The epibiotic relationship between mussels and barnacles
- Authors: Bell, Caroline Margaret
- Date: 2014
- Subjects: Epibiosis , Mussels -- Ecology -- South Africa , Mussels -- Behavior -- South Africa , Mussels -- Habitat -- South Africa , Barnacles -- Ecology -- South Africa , Barnacles -- Behavior -- South Africa , Barnacles -- Habitat -- South Africa , Perna -- Behavior -- South Africa , Mytilus galloprovincialis -- Behavior -- South Africa , Marine biodiversity -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5847 , http://hdl.handle.net/10962/d1011460 , Epibiosis , Mussels -- Ecology -- South Africa , Mussels -- Behavior -- South Africa , Mussels -- Habitat -- South Africa , Barnacles -- Ecology -- South Africa , Barnacles -- Behavior -- South Africa , Barnacles -- Habitat -- South Africa , Perna -- Behavior -- South Africa , Mytilus galloprovincialis -- Behavior -- South Africa , Marine biodiversity -- South Africa
- Description: Epibiosis is an ecological relationship that has been described as one of the closest possible associations in marine ecosystems. In the space limited rocky intertidal, mussel beds provide important secondary space for barnacles. The epibiotic relationship between mussels and barnacles on the south-east coast of South Africa was considered at different scales, from large-scale, natural patterns of epibiosis on the rocky shore, to fine-scale settlement choices of barnacles and the effects on the condition and growth rates of individual mussels. Mussel and barnacle assemblages were generally stable over a 12-month period. The tracking of individual mussels with and without barnacle epibionts resulted in a significant increase in mortality rate of mussels with epibionts over 12 months (two-way ANOVA, p = 0.028). Barnacles on rocks, as well as on mussels, were also tracked with no significant effect of substratum on mortality of barnacles (two-way ANOVA, p = 0.119). Prevalence and intensity of barnacle infestations was also examined in relation to coastline topography on two co-occurring mussel species, the indigenous Perna perna and invasive Mytilus galloprovincialis. The results were complex, but bay status had significant effects on prevalence and intensity for both mussel species, depending on the time and zone. The effect of bay in relation to time was particularly relevant for M. galloprovincialis (four-way nested ANOVA, Season X Site(Bay): p = 0.0002), where summer prevalence was higher than that of winter in bays, regardless of zone, while in open coast sites, the effect of season was only significant in the mid zone. Patterns of intensity generally showed higher values in summer. Substratum preference by barnacles was investigated by recording settlement, survival and mortality of Chthamalus dentatus barnacles on various treatments. There was a strong preference for the rock-like plastic substratum by primary settlers (pair-wise tests of PERMANOVA: Dead < Rock mimic (p = 0.0001); Replica < Rock mimic (p = 0.019) and Live < Rock mimic (p = 0.0001)). This indicates that barnacles settle on mussel shells only as a secondary choice and that micro-topography is an important variable in barnacle settlement. The effect of barnacle epibiosis on condition index and growth of P. perna and M. galloprovincialis was also examined as a direct indication of the health of mussels subjected to the biological stress of epibiosis. Although not significant (PERMANOVA: P. perna: p(perm) = 0.890; M. galloprovincialis: p(perm) = 0.395), growth for both mussel species was slower for barnacle-infested individuals in summer, which is the main growing season for mussels in the region. Results from condition index calculations, however, showed no negative impacts of epibiotic barnacles (three-way ANCOVA: P. perna: p = 0.372; M. galloprovincialis: p = 0.762). Barnacle epibionts create a new interface between the mussel and its environment and this interaction can affect other members of the community. The possibility of the barnacle epibiont causing increased drag also needs further investigation. Biological processes operating within a wide range of physical stressors drive the interactions on the rocky shore, such as epibiosis. Overall, the results of this study suggest that the epibiotic relationship between mussels and barnacles on the south-east coast of South Africa does not significantly affect the mussel species present and that barnacles only use mussel shells as a secondary choice of substratum.
- Full Text:
- Authors: Bell, Caroline Margaret
- Date: 2014
- Subjects: Epibiosis , Mussels -- Ecology -- South Africa , Mussels -- Behavior -- South Africa , Mussels -- Habitat -- South Africa , Barnacles -- Ecology -- South Africa , Barnacles -- Behavior -- South Africa , Barnacles -- Habitat -- South Africa , Perna -- Behavior -- South Africa , Mytilus galloprovincialis -- Behavior -- South Africa , Marine biodiversity -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5847 , http://hdl.handle.net/10962/d1011460 , Epibiosis , Mussels -- Ecology -- South Africa , Mussels -- Behavior -- South Africa , Mussels -- Habitat -- South Africa , Barnacles -- Ecology -- South Africa , Barnacles -- Behavior -- South Africa , Barnacles -- Habitat -- South Africa , Perna -- Behavior -- South Africa , Mytilus galloprovincialis -- Behavior -- South Africa , Marine biodiversity -- South Africa
- Description: Epibiosis is an ecological relationship that has been described as one of the closest possible associations in marine ecosystems. In the space limited rocky intertidal, mussel beds provide important secondary space for barnacles. The epibiotic relationship between mussels and barnacles on the south-east coast of South Africa was considered at different scales, from large-scale, natural patterns of epibiosis on the rocky shore, to fine-scale settlement choices of barnacles and the effects on the condition and growth rates of individual mussels. Mussel and barnacle assemblages were generally stable over a 12-month period. The tracking of individual mussels with and without barnacle epibionts resulted in a significant increase in mortality rate of mussels with epibionts over 12 months (two-way ANOVA, p = 0.028). Barnacles on rocks, as well as on mussels, were also tracked with no significant effect of substratum on mortality of barnacles (two-way ANOVA, p = 0.119). Prevalence and intensity of barnacle infestations was also examined in relation to coastline topography on two co-occurring mussel species, the indigenous Perna perna and invasive Mytilus galloprovincialis. The results were complex, but bay status had significant effects on prevalence and intensity for both mussel species, depending on the time and zone. The effect of bay in relation to time was particularly relevant for M. galloprovincialis (four-way nested ANOVA, Season X Site(Bay): p = 0.0002), where summer prevalence was higher than that of winter in bays, regardless of zone, while in open coast sites, the effect of season was only significant in the mid zone. Patterns of intensity generally showed higher values in summer. Substratum preference by barnacles was investigated by recording settlement, survival and mortality of Chthamalus dentatus barnacles on various treatments. There was a strong preference for the rock-like plastic substratum by primary settlers (pair-wise tests of PERMANOVA: Dead < Rock mimic (p = 0.0001); Replica < Rock mimic (p = 0.019) and Live < Rock mimic (p = 0.0001)). This indicates that barnacles settle on mussel shells only as a secondary choice and that micro-topography is an important variable in barnacle settlement. The effect of barnacle epibiosis on condition index and growth of P. perna and M. galloprovincialis was also examined as a direct indication of the health of mussels subjected to the biological stress of epibiosis. Although not significant (PERMANOVA: P. perna: p(perm) = 0.890; M. galloprovincialis: p(perm) = 0.395), growth for both mussel species was slower for barnacle-infested individuals in summer, which is the main growing season for mussels in the region. Results from condition index calculations, however, showed no negative impacts of epibiotic barnacles (three-way ANCOVA: P. perna: p = 0.372; M. galloprovincialis: p = 0.762). Barnacle epibionts create a new interface between the mussel and its environment and this interaction can affect other members of the community. The possibility of the barnacle epibiont causing increased drag also needs further investigation. Biological processes operating within a wide range of physical stressors drive the interactions on the rocky shore, such as epibiosis. Overall, the results of this study suggest that the epibiotic relationship between mussels and barnacles on the south-east coast of South Africa does not significantly affect the mussel species present and that barnacles only use mussel shells as a secondary choice of substratum.
- Full Text:
The feasibility of reintroducing African wild dogs (Lycaon pictus) into the Great Fish River Nature Reserve, Eastern Cape, South Africa
- Authors: Page, Samantha Karin
- Date: 2014
- Subjects: Great Fish River Nature Reserve (South Africa) , African wild dog -- South Africa -- Eastern Cape , Population biology -- South Africa -- Eastern Cape , African wild dog -- Reintroduction -- South Africa -- Eastern Cape , African wild dog -- Population viability analysis -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5915 , http://hdl.handle.net/10962/d1016078
- Description: With a declining population of roughly 3000-5000 individuals in Africa, African wild dogs (Lycaon pictus) are one of the most endangered carnivores in the world. As the global human population expands, it is becoming increasingly unlikely that large portions of land will be set aside for conservation, especially in developing countries. Thus, recent wild dog conservation efforts in South Africa have concentrated on establishing a managed metapopulation. A metapopulation is a group of geographically isolated subpopulations of a species that are managed (using supplementation and harvesting) to mimic natural gene flow. The Great Fish River Nature Reserve (GFRNR) in the Eastern Cape Province of South Africa has been identified as a potential reserve to become part of the national wild dog metapopulation. My research aimed to conduct a feasibility assessment of the long-term (~ 25 years) success of a wild dog reintroduction into the GFRNR. This assessment included biological modelling of wild dogs and their expected prey, and determining the potential anthropogenic threats to wild dogs on the private and communal land surrounding the reserve. I used VORTEX population modelling and determined that the GFRNR is likely to have a wild dog carrying capacity of ~22 individuals. Using a 25-year modelling simulation, the most appropriate wild dog reintroduction scenario would be to reintroduce six females and four males initially and supplement the population with one female and two males in years 3, 10, 15 and 23. In addition, the harvesting/removal of one male and one female in years 10 and 20 would be required to ensure 100% population persistence and adequate genetic diversity. Kudu (Tragelaphus strepsiceros) and bushbuck (Tragelaphus scriptus) are expected to be the two most important prey species for reintroduced wild dogs in the GFRNR. Furthermore, wild dogs are likely to prefer the north-western and south-western sectors of the reserve because of the relatively high prey densities in these areas. However, regular monitoring of both the potential prey and the wild dog populations is essential to ensure persistence of the wild dogs and to prevent prey populations decreasing precipitously. Using structured questionnaire interviews (n = 128), I found that while neighbouring land owners and local communities were generally positive about the potential wild dog reintroduction (56 % of all respondents), several threats to wild dogs were identified along the reserve boundary and on the adjoining unprotected land. Some private landowners and members of rural communities around the reserve (34 %) stated that they would kill any wild dogs that dispersed onto their land. In addition, some respondents (8 %) admitted to believing in traditional uses for wild dog products (e.g. fur) which could result in the illegal killing of wild dogs outside of the GFRNR for traditional purposes. Poaching and the presence of unvaccinated domestic dogs on neighbouring land were also identified as being potential threats to a reintroduced wild dog population. However, such anthropogenic threats appear to be localised to the western and southern boundaries of the reserve. Therefore, by implementing preventative measures (such as anti-snare collars, anti-poaching patrols and vaccination against rabies and canine distemper) the likelihood of such threats occurring can be reduced. I conclude that the GFRNR can sustain a population of wild dogs and successfully contribute to South Africa‘s national metapopulation. An additional reserve will benefit the country‘s metapopulation by increasing the number of wild dogs available for translocation, thereby increasing genetic diversity and overall resilience (to environmental change, disease etc.) of South Africa‘s wild dog population. This will contribute towards the future conservation of this endangered species.
