Improved singlet oxygen generation by a novel bodipy dye and a study of upconverison nanoparticles mixed with a functionalized bodipy compound
- Wildervanck, Martijn Johannes
- Authors: Wildervanck, Martijn Johannes
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3718 , vital:20538
- Description: This research explores the use of the versatile 4,4-difluoro-4-boro-3a,4a-diaza-s-indacene (BODIPY) dyes and the modification of their spectroscopic properties. The synthesis of a tetramethyl-BODIPY bearing a sterically hindered meso-phenyl ring with an ethynyl functional group at the para-position was compared to that of its freely rotating counterpart with no methyl substituents on the BODIPY core, with the fluorescence properties in particular proving to be markedly different. These phenyl-ethynyl-substituted BODIPYs were used as the starting materials for the synthesis of novel BODIPY dyes for sensor applications via Sonogashira coupling reactions at the ethynyl position, but this resulted instead in the serendipitous synthesis of a novel BODIPY dimer in which the para-positions of the meso-phenyl rings are linked by a diethynyl bridge. Following iodination at the 2, 6-positions, the dimer was found to have a singlet oxygen quantum yield of 0.88, compared to the value of 0.86 that was obtained for the analogous monomer. Since the εmax values for the main spectral bands of the dimers are significantly higher, the compounds may be of interest for singlet oxygen generation applications. A second study was carried out on the interaction between methyl ester functionalized BODIPY dyes and upconversion nanoparticles (UCNPs) to explore the possible use of BODIPY-UCNP conjugates in biomedical applications. The singlet oxygen generation properties of the BODIPY were tested following iodination at the 2, 6-positions, a singlet oxygen quantum yield value of 0.86 was obtained. Three sets of oleate capped UCNPs were synthesized with different diameters and were rendered water dispersible with the addition of a silica shell. The necessary scaffolding for conjugation to the BODIPY was provided by amine groups following functionalization of this shell. All of the sets of oleate capped and silica coated UCNPs were characterized by transmission electron microscopy (TEM) and X-ray diffractometry (XRD) and their emission properties were studied upon excitation at 978 nm with a diode laser with a Picoquant Fluotime 300 spectrophotometer that enables the measurement of anti-Stokes emission. The potential utility of UCNP-BODIPY conjugates for singlet oxygen applications, such as PDT, was then assessed.
- Full Text:
- Date Issued: 2016
- Authors: Wildervanck, Martijn Johannes
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3718 , vital:20538
- Description: This research explores the use of the versatile 4,4-difluoro-4-boro-3a,4a-diaza-s-indacene (BODIPY) dyes and the modification of their spectroscopic properties. The synthesis of a tetramethyl-BODIPY bearing a sterically hindered meso-phenyl ring with an ethynyl functional group at the para-position was compared to that of its freely rotating counterpart with no methyl substituents on the BODIPY core, with the fluorescence properties in particular proving to be markedly different. These phenyl-ethynyl-substituted BODIPYs were used as the starting materials for the synthesis of novel BODIPY dyes for sensor applications via Sonogashira coupling reactions at the ethynyl position, but this resulted instead in the serendipitous synthesis of a novel BODIPY dimer in which the para-positions of the meso-phenyl rings are linked by a diethynyl bridge. Following iodination at the 2, 6-positions, the dimer was found to have a singlet oxygen quantum yield of 0.88, compared to the value of 0.86 that was obtained for the analogous monomer. Since the εmax values for the main spectral bands of the dimers are significantly higher, the compounds may be of interest for singlet oxygen generation applications. A second study was carried out on the interaction between methyl ester functionalized BODIPY dyes and upconversion nanoparticles (UCNPs) to explore the possible use of BODIPY-UCNP conjugates in biomedical applications. The singlet oxygen generation properties of the BODIPY were tested following iodination at the 2, 6-positions, a singlet oxygen quantum yield value of 0.86 was obtained. Three sets of oleate capped UCNPs were synthesized with different diameters and were rendered water dispersible with the addition of a silica shell. The necessary scaffolding for conjugation to the BODIPY was provided by amine groups following functionalization of this shell. All of the sets of oleate capped and silica coated UCNPs were characterized by transmission electron microscopy (TEM) and X-ray diffractometry (XRD) and their emission properties were studied upon excitation at 978 nm with a diode laser with a Picoquant Fluotime 300 spectrophotometer that enables the measurement of anti-Stokes emission. The potential utility of UCNP-BODIPY conjugates for singlet oxygen applications, such as PDT, was then assessed.
- Full Text:
- Date Issued: 2016
In silico analysis of the effects of non-synonymous single nucleotide polymorphisms on the human macrophage migration inhibitory factor gene and their possible role in human African trypanosomiasis susceptibility
- Authors: Kimuda, Magambo Philip
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3047 , vital:20355
- Description: Human African trypanosomiasis (HAT) is a public health problem in sub-Saharan Africa, with approximately 10,000 cases being reported per year. The Macrophage Migration Inhibitory Factor (MIF) which is encoded by a functionally polymorphic gene is important in both innate andadaptive immune responses, and has been implicated in affecting the outcome and processes of several inflammatory conditions. A recent study in mice to that effect showed that MIF deficient and anti-MIF antibody treated mice showed lowered inflammatory responses, liver damage and anaemia than the wild type mice when experimentally challenged with Trypanosomes. These findings could mean that the transcript levels and/or polymorphisms in this gene can possibly affect individual risk to trypanosomiasis. This is especially of interest because there have been reports of spontaneous recovery i.e self-cure/resistance in some HAT cases in West Africa. Prior to this discovery the general paradigm was that trypanosomiasis is fatal if left untreated. The aim of this study was to gain insights into how human genetic variation in forms of nonsynonymous SNPs affects the MIF structure and function and possibly HAT susceptibility. NsSNPs in the mif gene were obtained from dbSNP. Through homology modeling, SNP prediction tools, protein interface analysis, alanine scanning, changes in free energy of folding, protein interactions calculator (PIC), and molecular dynamics simulations, SNP effects on the protein structure and function were studied. The study cohort comprised of human genome sequence data from 50 North Western Uganda Lugbara endemic individuals of whom 20 were cases (previous HAT patients) and 30 were controls (HAT free individuals). None of the 26 nsSNPs retrieved from dbSNP (July 2015) were present in the mif gene region in the study cohort. Out of the eight variants called in the mif coding region there was only one missense variant rs36065127 whose clinical significance is unknown. It was not possible to test for association of this variant with HAT due to its low global MAF that was less than 0.05. Alanine scanning provided a fast and computationally cheap means of quickly assessing nsSNPs of importance. NsSNPs that were interface residues were more likely to be hotspots (important in protein stability). Assessment of possible compensatory mutations using PIC analysis showed that some nsSNP sites were interacting with others, but this requires further experimentation. Analysis of changes in free energy using FOLDX was not enough to predict which nsSNPs would adversely affect protein structure, function and kinetics. The MD simulations were unfortunately too short to glean any meaningful inferences. This was the first genetic study carried out on the people of Lugbara ethnicity from North Western Uganda.
- Full Text:
- Date Issued: 2016
- Authors: Kimuda, Magambo Philip
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3047 , vital:20355
- Description: Human African trypanosomiasis (HAT) is a public health problem in sub-Saharan Africa, with approximately 10,000 cases being reported per year. The Macrophage Migration Inhibitory Factor (MIF) which is encoded by a functionally polymorphic gene is important in both innate andadaptive immune responses, and has been implicated in affecting the outcome and processes of several inflammatory conditions. A recent study in mice to that effect showed that MIF deficient and anti-MIF antibody treated mice showed lowered inflammatory responses, liver damage and anaemia than the wild type mice when experimentally challenged with Trypanosomes. These findings could mean that the transcript levels and/or polymorphisms in this gene can possibly affect individual risk to trypanosomiasis. This is especially of interest because there have been reports of spontaneous recovery i.e self-cure/resistance in some HAT cases in West Africa. Prior to this discovery the general paradigm was that trypanosomiasis is fatal if left untreated. The aim of this study was to gain insights into how human genetic variation in forms of nonsynonymous SNPs affects the MIF structure and function and possibly HAT susceptibility. NsSNPs in the mif gene were obtained from dbSNP. Through homology modeling, SNP prediction tools, protein interface analysis, alanine scanning, changes in free energy of folding, protein interactions calculator (PIC), and molecular dynamics simulations, SNP effects on the protein structure and function were studied. The study cohort comprised of human genome sequence data from 50 North Western Uganda Lugbara endemic individuals of whom 20 were cases (previous HAT patients) and 30 were controls (HAT free individuals). None of the 26 nsSNPs retrieved from dbSNP (July 2015) were present in the mif gene region in the study cohort. Out of the eight variants called in the mif coding region there was only one missense variant rs36065127 whose clinical significance is unknown. It was not possible to test for association of this variant with HAT due to its low global MAF that was less than 0.05. Alanine scanning provided a fast and computationally cheap means of quickly assessing nsSNPs of importance. NsSNPs that were interface residues were more likely to be hotspots (important in protein stability). Assessment of possible compensatory mutations using PIC analysis showed that some nsSNP sites were interacting with others, but this requires further experimentation. Analysis of changes in free energy using FOLDX was not enough to predict which nsSNPs would adversely affect protein structure, function and kinetics. The MD simulations were unfortunately too short to glean any meaningful inferences. This was the first genetic study carried out on the people of Lugbara ethnicity from North Western Uganda.
- Full Text:
- Date Issued: 2016
Information security concerns around enterprise bring your own device adoption in South African higher education institutions
- Authors: Sauls, Gershwin Ashton
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3619 , vital:20530
- Description: The research carried out in this thesis is an investigation into the information security concerns around the use of personally-owned mobile devices within South African universities. This concept, which is more commonly known as Bring Your Own Device or BYOD has raised many data loss concerns for organizational IT Departments across various industries worldwide. Universities as institutions are designed to facilitate research and learning and as such, have a strong culture toward the sharing of information which complicates management of these data loss concerns even further. As such, the objectives of the research were to determine the acceptance levels of BYOD within South African universities in relation to the perceived security risks. Thereafter, an investigation into which security practices, if any, that South African universities are using to minimize the information security concerns was carried out by means of a targeted online questionnaire. An extensive literature review was first carried out to evaluate the motivation for the research and to assess advantages of using Smartphone and Tablet PC’s for work related purposes. Thereafter, to determine security concerns, other surveys and related work was consulted to determine the relevant questions needed by the online questionnaire. The quantity of comprehensive academic studies concerning the security aspects of BYOD within organizations was very limited and because of this reason, the research took on a highly exploratory design. Finally, the research deliberated on the results of the online questionnaire and concluded with a strategy for the implementation of a mobile device security strategy for using personally-owned devices in a work-related environment.
- Full Text:
- Date Issued: 2016
- Authors: Sauls, Gershwin Ashton
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3619 , vital:20530
- Description: The research carried out in this thesis is an investigation into the information security concerns around the use of personally-owned mobile devices within South African universities. This concept, which is more commonly known as Bring Your Own Device or BYOD has raised many data loss concerns for organizational IT Departments across various industries worldwide. Universities as institutions are designed to facilitate research and learning and as such, have a strong culture toward the sharing of information which complicates management of these data loss concerns even further. As such, the objectives of the research were to determine the acceptance levels of BYOD within South African universities in relation to the perceived security risks. Thereafter, an investigation into which security practices, if any, that South African universities are using to minimize the information security concerns was carried out by means of a targeted online questionnaire. An extensive literature review was first carried out to evaluate the motivation for the research and to assess advantages of using Smartphone and Tablet PC’s for work related purposes. Thereafter, to determine security concerns, other surveys and related work was consulted to determine the relevant questions needed by the online questionnaire. The quantity of comprehensive academic studies concerning the security aspects of BYOD within organizations was very limited and because of this reason, the research took on a highly exploratory design. Finally, the research deliberated on the results of the online questionnaire and concluded with a strategy for the implementation of a mobile device security strategy for using personally-owned devices in a work-related environment.
