Liver steatosis and insulin-resistance : reversal by Sutherlandia frutescens
- Authors: Clarke, Stephen
- Date: 2014
- Subjects: Insulin resistance , Diabetes -- Treatment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10348 , http://hdl.handle.net/10948/d1020788
- Description: Type 2 diabetes mellitus (T2DM) is rapidly emerging as one of the greatest global health issues of the 21st century. Insulin-resistance is a condition associated with T2DM and in the cell it is defined as the inadequate strength of insulin signalling from the insulin receptor downstream to the final substrates of insulin action involved in multiple metabolic, gene expression, and mitogenic aspects of cellular function. To investigate the potential mechanisms involved in the development of insulin-resistance, two in vitro liver cell models were established using palmitate or a combination of insulin and fructose as inducers. The development of insulin-resistance was determined via the capacity of the hepatocytes to maintain normal glucose metabolism functionality by measuring hepatic gluconeogenesis and glycogenolysis. It was established that the treatments induced the development of insulinresistance after 24 hours chronic exposure. Previous studies have investigated the potential of Sutherlandia frutescens extracts as therapeutic agents for insulin-resistance. The aim of this study was thus to investigate the ability of a hot aqueous extract of S. frutescens to reverse the insulin-resistant state, via measuring gluconeogenesis and glycogenolysis, the associated changes in cellular physiology (lipid accumulation, oxidative stress, and acetyl- CoA levels), and changes in mRNA expression. The results showed that S. frutescens had a significant effect on reversing the insulin-resistant state in both models of insulin-resistance. Furthermore, S. frutescens was capable of reducing lipid accumulation in the form of triacylglycerol in the high insulin/fructose model, while this was unaffected in the palmitate model. However, S. frutescens did reduce the accumulation of diacylglycerol in the palmitate model. Oxidative stress, seen to be associated with the insulin-resistant state, was successfully treated using the extract, as indicated by a reduction in reactive oxygen species. However no change was seen in the nitric oxide levels, in either model. Interestingly, although S. frutescens had no effect on the level of acetyl-CoA in the insulin/fructose model, it was found to increase this in the palmitate model. It is suggested that this may be due to increased β-oxidation and metabolic activity induced by the extract. The analysis of mRNA expression gave some insight into possible mechanisms by which insulin-resistance develops, although the results were inconclusive due to high variability in samples and the possibility of the RNA being compromised. Future studies will address this issue. The results of this study reflect different proposed clinical causes of insulin-resistance through the responses seen in the two cell models. These indicate that liver steatosis and insulin-resistance are induced by high palmitate as well as high insulin and fructose levels, and reversed by S. frutescens. Therefore the potential of S. frutescens to be used as a therapeutic agent in the treatment of insulin-resistance is indicated by this study.
- Full Text:
- Date Issued: 2014
- Authors: Clarke, Stephen
- Date: 2014
- Subjects: Insulin resistance , Diabetes -- Treatment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10348 , http://hdl.handle.net/10948/d1020788
- Description: Type 2 diabetes mellitus (T2DM) is rapidly emerging as one of the greatest global health issues of the 21st century. Insulin-resistance is a condition associated with T2DM and in the cell it is defined as the inadequate strength of insulin signalling from the insulin receptor downstream to the final substrates of insulin action involved in multiple metabolic, gene expression, and mitogenic aspects of cellular function. To investigate the potential mechanisms involved in the development of insulin-resistance, two in vitro liver cell models were established using palmitate or a combination of insulin and fructose as inducers. The development of insulin-resistance was determined via the capacity of the hepatocytes to maintain normal glucose metabolism functionality by measuring hepatic gluconeogenesis and glycogenolysis. It was established that the treatments induced the development of insulinresistance after 24 hours chronic exposure. Previous studies have investigated the potential of Sutherlandia frutescens extracts as therapeutic agents for insulin-resistance. The aim of this study was thus to investigate the ability of a hot aqueous extract of S. frutescens to reverse the insulin-resistant state, via measuring gluconeogenesis and glycogenolysis, the associated changes in cellular physiology (lipid accumulation, oxidative stress, and acetyl- CoA levels), and changes in mRNA expression. The results showed that S. frutescens had a significant effect on reversing the insulin-resistant state in both models of insulin-resistance. Furthermore, S. frutescens was capable of reducing lipid accumulation in the form of triacylglycerol in the high insulin/fructose model, while this was unaffected in the palmitate model. However, S. frutescens did reduce the accumulation of diacylglycerol in the palmitate model. Oxidative stress, seen to be associated with the insulin-resistant state, was successfully treated using the extract, as indicated by a reduction in reactive oxygen species. However no change was seen in the nitric oxide levels, in either model. Interestingly, although S. frutescens had no effect on the level of acetyl-CoA in the insulin/fructose model, it was found to increase this in the palmitate model. It is suggested that this may be due to increased β-oxidation and metabolic activity induced by the extract. The analysis of mRNA expression gave some insight into possible mechanisms by which insulin-resistance develops, although the results were inconclusive due to high variability in samples and the possibility of the RNA being compromised. Future studies will address this issue. The results of this study reflect different proposed clinical causes of insulin-resistance through the responses seen in the two cell models. These indicate that liver steatosis and insulin-resistance are induced by high palmitate as well as high insulin and fructose levels, and reversed by S. frutescens. Therefore the potential of S. frutescens to be used as a therapeutic agent in the treatment of insulin-resistance is indicated by this study.
- Full Text:
- Date Issued: 2014
Modelling the spatial and genetic response of the endemic sparid: Polysteganus praeorbitalis (Pisces: Sparidae) to climate change in the Agulhas Current system
- Authors: Isemonger, Devin Neil
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54509 , vital:26576
- Description: The Scotsman Seabream, Polysteganus praeorbitalis, is one of several large, slow-growing members of the Sparidae family of fishes endemic to the Agulhas Current system in the Western Indian Ocean (WIO). Relatively little research has been conducted on this species despite its importance to both recreational and commercial line fisheries in South Africa and the drastic decline in catch per unit effort (CPUE) that has been recorded since the 1940s. Changing sea temperatures as a result of global climate change are further expected to affect the distribution and abundance of many fish species based on their thermal tolerances, life histories and population structures. The ability of these species to shift their distribution and adapt to new environments and thermal conditions will depend to some degree on the levels of genetic variation and gene flow, within and between populations. A combined approach using species distribution modelling and genetic analyses may prove to be a useful tool in investigating the potential effects of climate change on the distribution and genetic diversity of species. An ensemble species distribution model (SDM) based on 205 occurrence records and 30 years of Reynolds Optimum Interpolated (OI) sea surface temperature data was constructed to predict the distributional response of P. praeorbitalis to climate change in the Agulhas Current system. The ensemble SDM displayed a true skill statistic (TSS) of 0.975 and an area under the receiver operating curve (ROC) of 0.999, indicating good model fit. Autumn and winter minimum temperatures, as well as bathymetry, were the most important predictor variables in the majority of models, indicating that these variables may directly constrain the distribution of P. praeorbitalis. In particular, the southern range edge of this species appeared to be constrained by autumn and winter minima, with high model agreement on this range edge. Conversely, the northern range limit showed poor model agreement leading to a gradual reduction in occurrence. This indicates that this range edge may be constrained by other factors not included in the models such as species interactions. The ensemble SDM projected the current range of P. praeorbitalis to be 1500 km², smaller than the published range for this species. The model underestimated the northern range edge of this species by approximately 5° latitude when binary transformed. This is probably due to the rarity of this species in the landings of the Mozambican linefishery, which was assumed to be an indication of low abundance of P. praeorbitalis in these waters. The absence of a specimen to verify the published northern range edge of this species indicates that the northern range edge produced by this model is likely to be closer to the actual range limit of the species. A range contraction of 30% occurring at both the northern and southern edge of P. praeorbitalis’ range and range fragmentation occurring, towards its northern range edge by 2030, was predicted. These changes are modelled to be the results of cooling related to the intensification of the Port Alfred upwelling cell and of warming predicted north of the Natal Bight and in southern Mozambique. Genetic analyses of the nuclear DNA (nDNA) S7 intron 1 and mitochondrial DNA (mtDNA) control region genes were carried out using 118 tissue samples of P. praeorbitalis collected at four main localities: the Eastern Cape, Transkei, southern KwaZulu-Natal and northern KwaZulu-Natal. Analyses of genetic diversity levels revealed relatively low diversity in the mtDNA dataset (Hd = 0.488; π = 0.004) and moderate levels of diversity in the nDNA dataset (Ad = 0.922; π = 0.005). The low levels of diversity observed in the mtDNA dataset might be explained by a number of factors, including high variation in spawning success, the negative effects of over-harvesting, or a recent population bottleneck. The last explanation is supported by characteristic star-shaped haplotype networks and unimodal mismatch distributions displayed by both datasets. These results, in conjunction with a significant (p = 0.005) negative Tajimas D value (-2.029) in the mtDNA dataset and significant (p = 0.0005) negative Fu’s F statistic in both the nDNA (F = -26.5) and mtDNA (F = -11.9) datasets, provide strong evidence for a recent population expansion after a bottleneck event in this species. Spatially, mtDNA diversity was highest in the Eastern Cape and lowest in the middle localities, while nDNA diversity showed the opposite pattern. These results may be indicative of differences in the sex ratio between localities, possibly as a result of the protogynous hermaphroditism that has been postulated for this species. Although pairwise comparisons and exact tests of population differentiation revealed no significant geneticdifferentiation between populations in the mtDNA dataset, there was some evidence of low levels of differentiation in the nDNA dataset. This occurred for comparisons between the Eastern Cape and Transkei (Fst = 0.039; p <0.05), and the northern KwaZulu-Natal (Fst = 0.045; p < 0.05).. This might be the result of one or a combination of factors including the effects of the Port Alfred upwelling cell on dispersal and gene flow, or the possibility of more than one spawning ground for this species promoting sub-structuring. A SAMOVA analyses run on the nDNA dataset maximised variance by grouping the Eastern Cape and southern KwaZulu-Natal together and Transkei and northern KwaZulu-Natal together in two groups. This revealed no evidence of spatial structure (p = 0.36), with only 3.30% of variation explained by this grouping. The removal of individuals below the estimated length at 50% maturity in the nDNA dataset, in order to test for temporal structure, resulted in stronger evidence of differentiation between the Eastern Cape and all other localities: Transkei (Fst = 0.081; p< 0.05), southern KwaZulu-Natal (Fst = 0.031; p<0.05), and northern KwaZulu-Natal (Fst = 0.078; p< 0.05). This indicates that some temporal genetic structure may exist between age classes within this species. The differentiation observed between the Eastern Cape and other localities, coupled with the high percentage of private haplotypes in the mtDNA dataset in this locality, indicates that this area is where P. praeorbitalis is most vulnerable to the potential negative effects of climate change on its genetic diversity. However, the vast majority of this species genetic diversity appears to reside towards the centre of its range where it is most abundant and the lack of strong genetic structure indicates high levels of gene flow. In conclusion, while P. praeorbitalis is vulnerable to range loss as a result of climate change, its genetic diversity is unlikely to be greatly affected.
- Full Text:
- Date Issued: 2014
- Authors: Isemonger, Devin Neil
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54509 , vital:26576
- Description: The Scotsman Seabream, Polysteganus praeorbitalis, is one of several large, slow-growing members of the Sparidae family of fishes endemic to the Agulhas Current system in the Western Indian Ocean (WIO). Relatively little research has been conducted on this species despite its importance to both recreational and commercial line fisheries in South Africa and the drastic decline in catch per unit effort (CPUE) that has been recorded since the 1940s. Changing sea temperatures as a result of global climate change are further expected to affect the distribution and abundance of many fish species based on their thermal tolerances, life histories and population structures. The ability of these species to shift their distribution and adapt to new environments and thermal conditions will depend to some degree on the levels of genetic variation and gene flow, within and between populations. A combined approach using species distribution modelling and genetic analyses may prove to be a useful tool in investigating the potential effects of climate change on the distribution and genetic diversity of species. An ensemble species distribution model (SDM) based on 205 occurrence records and 30 years of Reynolds Optimum Interpolated (OI) sea surface temperature data was constructed to predict the distributional response of P. praeorbitalis to climate change in the Agulhas Current system. The ensemble SDM displayed a true skill statistic (TSS) of 0.975 and an area under the receiver operating curve (ROC) of 0.999, indicating good model fit. Autumn and winter minimum temperatures, as well as bathymetry, were the most important predictor variables in the majority of models, indicating that these variables may directly constrain the distribution of P. praeorbitalis. In particular, the southern range edge of this species appeared to be constrained by autumn and winter minima, with high model agreement on this range edge. Conversely, the northern range limit showed poor model agreement leading to a gradual reduction in occurrence. This indicates that this range edge may be constrained by other factors not included in the models such as species interactions. The ensemble SDM projected the current range of P. praeorbitalis to be 1500 km², smaller than the published range for this species. The model underestimated the northern range edge of this species by approximately 5° latitude when binary transformed. This is probably due to the rarity of this species in the landings of the Mozambican linefishery, which was assumed to be an indication of low abundance of P. praeorbitalis in these waters. The absence of a specimen to verify the published northern range edge of this species indicates that the northern range edge produced by this model is likely to be closer to the actual range limit of the species. A range contraction of 30% occurring at both the northern and southern edge of P. praeorbitalis’ range and range fragmentation occurring, towards its northern range edge by 2030, was predicted. These changes are modelled to be the results of cooling related to the intensification of the Port Alfred upwelling cell and of warming predicted north of the Natal Bight and in southern Mozambique. Genetic analyses of the nuclear DNA (nDNA) S7 intron 1 and mitochondrial DNA (mtDNA) control region genes were carried out using 118 tissue samples of P. praeorbitalis collected at four main localities: the Eastern Cape, Transkei, southern KwaZulu-Natal and northern KwaZulu-Natal. Analyses of genetic diversity levels revealed relatively low diversity in the mtDNA dataset (Hd = 0.488; π = 0.004) and moderate levels of diversity in the nDNA dataset (Ad = 0.922; π = 0.005). The low levels of diversity observed in the mtDNA dataset might be explained by a number of factors, including high variation in spawning success, the negative effects of over-harvesting, or a recent population bottleneck. The last explanation is supported by characteristic star-shaped haplotype networks and unimodal mismatch distributions displayed by both datasets. These results, in conjunction with a significant (p = 0.005) negative Tajimas D value (-2.029) in the mtDNA dataset and significant (p = 0.0005) negative Fu’s F statistic in both the nDNA (F = -26.5) and mtDNA (F = -11.9) datasets, provide strong evidence for a recent population expansion after a bottleneck event in this species. Spatially, mtDNA diversity was highest in the Eastern Cape and lowest in the middle localities, while nDNA diversity showed the opposite pattern. These results may be indicative of differences in the sex ratio between localities, possibly as a result of the protogynous hermaphroditism that has been postulated for this species. Although pairwise comparisons and exact tests of population differentiation revealed no significant geneticdifferentiation between populations in the mtDNA dataset, there was some evidence of low levels of differentiation in the nDNA dataset. This occurred for comparisons between the Eastern Cape and Transkei (Fst = 0.039; p <0.05), and the northern KwaZulu-Natal (Fst = 0.045; p < 0.05).. This might be the result of one or a combination of factors including the effects of the Port Alfred upwelling cell on dispersal and gene flow, or the possibility of more than one spawning ground for this species promoting sub-structuring. A SAMOVA analyses run on the nDNA dataset maximised variance by grouping the Eastern Cape and southern KwaZulu-Natal together and Transkei and northern KwaZulu-Natal together in two groups. This revealed no evidence of spatial structure (p = 0.36), with only 3.30% of variation explained by this grouping. The removal of individuals below the estimated length at 50% maturity in the nDNA dataset, in order to test for temporal structure, resulted in stronger evidence of differentiation between the Eastern Cape and all other localities: Transkei (Fst = 0.081; p< 0.05), southern KwaZulu-Natal (Fst = 0.031; p<0.05), and northern KwaZulu-Natal (Fst = 0.078; p< 0.05). This indicates that some temporal genetic structure may exist between age classes within this species. The differentiation observed between the Eastern Cape and other localities, coupled with the high percentage of private haplotypes in the mtDNA dataset in this locality, indicates that this area is where P. praeorbitalis is most vulnerable to the potential negative effects of climate change on its genetic diversity. However, the vast majority of this species genetic diversity appears to reside towards the centre of its range where it is most abundant and the lack of strong genetic structure indicates high levels of gene flow. In conclusion, while P. praeorbitalis is vulnerable to range loss as a result of climate change, its genetic diversity is unlikely to be greatly affected.