- Full Text:
- Authors: Page, Samantha Karin
- Date: 2014
- Subjects: Great Fish River Nature Reserve (South Africa) , African wild dog -- South Africa -- Eastern Cape , Population biology -- South Africa -- Eastern Cape , African wild dog -- Reintroduction -- South Africa -- Eastern Cape , African wild dog -- Population viability analysis -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5915 , http://hdl.handle.net/10962/d1016078
- Description: With a declining population of roughly 3000-5000 individuals in Africa, African wild dogs (Lycaon pictus) are one of the most endangered carnivores in the world. As the global human population expands, it is becoming increasingly unlikely that large portions of land will be set aside for conservation, especially in developing countries. Thus, recent wild dog conservation efforts in South Africa have concentrated on establishing a managed metapopulation. A metapopulation is a group of geographically isolated subpopulations of a species that are managed (using supplementation and harvesting) to mimic natural gene flow. The Great Fish River Nature Reserve (GFRNR) in the Eastern Cape Province of South Africa has been identified as a potential reserve to become part of the national wild dog metapopulation. My research aimed to conduct a feasibility assessment of the long-term (~ 25 years) success of a wild dog reintroduction into the GFRNR. This assessment included biological modelling of wild dogs and their expected prey, and determining the potential anthropogenic threats to wild dogs on the private and communal land surrounding the reserve. I used VORTEX population modelling and determined that the GFRNR is likely to have a wild dog carrying capacity of ~22 individuals. Using a 25-year modelling simulation, the most appropriate wild dog reintroduction scenario would be to reintroduce six females and four males initially and supplement the population with one female and two males in years 3, 10, 15 and 23. In addition, the harvesting/removal of one male and one female in years 10 and 20 would be required to ensure 100% population persistence and adequate genetic diversity. Kudu (Tragelaphus strepsiceros) and bushbuck (Tragelaphus scriptus) are expected to be the two most important prey species for reintroduced wild dogs in the GFRNR. Furthermore, wild dogs are likely to prefer the north-western and south-western sectors of the reserve because of the relatively high prey densities in these areas. However, regular monitoring of both the potential prey and the wild dog populations is essential to ensure persistence of the wild dogs and to prevent prey populations decreasing precipitously. Using structured questionnaire interviews (n = 128), I found that while neighbouring land owners and local communities were generally positive about the potential wild dog reintroduction (56 % of all respondents), several threats to wild dogs were identified along the reserve boundary and on the adjoining unprotected land. Some private landowners and members of rural communities around the reserve (34 %) stated that they would kill any wild dogs that dispersed onto their land. In addition, some respondents (8 %) admitted to believing in traditional uses for wild dog products (e.g. fur) which could result in the illegal killing of wild dogs outside of the GFRNR for traditional purposes. Poaching and the presence of unvaccinated domestic dogs on neighbouring land were also identified as being potential threats to a reintroduced wild dog population. However, such anthropogenic threats appear to be localised to the western and southern boundaries of the reserve. Therefore, by implementing preventative measures (such as anti-snare collars, anti-poaching patrols and vaccination against rabies and canine distemper) the likelihood of such threats occurring can be reduced. I conclude that the GFRNR can sustain a population of wild dogs and successfully contribute to South Africa‘s national metapopulation. An additional reserve will benefit the country‘s metapopulation by increasing the number of wild dogs available for translocation, thereby increasing genetic diversity and overall resilience (to environmental change, disease etc.) of South Africa‘s wild dog population. This will contribute towards the future conservation of this endangered species.
- Full Text:
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:
- 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:
The geographic stock structure of chokka squid, Loligo Reynaudi, and its implications for management of the fishery
- Van der Vyver, Johan Samuel Frederik
- Authors: Van der Vyver, Johan Samuel Frederik
- Date: 2014
- Subjects: Squids -- Geographical distribution , Loligo fisheries -- Africa, Southern , Fishery management -- Africa, Southern , Squids -- Africa, Southern , Squid fisheries -- Africa, Southern , Loliginidae -- Africa, Southern , Fish stock assessment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5363 , http://hdl.handle.net/10962/d1012973
- Description: It is currently hypothesised that the chokka squid (Loligo reynaudi) consist of a single stock. This was tested through a spatial comparison of the morphology of this species. Forty three morphometric characters were measured from 1079 chokka squid collected from three regions: the south coast of South Africa, the west coast of South Africa, and southern Angola. While no significant differences were found for the hard body parts, results from discriminant function analyses showed the soft body morphometric characters from each of the three regions differed, with an overall correct classification rate of 100% for males and 99% for females in all three regions. Due to the existing model being used to assess the resource currently being updated it was not feasible to apply this model to the area-disaggregated data from this study. Rather, the CPUE trends and catches from the area-disaggregated data were compared against those of the area-aggregated data, as a first attempt to discern any appreciable differences which would suggest the use of disaggregated data in future assessments. Both the trawl and jig CPUE trends from the area-disaggregated analysis differed only slightly from those of the area-aggregated data. Similarly, the spring and autumn biomass trends for the main spawning area (east of 22°E) followed the same trends as for the full area. It is therefore concluded that there is currently no need to assess the resource on an area-disaggregated basis.
- Full Text:
- Authors: Van der Vyver, Johan Samuel Frederik
- Date: 2014
- Subjects: Squids -- Geographical distribution , Loligo fisheries -- Africa, Southern , Fishery management -- Africa, Southern , Squids -- Africa, Southern , Squid fisheries -- Africa, Southern , Loliginidae -- Africa, Southern , Fish stock assessment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5363 , http://hdl.handle.net/10962/d1012973
- Description: It is currently hypothesised that the chokka squid (Loligo reynaudi) consist of a single stock. This was tested through a spatial comparison of the morphology of this species. Forty three morphometric characters were measured from 1079 chokka squid collected from three regions: the south coast of South Africa, the west coast of South Africa, and southern Angola. While no significant differences were found for the hard body parts, results from discriminant function analyses showed the soft body morphometric characters from each of the three regions differed, with an overall correct classification rate of 100% for males and 99% for females in all three regions. Due to the existing model being used to assess the resource currently being updated it was not feasible to apply this model to the area-disaggregated data from this study. Rather, the CPUE trends and catches from the area-disaggregated data were compared against those of the area-aggregated data, as a first attempt to discern any appreciable differences which would suggest the use of disaggregated data in future assessments. Both the trawl and jig CPUE trends from the area-disaggregated analysis differed only slightly from those of the area-aggregated data. Similarly, the spring and autumn biomass trends for the main spawning area (east of 22°E) followed the same trends as for the full area. It is therefore concluded that there is currently no need to assess the resource on an area-disaggregated basis.
- Full Text:
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:
- 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:
The involvement of TRAP1 in the mitochondrial localization of STAT3 in mammalian cells
- Authors: Kadye, Rose
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/55760 , vital:26731
- Description: STAT3 (signal transducer and activator of transcription 3), an oncogene and transcription factor of genes involved in cellular differentiation, proliferation and immune function, that classically localizes in the cytosol and nucleus has also been found in the mitochondria. However, STAT3 does not have a mitochondrial transit peptide, and its mechanism for mitochondrial localization is unknown. Cytosolic Hsp90s chaperone STAT3 to the nucleus therefore we investigated the involvement of the nuclear-encoded mitochondrial Hsp90 molecular chaperone tumor necrosis receptor associated protein 1 (TRAP1) in STAT3’s mitochondrial localization. Using TRAP1 transient over-expression, STAT3 inhibitor S3I- 201 and Hsp90 inhibitor geldanamycin, we demonstrate that TRAP1 and STAT3 co-localize and co-immunoprecipitates in mammalian systems. Taken together with the observation that STAT3 potentially directly interacts with TRAP1, these data suggest that TRAP1 plays a role in the mitochondrial localization of STAT3.
- Full Text:
- Authors: Kadye, Rose
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/55760 , vital:26731
- Description: STAT3 (signal transducer and activator of transcription 3), an oncogene and transcription factor of genes involved in cellular differentiation, proliferation and immune function, that classically localizes in the cytosol and nucleus has also been found in the mitochondria. However, STAT3 does not have a mitochondrial transit peptide, and its mechanism for mitochondrial localization is unknown. Cytosolic Hsp90s chaperone STAT3 to the nucleus therefore we investigated the involvement of the nuclear-encoded mitochondrial Hsp90 molecular chaperone tumor necrosis receptor associated protein 1 (TRAP1) in STAT3’s mitochondrial localization. Using TRAP1 transient over-expression, STAT3 inhibitor S3I- 201 and Hsp90 inhibitor geldanamycin, we demonstrate that TRAP1 and STAT3 co-localize and co-immunoprecipitates in mammalian systems. Taken together with the observation that STAT3 potentially directly interacts with TRAP1, these data suggest that TRAP1 plays a role in the mitochondrial localization of STAT3.
- Full Text:
The Kansanshi Cu-Au deposit, Domes region, Zambia : geology, mineralisation and alteration characteristics in the main pit
- Authors: Chinyuku, Donald Tichaona
- Date: 2014
- Subjects: Kansanshi Mine -- Zambia , Copper mines and mining -- Zambia , Gold mines and mining -- Zambia , Gold -- Assaying -- Zambia , Geology -- Zambia , Mineralogy -- Zambia , Tillite
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5051 , http://hdl.handle.net/10962/d1011758 , Kansanshi Mine -- Zambia , Copper mines and mining -- Zambia , Gold mines and mining -- Zambia , Gold -- Assaying -- Zambia , Geology -- Zambia , Mineralogy -- Zambia , Tillite
- Description: The Kansanshi Cu-Au deposit located in the Domes region of the North West province of Zambia is characterised by structurally controlled high angle veins and associated alteration halos. The northwest trending Kansanshi antiform flanks the Solwezi syncline to the north and hosts the Kansanshi deposit and consists of tillites and metasedimentary rocks. Mineralisation is associated with Neoproterozoic Pan African deformation events experienced during the formation of the Lufilian fold belt; however recent findings confirm that structures in the form of reverse and normal faults and drag folds are critical controls on mineralisation within the deposit, Main pit in particular. Low angle faults occurring below the current pit are believed to have served as major fluid pathways during mineralisation. Age dating data from the Kansanshi deposit suggest that mineralisation took place between 512 and 503 Ma indicating that the event was associated with metamorphism. Two types of alteration are dominant within the Main pit (Kansanshi deposit) with the type and intensity of alteration being largely controlled by lithological units. Albite alteration occurs dominantly in phyllites and schists whereas dolomitisation is prevalent in calcareous units. Alteration is associated with mineralisation, and therefore is used as a condition for predicting vein or disseminated mineralisation. The high Au tenor at Kansanshi can be attributed to gold grains occurring in association with melonite (NiTe₂) and microfractured pyrite intergrown with chalcopyrite in sulphide and quartz dominated veins and veinlets. Analysis of gold grade distribution within the Main pit shows a clear concentration of the element along the major north-south trending structures like the 4800 and 5400 zones, possibly through supergene enrichment in the oxide-transition-sulphide zones. It is imperative that exploration for Kansanshi-type deposits will require geochemical and geophysical studies, understanding of the geology of an area to identify the three lithostratigraphic units (red beds, evaporites and reducing strata).
- Full Text:
- Authors: Chinyuku, Donald Tichaona
- Date: 2014
- Subjects: Kansanshi Mine -- Zambia , Copper mines and mining -- Zambia , Gold mines and mining -- Zambia , Gold -- Assaying -- Zambia , Geology -- Zambia , Mineralogy -- Zambia , Tillite
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5051 , http://hdl.handle.net/10962/d1011758 , Kansanshi Mine -- Zambia , Copper mines and mining -- Zambia , Gold mines and mining -- Zambia , Gold -- Assaying -- Zambia , Geology -- Zambia , Mineralogy -- Zambia , Tillite
- Description: The Kansanshi Cu-Au deposit located in the Domes region of the North West province of Zambia is characterised by structurally controlled high angle veins and associated alteration halos. The northwest trending Kansanshi antiform flanks the Solwezi syncline to the north and hosts the Kansanshi deposit and consists of tillites and metasedimentary rocks. Mineralisation is associated with Neoproterozoic Pan African deformation events experienced during the formation of the Lufilian fold belt; however recent findings confirm that structures in the form of reverse and normal faults and drag folds are critical controls on mineralisation within the deposit, Main pit in particular. Low angle faults occurring below the current pit are believed to have served as major fluid pathways during mineralisation. Age dating data from the Kansanshi deposit suggest that mineralisation took place between 512 and 503 Ma indicating that the event was associated with metamorphism. Two types of alteration are dominant within the Main pit (Kansanshi deposit) with the type and intensity of alteration being largely controlled by lithological units. Albite alteration occurs dominantly in phyllites and schists whereas dolomitisation is prevalent in calcareous units. Alteration is associated with mineralisation, and therefore is used as a condition for predicting vein or disseminated mineralisation. The high Au tenor at Kansanshi can be attributed to gold grains occurring in association with melonite (NiTe₂) and microfractured pyrite intergrown with chalcopyrite in sulphide and quartz dominated veins and veinlets. Analysis of gold grade distribution within the Main pit shows a clear concentration of the element along the major north-south trending structures like the 4800 and 5400 zones, possibly through supergene enrichment in the oxide-transition-sulphide zones. It is imperative that exploration for Kansanshi-type deposits will require geochemical and geophysical studies, understanding of the geology of an area to identify the three lithostratigraphic units (red beds, evaporites and reducing strata).
- Full Text:
The large scale bioinformatics analysis of auxiliary activity family 9 enzymes
- Authors: Moses, Vuyani
- Date: 2014
- Subjects: Bioinformatics -- Analysis , Cellulose -- Biodegradation , Biomass energy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4145 , http://hdl.handle.net/10962/d1016356
- Description: Biofuels have been proposed to be a suitable replacement to the already depleting fossil fuels. The complex structures of plant biomasses present a challenge the production of biofuels due to recalcitrance. The complex cellulose structure and hydrogen bonding between repeat units of cellulose is believed to be a major contributor to the recalcitrance of cellulose. Fungal organisms come equipped with various oxidative enzymes involved in degradation of plant biomass. The exact mechanism of cellulose degradation remains elusive. The GH61 is a group of proteins which are PMOs. GH61 sequences where previously described as endoglucanases due to weak endoglucanase activity. These enzymes were later found not possess any enzyme activity of their own however they could enhance the activity of other cellulose degrading enzymes. As a result reclassification of these enzymes as AA9 has been implemented. AA9 proteins have been reported to share structural homology with the bacterial AA10 group of enzymes. Based on cleavage products that are produced when AA9 proteins interact with cellulose, AA9 proteins have been grouped into three types. To date the exact mechanism and the sequence and structural basis for differentiating between the various AA9 types remains unknown. Using various bionformatic techniques sequence and structural elements were identified for distinguishing between the AA9 types. A large dataset of sequences was obtained from the Pfam database from UNIPROT entries. Due to high divergence of AA9 sequences, a smaller dataset with the more divergent sequences removed was created. The inclusion of the reference sequences to the data set was done to observe which sequences belong to a certain type. Phylogenetic analysis was able to group AA9 proteins into three distinct groups. MSA and motif analysis revealed that the N-Terminus of these proteins is mostly responsible for type specificity. Structural analysis of AA9 PDB structures and homology models allowed the effect of physicochemical properties to be gauged structurally. The presence of 310 helices and aromatic residues the surface of AA9 sequences is an observation which still warrants further investigation.
- Full Text:
- Authors: Moses, Vuyani
- Date: 2014
- Subjects: Bioinformatics -- Analysis , Cellulose -- Biodegradation , Biomass energy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4145 , http://hdl.handle.net/10962/d1016356
- Description: Biofuels have been proposed to be a suitable replacement to the already depleting fossil fuels. The complex structures of plant biomasses present a challenge the production of biofuels due to recalcitrance. The complex cellulose structure and hydrogen bonding between repeat units of cellulose is believed to be a major contributor to the recalcitrance of cellulose. Fungal organisms come equipped with various oxidative enzymes involved in degradation of plant biomass. The exact mechanism of cellulose degradation remains elusive. The GH61 is a group of proteins which are PMOs. GH61 sequences where previously described as endoglucanases due to weak endoglucanase activity. These enzymes were later found not possess any enzyme activity of their own however they could enhance the activity of other cellulose degrading enzymes. As a result reclassification of these enzymes as AA9 has been implemented. AA9 proteins have been reported to share structural homology with the bacterial AA10 group of enzymes. Based on cleavage products that are produced when AA9 proteins interact with cellulose, AA9 proteins have been grouped into three types. To date the exact mechanism and the sequence and structural basis for differentiating between the various AA9 types remains unknown. Using various bionformatic techniques sequence and structural elements were identified for distinguishing between the AA9 types. A large dataset of sequences was obtained from the Pfam database from UNIPROT entries. Due to high divergence of AA9 sequences, a smaller dataset with the more divergent sequences removed was created. The inclusion of the reference sequences to the data set was done to observe which sequences belong to a certain type. Phylogenetic analysis was able to group AA9 proteins into three distinct groups. MSA and motif analysis revealed that the N-Terminus of these proteins is mostly responsible for type specificity. Structural analysis of AA9 PDB structures and homology models allowed the effect of physicochemical properties to be gauged structurally. The presence of 310 helices and aromatic residues the surface of AA9 sequences is an observation which still warrants further investigation.
- Full Text:
The natural history of the humpback dolphin, Sousa chinensis, in KwaZulu-Natal, South Africa : age, growth and reproduction
- Authors: Nolte, Zianca
- Date: 2014
- Subjects: Sousa -- South Africa -- KwaZulu-Natal , Dolphins -- Behavior -- South Africa -- KwaZulu-Natal , Dolphins -- Age determination -- South Africa -- KwaZulu-Natal , Dolphins -- Development -- South Africa -- KwaZulu-Natal , Dolphins -- South Africa -- KwaZulu-Natal -- Reproduction , Dolphins -- Physiology -- South Africa -- KwaZulu-Natal
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5878 , http://hdl.handle.net/10962/d1013178
- Description: Globally, inshore cetaceans are being threatened by a number of anthropogenic activities. The Indo-Pacific humpback dolphin, Sousa chinensis, is currently listed as ‘near threatened’ by the International Union for the Conservation of Nature (IUCN). In order to be able to advise on management and conservation strategies, knowledge on the life history of the species is required. To date very little is known about the biology of humpback dolphins. The aim of the present study was to determine basic life history parameters, including age, growth and reproduction of humpback dolphins incidentally caught in shark nets. Age was estimated by counting the growth layer groups (GLGs) in the dentine and cementum of sectioned and stained teeth. Both a Von Bertalanffy and a Gompertz growth curve fitted well to the data, but for comparison with previous studies on Sousa, the Gompertz growth function was adopted to describe the relationship between length and age for KwaZulu-Natal populations. Length at birth was estimated between 104.33 and 111.57 cm for males and females, respectively. Asymptotic length was reached at 266.48 cm and 239.29 cm for males and females, respectively. This corresponds to the attainment of physical maturity at 24 GLGs in males and 16 GLGs in females. Asymptotic mass for males could not be determined, while for females it occurred around 160 kg. The maximum age estimates and recorded lengths were 24 GLGs and 279 cm for males and 17.7 GLGs and 249 cm for females. Differences in length-at-age and mass-at-age for S. chinensis suggest sexual dimorphism. The attainment of sexual maturity in males occurred between 9 and 10 GLGs, corresponding to 230 cm total body length and 140 kg. The maximum combined testis mass of mature males comprised 0.42% of total body mass, and a roving male mating system was proposed. In females, sexual maturity occurred around 7.6 GLG, between 220 and 222 cm and 104 - 140 kg. The ovulation rate is estimated at 0.2 ovulations per annum, suggesting a calving interval of five years. It is evident from the results obtained in the present study that geographical differences exist in the life history parameters of S. chinensis. As a result, regional conservation and management strategies are imperative. Results from this study can therefore assist in assessing the status of existing population structures in the KwaZulu-Natal coastal waters, and the implementation of regional mitigation strategies to ensure the continued survival of humpback dolphins in the region.
- Full Text:
- Authors: Nolte, Zianca
- Date: 2014
- Subjects: Sousa -- South Africa -- KwaZulu-Natal , Dolphins -- Behavior -- South Africa -- KwaZulu-Natal , Dolphins -- Age determination -- South Africa -- KwaZulu-Natal , Dolphins -- Development -- South Africa -- KwaZulu-Natal , Dolphins -- South Africa -- KwaZulu-Natal -- Reproduction , Dolphins -- Physiology -- South Africa -- KwaZulu-Natal
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5878 , http://hdl.handle.net/10962/d1013178
- Description: Globally, inshore cetaceans are being threatened by a number of anthropogenic activities. The Indo-Pacific humpback dolphin, Sousa chinensis, is currently listed as ‘near threatened’ by the International Union for the Conservation of Nature (IUCN). In order to be able to advise on management and conservation strategies, knowledge on the life history of the species is required. To date very little is known about the biology of humpback dolphins. The aim of the present study was to determine basic life history parameters, including age, growth and reproduction of humpback dolphins incidentally caught in shark nets. Age was estimated by counting the growth layer groups (GLGs) in the dentine and cementum of sectioned and stained teeth. Both a Von Bertalanffy and a Gompertz growth curve fitted well to the data, but for comparison with previous studies on Sousa, the Gompertz growth function was adopted to describe the relationship between length and age for KwaZulu-Natal populations. Length at birth was estimated between 104.33 and 111.57 cm for males and females, respectively. Asymptotic length was reached at 266.48 cm and 239.29 cm for males and females, respectively. This corresponds to the attainment of physical maturity at 24 GLGs in males and 16 GLGs in females. Asymptotic mass for males could not be determined, while for females it occurred around 160 kg. The maximum age estimates and recorded lengths were 24 GLGs and 279 cm for males and 17.7 GLGs and 249 cm for females. Differences in length-at-age and mass-at-age for S. chinensis suggest sexual dimorphism. The attainment of sexual maturity in males occurred between 9 and 10 GLGs, corresponding to 230 cm total body length and 140 kg. The maximum combined testis mass of mature males comprised 0.42% of total body mass, and a roving male mating system was proposed. In females, sexual maturity occurred around 7.6 GLG, between 220 and 222 cm and 104 - 140 kg. The ovulation rate is estimated at 0.2 ovulations per annum, suggesting a calving interval of five years. It is evident from the results obtained in the present study that geographical differences exist in the life history parameters of S. chinensis. As a result, regional conservation and management strategies are imperative. Results from this study can therefore assist in assessing the status of existing population structures in the KwaZulu-Natal coastal waters, and the implementation of regional mitigation strategies to ensure the continued survival of humpback dolphins in the region.
- Full Text:
The origin of endorheic pans on the African erosion surface North of Grahamstown, South Africa
- Authors: Alistoun, Judith Robyn
- Date: 2014
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4775 , http://hdl.handle.net/10962/d1011048
- Description: Pans on the African Erosion Surface near Grahamstown are small features, which, perhaps due to their small size have been neglected by researchers. From the outset the striking difference of these pans relative to other pans in southern Africa, is that the host rock is silcrete, a highly resistant rock well known as being associated with deeply weathered plateaus. The dominant origin theory for pans in southern Africa was developed by Goudie and Thomas (1985), and focuses on mechanisms relating to erosion and deflation. This model does not fit in well with the pans that have formed on substrate that has largely been unaffected by erosion in recent geological history (thousands to 10 000 years). As such this study examined the role of prolonged chemical weathering of Dwyka Tillite, that has led to the formation of silcrete. The hypothesis was that such deep weathering is responsible for local scale volume changes, which have in turn led to the formation of a depression. The centre of the pan indicated the highest concentration of Al₂O₃ and kaolinite at mid depths, and their concentrations decreased vertically away from these depths, and laterally towards the margins of the pan. Similar results were noted for SiO₂, while CaO and MgO (and calcite and dolomite) were highest at mid depths along the margins of the pan, and decreased laterally toward the centre of the pan. Results indicated that there was a positive relationship in the centre of the pan between: - the degree of chemical weathering and volume losses, - relative elevation of the pan and volume changes. Geochemically and mineralogically, there was a link between the high concentrations of Ca and Mg carbonates and volume gains in the margin of the pans. It is proposed that transpiration of vegetation along the margin of the pan caused the lateral movement of solutes, and the selective exclusion of these solutes by plants was associated with carbonate precipitation, leading to the creation of local relief. These results provide evidence to suggest that weathering and precipitation processes occurring over geological time scales are responsible for minor scale relief features, whose origin has been mistakenly attributed to deflation processes occurring over hundreds to thousands of years.
- Full Text:
- Authors: Alistoun, Judith Robyn
- Date: 2014
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4775 , http://hdl.handle.net/10962/d1011048
- Description: Pans on the African Erosion Surface near Grahamstown are small features, which, perhaps due to their small size have been neglected by researchers. From the outset the striking difference of these pans relative to other pans in southern Africa, is that the host rock is silcrete, a highly resistant rock well known as being associated with deeply weathered plateaus. The dominant origin theory for pans in southern Africa was developed by Goudie and Thomas (1985), and focuses on mechanisms relating to erosion and deflation. This model does not fit in well with the pans that have formed on substrate that has largely been unaffected by erosion in recent geological history (thousands to 10 000 years). As such this study examined the role of prolonged chemical weathering of Dwyka Tillite, that has led to the formation of silcrete. The hypothesis was that such deep weathering is responsible for local scale volume changes, which have in turn led to the formation of a depression. The centre of the pan indicated the highest concentration of Al₂O₃ and kaolinite at mid depths, and their concentrations decreased vertically away from these depths, and laterally towards the margins of the pan. Similar results were noted for SiO₂, while CaO and MgO (and calcite and dolomite) were highest at mid depths along the margins of the pan, and decreased laterally toward the centre of the pan. Results indicated that there was a positive relationship in the centre of the pan between: - the degree of chemical weathering and volume losses, - relative elevation of the pan and volume changes. Geochemically and mineralogically, there was a link between the high concentrations of Ca and Mg carbonates and volume gains in the margin of the pans. It is proposed that transpiration of vegetation along the margin of the pan caused the lateral movement of solutes, and the selective exclusion of these solutes by plants was associated with carbonate precipitation, leading to the creation of local relief. These results provide evidence to suggest that weathering and precipitation processes occurring over geological time scales are responsible for minor scale relief features, whose origin has been mistakenly attributed to deflation processes occurring over hundreds to thousands of years.
- Full Text:
The preparation of antigen for the generation of polyclonal antibodies against the capsid subunit, VP1, and the viral protease, 3Cpro, of Theiler's murine encephalomyelitis virus (TMEV)
- Authors: Moetlhoa, Boitumelo
- Date: 2014
- Subjects: Enteroviruses , Encephalomyelitis , Antigens
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4118 , http://hdl.handle.net/10962/d1013225
- Description: The Picornaviridae is a family of viruses of economic importance that have a major impact on human and animal health. Some of the major genera found in the Picornaviridae family are Enterovirus which includes Poliovirus (PV) and Human Rhinovirus (HRV), Cardiovirus which includes Theiler’s murine encephalomyelitis virus (TMEV) and Saffold virus (SAFV), Aphthovirus of which the Foot and Mouth disease virus (FMDV) is a member and Hepatovirus which includes Hepatitis A virus (HAV). Picornaviruses have a single stranded, positive sense RNA genome which is approximately 7.5-8.4 kb pairs in size. The picornavirus genome is translated into a large polyprotein and is proteolytically cleaved by viral proteases namely 2Apro, 3Cpro and 3CDpro into mature viral structural and non-structural polypeptides encoded by the P1, P2 and P3 domains. Picornaviruses utilise host cell machinery and cellular pathways for entry and uncoating, genome replication and capsid assembly. In our laboratory, we are studying the mechanisms by which TMEV interacts with host cell components and our recent research shows that molecular chaperones are required for a production infection. To follow up on this observation, the overall aim of this study was to prepare antigen for the generation of polyclonal antibodies against the TMEV VP1 and 3Cpro proteins. To this end, the TMEV VP1 and 3Cpro amino acid sequences were analysed to identify hydrophobic, hydrophilic and antigenic regions. Homology modelling was performed in order to predict linear B cell epitopes exposed on the surface of the protein structures. The full length coding sequences of VP1 and 3Cpro were selected for amplification by the PCR and cloning into pQE-80L for expression in a bacterial system. Time course induction studies of recombinant VP1 and 3Cpro showed that the proteins were maximally expressed at 6 hrs and 4 hrs respectively. Recombinant VP1 was solubilised using the detergent, Sarcosyl and purified by Nickel affinity chromatography under native conditions. Because recombinant VP1 co-purified with an unidentified protein, the pET expression system was used. Although no protein of the estimated size was observed by SDS-PAGE analysis in the time course induction study, Western analysis using anti-His6 (2) antibodies detected a signal of ~35 kDa. Solubility studies resulted in the presence of two protein bands in the insoluble fraction resolved between 35 and 40 kDa. Recombinant 3Cpro expressed in a bacterial system was predominantly present in the insoluble fraction. Treatment with Sarcosyl had no effect on the solubility of the recombinant protein and it was therefore purified under denaturing conditions using 8M urea. Following dialysis, 3Cpro was used for immunisation of rabbits. Crude anti-TMEV 3Cpro antibodies were able to detect as little as 107 ng of bacterially expressed antigen at a dilution of 1:100 000 by Western analysis. The presence of contaminating proteins was reduced using pre-cleared anti-TMEV 3Cpro antibodies. The antibodies were unable to detect virally expressed 3Cpro in BHK-21 cell lysate supernatant. In an attempt to determine whether TMEV 3Cpro is present in the insoluble fraction, anti-TMEV 3Cpro antibodies were tested using total protein prepared from infected and mock-infected cell lysates. Once again, no protein band the size of 3Cpro was detected. The antibodies were further tested for detection of 3Cpro in TMEV-infected cells by indirect immunofluorescence and confocal microscopy. A diffuse cytoplasmic and perinuclear distribution, as well as nuclear staining, was observed in infected BHK-21 cells. This staining pattern resembled that observed for the HRV, FMDV and EMCV 3Cpro in similar experiments. Further experiments are required to confirm specificity of these antibodies for virally-expressed 3Cpro by Western analysis and indirect immunofluorescence.
- Full Text:
- Authors: Moetlhoa, Boitumelo
- Date: 2014
- Subjects: Enteroviruses , Encephalomyelitis , Antigens
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4118 , http://hdl.handle.net/10962/d1013225
- Description: The Picornaviridae is a family of viruses of economic importance that have a major impact on human and animal health. Some of the major genera found in the Picornaviridae family are Enterovirus which includes Poliovirus (PV) and Human Rhinovirus (HRV), Cardiovirus which includes Theiler’s murine encephalomyelitis virus (TMEV) and Saffold virus (SAFV), Aphthovirus of which the Foot and Mouth disease virus (FMDV) is a member and Hepatovirus which includes Hepatitis A virus (HAV). Picornaviruses have a single stranded, positive sense RNA genome which is approximately 7.5-8.4 kb pairs in size. The picornavirus genome is translated into a large polyprotein and is proteolytically cleaved by viral proteases namely 2Apro, 3Cpro and 3CDpro into mature viral structural and non-structural polypeptides encoded by the P1, P2 and P3 domains. Picornaviruses utilise host cell machinery and cellular pathways for entry and uncoating, genome replication and capsid assembly. In our laboratory, we are studying the mechanisms by which TMEV interacts with host cell components and our recent research shows that molecular chaperones are required for a production infection. To follow up on this observation, the overall aim of this study was to prepare antigen for the generation of polyclonal antibodies against the TMEV VP1 and 3Cpro proteins. To this end, the TMEV VP1 and 3Cpro amino acid sequences were analysed to identify hydrophobic, hydrophilic and antigenic regions. Homology modelling was performed in order to predict linear B cell epitopes exposed on the surface of the protein structures. The full length coding sequences of VP1 and 3Cpro were selected for amplification by the PCR and cloning into pQE-80L for expression in a bacterial system. Time course induction studies of recombinant VP1 and 3Cpro showed that the proteins were maximally expressed at 6 hrs and 4 hrs respectively. Recombinant VP1 was solubilised using the detergent, Sarcosyl and purified by Nickel affinity chromatography under native conditions. Because recombinant VP1 co-purified with an unidentified protein, the pET expression system was used. Although no protein of the estimated size was observed by SDS-PAGE analysis in the time course induction study, Western analysis using anti-His6 (2) antibodies detected a signal of ~35 kDa. Solubility studies resulted in the presence of two protein bands in the insoluble fraction resolved between 35 and 40 kDa. Recombinant 3Cpro expressed in a bacterial system was predominantly present in the insoluble fraction. Treatment with Sarcosyl had no effect on the solubility of the recombinant protein and it was therefore purified under denaturing conditions using 8M urea. Following dialysis, 3Cpro was used for immunisation of rabbits. Crude anti-TMEV 3Cpro antibodies were able to detect as little as 107 ng of bacterially expressed antigen at a dilution of 1:100 000 by Western analysis. The presence of contaminating proteins was reduced using pre-cleared anti-TMEV 3Cpro antibodies. The antibodies were unable to detect virally expressed 3Cpro in BHK-21 cell lysate supernatant. In an attempt to determine whether TMEV 3Cpro is present in the insoluble fraction, anti-TMEV 3Cpro antibodies were tested using total protein prepared from infected and mock-infected cell lysates. Once again, no protein band the size of 3Cpro was detected. The antibodies were further tested for detection of 3Cpro in TMEV-infected cells by indirect immunofluorescence and confocal microscopy. A diffuse cytoplasmic and perinuclear distribution, as well as nuclear staining, was observed in infected BHK-21 cells. This staining pattern resembled that observed for the HRV, FMDV and EMCV 3Cpro in similar experiments. Further experiments are required to confirm specificity of these antibodies for virally-expressed 3Cpro by Western analysis and indirect immunofluorescence.
- Full Text:
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:
- 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:
The water and nutrient potential of brewery effluent for hydroponic tomato production
- Authors: Power, Sean Duncan
- Date: 2014
- Subjects: Hydroponics , Tomatoes -- Breeding , Brewery waste , Water -- Purification , Algae culture , Algae -- Biotechnology , Nitric acid , Phosphoric acid
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5358 , http://hdl.handle.net/10962/d1011604 , Hydroponics , Tomatoes -- Breeding , Brewery waste , Water -- Purification , Algae culture , Algae -- Biotechnology , Nitric acid , Phosphoric acid
- Description: Brewery effluent that had undergone treatment in an anaerobic digester (AD) was used as an alternative water and nutrient source for hydroponic crop production. Brewery effluent was demonstrated to contain sufficient nutrients to support the growth, flowering and fruiting of Lycopersicum escolentum "Moneymaker" tomato crops. The adjustment of the effluent pH with phosphoric acid to between pH 6.0 and 6.5 increased the development of the crops by around 100% compared to crops grown in unaltered effluent. The pH adjusted effluent-grown plants grew to a mean height of 831.4 ± 21.1 mm and a dry biomass weight of 42.34 ± 2.76 g compared to the unaltered pH effluent plants which grew to a height of 410.6 ± 20.5 mm and a weight of 7.65 ± 0.68 g after 49 days. Effluent treatment in high-rate algal ponds (HRAP) was determined to have no positive effect on the nutritional potential of the effluent for Moneymaker production. The effluent-grown plants did not perform as well as plants grown in inorganic-fertilizer and municipal water. Plants grown in effluent grew taller but did not produce significantly more fruit when phosphoric acid (height: 1573.3 ± 50.4 mm, 19.4 ± 1.4 fruit per plant) was compared to nitric acid (height: 1254.1 ± 25.4 mm, 15.6 ± 1.5 fruit per plant) as the pH adjustment over 72 days. Direct and secondary plant stresses from effluent alkalinity, ammonium nutrition, nitrogen limitation, sodium concentrations and heat stress among other factors were probably confounding variables in these trials and require further investigation. Considering the raw effluent composition and manipulating the AD operation is a potential opportunity to improve overall AD performance, reduce chemical inputs in the effluent treatment process, reduce the final effluent alkalinity, and increase available nitrogen content in the final effluent. The anaerobic digester discharging >1000 m³ of nutrient enriched effluent every day is a resource with considerable potential. The benefits of developing this resource can contribute to cost-reduction at the brewery, more efficient water, nutrient and energy management at the brewery, and offer opportunities for job creation and potentially benefit local food security.
- Full Text:
- Authors: Power, Sean Duncan
- Date: 2014
- Subjects: Hydroponics , Tomatoes -- Breeding , Brewery waste , Water -- Purification , Algae culture , Algae -- Biotechnology , Nitric acid , Phosphoric acid
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5358 , http://hdl.handle.net/10962/d1011604 , Hydroponics , Tomatoes -- Breeding , Brewery waste , Water -- Purification , Algae culture , Algae -- Biotechnology , Nitric acid , Phosphoric acid
- Description: Brewery effluent that had undergone treatment in an anaerobic digester (AD) was used as an alternative water and nutrient source for hydroponic crop production. Brewery effluent was demonstrated to contain sufficient nutrients to support the growth, flowering and fruiting of Lycopersicum escolentum "Moneymaker" tomato crops. The adjustment of the effluent pH with phosphoric acid to between pH 6.0 and 6.5 increased the development of the crops by around 100% compared to crops grown in unaltered effluent. The pH adjusted effluent-grown plants grew to a mean height of 831.4 ± 21.1 mm and a dry biomass weight of 42.34 ± 2.76 g compared to the unaltered pH effluent plants which grew to a height of 410.6 ± 20.5 mm and a weight of 7.65 ± 0.68 g after 49 days. Effluent treatment in high-rate algal ponds (HRAP) was determined to have no positive effect on the nutritional potential of the effluent for Moneymaker production. The effluent-grown plants did not perform as well as plants grown in inorganic-fertilizer and municipal water. Plants grown in effluent grew taller but did not produce significantly more fruit when phosphoric acid (height: 1573.3 ± 50.4 mm, 19.4 ± 1.4 fruit per plant) was compared to nitric acid (height: 1254.1 ± 25.4 mm, 15.6 ± 1.5 fruit per plant) as the pH adjustment over 72 days. Direct and secondary plant stresses from effluent alkalinity, ammonium nutrition, nitrogen limitation, sodium concentrations and heat stress among other factors were probably confounding variables in these trials and require further investigation. Considering the raw effluent composition and manipulating the AD operation is a potential opportunity to improve overall AD performance, reduce chemical inputs in the effluent treatment process, reduce the final effluent alkalinity, and increase available nitrogen content in the final effluent. The anaerobic digester discharging >1000 m³ of nutrient enriched effluent every day is a resource with considerable potential. The benefits of developing this resource can contribute to cost-reduction at the brewery, more efficient water, nutrient and energy management at the brewery, and offer opportunities for job creation and potentially benefit local food security.
- Full Text:
Thermoluminescence characteristics of synthetic quartz
- Authors: Niyonzima, Pontien
- Date: 2014
- Subjects: Thermoluminescence , Quartz , Emission spectroscopy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5538 , http://hdl.handle.net/10962/d1013190
- Description: Quartz is one of the most abundant natural minerals in the crust of the earth. Due to its dosimetric luminescence properties, it is employed in retrospective dosimetry, archaeological and geological dating. The intensity and the structure of the TL glow curves of quartz are strongly dependent upon the origin, impurity content, formation condition and pre-irradiation heat treatment. The aim of this project is to study the mechanisms of thermoluminescence (TL), Phototranssferred thermoluminescence (PTTL) and radioluminescence (RL) in synthetic quartz and to discuss the results in terms of physical characteristics of point defects involved. Thermoluminescence measurements were made on a sample of synthetic quartz in its as-received state (unannealed) synthetic quartz annealed at 500˚C for 10 minutes. The unannealed sample shows six TL glow peaks located at 94, 116, 176, 212, 280 and 348˚C at a heating rate of 5˚Cs⁻¹. The annealed sample shows seven TL peaks at 115, 148, 214, 246, 300, 348 and 412˚C at a heating rate of 5˚Cs⁻¹. The intensity of peak I, at 94 and 115˚C for the unannealed and annealed samples respectively, increases with irradiation. Peak I has an activation energy of approximately 0.90 eV and a frequency factor of the order of 10¹¹ s⁻¹. The order of kinetics is between 0.9 and 1.2. The unannealed synthetic quartz shows phototransferred thermoluminescence (PTTL) at the position of peak I after removal of the first three peaks followed by illumination. The PTTL intensities show peak shaped behaviour when plotted against illumination time. The PTTL showed a quadratic increase with dose. The material exhibits fading of PTTL intensity with delay time. Radioluminescence was measured on synthetic quartz unannealed and annealed annealed at 500, 600, 700, 800, 900 and 1000˚C for 10 to 60 min. The emission spectra of synthetic quartz show seven emission bands. The effect of irradiation on the RL spectra is to increase the intensity of all emission bands for samples annealed at temperatures less than or equal to 700˚C. The effect of annealing time is to increase the RL amplitude for the samples annealed at temperatures greater than 700˚C. The annealing temperature increases the RL amplitude of all emission bands of the spectrum for all samples.
- Full Text:
- Authors: Niyonzima, Pontien
- Date: 2014
- Subjects: Thermoluminescence , Quartz , Emission spectroscopy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5538 , http://hdl.handle.net/10962/d1013190
- Description: Quartz is one of the most abundant natural minerals in the crust of the earth. Due to its dosimetric luminescence properties, it is employed in retrospective dosimetry, archaeological and geological dating. The intensity and the structure of the TL glow curves of quartz are strongly dependent upon the origin, impurity content, formation condition and pre-irradiation heat treatment. The aim of this project is to study the mechanisms of thermoluminescence (TL), Phototranssferred thermoluminescence (PTTL) and radioluminescence (RL) in synthetic quartz and to discuss the results in terms of physical characteristics of point defects involved. Thermoluminescence measurements were made on a sample of synthetic quartz in its as-received state (unannealed) synthetic quartz annealed at 500˚C for 10 minutes. The unannealed sample shows six TL glow peaks located at 94, 116, 176, 212, 280 and 348˚C at a heating rate of 5˚Cs⁻¹. The annealed sample shows seven TL peaks at 115, 148, 214, 246, 300, 348 and 412˚C at a heating rate of 5˚Cs⁻¹. The intensity of peak I, at 94 and 115˚C for the unannealed and annealed samples respectively, increases with irradiation. Peak I has an activation energy of approximately 0.90 eV and a frequency factor of the order of 10¹¹ s⁻¹. The order of kinetics is between 0.9 and 1.2. The unannealed synthetic quartz shows phototransferred thermoluminescence (PTTL) at the position of peak I after removal of the first three peaks followed by illumination. The PTTL intensities show peak shaped behaviour when plotted against illumination time. The PTTL showed a quadratic increase with dose. The material exhibits fading of PTTL intensity with delay time. Radioluminescence was measured on synthetic quartz unannealed and annealed annealed at 500, 600, 700, 800, 900 and 1000˚C for 10 to 60 min. The emission spectra of synthetic quartz show seven emission bands. The effect of irradiation on the RL spectra is to increase the intensity of all emission bands for samples annealed at temperatures less than or equal to 700˚C. The effect of annealing time is to increase the RL amplitude for the samples annealed at temperatures greater than 700˚C. The annealing temperature increases the RL amplitude of all emission bands of the spectrum for all samples.
- Full Text:
Thermoluminescence of natural quartz
- Authors: Lontsi Sob, Aaron Joel
- Date: 2014
- Subjects: Thermoluminescence , Quartz , Thermoluminescence dosimetry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5543 , http://hdl.handle.net/10962/d1013358
- Description: The kinetic and dosimetric features of the main thermoluminescence peak of quartz have been investigated in unannealed as well in quartz annealed at 500˚C for 10 minutes. The main peak is found at 92 and 86˚C respectively for aliquots of unannealed and annealed samples irradiated to 10 Gy and heated at 5.0˚C/s. For each sample, the intensity of the main peak is enhanced with repetitive measurement whereas its maximum temperature is unaffected. The peak position of the main peak in each sample is independent of the irradiation dose and this, together with its fading characteristics are consistent with first-order kinetics. For low doses, typically between 2 and 10 Gy, the dose response of the main peak in each sample is linear. In the intermediate dose range from 10 to 60 Gy, the growth of the main peak in each sample is sub-linear and for greater doses, in the range from 60 Gy to 151 Gy, it is linear again. The half-life of the main peak of the unannealed sample is about 1.3 h whereas that of the annealed sample is about 1.2 h. The main peak in each sample can be approximated to a first-order glow peak. As the heating rate increases, the intensity of the main peak in each sample decreases. This is evidence of thermal quenching. The main peak in each sample is the only peak regenerated by phototransfer. The resulting phototransferred peak occurs at the same temperature as the original peak and has similar kinetic and dosimetric features. For a preheat temperature of 120˚C, the intensity of the phototransferred peak in each sample increases with illumination time up to a maximum and decreases afterwards. At longer illumination times (such as 30 min up to 1 h), no further decrease in the intensity of the phototransferred peak is observed. The traps associated with the 325˚C peak are the main source of the electrons responsible for the regenerated peak. Radioluminescence emission spectra were also measured for quartz annealed at various temperatures. Emission bands in quartz are affected by annealing and irradiation. A strong enhancement of the 3.4 eV (~366 nm) emission band is observed in quartz annealed at 500˚C. A new emission band which grows with annealing up to 1000˚C is observed at 3.7 eV (~330 nm) for quartz annealed at 600˚C. An attempt has been made to correlate the changes in radioluminescence emission spectra due to annealing with the influence of annealing on luminescence lifetimes in quartz.
- Full Text:
- Authors: Lontsi Sob, Aaron Joel
- Date: 2014
- Subjects: Thermoluminescence , Quartz , Thermoluminescence dosimetry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5543 , http://hdl.handle.net/10962/d1013358
- Description: The kinetic and dosimetric features of the main thermoluminescence peak of quartz have been investigated in unannealed as well in quartz annealed at 500˚C for 10 minutes. The main peak is found at 92 and 86˚C respectively for aliquots of unannealed and annealed samples irradiated to 10 Gy and heated at 5.0˚C/s. For each sample, the intensity of the main peak is enhanced with repetitive measurement whereas its maximum temperature is unaffected. The peak position of the main peak in each sample is independent of the irradiation dose and this, together with its fading characteristics are consistent with first-order kinetics. For low doses, typically between 2 and 10 Gy, the dose response of the main peak in each sample is linear. In the intermediate dose range from 10 to 60 Gy, the growth of the main peak in each sample is sub-linear and for greater doses, in the range from 60 Gy to 151 Gy, it is linear again. The half-life of the main peak of the unannealed sample is about 1.3 h whereas that of the annealed sample is about 1.2 h. The main peak in each sample can be approximated to a first-order glow peak. As the heating rate increases, the intensity of the main peak in each sample decreases. This is evidence of thermal quenching. The main peak in each sample is the only peak regenerated by phototransfer. The resulting phototransferred peak occurs at the same temperature as the original peak and has similar kinetic and dosimetric features. For a preheat temperature of 120˚C, the intensity of the phototransferred peak in each sample increases with illumination time up to a maximum and decreases afterwards. At longer illumination times (such as 30 min up to 1 h), no further decrease in the intensity of the phototransferred peak is observed. The traps associated with the 325˚C peak are the main source of the electrons responsible for the regenerated peak. Radioluminescence emission spectra were also measured for quartz annealed at various temperatures. Emission bands in quartz are affected by annealing and irradiation. A strong enhancement of the 3.4 eV (~366 nm) emission band is observed in quartz annealed at 500˚C. A new emission band which grows with annealing up to 1000˚C is observed at 3.7 eV (~330 nm) for quartz annealed at 600˚C. An attempt has been made to correlate the changes in radioluminescence emission spectra due to annealing with the influence of annealing on luminescence lifetimes in quartz.
- Full Text:
Thermoluminescence of secondary glow peaks in carbon-doped aluminium oxide
- Authors: Seneza, Cleophace
- Date: 2014
- Subjects: Thermoluminescence , Aluminum oxide , Thermoluminescence dosimetry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5537 , http://hdl.handle.net/10962/d1013053
- Description: Carbon-doped aluminium oxide, α-Al₂O₃ : C, is a highly sensitive luminescence dosimeter. The high sensitivity of α-Al₂O₃ : C has been attributed to large concentrations of oxygen vacancies, F and F⁺ centres, induced in the material during its preparation. The material is prepared in a highly reducing atmosphere in the presence of carbon. In the luminescence process, electrons are trapped in F-centre defects as a result of irradiation of the material. Thermal or optical release of trapped electrons leads to emission of light, thermoluminescence (TL) or optically stimulated light (OSL) respectively. The thermoluminescence technique is used to study point defects involved in luminescence of α-Al₂O₃ : C. A glow curve of α-Al₂O₃ : C, generally, shows three peaks; the main dosimetric peak of high intensity (peak II) and two other peaks of lower intensity called secondary glow peaks (peaks I and III). The overall aim of our work was to study the TL mechanisms responsible for secondary glow peaks in α-Al₂O₃ : C. The dynamics of charge movement between centres during the TL process was studied. The phototransferred thermoluminescence (PTTL) from secondary glow peaks was also studied. The kinetic analysis of TL from secondary peaks has shown that the activation energy of peak I is 0.7 eV and that of peak III, 1.2 eV. The frequency factor, the frequency at which an electron attempts to escape a trap, was found near the range of the Debye vibration frequency. Values of the activation energy are consistent within a variety of methods used. The two peaks follow first order kinetics as confirmed by the TM-Tstop method. A linear dependence of TL from peak I on dose is observed at various doses from 0.5 to 2.5 Gy. The peak position for peak I was also independent on dose, further confirmation that peak I is of first order kinetics. Peak I suffers from thermal fading with storage with a half-life of about 120 s. The dependence of TL intensity for peak I increased as a function of heating rate from 0.2 to 6ºCs⁻¹. In contrast to the TL intensity for peak I, the intensity of TL for peak III decreases with an increase of heating rate from 0.2 to 6ºCs⁻¹. This is evidence of thermal quenching for peak III. Parameters W = 1.48 ± 0:10 eV and C = 4 x 10¹³ of thermal quenching were calculated from peak III intensities at different heating rates. Thermal cleaning of peak III and the glow curve deconvolution methods confirmed that the main peak is actually overlapped by a small peak (labeled peak IIA). The kinetic analysis of peak IIA showed that it is of first order kinetics and that its activation energy is 1:0 eV. In addition, the peak IIA is affected by thermal quenching. Another secondary peak appears at 422ºC (peak IV). However, the kinetic analysis of TL from peak IV was not studied because its intensity is not well defined. A heating rate of 0.4ºCs⁻¹ was used after a dose of 3 Gy in kinetic analysis of peaks IIA and III. The study of the PTTL showed that peaks I and II were regenerated under PTTL but peak III was not. Various effects of the PTTL for peaks I and II for different preheating temperatures in different samples were observed. The effect of annealing at 900ºC for 15 minutes between measurements following each illumination time was studied. The effect of dose on secondary peaks was also studied in this work. The kinetic analysis of the PTTL intensity for peak I showed that its activation energy is 0.7 eV, consistent with the activation energy of the normal TL for peak I. The PTTL intensity from peak I fades rapidly with storage compared with the thermal fading from peak I of the normal TL. The PTTL intensity for peak I decreases as a function of heating rate. This decrease was attributed to thermal quenching. Thermal quenching was not observed in the case of the normal TL intensity. The cause of this contrast requires further study.
- Full Text:
- Authors: Seneza, Cleophace
- Date: 2014
- Subjects: Thermoluminescence , Aluminum oxide , Thermoluminescence dosimetry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5537 , http://hdl.handle.net/10962/d1013053
- Description: Carbon-doped aluminium oxide, α-Al₂O₃ : C, is a highly sensitive luminescence dosimeter. The high sensitivity of α-Al₂O₃ : C has been attributed to large concentrations of oxygen vacancies, F and F⁺ centres, induced in the material during its preparation. The material is prepared in a highly reducing atmosphere in the presence of carbon. In the luminescence process, electrons are trapped in F-centre defects as a result of irradiation of the material. Thermal or optical release of trapped electrons leads to emission of light, thermoluminescence (TL) or optically stimulated light (OSL) respectively. The thermoluminescence technique is used to study point defects involved in luminescence of α-Al₂O₃ : C. A glow curve of α-Al₂O₃ : C, generally, shows three peaks; the main dosimetric peak of high intensity (peak II) and two other peaks of lower intensity called secondary glow peaks (peaks I and III). The overall aim of our work was to study the TL mechanisms responsible for secondary glow peaks in α-Al₂O₃ : C. The dynamics of charge movement between centres during the TL process was studied. The phototransferred thermoluminescence (PTTL) from secondary glow peaks was also studied. The kinetic analysis of TL from secondary peaks has shown that the activation energy of peak I is 0.7 eV and that of peak III, 1.2 eV. The frequency factor, the frequency at which an electron attempts to escape a trap, was found near the range of the Debye vibration frequency. Values of the activation energy are consistent within a variety of methods used. The two peaks follow first order kinetics as confirmed by the TM-Tstop method. A linear dependence of TL from peak I on dose is observed at various doses from 0.5 to 2.5 Gy. The peak position for peak I was also independent on dose, further confirmation that peak I is of first order kinetics. Peak I suffers from thermal fading with storage with a half-life of about 120 s. The dependence of TL intensity for peak I increased as a function of heating rate from 0.2 to 6ºCs⁻¹. In contrast to the TL intensity for peak I, the intensity of TL for peak III decreases with an increase of heating rate from 0.2 to 6ºCs⁻¹. This is evidence of thermal quenching for peak III. Parameters W = 1.48 ± 0:10 eV and C = 4 x 10¹³ of thermal quenching were calculated from peak III intensities at different heating rates. Thermal cleaning of peak III and the glow curve deconvolution methods confirmed that the main peak is actually overlapped by a small peak (labeled peak IIA). The kinetic analysis of peak IIA showed that it is of first order kinetics and that its activation energy is 1:0 eV. In addition, the peak IIA is affected by thermal quenching. Another secondary peak appears at 422ºC (peak IV). However, the kinetic analysis of TL from peak IV was not studied because its intensity is not well defined. A heating rate of 0.4ºCs⁻¹ was used after a dose of 3 Gy in kinetic analysis of peaks IIA and III. The study of the PTTL showed that peaks I and II were regenerated under PTTL but peak III was not. Various effects of the PTTL for peaks I and II for different preheating temperatures in different samples were observed. The effect of annealing at 900ºC for 15 minutes between measurements following each illumination time was studied. The effect of dose on secondary peaks was also studied in this work. The kinetic analysis of the PTTL intensity for peak I showed that its activation energy is 0.7 eV, consistent with the activation energy of the normal TL for peak I. The PTTL intensity from peak I fades rapidly with storage compared with the thermal fading from peak I of the normal TL. The PTTL intensity for peak I decreases as a function of heating rate. This decrease was attributed to thermal quenching. Thermal quenching was not observed in the case of the normal TL intensity. The cause of this contrast requires further study.
- Full Text:
Towards understanding the effects of stocking density on farmed South African abalone, Haliotis Midae
- Authors: Nicholson, Gareth Hurst
- Date: 2014
- Subjects: Haliotis midae -- South Africa , Haliotis midae fisheries -- South Africa , Abalones -- South Africa , Fish stocking -- South Africa , Abalone populations -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5371 , http://hdl.handle.net/10962/d1015646
- Description: The profitability of abalone farms is heavily influenced by their production per unit of grow-out space. With farms having physically expanded to the maximum, and with increasing production costs, one of the most realistic ways for farms to increase their production is through optimizing stocking densities. The effect of stocking density on Haliotis midae performance is undocumented and optimal stocking densities for this species have not been determined. Experiments were conducted under farm conditions to investigate the effects of four different stocking densities (16 %, 20 %, 22 % and 24 % of available surface area) on growth, production and health of three different size classes of abalone (15-35 g, 45-65 g, and 70-90 g start weight). Each treatment was replicated four times and trials ran over a period of eight months with measurements being made at four month intervals. Abalone behaviour was observed during the trials in the experimental tanks. Weight gain per abalone decreased with an increase in density for all tested size classes (5.04 ± 0.18 to 2.38 ± 0.17; 5.35 ± 0.21 to 4.62 ± 0.29; 7.97 ± 0.37 to 6.53 ± 0.28 g.abalone-1.month-1 for the 15-35, 45-65 and 70-90 g classes respectively, with an increased density of 16 to 24 %). Individual weight gain of 15-35 g abalone was similar at stocking densities of 16 % and 20 % while weight gain of 45-65 g and 70-90 g abalone decreased when density was increased above 16 %. Biomass gain (kg.basket-1.month-1) was not affected by stocking density in the 15-35 g and 45-65 g size classes (1.29 ± 0.02 and 0.97 ± 0.02 kg.basket-1.month-1 respectively). However, the biomass gained by baskets stocked with 70-90 g abalone increased with stocking density (1.08 ± 0.02 to 1.33 ± 0.02 kg.basket-1.month-1) with an increased density of 16 to 24 %) and did not appear to plateau within the tested density range (16 to 24 %). Food conversion ratio did not differ significantly between densities across all size classes. Stocking density did not have a significant effect on abalone condition factor or health indices. The proportion of abalone above the level of the feeder plate increased with density (7.26 ± 1.33 to 16.44 ± 1.33 with an increased density of 16 to 24 %). As a proportion of abalone situated in the area of the basket, the same proportions were situated on the walls above the feeder plate and on the feeder plate itself irrespective of stocking density (p > 0.05). Higher proportions of animals had restricted access to feed at higher stocking densities (p = 0.03). The amount of formulated feed available on the feeder plate did not differ between stocking densities throughout the night (p = 0.19). Individual abalone spent more time above the feeder plate at higher stocking densities (p < 0.05). The percentage of time above the feeder plate, spent on the walls of the basket and on the feeding surface was not significantly different at densities of 20 %, 22 % and 24 % (p > 0.05) but abalone stocked at 16 % spent a greater percentage of time above the feeder plate on the feeding surface (83.99 ± 6.26 %) than on the basket walls (16.01 ± 6.26 %). Stocking density did not affect the positioning of abalone within a basket during the day or at night. Different size H. midae are affected differently by increases in stocking density in terms of growth performance. Findings from this research may be implemented into farm management strategies to best suit production goals, whether in terms of biomass production or individual weight gain. The fundamental mechanisms resulting in reduced growth at higher densities are not well understood, however results from behaviour observations suggest that competition for preferred attachment space and feed availability are contributing to decreased growth rates. With knowledge of abalone behaviour at different densities, innovative tank designs may be established in order to counter the reduction in growth at higher densities.
- Full Text:
- Authors: Nicholson, Gareth Hurst
- Date: 2014
- Subjects: Haliotis midae -- South Africa , Haliotis midae fisheries -- South Africa , Abalones -- South Africa , Fish stocking -- South Africa , Abalone populations -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5371 , http://hdl.handle.net/10962/d1015646
- Description: The profitability of abalone farms is heavily influenced by their production per unit of grow-out space. With farms having physically expanded to the maximum, and with increasing production costs, one of the most realistic ways for farms to increase their production is through optimizing stocking densities. The effect of stocking density on Haliotis midae performance is undocumented and optimal stocking densities for this species have not been determined. Experiments were conducted under farm conditions to investigate the effects of four different stocking densities (16 %, 20 %, 22 % and 24 % of available surface area) on growth, production and health of three different size classes of abalone (15-35 g, 45-65 g, and 70-90 g start weight). Each treatment was replicated four times and trials ran over a period of eight months with measurements being made at four month intervals. Abalone behaviour was observed during the trials in the experimental tanks. Weight gain per abalone decreased with an increase in density for all tested size classes (5.04 ± 0.18 to 2.38 ± 0.17; 5.35 ± 0.21 to 4.62 ± 0.29; 7.97 ± 0.37 to 6.53 ± 0.28 g.abalone-1.month-1 for the 15-35, 45-65 and 70-90 g classes respectively, with an increased density of 16 to 24 %). Individual weight gain of 15-35 g abalone was similar at stocking densities of 16 % and 20 % while weight gain of 45-65 g and 70-90 g abalone decreased when density was increased above 16 %. Biomass gain (kg.basket-1.month-1) was not affected by stocking density in the 15-35 g and 45-65 g size classes (1.29 ± 0.02 and 0.97 ± 0.02 kg.basket-1.month-1 respectively). However, the biomass gained by baskets stocked with 70-90 g abalone increased with stocking density (1.08 ± 0.02 to 1.33 ± 0.02 kg.basket-1.month-1) with an increased density of 16 to 24 %) and did not appear to plateau within the tested density range (16 to 24 %). Food conversion ratio did not differ significantly between densities across all size classes. Stocking density did not have a significant effect on abalone condition factor or health indices. The proportion of abalone above the level of the feeder plate increased with density (7.26 ± 1.33 to 16.44 ± 1.33 with an increased density of 16 to 24 %). As a proportion of abalone situated in the area of the basket, the same proportions were situated on the walls above the feeder plate and on the feeder plate itself irrespective of stocking density (p > 0.05). Higher proportions of animals had restricted access to feed at higher stocking densities (p = 0.03). The amount of formulated feed available on the feeder plate did not differ between stocking densities throughout the night (p = 0.19). Individual abalone spent more time above the feeder plate at higher stocking densities (p < 0.05). The percentage of time above the feeder plate, spent on the walls of the basket and on the feeding surface was not significantly different at densities of 20 %, 22 % and 24 % (p > 0.05) but abalone stocked at 16 % spent a greater percentage of time above the feeder plate on the feeding surface (83.99 ± 6.26 %) than on the basket walls (16.01 ± 6.26 %). Stocking density did not affect the positioning of abalone within a basket during the day or at night. Different size H. midae are affected differently by increases in stocking density in terms of growth performance. Findings from this research may be implemented into farm management strategies to best suit production goals, whether in terms of biomass production or individual weight gain. The fundamental mechanisms resulting in reduced growth at higher densities are not well understood, however results from behaviour observations suggest that competition for preferred attachment space and feed availability are contributing to decreased growth rates. With knowledge of abalone behaviour at different densities, innovative tank designs may be established in order to counter the reduction in growth at higher densities.
- Full Text:
Trends in the fish assemblage structure of two South African transition-zone estuaries : can these trends be linked to climate change?
- Authors: Midgley, Craig
- Date: 2014
- Subjects: Estuarine fishes -- South Africa -- Climatic factors , Fish communities -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5368 , http://hdl.handle.net/10962/d1013173
- Description: Changes in the fish communities of the Breede and Mbashe estuaries were investigated in relation to the environmental variables that influence the fish assemblages in these systems. The Breede Estuary (34° 24’21.6”S, 20° 51’ 08.2”E) occurs within the warm-temperate/cool-temperate transition-zone, while the Mbashe Estuary (32o 14' 55.4"S, 28o 54' 03.7"E) falls within the subtropical/warm-temperate transition-zone along the South African coastline. The Breede Estuary was sampled (seine and gill nets) during summer (January-March) over a period of 10 years (2002-2012), while the Mbashe Estuary was sampled (seine net) during spring (October) over a period of three years (2010-2012). The proportion of tropical fish species was higher in the Mbashe Estuary compared to the Breede Estuary, while the Breede Estuary contained a higher proportion of temperate species than the Mbashe Estuary. Although the abundance of individual species in both estuaries varied, the ranking of species in the Breede Estuary was stable over the 10 year period. Multivariate analysis showed that the fish communities within each reach (upper, middle, lower) of the Breede Estuary remained similar, regardless of year. In contrast, species composition in the Mbashe Estuary differed significantly between years mainly due to differences in the river flow regime during the study period. Environmental variables responsible for structuring the fish assemblage in each estuary differed. Salinity significantly impacted the spatial fish assemblage structure of the Breede Estuary, with most of the species recorded being associated with the more saline lower reaches. The abundance of tropical species near their distributional limit in the Breede Estuary appeared to be impacted by sea surface temperature (SST) as peak total abundance of these species coincided with the warmest SST, while the lowest total abundance coincided with the coldest annual SST during the study period. The fish assemblage structure in the Mbashe Estuary was impacted by differing freshwater input prior to sampling, with flooding negatively impacting the mean total abundance, species composition and diversity in this system. The variables that influenced the fish assemblage structure of both transition-zone estuaries will be affected by climate change in the future. These variables will, in turn, determine the composition, abundance and diversity of species within these important estuarine systems. In order to measure these impacts with any degree of understanding, long-term studies on the abiotic and biotic (including the ichthyofauna) features of these estuaries are required to interpret climate change trends.
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- Authors: Midgley, Craig
- Date: 2014
- Subjects: Estuarine fishes -- South Africa -- Climatic factors , Fish communities -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5368 , http://hdl.handle.net/10962/d1013173
- Description: Changes in the fish communities of the Breede and Mbashe estuaries were investigated in relation to the environmental variables that influence the fish assemblages in these systems. The Breede Estuary (34° 24’21.6”S, 20° 51’ 08.2”E) occurs within the warm-temperate/cool-temperate transition-zone, while the Mbashe Estuary (32o 14' 55.4"S, 28o 54' 03.7"E) falls within the subtropical/warm-temperate transition-zone along the South African coastline. The Breede Estuary was sampled (seine and gill nets) during summer (January-March) over a period of 10 years (2002-2012), while the Mbashe Estuary was sampled (seine net) during spring (October) over a period of three years (2010-2012). The proportion of tropical fish species was higher in the Mbashe Estuary compared to the Breede Estuary, while the Breede Estuary contained a higher proportion of temperate species than the Mbashe Estuary. Although the abundance of individual species in both estuaries varied, the ranking of species in the Breede Estuary was stable over the 10 year period. Multivariate analysis showed that the fish communities within each reach (upper, middle, lower) of the Breede Estuary remained similar, regardless of year. In contrast, species composition in the Mbashe Estuary differed significantly between years mainly due to differences in the river flow regime during the study period. Environmental variables responsible for structuring the fish assemblage in each estuary differed. Salinity significantly impacted the spatial fish assemblage structure of the Breede Estuary, with most of the species recorded being associated with the more saline lower reaches. The abundance of tropical species near their distributional limit in the Breede Estuary appeared to be impacted by sea surface temperature (SST) as peak total abundance of these species coincided with the warmest SST, while the lowest total abundance coincided with the coldest annual SST during the study period. The fish assemblage structure in the Mbashe Estuary was impacted by differing freshwater input prior to sampling, with flooding negatively impacting the mean total abundance, species composition and diversity in this system. The variables that influenced the fish assemblage structure of both transition-zone estuaries will be affected by climate change in the future. These variables will, in turn, determine the composition, abundance and diversity of species within these important estuarine systems. In order to measure these impacts with any degree of understanding, long-term studies on the abiotic and biotic (including the ichthyofauna) features of these estuaries are required to interpret climate change trends.
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Validation of an assessment tool for mental fatigue applied to rotational shift work
- Authors: Huysamen, Kirsten Christina
- Date: 2014
- Subjects: Mental fatigue , Shift systems , Performance , Motor ability , Memory
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5154 , http://hdl.handle.net/10962/d1013551
- Description: Mental fatigue has been proven to be highly prominent during shift work, due to long, irregular working hours and disruption of the circadian rhythm. Measuring mental fatigue has been a challenge for many years, where commonly cognitive test tasks are used to assess mental fatigue. Moreover, these test tasks do not isolate where fatigue is occurring during human information processing. The human information processing system consists of four core stages, each of which requires numerous cognitive functions in order to process information. The Human Kinetics and Ergonomics Department at Rhodes University has developed six cognitive test tasks where each isolates a cognitive function: an accommodation test task, a visual detection test task, a reading test task, a memory test task, a tapping test task and a neural control test task. The cognitive functions include: eye accommodation, visual discrimination, visual pattern recognition, memory duration, motor programming and peripheral neural control. General task-related effect can also be examined for each of these cognitive test tasks which include choice reaction time, visual detection, reading performance, short-term memory, motor control and tracking performance. Additionally, a simple reaction time test task has been developed to analyse simple reaction time. This test task does not isolate a cognitive function. One or more parameters can be examined for each cognitive function and task-related effect. The first aim of this study was to validate numerous cognitive test tasks for mental fatigue in a simulated shift work laboratory setting. The second aim was to assess the validated cognitive test tasks in Phase 1 in a field-based rotational shift work setting. Parameters revealing sensitivity to mental fatigue would be validated for mental fatigue applied to rotational shift work and would be inserted into an assessment tool. In the laboratory setting, the seven cognitive test tasks were examined on four different types of shift work regimes. The first regime was a standard eight-hour shift work system, and the other three were non-conventional shift work regimes. Participants (n = 12 per regime) were required to complete one day shift followed by four night shifts, where testing occurred before and after each shift and four times within each shift. The cognitive test tasks revealing sensitivity to fatigue included: visual detection test task, reading test task, memory test task, tapping test task, neural control test task and simple reaction time test task. The testing of Phase 2 was conducted in three different companies, where each performed a different type of rotational shift work. The six cognitive test tasks validated for mental fatigue in Phase 1 were tested before and after work for each shift type within the rotational shift work system adopted by each company. Company A (n = 18) and Company B (n = 24) performed two-shift rotational shift work systems, where the shift length of Company A was 12-hours and the shift length of Company B was irregular hours. Company C (n = 21) performed an eight-hour three-shift rotational shift work system. Nine parameters revealed fatiguing effects and were inserted into the assessment tool, five of which provided information on a specific cognitive function: error rate for visual discrimination, processing time for visual pattern recognition, error rate for visual pattern recognition, impact of rehearsal time on memory recall rate for memory duration and the high-precision condition for motor programming time. The remaining four parameters provided information on general task-related effects: reading speed for reading performance, recall rate for short-term memory, reaction time for motor control and simple reaction time. Therefore, an assessment tool comprising nine parameters was validated for mental fatigue applied to rotational shift work, where five of the parameters were able to isolate exactly where fatigue was occurring during human information processing and the other four parameters were able to assess fatigue occurring throughout the human information processing chain.
- Full Text:
- Authors: Huysamen, Kirsten Christina
- Date: 2014
- Subjects: Mental fatigue , Shift systems , Performance , Motor ability , Memory
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5154 , http://hdl.handle.net/10962/d1013551
- Description: Mental fatigue has been proven to be highly prominent during shift work, due to long, irregular working hours and disruption of the circadian rhythm. Measuring mental fatigue has been a challenge for many years, where commonly cognitive test tasks are used to assess mental fatigue. Moreover, these test tasks do not isolate where fatigue is occurring during human information processing. The human information processing system consists of four core stages, each of which requires numerous cognitive functions in order to process information. The Human Kinetics and Ergonomics Department at Rhodes University has developed six cognitive test tasks where each isolates a cognitive function: an accommodation test task, a visual detection test task, a reading test task, a memory test task, a tapping test task and a neural control test task. The cognitive functions include: eye accommodation, visual discrimination, visual pattern recognition, memory duration, motor programming and peripheral neural control. General task-related effect can also be examined for each of these cognitive test tasks which include choice reaction time, visual detection, reading performance, short-term memory, motor control and tracking performance. Additionally, a simple reaction time test task has been developed to analyse simple reaction time. This test task does not isolate a cognitive function. One or more parameters can be examined for each cognitive function and task-related effect. The first aim of this study was to validate numerous cognitive test tasks for mental fatigue in a simulated shift work laboratory setting. The second aim was to assess the validated cognitive test tasks in Phase 1 in a field-based rotational shift work setting. Parameters revealing sensitivity to mental fatigue would be validated for mental fatigue applied to rotational shift work and would be inserted into an assessment tool. In the laboratory setting, the seven cognitive test tasks were examined on four different types of shift work regimes. The first regime was a standard eight-hour shift work system, and the other three were non-conventional shift work regimes. Participants (n = 12 per regime) were required to complete one day shift followed by four night shifts, where testing occurred before and after each shift and four times within each shift. The cognitive test tasks revealing sensitivity to fatigue included: visual detection test task, reading test task, memory test task, tapping test task, neural control test task and simple reaction time test task. The testing of Phase 2 was conducted in three different companies, where each performed a different type of rotational shift work. The six cognitive test tasks validated for mental fatigue in Phase 1 were tested before and after work for each shift type within the rotational shift work system adopted by each company. Company A (n = 18) and Company B (n = 24) performed two-shift rotational shift work systems, where the shift length of Company A was 12-hours and the shift length of Company B was irregular hours. Company C (n = 21) performed an eight-hour three-shift rotational shift work system. Nine parameters revealed fatiguing effects and were inserted into the assessment tool, five of which provided information on a specific cognitive function: error rate for visual discrimination, processing time for visual pattern recognition, error rate for visual pattern recognition, impact of rehearsal time on memory recall rate for memory duration and the high-precision condition for motor programming time. The remaining four parameters provided information on general task-related effects: reading speed for reading performance, recall rate for short-term memory, reaction time for motor control and simple reaction time. Therefore, an assessment tool comprising nine parameters was validated for mental fatigue applied to rotational shift work, where five of the parameters were able to isolate exactly where fatigue was occurring during human information processing and the other four parameters were able to assess fatigue occurring throughout the human information processing chain.
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Web-based M-learning system for ad-hoc learning of mathematical concepts amongst first year students at the University of Namibia
- Authors: Ntinda, Maria Ndapewa
- Date: 2014
- Subjects: Mathematics -- Study and teaching (Higher) -- Namibia , Mathematics -- Technological innovations , Mobile communication systems in education , Teaching -- Aids and devices , Educational innovations , Open source software
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4701 , http://hdl.handle.net/10962/d1013174
- Description: In the last decade, there has been an increase in the number of web-enabled mobile devices, offering a new platform that can be targeted for the development of learning applications. Worldwide, developers have taken initiatives in developing mobile learning (M-learning) systems to provide students with access to learning materials regardless of time and location. The purpose of this study was to investigate whether it is viable for first year students enrolled at the University of Namibia (UNAM) to use mobile phones for ad-hoc learning of mathematical concepts. A system, EnjoyMath, aiming to assist students in preparing for tests, examinations, review contents and reinforce knowledge acquired during traditional classroom interactions was designed and implemented. The EnjoyMath system was designed and implemented through the use of the Human Centred Design (HCD) methodology. Two revolutions of the four-step process of the HCD cycle were completed in this study. Due to the distance between UNAM and Rhodes University (where the researcher was based), the researcher could not always work in close relation with the UNAM students. Students from the Extended Study Unit (ESU) at Rhodes University were therefore selected in the first iteration of the project due to their proximity to the researcher and their similar demographics to the first year UNAM students, while the UNAM students were targeted in the second iteration of the study. This thesis presents the outcome of the two pre-intervention studies of the first-year students' perceptions about M-learning conducted at Rhodes University and UNAM. The results of the pre-intervention studies showed that the students are enthusiastic about using an M-learning system, because it would allow them to put in more time to practice their skills whenever and wherever they are. Moreover, the thesis presents the different stages undertaken to develop the EnjoyMath system using Open Source Software (PHP and MySQL). The results of a user study (post-intervention) conducted with participants at UNAM, ascertained the participants' perception of the usability of the EnjoyMath system and are also presented in this thesis. The EnjoyMath system was perceived by the participants to be "passable"; hence an M-learning system could be used to compliment an E-learning system at UNAM.
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- Authors: Ntinda, Maria Ndapewa
- Date: 2014
- Subjects: Mathematics -- Study and teaching (Higher) -- Namibia , Mathematics -- Technological innovations , Mobile communication systems in education , Teaching -- Aids and devices , Educational innovations , Open source software
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4701 , http://hdl.handle.net/10962/d1013174
- Description: In the last decade, there has been an increase in the number of web-enabled mobile devices, offering a new platform that can be targeted for the development of learning applications. Worldwide, developers have taken initiatives in developing mobile learning (M-learning) systems to provide students with access to learning materials regardless of time and location. The purpose of this study was to investigate whether it is viable for first year students enrolled at the University of Namibia (UNAM) to use mobile phones for ad-hoc learning of mathematical concepts. A system, EnjoyMath, aiming to assist students in preparing for tests, examinations, review contents and reinforce knowledge acquired during traditional classroom interactions was designed and implemented. The EnjoyMath system was designed and implemented through the use of the Human Centred Design (HCD) methodology. Two revolutions of the four-step process of the HCD cycle were completed in this study. Due to the distance between UNAM and Rhodes University (where the researcher was based), the researcher could not always work in close relation with the UNAM students. Students from the Extended Study Unit (ESU) at Rhodes University were therefore selected in the first iteration of the project due to their proximity to the researcher and their similar demographics to the first year UNAM students, while the UNAM students were targeted in the second iteration of the study. This thesis presents the outcome of the two pre-intervention studies of the first-year students' perceptions about M-learning conducted at Rhodes University and UNAM. The results of the pre-intervention studies showed that the students are enthusiastic about using an M-learning system, because it would allow them to put in more time to practice their skills whenever and wherever they are. Moreover, the thesis presents the different stages undertaken to develop the EnjoyMath system using Open Source Software (PHP and MySQL). The results of a user study (post-intervention) conducted with participants at UNAM, ascertained the participants' perception of the usability of the EnjoyMath system and are also presented in this thesis. The EnjoyMath system was perceived by the participants to be "passable"; hence an M-learning system could be used to compliment an E-learning system at UNAM.
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