- Full Text:
- Date Issued: 2016
Internal fingerprint extraction
- Authors: Darlow, Luke Nicholas
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2959 , vital:20347
- Description: Fingerprints are a non-invasive biometric that possess significant advantages. However, they are subject to surface erosion and damage; distortion upon scanning; and are vulnerable to fingerprint spoofing. The internal fingerprint exists as the undulations of the papillary junction - an intermediary layer of skin - and provides a solution to these disadvantages. Optical coherence tomography is used to capture the internal fingerprint. A depth profile of the papillary junction throughout the OCT scans is first constructed using fuzzy c-means clustering and a fine-tuning procedure. This information is then used to define localised regions over which to average pixels for the resultant internal fingerprint. When compared to a ground-truth internal fingerprint zone, the internal fingerprint zone detected automatically is within the measured bounds of human error. With a mean- squared-error of 21.3 and structural similarity of 96.4%, the internal fingerprint zone was successfully found and described. The extracted fingerprints exceed their surface counterparts with respect to orientation certainty and NFIQ scores (both of which are respected fingerprint quality assessment criteria). Internal to surface fingerprint correspondence and internal fingerprint cross correspondence were also measured. A larger scanned region is shown to be advantageous as internal fingerprints extracted from these scans have good surface correspondence (75% had at least one true match with a surface counterpart). It is also evidenced that internal fingerprints can constitute a fingerprint database. 96% of the internal fingerprints extracted had at least one corresponding match with another internal fingerprint. When compared to surface fingerprints cropped to match the internal fingerprints’ representative area and locality, the internal fingerprints outperformed these cropped surface counterparts. The internal fingerprint is an attractive biometric solution. This research develops a novel approach to extracting the internal fingerprint and is an asset to the further development of technologies surrounding fingerprint extraction from OCT scans. No earlier work has extracted or tested the internal fingerprint to the degree that this research has.
- Full Text:
- Date Issued: 2016
- Authors: Darlow, Luke Nicholas
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2959 , vital:20347
- Description: Fingerprints are a non-invasive biometric that possess significant advantages. However, they are subject to surface erosion and damage; distortion upon scanning; and are vulnerable to fingerprint spoofing. The internal fingerprint exists as the undulations of the papillary junction - an intermediary layer of skin - and provides a solution to these disadvantages. Optical coherence tomography is used to capture the internal fingerprint. A depth profile of the papillary junction throughout the OCT scans is first constructed using fuzzy c-means clustering and a fine-tuning procedure. This information is then used to define localised regions over which to average pixels for the resultant internal fingerprint. When compared to a ground-truth internal fingerprint zone, the internal fingerprint zone detected automatically is within the measured bounds of human error. With a mean- squared-error of 21.3 and structural similarity of 96.4%, the internal fingerprint zone was successfully found and described. The extracted fingerprints exceed their surface counterparts with respect to orientation certainty and NFIQ scores (both of which are respected fingerprint quality assessment criteria). Internal to surface fingerprint correspondence and internal fingerprint cross correspondence were also measured. A larger scanned region is shown to be advantageous as internal fingerprints extracted from these scans have good surface correspondence (75% had at least one true match with a surface counterpart). It is also evidenced that internal fingerprints can constitute a fingerprint database. 96% of the internal fingerprints extracted had at least one corresponding match with another internal fingerprint. When compared to surface fingerprints cropped to match the internal fingerprints’ representative area and locality, the internal fingerprints outperformed these cropped surface counterparts. The internal fingerprint is an attractive biometric solution. This research develops a novel approach to extracting the internal fingerprint and is an asset to the further development of technologies surrounding fingerprint extraction from OCT scans. No earlier work has extracted or tested the internal fingerprint to the degree that this research has.
- Full Text:
- Date Issued: 2016
Investigating soil microbial interactions of Portulacaria afra
- Authors: Fulmaka, Aviwe
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54598 , vital:26592
- Description: Portulacaria afra commonly known as Spekboom contributes significantly to carbon sequestration and has been widely planted in degraded areas of the Eastern Cape. Approximately 50% of planted cuttings do not survive although the cause of this decline is unknown. Like many indigenous plants, Spekboom forms a symbiotic relationship with mycorrhizal fungi and the interaction with rhizobacteria may enhance and improve plant growth and establishment. This study aims to investigate these relationships which will include a survey of the arbuscular mycorrhizal (AM) fungal populations associated with Spekboom, determination of the causal agent of Spekboom decline, isolation and identification of the associated rhizobacteria and investigation of their plant growth promotion properties and assessing the ability of arbuscular mycorrhizal fungi and selected rhizobacteria to enhance establishment and growth of Spekboom. Soil and root samples from selected trial sites were used to assess AM fungal spore abundance and colonisation; isolation, characterization, and identification of rhizobacteria and determine the interaction of the microbes on Spekboom growth and tolerance to Fusarium. AM spore abundance and percentage root colonisation did not differ between the three Spekboom plots. Molecular analyses of the SSU region from the plots showed 4 families of AM fungi and were identified as Ambisporaceae, Glomeraceae, Claroideoglomeraceae and Paraglomeraceae. A suspected Fusarium pathogen was isolated and molecularly identified. Pathogenicity tests indicated reduced Spekboom growth with poor root development. Thirty four rhizobacterial isolates were tested for various plant growth promoting abilities. Of these, 6 were able to produce IAA which may promote plant root growth, 27 siderophores and 23 were phosphate solubilisers. Bacterial isolates were molecularly identified to be from various species of Bacillus, with some Arthrobacter, Enterobacter, Pseudomonas and Microbacterium. Inoculation of Spekboom cuttings with mycorrhizal fungi and selected rhizobacterial isolates significantly improved shoot height. Spekboom cuttings challenged with Fusarium and inoculated with mycorrhizal fungi and two rhizobacterial isolates significantly improved growth. The inoculation of cuttings in the nursery with mycorrhizal fungi and selected rhizobacteria is recommended prior to establishing Spekboom in the field.
- Full Text:
- Date Issued: 2016
- Authors: Fulmaka, Aviwe
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54598 , vital:26592
- Description: Portulacaria afra commonly known as Spekboom contributes significantly to carbon sequestration and has been widely planted in degraded areas of the Eastern Cape. Approximately 50% of planted cuttings do not survive although the cause of this decline is unknown. Like many indigenous plants, Spekboom forms a symbiotic relationship with mycorrhizal fungi and the interaction with rhizobacteria may enhance and improve plant growth and establishment. This study aims to investigate these relationships which will include a survey of the arbuscular mycorrhizal (AM) fungal populations associated with Spekboom, determination of the causal agent of Spekboom decline, isolation and identification of the associated rhizobacteria and investigation of their plant growth promotion properties and assessing the ability of arbuscular mycorrhizal fungi and selected rhizobacteria to enhance establishment and growth of Spekboom. Soil and root samples from selected trial sites were used to assess AM fungal spore abundance and colonisation; isolation, characterization, and identification of rhizobacteria and determine the interaction of the microbes on Spekboom growth and tolerance to Fusarium. AM spore abundance and percentage root colonisation did not differ between the three Spekboom plots. Molecular analyses of the SSU region from the plots showed 4 families of AM fungi and were identified as Ambisporaceae, Glomeraceae, Claroideoglomeraceae and Paraglomeraceae. A suspected Fusarium pathogen was isolated and molecularly identified. Pathogenicity tests indicated reduced Spekboom growth with poor root development. Thirty four rhizobacterial isolates were tested for various plant growth promoting abilities. Of these, 6 were able to produce IAA which may promote plant root growth, 27 siderophores and 23 were phosphate solubilisers. Bacterial isolates were molecularly identified to be from various species of Bacillus, with some Arthrobacter, Enterobacter, Pseudomonas and Microbacterium. Inoculation of Spekboom cuttings with mycorrhizal fungi and selected rhizobacterial isolates significantly improved shoot height. Spekboom cuttings challenged with Fusarium and inoculated with mycorrhizal fungi and two rhizobacterial isolates significantly improved growth. The inoculation of cuttings in the nursery with mycorrhizal fungi and selected rhizobacteria is recommended prior to establishing Spekboom in the field.
- Full Text:
- Date Issued: 2016
Investigating the role of Hsp90 and LRP1 in FN matrix dynamics
- Authors: Boël, Natasha Marie-Eraine
- Date: 2016
- Subjects: Extracellular matrix , Molecular chaperones , Heat shock proteins , Cancer , Fibronectins
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2713 , vital:20319
- Description: Fibronectin (FN), a matrix protein responsible for regulating processes including migration and differentiation, is secreted as a soluble dimer which is assembled into an insoluble extracellular matrix. The dynamics of FN matrix assembly and degradation play a large role in cell migration and invasion contributing to the metastatic potential of cancer cells. Previous studies from our group have shown the direct binding of Hsp90 and FN in vitro and that inhibition of Hsp90 with novobiocin (NOV) caused internalisation of the FN matrix. However, the receptor mediating this internalisation is currently unknown. Low density lipoprotein 1 (LRP1) is a likely candidate as it is a ubiquitous receptor responsible for regulating internalisation of diverse ligands and is known to bind both Hsp90 and FN. We used wild type and knockout LRP1 cell lines to study the endocytosis of FN via this receptor. Here, we demonstrate that LRP1-deficient cells accumulated greatly increased levels of FN and were found to be less sensitive to pharmacological inhibition of Hsp90 by NOV. LRP1-expressing MEF-1 and Hs578T breast cancer cells experienced an increase in total FN in response to NOV, at concentrations below the EC50 value, followed by a dose-dependent loss of FN. We attributed greater FN levels to a loss of extracellular FN matrix coupled with increased internalisation of FN. Cell-surface biotinylation and DOC assays showed that loss of extracellular FN was specific to LRP1-expressing MEF-1 cells. Furthermore, we demonstrate that the loss of extracellular FN is not affected by changes in FN mRNA levels as determined by qRT-PCR, and that treatment with NOV resulted in the accelerated degradation of FN in the presence of cycloheximide. Immunoprecipitation studies reveal a putative complex exists between FN, Hsp90 and LRP1 in both cancer and non-cancer cells which is not perturbed by NOV. Western analyses revealed increased proteolytic processing of LRP1 in response to NOV which we proposed, based on literature, to modulate signalling pathways as a potential mechanism for regulating FN turnover. Moreover, using wound healing assays we identified increased migration to be one of the consequences associated with loss of extracellular FN by Hsp90 inhibition but only in cells containing LRP1. In summary, this study provides new insights into the Hsp90-LRP1 mediated loss of FN matrix and also reveals for the first time the functional consequence related to FN turnover by NOV was an increase in migration in LRP1-expressing cells.
- Full Text:
- Date Issued: 2016
- Authors: Boël, Natasha Marie-Eraine
- Date: 2016
- Subjects: Extracellular matrix , Molecular chaperones , Heat shock proteins , Cancer , Fibronectins
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2713 , vital:20319
- Description: Fibronectin (FN), a matrix protein responsible for regulating processes including migration and differentiation, is secreted as a soluble dimer which is assembled into an insoluble extracellular matrix. The dynamics of FN matrix assembly and degradation play a large role in cell migration and invasion contributing to the metastatic potential of cancer cells. Previous studies from our group have shown the direct binding of Hsp90 and FN in vitro and that inhibition of Hsp90 with novobiocin (NOV) caused internalisation of the FN matrix. However, the receptor mediating this internalisation is currently unknown. Low density lipoprotein 1 (LRP1) is a likely candidate as it is a ubiquitous receptor responsible for regulating internalisation of diverse ligands and is known to bind both Hsp90 and FN. We used wild type and knockout LRP1 cell lines to study the endocytosis of FN via this receptor. Here, we demonstrate that LRP1-deficient cells accumulated greatly increased levels of FN and were found to be less sensitive to pharmacological inhibition of Hsp90 by NOV. LRP1-expressing MEF-1 and Hs578T breast cancer cells experienced an increase in total FN in response to NOV, at concentrations below the EC50 value, followed by a dose-dependent loss of FN. We attributed greater FN levels to a loss of extracellular FN matrix coupled with increased internalisation of FN. Cell-surface biotinylation and DOC assays showed that loss of extracellular FN was specific to LRP1-expressing MEF-1 cells. Furthermore, we demonstrate that the loss of extracellular FN is not affected by changes in FN mRNA levels as determined by qRT-PCR, and that treatment with NOV resulted in the accelerated degradation of FN in the presence of cycloheximide. Immunoprecipitation studies reveal a putative complex exists between FN, Hsp90 and LRP1 in both cancer and non-cancer cells which is not perturbed by NOV. Western analyses revealed increased proteolytic processing of LRP1 in response to NOV which we proposed, based on literature, to modulate signalling pathways as a potential mechanism for regulating FN turnover. Moreover, using wound healing assays we identified increased migration to be one of the consequences associated with loss of extracellular FN by Hsp90 inhibition but only in cells containing LRP1. In summary, this study provides new insights into the Hsp90-LRP1 mediated loss of FN matrix and also reveals for the first time the functional consequence related to FN turnover by NOV was an increase in migration in LRP1-expressing cells.
- Full Text:
- Date Issued: 2016
Investigating the use of Arbuscular Mycorrhizas and Plant Growth Promoting Bacteria to improve the drought tolerance of maize (Zea mays L.)
- Authors: Moore, Nicolle Maureen
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54587 , vital:26591
- Description: Maize (Zea mays L.) is a direct staple food crop in Africa and remains an essential component of global food security, with maize crops accounting for over 60% of the total harvested area of annual food crops. Stress caused by drought and high soil salinity limits crop growth and productivity more than any other single environmental factor, with grain yield reductions up to 76% depending on the severity of the drought and the plant growth stage. Arbuscular mycorrhizal (AM) fungi and Plant Growth Promotion Rhizobacteria (PGPR) have previously been shown to improve tolerance of plants to drought stress through a number of chemical and physiological processes. The aim of this investigation was to determine whether mycorrhizal fungi and rhizobacteria adapted to drought and saline conditions and possessing plant growth promoting (PGP) traits were able to stimulate plant growth responses when applied to Zea mays seeds growing under greenhouse conditions Bacterial isolates selected were tolerant to concentrations of NaCl up to 600 mM and maintained 50% growth at low water potentials (-1.44 MPa). They were positive for Indole Acetic Acid (IAA) production, phosphate solubilisation and secretion of siderophores. Bacterial isolates showing plant growth promoting potential were identified using 16S rDNA gene sequencing as Achromobacter xylosoxidans strains A8 and C54 and Klebsiella oxytoca strain M1. Mixed inoculum was prepared from indigenous communities of mycorrhizas in soils sampled from the Cerebos Salt Pan and the Kalahari Desert. Mycorrhizal diversity was investigated using 454-Pyrosequencing which revealed that the community composition was dominated by species in the Ambispora, Glomus and Paraglomus genera with a rare component represented by species in the Redeckera, Archaeospora and Geosiphon genera. Microscopic examination of plant roots at the end of the trial revealed the presence of diagnostic mycorrhizal structures within the root cells, confirming that colonization was successful. Plant growth response to microbial inoculation was assessed by monitoring changes in plant photosynthetic capacity over the duration of a 7 week pot trial. A significant difference in photosynthetic and biomass data was observed between drought and well-watered groups but no mycorrhizal or bacterial treatment effect was evident within the groups, despite the high levels of colonization by mycorrhizas. These results suggest that the beneficial effects of mycorrhizal colonization may be primarily attributed to improved nutrient and mineral uptake in conditions where nutrients are limiting, resulting in improved growth. The improved growth may then have secondary effects on the plant‟s ability to withstand drought. Having controlled for nutrient deficiency, it was not evident in this study that mycorrhizal fungi were able to stimulate a change in plant physiology and confer drought tolerance under the conditions imposed.
- Full Text:
- Date Issued: 2016
- Authors: Moore, Nicolle Maureen
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54587 , vital:26591
- Description: Maize (Zea mays L.) is a direct staple food crop in Africa and remains an essential component of global food security, with maize crops accounting for over 60% of the total harvested area of annual food crops. Stress caused by drought and high soil salinity limits crop growth and productivity more than any other single environmental factor, with grain yield reductions up to 76% depending on the severity of the drought and the plant growth stage. Arbuscular mycorrhizal (AM) fungi and Plant Growth Promotion Rhizobacteria (PGPR) have previously been shown to improve tolerance of plants to drought stress through a number of chemical and physiological processes. The aim of this investigation was to determine whether mycorrhizal fungi and rhizobacteria adapted to drought and saline conditions and possessing plant growth promoting (PGP) traits were able to stimulate plant growth responses when applied to Zea mays seeds growing under greenhouse conditions Bacterial isolates selected were tolerant to concentrations of NaCl up to 600 mM and maintained 50% growth at low water potentials (-1.44 MPa). They were positive for Indole Acetic Acid (IAA) production, phosphate solubilisation and secretion of siderophores. Bacterial isolates showing plant growth promoting potential were identified using 16S rDNA gene sequencing as Achromobacter xylosoxidans strains A8 and C54 and Klebsiella oxytoca strain M1. Mixed inoculum was prepared from indigenous communities of mycorrhizas in soils sampled from the Cerebos Salt Pan and the Kalahari Desert. Mycorrhizal diversity was investigated using 454-Pyrosequencing which revealed that the community composition was dominated by species in the Ambispora, Glomus and Paraglomus genera with a rare component represented by species in the Redeckera, Archaeospora and Geosiphon genera. Microscopic examination of plant roots at the end of the trial revealed the presence of diagnostic mycorrhizal structures within the root cells, confirming that colonization was successful. Plant growth response to microbial inoculation was assessed by monitoring changes in plant photosynthetic capacity over the duration of a 7 week pot trial. A significant difference in photosynthetic and biomass data was observed between drought and well-watered groups but no mycorrhizal or bacterial treatment effect was evident within the groups, despite the high levels of colonization by mycorrhizas. These results suggest that the beneficial effects of mycorrhizal colonization may be primarily attributed to improved nutrient and mineral uptake in conditions where nutrients are limiting, resulting in improved growth. The improved growth may then have secondary effects on the plant‟s ability to withstand drought. Having controlled for nutrient deficiency, it was not evident in this study that mycorrhizal fungi were able to stimulate a change in plant physiology and confer drought tolerance under the conditions imposed.
- Full Text:
- Date Issued: 2016
Isolation, characterization and biomimetic oxidation of selected marine natural products and their analogues
- Authors: Mutsvairo, Tafadzwa
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/64685 , vital:28592
- Description: Marine brown algae produce a variety of terpenes with a wide range of biological activities. However, very few phytochemical studies of brown algae have been conducted in South Africa. Therefore, in our continued search for biologically active natural products, we examined the South African brown alga Brassicophycus brassicaeformis. The dichloromethane-methanol extract of B.brassicaeformis was fractionated by silica gel column chromatography followed by normal phase HPLC to give pure four pure compounds which were identified by spectroscopic methods as; fucosterol, fucoxanthin and two monogalactosyldiacylglycerol lipids. Many potential drug molecules such as natural products have failed to reach the market due to poor pharmacokinetic and metabolic profiles despite having potent biological activity. Therefore the importance of early drug metabolism studies in the drug development process is clear. A biomimetic oxidation model was used for in vitro drug metabolism studies to predict any possible metabolites that could be produced by these natural products. Two biomimetic oxidation models catalyzed by two water soluble metalloporphyrins as biomimics of cytochrome P450, in the presence of two terminal oxidants either hydrogen peroxide or iodobenzene diacetete were successfully developed. The models were applied to a range of natural products. The oxidation of the quinone natural products, sargahydroquinoic acid, and lapachol was most easily achieved by metalloporphyrins employed in this study.
- Full Text:
- Date Issued: 2016
- Authors: Mutsvairo, Tafadzwa
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/64685 , vital:28592
- Description: Marine brown algae produce a variety of terpenes with a wide range of biological activities. However, very few phytochemical studies of brown algae have been conducted in South Africa. Therefore, in our continued search for biologically active natural products, we examined the South African brown alga Brassicophycus brassicaeformis. The dichloromethane-methanol extract of B.brassicaeformis was fractionated by silica gel column chromatography followed by normal phase HPLC to give pure four pure compounds which were identified by spectroscopic methods as; fucosterol, fucoxanthin and two monogalactosyldiacylglycerol lipids. Many potential drug molecules such as natural products have failed to reach the market due to poor pharmacokinetic and metabolic profiles despite having potent biological activity. Therefore the importance of early drug metabolism studies in the drug development process is clear. A biomimetic oxidation model was used for in vitro drug metabolism studies to predict any possible metabolites that could be produced by these natural products. Two biomimetic oxidation models catalyzed by two water soluble metalloporphyrins as biomimics of cytochrome P450, in the presence of two terminal oxidants either hydrogen peroxide or iodobenzene diacetete were successfully developed. The models were applied to a range of natural products. The oxidation of the quinone natural products, sargahydroquinoic acid, and lapachol was most easily achieved by metalloporphyrins employed in this study.
- Full Text:
- Date Issued: 2016
Leopard population density and community attitudes towards leopards in and around Debshan Ranch, Shangani, Zimbabwe
- Authors: Nyoni, Phumuzile
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5946 , http://hdl.handle.net/10962/d1020838
- Description: Leopards (Panthera pardus) are regarded as one of the most resilient large carnivore species in the world and can persist in human dominated landscapes, areas with low prey availability nd highly fragmented habitats. However, recent evidence across much of their range reveals declining populations. In Zimbabwe, 500 Convention for the International Trade in Endangered Species (CITES) export tags are available annually for leopards as hunting trophies, despite limited accurate data on the leopard populations of the country. Moreover, when coupled with the massive land conversions under the controversial National Land Reform Programme (NLRP), leopard populations in Zimbabwe are in dire need of assessment. My study was conducted on Debshan ranch, Shangani, Zimbabwe, which is a commercial cattle (Bos indicus) ranch but also supports a high diversity of indigenous wildlife including an apparently healthy leopard population. However, the NLRP has resulted in an increase in small-holder subsistence farming communities around the ranch (the land was previously privately owned and divided into larger sub-units). This change in land-use means that both human and livestock densities have increased and the potential for human leopard conflict has increased. I estimated the leopard population density of the ranch and assessed community attitudes towards leopards in the communities surrounding the ranch. To estimate population densities, I performed spoor counts and conducted a camera trapping survey. Questionnaire interviews were used to assess community attitudes. My spoor counts provided a leopard density estimate of 13.57 leopards/100km2 compared to the camera trapping estimate of between 2.0 and 6.9 leopards/100km2. Although the high density estimate derived from the spoor counts is possible for Debshan because leopards are the apex predators and are adequately protected, potential edge effects are not yet fully understood. Thus, the more conservative estimate of 2.0 leopards/100km2, derived from the camera trapping survey, is probably more appropriate. Attitudes towards predators amongst respondents surrounding Debshan (n = 140) were neither too negative nor positive, attitude index had a mean score of 1.7 ± 3.8 (range: -7 – 10). No single predictor variable used in my analysis was able to adequately explain why the communities held these negative views. However, livestock losses were repeatedly listed by respondents as being one of the main reasons for their lack of tolerance towards predators. The density estimate of 2.0 leopards/100km2 translates to a population of 9 – 26 leopards within Debshan ranch. This density estimate is too low considering the habitat type at Debshan ranch but should be interpreted with caution as it lacks fundamental elements like age and sex ratio. Moreover, the interaction of the leopard population with the surrounding communities is currently unclear. As a precautionary measure, I recommended reducing the annual hunting quota for Debshan from five to one leopard. Future work should aim to improve the attitudes of the surrounding communities to secure broader landscapes for leopard conservation while also reconciling density estimates to fully understand the leopard population of the region.
