Investigation of the potency of topical corticosteroids using the vasoconstrictor assay
- Authors: Zvidzayi, Kudzayi Michael
- Date: 2017
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/65279 , vital:28717
- Description: Expected release date-May 2019
- Full Text:
- Authors: Zvidzayi, Kudzayi Michael
- Date: 2017
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/65279 , vital:28717
- Description: Expected release date-May 2019
- Full Text:
Ionospheric disturbances during magnetic storms at SANAE
- Authors: Hiyadutuje, Alicreance
- Date: 2017
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54956 , vital:26639
- Description: The coronal mass ejections (CMEs) and solar flares associated with extreme solar activity may strike the Earth's magnetosphere and give rise to geomagnetic storms. During geomagnetic storms, the polar plasma dynamics may influence the middle and low-latitude ionosphere via travelling ionospheric disturbances (TIDs). These are wave-like electron density disturbances caused by atmospheric gravity waves propagating in the ionosphere. TIDs focus and defocus SuperDARN signals producing a characteristic pattern of ground backscattered power (Samson et al., 1989). Geomagnetic storms may cause a decrease of total electron content (TEC), i.e. a negative storm effect, or/and an increase of TEC, i.e. a positive storm effect. The aim of this project was to investigate the ionospheric response to strong storms (Dst < -100 nT) between 2011 and 2015, using TEC and scintillation measurements derived from GPS receivers as well as SuperDARN power, Doppler velocity and convection maps. In this study the ionosphere's response to geomagnetic storms is determined by the magnitude and time of occurrence of the geomagnetic storm. The ionospheric TEC results of this study show that most of the storm effects observed were a combination of both negative and positive per storm per station (77.8%), and only 8.9% and 13.3% of effects on TEC were negative and positive respectively. The highest number of storm effects occurred in autumn (36.4%), while 31.6%, 28.4% and 3.6% occurred in winter, spring and summer respectively. During the storms studied, 71.4% had phase scintillation in the range of 0.7 - 1 radians, and only 14.3% of the storms had amplitude scintillations near 0.4. The storms studied at SANAE station generated TIDs with periods of less than an hour and amplitudes in the range 0.2 - 5 TECU. These TIDs were found to originate from the high-velocity plasma flows, some of which are visible in SuperDARN convection maps. Early studies concluded that likely sources of these disturbances correspond to ionospheric current surges (Bristow et al., 1994) in the dayside auroral zone (Huang et al., 1998).
- Full Text:
- Authors: Hiyadutuje, Alicreance
- Date: 2017
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54956 , vital:26639
- Description: The coronal mass ejections (CMEs) and solar flares associated with extreme solar activity may strike the Earth's magnetosphere and give rise to geomagnetic storms. During geomagnetic storms, the polar plasma dynamics may influence the middle and low-latitude ionosphere via travelling ionospheric disturbances (TIDs). These are wave-like electron density disturbances caused by atmospheric gravity waves propagating in the ionosphere. TIDs focus and defocus SuperDARN signals producing a characteristic pattern of ground backscattered power (Samson et al., 1989). Geomagnetic storms may cause a decrease of total electron content (TEC), i.e. a negative storm effect, or/and an increase of TEC, i.e. a positive storm effect. The aim of this project was to investigate the ionospheric response to strong storms (Dst < -100 nT) between 2011 and 2015, using TEC and scintillation measurements derived from GPS receivers as well as SuperDARN power, Doppler velocity and convection maps. In this study the ionosphere's response to geomagnetic storms is determined by the magnitude and time of occurrence of the geomagnetic storm. The ionospheric TEC results of this study show that most of the storm effects observed were a combination of both negative and positive per storm per station (77.8%), and only 8.9% and 13.3% of effects on TEC were negative and positive respectively. The highest number of storm effects occurred in autumn (36.4%), while 31.6%, 28.4% and 3.6% occurred in winter, spring and summer respectively. During the storms studied, 71.4% had phase scintillation in the range of 0.7 - 1 radians, and only 14.3% of the storms had amplitude scintillations near 0.4. The storms studied at SANAE station generated TIDs with periods of less than an hour and amplitudes in the range 0.2 - 5 TECU. These TIDs were found to originate from the high-velocity plasma flows, some of which are visible in SuperDARN convection maps. Early studies concluded that likely sources of these disturbances correspond to ionospheric current surges (Bristow et al., 1994) in the dayside auroral zone (Huang et al., 1998).
- Full Text:
Linking livelihood and ecosystem change in two dryland sites in Southern Africa over a period of 30 years
- Authors: Masunungure, Current
- Date: 2017
- Subjects: Marwendo Village (Zimbabwe) -- Social conditions , Tshivhulani Village (South Africa) -- Social conditions , Marwendo Village (Zimbabwe) -- Environmental conditions , Tshivhulani Village (South Africa) -- Environmental conditions , Climatic changes -- South Africa -- Tshivhulani Village , Climatic changes -- Zimbabwe -- Marwendo Village
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/4819 , vital:20732
- Description: The ongoing and rapid change (from global to local level) in climate, populations, governments, cultures, environment, land use and economies are critical issues, especially for poor rural communities found in the dryland parts of southern Africa. The manifestations of change can combine to increase rural livelihood vulnerability, through the erosion of assets and insecurity, but can at the same time create new opportunities. Studies that consider the complex nature of change across scales and how it affects changes in livelihoods, ecosystems and responses at local level, are increasingly needed. This study, carried out in two purposefully selected study sites in the communal drylands of south-eastern Zimbabwe (Marwendo village) and Limpopo province in South Africa (Tshivhulani village), examined the complex nature of change across scales by assessing the way in which change at the global scale results in localised trends, shocks and stressors, and its impacts on livelihoods and ecosystems and responses over the past 30 years. The study applies social-ecological system thinking in understanding human-environment change. Particular emphasis was put on the role of social protection and natural resources in responding to change, shocks and stressors. The study employed a mixed method approach to gather data which included a household survey, life history interviews, transect walks, focus group discussions as well as secondary sources of information. The results of the study illustrate that shocks and stressors are common in both villages and are likely to increase in severity and frequency with ongoing and rapid human-environmental change, especially climate change. The local responses to change, shocks and stressors are primarily reactive and mainly intensify exploitation of existing natural resources and social protection as safety-nets. In Marwendo village, the villagers relied more on the use and sale of natural resource products readily available to them, whereas in Tshivhulani village they mainly tend to rely on social grants. Thus, in the future, households’ vulnerability might increase, and may be worse in Marwendo village, since important components of current livelihoods remain natural resource-based and climate sensitive. In Tshivhulani village, livelihoods characterised by high dependence on social grants can have severe consequences for households as children get older or elderly members die and grants cease to be available. Social grants therefore only really offer a temporary relief. This coupled with environmentally destructive practices such as brick-moulding in Marwendo village and uncontrolled settlements in Tshivhulani village may reinforce the negative impacts of change and thus undermine sustainable adaptation. The study concludes that multiple lenses for understanding the links between livelihood and ecosystem vulnerability in the context of the ongoing and rapid change are essential, and these provide insights into how different policy options for livelihood improvement and social protection might be appropriate for reducing household and ecosystem vulnerabilities in the future.
- Full Text:
- Authors: Masunungure, Current
- Date: 2017
- Subjects: Marwendo Village (Zimbabwe) -- Social conditions , Tshivhulani Village (South Africa) -- Social conditions , Marwendo Village (Zimbabwe) -- Environmental conditions , Tshivhulani Village (South Africa) -- Environmental conditions , Climatic changes -- South Africa -- Tshivhulani Village , Climatic changes -- Zimbabwe -- Marwendo Village
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/4819 , vital:20732
- Description: The ongoing and rapid change (from global to local level) in climate, populations, governments, cultures, environment, land use and economies are critical issues, especially for poor rural communities found in the dryland parts of southern Africa. The manifestations of change can combine to increase rural livelihood vulnerability, through the erosion of assets and insecurity, but can at the same time create new opportunities. Studies that consider the complex nature of change across scales and how it affects changes in livelihoods, ecosystems and responses at local level, are increasingly needed. This study, carried out in two purposefully selected study sites in the communal drylands of south-eastern Zimbabwe (Marwendo village) and Limpopo province in South Africa (Tshivhulani village), examined the complex nature of change across scales by assessing the way in which change at the global scale results in localised trends, shocks and stressors, and its impacts on livelihoods and ecosystems and responses over the past 30 years. The study applies social-ecological system thinking in understanding human-environment change. Particular emphasis was put on the role of social protection and natural resources in responding to change, shocks and stressors. The study employed a mixed method approach to gather data which included a household survey, life history interviews, transect walks, focus group discussions as well as secondary sources of information. The results of the study illustrate that shocks and stressors are common in both villages and are likely to increase in severity and frequency with ongoing and rapid human-environmental change, especially climate change. The local responses to change, shocks and stressors are primarily reactive and mainly intensify exploitation of existing natural resources and social protection as safety-nets. In Marwendo village, the villagers relied more on the use and sale of natural resource products readily available to them, whereas in Tshivhulani village they mainly tend to rely on social grants. Thus, in the future, households’ vulnerability might increase, and may be worse in Marwendo village, since important components of current livelihoods remain natural resource-based and climate sensitive. In Tshivhulani village, livelihoods characterised by high dependence on social grants can have severe consequences for households as children get older or elderly members die and grants cease to be available. Social grants therefore only really offer a temporary relief. This coupled with environmentally destructive practices such as brick-moulding in Marwendo village and uncontrolled settlements in Tshivhulani village may reinforce the negative impacts of change and thus undermine sustainable adaptation. The study concludes that multiple lenses for understanding the links between livelihood and ecosystem vulnerability in the context of the ongoing and rapid change are essential, and these provide insights into how different policy options for livelihood improvement and social protection might be appropriate for reducing household and ecosystem vulnerabilities in the future.
- Full Text:
MEQSILHOUETTE: a mm-VLBI observation and signal corruption simulator
- Authors: Blecher, Tariq
- Date: 2017
- Subjects: Large astronomical telescopes , Very long baseline interferometry , MEQSILHOUETTE (Software) , Event horizon telescope
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/40713 , vital:25019
- Description: The Event Horizon Telescope (EHT) aims to resolve the innermost emission of nearby supermassive black holes, Sgr A* and M87, on event horizon scales. This emission is predicted to be gravitationally lensed by the black hole which should produce a shadow (or silhouette) feature, a precise measurement of which is a test of gravity in the strong-field regime. This emission is also an ideal probe of the innermost accretion and jet-launch physics, offering the new insights into this data-limited observing regime. The EHT will use the technique of Very Long Baseline Interferometry (VLBI) at (sub)millimetre wavelengths, which has a diffraction limited angular resolution of order ~ 10 µ-arcsec. However, this technique suffers from unique challenges, including scattering and attenuation in the troposphere and interstellar medium; variable source structure; as well as antenna pointing errors comparable to the size of the primary beam. In this thesis, we present the meqsilhouette software package which is focused towards simulating realistic EHT data. It has the capability to simulate a time-variable source, and includes realistic descriptions of the effects of the troposphere, the interstellar medium as well as primary beams and associated antenna pointing errors. We have demonstrated through several examples simulations that these effects can limit the ability to measure the key science parameters. This simulator can be used to research calibration, parameter estimation and imaging strategies, as well as gain insight into possible systematic uncertainties.
