Assessing the value of public investment into biological control research for invasive alien plants : the ARC PPRI Weeds Research Division
- Authors: Scarr, Lowell Martin
- Date: 2016
- Subjects: Alien plants -- Biological control , Invasive plants -- Biological control , Alien plants -- Economic aspects , Invasive plants -- Economic aspects , Weeds -- Biological control
- Language: English
- Type: Thesis , Masters , MCom
- Identifier: vital:1126 , http://hdl.handle.net/10962/d1020604
- Description: This study investigates the economic impact of the ARC PPRI Weeds Research Division. The Division researches appropriate methods of biological control for invasive alien plants (IAPs). These plants pose an increasing threat to environmental integrity and ecosystem service provision impacting on economic potential. Since the work of the Division is considered a public good, a predominantly descriptive approach has been adopted for the valuation process. A combination of quantitative cost analysis and a qualitative study of the impacts of research and invasive alien plants is used to deal with the challenges associated with non-market valuation. The study found that investment into the Weeds Division is a valuable activity that supports the long-term growth potential of the South African economy. The role of a well-functioning environment is highlighted as an essential base for the creation of sustained growth opportunities in any society. It was determined that investment into the Division should be increased into the future to support efficient spending of scarce state funds. Biological control research was found to provide strategic future growth potential, creating opportunities for the development of a competitive advantage in the biotechnology and environmental management sectors. The study adds to the increasing move towards a more holistic view of economic valuation, taking factors other than pure finance and econometrics into consideration. This is an important shift in prevailing economic thought, as a realisation is reached that a single, or even triple, bottom line is an outdated and insufficient decision making basis.
- Full Text:
- Authors: Scarr, Lowell Martin
- Date: 2016
- Subjects: Alien plants -- Biological control , Invasive plants -- Biological control , Alien plants -- Economic aspects , Invasive plants -- Economic aspects , Weeds -- Biological control
- Language: English
- Type: Thesis , Masters , MCom
- Identifier: vital:1126 , http://hdl.handle.net/10962/d1020604
- Description: This study investigates the economic impact of the ARC PPRI Weeds Research Division. The Division researches appropriate methods of biological control for invasive alien plants (IAPs). These plants pose an increasing threat to environmental integrity and ecosystem service provision impacting on economic potential. Since the work of the Division is considered a public good, a predominantly descriptive approach has been adopted for the valuation process. A combination of quantitative cost analysis and a qualitative study of the impacts of research and invasive alien plants is used to deal with the challenges associated with non-market valuation. The study found that investment into the Weeds Division is a valuable activity that supports the long-term growth potential of the South African economy. The role of a well-functioning environment is highlighted as an essential base for the creation of sustained growth opportunities in any society. It was determined that investment into the Division should be increased into the future to support efficient spending of scarce state funds. Biological control research was found to provide strategic future growth potential, creating opportunities for the development of a competitive advantage in the biotechnology and environmental management sectors. The study adds to the increasing move towards a more holistic view of economic valuation, taking factors other than pure finance and econometrics into consideration. This is an important shift in prevailing economic thought, as a realisation is reached that a single, or even triple, bottom line is an outdated and insufficient decision making basis.
- Full Text:
Assessment of fluctuating asymmetry as an indicator of water quality stress in South Africa
- Authors: Holland, Alexandra Jennifer
- Date: 2016
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/430 , vital:19958
- Description: South Africa’s freshwater resources are facing numerous water quality challenges and need to be protected from degradation and pollution by appropriate management strategies as they are a limited and shared resource. The South African Scoring System (SASS5), which assesses macroinvertebrate communities at family level, is used in routine monitoring of riverine ecosystems in South Africa. Assessing the condition of these ecosystems is limited as SASS5 does not allow for changes at lower levels of biological organisation to be detected. Fluctuating asymmetry (FA) - small random deviations from perfect symmetry - is considered a direct measure of developmental instability. This phenotypical response results from numerous internal and external factors and has a low level of heritability. FA is based on sound scientific principles, easy to measure, biologically robust and cost-effective. It reflects synergistic interactions between stressors and provides an integrated measure of several anthropogenic stresses, which strengthens the assertion that FA is an environmental indicator of water quality stress, and can potentially be used to detect stress in populations before irreversible effects manifest. FA responses were investigated by (1) exposing freshwater shrimp to increasing concentrations of cadmium chloride in a long-term experiment and (2) comparing FA responses to water quality changes and macroinvertebrate community responses in two case studies (Kwazulu-Natal and Limpopo Province) in South Africa. Although no consistent concentration-response curve could be established, this study suggests that FA responses can be used as a sublethal endpoint in exposure experiments. Determining water quality parameters causing FA responses was not possible in field collected freshwater shrimp in either case study. Although FA did not specifically respond to any of the measured water quality parameters identified in the case studies, it has potential as a general indicator of water quality stress in freshwater shrimp. This study shows that FA responses are potentially more sensitive than macroinvertebrate community responses to pollution since it is not affected by habitat. Since FA has the potential to be a general indicator of population quality, particularly where there are natural habitat differences, it can be useful at the level of biomonitoring required for routine basic river status assessments in South Africa. However, in order for FA to become a robust tool that can be used routinely in conjunction with SASS5 more research is required.
- Full Text:
- Authors: Holland, Alexandra Jennifer
- Date: 2016
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/430 , vital:19958
- Description: South Africa’s freshwater resources are facing numerous water quality challenges and need to be protected from degradation and pollution by appropriate management strategies as they are a limited and shared resource. The South African Scoring System (SASS5), which assesses macroinvertebrate communities at family level, is used in routine monitoring of riverine ecosystems in South Africa. Assessing the condition of these ecosystems is limited as SASS5 does not allow for changes at lower levels of biological organisation to be detected. Fluctuating asymmetry (FA) - small random deviations from perfect symmetry - is considered a direct measure of developmental instability. This phenotypical response results from numerous internal and external factors and has a low level of heritability. FA is based on sound scientific principles, easy to measure, biologically robust and cost-effective. It reflects synergistic interactions between stressors and provides an integrated measure of several anthropogenic stresses, which strengthens the assertion that FA is an environmental indicator of water quality stress, and can potentially be used to detect stress in populations before irreversible effects manifest. FA responses were investigated by (1) exposing freshwater shrimp to increasing concentrations of cadmium chloride in a long-term experiment and (2) comparing FA responses to water quality changes and macroinvertebrate community responses in two case studies (Kwazulu-Natal and Limpopo Province) in South Africa. Although no consistent concentration-response curve could be established, this study suggests that FA responses can be used as a sublethal endpoint in exposure experiments. Determining water quality parameters causing FA responses was not possible in field collected freshwater shrimp in either case study. Although FA did not specifically respond to any of the measured water quality parameters identified in the case studies, it has potential as a general indicator of water quality stress in freshwater shrimp. This study shows that FA responses are potentially more sensitive than macroinvertebrate community responses to pollution since it is not affected by habitat. Since FA has the potential to be a general indicator of population quality, particularly where there are natural habitat differences, it can be useful at the level of biomonitoring required for routine basic river status assessments in South Africa. However, in order for FA to become a robust tool that can be used routinely in conjunction with SASS5 more research is required.
- Full Text:
Assessment of water quality based on diatom indices in a small temperate river system, Kowie River, South Africa
- Dalu, Tatenda, Bere, Taurai, Froneman, P William
- Authors: Dalu, Tatenda , Bere, Taurai , Froneman, P William
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/123896 , vital:35514 , http://dx.doi.org/10.4314/wsa.v42i2.02
- Description: This study aimed to assess the impact of land use patterns on water quality and benthic diatom community structure and to test the applicability of diatom indices developed in other regions of the world to a small temperate southern African river system. Sampling was conducted at eight study sites along the length of the river on four separate occasions. Multivariate data analyses were performed on the diatom community dataset to specify the main gradients of floristic variation and to detect and visualize similarities in diatom samples in relation to land-use patterns within the catchment. One hundred and twelve (112) diatom species belonging to 36 genera were recorded during the study. Canonical correspondence analysis (CCA) demonstrated that variations in the benthic diatom community structure were best explained by ammonium, nitrate, conductivity, pH, temperature, resistivity and water flow. OMNIDIA was used for calculation of selected diatom water quality indices. A number of the indices, e.g., the trophic diatom index (TDI), eutrophication/pollution index and biological index of water quality (BIWQ), either under- or over-estimated the water quality of the system. With few exceptions, there were no significant correlations (p> 0.05) between the diatom indices’ values and the nutrient variables. The absence of any significant correlations between the diatom indices’ values and selected physico-chemical variables suggests that indices developed in other regions of the world may not be suitable for temperate southern African rivers.
