An investigation of the XMOS XSl architecture as a platform for development of audio control standards
- Authors: Dibley, James
- Date: 2014
- Subjects: Microcontrollers -- Research , Streaming audio -- Standards -- Research , Computer sound processing -- Research , Computer network protocols -- Standards -- Research , Communication -- Technological innovations -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4694 , http://hdl.handle.net/10962/d1011789 , Microcontrollers -- Research , Streaming audio -- Standards -- Research , Computer sound processing -- Research , Computer network protocols -- Standards -- Research , Communication -- Technological innovations -- Research
- Description: This thesis investigates the feasiblity of using a new microcontroller architecture, the XMOS XS1, in the research and development of control standards for audio distribution networks. This investigation is conducted in the context of an emerging audio distribution network standard, Ethernet Audio/Video Bridging (`Ethernet AVB'), and an emerging audio control standard, AES-64. The thesis describes these emerging standards, the XMOS XS1 architecture (including its associated programming language, XC), and the open-source implementation of an Ethernet AVB streaming audio device based on the XMOS XS1 architecture. It is shown how the XMOS XS1 architecture and its associated features, focusing on the XC language's mechanisms for concurrency, event-driven programming, and integration of C software modules, enable a powerful implementation of the AES-64 control standard. Feasibility is demonstrated by the implementation of an AES-64 protocol stack and its integration into an XMOS XS1-based Ethernet AVB streaming audio device, providing control of Ethernet AVB features and audio hardware, as well as implementations of advanced AES-64 control mechanisms. It is demonstrated that the XMOS XS1 architecture is a compelling platform for the development of audio control standards, and has enabled the implementation of AES-64 connection management and control over standards-compliant Ethernet AVB streaming audio devices where no such implementation previously existed. The research additionally describes a linear design method for applications based on the XMOS XS1 architecture, and provides a baseline implementation reference for the AES-64 control standard where none previously existed.
- Full Text:
- Authors: Dibley, James
- Date: 2014
- Subjects: Microcontrollers -- Research , Streaming audio -- Standards -- Research , Computer sound processing -- Research , Computer network protocols -- Standards -- Research , Communication -- Technological innovations -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4694 , http://hdl.handle.net/10962/d1011789 , Microcontrollers -- Research , Streaming audio -- Standards -- Research , Computer sound processing -- Research , Computer network protocols -- Standards -- Research , Communication -- Technological innovations -- Research
- Description: This thesis investigates the feasiblity of using a new microcontroller architecture, the XMOS XS1, in the research and development of control standards for audio distribution networks. This investigation is conducted in the context of an emerging audio distribution network standard, Ethernet Audio/Video Bridging (`Ethernet AVB'), and an emerging audio control standard, AES-64. The thesis describes these emerging standards, the XMOS XS1 architecture (including its associated programming language, XC), and the open-source implementation of an Ethernet AVB streaming audio device based on the XMOS XS1 architecture. It is shown how the XMOS XS1 architecture and its associated features, focusing on the XC language's mechanisms for concurrency, event-driven programming, and integration of C software modules, enable a powerful implementation of the AES-64 control standard. Feasibility is demonstrated by the implementation of an AES-64 protocol stack and its integration into an XMOS XS1-based Ethernet AVB streaming audio device, providing control of Ethernet AVB features and audio hardware, as well as implementations of advanced AES-64 control mechanisms. It is demonstrated that the XMOS XS1 architecture is a compelling platform for the development of audio control standards, and has enabled the implementation of AES-64 connection management and control over standards-compliant Ethernet AVB streaming audio devices where no such implementation previously existed. The research additionally describes a linear design method for applications based on the XMOS XS1 architecture, and provides a baseline implementation reference for the AES-64 control standard where none previously existed.
- Full Text:
Analysis of the interaction of Hsp90 with the extracellular matrix protein fibronectin (FN)
- Authors: Hunter, Morgan Campbell
- Date: 2014
- Subjects: Heat shock proteins , Fibronectins , Extracellular matrix proteins , Breast -- Cancer
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4170 , http://hdl.handle.net/10962/d1020960
- Description: Mounting evidence suggests that Hsp90 is present and functionally active in the extracellular space. The biological function of extracellular Hsp90 (eHsp90) remains relatively uncharacterized compared to that of intracellular Hsp90. eHsp90 has been shown to interact with a finite number of extracellular proteins, however, despite the identification of eHsp90 interacting proteins, the function of eHsp90 in these complexes is unknown. Several reports suggest a role for eHsp90α in cell migration and invasion. Reported targets for eHsp90 stimulated cell migration include MMPs, LRP-1, tyrosine kinase receptors and possible others unidentified. Limited studies report a role for eHsp90β. Recently, Hsp90α and Hsp90β were isolated in a complex containing fibronectin (FN) on the surface of MDA-MB-231 breast cancer cells. Herein, we report direct binding of Hsp90α and Hsp90β to FN using a solid phase binding assay and surface plasmon resonance (SPR) spectroscopy. SPR spectroscopy showed that Hsp90β bound the 70 kDa amino-terminal fragment of FN (FN70), but that binding of FN to Hsp90β was not limited to FN70. Confocal microscopy showed regions of colocalization of Hsp90 with extracellular FN matrix fibrils in Hs578T breast cancer cell lines. Treatment of Hs578T breast cancer cells with novobiocin (an Hsp90 inhibitor) and an LRP-1 blocking antibody resulted in a loss of FN matrix and FN endocytosis (novobiocin treated). Addition of exogenous Hsp90β was able to recover such effect after both treatments. FN was shown to colocalize with intracellular LRP-1 in novobiocin treated Hs578T cells. Immunoprecipitation of an LRP-1 containing complex showed the presence of Hsp90 and 70 and 120+ kDa FN fragments. Treatment of Hs578T cells with novobiocin increased the level of FN120+ bound in LRP-1 immunoprecipitate. Exogenous Hsp90β decreased the level of low and high molecular weight FN fragments in a complex with LRP-1, despite the fact that higher levels of lower molecular weight FN fragments were detected in this cell lysate compared to the other treatments. We report FN as a novel interacting protein of eHsp90. Taken together, we provide evidence for a direct role of eHsp90β in FN matrix remodeling. We suggest that Hsp90 plays a direct role in FN matrix dynamics through interaction with FN and LRP-1. The identification of FN as a novel interacting protein of eHsp90 suggests a role for Hsp90 in FN matrix remodeling, which is important for a number of fundamental cellular processes including cell migration and metastasis.
- Full Text:
- Authors: Hunter, Morgan Campbell
- Date: 2014
- Subjects: Heat shock proteins , Fibronectins , Extracellular matrix proteins , Breast -- Cancer
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4170 , http://hdl.handle.net/10962/d1020960
- Description: Mounting evidence suggests that Hsp90 is present and functionally active in the extracellular space. The biological function of extracellular Hsp90 (eHsp90) remains relatively uncharacterized compared to that of intracellular Hsp90. eHsp90 has been shown to interact with a finite number of extracellular proteins, however, despite the identification of eHsp90 interacting proteins, the function of eHsp90 in these complexes is unknown. Several reports suggest a role for eHsp90α in cell migration and invasion. Reported targets for eHsp90 stimulated cell migration include MMPs, LRP-1, tyrosine kinase receptors and possible others unidentified. Limited studies report a role for eHsp90β. Recently, Hsp90α and Hsp90β were isolated in a complex containing fibronectin (FN) on the surface of MDA-MB-231 breast cancer cells. Herein, we report direct binding of Hsp90α and Hsp90β to FN using a solid phase binding assay and surface plasmon resonance (SPR) spectroscopy. SPR spectroscopy showed that Hsp90β bound the 70 kDa amino-terminal fragment of FN (FN70), but that binding of FN to Hsp90β was not limited to FN70. Confocal microscopy showed regions of colocalization of Hsp90 with extracellular FN matrix fibrils in Hs578T breast cancer cell lines. Treatment of Hs578T breast cancer cells with novobiocin (an Hsp90 inhibitor) and an LRP-1 blocking antibody resulted in a loss of FN matrix and FN endocytosis (novobiocin treated). Addition of exogenous Hsp90β was able to recover such effect after both treatments. FN was shown to colocalize with intracellular LRP-1 in novobiocin treated Hs578T cells. Immunoprecipitation of an LRP-1 containing complex showed the presence of Hsp90 and 70 and 120+ kDa FN fragments. Treatment of Hs578T cells with novobiocin increased the level of FN120+ bound in LRP-1 immunoprecipitate. Exogenous Hsp90β decreased the level of low and high molecular weight FN fragments in a complex with LRP-1, despite the fact that higher levels of lower molecular weight FN fragments were detected in this cell lysate compared to the other treatments. We report FN as a novel interacting protein of eHsp90. Taken together, we provide evidence for a direct role of eHsp90β in FN matrix remodeling. We suggest that Hsp90 plays a direct role in FN matrix dynamics through interaction with FN and LRP-1. The identification of FN as a novel interacting protein of eHsp90 suggests a role for Hsp90 in FN matrix remodeling, which is important for a number of fundamental cellular processes including cell migration and metastasis.
- Full Text:
Analysis of transcription factor binding specificity using ChIP-seq data.
- Authors: Kibet, Caleb Kipkurui
- Date: 2014
- Subjects: Transcription factors , Chronic myeloid leukemia , Antioncogenes , Cancer cells -- Growth -- Regulation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4115 , http://hdl.handle.net/10962/d1013131
- Description: Transcription factors (TFs) are key regulators of gene expression whose failure has been implicated in many diseases, including cancer. They bind at various sites at different specificity depending on the prevailing cellular conditions, disease, development stage or environmental conditions of the cell. TF binding specificity is how well a TF distinguishes functional sites from potential non-functional sites to form a useful regulatory network. Owing to its role in diseases, various techniques have been used to determine TF binding specificity in vitro and in vivo, including chromatin immuno-precipitation followed by massively parallel sequencing (ChIP-seq). ChIP-seq is an in vivo technique that considers how the chromatin landscape affects TF binding. Motif enrichment analysis (MEA) tools are used to identify motifs that are over-represented in ChIP-seq peak regions. One such tool, CentriMo, finds over-represented motifs at the center since peak calling software are biased to declaring binding regions centered at the TF binding site. In this study, we investigate the use of CentriMo and other MEA tools to determine the difference in motif enrichment attributed presence of Chronic Myeloid leukemia (CML)), treatment with Interferon (IFN) and Dexamethasone (DEX) compared to control based on Fisher’s exact test; using uniform peaks ChIP-seq data generated by the ENCODE consortium. CentriMo proved to be capable. We observed differential motif enrichment of TFs with tumor promoter activity: YY1, CEBPA, Egr1, Cmyc family, Gata1 and JunD in K562 while Stat1, Irf1, and Runx1 in Gm12878. Enrichment of CTCF in Gm12878 with YY1 as the immuno-precipitated (ChIP-ed) factor and the presence of significant spacing (SpaMo analysis) of CTCF and YY1 in Gm12878 but not in K562 could show that CTCF, as a repressor, helps in maintaining the required YY1 level in a normal cell line. IFN might reduce Cmyc and the Jun family of TFs binding via the repressive action of CTCF and E2f2. We also show that the concentration of DEX treatment affects motif enrichment with 50nm being an optimum concentration for Gr binding by maintaining open chromatin via AP1 TF. This study has demonstrated the usefulness of CentriMo for TF binding specificity analysis.
- Full Text:
- Authors: Kibet, Caleb Kipkurui
- Date: 2014
- Subjects: Transcription factors , Chronic myeloid leukemia , Antioncogenes , Cancer cells -- Growth -- Regulation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4115 , http://hdl.handle.net/10962/d1013131
- Description: Transcription factors (TFs) are key regulators of gene expression whose failure has been implicated in many diseases, including cancer. They bind at various sites at different specificity depending on the prevailing cellular conditions, disease, development stage or environmental conditions of the cell. TF binding specificity is how well a TF distinguishes functional sites from potential non-functional sites to form a useful regulatory network. Owing to its role in diseases, various techniques have been used to determine TF binding specificity in vitro and in vivo, including chromatin immuno-precipitation followed by massively parallel sequencing (ChIP-seq). ChIP-seq is an in vivo technique that considers how the chromatin landscape affects TF binding. Motif enrichment analysis (MEA) tools are used to identify motifs that are over-represented in ChIP-seq peak regions. One such tool, CentriMo, finds over-represented motifs at the center since peak calling software are biased to declaring binding regions centered at the TF binding site. In this study, we investigate the use of CentriMo and other MEA tools to determine the difference in motif enrichment attributed presence of Chronic Myeloid leukemia (CML)), treatment with Interferon (IFN) and Dexamethasone (DEX) compared to control based on Fisher’s exact test; using uniform peaks ChIP-seq data generated by the ENCODE consortium. CentriMo proved to be capable. We observed differential motif enrichment of TFs with tumor promoter activity: YY1, CEBPA, Egr1, Cmyc family, Gata1 and JunD in K562 while Stat1, Irf1, and Runx1 in Gm12878. Enrichment of CTCF in Gm12878 with YY1 as the immuno-precipitated (ChIP-ed) factor and the presence of significant spacing (SpaMo analysis) of CTCF and YY1 in Gm12878 but not in K562 could show that CTCF, as a repressor, helps in maintaining the required YY1 level in a normal cell line. IFN might reduce Cmyc and the Jun family of TFs binding via the repressive action of CTCF and E2f2. We also show that the concentration of DEX treatment affects motif enrichment with 50nm being an optimum concentration for Gr binding by maintaining open chromatin via AP1 TF. This study has demonstrated the usefulness of CentriMo for TF binding specificity analysis.
- Full Text:
Assessing the genetic diversity of catface rockcod epinephelus andersoni in the subtropical Western Indian Ocean and modelling the effects of climate change on their distribution
- Authors: Coppinger, Christine Rose
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54499 , vital:26570
- Description: The catface rockcod Epinephelus andersoni is a range-restricted species that is endemic to the southeast coast of Africa from Quissico in Mozambique (subtropical) to Knysna in South Africa (warmtemperate). Its complex life-history, long-lived nature and high residency make E. andersoni potentially vulnerable to over-exploitation. Epinephelus andersoni is an important fishery species and has shown signs of depletion. Due to inadequate information necessary for management and conservation, further research is vital, particularly in the face of potentially significant climatic changes which could put further pressure on E. andersoni. The aim of the study was to provide information for the management of E. andersoni, with considerations for the possibly detrimental effects of future climate change. The objectives of this study were to describe the genetic structure and diversity of E. andersoni and to determine possible range shifts of E. andersoni with future changes in sea surface temperature. Genetic samples were collected throughout the distribution of E. andersoni. Standard DNA extraction and PCR using universal primers were conducted and nuclear (RPS7-1) and mitochondrial (cytochrome b) data were analysed to determine genetic diversity. A combination of nuclear and mitochondrial markers was used to ensure that the results were robust. RPS7-1 haplotype diversity was high (0.801) and an AMOVA on the RPS7-1 data showed significantly high among group variation (ΦCT = 0.204, p < 0.05) between five groups: 1. Quissico to Inhaca; 2. Cape Vidal to Port Edward; 3 Port St Johns to Coffee Bay; 4. Mbashe; 5. Port Alfred. This geographic structuring could be attributed to low gene flow across barriers such as the Port Alfred upwelling cell, the Mozambique Channel eddies and smaller more localised upwelling cells such as the Port St Johns cell. The cytochrome b results contrastingly indicate low haplotype diversity (0.309) and no differentiation (ΦCT = 0.265, p = 0.074) between groups and support the hypothesis of a historical population bottleneck. This may be due to an unusually slower mutation rate of the cytochrome b region than the RPS7-1 region, resulting in the RPS7-1 data showing a more recent picture of diversification. To complement the genetic results, niche modelling techniques were used to determine range shifts of E. andersoni with future temperature trends using species distribution and climatic data. The model illustrated a contraction of the E. andersoni distribution as well as future intensification of various upwelling cells along the south-east African coast including the Port Alfred upwelling cell. Due to the low gene flow across these barriers this intensification could decrease the resilience of E. andersoni, as its range becomes more limited with global change. The genetic data and modelling results combined provide useful information on which to base future fisheries management.
- Full Text:
- Authors: Coppinger, Christine Rose
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54499 , vital:26570
- Description: The catface rockcod Epinephelus andersoni is a range-restricted species that is endemic to the southeast coast of Africa from Quissico in Mozambique (subtropical) to Knysna in South Africa (warmtemperate). Its complex life-history, long-lived nature and high residency make E. andersoni potentially vulnerable to over-exploitation. Epinephelus andersoni is an important fishery species and has shown signs of depletion. Due to inadequate information necessary for management and conservation, further research is vital, particularly in the face of potentially significant climatic changes which could put further pressure on E. andersoni. The aim of the study was to provide information for the management of E. andersoni, with considerations for the possibly detrimental effects of future climate change. The objectives of this study were to describe the genetic structure and diversity of E. andersoni and to determine possible range shifts of E. andersoni with future changes in sea surface temperature. Genetic samples were collected throughout the distribution of E. andersoni. Standard DNA extraction and PCR using universal primers were conducted and nuclear (RPS7-1) and mitochondrial (cytochrome b) data were analysed to determine genetic diversity. A combination of nuclear and mitochondrial markers was used to ensure that the results were robust. RPS7-1 haplotype diversity was high (0.801) and an AMOVA on the RPS7-1 data showed significantly high among group variation (ΦCT = 0.204, p < 0.05) between five groups: 1. Quissico to Inhaca; 2. Cape Vidal to Port Edward; 3 Port St Johns to Coffee Bay; 4. Mbashe; 5. Port Alfred. This geographic structuring could be attributed to low gene flow across barriers such as the Port Alfred upwelling cell, the Mozambique Channel eddies and smaller more localised upwelling cells such as the Port St Johns cell. The cytochrome b results contrastingly indicate low haplotype diversity (0.309) and no differentiation (ΦCT = 0.265, p = 0.074) between groups and support the hypothesis of a historical population bottleneck. This may be due to an unusually slower mutation rate of the cytochrome b region than the RPS7-1 region, resulting in the RPS7-1 data showing a more recent picture of diversification. To complement the genetic results, niche modelling techniques were used to determine range shifts of E. andersoni with future temperature trends using species distribution and climatic data. The model illustrated a contraction of the E. andersoni distribution as well as future intensification of various upwelling cells along the south-east African coast including the Port Alfred upwelling cell. Due to the low gene flow across these barriers this intensification could decrease the resilience of E. andersoni, as its range becomes more limited with global change. The genetic data and modelling results combined provide useful information on which to base future fisheries management.
- Full Text:
Assessment of the Lake Liambezi fishery, Zambezi region, Namibia
- Authors: Simasiku, Evans Kamwi
- Date: 2014
- Subjects: Fishery management -- Namibia -- Lake Liambezi , Seines -- Namibia -- Lake Liambezi , Gillnetting -- Namibia -- Lake Liambezi , Fishes -- Namibia -- Lake Liambezi , Fisheries -- Catch effort -- Namibia -- Lake Liambezi
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5366 , http://hdl.handle.net/10962/d1013036
- Description: Lake Liambezi in the Zambezi Region of Namibia, formerly known as the Caprivi Region, is shallow (<6m deep) and characterised by cyclic episodes of filling and drying. When full the lake supports a highly productive fishery and when dry the lake is completely dry and used for agriculture and grazing. In 2000 the lake filled, and between May 2011 and April 2012 was surveyed using beach seine, experimental gillnets and catch landing surveys to obtain information for conservation and management recommendations for the fishery. Littoral fishes in Lake Liambezi and the Kavango floodplain were sampled using seine net and physicochemical properties were measured. Seine net surveys demonstrated that Lake Liambezi littoral zones were dominated by fishes of the family Alestidae (59.7%) while Cichlids constituted the most diverse family. Juvenile Tilapia rendalli and Oreochromis macrochir were among the five most important species in the littoral zone, indicating that these commercially important species use the littoral zone as a nursery ground. Since T. rendalli and O. macrochir are commercially important species, because of this, it is advised that seine nets should not be used. Catch efficiency between monofilament and multifilament gillnets in Lake Liambezi offshore waters were assessed. Catch efficiency experimental fishing trials showed that monofilament gillnets catch per unit effort (CPUE) was three times higher than that of multifilament gillnets for Oreochromis andersonii, O. macrochir, T. rendalli, Serranochromis macrocephalus and Clarias spp. Oreochromis andersonii comprised over 66% of the overall CPUE for both net types combined indicating the importance of this species in the gillnet fishery on the lake. A fishery has been established on the lake with more than 300 canoes and 120 fishermen using monofilament and multifilament gillnets. CPUE was 15 kg/canoe/day and was significantly (P < 0.05) associated with monthly temperature and moon phase parameters indicating that the fishery of Lake Liambezi may be altered by climate and environmental factors. Annual catch from Lake Liambezi was estimated at 3193t with an estimated productivity of 106kg/ha, suggesting that Lake Liambezi makes a significant contribution to the fish supply in the Zambezi Region. Recommendations were made to manage the Lake Liambezi fishery by imposing restrictions on effort (number of fishing boats), gear type, mesh sizes and access. Proper fisheries management and monitoring should incorporate climatic and environmental factors such as temperature and moon phase to meet the challenges of global climatic changes as well as other environmental issues.
- Full Text:
- Authors: Simasiku, Evans Kamwi
- Date: 2014
- Subjects: Fishery management -- Namibia -- Lake Liambezi , Seines -- Namibia -- Lake Liambezi , Gillnetting -- Namibia -- Lake Liambezi , Fishes -- Namibia -- Lake Liambezi , Fisheries -- Catch effort -- Namibia -- Lake Liambezi
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5366 , http://hdl.handle.net/10962/d1013036
- Description: Lake Liambezi in the Zambezi Region of Namibia, formerly known as the Caprivi Region, is shallow (<6m deep) and characterised by cyclic episodes of filling and drying. When full the lake supports a highly productive fishery and when dry the lake is completely dry and used for agriculture and grazing. In 2000 the lake filled, and between May 2011 and April 2012 was surveyed using beach seine, experimental gillnets and catch landing surveys to obtain information for conservation and management recommendations for the fishery. Littoral fishes in Lake Liambezi and the Kavango floodplain were sampled using seine net and physicochemical properties were measured. Seine net surveys demonstrated that Lake Liambezi littoral zones were dominated by fishes of the family Alestidae (59.7%) while Cichlids constituted the most diverse family. Juvenile Tilapia rendalli and Oreochromis macrochir were among the five most important species in the littoral zone, indicating that these commercially important species use the littoral zone as a nursery ground. Since T. rendalli and O. macrochir are commercially important species, because of this, it is advised that seine nets should not be used. Catch efficiency between monofilament and multifilament gillnets in Lake Liambezi offshore waters were assessed. Catch efficiency experimental fishing trials showed that monofilament gillnets catch per unit effort (CPUE) was three times higher than that of multifilament gillnets for Oreochromis andersonii, O. macrochir, T. rendalli, Serranochromis macrocephalus and Clarias spp. Oreochromis andersonii comprised over 66% of the overall CPUE for both net types combined indicating the importance of this species in the gillnet fishery on the lake. A fishery has been established on the lake with more than 300 canoes and 120 fishermen using monofilament and multifilament gillnets. CPUE was 15 kg/canoe/day and was significantly (P < 0.05) associated with monthly temperature and moon phase parameters indicating that the fishery of Lake Liambezi may be altered by climate and environmental factors. Annual catch from Lake Liambezi was estimated at 3193t with an estimated productivity of 106kg/ha, suggesting that Lake Liambezi makes a significant contribution to the fish supply in the Zambezi Region. Recommendations were made to manage the Lake Liambezi fishery by imposing restrictions on effort (number of fishing boats), gear type, mesh sizes and access. Proper fisheries management and monitoring should incorporate climatic and environmental factors such as temperature and moon phase to meet the challenges of global climatic changes as well as other environmental issues.
- Full Text:
Bacterial degradation of waste coal
- Authors: Madikiza, Lwazikazi
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54576 , vital:26590
- Description: As an energy source coal has one of the largest agglomerations in the world. Consequently mining of coal creates large volumes of waste in the form of low ranks coals. The complex structure of coal makes it difficult for the microorganisms to degrade and relatively few bacteria and fungi have been shown to break down coal. This study aimed to investigate bacteria not previously known to degrade coal. In this study bacteria were isolated from hydrocarbon contaminated sites and inoculated in coal medium where coal served as the only carbon source. Three strains produced a yellow – brown supernatant after 14 d of incubation at 30 °C. Bacteria generating a yellow – brown coloured supernatant were presumed to possess coal degrading capabilities and the best performing of these bacterial species was identified using 16s rDNA as Bacillus flexus. Scanning electron microscopy showed that there was a close association between the bacterium and substrate coal. The close association of bacteria to substrate suggested that these organisms were able to maximize solubilisation. FT-IR spectroscopic analysis demonstrated the addition of single bonded compounds COOH, OH, CN and CH that were absent prior to bacterial interaction. The increase in oxygen rich regions indicated degradation of the coal substrate. Elemental analysis showed that there was a decrease in carbon content from 47 % to 24 % during the 14 day incubation period. Reduction in coal carbon content was assumed to be due to bacterial utilization for metabolism and growth particularly as untreated coal substrate showed minimal loss of carbon. Analysis of the residual culture medium revealed that there was a linear increase in humic-like substance concentration for 8 d, coincident with increased coal biosolubilisation and colour change. Laccase activity was insignificant, and at 13 d enzyme activity was only 5×10-3 U/L suggesting that B. flexus may use a different mechanism to degrade coal. Residual culture medium remaining after bacterial action on the coal substrate appeared to possess plant growth promoting activity. This soluble biodegradation product with characteristics similar to humic acid-like substances was shown to impact growth of radish cotyledons. Expansion of isolated radish cotyledons was enhanced by 140% when incubated in coal biodegradation product. In conclusion, this study has yielded B. flexus and two other unidentified bacteria, isolated from polyaromatic hydrocarbon contaminated soils, and demonstrated the ability of these microorganisms to degrade waste coal. Further studies to elucidate the mechanism of coal breakdown by B. flexus, synergies with other coal degrading microorganisms, and incorporation of bacterium into Fungcoal bioprocess technology is imminent.
- Full Text:
- Authors: Madikiza, Lwazikazi
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54576 , vital:26590
- Description: As an energy source coal has one of the largest agglomerations in the world. Consequently mining of coal creates large volumes of waste in the form of low ranks coals. The complex structure of coal makes it difficult for the microorganisms to degrade and relatively few bacteria and fungi have been shown to break down coal. This study aimed to investigate bacteria not previously known to degrade coal. In this study bacteria were isolated from hydrocarbon contaminated sites and inoculated in coal medium where coal served as the only carbon source. Three strains produced a yellow – brown supernatant after 14 d of incubation at 30 °C. Bacteria generating a yellow – brown coloured supernatant were presumed to possess coal degrading capabilities and the best performing of these bacterial species was identified using 16s rDNA as Bacillus flexus. Scanning electron microscopy showed that there was a close association between the bacterium and substrate coal. The close association of bacteria to substrate suggested that these organisms were able to maximize solubilisation. FT-IR spectroscopic analysis demonstrated the addition of single bonded compounds COOH, OH, CN and CH that were absent prior to bacterial interaction. The increase in oxygen rich regions indicated degradation of the coal substrate. Elemental analysis showed that there was a decrease in carbon content from 47 % to 24 % during the 14 day incubation period. Reduction in coal carbon content was assumed to be due to bacterial utilization for metabolism and growth particularly as untreated coal substrate showed minimal loss of carbon. Analysis of the residual culture medium revealed that there was a linear increase in humic-like substance concentration for 8 d, coincident with increased coal biosolubilisation and colour change. Laccase activity was insignificant, and at 13 d enzyme activity was only 5×10-3 U/L suggesting that B. flexus may use a different mechanism to degrade coal. Residual culture medium remaining after bacterial action on the coal substrate appeared to possess plant growth promoting activity. This soluble biodegradation product with characteristics similar to humic acid-like substances was shown to impact growth of radish cotyledons. Expansion of isolated radish cotyledons was enhanced by 140% when incubated in coal biodegradation product. In conclusion, this study has yielded B. flexus and two other unidentified bacteria, isolated from polyaromatic hydrocarbon contaminated soils, and demonstrated the ability of these microorganisms to degrade waste coal. Further studies to elucidate the mechanism of coal breakdown by B. flexus, synergies with other coal degrading microorganisms, and incorporation of bacterium into Fungcoal bioprocess technology is imminent.
- Full Text:
Biological control as an integrated control method in the management of aquatic weeds in an urban environmental and socio-political landscape : case study : Cape Town Metropolitan Area
- Authors: Stafford, Martha Louise
- Date: 2014
- Subjects: Aquatic weeds -- South Africa -- Cape Town , Aquatic weeds -- Biological control -- South Africa -- Cape Town , Water hyacinth -- Biological control -- South Africa -- Cape Town , Metropolitan areas -- South Africa -- Cape Town
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5874 , http://hdl.handle.net/10962/d1013015
- Description: Aquatic weeds transform and degrade the ecosystems which they invade, impacting various aspects of their surroundings ranging from the community level to disrupting important processes affecting ecosystem services. All of the major aquatic weeds of South Africa are found in the Cape Town Metropolitan Area. Landowners, whether private or public, are legally obliged to manage the listed invasive species through applying environmentally acceptable methodologies. This thesis provides an overview of the strategic management options, prevention, early detection, rapid response and eradication of new invasions, and containment and control species of established species. It discusses the different control methods available for managing aquatic weeds, namely mechanical, manual, chemical and biological, and the integration of different methods to improve their effectiveness. Although various studies have shown that biological control is the most cost–effective, environmentally-friendly and sustainable method, it is not yet fully integrated into weed management programmes in South Africa. In addition, the successes achieved in other parts of the world with the control of water hyacinth through biological control have not been repeated in the urban environment, despite the fact that South Africa has the highest number of biological control agents available for the weed. Urbanisation puts pressure on the natural environment and ecosystem functioning. Nutrient-enriched waters support aquatic weed growth and pose a challenge to the management thereof, in particular with regard to integrating biological control into management programmes. The aims of this study were to determine the reasons for the lack of integration of biological control into weed management programmes in South Africa, to determine the feasibility of integrating biological control in aquatic weed management programmes in a complex urban environmental and socio-political landscape by means of three case studies in the Cape Town Metropolitan Area, which showed that biological control is feasible in urban environments and should be considered. Two surveys were conducted to determine the reasons for the lack of integration of biological control into weed management programmes. The surveys showed that there is a gap between research and implementation as a result of poor communication, non-supporting institutional arrangements and a lack of appropriate capacity and skills at the implementation level. Recommendations were offered to address these issues.
- Full Text:
- Authors: Stafford, Martha Louise
- Date: 2014
- Subjects: Aquatic weeds -- South Africa -- Cape Town , Aquatic weeds -- Biological control -- South Africa -- Cape Town , Water hyacinth -- Biological control -- South Africa -- Cape Town , Metropolitan areas -- South Africa -- Cape Town
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5874 , http://hdl.handle.net/10962/d1013015
- Description: Aquatic weeds transform and degrade the ecosystems which they invade, impacting various aspects of their surroundings ranging from the community level to disrupting important processes affecting ecosystem services. All of the major aquatic weeds of South Africa are found in the Cape Town Metropolitan Area. Landowners, whether private or public, are legally obliged to manage the listed invasive species through applying environmentally acceptable methodologies. This thesis provides an overview of the strategic management options, prevention, early detection, rapid response and eradication of new invasions, and containment and control species of established species. It discusses the different control methods available for managing aquatic weeds, namely mechanical, manual, chemical and biological, and the integration of different methods to improve their effectiveness. Although various studies have shown that biological control is the most cost–effective, environmentally-friendly and sustainable method, it is not yet fully integrated into weed management programmes in South Africa. In addition, the successes achieved in other parts of the world with the control of water hyacinth through biological control have not been repeated in the urban environment, despite the fact that South Africa has the highest number of biological control agents available for the weed. Urbanisation puts pressure on the natural environment and ecosystem functioning. Nutrient-enriched waters support aquatic weed growth and pose a challenge to the management thereof, in particular with regard to integrating biological control into management programmes. The aims of this study were to determine the reasons for the lack of integration of biological control into weed management programmes in South Africa, to determine the feasibility of integrating biological control in aquatic weed management programmes in a complex urban environmental and socio-political landscape by means of three case studies in the Cape Town Metropolitan Area, which showed that biological control is feasible in urban environments and should be considered. Two surveys were conducted to determine the reasons for the lack of integration of biological control into weed management programmes. The surveys showed that there is a gap between research and implementation as a result of poor communication, non-supporting institutional arrangements and a lack of appropriate capacity and skills at the implementation level. Recommendations were offered to address these issues.
- Full Text:
Cardiovascular disease risk in Black African females and the efficacy of a walking programme on blood pressure in a sub-sample
- Authors: Crymble, Tegan
- Date: 2014
- Subjects: Cardiovascular system -- Diseases -- South Africa -- Eastern Cape , Women -- Health and hygiene -- South Africa -- Eastern Cape , Obesity -- South Africa -- Eastern Cape , Hypertension -- South Africa -- Eastern Cape , Walking -- South Africa -- Eastern Cape -- Physiological aspects , Lifestyles -- Health aspects -- South Africa -- Eastern Cape , Health attitudes -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5152 , http://hdl.handle.net/10962/d1013234
- Description: The purpose of the study was to investigate the cardiovascular disease (CVD) risk profile of black African females in the Makana region, Eastern Cape, South Africa. Baseline measures from 40 participants, who met the criteria, were compared against the 2003 South African Demographic and Health Survey (SADHS) and the 2013 South African National Health and Nutritional Examination Survey (SANHANES-1). The risk factors measured were anthropometric (stature, body mass and body mass index (BMI)), morphological (waist circumference (WC), fat mass and lean mass), cardiovascular (heart rate and blood pressure (BP)), physical activity (step count and energy expenditure), biochemical (glycated haemoglobin and full blood lipid profile) and behavioural (alcohol and tobacco use). Results showed significantly higher (p≤0.05) values for overweight/obesity (BMI 37.60 kg.m⁻²; WC 1130.58 mm; fat mass 45.23%) and high BP (130/88 mmHg) compared to the previous national surveys, highlighting these CVD risk factors as problematic. The subsequent sub-study aimed to assess the efficacy of a pedometer-based walking intervention on high BP. The walking programme (n=25) was based on individual step goals to be completed at a moderate-intensity on five days.week⁻¹ for 12 weeks. The same measurements were taken at monthly intervals, Week 0, Week 4, Week 8 and Week 12, with the addition of dietary intake and fitness level, and the exclusion of the behavioural variables. There were no significant differences (p≤0.05) in systolic and diastolic BP with the exercise intervention, although there was a strong, negative relationship with time for diastolic BP (r²=0.9857). This trend suggests that the lack of significance may be a result of poor compliance and/or the small sample size. Individual results, however, showed no compliance-result relationship for the two risk factors of interest: overweight/obesity and high BP. Future recommendations include supervised or group-based exercise interventions to improve compliance, and the addition of resistance training to the aerobic programme.
- Full Text:
- Authors: Crymble, Tegan
- Date: 2014
- Subjects: Cardiovascular system -- Diseases -- South Africa -- Eastern Cape , Women -- Health and hygiene -- South Africa -- Eastern Cape , Obesity -- South Africa -- Eastern Cape , Hypertension -- South Africa -- Eastern Cape , Walking -- South Africa -- Eastern Cape -- Physiological aspects , Lifestyles -- Health aspects -- South Africa -- Eastern Cape , Health attitudes -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5152 , http://hdl.handle.net/10962/d1013234
- Description: The purpose of the study was to investigate the cardiovascular disease (CVD) risk profile of black African females in the Makana region, Eastern Cape, South Africa. Baseline measures from 40 participants, who met the criteria, were compared against the 2003 South African Demographic and Health Survey (SADHS) and the 2013 South African National Health and Nutritional Examination Survey (SANHANES-1). The risk factors measured were anthropometric (stature, body mass and body mass index (BMI)), morphological (waist circumference (WC), fat mass and lean mass), cardiovascular (heart rate and blood pressure (BP)), physical activity (step count and energy expenditure), biochemical (glycated haemoglobin and full blood lipid profile) and behavioural (alcohol and tobacco use). Results showed significantly higher (p≤0.05) values for overweight/obesity (BMI 37.60 kg.m⁻²; WC 1130.58 mm; fat mass 45.23%) and high BP (130/88 mmHg) compared to the previous national surveys, highlighting these CVD risk factors as problematic. The subsequent sub-study aimed to assess the efficacy of a pedometer-based walking intervention on high BP. The walking programme (n=25) was based on individual step goals to be completed at a moderate-intensity on five days.week⁻¹ for 12 weeks. The same measurements were taken at monthly intervals, Week 0, Week 4, Week 8 and Week 12, with the addition of dietary intake and fitness level, and the exclusion of the behavioural variables. There were no significant differences (p≤0.05) in systolic and diastolic BP with the exercise intervention, although there was a strong, negative relationship with time for diastolic BP (r²=0.9857). This trend suggests that the lack of significance may be a result of poor compliance and/or the small sample size. Individual results, however, showed no compliance-result relationship for the two risk factors of interest: overweight/obesity and high BP. Future recommendations include supervised or group-based exercise interventions to improve compliance, and the addition of resistance training to the aerobic programme.
- Full Text:
Characterization and application of phthalocyanine-magnetic nanoparticle conjugates anchored to electrospun polyamide nanofibers
- Authors: Ledwaba, Mpho
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54610 , vital:26593
- Description: This work presents the syntheses, photophysical and photochemical characterization of zinc tetracarboxyphenoxy phthalocyanine (ZnTCPPc, 3) and its gadolinium oxide nanoparticle conjugate (4). By means of spectroscopic and microscopic characterization, the conjugation of the ZnTCPPc to the silica coated gadolinium oxide nanoparticles (Si-Gd2O3 NPs, 2) through an amide bond was confirmed. The thermal stability, morphology, nanoparticle sizes and their conjugates with the Pc were studied using ThermoGravimetric Analysis (TGA), Fourier Transform Infrared spectroscopy (FTIR), Transmission Electron Microscopy (TEM) and powder X-ray diffractometry (XRD). Conjugation of ZnTCPPc to the magnetic nanoparticles, proved to have a negligible effect on the photophysical parameters of the phthalocyanine, where a slight decrease in fluorescence and triplet quantum yields and lifetimes was observed. The singlet oxygen quantum yield, however, increased slightly upon conjugation, suggesting that the overall efficiency of the ZnTCPPc as a photosensitizer had improved. Physical mixing of the ZnTCPPc and the silica-coated gadolinium nanoparticles also showed an improvement in the singlet oxygen quantum yield and triplet lifetime, also showing an enhanced efficiency for the photosensitizer and therefore photocatalysis. ZnTCPPc (3) alone and the Pc-gadolinium oxide nanoparticle conjugate (4) were therefore electrospun into nanofibers to create a solid support. The fibers were characterized and their diameter sizes and composition was studied confirming the incorporation of the phthalocyanine and gadolinium oxide nanoparticle. Increased singlet oxygen generation resulted in increased Photodegradation of the environmental pollutant Orange G and the fibers were found to be more efficient as photocatalysts compared to the photosensitizer in solution. The nanomaterial may therefore be applied to the photodegradation of Orange G.
- Full Text:
- Authors: Ledwaba, Mpho
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54610 , vital:26593
- Description: This work presents the syntheses, photophysical and photochemical characterization of zinc tetracarboxyphenoxy phthalocyanine (ZnTCPPc, 3) and its gadolinium oxide nanoparticle conjugate (4). By means of spectroscopic and microscopic characterization, the conjugation of the ZnTCPPc to the silica coated gadolinium oxide nanoparticles (Si-Gd2O3 NPs, 2) through an amide bond was confirmed. The thermal stability, morphology, nanoparticle sizes and their conjugates with the Pc were studied using ThermoGravimetric Analysis (TGA), Fourier Transform Infrared spectroscopy (FTIR), Transmission Electron Microscopy (TEM) and powder X-ray diffractometry (XRD). Conjugation of ZnTCPPc to the magnetic nanoparticles, proved to have a negligible effect on the photophysical parameters of the phthalocyanine, where a slight decrease in fluorescence and triplet quantum yields and lifetimes was observed. The singlet oxygen quantum yield, however, increased slightly upon conjugation, suggesting that the overall efficiency of the ZnTCPPc as a photosensitizer had improved. Physical mixing of the ZnTCPPc and the silica-coated gadolinium nanoparticles also showed an improvement in the singlet oxygen quantum yield and triplet lifetime, also showing an enhanced efficiency for the photosensitizer and therefore photocatalysis. ZnTCPPc (3) alone and the Pc-gadolinium oxide nanoparticle conjugate (4) were therefore electrospun into nanofibers to create a solid support. The fibers were characterized and their diameter sizes and composition was studied confirming the incorporation of the phthalocyanine and gadolinium oxide nanoparticle. Increased singlet oxygen generation resulted in increased Photodegradation of the environmental pollutant Orange G and the fibers were found to be more efficient as photocatalysts compared to the photosensitizer in solution. The nanomaterial may therefore be applied to the photodegradation of Orange G.
- Full Text:
Classification of the difficulty in accelerating problems using GPUs
- Authors: Tristram, Uvedale Roy
- Date: 2014
- Subjects: Graphics processing units , Computer algorithms , Computer programming , Problem solving -- Data processing
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4699 , http://hdl.handle.net/10962/d1012978
- Description: Scientists continually require additional processing power, as this enables them to compute larger problem sizes, use more complex models and algorithms, and solve problems previously thought computationally impractical. General-purpose computation on graphics processing units (GPGPU) can help in this regard, as there is great potential in using graphics processors to accelerate many scientific models and algorithms. However, some problems are considerably harder to accelerate than others, and it may be challenging for those new to GPGPU to ascertain the difficulty of accelerating a particular problem or seek appropriate optimisation guidance. Through what was learned in the acceleration of a hydrological uncertainty ensemble model, large numbers of k-difference string comparisons, and a radix sort, problem attributes have been identified that can assist in the evaluation of the difficulty in accelerating a problem using GPUs. The identified attributes are inherent parallelism, branch divergence, problem size, required computational parallelism, memory access pattern regularity, data transfer overhead, and thread cooperation. Using these attributes as difficulty indicators, an initial problem difficulty classification framework has been created that aids in GPU acceleration difficulty evaluation. This framework further facilitates directed guidance on suggested optimisations and required knowledge based on problem classification, which has been demonstrated for the aforementioned accelerated problems. It is anticipated that this framework, or a derivative thereof, will prove to be a useful resource for new or novice GPGPU developers in the evaluation of potential problems for GPU acceleration.
- Full Text:
- Authors: Tristram, Uvedale Roy
- Date: 2014
- Subjects: Graphics processing units , Computer algorithms , Computer programming , Problem solving -- Data processing
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4699 , http://hdl.handle.net/10962/d1012978
- Description: Scientists continually require additional processing power, as this enables them to compute larger problem sizes, use more complex models and algorithms, and solve problems previously thought computationally impractical. General-purpose computation on graphics processing units (GPGPU) can help in this regard, as there is great potential in using graphics processors to accelerate many scientific models and algorithms. However, some problems are considerably harder to accelerate than others, and it may be challenging for those new to GPGPU to ascertain the difficulty of accelerating a particular problem or seek appropriate optimisation guidance. Through what was learned in the acceleration of a hydrological uncertainty ensemble model, large numbers of k-difference string comparisons, and a radix sort, problem attributes have been identified that can assist in the evaluation of the difficulty in accelerating a problem using GPUs. The identified attributes are inherent parallelism, branch divergence, problem size, required computational parallelism, memory access pattern regularity, data transfer overhead, and thread cooperation. Using these attributes as difficulty indicators, an initial problem difficulty classification framework has been created that aids in GPU acceleration difficulty evaluation. This framework further facilitates directed guidance on suggested optimisations and required knowledge based on problem classification, which has been demonstrated for the aforementioned accelerated problems. It is anticipated that this framework, or a derivative thereof, will prove to be a useful resource for new or novice GPGPU developers in the evaluation of potential problems for GPU acceleration.
- Full Text:
Cloud information security : a higher education perspective
- Authors: Van der Schyff, Karl Izak
- Date: 2014
- Subjects: Cloud computing -- Security measures , Information technology -- Security measures , Data protection , Internet in higher education , Education, Higher -- Technological innovations
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4692 , http://hdl.handle.net/10962/d1011607 , Cloud computing -- Security measures , Information technology -- Security measures , Data protection , Internet in higher education , Education, Higher -- Technological innovations
- Description: In recent years higher education institutions have come under increasing financial pressure. This has not only prompted universities to investigate more cost effective means of delivering course content and maintaining research output, but also to investigate the administrative functions that accompany them. As such, many South African universities have either adopted or are in the process of adopting some form of cloud computing given the recent drop in bandwidth costs. However, this adoption process has raised concerns about the security of cloud-based information and this has, in some cases, had a negative impact on the adoption process. In an effort to study these concerns many researchers have employed a positivist approach with little, if any, focus on the operational context of these universities. Moreover, there has been very little research, specifically within the South African context. This study addresses some of these concerns by investigating the threats and security incident response life cycle within a higher education cloud. This was done by initially conducting a small scale survey and a detailed thematic analysis of twelve interviews from three South African universities. The identified themes and their corresponding analyses and interpretation contribute on both a practical and theoretical level with the practical contributions relating to a set of security driven criteria for selecting cloud providers as well as recommendations for universities who have or are in the process of adopting cloud computing. Theoretically several conceptual frameworks are offered allowing the researcher to convey his understanding of how the aforementioned practical concepts relate to each other as well as the concepts that constitute the research questions of this study.
- Full Text:
- Authors: Van der Schyff, Karl Izak
- Date: 2014
- Subjects: Cloud computing -- Security measures , Information technology -- Security measures , Data protection , Internet in higher education , Education, Higher -- Technological innovations
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4692 , http://hdl.handle.net/10962/d1011607 , Cloud computing -- Security measures , Information technology -- Security measures , Data protection , Internet in higher education , Education, Higher -- Technological innovations
- Description: In recent years higher education institutions have come under increasing financial pressure. This has not only prompted universities to investigate more cost effective means of delivering course content and maintaining research output, but also to investigate the administrative functions that accompany them. As such, many South African universities have either adopted or are in the process of adopting some form of cloud computing given the recent drop in bandwidth costs. However, this adoption process has raised concerns about the security of cloud-based information and this has, in some cases, had a negative impact on the adoption process. In an effort to study these concerns many researchers have employed a positivist approach with little, if any, focus on the operational context of these universities. Moreover, there has been very little research, specifically within the South African context. This study addresses some of these concerns by investigating the threats and security incident response life cycle within a higher education cloud. This was done by initially conducting a small scale survey and a detailed thematic analysis of twelve interviews from three South African universities. The identified themes and their corresponding analyses and interpretation contribute on both a practical and theoretical level with the practical contributions relating to a set of security driven criteria for selecting cloud providers as well as recommendations for universities who have or are in the process of adopting cloud computing. Theoretically several conceptual frameworks are offered allowing the researcher to convey his understanding of how the aforementioned practical concepts relate to each other as well as the concepts that constitute the research questions of this study.
- Full Text:
Comparative phylogeography of five swallowtail butterfly species (Lepidoptera: Papilionidae) in South Africa : ecological and taxonomic implications.
- Authors: Neef, Götz-Georg
- Date: 2014
- Subjects: Swallowtail butterflies , Papilionidae -- South Africa , Phylogeography -- South Africa , Swallowtail butterflies -- Effect of habitat modification on , Biodiversity -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4266 , http://hdl.handle.net/10962/d1013574
- Description: With current biota under constant threat of extinction, it is important to ascertain where and how biological diversity is generated and partitioned. Phylogeographic studies can assist in the identification of places and processes that indicate the origin and maintenance of biodiversity. Forest fragmentation has a big effect on local extinction and loss of genetic diversity of forest-restricted taxa, along with divergence and speciation of forest biota. This study aims to understand the effects of these processes on a number of forest-dwelling butterflies using a comparative phylogeographic approach. Mitochondrial DNA of five different Papilio species with different degrees of forest specificity was analysed using phylogenetic methods. In addition, the subspecific taxonomy of P. ophidicephalus was investigated using morphometrics of discal spots on the wings and nuclear DNA analysis along with mitochondrial DNA analysis. The results show that the forest-restricted species (P. ophidicephalus and P. echerioides) have more genetic structure and less genetic diversity than the more generalist species (P. dardanus, P. demodocus and P. nireus). This could be due to inbreeding depression and bottlenecks caused by forest fragmentation. As forest patches become smaller, the population size is affected and that causes a loss in genetic diversity, and increasing habitat fragmentation disrupts gene flow. The intraspecific taxonomy of P. ophidicephalus is far from revealed. However, this study shows there is evidence for the different subspecies when comparing morphological results and genetic results. From the evidence provided here it is suggested that P. ophidicephalus should be divided into two separate species rather than five subspecies.
- Full Text:
- Authors: Neef, Götz-Georg
- Date: 2014
- Subjects: Swallowtail butterflies , Papilionidae -- South Africa , Phylogeography -- South Africa , Swallowtail butterflies -- Effect of habitat modification on , Biodiversity -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4266 , http://hdl.handle.net/10962/d1013574
- Description: With current biota under constant threat of extinction, it is important to ascertain where and how biological diversity is generated and partitioned. Phylogeographic studies can assist in the identification of places and processes that indicate the origin and maintenance of biodiversity. Forest fragmentation has a big effect on local extinction and loss of genetic diversity of forest-restricted taxa, along with divergence and speciation of forest biota. This study aims to understand the effects of these processes on a number of forest-dwelling butterflies using a comparative phylogeographic approach. Mitochondrial DNA of five different Papilio species with different degrees of forest specificity was analysed using phylogenetic methods. In addition, the subspecific taxonomy of P. ophidicephalus was investigated using morphometrics of discal spots on the wings and nuclear DNA analysis along with mitochondrial DNA analysis. The results show that the forest-restricted species (P. ophidicephalus and P. echerioides) have more genetic structure and less genetic diversity than the more generalist species (P. dardanus, P. demodocus and P. nireus). This could be due to inbreeding depression and bottlenecks caused by forest fragmentation. As forest patches become smaller, the population size is affected and that causes a loss in genetic diversity, and increasing habitat fragmentation disrupts gene flow. The intraspecific taxonomy of P. ophidicephalus is far from revealed. However, this study shows there is evidence for the different subspecies when comparing morphological results and genetic results. From the evidence provided here it is suggested that P. ophidicephalus should be divided into two separate species rather than five subspecies.
- Full Text:
Correlation and comparative analysis of traffic across five network telescopes
- Nkhumeleni, Thizwilondi Moses
- Authors: Nkhumeleni, Thizwilondi Moses
- Date: 2014
- Subjects: Sensor networks , Computer networks , TCP/IP (Computer network protocol) , Computer networks -- Management , Electronic data processing -- Management
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4693 , http://hdl.handle.net/10962/d1011668 , Sensor networks , Computer networks , TCP/IP (Computer network protocol) , Computer networks -- Management , Electronic data processing -- Management
- Description: Monitoring unused IP address space by using network telescopes provides a favourable environment for researchers to study and detect malware, worms, denial of service and scanning activities. Research in the field of network telescopes has progressed over the past decade resulting in the development of an increased number of overlapping datasets. Rhodes University's network of telescope sensors has continued to grow with additional network telescopes being brought online. At the time of writing, Rhodes University has a distributed network of five relatively small /24 network telescopes. With five network telescope sensors, this research focuses on comparative and correlation analysis of traffic activity across the network of telescope sensors. To aid summarisation and visualisation techniques, time series' representing time-based traffic activity, are constructed. By employing an iterative experimental process of captured traffic, two natural categories of the five network telescopes are presented. Using the cross- and auto-correlation methods of time series analysis, moderate correlation of traffic activity was achieved between telescope sensors in each category. Weak to moderate correlation was calculated when comparing category A and category B network telescopes' datasets. Results were significantly improved by studying TCP traffic separately. Moderate to strong correlation coefficients in each category were calculated when using TCP traffic only. UDP traffic analysis showed weaker correlation between sensors, however the uniformity of ICMP traffic showed correlation of traffic activity across all sensors. The results confirmed the visual observation of traffic relativity in telescope sensors within the same category and quantitatively analysed the correlation of network telescopes' traffic activity.
- Full Text:
- Authors: Nkhumeleni, Thizwilondi Moses
- Date: 2014
- Subjects: Sensor networks , Computer networks , TCP/IP (Computer network protocol) , Computer networks -- Management , Electronic data processing -- Management
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4693 , http://hdl.handle.net/10962/d1011668 , Sensor networks , Computer networks , TCP/IP (Computer network protocol) , Computer networks -- Management , Electronic data processing -- Management
- Description: Monitoring unused IP address space by using network telescopes provides a favourable environment for researchers to study and detect malware, worms, denial of service and scanning activities. Research in the field of network telescopes has progressed over the past decade resulting in the development of an increased number of overlapping datasets. Rhodes University's network of telescope sensors has continued to grow with additional network telescopes being brought online. At the time of writing, Rhodes University has a distributed network of five relatively small /24 network telescopes. With five network telescope sensors, this research focuses on comparative and correlation analysis of traffic activity across the network of telescope sensors. To aid summarisation and visualisation techniques, time series' representing time-based traffic activity, are constructed. By employing an iterative experimental process of captured traffic, two natural categories of the five network telescopes are presented. Using the cross- and auto-correlation methods of time series analysis, moderate correlation of traffic activity was achieved between telescope sensors in each category. Weak to moderate correlation was calculated when comparing category A and category B network telescopes' datasets. Results were significantly improved by studying TCP traffic separately. Moderate to strong correlation coefficients in each category were calculated when using TCP traffic only. UDP traffic analysis showed weaker correlation between sensors, however the uniformity of ICMP traffic showed correlation of traffic activity across all sensors. The results confirmed the visual observation of traffic relativity in telescope sensors within the same category and quantitatively analysed the correlation of network telescopes' traffic activity.
- Full Text:
Data-centric security : towards a utopian model for protecting corporate data on mobile devices
- Authors: Mayisela, Simphiwe Hector
- Date: 2014
- Subjects: Computer security , Computer networks -- Security measures , Business enterprises -- Computer networks -- Security measures , Mobile computing -- Security measures , Mobile communication systems -- Security measures
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4688 , http://hdl.handle.net/10962/d1011094 , Computer security , Computer networks -- Security measures , Business enterprises -- Computer networks -- Security measures , Mobile computing -- Security measures , Mobile communication systems -- Security measures
- Description: Data-centric security is significant in understanding, assessing and mitigating the various risks and impacts of sharing information outside corporate boundaries. Information generally leaves corporate boundaries through mobile devices. Mobile devices continue to evolve as multi-functional tools for everyday life, surpassing their initial intended use. This added capability and increasingly extensive use of mobile devices does not come without a degree of risk - hence the need to guard and protect information as it exists beyond the corporate boundaries and throughout its lifecycle. Literature on existing models crafted to protect data, rather than infrastructure in which the data resides, is reviewed. Technologies that organisations have implemented to adopt the data-centric model are studied. A utopian model that takes into account the shortcomings of existing technologies and deficiencies of common theories is proposed. Two sets of qualitative studies are reported; the first is a preliminary online survey to assess the ubiquity of mobile devices and extent of technology adoption towards implementation of data-centric model; and the second comprises of a focus survey and expert interviews pertaining on technologies that organisations have implemented to adopt the data-centric model. The latter study revealed insufficient data at the time of writing for the results to be statistically significant; however; indicative trends supported the assertions documented in the literature review. The question that this research answers is whether or not current technology implementations designed to mitigate risks from mobile devices, actually address business requirements. This research question, answered through these two sets qualitative studies, discovered inconsistencies between the technology implementations and business requirements. The thesis concludes by proposing a realistic model, based on the outcome of the qualitative study, which bridges the gap between the technology implementations and business requirements. Future work which could perhaps be conducted in light of the findings and the comments from this research is also considered.
- Full Text:
- Authors: Mayisela, Simphiwe Hector
- Date: 2014
- Subjects: Computer security , Computer networks -- Security measures , Business enterprises -- Computer networks -- Security measures , Mobile computing -- Security measures , Mobile communication systems -- Security measures
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4688 , http://hdl.handle.net/10962/d1011094 , Computer security , Computer networks -- Security measures , Business enterprises -- Computer networks -- Security measures , Mobile computing -- Security measures , Mobile communication systems -- Security measures
- Description: Data-centric security is significant in understanding, assessing and mitigating the various risks and impacts of sharing information outside corporate boundaries. Information generally leaves corporate boundaries through mobile devices. Mobile devices continue to evolve as multi-functional tools for everyday life, surpassing their initial intended use. This added capability and increasingly extensive use of mobile devices does not come without a degree of risk - hence the need to guard and protect information as it exists beyond the corporate boundaries and throughout its lifecycle. Literature on existing models crafted to protect data, rather than infrastructure in which the data resides, is reviewed. Technologies that organisations have implemented to adopt the data-centric model are studied. A utopian model that takes into account the shortcomings of existing technologies and deficiencies of common theories is proposed. Two sets of qualitative studies are reported; the first is a preliminary online survey to assess the ubiquity of mobile devices and extent of technology adoption towards implementation of data-centric model; and the second comprises of a focus survey and expert interviews pertaining on technologies that organisations have implemented to adopt the data-centric model. The latter study revealed insufficient data at the time of writing for the results to be statistically significant; however; indicative trends supported the assertions documented in the literature review. The question that this research answers is whether or not current technology implementations designed to mitigate risks from mobile devices, actually address business requirements. This research question, answered through these two sets qualitative studies, discovered inconsistencies between the technology implementations and business requirements. The thesis concludes by proposing a realistic model, based on the outcome of the qualitative study, which bridges the gap between the technology implementations and business requirements. Future work which could perhaps be conducted in light of the findings and the comments from this research is also considered.
- Full Text:
Dietary aspects of establishing a mainland-based colony of the endangered African Penguin (Spheniscus demersus) in St Francis Bay, South Africa
- Authors: Voogt, Nina Margaret
- Date: 2014
- Subjects: African penguin -- South Africa -- Cape Saint Francis , African penguin -- Food -- South Africa -- Algoa Bay , African penguin -- Habitat suitability index models -- South Africa -- Cape Saint Francis , Stable isotopes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5875 , http://hdl.handle.net/10962/d1013115
- Description: Cape St Francis, Eastern Cape, has been identified as one of four potential sites for establishing a mainland-based African penguin (Spheniscus demersus) colony. This thesis comprises three main components: a verification of a preparation method for stable isotope samples from penguin feathers; a dietary analysis of the penguins on Bird Island, Algoa Bay, though stable isotope analysis of whole blood and feathers (2012 and 2013); and an estimation of available fish surplus that could potentially support a colony of penguins at Cape St Francis. Each component contributes towards the next, all building towards answering the main research question: Will there be enough food around St Francis Bay to support a colony of penguins and sustain the already established fisheries industry within the bay? Stable isotope analysis of whole blood and feathers from breeding adults and whole blood from juveniles provided insight into the variability of African penguins’ diets at different stages in their life history. Stable isotope mixing models indicated that the predicted proportions that each prey species could potentially contribute to diet conflicted with published stomach sample data. This might arise from inaccurate trophic enrichment factors used in the model, or from systematic biases in the published stomach sampling techniques, or both. Dietary sexual dimorphism was not demonstrated by the isotope signatures of breeding penguins. Based on official catch data, the fisheries activity on the south coast, and especially around the potential colony site at St Francis, is much lower than around the west coast’s penguin colonies. The model provided a first-order estimate for fish supply around the potential colony site at St Francis both at a large coastal scale and a local small scale. At both scales the estimate indicated an ample availability of fish at current fishing levels. The model in Chapter 4 can also be applied to refining the assessments of other potential colony sites on the south coast. In conclusion, the south coast is a promising area for a new colony of penguins in terms of food availability. There is relatively low fishing activity in the area and, as suggested by the large-scale model in Chapter 4, an ample fish resource. The final chapter briefly discusses factors that need to be considered before attempting to establish a mainland-based colony of African penguins.
- Full Text:
- Authors: Voogt, Nina Margaret
- Date: 2014
- Subjects: African penguin -- South Africa -- Cape Saint Francis , African penguin -- Food -- South Africa -- Algoa Bay , African penguin -- Habitat suitability index models -- South Africa -- Cape Saint Francis , Stable isotopes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5875 , http://hdl.handle.net/10962/d1013115
- Description: Cape St Francis, Eastern Cape, has been identified as one of four potential sites for establishing a mainland-based African penguin (Spheniscus demersus) colony. This thesis comprises three main components: a verification of a preparation method for stable isotope samples from penguin feathers; a dietary analysis of the penguins on Bird Island, Algoa Bay, though stable isotope analysis of whole blood and feathers (2012 and 2013); and an estimation of available fish surplus that could potentially support a colony of penguins at Cape St Francis. Each component contributes towards the next, all building towards answering the main research question: Will there be enough food around St Francis Bay to support a colony of penguins and sustain the already established fisheries industry within the bay? Stable isotope analysis of whole blood and feathers from breeding adults and whole blood from juveniles provided insight into the variability of African penguins’ diets at different stages in their life history. Stable isotope mixing models indicated that the predicted proportions that each prey species could potentially contribute to diet conflicted with published stomach sample data. This might arise from inaccurate trophic enrichment factors used in the model, or from systematic biases in the published stomach sampling techniques, or both. Dietary sexual dimorphism was not demonstrated by the isotope signatures of breeding penguins. Based on official catch data, the fisheries activity on the south coast, and especially around the potential colony site at St Francis, is much lower than around the west coast’s penguin colonies. The model provided a first-order estimate for fish supply around the potential colony site at St Francis both at a large coastal scale and a local small scale. At both scales the estimate indicated an ample availability of fish at current fishing levels. The model in Chapter 4 can also be applied to refining the assessments of other potential colony sites on the south coast. In conclusion, the south coast is a promising area for a new colony of penguins in terms of food availability. There is relatively low fishing activity in the area and, as suggested by the large-scale model in Chapter 4, an ample fish resource. The final chapter briefly discusses factors that need to be considered before attempting to establish a mainland-based colony of African penguins.
- Full Text:
Distribution of heavy minerals sand in Namalope deposit, Moma district, Mozambique
- Authors: Assane, Ali Ossufo
- Date: 2014
- Subjects: Heavy minerals -- Mozambique -- Moma District , Prospecting -- Mozambique -- Moma District , Mines and mineral resources -- Mozambique -- Moma District , Ilmenite -- Research , Zircon -- Research , Rutile -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5056 , http://hdl.handle.net/10962/d1012169 , Heavy minerals -- Mozambique -- Moma District , Prospecting -- Mozambique -- Moma District , Mines and mineral resources -- Mozambique -- Moma District , Ilmenite -- Research , Zircon -- Research , Rutile -- Research
- Description: The spatial distribution of heavy minerals along the mine paths 2014 and 2015 at the wet concentrate plant B shows an increase of heavy minerals sand concentration northwards and slime contents southwards, and it is commonly associated with depth and grain sorting; the increase of heavy minerals concentration with depth is considered to be from the surface formed by Unit 6 to the bottom of Unit 7. The Unit 82 is characterized by low heavy minerals concentrations and high slime contents declining northwards. The mineral proportion estimation suggests that ilmenite is the most abundant heavy mineral in the entire area followed by zircon, rutile and mozanite, and some accessory minerals such as chromite, kyanite, staurolite, tourmaline, epidote, spinel and quartz. The ilmenite occurrence is divided into ilmenite low (< 53% TiO₂) and high (> 53% TiO₂); the ilmenite high with zircon and rutile shows tendency to increase northwards while ilmenite low increase southwards. Zircon, monazite, rutile, chromite, kyanite and staurolite show low variability, which is probably associated with high resistance of minerals for abrasion during transportation and diagenesis. The depositional model of the Namalope deposit, in the flat area and wet concentrate plant B in particular, suggests deposition in a shallow marine environment associated with regression for deposition of Unit 6, 7 and 9 and transgression during deposition of Unit 82. The spatial distribution of heavy minerals in the Namalope deposit and its environment of deposition are the key points for discovery of new deposits around the Namalope with the same characteristic of mineral assemblage and they are used for mine strategic plans such as update block model and mine design.
- Full Text:
- Authors: Assane, Ali Ossufo
- Date: 2014
- Subjects: Heavy minerals -- Mozambique -- Moma District , Prospecting -- Mozambique -- Moma District , Mines and mineral resources -- Mozambique -- Moma District , Ilmenite -- Research , Zircon -- Research , Rutile -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5056 , http://hdl.handle.net/10962/d1012169 , Heavy minerals -- Mozambique -- Moma District , Prospecting -- Mozambique -- Moma District , Mines and mineral resources -- Mozambique -- Moma District , Ilmenite -- Research , Zircon -- Research , Rutile -- Research
- Description: The spatial distribution of heavy minerals along the mine paths 2014 and 2015 at the wet concentrate plant B shows an increase of heavy minerals sand concentration northwards and slime contents southwards, and it is commonly associated with depth and grain sorting; the increase of heavy minerals concentration with depth is considered to be from the surface formed by Unit 6 to the bottom of Unit 7. The Unit 82 is characterized by low heavy minerals concentrations and high slime contents declining northwards. The mineral proportion estimation suggests that ilmenite is the most abundant heavy mineral in the entire area followed by zircon, rutile and mozanite, and some accessory minerals such as chromite, kyanite, staurolite, tourmaline, epidote, spinel and quartz. The ilmenite occurrence is divided into ilmenite low (< 53% TiO₂) and high (> 53% TiO₂); the ilmenite high with zircon and rutile shows tendency to increase northwards while ilmenite low increase southwards. Zircon, monazite, rutile, chromite, kyanite and staurolite show low variability, which is probably associated with high resistance of minerals for abrasion during transportation and diagenesis. The depositional model of the Namalope deposit, in the flat area and wet concentrate plant B in particular, suggests deposition in a shallow marine environment associated with regression for deposition of Unit 6, 7 and 9 and transgression during deposition of Unit 82. The spatial distribution of heavy minerals in the Namalope deposit and its environment of deposition are the key points for discovery of new deposits around the Namalope with the same characteristic of mineral assemblage and they are used for mine strategic plans such as update block model and mine design.
- Full Text:
Distribution of iron-titanium oxides in the vanadiferous main magnetite seam of the upper zone : Northern limb, Bushveld complex
- Authors: Gwatinetsa, Demand
- Date: 2014
- Subjects: Igneous rocks -- South Africa -- Bushveld Complex , Sulfide minerals -- South Africa -- Bushveld Complex , Vanadium -- South Africa -- Bushveld Complex , Titanium dioxide -- South Africa -- Bushveld Complex , Ferric oxide -- South Africa -- Bushveld Complex , Geology -- South Africa -- Bushveld Complex , Mineralogy -- South Africa -- Bushveld Complex , Mines and mineral resources -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5063 , http://hdl.handle.net/10962/d1013281
- Description: The main magnetite seam of the Upper Zone of the Rustenburg Layered Suite (SACS, 1980) on the Bushveld Complex is known to host the world‘s largest vanadium bearing titaniferous iron ores. The vanadiferous titanomagnetites, contain vanadium in sufficient concentrations (1.2 - 2.2 per cent V₂O₅) to be considered as resources and vanadium has been mined historically by a number of companies among them Anglo-American, Highveld Steel and Vanadium and VanMag Resources as well as currently by Evraz Highveld Steel and Vanadium Limited of South Africa. The titanomagnetites contain iron ore in the form of magnetite and titanium with concentrations averaging 50-75 per cent FeO and 12-21 per cent TiO₂. The titaniferous iron ores have been historically dismissed as a source of iron and titanium, due to the known difficulties of using iron ore with high titania content in blast furnaces. The economic potential for the extractability of the titaniferous magnetites lies in the capacity of the ores to be separated into iron rich and titanium rich concentrates usually through, crushing, grinding and magnetic separation. The separatability of iron oxides and titanium oxides, is dependent on the nature in which the titanium oxide occurs, with granular ilmenite being the most favourable since it can be separated from magnetite via magnetic separation. Titanium that occurs as finely exsolved lamellae or as iron-titanium oxides with low titania content such as ulvospinel render the potential recoverability of titanium poor. The Upper Zone vanadiferous titanomagnetites contain titanium in various forms varying from discrete granular ilmenite to finely exsolved lamellae as well as occurring as part of the minerals ulvospinel (Fe₂TiO₄) and titanomagnetite (a solid solution series between ulvospinel and magnetite) . Discrete ilmenite constitutes between 3-5 per cent by volume of the massive titanomagnetite ores, and between 5-10 per cent by volume of the magnetite-plagioclase cumulates with more than 50 per cent opaque oxide minerals. The purpose of this research was to investigate the mineralogical setting and distribution of the iron and titanium oxides within the magnetitite layers from top to bottom as well as spatially along a strike length of 2 000m to determine the potential for the titanium to be extracted from the titanomagnetite ores. The titanomagnetites of the Upper Zone of the Bushveld Complex with particular reference to the Northern Limb where this research was conducted contains titanium oxides as discrete ilmenite grains but in low concentrations whose potential for separate economic extraction will be challenging. The highest concentration of titanium in the magnetite ores is not contained in the granular ilmenite, but rather in ulvospinel and titanomagnetite as illustrated by the marked higher concentration of TiO₂ in the massive ores which contain less granular ilmenite in comparison to the disseminated ores which contain 3 to 8 percentage points higher granular ilmenite than the massive ores. On the scale of the main magnetite seam, the TiO₂ content increases with increasing stratigraphic height from being completely absent in the footwall anorthosite. The V₂2O₅ content also increases with stratigraphic height except for in one of the 3 boreholes where it drops with increasing height. The decrease or increase patterns are repeated in every seam. The titanomagnetites of the main magnetite seam display a variety of textures from coarse granular magnetite and ilmenite, to trellis ilmenite lamellae, intergranular ilmenite and magnesian spinels and fine exsolution lamellae of ulvospinel and ferro-magnesian spinels parallel to the magnetite cleavage. The bottom contact of the main magnetite seam is very sharp and there is no titanium or vanadium in the footwall barely 10cm below the contact. Chromium is present in the bottom of the 4 layers that constitute the main magnetite seam and it upwards decreases rapidly. In boreholes P21 and P55, there are slight reversals in the TiO₂ and V₂O₅ content towards the top of the magnetite seams.
- Full Text:
- Authors: Gwatinetsa, Demand
- Date: 2014
- Subjects: Igneous rocks -- South Africa -- Bushveld Complex , Sulfide minerals -- South Africa -- Bushveld Complex , Vanadium -- South Africa -- Bushveld Complex , Titanium dioxide -- South Africa -- Bushveld Complex , Ferric oxide -- South Africa -- Bushveld Complex , Geology -- South Africa -- Bushveld Complex , Mineralogy -- South Africa -- Bushveld Complex , Mines and mineral resources -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5063 , http://hdl.handle.net/10962/d1013281
- Description: The main magnetite seam of the Upper Zone of the Rustenburg Layered Suite (SACS, 1980) on the Bushveld Complex is known to host the world‘s largest vanadium bearing titaniferous iron ores. The vanadiferous titanomagnetites, contain vanadium in sufficient concentrations (1.2 - 2.2 per cent V₂O₅) to be considered as resources and vanadium has been mined historically by a number of companies among them Anglo-American, Highveld Steel and Vanadium and VanMag Resources as well as currently by Evraz Highveld Steel and Vanadium Limited of South Africa. The titanomagnetites contain iron ore in the form of magnetite and titanium with concentrations averaging 50-75 per cent FeO and 12-21 per cent TiO₂. The titaniferous iron ores have been historically dismissed as a source of iron and titanium, due to the known difficulties of using iron ore with high titania content in blast furnaces. The economic potential for the extractability of the titaniferous magnetites lies in the capacity of the ores to be separated into iron rich and titanium rich concentrates usually through, crushing, grinding and magnetic separation. The separatability of iron oxides and titanium oxides, is dependent on the nature in which the titanium oxide occurs, with granular ilmenite being the most favourable since it can be separated from magnetite via magnetic separation. Titanium that occurs as finely exsolved lamellae or as iron-titanium oxides with low titania content such as ulvospinel render the potential recoverability of titanium poor. The Upper Zone vanadiferous titanomagnetites contain titanium in various forms varying from discrete granular ilmenite to finely exsolved lamellae as well as occurring as part of the minerals ulvospinel (Fe₂TiO₄) and titanomagnetite (a solid solution series between ulvospinel and magnetite) . Discrete ilmenite constitutes between 3-5 per cent by volume of the massive titanomagnetite ores, and between 5-10 per cent by volume of the magnetite-plagioclase cumulates with more than 50 per cent opaque oxide minerals. The purpose of this research was to investigate the mineralogical setting and distribution of the iron and titanium oxides within the magnetitite layers from top to bottom as well as spatially along a strike length of 2 000m to determine the potential for the titanium to be extracted from the titanomagnetite ores. The titanomagnetites of the Upper Zone of the Bushveld Complex with particular reference to the Northern Limb where this research was conducted contains titanium oxides as discrete ilmenite grains but in low concentrations whose potential for separate economic extraction will be challenging. The highest concentration of titanium in the magnetite ores is not contained in the granular ilmenite, but rather in ulvospinel and titanomagnetite as illustrated by the marked higher concentration of TiO₂ in the massive ores which contain less granular ilmenite in comparison to the disseminated ores which contain 3 to 8 percentage points higher granular ilmenite than the massive ores. On the scale of the main magnetite seam, the TiO₂ content increases with increasing stratigraphic height from being completely absent in the footwall anorthosite. The V₂2O₅ content also increases with stratigraphic height except for in one of the 3 boreholes where it drops with increasing height. The decrease or increase patterns are repeated in every seam. The titanomagnetites of the main magnetite seam display a variety of textures from coarse granular magnetite and ilmenite, to trellis ilmenite lamellae, intergranular ilmenite and magnesian spinels and fine exsolution lamellae of ulvospinel and ferro-magnesian spinels parallel to the magnetite cleavage. The bottom contact of the main magnetite seam is very sharp and there is no titanium or vanadium in the footwall barely 10cm below the contact. Chromium is present in the bottom of the 4 layers that constitute the main magnetite seam and it upwards decreases rapidly. In boreholes P21 and P55, there are slight reversals in the TiO₂ and V₂O₅ content towards the top of the magnetite seams.
- Full Text:
DNS traffic based classifiers for the automatic classification of botnet domains
- Authors: Stalmans, Etienne Raymond
- Date: 2014
- Subjects: Denial of service attacks -- Research , Computer security -- Research , Internet -- Security measures -- Research , Malware (Computer software) , Spam (Electronic mail) , Phishing , Command and control systems
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4684 , http://hdl.handle.net/10962/d1007739
- Description: Networks of maliciously compromised computers, known as botnets, consisting of thousands of hosts have emerged as a serious threat to Internet security in recent years. These compromised systems, under the control of an operator are used to steal data, distribute malware and spam, launch phishing attacks and in Distributed Denial-of-Service (DDoS) attacks. The operators of these botnets use Command and Control (C2) servers to communicate with the members of the botnet and send commands. The communications channels between the C2 nodes and endpoints have employed numerous detection avoidance mechanisms to prevent the shutdown of the C2 servers. Two prevalent detection avoidance techniques used by current botnets are algorithmically generated domain names and DNS Fast-Flux. The use of these mechanisms can however be observed and used to create distinct signatures that in turn can be used to detect DNS domains being used for C2 operation. This report details research conducted into the implementation of three classes of classification techniques that exploit these signatures in order to accurately detect botnet traffic. The techniques described make use of the traffic from DNS query responses created when members of a botnet try to contact the C2 servers. Traffic observation and categorisation is passive from the perspective of the communicating nodes. The first set of classifiers explored employ frequency analysis to detect the algorithmically generated domain names used by botnets. These were found to have a high degree of accuracy with a low false positive rate. The characteristics of Fast-Flux domains are used in the second set of classifiers. It is shown that using these characteristics Fast-Flux domains can be accurately identified and differentiated from legitimate domains (such as Content Distribution Networks exhibit similar behaviour). The final set of classifiers use spatial autocorrelation to detect Fast-Flux domains based on the geographic distribution of the botnet C2 servers to which the detected domains resolve. It is shown that botnet C2 servers can be detected solely based on their geographic location. This technique is shown to clearly distinguish between malicious and legitimate domains. The implemented classifiers are lightweight and use existing network traffic to detect botnets and thus do not require major architectural changes to the network. The performance impact of implementing classification of DNS traffic is examined and it is shown that the performance impact is at an acceptable level.
- Full Text:
- Authors: Stalmans, Etienne Raymond
- Date: 2014
- Subjects: Denial of service attacks -- Research , Computer security -- Research , Internet -- Security measures -- Research , Malware (Computer software) , Spam (Electronic mail) , Phishing , Command and control systems
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4684 , http://hdl.handle.net/10962/d1007739
- Description: Networks of maliciously compromised computers, known as botnets, consisting of thousands of hosts have emerged as a serious threat to Internet security in recent years. These compromised systems, under the control of an operator are used to steal data, distribute malware and spam, launch phishing attacks and in Distributed Denial-of-Service (DDoS) attacks. The operators of these botnets use Command and Control (C2) servers to communicate with the members of the botnet and send commands. The communications channels between the C2 nodes and endpoints have employed numerous detection avoidance mechanisms to prevent the shutdown of the C2 servers. Two prevalent detection avoidance techniques used by current botnets are algorithmically generated domain names and DNS Fast-Flux. The use of these mechanisms can however be observed and used to create distinct signatures that in turn can be used to detect DNS domains being used for C2 operation. This report details research conducted into the implementation of three classes of classification techniques that exploit these signatures in order to accurately detect botnet traffic. The techniques described make use of the traffic from DNS query responses created when members of a botnet try to contact the C2 servers. Traffic observation and categorisation is passive from the perspective of the communicating nodes. The first set of classifiers explored employ frequency analysis to detect the algorithmically generated domain names used by botnets. These were found to have a high degree of accuracy with a low false positive rate. The characteristics of Fast-Flux domains are used in the second set of classifiers. It is shown that using these characteristics Fast-Flux domains can be accurately identified and differentiated from legitimate domains (such as Content Distribution Networks exhibit similar behaviour). The final set of classifiers use spatial autocorrelation to detect Fast-Flux domains based on the geographic distribution of the botnet C2 servers to which the detected domains resolve. It is shown that botnet C2 servers can be detected solely based on their geographic location. This technique is shown to clearly distinguish between malicious and legitimate domains. The implemented classifiers are lightweight and use existing network traffic to detect botnets and thus do not require major architectural changes to the network. The performance impact of implementing classification of DNS traffic is examined and it is shown that the performance impact is at an acceptable level.
- Full Text:
Effect of diet and sex-sorting on growth and gonad development in farmed South African abalone, Haliotis midae
- Authors: Ayres, Devin William Philip
- Date: 2014
- Subjects: Haliotis midae -- South Africa , Haliotis midae fisheries -- South Africa , Abalone culture -- South Africa , Abalones -- Physiology -- South Africa , Abalones -- South Africa -- Growth , Abalones -- Feeding and feeds -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5357 , http://hdl.handle.net/10962/d1010856 , Haliotis midae -- South Africa , Haliotis midae fisheries -- South Africa , Abalone culture -- South Africa , Abalones -- Physiology -- South Africa , Abalones -- South Africa -- Growth , Abalones -- Feeding and feeds -- South Africa
- Description: Abalone, Haliotis midae, farmers in South Africa that feed formulated diets reported a periodic drop in abalone growth during periods of increased gonad development. A large drop in abalone biomass was noticed after presumed spawning events. This study was aimed to determine the effect of diet and sex-sorting on gonad development in abalone. Experiments were conducted on a commercial abalone farm from July 2012 to the end of June 2013. Isonitrogenous and isoenergetic diets were formulated with two protein sources. A fishmeal and soybean meal (S-diet) diet and a fishmeal only (F-diet) diet were fed to abalone (50 - 70 g abalone⁻¹) over 12 months. Weight and length gain, gonad bulk index (GBI), visceral index (%) and meat mass index (%) were determined monthly and seasonally. A histological study on the female gonads was conducted. This study also included an experiment to test the effect of sex-sorting (70 - 80 g abalone⁻¹) on growth and body composition with treatments including males (M), females (F) and equal numbers of males and females (MF). Weight gain and length gain were faster in S-diet-fed abalone (RM-ANOVA, F ₍₁, ₁₆₎ = 7.77, p = 0.01; F ₍₁, ₆₉₎ = 49.9, p < 0.001, respectively). Gonad development was significantly affected by the inclusion of soybean meal with S-diet-fed abalone showing higher GBI-values than F-diet-fed abalone (RM-ANOVA, F ₍₁, ₃₃)= 16.22, p = 0.0003). Male abalone had higher GBI-values than females (RM-ANOVA, F ₍₁, ₃₃₎ = 39.87, p < 0.0001). There was no significant difference in average feed conversion ratio (FCR) between diets over time (RM-ANOVA, F ₍₁, ₂₁₎ = 0.008, p = 0.97). However, average FCR-values were significantly highest between November 2012 and March 2013, the presumed spawning season. The visceral mass (gut and gonad) as a proportion of whole mass (visceral index, %) was significantly higher in abalone fed the S-diet (RM-ANOVA; F ₍₁, ₆₉₎ = 68.06, p < 0.0001). There was no difference in meat mass index (%) between diets for both male and female abalone (RM-ANOVA; F ₍₇, ₂₄₈₎ = 0.80, p = 0.60; F ₍₇, ₂₄₁₎ = 1.7, p = 0.11,respectively). Meat mass index significantly decreased from September 2012 to February 2013 coinciding with the period of high GBI-values. The distribution of oocyte maturity stages differed between diets. The majority of oocytes within S-diet-fed abalone were fully mature stage 8 oocytes compared to a majority of stage 7 oocytes in F-diet-fed abalone. Histology corroborated peaks in GBI-values for abalone fed both diets. There was no significant difference in growth, GBI, visceral index (%) and meat mass index (%) between abalone sorted into monosex and mixed-sex populations. Thus, the presence of the opposite sex did not have an effect on growth and gonad mass in H. midae. The phytoestrogens daidzin, glycitin, genistin, daidzein, glycitein and genistein were present in soybean meal and only traceable amounts were found in the F-diet. This study provided evidence that soybean meal present in formulated feed affected growth and gonad development in H.midae. The difference in the distribution of the maturity stages of oocytes was affected by diet. Sex-sorting abalone into monosex and mixed-sex populations had no influence on weight and length gain and gonad development.
- Full Text:
- Authors: Ayres, Devin William Philip
- Date: 2014
- Subjects: Haliotis midae -- South Africa , Haliotis midae fisheries -- South Africa , Abalone culture -- South Africa , Abalones -- Physiology -- South Africa , Abalones -- South Africa -- Growth , Abalones -- Feeding and feeds -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5357 , http://hdl.handle.net/10962/d1010856 , Haliotis midae -- South Africa , Haliotis midae fisheries -- South Africa , Abalone culture -- South Africa , Abalones -- Physiology -- South Africa , Abalones -- South Africa -- Growth , Abalones -- Feeding and feeds -- South Africa
- Description: Abalone, Haliotis midae, farmers in South Africa that feed formulated diets reported a periodic drop in abalone growth during periods of increased gonad development. A large drop in abalone biomass was noticed after presumed spawning events. This study was aimed to determine the effect of diet and sex-sorting on gonad development in abalone. Experiments were conducted on a commercial abalone farm from July 2012 to the end of June 2013. Isonitrogenous and isoenergetic diets were formulated with two protein sources. A fishmeal and soybean meal (S-diet) diet and a fishmeal only (F-diet) diet were fed to abalone (50 - 70 g abalone⁻¹) over 12 months. Weight and length gain, gonad bulk index (GBI), visceral index (%) and meat mass index (%) were determined monthly and seasonally. A histological study on the female gonads was conducted. This study also included an experiment to test the effect of sex-sorting (70 - 80 g abalone⁻¹) on growth and body composition with treatments including males (M), females (F) and equal numbers of males and females (MF). Weight gain and length gain were faster in S-diet-fed abalone (RM-ANOVA, F ₍₁, ₁₆₎ = 7.77, p = 0.01; F ₍₁, ₆₉₎ = 49.9, p < 0.001, respectively). Gonad development was significantly affected by the inclusion of soybean meal with S-diet-fed abalone showing higher GBI-values than F-diet-fed abalone (RM-ANOVA, F ₍₁, ₃₃)= 16.22, p = 0.0003). Male abalone had higher GBI-values than females (RM-ANOVA, F ₍₁, ₃₃₎ = 39.87, p < 0.0001). There was no significant difference in average feed conversion ratio (FCR) between diets over time (RM-ANOVA, F ₍₁, ₂₁₎ = 0.008, p = 0.97). However, average FCR-values were significantly highest between November 2012 and March 2013, the presumed spawning season. The visceral mass (gut and gonad) as a proportion of whole mass (visceral index, %) was significantly higher in abalone fed the S-diet (RM-ANOVA; F ₍₁, ₆₉₎ = 68.06, p < 0.0001). There was no difference in meat mass index (%) between diets for both male and female abalone (RM-ANOVA; F ₍₇, ₂₄₈₎ = 0.80, p = 0.60; F ₍₇, ₂₄₁₎ = 1.7, p = 0.11,respectively). Meat mass index significantly decreased from September 2012 to February 2013 coinciding with the period of high GBI-values. The distribution of oocyte maturity stages differed between diets. The majority of oocytes within S-diet-fed abalone were fully mature stage 8 oocytes compared to a majority of stage 7 oocytes in F-diet-fed abalone. Histology corroborated peaks in GBI-values for abalone fed both diets. There was no significant difference in growth, GBI, visceral index (%) and meat mass index (%) between abalone sorted into monosex and mixed-sex populations. Thus, the presence of the opposite sex did not have an effect on growth and gonad mass in H. midae. The phytoestrogens daidzin, glycitin, genistin, daidzein, glycitein and genistein were present in soybean meal and only traceable amounts were found in the F-diet. This study provided evidence that soybean meal present in formulated feed affected growth and gonad development in H.midae. The difference in the distribution of the maturity stages of oocytes was affected by diet. Sex-sorting abalone into monosex and mixed-sex populations had no influence on weight and length gain and gonad development.
- Full Text:
Electrospun sorbents for solid phase extraction (SPE) and colorimetric detection of pesticides
- Authors: Gulamussen, Noor Jehan
- Date: 2014
- Subjects: Sorbents , Electrospinning , Extraction (Chemistry) , Colorimetry , Pesticides , Water -- Pesticide content -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4501 , http://hdl.handle.net/10962/d1013241
- Description: The thesis presents the evaluation of polysulfone sorbents for solid phase extraction (SPE) and the development of colorimetric probes for pesticides analysis in water. Through electrospraying and electrospinning techniques, different morphologies of sorbents (particles, beaded fibers and bead-free fibers) were fabricated. The sorbents were morphologically characterized by scanning electron microscopy. Adsorption capacities of sorbents were evaluated by conducting recoveries studies for model pesticides; atrazine, chlorpyrifos and DDT using batch and column SPE modes. Better recovery results were achieved by employing the batch mode of fibers, as values ranged from 98 to 105percent. Further sorbent evaluation was conducted using breakthrough experiments and static experiments. The breakthrough studies indicated that 1700 μL was the sample volume that could be percolated with no breakthrough of the analyte that correspond to a concentration of 150 mg/g of sorbent that can be extracted without any loss of analyte. From static studies, quantities of each model compound adsorbed into the fiber at the equilibrium time were evaluated. The adsorbed atrazine was 65, chlorpyrifos 250 and DDT 400 mg/g of sorbent. Kinetic studies suggested retention mechanism following pseudo first and second order model observed by high correlation coefficients (> 0. 96), demonstrating the fiber affinity to retain both polar and non-polar compounds opening a possibility to be used as sorbent for sample preparation of different classes of pesticides in water. For the second part of the study simple strategies for colorimetric sensing based on silver nanoparticles and polivinylpyrrolidone capped nanoparticles were developed, respectively for atrazine and chlorpyrifos detection. The limits of detection of the methods were 3.32 and 0.88 mg/L for atrazine and chlorpyrifos respectively. The applicability of the probe in real samples was demonstrated by the recoveries studies of tap water varying from 94 to 104 percent. The versatility of the probe was demonstrated by affording a simple, rapid and selective detection of atrazine and chlorpyrifos in the presence of other pesticides by direct analysis without employing any sample handling steps. Attempt to incorporate the probes in a solid support was achieved by using nylon 6 as solid support polymer proving to be fast and useful for on-site detection.
- Full Text:
- Authors: Gulamussen, Noor Jehan
- Date: 2014
- Subjects: Sorbents , Electrospinning , Extraction (Chemistry) , Colorimetry , Pesticides , Water -- Pesticide content -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4501 , http://hdl.handle.net/10962/d1013241
- Description: The thesis presents the evaluation of polysulfone sorbents for solid phase extraction (SPE) and the development of colorimetric probes for pesticides analysis in water. Through electrospraying and electrospinning techniques, different morphologies of sorbents (particles, beaded fibers and bead-free fibers) were fabricated. The sorbents were morphologically characterized by scanning electron microscopy. Adsorption capacities of sorbents were evaluated by conducting recoveries studies for model pesticides; atrazine, chlorpyrifos and DDT using batch and column SPE modes. Better recovery results were achieved by employing the batch mode of fibers, as values ranged from 98 to 105percent. Further sorbent evaluation was conducted using breakthrough experiments and static experiments. The breakthrough studies indicated that 1700 μL was the sample volume that could be percolated with no breakthrough of the analyte that correspond to a concentration of 150 mg/g of sorbent that can be extracted without any loss of analyte. From static studies, quantities of each model compound adsorbed into the fiber at the equilibrium time were evaluated. The adsorbed atrazine was 65, chlorpyrifos 250 and DDT 400 mg/g of sorbent. Kinetic studies suggested retention mechanism following pseudo first and second order model observed by high correlation coefficients (> 0. 96), demonstrating the fiber affinity to retain both polar and non-polar compounds opening a possibility to be used as sorbent for sample preparation of different classes of pesticides in water. For the second part of the study simple strategies for colorimetric sensing based on silver nanoparticles and polivinylpyrrolidone capped nanoparticles were developed, respectively for atrazine and chlorpyrifos detection. The limits of detection of the methods were 3.32 and 0.88 mg/L for atrazine and chlorpyrifos respectively. The applicability of the probe in real samples was demonstrated by the recoveries studies of tap water varying from 94 to 104 percent. The versatility of the probe was demonstrated by affording a simple, rapid and selective detection of atrazine and chlorpyrifos in the presence of other pesticides by direct analysis without employing any sample handling steps. Attempt to incorporate the probes in a solid support was achieved by using nylon 6 as solid support polymer proving to be fast and useful for on-site detection.
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