- Full Text:
- Date Issued: 2014
Models for forecasting residential property prices using paired comparisons
- Authors: Mpapela, Sinazo
- Date: 2014
- Subjects: Paired comparisons (Statistics) , Statistics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/5839 , vital:21006
- Description: Residential real estate forecasting has become a part of the larger process of business planning and strategic management. Several studies of housing price trends recommend confining statistical analysis to repeated sales of residential property. This study presents an alternate methodology which combines information only on repeated residential sales regardless of the changes that has been made in the house in-between the sales. Additive and multiplicative models were used to forecast the residential property prices in Nelson Mandela Metropole. Data was collected from various sources and was reconciled into one data set for analysis through a process of data screening.
- Full Text:
- Date Issued: 2014
- Authors: Mpapela, Sinazo
- Date: 2014
- Subjects: Paired comparisons (Statistics) , Statistics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/5839 , vital:21006
- Description: Residential real estate forecasting has become a part of the larger process of business planning and strategic management. Several studies of housing price trends recommend confining statistical analysis to repeated sales of residential property. This study presents an alternate methodology which combines information only on repeated residential sales regardless of the changes that has been made in the house in-between the sales. Additive and multiplicative models were used to forecast the residential property prices in Nelson Mandela Metropole. Data was collected from various sources and was reconciled into one data set for analysis through a process of data screening.
- Full Text:
- Date Issued: 2014
New geochemical constraints on the genesis of the Gamsberg zinc deposit, Namaqualand Metamorphic Province, South Africa
- Authors: Foulkes, Susan Elizabeth
- Date: 2014
- Subjects: Zinc ores -- South Africa -- Gamsberg , Mines and mineral resources -- South Africa -- Gamsberg , Mineralogy -- South Africa -- Gamsberg , Molecular evolution , Geology -- South Africa -- Namaqualand
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5054 , http://hdl.handle.net/10962/d1012084 , Zinc ores -- South Africa -- Gamsberg , Mines and mineral resources -- South Africa -- Gamsberg , Mineralogy -- South Africa -- Gamsberg , Molecular evolution , Geology -- South Africa -- Namaqualand
- Description: The base metal massive sulfide deposits of the Aggeneys-Gamsberg (A-G) District are hosted within the Mesoproterozoic Bushmanland Group of the Namaqua-Natal Metamorphic Complex in the Northern Cape Province of South Africa. The district displays an apparent eastward trend in the economic concentration of base metals (+ barite) from relatively Cu-Pb-rich, Ba-poor mineralisation at Black Mountain to Zn- and Ba-rich ores at Gamsberg. Base metal sulfides at Gamsberg are restricted to the so called Gams (Iron) Formation which comprises a sulfidic mineralized unit (“B”) enveloped within a sequence of meta-sedimentary units (“A” and “C”). The aim of the study was to shed further light on the genesis and chemical evolution of the sulfide mineralisation at Gamsberg in the context of the entire A-G District, by interrogating further the apparent district-wide trend in base metal distribution. The Gams Iron Formation was sampled and studied from one key drill core intersection (“G1”) which intersects the largest part of it as described elsewhere; a small number of additional samples from a second drill core (“G2”) complemented the main sample suite. Minerals that make up the silicate assemblages across the studied section include quartz, garnet, pyroxene, pyroxenoid, phyllosilicates, carbonates, amphiboles, oxides (chiefly magnetite) and graphite. In a stratigraphic context, the mineralogical variations conform directly to those documented in the relevant literature from the Gamsberg locality. These are coupled, where possible, with mineral-chemical profiles of selected silicate species which replicate those of bulk-rock compositions, particularly with respect to Mn, Fe and Ca in the upper C Unit of the studied section. These signals collectively track the characteristic transition from a terrigenous, siliciclastic sediment-dominated footwall to an exhalative sediment-dominated hanging wall to the sulfide mineralisation as also seen in similar deposits elsewhere, particularly with respect to the characteristic Mn-rich signature increasingly observed in the hanging wall C Unit. The foregoing suggests that the examined section faithfully records the interpreted primary stratigraphy of the deposits, despite the complex structural and metamorphic overprint that characterises the region. This facilitates a stratigraphic analytical approach on the sulfidic Unit B, through a combination of mineral-chemical and stable isotope analyses. Dominant sulfides in Unit B are sphalerite and pyrite, with lesser pyrrhotite and minor galena. Sphalerite shows high and generally invariant contents of Fe (mean 12.18wt%, as FeS) whereas Zn anti-correlates with Mn (mean 5.58wt%, as MnS). Isotopic analyses for S, Fe and Zn in hand-picked sphalerite and pyrite separates were used with a view to providing new evidence for chemical and isotopic variation within the sulfide ore-body in a vertical (i.e. stratigraphic) sense, discuss the implications thereof, and ultimately interpret the new data in light of similar existing data from the A-G District and elsewhere. The δ³⁴S data for pyrite (plus a single pyrrhotite grain) and sphalerite from both cores G1 and G2 show comparable compositional ranges between 22.9 and 30.4‰ and between 27 and 30.1‰ respectively. The δ⁵⁶Fe data for pyrite show a range between -1.85 and 0.19‰, whereas seven sphalerite separates have a very narrow range of δ⁶⁶Zn from 0.06 to 0.20‰. The atypically high sulfur isotope data reported in this study are interpreted to reflect sedimentary deposition of primary sulfide ore at Gamsberg from an isotopically highly evolved seawater sulfate source through large-scale Rayleigh fractionation processes. Thermogenic sulfate reduction is proposed to have been the main reductive mechanism from seawater sulfate to sulfide, given the absence of very low δ³⁴S data for sulfides anywhere in the A-G District. By contrast, the δ⁶⁶Zn values for sphalerite are for all intents and purposes invariant and very close to 0‰, and therefore suggest little Zn isotope fractionation from an original exhalative fluid source. On this evidence alone, Zn isotopes therefore appear to hold little promise as a proxy of the chemical and isotopic evolution of SEDEX deposits in space and time, although this can only be verified through further application in the broader A-G District and similar deposits elsewhere. The apparent decoupling of Zn and S isotopes in the Gamsberg sulfide deposit, however, points towards diverse sources of these two components, i.e. ascending metalliferous brines versus seawater respectively. Finally, pyrite δ⁵⁶Fe data do show a stratigraphic trend of generally declining values up-section, which are interpreted to reflect the influence of broadly coeval precipitation of isotopically heavy Fe-oxides on a broader-scale – now preserved as abundant magnetite through metamorphism. Further work on the iron isotope composition of silicate-and oxide-hosted Fe on a local-to-district scale will assist in testing this interpretation.
- Full Text:
- Date Issued: 2014
- Authors: Foulkes, Susan Elizabeth
- Date: 2014
- Subjects: Zinc ores -- South Africa -- Gamsberg , Mines and mineral resources -- South Africa -- Gamsberg , Mineralogy -- South Africa -- Gamsberg , Molecular evolution , Geology -- South Africa -- Namaqualand
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5054 , http://hdl.handle.net/10962/d1012084 , Zinc ores -- South Africa -- Gamsberg , Mines and mineral resources -- South Africa -- Gamsberg , Mineralogy -- South Africa -- Gamsberg , Molecular evolution , Geology -- South Africa -- Namaqualand
- Description: The base metal massive sulfide deposits of the Aggeneys-Gamsberg (A-G) District are hosted within the Mesoproterozoic Bushmanland Group of the Namaqua-Natal Metamorphic Complex in the Northern Cape Province of South Africa. The district displays an apparent eastward trend in the economic concentration of base metals (+ barite) from relatively Cu-Pb-rich, Ba-poor mineralisation at Black Mountain to Zn- and Ba-rich ores at Gamsberg. Base metal sulfides at Gamsberg are restricted to the so called Gams (Iron) Formation which comprises a sulfidic mineralized unit (“B”) enveloped within a sequence of meta-sedimentary units (“A” and “C”). The aim of the study was to shed further light on the genesis and chemical evolution of the sulfide mineralisation at Gamsberg in the context of the entire A-G District, by interrogating further the apparent district-wide trend in base metal distribution. The Gams Iron Formation was sampled and studied from one key drill core intersection (“G1”) which intersects the largest part of it as described elsewhere; a small number of additional samples from a second drill core (“G2”) complemented the main sample suite. Minerals that make up the silicate assemblages across the studied section include quartz, garnet, pyroxene, pyroxenoid, phyllosilicates, carbonates, amphiboles, oxides (chiefly magnetite) and graphite. In a stratigraphic context, the mineralogical variations conform directly to those documented in the relevant literature from the Gamsberg locality. These are coupled, where possible, with mineral-chemical profiles of selected silicate species which replicate those of bulk-rock compositions, particularly with respect to Mn, Fe and Ca in the upper C Unit of the studied section. These signals collectively track the characteristic transition from a terrigenous, siliciclastic sediment-dominated footwall to an exhalative sediment-dominated hanging wall to the sulfide mineralisation as also seen in similar deposits elsewhere, particularly with respect to the characteristic Mn-rich signature increasingly observed in the hanging wall C Unit. The foregoing suggests that the examined section faithfully records the interpreted primary stratigraphy of the deposits, despite the complex structural and metamorphic overprint that characterises the region. This facilitates a stratigraphic analytical approach on the sulfidic Unit B, through a combination of mineral-chemical and stable isotope analyses. Dominant sulfides in Unit B are sphalerite and pyrite, with lesser pyrrhotite and minor galena. Sphalerite shows high and generally invariant contents of Fe (mean 12.18wt%, as FeS) whereas Zn anti-correlates with Mn (mean 5.58wt%, as MnS). Isotopic analyses for S, Fe and Zn in hand-picked sphalerite and pyrite separates were used with a view to providing new evidence for chemical and isotopic variation within the sulfide ore-body in a vertical (i.e. stratigraphic) sense, discuss the implications thereof, and ultimately interpret the new data in light of similar existing data from the A-G District and elsewhere. The δ³⁴S data for pyrite (plus a single pyrrhotite grain) and sphalerite from both cores G1 and G2 show comparable compositional ranges between 22.9 and 30.4‰ and between 27 and 30.1‰ respectively. The δ⁵⁶Fe data for pyrite show a range between -1.85 and 0.19‰, whereas seven sphalerite separates have a very narrow range of δ⁶⁶Zn from 0.06 to 0.20‰. The atypically high sulfur isotope data reported in this study are interpreted to reflect sedimentary deposition of primary sulfide ore at Gamsberg from an isotopically highly evolved seawater sulfate source through large-scale Rayleigh fractionation processes. Thermogenic sulfate reduction is proposed to have been the main reductive mechanism from seawater sulfate to sulfide, given the absence of very low δ³⁴S data for sulfides anywhere in the A-G District. By contrast, the δ⁶⁶Zn values for sphalerite are for all intents and purposes invariant and very close to 0‰, and therefore suggest little Zn isotope fractionation from an original exhalative fluid source. On this evidence alone, Zn isotopes therefore appear to hold little promise as a proxy of the chemical and isotopic evolution of SEDEX deposits in space and time, although this can only be verified through further application in the broader A-G District and similar deposits elsewhere. The apparent decoupling of Zn and S isotopes in the Gamsberg sulfide deposit, however, points towards diverse sources of these two components, i.e. ascending metalliferous brines versus seawater respectively. Finally, pyrite δ⁵⁶Fe data do show a stratigraphic trend of generally declining values up-section, which are interpreted to reflect the influence of broadly coeval precipitation of isotopically heavy Fe-oxides on a broader-scale – now preserved as abundant magnetite through metamorphism. Further work on the iron isotope composition of silicate-and oxide-hosted Fe on a local-to-district scale will assist in testing this interpretation.
- Full Text:
- Date Issued: 2014
Optimizing MIDAS III over South Africa
- Authors: Giday, Nigussie Mezgebe
- Date: 2014
- Subjects: Multi-Instrument Data Analysis System (MIDAS) , Global Positioning System , Ionosphere -- South Africa , Ionospheric electron density -- South Africa , Ionosondes -- South Africa , Tomography -- Scientific applications -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5517 , http://hdl.handle.net/10962/d1011277 , Multi-Instrument Data Analysis System (MIDAS) , Global Positioning System , Ionosphere -- South Africa , Ionospheric electron density -- South Africa , Ionosondes -- South Africa , Tomography -- Scientific applications -- South Africa
- Description: In this thesis an ionospheric tomographic algorithm called Multi-Instrument Data Anal- ysis System (MIDAS) is used to reconstruct electron density profiles using the Global Positioning System (GPS) data recorded from 53 GPS receivers over the South African region. MIDAS, developed by the Invert group at the University of Bath in the UK, is an inversion algorithm that produces a time dependent 3D image of the electron density of the ionosphere. GPS receivers record the time delay and phase advance of the trans- ionospheric GPS signals that traverse through the ionosphere from which the ionospheric parameter called Total Electron Content (TEC) can be computed. TEC, the line integral of the electron density along the satellite-receiver signal path, is ingested by ionospheric tomographic algorithms such as MIDAS to produce a time dependent 3D electron density profile. In order to validate electron density profiles from MIDAS, MIDAS derived NmF2 values were compared with ionosonde derived NmF2 values extracted from their respective 1D electron density profiles at 15 minute intervals for all four South African ionosonde stations (Grahamstown, Hermanus, Louisvale, and Madimbo). MIDAS 2D images of the electron density showed good diurnal and seasonal patterns; where a comparison of the 2D images at 12h00 UT for all the validation days exhibited maximum electron concentration during the autumn and summer and a minimum during the winter. A root mean square error (rmse) value as small as 0.88x 10¹¹[el=m³] was calculated for the Louisvale ionosonde station during the winter season and a maximum rmse value of 1.92x 10¹¹[el=m³] was ob- tained during the autumn season. The r² values were the least during the autumn and relatively large during summer and winter; similarly the rmse values were found to be a maximum during the autumn and a minimum during the winter indicating that MIDAS performs better during the winter than during the autumn and spring seasons. It is also observed that MIDAS performs better at Louisvale and Madimbo than at Grahamstown and Hermanus. In conclusion, the MIDAS reconstruction has showed good agreement with the ionosonde measurements; therefore, MIDAS can be considered a useful tool to study the ionosphere over the South African region.
- Full Text:
- Date Issued: 2014
- Authors: Giday, Nigussie Mezgebe
- Date: 2014
- Subjects: Multi-Instrument Data Analysis System (MIDAS) , Global Positioning System , Ionosphere -- South Africa , Ionospheric electron density -- South Africa , Ionosondes -- South Africa , Tomography -- Scientific applications -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5517 , http://hdl.handle.net/10962/d1011277 , Multi-Instrument Data Analysis System (MIDAS) , Global Positioning System , Ionosphere -- South Africa , Ionospheric electron density -- South Africa , Ionosondes -- South Africa , Tomography -- Scientific applications -- South Africa
- Description: In this thesis an ionospheric tomographic algorithm called Multi-Instrument Data Anal- ysis System (MIDAS) is used to reconstruct electron density profiles using the Global Positioning System (GPS) data recorded from 53 GPS receivers over the South African region. MIDAS, developed by the Invert group at the University of Bath in the UK, is an inversion algorithm that produces a time dependent 3D image of the electron density of the ionosphere. GPS receivers record the time delay and phase advance of the trans- ionospheric GPS signals that traverse through the ionosphere from which the ionospheric parameter called Total Electron Content (TEC) can be computed. TEC, the line integral of the electron density along the satellite-receiver signal path, is ingested by ionospheric tomographic algorithms such as MIDAS to produce a time dependent 3D electron density profile. In order to validate electron density profiles from MIDAS, MIDAS derived NmF2 values were compared with ionosonde derived NmF2 values extracted from their respective 1D electron density profiles at 15 minute intervals for all four South African ionosonde stations (Grahamstown, Hermanus, Louisvale, and Madimbo). MIDAS 2D images of the electron density showed good diurnal and seasonal patterns; where a comparison of the 2D images at 12h00 UT for all the validation days exhibited maximum electron concentration during the autumn and summer and a minimum during the winter. A root mean square error (rmse) value as small as 0.88x 10¹¹[el=m³] was calculated for the Louisvale ionosonde station during the winter season and a maximum rmse value of 1.92x 10¹¹[el=m³] was ob- tained during the autumn season. The r² values were the least during the autumn and relatively large during summer and winter; similarly the rmse values were found to be a maximum during the autumn and a minimum during the winter indicating that MIDAS performs better during the winter than during the autumn and spring seasons. It is also observed that MIDAS performs better at Louisvale and Madimbo than at Grahamstown and Hermanus. In conclusion, the MIDAS reconstruction has showed good agreement with the ionosonde measurements; therefore, MIDAS can be considered a useful tool to study the ionosphere over the South African region.
- Full Text:
- Date Issued: 2014
Options for eland: a multi-scale assessment of antipredatory responses of a vulnerable prey species to their dominant predator in the Eastern Cape, South Africa
- Authors: Leaver, Jessica
- Date: 2014
- Subjects: Endangered species -- South Africa -- Eastern Cape , Predatory animals -- Control -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/6570 , vital:21113
- Description: Eland Tragelaphus oryx are the largest and slowest African antelope, falling within the preferred weight range of the prey of lions Panthera leo. Little is known, however, about the antipredatory strategies employed by eland. Rapid population declines in several small reserves following the reintroduction of lions suggest that the antipredatory strategies of eland may be compromised in spatially limited areas. This emphasises the need for research aimed at investigating how eland respond to lions, particularly in the spatial context, given that lions are increasingly being reintroduced into small reserves in South Africa. This study aimed to investigate lion-eland interactions at multiple scales and determine where on the landscape eland were vulnerable to predation. Adult female eland (n = 3 per site) in breeding herds were collared with GPS satellite collars in two study sites; the Nyathi section of Addo Elephant National Park (Nyathi) and Mountain Zebra National Park (MZNP) in the Eastern Cape, South Africa. A reintroduced population of lions, comprising two males and one female, was present in each study site, with individuals fitted with GPS satellite collars. At a broad spatiotemporal scale, eland did not avoid lions and there was considerable overlap between eland and lion home ranges in both study sites. At a finer spatiotemporal scale however, eland and lion space use was asynchronous in time, except in the case of the female lion in Nyathi where there was considerable overlap at the finest temporal scale investigated (i.e. monthly). Herd-associated eland in Nyathi were killed most frequently in areas associated with high long-term use by the female lion, showing that failure to avoid the female lion at a fine scale increased predation risk for eland. Secondly, eland in Nyathi were killed most frequently in habitat types of intermediate structural density (i.e. mixed habitats), which limited the viewshed of eland but presumably offered increased forage. This habitat type was selected for by eland, despite it being associated with a higher level of predation risk. This suggested that eland in Nyathi traded off safety for forage. In MZNP, predation of herd-associated eland was low which reflected the limited spatial overlap between eland and lion at a fine scale in this reserve. In Nyathi, but not in MZNP, eland responded to lions within 1.5 km by increasing their movement rate, with this response particularly strong at night. The findings of this study show that eland responses to lions are scale-dependent and site-specific. Furthermore, eland responses to lions were shown to be lion gender-specific. This study has increased our understanding of the antipredatory behaviours of eland and demonstrated the importance of investigating prey responses to predation risk at multiple scales.
- Full Text:
- Date Issued: 2014
- Authors: Leaver, Jessica
- Date: 2014
- Subjects: Endangered species -- South Africa -- Eastern Cape , Predatory animals -- Control -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/6570 , vital:21113
- Description: Eland Tragelaphus oryx are the largest and slowest African antelope, falling within the preferred weight range of the prey of lions Panthera leo. Little is known, however, about the antipredatory strategies employed by eland. Rapid population declines in several small reserves following the reintroduction of lions suggest that the antipredatory strategies of eland may be compromised in spatially limited areas. This emphasises the need for research aimed at investigating how eland respond to lions, particularly in the spatial context, given that lions are increasingly being reintroduced into small reserves in South Africa. This study aimed to investigate lion-eland interactions at multiple scales and determine where on the landscape eland were vulnerable to predation. Adult female eland (n = 3 per site) in breeding herds were collared with GPS satellite collars in two study sites; the Nyathi section of Addo Elephant National Park (Nyathi) and Mountain Zebra National Park (MZNP) in the Eastern Cape, South Africa. A reintroduced population of lions, comprising two males and one female, was present in each study site, with individuals fitted with GPS satellite collars. At a broad spatiotemporal scale, eland did not avoid lions and there was considerable overlap between eland and lion home ranges in both study sites. At a finer spatiotemporal scale however, eland and lion space use was asynchronous in time, except in the case of the female lion in Nyathi where there was considerable overlap at the finest temporal scale investigated (i.e. monthly). Herd-associated eland in Nyathi were killed most frequently in areas associated with high long-term use by the female lion, showing that failure to avoid the female lion at a fine scale increased predation risk for eland. Secondly, eland in Nyathi were killed most frequently in habitat types of intermediate structural density (i.e. mixed habitats), which limited the viewshed of eland but presumably offered increased forage. This habitat type was selected for by eland, despite it being associated with a higher level of predation risk. This suggested that eland in Nyathi traded off safety for forage. In MZNP, predation of herd-associated eland was low which reflected the limited spatial overlap between eland and lion at a fine scale in this reserve. In Nyathi, but not in MZNP, eland responded to lions within 1.5 km by increasing their movement rate, with this response particularly strong at night. The findings of this study show that eland responses to lions are scale-dependent and site-specific. Furthermore, eland responses to lions were shown to be lion gender-specific. This study has increased our understanding of the antipredatory behaviours of eland and demonstrated the importance of investigating prey responses to predation risk at multiple scales.
- Full Text:
- Date Issued: 2014
Ore distribution controls of the Navachab Gold Mine, Damara Belt, Karibib District, Namibia
- Authors: Slabbert, W L
- Date: 2014
- Subjects: Gold ores -- Namibia , Ore deposits -- Namibia
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5082 , http://hdl.handle.net/10962/d1016364
- Description: The Navachab Gold mine, an orogenic lode gold deposit, is located in the Karibib region of the Pan-African (ca. 550-500) Damara belt of central Namibia. Gold mineralisation is developed within the steeply NW dipping limb of the Karibib dome. Here, ore envelopes trend along three main orientations: a) trends shallowly towards the NE (the down plunge extent), b) trends sub-vertically in and along the down plunge extent and c) trends sub-horizontally across the down plunge extent. The down plunge extent represents the bulk of the gold mineralisation, hosting the only high grade ores mined at Navachab. As such, past work primarily focused on establishing the controls to the mineralisation observed here. The sub-vertical and sub–horizontal ore trends are seen as secondary, lower grade, being hosted in the footwall. By cutting pushbacks into the footwall, in an effort to regain access to high grade pit bottom, future gold production almost exclusively relies upon optimally mining these ores. This underlines the importance to investigate and outline the mineralising controls to the secondary ore trends. This study identified the following prevailing quartz vein sets developed within the footwall, set (1) dips shallowly towards the NE (conjugate vein set), (2) steeply towards the NW (bedding parallel veins) and (3) steeply towards the SE (S2 foliation parallel). The NW and SE dipping sets contain high average gold grades, occurring at an infrequent vein density. The NE dipping veins, as a result of occurrence density alone, was highlighted as the dominant gold hosting set. Veining occurred during the late stages of the NW-SE directed, sub-horizontal shortening (D2) event and is associated with top-to-the-NW thrusting and NW-verging folds. Re-Os molybdenite dating from auriferous quartz veins indicates mineralisation occurred at 525-520 Ma. As crustal shortening amplified the Karibib dome, flexural flow developed fractures along bedding planes, providing the control to bedding parallel veins (NW dipping). With continued crustal compression the dome later experienced fold lock up associated with reduced mean rock stress and sub-horizontal extension occurred along the steeply NW dipping limb. Horizontal extensional gashes sucked in fluids to form the shallowly NE dipping conjugate vein set. These features suggest the regional D2 strain as the first-order control to quartz vein development, down plunge and within the footwall ores. To further define the secondary ores, lithological and structural controls were evaluated on a more detailed local scale. With equal amounts of biotite schist and calc-silicate host rock (bulk of the footwall lithology) material analysed, the biotite schist units were found to contain a larger volume amount of quartz veins. The mineralisation incurred is also developed at higher average gold grades compared to that of the calc-silicates, demonstrating biotite schist having the optimal rheology for quartz vein emplacement. Normal faulting and thrusting occurs widespread, at all scale levels, across the footwall. These were primarily observed along bedding foliations and secondly at higher angles cutting across foliation. The study did not constrain the extent of these, but can conclude faulting plays a very prominent role in re-distributing the secondary ores parallel to bedding along sub-vertical trend planes. Great care should be placed in properly modelling these with 3D software such as Leapfrog. The Navachab gold mineralisation came about as a result of convergent and collisional tectonics activating metamorphic dehydration of the crustal metapelites. As these fluids ascended they absorbed gold from the crust, emplaced by either a magmatic or paleo-placer source. The gold enriched hydrothermal fluids amalgamated in large scale 1ste order structures (shearing of the steep NW limb of the Karibib Dome, the Mon Repos Thrust Zone) that acted as primary active fluid path ways. In the case of Navachab the gold enriched fluid fluxed along these pathways while interacting with fluid sinks related to a physical throttle (brittle schist, folding, bedding parallel shears) and/or a chemical trap (marbles). By summarising and detailing the fluid sinks and active fluid pathways identified by this and previous works, it is strongly recommended that a mineral approach system be designed and implemented as targeting model to lead future exploration endeavours.
- Full Text:
- Date Issued: 2014
- Authors: Slabbert, W L
- Date: 2014
- Subjects: Gold ores -- Namibia , Ore deposits -- Namibia
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5082 , http://hdl.handle.net/10962/d1016364
- Description: The Navachab Gold mine, an orogenic lode gold deposit, is located in the Karibib region of the Pan-African (ca. 550-500) Damara belt of central Namibia. Gold mineralisation is developed within the steeply NW dipping limb of the Karibib dome. Here, ore envelopes trend along three main orientations: a) trends shallowly towards the NE (the down plunge extent), b) trends sub-vertically in and along the down plunge extent and c) trends sub-horizontally across the down plunge extent. The down plunge extent represents the bulk of the gold mineralisation, hosting the only high grade ores mined at Navachab. As such, past work primarily focused on establishing the controls to the mineralisation observed here. The sub-vertical and sub–horizontal ore trends are seen as secondary, lower grade, being hosted in the footwall. By cutting pushbacks into the footwall, in an effort to regain access to high grade pit bottom, future gold production almost exclusively relies upon optimally mining these ores. This underlines the importance to investigate and outline the mineralising controls to the secondary ore trends. This study identified the following prevailing quartz vein sets developed within the footwall, set (1) dips shallowly towards the NE (conjugate vein set), (2) steeply towards the NW (bedding parallel veins) and (3) steeply towards the SE (S2 foliation parallel). The NW and SE dipping sets contain high average gold grades, occurring at an infrequent vein density. The NE dipping veins, as a result of occurrence density alone, was highlighted as the dominant gold hosting set. Veining occurred during the late stages of the NW-SE directed, sub-horizontal shortening (D2) event and is associated with top-to-the-NW thrusting and NW-verging folds. Re-Os molybdenite dating from auriferous quartz veins indicates mineralisation occurred at 525-520 Ma. As crustal shortening amplified the Karibib dome, flexural flow developed fractures along bedding planes, providing the control to bedding parallel veins (NW dipping). With continued crustal compression the dome later experienced fold lock up associated with reduced mean rock stress and sub-horizontal extension occurred along the steeply NW dipping limb. Horizontal extensional gashes sucked in fluids to form the shallowly NE dipping conjugate vein set. These features suggest the regional D2 strain as the first-order control to quartz vein development, down plunge and within the footwall ores. To further define the secondary ores, lithological and structural controls were evaluated on a more detailed local scale. With equal amounts of biotite schist and calc-silicate host rock (bulk of the footwall lithology) material analysed, the biotite schist units were found to contain a larger volume amount of quartz veins. The mineralisation incurred is also developed at higher average gold grades compared to that of the calc-silicates, demonstrating biotite schist having the optimal rheology for quartz vein emplacement. Normal faulting and thrusting occurs widespread, at all scale levels, across the footwall. These were primarily observed along bedding foliations and secondly at higher angles cutting across foliation. The study did not constrain the extent of these, but can conclude faulting plays a very prominent role in re-distributing the secondary ores parallel to bedding along sub-vertical trend planes. Great care should be placed in properly modelling these with 3D software such as Leapfrog. The Navachab gold mineralisation came about as a result of convergent and collisional tectonics activating metamorphic dehydration of the crustal metapelites. As these fluids ascended they absorbed gold from the crust, emplaced by either a magmatic or paleo-placer source. The gold enriched hydrothermal fluids amalgamated in large scale 1ste order structures (shearing of the steep NW limb of the Karibib Dome, the Mon Repos Thrust Zone) that acted as primary active fluid path ways. In the case of Navachab the gold enriched fluid fluxed along these pathways while interacting with fluid sinks related to a physical throttle (brittle schist, folding, bedding parallel shears) and/or a chemical trap (marbles). By summarising and detailing the fluid sinks and active fluid pathways identified by this and previous works, it is strongly recommended that a mineral approach system be designed and implemented as targeting model to lead future exploration endeavours.
- Full Text:
- Date Issued: 2014
Petrography, geochemistry and origin of atypical sedimentary-igneous contact relationships at the base of the Hotazel Formation around Middelplaats, Northern Cape Province, RSA
- Authors: Terracin, Matthew Theodore
- Date: 2014
- Subjects: Petrology -- South Africa , Geochemistry -- South Africa , Igneous rocks -- South Africa , Manganese ores -- South Africa , Manganese ores -- Geology -- South Africa , Metasomatism (Mineralogy) , Potassium
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5059 , http://hdl.handle.net/10962/d1012985
- Description: In the Middelplaats mine area of the Kalahari manganese field, two drill holes (MP53 and MP54) intersected anomalously high-grade manganese ore sitting stratigraphically just above an igneous body (likely a dike or sill). Manganese ore located within approximate 5 meters of the contact with the underlying igneous rocks has been substantially metasomatically upgraded from 25 percent manganese, to over 40 percent whilst the dominant manganese species within the ore has been altered to hausmannite. This report demonstrates the metasomatic alteration is related to devolatilization (removal and/or remobilization of H₂O, CO₂ and CaO) due to contact metamorphism caused by the underlying igneous rocks. The Middelplaats mine is situated in the southwest corner of the Kalahari manganese field where the paleo basin shallows out and ends. Within the mine area, several stratigraphic units pinch out or are truncated by the side of the basin. This pinching out of lithological formations has led to the underlying Ongeluk Formation being in contact with the much younger units of the Hotazel Formation. Therefore, geochemical investigation into the nature and source of the igneous rocks was also undertaken to see if the rocks from the two drill holes were related to one another and/or the underlying Ongeluk Formation. Results of these geochemical studies have demonstrated that the Middelplaats igneous rocks (dolerites) from the two drill holes (MP53 and MP54) share a co-genetic source region. There is also reasonable geochemical evidence that the source region of the Middelplaats igneous rocks was substantially similar to the source region of the Ongeluk Formation. This may indicate that the source region of the Ongeluk Formation was reactivated at some later stage resulting in the emplacement of doleritic dikes or sills in the Middelplaats mine area. The Middelplaats igneous rocks were also found to have undergone a slight but pervasive potassic alteration; with most of the original plagioclase feldspar showing some level of replacement by a potassium enriched feldspar. Although no source for this potassic fluid was found, the devolatilization reaction within the manganese ore appears to have released some potassium into the surrounding rocks. This additional potassium may be responsible for some localized potassic alteration.
- Full Text:
- Date Issued: 2014
- Authors: Terracin, Matthew Theodore
- Date: 2014
- Subjects: Petrology -- South Africa , Geochemistry -- South Africa , Igneous rocks -- South Africa , Manganese ores -- South Africa , Manganese ores -- Geology -- South Africa , Metasomatism (Mineralogy) , Potassium
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5059 , http://hdl.handle.net/10962/d1012985
- Description: In the Middelplaats mine area of the Kalahari manganese field, two drill holes (MP53 and MP54) intersected anomalously high-grade manganese ore sitting stratigraphically just above an igneous body (likely a dike or sill). Manganese ore located within approximate 5 meters of the contact with the underlying igneous rocks has been substantially metasomatically upgraded from 25 percent manganese, to over 40 percent whilst the dominant manganese species within the ore has been altered to hausmannite. This report demonstrates the metasomatic alteration is related to devolatilization (removal and/or remobilization of H₂O, CO₂ and CaO) due to contact metamorphism caused by the underlying igneous rocks. The Middelplaats mine is situated in the southwest corner of the Kalahari manganese field where the paleo basin shallows out and ends. Within the mine area, several stratigraphic units pinch out or are truncated by the side of the basin. This pinching out of lithological formations has led to the underlying Ongeluk Formation being in contact with the much younger units of the Hotazel Formation. Therefore, geochemical investigation into the nature and source of the igneous rocks was also undertaken to see if the rocks from the two drill holes were related to one another and/or the underlying Ongeluk Formation. Results of these geochemical studies have demonstrated that the Middelplaats igneous rocks (dolerites) from the two drill holes (MP53 and MP54) share a co-genetic source region. There is also reasonable geochemical evidence that the source region of the Middelplaats igneous rocks was substantially similar to the source region of the Ongeluk Formation. This may indicate that the source region of the Ongeluk Formation was reactivated at some later stage resulting in the emplacement of doleritic dikes or sills in the Middelplaats mine area. The Middelplaats igneous rocks were also found to have undergone a slight but pervasive potassic alteration; with most of the original plagioclase feldspar showing some level of replacement by a potassium enriched feldspar. Although no source for this potassic fluid was found, the devolatilization reaction within the manganese ore appears to have released some potassium into the surrounding rocks. This additional potassium may be responsible for some localized potassic alteration.
- Full Text:
- Date Issued: 2014
Petrological, mineralogical and geochemical studies of Zhongchang and Yantiangou ultramafic intrusions from the Panxi region, Sichuan Province, S-W China. Metallogenic and Exploration implications
- Authors: Malatji, Tsholofelo S
- Date: 2014
- Subjects: Mineralogy -- China , Geochemistry -- China
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5057 , http://hdl.handle.net/10962/d1012951
- Description: The Emeishan Large Igneous Province is one of the largest igneous provinces in the world. It is marked by basaltic extrusives that vary in Ti amount, classified as high Ti and low Ti. Several mafic to ultramafic intrusions occur in the province as well as granitic intrusions. The mafic-ultramafic intrusions are associated with mineralization; large layered utlramafic intrusions bearing Fe-Ti-V mineralization, while small dyke like or sill like intrusions contain Cu-Ni-PGE mineralization. The Zhongchang and Yantiangou mafic- ultramafic intrusions are small such intrusions bearing Ni-Cu-PGE mineralization. The deposits show a lot of similarities in source magma, evolution and mineralization. Parental magma for both deposits show alkaline tendencies, and a high Mg # indicative of primitive magma that underwent little crustal contamination. Mantle range Cu/Pd ratios show parental magma fertile in chalcophile elements and both deposits proceed to show depleted mantle normalized values as a result of sulphide saturation and subsequent mineralization. Mineralization in Zhongchang is hosted at the contact between peridotite and pyroxenite, interstitial to olivine and clinopyroxene. Alteration minerals include epidote and chlorite. High Cu/Pd ratios suggest earlier sulphide saturation and removal of a PGE sulphide, and a second sulphide saturation phase resulted in Ni-Cu mineralization. Mineralization in Yantiangou is hosted in biotite effectively following fractionation of olivine and clinopyroxene after which sulphide saturation occurred, precipitating sulphide minerals in biotite. Pyrite and millerite occur as a result of late stage hydrothermal alteration. Cu/Pd ratios are high indicating prior sulphide saturation occurred where PGE partitioned into sulphides. Ni/MgO ratios observed for both deposits indicate a state of sulphide under saturation where PGE partitioned into tellurides and bismurthinides and Ni into olivine. Average tenors for mineralized units are; Zhongchang at 5%Ni, 9% Cu, 4300ppb Pt and 2000ppb Pd, and Yantiangou having relatively lower tenors at 3.2%Ni, 6.5% Cu, 3000ppb Pt and 1300 ppb Pd.
- Full Text:
- Date Issued: 2014
- Authors: Malatji, Tsholofelo S
- Date: 2014
- Subjects: Mineralogy -- China , Geochemistry -- China
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5057 , http://hdl.handle.net/10962/d1012951
- Description: The Emeishan Large Igneous Province is one of the largest igneous provinces in the world. It is marked by basaltic extrusives that vary in Ti amount, classified as high Ti and low Ti. Several mafic to ultramafic intrusions occur in the province as well as granitic intrusions. The mafic-ultramafic intrusions are associated with mineralization; large layered utlramafic intrusions bearing Fe-Ti-V mineralization, while small dyke like or sill like intrusions contain Cu-Ni-PGE mineralization. The Zhongchang and Yantiangou mafic- ultramafic intrusions are small such intrusions bearing Ni-Cu-PGE mineralization. The deposits show a lot of similarities in source magma, evolution and mineralization. Parental magma for both deposits show alkaline tendencies, and a high Mg # indicative of primitive magma that underwent little crustal contamination. Mantle range Cu/Pd ratios show parental magma fertile in chalcophile elements and both deposits proceed to show depleted mantle normalized values as a result of sulphide saturation and subsequent mineralization. Mineralization in Zhongchang is hosted at the contact between peridotite and pyroxenite, interstitial to olivine and clinopyroxene. Alteration minerals include epidote and chlorite. High Cu/Pd ratios suggest earlier sulphide saturation and removal of a PGE sulphide, and a second sulphide saturation phase resulted in Ni-Cu mineralization. Mineralization in Yantiangou is hosted in biotite effectively following fractionation of olivine and clinopyroxene after which sulphide saturation occurred, precipitating sulphide minerals in biotite. Pyrite and millerite occur as a result of late stage hydrothermal alteration. Cu/Pd ratios are high indicating prior sulphide saturation occurred where PGE partitioned into sulphides. Ni/MgO ratios observed for both deposits indicate a state of sulphide under saturation where PGE partitioned into tellurides and bismurthinides and Ni into olivine. Average tenors for mineralized units are; Zhongchang at 5%Ni, 9% Cu, 4300ppb Pt and 2000ppb Pd, and Yantiangou having relatively lower tenors at 3.2%Ni, 6.5% Cu, 3000ppb Pt and 1300 ppb Pd.
- Full Text:
- Date Issued: 2014
Polynuclear biomolecular-supported rare earth coordination compounds : towards a new generation of lanthanide-based drugs
- Authors: Clark, Candyce
- Date: 2014
- Subjects: Polyols , Hydroxyl group , Rare earth metals
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10439 , http://hdl.handle.net/10948/d1020778
- Description: Galactitol and cis,cis,cis-1,3,5-cyclohexanetriol are polyols that are ideal examples of model compounds for ligands with lanthanide ions as they have their hydroxyl groups in favourable steric arrangement. Several complexes were synthesised with both lanthanide chloride and lanthanide nitrate salts with galactitol, and a variety of structures, both polymeric and monomeric, were observed. In all these complexes, galactitol acted as a bridging molecule between the lanthanide ions. A notable difference was the lanthanum chloride–galactitol complex that showed both chloride and galactitol bridging. The lanthanide nitrate salts formed only polymeric complexes with galactitol. Not all of the complexes showed nitrate ions coordinated to the metal centre, and in the neodymium nitrate– galactitol complex, which shows both monodentate and bidentate coordination of the nitrate groups. The coordination of the nitrate ions was confirmed using both XRD and IR analysis. Two complexes with lanthanide chloride salts and cis,cis,cis-1,3,5-cyclohexanetriol were synthesised and analysed. Lanthanum chloride formed a polymeric complex, which showed extensive chloride bridging between the metal centres. Praseodymium chloride formed a dimeric complex. All complexes were analysed with single-crystal X-ray diffraction, 1H NMR, 13C NMR and IR spectroscopy.
- Full Text:
- Date Issued: 2014
- Authors: Clark, Candyce
- Date: 2014
- Subjects: Polyols , Hydroxyl group , Rare earth metals
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10439 , http://hdl.handle.net/10948/d1020778
- Description: Galactitol and cis,cis,cis-1,3,5-cyclohexanetriol are polyols that are ideal examples of model compounds for ligands with lanthanide ions as they have their hydroxyl groups in favourable steric arrangement. Several complexes were synthesised with both lanthanide chloride and lanthanide nitrate salts with galactitol, and a variety of structures, both polymeric and monomeric, were observed. In all these complexes, galactitol acted as a bridging molecule between the lanthanide ions. A notable difference was the lanthanum chloride–galactitol complex that showed both chloride and galactitol bridging. The lanthanide nitrate salts formed only polymeric complexes with galactitol. Not all of the complexes showed nitrate ions coordinated to the metal centre, and in the neodymium nitrate– galactitol complex, which shows both monodentate and bidentate coordination of the nitrate groups. The coordination of the nitrate ions was confirmed using both XRD and IR analysis. Two complexes with lanthanide chloride salts and cis,cis,cis-1,3,5-cyclohexanetriol were synthesised and analysed. Lanthanum chloride formed a polymeric complex, which showed extensive chloride bridging between the metal centres. Praseodymium chloride formed a dimeric complex. All complexes were analysed with single-crystal X-ray diffraction, 1H NMR, 13C NMR and IR spectroscopy.
- Full Text:
- Date Issued: 2014
Potential for human exposure to Beta-N-methylamino-L-alanine in a freshwater system
- Authors: Scott, Laura Louise
- Date: 2014
- Subjects: Water quality biological assessment , Cyanobacteria , Neurotoxic agents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/5159 , vital:20816
- Description: β-N-methylamino-L-alanine (BMAA) is a non-proteinogenic amino acid associated with human neurodegenerative diseases. The content of BMAA in cyanobacteria is modulated by nitrogen in laboratory cultures. In order to evaluate the potential for human exposure, the nitrogen modulation of BMAA content needed verification in a natural environment. In accordance with laboratory culture studies, data presented in this study show that combined nitrogen was the most significant modulator of both cellular microcystin (MC) and BMAA content in phytoplankton in an environmental cyanobacterial bloom. While BMAA is produced upon nitrogen deprivation, MC is only produced at a specific nitrogen threshold where the rate of increase of nitrogen in the cell exceeds the carbon fixation rate. As BMAA and MC were detected in phytoplankton sourced from the Hartbeespoort Dam reservoir, the transfer of these cyanotoxins to organisms of higher trophic levels was investigated. Both BMAA and MC were detected at high concentrations in the liver and muscle tissue of fish sourced from the Hartbeespoort Dam reservoir indicating that consumption of fish from this reservoir constitutes a serious risk of exposure to cyanotoxins. In addition to the dietary exposure route to BMAA, two recent studies reported a correlation between Amyotrophic Lateral Sclerosis (ALS) incidence and the potential for aerosol exposure to cyanobacteria. With the absence of any evidence of the systemic distribution of BMAA following inhalation, an evaluation of the potential exposure risk associated with living in close proximity to this reservoir was deemed premature. A laboratory experiment investigating the effect and systemic fate of inhaled aerosolised BMAA was therefore conducted in order to determine the feasibility of inhalation as a potential BMAA exposure route. Data from the rat inhalation exposure study, however, showed that in rats BMAA inhalation may not constitute a significant mechanism of toxicity at environmental BMAA levels.
- Full Text:
- Date Issued: 2014
- Authors: Scott, Laura Louise
- Date: 2014
- Subjects: Water quality biological assessment , Cyanobacteria , Neurotoxic agents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/5159 , vital:20816
- Description: β-N-methylamino-L-alanine (BMAA) is a non-proteinogenic amino acid associated with human neurodegenerative diseases. The content of BMAA in cyanobacteria is modulated by nitrogen in laboratory cultures. In order to evaluate the potential for human exposure, the nitrogen modulation of BMAA content needed verification in a natural environment. In accordance with laboratory culture studies, data presented in this study show that combined nitrogen was the most significant modulator of both cellular microcystin (MC) and BMAA content in phytoplankton in an environmental cyanobacterial bloom. While BMAA is produced upon nitrogen deprivation, MC is only produced at a specific nitrogen threshold where the rate of increase of nitrogen in the cell exceeds the carbon fixation rate. As BMAA and MC were detected in phytoplankton sourced from the Hartbeespoort Dam reservoir, the transfer of these cyanotoxins to organisms of higher trophic levels was investigated. Both BMAA and MC were detected at high concentrations in the liver and muscle tissue of fish sourced from the Hartbeespoort Dam reservoir indicating that consumption of fish from this reservoir constitutes a serious risk of exposure to cyanotoxins. In addition to the dietary exposure route to BMAA, two recent studies reported a correlation between Amyotrophic Lateral Sclerosis (ALS) incidence and the potential for aerosol exposure to cyanobacteria. With the absence of any evidence of the systemic distribution of BMAA following inhalation, an evaluation of the potential exposure risk associated with living in close proximity to this reservoir was deemed premature. A laboratory experiment investigating the effect and systemic fate of inhaled aerosolised BMAA was therefore conducted in order to determine the feasibility of inhalation as a potential BMAA exposure route. Data from the rat inhalation exposure study, however, showed that in rats BMAA inhalation may not constitute a significant mechanism of toxicity at environmental BMAA levels.
- Full Text:
- Date Issued: 2014
Predation by alien largemouth bass, Micropterus salmoides Lacepéde 1802 (Centrarchidae: Perciformes), on indigenous marine fish species in the Kowie System, South Africa
- Authors: Magoro, Mandla Leon
- Date: 2014
- Subjects: Largemouth bass -- South Africa -- Port Alfred , Largemouth bass -- Food -- South Africa -- Port Alfred , Estuarine fishes -- South Africa -- Port Alfred , Estuarine fishes -- Predators of , Centrarchidae , Fishes -- Effect of human beings on
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5851 , http://hdl.handle.net/10962/d1011939 , Largemouth bass -- South Africa -- Port Alfred , Largemouth bass -- Food -- South Africa -- Port Alfred , Estuarine fishes -- South Africa -- Port Alfred , Estuarine fishes -- Predators of , Centrarchidae , Fishes -- Effect of human beings on
- Description: Estuaries serve as nursery areas for a large number of estuary-associated fish species. Some of these taxa also use river catchments as nursery areas. During the upstream migration of this latter group, the juveniles are prone to predation by native and alien predatory fish inhabiting the system. The rate of invasion of ecosystems by alien organisms can be directly linked to anthropogenic influences, including both intentional and unintentional introductions by alien organisms into new regions. The largemouth bass, Micropterus salmoides, is a facultative piscivorous fish that has been successfully introduced worldwide for the main purpose of sport fishing. Where introduced, it has been found to negatively impact native fish and invertebrate species through predation, competitive exclusion and displacement of indigenous fish species. The aim of this thesis was to investigate the predatory impact of largemouth bass on the estuary-associated Cape moony Monodactylus falciformis, Cape stumpnose Rhabdosargus holubi and freshwater mullet Myxus capensis in the lower Kowie River of the Eastern Cape Province, South Africa. A combination of approaches was employed during this study. Stomach contents, stable isotopes and fatty acid analyses were employed for the reconstruction of the diet of largemouth bass. Acoustic telemetry was used to elucidate largemouth bass movements, particularly their ability to enter the upper reaches of the Kowie Estuary. Stomach contents and stable isotopes analyses showed that M. salmoides exhibit an ontogenic shift in diet, with small and medium sized individuals consuming the higher proportion of fish prey, while large sized individuals mostly consumed invertebrates such as crabs (Potamonautes sidneyi) and Odonata larvae, while consuming only a small proportion of estuary-associated fish. Fatty acid analysis only showed a direct connection between the fatty acid profiles of largemouth bass and those of M. capensis and M. falciformis. The acoustic telemetry results indicated that some M. salmoides individuals periodically move into the upper reaches of the estuary following river flood events. The results obtained from all these approaches highlight the risk posed by largemouth bass introductions on indigenous fish species, particularly those that enter the areas occupied by these top predators.
- Full Text:
- Date Issued: 2014
- Authors: Magoro, Mandla Leon
- Date: 2014
- Subjects: Largemouth bass -- South Africa -- Port Alfred , Largemouth bass -- Food -- South Africa -- Port Alfred , Estuarine fishes -- South Africa -- Port Alfred , Estuarine fishes -- Predators of , Centrarchidae , Fishes -- Effect of human beings on
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5851 , http://hdl.handle.net/10962/d1011939 , Largemouth bass -- South Africa -- Port Alfred , Largemouth bass -- Food -- South Africa -- Port Alfred , Estuarine fishes -- South Africa -- Port Alfred , Estuarine fishes -- Predators of , Centrarchidae , Fishes -- Effect of human beings on
- Description: Estuaries serve as nursery areas for a large number of estuary-associated fish species. Some of these taxa also use river catchments as nursery areas. During the upstream migration of this latter group, the juveniles are prone to predation by native and alien predatory fish inhabiting the system. The rate of invasion of ecosystems by alien organisms can be directly linked to anthropogenic influences, including both intentional and unintentional introductions by alien organisms into new regions. The largemouth bass, Micropterus salmoides, is a facultative piscivorous fish that has been successfully introduced worldwide for the main purpose of sport fishing. Where introduced, it has been found to negatively impact native fish and invertebrate species through predation, competitive exclusion and displacement of indigenous fish species. The aim of this thesis was to investigate the predatory impact of largemouth bass on the estuary-associated Cape moony Monodactylus falciformis, Cape stumpnose Rhabdosargus holubi and freshwater mullet Myxus capensis in the lower Kowie River of the Eastern Cape Province, South Africa. A combination of approaches was employed during this study. Stomach contents, stable isotopes and fatty acid analyses were employed for the reconstruction of the diet of largemouth bass. Acoustic telemetry was used to elucidate largemouth bass movements, particularly their ability to enter the upper reaches of the Kowie Estuary. Stomach contents and stable isotopes analyses showed that M. salmoides exhibit an ontogenic shift in diet, with small and medium sized individuals consuming the higher proportion of fish prey, while large sized individuals mostly consumed invertebrates such as crabs (Potamonautes sidneyi) and Odonata larvae, while consuming only a small proportion of estuary-associated fish. Fatty acid analysis only showed a direct connection between the fatty acid profiles of largemouth bass and those of M. capensis and M. falciformis. The acoustic telemetry results indicated that some M. salmoides individuals periodically move into the upper reaches of the estuary following river flood events. The results obtained from all these approaches highlight the risk posed by largemouth bass introductions on indigenous fish species, particularly those that enter the areas occupied by these top predators.
- Full Text:
- Date Issued: 2014
Prevalence and molecular epidemiology of extended-spectrum beta-lactamase-producing and carbapenem-resistant enterobacteriaceae, acinetobacter baumannii and pseudomonas aeruginosa in Port Elizabeth
- Authors: Gqunta, Kwanele
- Date: 2014
- Subjects: Beta lactamases , Enterobacteriaceae -- South Africa -- Port Elizabeth
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10353 , http://hdl.handle.net/10948/d1020944
- Description: Multidrug resistant (MDR) extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant Gram-negative bacteria have become an international health issue limiting treatment options. The objective of this study was to determine the prevalence of carbapenem-susceptible (CS) and carbapenem-resistant (CR) Enterobacteriaceae, Acinetobacter baumannii and Pseudomonas aeruginosa and investigate clinical isolates for their resistant genes/ determinants. A total of 98 bacterial isolates (59 CS and 39 CR) were collected between February 2012 and February 2013 at NHLS, after being recovered from various clinical specimens from PE hospital complex. Antimicrobial susceptibility testing was performed using the VITEK 2® system, E-test and microbroth dilution method. PCR and DNA sequencing were used to investigate: (i) ESBLs: CTX-M, TEM, SHV and OXA-1; (ii) plasmidmediated quinolone resistance (PMQR) genes: qnrA, qnrB, qnrC, qnrD, qnrS, qepA and aac(6’)-lb-cr; (iii) Escherichia coli sequence type 131 (ST131); (iv) carbapenemases: NDM, VIM, IMP, KPC, BIC, SME, IMI, NMC-A, GES, OXA-23, OXA-24, OXA-48, OXA-51 and OXA-58; and (v) insertion sequence ISAba1 upstream blaOXA-23/-24/-51/-58 genes. Porin loss in CR isolates was determined by SDSPAGE while genetic relatedness between E. coli ST131 isolates was determined by pulsed-field gel electrophoresis (PFGE). MDR ESBL-producing Enterobacteriaceae (mainly K. pneumoniae) and CR A. baumannii isolates were recovered from neonatal/ infant specimens. The majority of CS and CR isolates were MDR, possessing multiple ESBL genotypes (CTX-M, TEM, SHV and OXA-1). ESBL variants identified included: CTX-M-1, CTX-M-3, CTX-M-15, CTX-M-22, CTX-M-9, CTX-M-14, TEM-1, SHV-1, SHV-11 and OXA-1. PMQRs identified included: aac(6’)- lb-cr, qnrB1, qnrB2, qnrB13 and qnrS1. Twelve of 21 (57.1 percent) E. coli isolates belonged to the ST131 clonal complex and were genetically diverse, mainly producing CTX-M-15. Carbapenem resistance mechanisms identified included: (i) OXA-23 preceded by ISAba1 in 10 A. baumannii and 2 P. aeruginosa isolates; (ii) IMI-2 carbapenemase in an E. asburiae isolate; and (iii) combination of porin loss and ESBL production in 1 K. pneumoniae and 1 E. coli isolate. This is the first report in South Africa describing the occurrence of CTX-M-9, CTX-M-22 and IMI-2 among Enterobacteriaceae; CTX-M-15 in A. baumannii; and OXA-23 in combination with OXA-51 in P. aeruginosa. However, resistance determinants could not be detected for 24 carbapenem-resistant isolates which requires further investigation.
- Full Text:
- Date Issued: 2014
- Authors: Gqunta, Kwanele
- Date: 2014
- Subjects: Beta lactamases , Enterobacteriaceae -- South Africa -- Port Elizabeth
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10353 , http://hdl.handle.net/10948/d1020944
- Description: Multidrug resistant (MDR) extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant Gram-negative bacteria have become an international health issue limiting treatment options. The objective of this study was to determine the prevalence of carbapenem-susceptible (CS) and carbapenem-resistant (CR) Enterobacteriaceae, Acinetobacter baumannii and Pseudomonas aeruginosa and investigate clinical isolates for their resistant genes/ determinants. A total of 98 bacterial isolates (59 CS and 39 CR) were collected between February 2012 and February 2013 at NHLS, after being recovered from various clinical specimens from PE hospital complex. Antimicrobial susceptibility testing was performed using the VITEK 2® system, E-test and microbroth dilution method. PCR and DNA sequencing were used to investigate: (i) ESBLs: CTX-M, TEM, SHV and OXA-1; (ii) plasmidmediated quinolone resistance (PMQR) genes: qnrA, qnrB, qnrC, qnrD, qnrS, qepA and aac(6’)-lb-cr; (iii) Escherichia coli sequence type 131 (ST131); (iv) carbapenemases: NDM, VIM, IMP, KPC, BIC, SME, IMI, NMC-A, GES, OXA-23, OXA-24, OXA-48, OXA-51 and OXA-58; and (v) insertion sequence ISAba1 upstream blaOXA-23/-24/-51/-58 genes. Porin loss in CR isolates was determined by SDSPAGE while genetic relatedness between E. coli ST131 isolates was determined by pulsed-field gel electrophoresis (PFGE). MDR ESBL-producing Enterobacteriaceae (mainly K. pneumoniae) and CR A. baumannii isolates were recovered from neonatal/ infant specimens. The majority of CS and CR isolates were MDR, possessing multiple ESBL genotypes (CTX-M, TEM, SHV and OXA-1). ESBL variants identified included: CTX-M-1, CTX-M-3, CTX-M-15, CTX-M-22, CTX-M-9, CTX-M-14, TEM-1, SHV-1, SHV-11 and OXA-1. PMQRs identified included: aac(6’)- lb-cr, qnrB1, qnrB2, qnrB13 and qnrS1. Twelve of 21 (57.1 percent) E. coli isolates belonged to the ST131 clonal complex and were genetically diverse, mainly producing CTX-M-15. Carbapenem resistance mechanisms identified included: (i) OXA-23 preceded by ISAba1 in 10 A. baumannii and 2 P. aeruginosa isolates; (ii) IMI-2 carbapenemase in an E. asburiae isolate; and (iii) combination of porin loss and ESBL production in 1 K. pneumoniae and 1 E. coli isolate. This is the first report in South Africa describing the occurrence of CTX-M-9, CTX-M-22 and IMI-2 among Enterobacteriaceae; CTX-M-15 in A. baumannii; and OXA-23 in combination with OXA-51 in P. aeruginosa. However, resistance determinants could not be detected for 24 carbapenem-resistant isolates which requires further investigation.
- Full Text:
- Date Issued: 2014
Prioritising native fish populations for conservation using genetics in the Groot Marico catchment, North West Province, South Africa
- Authors: Van der Walt, Kerry-Ann
- Date: 2014
- Subjects: Native fishes Fishery management -- South Africa -- North West Fish populations Fishes -- Conservation -- South Africa -- Western Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/69102 , vital:29390
- Description: The Groot Marico catchment in the North West Province is a National Freshwater Ecosystem Priority Area (NFEPA) because it represents unique landscape features with unique biodiversity that are considered to be of special ecological significance. Three native freshwater species Amphilius uranoscopus, Chiloglanis pretoriae and Barbus motebensis, have high local conservation importance and B. motebensis is endemic to the catchment and is IUCN-listed as vulnerable. The main objective of this study is to contribute towards the effective conservation of these three species in the Groot Marico River system by assessing their genetic structure to determine whether tributary populations of the three species comprise of one genetic population or whether they are divided into genetically distinct subpopulations, in order to prioritise areas for conservation. The central null hypothesis was that there is no genetic differentiation between tributary populations (i.e., panmixia) of B. motebensis, A. uranoscopus and C. pretoriae in the Groot Marico catchment, North West Province. In total, 80 individuals per species were collected, targeting at least 10 individuals per population from a total of eight populations (seven tributaries and the Groot Marico main stem) and across the study area. Samples were collected by electrofishing and specimens were euthanized using an overdose of clove oil. A sample of muscle tissue was removed for genetic evaluation and the remainder of the specimens served as voucher specimens. For the genetic evaluation, mitochondrial (ND2, cyt b) and nuclear (S7) genes were used. Genetic techniques used were DNA extraction, polymerase chain reaction (PCR), purification and sequencing. From the 240 individuals collected, 123 sequences for B. motebensis, 111 sequences for A. uranoscopus and 103 sequences for C. pretoriae were analysed across all three genes. Statistical analysis included looking at cleaned sequences in order to obtain models using MODELTEST (version 3.06). Population structuring and phylogeographic analysis was performed in Arlequin (version 2000), TCS (version 1.2.1) and PAUP*. Results indicated that for B. motebensis the null hypothesis could be rejected as there were two distinct lineages (the Draai and Eastern lineages) that demonstrated significant divergence in both the ND2 and S7 genes, suggesting historical isolation. The low divergence in the mitochondrial cytochrome b gene (0% < D < 0.8%) suggests that this isolation is not very old and is probably not comparable to species level differentiation. The null hypothesis was also rejected for A. uranoscopus as there were also significant levels of differentiation between tributary populations resulting in the identification of two lineages (the Ribbok and Western lineages). However, for C. pretoriae, the null hypothesis could not be rejected as there was no genetic differentiation between tributary populations i.e., one panmictic population. Therefore, due to each species showing different genetic structuring within the tributary populations, more than one priority area for conservation needs to be implemented. These priority areas of conservation where therefore evaluated based on the current conservation status of the species (B. motebensis being vulnerable on the IUCN Red List), the number of Evolutionary Significant Units for each species and the overall genetic diversity of all three species in the Groot Marico catchment. In total, four tributary populations were conservation priorities areas, these were the Draai, Vanstraatens, Ribbok and Kaaloog tributaries. The Draai, Vanstraatens and Kaaloog tributaries were selected as priority areas for B. motebensis (B. motebensis is considered to be the most vulnerable of all three species). The Draai tributary was selected due to the B. motebensis population within the tributary showing isolation from the rest of the tributary populations. In order to conserve B. motebensis from the Southern lineage, the Vanstraatens and Kaaloog tributaries were selected. Reasons for selecting these two specific tributaries within the Southern lineage were that the Vanstraatens tributary had unique alleles (three Evolutionary Significant Units) for B. motebensis and the Kaaloog tributary had high genetic diversity (HD = 0.889, ND2 gene) when compared to the other tributary populations. The Ribbok and Vanstraatens tributaries were selected as priority areas for the conservation of A. uranoscopus. The Ribbok tributary was selected as it showed isolation from the rest of the tributary populations, as seen with the Draai tributary (B. motebensis) and the Vanstraatens tributary was selected to represent the Western lineage as it had the highest diversity for both genes (ND2 and S7). The Ribbok tributary has the highest prioritisation when compared to the Vanstraatens tributary. Chiloglanis pretoriae occurs within the Draai, Vanstraatens, Ribbok and Kaaloog tributaries, therefore by prioritising these tributaries for conservation, C. pretoriae will in turn be conserved.
- Full Text:
- Date Issued: 2014
- Authors: Van der Walt, Kerry-Ann
- Date: 2014
- Subjects: Native fishes Fishery management -- South Africa -- North West Fish populations Fishes -- Conservation -- South Africa -- Western Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/69102 , vital:29390
- Description: The Groot Marico catchment in the North West Province is a National Freshwater Ecosystem Priority Area (NFEPA) because it represents unique landscape features with unique biodiversity that are considered to be of special ecological significance. Three native freshwater species Amphilius uranoscopus, Chiloglanis pretoriae and Barbus motebensis, have high local conservation importance and B. motebensis is endemic to the catchment and is IUCN-listed as vulnerable. The main objective of this study is to contribute towards the effective conservation of these three species in the Groot Marico River system by assessing their genetic structure to determine whether tributary populations of the three species comprise of one genetic population or whether they are divided into genetically distinct subpopulations, in order to prioritise areas for conservation. The central null hypothesis was that there is no genetic differentiation between tributary populations (i.e., panmixia) of B. motebensis, A. uranoscopus and C. pretoriae in the Groot Marico catchment, North West Province. In total, 80 individuals per species were collected, targeting at least 10 individuals per population from a total of eight populations (seven tributaries and the Groot Marico main stem) and across the study area. Samples were collected by electrofishing and specimens were euthanized using an overdose of clove oil. A sample of muscle tissue was removed for genetic evaluation and the remainder of the specimens served as voucher specimens. For the genetic evaluation, mitochondrial (ND2, cyt b) and nuclear (S7) genes were used. Genetic techniques used were DNA extraction, polymerase chain reaction (PCR), purification and sequencing. From the 240 individuals collected, 123 sequences for B. motebensis, 111 sequences for A. uranoscopus and 103 sequences for C. pretoriae were analysed across all three genes. Statistical analysis included looking at cleaned sequences in order to obtain models using MODELTEST (version 3.06). Population structuring and phylogeographic analysis was performed in Arlequin (version 2000), TCS (version 1.2.1) and PAUP*. Results indicated that for B. motebensis the null hypothesis could be rejected as there were two distinct lineages (the Draai and Eastern lineages) that demonstrated significant divergence in both the ND2 and S7 genes, suggesting historical isolation. The low divergence in the mitochondrial cytochrome b gene (0% < D < 0.8%) suggests that this isolation is not very old and is probably not comparable to species level differentiation. The null hypothesis was also rejected for A. uranoscopus as there were also significant levels of differentiation between tributary populations resulting in the identification of two lineages (the Ribbok and Western lineages). However, for C. pretoriae, the null hypothesis could not be rejected as there was no genetic differentiation between tributary populations i.e., one panmictic population. Therefore, due to each species showing different genetic structuring within the tributary populations, more than one priority area for conservation needs to be implemented. These priority areas of conservation where therefore evaluated based on the current conservation status of the species (B. motebensis being vulnerable on the IUCN Red List), the number of Evolutionary Significant Units for each species and the overall genetic diversity of all three species in the Groot Marico catchment. In total, four tributary populations were conservation priorities areas, these were the Draai, Vanstraatens, Ribbok and Kaaloog tributaries. The Draai, Vanstraatens and Kaaloog tributaries were selected as priority areas for B. motebensis (B. motebensis is considered to be the most vulnerable of all three species). The Draai tributary was selected due to the B. motebensis population within the tributary showing isolation from the rest of the tributary populations. In order to conserve B. motebensis from the Southern lineage, the Vanstraatens and Kaaloog tributaries were selected. Reasons for selecting these two specific tributaries within the Southern lineage were that the Vanstraatens tributary had unique alleles (three Evolutionary Significant Units) for B. motebensis and the Kaaloog tributary had high genetic diversity (HD = 0.889, ND2 gene) when compared to the other tributary populations. The Ribbok and Vanstraatens tributaries were selected as priority areas for the conservation of A. uranoscopus. The Ribbok tributary was selected as it showed isolation from the rest of the tributary populations, as seen with the Draai tributary (B. motebensis) and the Vanstraatens tributary was selected to represent the Western lineage as it had the highest diversity for both genes (ND2 and S7). The Ribbok tributary has the highest prioritisation when compared to the Vanstraatens tributary. Chiloglanis pretoriae occurs within the Draai, Vanstraatens, Ribbok and Kaaloog tributaries, therefore by prioritising these tributaries for conservation, C. pretoriae will in turn be conserved.
- Full Text:
- Date Issued: 2014
Problems experienced by project managers on housing projects
- Mtshekexe, Ntombesibini Octavia
- Authors: Mtshekexe, Ntombesibini Octavia
- Date: 2014
- Subjects: Project management , Housing rehabilitation , Public housing -- South Africa , Building -- Superintendence
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:9675 , http://hdl.handle.net/10948/d1020930
- Description: Housing projects are amongst the South African (SA) Government’s major focus points with reference to budgeting for its financial years. The delivery of these housing projects is taking place at a slower rate than anticipated due to the problems experienced in the processes involved in their management. The project management shortcomings are a major setback with reference to the delivery of houses to the communities. It is, however, stated by the Constitution of the Republic of South Africa (RSA) that every South African citizen has a right to housing and that the Local Government, as the closest entity to communities, must do whatever it possibly can to ensure timeous service delivery to its communities. The objective of this research is to ascertain the nature and extent of project management problems experienced by municipal project managers, the impact thereof and potential solutions to the identified problems. The study is intended to advise on possible ways to address project management problems arising during the implementation of housing projects in the Nelson Mandela Bay Municipality (NMBM) through investigation and analysis of information gathered in both theory and practice. Project management is a process of controlling the achievement of project objectives through the application of knowledge, skills, tools and techniques. For a housing project the main objective is to deliver safe, quality houses on time and within budget. Problems which hinder the delivery of housing projects relate to cost, time and the quality of housing projects delivered. The fact that these key project objectives are not met needs to be addressed urgently in order to improve the housing delivery. The literature reviewed and the feedback from the surveys; indicate that these problems have a vast impact on housing projects. The survey also reveals that it is not only housing Project Managers (PMs) that are unable to perform well, but also other parties involved in the project management of housing projects and which play a great role in project management failures of housing projects. Some of these parties are consultants and contractors. The lack of performance by project managers affects the delivery of houses negatively in the NMBM.
- Full Text:
- Date Issued: 2014
- Authors: Mtshekexe, Ntombesibini Octavia
- Date: 2014
- Subjects: Project management , Housing rehabilitation , Public housing -- South Africa , Building -- Superintendence
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:9675 , http://hdl.handle.net/10948/d1020930
- Description: Housing projects are amongst the South African (SA) Government’s major focus points with reference to budgeting for its financial years. The delivery of these housing projects is taking place at a slower rate than anticipated due to the problems experienced in the processes involved in their management. The project management shortcomings are a major setback with reference to the delivery of houses to the communities. It is, however, stated by the Constitution of the Republic of South Africa (RSA) that every South African citizen has a right to housing and that the Local Government, as the closest entity to communities, must do whatever it possibly can to ensure timeous service delivery to its communities. The objective of this research is to ascertain the nature and extent of project management problems experienced by municipal project managers, the impact thereof and potential solutions to the identified problems. The study is intended to advise on possible ways to address project management problems arising during the implementation of housing projects in the Nelson Mandela Bay Municipality (NMBM) through investigation and analysis of information gathered in both theory and practice. Project management is a process of controlling the achievement of project objectives through the application of knowledge, skills, tools and techniques. For a housing project the main objective is to deliver safe, quality houses on time and within budget. Problems which hinder the delivery of housing projects relate to cost, time and the quality of housing projects delivered. The fact that these key project objectives are not met needs to be addressed urgently in order to improve the housing delivery. The literature reviewed and the feedback from the surveys; indicate that these problems have a vast impact on housing projects. The survey also reveals that it is not only housing Project Managers (PMs) that are unable to perform well, but also other parties involved in the project management of housing projects and which play a great role in project management failures of housing projects. Some of these parties are consultants and contractors. The lack of performance by project managers affects the delivery of houses negatively in the NMBM.
- Full Text:
- Date Issued: 2014
Regional connectivity, differentiation and biogeography of three species of the genus Lutjanus in the western Indian Ocean
- Authors: Morallana, Jonas Moqebelo
- Date: 2014
- Subjects: Lutjanus -- Indian Ocean , Biogeography -- Indian Ocean , Phylogeography -- Indian Ocean , Lutjanus -- Geographical distribution , Lutjanus -- Variation , Mitochondrial DNA , Animal genetics , Variation (Biology)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5369 , http://hdl.handle.net/10962/d1013293
- Description: Snappers of the genus Lutjanus are small to large predatory fishes occurring in inshore circumtropical and subtropical waters throughout the world. These fishes support fisheries across their distribution range. Within the Western Indian Ocean (WIO), previous studies on Lutjanus kasmira revealed limited spatial genetic differentiation, whereas Lutjanus fulviflamma showed high genetic connectivity. The phylogenetic relationships among WIO snappers are unknown. Previous studies in the Indo-Pacific (IP) did not include any WIO representatives. This study examined (1) the phylogeographic patterns in Lutjanus bohar, L. fulviflamma and L. lutjanus to understand the origins and factors influencing the distribution of diversity in the region, (2) how the physical environment, biological, and ecological factors influence genetic diversity, (3) the placement of WIO snappers in context to those from the IP, as well as the placement of taxa not included previously, (4) extent of differentiation among conspecifics from the two regions, and (5) the relationship of the Caesionidae to the Lutjanidae. Samples were sourced from across the WIO and from peripheral localities, where possible. DNA sequence data were generated from two mitochondrial gene regions (cyt-b and NADH-2) and a nuclear gene region (S7 intron 1). Data were analysed under a phylogeographic framework to examine genetic structure, diversity and differentiation among identified regions for each of the three species. Other sequence data were generated from two mitochondrial gene regions (COII and 16S rDNA) to examine the phylogenetic placement of WIO snappers in context of the IP snappers and the relationship of the Caesionidae to the Lutjanidae. Lutjanus bohar and L. fulviflamma displayed high genetic diversity, but lower diversities were observed for L. lutjanus. Genetic differentiation was observed between Mozambique and Maldives in L. bohar. Lutjanus fulviflamma was differentiated in South Africa, Mozambique, Mauritius and Thailand, while differentiation was observed between Kenya and Tanzania in Lutjanus lutjanus. Overall, low genetic differentiation and high connectivity were observed for each of the three species. This differentiation may result from intrinsic features of the species and extrinsic features of the environment, whereas the connectivity is mainly influenced by the pelagic larval duration. These patterns of differentiation are in accordance with a proposed vicariant biogeographic hypothesis for the origins of regional faunas of the IP. Phylogenies were similar to those published, with additional taxa not altering the previous groupings found. Conspecifics from the two regions clustered together, with varying degrees of differentiation among the WIO and IP, depending on the species. Members of the Caesionidae were nested within Lutjanidae, suggesting that morphological characters separating the two families are taxonomically insignificant. This affirms previous notions that the Caesionidae should be a subfamily within the Lutjanidae. This is the first multi-gene study, examining differentiation in multiple species of snapper over a wide geographic area in the WIO, and the results of this study could have potential implications for fisheries management and conservation.
- Full Text:
- Date Issued: 2014
- Authors: Morallana, Jonas Moqebelo
- Date: 2014
- Subjects: Lutjanus -- Indian Ocean , Biogeography -- Indian Ocean , Phylogeography -- Indian Ocean , Lutjanus -- Geographical distribution , Lutjanus -- Variation , Mitochondrial DNA , Animal genetics , Variation (Biology)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5369 , http://hdl.handle.net/10962/d1013293
- Description: Snappers of the genus Lutjanus are small to large predatory fishes occurring in inshore circumtropical and subtropical waters throughout the world. These fishes support fisheries across their distribution range. Within the Western Indian Ocean (WIO), previous studies on Lutjanus kasmira revealed limited spatial genetic differentiation, whereas Lutjanus fulviflamma showed high genetic connectivity. The phylogenetic relationships among WIO snappers are unknown. Previous studies in the Indo-Pacific (IP) did not include any WIO representatives. This study examined (1) the phylogeographic patterns in Lutjanus bohar, L. fulviflamma and L. lutjanus to understand the origins and factors influencing the distribution of diversity in the region, (2) how the physical environment, biological, and ecological factors influence genetic diversity, (3) the placement of WIO snappers in context to those from the IP, as well as the placement of taxa not included previously, (4) extent of differentiation among conspecifics from the two regions, and (5) the relationship of the Caesionidae to the Lutjanidae. Samples were sourced from across the WIO and from peripheral localities, where possible. DNA sequence data were generated from two mitochondrial gene regions (cyt-b and NADH-2) and a nuclear gene region (S7 intron 1). Data were analysed under a phylogeographic framework to examine genetic structure, diversity and differentiation among identified regions for each of the three species. Other sequence data were generated from two mitochondrial gene regions (COII and 16S rDNA) to examine the phylogenetic placement of WIO snappers in context of the IP snappers and the relationship of the Caesionidae to the Lutjanidae. Lutjanus bohar and L. fulviflamma displayed high genetic diversity, but lower diversities were observed for L. lutjanus. Genetic differentiation was observed between Mozambique and Maldives in L. bohar. Lutjanus fulviflamma was differentiated in South Africa, Mozambique, Mauritius and Thailand, while differentiation was observed between Kenya and Tanzania in Lutjanus lutjanus. Overall, low genetic differentiation and high connectivity were observed for each of the three species. This differentiation may result from intrinsic features of the species and extrinsic features of the environment, whereas the connectivity is mainly influenced by the pelagic larval duration. These patterns of differentiation are in accordance with a proposed vicariant biogeographic hypothesis for the origins of regional faunas of the IP. Phylogenies were similar to those published, with additional taxa not altering the previous groupings found. Conspecifics from the two regions clustered together, with varying degrees of differentiation among the WIO and IP, depending on the species. Members of the Caesionidae were nested within Lutjanidae, suggesting that morphological characters separating the two families are taxonomically insignificant. This affirms previous notions that the Caesionidae should be a subfamily within the Lutjanidae. This is the first multi-gene study, examining differentiation in multiple species of snapper over a wide geographic area in the WIO, and the results of this study could have potential implications for fisheries management and conservation.
- Full Text:
- Date Issued: 2014
Relative contribution of wild foods to individual and household food security in the context of increasing vulnerability due to HIV/AIDS and climate variability
- Abu-Basutu, Keitometsi Ngulube
- Authors: Abu-Basutu, Keitometsi Ngulube
- Date: 2014
- Subjects: Wild foods -- South Africa -- Eastern Cape , Food security -- South Africa , Food supply -- South Africa , AIDS (Disease) -- Social aspects -- South Africa , HIV infections -- Social aspects -- South Africa , Chronically ill -- South Africa -- Economic conditions , Chronically ill -- South Africa -- Social conditions , Food -- Social aspects -- South Africa , Food -- Economic aspects -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4774 , http://hdl.handle.net/10962/d1010864 , Wild foods -- South Africa -- Eastern Cape , Food security -- South Africa , Food supply -- South Africa , AIDS (Disease) -- Social aspects -- South Africa , HIV infections -- Social aspects -- South Africa , Chronically ill -- South Africa -- Economic conditions , Chronically ill -- South Africa -- Social conditions , Food -- Social aspects -- South Africa , Food -- Economic aspects -- South Africa
- Description: Wild foods are an integral component of the household food basket, yet their quantified contribution to food security relative to other sources in the context of HIV/AIDS, climate change and variability remains underexplored. This study was carried out in Willowvale and Lesseyton which are rural communities in the Eastern Cape province of South Africa. Willowvale is a relatively remote, medium-rainfall coastal community, while Lesseyton is a peri-urban low rainfall inland community. Qualitative and quantitative methods were used to collect data from 78 HIV/AIDS afflicted households with 329 individuals and 87 non-afflicted households with 365 individuals in the two study sites. Households were visited quarterly over 12 months to assess food acquisition methods, dietary intake and quality, and levels of food security, and to determine strategies employed by households to cope with droughts. The wild foods investigated were wild meat, wild birds, wild fish, wild mushrooms, wild leafy vegetables and wild fruits. Diets were moderately well-balanced and limited in variety, with cereal items contributing 52 % to total calorie intake. Mid-upper arm circumference measurements showed that all respondents were adequately nourished. The bulk of the food consumed by households was purchased, with supplementation from own production, wild vegetables and wild fruits. In Willowvale, wild vegetables comprised 46 % of overall vegetable consumption for afflicted households and 32 % for non-afflicted households, while own fruit production comprised 100 % of fruit consumption. In Lesseyton, wild vegetables comprised only 6 % and 4 % of vegetable consumption for afflicted and non-afflicted households, while wild fruit comprised 63 % and 41 % for afflicted and non-afflicted households. More than 80 % of respondents from both afflicted and non-afflicted households had sufficient daily kilocalories, although the majority of afflicted households felt they were food insecure and sometimes collected wild foods as one of their multiple coping strategies. Hunting and gathering of wild foods was associated with site, household affliction status, gender, age and season. More than 80 % of respondents ate wild vegetables and said they were more drought tolerant than conventional vegetables, making them the most consumed wild food and approximately 16 % of respondents ate wild birds, making them the least consumed wild food. Approximately 14 % of respondents from afflicted households in Willowvale sold wild fish, whilst 34 % of respondents from afflicted households and 7 % from non-afflicted households sold wild fruits in Lesseyton. Strategies adopted by households to cope with droughts were different between the two study sites, and households in Willowvale used a wider range of strategies. Given the devastating effects of HIV/AIDS coupled with the drawbacks of climate change and variability on food security, wild foods represent a free and easy way for vulnerable households to obtain food.
- Full Text:
- Date Issued: 2014
- Authors: Abu-Basutu, Keitometsi Ngulube
- Date: 2014
- Subjects: Wild foods -- South Africa -- Eastern Cape , Food security -- South Africa , Food supply -- South Africa , AIDS (Disease) -- Social aspects -- South Africa , HIV infections -- Social aspects -- South Africa , Chronically ill -- South Africa -- Economic conditions , Chronically ill -- South Africa -- Social conditions , Food -- Social aspects -- South Africa , Food -- Economic aspects -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4774 , http://hdl.handle.net/10962/d1010864 , Wild foods -- South Africa -- Eastern Cape , Food security -- South Africa , Food supply -- South Africa , AIDS (Disease) -- Social aspects -- South Africa , HIV infections -- Social aspects -- South Africa , Chronically ill -- South Africa -- Economic conditions , Chronically ill -- South Africa -- Social conditions , Food -- Social aspects -- South Africa , Food -- Economic aspects -- South Africa
- Description: Wild foods are an integral component of the household food basket, yet their quantified contribution to food security relative to other sources in the context of HIV/AIDS, climate change and variability remains underexplored. This study was carried out in Willowvale and Lesseyton which are rural communities in the Eastern Cape province of South Africa. Willowvale is a relatively remote, medium-rainfall coastal community, while Lesseyton is a peri-urban low rainfall inland community. Qualitative and quantitative methods were used to collect data from 78 HIV/AIDS afflicted households with 329 individuals and 87 non-afflicted households with 365 individuals in the two study sites. Households were visited quarterly over 12 months to assess food acquisition methods, dietary intake and quality, and levels of food security, and to determine strategies employed by households to cope with droughts. The wild foods investigated were wild meat, wild birds, wild fish, wild mushrooms, wild leafy vegetables and wild fruits. Diets were moderately well-balanced and limited in variety, with cereal items contributing 52 % to total calorie intake. Mid-upper arm circumference measurements showed that all respondents were adequately nourished. The bulk of the food consumed by households was purchased, with supplementation from own production, wild vegetables and wild fruits. In Willowvale, wild vegetables comprised 46 % of overall vegetable consumption for afflicted households and 32 % for non-afflicted households, while own fruit production comprised 100 % of fruit consumption. In Lesseyton, wild vegetables comprised only 6 % and 4 % of vegetable consumption for afflicted and non-afflicted households, while wild fruit comprised 63 % and 41 % for afflicted and non-afflicted households. More than 80 % of respondents from both afflicted and non-afflicted households had sufficient daily kilocalories, although the majority of afflicted households felt they were food insecure and sometimes collected wild foods as one of their multiple coping strategies. Hunting and gathering of wild foods was associated with site, household affliction status, gender, age and season. More than 80 % of respondents ate wild vegetables and said they were more drought tolerant than conventional vegetables, making them the most consumed wild food and approximately 16 % of respondents ate wild birds, making them the least consumed wild food. Approximately 14 % of respondents from afflicted households in Willowvale sold wild fish, whilst 34 % of respondents from afflicted households and 7 % from non-afflicted households sold wild fruits in Lesseyton. Strategies adopted by households to cope with droughts were different between the two study sites, and households in Willowvale used a wider range of strategies. Given the devastating effects of HIV/AIDS coupled with the drawbacks of climate change and variability on food security, wild foods represent a free and easy way for vulnerable households to obtain food.
- Full Text:
- Date Issued: 2014
Screening of entomopathogenic fungi against citrus mealybug (Planococcus citri (Risso)) and citrus thrips (Scirtothrips aurantii (Faure))
- FitzGerald, Véronique Chartier
- Authors: FitzGerald, Véronique Chartier
- Date: 2014
- Subjects: Entomopathogenic fungi , Citrus mealybug -- South Africa -- Eastern Cape , Citrus thrips -- South Africa -- Eastern Cape , Citrus -- Diseases and pests , Citrus mealybug -- Biological control , Citrus thrips -- Biological control , Biological pest control agents , Scanning electron microscopy , Mycoses
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4166 , http://hdl.handle.net/10962/d1020887
- Description: Mealybugs (Planococcus citri) and thrips (Scirtothrips aurantii) are common and extremely damaging citrus crop pests which have proven difficult to control via conventional methods, such as chemical pesticides and insect growth regulators. The objective of this study was to determine the efficacy of entomopathogenic fungi against these pests in laboratory bioassays. Isolates of Metarhizium anisopliae and Beauveria bassiana from citrus orchards in the Eastern Cape, South Africa were maintained on Sabouraud Dextrose 4% Agar supplemented with Dodine, chloramphenicol and rifampicin at 25°C. Infectivity of the fungal isolates was initially assessed using 5th instar false codling moth, Thaumatotibia leucotreta, larvae. Mealybug bioassays were performed in 24 well plates using 1 x 107 ml-1 conidial suspensions and kept at 26°C for 5 days with a photoperiod of 12 L:12 D. A Beauveria commercial product and an un-inoculated control were also screened for comparison. Isolates GAR 17 B3 (B. bassiana) and FCM AR 23 B3 (M. anisopliae) both resulted in 67.5% mealybug crawler mortality and GB AR 23 13 3 (B. bassiana) resulted in 64% crawler mortality. These 3 isolates were further tested in dose-dependent assays. Probit analyses were conducted on the dose-dependent assays data using PROBAN to determine LC₅₀ values. For both the mealybug adult and crawlers FCM AR 23 B3 required the lowest concentration to achieve LC₅₀ at 4.96 x 10⁶ conidia ml-1 and 5.29 x 10⁵ conidia ml-1, respectively. Bioassays on adult thrips were conducted in munger cells with leaf buds inoculated with the conidial suspensions. Isolate GAR 17 B3 had the highest mortality rate at 70% on thrips while FCM AR 23 B3 resulted in 60% mortality. Identification of the isolates, FCM AR 23 B3, GAR 17 B3 and GB AR 23 13 3, were confirmed to be correct using both microscopic and molecularly techniques. ITS sequences were compared to other sequences from GenBank and confirmed phylogenetically using MEGA6. Mealybug infection was investigated using scanning electron microscopy, mycosis was confirmed but the infection process could not be followed due to the extensive waxy cuticle. These results indicate that there is potential for the isolates FCM AR 23 B3 and GAR 17 B3 to be developed as biological control agents for the control of citrus mealybug and thrips. Further research would be required to determine their ability to perform under field conditions.
- Full Text:
- Date Issued: 2014
- Authors: FitzGerald, Véronique Chartier
- Date: 2014
- Subjects: Entomopathogenic fungi , Citrus mealybug -- South Africa -- Eastern Cape , Citrus thrips -- South Africa -- Eastern Cape , Citrus -- Diseases and pests , Citrus mealybug -- Biological control , Citrus thrips -- Biological control , Biological pest control agents , Scanning electron microscopy , Mycoses
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4166 , http://hdl.handle.net/10962/d1020887
- Description: Mealybugs (Planococcus citri) and thrips (Scirtothrips aurantii) are common and extremely damaging citrus crop pests which have proven difficult to control via conventional methods, such as chemical pesticides and insect growth regulators. The objective of this study was to determine the efficacy of entomopathogenic fungi against these pests in laboratory bioassays. Isolates of Metarhizium anisopliae and Beauveria bassiana from citrus orchards in the Eastern Cape, South Africa were maintained on Sabouraud Dextrose 4% Agar supplemented with Dodine, chloramphenicol and rifampicin at 25°C. Infectivity of the fungal isolates was initially assessed using 5th instar false codling moth, Thaumatotibia leucotreta, larvae. Mealybug bioassays were performed in 24 well plates using 1 x 107 ml-1 conidial suspensions and kept at 26°C for 5 days with a photoperiod of 12 L:12 D. A Beauveria commercial product and an un-inoculated control were also screened for comparison. Isolates GAR 17 B3 (B. bassiana) and FCM AR 23 B3 (M. anisopliae) both resulted in 67.5% mealybug crawler mortality and GB AR 23 13 3 (B. bassiana) resulted in 64% crawler mortality. These 3 isolates were further tested in dose-dependent assays. Probit analyses were conducted on the dose-dependent assays data using PROBAN to determine LC₅₀ values. For both the mealybug adult and crawlers FCM AR 23 B3 required the lowest concentration to achieve LC₅₀ at 4.96 x 10⁶ conidia ml-1 and 5.29 x 10⁵ conidia ml-1, respectively. Bioassays on adult thrips were conducted in munger cells with leaf buds inoculated with the conidial suspensions. Isolate GAR 17 B3 had the highest mortality rate at 70% on thrips while FCM AR 23 B3 resulted in 60% mortality. Identification of the isolates, FCM AR 23 B3, GAR 17 B3 and GB AR 23 13 3, were confirmed to be correct using both microscopic and molecularly techniques. ITS sequences were compared to other sequences from GenBank and confirmed phylogenetically using MEGA6. Mealybug infection was investigated using scanning electron microscopy, mycosis was confirmed but the infection process could not be followed due to the extensive waxy cuticle. These results indicate that there is potential for the isolates FCM AR 23 B3 and GAR 17 B3 to be developed as biological control agents for the control of citrus mealybug and thrips. Further research would be required to determine their ability to perform under field conditions.
- Full Text:
- Date Issued: 2014
Structural bioinformatics analysis of the Hsp40 and Hsp70 molecular chaperones from humans
- Authors: Adeyemi, Samson Adebowale
- Date: 2014
- Subjects: Structural bioinformatics , Molecular chaperones , Heat shock proteins , Protein-protein interactions , Biomolecules
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4171 , http://hdl.handle.net/10962/d1020962
- Description: HSP70 is one of the most important families of molecular chaperone that regulate the folding and transport of client proteins in an ATP dependent manner. The ATPase activity of HSP70 is stimulated through an interaction with its family of HSP40 co-chaperones. There is evidence to suggest that specific partnerships occur between the different HSP40 and HSP70 isoforms. While some of the residues involved in the interaction are known, many of the residues governing the specificity of HSP40-HSP70 partnerships are not precisely defined. It is not currently possible to predict which HSP40 and HSP70 isoforms will interact. We attempted to use bioinformatics to identify residues involved in the specificity of the interaction between the J domain from HSP40 and the ATPase domain from the HSP70 isoforms from humans. A total of 49 HSP40 and 13 HSP70 sequences from humans were retrieved and used for subsequent analyses. The HSP40 J domains and HSP70 ATPase domains were extracted using python scripts and classified according to the subcellular localization of the proteins using localization prediction programs. Motif analysis was carried out using the full length HSP40 proteins and Multiple Sequence Alignment (MSA) was performed to identify conserved residues that may contribute to the J domain – ATPase domain interactions. Phylogenetic inference of the proteins was also performed in order to study their evolutionary relationship. Homology models of the J domains and ATPase domains were generated. The corresponding models were docked using HADDOCK server in order to analyze possible putative interactions between the partner proteins using the Protein Interactions Calculator (PIC). The level of residue conservation was found to be higher in Type I and II HSP40 than in Type III J proteins. While highly conserved residues on helixes II and III could play critical roles in J domain interactions with corresponding HSP70s, conserved residues on helixes I and IV seemed to be significant in keeping the J domain in its right orientation for functional interactions with HSP70s. Our results also showed that helixes II and III formed the interaction interface for binding to HSP70 ATPase domain as well as the linker residues. Finally, data based docking procedures, such as applied in this study, could be an effective method to investigate protein-protein interactions complex of biomolecules.
- Full Text:
- Date Issued: 2014
- Authors: Adeyemi, Samson Adebowale
- Date: 2014
- Subjects: Structural bioinformatics , Molecular chaperones , Heat shock proteins , Protein-protein interactions , Biomolecules
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4171 , http://hdl.handle.net/10962/d1020962
- Description: HSP70 is one of the most important families of molecular chaperone that regulate the folding and transport of client proteins in an ATP dependent manner. The ATPase activity of HSP70 is stimulated through an interaction with its family of HSP40 co-chaperones. There is evidence to suggest that specific partnerships occur between the different HSP40 and HSP70 isoforms. While some of the residues involved in the interaction are known, many of the residues governing the specificity of HSP40-HSP70 partnerships are not precisely defined. It is not currently possible to predict which HSP40 and HSP70 isoforms will interact. We attempted to use bioinformatics to identify residues involved in the specificity of the interaction between the J domain from HSP40 and the ATPase domain from the HSP70 isoforms from humans. A total of 49 HSP40 and 13 HSP70 sequences from humans were retrieved and used for subsequent analyses. The HSP40 J domains and HSP70 ATPase domains were extracted using python scripts and classified according to the subcellular localization of the proteins using localization prediction programs. Motif analysis was carried out using the full length HSP40 proteins and Multiple Sequence Alignment (MSA) was performed to identify conserved residues that may contribute to the J domain – ATPase domain interactions. Phylogenetic inference of the proteins was also performed in order to study their evolutionary relationship. Homology models of the J domains and ATPase domains were generated. The corresponding models were docked using HADDOCK server in order to analyze possible putative interactions between the partner proteins using the Protein Interactions Calculator (PIC). The level of residue conservation was found to be higher in Type I and II HSP40 than in Type III J proteins. While highly conserved residues on helixes II and III could play critical roles in J domain interactions with corresponding HSP70s, conserved residues on helixes I and IV seemed to be significant in keeping the J domain in its right orientation for functional interactions with HSP70s. Our results also showed that helixes II and III formed the interaction interface for binding to HSP70 ATPase domain as well as the linker residues. Finally, data based docking procedures, such as applied in this study, could be an effective method to investigate protein-protein interactions complex of biomolecules.
- Full Text:
- Date Issued: 2014
Synthesis and characterization of NaYGdF4 upconversion nanoparticles and an investigation of their effects on the spectroscopic properties of two phthalocyanine dyes
- Authors: Taylor, Jessica Mary
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54621 , vital:26594
- Description: Sphere and star shaped NaYGdF4:Yb/Er(Tm) upconversion nanoparticles were successfully synthesized utilizing a methanol assisted thermal decomposition approach and their chemical, spectroscopic and fluorescence properties were fully characterized. In addition, their influence on the spectroscopic and fluorescence properties of two phthalocyanines (Pcs) (unsubstituted tetrathiophenoxy phthalocyanine (H2Pc) and aluminium octacarboxy phthalocyanine (Cl)AlOCPc) was investigated. Upconversion nanoparticles were found to produce characteristic upconversion fluorescence emissions in the blue, green, red and NIR regions and were also shown to possess paramagnetic properties. Simple mixing with an H2Pc in toluene was found to exert no change on the spectroscopic or fluorescence properties of the Pc while covalent conjugation to a (Cl)AlOCPc resulted in a large Q band blue shift accompanied by a decrease in fluorescence lifetimes in DMSO. The red light excitation mediated singlet oxygen generation of the H2Pc mixed with upconversion nanoparticles was investigated and singlet oxygen fluorescence lifetimes were found to decrease in the presence of the nanoparticles. Upconversion mediated singlet oxygen generation, by way of resonance energy transfer to the Pc, was also attempted using 972 nm excitation; however, no singlet oxygen was detected utilizing singlet oxygen NIR emission detection. Pending further work using alternative singlet oxygen detection methods, this suggests that while upconversion nanoparticles possess excellent fluorescent imaging capabilities, they are relatively inefficient in inducing singlet oxygen production simply when mixed with phthalocyanines. Despite this, by combining phthalocyanines and upconversion nanoparticles, we present a system capable of: multimodal imaging, using both upconversion and phthalocyanines emissions, singlet oxygen generation, via direct excitation of the phthalocyanine with red laser light, and, possibly, magnetic resonance imaging, as a result of doping the upconversion nanoparticles with Gd3+ ions.
- Full Text:
- Date Issued: 2014
- Authors: Taylor, Jessica Mary
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54621 , vital:26594
- Description: Sphere and star shaped NaYGdF4:Yb/Er(Tm) upconversion nanoparticles were successfully synthesized utilizing a methanol assisted thermal decomposition approach and their chemical, spectroscopic and fluorescence properties were fully characterized. In addition, their influence on the spectroscopic and fluorescence properties of two phthalocyanines (Pcs) (unsubstituted tetrathiophenoxy phthalocyanine (H2Pc) and aluminium octacarboxy phthalocyanine (Cl)AlOCPc) was investigated. Upconversion nanoparticles were found to produce characteristic upconversion fluorescence emissions in the blue, green, red and NIR regions and were also shown to possess paramagnetic properties. Simple mixing with an H2Pc in toluene was found to exert no change on the spectroscopic or fluorescence properties of the Pc while covalent conjugation to a (Cl)AlOCPc resulted in a large Q band blue shift accompanied by a decrease in fluorescence lifetimes in DMSO. The red light excitation mediated singlet oxygen generation of the H2Pc mixed with upconversion nanoparticles was investigated and singlet oxygen fluorescence lifetimes were found to decrease in the presence of the nanoparticles. Upconversion mediated singlet oxygen generation, by way of resonance energy transfer to the Pc, was also attempted using 972 nm excitation; however, no singlet oxygen was detected utilizing singlet oxygen NIR emission detection. Pending further work using alternative singlet oxygen detection methods, this suggests that while upconversion nanoparticles possess excellent fluorescent imaging capabilities, they are relatively inefficient in inducing singlet oxygen production simply when mixed with phthalocyanines. Despite this, by combining phthalocyanines and upconversion nanoparticles, we present a system capable of: multimodal imaging, using both upconversion and phthalocyanines emissions, singlet oxygen generation, via direct excitation of the phthalocyanine with red laser light, and, possibly, magnetic resonance imaging, as a result of doping the upconversion nanoparticles with Gd3+ ions.
- Full Text:
- Date Issued: 2014