- Full Text:
- Date Issued: 2016
- Authors: Nyoni, Phumuzile
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5946 , http://hdl.handle.net/10962/d1020838
- Description: Leopards (Panthera pardus) are regarded as one of the most resilient large carnivore species in the world and can persist in human dominated landscapes, areas with low prey availability nd highly fragmented habitats. However, recent evidence across much of their range reveals declining populations. In Zimbabwe, 500 Convention for the International Trade in Endangered Species (CITES) export tags are available annually for leopards as hunting trophies, despite limited accurate data on the leopard populations of the country. Moreover, when coupled with the massive land conversions under the controversial National Land Reform Programme (NLRP), leopard populations in Zimbabwe are in dire need of assessment. My study was conducted on Debshan ranch, Shangani, Zimbabwe, which is a commercial cattle (Bos indicus) ranch but also supports a high diversity of indigenous wildlife including an apparently healthy leopard population. However, the NLRP has resulted in an increase in small-holder subsistence farming communities around the ranch (the land was previously privately owned and divided into larger sub-units). This change in land-use means that both human and livestock densities have increased and the potential for human leopard conflict has increased. I estimated the leopard population density of the ranch and assessed community attitudes towards leopards in the communities surrounding the ranch. To estimate population densities, I performed spoor counts and conducted a camera trapping survey. Questionnaire interviews were used to assess community attitudes. My spoor counts provided a leopard density estimate of 13.57 leopards/100km2 compared to the camera trapping estimate of between 2.0 and 6.9 leopards/100km2. Although the high density estimate derived from the spoor counts is possible for Debshan because leopards are the apex predators and are adequately protected, potential edge effects are not yet fully understood. Thus, the more conservative estimate of 2.0 leopards/100km2, derived from the camera trapping survey, is probably more appropriate. Attitudes towards predators amongst respondents surrounding Debshan (n = 140) were neither too negative nor positive, attitude index had a mean score of 1.7 ± 3.8 (range: -7 – 10). No single predictor variable used in my analysis was able to adequately explain why the communities held these negative views. However, livestock losses were repeatedly listed by respondents as being one of the main reasons for their lack of tolerance towards predators. The density estimate of 2.0 leopards/100km2 translates to a population of 9 – 26 leopards within Debshan ranch. This density estimate is too low considering the habitat type at Debshan ranch but should be interpreted with caution as it lacks fundamental elements like age and sex ratio. Moreover, the interaction of the leopard population with the surrounding communities is currently unclear. As a precautionary measure, I recommended reducing the annual hunting quota for Debshan from five to one leopard. Future work should aim to improve the attitudes of the surrounding communities to secure broader landscapes for leopard conservation while also reconciling density estimates to fully understand the leopard population of the region.
- Full Text:
- Date Issued: 2016
Local versus landscape effects of bush encroachment on plant available light, soil moisture, frost occurrence and herbaceous productivity and composition
- Authors: Klopper, Chrisna
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3137 , vital:20376
- Description: Bush encroachment is a global phenomenon and a pressing concern for South Africa rangelands. The expansion and increase in density of Vachellia karroo (hereafter referred to aAcacia karroo) has been documented in the Eastern Cape and KwaZulu Natal in South Africa. This increase in woody species in savannas is often at the expense of grass cover and thus is causing concern about how this will impact agriculture due to possible loss of grazing capacity. To understand the impacts of bush encroachment the effect of trees on their micro-climate and abiotic factors and in turn on the herbaceous layer needs to be examined. The objective of this study was to quantify the effect of Acacia karroo encroachment on the light environment, soil moisture and frost occurrence in the sub-canopy and inter-canopy micro-habitats, and how these changes affected herbaceous player productivity and composition. Another question that is being addressed here is whether, and how, the local tree effects scale up in the landscape and whether prediction can be made based on the effects of individual trees. The study was undertaken on a farm, Endwell, in the Smaldeel, Eastern Cape. At the study site, a semi-arid savanna, Acacia karroo has been encroaching since the 1980’s. The study was conducted at three scales: landscape, stand-wide and local scale. The landscape scale was represented by four areas with 0, 21, 45 and 72% tree canopy cover, the stand-wide scale consisted of transects with varying percentages of tree canopy cover within each of the four levels of encroachment. The local scale was represented by the sub-canopy and inter-canopy environment to test the effect of trees. At the local scale plant available light and soil moisture were lower in the sub-canopy than intercanopy regions, with leaf area index being higher in the sub-canopy. This local negative effect of the tree canopy on light and soil moisture in the sub-canopy did not scale up predictably in the landscape. At the stand-wide scale light in the inter-canopy was reduced as shading increased. Frost was excluded from under the canopies and frost incidence decreased at higher tree cover. Grass productivity was reduced in the sub-canopy, possibly due to lower light and soil moisture. Overall biomass increased from the low to medium level of encroachment but lowest at the high level of encroachment. Grass composition and cover was only slightly affected by tree canopies cover and C4 grass species were still present in the sub-canopy and at lower light environments. At the levels of Acacia karroo encroachment encountered at this study site, it seems unlikely that palatable or desirable C4 would be excluded from the system and that a shift from C4 to shade-tolerant species would occur. This is due to tree canopies at the site not reducing light to such anextent that they would outcompete grasses, and likely the very low grazing pressure at thesesites. Herbaceous biomass at these sites were still sufficient to carry a fire in the inter-canopyregion and sufficient grazing for herbivores. In the sub-canopy region fires will be excluded thus with higher the portion of sub-canopy areas increasing at the high levels of encroachment they may interrupt fire spread. Thus it was concluded that Acacia karroo encroachment up to 45% tree cover is currently not creating negative feedback on herbivory, but low stocking rates appear to be key to maintain this.
- Full Text:
- Date Issued: 2016
- Authors: Klopper, Chrisna
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3137 , vital:20376
- Description: Bush encroachment is a global phenomenon and a pressing concern for South Africa rangelands. The expansion and increase in density of Vachellia karroo (hereafter referred to aAcacia karroo) has been documented in the Eastern Cape and KwaZulu Natal in South Africa. This increase in woody species in savannas is often at the expense of grass cover and thus is causing concern about how this will impact agriculture due to possible loss of grazing capacity. To understand the impacts of bush encroachment the effect of trees on their micro-climate and abiotic factors and in turn on the herbaceous layer needs to be examined. The objective of this study was to quantify the effect of Acacia karroo encroachment on the light environment, soil moisture and frost occurrence in the sub-canopy and inter-canopy micro-habitats, and how these changes affected herbaceous player productivity and composition. Another question that is being addressed here is whether, and how, the local tree effects scale up in the landscape and whether prediction can be made based on the effects of individual trees. The study was undertaken on a farm, Endwell, in the Smaldeel, Eastern Cape. At the study site, a semi-arid savanna, Acacia karroo has been encroaching since the 1980’s. The study was conducted at three scales: landscape, stand-wide and local scale. The landscape scale was represented by four areas with 0, 21, 45 and 72% tree canopy cover, the stand-wide scale consisted of transects with varying percentages of tree canopy cover within each of the four levels of encroachment. The local scale was represented by the sub-canopy and inter-canopy environment to test the effect of trees. At the local scale plant available light and soil moisture were lower in the sub-canopy than intercanopy regions, with leaf area index being higher in the sub-canopy. This local negative effect of the tree canopy on light and soil moisture in the sub-canopy did not scale up predictably in the landscape. At the stand-wide scale light in the inter-canopy was reduced as shading increased. Frost was excluded from under the canopies and frost incidence decreased at higher tree cover. Grass productivity was reduced in the sub-canopy, possibly due to lower light and soil moisture. Overall biomass increased from the low to medium level of encroachment but lowest at the high level of encroachment. Grass composition and cover was only slightly affected by tree canopies cover and C4 grass species were still present in the sub-canopy and at lower light environments. At the levels of Acacia karroo encroachment encountered at this study site, it seems unlikely that palatable or desirable C4 would be excluded from the system and that a shift from C4 to shade-tolerant species would occur. This is due to tree canopies at the site not reducing light to such anextent that they would outcompete grasses, and likely the very low grazing pressure at thesesites. Herbaceous biomass at these sites were still sufficient to carry a fire in the inter-canopyregion and sufficient grazing for herbivores. In the sub-canopy region fires will be excluded thus with higher the portion of sub-canopy areas increasing at the high levels of encroachment they may interrupt fire spread. Thus it was concluded that Acacia karroo encroachment up to 45% tree cover is currently not creating negative feedback on herbivory, but low stocking rates appear to be key to maintain this.
- Full Text:
- Date Issued: 2016
Localizing selected endocytosis protein candidates in Plasmodium falciparum using GFP-tagged fusion constructs
- Authors: Basson, Travis
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2680 , vital:20316
- Description: Malaria is a mosquito-borne infectious disease caused by several obligate intracellular protozoan parasites in the Plasmodium genus, with Plasmodium falciparum causing the most widespread cases and malaria deaths. In 2013 there were approximately 190 million cases of the disease and between 584,000 and 855,000 deaths. It is essential to identify novel drug targets and develop novel drug candidates due to the increase in resistance of P. falciparum parasites to the current arsenal of antimalarial drugs. Endocytosis is an essential process in eukaryotic cells in which the external environment is internalized by the cell in order to obtain various particles from the extracellular space. This extracellular cytoplasm is internalized in membrane-bound invaginations at the plasma membrane. During the blood stage of malaria infection, the parasite requires nutrients from the host red blood cell. To obtain these nutrients, the parasite internalizes haemoglobin in large amounts and degrades it in an acidic, lysosome-like organelle, known as the digestive vacuole. Whilst the exact molecular mechanism of malaria parasite endocytosis is not yet fully understood, a number of proteins have been suggested to be involved. The most expedient approach in identifying candidate endocytosis proteins is to investigate parasite homologues of proteins known to be involved in endocytosis in mammalian cells. The three proteins selected for investigation in this study were the P. falciparum homologues of coronin, dynamin 2, and μ4. The coding sequences for the candidate endocytosis proteins were amplified by PCR and cloned into the pARL2-GFP expression vector. P. falciparum 3D7 parasites were transfected with these vectors and the episomal expression of full-length GFP-tagged fusion protein was confirmed by Western blot analysis using commercially available anti-GFP antibodies. Microscopic analysis of live parasites using fluorescence and confocal microscopy was used to determine the localization of the candidate endocytosis proteins. Coronin appeared to display diffuse cytoplasmic GFP localization during the trophozoite stage, arguing against a role in endocytosis. However, distinct localization during the schizont stage at what appears to be the inner membrane complex was observed. Coronin is thus likely required to coordinate the formation of the actin network between the merozoite IMC and the plasma membrane on which the glideosome is dependant for generating the motile forces required for the merozoite motility and invasion of RBCs. Dynamin 2 displayed localization at three potential locii: the parasite periphery (plasma membrane), punctuate regions within the cytoplasm (potentially at membrane bound organelles) and at the parasite food vacuole. The data suggested that dynamin 2 is involved in endocytosis and membrane trafficking in a similar manner to classical dynamins, potentially as a vesicle scission molecule at the plasma membrane, mediating vesicle formation at the food vacuole to recycle membrane to the plasma membrane, and possibly mitochondria organelle division. μ4 displayed transient localization, cycling between cytosolic localization, and localization to distinct regions at the plasma membrane and the food vacuole. Localization of Pfμ4 to the plasma membrane is indicative of a role for μ4 as a part of an adaptor protein (AP) complex which may be responsible for recruitment of clathrin to initiate endocytosis in a manner similar to mammalian AP-2. As was observed with PfDYN2, Pfμ4 localizes to the FV, which suggests that Pfμ4 forms part of a coat complex that mediates the formation of vesicles that recycle membrane from the FV to the parasite plasma membrane. This study showed that expressing proteins as full-length GFP-tagged fusion constructs is an effective approach in the early stages of determining the localization and function of P. falciparum proteins in vitro, and distinguishing between candidates that have a potential role in endocytosis and those that are unlikely to do so.
- Full Text:
- Date Issued: 2016
- Authors: Basson, Travis
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2680 , vital:20316
- Description: Malaria is a mosquito-borne infectious disease caused by several obligate intracellular protozoan parasites in the Plasmodium genus, with Plasmodium falciparum causing the most widespread cases and malaria deaths. In 2013 there were approximately 190 million cases of the disease and between 584,000 and 855,000 deaths. It is essential to identify novel drug targets and develop novel drug candidates due to the increase in resistance of P. falciparum parasites to the current arsenal of antimalarial drugs. Endocytosis is an essential process in eukaryotic cells in which the external environment is internalized by the cell in order to obtain various particles from the extracellular space. This extracellular cytoplasm is internalized in membrane-bound invaginations at the plasma membrane. During the blood stage of malaria infection, the parasite requires nutrients from the host red blood cell. To obtain these nutrients, the parasite internalizes haemoglobin in large amounts and degrades it in an acidic, lysosome-like organelle, known as the digestive vacuole. Whilst the exact molecular mechanism of malaria parasite endocytosis is not yet fully understood, a number of proteins have been suggested to be involved. The most expedient approach in identifying candidate endocytosis proteins is to investigate parasite homologues of proteins known to be involved in endocytosis in mammalian cells. The three proteins selected for investigation in this study were the P. falciparum homologues of coronin, dynamin 2, and μ4. The coding sequences for the candidate endocytosis proteins were amplified by PCR and cloned into the pARL2-GFP expression vector. P. falciparum 3D7 parasites were transfected with these vectors and the episomal expression of full-length GFP-tagged fusion protein was confirmed by Western blot analysis using commercially available anti-GFP antibodies. Microscopic analysis of live parasites using fluorescence and confocal microscopy was used to determine the localization of the candidate endocytosis proteins. Coronin appeared to display diffuse cytoplasmic GFP localization during the trophozoite stage, arguing against a role in endocytosis. However, distinct localization during the schizont stage at what appears to be the inner membrane complex was observed. Coronin is thus likely required to coordinate the formation of the actin network between the merozoite IMC and the plasma membrane on which the glideosome is dependant for generating the motile forces required for the merozoite motility and invasion of RBCs. Dynamin 2 displayed localization at three potential locii: the parasite periphery (plasma membrane), punctuate regions within the cytoplasm (potentially at membrane bound organelles) and at the parasite food vacuole. The data suggested that dynamin 2 is involved in endocytosis and membrane trafficking in a similar manner to classical dynamins, potentially as a vesicle scission molecule at the plasma membrane, mediating vesicle formation at the food vacuole to recycle membrane to the plasma membrane, and possibly mitochondria organelle division. μ4 displayed transient localization, cycling between cytosolic localization, and localization to distinct regions at the plasma membrane and the food vacuole. Localization of Pfμ4 to the plasma membrane is indicative of a role for μ4 as a part of an adaptor protein (AP) complex which may be responsible for recruitment of clathrin to initiate endocytosis in a manner similar to mammalian AP-2. As was observed with PfDYN2, Pfμ4 localizes to the FV, which suggests that Pfμ4 forms part of a coat complex that mediates the formation of vesicles that recycle membrane from the FV to the parasite plasma membrane. This study showed that expressing proteins as full-length GFP-tagged fusion constructs is an effective approach in the early stages of determining the localization and function of P. falciparum proteins in vitro, and distinguishing between candidates that have a potential role in endocytosis and those that are unlikely to do so.
- Full Text:
- Date Issued: 2016
Mapping Nitrogen Loading in Freshwater Systems: Using Aquatic Biota to Trace Nutrients
- Authors: Motitsoe, Samuel Nkopane
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5945 , http://hdl.handle.net/10962/d1020819
- Description: The majority of river systems in developing countries like South Africa, are found in catchments areas that are densely human populated, therefore are subjected to intense land-use and developmental pressures. Anthropogenic nutrient pollution or the excessive addition of nutrients is one important type of stressors that river systems often experience through intense land-use, which includes poor waste management and agricultural practices. Such events are referred to as the “urban syndrome”, were human populations and developmental demands outpace ecosystem services. Traditional measurements of water quality (e.g. physicochemical and micro-nutrient assessments) and biological monitoring (e.g. South African Scoring System 5, SASS5) techniques for assessing ecosystem health have being widely used to reflect the ecological health and status of river systems. However these techniques have a number of challenges associated with their application. SASS5 which is used most prevalently in southern Africa for example, can only be applied in lotic systems, it is habitat dependent and finally (but arguably most importantly) it cannot identify the source of pollution inputs. Recent laboratory studies using stable isotopic ratios (δ15N and δ13C) of aquatic macrophytes (duckweed: Spirodela sp.) have shown successful differentiation between different N-sources and the mapping of temporal and spatial nitrogen dynamics in freshwater systems. Furthermore δ15N isotopic values of Spirodela sp. showed the capability to act as an early warning indicator of eutrophication, before the onset of aquatic ecosystem degradation. Therefore, this study aimed to field test the potential of sewage plume mapping using the stable isotopic values of Spirodela sp. and aquatic macroinvertebrates at nine study sites on the Bloukrans-Kowie River and ten study sites on the Bushman-New Year’s River systems in the Eastern Cape, South Africa. And more...
- Full Text:
- Date Issued: 2016
- Authors: Motitsoe, Samuel Nkopane
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5945 , http://hdl.handle.net/10962/d1020819
- Description: The majority of river systems in developing countries like South Africa, are found in catchments areas that are densely human populated, therefore are subjected to intense land-use and developmental pressures. Anthropogenic nutrient pollution or the excessive addition of nutrients is one important type of stressors that river systems often experience through intense land-use, which includes poor waste management and agricultural practices. Such events are referred to as the “urban syndrome”, were human populations and developmental demands outpace ecosystem services. Traditional measurements of water quality (e.g. physicochemical and micro-nutrient assessments) and biological monitoring (e.g. South African Scoring System 5, SASS5) techniques for assessing ecosystem health have being widely used to reflect the ecological health and status of river systems. However these techniques have a number of challenges associated with their application. SASS5 which is used most prevalently in southern Africa for example, can only be applied in lotic systems, it is habitat dependent and finally (but arguably most importantly) it cannot identify the source of pollution inputs. Recent laboratory studies using stable isotopic ratios (δ15N and δ13C) of aquatic macrophytes (duckweed: Spirodela sp.) have shown successful differentiation between different N-sources and the mapping of temporal and spatial nitrogen dynamics in freshwater systems. Furthermore δ15N isotopic values of Spirodela sp. showed the capability to act as an early warning indicator of eutrophication, before the onset of aquatic ecosystem degradation. Therefore, this study aimed to field test the potential of sewage plume mapping using the stable isotopic values of Spirodela sp. and aquatic macroinvertebrates at nine study sites on the Bloukrans-Kowie River and ten study sites on the Bushman-New Year’s River systems in the Eastern Cape, South Africa. And more...
- Full Text:
- Date Issued: 2016
Measuring changes in residential segregation in Port Elizabeth, South Africa, from 1996-2011
- Authors: Odayar, Luveshni
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3641 , vital:20532
- Description: Racial segregation and inequality were the prime objectives of the colonial and apartheid spatial planning policies that governed the spatial development of the South African urban landscape. Since South Africa’s democratic transition after 1994, efforts have been made by government to facilitate racial integration and transform the apartheid urban fabric. Research into post-apartheid segregation is crucial to assess the success of governmental actions enacted thus far, while informing future spatial planning strategies. Most studies of these processes have relied solely on dichotomous indices to measure the extent of segregation between two groups. Few have utilized multi-group indices, which are more suited to investigating changes in multi-ethnic cases. Furthermore, the segregation indices used are typically aspatial. This study investigates the extent to which the segregationist legacy prevails in Port Elizabeth, a place widely considered to be the founding city of urban racial segregation. It also aims to investigate the impact of geographical scale on segregation. Theil’s multi-group Entropy Index and Duncan and Duncan’s Dissimilarity Index were derived from racial population data from the 1996, 2001 and 2011 National Censuses, and GIS was used to map changes in racial diversity both at tract level and across a range of geographical scales. To generate a more holistic understanding of the observed trends, statistical tests were performed to relate the observed patterns to socio-economic determinants, and feedback from the relevant government department was obtained. The results from the entropy indices reveal that segregation levels in Port Elizabeth have declined but still remain high: 84.6 % (1996), 79.2 % (2001) to 71.5 % (2011). This is a similar trend to those found in Cape Town and Johannesburg. The integration that did occur was characterized by one-way patterns of movement into former-White areas; this was predominantly confined to the Indian population, and to a lesser extent, the Coloured population. The vast majority of the African population remains confined to their former designated location areas. The White population remains the most segregated group, despite most of the racial integration occurring in former-White areas. Interview results and statistical tests revealed that persisting racial discrepancies in socio-economic factors (income, employment and education) can be considered major drivers influencing the observed trends in racial integration and persisting desegregation, as well as self-segregation.
- Full Text:
- Date Issued: 2016
- Authors: Odayar, Luveshni
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3641 , vital:20532
- Description: Racial segregation and inequality were the prime objectives of the colonial and apartheid spatial planning policies that governed the spatial development of the South African urban landscape. Since South Africa’s democratic transition after 1994, efforts have been made by government to facilitate racial integration and transform the apartheid urban fabric. Research into post-apartheid segregation is crucial to assess the success of governmental actions enacted thus far, while informing future spatial planning strategies. Most studies of these processes have relied solely on dichotomous indices to measure the extent of segregation between two groups. Few have utilized multi-group indices, which are more suited to investigating changes in multi-ethnic cases. Furthermore, the segregation indices used are typically aspatial. This study investigates the extent to which the segregationist legacy prevails in Port Elizabeth, a place widely considered to be the founding city of urban racial segregation. It also aims to investigate the impact of geographical scale on segregation. Theil’s multi-group Entropy Index and Duncan and Duncan’s Dissimilarity Index were derived from racial population data from the 1996, 2001 and 2011 National Censuses, and GIS was used to map changes in racial diversity both at tract level and across a range of geographical scales. To generate a more holistic understanding of the observed trends, statistical tests were performed to relate the observed patterns to socio-economic determinants, and feedback from the relevant government department was obtained. The results from the entropy indices reveal that segregation levels in Port Elizabeth have declined but still remain high: 84.6 % (1996), 79.2 % (2001) to 71.5 % (2011). This is a similar trend to those found in Cape Town and Johannesburg. The integration that did occur was characterized by one-way patterns of movement into former-White areas; this was predominantly confined to the Indian population, and to a lesser extent, the Coloured population. The vast majority of the African population remains confined to their former designated location areas. The White population remains the most segregated group, despite most of the racial integration occurring in former-White areas. Interview results and statistical tests revealed that persisting racial discrepancies in socio-economic factors (income, employment and education) can be considered major drivers influencing the observed trends in racial integration and persisting desegregation, as well as self-segregation.
- Full Text:
- Date Issued: 2016
Mesopredator release and the effectiveness of camera traps for estimating mammal abundances in the Eastern Cape, South Africa
- Authors: Taylor, Jonathan Michael
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3587 , vital:20527
- Description: Remotely operated cameras (camera traps) have become an indispensable tool for many ecologists, particularly those studying rare and elusive animals. A plethora of camera trap makes and models are now commercially available, yet the effects of their varying design features on the quality and quantity of data recorded remains principally unknown. Better understanding of differing camera trap designs is needed before adequate management policies can be implemented, especially when the aim is to protect vulnerable and endangered species such as many carnivores. Habitat loss and human conflict has prompted worldwide declines of apex predator populations. Following this, many smaller predators have undergone population ‘explosions’ due to the lack of top-down forcing, a phenomenon known as mesopredator release. Land use changes in the Eastern Cape of South Africa have caused extensive degradation and fragmentation of the Subtropical Thicket Biome. In addition, coupled with anthropogenic persecution, apex predators including lions (Panthera leo), leopards (P. pardus), and brown hyaenas (Hyaena brunnea) have been extirpated from large areas of their historic range. Removal of these apex predators may provide opportunity for mesopredators, such as black-backed jackals (Canis mesomelas) and caracals (Caracal caracal), to be released from top-down forcing and possibly initiate trophic cascade effects. Therefore, using randomly distributed camera traps, my study aimed to explore the quality and quantity of data collected by different camera trap designs, and to investigate the mesopredator release hypothesis in the Eastern Cape of South Africa. A total of 2,989 trap nights was used to compare camera trap designs. Camera traps with narrow detection zones and fast trigger speeds (≤ 0.25 seconds) recorded a higher diversity of carnivores, but there was no significant difference in the relative abundances of carnivore species recorded by different camera trap models. A total of 19,659 trap nights was used to assess mesopredator relative abundance, occupancy, distribution and daily activity patterns at one site with, and one site without, apex predators. Consistent with the mesopredator release hypothesis, black-backed jackal relative abundance was significantly higher in the absence of apex predators, and this was supported by occupancy analyses. Further, black-backed jackal distribution was significantly concentrated in areas where apex predator activity was low, possibly indicating spatial avoidance. There was no significant difference in caracal relative abundance, occupancy, distribution, or daily activity between sites. These results provide the first indication of mesopredator release of blackbacked jackals in the Eastern Cape. The implications of black-backed jackal release including prey population structure, local extinctions, altered seed dispersal and disease dynamics are discussed.
- Full Text:
- Date Issued: 2016
- Authors: Taylor, Jonathan Michael
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3587 , vital:20527
- Description: Remotely operated cameras (camera traps) have become an indispensable tool for many ecologists, particularly those studying rare and elusive animals. A plethora of camera trap makes and models are now commercially available, yet the effects of their varying design features on the quality and quantity of data recorded remains principally unknown. Better understanding of differing camera trap designs is needed before adequate management policies can be implemented, especially when the aim is to protect vulnerable and endangered species such as many carnivores. Habitat loss and human conflict has prompted worldwide declines of apex predator populations. Following this, many smaller predators have undergone population ‘explosions’ due to the lack of top-down forcing, a phenomenon known as mesopredator release. Land use changes in the Eastern Cape of South Africa have caused extensive degradation and fragmentation of the Subtropical Thicket Biome. In addition, coupled with anthropogenic persecution, apex predators including lions (Panthera leo), leopards (P. pardus), and brown hyaenas (Hyaena brunnea) have been extirpated from large areas of their historic range. Removal of these apex predators may provide opportunity for mesopredators, such as black-backed jackals (Canis mesomelas) and caracals (Caracal caracal), to be released from top-down forcing and possibly initiate trophic cascade effects. Therefore, using randomly distributed camera traps, my study aimed to explore the quality and quantity of data collected by different camera trap designs, and to investigate the mesopredator release hypothesis in the Eastern Cape of South Africa. A total of 2,989 trap nights was used to compare camera trap designs. Camera traps with narrow detection zones and fast trigger speeds (≤ 0.25 seconds) recorded a higher diversity of carnivores, but there was no significant difference in the relative abundances of carnivore species recorded by different camera trap models. A total of 19,659 trap nights was used to assess mesopredator relative abundance, occupancy, distribution and daily activity patterns at one site with, and one site without, apex predators. Consistent with the mesopredator release hypothesis, black-backed jackal relative abundance was significantly higher in the absence of apex predators, and this was supported by occupancy analyses. Further, black-backed jackal distribution was significantly concentrated in areas where apex predator activity was low, possibly indicating spatial avoidance. There was no significant difference in caracal relative abundance, occupancy, distribution, or daily activity between sites. These results provide the first indication of mesopredator release of blackbacked jackals in the Eastern Cape. The implications of black-backed jackal release including prey population structure, local extinctions, altered seed dispersal and disease dynamics are discussed.
- Full Text:
- Date Issued: 2016
Mesoscale mechanisms of larval transport and settlement in relation to physical factors off the south coast of South Africa: a topographic approach
- Authors: Mian, Shana Iva
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5947 , http://hdl.handle.net/10962/d1020844
- Description: The majority of benthic marine invertebrate life cycles include a meroplanktonic phase. Most marine biologists recognise that this stage could play an important role in dispersal, especially for sedentary or sessile organisms. Recent studies on larval dispersal have found that dispersal does not occur to the extent that was previously believed. Some larvae instead remain close to their natal populations through larval nearshore retention mechanisms, both active and passive. This study attempted to a) describe nearshore distribution patterns of several intertidal larvae in relation to nearshore hydrodynamics, b) infer whether larvae are active or passive in the water column and whether this differs among taxa and c) compare pelagic mussel larval abundance with settlement rates, at 2 bay and 2 open coast sites on the south coast of South Africa to note any topographical effects. At each of the four sites, pelagic samples were collected along 2 transects. Larvae and current speed data were collected at various depths (surface, mid-depth and bottom) at distances of 200, 400, 900 and 2400m offshore of the coast. Settlement samples were collected at sites that were onshore of the pelagic transects using plastic souring pads following previous studies. Pelagic larval distribution showed no effect of topography. Instead larval abundance was highly variable among sample periods and among different taxa. Slow swimming D-stage mussel larvae were found to be positively correlated with both upwelling and turbulence indices suggesting that they behave as passive particles in the water column. The abundances of larval taxa with faster swimming speeds than the D-larvae were negatively correlated with upwelling and did not correlate with turbulence. This suggests that these larvae are more active within the water column than the D-larvae which would theoretically allow them to maintain their position in the water column. Further analysis revealed that mean larval depth correlated with mean depth of shoreward moving water masses regardless of the state of upwelling. These results suggest that larvae were actively selecting the depth at which they were found presumably in order to associate themselves with shoreward moving currents. This interpretation was supported by ontogenetic patterns in the behaviour of barnacle larvae, the nauplii of which were found further offshore as they aged, and closer onshore again once they reach the faster swimming cyprid stage. Although there was no detectable effect of topography on the abundances of planktonic larvae, the settlement section of this study revealed an effect of topography, with higher settlement and recruitment rates at bay sites than at the open coast sites. Settlement rates were seen to be negatively correlated with turbulence at bay sites but not open coast sites. Recruitment rates for each sample event were positively correlated with upwelling at each site. This study found pelagic larvae to be generally active within the water column which allowed them to remain close to the shore regardless of topography and upwelling/turbulence regimes. Although meaningful correlation analyses between pelagic larval supply and settlement rates could not be conducted due to loss of settlement collectors, settlement rates were affected by local topography with higher settlement and recruitment in bay sites.
- Full Text:
- Date Issued: 2016
- Authors: Mian, Shana Iva
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5947 , http://hdl.handle.net/10962/d1020844
- Description: The majority of benthic marine invertebrate life cycles include a meroplanktonic phase. Most marine biologists recognise that this stage could play an important role in dispersal, especially for sedentary or sessile organisms. Recent studies on larval dispersal have found that dispersal does not occur to the extent that was previously believed. Some larvae instead remain close to their natal populations through larval nearshore retention mechanisms, both active and passive. This study attempted to a) describe nearshore distribution patterns of several intertidal larvae in relation to nearshore hydrodynamics, b) infer whether larvae are active or passive in the water column and whether this differs among taxa and c) compare pelagic mussel larval abundance with settlement rates, at 2 bay and 2 open coast sites on the south coast of South Africa to note any topographical effects. At each of the four sites, pelagic samples were collected along 2 transects. Larvae and current speed data were collected at various depths (surface, mid-depth and bottom) at distances of 200, 400, 900 and 2400m offshore of the coast. Settlement samples were collected at sites that were onshore of the pelagic transects using plastic souring pads following previous studies. Pelagic larval distribution showed no effect of topography. Instead larval abundance was highly variable among sample periods and among different taxa. Slow swimming D-stage mussel larvae were found to be positively correlated with both upwelling and turbulence indices suggesting that they behave as passive particles in the water column. The abundances of larval taxa with faster swimming speeds than the D-larvae were negatively correlated with upwelling and did not correlate with turbulence. This suggests that these larvae are more active within the water column than the D-larvae which would theoretically allow them to maintain their position in the water column. Further analysis revealed that mean larval depth correlated with mean depth of shoreward moving water masses regardless of the state of upwelling. These results suggest that larvae were actively selecting the depth at which they were found presumably in order to associate themselves with shoreward moving currents. This interpretation was supported by ontogenetic patterns in the behaviour of barnacle larvae, the nauplii of which were found further offshore as they aged, and closer onshore again once they reach the faster swimming cyprid stage. Although there was no detectable effect of topography on the abundances of planktonic larvae, the settlement section of this study revealed an effect of topography, with higher settlement and recruitment rates at bay sites than at the open coast sites. Settlement rates were seen to be negatively correlated with turbulence at bay sites but not open coast sites. Recruitment rates for each sample event were positively correlated with upwelling at each site. This study found pelagic larvae to be generally active within the water column which allowed them to remain close to the shore regardless of topography and upwelling/turbulence regimes. Although meaningful correlation analyses between pelagic larval supply and settlement rates could not be conducted due to loss of settlement collectors, settlement rates were affected by local topography with higher settlement and recruitment in bay sites.
- Full Text:
- Date Issued: 2016
Movement patterns of Cape stumpnose, Rhabdosargus holubi (Sparidae), in the Kowie Estuary, South Africa
- Authors: Grant, Gareth Neil
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/982 , vital:20010
- Description: Rhabdosargus holubi is an ubiquitous estuary-dependent fishery species endemic to southern Africa. Although aspects of its recruitment dynamics from sea to estuary have received considerable research attention, little is known about its movement behaviour within estuarine systems. Fishery surveys have also revealed that R. holubi is a dominant species in catches within several temperate estuaries in South Africa. Therefore, investigating movement behaviour is fundamental to understanding the ecology of this species and providing a means for implementing effective fisheries management strategies. This study made use of passive acoustic telemetry to quantify the movement patterns of juvenile R. holubi in the Kowie Estuary, in the Eastern Cape Province of South Africa. Previous studies have revealed that surgically implanted transmitters may have adverse effects on the physiology and behaviour of tagged fish. Therefore, due to the small size of juvenile R. holubi, an a priori transmitter-effect experiment was undertaken. This experiment revealed that juvenile R. holubi (146-217 mm fork length) were not adversely affected by the surgical implantation of acoustic transmitters (7 mm Ø, 1.6 g out of water) and hence acoustic telemetry was well suited to monitoring the movements of this species. A 4-month telemetry study evaluated the movement patterns of 21 juveniles (140-190 mm fork length) tagged in three equal batches along the length of the estuary. Specific aspects of their movement included space use patterns, habitat connectivity, and the influences of geophysical cycles and environmental variables. Tagged fish exhibited high residency, which varied between each release site area. The mean length of estuary used was greater for the upper batch (15.65 ± 6.49 km) than the middle and lower batches (7.36 ± 3.68 and 2.67 ± 2 km, respectively). In terms of habitat connectivity, once the tagged fish left the estuary, they generally did not return. Tagged R. holubi spent the majority (83%) of their monitoring periods within the estuarine environment, with the sea (16%) and riverine (1%) environments being utilised to a lesser extent. Diel and tidal cycles influenced the movement patterns of juvenile R. holubi. However, the high levels of residency meant that fine-scale movements were difficult to detect due to the acoustic receiver deployment configuration (i.e. receivers moored one kilometer apart). The influence of environmental variables on the movement of individuals, modelled with general linear mixed models (GLMMs), revealed that the effects of river inflow and water temperature were greatest. Increased river inflow caused individuals to use larger portions of the estuary. Increased water temperature, particularly river temperature, caused individuals to shift their distributions downstream (towards the mouth of the estuary). This study highlighted the importance of estuarine nursery habitats to R. holubi, suggesting that a loss or reduction of healthy estuarine habitats may lead to significant declines in the abundance of this species. Furthermore, extreme resident behaviour suggests that no-take area closures (estuarine protected areas) would be an effective management strategy for this important fishery species.
- Full Text:
- Date Issued: 2016
- Authors: Grant, Gareth Neil
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/982 , vital:20010
- Description: Rhabdosargus holubi is an ubiquitous estuary-dependent fishery species endemic to southern Africa. Although aspects of its recruitment dynamics from sea to estuary have received considerable research attention, little is known about its movement behaviour within estuarine systems. Fishery surveys have also revealed that R. holubi is a dominant species in catches within several temperate estuaries in South Africa. Therefore, investigating movement behaviour is fundamental to understanding the ecology of this species and providing a means for implementing effective fisheries management strategies. This study made use of passive acoustic telemetry to quantify the movement patterns of juvenile R. holubi in the Kowie Estuary, in the Eastern Cape Province of South Africa. Previous studies have revealed that surgically implanted transmitters may have adverse effects on the physiology and behaviour of tagged fish. Therefore, due to the small size of juvenile R. holubi, an a priori transmitter-effect experiment was undertaken. This experiment revealed that juvenile R. holubi (146-217 mm fork length) were not adversely affected by the surgical implantation of acoustic transmitters (7 mm Ø, 1.6 g out of water) and hence acoustic telemetry was well suited to monitoring the movements of this species. A 4-month telemetry study evaluated the movement patterns of 21 juveniles (140-190 mm fork length) tagged in three equal batches along the length of the estuary. Specific aspects of their movement included space use patterns, habitat connectivity, and the influences of geophysical cycles and environmental variables. Tagged fish exhibited high residency, which varied between each release site area. The mean length of estuary used was greater for the upper batch (15.65 ± 6.49 km) than the middle and lower batches (7.36 ± 3.68 and 2.67 ± 2 km, respectively). In terms of habitat connectivity, once the tagged fish left the estuary, they generally did not return. Tagged R. holubi spent the majority (83%) of their monitoring periods within the estuarine environment, with the sea (16%) and riverine (1%) environments being utilised to a lesser extent. Diel and tidal cycles influenced the movement patterns of juvenile R. holubi. However, the high levels of residency meant that fine-scale movements were difficult to detect due to the acoustic receiver deployment configuration (i.e. receivers moored one kilometer apart). The influence of environmental variables on the movement of individuals, modelled with general linear mixed models (GLMMs), revealed that the effects of river inflow and water temperature were greatest. Increased river inflow caused individuals to use larger portions of the estuary. Increased water temperature, particularly river temperature, caused individuals to shift their distributions downstream (towards the mouth of the estuary). This study highlighted the importance of estuarine nursery habitats to R. holubi, suggesting that a loss or reduction of healthy estuarine habitats may lead to significant declines in the abundance of this species. Furthermore, extreme resident behaviour suggests that no-take area closures (estuarine protected areas) would be an effective management strategy for this important fishery species.
- Full Text:
- Date Issued: 2016
Penguin parenting : assortative mating, nest attendance and sex-specific chick provisioning in the African Penguin (Spheniscus demersus)
- Authors: Smith, Diane Lauren
- Date: 2016
- Subjects: African penguin , Penguins -- South Africa , Penguins -- Sexual behavior , Parental behavior in animals
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5943 , http://hdl.handle.net/10962/d1019993
- Description: Animal behaviour is especially sensitive to environmental variability and prey availability during the breeding season, and this is particularly true for non-volant, central place foragers such as the endangered African Penguin (Spheniscus demersus). Individual sex and morphology, as well as the level of assortment within mated pairs can influence both the behaviour and the reproductive success of species exhibiting biparental care. This study made use of a large biometric database and nest attendance video footage to determine the influence of intrinsic (assortative mating, brood size and chick age) and extrinsic (environmental conditions, anthropic disturbance) factors on breeding behaviour and performance of African Penguins on Bird Island, Algoa Bay, during peak breeding (March - July) in 2013. While sexual dimorphism in African Penguins is subtle, the colony-specific discriminant functions presented here provide an accurate sexing tool when only bill and flipper length are available. Despite the premise that selection of a large, high-quality mate in this longlived, monogamous seabird governs lifetime fitness, only low levels of assortative mating were found, and this only for earlier breeders, when larger females (but not males) bred. The 2013 season was a particularly successful one, coinciding with above-average sardine and anchovy abundance, and almost 80 percent of monitored nests were double-brooded, with very low levels of mortality. A- and B-chicks of double broods and singleton chicks grew at similar rates and exhibited similar body condition indices. In these conditions, chick developmental rates were independent of parental size, assortment or provisioning behaviour. Females raising a double brood were significantly lighter and in poorer body condition than those raising a single chick, although the same trend was not evident in males. Offspring sex ratio in 2013 (2.27:1) favoured male chicks, suggesting that there is potential to over-produce the larger sex when resources are plentiful. Peak nest arrival and departure times of parents did not change over the course of monitored breeding attempts (March-June), nor were they different for disturbed and undisturbed nests or for a single or double brood. The increase in CCTV-observed provisioning rate as chicks grew larger was best explained by brood size, at-sea chlorophyll a concentration, and maximum air temperature, but was unrelated to parental morphology or assortative index. Importantly, parental absenteeism commenced earlier and was markedly greater in nests frequently handled by researchers than in undisturbed nests. Both the time spent together by parents, and absenteeism were measurably affected by maximum afternoon air temperatures, the effects of which are expected to be exacerbated by poorer foraging conditions and climate change. A third of manually-monitored nests shared chick-guarding duties unequally, although this phenomenon was independent of parental sex or morphology. The adaptive benefits of mating patterns and division of labour during chick-rearing may only become apparent in a year of below-average food availability and it is highly recommended that this study be repeated in a year of scarce food resources. These findings augment past foraging ecology studies and demonstrate that investigator disturbance and environmental conditions can affect the nesting behaviour of this highly threatened seabird.
- Full Text:
- Date Issued: 2016
- Authors: Smith, Diane Lauren
- Date: 2016
- Subjects: African penguin , Penguins -- South Africa , Penguins -- Sexual behavior , Parental behavior in animals
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5943 , http://hdl.handle.net/10962/d1019993
- Description: Animal behaviour is especially sensitive to environmental variability and prey availability during the breeding season, and this is particularly true for non-volant, central place foragers such as the endangered African Penguin (Spheniscus demersus). Individual sex and morphology, as well as the level of assortment within mated pairs can influence both the behaviour and the reproductive success of species exhibiting biparental care. This study made use of a large biometric database and nest attendance video footage to determine the influence of intrinsic (assortative mating, brood size and chick age) and extrinsic (environmental conditions, anthropic disturbance) factors on breeding behaviour and performance of African Penguins on Bird Island, Algoa Bay, during peak breeding (March - July) in 2013. While sexual dimorphism in African Penguins is subtle, the colony-specific discriminant functions presented here provide an accurate sexing tool when only bill and flipper length are available. Despite the premise that selection of a large, high-quality mate in this longlived, monogamous seabird governs lifetime fitness, only low levels of assortative mating were found, and this only for earlier breeders, when larger females (but not males) bred. The 2013 season was a particularly successful one, coinciding with above-average sardine and anchovy abundance, and almost 80 percent of monitored nests were double-brooded, with very low levels of mortality. A- and B-chicks of double broods and singleton chicks grew at similar rates and exhibited similar body condition indices. In these conditions, chick developmental rates were independent of parental size, assortment or provisioning behaviour. Females raising a double brood were significantly lighter and in poorer body condition than those raising a single chick, although the same trend was not evident in males. Offspring sex ratio in 2013 (2.27:1) favoured male chicks, suggesting that there is potential to over-produce the larger sex when resources are plentiful. Peak nest arrival and departure times of parents did not change over the course of monitored breeding attempts (March-June), nor were they different for disturbed and undisturbed nests or for a single or double brood. The increase in CCTV-observed provisioning rate as chicks grew larger was best explained by brood size, at-sea chlorophyll a concentration, and maximum air temperature, but was unrelated to parental morphology or assortative index. Importantly, parental absenteeism commenced earlier and was markedly greater in nests frequently handled by researchers than in undisturbed nests. Both the time spent together by parents, and absenteeism were measurably affected by maximum afternoon air temperatures, the effects of which are expected to be exacerbated by poorer foraging conditions and climate change. A third of manually-monitored nests shared chick-guarding duties unequally, although this phenomenon was independent of parental sex or morphology. The adaptive benefits of mating patterns and division of labour during chick-rearing may only become apparent in a year of below-average food availability and it is highly recommended that this study be repeated in a year of scarce food resources. These findings augment past foraging ecology studies and demonstrate that investigator disturbance and environmental conditions can affect the nesting behaviour of this highly threatened seabird.
- Full Text:
- Date Issued: 2016
Petrogenetic implications for the Merensky Reef: a platinum-group element distribution study from wide-reef facies in the western Bushveld Complex, RSA
- Authors: Largatzis, Savvas Anthony
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3167 , vital:20380
- Description: Despite decades of research and its economic importance, the formation of the Merensky Reef still remains controversial. This study reports on the distribution of platinum-group elements within widereef facies in an attempt to identify petrogenetic controls in the formation of the Merensky Reef. Widereef Merensky was sampled from Eland Platinum Mines in the western Bushveld. Macroscopic investigation of the drillcore identified a basal chromitite stringer overlying an anorthositic footwall. The reef comprised a pyroxenite unit while the hangingwall comprised noritic, leuconoritic and anorthositic units (upwards the stratigraphy). Furthermore, an anorthositic seam was identified within the pyroxenite reef, near the top of the unit. Ophitic textures of orthopyroxene oikocrysts comprising inclusions of plagioclase chadacrysts suggest that the crystallization of plagioclase preceded the crystallization of orthopyroxene. Furthermore, plagioclase and orthopyroxene were shown to be in mineral disequilibrium with one another. Pervasive hydrous alteration features throughout the Merensky Reef suggest late stage deuteric alteration. Mineral chemistry of plagioclase cores recorded ranges for An content in the Merensky Reef as follows: An72-79 in the anorthositic footwall, An71-77 in the chromitite stringer, An45-78 in the pyroxenite reef unit, An47-73 in the anorthosite reef unit, An72-76 in the norite hangingwall, An75-77 in the leuconorite hangingwall and An72-77 in the anorthosite hangingwall. This suggest that the reef units were more evolved than the footwall and hangingwall units. Furthermore, plagioclase showed reverse zoning in the anorthosite footwall unit while normal zoning was identified in the anorthosite reef unit. This suggested that the footwall unit underwent reheating and re-equilibration with a hotter, more primitive magma (also evident in recrystallization textures) while the anorthositic reef unit cooled relatively slowly and interstitial plagioclase present within this unit equilibrated with a trapped, more evolved liquid. The pyroxenite reef unit shows enrichment in incompatible elements and corresponding negative Eu anomalies, indicating the presence of trapped liquids. Cu, Ni and S concentrations remained low throughout the reef with the exception of a peak underlying the anorthositic seam and further enrichment underlying this peak. Platinum-group element geochemistry identified two major peaks: an upper peak which coincided with the peaks for Cu, Ni and S, and showed preferential enrichment in Pd and Au relative to other PGE, and a lower peak which coincided with the presence of chromitite and showed the preferential enrichment of Os, Ir, Ru, Rh and Pt relative to Pd, Au, Cu and Ni. The formation of the lower peak was consistent with a model involving the co-precipitation of chromite and PGE clusters (as PGM) while the upper peak was attributed to a model involving the collection of PGE by an immiscible sulphide liquid. Moreover, high Cu/Pd and Pt/Pd ratios in the lower pyroxenite unit indicated a process involving sulphide fractional segregation and scavenging while the inverse, present within the upper pyroxenite unit, suggested a more dynamic system involving the introduction of PGE-undepleted magma and S during simultaneous sulphide precipitation. Furthermore, a separation of PPGE peaks from IPGE peaks was observed within the pyroxenite unit, indicating a different partitioning behavior between PPGE and IPGE. The separation of these peaks is attributed to a sulphide liquid fractionation model while depletion haloes occurring in the proximity of the main PGE peaks was suggested to form through an Ostwald-ripening type mechanism. The results of this study are consistent with a model for the formation of the Merensky Reef involving a combination of geochemical processes, including sulphide segregation and fractionation, as well as multiple replenishments of magma.
- Full Text:
- Date Issued: 2016
- Authors: Largatzis, Savvas Anthony
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3167 , vital:20380
- Description: Despite decades of research and its economic importance, the formation of the Merensky Reef still remains controversial. This study reports on the distribution of platinum-group elements within widereef facies in an attempt to identify petrogenetic controls in the formation of the Merensky Reef. Widereef Merensky was sampled from Eland Platinum Mines in the western Bushveld. Macroscopic investigation of the drillcore identified a basal chromitite stringer overlying an anorthositic footwall. The reef comprised a pyroxenite unit while the hangingwall comprised noritic, leuconoritic and anorthositic units (upwards the stratigraphy). Furthermore, an anorthositic seam was identified within the pyroxenite reef, near the top of the unit. Ophitic textures of orthopyroxene oikocrysts comprising inclusions of plagioclase chadacrysts suggest that the crystallization of plagioclase preceded the crystallization of orthopyroxene. Furthermore, plagioclase and orthopyroxene were shown to be in mineral disequilibrium with one another. Pervasive hydrous alteration features throughout the Merensky Reef suggest late stage deuteric alteration. Mineral chemistry of plagioclase cores recorded ranges for An content in the Merensky Reef as follows: An72-79 in the anorthositic footwall, An71-77 in the chromitite stringer, An45-78 in the pyroxenite reef unit, An47-73 in the anorthosite reef unit, An72-76 in the norite hangingwall, An75-77 in the leuconorite hangingwall and An72-77 in the anorthosite hangingwall. This suggest that the reef units were more evolved than the footwall and hangingwall units. Furthermore, plagioclase showed reverse zoning in the anorthosite footwall unit while normal zoning was identified in the anorthosite reef unit. This suggested that the footwall unit underwent reheating and re-equilibration with a hotter, more primitive magma (also evident in recrystallization textures) while the anorthositic reef unit cooled relatively slowly and interstitial plagioclase present within this unit equilibrated with a trapped, more evolved liquid. The pyroxenite reef unit shows enrichment in incompatible elements and corresponding negative Eu anomalies, indicating the presence of trapped liquids. Cu, Ni and S concentrations remained low throughout the reef with the exception of a peak underlying the anorthositic seam and further enrichment underlying this peak. Platinum-group element geochemistry identified two major peaks: an upper peak which coincided with the peaks for Cu, Ni and S, and showed preferential enrichment in Pd and Au relative to other PGE, and a lower peak which coincided with the presence of chromitite and showed the preferential enrichment of Os, Ir, Ru, Rh and Pt relative to Pd, Au, Cu and Ni. The formation of the lower peak was consistent with a model involving the co-precipitation of chromite and PGE clusters (as PGM) while the upper peak was attributed to a model involving the collection of PGE by an immiscible sulphide liquid. Moreover, high Cu/Pd and Pt/Pd ratios in the lower pyroxenite unit indicated a process involving sulphide fractional segregation and scavenging while the inverse, present within the upper pyroxenite unit, suggested a more dynamic system involving the introduction of PGE-undepleted magma and S during simultaneous sulphide precipitation. Furthermore, a separation of PPGE peaks from IPGE peaks was observed within the pyroxenite unit, indicating a different partitioning behavior between PPGE and IPGE. The separation of these peaks is attributed to a sulphide liquid fractionation model while depletion haloes occurring in the proximity of the main PGE peaks was suggested to form through an Ostwald-ripening type mechanism. The results of this study are consistent with a model for the formation of the Merensky Reef involving a combination of geochemical processes, including sulphide segregation and fractionation, as well as multiple replenishments of magma.
- Full Text:
- Date Issued: 2016
Population assessment and feeding ecology of brown hyenas (hyaena brunnea) in Mountain Zebra National Park, Eastern Cape, South Africa
- Authors: Comley, Jessica
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2862 , vital:20336
- Description: The development of many small (<400 km2), enclosed game reserves in the Eastern Cape Province of South Africa over the past 25 years has contributed greatly to the conservation of large carnivores. However, the brown hyena (Hyaena brunnea) is one of the least studied large carnivores in South Africa. Nevertheless, the reintroduction of this species (n=3 in 2008) into Mountain Zebra National Park (MZNP) provided the perfect opportunity to broaden our understanding of the role that this carnivore plays in an enclosed system. Camera trap data was collected for just over a year from April 2014 to April 2015 and brown hyena density estimates were calculated using spatially explicit capture-recapture analysis. Left-side images of brown hyenas were used in the analysis and 12 individuals were positively identified. The best model to estimate brown hyena density included a road covariate and estimated brown hyena density to be 6-10 individuals/100 km2 (an absolute abundance of between 12 and 21 individuals), which is higher than densities calculated for brown hyenas in other arid, open systems. In, addition, brown hyena scat samples were collected over a five year period from April 2011 to June 2015 and standard techniques for scat analysis were used to identify prey items. Cheetah (Acinonyx jubatus) and lion (Panthera leo) kill site data were used to investigate the impacts of these species on the diet of brown hyenas. Before the release of lions brown hyenas predominantly scavenged on medium-sized mammals, which was what the cheetahs mainly killed. However, after the release of the lions, brown hyenas predominantly scavenged on large mammals, which was what the lions primarily killed. The results from my study indicate that brown hyenas are most likely reaching high densities in enclosed systems, due to increased scavenging opportunities provided by other large predators. The rapid increase of brown hyena densities from small founder populations in enclosed reserves could result in inbreeding. Therefore, in order to successfully conserve brown hyenas and other large carnivores in South Africa, continual post-release monitoring and possible implementation of meta-population management schemes is required.
- Full Text:
- Date Issued: 2016
- Authors: Comley, Jessica
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2862 , vital:20336
- Description: The development of many small (<400 km2), enclosed game reserves in the Eastern Cape Province of South Africa over the past 25 years has contributed greatly to the conservation of large carnivores. However, the brown hyena (Hyaena brunnea) is one of the least studied large carnivores in South Africa. Nevertheless, the reintroduction of this species (n=3 in 2008) into Mountain Zebra National Park (MZNP) provided the perfect opportunity to broaden our understanding of the role that this carnivore plays in an enclosed system. Camera trap data was collected for just over a year from April 2014 to April 2015 and brown hyena density estimates were calculated using spatially explicit capture-recapture analysis. Left-side images of brown hyenas were used in the analysis and 12 individuals were positively identified. The best model to estimate brown hyena density included a road covariate and estimated brown hyena density to be 6-10 individuals/100 km2 (an absolute abundance of between 12 and 21 individuals), which is higher than densities calculated for brown hyenas in other arid, open systems. In, addition, brown hyena scat samples were collected over a five year period from April 2011 to June 2015 and standard techniques for scat analysis were used to identify prey items. Cheetah (Acinonyx jubatus) and lion (Panthera leo) kill site data were used to investigate the impacts of these species on the diet of brown hyenas. Before the release of lions brown hyenas predominantly scavenged on medium-sized mammals, which was what the cheetahs mainly killed. However, after the release of the lions, brown hyenas predominantly scavenged on large mammals, which was what the lions primarily killed. The results from my study indicate that brown hyenas are most likely reaching high densities in enclosed systems, due to increased scavenging opportunities provided by other large predators. The rapid increase of brown hyena densities from small founder populations in enclosed reserves could result in inbreeding. Therefore, in order to successfully conserve brown hyenas and other large carnivores in South Africa, continual post-release monitoring and possible implementation of meta-population management schemes is required.
- Full Text:
- Date Issued: 2016
Potential benefits and experienced challenges of small household biogas-digesters for rural households
- Authors: Langley, Kyle Anthony
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4789 , http://hdl.handle.net/10962/d1021268
- Description: Access to renewable energy supplies is a critical foundation for sustainable development and poverty alleviation. Anaerobic biogas-digesters also referred to as bio-digesters, have been identified as one of the leading technologies with regards to assisting in improving energy access for remote rural areas that still remain dependent upon biomass usage. This thesis assesses the potential feasibility of bio-digesters for rural households in South Africa by focusing on the experiences of a remote and rural community in Eastern Cape. A standardised survey was used to capture household details and energy use patterns of households with 180 interviews being conducted. Field observations were also conducted on the five bio-digesters installed in the community over a three month period. Despite the predominance of electrification in the community, households were heavily reliant upon biomass in the form of fuelwood and cattle dung to supplement their energy needs. Households supplemented their energy usage with alternative energy sources such as LPG gas and paraffin, especially during periods when electricity was unavailable or deemed too expensive. Initial knowledge of bio-digester technology in the community was non-existent, however with the installation of bio-digesters within the targeted villages, social learning was observed. Despite low temperatures bio-digesters continued to function throughout the study period, though malfunctions did occur and gas production did not reach optimal levels. Primary challenges encountered were the lack of financial subsidies for wide-spread adoption; the limited technical capacity of the community to conduct repairs and minimal gas production due to a build-up of ligneous materials within the gas chamber of the bio-digesters. Bio-digesters were found to provide significant benefits for households and further studies into maximising their effectiveness for rural South African households are recommended.
- Full Text:
- Date Issued: 2016
- Authors: Langley, Kyle Anthony
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4789 , http://hdl.handle.net/10962/d1021268
- Description: Access to renewable energy supplies is a critical foundation for sustainable development and poverty alleviation. Anaerobic biogas-digesters also referred to as bio-digesters, have been identified as one of the leading technologies with regards to assisting in improving energy access for remote rural areas that still remain dependent upon biomass usage. This thesis assesses the potential feasibility of bio-digesters for rural households in South Africa by focusing on the experiences of a remote and rural community in Eastern Cape. A standardised survey was used to capture household details and energy use patterns of households with 180 interviews being conducted. Field observations were also conducted on the five bio-digesters installed in the community over a three month period. Despite the predominance of electrification in the community, households were heavily reliant upon biomass in the form of fuelwood and cattle dung to supplement their energy needs. Households supplemented their energy usage with alternative energy sources such as LPG gas and paraffin, especially during periods when electricity was unavailable or deemed too expensive. Initial knowledge of bio-digester technology in the community was non-existent, however with the installation of bio-digesters within the targeted villages, social learning was observed. Despite low temperatures bio-digesters continued to function throughout the study period, though malfunctions did occur and gas production did not reach optimal levels. Primary challenges encountered were the lack of financial subsidies for wide-spread adoption; the limited technical capacity of the community to conduct repairs and minimal gas production due to a build-up of ligneous materials within the gas chamber of the bio-digesters. Bio-digesters were found to provide significant benefits for households and further studies into maximising their effectiveness for rural South African households are recommended.
- Full Text:
- Date Issued: 2016