- Full Text:
- Authors: Dalu, Tatenda , Bere, Taurai , Froneman, P William
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/123896 , vital:35514 , http://dx.doi.org/10.4314/wsa.v42i2.02
- Description: This study aimed to assess the impact of land use patterns on water quality and benthic diatom community structure and to test the applicability of diatom indices developed in other regions of the world to a small temperate southern African river system. Sampling was conducted at eight study sites along the length of the river on four separate occasions. Multivariate data analyses were performed on the diatom community dataset to specify the main gradients of floristic variation and to detect and visualize similarities in diatom samples in relation to land-use patterns within the catchment. One hundred and twelve (112) diatom species belonging to 36 genera were recorded during the study. Canonical correspondence analysis (CCA) demonstrated that variations in the benthic diatom community structure were best explained by ammonium, nitrate, conductivity, pH, temperature, resistivity and water flow. OMNIDIA was used for calculation of selected diatom water quality indices. A number of the indices, e.g., the trophic diatom index (TDI), eutrophication/pollution index and biological index of water quality (BIWQ), either under- or over-estimated the water quality of the system. With few exceptions, there were no significant correlations (p> 0.05) between the diatom indices’ values and the nutrient variables. The absence of any significant correlations between the diatom indices’ values and selected physico-chemical variables suggests that indices developed in other regions of the world may not be suitable for temperate southern African rivers.
- Full Text:
Assimilation of organic and inorganic nutrients by Erica root fungi from the fynbos ecosystem
- Bizabani, Christine, Dames, Joanna F
- Authors: Bizabani, Christine , Dames, Joanna F
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/444079 , vital:74183 , https://doi.org/10.1016/j.funbio.2015.11.006
- Description: Erica dominate the fynbos ecosystem, which is characterized by acidic soils that are rich in organic matter. The ericaceae associate with ericoid mycorrhizal (ERM) fungi for survival. In this study fungal biomass accumulation in vitro was used to determine nutrient utilisation of various inorganic and organic substrates. This is an initial step towards establishment of the ecological roles of typical ERM fungi and other root fungi associated with Erica plants, with regard to host nutrition. Meliniomyces sp., Acremonium implicatum, Leohumicola sp., Cryptosporiopsis erica, Oidiodendron maius and an unidentified Helotiales fungus were selected from fungi previously isolated and identified from Erica roots. Sole nitrogen sources ammonium, nitrate, arginine and Bovine Serum Albumin (BSA) were tested. Meliniomyces and Leohumicola species were able to utilise BSA effectively. Phosphorus nutrition was tested using orthophosphate, sodium inositol hexaphosphate and DNA. Most isolates preferred orthophosphate. Meliniomyces sp. and A. implicatum were able to accumulate significant biomass using DNA. Carbon utilisation was tested using glucose, cellobiose, carboxymethylcellulose, pectin and tannic acid substrates. All fungal isolates produced high biomass on glucose and cellobiose. The ability to utilize organic nutrient sources in culture, illustrates their potential role of these fungi in host nutrition in the fynbos ecosystem.
- Full Text:
- Authors: Bizabani, Christine , Dames, Joanna F
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/444079 , vital:74183 , https://doi.org/10.1016/j.funbio.2015.11.006
- Description: Erica dominate the fynbos ecosystem, which is characterized by acidic soils that are rich in organic matter. The ericaceae associate with ericoid mycorrhizal (ERM) fungi for survival. In this study fungal biomass accumulation in vitro was used to determine nutrient utilisation of various inorganic and organic substrates. This is an initial step towards establishment of the ecological roles of typical ERM fungi and other root fungi associated with Erica plants, with regard to host nutrition. Meliniomyces sp., Acremonium implicatum, Leohumicola sp., Cryptosporiopsis erica, Oidiodendron maius and an unidentified Helotiales fungus were selected from fungi previously isolated and identified from Erica roots. Sole nitrogen sources ammonium, nitrate, arginine and Bovine Serum Albumin (BSA) were tested. Meliniomyces and Leohumicola species were able to utilise BSA effectively. Phosphorus nutrition was tested using orthophosphate, sodium inositol hexaphosphate and DNA. Most isolates preferred orthophosphate. Meliniomyces sp. and A. implicatum were able to accumulate significant biomass using DNA. Carbon utilisation was tested using glucose, cellobiose, carboxymethylcellulose, pectin and tannic acid substrates. All fungal isolates produced high biomass on glucose and cellobiose. The ability to utilize organic nutrient sources in culture, illustrates their potential role of these fungi in host nutrition in the fynbos ecosystem.
- Full Text:
Audit, investigation, search, seizure and access to information
- Arendse, Jacqueline A, Clegg, David, Williams, Robert C
- Authors: Arendse, Jacqueline A , Clegg, David , Williams, Robert C
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/131245 , vital:36541 , https://store.lexisnexis.co.za/products/silke-on-tax-administration-skuZASKUPG1440
- Description: Chapter 5 of the Tax Administration Act, which supplements the various fiscal statutes, empowers SARS to call for information on taxpayers, conduct audits, investigations and in certain instances to search premises and seize goods and records. For this purpose, taxpayers are required to keep proper books and records (see § 8.2 and § 4). The purpose of a tax audit is to verify the accuracy and timing of an assessment, but more specifically to ensure accuracy and full disclosure in terms of the law. In the event that an audit reveals non-compliance, criminal and/or civil charges may be initiated by SARS (see § 8.5).
- Full Text: false
- Authors: Arendse, Jacqueline A , Clegg, David , Williams, Robert C
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/131245 , vital:36541 , https://store.lexisnexis.co.za/products/silke-on-tax-administration-skuZASKUPG1440
- Description: Chapter 5 of the Tax Administration Act, which supplements the various fiscal statutes, empowers SARS to call for information on taxpayers, conduct audits, investigations and in certain instances to search premises and seize goods and records. For this purpose, taxpayers are required to keep proper books and records (see § 8.2 and § 4). The purpose of a tax audit is to verify the accuracy and timing of an assessment, but more specifically to ensure accuracy and full disclosure in terms of the law. In the event that an audit reveals non-compliance, criminal and/or civil charges may be initiated by SARS (see § 8.5).
- Full Text: false
Back to the future: revival, relevance and route of an anarchist/syndicalist approach for twenty-first-century left, labour and national liberation movements
- Authors: Van der Walt, Lucien
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/144812 , vital:38381 , DOI: 10.1080/02589001.2016.1235365
- Description: The failings of classical Marxism, social democracy and anti-imperialist nationalism point to the need for a radical left politics at a distance from the state. This paper examines the impact, revival and promise of the anarchist/syndicalist tradition, a rich, continuous praxis in labour, left, anti-imperialist, anti-racist and egalitarian movements, worldwide, since the 1860s. Outlining its core ideas – anti-hierarchy, anti-capitalism, anti-statism, opposition to social and economic inequality, internationalist class-based mobilisation – and critique of mainstream Marxism and nationalism, it highlights the arguments there is a basic incompatibility between state rule, and bottom-up, egalitarian, democratic, socialist relationships. The anarchist/syndicalist project cannot be reduced to an organising style, protest politics or spontaneism: for it, transition to a just, self-managed society requires organised popular capacity for a revolutionary rupture, developed through prefigurative, class-based, democratic organs of counter-power, including syndicalist unions aiming at collectivised property, and revolutionary counter-culture. Success needs formal organisation, unified strategy and anarchist / syndicalist political organisations.
- Full Text:
- Authors: Van der Walt, Lucien
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/144812 , vital:38381 , DOI: 10.1080/02589001.2016.1235365
- Description: The failings of classical Marxism, social democracy and anti-imperialist nationalism point to the need for a radical left politics at a distance from the state. This paper examines the impact, revival and promise of the anarchist/syndicalist tradition, a rich, continuous praxis in labour, left, anti-imperialist, anti-racist and egalitarian movements, worldwide, since the 1860s. Outlining its core ideas – anti-hierarchy, anti-capitalism, anti-statism, opposition to social and economic inequality, internationalist class-based mobilisation – and critique of mainstream Marxism and nationalism, it highlights the arguments there is a basic incompatibility between state rule, and bottom-up, egalitarian, democratic, socialist relationships. The anarchist/syndicalist project cannot be reduced to an organising style, protest politics or spontaneism: for it, transition to a just, self-managed society requires organised popular capacity for a revolutionary rupture, developed through prefigurative, class-based, democratic organs of counter-power, including syndicalist unions aiming at collectivised property, and revolutionary counter-culture. Success needs formal organisation, unified strategy and anarchist / syndicalist political organisations.