- Full Text:
- Authors: Blecher, Tariq
- Date: 2017
- Subjects: Large astronomical telescopes , Very long baseline interferometry , MEQSILHOUETTE (Software) , Event horizon telescope
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/40713 , vital:25019
- Description: The Event Horizon Telescope (EHT) aims to resolve the innermost emission of nearby supermassive black holes, Sgr A* and M87, on event horizon scales. This emission is predicted to be gravitationally lensed by the black hole which should produce a shadow (or silhouette) feature, a precise measurement of which is a test of gravity in the strong-field regime. This emission is also an ideal probe of the innermost accretion and jet-launch physics, offering the new insights into this data-limited observing regime. The EHT will use the technique of Very Long Baseline Interferometry (VLBI) at (sub)millimetre wavelengths, which has a diffraction limited angular resolution of order ~ 10 µ-arcsec. However, this technique suffers from unique challenges, including scattering and attenuation in the troposphere and interstellar medium; variable source structure; as well as antenna pointing errors comparable to the size of the primary beam. In this thesis, we present the meqsilhouette software package which is focused towards simulating realistic EHT data. It has the capability to simulate a time-variable source, and includes realistic descriptions of the effects of the troposphere, the interstellar medium as well as primary beams and associated antenna pointing errors. We have demonstrated through several examples simulations that these effects can limit the ability to measure the key science parameters. This simulator can be used to research calibration, parameter estimation and imaging strategies, as well as gain insight into possible systematic uncertainties.
- Full Text:
Mineralogical and geochemical constraints on the origin, alteration history and metallogenic significance of the Manganore iron-formation, Northern Cape Province, South Africa
- Authors: Papadopoulos, Vlassis
- Date: 2017
- Subjects: Banded iron formation , Transvaal Supergroup (South Africa) , Groups (Stratigraphy) South Africa , Lithostratigraphy , Petrology South Africa , Geochemistry South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/65189 , vital:28702
- Description: The Manganore iron-formation (MIF) of the Transvaal Supergroup is host to the most important high-grade iron ore bodies in South Africa. Prevailing models for ore genesis invoke supergene processes performing during a long period of erosion, oxidation and weathering under tropical lateritic conditions while the role of potential hydrothermal processes is not addressed. Lack of detailed petrographical and geochemical data necessitated reexamination of the MIF through new and existing drill core exploration material. Thorough petrographical investigation revealed a multi-event complex alteration history involving hydrothermal activity. Iron and silica mobility during alteration is demonstrated by a series of replacement, overprinting, crosscutting textures, extensive silicification and hematitization. Metasomatized textures such as pseudomorphs of primary magnetite, carbonate minerals and chert pods/lenses point to an alteration occurring in layer- controlled fronts and link stratigraphically the MIF to Kuruman and Griquatown iron- formations. Whole-rock geochemical data verify textural observations suggesting strong enrichment of iron or silica in meter-scale horizons, expressed by different generations of quartz and hematite. High-grade iron ore is highly enriched in TiO2 and Al2O3 compared to the protolith while both BIF and iron ore display highly increased concentrations of trace elements (transition metals and HFSE). Oxygen isotopes from different quartz textures reveal little to none isotopic exchangement during alteration whereas O isotopes from hematite are in concert to values from literature and suggest two different generations of hematite. A total of 20 minerals apart from quartz and hematite were documented. An earlier alkali/HFSE alteration event that is believed to have affected the overlying Gamagara shales is recorded in the BIF by the presence of muscovite, apatite, rutile, zircon and xenotime. A later and possibly ongoing event of succeeding hydrothermal pulses involves mainly sulphates (gypsum, baryte, celestine), pyrite, carbonates (siderite, calcite) and silicates (berthierine and tourmaline). Alkali-bearing brines persistently exploit the BIF mainly through karstification-related secondary porosity, are evidently carrying iron and are proposed to participate in or control the iron enrichment by facilitating removal of silica. The source of metals, sulfur and carbon is attributed to the underlying Campbellrand dolomites and especially to the upper Gamogaan Formation. The unconformable contact between BIF and the overlying shales is suggested as a suitable fluid conduit for the development of the observed BIF and shale-derived high-grade hematite iron ore.
- Full Text:
- Authors: Papadopoulos, Vlassis
- Date: 2017
- Subjects: Banded iron formation , Transvaal Supergroup (South Africa) , Groups (Stratigraphy) South Africa , Lithostratigraphy , Petrology South Africa , Geochemistry South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/65189 , vital:28702
- Description: The Manganore iron-formation (MIF) of the Transvaal Supergroup is host to the most important high-grade iron ore bodies in South Africa. Prevailing models for ore genesis invoke supergene processes performing during a long period of erosion, oxidation and weathering under tropical lateritic conditions while the role of potential hydrothermal processes is not addressed. Lack of detailed petrographical and geochemical data necessitated reexamination of the MIF through new and existing drill core exploration material. Thorough petrographical investigation revealed a multi-event complex alteration history involving hydrothermal activity. Iron and silica mobility during alteration is demonstrated by a series of replacement, overprinting, crosscutting textures, extensive silicification and hematitization. Metasomatized textures such as pseudomorphs of primary magnetite, carbonate minerals and chert pods/lenses point to an alteration occurring in layer- controlled fronts and link stratigraphically the MIF to Kuruman and Griquatown iron- formations. Whole-rock geochemical data verify textural observations suggesting strong enrichment of iron or silica in meter-scale horizons, expressed by different generations of quartz and hematite. High-grade iron ore is highly enriched in TiO2 and Al2O3 compared to the protolith while both BIF and iron ore display highly increased concentrations of trace elements (transition metals and HFSE). Oxygen isotopes from different quartz textures reveal little to none isotopic exchangement during alteration whereas O isotopes from hematite are in concert to values from literature and suggest two different generations of hematite. A total of 20 minerals apart from quartz and hematite were documented. An earlier alkali/HFSE alteration event that is believed to have affected the overlying Gamagara shales is recorded in the BIF by the presence of muscovite, apatite, rutile, zircon and xenotime. A later and possibly ongoing event of succeeding hydrothermal pulses involves mainly sulphates (gypsum, baryte, celestine), pyrite, carbonates (siderite, calcite) and silicates (berthierine and tourmaline). Alkali-bearing brines persistently exploit the BIF mainly through karstification-related secondary porosity, are evidently carrying iron and are proposed to participate in or control the iron enrichment by facilitating removal of silica. The source of metals, sulfur and carbon is attributed to the underlying Campbellrand dolomites and especially to the upper Gamogaan Formation. The unconformable contact between BIF and the overlying shales is suggested as a suitable fluid conduit for the development of the observed BIF and shale-derived high-grade hematite iron ore.
- Full Text:
Mineralogical variation in the basal Upper Zone, Bushveld Igneous Complex, South Africa: implications for ore genesis and mineral extraction
- Van Huyssteen, Darryn Ashley
- Authors: Van Huyssteen, Darryn Ashley
- Date: 2017
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5060 , vital:20762
- Full Text:
- Authors: Van Huyssteen, Darryn Ashley
- Date: 2017
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5060 , vital:20762
- Full Text:
Mineralogy and geochemistry of structurally-controlled metasomatic alteration of carbonate-rich manganese ore at Mamatwan Mine, Kalahari Manganese Field
- Authors: Harawa, Esau Tonderai
- Date: 2017
- Subjects: Metasomatism (Mineralogy) , Manganese ores -- Geology -- South Africa , Geology -- South Africa , Mamatwan Mine (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/4717 , vital:20715
- Description: The Kalahari Manganese Field (KMF) located in the Northern Cape Province about 700km south west of Johannesburg contains 80% of the world manganese ore reserves. Mamatwan Mine is hosted within the low grade Mamatwan type ore and is located in the southernmost tip of the KMF. This mine is an open pit mine which is divided into three benches namely the top cut, middle cut and bottom cut. These three benches are structurally controlled by faults which influence the overall grade of the manganese ore. This study is a follow up work to the previous two studies carried out at Wessels Mine and Mamatwan Mine by (Gutzmer and Beukes) in 1995 and 1996 respectively with regards to alteration processes around fault controlled systems in which they concluded that epithermal fluids caused local reduction and bleaching of ore followed by oxidation and carbonate leaching of manganese ore through ascending oxidized groundwater. Metasomatic activity around fault controlled systems is controlled by three main processes namely redistribution, enrichment and depletion. These processes are determined by mobility/immobility of elements from the fault which are introduced into the pre-existing braunite carbonate rich ore. Elements such as Ca, Mg, Si, Fe, C and Mn interact with pre-existing ore due to temperature, fluid pressure, physico-chemical property of fluid gradient. Structurally, faulting and folding contribute to the movement of elements as one end of the system gets depleted the other end of the system gets enriched and vice versa. To better understand this metasomatic activity, it is crucial to conduct mass balance studies of these elements. Grant (1986) introduced the isocon diagram which is a modification of Gresen’s equation (1967) to ascertain which elements are directly or indirectly related to alteration through enrichment and depletion of Ca, Mg, Si, Fe, C and Mn. As the section approaches from altered to less altered manganese ore the mineral chemistry gradually changes from a manganese rich matrix composed of manganomelane and todorokite to a carbonate rich matrix composed of braunite, dolomite, kutnohorite and Mn-rich calcites.
- Full Text:
- Authors: Harawa, Esau Tonderai
- Date: 2017
- Subjects: Metasomatism (Mineralogy) , Manganese ores -- Geology -- South Africa , Geology -- South Africa , Mamatwan Mine (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/4717 , vital:20715
- Description: The Kalahari Manganese Field (KMF) located in the Northern Cape Province about 700km south west of Johannesburg contains 80% of the world manganese ore reserves. Mamatwan Mine is hosted within the low grade Mamatwan type ore and is located in the southernmost tip of the KMF. This mine is an open pit mine which is divided into three benches namely the top cut, middle cut and bottom cut. These three benches are structurally controlled by faults which influence the overall grade of the manganese ore. This study is a follow up work to the previous two studies carried out at Wessels Mine and Mamatwan Mine by (Gutzmer and Beukes) in 1995 and 1996 respectively with regards to alteration processes around fault controlled systems in which they concluded that epithermal fluids caused local reduction and bleaching of ore followed by oxidation and carbonate leaching of manganese ore through ascending oxidized groundwater. Metasomatic activity around fault controlled systems is controlled by three main processes namely redistribution, enrichment and depletion. These processes are determined by mobility/immobility of elements from the fault which are introduced into the pre-existing braunite carbonate rich ore. Elements such as Ca, Mg, Si, Fe, C and Mn interact with pre-existing ore due to temperature, fluid pressure, physico-chemical property of fluid gradient. Structurally, faulting and folding contribute to the movement of elements as one end of the system gets depleted the other end of the system gets enriched and vice versa. To better understand this metasomatic activity, it is crucial to conduct mass balance studies of these elements. Grant (1986) introduced the isocon diagram which is a modification of Gresen’s equation (1967) to ascertain which elements are directly or indirectly related to alteration through enrichment and depletion of Ca, Mg, Si, Fe, C and Mn. As the section approaches from altered to less altered manganese ore the mineral chemistry gradually changes from a manganese rich matrix composed of manganomelane and todorokite to a carbonate rich matrix composed of braunite, dolomite, kutnohorite and Mn-rich calcites.
- Full Text:
Missing values: a closer look
- Authors: Thorpe, Kerri
- Date: 2017
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/d1017827 , vital:20798
- Description: Problem: In today’s world, missing values are more present than ever. Due to the ever-changing and fast paced global society in which we live, most business and research data produced around the world contain missing data. This means that locating data which is meticulously precise can be a hard task in itself, but at times may prove essential as the consequences of making use of incomplete data could be disastrous. The reasons for missing data cropping up in almost all forms of work are numerous and shall be discussed in this dissertation. For example, those being interviewed or polled may choose to simply ignore questions which are posed to them, recording equipment may malfunction or be misplaced, or organisers may not be able to locate the respondent in order to rectify the missing data. Whatever the reasons for data being incomplete, it is necessary to avoid having to use inefficient and incomplete data as a result from the above problems. Therefore, various strategies or methods have been developed in order to handle these missing values. It is important, however, that these strategies or methods are utilised effectively as missing data treatment can introduce bias into the analysis. This dissertation shall look at these and other problems in more detail by using a data set which consists of records for 581 children who were interviewed in 1990 as part of the National Longitudinal Survey of Youth (NLSY). Approach: As mentioned above, many strategies or methods have been developed in order to deal with missing values. More specifically, traditional methods such as complete case analysis, available case analysis or single imputation are widely used by researchers and shall be discussed herein. Although these methods are simple and easy to implement, they require assumptions about the data that are not often satisfied in practice. Over the years, more up to date and relevant methods, such as multiple imputation and maximum likelihood have been developed. These methods rely on weaker assumptions and contain superior statistical properties when compared to the traditional techniques. In this dissertation, these traditional methods shall be reviewed and assessed in SAS and shall be compared to the more modern techniques. Results: The ad hoc techniques for handling missing data such as complete case and available case methods produce biased parameter estimates when the data is not missing completely at random (MCAR). Single imputation techniques likewise produce biased estimates as well as result in the underestimation of standard errors. Although the expectation maximisation (EM) algorithm yields unbiased parameter estimates, the lack of convenient standard errors suggests that using this algorithm for hypothesis testing is not a good idea. Multiple imputation, however, yields unbiased parameter estimates and correctly estimates standard errors. Conclusion: Ignoring missing data in any analysis produces biased parameter estimates. Using single imputation to handle missing values is not recommended, as using a single value to replace missing values does not account for the variation that would have been present if the variables were observed. As a result, the variance will be greatly underestimated. The more modern missing data methods such as the EM algorithm and multiple imputation are preferred over the traditional techniques as they require less stringent assumptions and they also mitigate the downsides of the older methods.
- Full Text:
- Authors: Thorpe, Kerri
- Date: 2017
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/d1017827 , vital:20798
- Description: Problem: In today’s world, missing values are more present than ever. Due to the ever-changing and fast paced global society in which we live, most business and research data produced around the world contain missing data. This means that locating data which is meticulously precise can be a hard task in itself, but at times may prove essential as the consequences of making use of incomplete data could be disastrous. The reasons for missing data cropping up in almost all forms of work are numerous and shall be discussed in this dissertation. For example, those being interviewed or polled may choose to simply ignore questions which are posed to them, recording equipment may malfunction or be misplaced, or organisers may not be able to locate the respondent in order to rectify the missing data. Whatever the reasons for data being incomplete, it is necessary to avoid having to use inefficient and incomplete data as a result from the above problems. Therefore, various strategies or methods have been developed in order to handle these missing values. It is important, however, that these strategies or methods are utilised effectively as missing data treatment can introduce bias into the analysis. This dissertation shall look at these and other problems in more detail by using a data set which consists of records for 581 children who were interviewed in 1990 as part of the National Longitudinal Survey of Youth (NLSY). Approach: As mentioned above, many strategies or methods have been developed in order to deal with missing values. More specifically, traditional methods such as complete case analysis, available case analysis or single imputation are widely used by researchers and shall be discussed herein. Although these methods are simple and easy to implement, they require assumptions about the data that are not often satisfied in practice. Over the years, more up to date and relevant methods, such as multiple imputation and maximum likelihood have been developed. These methods rely on weaker assumptions and contain superior statistical properties when compared to the traditional techniques. In this dissertation, these traditional methods shall be reviewed and assessed in SAS and shall be compared to the more modern techniques. Results: The ad hoc techniques for handling missing data such as complete case and available case methods produce biased parameter estimates when the data is not missing completely at random (MCAR). Single imputation techniques likewise produce biased estimates as well as result in the underestimation of standard errors. Although the expectation maximisation (EM) algorithm yields unbiased parameter estimates, the lack of convenient standard errors suggests that using this algorithm for hypothesis testing is not a good idea. Multiple imputation, however, yields unbiased parameter estimates and correctly estimates standard errors. Conclusion: Ignoring missing data in any analysis produces biased parameter estimates. Using single imputation to handle missing values is not recommended, as using a single value to replace missing values does not account for the variation that would have been present if the variables were observed. As a result, the variance will be greatly underestimated. The more modern missing data methods such as the EM algorithm and multiple imputation are preferred over the traditional techniques as they require less stringent assumptions and they also mitigate the downsides of the older methods.
- Full Text:
Modelling water quality : complexity versus simplicity
- Authors: Jacobs, Haden
- Date: 2017
- Subjects: Water quality management -- Mathematical models , Water quality -- Measurement , Water quality biological assessment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/4754 , vital:20721
- Description: Water quality management makes use of water quality models as decision making tools. Water quality management decisions need to be informed by information that is as reliable as possible. There are many situations where observational data are limited and therefore models or simulation methods have a significant role to play in providing some information that can be used to guide management decisions. Water quality modelling is the use of mathematical equations and statistics to represent the processes affecting water quality in the natural environment. Water quality data are expensive and difficult to obtain. Nutrient sampling requires a technician to obtain ‘grab samples’ which need to be kept at low temperatures and analysed in a laboratory. The laboratory analyses of nutrients is expensive and time consuming. The data required by water quality models are seldom available as complete datasets of sufficient length. This is especially true for ungauged regions, either in small rural catchments or even major rivers in developing countries. Water quality modelling requires simulated or observed water quantity data as water quality is affected by water quantity. Both the water quality modelling and water quantity modelling require data to simulate the required processes. Data are necessary for both model structure as well as model set up for calibration and validation. This study aimed to investigate the simulation of water quality in a low order stream with limited observed data using a relatively complex as well as a much simpler water quality model, represented by QUAL2K and an in-house developed Mass Balance Nutrient (MBN) model, respectively. The two models differ greatly in the approach adopted for water quality modelling, with QUAL2K being an instream water quality fate model and the MBN model being a catchment scale model that links water quantity and quality. The MBN model uses hydrological routines to simulate those components of the hydrological cycle that are expected to differ with respect to their water quality signatures (low flows, high flows, etc.). Incremental flows are broken down into flow fractions, and nutrient signatures are assigned to fractions to represent catchment nutrient load input. A linear regression linked to an urban runoff model was used to simulate water quality entering the river system from failing municipal infrastructure, which was found to be a highly variable source of nutrients within the system. A simple algal model was adapted from CE-QUAL-W2 to simulate nutrient assimilation by benthic algae. QUAL2K, an instream water quality fate model, proved unsuitable for modelling diffuse sources for a wide range of conditions and was data intensive when compared to the data requirements of the MBN model. QUAL2K did not simulate water quality accurately over a wide range of flow conditions and was found to be more suitable to simulating point sources. The MBN model did not provide accurate results in terms of the simulation of individual daily water quality values; however, the general trends and frequency characteristics of the simulations were satisfactory. Despite some uncertainties, the MBN model remains useful for extending data for catchments with limited observed water quality data. The MBN model was found to be more suitable for South African conditions than QUAL2K, given the data requirements of each model and water quality and flow data available from the Department of Water and Sanitation. The MBN model was found to be particularly useful by providing frequency distributions of water quality loads or concentrations using minimal data that can be related to the risks of exceeding management thresholds.
- Full Text:
- Authors: Jacobs, Haden
- Date: 2017
- Subjects: Water quality management -- Mathematical models , Water quality -- Measurement , Water quality biological assessment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/4754 , vital:20721
- Description: Water quality management makes use of water quality models as decision making tools. Water quality management decisions need to be informed by information that is as reliable as possible. There are many situations where observational data are limited and therefore models or simulation methods have a significant role to play in providing some information that can be used to guide management decisions. Water quality modelling is the use of mathematical equations and statistics to represent the processes affecting water quality in the natural environment. Water quality data are expensive and difficult to obtain. Nutrient sampling requires a technician to obtain ‘grab samples’ which need to be kept at low temperatures and analysed in a laboratory. The laboratory analyses of nutrients is expensive and time consuming. The data required by water quality models are seldom available as complete datasets of sufficient length. This is especially true for ungauged regions, either in small rural catchments or even major rivers in developing countries. Water quality modelling requires simulated or observed water quantity data as water quality is affected by water quantity. Both the water quality modelling and water quantity modelling require data to simulate the required processes. Data are necessary for both model structure as well as model set up for calibration and validation. This study aimed to investigate the simulation of water quality in a low order stream with limited observed data using a relatively complex as well as a much simpler water quality model, represented by QUAL2K and an in-house developed Mass Balance Nutrient (MBN) model, respectively. The two models differ greatly in the approach adopted for water quality modelling, with QUAL2K being an instream water quality fate model and the MBN model being a catchment scale model that links water quantity and quality. The MBN model uses hydrological routines to simulate those components of the hydrological cycle that are expected to differ with respect to their water quality signatures (low flows, high flows, etc.). Incremental flows are broken down into flow fractions, and nutrient signatures are assigned to fractions to represent catchment nutrient load input. A linear regression linked to an urban runoff model was used to simulate water quality entering the river system from failing municipal infrastructure, which was found to be a highly variable source of nutrients within the system. A simple algal model was adapted from CE-QUAL-W2 to simulate nutrient assimilation by benthic algae. QUAL2K, an instream water quality fate model, proved unsuitable for modelling diffuse sources for a wide range of conditions and was data intensive when compared to the data requirements of the MBN model. QUAL2K did not simulate water quality accurately over a wide range of flow conditions and was found to be more suitable to simulating point sources. The MBN model did not provide accurate results in terms of the simulation of individual daily water quality values; however, the general trends and frequency characteristics of the simulations were satisfactory. Despite some uncertainties, the MBN model remains useful for extending data for catchments with limited observed water quality data. The MBN model was found to be more suitable for South African conditions than QUAL2K, given the data requirements of each model and water quality and flow data available from the Department of Water and Sanitation. The MBN model was found to be particularly useful by providing frequency distributions of water quality loads or concentrations using minimal data that can be related to the risks of exceeding management thresholds.
- Full Text:
Molecular cloning and expression of equine CYP1A2 in Escherichia coli
- Authors: Mkabayi, Lithalethu
- Date: 2017
- Subjects: Escherichia coli , Escherichia coli infections in animals , Cytochrome P-450 , Cytochromes , Horses -- Effect of drugs on
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/4830 , vital:20734
- Description: Information regarding drug metabolism in veterinary species, especially horses, remains fragmented and incomplete. This information is essential for detection of metabolites of potential performance-enhancing substances in horseracing and for veterinary drug development. Equine liver microsomes have been used to study metabolism of a limited number of drugs, but these provide little information about individual drug metabolizing enzymes. Recombinant CYP enzyme systems are commonly used to determine contribution of individual CYP to metabolism of specific drugs. A limited number of recombinant equine CYPs have been expressed in insect cells and mammalian cell lines. However, there are no reports of recombinant equine CYP1A2 enzyme. In this study, equine CYP1A2 was identified, codon-optimized, cloned and expressed in E. coli BL21 cells. Multiple sequence alignments of equine CYP1A2 revealed an amino acid sequence identity of 83.69% to its human homolog which has previously been expressed in E. coli. The enzyme was expressed using both auto-induction and IPTG induction. Expressed equine CYP1A2 had a size of about 55 kDa, and was insoluble after cell lysis. Sarkosyl- solubilized CYP1A2 was purified using nickel affinity chromatography and gel filtration. For activity reconstitution, yeast NADPH-cytochrome P450 reductase was first expressed in E. coli BL21 cells and exhibited activity of 0.13 U/ml. Activity assay with Glo-P450 CYP1A2 assay kit indicated that CYP1A2 was inactive. Despite numerous attempts to obtain the activity, the CYP1A2 remained inactive. Although expression of equine CYP1A2 in E. coli produced non- catalytically active enzyme, this study could be used as the first step in an effort to fully develop a recombinant equine CYP1A2 system.
- Full Text:
- Authors: Mkabayi, Lithalethu
- Date: 2017
- Subjects: Escherichia coli , Escherichia coli infections in animals , Cytochrome P-450 , Cytochromes , Horses -- Effect of drugs on
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/4830 , vital:20734
- Description: Information regarding drug metabolism in veterinary species, especially horses, remains fragmented and incomplete. This information is essential for detection of metabolites of potential performance-enhancing substances in horseracing and for veterinary drug development. Equine liver microsomes have been used to study metabolism of a limited number of drugs, but these provide little information about individual drug metabolizing enzymes. Recombinant CYP enzyme systems are commonly used to determine contribution of individual CYP to metabolism of specific drugs. A limited number of recombinant equine CYPs have been expressed in insect cells and mammalian cell lines. However, there are no reports of recombinant equine CYP1A2 enzyme. In this study, equine CYP1A2 was identified, codon-optimized, cloned and expressed in E. coli BL21 cells. Multiple sequence alignments of equine CYP1A2 revealed an amino acid sequence identity of 83.69% to its human homolog which has previously been expressed in E. coli. The enzyme was expressed using both auto-induction and IPTG induction. Expressed equine CYP1A2 had a size of about 55 kDa, and was insoluble after cell lysis. Sarkosyl- solubilized CYP1A2 was purified using nickel affinity chromatography and gel filtration. For activity reconstitution, yeast NADPH-cytochrome P450 reductase was first expressed in E. coli BL21 cells and exhibited activity of 0.13 U/ml. Activity assay with Glo-P450 CYP1A2 assay kit indicated that CYP1A2 was inactive. Despite numerous attempts to obtain the activity, the CYP1A2 remained inactive. Although expression of equine CYP1A2 in E. coli produced non- catalytically active enzyme, this study could be used as the first step in an effort to fully develop a recombinant equine CYP1A2 system.
- Full Text:
Nonlinear optical properties of Sn(IV) phthalocyanines: experimental and theoretical approach
- Authors: Louzada, Marcel Severiano
- Date: 2017
- Subjects: Phthalocyanines , Nonlinear optics
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/57852 , vital:26996
- Description: This work presents the nonlinear properties of six Sn(IV) Phthalocyanines. Three of the phthalocyanines are linked by an alkylthiol substituent and the rest are linked with a phenoxy substituent. For all six compounds non-linear optic analysis was carried out in four solvents: chloroform, toluene, dichloromethane, and tetrahydrofuran, and their differences were recorded. Calculation of the linear, singlet excited, triplet excited and two photon absorption cross-sections were also carried out and the results compared. To form a comparison the first order hyperpolarizabilities, DFT calculations were also performed and the results compared to see if the behaviour between the two properties can be predicted using DFT.
- Full Text:
- Authors: Louzada, Marcel Severiano
- Date: 2017
- Subjects: Phthalocyanines , Nonlinear optics
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/57852 , vital:26996
- Description: This work presents the nonlinear properties of six Sn(IV) Phthalocyanines. Three of the phthalocyanines are linked by an alkylthiol substituent and the rest are linked with a phenoxy substituent. For all six compounds non-linear optic analysis was carried out in four solvents: chloroform, toluene, dichloromethane, and tetrahydrofuran, and their differences were recorded. Calculation of the linear, singlet excited, triplet excited and two photon absorption cross-sections were also carried out and the results compared. To form a comparison the first order hyperpolarizabilities, DFT calculations were also performed and the results compared to see if the behaviour between the two properties can be predicted using DFT.
- Full Text:
Oxygen limitation and thermal tolerance: a comparison of pulmonate and patellogastropod limpets
- Authors: Kankondi, Sebbi
- Date: 2017
- Subjects: Thermal tolerance (Physiology) , Limpets -- Physiology , Limpets -- Effect of temperature on , Oxygen consumption (Physiology)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/7570 , vital:21274
- Description: Since the scientific community anticipates a general change in the global climate, it has become increasingly important to develop predictive models which encompass mechanisms to generate reliable forecasts of the effects this change on ecological communities and processes. To this end, the oxygen- and capacity- limited thermal tolerance (OCLTT) theory has been developed as a link between various physiological processes, the thermal aspect of climate change and the associated shifts at different levels of biological organization. This study set out to assess the general applicability of the OCLTT theory in eurythermal pulmonate and patellogastropod limpets, whose distributions overlap on the high shore rocks of the warm temperate, south-east coast of South Africa.This was done by determining their microhabitat use, median lethal temperatures and cardiac, Arrhenius breakpoint temperatures as measures of their upper thermal tolerance limits, in both air and water. The main hypotheses of the study were that the pulmonate limpets would be more common than the patellogastropods in warmer microhabitats during low tide and would have higher thermal limits than the patellogastropods in air and vice versa in water. This was based on the assumption that the two limpet groups have different capabilities of oxygen consumption in air and water, due to differences in their respiratory organs and that this would be reflected in their thermal tolerances based on predictions made by the OCLTT. This assumption was important because oxygen consumption was not measured in this study. Previous research (e.g. Garrity, 1984), showed that a thermal stress gradient exists among rocky intertidal microhabitats. From most to least thermally stressful the gradient is horizontal surfaces> slopes> vertical surfaces> tide pools> crevices. The current study found that, while the pulmonate limpets, Siphonaria capensis and S. serrata, preferred rock pools, sloped, vertical and horizontal rock surfaces, the patellogastropod limpets, Cellana capensis and Scutellastra granularis, preferred rock pools and vertical rock surfaces. Furthermore, the pulmonate limpets were only common on horizontal rock surfaces where specific ameliorating conditions would have mitigated thermal stress there. In addition, C. capensis had similar thermal tolerance limits to the pulmonate limpets in air and the pulmonate limpets had similar and/or higher thermal tolerance limits compared to S. granularis in water. This indicates that the pulmonate limpets did not necessarily prefer warmer microhabitats than the patellogastropod limpets and that there were no differences in the collective upper thermal tolerance limits between the two limpet groups in either medium.Consequently, there was no indication from this study that an assumed superior capacity for oxygen supply translates into greater thermal tolerance and that the hypotheses based on the OCLTT were not supported. Although this was an indirect test of the OCLTT theory, I conclude that this study does not support the notion of its general applicability and that mechanisms other than those outlined by the OCLTT theory may help explain the patterns of thermal limitation observed in the current study.
- Full Text:
- Authors: Kankondi, Sebbi
- Date: 2017
- Subjects: Thermal tolerance (Physiology) , Limpets -- Physiology , Limpets -- Effect of temperature on , Oxygen consumption (Physiology)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/7570 , vital:21274
- Description: Since the scientific community anticipates a general change in the global climate, it has become increasingly important to develop predictive models which encompass mechanisms to generate reliable forecasts of the effects this change on ecological communities and processes. To this end, the oxygen- and capacity- limited thermal tolerance (OCLTT) theory has been developed as a link between various physiological processes, the thermal aspect of climate change and the associated shifts at different levels of biological organization. This study set out to assess the general applicability of the OCLTT theory in eurythermal pulmonate and patellogastropod limpets, whose distributions overlap on the high shore rocks of the warm temperate, south-east coast of South Africa.This was done by determining their microhabitat use, median lethal temperatures and cardiac, Arrhenius breakpoint temperatures as measures of their upper thermal tolerance limits, in both air and water. The main hypotheses of the study were that the pulmonate limpets would be more common than the patellogastropods in warmer microhabitats during low tide and would have higher thermal limits than the patellogastropods in air and vice versa in water. This was based on the assumption that the two limpet groups have different capabilities of oxygen consumption in air and water, due to differences in their respiratory organs and that this would be reflected in their thermal tolerances based on predictions made by the OCLTT. This assumption was important because oxygen consumption was not measured in this study. Previous research (e.g. Garrity, 1984), showed that a thermal stress gradient exists among rocky intertidal microhabitats. From most to least thermally stressful the gradient is horizontal surfaces> slopes> vertical surfaces> tide pools> crevices. The current study found that, while the pulmonate limpets, Siphonaria capensis and S. serrata, preferred rock pools, sloped, vertical and horizontal rock surfaces, the patellogastropod limpets, Cellana capensis and Scutellastra granularis, preferred rock pools and vertical rock surfaces. Furthermore, the pulmonate limpets were only common on horizontal rock surfaces where specific ameliorating conditions would have mitigated thermal stress there. In addition, C. capensis had similar thermal tolerance limits to the pulmonate limpets in air and the pulmonate limpets had similar and/or higher thermal tolerance limits compared to S. granularis in water. This indicates that the pulmonate limpets did not necessarily prefer warmer microhabitats than the patellogastropod limpets and that there were no differences in the collective upper thermal tolerance limits between the two limpet groups in either medium.Consequently, there was no indication from this study that an assumed superior capacity for oxygen supply translates into greater thermal tolerance and that the hypotheses based on the OCLTT were not supported. Although this was an indirect test of the OCLTT theory, I conclude that this study does not support the notion of its general applicability and that mechanisms other than those outlined by the OCLTT theory may help explain the patterns of thermal limitation observed in the current study.
- Full Text:
Patterns of plant diversity and cultural meaning in a rural landscape in the Albany Thicket: effects of land-use and topography
- Authors: Ngqiyaza, Nozuko Princess
- Date: 2017
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/50237 , vital:25969
- Description: South Africa is the world's third most bio-diverse country, but pressures on this biodiversity are many and widespread. It is now well recognised that protected areas on their own are insufficient to protect biodiversity, and increasing emphasis is placed on developing models for ensuring the persistence of biodiversity in agricultural and rural landscapes. One of the major challenges, especially in rural areas, is the need to reconcile people’s need to use natural resources with biodiversity conservation. This study aimed to (1) examine the ecosystem services people derive from the natural vegetation and how this is distributed in space and (2) the effects of land use and topo-edaphic factors on species richness, composition and structure and how this is spatially distributed. I investigated two land-use types, i.e. a rural village and adjacent lightly used game farm(s) by comparing 20 sites under each land-use representing the range of topographic position. I sampled respondent’s uses and values, species richness and composition, woody density, structure and composition at these 40 sites. This allowed for comparison between the two land uses but also allowed me to examine the effect of topography and relative soil moisture (both known to have a string influence on vegetation in semi-arid areas), and to relate the ecosystem services to plant species richness, structure and woody composition. People derived a wide range of ecosystem services and this differed with distance from the village and vegetation type. Men and women performed different tasks and had different feelings and derived different use values across the landscapes. Both men and women showed a great appreciation for the thicket forest, Pteronia-dominated and grasslands sites. They recognised these areas and as sacred grounds where they have a strong connection with their ancestors. Women preferred utilising areas closer to the village because they feared crime and wild animals in more remote thicket or forest, while men utilised all areas across the land, but more frequently closer to the village. The older generation had a strong attachment to nature, perceiving it as a provider. The younger generation, especially the young women did not express such a deeply felt connection, but enjoyed getting to see where some of the medicinal plants and useful wood structures were harvested. Younger men would go far into the forest quite regularly, often as far the Great Fish River, when they hunt with their peers. Although a diversity of perceptions were presented, and not all conformed to traditional views and practices, most respondents derived a mix of ecosystem services, with the areas closer to the village providing recreational and direct use value to more people on a more regular basis but spiritual values associated with deep forest persisted, especially among the older generation. Species richness and composition was analysed in relation to Topographic Relative Moisture Index (TRMI), land use and distance from the village to see the effect of topography versus land use on the vegetation. The total number of plant species recorded was 386 for both study sites. Two hundred and ninety two species were recorded in Ntloko and 265 on the game farms. Of the species that were sampled, 121 were recorded in Ntloko only, 94 in the game farms only, and 171 species were shared. The number of useful plant species (fuel, medicine, forage, cultural and edibles) was recorded to be 110, 83 in Ntloko and 63 on the game farms. There was no significant difference in species richness and alpha diversity between the study sites, but the game farms had a higher projected total number of species, reflecting higher beta diversity in the game farms than the communal area. The point-centered quarter method (PCQ) was used to describe woody plant composition, tree density and structure. The woody structure and composition was analysed in relation to the above-mentioned factors and I found no significant difference in the density and overall woody structure and composition between the two study sites. Sites at Ntloko had a positive correlation between soil moisture and woody plant density and a higher density of palatable and unpalatable species. The game farms showed no significant changes in woody plant density with TRMI. This study showed that the communal area maintained comparable plant species richness and vegetation structure and composition to game farms. The rural landscape comprised a gradient from sites close to the village that were heavily impacted, not considered particularly special or sacred but safe, familiar and of utilitarian importance, to sites farther away with denser, less transformed thicket vegetation, which are considered to be of greater cultural, spiritual and aesthetic importance but less safe, familiar and accessible. This suggests that conservation outcomes can be achieved outside protected areas, and that biodiversity is valuable to local residents. Resource management should be implemented to maintain the ecosystem services provided in rural areas in a way that integrates local peoples’ perceptions, goals and values with ecological evidence.
- Full Text:
- Authors: Ngqiyaza, Nozuko Princess
- Date: 2017
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/50237 , vital:25969
- Description: South Africa is the world's third most bio-diverse country, but pressures on this biodiversity are many and widespread. It is now well recognised that protected areas on their own are insufficient to protect biodiversity, and increasing emphasis is placed on developing models for ensuring the persistence of biodiversity in agricultural and rural landscapes. One of the major challenges, especially in rural areas, is the need to reconcile people’s need to use natural resources with biodiversity conservation. This study aimed to (1) examine the ecosystem services people derive from the natural vegetation and how this is distributed in space and (2) the effects of land use and topo-edaphic factors on species richness, composition and structure and how this is spatially distributed. I investigated two land-use types, i.e. a rural village and adjacent lightly used game farm(s) by comparing 20 sites under each land-use representing the range of topographic position. I sampled respondent’s uses and values, species richness and composition, woody density, structure and composition at these 40 sites. This allowed for comparison between the two land uses but also allowed me to examine the effect of topography and relative soil moisture (both known to have a string influence on vegetation in semi-arid areas), and to relate the ecosystem services to plant species richness, structure and woody composition. People derived a wide range of ecosystem services and this differed with distance from the village and vegetation type. Men and women performed different tasks and had different feelings and derived different use values across the landscapes. Both men and women showed a great appreciation for the thicket forest, Pteronia-dominated and grasslands sites. They recognised these areas and as sacred grounds where they have a strong connection with their ancestors. Women preferred utilising areas closer to the village because they feared crime and wild animals in more remote thicket or forest, while men utilised all areas across the land, but more frequently closer to the village. The older generation had a strong attachment to nature, perceiving it as a provider. The younger generation, especially the young women did not express such a deeply felt connection, but enjoyed getting to see where some of the medicinal plants and useful wood structures were harvested. Younger men would go far into the forest quite regularly, often as far the Great Fish River, when they hunt with their peers. Although a diversity of perceptions were presented, and not all conformed to traditional views and practices, most respondents derived a mix of ecosystem services, with the areas closer to the village providing recreational and direct use value to more people on a more regular basis but spiritual values associated with deep forest persisted, especially among the older generation. Species richness and composition was analysed in relation to Topographic Relative Moisture Index (TRMI), land use and distance from the village to see the effect of topography versus land use on the vegetation. The total number of plant species recorded was 386 for both study sites. Two hundred and ninety two species were recorded in Ntloko and 265 on the game farms. Of the species that were sampled, 121 were recorded in Ntloko only, 94 in the game farms only, and 171 species were shared. The number of useful plant species (fuel, medicine, forage, cultural and edibles) was recorded to be 110, 83 in Ntloko and 63 on the game farms. There was no significant difference in species richness and alpha diversity between the study sites, but the game farms had a higher projected total number of species, reflecting higher beta diversity in the game farms than the communal area. The point-centered quarter method (PCQ) was used to describe woody plant composition, tree density and structure. The woody structure and composition was analysed in relation to the above-mentioned factors and I found no significant difference in the density and overall woody structure and composition between the two study sites. Sites at Ntloko had a positive correlation between soil moisture and woody plant density and a higher density of palatable and unpalatable species. The game farms showed no significant changes in woody plant density with TRMI. This study showed that the communal area maintained comparable plant species richness and vegetation structure and composition to game farms. The rural landscape comprised a gradient from sites close to the village that were heavily impacted, not considered particularly special or sacred but safe, familiar and of utilitarian importance, to sites farther away with denser, less transformed thicket vegetation, which are considered to be of greater cultural, spiritual and aesthetic importance but less safe, familiar and accessible. This suggests that conservation outcomes can be achieved outside protected areas, and that biodiversity is valuable to local residents. Resource management should be implemented to maintain the ecosystem services provided in rural areas in a way that integrates local peoples’ perceptions, goals and values with ecological evidence.
- Full Text:
Perceptions and livelihood uses of an invasive alien tree (acacia dealbata) by rural communities in the Eastern Cape
- Authors: Agripa, Ngorima
- Date: 2017
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5326 , vital:20813
- Description: The negative impacts which invasive alien species have on ecosystems are well documented but there is paucity of information on their impacts on rural communities. Due to ecological impacts that may be associated with Acacia dealbata invasions the Agricultural Research Council Plant Protection Institute is considering releasing a biocontrol agent for A. dealbata. The actual social impacts of A. dealbata invasion and control are likely to be related to its importance in rural livelihoods. This thesis reports on the perceptions and livelihood uses of A. dealbata in the Eastern Cape. Three study sites were assessed, Matatiele, Mount Fletcher and Maclear. The study involved 150 household surveys, one focus group discussion and one transect walk at each site, key informant interviews and frequent house visits to acquire reliable data. Results show that 100 % of households in the three sites use Silver Wattle extensively for firewood. In Matatiele 64 %, 72 % in Mount Fletcher and 84 % of households in Maclear use Silver Wattle for fencing. To carve tools 76 % in Matatiele, 76 % in Mount Fletcher and 84 % households in Maclear use Silver Wattle. For medicinal purposes 18 % in Matatiele, 20 % in Mount Fletcher and 16 % in Maclear use Silver Wattle, whilst 78 % in Matatiele, 80 % in Mount Fletcher and 80 % in Maclear use it for fodder purposes. Many respondents felt that Silver Wattle is too abundant within their areas such that it now has many negative impacts associated with it. Perceptions of local people towards A. dealbata are neither static nor uniform, but are influenced by time since the invasion and now abundance of the species. There are no alternatives which provide the same services provided by Silver Wattle. Benefits and constraints due to A. dealbata invasion are experienced by everyone irrespective of wealth and gender. In conclusion, Silver Wattle is a valuable resource to these rural communities, but increasing abundance is incurring high costs to grazing resources and landscape accessibility.
- Full Text:
- Authors: Agripa, Ngorima
- Date: 2017
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5326 , vital:20813
- Description: The negative impacts which invasive alien species have on ecosystems are well documented but there is paucity of information on their impacts on rural communities. Due to ecological impacts that may be associated with Acacia dealbata invasions the Agricultural Research Council Plant Protection Institute is considering releasing a biocontrol agent for A. dealbata. The actual social impacts of A. dealbata invasion and control are likely to be related to its importance in rural livelihoods. This thesis reports on the perceptions and livelihood uses of A. dealbata in the Eastern Cape. Three study sites were assessed, Matatiele, Mount Fletcher and Maclear. The study involved 150 household surveys, one focus group discussion and one transect walk at each site, key informant interviews and frequent house visits to acquire reliable data. Results show that 100 % of households in the three sites use Silver Wattle extensively for firewood. In Matatiele 64 %, 72 % in Mount Fletcher and 84 % of households in Maclear use Silver Wattle for fencing. To carve tools 76 % in Matatiele, 76 % in Mount Fletcher and 84 % households in Maclear use Silver Wattle. For medicinal purposes 18 % in Matatiele, 20 % in Mount Fletcher and 16 % in Maclear use Silver Wattle, whilst 78 % in Matatiele, 80 % in Mount Fletcher and 80 % in Maclear use it for fodder purposes. Many respondents felt that Silver Wattle is too abundant within their areas such that it now has many negative impacts associated with it. Perceptions of local people towards A. dealbata are neither static nor uniform, but are influenced by time since the invasion and now abundance of the species. There are no alternatives which provide the same services provided by Silver Wattle. Benefits and constraints due to A. dealbata invasion are experienced by everyone irrespective of wealth and gender. In conclusion, Silver Wattle is a valuable resource to these rural communities, but increasing abundance is incurring high costs to grazing resources and landscape accessibility.
- Full Text:
Phenomenology: preconceptions and experiences of non-chemists at Rhodes University using milk paint
- Authors: Kelly, Kelvin Leigh
- Date: 2017
- Subjects: Phenomenology , Art and science , Casein , Paint , Chemistry -- Study and teaching , Science -- Study and teaching -- Philosophy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/37942 , vital:24711
- Description: There exists an ever-increasing crisis in science education where students experience disinterest because of an inability to grasp true understanding of scientific subjects, and therefore there should be a call to increase the research of phenomenology in combination with science education. A rebalance and paradigm shift in the focus of the modes of teaching could result in a great improvement in the learning, comprehension, and intellectual self-confidence of students interested in the sciences. To study this, three research questions were established: How is chemistry perceived by non-chemists; what is the experience of the participants’ during the chemistry practical in a laboratory and; do the participants’ perspectives about chemistry change during the experience. The performed study consisted of a chemistry practical, two art works and, in some cases, an interview. Nine participants were asked to create the art under specific instructions of points of focus, namely their preconceptions prior to the practical (Artwork 1) and their lived experience during the practical (Artwork 2). Participants’ artworks were examined using methods of visual semiotics and classical art analysis techniques, looking at line, shape, and colour choice. The iterative analysis of the interviews from participants 1, 2, 7, and 9 coded with ATLAS.ti 7 software, led to the emergence of themes that constitute the core of the participants’ experience. This phenomenological study presents a path to engage the non-chemist with processes taking place in the laboratory by using ‘Kitchen Chemistry’ and illustrates how a phenomenological engagement with chemistry can make the subject more applicable to the general population of non-chemists.
- Full Text:
- Authors: Kelly, Kelvin Leigh
- Date: 2017
- Subjects: Phenomenology , Art and science , Casein , Paint , Chemistry -- Study and teaching , Science -- Study and teaching -- Philosophy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/37942 , vital:24711
- Description: There exists an ever-increasing crisis in science education where students experience disinterest because of an inability to grasp true understanding of scientific subjects, and therefore there should be a call to increase the research of phenomenology in combination with science education. A rebalance and paradigm shift in the focus of the modes of teaching could result in a great improvement in the learning, comprehension, and intellectual self-confidence of students interested in the sciences. To study this, three research questions were established: How is chemistry perceived by non-chemists; what is the experience of the participants’ during the chemistry practical in a laboratory and; do the participants’ perspectives about chemistry change during the experience. The performed study consisted of a chemistry practical, two art works and, in some cases, an interview. Nine participants were asked to create the art under specific instructions of points of focus, namely their preconceptions prior to the practical (Artwork 1) and their lived experience during the practical (Artwork 2). Participants’ artworks were examined using methods of visual semiotics and classical art analysis techniques, looking at line, shape, and colour choice. The iterative analysis of the interviews from participants 1, 2, 7, and 9 coded with ATLAS.ti 7 software, led to the emergence of themes that constitute the core of the participants’ experience. This phenomenological study presents a path to engage the non-chemist with processes taking place in the laboratory by using ‘Kitchen Chemistry’ and illustrates how a phenomenological engagement with chemistry can make the subject more applicable to the general population of non-chemists.
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Photophysical studies of conjugates of upconversion nanoparticles with aluminium phthalocyanines
- Authors: Watkins, Zane
- Date: 2017
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/4964 , vital:20747
- Description: NaYF4 :Yb/Er/Gd upconversion nanoparticles (UCNP) were synthesised and their photoemission stabilised by embedding these nanoparticles in electrospun fibres. The photophysical behaviour of chloro aluminium tetrasulfo-phthalocyanine chloride (ClAlTSPc) was studied in the presence of UCNPs on mixing the two species in solution. The fluorescence lifetimes for UCNPs were shortened at 658 nm in the presence of ClAlTSPc when the former was embedded in fibre and suspended in a dimethyl sulfoxide solution of the latter. A clear singlet oxygen generation by ClAlTSPc through Forster resonance energy transfer (FRET) was demonstrated using a singlet oxygen quencher, 1,3-diphenylisobenzofuran. UCNP capped with amino groups were then covalently attached to chloro aluminium tetrasulphonated phthalocyanine (ClAlTSPc) and chloro aluminium tetracarboxy phthalocyanine (ClAlTCPc). The conjugates were characterized using different techniques such as infrared spectroscopy (IR), X-ray photoelectron spectroscopy (XPS) and Transmission electron microscopy (TEM). There was a decrease in fluorescence emission spectra of the UCNPs at 658 nm in the presence of the phthalocyanines. This decrease indicates an energy transfer between the donor UCNP and conjugated accepting phthalocyanine (Pc), due to FRET. Low FRET efficiencies of 18 and 21 % for ClAlTSPc and ClAlTCPc, respectively, were obtained.
- Full Text:
- Authors: Watkins, Zane
- Date: 2017
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/4964 , vital:20747
- Description: NaYF4 :Yb/Er/Gd upconversion nanoparticles (UCNP) were synthesised and their photoemission stabilised by embedding these nanoparticles in electrospun fibres. The photophysical behaviour of chloro aluminium tetrasulfo-phthalocyanine chloride (ClAlTSPc) was studied in the presence of UCNPs on mixing the two species in solution. The fluorescence lifetimes for UCNPs were shortened at 658 nm in the presence of ClAlTSPc when the former was embedded in fibre and suspended in a dimethyl sulfoxide solution of the latter. A clear singlet oxygen generation by ClAlTSPc through Forster resonance energy transfer (FRET) was demonstrated using a singlet oxygen quencher, 1,3-diphenylisobenzofuran. UCNP capped with amino groups were then covalently attached to chloro aluminium tetrasulphonated phthalocyanine (ClAlTSPc) and chloro aluminium tetracarboxy phthalocyanine (ClAlTCPc). The conjugates were characterized using different techniques such as infrared spectroscopy (IR), X-ray photoelectron spectroscopy (XPS) and Transmission electron microscopy (TEM). There was a decrease in fluorescence emission spectra of the UCNPs at 658 nm in the presence of the phthalocyanines. This decrease indicates an energy transfer between the donor UCNP and conjugated accepting phthalocyanine (Pc), due to FRET. Low FRET efficiencies of 18 and 21 % for ClAlTSPc and ClAlTCPc, respectively, were obtained.
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Photosynthetic and growth responses of C3 and C4 grasses to short- duration sunflecks and resultant consequences for their performance in understory environments
- Authors: Adams, Claire Elizabeth
- Date: 2017
- Subjects: Understory plants -- Effect of light on , Grasses -- Effect of light on -- South Africa , Erharta -- Effect of light on , Brachiara -- Effect of light on
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5016 , vital:20753
- Description: Low C4 grass species abundance in understory environments is thought to be as a result of their high-light requirements, lack of photosynthetic advantage relative to C3 species in cooler environments, and an inability to adequately utilise sunflecks. This study sets out to investigate this theory, hypothesizing that C3 grass species outperform C4 grass species under the canopy, not as a result of quantum efficiency temperature effects, but as a result of C4 species inability to utilize short-duration sunflecks. Short sunflecks could result in a breakdown in assimilate movement between the mesophyll (MSC) and bundle sheath (BSC) cells. The role of BSC leakiness, stomata and PSII efficiency on the ability of C3 and C4 Alloteropsis semialata to utilize short-duration sunflecks was investigated using gaseous exchange and chlorophyll fluorescence techniques, while the growth of both subspecies under a simulated flecking-light environment tested whether these measured responses translated into effects on growth. As C3 grasses are known to possess higher levels of stomatal conductance in relation to C4 species, results showed that C3 A. semialata was able to utilize short-duration sunflecks as a result of increased stomatal conductance and an ability to induce photosynthesis under various light flecking conditions. In contrast, C4 A. semialata was unable to utilize sunflecks possibly as a result of energetic limitations of the carboxylation mechanism (PSII) and not because of increased bundle sheath leakiness. These photosynthetic responses translated into growth differences when both types were grown in an artificially flecking light environment. The photosynthetic differences noted for C3 and C4 A.semialata were also evident in shade adapted understory grasses; Erharta erecta (C3), Dactylotenium australe (C4) and Brachiaria chusqueoides (C4). As photosynthetic induction was marginally more rapid in all species relative to A. semialata it suggests some degree of adaptation in shade grasses, however the inability of the C4 species to utilise short sunflecks remained. As a result, it was hypothesized that C3 shade adapted E. erecta and C4 B. chusqueoides, co-inhabiting the same forest understory, are able to do so because of differences in light micro-environments associated with each species. However, canopy openness and light profiles determined for theses micro-climates showed no differences and that both species have persisted within a relatively stable understory environment. The coexistence was possible as the understory was supplied with a significant proportion of its daily light in flecks sufficiently long as to not compromise C4 productivity. A survey of 10 species of grasses under various canopy densities and in the open showed a strong negative linear relationship between canopy openness and the rate at which photosynthesis was induced by flecking light, which has not been shown before. This did not result from the phylogenetic relationship between species and could be shown for a single species (E. erecta) growing in a range of light environments. This demonstrates that C4 grasses, despite adaptation, would be limited from sunfleck environments if a significant proportion of the daily light available consists of flecks of short-duration. The generation of such environments may occur as a result of woody thickening and could help explain the observed decline in C4 grasses under these conditions.
- Full Text:
- Authors: Adams, Claire Elizabeth
- Date: 2017
- Subjects: Understory plants -- Effect of light on , Grasses -- Effect of light on -- South Africa , Erharta -- Effect of light on , Brachiara -- Effect of light on
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5016 , vital:20753
- Description: Low C4 grass species abundance in understory environments is thought to be as a result of their high-light requirements, lack of photosynthetic advantage relative to C3 species in cooler environments, and an inability to adequately utilise sunflecks. This study sets out to investigate this theory, hypothesizing that C3 grass species outperform C4 grass species under the canopy, not as a result of quantum efficiency temperature effects, but as a result of C4 species inability to utilize short-duration sunflecks. Short sunflecks could result in a breakdown in assimilate movement between the mesophyll (MSC) and bundle sheath (BSC) cells. The role of BSC leakiness, stomata and PSII efficiency on the ability of C3 and C4 Alloteropsis semialata to utilize short-duration sunflecks was investigated using gaseous exchange and chlorophyll fluorescence techniques, while the growth of both subspecies under a simulated flecking-light environment tested whether these measured responses translated into effects on growth. As C3 grasses are known to possess higher levels of stomatal conductance in relation to C4 species, results showed that C3 A. semialata was able to utilize short-duration sunflecks as a result of increased stomatal conductance and an ability to induce photosynthesis under various light flecking conditions. In contrast, C4 A. semialata was unable to utilize sunflecks possibly as a result of energetic limitations of the carboxylation mechanism (PSII) and not because of increased bundle sheath leakiness. These photosynthetic responses translated into growth differences when both types were grown in an artificially flecking light environment. The photosynthetic differences noted for C3 and C4 A.semialata were also evident in shade adapted understory grasses; Erharta erecta (C3), Dactylotenium australe (C4) and Brachiaria chusqueoides (C4). As photosynthetic induction was marginally more rapid in all species relative to A. semialata it suggests some degree of adaptation in shade grasses, however the inability of the C4 species to utilise short sunflecks remained. As a result, it was hypothesized that C3 shade adapted E. erecta and C4 B. chusqueoides, co-inhabiting the same forest understory, are able to do so because of differences in light micro-environments associated with each species. However, canopy openness and light profiles determined for theses micro-climates showed no differences and that both species have persisted within a relatively stable understory environment. The coexistence was possible as the understory was supplied with a significant proportion of its daily light in flecks sufficiently long as to not compromise C4 productivity. A survey of 10 species of grasses under various canopy densities and in the open showed a strong negative linear relationship between canopy openness and the rate at which photosynthesis was induced by flecking light, which has not been shown before. This did not result from the phylogenetic relationship between species and could be shown for a single species (E. erecta) growing in a range of light environments. This demonstrates that C4 grasses, despite adaptation, would be limited from sunfleck environments if a significant proportion of the daily light available consists of flecks of short-duration. The generation of such environments may occur as a result of woody thickening and could help explain the observed decline in C4 grasses under these conditions.
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Population genomics analysis of yellowfin tuna Thunnus albacares off South Africa reveals need for a shifted management boundary
- Authors: Mullins, Rachel Brenna
- Date: 2017
- Subjects: Yellowfin tuna fisheries -- South Africa -- Western Cape , Genomics , Tuna fisheries -- South Africa , Fishery management -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/57819 , vital:26992
- Description: Yellowfin tuna Thunnus albacares is a commercially and economically important fisheries species, which comprises the second largest component of South Africa’s catch of tuna and tuna-like species. Catches of the species off South Africa are treated as two discrete stocks by the two tuna Regional Fisheries Management Organisations (tRFMOs) under whose jurisdictions they fall. Individuals caught off the Western Cape, west of the boundary between the tRFMOs at 20°E, are included in assessment and management of the Atlantic Ocean yellowfin tuna stock by the International Commission for the Conservation of Atlantic Tunas (ICCAT), and those caught east of this boundary are assessed and managed as part of the Indian Ocean stock by the Indian Ocean Tuna Commission (IOTC). The boundary between these stocks is based on the confluence of the two oceans in this region and does not incorporate the population structure of species. For sustainable exploitation of fisheries resources, it is important that the definition of management stocks reflects species’ biological population structure; the fine-scale stock structure of yellowfin tuna off South Africa is therefore a research priority which this study aimed to address by means of population genomics analyses. Yellowfin tuna exhibit shallow genetic differentiation over wide geographic areas, and as such traditional population genetic approaches have limited power in resolving fishery significant population structure in the species. Herein, a population genomic approach was employed, specifically, genome-wide analysis of single nucleotide polymorphisms (SNPs) discovered using a next-generation DNA sequencing approach, to confer (i) increased statistical power to detect neutral structuring reflecting population connectivity patterns and (ii) signatures of local adaptation. The mitochondrial Control Region (mtDNA CR) was also sequenced to compare the resolving power of different approaches and to permit coalescent based analyses of the species evolutionary history in the region. Neutral SNP loci revealed significant structure within the dataset (Fst=0.0043; P<0.0001); partitioning of this differentiation within the dataset indicated significant differentiation between yellowfin tuna from the Western Cape and the Gulf of Guinea in the eastern Atlantic Ocean, with no significant differentiation between individuals from the Western Cape and Western Indian Ocean regions. This indicates two population units wherein there is a separation of the Gulf of Guinea from the remaining samples (Indian Ocean including Western Cape) that are largely derived from a single genetic population. This pattern was also supported by assignment tests. Positive outlier SNPs, exhibiting signatures of diversifying selection, suggest that individuals from these regions may be locally adapted, as well as demographically isolated. The mtDNA CR did not reveal any significant genetic structure among samples (Fst=0.0030; P=0.309), demonstrating the increased resolving power provided by population genomics approaches, but revealed signatures of historical demographic fluctuations associated with glacial cycles. Based on the findings of this study, it is suggested that yellowfin tuna caught off the Western Cape of South Africa are migrants from the Indian Ocean population, exhibiting significant genetic differentiation from the Atlantic Ocean Gulf of Guinea individuals, and should thus be included in the assessment and management of the Indian Ocean stock. It is therefore recommended that the boundary between the Atlantic and Indian Ocean yellowfin tuna stocks, under the mandates of ICCAT and the IOTC respectively, should be shifted to approximately 13.35°E to include all individuals caught in South African waters in the Indian Ocean stock.
- Full Text:
- Authors: Mullins, Rachel Brenna
- Date: 2017
- Subjects: Yellowfin tuna fisheries -- South Africa -- Western Cape , Genomics , Tuna fisheries -- South Africa , Fishery management -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/57819 , vital:26992
- Description: Yellowfin tuna Thunnus albacares is a commercially and economically important fisheries species, which comprises the second largest component of South Africa’s catch of tuna and tuna-like species. Catches of the species off South Africa are treated as two discrete stocks by the two tuna Regional Fisheries Management Organisations (tRFMOs) under whose jurisdictions they fall. Individuals caught off the Western Cape, west of the boundary between the tRFMOs at 20°E, are included in assessment and management of the Atlantic Ocean yellowfin tuna stock by the International Commission for the Conservation of Atlantic Tunas (ICCAT), and those caught east of this boundary are assessed and managed as part of the Indian Ocean stock by the Indian Ocean Tuna Commission (IOTC). The boundary between these stocks is based on the confluence of the two oceans in this region and does not incorporate the population structure of species. For sustainable exploitation of fisheries resources, it is important that the definition of management stocks reflects species’ biological population structure; the fine-scale stock structure of yellowfin tuna off South Africa is therefore a research priority which this study aimed to address by means of population genomics analyses. Yellowfin tuna exhibit shallow genetic differentiation over wide geographic areas, and as such traditional population genetic approaches have limited power in resolving fishery significant population structure in the species. Herein, a population genomic approach was employed, specifically, genome-wide analysis of single nucleotide polymorphisms (SNPs) discovered using a next-generation DNA sequencing approach, to confer (i) increased statistical power to detect neutral structuring reflecting population connectivity patterns and (ii) signatures of local adaptation. The mitochondrial Control Region (mtDNA CR) was also sequenced to compare the resolving power of different approaches and to permit coalescent based analyses of the species evolutionary history in the region. Neutral SNP loci revealed significant structure within the dataset (Fst=0.0043; P<0.0001); partitioning of this differentiation within the dataset indicated significant differentiation between yellowfin tuna from the Western Cape and the Gulf of Guinea in the eastern Atlantic Ocean, with no significant differentiation between individuals from the Western Cape and Western Indian Ocean regions. This indicates two population units wherein there is a separation of the Gulf of Guinea from the remaining samples (Indian Ocean including Western Cape) that are largely derived from a single genetic population. This pattern was also supported by assignment tests. Positive outlier SNPs, exhibiting signatures of diversifying selection, suggest that individuals from these regions may be locally adapted, as well as demographically isolated. The mtDNA CR did not reveal any significant genetic structure among samples (Fst=0.0030; P=0.309), demonstrating the increased resolving power provided by population genomics approaches, but revealed signatures of historical demographic fluctuations associated with glacial cycles. Based on the findings of this study, it is suggested that yellowfin tuna caught off the Western Cape of South Africa are migrants from the Indian Ocean population, exhibiting significant genetic differentiation from the Atlantic Ocean Gulf of Guinea individuals, and should thus be included in the assessment and management of the Indian Ocean stock. It is therefore recommended that the boundary between the Atlantic and Indian Ocean yellowfin tuna stocks, under the mandates of ICCAT and the IOTC respectively, should be shifted to approximately 13.35°E to include all individuals caught in South African waters in the Indian Ocean stock.
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Post-release evaluation and thermal physiology of the Pereskia stem-wilter, Catorhintha schaffneri (Coreidae), a new biological control agent for Pereskia aculeata (Cactaceae)
- Authors: Muskett, Phillippa Claire
- Date: 2017
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/36094 , vital:24477
- Description: Catorhintha schaffneri Brailovsky and Garcia (Hemiptera: Coreidae) is a biological control agent that was recently accepted for release in South Africa to control Pereskia aculeata Miller (Cactaceae), an invasive creeping cactus. The aim of this thesis was to conduct post-release research to ensure that C. schaffneri is utilised to its full potential. To achieve this aim, and focus release efforts, the thermal physiology of C. schaffneri was investigated to predict where in South Africa the agent is most likely to establish. These predictions were then tested by releasing the agent at field sites with a wide variety of climatic conditions and evaluating establishment success. When invasive plants invade a wide distribution, made up of areas with different climatic conditions, biological control agents may not establish or be effective throughout the invaded distribution. According to the thermal physiology of C. schaffneri, it is most likely to establish and become effective in the subtropical region of South Africa, along the coast of KwaZulu- Natal. Cold winters, or generally low year-round temperatures, may limit establishment in the more temperate areas of South Africa in the Eastern and Western Cape as well as inland in the Highveld region. These predictions can be used to focus release efforts to climatically suitable regions and stop releases in areas where C. schaffneri cannot survive. Predictions based on thermal physiology may not account for all of the variables which affect establishment. To account for other variables, the establishment of C. schaffneri was tested using closely monitored field release studies. During these studies the effect of other variables such as; microclimate temperature, humidity, precipitation, plant quality and release strategy were considered. Low humidity, precipitation and plant quality appear to affect the establishment of C. schaffneri in the subtropical areas of South Africa. The experiment was conducted during a period of drought, and this may have resulted in lower establishment rates. The most successful release strategy for C. schaffneri was the use of multiple, small releases rather than single releases of the same number of individuals. The field based study was therefore able to improve the biological control of P. aculeata by increasing the chance that each release of C. schaffneri results in establishment. The post-release studies presented in this thesis will increase the impact of C. schaffneri by focussing release efforts to climatically suitable sites, releasing at appropriate times of year and releasing the agent in a manner that increases establishment success. Post-release studies, such as those presented here, can make biological control programmes more efficient and effective.
- Full Text:
- Authors: Muskett, Phillippa Claire
- Date: 2017
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/36094 , vital:24477
- Description: Catorhintha schaffneri Brailovsky and Garcia (Hemiptera: Coreidae) is a biological control agent that was recently accepted for release in South Africa to control Pereskia aculeata Miller (Cactaceae), an invasive creeping cactus. The aim of this thesis was to conduct post-release research to ensure that C. schaffneri is utilised to its full potential. To achieve this aim, and focus release efforts, the thermal physiology of C. schaffneri was investigated to predict where in South Africa the agent is most likely to establish. These predictions were then tested by releasing the agent at field sites with a wide variety of climatic conditions and evaluating establishment success. When invasive plants invade a wide distribution, made up of areas with different climatic conditions, biological control agents may not establish or be effective throughout the invaded distribution. According to the thermal physiology of C. schaffneri, it is most likely to establish and become effective in the subtropical region of South Africa, along the coast of KwaZulu- Natal. Cold winters, or generally low year-round temperatures, may limit establishment in the more temperate areas of South Africa in the Eastern and Western Cape as well as inland in the Highveld region. These predictions can be used to focus release efforts to climatically suitable regions and stop releases in areas where C. schaffneri cannot survive. Predictions based on thermal physiology may not account for all of the variables which affect establishment. To account for other variables, the establishment of C. schaffneri was tested using closely monitored field release studies. During these studies the effect of other variables such as; microclimate temperature, humidity, precipitation, plant quality and release strategy were considered. Low humidity, precipitation and plant quality appear to affect the establishment of C. schaffneri in the subtropical areas of South Africa. The experiment was conducted during a period of drought, and this may have resulted in lower establishment rates. The most successful release strategy for C. schaffneri was the use of multiple, small releases rather than single releases of the same number of individuals. The field based study was therefore able to improve the biological control of P. aculeata by increasing the chance that each release of C. schaffneri results in establishment. The post-release studies presented in this thesis will increase the impact of C. schaffneri by focussing release efforts to climatically suitable sites, releasing at appropriate times of year and releasing the agent in a manner that increases establishment success. Post-release studies, such as those presented here, can make biological control programmes more efficient and effective.
- Full Text:
Post-release evaluation of the biological control programme against Cereus jamacaru De Candolle (Cactaceae), in South Africa
- Authors: Sutton, Guy Frederick
- Date: 2017
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/7982 , vital:21330
- Description: Cereus jamacaru De Candolle (Cactaceae) is an environment-transforming weed of both agricultural and wildlife habitats in South Africa. Weed infestations reduce carrying capacity of the land, and pose a risk to livestock, wildlife and human safety due to the plant’s spiny thorns. The weed is considered to be under complete biological control in South Africa, due to its introduced control agent, Hypogeococcus festerianus Lizer y Trelles (Hemiptera: Pseudococcidae), although observational reports suggest that the level of success achieved is variable. In this thesis, a formal post-release evaluation of this biological control programme was conducted, specifically to determine the efficacy of H. festerianus as a biological control agent, and to identify factors which may limit or constrain the level of success achieved by the control agent. These data were collected with the intention of improving the control of C. jamacaru in South Africa. A field-based study of C. jamacaru population demographics investigated the efficacy of H. festerianus as a biological control agent of the weed, by integrating weed growth, fecundity and survival metrics with C. jamacaru population dynamics and demographic patterns from 8 sites where H. festerianus was present and 14 sites where the control agent was absent. The findings indicated that H. festerianus significantly reduced weed fecundity, which resulted in fewer seedling recruits, and that levels of plant mortality were greater at sites where H. festerianus was present. The reduction in weed fecundity and survival translated into negative population-level consequences for H. festerianus. Weed-population age frequency distributions in the absence of H. festerianus demonstrated a “reverse J-shaped” distribution, indicative of high recruitment rates and population stability, while C. jamacaru populations infected with H. festerianus were described by bell-shaped distributions, and were typified by limited recruitment, or a complete lack thereof. By constraining recruitment and inhibiting selfregeneration, H. festerianus appears to regulate populations of C. jamacaru. Predation and parasitism of H. festerianus was believed to be a limiting factor for the biological control programme against C. jamacaru in South Africa, although no formal evaluation of this claim had been undertaken. Accordingly, the assemblage of natural enemies acquired by H. festerianus in South Africa was identified by field-collections of infected H. festerianus gall-material. Further, timed point-count surveys of natural enemies associated with H. festerianus were performed and integrated with the data on the impact of H. festerianus on weed population dynamics to assess the impact of two prominent predaceous taxa on H. festerianus efficacy as a biological control agent. Although H. festerianus had acquired a diverse suite of novel natural enemies in South Africa, this has not prevented the biocontrol agent from having an impact on C. jamacaru populations, although other subtler effects cannot be ruled out. This study showed that biological control efforts employing H. festerianus for the management of C. jamacaru have been successful. Furthermore, these data demonstrated the utility of retrospective analyses in developing and improving the science of biological control, specifically how to improve candidate agent prioritisation, determining how many agents are required for successful biological control, and how to evaluate the success of biological control efforts. Improvements in our theoretical understanding of biological control will undoubtedly reduce costs of biological control programmes, improve success rates, and increase the predictability of biological control.
- Full Text:
- Authors: Sutton, Guy Frederick
- Date: 2017
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/7982 , vital:21330
- Description: Cereus jamacaru De Candolle (Cactaceae) is an environment-transforming weed of both agricultural and wildlife habitats in South Africa. Weed infestations reduce carrying capacity of the land, and pose a risk to livestock, wildlife and human safety due to the plant’s spiny thorns. The weed is considered to be under complete biological control in South Africa, due to its introduced control agent, Hypogeococcus festerianus Lizer y Trelles (Hemiptera: Pseudococcidae), although observational reports suggest that the level of success achieved is variable. In this thesis, a formal post-release evaluation of this biological control programme was conducted, specifically to determine the efficacy of H. festerianus as a biological control agent, and to identify factors which may limit or constrain the level of success achieved by the control agent. These data were collected with the intention of improving the control of C. jamacaru in South Africa. A field-based study of C. jamacaru population demographics investigated the efficacy of H. festerianus as a biological control agent of the weed, by integrating weed growth, fecundity and survival metrics with C. jamacaru population dynamics and demographic patterns from 8 sites where H. festerianus was present and 14 sites where the control agent was absent. The findings indicated that H. festerianus significantly reduced weed fecundity, which resulted in fewer seedling recruits, and that levels of plant mortality were greater at sites where H. festerianus was present. The reduction in weed fecundity and survival translated into negative population-level consequences for H. festerianus. Weed-population age frequency distributions in the absence of H. festerianus demonstrated a “reverse J-shaped” distribution, indicative of high recruitment rates and population stability, while C. jamacaru populations infected with H. festerianus were described by bell-shaped distributions, and were typified by limited recruitment, or a complete lack thereof. By constraining recruitment and inhibiting selfregeneration, H. festerianus appears to regulate populations of C. jamacaru. Predation and parasitism of H. festerianus was believed to be a limiting factor for the biological control programme against C. jamacaru in South Africa, although no formal evaluation of this claim had been undertaken. Accordingly, the assemblage of natural enemies acquired by H. festerianus in South Africa was identified by field-collections of infected H. festerianus gall-material. Further, timed point-count surveys of natural enemies associated with H. festerianus were performed and integrated with the data on the impact of H. festerianus on weed population dynamics to assess the impact of two prominent predaceous taxa on H. festerianus efficacy as a biological control agent. Although H. festerianus had acquired a diverse suite of novel natural enemies in South Africa, this has not prevented the biocontrol agent from having an impact on C. jamacaru populations, although other subtler effects cannot be ruled out. This study showed that biological control efforts employing H. festerianus for the management of C. jamacaru have been successful. Furthermore, these data demonstrated the utility of retrospective analyses in developing and improving the science of biological control, specifically how to improve candidate agent prioritisation, determining how many agents are required for successful biological control, and how to evaluate the success of biological control efforts. Improvements in our theoretical understanding of biological control will undoubtedly reduce costs of biological control programmes, improve success rates, and increase the predictability of biological control.
- Full Text: