Phylogeography and epifauna of two intertidal seaweeds on the coast of South Africa
- Authors: Mmonwa, Lucas Kolobe
- Date: 2009
- Subjects: Phylogeography -- South Africa , Marine algae -- South Africa , Red algae -- South Africa , Gelidium -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5738 , http://hdl.handle.net/10962/d1005424 , Phylogeography -- South Africa , Marine algae -- South Africa , Red algae -- South Africa , Gelidium -- South Africa
- Description: Southern African biogeographic boundaries delimit the phylogeographic distribution of some coastal and estuarine invertebrates. This study investigated the impact of these boundaries on the phylogeographic distribution of two intertidal red seaweeds, Gelidium pristoides and Hypnea spicifera using the mitochondrial Cox2-3 spacer and the nuclear ITS1 regions. G. pristoides spores have short distance-dispersal, while long distance-dispersal is more likely in H. spicifera via spores and drifting fertile thallus fragments. Both markers revealed a south-western and south-eastern lineage within G. pristoides but the breaks between lineages do not coincide with any recognised biogeographic limits. The Cox2-3 spacer revealed a boundary between the two lineages at the Alexandria Coastal Dunefield (ACD) and ITS1 at the Gamtoos-Van Stadens Dunefields (GVD) which is approximately 80km west of the ACD. The minor difference between the two markers regarding location of the phylogeographic boundary is probably due to the dating differences between the two dunefields. The ACD as developed currently is superimposed on the ancient dunefields which formed during the Pleistocene, coinciding with the Cox2-3 spacer sequences divergence which dates back 500,000 - 580,000 years. The GVD formed during the Holocene (6,500 - 4,000 years ago), coinciding with the ITS1 sequences divergence which dates 4,224 - 4,928 years ago. Thus, these phylogeographic boundaries probably appeared without the influence of biogeographic boundaries, but rather due to the lack of suitable habitat in the dunefields, coupled with short dispersal-distances of the spores. Analysis of the ITS1 and Cox2-3 spacer regions in H. spicifera revealed that the species is characterized by uniform genetic structure along the coastline. This reflects the species`s potential for long range expansion as it inhabits both the intertidal and subtidal zones; and this presumably leads to high gene flow among populations. The ITS1 sequences showed minimal genetic variation of one substitution between the gametophyte and tetrasporophyte generations within H. spicifera. This suggests the predominance of asexual reproduction, which reduces gene flow and fixes alleles between generations. ANOSIM and Bray-Curtis cluster analyses showed scale-dependant variation in the abundances of epifauna (mainly amphipod, isopod, mollusc and polychaete species) on G. pristoides. At small local (within site) and large (among sites) scales, there were weak and no structure in epifaunal abundances respectively. However, at larger, biogeographic scales, samples from the same biogeographic region tended to be clustered together. Thus, there was a group containing predominantly south coast samples and a group containing east coast samples mixed with the remaining south coast samples. Such scale-dependant variation in epifaunal abundances is probably due to the effects of factors driving species richness at small local (within site) scales (e.g. wave exposure, seaweed biomass) and at larger, biogeographic scales (e.g. surface sea temperature). Moreover, at very small (individual samples) scales; there was no correlation between epifauna composition and genotype of the seaweed. Seaweed samples characterized by distinct ITS1 or Cox2-3 spacer sequences did not show any significant differences in epifaunal composition. Although the distributional pattern of the epifaunal community observed at large biogeographic scale is not clear, it seems to be associated with the biogeographic regions. However, phylogeographic distribution of Gelidium pristoides is not connected to biogeographic regions. Thus, at larger, biogeographic scales, there is no correlation between phylogeographic distribution of G. pristoides and distribution of the associated fauna
- Full Text:
- Date Issued: 2009
- Authors: Mmonwa, Lucas Kolobe
- Date: 2009
- Subjects: Phylogeography -- South Africa , Marine algae -- South Africa , Red algae -- South Africa , Gelidium -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5738 , http://hdl.handle.net/10962/d1005424 , Phylogeography -- South Africa , Marine algae -- South Africa , Red algae -- South Africa , Gelidium -- South Africa
- Description: Southern African biogeographic boundaries delimit the phylogeographic distribution of some coastal and estuarine invertebrates. This study investigated the impact of these boundaries on the phylogeographic distribution of two intertidal red seaweeds, Gelidium pristoides and Hypnea spicifera using the mitochondrial Cox2-3 spacer and the nuclear ITS1 regions. G. pristoides spores have short distance-dispersal, while long distance-dispersal is more likely in H. spicifera via spores and drifting fertile thallus fragments. Both markers revealed a south-western and south-eastern lineage within G. pristoides but the breaks between lineages do not coincide with any recognised biogeographic limits. The Cox2-3 spacer revealed a boundary between the two lineages at the Alexandria Coastal Dunefield (ACD) and ITS1 at the Gamtoos-Van Stadens Dunefields (GVD) which is approximately 80km west of the ACD. The minor difference between the two markers regarding location of the phylogeographic boundary is probably due to the dating differences between the two dunefields. The ACD as developed currently is superimposed on the ancient dunefields which formed during the Pleistocene, coinciding with the Cox2-3 spacer sequences divergence which dates back 500,000 - 580,000 years. The GVD formed during the Holocene (6,500 - 4,000 years ago), coinciding with the ITS1 sequences divergence which dates 4,224 - 4,928 years ago. Thus, these phylogeographic boundaries probably appeared without the influence of biogeographic boundaries, but rather due to the lack of suitable habitat in the dunefields, coupled with short dispersal-distances of the spores. Analysis of the ITS1 and Cox2-3 spacer regions in H. spicifera revealed that the species is characterized by uniform genetic structure along the coastline. This reflects the species`s potential for long range expansion as it inhabits both the intertidal and subtidal zones; and this presumably leads to high gene flow among populations. The ITS1 sequences showed minimal genetic variation of one substitution between the gametophyte and tetrasporophyte generations within H. spicifera. This suggests the predominance of asexual reproduction, which reduces gene flow and fixes alleles between generations. ANOSIM and Bray-Curtis cluster analyses showed scale-dependant variation in the abundances of epifauna (mainly amphipod, isopod, mollusc and polychaete species) on G. pristoides. At small local (within site) and large (among sites) scales, there were weak and no structure in epifaunal abundances respectively. However, at larger, biogeographic scales, samples from the same biogeographic region tended to be clustered together. Thus, there was a group containing predominantly south coast samples and a group containing east coast samples mixed with the remaining south coast samples. Such scale-dependant variation in epifaunal abundances is probably due to the effects of factors driving species richness at small local (within site) scales (e.g. wave exposure, seaweed biomass) and at larger, biogeographic scales (e.g. surface sea temperature). Moreover, at very small (individual samples) scales; there was no correlation between epifauna composition and genotype of the seaweed. Seaweed samples characterized by distinct ITS1 or Cox2-3 spacer sequences did not show any significant differences in epifaunal composition. Although the distributional pattern of the epifaunal community observed at large biogeographic scale is not clear, it seems to be associated with the biogeographic regions. However, phylogeographic distribution of Gelidium pristoides is not connected to biogeographic regions. Thus, at larger, biogeographic scales, there is no correlation between phylogeographic distribution of G. pristoides and distribution of the associated fauna
- Full Text:
- Date Issued: 2009
Polymers, catalysts and nanostructures a hybrid approach to biomolecule detection
- Authors: Frith, Kelly-Anne
- Date: 2009
- Subjects: Polymers , Nanostructured materials , Biomolecules , Tryptophan , Melatonin , Electrodes , Electrochemistry , Tryptophan oxygenase
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3980 , http://hdl.handle.net/10962/d1004039 , Polymers , Nanostructured materials , Biomolecules , Tryptophan , Melatonin , Electrodes , Electrochemistry , Tryptophan oxygenase
- Description: The main goals in electroanalytical sensing are towards improved sensitivity and selectivity, or specificity, of an analyte. There are several approaches to achieving these goals with the main approach being modification of an electrode surface with synthetic or natural catalysts (enzymes), polymers and also utilisation of nanostructured materials. At present, there is a strong movement towards hybrid sensing which couple different properties of two or more surface modification approaches. In this thesis, a range of these surface modifications were explored for analysis and detection of two main analytes: the amino acid, tryptophan (Trp); and, the neurotransmitter, dopamine (DA). Specifically, this thesis aimed to utilise these methods to enhance the sensitivity and selectivity for Trp over an interferent, the indoleamine, melatonin (Mel); and, DA over the vitamin, ascorbic acid (AA). For Trp detection, immobilisation of an enzyme, Tryptophanase (Trpase) resulted in poor selectivity for the analyte. However, enhanced sensitivity and selectivity was achieved through pH manipulation of the electrolyte medium at a Nafion®-modified electrode surface for both Trp and Mel. At pH 3.0, the Mel and Trp anodic peak potentials were sufficiently resolved allowing for an LOD of 1.60 and 1.62 nM,respectively, and permitting the accurate analysis of Trp in a dietary supplement containing Mel. Multi-walled carbon nanotubes (MWCNTs) suspended in Nafion® exhibited further increases in the signal responses of these analytes at pH 3.0 and 7.4 with minimal change in the resolution of the anodic peaks. A lower sensitivity was, therefore, observed at the Nafion® and MWCNT modified electrode compared to the Nafion®-modified electrode at pH 3.0 with LODs of 0.59 and 0.80 nM exhibited for Trp and Mel, respectively. Enhanced selectivity for Trp in the presence of Mel can be achieved with MWCNTs in the presence of metallotetrasulphonated phthalocyanines (MTSPcs) particularly at pH 3.0, owing to cation exchange effects. However, the lack of sensitivity towards Trp, and even Mel, at this CoTSPc and MWCNT modified electrode remains a drawback. For DA, detection at the MWCNT and Nafion® surface resulted in improved sensitivity over that of both the bare electrode (613.0 nM) and the Nafion® modified electrode (1045.1 nM) with a calculated LOD of 133.9 nM at this layer. Furthermore, improvements in the selectivity of DA were achieved at the Nafion® and MWCNT modified electrode as exclusion of AA (150 μM) was achieved. At the MWCNT and CoTSPc surface, AA was excluded up to 130 μM with sensitivity for DA extending as low as 14.3 nM, far greater than observed for Trp and Mel. These concentrations are well within physiological concentration ranges and represent the most significant solution yet in terms of AA exclusion and enhanced sensitivity for DA. An examination of the surface layering by impedance spectroscopy and atomic force microscopy indicates that the success of the hybrid sensor utilising CoTSPc and MWCNTs lay in improved dispersion of MWCNTs and improved electron transfer kinetics, facilitated by the net charge of the materials present. This thesis, thus, showed the utility of a judicious selection of synthetic and biological catalysts, polymers and carbon nanomaterials towards a hybrid approach to the electrochemical sensing of Trp, Mel, DA and AA with focus on sensitivity and selectivity of these analytes.
- Full Text:
- Date Issued: 2009
- Authors: Frith, Kelly-Anne
- Date: 2009
- Subjects: Polymers , Nanostructured materials , Biomolecules , Tryptophan , Melatonin , Electrodes , Electrochemistry , Tryptophan oxygenase
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3980 , http://hdl.handle.net/10962/d1004039 , Polymers , Nanostructured materials , Biomolecules , Tryptophan , Melatonin , Electrodes , Electrochemistry , Tryptophan oxygenase
- Description: The main goals in electroanalytical sensing are towards improved sensitivity and selectivity, or specificity, of an analyte. There are several approaches to achieving these goals with the main approach being modification of an electrode surface with synthetic or natural catalysts (enzymes), polymers and also utilisation of nanostructured materials. At present, there is a strong movement towards hybrid sensing which couple different properties of two or more surface modification approaches. In this thesis, a range of these surface modifications were explored for analysis and detection of two main analytes: the amino acid, tryptophan (Trp); and, the neurotransmitter, dopamine (DA). Specifically, this thesis aimed to utilise these methods to enhance the sensitivity and selectivity for Trp over an interferent, the indoleamine, melatonin (Mel); and, DA over the vitamin, ascorbic acid (AA). For Trp detection, immobilisation of an enzyme, Tryptophanase (Trpase) resulted in poor selectivity for the analyte. However, enhanced sensitivity and selectivity was achieved through pH manipulation of the electrolyte medium at a Nafion®-modified electrode surface for both Trp and Mel. At pH 3.0, the Mel and Trp anodic peak potentials were sufficiently resolved allowing for an LOD of 1.60 and 1.62 nM,respectively, and permitting the accurate analysis of Trp in a dietary supplement containing Mel. Multi-walled carbon nanotubes (MWCNTs) suspended in Nafion® exhibited further increases in the signal responses of these analytes at pH 3.0 and 7.4 with minimal change in the resolution of the anodic peaks. A lower sensitivity was, therefore, observed at the Nafion® and MWCNT modified electrode compared to the Nafion®-modified electrode at pH 3.0 with LODs of 0.59 and 0.80 nM exhibited for Trp and Mel, respectively. Enhanced selectivity for Trp in the presence of Mel can be achieved with MWCNTs in the presence of metallotetrasulphonated phthalocyanines (MTSPcs) particularly at pH 3.0, owing to cation exchange effects. However, the lack of sensitivity towards Trp, and even Mel, at this CoTSPc and MWCNT modified electrode remains a drawback. For DA, detection at the MWCNT and Nafion® surface resulted in improved sensitivity over that of both the bare electrode (613.0 nM) and the Nafion® modified electrode (1045.1 nM) with a calculated LOD of 133.9 nM at this layer. Furthermore, improvements in the selectivity of DA were achieved at the Nafion® and MWCNT modified electrode as exclusion of AA (150 μM) was achieved. At the MWCNT and CoTSPc surface, AA was excluded up to 130 μM with sensitivity for DA extending as low as 14.3 nM, far greater than observed for Trp and Mel. These concentrations are well within physiological concentration ranges and represent the most significant solution yet in terms of AA exclusion and enhanced sensitivity for DA. An examination of the surface layering by impedance spectroscopy and atomic force microscopy indicates that the success of the hybrid sensor utilising CoTSPc and MWCNTs lay in improved dispersion of MWCNTs and improved electron transfer kinetics, facilitated by the net charge of the materials present. This thesis, thus, showed the utility of a judicious selection of synthetic and biological catalysts, polymers and carbon nanomaterials towards a hybrid approach to the electrochemical sensing of Trp, Mel, DA and AA with focus on sensitivity and selectivity of these analytes.
- Full Text:
- Date Issued: 2009
Predictability of Geomagnetically Induced Currents using neural networks
- Authors: Lotz, Stefan
- Date: 2009
- Subjects: Advanced Composition Explorer (Artificial satellite) , Geomagnetism , Electromagnetic induction , Neural networks (Computer science) , Artificial intelligence
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5483 , http://hdl.handle.net/10962/d1005269 , Advanced Composition Explorer (Artificial satellite) , Geomagnetism , Electromagnetic induction , Neural networks (Computer science) , Artificial intelligence
- Description: It is a well documented fact that Geomagnetically Induced Currents (GIC’s) poses a significant threat to ground-based electric conductor networks like oil pipelines, railways and powerline networks. A study is undertaken to determine the feasibility of using artificial neural network models to predict GIC occurrence in the Southern African power grid. The magnitude of an induced current at a specific location on the Earth’s surface is directly related to the temporal derivative of the geomagnetic field (specifically its horizontal components) at that point. Hence, the focus of the problem is on the prediction of the temporal variations in the horizontal geomagnetic field (@Bx/@t and @By/@t). Artificial neural networks are used to predict @Bx/@t and @By/@t measured at Hermanus, South Africa (34.27◦ S, 19.12◦ E) with a 30 minute prediction lead time. As input parameters to the neural networks, insitu solar wind measurements made by the Advanced Composition Explorer (ACE) satellite are used. The results presented here compare well with similar models developed at high-latitude locations (e.g. Sweden, Finland, Canada) where extensive GIC research has been undertaken. It is concluded that it would indeed be feasible to use a neural network model to predict GIC occurrence in the Southern African power grid, provided that GIC measurements, powerline configuration and network parameters are made available.
- Full Text:
- Date Issued: 2009
- Authors: Lotz, Stefan
- Date: 2009
- Subjects: Advanced Composition Explorer (Artificial satellite) , Geomagnetism , Electromagnetic induction , Neural networks (Computer science) , Artificial intelligence
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5483 , http://hdl.handle.net/10962/d1005269 , Advanced Composition Explorer (Artificial satellite) , Geomagnetism , Electromagnetic induction , Neural networks (Computer science) , Artificial intelligence
- Description: It is a well documented fact that Geomagnetically Induced Currents (GIC’s) poses a significant threat to ground-based electric conductor networks like oil pipelines, railways and powerline networks. A study is undertaken to determine the feasibility of using artificial neural network models to predict GIC occurrence in the Southern African power grid. The magnitude of an induced current at a specific location on the Earth’s surface is directly related to the temporal derivative of the geomagnetic field (specifically its horizontal components) at that point. Hence, the focus of the problem is on the prediction of the temporal variations in the horizontal geomagnetic field (@Bx/@t and @By/@t). Artificial neural networks are used to predict @Bx/@t and @By/@t measured at Hermanus, South Africa (34.27◦ S, 19.12◦ E) with a 30 minute prediction lead time. As input parameters to the neural networks, insitu solar wind measurements made by the Advanced Composition Explorer (ACE) satellite are used. The results presented here compare well with similar models developed at high-latitude locations (e.g. Sweden, Finland, Canada) where extensive GIC research has been undertaken. It is concluded that it would indeed be feasible to use a neural network model to predict GIC occurrence in the Southern African power grid, provided that GIC measurements, powerline configuration and network parameters are made available.
- Full Text:
- Date Issued: 2009
Production of biologically active recombinant HIV-1 protease and intehrase for the purpose of screening medicianl plant extracts
- Authors: Bosch, Janine
- Date: 2009
- Subjects: Medicinal plants -- South Africa , HIV infections -- Alternative treatment -- South Africa , Materia medica, Vegetable -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10325 , http://hdl.handle.net/10948/1056 , Medicinal plants -- South Africa , HIV infections -- Alternative treatment -- South Africa , Materia medica, Vegetable -- South Africa
- Description: Human immunodeficiency virus (HIV) and its gradual weakening of the immune system is an ever growing threat. Acquired immune deficiency syndrome (AIDS), the final stage of HIV, renders a person vulnerable to various opportunistic infections, which in the end lead to death. Apart from intensive vaccine studies, treatment research mainly focuses on preventing the individual HIV enzymes (reverse transcriptase, integrase and protease) from performing their functions. Entry inhibitors, however, block viral entry into the cell, while antisense drugs lock onto the viral genome to keep it from functioning. In this study production of active recombinant HIV-1 protease and integrase was attempted for future drug screening programs. HIV-1 protease was cloned into a pET28b(+) vector and expressed in ROSETTA(DE3)pLysS cells. The protein was purified using a nickel-affinity column utilizing the hexa-histidine tag encoded by the vector. Gel filtration chromatography was attempted after refolding of the protease, but protease yield seemed to decrease with the additional purification step. Partially purified protease was characterized with kinetic studies. Kinetic parameters of HIV-1 protease were determined to be Km = 592 μM, Vmax = 0.59 μM/min and kcat = 31 s-1. HIV-1 integrase, which was cloned into a pET15b vector, was expressed in E. coli BL21(DE3) cells. The coding sequence had been mutated to introduce the amino acid substitutions F185K and C280S, increasing solubility of the protein. The first step in purification of this protein was nickel-affinity chromatography, after which cation exchange chromatography was attempted. HIV-1 integrase concentration was low throughout experiments and no clear elution from the cation exchange column could be observed. A non-radioactive enzyme linked HIV-1 integrase assay failed to detect integrase activity. Modifications to future studies of the integrase are suggested in the chapter involved.
- Full Text:
- Date Issued: 2009
- Authors: Bosch, Janine
- Date: 2009
- Subjects: Medicinal plants -- South Africa , HIV infections -- Alternative treatment -- South Africa , Materia medica, Vegetable -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10325 , http://hdl.handle.net/10948/1056 , Medicinal plants -- South Africa , HIV infections -- Alternative treatment -- South Africa , Materia medica, Vegetable -- South Africa
- Description: Human immunodeficiency virus (HIV) and its gradual weakening of the immune system is an ever growing threat. Acquired immune deficiency syndrome (AIDS), the final stage of HIV, renders a person vulnerable to various opportunistic infections, which in the end lead to death. Apart from intensive vaccine studies, treatment research mainly focuses on preventing the individual HIV enzymes (reverse transcriptase, integrase and protease) from performing their functions. Entry inhibitors, however, block viral entry into the cell, while antisense drugs lock onto the viral genome to keep it from functioning. In this study production of active recombinant HIV-1 protease and integrase was attempted for future drug screening programs. HIV-1 protease was cloned into a pET28b(+) vector and expressed in ROSETTA(DE3)pLysS cells. The protein was purified using a nickel-affinity column utilizing the hexa-histidine tag encoded by the vector. Gel filtration chromatography was attempted after refolding of the protease, but protease yield seemed to decrease with the additional purification step. Partially purified protease was characterized with kinetic studies. Kinetic parameters of HIV-1 protease were determined to be Km = 592 μM, Vmax = 0.59 μM/min and kcat = 31 s-1. HIV-1 integrase, which was cloned into a pET15b vector, was expressed in E. coli BL21(DE3) cells. The coding sequence had been mutated to introduce the amino acid substitutions F185K and C280S, increasing solubility of the protein. The first step in purification of this protein was nickel-affinity chromatography, after which cation exchange chromatography was attempted. HIV-1 integrase concentration was low throughout experiments and no clear elution from the cation exchange column could be observed. A non-radioactive enzyme linked HIV-1 integrase assay failed to detect integrase activity. Modifications to future studies of the integrase are suggested in the chapter involved.
- Full Text:
- Date Issued: 2009
Protein secondary structure prediction using neural networks and support vector machines
- Authors: Tsilo, Lipontseng Cecilia
- Date: 2009
- Subjects: Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5569 , http://hdl.handle.net/10962/d1002809 , Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Description: Predicting the secondary structure of proteins is important in biochemistry because the 3D structure can be determined from the local folds that are found in secondary structures. Moreover, knowing the tertiary structure of proteins can assist in determining their functions. The objective of this thesis is to compare the performance of Neural Networks (NN) and Support Vector Machines (SVM) in predicting the secondary structure of 62 globular proteins from their primary sequence. For each NN and SVM, we created six binary classifiers to distinguish between the classes’ helices (H) strand (E), and coil (C). For NN we use Resilient Backpropagation training with and without early stopping. We use NN with either no hidden layer or with one hidden layer with 1,2,...,40 hidden neurons. For SVM we use a Gaussian kernel with parameter fixed at = 0.1 and varying cost parameters C in the range [0.1,5]. 10- fold cross-validation is used to obtain overall estimates for the probability of making a correct prediction. Our experiments indicate for NN and SVM that the different binary classifiers have varying accuracies: from 69% correct predictions for coils vs. non-coil up to 80% correct predictions for stand vs. non-strand. It is further demonstrated that NN with no hidden layer or not more than 2 hidden neurons in the hidden layer are sufficient for better predictions. For SVM we show that the estimated accuracies do not depend on the value of the cost parameter. As a major result, we will demonstrate that the accuracy estimates of NN and SVM binary classifiers cannot distinguish. This contradicts a modern belief in bioinformatics that SVM outperforms other predictors.
- Full Text:
- Date Issued: 2009
- Authors: Tsilo, Lipontseng Cecilia
- Date: 2009
- Subjects: Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5569 , http://hdl.handle.net/10962/d1002809 , Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Description: Predicting the secondary structure of proteins is important in biochemistry because the 3D structure can be determined from the local folds that are found in secondary structures. Moreover, knowing the tertiary structure of proteins can assist in determining their functions. The objective of this thesis is to compare the performance of Neural Networks (NN) and Support Vector Machines (SVM) in predicting the secondary structure of 62 globular proteins from their primary sequence. For each NN and SVM, we created six binary classifiers to distinguish between the classes’ helices (H) strand (E), and coil (C). For NN we use Resilient Backpropagation training with and without early stopping. We use NN with either no hidden layer or with one hidden layer with 1,2,...,40 hidden neurons. For SVM we use a Gaussian kernel with parameter fixed at = 0.1 and varying cost parameters C in the range [0.1,5]. 10- fold cross-validation is used to obtain overall estimates for the probability of making a correct prediction. Our experiments indicate for NN and SVM that the different binary classifiers have varying accuracies: from 69% correct predictions for coils vs. non-coil up to 80% correct predictions for stand vs. non-strand. It is further demonstrated that NN with no hidden layer or not more than 2 hidden neurons in the hidden layer are sufficient for better predictions. For SVM we show that the estimated accuracies do not depend on the value of the cost parameter. As a major result, we will demonstrate that the accuracy estimates of NN and SVM binary classifiers cannot distinguish. This contradicts a modern belief in bioinformatics that SVM outperforms other predictors.
- Full Text:
- Date Issued: 2009
Purification and characterization of fructosyltransferase for the synthesis of short-chain fructo-oligosaccharides and investigation into thier anti-carcinogenic properties
- Authors: Nemukula, Aluwani
- Date: 2009
- Subjects: Oligosaccharides , Polygalacturonase , Aspergillus , Fructose , Inulin , Cancer -- Prevention , Cancer -- Research , Carcinogens , High performance liquid chromatography
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3927 , http://hdl.handle.net/10962/d1003986 , Oligosaccharides , Polygalacturonase , Aspergillus , Fructose , Inulin , Cancer -- Prevention , Cancer -- Research , Carcinogens , High performance liquid chromatography
- Description: There is a growing attention in the synthesis of fructo-oligosaccharides (FOS) due to their excellent bio-functional and health-promoting properties. The current production processes are limited to chemical hydrolysis reactions of plant extracts, which are often associated with several drawbacks. In this study, fructosyltransferase (FTase) and polygalacturonase (PGase) activities, present in a commercial enzyme preparation (Pectinex® Ultra SP-L) sourced from Aspergillus aculeatus, have been separated and fully purified by anion-exchange and sizeexclusion chromatography. The FTase possesses fructosyl transfer activity for FOS synthesis and the PGase has pectin hydrolytic activity. Fructosyltransferase is a single-band protein with a molecular weight of 85 kDa, whereas PGase is a distinct protein of 40 kDa. The temperature and pH optima of FTase were 60 ºC and 6.0, with a half-life of 8 h; while that for PGase were 40 ºC and 6.0, respectively. FTase was slightly inhibited in the presence of Ni²⁺, Mg²⁺ and urea; but PGase was more susceptible to divalent ions such as Ca²⁺, Mg²⁺ and Mn²⁺. The kinetic parameters (Km and Vmax) of FTase for the hydrolysis of β-(2→1) linkages from sucrose were 752.3 mM and 120.5 μmol.min⁻¹.mL⁻¹, respectively; whereas the same parameters for pectin hydrolysis by PGase were 13.0 mg.mL⁻¹ and 263 μmol.min-1.mL⁻¹, respectively. The purified FTase was able to transfer fructosyl residues from sucrose, synthesizing the corresponding chains of FOS. PGase was relatively stable at 40 ºC (t½ > 3 h), depolymerizing the pectin backbone while releasing the inulins from within the chicory roots. Analysis of various mixtures of FOS by mass spectrometry, HPLC and ¹H-NMR was undertaken. Results indicated that MS with electrospray ionization and ¹H-NMR are capable of providing relative quantitative data of the FOS present in the mixtures. The pharmaceutical effects of various sc-FOS (0.5%, v/v) and SCFA (0.3%, v/v) on certain bacterial enzymes (β-glucuronidase, urease and β-glucosidase) associated with the formation of carcinogens were also studied. These enzyme activities were not directly influenced by the sc-FOS, but were found to be remarkably decreased by SCFA, pointing toward the prebiotic effect of FOS in intestinal microflora modulation.
- Full Text:
- Date Issued: 2009
- Authors: Nemukula, Aluwani
- Date: 2009
- Subjects: Oligosaccharides , Polygalacturonase , Aspergillus , Fructose , Inulin , Cancer -- Prevention , Cancer -- Research , Carcinogens , High performance liquid chromatography
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3927 , http://hdl.handle.net/10962/d1003986 , Oligosaccharides , Polygalacturonase , Aspergillus , Fructose , Inulin , Cancer -- Prevention , Cancer -- Research , Carcinogens , High performance liquid chromatography
- Description: There is a growing attention in the synthesis of fructo-oligosaccharides (FOS) due to their excellent bio-functional and health-promoting properties. The current production processes are limited to chemical hydrolysis reactions of plant extracts, which are often associated with several drawbacks. In this study, fructosyltransferase (FTase) and polygalacturonase (PGase) activities, present in a commercial enzyme preparation (Pectinex® Ultra SP-L) sourced from Aspergillus aculeatus, have been separated and fully purified by anion-exchange and sizeexclusion chromatography. The FTase possesses fructosyl transfer activity for FOS synthesis and the PGase has pectin hydrolytic activity. Fructosyltransferase is a single-band protein with a molecular weight of 85 kDa, whereas PGase is a distinct protein of 40 kDa. The temperature and pH optima of FTase were 60 ºC and 6.0, with a half-life of 8 h; while that for PGase were 40 ºC and 6.0, respectively. FTase was slightly inhibited in the presence of Ni²⁺, Mg²⁺ and urea; but PGase was more susceptible to divalent ions such as Ca²⁺, Mg²⁺ and Mn²⁺. The kinetic parameters (Km and Vmax) of FTase for the hydrolysis of β-(2→1) linkages from sucrose were 752.3 mM and 120.5 μmol.min⁻¹.mL⁻¹, respectively; whereas the same parameters for pectin hydrolysis by PGase were 13.0 mg.mL⁻¹ and 263 μmol.min-1.mL⁻¹, respectively. The purified FTase was able to transfer fructosyl residues from sucrose, synthesizing the corresponding chains of FOS. PGase was relatively stable at 40 ºC (t½ > 3 h), depolymerizing the pectin backbone while releasing the inulins from within the chicory roots. Analysis of various mixtures of FOS by mass spectrometry, HPLC and ¹H-NMR was undertaken. Results indicated that MS with electrospray ionization and ¹H-NMR are capable of providing relative quantitative data of the FOS present in the mixtures. The pharmaceutical effects of various sc-FOS (0.5%, v/v) and SCFA (0.3%, v/v) on certain bacterial enzymes (β-glucuronidase, urease and β-glucosidase) associated with the formation of carcinogens were also studied. These enzyme activities were not directly influenced by the sc-FOS, but were found to be remarkably decreased by SCFA, pointing toward the prebiotic effect of FOS in intestinal microflora modulation.
- Full Text:
- Date Issued: 2009
Purification and characterization of serine proteinase inhibitors from two South African indigenous plants, Acacia karoo and Acacia schweinfurthii
- Authors: Odei-Addo, Frank
- Date: 2009
- Subjects: Proteinase -- Inhibitors
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10319 , http://hdl.handle.net/10948/1291 , Proteinase -- Inhibitors
- Description: Serine proteases are known to perform a wide range of functions essential to life; however there has to be some form of control mechanism in place. One of the many control mechanisms is their specific inhibition by protein proteinase inhibitors. Proteinase inhibitors in plants, present in their seeds, participate in defense mechanisms and their production is induced by herbivory or wounding. Plant proteinase inhibitors have been reported to inhibit a variety of serine proteinases, including enzymes of the blood coagulation cascade. In this study, various indigenous seed extracts were screened for potential serine proteinase inhibition. Acacia schweinfurthii was selected as a potential inhibitor that inhibited trypsin and factor X. The AS inhibitor was successfully purified to homogeneity by precipitating with 80 percent (v/v) acetone and the sequential chromatographic steps including ion-exchange chromatography, size exclusion chromatography, affinity purification on a trypsin-agarose column and RP-HPLC. Reducing SDS-PAGE conditions revealed an inhibitor of two polypeptide chains A and B of approximate molecular weights 16 and 10 kDa, respectively, and under non-reducing conditions, 25 kDa was observed. The inhibitor was shown to inhibit trypsin, chymotrypsin and factor X indicating the dynamic nature of the reactive site. An enzyme: inhibitor ratio of 1:1, and a Ki of 3.45nM was determined for the AS inhibitor on trypsin, and the inhibitor also weakly inhibit chymotrypsin. AS inhibitor and STI inhibited factor X with a Ki values of 13.7nM and 77.5μM respectively. Amino acid analysis revealed Mmin values of the A- and B- chain of 15,000 and 7,800, respectively. The effect of seed extracts on the activated partial thrombin time (APTT) and prothrombin time (PT) was tested. No prolongation of the PT was obtained. For the crude extracts of AK and AS, IC200 values of 4.6 and 189.62 μg/mL, were respectively obtained. For the purified fractions of STI, AS and AK, IC200 values of 51.5, 114.31 and 893.8 μg/ml were observed, respectively. Keywords: proteinase inhibitors, Acacia species, trypsin inhibitor, FX inhibitor.
- Full Text:
- Date Issued: 2009
- Authors: Odei-Addo, Frank
- Date: 2009
- Subjects: Proteinase -- Inhibitors
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10319 , http://hdl.handle.net/10948/1291 , Proteinase -- Inhibitors
- Description: Serine proteases are known to perform a wide range of functions essential to life; however there has to be some form of control mechanism in place. One of the many control mechanisms is their specific inhibition by protein proteinase inhibitors. Proteinase inhibitors in plants, present in their seeds, participate in defense mechanisms and their production is induced by herbivory or wounding. Plant proteinase inhibitors have been reported to inhibit a variety of serine proteinases, including enzymes of the blood coagulation cascade. In this study, various indigenous seed extracts were screened for potential serine proteinase inhibition. Acacia schweinfurthii was selected as a potential inhibitor that inhibited trypsin and factor X. The AS inhibitor was successfully purified to homogeneity by precipitating with 80 percent (v/v) acetone and the sequential chromatographic steps including ion-exchange chromatography, size exclusion chromatography, affinity purification on a trypsin-agarose column and RP-HPLC. Reducing SDS-PAGE conditions revealed an inhibitor of two polypeptide chains A and B of approximate molecular weights 16 and 10 kDa, respectively, and under non-reducing conditions, 25 kDa was observed. The inhibitor was shown to inhibit trypsin, chymotrypsin and factor X indicating the dynamic nature of the reactive site. An enzyme: inhibitor ratio of 1:1, and a Ki of 3.45nM was determined for the AS inhibitor on trypsin, and the inhibitor also weakly inhibit chymotrypsin. AS inhibitor and STI inhibited factor X with a Ki values of 13.7nM and 77.5μM respectively. Amino acid analysis revealed Mmin values of the A- and B- chain of 15,000 and 7,800, respectively. The effect of seed extracts on the activated partial thrombin time (APTT) and prothrombin time (PT) was tested. No prolongation of the PT was obtained. For the crude extracts of AK and AS, IC200 values of 4.6 and 189.62 μg/mL, were respectively obtained. For the purified fractions of STI, AS and AK, IC200 values of 51.5, 114.31 and 893.8 μg/ml were observed, respectively. Keywords: proteinase inhibitors, Acacia species, trypsin inhibitor, FX inhibitor.
- Full Text:
- Date Issued: 2009
Purification and partial characterisation of cathepsin D from ostrich skeletal muscle, and its activity during meat maturation
- Authors: Krause, Jason
- Date: 2009
- Subjects: Proteolytic enzymes , Ostrich products industry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10313 , http://hdl.handle.net/10948/1461 , Proteolytic enzymes , Ostrich products industry
- Description: Cathepsin D, a muscle proteinase, participates in lysosomally mediated protein degradation in vivo. This enzyme has been proposed to play a significant role in the postmortem proteolysis process apparently associated with tenderisation. The lack of data on the postmortem characteristics of ostrich meat, especially on the ageing process and its influence on meat tenderness, called for an investigation into this process. There is no data available for purified ostrich cathepsin D, and the aim of this study was, therefore, to isolate, purify and characterise cathepsin D from ostrich skeletal muscle and subsequently investigate the possible role that it may have in the tenderisation process of meat. Cathepsin D was successfully isolated and purified from ostrich skeletal muscle using pepstatin A-agarose chromatography. The purified enzyme was composed of two subunits (14 and 29kDa). The amino acid composition as well as the N-terminal amino acid sequence of both subunits were determined. Kinetic parameters (Km and Vm), thermodynamic parameters (Ea, ∆H, ∆S and ∆G) and functional characteristics (effect of pH, temperature and various inhibitors on cathepsin D activity) were determined and are reported in this study. Ostrich muscle cathepsin D showed a pH optimum of 4 and a temperature optimum of 45°C. The activity of cathepsin D was strongly inhibited by pepstatin A and DTT. Purified ostrich cathepsin D displayed kinetic and functional properties similar to previously reported values from various species. The effect of storage on the activity of cathepsin D was investigated over a 30 day period. It was established that substantial postmortem cathepsin D activity remained throughout the storage period, to implicate cathepsin D, fulfilling a possible role in meat maturation.
- Full Text:
- Date Issued: 2009
- Authors: Krause, Jason
- Date: 2009
- Subjects: Proteolytic enzymes , Ostrich products industry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10313 , http://hdl.handle.net/10948/1461 , Proteolytic enzymes , Ostrich products industry
- Description: Cathepsin D, a muscle proteinase, participates in lysosomally mediated protein degradation in vivo. This enzyme has been proposed to play a significant role in the postmortem proteolysis process apparently associated with tenderisation. The lack of data on the postmortem characteristics of ostrich meat, especially on the ageing process and its influence on meat tenderness, called for an investigation into this process. There is no data available for purified ostrich cathepsin D, and the aim of this study was, therefore, to isolate, purify and characterise cathepsin D from ostrich skeletal muscle and subsequently investigate the possible role that it may have in the tenderisation process of meat. Cathepsin D was successfully isolated and purified from ostrich skeletal muscle using pepstatin A-agarose chromatography. The purified enzyme was composed of two subunits (14 and 29kDa). The amino acid composition as well as the N-terminal amino acid sequence of both subunits were determined. Kinetic parameters (Km and Vm), thermodynamic parameters (Ea, ∆H, ∆S and ∆G) and functional characteristics (effect of pH, temperature and various inhibitors on cathepsin D activity) were determined and are reported in this study. Ostrich muscle cathepsin D showed a pH optimum of 4 and a temperature optimum of 45°C. The activity of cathepsin D was strongly inhibited by pepstatin A and DTT. Purified ostrich cathepsin D displayed kinetic and functional properties similar to previously reported values from various species. The effect of storage on the activity of cathepsin D was investigated over a 30 day period. It was established that substantial postmortem cathepsin D activity remained throughout the storage period, to implicate cathepsin D, fulfilling a possible role in meat maturation.
- Full Text:
- Date Issued: 2009
Raman spectroscopy of ternary III-V semiconducting films
- Authors: Mashigo, Donald
- Date: 2009
- Subjects: Raman spectroscopy , Semiconductor films , Compound semiconductors
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10522 , http://hdl.handle.net/10948/1011 , Raman spectroscopy , Semiconductor films , Compound semiconductors
- Description: The III-V semiconductor compounds (i.e. In Ga As x 1-x , 1 x x InAs Sb - , In Ga Sb x 1-x and Al Ga As x 1-x ) have been studied using room temperature Raman spectroscopy. X-ray diffraction has been used as a complementary characterization technique. In this study all the III-V semiconductor compounds were grown by metal organic chemical vapour deposition (MOCVD) on GaAs and GaSb substrates. The layers were studied with respect to composition, strain variation and critical thickness. Raman spectroscopy has been employed to assess the composition dependence of optical phonons in the layers. The alloy composition was varied, while the thickness was kept constant in order to investigate compositional effects. A significant frequency shift of the phonon modes were observed as the composition changed. The composition dependence of the phonon frequencies were described by linear and polynomial expressions. The results of this study were compared with previous Raman and infrared work on III-V semiconductor compounds. Strain relaxation in InGaAs and InGaSb has been investigated by Raman and X-ray diffraction. Measurements were performed on several series of layers. For each series, the thickness was varied, while keeping the composition constant. For a given composition, the layer thicknesses were such that some layers should be fully strained, some partially relaxed and some fully relaxed. The Raman peak shifts and XRD confirm that a layer grows up to the critical thickness and then releases the strain as the thickness increases. Critical layer thickness values measured in this study were compared with published data, in which various techniques had been used to estimate the critical thickness.
- Full Text:
- Date Issued: 2009
- Authors: Mashigo, Donald
- Date: 2009
- Subjects: Raman spectroscopy , Semiconductor films , Compound semiconductors
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10522 , http://hdl.handle.net/10948/1011 , Raman spectroscopy , Semiconductor films , Compound semiconductors
- Description: The III-V semiconductor compounds (i.e. In Ga As x 1-x , 1 x x InAs Sb - , In Ga Sb x 1-x and Al Ga As x 1-x ) have been studied using room temperature Raman spectroscopy. X-ray diffraction has been used as a complementary characterization technique. In this study all the III-V semiconductor compounds were grown by metal organic chemical vapour deposition (MOCVD) on GaAs and GaSb substrates. The layers were studied with respect to composition, strain variation and critical thickness. Raman spectroscopy has been employed to assess the composition dependence of optical phonons in the layers. The alloy composition was varied, while the thickness was kept constant in order to investigate compositional effects. A significant frequency shift of the phonon modes were observed as the composition changed. The composition dependence of the phonon frequencies were described by linear and polynomial expressions. The results of this study were compared with previous Raman and infrared work on III-V semiconductor compounds. Strain relaxation in InGaAs and InGaSb has been investigated by Raman and X-ray diffraction. Measurements were performed on several series of layers. For each series, the thickness was varied, while keeping the composition constant. For a given composition, the layer thicknesses were such that some layers should be fully strained, some partially relaxed and some fully relaxed. The Raman peak shifts and XRD confirm that a layer grows up to the critical thickness and then releases the strain as the thickness increases. Critical layer thickness values measured in this study were compared with published data, in which various techniques had been used to estimate the critical thickness.
- Full Text:
- Date Issued: 2009
Reeds as indicators of nutrient enrichment in the East Kleinemonde Estuary
- Authors: Human, Lucienne Ryno Daniel
- Date: 2009
- Subjects: Estuaries -- South Africa -- Eastern Cape -- East Kleinemonde Estuary , Nutrient cycles -- South Africa -- Eastern Cape -- East Kleinemonde Estuary
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10615 , http://hdl.handle.net/10948/1252 , Estuaries -- South Africa -- Eastern Cape -- East Kleinemonde Estuary , Nutrient cycles -- South Africa -- Eastern Cape -- East Kleinemonde Estuary
- Description: The release of nutrients (nitrogen and phosphorus) via land clearing, application of fertilisers, discharge of human waste and combustion of fossil fuels, is one of the most harmful effects of anthropogenic stresses on aquatic environments. This study investigated the use of reeds as indicators of nutrient input to estuaries. Small estuaries such as the oligotrophic East Kleinemonde where the research was mostly conducted are sensitive to nutrient enrichment from septic tanks, stormwater runoff and fertiliser application to lawns in close proximity to the estuary. Nutrient concentrations were sampled at different positions, in the groundwater, at the water’s edge, in the reed bed and in the main estuary channel at five sites in the East Kleinemonde Estuary. The NH4+ and SRP concentrations showed a definite trend as concentrations decreased from the groundwater or water’s edge into the main estuary channel. Groundwater introduced nutrients to the estuary which were then taken up by the fringing reeds (Phragmites australis (Cavinelles) Trinius ex Steudel). The water column nutrients were either below detectable limits or in very low concentrations. Low TOxN concentrations were consistently found at the different sites and probably resulted from P. australis assimilating N-TOxN for growth more efficiently than N- NH4+. The roots, rhizomes, stems and leaves of the reeds were measured for δ15N as an indicator of nutrient enrichment as nitrogen stable isotope analysis of plant tissue is an effective method for assessing and monitoring septic tank and other anthropogenic inputs. All plant parts for the three sampling sessions at Site 1 (mouth region) in the East Kleinemonde Estuary had significantly higher δ15N signatures (~20 percent) than the leaves at Site 5 (upper reaches). These differences were related to the surrounding land-use of the East Kleinemonde catchment, where the lower part of the estuary has moderate to low residential development and the upper reaches are utilized mainly for livestock farming. The high δ15N signatures at Site 1 were attributed to septic tank wastewater and stormwater run-off entering the estuary. Nutrient enrichment also influenced the morphology of the reeds. Reed biomass, height and stem density was significantly higher at Site 1 compared to Site 5. Similar studies were conducted in August 2008 in the Sundays Estuary and October 2008 in the nearby Mtati and Mpekweni estuaries to see if the results were similar. iii The same patterns were found where the groundwater NH4+ and SRP concentrations were higher than the estuary channel in the Mtati and Mpekweni estuaries. In the Mpekweni and Sundays estuaries Phragmites australis leaves had high δ15N signatures (10 and 11 percent) similar to that of Site 1 in the East Kleinemonde Estuary. Lower signatures (-2 to +4 percent) were found in the Mtati Estuary. This sampling site was sheltered by a bridge with a steep slope and the concentrations were similar to Site 3 and 5 in the East Kleinemonde Estuary where the derived nutrient was the result of stormwater runoff or fertilisers. Density and biomass of reeds in the Sundays and East Kleinemonde (Site 1) estuaries were similar and this could be related to different nutrient sources, agricultural return flow and septic tank input respectively. Reeds in the Sundays Estuary were significantly taller than in the other estuaries which showed that factors such as shelter and salinity also influence reed growth and therefore morphology alone would not be a good indicator of nutrient enrichment. Indicators of nutrient enrichment are important as the status of temporarily open / closed estuaries in South Africa is threatened by deteriorating water quality. Measurements of the water column may provide an inaccurate assessment of water quality whereas macrophytes are outstanding potential indicators of nutrient enrichment as they are widely distributed, abundant and long-lived. The findings from this study indicate that δ15N concentrations in reeds can be used to indicate nutrient loading.
- Full Text:
- Date Issued: 2009
- Authors: Human, Lucienne Ryno Daniel
- Date: 2009
- Subjects: Estuaries -- South Africa -- Eastern Cape -- East Kleinemonde Estuary , Nutrient cycles -- South Africa -- Eastern Cape -- East Kleinemonde Estuary
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10615 , http://hdl.handle.net/10948/1252 , Estuaries -- South Africa -- Eastern Cape -- East Kleinemonde Estuary , Nutrient cycles -- South Africa -- Eastern Cape -- East Kleinemonde Estuary
- Description: The release of nutrients (nitrogen and phosphorus) via land clearing, application of fertilisers, discharge of human waste and combustion of fossil fuels, is one of the most harmful effects of anthropogenic stresses on aquatic environments. This study investigated the use of reeds as indicators of nutrient input to estuaries. Small estuaries such as the oligotrophic East Kleinemonde where the research was mostly conducted are sensitive to nutrient enrichment from septic tanks, stormwater runoff and fertiliser application to lawns in close proximity to the estuary. Nutrient concentrations were sampled at different positions, in the groundwater, at the water’s edge, in the reed bed and in the main estuary channel at five sites in the East Kleinemonde Estuary. The NH4+ and SRP concentrations showed a definite trend as concentrations decreased from the groundwater or water’s edge into the main estuary channel. Groundwater introduced nutrients to the estuary which were then taken up by the fringing reeds (Phragmites australis (Cavinelles) Trinius ex Steudel). The water column nutrients were either below detectable limits or in very low concentrations. Low TOxN concentrations were consistently found at the different sites and probably resulted from P. australis assimilating N-TOxN for growth more efficiently than N- NH4+. The roots, rhizomes, stems and leaves of the reeds were measured for δ15N as an indicator of nutrient enrichment as nitrogen stable isotope analysis of plant tissue is an effective method for assessing and monitoring septic tank and other anthropogenic inputs. All plant parts for the three sampling sessions at Site 1 (mouth region) in the East Kleinemonde Estuary had significantly higher δ15N signatures (~20 percent) than the leaves at Site 5 (upper reaches). These differences were related to the surrounding land-use of the East Kleinemonde catchment, where the lower part of the estuary has moderate to low residential development and the upper reaches are utilized mainly for livestock farming. The high δ15N signatures at Site 1 were attributed to septic tank wastewater and stormwater run-off entering the estuary. Nutrient enrichment also influenced the morphology of the reeds. Reed biomass, height and stem density was significantly higher at Site 1 compared to Site 5. Similar studies were conducted in August 2008 in the Sundays Estuary and October 2008 in the nearby Mtati and Mpekweni estuaries to see if the results were similar. iii The same patterns were found where the groundwater NH4+ and SRP concentrations were higher than the estuary channel in the Mtati and Mpekweni estuaries. In the Mpekweni and Sundays estuaries Phragmites australis leaves had high δ15N signatures (10 and 11 percent) similar to that of Site 1 in the East Kleinemonde Estuary. Lower signatures (-2 to +4 percent) were found in the Mtati Estuary. This sampling site was sheltered by a bridge with a steep slope and the concentrations were similar to Site 3 and 5 in the East Kleinemonde Estuary where the derived nutrient was the result of stormwater runoff or fertilisers. Density and biomass of reeds in the Sundays and East Kleinemonde (Site 1) estuaries were similar and this could be related to different nutrient sources, agricultural return flow and septic tank input respectively. Reeds in the Sundays Estuary were significantly taller than in the other estuaries which showed that factors such as shelter and salinity also influence reed growth and therefore morphology alone would not be a good indicator of nutrient enrichment. Indicators of nutrient enrichment are important as the status of temporarily open / closed estuaries in South Africa is threatened by deteriorating water quality. Measurements of the water column may provide an inaccurate assessment of water quality whereas macrophytes are outstanding potential indicators of nutrient enrichment as they are widely distributed, abundant and long-lived. The findings from this study indicate that δ15N concentrations in reeds can be used to indicate nutrient loading.
- Full Text:
- Date Issued: 2009
Restoration of degraded subtropical thickets in the Baviaanskloof Megareserve, South Africa: the role of carbon stocks and Portulacaria afra survivorship
- Authors: Powell, Michael John
- Date: 2009
- Subjects: Portulacaria afra -- South Africa -- Eastern Cape , Portulacaceae -- South Africa -- Eastern Cape , Biodiversity conservation -- South Africa -- Eastern Cape , Plant conservation -- South Africa -- Eastern Cape , Shrubs -- South Africa -- Eastern Cape , Succulent plants -- South Africa -- Eastern Cape , Baviaanskloof (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4764 , http://hdl.handle.net/10962/d1007164 , Portulacaria afra -- South Africa -- Eastern Cape , Portulacaceae -- South Africa -- Eastern Cape , Biodiversity conservation -- South Africa -- Eastern Cape , Plant conservation -- South Africa -- Eastern Cape , Shrubs -- South Africa -- Eastern Cape , Succulent plants -- South Africa -- Eastern Cape , Baviaanskloof (South Africa)
- Description: The semi-arid forms of subtropical thicket in the Eastern and Western Cape have been heavily degraded through unsustainable pastoralism over the last century or more. The degraded areas exhibit a significant loss of above-ground and belowground carbon stocks, and consequently provide an opportunity for restoration through the formal and informal carbon markets. A prerequisite for the attainment of carbon credits is to ensure sound carbon stock baselines prior to effecting restoration. I report on the carbon stocks (including sub-pools) for a number of intact subtropical thicket types, as well as the differentials between the intact and degraded states (including the sub-pools). Total carbon stocks (TCS in t C ha⁻¹) for intact vegetation (to a soil depth 0–25 cm), ranged from 87.73±6.51 to 70.64±17.24. For degraded vegetation (including old lands), TCS (t C ha⁻¹) ranged from 34.05±3.61 to 21.03±2.70. For all vegetation types, the differentials in TCS along the degradation gradient (0–25 cm) are highly significant and strengthen the possibility for carbon credit financing to catalyse the restoration of the degraded semi-arid subtropical thickets. This study has shown a mean loss of 57.23 t C ha⁻¹ in Baviaanskloof spekboom thickets, when measured to a soil depth of 25 cm. Portulacaria afra is a key species within the semi-arid subtropical thickets, being a canopy dominant and a driver of soil nutrient status, but has been largely lost from the degraded landscapes. Degraded semi-arid subtropical thicket vegetation lacks regeneration via seedling recruitment; restoration therefore requires the manual replanting of P. afra using cut truncheons. Survivorship trials were undertaken infield in 2005 to establish restoration protocols for P. afra, with survivorship being recorded in 2006 and 2008. Overall survivorship for all treatments was found to be 43.2±2.8% in 2006, dropping to 35.8±2.7% in 2008. Planting posture (flat or upright) showed the most significant results of all the factors tested in 2006 and 2008. Micro-damming also influenced survivorship in that micro-damming was associated with marginally higher survivorship (47.4 ±2.0% with damming vs. 39.1±1.5% without damming in 2006, and 39.3±1.9% vs. 32.3±1.5% in 2008). Higher planting density only showed a significant positive impact on survivorship in 2008. Neither stem diameter nor clumping significantly affected degree of survival. A key finding in the study has been the non-static nature of P. afra truncheon survivorship, even after being well established (three years since planting). The results from the study will guide the restoration protocols for the restoration of degraded subtropical thickets, where P. afra requires replanting.
- Full Text:
- Date Issued: 2009
- Authors: Powell, Michael John
- Date: 2009
- Subjects: Portulacaria afra -- South Africa -- Eastern Cape , Portulacaceae -- South Africa -- Eastern Cape , Biodiversity conservation -- South Africa -- Eastern Cape , Plant conservation -- South Africa -- Eastern Cape , Shrubs -- South Africa -- Eastern Cape , Succulent plants -- South Africa -- Eastern Cape , Baviaanskloof (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4764 , http://hdl.handle.net/10962/d1007164 , Portulacaria afra -- South Africa -- Eastern Cape , Portulacaceae -- South Africa -- Eastern Cape , Biodiversity conservation -- South Africa -- Eastern Cape , Plant conservation -- South Africa -- Eastern Cape , Shrubs -- South Africa -- Eastern Cape , Succulent plants -- South Africa -- Eastern Cape , Baviaanskloof (South Africa)
- Description: The semi-arid forms of subtropical thicket in the Eastern and Western Cape have been heavily degraded through unsustainable pastoralism over the last century or more. The degraded areas exhibit a significant loss of above-ground and belowground carbon stocks, and consequently provide an opportunity for restoration through the formal and informal carbon markets. A prerequisite for the attainment of carbon credits is to ensure sound carbon stock baselines prior to effecting restoration. I report on the carbon stocks (including sub-pools) for a number of intact subtropical thicket types, as well as the differentials between the intact and degraded states (including the sub-pools). Total carbon stocks (TCS in t C ha⁻¹) for intact vegetation (to a soil depth 0–25 cm), ranged from 87.73±6.51 to 70.64±17.24. For degraded vegetation (including old lands), TCS (t C ha⁻¹) ranged from 34.05±3.61 to 21.03±2.70. For all vegetation types, the differentials in TCS along the degradation gradient (0–25 cm) are highly significant and strengthen the possibility for carbon credit financing to catalyse the restoration of the degraded semi-arid subtropical thickets. This study has shown a mean loss of 57.23 t C ha⁻¹ in Baviaanskloof spekboom thickets, when measured to a soil depth of 25 cm. Portulacaria afra is a key species within the semi-arid subtropical thickets, being a canopy dominant and a driver of soil nutrient status, but has been largely lost from the degraded landscapes. Degraded semi-arid subtropical thicket vegetation lacks regeneration via seedling recruitment; restoration therefore requires the manual replanting of P. afra using cut truncheons. Survivorship trials were undertaken infield in 2005 to establish restoration protocols for P. afra, with survivorship being recorded in 2006 and 2008. Overall survivorship for all treatments was found to be 43.2±2.8% in 2006, dropping to 35.8±2.7% in 2008. Planting posture (flat or upright) showed the most significant results of all the factors tested in 2006 and 2008. Micro-damming also influenced survivorship in that micro-damming was associated with marginally higher survivorship (47.4 ±2.0% with damming vs. 39.1±1.5% without damming in 2006, and 39.3±1.9% vs. 32.3±1.5% in 2008). Higher planting density only showed a significant positive impact on survivorship in 2008. Neither stem diameter nor clumping significantly affected degree of survival. A key finding in the study has been the non-static nature of P. afra truncheon survivorship, even after being well established (three years since planting). The results from the study will guide the restoration protocols for the restoration of degraded subtropical thickets, where P. afra requires replanting.
- Full Text:
- Date Issued: 2009
Salinity induced physiological responses in juvenile dusky kob, Argyrosomus japonicus (Sciaenidae)
- Authors: Bernatzeder, Andrea Katinka
- Date: 2009
- Subjects: Osmoregulation , Argyrosomus -- Effects of salt on -- South Africa , Sciaenidae -- Effects of salt on -- South Africa , Argyrosomus -- Physiology , Sciaenidae -- Physiology , Fishes -- Physiology , Biological control systems , Marine ecology -- South Africa , Fishery management -- South Africa , Mariculture -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5318 , http://hdl.handle.net/10962/d1005163 , Osmoregulation , Argyrosomus -- Effects of salt on -- South Africa , Sciaenidae -- Effects of salt on -- South Africa , Argyrosomus -- Physiology , Sciaenidae -- Physiology , Fishes -- Physiology , Biological control systems , Marine ecology -- South Africa , Fishery management -- South Africa , Mariculture -- South Africa
- Description: Fisheries management regulations for dusky kob Argyrosomus japonicus, an important commercial and recreational fisheries species, have failed and the stock is considered collapsed. It is important to take an ecosystems approach to management which includes understanding the effect of environmental factors on recruitment, abundance and distribution. The distribution of early juveniles (20-150 mm TL) in the wild appears to be restricted to the upper reaches of estuaries at salinities below 5 psu. Food availability could not explain the distribution of early juveniles. The aim of this study was to investigate the role of salinity on the distribution of early juvenile dusky kob (<150 mm TL) by examining physiological responses of juveniles exposed to a range of salinities under laboratory conditions. The hypothesis was that the physiological functioning of early juveniles would be optimised at the reduced salinities which they naturally occur at. The objectives of this study were to investigate the effect of salinity on: i) plasma osmolality; ii) growth, food conversion ratio and condition factor; and iii) gill histology with emphasis on chloride cell size and number. A preliminary study was undertaken to determine whether the use of 2-phenoxyethanol had an effect on plasma osmolality. Juveniles pithed prior to blood sampling were used as the control. Plasma osmolality was not affected by exposure or duration of exposure (2, 4, 6, 8, 10 min) to 2-phenoxyethanol. The ability of teleosts to regulate plasma osmolality over a wide range of salinities indicates their degree of ‘physiological euryhalinity’. Plasma osmolality of juveniles exposed to 5, 12 and 35 psu was measured every two weeks over a total of six weeks. Although juveniles were able to regulate plasma osmolality over the duration of the experiment, plasma osmolality at 5 and 12 psu was significantly lower than in fish maintained at 35 psu. Growth is used as an indicator of the relative energy used for osmoregulation at different salinities, as the energy used for osmoregulation becomes unavailable for growth. A nineweek growth experiment was conducted on juveniles exposed to 5, 12 and 35 psu. Juveniles grew and survived at all three salinities. However, growth of juveniles at 5 psu was significantly lower than at 12 and 35 psu. Other than a significantly greater weight gain at 35 psu relative to 12 psu, there was no significant difference in specific growth and length gain between juveniles at 12 and 35 psu. Food conversion ratio and condition factor at 12 and 35 psu were not significantly different, but food conversion ratio and condition factor at 5 psu was significantly greater and lower than at 35 psu respectively. In fish, gills are considered the major organ involved in osmoregulation. Within the gills, chloride cells are the predominant site of ion exchange which is driven by the Na⁺, K⁺- ATPase enzyme. Gill samples of juveniles exposed to 5, 12 and 35 psu for six weeks were examined histologically using light microscopy. Chloride cells of juveniles maintained at 5 psu were significantly more abundant than in juveniles at 12 and 35 psu. Chloride cells of juveniles at 5 psu were significantly larger than in juveniles kept at 12 psu, but not significantly different to those of juveniles kept at 35 psu. The ability of the juvenile fish to regulate plasma osmolality indicates that they are 'physiologically euryhaline', but the reduced growth and proliferation of chloride cells at 5 psu suggests that energy expenditure for osmoregulation is increased at hypoosmotic salinities. Salinity induced physiological responses could therefore not explain the natural distribution of early juvenile dusky kob and it is proposed that other environmental factors (e.g. temperature) are also important. It is also hypothesised that the high conductivity of an estuary in South Africa, to which our understanding is limited, may negate the effect of reduced salinity. Although freshwater input into estuaries is an important factor, further investigations to explain the distribution and abundance of early juveniles is required to make management recommendations. Dusky kob is also becoming an increasingly popular aquaculture species in South Africa. In this regard, early juvenile dusky kob can be grown at salinities as low as 12 psu without negatively affecting growth and production.
- Full Text:
- Date Issued: 2009
- Authors: Bernatzeder, Andrea Katinka
- Date: 2009
- Subjects: Osmoregulation , Argyrosomus -- Effects of salt on -- South Africa , Sciaenidae -- Effects of salt on -- South Africa , Argyrosomus -- Physiology , Sciaenidae -- Physiology , Fishes -- Physiology , Biological control systems , Marine ecology -- South Africa , Fishery management -- South Africa , Mariculture -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5318 , http://hdl.handle.net/10962/d1005163 , Osmoregulation , Argyrosomus -- Effects of salt on -- South Africa , Sciaenidae -- Effects of salt on -- South Africa , Argyrosomus -- Physiology , Sciaenidae -- Physiology , Fishes -- Physiology , Biological control systems , Marine ecology -- South Africa , Fishery management -- South Africa , Mariculture -- South Africa
- Description: Fisheries management regulations for dusky kob Argyrosomus japonicus, an important commercial and recreational fisheries species, have failed and the stock is considered collapsed. It is important to take an ecosystems approach to management which includes understanding the effect of environmental factors on recruitment, abundance and distribution. The distribution of early juveniles (20-150 mm TL) in the wild appears to be restricted to the upper reaches of estuaries at salinities below 5 psu. Food availability could not explain the distribution of early juveniles. The aim of this study was to investigate the role of salinity on the distribution of early juvenile dusky kob (<150 mm TL) by examining physiological responses of juveniles exposed to a range of salinities under laboratory conditions. The hypothesis was that the physiological functioning of early juveniles would be optimised at the reduced salinities which they naturally occur at. The objectives of this study were to investigate the effect of salinity on: i) plasma osmolality; ii) growth, food conversion ratio and condition factor; and iii) gill histology with emphasis on chloride cell size and number. A preliminary study was undertaken to determine whether the use of 2-phenoxyethanol had an effect on plasma osmolality. Juveniles pithed prior to blood sampling were used as the control. Plasma osmolality was not affected by exposure or duration of exposure (2, 4, 6, 8, 10 min) to 2-phenoxyethanol. The ability of teleosts to regulate plasma osmolality over a wide range of salinities indicates their degree of ‘physiological euryhalinity’. Plasma osmolality of juveniles exposed to 5, 12 and 35 psu was measured every two weeks over a total of six weeks. Although juveniles were able to regulate plasma osmolality over the duration of the experiment, plasma osmolality at 5 and 12 psu was significantly lower than in fish maintained at 35 psu. Growth is used as an indicator of the relative energy used for osmoregulation at different salinities, as the energy used for osmoregulation becomes unavailable for growth. A nineweek growth experiment was conducted on juveniles exposed to 5, 12 and 35 psu. Juveniles grew and survived at all three salinities. However, growth of juveniles at 5 psu was significantly lower than at 12 and 35 psu. Other than a significantly greater weight gain at 35 psu relative to 12 psu, there was no significant difference in specific growth and length gain between juveniles at 12 and 35 psu. Food conversion ratio and condition factor at 12 and 35 psu were not significantly different, but food conversion ratio and condition factor at 5 psu was significantly greater and lower than at 35 psu respectively. In fish, gills are considered the major organ involved in osmoregulation. Within the gills, chloride cells are the predominant site of ion exchange which is driven by the Na⁺, K⁺- ATPase enzyme. Gill samples of juveniles exposed to 5, 12 and 35 psu for six weeks were examined histologically using light microscopy. Chloride cells of juveniles maintained at 5 psu were significantly more abundant than in juveniles at 12 and 35 psu. Chloride cells of juveniles at 5 psu were significantly larger than in juveniles kept at 12 psu, but not significantly different to those of juveniles kept at 35 psu. The ability of the juvenile fish to regulate plasma osmolality indicates that they are 'physiologically euryhaline', but the reduced growth and proliferation of chloride cells at 5 psu suggests that energy expenditure for osmoregulation is increased at hypoosmotic salinities. Salinity induced physiological responses could therefore not explain the natural distribution of early juvenile dusky kob and it is proposed that other environmental factors (e.g. temperature) are also important. It is also hypothesised that the high conductivity of an estuary in South Africa, to which our understanding is limited, may negate the effect of reduced salinity. Although freshwater input into estuaries is an important factor, further investigations to explain the distribution and abundance of early juveniles is required to make management recommendations. Dusky kob is also becoming an increasingly popular aquaculture species in South Africa. In this regard, early juvenile dusky kob can be grown at salinities as low as 12 psu without negatively affecting growth and production.
- Full Text:
- Date Issued: 2009
Seed dynamics and seedling survival in mainland thicket of the Eastern Cape
- Weatherall-Thomas, Clayton Richard
- Authors: Weatherall-Thomas, Clayton Richard
- Date: 2009
- Subjects: Seeds -- Growth , Germination , Seedlings -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10601 , http://hdl.handle.net/10948/1048 , Seeds -- Growth , Germination , Seedlings -- South Africa -- Eastern Cape
- Description: Subtropical Thicket is the dominant vegetation biome in the Eastern Cape. Little regeneration through seedlings has been observed in Thicket. This is of serious concern, as Thicket has been degraded over large areas of its distribution. An understanding of the seed dynamics is necessary for any restoration project. A number of possible causes for the lack of seedlings were therefore investigated. Study sites were best classified according to the biogeographical regions of the Subtropical Thicket Ecosystem Planning (STEP) project. The seed bank of Thicket is dissimilar to the aboveground vegetation, as it lacks woody species and is dominated by herbs and grasses, making little contribution to the regeneration of Thicket species. An increase in canopy cover resulted in lower soil and air temperatures, as well as light, and an increase in litter depth. Seedling abundance and species richness increases with mean annual rainfall, with woody seedlings being dominant in the higher rainfall areas, and succulent species in the lower rainfall regions. Anemochorous species dominated the germinable seed bank, and zoochorous species were more prevalent underneath the canopy, compared to open areas, an indication of active seed dispersal. No germination was recorded in many Thicket species, and dormancy mechanisms were lacking in many of the species that did germinate. Immersion in hot water increased germination in the hard seeds of Acacia karroo, whereas shade enhanced germination in small seeded Burchellia bubalina. The response of seedlings of four Thicket species with varying distribution to shade and drought was studied. Ptaeroxylon obliquum and Aloe africana are drought tolerant species, whereas Burchellia bubalina and Rhus dentata were intolerant to low soil moisture. All four species were able to grow in deep shade, although Rhus dentata would be classified as a shade avoider, unlike the other three species that are shade tolerant. This results in the four species having different regeneration niches. It was concluded that dispersal and the lack of “safe sites” for seedlings were the main limitations to seedling establishment in Mainland Thicket.
- Full Text:
- Date Issued: 2009
- Authors: Weatherall-Thomas, Clayton Richard
- Date: 2009
- Subjects: Seeds -- Growth , Germination , Seedlings -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10601 , http://hdl.handle.net/10948/1048 , Seeds -- Growth , Germination , Seedlings -- South Africa -- Eastern Cape
- Description: Subtropical Thicket is the dominant vegetation biome in the Eastern Cape. Little regeneration through seedlings has been observed in Thicket. This is of serious concern, as Thicket has been degraded over large areas of its distribution. An understanding of the seed dynamics is necessary for any restoration project. A number of possible causes for the lack of seedlings were therefore investigated. Study sites were best classified according to the biogeographical regions of the Subtropical Thicket Ecosystem Planning (STEP) project. The seed bank of Thicket is dissimilar to the aboveground vegetation, as it lacks woody species and is dominated by herbs and grasses, making little contribution to the regeneration of Thicket species. An increase in canopy cover resulted in lower soil and air temperatures, as well as light, and an increase in litter depth. Seedling abundance and species richness increases with mean annual rainfall, with woody seedlings being dominant in the higher rainfall areas, and succulent species in the lower rainfall regions. Anemochorous species dominated the germinable seed bank, and zoochorous species were more prevalent underneath the canopy, compared to open areas, an indication of active seed dispersal. No germination was recorded in many Thicket species, and dormancy mechanisms were lacking in many of the species that did germinate. Immersion in hot water increased germination in the hard seeds of Acacia karroo, whereas shade enhanced germination in small seeded Burchellia bubalina. The response of seedlings of four Thicket species with varying distribution to shade and drought was studied. Ptaeroxylon obliquum and Aloe africana are drought tolerant species, whereas Burchellia bubalina and Rhus dentata were intolerant to low soil moisture. All four species were able to grow in deep shade, although Rhus dentata would be classified as a shade avoider, unlike the other three species that are shade tolerant. This results in the four species having different regeneration niches. It was concluded that dispersal and the lack of “safe sites” for seedlings were the main limitations to seedling establishment in Mainland Thicket.
- Full Text:
- Date Issued: 2009
Size prediction for plus-size women's intimate apparel using a 3D body scanner
- Authors: Pandarum, Krishnavellie
- Date: 2009
- Subjects: Lingerie , Lingerie -- Design , Overweight women
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10450 , http://hdl.handle.net/10948/1153 , http://hdl.handle.net/10948/d1012020 , Lingerie , Lingerie -- Design , Overweight women
- Description: Garment “fitting” from tailor-made to ready-to-wear clothing, has evolved over time. Ready to-wear and standardized sizes appeared in the middle 19th century. Today garment fitting is one of the most important criteria in the consumer buying decision making process. This is particularly so with “body hugging” garments, such as intimate apparel; or the bra that moulds the form of the wearer to produce “smooth” outer garment silhouettes. The South African bra retailer and manufacturers sizing charts are generally based upon body dimension data collected using traditional anthropometric methods. Professional measurers are not able to capture the hidden areas of the breast such as the inframmatory fold line, the volume, shape and contour of the breast using tape measures, calipers and other measuring devices. Traditional anthropometry also does not have the ability to systemically observe the bottom line of the breast base and extract accurate data on breast volume which are key factors in designing underwire bras and in the pattern making of the bra cup panels. Exploratory retail and consumer studies have indicated that consumers, notably plus size women, experience considerable problems and dissatisfaction with poorly fitting bras. There is therefore clearly a need in South Africa to conduct a 3D anthropometric study, focusing especially on the plus-sized women’s bra market segment, as there is very little or limited studies, to date, conduct for this market segment of the population. This pilot study collected 3D torso body measurement data from a convenient sample of 176 plus sized women, recruited from Playtex (Pty) Ltd. situated in Durban, KwaZulu Natal, South Africa. The study evaluates the 3D breast volume measurement data extraction process, using an expert system developed by [TC]2 integrated into the propriety NX12-3D full body scanner software and that taken using the traditional dress-makers tape-measure. The objective is to establish the relationship between the 3D torso and breast volume data measurement output as extracted by the expert system when compared to the South African bra manufacturers sizing chart, for use in pattern making for bra cup panel designs and in the designing of underwire bras for large breasted or plus size women. The results contained in this dissertation cannot be extrapolated to the larger population of South Africa and is limited to the 176 plus size women selected by Body Mass Index; recruited from KwaZulu Natal, South Africa.
- Full Text:
- Date Issued: 2009
- Authors: Pandarum, Krishnavellie
- Date: 2009
- Subjects: Lingerie , Lingerie -- Design , Overweight women
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10450 , http://hdl.handle.net/10948/1153 , http://hdl.handle.net/10948/d1012020 , Lingerie , Lingerie -- Design , Overweight women
- Description: Garment “fitting” from tailor-made to ready-to-wear clothing, has evolved over time. Ready to-wear and standardized sizes appeared in the middle 19th century. Today garment fitting is one of the most important criteria in the consumer buying decision making process. This is particularly so with “body hugging” garments, such as intimate apparel; or the bra that moulds the form of the wearer to produce “smooth” outer garment silhouettes. The South African bra retailer and manufacturers sizing charts are generally based upon body dimension data collected using traditional anthropometric methods. Professional measurers are not able to capture the hidden areas of the breast such as the inframmatory fold line, the volume, shape and contour of the breast using tape measures, calipers and other measuring devices. Traditional anthropometry also does not have the ability to systemically observe the bottom line of the breast base and extract accurate data on breast volume which are key factors in designing underwire bras and in the pattern making of the bra cup panels. Exploratory retail and consumer studies have indicated that consumers, notably plus size women, experience considerable problems and dissatisfaction with poorly fitting bras. There is therefore clearly a need in South Africa to conduct a 3D anthropometric study, focusing especially on the plus-sized women’s bra market segment, as there is very little or limited studies, to date, conduct for this market segment of the population. This pilot study collected 3D torso body measurement data from a convenient sample of 176 plus sized women, recruited from Playtex (Pty) Ltd. situated in Durban, KwaZulu Natal, South Africa. The study evaluates the 3D breast volume measurement data extraction process, using an expert system developed by [TC]2 integrated into the propriety NX12-3D full body scanner software and that taken using the traditional dress-makers tape-measure. The objective is to establish the relationship between the 3D torso and breast volume data measurement output as extracted by the expert system when compared to the South African bra manufacturers sizing chart, for use in pattern making for bra cup panel designs and in the designing of underwire bras for large breasted or plus size women. The results contained in this dissertation cannot be extrapolated to the larger population of South Africa and is limited to the 176 plus size women selected by Body Mass Index; recruited from KwaZulu Natal, South Africa.
- Full Text:
- Date Issued: 2009
Socio-economic and ecological correlates of leopard-stock farmer conflict in the Baviaanskloof mega-reserve, Eastern Cape
- Authors: Minnie, Liaan
- Date: 2009
- Subjects: Leopard -- Ecology -- South Africa -- Eastern Cape , Leopard -- Conservation -- South Africa -- Baviaanskloof , Leopard -- Conservation -- South Africa -- Eastern Cape , Wildlife conservation -- South Africa -- Eastern Cape , Leopard -- Effect of human beings on
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10702 , http://hdl.handle.net/10948/1044 , Leopard -- Ecology -- South Africa -- Eastern Cape , Leopard -- Conservation -- South Africa -- Baviaanskloof , Leopard -- Conservation -- South Africa -- Eastern Cape , Wildlife conservation -- South Africa -- Eastern Cape , Leopard -- Effect of human beings on
- Description: The leopard, Panthera pardus, is particularly threatened outside conservation areas in South Africa. This has been attributed to a reduction in natural habitat, decreasing natural prey populations, and commercial exploitation such as trophy hunting, and most importantly, persecution by stock farmers (Woodroffe 2001). The leopard population in the Baviaanskloof Mega-Reserve (BMR) has undergone a substantial decrease in range and numbers in the past 200 years, resulting in a highly fragmented population in the Baviaanskloof Mega-Reserve, and is regarded as being insecure. There is thus a need to investigate the nature and extent of leopard-stock farmer interactions to provide the foundation for an effective leopard conservation plan. Here I investigated the ecological and socio-economic factors influencing leopard-stock farmer conflict via landowner surveys and estimated potential leopard numbers using a prey-based density model. Leopards are not necessarily the most important causes of livestock mortality in the BMR. On average, leopards killed significantly less livestock (0.7 percent livestock per year) than black-backed jackals (4.7 percent per year) and caracal (2.5 percent per year), yet 67 percent of farmers had negative attitudes towards leopards. These negative attitudes were not significantly related to stock losses. However, most of the farmers that had negative attitudes towards leopards did not have any stock losses attributed to leopards. Thus if predator-stock conflict is not reduced it will result in the retaliatory killing of leopards. This will have severe consequences for this relatively small population (estimated at 59 – 104 individuals by the prey-based model), which may ultimately lead to the local extinction of these leopards (Woodroffe & Ginsberg 1998).
- Full Text:
- Date Issued: 2009
- Authors: Minnie, Liaan
- Date: 2009
- Subjects: Leopard -- Ecology -- South Africa -- Eastern Cape , Leopard -- Conservation -- South Africa -- Baviaanskloof , Leopard -- Conservation -- South Africa -- Eastern Cape , Wildlife conservation -- South Africa -- Eastern Cape , Leopard -- Effect of human beings on
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10702 , http://hdl.handle.net/10948/1044 , Leopard -- Ecology -- South Africa -- Eastern Cape , Leopard -- Conservation -- South Africa -- Baviaanskloof , Leopard -- Conservation -- South Africa -- Eastern Cape , Wildlife conservation -- South Africa -- Eastern Cape , Leopard -- Effect of human beings on
- Description: The leopard, Panthera pardus, is particularly threatened outside conservation areas in South Africa. This has been attributed to a reduction in natural habitat, decreasing natural prey populations, and commercial exploitation such as trophy hunting, and most importantly, persecution by stock farmers (Woodroffe 2001). The leopard population in the Baviaanskloof Mega-Reserve (BMR) has undergone a substantial decrease in range and numbers in the past 200 years, resulting in a highly fragmented population in the Baviaanskloof Mega-Reserve, and is regarded as being insecure. There is thus a need to investigate the nature and extent of leopard-stock farmer interactions to provide the foundation for an effective leopard conservation plan. Here I investigated the ecological and socio-economic factors influencing leopard-stock farmer conflict via landowner surveys and estimated potential leopard numbers using a prey-based density model. Leopards are not necessarily the most important causes of livestock mortality in the BMR. On average, leopards killed significantly less livestock (0.7 percent livestock per year) than black-backed jackals (4.7 percent per year) and caracal (2.5 percent per year), yet 67 percent of farmers had negative attitudes towards leopards. These negative attitudes were not significantly related to stock losses. However, most of the farmers that had negative attitudes towards leopards did not have any stock losses attributed to leopards. Thus if predator-stock conflict is not reduced it will result in the retaliatory killing of leopards. This will have severe consequences for this relatively small population (estimated at 59 – 104 individuals by the prey-based model), which may ultimately lead to the local extinction of these leopards (Woodroffe & Ginsberg 1998).
- Full Text:
- Date Issued: 2009
Solvent-free synthesis of bisferrocenylimines and their coordination to rhodium (I)
- Authors: Kleyi, Phumelele Eldridge
- Date: 2009
- Subjects: Organic compounds -- Synthesis , Organic solvents , Solution (Chemistry) , Chemistry, Organic , Coordination compounds
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10393 , http://hdl.handle.net/10948/1053 , Organic compounds -- Synthesis , Organic solvents , Solution (Chemistry) , Chemistry, Organic , Coordination compounds
- Description: Solvent-free reactions possess advantages compared to the solvent route, such as shorter reaction times, less use of energy, better yields, etc. Herein, the synthesis and characterization of bisferrocenylimines and arylbisamines are described. Reduction of the above compounds with LAH resulted in the formation of bisferrocenylamines and arylbisamines, respectively. The coordination chemistry of all the above compounds to rhodium(I) is also discussed in the prepared complexes [Rh(COD)(NN)]ClO4, where NN = bisferrocenylimines, and [Rh(COD)(NN)]BF4, where NN = bisferrocenylamines and arylbisamines. X-ray crystal structures of the complexes [Rh(COD)(NN)]ClO4 ([3.2] and [3.3]) have been obtained. Complexes of the type [Rh(COD)(NN)]BF4 were characterized with IR and UV-vis spectroscopy, cyclic voltammetry and conductometry. The catalytic activity of the complexes was also investigated: [Rh(COD)(NN)]ClO4 for the polymerization of phenylacetylene and [Rh(COD)(NN)]BF4 for the hydroformylation of styrene.
- Full Text:
- Date Issued: 2009
- Authors: Kleyi, Phumelele Eldridge
- Date: 2009
- Subjects: Organic compounds -- Synthesis , Organic solvents , Solution (Chemistry) , Chemistry, Organic , Coordination compounds
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10393 , http://hdl.handle.net/10948/1053 , Organic compounds -- Synthesis , Organic solvents , Solution (Chemistry) , Chemistry, Organic , Coordination compounds
- Description: Solvent-free reactions possess advantages compared to the solvent route, such as shorter reaction times, less use of energy, better yields, etc. Herein, the synthesis and characterization of bisferrocenylimines and arylbisamines are described. Reduction of the above compounds with LAH resulted in the formation of bisferrocenylamines and arylbisamines, respectively. The coordination chemistry of all the above compounds to rhodium(I) is also discussed in the prepared complexes [Rh(COD)(NN)]ClO4, where NN = bisferrocenylimines, and [Rh(COD)(NN)]BF4, where NN = bisferrocenylamines and arylbisamines. X-ray crystal structures of the complexes [Rh(COD)(NN)]ClO4 ([3.2] and [3.3]) have been obtained. Complexes of the type [Rh(COD)(NN)]BF4 were characterized with IR and UV-vis spectroscopy, cyclic voltammetry and conductometry. The catalytic activity of the complexes was also investigated: [Rh(COD)(NN)]ClO4 for the polymerization of phenylacetylene and [Rh(COD)(NN)]BF4 for the hydroformylation of styrene.
- Full Text:
- Date Issued: 2009
Statistical models for pricing weather derivatives for Port Elizabeth
- Authors: Nasila, Mark Wopicho
- Date: 2009
- Subjects: Weather derivatives -- Prices -- South Africa -- Port Elizabeth
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10567 , http://hdl.handle.net/10948/1018 , Weather derivatives -- Prices -- South Africa -- Port Elizabeth
- Description: Weather has a significant impact on business activities of many kinds. The list of economic activities subjected to the risk of the weather include: the energy producers and consumers, the industry of leisure, the insurance industry, the food industry and the agricultural industries but the primary industry, namely the energy industry, has given rise to the demand for weather derivatives and has caused the weather risk management industry to evolve actively. A derivative is a contract or security, whose payoffs depend upon the price of an underlying asset price, and is used to control the risks of naturally-arising exposures to such an asset price. Therefore weather derivatives are financial contracts with payouts that depend on weather in some form. It is a contract that provides a payoff in response to an index level based on weather phenomena (West, 2002).The underlying variable can be for example humidity, rain, snowfall, temperature, or even sunshine. The main players who take part in the weather derivatives markets industry can be grouped in to five main categories, namely: 1) End users who are also referred to as hedgers 2) Speculators 3) Market makers 4) Brokers 5) Insurance and re-insurance companies. Since the late 90’s when the first weather derivatives transactions were recorded, the underlying market has witnessed the development of a new derivative market in the United States, which is gradually expanding across Europe. However, the newly developed market for weather derivatives is not liquid in Africa and specifically South Africa mainly due to the following factors: 1) Many companies and business organisations have not yet established a hedging policy or even figured out how their businesses or industries are exposed to weather risks. 2 2) “Since many companies and industries depend on insurance companies to cover their risks, it is possible that the solutions suggested by these companies or industries looking for protection from weather risks differ according to the cover provided by these insurance organisations “(Micali, 2008). The main aim of this study is to review available statistical models for pricing derivatives, with temperature as the underlying which could enable industries, businesses and other organisations in South Africa to protect themselves against losses due to fluctuations in the weather and therefore hedge their risks.
- Full Text:
- Date Issued: 2009
- Authors: Nasila, Mark Wopicho
- Date: 2009
- Subjects: Weather derivatives -- Prices -- South Africa -- Port Elizabeth
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10567 , http://hdl.handle.net/10948/1018 , Weather derivatives -- Prices -- South Africa -- Port Elizabeth
- Description: Weather has a significant impact on business activities of many kinds. The list of economic activities subjected to the risk of the weather include: the energy producers and consumers, the industry of leisure, the insurance industry, the food industry and the agricultural industries but the primary industry, namely the energy industry, has given rise to the demand for weather derivatives and has caused the weather risk management industry to evolve actively. A derivative is a contract or security, whose payoffs depend upon the price of an underlying asset price, and is used to control the risks of naturally-arising exposures to such an asset price. Therefore weather derivatives are financial contracts with payouts that depend on weather in some form. It is a contract that provides a payoff in response to an index level based on weather phenomena (West, 2002).The underlying variable can be for example humidity, rain, snowfall, temperature, or even sunshine. The main players who take part in the weather derivatives markets industry can be grouped in to five main categories, namely: 1) End users who are also referred to as hedgers 2) Speculators 3) Market makers 4) Brokers 5) Insurance and re-insurance companies. Since the late 90’s when the first weather derivatives transactions were recorded, the underlying market has witnessed the development of a new derivative market in the United States, which is gradually expanding across Europe. However, the newly developed market for weather derivatives is not liquid in Africa and specifically South Africa mainly due to the following factors: 1) Many companies and business organisations have not yet established a hedging policy or even figured out how their businesses or industries are exposed to weather risks. 2 2) “Since many companies and industries depend on insurance companies to cover their risks, it is possible that the solutions suggested by these companies or industries looking for protection from weather risks differ according to the cover provided by these insurance organisations “(Micali, 2008). The main aim of this study is to review available statistical models for pricing derivatives, with temperature as the underlying which could enable industries, businesses and other organisations in South Africa to protect themselves against losses due to fluctuations in the weather and therefore hedge their risks.
- Full Text:
- Date Issued: 2009
Statistical relationship of customer behavioral characteristics in personal banking
- Authors: Rasuba, Maanda
- Date: 2009
- Subjects: Customer relations -- South Africa -- Management , Consumer behavior -- South Africa , Banks and banking -- Customer services -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10566 , http://hdl.handle.net/10948/1165 , Customer relations -- South Africa -- Management , Consumer behavior -- South Africa , Banks and banking -- Customer services -- South Africa
- Description: This study investigates the relationship of bank customers’ behavioural patterns based on the customers past transactions, with respect to their profile characteristics. The main aim of this study is to illustrate that different categories of customers (based on demographical variables such as race, gender and age) have statistically significant differences in behaviour, with respect to how they operate their accounts. A theoretical overview on the literature of customer relationship management in the banking sector emphasises the importance of understanding customers to ensure that a business is successful. Four null-hypotheses where formulated based on a general research hypothesis. The data base provided a major South African bank is used to achieve the objectives. Extensive cleaning of the data set was necessary to ensure the validity of the results. The data set had 7860 customer keys. The large data base used contributed to the reliability of the results. The following behavioural variables were used in the study namely, transaction data, average debit and credit transaction amounts and average number of transactions per month. The main results of study indicate that different customer categories have statistically significant differences in behaviour, with respect to how customers operate their accounts. This implies that it is important for the banking sector to consider customer gender differences, age differences and race group differences in the relationship strategies which they employ in their multicultural environment. Further research in the area may be necessary before generalisation can be made on all banking customers.
- Full Text:
- Date Issued: 2009
- Authors: Rasuba, Maanda
- Date: 2009
- Subjects: Customer relations -- South Africa -- Management , Consumer behavior -- South Africa , Banks and banking -- Customer services -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10566 , http://hdl.handle.net/10948/1165 , Customer relations -- South Africa -- Management , Consumer behavior -- South Africa , Banks and banking -- Customer services -- South Africa
- Description: This study investigates the relationship of bank customers’ behavioural patterns based on the customers past transactions, with respect to their profile characteristics. The main aim of this study is to illustrate that different categories of customers (based on demographical variables such as race, gender and age) have statistically significant differences in behaviour, with respect to how they operate their accounts. A theoretical overview on the literature of customer relationship management in the banking sector emphasises the importance of understanding customers to ensure that a business is successful. Four null-hypotheses where formulated based on a general research hypothesis. The data base provided a major South African bank is used to achieve the objectives. Extensive cleaning of the data set was necessary to ensure the validity of the results. The data set had 7860 customer keys. The large data base used contributed to the reliability of the results. The following behavioural variables were used in the study namely, transaction data, average debit and credit transaction amounts and average number of transactions per month. The main results of study indicate that different customer categories have statistically significant differences in behaviour, with respect to how customers operate their accounts. This implies that it is important for the banking sector to consider customer gender differences, age differences and race group differences in the relationship strategies which they employ in their multicultural environment. Further research in the area may be necessary before generalisation can be made on all banking customers.
- Full Text:
- Date Issued: 2009
Studies towards the synthesis of novel tridentate ligands for use in ruthenium metathesis catalysts
- Authors: Millward, Tanya
- Date: 2009
- Subjects: Ligands , Catalysis , Metathesis (Chemistry) , Ruthenium , Complex compounds
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4360 , http://hdl.handle.net/10962/d1005025 , Ligands , Catalysis , Metathesis (Chemistry) , Ruthenium , Complex compounds
- Description: This work has focussed on the preparation of a variety of tridentate ligands, designed to form ruthenium complexes as potential metathesis catalysts. Various approaches to the tridentate, malonate-tethered imidazolidine system have been investigated, and a promising route to accessing ligands of this type is discussed. A tridentate malonate-tethered pyridine ligand has been successfully prepared and its dithallium salt has been accessed by hydrolysis with thallium carbonate; approaches to a longer-chain analogue have also been investigated. A thallium pyridine-2,6- dicarboxylate ligand has been has been successfully prepared, as have a range of pyridine diamine ligands, with various alkyl and aromatic substituents on the amine donor atoms. Preliminary investigations into the potential of these compounds as ligands for alkylidene ruthenium complexes are reported using molecular modelling techniques. The geometries and steric energies of the ligands and their corresponding complexes have been analysed, and results obtained from two different software packages are compared. Finally, some preliminary complexation studies have been undertaken.
- Full Text:
- Date Issued: 2009
- Authors: Millward, Tanya
- Date: 2009
- Subjects: Ligands , Catalysis , Metathesis (Chemistry) , Ruthenium , Complex compounds
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4360 , http://hdl.handle.net/10962/d1005025 , Ligands , Catalysis , Metathesis (Chemistry) , Ruthenium , Complex compounds
- Description: This work has focussed on the preparation of a variety of tridentate ligands, designed to form ruthenium complexes as potential metathesis catalysts. Various approaches to the tridentate, malonate-tethered imidazolidine system have been investigated, and a promising route to accessing ligands of this type is discussed. A tridentate malonate-tethered pyridine ligand has been successfully prepared and its dithallium salt has been accessed by hydrolysis with thallium carbonate; approaches to a longer-chain analogue have also been investigated. A thallium pyridine-2,6- dicarboxylate ligand has been has been successfully prepared, as have a range of pyridine diamine ligands, with various alkyl and aromatic substituents on the amine donor atoms. Preliminary investigations into the potential of these compounds as ligands for alkylidene ruthenium complexes are reported using molecular modelling techniques. The geometries and steric energies of the ligands and their corresponding complexes have been analysed, and results obtained from two different software packages are compared. Finally, some preliminary complexation studies have been undertaken.
- Full Text:
- Date Issued: 2009
Synthesis and characterization of novel platinum complexes : their anticancer behaviour
- Authors: Myburgh, Jolanda
- Date: 2009
- Subjects: Complex compounds -- Synthesis , Platinum compounds , Antineoplastic agents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10429 , http://hdl.handle.net/10948/d1018621
- Description: In this dissertation novel non-leaving groups were employed to synthesize platinum complexes which can contribute to the understanding or improvement of anticancer action. These complexes basically consist of (NS)-chelate and amineplatinum complexes. Bidentate (NS)-donor ligands were used as non-leaving ligands in the syntheses of platinum(II) complexes with iodide, chloride, bromide and oxalate anions as leaving groups. These complexes were synthesized and studied since many questions regarding the interaction of sulfur donors and platinum still exists. These relate to thermodynamic and kinetic factors and their influence on anticancer action. In this dissertation the properties of novel platinum(II) complexes of a bidentate ligand having an aromatic nitrogen-donor atom in combination with a thioethereal sulfur atom capable of forming a five membered ring with platinum(II) were studied. The general structure of the (NS) -ligands used were N-alkyl-2-methylthioalkyl imidazole. Alkyl groups used were methyl, ethyl and propyl. Although amine complexes of platinum have been extensively studied there are some new aspects of these that are worthwhile investigating. In this dissertation amines having planar attachments which will be at an angle with the coordination plane viz. benzylamine and amines having cyclic aliphatic groups namely cyclopropyl and cyclohexyl were investigated. Some of the (NS) - and amineplatinum(II) complexes were oxidised to their mononitroplatinum(IV) analogues . The motivation for the synthesis of these complexes was the greater kinetic stability of platinum(IV) and recent research has shown that a specific type of platinum(IV) compound shows suitable properties as an anticancer agent. These complexes were characterised by a variety of spectral means (IR, NMR, mass spectroscopy) as well as elemental analysis, solubility determinations, thermal analysis (TGA), ionization studies and finally their anticancer behaviour towards three different cell lines(Hela, MCF 7, Ht29) and in this process they were compared to the behaviour of cisplatin as a reference. A few have shown promising anticancer behaviour.
- Full Text:
- Date Issued: 2009
- Authors: Myburgh, Jolanda
- Date: 2009
- Subjects: Complex compounds -- Synthesis , Platinum compounds , Antineoplastic agents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10429 , http://hdl.handle.net/10948/d1018621
- Description: In this dissertation novel non-leaving groups were employed to synthesize platinum complexes which can contribute to the understanding or improvement of anticancer action. These complexes basically consist of (NS)-chelate and amineplatinum complexes. Bidentate (NS)-donor ligands were used as non-leaving ligands in the syntheses of platinum(II) complexes with iodide, chloride, bromide and oxalate anions as leaving groups. These complexes were synthesized and studied since many questions regarding the interaction of sulfur donors and platinum still exists. These relate to thermodynamic and kinetic factors and their influence on anticancer action. In this dissertation the properties of novel platinum(II) complexes of a bidentate ligand having an aromatic nitrogen-donor atom in combination with a thioethereal sulfur atom capable of forming a five membered ring with platinum(II) were studied. The general structure of the (NS) -ligands used were N-alkyl-2-methylthioalkyl imidazole. Alkyl groups used were methyl, ethyl and propyl. Although amine complexes of platinum have been extensively studied there are some new aspects of these that are worthwhile investigating. In this dissertation amines having planar attachments which will be at an angle with the coordination plane viz. benzylamine and amines having cyclic aliphatic groups namely cyclopropyl and cyclohexyl were investigated. Some of the (NS) - and amineplatinum(II) complexes were oxidised to their mononitroplatinum(IV) analogues . The motivation for the synthesis of these complexes was the greater kinetic stability of platinum(IV) and recent research has shown that a specific type of platinum(IV) compound shows suitable properties as an anticancer agent. These complexes were characterised by a variety of spectral means (IR, NMR, mass spectroscopy) as well as elemental analysis, solubility determinations, thermal analysis (TGA), ionization studies and finally their anticancer behaviour towards three different cell lines(Hela, MCF 7, Ht29) and in this process they were compared to the behaviour of cisplatin as a reference. A few have shown promising anticancer behaviour.
- Full Text:
- Date Issued: 2009