- Full Text:
Bayesian accelerated life tests: exponential and Weibull models
- Authors: Izally, Sharkay Ruwade
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3003 , vital:20351
- Description: Reliability life testing is used for life data analysis in which samples are tested under normal conditions to obtain failure time data for reliability assessment. It can be costly and time consuming to obtain failure time data under normal operating conditions if the mean time to failure of a product is long. An alternative is to use failure time data from an accelerated life test (ALT) to extrapolate the reliability under normal conditions. In accelerated life testing, the units are placed under a higher than normal stress condition such as voltage, current, pressure, temperature, to make the items fail in a shorter period of time. The failure information is then transformed through an accelerated model commonly known as the time transformation function, to predict the reliability under normal operating conditions. The power law will be used as the time transformation function in this thesis. We will first consider a Bayesian inference model under the assumption that the underlying life distribution in the accelerated life test is exponentially distributed. The maximal data information (MDI) prior, the Ghosh Mergel and Liu (GML) prior and the Jeffreys prior will be derived for the exponential distribution. The propriety of the posterior distributions will be investigated. Results will be compared when using these non-informative priors in a simulation study by looking at the posterior variances. The Weibull distribution as the underlying life distribution in the accelerated life test will also be investigated. The maximal data information prior will be derived for the Weibull distribution using the power law. The uniform prior and a mixture of Gamma and uniform priors will be considered. The propriety of these posteriors will also be investigated. The predictive reliability at the use-stress will be computed for these models. The deviance information criterion will be used to compare these priors. As a result of using a time transformation function, Bayesian inference becomes analytically intractable and Markov Chain Monte Carlo (MCMC) methods will be used to alleviate this problem. The Metropolis-Hastings algorithm will be used to sample from the posteriors for the exponential model in the accelerated life test. The adaptive rejection sampling method will be used to sample from the posterior distributions when the Weibull model is considered.
- Full Text:
- Authors: Izally, Sharkay Ruwade
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3003 , vital:20351
- Description: Reliability life testing is used for life data analysis in which samples are tested under normal conditions to obtain failure time data for reliability assessment. It can be costly and time consuming to obtain failure time data under normal operating conditions if the mean time to failure of a product is long. An alternative is to use failure time data from an accelerated life test (ALT) to extrapolate the reliability under normal conditions. In accelerated life testing, the units are placed under a higher than normal stress condition such as voltage, current, pressure, temperature, to make the items fail in a shorter period of time. The failure information is then transformed through an accelerated model commonly known as the time transformation function, to predict the reliability under normal operating conditions. The power law will be used as the time transformation function in this thesis. We will first consider a Bayesian inference model under the assumption that the underlying life distribution in the accelerated life test is exponentially distributed. The maximal data information (MDI) prior, the Ghosh Mergel and Liu (GML) prior and the Jeffreys prior will be derived for the exponential distribution. The propriety of the posterior distributions will be investigated. Results will be compared when using these non-informative priors in a simulation study by looking at the posterior variances. The Weibull distribution as the underlying life distribution in the accelerated life test will also be investigated. The maximal data information prior will be derived for the Weibull distribution using the power law. The uniform prior and a mixture of Gamma and uniform priors will be considered. The propriety of these posteriors will also be investigated. The predictive reliability at the use-stress will be computed for these models. The deviance information criterion will be used to compare these priors. As a result of using a time transformation function, Bayesian inference becomes analytically intractable and Markov Chain Monte Carlo (MCMC) methods will be used to alleviate this problem. The Metropolis-Hastings algorithm will be used to sample from the posteriors for the exponential model in the accelerated life test. The adaptive rejection sampling method will be used to sample from the posterior distributions when the Weibull model is considered.
- Full Text:
Behaviour and trophic ecology of oceanic triggerfish (Canthidermis maculata) and rainbow runner (Elagatis bipinnulata) associated with floating objects in the open ocean
- Forget, Fabien Rocky Gilbert
- Authors: Forget, Fabien Rocky Gilbert
- Date: 2016
- Subjects: Uncatalogued
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/193531 , vital:45340
- Description: The oceanic triggerfish (Canthidermis maculata) and rainbow runner (Elagatis bipinnulata) are epipelagic species that commonly associate with floating objects throughout the world’s tropical oceans. Besides tunas, these two species often form the bulk of the aggregation and are major non-target species (bycatch) incidentally captured at fish aggregation devices (FADs) by tropical tuna purse seiners. Despite being abundant, little is known about their basic biology, ecology and associative behavior with floating objects. This thesis aims to address knowledge gaps in their associative behavior and ecology at floating objects and attempts to explore potential bycatch mitigation methods. Acoustic telemetry was used to characterise several aspects of the two species’ behavior at floating objects. Fish were captured and tagged at drifting FADs in the core of the western Indian Ocean tuna fishing grounds. Prolonged remote observations were obtained through satellite linked receivers which provided fine-scale data on the behavior of oceanic triggerfish (n= 46 919 cumulated observation days) and rainbow runner (n= 24 538 cumulated observation days). The two species remained associated with the same floating object for periods extending up to several months. The mean residence time estimated using a survival analysis was 65 days for oceanic triggerfish and 94 days for rainbow runner. A distinct diel pattern in association was observed; the two species were closely associated to the FAD during the night and increased their home range during the day while performing short excursions (oceanic triggerfish mean: 2.0 hours ±1.6 SD; rainbow runner mean: 2.4 hours ±2.2 SD) away from the FAD. Similarly, distinct patterns in the vertical movements and locomotory activity (measured using accelerometer tags) were observed as the two species increased their vertical movements and activity levels during the day. Generally, their vertical movements were largely restricted to the mixed layer (< 60 m). At night, the two species remained close to the surface (0-5 m) where they appear to be in a resting state. An interesting behavioural switch in activity levels and vertical distribution was observed for oceanic triggerfish which coincided with a change in the environment as the FAD drifted close to a cold-core cyclonic eddy. Ambient light appears to be the key stimulus triggering the observed diel behavioural patterns. species-specific vulnerability for target species, skipjack (Katsuwonus pelamis), yellowfin (Thunnus albacares), bigeye tuna (Thunnus obesus) and non-target species, including silky shark (Carcharhinus falciformis), oceanic triggerfish, and rainbow runner, to the purse seine fishing gear were investigated. Hourly presence rates at FADs over 24 hours were examined to assess whether the capture rate of non-target species could be reduced at specific times during the day. Silky sharks displayed a similar associative pattern to that of targeted tunas. Moreover, the vulnerability of both target and non-target species were close to the maximum during the period of behavioural transitions at sunrise when the majority of the fishing sets are made. As such, a change in set time in the western Indian Ocean does not appear to be a feasible method to reduce capture rates of non-target species. Stomach content and stable isotope analysis were conducted on oceanic triggerfish (stomach n = 152, isotope n = 65) and rainbow runner (stomach n = 156, isotope n = 71) incidentally captured individuals at FADs by purse seiners. Typical FAD-associated prey items represented a minor component of their diet as they predominantly foraged on zooplankton and micronekton in the water column, suggesting that oceanic triggerfish and rainbow runner do not associate to floating objects for direct trophic advantages. Overlap in their dietary and isotopic niches indicates an intermediate level of competition. Overall, the spatial and trophic ecology of both species are remarkably similar and prolonged associations with FADs indicates that floating objects play a significant ecological role in the pelagic environment for the two species. , Thesis (PhD) -- Faculty of Science, Ichthyology and Fisheries Science, 2016
- Full Text:
- Authors: Forget, Fabien Rocky Gilbert
- Date: 2016
- Subjects: Uncatalogued
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/193531 , vital:45340
- Description: The oceanic triggerfish (Canthidermis maculata) and rainbow runner (Elagatis bipinnulata) are epipelagic species that commonly associate with floating objects throughout the world’s tropical oceans. Besides tunas, these two species often form the bulk of the aggregation and are major non-target species (bycatch) incidentally captured at fish aggregation devices (FADs) by tropical tuna purse seiners. Despite being abundant, little is known about their basic biology, ecology and associative behavior with floating objects. This thesis aims to address knowledge gaps in their associative behavior and ecology at floating objects and attempts to explore potential bycatch mitigation methods. Acoustic telemetry was used to characterise several aspects of the two species’ behavior at floating objects. Fish were captured and tagged at drifting FADs in the core of the western Indian Ocean tuna fishing grounds. Prolonged remote observations were obtained through satellite linked receivers which provided fine-scale data on the behavior of oceanic triggerfish (n= 46 919 cumulated observation days) and rainbow runner (n= 24 538 cumulated observation days). The two species remained associated with the same floating object for periods extending up to several months. The mean residence time estimated using a survival analysis was 65 days for oceanic triggerfish and 94 days for rainbow runner. A distinct diel pattern in association was observed; the two species were closely associated to the FAD during the night and increased their home range during the day while performing short excursions (oceanic triggerfish mean: 2.0 hours ±1.6 SD; rainbow runner mean: 2.4 hours ±2.2 SD) away from the FAD. Similarly, distinct patterns in the vertical movements and locomotory activity (measured using accelerometer tags) were observed as the two species increased their vertical movements and activity levels during the day. Generally, their vertical movements were largely restricted to the mixed layer (< 60 m). At night, the two species remained close to the surface (0-5 m) where they appear to be in a resting state. An interesting behavioural switch in activity levels and vertical distribution was observed for oceanic triggerfish which coincided with a change in the environment as the FAD drifted close to a cold-core cyclonic eddy. Ambient light appears to be the key stimulus triggering the observed diel behavioural patterns. species-specific vulnerability for target species, skipjack (Katsuwonus pelamis), yellowfin (Thunnus albacares), bigeye tuna (Thunnus obesus) and non-target species, including silky shark (Carcharhinus falciformis), oceanic triggerfish, and rainbow runner, to the purse seine fishing gear were investigated. Hourly presence rates at FADs over 24 hours were examined to assess whether the capture rate of non-target species could be reduced at specific times during the day. Silky sharks displayed a similar associative pattern to that of targeted tunas. Moreover, the vulnerability of both target and non-target species were close to the maximum during the period of behavioural transitions at sunrise when the majority of the fishing sets are made. As such, a change in set time in the western Indian Ocean does not appear to be a feasible method to reduce capture rates of non-target species. Stomach content and stable isotope analysis were conducted on oceanic triggerfish (stomach n = 152, isotope n = 65) and rainbow runner (stomach n = 156, isotope n = 71) incidentally captured individuals at FADs by purse seiners. Typical FAD-associated prey items represented a minor component of their diet as they predominantly foraged on zooplankton and micronekton in the water column, suggesting that oceanic triggerfish and rainbow runner do not associate to floating objects for direct trophic advantages. Overlap in their dietary and isotopic niches indicates an intermediate level of competition. Overall, the spatial and trophic ecology of both species are remarkably similar and prolonged associations with FADs indicates that floating objects play a significant ecological role in the pelagic environment for the two species. , Thesis (PhD) -- Faculty of Science, Ichthyology and Fisheries Science, 2016
- Full Text:
Being a black mine worker in South Africa: the case of Anglo Platinum Mine
- Authors: Maseko, Robert
- Date: 2016
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/651 , vital:19978
- Description: This thesis presents a decolonial perspective on the experience of being a black mineworker in post-apartheid South Africa with specific reference to the Platinum Belt. It seeks to understand what it means to be a black mineworker by unmasking and analysing the existence and prevalence of coloniality in contemporary South Africa despite the end of formal colonialism (i.e. apartheid). As a world-wide system, coloniality has different dimensions which all speak to and highlight continuities between the period of colonialism and the post-colonial period. These dimensions are coloniality of power, coloniality of being and coloniality of knowledge. The power structure of coloniality produces and reproduces the identity of the black mineworker in present-day South Africa as a sub-ontological being devoid of an authentic humanity such that the mineworker is depicted as incapable of rational thought and knowledge. The existential condition of the black mineworker is symptomatic of the generic experience of being a racialised subject of colour in the current global power structure predicated on the dominance and hegemony of Western-centred modernity. The black mineworker exists on the darker side of Western-centred modernity, living a life of wretchedness and continuing to suffer the colonial wound in the absence of formal colonialism and apartheid. The mineworker is disposable and dispensable and lives and works in the shadow of death. In pursuing this course of reasoning, I deploy the epistemic method of ‘shifting the geography of reason’ in order to read the experience of mineworkers in South Africa from the locus of enunciation of the oppressed subject within the scheme of a colonial power differential based on a hierarchy of humanity. This method allows me to speak with and from the perspective of the black mineworkers in the Platinum Belt as opposed to speaking for and about them. I reach the conclusion that being a platinum mineworker in post-apartheid South Africa is a racial and market determined identity of colonialised subjectivity that relegates the dominated subject (the black mineworker) to the realm of the subhuman. In setting the context for this claim, I trace the origins and development of the black mineworker in South Africa with reference to historical processes such as dispossession and proletarianisation. Empirically, the thesis is rooted in a contemporary case study of mainly Anglo Platinum Mine, which involved comprehensive fieldwork focusing on the present lived realities of platinum mineworkers. The dignity and humanity of these black mineworkers has still not returned despite twenty years of democratic rule in South Africa, such that race remains a crucial organising principle in postapartheid South Africa.
- Full Text:
- Authors: Maseko, Robert
- Date: 2016
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/651 , vital:19978
- Description: This thesis presents a decolonial perspective on the experience of being a black mineworker in post-apartheid South Africa with specific reference to the Platinum Belt. It seeks to understand what it means to be a black mineworker by unmasking and analysing the existence and prevalence of coloniality in contemporary South Africa despite the end of formal colonialism (i.e. apartheid). As a world-wide system, coloniality has different dimensions which all speak to and highlight continuities between the period of colonialism and the post-colonial period. These dimensions are coloniality of power, coloniality of being and coloniality of knowledge. The power structure of coloniality produces and reproduces the identity of the black mineworker in present-day South Africa as a sub-ontological being devoid of an authentic humanity such that the mineworker is depicted as incapable of rational thought and knowledge. The existential condition of the black mineworker is symptomatic of the generic experience of being a racialised subject of colour in the current global power structure predicated on the dominance and hegemony of Western-centred modernity. The black mineworker exists on the darker side of Western-centred modernity, living a life of wretchedness and continuing to suffer the colonial wound in the absence of formal colonialism and apartheid. The mineworker is disposable and dispensable and lives and works in the shadow of death. In pursuing this course of reasoning, I deploy the epistemic method of ‘shifting the geography of reason’ in order to read the experience of mineworkers in South Africa from the locus of enunciation of the oppressed subject within the scheme of a colonial power differential based on a hierarchy of humanity. This method allows me to speak with and from the perspective of the black mineworkers in the Platinum Belt as opposed to speaking for and about them. I reach the conclusion that being a platinum mineworker in post-apartheid South Africa is a racial and market determined identity of colonialised subjectivity that relegates the dominated subject (the black mineworker) to the realm of the subhuman. In setting the context for this claim, I trace the origins and development of the black mineworker in South Africa with reference to historical processes such as dispossession and proletarianisation. Empirically, the thesis is rooted in a contemporary case study of mainly Anglo Platinum Mine, which involved comprehensive fieldwork focusing on the present lived realities of platinum mineworkers. The dignity and humanity of these black mineworkers has still not returned despite twenty years of democratic rule in South Africa, such that race remains a crucial organising principle in postapartheid South Africa.
- Full Text:
Being civil
- Matshoba, Zongezile Theophilus
- Authors: Matshoba, Zongezile Theophilus
- Date: 2016
- Language: English , Xhosa
- Type: Thesis , Masters , MA
- Identifier: vital:6017 , http://hdl.handle.net/10962/d1021237
- Description: My collection of short stories delves into government and governance, democracy, citizenship, civil servants, poverty, corruption and nepotism. My stories draw on the traditions of gritty urban crime fiction uncovering crimes of violence, service delivery, vandalism and corruption. They explore themes of mental cruelty and greed, self- preservation and community in rural areas, farms, townships and cities characterized by wrenching contradictions and inequalities. , This epic dramatic poetic verse delves into government and school governance, labour unions, liberation struggle, parenting and a wide range of school perceptions. It interrogates the roles of parents, teachers, students, department of education officials and that of other stakeholders that make use of schools. Influenced by William Wellington Gqoba’s ‘A great debate on education: a Parable’ wayback, it continues the education debate in the current post-democratic South Africa characterized by wrenching contradictions and inequalities. , This thesis is presented in two parts: English and isiXhosa.
- Full Text:
- Authors: Matshoba, Zongezile Theophilus
- Date: 2016
- Language: English , Xhosa
- Type: Thesis , Masters , MA
- Identifier: vital:6017 , http://hdl.handle.net/10962/d1021237
- Description: My collection of short stories delves into government and governance, democracy, citizenship, civil servants, poverty, corruption and nepotism. My stories draw on the traditions of gritty urban crime fiction uncovering crimes of violence, service delivery, vandalism and corruption. They explore themes of mental cruelty and greed, self- preservation and community in rural areas, farms, townships and cities characterized by wrenching contradictions and inequalities. , This epic dramatic poetic verse delves into government and school governance, labour unions, liberation struggle, parenting and a wide range of school perceptions. It interrogates the roles of parents, teachers, students, department of education officials and that of other stakeholders that make use of schools. Influenced by William Wellington Gqoba’s ‘A great debate on education: a Parable’ wayback, it continues the education debate in the current post-democratic South Africa characterized by wrenching contradictions and inequalities. , This thesis is presented in two parts: English and isiXhosa.
- Full Text:
Being for the Other: Surveillance and Depictions of Race, Gender, and Animals in Contemporary South African Fiction
- Authors: Laue, Kharys Ateh
- Date: 2016
- Language: English
- Type: Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/3848 , vital:20549
- Description: This thesis examines the depiction, in contemporary South African fiction, of irresponsibility and responsibility in relation to the raced, gendered, and animal Other. Through a close analysis of Jeremy Bentham’s Panopticon prison and Michel Foucault’s study of this design, I establish the notion of disciplinary surveillance or panopticism. This I take to be a mode of power that seeks, by means of an invisible gaze, to render its subjects docile. In my readings of J. M. Coetzee’s Waiting for the Barbarians, Zoë Wicomb’s Playing in the Light, Justin Cartwright’s White Lightning, and selected short stories from Wicomb’s You Can’t Get Lost in Cape Town and The One That Got Away, I demonstrate that oppressive authoritarian regimes are rooted in Benthamic principles of hyper-visibility and concealment. Disciplinary power, I contend, is effective precisely because it places an individual in a constant state of Being-for-Others, a term coined by Jean-Paul Sartre to describe the experience of objectification through another’s look. Judith Butler’s concept of gender performativity and W. E. B. Du Bois’s notion of black double consciousness frame my examination of, respectively, gender and racial oppression, while my discussion of animals appeals to Jacques Derrida’s work on the non-human. I show how surveillance, in each of the selected texts, functions through a racist and/or sexist and/or speciesist gaze that facilitates violent, irresponsible relationships with the human and non-human Other. The texts under discussion, however, also depict ways in which the Other actively resists and subverts regimes of oppression, often by means of a counter gaze that compels the protagonist, or the reader, to take up responsibility for Others. Ultimately, my study concludes that the fictional works of Coetzee, Wicomb, and Cartwright offer an ethics of empathetic responsibility, which I term Being for the Other, in opposition to mechanisms of disciplinary surveillance that seek to oppress, conceal, and dominate.
- Full Text:
- Authors: Laue, Kharys Ateh
- Date: 2016
- Language: English
- Type: Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/3848 , vital:20549
- Description: This thesis examines the depiction, in contemporary South African fiction, of irresponsibility and responsibility in relation to the raced, gendered, and animal Other. Through a close analysis of Jeremy Bentham’s Panopticon prison and Michel Foucault’s study of this design, I establish the notion of disciplinary surveillance or panopticism. This I take to be a mode of power that seeks, by means of an invisible gaze, to render its subjects docile. In my readings of J. M. Coetzee’s Waiting for the Barbarians, Zoë Wicomb’s Playing in the Light, Justin Cartwright’s White Lightning, and selected short stories from Wicomb’s You Can’t Get Lost in Cape Town and The One That Got Away, I demonstrate that oppressive authoritarian regimes are rooted in Benthamic principles of hyper-visibility and concealment. Disciplinary power, I contend, is effective precisely because it places an individual in a constant state of Being-for-Others, a term coined by Jean-Paul Sartre to describe the experience of objectification through another’s look. Judith Butler’s concept of gender performativity and W. E. B. Du Bois’s notion of black double consciousness frame my examination of, respectively, gender and racial oppression, while my discussion of animals appeals to Jacques Derrida’s work on the non-human. I show how surveillance, in each of the selected texts, functions through a racist and/or sexist and/or speciesist gaze that facilitates violent, irresponsible relationships with the human and non-human Other. The texts under discussion, however, also depict ways in which the Other actively resists and subverts regimes of oppression, often by means of a counter gaze that compels the protagonist, or the reader, to take up responsibility for Others. Ultimately, my study concludes that the fictional works of Coetzee, Wicomb, and Cartwright offer an ethics of empathetic responsibility, which I term Being for the Other, in opposition to mechanisms of disciplinary surveillance that seek to oppress, conceal, and dominate.
- Full Text:
Beta decay of 100/400 Zr produced in neutron-induced fission of natural uranium
- Authors: Kamoto, Thokozani
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3024 , vital:20353
- Description: Fission fragments, produced by neutron bombardment of natural uranium at the Physics Department, Jyväskylä, Finland, are studied in this work. The data had been sorted into 25 Y — y coincidence matrices which were then analysed. In this work we aimed to identify the fission products using Y-Y coincidence analysis and then study the beta-decay of some of the fission products. Sixteen fission products ranging from A = 94 to A = 136 were identified. Out of these fission products beta decay of the A = 100 (100/40 Zr – 100/41 Nb – 100/42 Mo) chain was studied in greater detail. We have also studied the variation of the relative intensities as a function of time of the 159-, 528-, 600-, 768-, 928- and 1502-keV Y-rav lines in 100/42 Mo and the profiles of the relative intensities have been modelled with the variation of the activity of 100/41 Nb against time. Configuration assignments of 100 Zr and 100/42 Mo are discussed.
- Full Text:
- Authors: Kamoto, Thokozani
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3024 , vital:20353
- Description: Fission fragments, produced by neutron bombardment of natural uranium at the Physics Department, Jyväskylä, Finland, are studied in this work. The data had been sorted into 25 Y — y coincidence matrices which were then analysed. In this work we aimed to identify the fission products using Y-Y coincidence analysis and then study the beta-decay of some of the fission products. Sixteen fission products ranging from A = 94 to A = 136 were identified. Out of these fission products beta decay of the A = 100 (100/40 Zr – 100/41 Nb – 100/42 Mo) chain was studied in greater detail. We have also studied the variation of the relative intensities as a function of time of the 159-, 528-, 600-, 768-, 928- and 1502-keV Y-rav lines in 100/42 Mo and the profiles of the relative intensities have been modelled with the variation of the activity of 100/41 Nb against time. Configuration assignments of 100 Zr and 100/42 Mo are discussed.
- Full Text:
Between sentences
- Authors: Thesen, Jo-Ann
- Date: 2016
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:6007 , http://hdl.handle.net/10962/1021215
- Description: My stories explore different forms, including flash fiction. Some use the fairy tale form to combine fiction and non-fiction in order to reach the essence of the story. In this I am influenced by Kate Bernheimer, who speaks of the “flatness, abstraction, intuitive logic and normalized magic” of traditional fairy tales. A number of stories are set in the places I worked as a newspaper reporter. Here I use my old press reports as starting points for the real or imagined story behind the news – often involving miscommunication, dominance, exploitation, the tension between isolation and belonging, and the nuances of family relationships.
- Full Text:
- Authors: Thesen, Jo-Ann
- Date: 2016
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:6007 , http://hdl.handle.net/10962/1021215
- Description: My stories explore different forms, including flash fiction. Some use the fairy tale form to combine fiction and non-fiction in order to reach the essence of the story. In this I am influenced by Kate Bernheimer, who speaks of the “flatness, abstraction, intuitive logic and normalized magic” of traditional fairy tales. A number of stories are set in the places I worked as a newspaper reporter. Here I use my old press reports as starting points for the real or imagined story behind the news – often involving miscommunication, dominance, exploitation, the tension between isolation and belonging, and the nuances of family relationships.
- Full Text:
Binding and entry of a non-enveloped T=4 insect RNA virus is triggered by alkaline pH
- Penkler, David L, Jiwaji, Meesbah, Domitrovic, Tatiana, Short, James R, Johnson, John E, Dorrington, Rosemary A
- Authors: Penkler, David L , Jiwaji, Meesbah , Domitrovic, Tatiana , Short, James R , Johnson, John E , Dorrington, Rosemary A
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/65995 , vital:28875 , https://doi.org/10.1016/j.virol.2016.08.028
- Description: publisher version , Tetraviruses are small, non-enveloped, RNA viruses that exclusively infect lepidopteran insects. Their particles comprise 240 copies of a single capsid protein precursor (CP), which undergoes autoproteolytic cleavage during maturation. The molecular mechanisms of capsid assembly and maturation are well understood, but little is known about the viral infectious lifecycle due to a lack of tissue culture cell lines that are susceptible to tetravirus infection. We show here that binding and entry of the alphatetravirus, Helicoverpa armigera stunt virus (HaSV), is triggered by alkaline pH. At pH 9.0, wild-type HaSV virus particles undergo conformational changes that induce membrane-lytic activity and binding to Spodoptera frugiperda Sf9 cells. Binding is followed by entry and infection, with virus replication complexes detected by immunofluorescence microscopy within 2 h post-infection and the CP after 12 h. HaSV particles produced in S. frugiperda Sf9 cells are infectious. Helicoverpa armigera larval virus biofeed assays showed that pre-treatment with the V-ATPase inhibitor, Bafilomycin A1, resulted in a 50% decrease in larval mortality and stunting, while incubation of virus particles at pH 9.0 prior to infection restored infectivity. Together, these data show that HaSV, and likely other tetraviruses, requires the alkaline environment of the lepidopteran larval midgut for binding and entry into host cells.
- Full Text: false
- Authors: Penkler, David L , Jiwaji, Meesbah , Domitrovic, Tatiana , Short, James R , Johnson, John E , Dorrington, Rosemary A
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/65995 , vital:28875 , https://doi.org/10.1016/j.virol.2016.08.028
- Description: publisher version , Tetraviruses are small, non-enveloped, RNA viruses that exclusively infect lepidopteran insects. Their particles comprise 240 copies of a single capsid protein precursor (CP), which undergoes autoproteolytic cleavage during maturation. The molecular mechanisms of capsid assembly and maturation are well understood, but little is known about the viral infectious lifecycle due to a lack of tissue culture cell lines that are susceptible to tetravirus infection. We show here that binding and entry of the alphatetravirus, Helicoverpa armigera stunt virus (HaSV), is triggered by alkaline pH. At pH 9.0, wild-type HaSV virus particles undergo conformational changes that induce membrane-lytic activity and binding to Spodoptera frugiperda Sf9 cells. Binding is followed by entry and infection, with virus replication complexes detected by immunofluorescence microscopy within 2 h post-infection and the CP after 12 h. HaSV particles produced in S. frugiperda Sf9 cells are infectious. Helicoverpa armigera larval virus biofeed assays showed that pre-treatment with the V-ATPase inhibitor, Bafilomycin A1, resulted in a 50% decrease in larval mortality and stunting, while incubation of virus particles at pH 9.0 prior to infection restored infectivity. Together, these data show that HaSV, and likely other tetraviruses, requires the alkaline environment of the lepidopteran larval midgut for binding and entry into host cells.
- Full Text: false
Bio-prospecting a Soil Metagenomic Library for Carbohydrate Active Esterases
- Authors: Shezi, Ntombifuthi
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4172 , http://hdl.handle.net/10962/d1021266
- Description: Lignocellulosic biomass is a promising renewable resource on earth. Plant biomass contains fermentable sugars and other moieties that can be converted to biofuels or other chemicals. Enzymatic hydrolysis of these biopolymers is significant in the liberation of sugars for fermentation into desired products. Owing to its complex structure, synergistic action of enzymes is required for its degradation. Enzymes that are involved in biomass degradation include cellulases, hemicellulases and the accessory enzymes acetyl xylan esterases and ferulic acid esterases. Ferulic acid esterases (FAEs, EC 3.1.1.73), represent a subclass of carboxylester hydrolases (EC 3.1.1.-) that catalyse the release of hydroxycinnamic acids (such as ferulic acid, p-coumaric, ferulic, sinapic and caffeic acid) that are generally found esterified to polysaccharides, such as arabinoxylans. Hydroxycinnamic acids have widespread potential applications due to their antimicrobial, photoprotectant and antioxidant properties, as well as their use as flavour precursors. Therefore, this interesting group of FAEs has a potentially wide variety of applications in agriculture, food and pharmaceutical industries. In the search for novel biocatalysts, metagenomics is considered as an alternative approach to conventional microbe screening, therefore, searching for novel biocatalysts from a soil metagenome that harbours a unique diversity of biocatalyst is significant. The aim of this study was to extract DNA from soil associated with cattle manure and construct a soil metagenomic library using a fosmid based plasmid vector and subsequently functionally screen for ferulic acid esterases using ethyl ferulate as a model substrate. A total of 59 recombinant fosmids conferring ferulic acid esterase phenotypes were identified (Hit rate 1:3122) and the two fosmids that consistently showed high FAE activities were selected for further study. Following nucleotide sequencing and translational analysis, two fae encoding open reading frames (FAE9 and FAE27) of approximately 274 and 322 aa, respectively, were identified. The amino acid sequence of the two ORFs contained a classical conserved esterase/lipase G-x-S-x-G sequence motif. The two genes (fae9 and fae27) were successfully expressed in Escherichia coli BL21 (DE3) and the purified enzymes exhibited respective temperature optima of 50 °C and 40 °C, and respective pH optima of 6.0 and 7.0. Further biochemical characterisation showed that FAE9 and FAE27 have high substrate specificity, following the fact that EFA is the preferred substrate for FAE9 (kcat/Km value of 128 s−1.mM-1) and also the preferred substrate for FAE27 (kcat/Km value of 137 s−1.mM-1). This work proves that soil is a valuable environmental source for novel esterase screening through functional based metagenomic approach. Therefore, this method may be used to screen for other valuable enzymes from environmental sources using inexpensive natural sources to encourage the screening of specific enzymes. Biochemistry of the two isolated enzymes makes these enzymes to be useful in industrial applications due to broad substrate activity that could replace the specialised enzymes to complete plant biomass degradation.
- Full Text:
- Authors: Shezi, Ntombifuthi
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4172 , http://hdl.handle.net/10962/d1021266
- Description: Lignocellulosic biomass is a promising renewable resource on earth. Plant biomass contains fermentable sugars and other moieties that can be converted to biofuels or other chemicals. Enzymatic hydrolysis of these biopolymers is significant in the liberation of sugars for fermentation into desired products. Owing to its complex structure, synergistic action of enzymes is required for its degradation. Enzymes that are involved in biomass degradation include cellulases, hemicellulases and the accessory enzymes acetyl xylan esterases and ferulic acid esterases. Ferulic acid esterases (FAEs, EC 3.1.1.73), represent a subclass of carboxylester hydrolases (EC 3.1.1.-) that catalyse the release of hydroxycinnamic acids (such as ferulic acid, p-coumaric, ferulic, sinapic and caffeic acid) that are generally found esterified to polysaccharides, such as arabinoxylans. Hydroxycinnamic acids have widespread potential applications due to their antimicrobial, photoprotectant and antioxidant properties, as well as their use as flavour precursors. Therefore, this interesting group of FAEs has a potentially wide variety of applications in agriculture, food and pharmaceutical industries. In the search for novel biocatalysts, metagenomics is considered as an alternative approach to conventional microbe screening, therefore, searching for novel biocatalysts from a soil metagenome that harbours a unique diversity of biocatalyst is significant. The aim of this study was to extract DNA from soil associated with cattle manure and construct a soil metagenomic library using a fosmid based plasmid vector and subsequently functionally screen for ferulic acid esterases using ethyl ferulate as a model substrate. A total of 59 recombinant fosmids conferring ferulic acid esterase phenotypes were identified (Hit rate 1:3122) and the two fosmids that consistently showed high FAE activities were selected for further study. Following nucleotide sequencing and translational analysis, two fae encoding open reading frames (FAE9 and FAE27) of approximately 274 and 322 aa, respectively, were identified. The amino acid sequence of the two ORFs contained a classical conserved esterase/lipase G-x-S-x-G sequence motif. The two genes (fae9 and fae27) were successfully expressed in Escherichia coli BL21 (DE3) and the purified enzymes exhibited respective temperature optima of 50 °C and 40 °C, and respective pH optima of 6.0 and 7.0. Further biochemical characterisation showed that FAE9 and FAE27 have high substrate specificity, following the fact that EFA is the preferred substrate for FAE9 (kcat/Km value of 128 s−1.mM-1) and also the preferred substrate for FAE27 (kcat/Km value of 137 s−1.mM-1). This work proves that soil is a valuable environmental source for novel esterase screening through functional based metagenomic approach. Therefore, this method may be used to screen for other valuable enzymes from environmental sources using inexpensive natural sources to encourage the screening of specific enzymes. Biochemistry of the two isolated enzymes makes these enzymes to be useful in industrial applications due to broad substrate activity that could replace the specialised enzymes to complete plant biomass degradation.
- Full Text:
Biofuels and rural development: A case study of the Mapfura-Makhura Incubator and small-scale farmers in the Limpopo Province
- Authors: Mothupi, Frans Makwena
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSocSc
- Identifier: http://hdl.handle.net/10962/1488 , vital:20062
- Description: The primary objective of the study is to examine the livelihood impact of biofuel production on small-scale rural farmers participating in the MMI project in the local districts in Limpopo province. The study is theoretically underpinned by the sustainable livelihoods framework which provides a nuanced analysis of the complex nature of poverty and livelihoods. The framework was used to examine how MMI as a structure with its own processes (incubator model) plays a role in creating a means for farmers to have more access to livelihood assets which would help them achieve improved livelihoods outcome. The findings of this study reflect what has already been articulated in literature about small-scale biofuel projects. This study shows that MMI’s incubator plays an important role for 73% of the farmers to access all of the livelihood assets and ultimately improving their farm income and food security. Furthermore, 90% of the participants admitted to have received support from MMI in a number of ways. This includes the provision of farming inputs, labour and access to markets in addition to training, mentoring and coaching. The study also found that despite the overwhelming support, both MMI and farmers face a number of challenges. Farmers still lack adequate farming inputs, transport, access to markets and vulnerability to natural disasters. MMI faces challenges in raising funds to provide inputs to all their incubatees and lack of adequate mechanization. Lack of transportation affects both farmers and MMI in that farmers find it difficult to access MMI service. In the same light, MMI has found it difficult to reach farmers for post-incubation, coaching and mentoring or delivering inputs; this can be challenging and a costly process. MMI’s biofuel production project has the capability for improving rural livelihoods through agriculture. The study concludes by recommending that MMI should improve its own capacity in order for them to better the lives of the farmers they assist. This study is significant for contributing to a field which has received less academic and research attention in South Africa. Its scholarly contribution will enhance the existing body of knowledge on biofuels and rural development in South Africa
- Full Text:
- Authors: Mothupi, Frans Makwena
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSocSc
- Identifier: http://hdl.handle.net/10962/1488 , vital:20062
- Description: The primary objective of the study is to examine the livelihood impact of biofuel production on small-scale rural farmers participating in the MMI project in the local districts in Limpopo province. The study is theoretically underpinned by the sustainable livelihoods framework which provides a nuanced analysis of the complex nature of poverty and livelihoods. The framework was used to examine how MMI as a structure with its own processes (incubator model) plays a role in creating a means for farmers to have more access to livelihood assets which would help them achieve improved livelihoods outcome. The findings of this study reflect what has already been articulated in literature about small-scale biofuel projects. This study shows that MMI’s incubator plays an important role for 73% of the farmers to access all of the livelihood assets and ultimately improving their farm income and food security. Furthermore, 90% of the participants admitted to have received support from MMI in a number of ways. This includes the provision of farming inputs, labour and access to markets in addition to training, mentoring and coaching. The study also found that despite the overwhelming support, both MMI and farmers face a number of challenges. Farmers still lack adequate farming inputs, transport, access to markets and vulnerability to natural disasters. MMI faces challenges in raising funds to provide inputs to all their incubatees and lack of adequate mechanization. Lack of transportation affects both farmers and MMI in that farmers find it difficult to access MMI service. In the same light, MMI has found it difficult to reach farmers for post-incubation, coaching and mentoring or delivering inputs; this can be challenging and a costly process. MMI’s biofuel production project has the capability for improving rural livelihoods through agriculture. The study concludes by recommending that MMI should improve its own capacity in order for them to better the lives of the farmers they assist. This study is significant for contributing to a field which has received less academic and research attention in South Africa. Its scholarly contribution will enhance the existing body of knowledge on biofuels and rural development in South Africa
- Full Text:
Bioinformatic characterization of type-specific sequence and structural features in auxiliary activity family 9 proteins:
- Moses, Vuyani, Hatherley, Rowan, Tastan Bishop, Özlem
- Authors: Moses, Vuyani , Hatherley, Rowan , Tastan Bishop, Özlem
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148358 , vital:38732 , DOI: 10.1186/s13068-016-0655-2
- Description: Due to the impending depletion of fossil fuels, it has become important to identify alternative energy sources. The biofuel industry has proven to be a promising alternative. However, owing to the complex nature of plant biomass, hence the degradation, biofuel production remains a challenge. The copper-dependent Auxiliary Activity family 9 (AA9) proteins have been found to act synergistically with other cellulose-degrading enzymes resulting in an increased rate of cellulose breakdown. AA9 proteins are lytic polysaccharide monooxygenase (LPMO) enzymes, otherwise known as polysaccharide monooxygenases (PMOs). They are further classified as Type 1, 2 or 3 PMOs, depending on the different cleavage products formed. As AA9 proteins are known to exhibit low sequence conservation, the analysis of unique features of AA9 domains of these enzymes should provide insights for the better understanding of how different AA9 PMO types function.
- Full Text:
- Authors: Moses, Vuyani , Hatherley, Rowan , Tastan Bishop, Özlem
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148358 , vital:38732 , DOI: 10.1186/s13068-016-0655-2
- Description: Due to the impending depletion of fossil fuels, it has become important to identify alternative energy sources. The biofuel industry has proven to be a promising alternative. However, owing to the complex nature of plant biomass, hence the degradation, biofuel production remains a challenge. The copper-dependent Auxiliary Activity family 9 (AA9) proteins have been found to act synergistically with other cellulose-degrading enzymes resulting in an increased rate of cellulose breakdown. AA9 proteins are lytic polysaccharide monooxygenase (LPMO) enzymes, otherwise known as polysaccharide monooxygenases (PMOs). They are further classified as Type 1, 2 or 3 PMOs, depending on the different cleavage products formed. As AA9 proteins are known to exhibit low sequence conservation, the analysis of unique features of AA9 domains of these enzymes should provide insights for the better understanding of how different AA9 PMO types function.
- Full Text:
Biological activity of extracellular and intracellular polysaccharides from Pleurotus tuber-regium hybrid and mutant strains
- Bamigboye, Comfort O, Oloke, Julius K, Dames, Joanna Felicity
- Authors: Bamigboye, Comfort O , Oloke, Julius K , Dames, Joanna Felicity
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/69056 , vital:29376 , http://pubs.sciepub.com/jfnr/4/7/2/
- Description: Publisher version , Pleurotus tuber-regium (Fr.) Singer (1951) is a unique sclerotium-forming edible and medicinal mushroom. Interestingly, both the sclerotium and mushroom are edible and are often used for curing various ailments. Previous studies have focused on the antimicrobial and antioxidant activity of the extracellular polysaccharide (EPS) from wild P. tuber-regium. There has been no report on the intracellular polysaccharide (IPS) of the wild mycelia, likewise there is very meager information on the improvement of the perceived potentials of P. tuber-regium. This research study analysed the EPS and IPS fractions of P. tuber-regium hybrid and mutant strains. The antimicrobial potential of the IPS and EPS fractions, their scavenging activity on 1, 1-diphenyl–2picryhydrazyl (DPPH) and Hydroxyl radicals were also determined. Both IPS and EPS fractions of P. tuber-regium hybrids and mutants showed increased DPPH and hydroxyl scavenging activity over the wild P. tuber-regium with an EC50 mostly 1 mg/ml. The antimicrobial activity of the IPS from a mutant strain had an IC50 of 15.6 mg/ml compared to the wild type (18.75 mg /ml). This study showed that selected mutant and hybrids of P. tuber-regium had increased radical scavenging activity indicating potentially increased biological activity that could offer increased benefit as a neutraceutical.
- Full Text: false
- Authors: Bamigboye, Comfort O , Oloke, Julius K , Dames, Joanna Felicity
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/69056 , vital:29376 , http://pubs.sciepub.com/jfnr/4/7/2/
- Description: Publisher version , Pleurotus tuber-regium (Fr.) Singer (1951) is a unique sclerotium-forming edible and medicinal mushroom. Interestingly, both the sclerotium and mushroom are edible and are often used for curing various ailments. Previous studies have focused on the antimicrobial and antioxidant activity of the extracellular polysaccharide (EPS) from wild P. tuber-regium. There has been no report on the intracellular polysaccharide (IPS) of the wild mycelia, likewise there is very meager information on the improvement of the perceived potentials of P. tuber-regium. This research study analysed the EPS and IPS fractions of P. tuber-regium hybrid and mutant strains. The antimicrobial potential of the IPS and EPS fractions, their scavenging activity on 1, 1-diphenyl–2picryhydrazyl (DPPH) and Hydroxyl radicals were also determined. Both IPS and EPS fractions of P. tuber-regium hybrids and mutants showed increased DPPH and hydroxyl scavenging activity over the wild P. tuber-regium with an EC50 mostly 1 mg/ml. The antimicrobial activity of the IPS from a mutant strain had an IC50 of 15.6 mg/ml compared to the wild type (18.75 mg /ml). This study showed that selected mutant and hybrids of P. tuber-regium had increased radical scavenging activity indicating potentially increased biological activity that could offer increased benefit as a neutraceutical.
