilitates the folding of proteins in all living cells and their role is more important to parasites because of their environmental changes, from vector to host. Hsp90s play a major role; therefore this justifies the need for a deeper analysis of the parasitic Hsp90s. Recent studies have revealed that, the Plasmodium sp. Hsp90 has an extended linker region which increases the protein’s affinity for ATP and its inhibitors. Therefore we hypothesize that there are also significant features in other parasitic Hsp90s which would lead to Hsp90 being defined as potential drug targets. In the present study an attempt was made to gain more insight into the differences in primary structure of human and parasitic Hsp90s. The sequences were retrieved from the NCBI database and analysis was done in three groups basing on the localization of the Hsp90. The physicochemical properties were calculated and in every group, the protozoan Hsp90s showed significant differences when compared to the human orthologs. Multiple sequence alignments (MSA) showed that endoplasmic reticulum Hsp90s have an extended region in the middle domain indicating their ability to bind to a unique subset of client proteins. Sequence identities between the human and parasites showed that the protozoan Hsp90s are less related to the human Hsp90s as compared to the other parasites. Likewise, motif analysis showed the trypanosomatids and apicomplexan groups have their own unique set of motifs and they were grouped together in the phylogenetic analysis. Phylogenetic analysis also showed that, the protozoan Hsp90s forms their own clades in each group while the helminths did not form in endoplasmic reticulum group. In this study, we concluded that, Hsp90 can be a potential drug target for the protozoan species and more specifically those from the apicomplexan and trypanosomatids groups.
- Full Text:
- Date Issued: 2014
- Authors: Faya, Ngonidzashe
- Date: 2014
- Subjects: Heat shock proteins -- Research , Malaria -- Chemotherapy -- Research , Antimalarials -- Development -- Research , Parasitic diseases -- Research , Plasmodium
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4110 , http://hdl.handle.net/10962/d1012993
- Description: Parasitic diseases remain a health burden affecting more than 500 million people worldwide with malaria having the highest mortality rate. The parasites can be transferred to the human bodies either through the mouth by ingestion of contaminated food and water or through the skin by bug bites or direct contact to environments harbouring them. Epidemiological control seems to be impossible since there is failure to control the insect vectors as well as practice of hygiene. Therefore, this has led to the development of a number of vaccines, chemotherapy and disease control programs. However, parasites have increasingly developed resistance to traditionally used anti-parasitic drugs and due to that fact there is need for alternative medication for parasitic diseases. Heat shock protein 90 (Hsp90) facilitates the folding of proteins in all living cells and their role is more important to parasites because of their environmental changes, from vector to host. Hsp90s play a major role; therefore this justifies the need for a deeper analysis of the parasitic Hsp90s. Recent studies have revealed that, the Plasmodium sp. Hsp90 has an extended linker region which increases the protein’s affinity for ATP and its inhibitors. Therefore we hypothesize that there are also significant features in other parasitic Hsp90s which would lead to Hsp90 being defined as potential drug targets. In the present study an attempt was made to gain more insight into the differences in primary structure of human and parasitic Hsp90s. The sequences were retrieved from the NCBI database and analysis was done in three groups basing on the localization of the Hsp90. The physicochemical properties were calculated and in every group, the protozoan Hsp90s showed significant differences when compared to the human orthologs. Multiple sequence alignments (MSA) showed that endoplasmic reticulum Hsp90s have an extended region in the middle domain indicating their ability to bind to a unique subset of client proteins. Sequence identities between the human and parasites showed that the protozoan Hsp90s are less related to the human Hsp90s as compared to the other parasites. Likewise, motif analysis showed the trypanosomatids and apicomplexan groups have their own unique set of motifs and they were grouped together in the phylogenetic analysis. Phylogenetic analysis also showed that, the protozoan Hsp90s forms their own clades in each group while the helminths did not form in endoplasmic reticulum group. In this study, we concluded that, Hsp90 can be a potential drug target for the protozoan species and more specifically those from the apicomplexan and trypanosomatids groups.
- Full Text:
- Date Issued: 2014
Screening of entomopathogenic fungi against citrus mealybug (Planococcus citri (Risso)) and citrus thrips (Scirtothrips aurantii (Faure))
- FitzGerald, Véronique Chartier
- Authors: FitzGerald, Véronique Chartier
- Date: 2014
- Subjects: Entomopathogenic fungi , Citrus mealybug -- South Africa -- Eastern Cape , Citrus thrips -- South Africa -- Eastern Cape , Citrus -- Diseases and pests , Citrus mealybug -- Biological control , Citrus thrips -- Biological control , Biological pest control agents , Scanning electron microscopy , Mycoses
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4166 , http://hdl.handle.net/10962/d1020887
- Description: Mealybugs (Planococcus citri) and thrips (Scirtothrips aurantii) are common and extremely damaging citrus crop pests which have proven difficult to control via conventional methods, such as chemical pesticides and insect growth regulators. The objective of this study was to determine the efficacy of entomopathogenic fungi against these pests in laboratory bioassays. Isolates of Metarhizium anisopliae and Beauveria bassiana from citrus orchards in the Eastern Cape, South Africa were maintained on Sabouraud Dextrose 4% Agar supplemented with Dodine, chloramphenicol and rifampicin at 25°C. Infectivity of the fungal isolates was initially assessed using 5th instar false codling moth, Thaumatotibia leucotreta, larvae. Mealybug bioassays were performed in 24 well plates using 1 x 107 ml-1 conidial suspensions and kept at 26°C for 5 days with a photoperiod of 12 L:12 D. A Beauveria commercial product and an un-inoculated control were also screened for comparison. Isolates GAR 17 B3 (B. bassiana) and FCM AR 23 B3 (M. anisopliae) both resulted in 67.5% mealybug crawler mortality and GB AR 23 13 3 (B. bassiana) resulted in 64% crawler mortality. These 3 isolates were further tested in dose-dependent assays. Probit analyses were conducted on the dose-dependent assays data using PROBAN to determine LC₅₀ values. For both the mealybug adult and crawlers FCM AR 23 B3 required the lowest concentration to achieve LC₅₀ at 4.96 x 10⁶ conidia ml-1 and 5.29 x 10⁵ conidia ml-1, respectively. Bioassays on adult thrips were conducted in munger cells with leaf buds inoculated with the conidial suspensions. Isolate GAR 17 B3 had the highest mortality rate at 70% on thrips while FCM AR 23 B3 resulted in 60% mortality. Identification of the isolates, FCM AR 23 B3, GAR 17 B3 and GB AR 23 13 3, were confirmed to be correct using both microscopic and molecularly techniques. ITS sequences were compared to other sequences from GenBank and confirmed phylogenetically using MEGA6. Mealybug infection was investigated using scanning electron microscopy, mycosis was confirmed but the infection process could not be followed due to the extensive waxy cuticle. These results indicate that there is potential for the isolates FCM AR 23 B3 and GAR 17 B3 to be developed as biological control agents for the control of citrus mealybug and thrips. Further research would be required to determine their ability to perform under field conditions.
- Full Text:
- Date Issued: 2014
- Authors: FitzGerald, Véronique Chartier
- Date: 2014
- Subjects: Entomopathogenic fungi , Citrus mealybug -- South Africa -- Eastern Cape , Citrus thrips -- South Africa -- Eastern Cape , Citrus -- Diseases and pests , Citrus mealybug -- Biological control , Citrus thrips -- Biological control , Biological pest control agents , Scanning electron microscopy , Mycoses
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4166 , http://hdl.handle.net/10962/d1020887
- Description: Mealybugs (Planococcus citri) and thrips (Scirtothrips aurantii) are common and extremely damaging citrus crop pests which have proven difficult to control via conventional methods, such as chemical pesticides and insect growth regulators. The objective of this study was to determine the efficacy of entomopathogenic fungi against these pests in laboratory bioassays. Isolates of Metarhizium anisopliae and Beauveria bassiana from citrus orchards in the Eastern Cape, South Africa were maintained on Sabouraud Dextrose 4% Agar supplemented with Dodine, chloramphenicol and rifampicin at 25°C. Infectivity of the fungal isolates was initially assessed using 5th instar false codling moth, Thaumatotibia leucotreta, larvae. Mealybug bioassays were performed in 24 well plates using 1 x 107 ml-1 conidial suspensions and kept at 26°C for 5 days with a photoperiod of 12 L:12 D. A Beauveria commercial product and an un-inoculated control were also screened for comparison. Isolates GAR 17 B3 (B. bassiana) and FCM AR 23 B3 (M. anisopliae) both resulted in 67.5% mealybug crawler mortality and GB AR 23 13 3 (B. bassiana) resulted in 64% crawler mortality. These 3 isolates were further tested in dose-dependent assays. Probit analyses were conducted on the dose-dependent assays data using PROBAN to determine LC₅₀ values. For both the mealybug adult and crawlers FCM AR 23 B3 required the lowest concentration to achieve LC₅₀ at 4.96 x 10⁶ conidia ml-1 and 5.29 x 10⁵ conidia ml-1, respectively. Bioassays on adult thrips were conducted in munger cells with leaf buds inoculated with the conidial suspensions. Isolate GAR 17 B3 had the highest mortality rate at 70% on thrips while FCM AR 23 B3 resulted in 60% mortality. Identification of the isolates, FCM AR 23 B3, GAR 17 B3 and GB AR 23 13 3, were confirmed to be correct using both microscopic and molecularly techniques. ITS sequences were compared to other sequences from GenBank and confirmed phylogenetically using MEGA6. Mealybug infection was investigated using scanning electron microscopy, mycosis was confirmed but the infection process could not be followed due to the extensive waxy cuticle. These results indicate that there is potential for the isolates FCM AR 23 B3 and GAR 17 B3 to be developed as biological control agents for the control of citrus mealybug and thrips. Further research would be required to determine their ability to perform under field conditions.
- Full Text:
- Date Issued: 2014
An exploration into the use of webinjects by financial malware
- Authors: Forrester, Jock Ingram
- Date: 2014
- Subjects: Malware (Computer software) -- Analysis , Internet fraud , Computer crimes , Computer security , Electronic commerce
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4697 , http://hdl.handle.net/10962/d1012079 , Malware (Computer software) -- Analysis , Internet fraud , Computer crimes , Computer security , Electronic commerce
- Description: As the number of computing devices connected to the Internet increases and the Internet itself becomes more pervasive, so does the opportunity for criminals to use these devices in cybercrimes. Supporting the increase in cybercrime is the growth and maturity of the digital underground economy with strong links to its more visible and physical counterpart. The digital underground economy provides software and related services to equip the entrepreneurial cybercriminal with the appropriate skills and required tools. Financial malware, particularly the capability for injection of code into web browsers, has become one of the more profitable cybercrime tool sets due to its versatility and adaptability when targeting clients of institutions with an online presence, both in and outside of the financial industry. There are numerous families of financial malware available for use, with perhaps the most prevalent being Zeus and SpyEye. Criminals create (or purchase) and grow botnets of computing devices infected with financial malware that has been configured to attack clients of certain websites. In the research data set there are 483 configuration files containing approximately 40 000 webinjects that were captured from various financial malware botnets between October 2010 and June 2012. They were processed and analysed to determine the methods used by criminals to defraud either the user of the computing device, or the institution of which the user is a client. The configuration files contain the injection code that is executed in the web browser to create a surrogate interface, which is then used by the criminal to interact with the user and institution in order to commit fraud. Demographics on the captured data set are presented and case studies are documented based on the various methods used to defraud and bypass financial security controls across multiple industries. The case studies cover techniques used in social engineering, bypassing security controls and automated transfers.
- Full Text:
- Date Issued: 2014
- Authors: Forrester, Jock Ingram
- Date: 2014
- Subjects: Malware (Computer software) -- Analysis , Internet fraud , Computer crimes , Computer security , Electronic commerce
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4697 , http://hdl.handle.net/10962/d1012079 , Malware (Computer software) -- Analysis , Internet fraud , Computer crimes , Computer security , Electronic commerce
- Description: As the number of computing devices connected to the Internet increases and the Internet itself becomes more pervasive, so does the opportunity for criminals to use these devices in cybercrimes. Supporting the increase in cybercrime is the growth and maturity of the digital underground economy with strong links to its more visible and physical counterpart. The digital underground economy provides software and related services to equip the entrepreneurial cybercriminal with the appropriate skills and required tools. Financial malware, particularly the capability for injection of code into web browsers, has become one of the more profitable cybercrime tool sets due to its versatility and adaptability when targeting clients of institutions with an online presence, both in and outside of the financial industry. There are numerous families of financial malware available for use, with perhaps the most prevalent being Zeus and SpyEye. Criminals create (or purchase) and grow botnets of computing devices infected with financial malware that has been configured to attack clients of certain websites. In the research data set there are 483 configuration files containing approximately 40 000 webinjects that were captured from various financial malware botnets between October 2010 and June 2012. They were processed and analysed to determine the methods used by criminals to defraud either the user of the computing device, or the institution of which the user is a client. The configuration files contain the injection code that is executed in the web browser to create a surrogate interface, which is then used by the criminal to interact with the user and institution in order to commit fraud. Demographics on the captured data set are presented and case studies are documented based on the various methods used to defraud and bypass financial security controls across multiple industries. The case studies cover techniques used in social engineering, bypassing security controls and automated transfers.
- Full Text:
- Date Issued: 2014
New geochemical constraints on the genesis of the Gamsberg zinc deposit, Namaqualand Metamorphic Province, South Africa
- Authors: Foulkes, Susan Elizabeth
- Date: 2014
- Subjects: Zinc ores -- South Africa -- Gamsberg , Mines and mineral resources -- South Africa -- Gamsberg , Mineralogy -- South Africa -- Gamsberg , Molecular evolution , Geology -- South Africa -- Namaqualand
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5054 , http://hdl.handle.net/10962/d1012084 , Zinc ores -- South Africa -- Gamsberg , Mines and mineral resources -- South Africa -- Gamsberg , Mineralogy -- South Africa -- Gamsberg , Molecular evolution , Geology -- South Africa -- Namaqualand
- Description: The base metal massive sulfide deposits of the Aggeneys-Gamsberg (A-G) District are hosted within the Mesoproterozoic Bushmanland Group of the Namaqua-Natal Metamorphic Complex in the Northern Cape Province of South Africa. The district displays an apparent eastward trend in the economic concentration of base metals (+ barite) from relatively Cu-Pb-rich, Ba-poor mineralisation at Black Mountain to Zn- and Ba-rich ores at Gamsberg. Base metal sulfides at Gamsberg are restricted to the so called Gams (Iron) Formation which comprises a sulfidic mineralized unit (“B”) enveloped within a sequence of meta-sedimentary units (“A” and “C”). The aim of the study was to shed further light on the genesis and chemical evolution of the sulfide mineralisation at Gamsberg in the context of the entire A-G District, by interrogating further the apparent district-wide trend in base metal distribution. The Gams Iron Formation was sampled and studied from one key drill core intersection (“G1”) which intersects the largest part of it as described elsewhere; a small number of additional samples from a second drill core (“G2”) complemented the main sample suite. Minerals that make up the silicate assemblages across the studied section include quartz, garnet, pyroxene, pyroxenoid, phyllosilicates, carbonates, amphiboles, oxides (chiefly magnetite) and graphite. In a stratigraphic context, the mineralogical variations conform directly to those documented in the relevant literature from the Gamsberg locality. These are coupled, where possible, with mineral-chemical profiles of selected silicate species which replicate those of bulk-rock compositions, particularly with respect to Mn, Fe and Ca in the upper C Unit of the studied section. These signals collectively track the characteristic transition from a terrigenous, siliciclastic sediment-dominated footwall to an exhalative sediment-dominated hanging wall to the sulfide mineralisation as also seen in similar deposits elsewhere, particularly with respect to the characteristic Mn-rich signature increasingly observed in the hanging wall C Unit. The foregoing suggests that the examined section faithfully records the interpreted primary stratigraphy of the deposits, despite the complex structural and metamorphic overprint that characterises the region. This facilitates a stratigraphic analytical approach on the sulfidic Unit B, through a combination of mineral-chemical and stable isotope analyses. Dominant sulfides in Unit B are sphalerite and pyrite, with lesser pyrrhotite and minor galena. Sphalerite shows high and generally invariant contents of Fe (mean 12.18wt%, as FeS) whereas Zn anti-correlates with Mn (mean 5.58wt%, as MnS). Isotopic analyses for S, Fe and Zn in hand-picked sphalerite and pyrite separates were used with a view to providing new evidence for chemical and isotopic variation within the sulfide ore-body in a vertical (i.e. stratigraphic) sense, discuss the implications thereof, and ultimately interpret the new data in light of similar existing data from the A-G District and elsewhere. The δ³⁴S data for pyrite (plus a single pyrrhotite grain) and sphalerite from both cores G1 and G2 show comparable compositional ranges between 22.9 and 30.4‰ and between 27 and 30.1‰ respectively. The δ⁵⁶Fe data for pyrite show a range between -1.85 and 0.19‰, whereas seven sphalerite separates have a very narrow range of δ⁶⁶Zn from 0.06 to 0.20‰. The atypically high sulfur isotope data reported in this study are interpreted to reflect sedimentary deposition of primary sulfide ore at Gamsberg from an isotopically highly evolved seawater sulfate source through large-scale Rayleigh fractionation processes. Thermogenic sulfate reduction is proposed to have been the main reductive mechanism from seawater sulfate to sulfide, given the absence of very low δ³⁴S data for sulfides anywhere in the A-G District. By contrast, the δ⁶⁶Zn values for sphalerite are for all intents and purposes invariant and very close to 0‰, and therefore suggest little Zn isotope fractionation from an original exhalative fluid source. On this evidence alone, Zn isotopes therefore appear to hold little promise as a proxy of the chemical and isotopic evolution of SEDEX deposits in space and time, although this can only be verified through further application in the broader A-G District and similar deposits elsewhere. The apparent decoupling of Zn and S isotopes in the Gamsberg sulfide deposit, however, points towards diverse sources of these two components, i.e. ascending metalliferous brines versus seawater respectively. Finally, pyrite δ⁵⁶Fe data do show a stratigraphic trend of generally declining values up-section, which are interpreted to reflect the influence of broadly coeval precipitation of isotopically heavy Fe-oxides on a broader-scale – now preserved as abundant magnetite through metamorphism. Further work on the iron isotope composition of silicate-and oxide-hosted Fe on a local-to-district scale will assist in testing this interpretation.
- Full Text:
- Date Issued: 2014
- Authors: Foulkes, Susan Elizabeth
- Date: 2014
- Subjects: Zinc ores -- South Africa -- Gamsberg , Mines and mineral resources -- South Africa -- Gamsberg , Mineralogy -- South Africa -- Gamsberg , Molecular evolution , Geology -- South Africa -- Namaqualand
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5054 , http://hdl.handle.net/10962/d1012084 , Zinc ores -- South Africa -- Gamsberg , Mines and mineral resources -- South Africa -- Gamsberg , Mineralogy -- South Africa -- Gamsberg , Molecular evolution , Geology -- South Africa -- Namaqualand
- Description: The base metal massive sulfide deposits of the Aggeneys-Gamsberg (A-G) District are hosted within the Mesoproterozoic Bushmanland Group of the Namaqua-Natal Metamorphic Complex in the Northern Cape Province of South Africa. The district displays an apparent eastward trend in the economic concentration of base metals (+ barite) from relatively Cu-Pb-rich, Ba-poor mineralisation at Black Mountain to Zn- and Ba-rich ores at Gamsberg. Base metal sulfides at Gamsberg are restricted to the so called Gams (Iron) Formation which comprises a sulfidic mineralized unit (“B”) enveloped within a sequence of meta-sedimentary units (“A” and “C”). The aim of the study was to shed further light on the genesis and chemical evolution of the sulfide mineralisation at Gamsberg in the context of the entire A-G District, by interrogating further the apparent district-wide trend in base metal distribution. The Gams Iron Formation was sampled and studied from one key drill core intersection (“G1”) which intersects the largest part of it as described elsewhere; a small number of additional samples from a second drill core (“G2”) complemented the main sample suite. Minerals that make up the silicate assemblages across the studied section include quartz, garnet, pyroxene, pyroxenoid, phyllosilicates, carbonates, amphiboles, oxides (chiefly magnetite) and graphite. In a stratigraphic context, the mineralogical variations conform directly to those documented in the relevant literature from the Gamsberg locality. These are coupled, where possible, with mineral-chemical profiles of selected silicate species which replicate those of bulk-rock compositions, particularly with respect to Mn, Fe and Ca in the upper C Unit of the studied section. These signals collectively track the characteristic transition from a terrigenous, siliciclastic sediment-dominated footwall to an exhalative sediment-dominated hanging wall to the sulfide mineralisation as also seen in similar deposits elsewhere, particularly with respect to the characteristic Mn-rich signature increasingly observed in the hanging wall C Unit. The foregoing suggests that the examined section faithfully records the interpreted primary stratigraphy of the deposits, despite the complex structural and metamorphic overprint that characterises the region. This facilitates a stratigraphic analytical approach on the sulfidic Unit B, through a combination of mineral-chemical and stable isotope analyses. Dominant sulfides in Unit B are sphalerite and pyrite, with lesser pyrrhotite and minor galena. Sphalerite shows high and generally invariant contents of Fe (mean 12.18wt%, as FeS) whereas Zn anti-correlates with Mn (mean 5.58wt%, as MnS). Isotopic analyses for S, Fe and Zn in hand-picked sphalerite and pyrite separates were used with a view to providing new evidence for chemical and isotopic variation within the sulfide ore-body in a vertical (i.e. stratigraphic) sense, discuss the implications thereof, and ultimately interpret the new data in light of similar existing data from the A-G District and elsewhere. The δ³⁴S data for pyrite (plus a single pyrrhotite grain) and sphalerite from both cores G1 and G2 show comparable compositional ranges between 22.9 and 30.4‰ and between 27 and 30.1‰ respectively. The δ⁵⁶Fe data for pyrite show a range between -1.85 and 0.19‰, whereas seven sphalerite separates have a very narrow range of δ⁶⁶Zn from 0.06 to 0.20‰. The atypically high sulfur isotope data reported in this study are interpreted to reflect sedimentary deposition of primary sulfide ore at Gamsberg from an isotopically highly evolved seawater sulfate source through large-scale Rayleigh fractionation processes. Thermogenic sulfate reduction is proposed to have been the main reductive mechanism from seawater sulfate to sulfide, given the absence of very low δ³⁴S data for sulfides anywhere in the A-G District. By contrast, the δ⁶⁶Zn values for sphalerite are for all intents and purposes invariant and very close to 0‰, and therefore suggest little Zn isotope fractionation from an original exhalative fluid source. On this evidence alone, Zn isotopes therefore appear to hold little promise as a proxy of the chemical and isotopic evolution of SEDEX deposits in space and time, although this can only be verified through further application in the broader A-G District and similar deposits elsewhere. The apparent decoupling of Zn and S isotopes in the Gamsberg sulfide deposit, however, points towards diverse sources of these two components, i.e. ascending metalliferous brines versus seawater respectively. Finally, pyrite δ⁵⁶Fe data do show a stratigraphic trend of generally declining values up-section, which are interpreted to reflect the influence of broadly coeval precipitation of isotopically heavy Fe-oxides on a broader-scale – now preserved as abundant magnetite through metamorphism. Further work on the iron isotope composition of silicate-and oxide-hosted Fe on a local-to-district scale will assist in testing this interpretation.
- Full Text:
- Date Issued: 2014
A study of South African computer users' password usage habits and attitude towards password security
- Authors: Friendman, Brandon
- Date: 2014
- Subjects: Computers -- Access control -- Passwords , Computer users -- Attitudes , Internet -- Access control , Internet -- Security measures , Internet -- Management , Data protection
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: vital:4700
- Description: The challenge of having to create and remember a secure password for each user account has become a problem for many computer users and can lead to bad password management practices. Simpler and less secure passwords are often selected and are regularly reused across multiple user accounts. Computer users within corporations and institutions are subject to password policies, policies which require users to create passwords of a specified length and composition and change passwords regularly. These policies often prevent users from reusing previous selected passwords. Security vendors and professionals have sought to improve or even replace password authentication. Technologies such as multi-factor authentication and single sign-on have been developed to complement or even replace password authentication. The objective of the study was to investigate the password habits of South African computer and internet users. The aim was to assess their attitudes toward password security, to determine whether password policies a↵ect the manner in which they manage their passwords and to investigate their exposure to alternate authentication technologies. The results from the online survey demonstrated that password practices of the participants across their professional and personal contexts were generally insecure. Participants often used shorter, simpler and ultimately less secure passwords. Participants would try to memorise all of their passwords or reuse the same password on most of their accounts. Many participants had not received any security awareness training, and additional security technologies (such as multi-factor authentication or password managers) were seldom used or provided to them. The password policies encountered by the participants in their organisations did little towards encouraging the users to apply more secure password practices. Users lack the knowledge and understanding about password security as they had received little or no training pertaining to it.
- Full Text:
- Date Issued: 2014
- Authors: Friendman, Brandon
- Date: 2014
- Subjects: Computers -- Access control -- Passwords , Computer users -- Attitudes , Internet -- Access control , Internet -- Security measures , Internet -- Management , Data protection
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: vital:4700
- Description: The challenge of having to create and remember a secure password for each user account has become a problem for many computer users and can lead to bad password management practices. Simpler and less secure passwords are often selected and are regularly reused across multiple user accounts. Computer users within corporations and institutions are subject to password policies, policies which require users to create passwords of a specified length and composition and change passwords regularly. These policies often prevent users from reusing previous selected passwords. Security vendors and professionals have sought to improve or even replace password authentication. Technologies such as multi-factor authentication and single sign-on have been developed to complement or even replace password authentication. The objective of the study was to investigate the password habits of South African computer and internet users. The aim was to assess their attitudes toward password security, to determine whether password policies a↵ect the manner in which they manage their passwords and to investigate their exposure to alternate authentication technologies. The results from the online survey demonstrated that password practices of the participants across their professional and personal contexts were generally insecure. Participants often used shorter, simpler and ultimately less secure passwords. Participants would try to memorise all of their passwords or reuse the same password on most of their accounts. Many participants had not received any security awareness training, and additional security technologies (such as multi-factor authentication or password managers) were seldom used or provided to them. The password policies encountered by the participants in their organisations did little towards encouraging the users to apply more secure password practices. Users lack the knowledge and understanding about password security as they had received little or no training pertaining to it.
- Full Text:
- Date Issued: 2014
Optimizing MIDAS III over South Africa
- Authors: Giday, Nigussie Mezgebe
- Date: 2014
- Subjects: Multi-Instrument Data Analysis System (MIDAS) , Global Positioning System , Ionosphere -- South Africa , Ionospheric electron density -- South Africa , Ionosondes -- South Africa , Tomography -- Scientific applications -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5517 , http://hdl.handle.net/10962/d1011277 , Multi-Instrument Data Analysis System (MIDAS) , Global Positioning System , Ionosphere -- South Africa , Ionospheric electron density -- South Africa , Ionosondes -- South Africa , Tomography -- Scientific applications -- South Africa
- Description: In this thesis an ionospheric tomographic algorithm called Multi-Instrument Data Anal- ysis System (MIDAS) is used to reconstruct electron density profiles using the Global Positioning System (GPS) data recorded from 53 GPS receivers over the South African region. MIDAS, developed by the Invert group at the University of Bath in the UK, is an inversion algorithm that produces a time dependent 3D image of the electron density of the ionosphere. GPS receivers record the time delay and phase advance of the trans- ionospheric GPS signals that traverse through the ionosphere from which the ionospheric parameter called Total Electron Content (TEC) can be computed. TEC, the line integral of the electron density along the satellite-receiver signal path, is ingested by ionospheric tomographic algorithms such as MIDAS to produce a time dependent 3D electron density profile. In order to validate electron density profiles from MIDAS, MIDAS derived NmF2 values were compared with ionosonde derived NmF2 values extracted from their respective 1D electron density profiles at 15 minute intervals for all four South African ionosonde stations (Grahamstown, Hermanus, Louisvale, and Madimbo). MIDAS 2D images of the electron density showed good diurnal and seasonal patterns; where a comparison of the 2D images at 12h00 UT for all the validation days exhibited maximum electron concentration during the autumn and summer and a minimum during the winter. A root mean square error (rmse) value as small as 0.88x 10¹¹[el=m³] was calculated for the Louisvale ionosonde station during the winter season and a maximum rmse value of 1.92x 10¹¹[el=m³] was ob- tained during the autumn season. The r² values were the least during the autumn and relatively large during summer and winter; similarly the rmse values were found to be a maximum during the autumn and a minimum during the winter indicating that MIDAS performs better during the winter than during the autumn and spring seasons. It is also observed that MIDAS performs better at Louisvale and Madimbo than at Grahamstown and Hermanus. In conclusion, the MIDAS reconstruction has showed good agreement with the ionosonde measurements; therefore, MIDAS can be considered a useful tool to study the ionosphere over the South African region.
- Full Text:
- Date Issued: 2014
- Authors: Giday, Nigussie Mezgebe
- Date: 2014
- Subjects: Multi-Instrument Data Analysis System (MIDAS) , Global Positioning System , Ionosphere -- South Africa , Ionospheric electron density -- South Africa , Ionosondes -- South Africa , Tomography -- Scientific applications -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5517 , http://hdl.handle.net/10962/d1011277 , Multi-Instrument Data Analysis System (MIDAS) , Global Positioning System , Ionosphere -- South Africa , Ionospheric electron density -- South Africa , Ionosondes -- South Africa , Tomography -- Scientific applications -- South Africa
- Description: In this thesis an ionospheric tomographic algorithm called Multi-Instrument Data Anal- ysis System (MIDAS) is used to reconstruct electron density profiles using the Global Positioning System (GPS) data recorded from 53 GPS receivers over the South African region. MIDAS, developed by the Invert group at the University of Bath in the UK, is an inversion algorithm that produces a time dependent 3D image of the electron density of the ionosphere. GPS receivers record the time delay and phase advance of the trans- ionospheric GPS signals that traverse through the ionosphere from which the ionospheric parameter called Total Electron Content (TEC) can be computed. TEC, the line integral of the electron density along the satellite-receiver signal path, is ingested by ionospheric tomographic algorithms such as MIDAS to produce a time dependent 3D electron density profile. In order to validate electron density profiles from MIDAS, MIDAS derived NmF2 values were compared with ionosonde derived NmF2 values extracted from their respective 1D electron density profiles at 15 minute intervals for all four South African ionosonde stations (Grahamstown, Hermanus, Louisvale, and Madimbo). MIDAS 2D images of the electron density showed good diurnal and seasonal patterns; where a comparison of the 2D images at 12h00 UT for all the validation days exhibited maximum electron concentration during the autumn and summer and a minimum during the winter. A root mean square error (rmse) value as small as 0.88x 10¹¹[el=m³] was calculated for the Louisvale ionosonde station during the winter season and a maximum rmse value of 1.92x 10¹¹[el=m³] was ob- tained during the autumn season. The r² values were the least during the autumn and relatively large during summer and winter; similarly the rmse values were found to be a maximum during the autumn and a minimum during the winter indicating that MIDAS performs better during the winter than during the autumn and spring seasons. It is also observed that MIDAS performs better at Louisvale and Madimbo than at Grahamstown and Hermanus. In conclusion, the MIDAS reconstruction has showed good agreement with the ionosonde measurements; therefore, MIDAS can be considered a useful tool to study the ionosphere over the South African region.
- Full Text:
- Date Issued: 2014
The role of computational thinking in introductory computer science
- Authors: Gouws, Lindsey Ann
- Date: 2014
- Subjects: Computer science , Computational complexity , Problem solving -- Study and teaching
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4690 , http://hdl.handle.net/10962/d1011152 , Computer science , Computational complexity , Problem solving -- Study and teaching
- Description: Computational thinking (CT) is gaining recognition as an important skill for students, both in computer science and other disciplines. Although there has been much focus on this field in recent years, it is rarely taught as a formal course, and there is little consensus on what exactly CT entails and how to teach and evaluate it. This research addresses the lack of resources for integrating CT into the introductory computer science curriculum. The question that we aim to answer is whether CT can be evaluated in a meaningful way. A CT framework that outlines the skills and techniques comprising CT and describes the nature of student engagement was developed; this is used as the basis for this research. An assessment (CT test) was then created to gauge the ability of incoming students, and a CT-specfic computer game was developed based on the analysis of an existing game. A set of problem solving strategies and practice activities were then recommended based on criteria defined in the framework. The results revealed that the CT abilities of first year university students are relatively poor, but that the students' scores for the CT test could be used as a predictor for their future success in computer science courses. The framework developed for this research proved successful when applied to the test, computer game evaluation, and classification of strategies and activities. Through this research, we established that CT is a skill that first year computer science students are lacking, and that using CT exercises alongside traditional programming instruction can improve students' learning experiences.
- Full Text:
- Date Issued: 2014
- Authors: Gouws, Lindsey Ann
- Date: 2014
- Subjects: Computer science , Computational complexity , Problem solving -- Study and teaching
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4690 , http://hdl.handle.net/10962/d1011152 , Computer science , Computational complexity , Problem solving -- Study and teaching
- Description: Computational thinking (CT) is gaining recognition as an important skill for students, both in computer science and other disciplines. Although there has been much focus on this field in recent years, it is rarely taught as a formal course, and there is little consensus on what exactly CT entails and how to teach and evaluate it. This research addresses the lack of resources for integrating CT into the introductory computer science curriculum. The question that we aim to answer is whether CT can be evaluated in a meaningful way. A CT framework that outlines the skills and techniques comprising CT and describes the nature of student engagement was developed; this is used as the basis for this research. An assessment (CT test) was then created to gauge the ability of incoming students, and a CT-specfic computer game was developed based on the analysis of an existing game. A set of problem solving strategies and practice activities were then recommended based on criteria defined in the framework. The results revealed that the CT abilities of first year university students are relatively poor, but that the students' scores for the CT test could be used as a predictor for their future success in computer science courses. The framework developed for this research proved successful when applied to the test, computer game evaluation, and classification of strategies and activities. Through this research, we established that CT is a skill that first year computer science students are lacking, and that using CT exercises alongside traditional programming instruction can improve students' learning experiences.
- Full Text:
- Date Issued: 2014