Towards understanding how exploitation influences the wild energetic response of marine fish to temperature variability
- Authors: Skeeles, Michael Richard
- Date: 2020
- Subjects: Chrysoblepus laticeps -- Climatic factors , Sparidae -- Genetics , Sparidae -- South Africa -- Climatic factors
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/145133 , vital:38411
- Description: Exploitation of fish populations can exacerbate the effects of climate change, yet our understanding of their synergistic effects remains limited. As fish are increasingly exposed to temperatures on the edges of their optimal thermal performance window, their physiological response is expected to shape their future performance. It is therefore concerning that exploitation can select for specific physiological phenotypes, as this may affect fished populations’ physiological response to temperature change. A recent laboratory study revealed fewer high-performance metabolic-scope phenotypes in an exploited population of the marine Sparid Chrysoblepus laticeps across a range of experimental temperatures in comparison to an unexploited population. This suggested that individuals in exploited populations may have less available energy for aerobic performance at thermal extremes, which may reduce the resilience of the population to changes in temperature. However, since laboratory experiments exclude numerous other variables that fish encounter in the wild, it was necessary to test this finding in a natural setting. This thesis aimed to further develop the laboratory study by assessing whether exploitation effects the wild energetic response of C. laticeps to thermal variability. To achieve this, the field metabolic rate of C. laticeps, a resident and endemic South African fish, from a near-pristine population (Tsitsikamma National Park) and a heavily exploited population (Port Elizabeth) was compared using acoustic accelerometry. A laboratory-based study using a swim-tunnel respirometer and accelerometer transmitters was conducted to develop a model to predict metabolic rate from acceleration data at temperatures from 10 to 22⁰C. Acceleration, temperature, mass and population (exploited/unexploited) were found to be the best predictors of the metabolic rate of C. laticeps and were incorporated into the model to estimate the field metabolic rate of fish tagged with acoustic accelerometers in the wild. To examine the combined effects of temperature and exploitation on the field metabolic rate of C. laticeps in their natural state, two fine-scale telemetry arrays with temperature loggers were used to assess the acceleration of the fish across different temperatures in the wild for three months during a period of high thermal variability. Ten fish from the exploited and unexploited populations were caught, surgically implanted with accelerometer transmitters and released back into the wild. Close to 500 000 and 400 000 acceleration estimates were recorded from wild exploited and unexploited fish, respectively. The field metabolic rate of both populations was estimated by combining the field acceleration and temperature data with the laboratory calibration model. The field metabolic rate of C. laticeps from the exploited population was constrained near cold and warm extremes compared to no constraints observed in the unexploited population. This was attributed to reduced inter-individual variability in the field metabolic rate-temperature relationship within the exploited population. There appeared to be a greater proportion of individuals that maintained a high field metabolic rate at extreme temperatures in the unexploited population. In contrast, all but one fish from the exploited population did not maintain a high field metabolic rate at extreme temperatures. These findings aligned with the laboratory-based metabolic-scope study on both populations of C. laticeps and demonstrate that passive-fishing may be removing thermally tolerant individuals and rendering exploited populations less resilient to thermal change. These findings are discussed in the context of fisheries management and particularly on the role that marine protected areas could play in maintaining physiological diversity, and therefore the resilience of fish in the Anthropocene. This study highlights the importance of applied conservation physiology in understanding the consequences of fisheries-induced evolution in an increasingly variable climate.
- Full Text:
- Date Issued: 2020
- Authors: Skeeles, Michael Richard
- Date: 2020
- Subjects: Chrysoblepus laticeps -- Climatic factors , Sparidae -- Genetics , Sparidae -- South Africa -- Climatic factors
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/145133 , vital:38411
- Description: Exploitation of fish populations can exacerbate the effects of climate change, yet our understanding of their synergistic effects remains limited. As fish are increasingly exposed to temperatures on the edges of their optimal thermal performance window, their physiological response is expected to shape their future performance. It is therefore concerning that exploitation can select for specific physiological phenotypes, as this may affect fished populations’ physiological response to temperature change. A recent laboratory study revealed fewer high-performance metabolic-scope phenotypes in an exploited population of the marine Sparid Chrysoblepus laticeps across a range of experimental temperatures in comparison to an unexploited population. This suggested that individuals in exploited populations may have less available energy for aerobic performance at thermal extremes, which may reduce the resilience of the population to changes in temperature. However, since laboratory experiments exclude numerous other variables that fish encounter in the wild, it was necessary to test this finding in a natural setting. This thesis aimed to further develop the laboratory study by assessing whether exploitation effects the wild energetic response of C. laticeps to thermal variability. To achieve this, the field metabolic rate of C. laticeps, a resident and endemic South African fish, from a near-pristine population (Tsitsikamma National Park) and a heavily exploited population (Port Elizabeth) was compared using acoustic accelerometry. A laboratory-based study using a swim-tunnel respirometer and accelerometer transmitters was conducted to develop a model to predict metabolic rate from acceleration data at temperatures from 10 to 22⁰C. Acceleration, temperature, mass and population (exploited/unexploited) were found to be the best predictors of the metabolic rate of C. laticeps and were incorporated into the model to estimate the field metabolic rate of fish tagged with acoustic accelerometers in the wild. To examine the combined effects of temperature and exploitation on the field metabolic rate of C. laticeps in their natural state, two fine-scale telemetry arrays with temperature loggers were used to assess the acceleration of the fish across different temperatures in the wild for three months during a period of high thermal variability. Ten fish from the exploited and unexploited populations were caught, surgically implanted with accelerometer transmitters and released back into the wild. Close to 500 000 and 400 000 acceleration estimates were recorded from wild exploited and unexploited fish, respectively. The field metabolic rate of both populations was estimated by combining the field acceleration and temperature data with the laboratory calibration model. The field metabolic rate of C. laticeps from the exploited population was constrained near cold and warm extremes compared to no constraints observed in the unexploited population. This was attributed to reduced inter-individual variability in the field metabolic rate-temperature relationship within the exploited population. There appeared to be a greater proportion of individuals that maintained a high field metabolic rate at extreme temperatures in the unexploited population. In contrast, all but one fish from the exploited population did not maintain a high field metabolic rate at extreme temperatures. These findings aligned with the laboratory-based metabolic-scope study on both populations of C. laticeps and demonstrate that passive-fishing may be removing thermally tolerant individuals and rendering exploited populations less resilient to thermal change. These findings are discussed in the context of fisheries management and particularly on the role that marine protected areas could play in maintaining physiological diversity, and therefore the resilience of fish in the Anthropocene. This study highlights the importance of applied conservation physiology in understanding the consequences of fisheries-induced evolution in an increasingly variable climate.
- Full Text:
- Date Issued: 2020
Understanding of the underlying resistance mechanism of the Kat-G protein against isoniazid in Mycobacterium tuberculosis using bioinformatics approaches
- Authors: Barozi, Victor
- Date: 2020
- Subjects: Mycobacterium tuberculosis , Isoniazid , Drug resistance in microorganisms , Proteins -- Microbiology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/146592 , vital:38540
- Description: Tuberculosis (TB) is a multi-organ infection caused by rod-shaped acid-fast Mycobacterium tuberculosis. The World Health Organization (WHO) ranks TB among the top 10 fatal infections and the leading the cause of death from a single infection. In 2017, TB was responsible for an estimated 1.3 million deaths among both the HIV negative and positive populations worldwide (WHO, 2018). Approximately 23% (roughly 1.7 billion) of the world’s population is estimated to have latent TB with a high risk of reverting to active TB infection. In 2017, an estimated 558,000 people developed drug resistant TB worldwide with 82% of the cases being multi-drug resistant TB (WHO, 2018). South Africa is ranked among the 30 high TB burdened countries with a TB incidence of 322,000 cases in 2017 accounting for 3% of the world’s TB cases. TB is curable and is clinically managed through a combination of intensive and continuation phases of first-line drugs (isoniazid, rifampicin, ethambutol, and pyrazinamide). Second-line drugs which include fluoroquinolones, injectable aminoglycoside and injectable polypeptides are used in cases of first line drug resistance. The third-line drugs include amoxicillin, clofazimine, linezolid and imipenem. These have variable but unproven efficacy to TB and are the last resort in cases of total drug resistance (Jilani et al., 2019). TB drug resistance to first-line drugs especially isoniazid in M. tuberculosis has been attributed to single nucleotide polymorphisms (SNPs) in the catalase peroxidase enzyme (katG), a protein important in the activation of the pro-drug isoniazid. The SNPs especially at position 315 of the katG enzyme are believed to reduce the sensitivity of the M. tuberculosis to isoniazid while still maintaining the enzyme’s catalytic activity - a mechanism not completely understood. KatG protein is important for protecting the bacteria from hydro peroxides and hydroxyl radicals present in an aerobic environment. This study focused on understanding the mechanism of isoniazid drug resistance in M. tuberculosis as a result of high confidence mutations in the katG through modelling the enzyme with its respective variants, performing MD simulations to explore the protein behaviour, calculating the dynamic residue network analysis (DRN) of the variants in respect to the wild type katG and finally performing alanine scanning. From the MD simulations, it was observed that the high confidence mutations i.e. S140R, S140N, G279D, G285D, S315T, S315I, S315R, S315N, G316D, S457I and G593D were not only reducing the backbone flexibility of the protein but also reducing the protein’s conformational variation and space. All the variant protein structures were observed to be more compact compared to the wild type. Residue fluctuation results indicated reduced residue flexibility across all variants in the loop region (position 26-110) responsible for katG dimerization. In addition, mutation S315T is believed to reduce the size of the active site access channel in the protein. From the DRN data, residues in the interface region between the N and C-terminal domains were observed to gain importance in the variants irrespective of the mutation location indicating an allosteric effect of the mutations on the interface region. Alanine scanning results established that residue Leucine at position 48 was not only important in the protein communication but also a destabilizing residue across all the variants. The study not only demonstrated change in the protein behaviour but also showed allosteric effect of the mutations in the katG protein.
- Full Text:
- Date Issued: 2020
- Authors: Barozi, Victor
- Date: 2020
- Subjects: Mycobacterium tuberculosis , Isoniazid , Drug resistance in microorganisms , Proteins -- Microbiology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/146592 , vital:38540
- Description: Tuberculosis (TB) is a multi-organ infection caused by rod-shaped acid-fast Mycobacterium tuberculosis. The World Health Organization (WHO) ranks TB among the top 10 fatal infections and the leading the cause of death from a single infection. In 2017, TB was responsible for an estimated 1.3 million deaths among both the HIV negative and positive populations worldwide (WHO, 2018). Approximately 23% (roughly 1.7 billion) of the world’s population is estimated to have latent TB with a high risk of reverting to active TB infection. In 2017, an estimated 558,000 people developed drug resistant TB worldwide with 82% of the cases being multi-drug resistant TB (WHO, 2018). South Africa is ranked among the 30 high TB burdened countries with a TB incidence of 322,000 cases in 2017 accounting for 3% of the world’s TB cases. TB is curable and is clinically managed through a combination of intensive and continuation phases of first-line drugs (isoniazid, rifampicin, ethambutol, and pyrazinamide). Second-line drugs which include fluoroquinolones, injectable aminoglycoside and injectable polypeptides are used in cases of first line drug resistance. The third-line drugs include amoxicillin, clofazimine, linezolid and imipenem. These have variable but unproven efficacy to TB and are the last resort in cases of total drug resistance (Jilani et al., 2019). TB drug resistance to first-line drugs especially isoniazid in M. tuberculosis has been attributed to single nucleotide polymorphisms (SNPs) in the catalase peroxidase enzyme (katG), a protein important in the activation of the pro-drug isoniazid. The SNPs especially at position 315 of the katG enzyme are believed to reduce the sensitivity of the M. tuberculosis to isoniazid while still maintaining the enzyme’s catalytic activity - a mechanism not completely understood. KatG protein is important for protecting the bacteria from hydro peroxides and hydroxyl radicals present in an aerobic environment. This study focused on understanding the mechanism of isoniazid drug resistance in M. tuberculosis as a result of high confidence mutations in the katG through modelling the enzyme with its respective variants, performing MD simulations to explore the protein behaviour, calculating the dynamic residue network analysis (DRN) of the variants in respect to the wild type katG and finally performing alanine scanning. From the MD simulations, it was observed that the high confidence mutations i.e. S140R, S140N, G279D, G285D, S315T, S315I, S315R, S315N, G316D, S457I and G593D were not only reducing the backbone flexibility of the protein but also reducing the protein’s conformational variation and space. All the variant protein structures were observed to be more compact compared to the wild type. Residue fluctuation results indicated reduced residue flexibility across all variants in the loop region (position 26-110) responsible for katG dimerization. In addition, mutation S315T is believed to reduce the size of the active site access channel in the protein. From the DRN data, residues in the interface region between the N and C-terminal domains were observed to gain importance in the variants irrespective of the mutation location indicating an allosteric effect of the mutations on the interface region. Alanine scanning results established that residue Leucine at position 48 was not only important in the protein communication but also a destabilizing residue across all the variants. The study not only demonstrated change in the protein behaviour but also showed allosteric effect of the mutations in the katG protein.
- Full Text:
- Date Issued: 2020
Understanding the relationship between mangrove composition, stand dynamics and resource use in the Ntafufu estuary, Eastern Cape, as basis for sustainable resource use
- Mvakade, Monica, Rajkaran, Anusha
- Authors: Mvakade, Monica , Rajkaran, Anusha
- Date: 2020
- Subjects: Estuarine ecology -- South Africa -- Eastern Cape , Aquatic ecology , Marine sciences , Fresh water
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49215 , vital:41611
- Description: Traditionally, coastal communities along the Wild Coast in the Eastern Cape, used mangrove forests for their livelihoods and socio-economic needs. Mangroves along the Eastern Cape coast are threatened by both natural and human factors. The wood obtained from the mangroves by rural households was used as poles for house and fence construction, firewood, and traditional medicine. This is a threat to the status of several mangrove species in this and surrounding areas. The harvesting of mangrove trees will have a direct and indirect effect on the other biotic and abiotic components of the mangrove ecosystems. The Department of Agriculture, Forestry and Fisheries (DAFF) (currently the Department of Environment, Forestry and Fisheries, or DEFF), through the National Forest Act no 84 of 1998, was directly responsible for the wellbeing of the national forests in South Africa. This also includes the mangroves as a specific national forest type. Several estuaries with mangroves occur within state forests. The harvesting and clear-felling of trees for timber and land conversion and associated waste of harvested mangrove poles and laths causes the many changes in mangrove forests. The aim of this study was to develop a framework for sustainable management of the mangroves for the Mtambalala forest management unit. This was done in relation to the requirements of the current legislation, policy guidelines and business plan of the management authority. The aim was pursued through two specific objectives. The first objective was to understand the variation in the composition in different parts of the Ntafufu Estuary, and the population dynamics of the main mangrove species, as basis for the development of sustainable resource use practices. Plots along transects were used to measure seedling to adult ratios, population structure and abiotic characteristics. The second objective was to understand the community use and requirements of mangrove wood from the Ntafufu Estuary. A participatory approach was followed to collect demographic data from each community, the requirements of mangrove poles and behaviour of harvesters. This was used to set up a framework to guide the sustainable management of mangroves based on the current status and stand dynamics of the mangrove communities. There are three mangrove species found in the Ntafufu Estuary: Bruguiera gymnorhiza (black mangrove) regenerates under the mangrove canopy and forms layers of even-aged stands. Avicennia marina (white mangrove) does not regenerate under a mangrove canopy i.e. the seedlings establish outside the canopy. A few Rhizophora mucronata (red mangrove) trees exist in the lower intertidal zone and form multiple stems on stilt roots. The mangrove associate, Hibiscus tiliaceus (wild cotton tree- mangrove associate), forms dense clusters of scrambling stems. Some of the Avicennia individuals show signs of mangrove bleeding and one individual of Bruguiera showed indications of disease. Mngazana and Ntafufu Estuaries had the highest tree densities of 2594 and 1402 trees ha-1 respectively, typical of riverine mangrove forest. The seedling to adult ratio was high in this study: 12.8 for B. gymnorrhiza and 24.3 for A. marina. Abandoned cut stems and laths were found during the study. Bark harvested for traditional medicine and cattle feeding in mangroves was also prevalent and expected to reduce the health of the forest. Mangroves in the Ntafufu Estuary are expanding, and the population structure of the three mangrove species showed a healthy balance between young and mature stems. The harvesting of Black mangrove (B. gymnorrhiza) poles for mainly roof construction is relatively limited. As part of the functions of the DAFF, the use of the mangrove resources has to be balanced with the resource availability from the mangroves, and this should result in a healthy functioning mangrove forest. Development of a participatory forest management (PFM) plan for a forest estate and its forest management unit, require an understanding of the mangrove communities and their dynamics, and the current level of resource use associated with the mangroves. The study recommended that a Mangrove Pole Harvesters Group is needed to practice silviculture through guidance of relevant governmental personnel.
- Full Text:
- Date Issued: 2020
- Authors: Mvakade, Monica , Rajkaran, Anusha
- Date: 2020
- Subjects: Estuarine ecology -- South Africa -- Eastern Cape , Aquatic ecology , Marine sciences , Fresh water
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49215 , vital:41611
- Description: Traditionally, coastal communities along the Wild Coast in the Eastern Cape, used mangrove forests for their livelihoods and socio-economic needs. Mangroves along the Eastern Cape coast are threatened by both natural and human factors. The wood obtained from the mangroves by rural households was used as poles for house and fence construction, firewood, and traditional medicine. This is a threat to the status of several mangrove species in this and surrounding areas. The harvesting of mangrove trees will have a direct and indirect effect on the other biotic and abiotic components of the mangrove ecosystems. The Department of Agriculture, Forestry and Fisheries (DAFF) (currently the Department of Environment, Forestry and Fisheries, or DEFF), through the National Forest Act no 84 of 1998, was directly responsible for the wellbeing of the national forests in South Africa. This also includes the mangroves as a specific national forest type. Several estuaries with mangroves occur within state forests. The harvesting and clear-felling of trees for timber and land conversion and associated waste of harvested mangrove poles and laths causes the many changes in mangrove forests. The aim of this study was to develop a framework for sustainable management of the mangroves for the Mtambalala forest management unit. This was done in relation to the requirements of the current legislation, policy guidelines and business plan of the management authority. The aim was pursued through two specific objectives. The first objective was to understand the variation in the composition in different parts of the Ntafufu Estuary, and the population dynamics of the main mangrove species, as basis for the development of sustainable resource use practices. Plots along transects were used to measure seedling to adult ratios, population structure and abiotic characteristics. The second objective was to understand the community use and requirements of mangrove wood from the Ntafufu Estuary. A participatory approach was followed to collect demographic data from each community, the requirements of mangrove poles and behaviour of harvesters. This was used to set up a framework to guide the sustainable management of mangroves based on the current status and stand dynamics of the mangrove communities. There are three mangrove species found in the Ntafufu Estuary: Bruguiera gymnorhiza (black mangrove) regenerates under the mangrove canopy and forms layers of even-aged stands. Avicennia marina (white mangrove) does not regenerate under a mangrove canopy i.e. the seedlings establish outside the canopy. A few Rhizophora mucronata (red mangrove) trees exist in the lower intertidal zone and form multiple stems on stilt roots. The mangrove associate, Hibiscus tiliaceus (wild cotton tree- mangrove associate), forms dense clusters of scrambling stems. Some of the Avicennia individuals show signs of mangrove bleeding and one individual of Bruguiera showed indications of disease. Mngazana and Ntafufu Estuaries had the highest tree densities of 2594 and 1402 trees ha-1 respectively, typical of riverine mangrove forest. The seedling to adult ratio was high in this study: 12.8 for B. gymnorrhiza and 24.3 for A. marina. Abandoned cut stems and laths were found during the study. Bark harvested for traditional medicine and cattle feeding in mangroves was also prevalent and expected to reduce the health of the forest. Mangroves in the Ntafufu Estuary are expanding, and the population structure of the three mangrove species showed a healthy balance between young and mature stems. The harvesting of Black mangrove (B. gymnorrhiza) poles for mainly roof construction is relatively limited. As part of the functions of the DAFF, the use of the mangrove resources has to be balanced with the resource availability from the mangroves, and this should result in a healthy functioning mangrove forest. Development of a participatory forest management (PFM) plan for a forest estate and its forest management unit, require an understanding of the mangrove communities and their dynamics, and the current level of resource use associated with the mangroves. The study recommended that a Mangrove Pole Harvesters Group is needed to practice silviculture through guidance of relevant governmental personnel.
- Full Text:
- Date Issued: 2020
Understanding the underlying resistance mechanism of Mycobacterium tuberculosis against Rifampicin by analyzing mutant DNA - directed RNA polymerase proteins via bioinformatics approaches
- Authors: Monama, Mokgerwa Zacharia
- Date: 2020
- Subjects: Mycobacterium tuberculosis , Rifampin , Drug resistance , Homology (Biology) , Tuberculosis -- Chemotherapy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167508 , vital:41487
- Description: Tuberculosis or TB is an airborne disease caused by the non-motile bacilli, Mycobacterium tuberculosis (MTB). There are two main forms of TB, namely, latent TB or LTB, asymptomatic and non-contagious version which according to the World Health Organization (WHO) is estimated to afflict over a third of the world’s population; and active TB or ATB, a symptomatic and contagious version which continues to spread, affecting millions worldwide. With the already high reported prevalence of TB, the emergence of drug-resistant strains has prompted the development of novel approaches to enhance the efficacy of known drugs and a desperate search for novel compounds to combat MTB infections. It was for this very purpose that this study was conducted. A look into the resistance mechanism of Rifampicin (Rifampin or RIF), one of the more potent first-line drugs, might prove beneficial in predicting the consequence of an introduced mutation (which usually occur as single nucleotide polymorphisms or SNPs) and perhaps even overcome it using appropriate therapeutic interventions that improve RIF’s efficacy. To accomplish this task, models of acceptable quality were generated for the WT and clinically relevant, RIF resistance conferring, SNPs occurring at codon positions D516, H526 and S531 (E .coli numbering system) using MODELLER. The models were accordingly ranked using GA341 and z-DOPE score, and subsequently validated with QMEAN, PROCHECK and VERIFY3D. MD simulations spanning 100 ns were run for RIF-bound (complex) and RIF-free (holo) DNA-directed RNA polymerase (DDRP) protein systems for the WT and SNP mutants using GROMACS. The MD frames were analyzed using RMSD, Rg and RMSF. For further analysis, MD-TASK was used to analyze the calculated dynamic residue networks (DRNs) from the generated MD frames, determining both change in average shortest path (ΔL) and betweenness centrality (ΔBC). The RMSD analysis revealed that all of the SNP complex models displayed a level instability higher than that of the WT complex. A majority of the SNP complex models were also observed to have similar compactness to the WT holo when looking at the calculated Rg. The RMSF results also hinted towards possible physiological consequences of the mutations (generally referred to as a fitness cost) highlighted by the increased fluctuations of the zinc-binding domain and the MTB SI α helical coiled coil. For the first time, to the knowledge of the authors, DRN analysis was employed for the DDRP protein for both holo and complex systems, revealing insightful information about the residues that play a key role in the change in distance between residue pairs along with residues that play an essential role in protein communication within the calculated RIN. Overall, the data supported the conclusions drawn by a recent study that only concentrated on RIF-resistance in rpoB models which suggested that the binding pocket for the SNP models may result in the changed coordination of RIF which may be the main contributor to its impaired efficacy.
- Full Text:
- Date Issued: 2020
- Authors: Monama, Mokgerwa Zacharia
- Date: 2020
- Subjects: Mycobacterium tuberculosis , Rifampin , Drug resistance , Homology (Biology) , Tuberculosis -- Chemotherapy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/167508 , vital:41487
- Description: Tuberculosis or TB is an airborne disease caused by the non-motile bacilli, Mycobacterium tuberculosis (MTB). There are two main forms of TB, namely, latent TB or LTB, asymptomatic and non-contagious version which according to the World Health Organization (WHO) is estimated to afflict over a third of the world’s population; and active TB or ATB, a symptomatic and contagious version which continues to spread, affecting millions worldwide. With the already high reported prevalence of TB, the emergence of drug-resistant strains has prompted the development of novel approaches to enhance the efficacy of known drugs and a desperate search for novel compounds to combat MTB infections. It was for this very purpose that this study was conducted. A look into the resistance mechanism of Rifampicin (Rifampin or RIF), one of the more potent first-line drugs, might prove beneficial in predicting the consequence of an introduced mutation (which usually occur as single nucleotide polymorphisms or SNPs) and perhaps even overcome it using appropriate therapeutic interventions that improve RIF’s efficacy. To accomplish this task, models of acceptable quality were generated for the WT and clinically relevant, RIF resistance conferring, SNPs occurring at codon positions D516, H526 and S531 (E .coli numbering system) using MODELLER. The models were accordingly ranked using GA341 and z-DOPE score, and subsequently validated with QMEAN, PROCHECK and VERIFY3D. MD simulations spanning 100 ns were run for RIF-bound (complex) and RIF-free (holo) DNA-directed RNA polymerase (DDRP) protein systems for the WT and SNP mutants using GROMACS. The MD frames were analyzed using RMSD, Rg and RMSF. For further analysis, MD-TASK was used to analyze the calculated dynamic residue networks (DRNs) from the generated MD frames, determining both change in average shortest path (ΔL) and betweenness centrality (ΔBC). The RMSD analysis revealed that all of the SNP complex models displayed a level instability higher than that of the WT complex. A majority of the SNP complex models were also observed to have similar compactness to the WT holo when looking at the calculated Rg. The RMSF results also hinted towards possible physiological consequences of the mutations (generally referred to as a fitness cost) highlighted by the increased fluctuations of the zinc-binding domain and the MTB SI α helical coiled coil. For the first time, to the knowledge of the authors, DRN analysis was employed for the DDRP protein for both holo and complex systems, revealing insightful information about the residues that play a key role in the change in distance between residue pairs along with residues that play an essential role in protein communication within the calculated RIN. Overall, the data supported the conclusions drawn by a recent study that only concentrated on RIF-resistance in rpoB models which suggested that the binding pocket for the SNP models may result in the changed coordination of RIF which may be the main contributor to its impaired efficacy.
- Full Text:
- Date Issued: 2020
Underutilisation of information communication and technology in the building construction industry case study: Department of Public Works in the Amathole district in the Eastern Cape
- Authors: Camngca, Vuyokazi Precious
- Date: 2020
- Subjects: Construction industry -- Information technology , Construction industry -- Data processing Information technology Communication and technology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/50632 , vital:42280
- Description: This study investigated the causes and effects of the underutilisation of Information Communication Technology (ICT) in the building section of the Amathole Region. The construction industry’s daily processes demand both heavy usages of data and data communication between project participants to meet client requirements. This industry is characterised by inaccurate and untimely communications that often result in costly delays and extensions of the project timeframe. ICT is a potential solution to this problem. The objectives of the study are, therefore, to determine why the above, a technically skilled occupational government institution in the Eastern Cape, does not employ ICT efficiently and optimally during this time of the looming global fourth industrial revolution. The literature review detailed the causes of and impact level of ICT’s utilisation and its potential benefits. For data collection, the researcher held unstructured interviews with a Chief Quantity Surveyor, Chief Architect, Engineer, Building Inspectors, and a Quantity Surveyor who dealt directly with construction projects. The key findings revealed that a lack of understanding of existing and newly available ICT software and hardware technology existed amongst certain senior officials within the building technology. The previously alluded, combined with the fear of the inability to learn and apply such new technology, has led to a culture of resistance to change from these more senior officials to utilise applications such as AutoCAD. The above-mentioned resistance, has also triggered the prevention of access to and lack of ICT resources, training, and inadequate funding, thereby eventually resulting in the underutilisation of ICT within the whole building section. This change also adversely affects all officials, especially the junior officials who have graduated using the most recent ICT technology during their studies. The researcher deduced, from the above findings, that adequate change management and continuous development, combined with the allocation of proper resources, would be necessary for all staff members. It was also determined that investments had to be made in the ICT equipment through the provision of a sufficient budget in the building section at AR.
- Full Text:
- Date Issued: 2020
- Authors: Camngca, Vuyokazi Precious
- Date: 2020
- Subjects: Construction industry -- Information technology , Construction industry -- Data processing Information technology Communication and technology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/50632 , vital:42280
- Description: This study investigated the causes and effects of the underutilisation of Information Communication Technology (ICT) in the building section of the Amathole Region. The construction industry’s daily processes demand both heavy usages of data and data communication between project participants to meet client requirements. This industry is characterised by inaccurate and untimely communications that often result in costly delays and extensions of the project timeframe. ICT is a potential solution to this problem. The objectives of the study are, therefore, to determine why the above, a technically skilled occupational government institution in the Eastern Cape, does not employ ICT efficiently and optimally during this time of the looming global fourth industrial revolution. The literature review detailed the causes of and impact level of ICT’s utilisation and its potential benefits. For data collection, the researcher held unstructured interviews with a Chief Quantity Surveyor, Chief Architect, Engineer, Building Inspectors, and a Quantity Surveyor who dealt directly with construction projects. The key findings revealed that a lack of understanding of existing and newly available ICT software and hardware technology existed amongst certain senior officials within the building technology. The previously alluded, combined with the fear of the inability to learn and apply such new technology, has led to a culture of resistance to change from these more senior officials to utilise applications such as AutoCAD. The above-mentioned resistance, has also triggered the prevention of access to and lack of ICT resources, training, and inadequate funding, thereby eventually resulting in the underutilisation of ICT within the whole building section. This change also adversely affects all officials, especially the junior officials who have graduated using the most recent ICT technology during their studies. The researcher deduced, from the above findings, that adequate change management and continuous development, combined with the allocation of proper resources, would be necessary for all staff members. It was also determined that investments had to be made in the ICT equipment through the provision of a sufficient budget in the building section at AR.
- Full Text:
- Date Issued: 2020
Unravelling the replication biology of Providence virus in a cell culturebased model system
- Authors: Jarvie, Rachel Anne
- Date: 2020
- Subjects: Virology -- Research , RNA viruses , Viruses -- Reproduction , Providence virus
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/142339 , vital:38071
- Description: There has been an increase in the number of viral outbreaks in the last decade; the majority of these are attributed to insect-human or animal-human transfer. Despite this awareness, there is limited understanding of the replication biology of the viruses causing the outbreaks and there are few model systems that are available to study RNA virus replication and viral persistence. In this study, we describe a Providence (PrV)-based model system to study virus replication biology. PrV is a single-stranded RNA virus that can cross Kingdom boundaries; it is capable of establishing a productive infection in insect and mammalian cell culture and it is also capable of replicating in plants. Only one other virus has been reported to infect a similar host range - the Nodavirus, Flock House virus (FHV). First, we performed a bioinformatic analysis of the PrV genome and validated the tools that were currently available to work with this model system in mammalian cells. Our data indicate that PrV infection of human cervical cancer (HeLa) cells results in the production of p130, p104/p40 and VCAP, albeit at low levels. While PrV replication in insect cells is associated with the Golgi apparatus and secretory vesicles, in HeLa cells, PrV replication is associated with the mitochondria. It is interesting to note that FHV replication factories are located on the outer mitochondrial membrane. In an attempt to study PrV virus replication in vitro, we adapted the BioID system reported by Roux et al. (2012). Here a promiscuous biotin ligase enzyme (BirA) was fused to a protein of interest and the expression of the fusion protein in mammalian cells resulted in the proximitybased biotinylation of proteins associated with the protein of interest. Using p40 as the protein of interest, we studied the fusion protein (BirA-p40) in transiently transfected HeLa cells and in a stable cell line, using western blot analysis and confocal microscopy. We faced challenges comparing the data collected using the two antibody-based detection techniques and the lack of BirA-p40 detection when using western analysis was attributed to the associated of p40 with detergent resistant membranes. BirA-p40 was subsequently expressed using in vitro coupled transcription/translation reactions, in the presence of excess biotin. While BirA-p40 was robustly expressed under these conditions, biotinylation of BirA-p40 was not detected. We attributed this to the conditions used in the experiments and given additional time, we would extend the duration of biotinylation, in vitro. PrV replication in mammalian cells was detectable using confocal microscopy however the levels of fluorescence were relatively low. The knowledge that p40 was associated with detergent resistant membranes led us to question the impact of detergent treatment of live cells on the detection of PrV replication. PrV-infected HeLa cells were treated with detergents with varying biochemical characteristics and the impact of these treatments on the detection of PrV replication were evaluated. We observed that linear and non-ionic detergents, namely NP-40 and Triton X-100, were most effective at enhancing the detection of viral replication in PrV-infected HeLa cells. Our data confirm that detergent treatment results in enhanced detection, and not enhanced PrV replication, in HeLa cells. Using the stable BirA-p40 expressing HeLa cell line, we showed that the protein is associated with membranes in vitro, and that the enhanced expression of BirA-p40 results in the formation of greater volumes of detergent-resistant membranes. In addition, detergent treatment of unfixed PrV-infected HeLa cells revealed the presence of the PrV p40 protein in the nucleoli of the cells. This is the first report of PrV proteins, which are translated in the cytosol of the mammalian cells, occurring in the nucleus. Our study has resulted in a deeper understanding of PrV replication in mammalian cell lines. A ‘simple RNA virus’ with only three predicted open reading frames has exhibited high levels of complexity within its elegant simplicity. This study has also highlighted the challenges associated with studying RNA virus replication biology in vitro. Looking forward, the identification of detergent-based enhancement for the detection of PrV replication provides the opportunity to perform more targeted PrV replication studies. The PrV-based model system can also be applied to the identification and analysis of potential broad-spectrum antiviral drugs in vitro. The latter application is particularly relevant considering the increase in the number of viral outbreaks over the last decade.
- Full Text:
- Date Issued: 2020
- Authors: Jarvie, Rachel Anne
- Date: 2020
- Subjects: Virology -- Research , RNA viruses , Viruses -- Reproduction , Providence virus
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/142339 , vital:38071
- Description: There has been an increase in the number of viral outbreaks in the last decade; the majority of these are attributed to insect-human or animal-human transfer. Despite this awareness, there is limited understanding of the replication biology of the viruses causing the outbreaks and there are few model systems that are available to study RNA virus replication and viral persistence. In this study, we describe a Providence (PrV)-based model system to study virus replication biology. PrV is a single-stranded RNA virus that can cross Kingdom boundaries; it is capable of establishing a productive infection in insect and mammalian cell culture and it is also capable of replicating in plants. Only one other virus has been reported to infect a similar host range - the Nodavirus, Flock House virus (FHV). First, we performed a bioinformatic analysis of the PrV genome and validated the tools that were currently available to work with this model system in mammalian cells. Our data indicate that PrV infection of human cervical cancer (HeLa) cells results in the production of p130, p104/p40 and VCAP, albeit at low levels. While PrV replication in insect cells is associated with the Golgi apparatus and secretory vesicles, in HeLa cells, PrV replication is associated with the mitochondria. It is interesting to note that FHV replication factories are located on the outer mitochondrial membrane. In an attempt to study PrV virus replication in vitro, we adapted the BioID system reported by Roux et al. (2012). Here a promiscuous biotin ligase enzyme (BirA) was fused to a protein of interest and the expression of the fusion protein in mammalian cells resulted in the proximitybased biotinylation of proteins associated with the protein of interest. Using p40 as the protein of interest, we studied the fusion protein (BirA-p40) in transiently transfected HeLa cells and in a stable cell line, using western blot analysis and confocal microscopy. We faced challenges comparing the data collected using the two antibody-based detection techniques and the lack of BirA-p40 detection when using western analysis was attributed to the associated of p40 with detergent resistant membranes. BirA-p40 was subsequently expressed using in vitro coupled transcription/translation reactions, in the presence of excess biotin. While BirA-p40 was robustly expressed under these conditions, biotinylation of BirA-p40 was not detected. We attributed this to the conditions used in the experiments and given additional time, we would extend the duration of biotinylation, in vitro. PrV replication in mammalian cells was detectable using confocal microscopy however the levels of fluorescence were relatively low. The knowledge that p40 was associated with detergent resistant membranes led us to question the impact of detergent treatment of live cells on the detection of PrV replication. PrV-infected HeLa cells were treated with detergents with varying biochemical characteristics and the impact of these treatments on the detection of PrV replication were evaluated. We observed that linear and non-ionic detergents, namely NP-40 and Triton X-100, were most effective at enhancing the detection of viral replication in PrV-infected HeLa cells. Our data confirm that detergent treatment results in enhanced detection, and not enhanced PrV replication, in HeLa cells. Using the stable BirA-p40 expressing HeLa cell line, we showed that the protein is associated with membranes in vitro, and that the enhanced expression of BirA-p40 results in the formation of greater volumes of detergent-resistant membranes. In addition, detergent treatment of unfixed PrV-infected HeLa cells revealed the presence of the PrV p40 protein in the nucleoli of the cells. This is the first report of PrV proteins, which are translated in the cytosol of the mammalian cells, occurring in the nucleus. Our study has resulted in a deeper understanding of PrV replication in mammalian cell lines. A ‘simple RNA virus’ with only three predicted open reading frames has exhibited high levels of complexity within its elegant simplicity. This study has also highlighted the challenges associated with studying RNA virus replication biology in vitro. Looking forward, the identification of detergent-based enhancement for the detection of PrV replication provides the opportunity to perform more targeted PrV replication studies. The PrV-based model system can also be applied to the identification and analysis of potential broad-spectrum antiviral drugs in vitro. The latter application is particularly relevant considering the increase in the number of viral outbreaks over the last decade.
- Full Text:
- Date Issued: 2020
Upwelling on the Southeast Madagascan shelf: frequency, extent, and driving mechanisms
- Authors: Collins, Matthew
- Date: 2020
- Subjects: Upwelling (Oceanography) -- Madagascar , Oceanography -- Research -- Madagascar Marine biology -- Indian Ocean
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49060 , vital:41597
- Description: The southeast coast of Madagascar, namely the region surrounding the town of Fort Dauphin, is an area that regularly experiences upwelling events. Two unique high frequency data sets, UTR data, and wind data retrieved from a nearby airport, are the primary data sets used to investigate the nature of the upwelling, i.e. the area that experiences upwelling, how often it occurs, and its mechanisms. To complement the in-situ data, several different satellite data sources are used alongside the in-situ data to study this relatively remote region, i.e. SST, chlorophyll-a concentration, current, and wind data. The results refine upon previous literature on the topic. The upwelling covers an area of 1o latitude by 1.3o longitude, and occurs on average 14 times per annum. The mechanism driving the upwelling can be attributed to both wind and current, with wind the more dominant driver along the south coast, and current more dominant along the east coast. Separate to the main objective of the thesis is the importance of in-situ data when analysing small scale events such as upwelling events. While the in-situ wind data were found to be unreliable due to its location within a valley, the UTR data were of vital importance in identifying and studying the finer details of the upwelling events. The satellite SST data, by comparison, were lacking in their ability to investigate the upwelling events. The satellite derived wind data, however, did prove useful when analysing the wind as a driver of the upwelling.
- Full Text:
- Date Issued: 2020
- Authors: Collins, Matthew
- Date: 2020
- Subjects: Upwelling (Oceanography) -- Madagascar , Oceanography -- Research -- Madagascar Marine biology -- Indian Ocean
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/49060 , vital:41597
- Description: The southeast coast of Madagascar, namely the region surrounding the town of Fort Dauphin, is an area that regularly experiences upwelling events. Two unique high frequency data sets, UTR data, and wind data retrieved from a nearby airport, are the primary data sets used to investigate the nature of the upwelling, i.e. the area that experiences upwelling, how often it occurs, and its mechanisms. To complement the in-situ data, several different satellite data sources are used alongside the in-situ data to study this relatively remote region, i.e. SST, chlorophyll-a concentration, current, and wind data. The results refine upon previous literature on the topic. The upwelling covers an area of 1o latitude by 1.3o longitude, and occurs on average 14 times per annum. The mechanism driving the upwelling can be attributed to both wind and current, with wind the more dominant driver along the south coast, and current more dominant along the east coast. Separate to the main objective of the thesis is the importance of in-situ data when analysing small scale events such as upwelling events. While the in-situ wind data were found to be unreliable due to its location within a valley, the UTR data were of vital importance in identifying and studying the finer details of the upwelling events. The satellite SST data, by comparison, were lacking in their ability to investigate the upwelling events. The satellite derived wind data, however, did prove useful when analysing the wind as a driver of the upwelling.
- Full Text:
- Date Issued: 2020
Using a spatial resilience lens to understand alignments and misalignments in South Africa’s marine governance system
- Authors: Hardisty, Shannon
- Date: 2020
- Subjects: Marine parks and reserves -- South Africa , Marine parks and reserves -- South Africa -- Management , Marine parks and reserves -- Government policy -- South Africa , Table Mountain National Park (South Africa) , Spatial ecology -- South Africa , Coastal zone management -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/164649 , vital:41152
- Description: In marine protected areas (MPAs), the radically open nature of marine ecosystems, the seemingly contradictory short-term goals of fisheries management (resource use) and conservation efforts (biodiversity protection), the variety of stakeholders, and the inherently political nature of space ha ve contributed to a disconnect between policy and practice. Many groups operate in an MPA at various spatial and socio-political scales, from national government bodies to local community groups, as such an MPA can be viewed as a complex, multi-scale and multi-level social-ecological system (SES). A greater understanding of the multi-scale processes driving the spatial resilience of SES can help address scale mismatches between continuous ecological change and the long-term governance of a seascape. South Africa has a long history of spaces and natural resources being politicised and faces high levels of unemployment and political frustration. Marine governance has been characterised as being siloed, lacking transparency regarding government processes and even between departments, and not properly addressing the needs of local communities; resulting in scale and level mismatches throughout the multi-scale processes (from national policies to local regulations)therefore, it is pertinent to understand the interactions between various national policies, their implementation, and their impacts. Using a spatial resilience lens, I set out to understand scale alignment in South Africa’s marine governance systems as it relates to MPAs. A spatial resilience lens emphasises analysis of both spatial and temporal scales, thus highlighting the multi-scale variables and interactions that occur within a system. I first sought to understand the policy and management across national and regional scales by conducting a series of semi-structured interviews with experts which were analysed using thematic analysis. I then approached the question of alignment from a local to national scale by using the Table Mountain National Park Marine Protected Area as a case study, here I carried out a series of workshops and interviews with line fishers, women’s groups, and eco-tourism operators from three different communities. Experts identified six themes when describing the structure of gove rnance in South African MPAs; they consisted of: government departments and marine legislation, management level factors, communication and information sharing, local level factors, biophysical factors, and scale. Communication and information sharing was the most mentioned referenced theme (40.26 %). The relationships between the communities and other actors (i.e. how communities are impacted, or impact on, the Department of Environmental Affairs , the Department of Agriculture Forestry and Fisheries, and Park Authorities) contributed 67.27 % to the total number of mentions, 91 % of which were from the following themes: communication and information sharing, local level factors, biophysical factors, and scale. My results indicate that weak, top-down relationships dominate the governance system in South Africa. During the Cape Town workshops I applied the spatial resilience lens in three ways. Firstly, the participants collaborated on a mapping exercise discussing the existing zone types within the MPA, as well as developing their own. There was an 87.87 % overlap of community designed zones on the existing MPA zones, however the types of zones designed by the community were different. Secondly, I carried out a document analysis and used information from the workshops to analyse the status and rights designation of important species for different user groups. The results show that the various stakeholder groups, while all active in the marine environment, interact with the ecosystem at different scales and with differing species. The differing interactions between groups result in challenges such as representation and complicated power dynamics between user groups. Finally, I asked participants to discuss factors that affect their ability to gain a livelihood from the sea. The external elements and their effects differed between the user groups, identifying important socio-political interactions. Whilst the external elements were all geographically distinct and localised, the spatial resilience lens allowed for a cross-scale, and to a certain extent cross-sector, understanding of these elements thus producing a more holistic understanding. My thesis shows that user groups operate on different spatial scales within the marine environment as a result of social, economic, and political influences leading to several scale-based challenges. The identified scale-based challenges have contributed to misalignments in marine governance in South Africa. My study shows that scale mismatches have important implications for understanding how marine policy influences user groups and identified pathways that affected policy implementation , and identifies future research application of a spatial resilience lens within social-ecological systems, for example it’s potential use in understanding the gendered nature of MPAs
- Full Text:
- Date Issued: 2020
- Authors: Hardisty, Shannon
- Date: 2020
- Subjects: Marine parks and reserves -- South Africa , Marine parks and reserves -- South Africa -- Management , Marine parks and reserves -- Government policy -- South Africa , Table Mountain National Park (South Africa) , Spatial ecology -- South Africa , Coastal zone management -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/164649 , vital:41152
- Description: In marine protected areas (MPAs), the radically open nature of marine ecosystems, the seemingly contradictory short-term goals of fisheries management (resource use) and conservation efforts (biodiversity protection), the variety of stakeholders, and the inherently political nature of space ha ve contributed to a disconnect between policy and practice. Many groups operate in an MPA at various spatial and socio-political scales, from national government bodies to local community groups, as such an MPA can be viewed as a complex, multi-scale and multi-level social-ecological system (SES). A greater understanding of the multi-scale processes driving the spatial resilience of SES can help address scale mismatches between continuous ecological change and the long-term governance of a seascape. South Africa has a long history of spaces and natural resources being politicised and faces high levels of unemployment and political frustration. Marine governance has been characterised as being siloed, lacking transparency regarding government processes and even between departments, and not properly addressing the needs of local communities; resulting in scale and level mismatches throughout the multi-scale processes (from national policies to local regulations)therefore, it is pertinent to understand the interactions between various national policies, their implementation, and their impacts. Using a spatial resilience lens, I set out to understand scale alignment in South Africa’s marine governance systems as it relates to MPAs. A spatial resilience lens emphasises analysis of both spatial and temporal scales, thus highlighting the multi-scale variables and interactions that occur within a system. I first sought to understand the policy and management across national and regional scales by conducting a series of semi-structured interviews with experts which were analysed using thematic analysis. I then approached the question of alignment from a local to national scale by using the Table Mountain National Park Marine Protected Area as a case study, here I carried out a series of workshops and interviews with line fishers, women’s groups, and eco-tourism operators from three different communities. Experts identified six themes when describing the structure of gove rnance in South African MPAs; they consisted of: government departments and marine legislation, management level factors, communication and information sharing, local level factors, biophysical factors, and scale. Communication and information sharing was the most mentioned referenced theme (40.26 %). The relationships between the communities and other actors (i.e. how communities are impacted, or impact on, the Department of Environmental Affairs , the Department of Agriculture Forestry and Fisheries, and Park Authorities) contributed 67.27 % to the total number of mentions, 91 % of which were from the following themes: communication and information sharing, local level factors, biophysical factors, and scale. My results indicate that weak, top-down relationships dominate the governance system in South Africa. During the Cape Town workshops I applied the spatial resilience lens in three ways. Firstly, the participants collaborated on a mapping exercise discussing the existing zone types within the MPA, as well as developing their own. There was an 87.87 % overlap of community designed zones on the existing MPA zones, however the types of zones designed by the community were different. Secondly, I carried out a document analysis and used information from the workshops to analyse the status and rights designation of important species for different user groups. The results show that the various stakeholder groups, while all active in the marine environment, interact with the ecosystem at different scales and with differing species. The differing interactions between groups result in challenges such as representation and complicated power dynamics between user groups. Finally, I asked participants to discuss factors that affect their ability to gain a livelihood from the sea. The external elements and their effects differed between the user groups, identifying important socio-political interactions. Whilst the external elements were all geographically distinct and localised, the spatial resilience lens allowed for a cross-scale, and to a certain extent cross-sector, understanding of these elements thus producing a more holistic understanding. My thesis shows that user groups operate on different spatial scales within the marine environment as a result of social, economic, and political influences leading to several scale-based challenges. The identified scale-based challenges have contributed to misalignments in marine governance in South Africa. My study shows that scale mismatches have important implications for understanding how marine policy influences user groups and identified pathways that affected policy implementation , and identifies future research application of a spatial resilience lens within social-ecological systems, for example it’s potential use in understanding the gendered nature of MPAs
- Full Text:
- Date Issued: 2020
Using sound localization to gain depth perception for the visually impaired through sensory substitution
- Authors: De Klerk, James Carmichael
- Date: 2020
- Subjects: People with visual disabilities Directional hearing--Physiological aspects
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/50779 , vital:42674
- Description: The visually impaired do not have the visual ability to localize objects in three-dimensional space, rather, they rely on their other senses to gain depth perception. Sensory substitution is the concept of substituting one sense for another, normally substituting an impaired sense with a functioning sense. Visual-to-auditory sensory substitution substitutes an impaired visual sense with a functioning auditory sense. This research aimed to investigate and develop techniques for visualto-auditory sensory substitution – using sound localization as a sensory substitution for depth perception. The research started by investigating the characteristics of human audition with a particular focus on how humans localize sounds. It then looked at existing visual-to-auditory sensory substitution systems and the techniques they used. From the existing systems, a system known as MeloSee was chosen as a baseline for developing and evaluating further sensory substitution prototypes. The baseline prototype (𝑃0) was then implemented and a preliminary study performed. Based on the knowledge gained from the preliminary study, baseline implementation and the background research, a set of improvement recommendations were generated. The next iteration – Prototype 1 (𝑃1) – was then developed based on the recommendations. A comparative study between 𝑃0 and 𝑃1 was then performed. Based on the study, another set of improvement recommendations were generated. From the recommendations, a final prototype was developed – Prototype 2 (𝑃2). The last comparative study was then performed between 𝑃0 and 𝑃2, with a third set of recommendations being generated as a result. From the studies it was found that participants using 𝑃0 were able to identify when they were approaching large objects such as walls. 𝑃1 built on that, improving the ability to identify the quadrant of a nearby isolated object. 𝑃2 built on 𝑃0 and 𝑃1, achieving similar results to 𝑃1 for identifying the quadrant of nearby isolated objects, and improving on 𝑃0 and 𝑃1 with regard to depth discrimination – especially for navigation tasks where there were no obstacles. Based on the three sets of recommendations and what was learnt over the course of the research, a set of visual-to-auditory sensory substitution techniques were presented. The techniques aim to be useful for implementing visual-to-auditory sensory substitution systems, which would provide the visually impaired with the visual ability to localize objects in three-dimensional space through sound.
- Full Text:
- Date Issued: 2020
- Authors: De Klerk, James Carmichael
- Date: 2020
- Subjects: People with visual disabilities Directional hearing--Physiological aspects
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/50779 , vital:42674
- Description: The visually impaired do not have the visual ability to localize objects in three-dimensional space, rather, they rely on their other senses to gain depth perception. Sensory substitution is the concept of substituting one sense for another, normally substituting an impaired sense with a functioning sense. Visual-to-auditory sensory substitution substitutes an impaired visual sense with a functioning auditory sense. This research aimed to investigate and develop techniques for visualto-auditory sensory substitution – using sound localization as a sensory substitution for depth perception. The research started by investigating the characteristics of human audition with a particular focus on how humans localize sounds. It then looked at existing visual-to-auditory sensory substitution systems and the techniques they used. From the existing systems, a system known as MeloSee was chosen as a baseline for developing and evaluating further sensory substitution prototypes. The baseline prototype (𝑃0) was then implemented and a preliminary study performed. Based on the knowledge gained from the preliminary study, baseline implementation and the background research, a set of improvement recommendations were generated. The next iteration – Prototype 1 (𝑃1) – was then developed based on the recommendations. A comparative study between 𝑃0 and 𝑃1 was then performed. Based on the study, another set of improvement recommendations were generated. From the recommendations, a final prototype was developed – Prototype 2 (𝑃2). The last comparative study was then performed between 𝑃0 and 𝑃2, with a third set of recommendations being generated as a result. From the studies it was found that participants using 𝑃0 were able to identify when they were approaching large objects such as walls. 𝑃1 built on that, improving the ability to identify the quadrant of a nearby isolated object. 𝑃2 built on 𝑃0 and 𝑃1, achieving similar results to 𝑃1 for identifying the quadrant of nearby isolated objects, and improving on 𝑃0 and 𝑃1 with regard to depth discrimination – especially for navigation tasks where there were no obstacles. Based on the three sets of recommendations and what was learnt over the course of the research, a set of visual-to-auditory sensory substitution techniques were presented. The techniques aim to be useful for implementing visual-to-auditory sensory substitution systems, which would provide the visually impaired with the visual ability to localize objects in three-dimensional space through sound.
- Full Text:
- Date Issued: 2020
Utility of construction automation and robotics in South Africa
- Mkunqwana, Khungelwa Sandisiwe
- Authors: Mkunqwana, Khungelwa Sandisiwe
- Date: 2020
- Subjects: Construction industry -- Automation , Construction industry -- South Africa -- Automation Robotics -- South Africa Robotics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/46174 , vital:39511
- Description: The construction industry demands active construction organisation, efficient construction processes and innovative construction techniques to effectively compete under increasing market competition and technological advancements in the twenty first century. The problems associated with construction, such as poor quality and slow productivity, labour shortages, occupational health and safety, and inferior working conditions, have opened the possibility of more revolutionary solutions within the industry. One such solution espoused as having tremendous potential to improve construction productivity whilst alleviating the problems associated with construction is Construction Automation and Robotics. Automation and robotics technologies encompass a wide range of innovative technologies using technologically advanced machinery to improve the speed and efficiency of a given process. The aim of this study is to analyse the extent of utility of construction automation and robotics in the South African construction industry. The research adopted the quantitative methodology and online survey to collect data. A detailed quantitative (statistical) data analysis was performed, using web-based software “QuestionPro,” including data analysis for investigating possible relationships between variables. Through this study it has been established that one of the prospective solutions to the problems associated with construction is in the implementation and utility of innovative technologies in construction such as automation and robotics. Moreover, the research found that automation and robotics in South Africa is at an interesting point whereby organisations are taking strides in accepting and implementing the technologies. It is envisaged that the utility of construction automation and robotics would improve the industry in terms of productivity, health and safety and quality.
- Full Text:
- Date Issued: 2020
- Authors: Mkunqwana, Khungelwa Sandisiwe
- Date: 2020
- Subjects: Construction industry -- Automation , Construction industry -- South Africa -- Automation Robotics -- South Africa Robotics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/46174 , vital:39511
- Description: The construction industry demands active construction organisation, efficient construction processes and innovative construction techniques to effectively compete under increasing market competition and technological advancements in the twenty first century. The problems associated with construction, such as poor quality and slow productivity, labour shortages, occupational health and safety, and inferior working conditions, have opened the possibility of more revolutionary solutions within the industry. One such solution espoused as having tremendous potential to improve construction productivity whilst alleviating the problems associated with construction is Construction Automation and Robotics. Automation and robotics technologies encompass a wide range of innovative technologies using technologically advanced machinery to improve the speed and efficiency of a given process. The aim of this study is to analyse the extent of utility of construction automation and robotics in the South African construction industry. The research adopted the quantitative methodology and online survey to collect data. A detailed quantitative (statistical) data analysis was performed, using web-based software “QuestionPro,” including data analysis for investigating possible relationships between variables. Through this study it has been established that one of the prospective solutions to the problems associated with construction is in the implementation and utility of innovative technologies in construction such as automation and robotics. Moreover, the research found that automation and robotics in South Africa is at an interesting point whereby organisations are taking strides in accepting and implementing the technologies. It is envisaged that the utility of construction automation and robotics would improve the industry in terms of productivity, health and safety and quality.
- Full Text:
- Date Issued: 2020
Waste management in the informal settlements of Msukaligwa Municipality
- Authors: Ngema, , Noxolo Nondumiso
- Date: 2020
- Subjects: Waste disposal in the ground -- South Africa -- Ermelo , Refuse and refuse disposal -- South Africa -- Ermelo Squatters -- South Africa -- Ermelo
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/46827 , vital:39665
- Description: This study focused on waste management, and, sought to evaluate the level of awareness on environmental impact of littering in vulnerable communities in the informal settlements of Msukaligwa municipality, in particular at Ward 16 which is Nyibe newly named as New Ermelo. This study was, thus, concerned with how solid waste is managed within the informal settlements. The study arose with the concern that the environment is mostly affected when informal settlements are developed. If informal settlements are less aware of the damage caused by littering and improper waste disposal, the waste management plan of a local municipality becomes ineffective where local communities do not assume their responsibilities for ensuring healthy and safe living environments. A quantitative research design was applied in this study. Population for this research comprised of Msukaligwa Local Municipality, with a study sample drawn from Ward 16 Nyibe households, church leaders, local business owners, and ward councillor. A nonprobability sampling technique for selection of study participants was used, and this technique applied in both households and stakeholders. Data was collected through self-administered survey questionnaires that were statistically analysed, weaving in filed observations, where deemed necessary. The researcher discovered that Nyibe (New Ermelo) community’s level of awareness of the environmental impact of littering is impressively above average. Majority of households’ respondents identified all the negative environmental impact caused by littering in vulnerable communities and the impact is considered a major challenge within Nyibe. Necessary waste disposal infrastructures are not provided at Nyibe leading to people littering on any open land, burning, or throwing solid waste in their family pit.
- Full Text:
- Date Issued: 2020
- Authors: Ngema, , Noxolo Nondumiso
- Date: 2020
- Subjects: Waste disposal in the ground -- South Africa -- Ermelo , Refuse and refuse disposal -- South Africa -- Ermelo Squatters -- South Africa -- Ermelo
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/46827 , vital:39665
- Description: This study focused on waste management, and, sought to evaluate the level of awareness on environmental impact of littering in vulnerable communities in the informal settlements of Msukaligwa municipality, in particular at Ward 16 which is Nyibe newly named as New Ermelo. This study was, thus, concerned with how solid waste is managed within the informal settlements. The study arose with the concern that the environment is mostly affected when informal settlements are developed. If informal settlements are less aware of the damage caused by littering and improper waste disposal, the waste management plan of a local municipality becomes ineffective where local communities do not assume their responsibilities for ensuring healthy and safe living environments. A quantitative research design was applied in this study. Population for this research comprised of Msukaligwa Local Municipality, with a study sample drawn from Ward 16 Nyibe households, church leaders, local business owners, and ward councillor. A nonprobability sampling technique for selection of study participants was used, and this technique applied in both households and stakeholders. Data was collected through self-administered survey questionnaires that were statistically analysed, weaving in filed observations, where deemed necessary. The researcher discovered that Nyibe (New Ermelo) community’s level of awareness of the environmental impact of littering is impressively above average. Majority of households’ respondents identified all the negative environmental impact caused by littering in vulnerable communities and the impact is considered a major challenge within Nyibe. Necessary waste disposal infrastructures are not provided at Nyibe leading to people littering on any open land, burning, or throwing solid waste in their family pit.
- Full Text:
- Date Issued: 2020
Wind damage impacts on Eucalyptus species performance in South Africa
- Authors: Hechter, Heinrich
- Date: 2020
- Subjects: Commercial forests -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/48368 , vital:40853
- Description: Commercial forestry plantations in South Africa play an important role in the economy of the country, contributing 1.2% towards the gross domestic product, as well as with job creation in rural communities. Currently plantation forests cover 1% (1.2 million hectares) of the South African land surface, of which ±75 000 hectares (±43 000 hectares to Eucalyptus species) are re-established each year. Different timber companies afforest areas with different species to satisfy specific management objectives, with the two main objectives being for either the production of saw-timber or pulpwood. Species of the Eucalyptus genera are preferred as they are fast growing and have desirable wood and pulping properties. However, their productive potential can be negatively impacted by numerous abiotic and biotic risk factors. Of the various risk factors that forest stands are exposed to, wind and wind-related tree damage has received very little attention, both nationally and internationally. Wind-related tree damage may result in wind-throw (uprooting or stem breakage), or trees that tilt (lean off vertical). Trees that are tilting can recover to an upright position, but are likely to retain some level of stem sinuosity or butt-sweep. Although strong winds increase the risk of tree damage, a number of other factors can also act to predispose trees to wind-related damage. These include choice of planting stock (genotype and type of plant stock), planting practices (including soil cultivation), site factors (wind exposure, rainfall, soil texture and soil fertility) or excessive weed competition. Most of the literature dealing with wind-related tree damage has focused on trees growing in natural forests, whereas trees in natural forests differ from forest grown plantation trees in terms of above- and below-ground morphological differences, as well as the stability factors of the trees. There is a need to not only understand the impacts of severe (catastrophic) wind events on mature trees, but also to test management strategies that prevent, or minimize damage prior to any severe wind events. Two existing eucalypt trials were used to provide information on the influence of selected re-establishment silvicultural practices on short-term pulpwood and long-term saw-timber survival, growth and uniformity when influenced by catastrophic wind events, within South Africa.
- Full Text:
- Date Issued: 2020
- Authors: Hechter, Heinrich
- Date: 2020
- Subjects: Commercial forests -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/48368 , vital:40853
- Description: Commercial forestry plantations in South Africa play an important role in the economy of the country, contributing 1.2% towards the gross domestic product, as well as with job creation in rural communities. Currently plantation forests cover 1% (1.2 million hectares) of the South African land surface, of which ±75 000 hectares (±43 000 hectares to Eucalyptus species) are re-established each year. Different timber companies afforest areas with different species to satisfy specific management objectives, with the two main objectives being for either the production of saw-timber or pulpwood. Species of the Eucalyptus genera are preferred as they are fast growing and have desirable wood and pulping properties. However, their productive potential can be negatively impacted by numerous abiotic and biotic risk factors. Of the various risk factors that forest stands are exposed to, wind and wind-related tree damage has received very little attention, both nationally and internationally. Wind-related tree damage may result in wind-throw (uprooting or stem breakage), or trees that tilt (lean off vertical). Trees that are tilting can recover to an upright position, but are likely to retain some level of stem sinuosity or butt-sweep. Although strong winds increase the risk of tree damage, a number of other factors can also act to predispose trees to wind-related damage. These include choice of planting stock (genotype and type of plant stock), planting practices (including soil cultivation), site factors (wind exposure, rainfall, soil texture and soil fertility) or excessive weed competition. Most of the literature dealing with wind-related tree damage has focused on trees growing in natural forests, whereas trees in natural forests differ from forest grown plantation trees in terms of above- and below-ground morphological differences, as well as the stability factors of the trees. There is a need to not only understand the impacts of severe (catastrophic) wind events on mature trees, but also to test management strategies that prevent, or minimize damage prior to any severe wind events. Two existing eucalypt trials were used to provide information on the influence of selected re-establishment silvicultural practices on short-term pulpwood and long-term saw-timber survival, growth and uniformity when influenced by catastrophic wind events, within South Africa.
- Full Text:
- Date Issued: 2020