- Full Text: false
Biology and ecology of Glossogobius callidus (Smith 1937) in irrigation impoundments in the Sundays River Valley of the Eastern Cape
- Authors: Mofu, Lubabalo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1136 , vital:20023
- Description: The River Goby Glossogobius callidus (Smith, 1937) is a native abundant fish in both freshwater and estuarine habitats in the Cape Fold Ecoregion, yet little information is available on its life-history. This study aims to contribute to knowledge on the age and growth, reproductive biology and the diet and feeding habits of G. callidus in irrigation impoundments. Glossogobius callidus was sampled monthly from August 2013 till March 2015; from the irrigation ponds in the Sundays River Valley, Eastern Cape Province, South Africa. To determine sex, gonads were visually assessed under a dissecting microscope to confirm the sex based on the shape of the urogenital papillae. Fish were then dissected to confirm sex and gonads were categorised into five macroscopic stages which were histologically validated. Microscopic stages of gonadal development were discerned based on nuclear and cytoplasmic characteristics of the oocyte or sperm. Ovaries and sperms were assigned stages based on the most advanced type of oocyte present. In total 2054 fishes ranging in length from 21.1 mm to 137.2 mm TL were sampled. The sex ratio (1.1 males: 1 females) did not differ from unity (x2 = 0.027, df = 1, p = 0.87). Length at 50% maturity (Lm) was 70 mm TL females and 72 mm TL for males. Spawning season was mid-spring and mid-summer and mean ± S.D absolute fecundity was estimated at 1028.2 ± 131.7 ova/fish. Relative fecundity (number of vitellogenic oocytes per gram of eviscerated fish mass) were estimated at 50 ± 18 ova/fish gram. Otoliths from 560 fish were used for ageing. Growth zone deposition rate was validated using edge analysis. As a unimodal periodic regression model best described the temporal proportion of opaque zone deposition on the edge of otoliths over a one-year period, growth zone deposition rate was validated as annual. The oldest female fish was a 4-year old 84.4 mm TL fish and the oldest male was a 7-year old 100.5 mm TL fish. The length-at-age for the entire population of 560 G. callidus provided von Bertalanffy parameters of Lt = 92 (1 - e -0.58(t + 0.4)) mm TL for the entire population, Lt = 70 (1 - e -1.8 (t + 0.06)) mm TL for males and Lt = 65 (1 - e -1.8 (t + 0.05)) mm TL for females. Converting length at maturity to age at maturity demonstrated that G. callidus attained maturity at an age of 2-years. Growth performance described using the phi-prime index showed that G. callidus had lower growth performance compared to the invasive Neogobius melanostomus. Using age structure, natural mortality was estimated at 1.31 yr-1 using catch curve analysis. Diet of G. callidus comprised of ten taxonomic groups. Among these, aquatic invertebrates were the most diverse group but while relative contribution of the dietary components varied across all size classes and seasons, the key prey items were consistently found in all size classes. These were Diptera, Hemiptera, Trichoptera, Odonata, Cladocera, Copepoda, Hydracarina, Amphipoda, Crustacea, and Mollusca. While dietary differences were observed between the size classes and throughout the seasons, G. callidus can be regarded as a generalist feeder preying on an array of different species. Given its abundance and diet, I suggest that G. callidus contribute considerably to the invertebrate predation pressure in these artificial aquatic environments in an arid region. In summary, medium fecundity, fast growth, moderate maturity, and a generalist feeding behaviour demonstrate that G. callidus is an equilibrium life strategist. In comparison with other species, the life-history traits of G. callidus from irrigation impoundments resemble those of other freshwater goby species, some of which are global invaders.
- Full Text:
- Authors: Mofu, Lubabalo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1136 , vital:20023
- Description: The River Goby Glossogobius callidus (Smith, 1937) is a native abundant fish in both freshwater and estuarine habitats in the Cape Fold Ecoregion, yet little information is available on its life-history. This study aims to contribute to knowledge on the age and growth, reproductive biology and the diet and feeding habits of G. callidus in irrigation impoundments. Glossogobius callidus was sampled monthly from August 2013 till March 2015; from the irrigation ponds in the Sundays River Valley, Eastern Cape Province, South Africa. To determine sex, gonads were visually assessed under a dissecting microscope to confirm the sex based on the shape of the urogenital papillae. Fish were then dissected to confirm sex and gonads were categorised into five macroscopic stages which were histologically validated. Microscopic stages of gonadal development were discerned based on nuclear and cytoplasmic characteristics of the oocyte or sperm. Ovaries and sperms were assigned stages based on the most advanced type of oocyte present. In total 2054 fishes ranging in length from 21.1 mm to 137.2 mm TL were sampled. The sex ratio (1.1 males: 1 females) did not differ from unity (x2 = 0.027, df = 1, p = 0.87). Length at 50% maturity (Lm) was 70 mm TL females and 72 mm TL for males. Spawning season was mid-spring and mid-summer and mean ± S.D absolute fecundity was estimated at 1028.2 ± 131.7 ova/fish. Relative fecundity (number of vitellogenic oocytes per gram of eviscerated fish mass) were estimated at 50 ± 18 ova/fish gram. Otoliths from 560 fish were used for ageing. Growth zone deposition rate was validated using edge analysis. As a unimodal periodic regression model best described the temporal proportion of opaque zone deposition on the edge of otoliths over a one-year period, growth zone deposition rate was validated as annual. The oldest female fish was a 4-year old 84.4 mm TL fish and the oldest male was a 7-year old 100.5 mm TL fish. The length-at-age for the entire population of 560 G. callidus provided von Bertalanffy parameters of Lt = 92 (1 - e -0.58(t + 0.4)) mm TL for the entire population, Lt = 70 (1 - e -1.8 (t + 0.06)) mm TL for males and Lt = 65 (1 - e -1.8 (t + 0.05)) mm TL for females. Converting length at maturity to age at maturity demonstrated that G. callidus attained maturity at an age of 2-years. Growth performance described using the phi-prime index showed that G. callidus had lower growth performance compared to the invasive Neogobius melanostomus. Using age structure, natural mortality was estimated at 1.31 yr-1 using catch curve analysis. Diet of G. callidus comprised of ten taxonomic groups. Among these, aquatic invertebrates were the most diverse group but while relative contribution of the dietary components varied across all size classes and seasons, the key prey items were consistently found in all size classes. These were Diptera, Hemiptera, Trichoptera, Odonata, Cladocera, Copepoda, Hydracarina, Amphipoda, Crustacea, and Mollusca. While dietary differences were observed between the size classes and throughout the seasons, G. callidus can be regarded as a generalist feeder preying on an array of different species. Given its abundance and diet, I suggest that G. callidus contribute considerably to the invertebrate predation pressure in these artificial aquatic environments in an arid region. In summary, medium fecundity, fast growth, moderate maturity, and a generalist feeding behaviour demonstrate that G. callidus is an equilibrium life strategist. In comparison with other species, the life-history traits of G. callidus from irrigation impoundments resemble those of other freshwater goby species, some of which are global invaders.
- Full Text:
Birders of Africa: History of a network
- Authors: Craig, Adrian J F K
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/465317 , vital:76594 , https://doi.org/10.1080/0035919X.2016.1176081
- Description: Opening with an account of the Greater Honeyguide and its long association with man in Africa, this book sets the scene for a new historical approach to how ornithology with its northern hemisphere traditions has interacted with information provided by African people. The title Birders of Africa suggests a wider readership than the academic target audience. ‘Birder’ in current popular usage implies recreational birders, who often focus on cataloguing and collecting experiences and photographs, rather than physical specimens in the tradition of many characters in this book. Readers who might categorise themselves as ‘birders’ would likely be discouraged by an introduction with quotations from theories relating to the asymmetries of knowledge, though they could find much of interest elsewhere in the text. The introduction needs to be read with close attention, since Nancy Jacobs sets out clearly her choice of terminology and the aims of her approach to the subject.
- Full Text:
- Authors: Craig, Adrian J F K
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/465317 , vital:76594 , https://doi.org/10.1080/0035919X.2016.1176081
- Description: Opening with an account of the Greater Honeyguide and its long association with man in Africa, this book sets the scene for a new historical approach to how ornithology with its northern hemisphere traditions has interacted with information provided by African people. The title Birders of Africa suggests a wider readership than the academic target audience. ‘Birder’ in current popular usage implies recreational birders, who often focus on cataloguing and collecting experiences and photographs, rather than physical specimens in the tradition of many characters in this book. Readers who might categorise themselves as ‘birders’ would likely be discouraged by an introduction with quotations from theories relating to the asymmetries of knowledge, though they could find much of interest elsewhere in the text. The introduction needs to be read with close attention, since Nancy Jacobs sets out clearly her choice of terminology and the aims of her approach to the subject.
- Full Text: