Identification of novel compounds against Plasmodium falciparum Cytochrome bc1 Complex inhibiting the trans-membrane electron transfer pathway: an In Silico study
- Authors: Chebon, Lorna Jemosop
- Date: 2022-10-14
- Subjects: Malaria , Plasmodium falciparum , Molecular dynamics , Antimalarials , Molecules Models , Docking , Cytochromes , Drug resistance , Computer simulation , Drugs Computer-aided design , System analysis
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365666 , vital:65774 , DOI https://doi.org/10.21504/10962/365666
- Description: Malaria continues to be a burden globally with a myriad of challenges deterring eradication efforts. With most antimalarials facing drug resistance, such as atovaquone (ATQ), alternative compounds that can withstand resistance are warranted. The Plasmodium falciparum cytochrome b (PfCytb), a subunit of P. falciparum cytochrome bc1 complex, is a validated drug target. Structurally, cytochrome b, cytochrome c1, and iron sulphur protein (ISP) subunits form the catalytic domain of the protein complex having heme bL, heme bH and iron-sulphur [2FE-2S] cluster cofactors. These cofactos have redox centres to aid in the electron transfer (ET) process. These subunits promote ET mainly through the enzyme’s ubiquinol oxidation (Qo) and ubiquinone reduction (Qi) processes in the catalytic domain. ATQ drug has been used in the prevention and treatment of uncomplicated malaria by targeting PfCytb protein. Once the mitochondrial transmembrane ET pathway is inhibited, it causes a collapse in its membrane potential. Previously reported ATQ drug resistance has been associated with the point mutations Y268C, Y268N and Y268S. Thus, in finding alternatives to the ATQ drug, this research aimed to: i) employ in silico approaches incorporating protein into phospholipid bilayer for the first time to understand the parasites’ resistance mechanism; ii) determine any sequence and structural differences that could be explored in drug design studies; and iii) screen for PfCytb-iron sulphur protein (Cytb-ISP) hit compounds from South African natural compound database (SANCDB) and Medicines for Malaria Venture (MMV) that can withstand the identified mutations. Using computational tools, comparative sequence and structural analyses were performed on the cytochrome b protein, where the ultimate focus was on P. falciparum cytochrome b and its human homolog. Through multiple sequence alignment, motif discovery and phylogeny, differences between P. falciparum and H. sapiens cytochrome b were identified. Protein modelling of both P. falciparum and H. sapiens cytochrome b - iron sulphur protein (PfCytb-ISP and HsCytb-ISP) was performed. Results showed that at the sequence level, there were few amino acid residue differences because the protein is highly conserved. Important to note is the four-residue deletion in Plasmodium spp. absent in the human homolog. Motif analysis discovered five unique motifs in P. falciparum cytochrome b protein which were mapped onto the predicted protein model. These motifs were not in regions of functional importance; hence their function is still unknown. At a structural level, the four-residue deletion was observed to alter the Qo substrate binding pocket as reported in previous studies and confirmed in this study. This deletion resulted in a 0.83 Å structural displacement. Also, there are currently no in silico studies that have performed experiments with P. falciparum cytochrome b protein incorporated into a phospholipid bilayer. Using 350 ns molecular dynamics (MD) simulations of the holo and ATQ-bound systems, the study highlighted the resistance mechanism of the parasite protein where the loss of active site residue-residue interactions was identified, all linked to the three mutations. The identified compromised interactions are likely to destabilise the protein’s function, specifically in the Qo substrate binding site. This showed the possible effect of mutations on ATQ drug activity, where all three mutations were reported to share a similar resistance mechanism. Thereafter, this research work utilised in silico approaches where both Qo active site and interface pocket were targeted by screening the South African natural compounds database (SANCDB) and Medicines for Malaria Venture (MMV) compounds to identify novel selective hits. SANCDB compounds are known for their structural complexity that preserves the potency of the drug molecule. Both SANCDB and MMV compounds have not been explored as inhibitors against the PfCytb drug target. Molecular docking, molecular dynamics (MD) simulations, principal component, and dynamic residue network (DRN; global and local) analyses were utilised to identify and confirm the potential selective inhibitors. Docking results identified compounds that bound selectively onto PfCytb-ISP with a binding energy ≤ -8.7 kcal/mol-1. Further, this work validated a total of eight potential selective compounds to inhibit PfCytb-ISP protein (Qo active site) not only in the wild-type but also in the presence of the point mutations Y268C, Y268N and Y268S. The selective binding of these hit compounds could be linked to the differences reported at sequence/residue level in chapter 3. DRN and residue contact map analyses of the eight compounds in holo and ligand-bound systems revealed reduced residue interactions and decreased protein communication. This suggests that the eight compounds show the possibility of inhibiting the parasite and disrupting important residue-residue interactions. Additionally, 13 selective compounds were identified to bind at the protein’s heterodimer interface, where global and local analysis confirmed their effect on active site residues (distal location) as well as on the communication network. Based on the sequence differences between PfCytb and the human homolog, these findings suggest these selective compounds as potential allosteric modulators of the parasite enzyme, which may serve as possible replacements of the already resistant ATQ drug. Therefore, these findings pave the way for further in vitro studies to establish their anti-plasmodial inhibition levels. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Authors: Chebon, Lorna Jemosop
- Date: 2022-10-14
- Subjects: Malaria , Plasmodium falciparum , Molecular dynamics , Antimalarials , Molecules Models , Docking , Cytochromes , Drug resistance , Computer simulation , Drugs Computer-aided design , System analysis
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365666 , vital:65774 , DOI https://doi.org/10.21504/10962/365666
- Description: Malaria continues to be a burden globally with a myriad of challenges deterring eradication efforts. With most antimalarials facing drug resistance, such as atovaquone (ATQ), alternative compounds that can withstand resistance are warranted. The Plasmodium falciparum cytochrome b (PfCytb), a subunit of P. falciparum cytochrome bc1 complex, is a validated drug target. Structurally, cytochrome b, cytochrome c1, and iron sulphur protein (ISP) subunits form the catalytic domain of the protein complex having heme bL, heme bH and iron-sulphur [2FE-2S] cluster cofactors. These cofactos have redox centres to aid in the electron transfer (ET) process. These subunits promote ET mainly through the enzyme’s ubiquinol oxidation (Qo) and ubiquinone reduction (Qi) processes in the catalytic domain. ATQ drug has been used in the prevention and treatment of uncomplicated malaria by targeting PfCytb protein. Once the mitochondrial transmembrane ET pathway is inhibited, it causes a collapse in its membrane potential. Previously reported ATQ drug resistance has been associated with the point mutations Y268C, Y268N and Y268S. Thus, in finding alternatives to the ATQ drug, this research aimed to: i) employ in silico approaches incorporating protein into phospholipid bilayer for the first time to understand the parasites’ resistance mechanism; ii) determine any sequence and structural differences that could be explored in drug design studies; and iii) screen for PfCytb-iron sulphur protein (Cytb-ISP) hit compounds from South African natural compound database (SANCDB) and Medicines for Malaria Venture (MMV) that can withstand the identified mutations. Using computational tools, comparative sequence and structural analyses were performed on the cytochrome b protein, where the ultimate focus was on P. falciparum cytochrome b and its human homolog. Through multiple sequence alignment, motif discovery and phylogeny, differences between P. falciparum and H. sapiens cytochrome b were identified. Protein modelling of both P. falciparum and H. sapiens cytochrome b - iron sulphur protein (PfCytb-ISP and HsCytb-ISP) was performed. Results showed that at the sequence level, there were few amino acid residue differences because the protein is highly conserved. Important to note is the four-residue deletion in Plasmodium spp. absent in the human homolog. Motif analysis discovered five unique motifs in P. falciparum cytochrome b protein which were mapped onto the predicted protein model. These motifs were not in regions of functional importance; hence their function is still unknown. At a structural level, the four-residue deletion was observed to alter the Qo substrate binding pocket as reported in previous studies and confirmed in this study. This deletion resulted in a 0.83 Å structural displacement. Also, there are currently no in silico studies that have performed experiments with P. falciparum cytochrome b protein incorporated into a phospholipid bilayer. Using 350 ns molecular dynamics (MD) simulations of the holo and ATQ-bound systems, the study highlighted the resistance mechanism of the parasite protein where the loss of active site residue-residue interactions was identified, all linked to the three mutations. The identified compromised interactions are likely to destabilise the protein’s function, specifically in the Qo substrate binding site. This showed the possible effect of mutations on ATQ drug activity, where all three mutations were reported to share a similar resistance mechanism. Thereafter, this research work utilised in silico approaches where both Qo active site and interface pocket were targeted by screening the South African natural compounds database (SANCDB) and Medicines for Malaria Venture (MMV) compounds to identify novel selective hits. SANCDB compounds are known for their structural complexity that preserves the potency of the drug molecule. Both SANCDB and MMV compounds have not been explored as inhibitors against the PfCytb drug target. Molecular docking, molecular dynamics (MD) simulations, principal component, and dynamic residue network (DRN; global and local) analyses were utilised to identify and confirm the potential selective inhibitors. Docking results identified compounds that bound selectively onto PfCytb-ISP with a binding energy ≤ -8.7 kcal/mol-1. Further, this work validated a total of eight potential selective compounds to inhibit PfCytb-ISP protein (Qo active site) not only in the wild-type but also in the presence of the point mutations Y268C, Y268N and Y268S. The selective binding of these hit compounds could be linked to the differences reported at sequence/residue level in chapter 3. DRN and residue contact map analyses of the eight compounds in holo and ligand-bound systems revealed reduced residue interactions and decreased protein communication. This suggests that the eight compounds show the possibility of inhibiting the parasite and disrupting important residue-residue interactions. Additionally, 13 selective compounds were identified to bind at the protein’s heterodimer interface, where global and local analysis confirmed their effect on active site residues (distal location) as well as on the communication network. Based on the sequence differences between PfCytb and the human homolog, these findings suggest these selective compounds as potential allosteric modulators of the parasite enzyme, which may serve as possible replacements of the already resistant ATQ drug. Therefore, these findings pave the way for further in vitro studies to establish their anti-plasmodial inhibition levels. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
Identification of selective novel hits against Mycobacterium tuberculosis KasA potential allosteric sites using bioinformatics approaches
- Authors: Hare, Fadzayi Faith
- Date: 2022-10-14
- Subjects: Tuberculosis , Docking , Molecules Models , Virtual screening , Multidrug-resistant tuberculosis , Fatty acids Synthesis , Drugs Design
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362842 , vital:65367
- Description: Tuberculosis (TB) is a global health threat that has led to approximately 1.5 million deaths annually. According to the World Health Organization (WHO), TB is among the top ten deadly diseases and is the leading cause of death due to a single infectious agent. The main challenge in the effective treatment and control of TB is the ongoing emergence of resistant strains of Mycobacterium tuberculosis (Mtb) which lead to multi-drug resistant (MDR) and extensive-drug resistant (XDR) TB. Hence, the identification and characterization of novel drug targets and drugs that modulate the activity of the pathogen are an urgent priority. The current situation even necessitates the reengineering or repurposing of drugs in order to achieve effective control. The β-ketoacyl-acyl carrier protein synthase I (KasA) of Mycobacterium tuberculosis is an essential enzyme in the mycobacterial fatty acid synthesis (FAS-II) pathway and is believed to be a promising target for drug discovery in TB. It is one of the five main proteins of the FAS-II pathway and catalyzes a key condensation reaction in the synthesis of meromycolate chains, the precursors of mycolic acids involved in cell wall formation. Although this protein has been extensively studied, little research has been devoted to the allosteric inhibition of potential drug compounds. The main aim of this research was to identify the allosteric sites on the protein that could be involved in the inhibition of substrate binding activities and novel drug compounds that bind to these sites by use of in-silico approaches. The bioinformatics approaches used in this study were divided into four main objectives namely identification of KasA homolog sequences, sequence analysis and protein characterization, allosteric site search and lastly virtual screening of DrugBank compounds via molecular docking. Fifteen homolog sequences were identified from the BLASTP analysis and were derived from bacteria, fungi and mammals. In order to discover important residues and regions within the KasA proteins, sequence alignment, motif analysis and phylogenetic studies were performed using Mtb KasA as a reference. Sequence alignment revealed conserved residues in all KasA proteins that have functional importance such as the catalytic triad residues (Cys171, His311 and His345). Motif analysis identified 18 highly conserved motifs within the KasA proteins with structural and functional roles. In addition, motifs unique to the Mtb KasA protein were also identified and explored for inhibitor drug design purposes. Phylogenetic analysis of the homolog sequences showed a distinct clustering of prokaryotes and eukaryotes. A distinctive clustering was also observed for species belonging to the same genus. Since the mechanism of action of most drugs involves the active site, allosteric site search was conducted on Mtb KasA and the human homolog protein using a combination of pocket detection algorithms with the aim of identifying sites that could be utilized in allosteric modulator drug discovery. This was followed by the virtual screening of 2089 FDA approved DrugBank compounds against the entire protein surfaces of Mtb KasA and Hsmt KasA, performed via molecular docking using AutoDock Vina. Screening of the compounds was based on the binding energies, with more focus on identifying ligands that bound exclusively to the acyl-binding tunnel of Mtb KasA. This reduced the data set to 27 promising drug compounds with a relatively high binding affinity for Mtb KasA, however, further experiments need to be performed to validate this result. Among these compounds were DB08889, DB06755, DB09270, DB11226, DB00392, DB12278, DB08936, DB00781, DB13720 and DB00392, which displayed relatively low binding energies for Mtb KasA when compared to the human homolog protein. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Authors: Hare, Fadzayi Faith
- Date: 2022-10-14
- Subjects: Tuberculosis , Docking , Molecules Models , Virtual screening , Multidrug-resistant tuberculosis , Fatty acids Synthesis , Drugs Design
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362842 , vital:65367
- Description: Tuberculosis (TB) is a global health threat that has led to approximately 1.5 million deaths annually. According to the World Health Organization (WHO), TB is among the top ten deadly diseases and is the leading cause of death due to a single infectious agent. The main challenge in the effective treatment and control of TB is the ongoing emergence of resistant strains of Mycobacterium tuberculosis (Mtb) which lead to multi-drug resistant (MDR) and extensive-drug resistant (XDR) TB. Hence, the identification and characterization of novel drug targets and drugs that modulate the activity of the pathogen are an urgent priority. The current situation even necessitates the reengineering or repurposing of drugs in order to achieve effective control. The β-ketoacyl-acyl carrier protein synthase I (KasA) of Mycobacterium tuberculosis is an essential enzyme in the mycobacterial fatty acid synthesis (FAS-II) pathway and is believed to be a promising target for drug discovery in TB. It is one of the five main proteins of the FAS-II pathway and catalyzes a key condensation reaction in the synthesis of meromycolate chains, the precursors of mycolic acids involved in cell wall formation. Although this protein has been extensively studied, little research has been devoted to the allosteric inhibition of potential drug compounds. The main aim of this research was to identify the allosteric sites on the protein that could be involved in the inhibition of substrate binding activities and novel drug compounds that bind to these sites by use of in-silico approaches. The bioinformatics approaches used in this study were divided into four main objectives namely identification of KasA homolog sequences, sequence analysis and protein characterization, allosteric site search and lastly virtual screening of DrugBank compounds via molecular docking. Fifteen homolog sequences were identified from the BLASTP analysis and were derived from bacteria, fungi and mammals. In order to discover important residues and regions within the KasA proteins, sequence alignment, motif analysis and phylogenetic studies were performed using Mtb KasA as a reference. Sequence alignment revealed conserved residues in all KasA proteins that have functional importance such as the catalytic triad residues (Cys171, His311 and His345). Motif analysis identified 18 highly conserved motifs within the KasA proteins with structural and functional roles. In addition, motifs unique to the Mtb KasA protein were also identified and explored for inhibitor drug design purposes. Phylogenetic analysis of the homolog sequences showed a distinct clustering of prokaryotes and eukaryotes. A distinctive clustering was also observed for species belonging to the same genus. Since the mechanism of action of most drugs involves the active site, allosteric site search was conducted on Mtb KasA and the human homolog protein using a combination of pocket detection algorithms with the aim of identifying sites that could be utilized in allosteric modulator drug discovery. This was followed by the virtual screening of 2089 FDA approved DrugBank compounds against the entire protein surfaces of Mtb KasA and Hsmt KasA, performed via molecular docking using AutoDock Vina. Screening of the compounds was based on the binding energies, with more focus on identifying ligands that bound exclusively to the acyl-binding tunnel of Mtb KasA. This reduced the data set to 27 promising drug compounds with a relatively high binding affinity for Mtb KasA, however, further experiments need to be performed to validate this result. Among these compounds were DB08889, DB06755, DB09270, DB11226, DB00392, DB12278, DB08936, DB00781, DB13720 and DB00392, which displayed relatively low binding energies for Mtb KasA when compared to the human homolog protein. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
Igniting a revolution at point zero? Exploring the barriers to early learning access in South Africa and the possibility of the social economy : a comparative analysis and study of Smartstart
- Authors: McCann, Claire Mary
- Date: 2022-10-14
- Subjects: Early childhood education South Africa , Social economy South Africa , Smart Start , Education and state South Africa , Social democracy , Dual economy South Africa , South Africa Economic conditions 1991-
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/403080 , vital:69920
- Description: Economic theory suggests that the greatest return to education investment is in the earliest years; early learning and childcare may enhance skill accumulation and mothers’ labour market choices. These services may be catalytic, igniting a revolution at point zero that transforms family outcomes and aids development. In South Africa, however, early learning deficits persist. This thesis explores barriers to quality early learning access and the possibility social economy initiatives offer, focusing on social franchises like SmartStart. Document analysis, comparative analysis, and interviews with SmartStart leaders suggest two key barriers. Firstly, where private firms are dominant and ability to pay for services is limited, low-income areas are under-served. For this reason, Polanyi claims that markets should be embedded in institutions. A post-Polanyian approach emphasises the role of social investment states, which focus spending on education and where social protection scaffolds markets, in this regard. The South African state seems to embrace this approach as ECD policy frames early learning as a public good and social investment. However, a second barrier is that an insulated state enables technocratic over democratic embeddedness, with powerful rights-based discourse but poor implementation. In particular, it seems that the state lacks a framework to progressively realise the right to quality early learning. Attempts to enforce high standards are not accompanied by sufficient resources, capacity or collaboration, resulting in sub-standard services and barriers to entry. Even in better resourced contexts (e.g., Basic Education), top-down, technocratic models (re)produce failing systems, where those with means exit in favour of market alternatives. An exploration of other developing countries suggests that this failure, with variations, prevails, but also that possibility exists. In these contexts, states seem more coordinated and responsive when partnering with civil society. In South Africa, the SmartStart model is based on partnership. SmartStart frames itself as a delivery platform, building relationships with local NGOs to simultaneously scale and deepen early learning. Partnerships with communities are crucial, to build demand in a sector whose association with social reproduction means that its economic significance may be overlooked. In addition, SmartStart puts forward a child-centred approach based on a prefigurative vision but also responsive to the realities of under-resourced contexts, aiming to progressively realise rights. Though with some limitations, SmartStart’s least-cost innovation for scale provides lessons for the state. As the state’s ECD mandate shifts to Basic Education, these findings serve to inform a more effective implementation model, leveraging resources that already exist. , Thesis (MEcon) -- Faculty of Commerce, Economics and Economic History, 2022
- Full Text:
- Authors: McCann, Claire Mary
- Date: 2022-10-14
- Subjects: Early childhood education South Africa , Social economy South Africa , Smart Start , Education and state South Africa , Social democracy , Dual economy South Africa , South Africa Economic conditions 1991-
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/403080 , vital:69920
- Description: Economic theory suggests that the greatest return to education investment is in the earliest years; early learning and childcare may enhance skill accumulation and mothers’ labour market choices. These services may be catalytic, igniting a revolution at point zero that transforms family outcomes and aids development. In South Africa, however, early learning deficits persist. This thesis explores barriers to quality early learning access and the possibility social economy initiatives offer, focusing on social franchises like SmartStart. Document analysis, comparative analysis, and interviews with SmartStart leaders suggest two key barriers. Firstly, where private firms are dominant and ability to pay for services is limited, low-income areas are under-served. For this reason, Polanyi claims that markets should be embedded in institutions. A post-Polanyian approach emphasises the role of social investment states, which focus spending on education and where social protection scaffolds markets, in this regard. The South African state seems to embrace this approach as ECD policy frames early learning as a public good and social investment. However, a second barrier is that an insulated state enables technocratic over democratic embeddedness, with powerful rights-based discourse but poor implementation. In particular, it seems that the state lacks a framework to progressively realise the right to quality early learning. Attempts to enforce high standards are not accompanied by sufficient resources, capacity or collaboration, resulting in sub-standard services and barriers to entry. Even in better resourced contexts (e.g., Basic Education), top-down, technocratic models (re)produce failing systems, where those with means exit in favour of market alternatives. An exploration of other developing countries suggests that this failure, with variations, prevails, but also that possibility exists. In these contexts, states seem more coordinated and responsive when partnering with civil society. In South Africa, the SmartStart model is based on partnership. SmartStart frames itself as a delivery platform, building relationships with local NGOs to simultaneously scale and deepen early learning. Partnerships with communities are crucial, to build demand in a sector whose association with social reproduction means that its economic significance may be overlooked. In addition, SmartStart puts forward a child-centred approach based on a prefigurative vision but also responsive to the realities of under-resourced contexts, aiming to progressively realise rights. Though with some limitations, SmartStart’s least-cost innovation for scale provides lessons for the state. As the state’s ECD mandate shifts to Basic Education, these findings serve to inform a more effective implementation model, leveraging resources that already exist. , Thesis (MEcon) -- Faculty of Commerce, Economics and Economic History, 2022
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In silico substrate binding profiling for SARS-COV-2 main protease (mpro) using hexapeptide substrates
- Authors: Zabo, Sophakama
- Date: 2022-10-14
- Subjects: COVID-19 (Disease) , Peptides , Chymotrypsin like , Chymotrypsin , Proteases , Proteolytic enzymes
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/365566 , vital:65760
- Description: COVID-19, as a disease resulting from SARS-CoV-2 infection, and a pandemic has had a devastating effect on the world. There are limited effective measures that control the spread and treatment of COVID-19 illness. The homodimeric cysteine main protease (Mpro) is crucial to the life cycle of the virus, as it cleaves the large polyproteins 1a and 1ab into matured, functional non-structural proteins. The Mpro exhibits high degrees of conservation in sequence, structure and specificity across coronavirus species, making it an ideal drug target. The Mpro substrate-binding profiles remain, despite the resolution of its recognition sequence and cleavage points (Leu-Gln↓(Ser/Ala/Gly)). In this study, a series of hexapeptide sequences containing the appropriate recognition sequence and cleavage points were generated and screened against the Mpro to study these binding profiles, and to further be the basis for efficiency-driven drug design. A multi-conformer hexapeptide substrate library comprising optimised 81000 models of 810 unique sequences was generated using RDKit within the context of python. Terminal capping with ACE and NMe was effected using SMILES and SMARTS matching. Multiple hexapeptides were complexed with chain B of crystallographic Mpro (PDS ID: 6XHM), following the validation of chain B for this purpose using AutoDock Vina at high levels of exhaustiveness (480). The resulting Vina scores ranged between -8.7 and -7.0 kcal.mol-1, and the reproducibility of best poses was validated through redocking. Ligand efficiency indices were calculated to identify substrate residues with high binding efficiency at their respective positions, revealing Val (P3), Ala (P1′); and Gly and Ala (P2′ and P3′) as leading efficient binders. Binding efficiencies were lowered by molecular weight. Substrate recognition was assessed by mapping of binding subsites, and Mpro specificity was evaluated through the resolution of intermolecular interaction at the binding interface. Molecular dynamics simulations for 20 ns were performed to assess the stability and behaviour of 132 Mpro systems complexed with KLQ*** substrates. Principal component analysis (PCA), was performed to assess II protein motions and conformational changes during the simulations. A strategy was formulated to classify and evaluate relations in the Mpro PCA motions, revealing four main clades of similarity. Similarity within a clade (Group 2) and dissimilarity between clades were confirmed. Trajectory visualisation revealed complex stability, substrate unbinding and dimer dissociation for various Mpro systems. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Authors: Zabo, Sophakama
- Date: 2022-10-14
- Subjects: COVID-19 (Disease) , Peptides , Chymotrypsin like , Chymotrypsin , Proteases , Proteolytic enzymes
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/365566 , vital:65760
- Description: COVID-19, as a disease resulting from SARS-CoV-2 infection, and a pandemic has had a devastating effect on the world. There are limited effective measures that control the spread and treatment of COVID-19 illness. The homodimeric cysteine main protease (Mpro) is crucial to the life cycle of the virus, as it cleaves the large polyproteins 1a and 1ab into matured, functional non-structural proteins. The Mpro exhibits high degrees of conservation in sequence, structure and specificity across coronavirus species, making it an ideal drug target. The Mpro substrate-binding profiles remain, despite the resolution of its recognition sequence and cleavage points (Leu-Gln↓(Ser/Ala/Gly)). In this study, a series of hexapeptide sequences containing the appropriate recognition sequence and cleavage points were generated and screened against the Mpro to study these binding profiles, and to further be the basis for efficiency-driven drug design. A multi-conformer hexapeptide substrate library comprising optimised 81000 models of 810 unique sequences was generated using RDKit within the context of python. Terminal capping with ACE and NMe was effected using SMILES and SMARTS matching. Multiple hexapeptides were complexed with chain B of crystallographic Mpro (PDS ID: 6XHM), following the validation of chain B for this purpose using AutoDock Vina at high levels of exhaustiveness (480). The resulting Vina scores ranged between -8.7 and -7.0 kcal.mol-1, and the reproducibility of best poses was validated through redocking. Ligand efficiency indices were calculated to identify substrate residues with high binding efficiency at their respective positions, revealing Val (P3), Ala (P1′); and Gly and Ala (P2′ and P3′) as leading efficient binders. Binding efficiencies were lowered by molecular weight. Substrate recognition was assessed by mapping of binding subsites, and Mpro specificity was evaluated through the resolution of intermolecular interaction at the binding interface. Molecular dynamics simulations for 20 ns were performed to assess the stability and behaviour of 132 Mpro systems complexed with KLQ*** substrates. Principal component analysis (PCA), was performed to assess II protein motions and conformational changes during the simulations. A strategy was formulated to classify and evaluate relations in the Mpro PCA motions, revealing four main clades of similarity. Similarity within a clade (Group 2) and dissimilarity between clades were confirmed. Trajectory visualisation revealed complex stability, substrate unbinding and dimer dissociation for various Mpro systems. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
Inadequate menstrual health management and human rights
- Authors: Hartley, Gemma-Maé
- Date: 2022-10-14
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422506 , vital:71953
- Description: Various human rights bodies have suggested that Inadequate Menstrual Health Management (MHM) could contribute to violations of human rights or, at the very least, is connected to the fulfilment of human rights. Despite recognition of this, there has not been thorough analysis of whether inadequate MHM is a violation of human rights, particularly in political discussions on the philosophy of human rights. Using a liberal cosmopolitan framework, this thesis attempts to bridge this gap and, ultimately, to argue that inadequate MHM constitutes a violation of human rights. This assertion brings with it various complications due to the heavily contested nature of human rights, their correlative duties, and the requirements for a lack of fulfilment to be considered a violation. I address each complication in turn. I argue that the traditional approach to human rights violations fails to consider the various ways that human rights are violated in our contemporary, globalised world. I suggest that structural violations of human rights should not be ruled out, particularly when we consider severe poverty and its by-products. Ultimately, the question of inadequate MHM is concerned with the content of human rights. If inadequate MHM were a violation, it would be a violation of women’s socio-economic rights. However, both group rights and socio-economic rights are contested. This thesis therefore justifies these rights. Group-differentiated rights are argued to be necessary for substantive equality. This is particularly the case when we consider the various risks women face simply because they are women. Women therefore need special protections and provisions for their human rights to be fulfilled. Socio-economic rights are necessary for the well-being and dignity of individuals everywhere. We can justify them even if they are costly, vague, and demanding on states, as critics argue they are. Therefore, if we can accept socio-economic rights and women’s rights, we can argue that inadequate MHM is a structural violation of human rights. Thinking about inadequate MHM in this way means we can respond to it with a level of urgency. This has the potential to improve the well-being, development, and dignity of women. , Thesis (MA) -- Faculty of Humanities, Political and International Studies, 2023
- Full Text:
- Authors: Hartley, Gemma-Maé
- Date: 2022-10-14
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422506 , vital:71953
- Description: Various human rights bodies have suggested that Inadequate Menstrual Health Management (MHM) could contribute to violations of human rights or, at the very least, is connected to the fulfilment of human rights. Despite recognition of this, there has not been thorough analysis of whether inadequate MHM is a violation of human rights, particularly in political discussions on the philosophy of human rights. Using a liberal cosmopolitan framework, this thesis attempts to bridge this gap and, ultimately, to argue that inadequate MHM constitutes a violation of human rights. This assertion brings with it various complications due to the heavily contested nature of human rights, their correlative duties, and the requirements for a lack of fulfilment to be considered a violation. I address each complication in turn. I argue that the traditional approach to human rights violations fails to consider the various ways that human rights are violated in our contemporary, globalised world. I suggest that structural violations of human rights should not be ruled out, particularly when we consider severe poverty and its by-products. Ultimately, the question of inadequate MHM is concerned with the content of human rights. If inadequate MHM were a violation, it would be a violation of women’s socio-economic rights. However, both group rights and socio-economic rights are contested. This thesis therefore justifies these rights. Group-differentiated rights are argued to be necessary for substantive equality. This is particularly the case when we consider the various risks women face simply because they are women. Women therefore need special protections and provisions for their human rights to be fulfilled. Socio-economic rights are necessary for the well-being and dignity of individuals everywhere. We can justify them even if they are costly, vague, and demanding on states, as critics argue they are. Therefore, if we can accept socio-economic rights and women’s rights, we can argue that inadequate MHM is a structural violation of human rights. Thinking about inadequate MHM in this way means we can respond to it with a level of urgency. This has the potential to improve the well-being, development, and dignity of women. , Thesis (MA) -- Faculty of Humanities, Political and International Studies, 2023
- Full Text:
Informal sector taxation: a lesson for South Africa
- Authors: Ledwaba, Sophy
- Date: 2022-10-14
- Subjects: Informal sector (Economics) Taxation South Africa , Turnover tax South Africa , Informal sector (Economics) Taxation Tanzania , Informal sector (Economics) Taxation Ghana , Informal sector (Economics) Taxation Zimbabwe , Small business Taxation Law and legislation South Africa
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/357571 , vital:64756
- Description: Most informal sector businesses in developing countries participate indirectly in the tax system through paying Value-Added Tax, as well as import and export duties, without being registered as taxpayers. This effectively results in the collection of lower tax revenue than the informal businesses would be liable for if they were registered as taxpayers. Additionally, the nonregistration of informal sector businesses in the tax system perpetuates a culture of non-tax compliance. Countries in sub-Saharan Africa have responded to this challenge by imposing direct taxes on revenue generated in the informal sector. This thesis discussed the informal sector taxation regimes adopted in Tanzania, Ghana and Zimbabwe, with the aim of identifying direct taxes that could be imposed in South Africa on the revenues generated in the informal sector. The goal of the research was to determine the nature of direct taxes that could be imposed in South Africa on the revenues generated in the informal sector, taking lessons from the sub- Saharan countries of Tanzania, Ghana and Zimbabwe. The research was based in the interpretivist paradigm. The data for the research consisted of documentary data dealing with the legislation and experiences of informal sector taxation in South Africa and the countries forming part of this research. The data were analysed using qualitative non-empirical research methods. South Africa has a presumptive tax model in the form of the Turnover Tax system, and it was recommended that this direct tax could be adapted to integrate the informal sector businesses into the tax base. The study made several recommendations to integrate informal sector businesses into the tax base. These recommendations include the implementation of the tax stamp system to tax informal businesses other than minibus taxi businesses, and an income tax sticker specifically designed for the informal minibus taxi industry. , Thesis (MCom) -- Faculty of Commerce, Accounting, 2022
- Full Text:
- Authors: Ledwaba, Sophy
- Date: 2022-10-14
- Subjects: Informal sector (Economics) Taxation South Africa , Turnover tax South Africa , Informal sector (Economics) Taxation Tanzania , Informal sector (Economics) Taxation Ghana , Informal sector (Economics) Taxation Zimbabwe , Small business Taxation Law and legislation South Africa
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/357571 , vital:64756
- Description: Most informal sector businesses in developing countries participate indirectly in the tax system through paying Value-Added Tax, as well as import and export duties, without being registered as taxpayers. This effectively results in the collection of lower tax revenue than the informal businesses would be liable for if they were registered as taxpayers. Additionally, the nonregistration of informal sector businesses in the tax system perpetuates a culture of non-tax compliance. Countries in sub-Saharan Africa have responded to this challenge by imposing direct taxes on revenue generated in the informal sector. This thesis discussed the informal sector taxation regimes adopted in Tanzania, Ghana and Zimbabwe, with the aim of identifying direct taxes that could be imposed in South Africa on the revenues generated in the informal sector. The goal of the research was to determine the nature of direct taxes that could be imposed in South Africa on the revenues generated in the informal sector, taking lessons from the sub- Saharan countries of Tanzania, Ghana and Zimbabwe. The research was based in the interpretivist paradigm. The data for the research consisted of documentary data dealing with the legislation and experiences of informal sector taxation in South Africa and the countries forming part of this research. The data were analysed using qualitative non-empirical research methods. South Africa has a presumptive tax model in the form of the Turnover Tax system, and it was recommended that this direct tax could be adapted to integrate the informal sector businesses into the tax base. The study made several recommendations to integrate informal sector businesses into the tax base. These recommendations include the implementation of the tax stamp system to tax informal businesses other than minibus taxi businesses, and an income tax sticker specifically designed for the informal minibus taxi industry. , Thesis (MCom) -- Faculty of Commerce, Accounting, 2022
- Full Text:
Investigating the roles of HOP isoforms in KSHV biology
- Matandirotya, Lorraine Tariro
- Authors: Matandirotya, Lorraine Tariro
- Date: 2022-10-14
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/365257 , vital:65721
- Description: Thesis embargoed. Possible release date set for early 2025. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Authors: Matandirotya, Lorraine Tariro
- Date: 2022-10-14
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/365257 , vital:65721
- Description: Thesis embargoed. Possible release date set for early 2025. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
Knowledge of and concern about global biodiversity loss vs local biodiversity loss in the Maputaland-Pondoland-Albany Hotspot (MPA)
- Authors: Toyisi, Zanele Jacqueline
- Date: 2022-10-14
- Subjects: Biodiversity Public opinion , Biodiversity conservation South Africa , Maputaland-Pondoland-Albany Hotspot , Biodiversity loss , Local knowledge
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/365025 , vital:65671
- Description: Biodiversity forms the basis of the ecosystem services that society depends on. However, humanity has caused an increase in the extinction rates up to 100 times higher than that of evolutionary background levels. Recent studies found that biodiversity conservation becomes successful when it is grounded in local support. Support for conservation of biodiversity depends on peoples’ knowledge of biodiversity, their attitudes and awareness of the number of species that are present and that are threatened with extinction. However, some studies have shown that the public has little knowledge about the concept of biodiversity and have poor biodiversity identification skills. There is growing concern that people know and are more concerned about global biodiversity loss than what is happening around them locally. The notion that people know and are more concerned about global biodiversity loss rather than local, has not been deeply studied. Most studies have been in developed countries, with limited studies in developing countries and countries that have high diversity such as South Africa. Having accurate knowledge about biodiversity and the environment is said to be the key predictor of intention to change behaviour in relation to biodiversity. Therefore, the purpose of this study was to understand the knowledge and concern (if any) people have of biodiversity at global and local scales. More so, it set out to determine how familiar people are with the term biodiversity, what they consider as forces leading to biodiversity decline, the level of concern that they have for biodiversity loss and if knowledge and concern is influenced by demographic profiles. To achieve this aim, a total of 220 random interviews were conducted in three towns within the Maputaland-Pondoland-Albany Hotspot in South Africa. The results show that respondents are familiar with the term biodiversity. There was a strong relationship between having heard of the term and the ability to define it with 55 % of the respondents aware of it and able to define it. Respondents had moderate knowledge general knowledge related to biodiversity. Gender, education and childhood background did play a role in the knowledge of biodiversity. Women had more knowledge about biodiversity than men, highly educated respondents knew more and the youth knew more than older respondents. The results of this study found that there were no respondents who could not name any local species from South Africa. However, things changed at global level with 32 % of the participants unable to name species at global level. Endangered species are still relatively unknown, as the majority of respondents could not name any at district (84 %) or at global level (61 %). Charismatic species were known the most by respondents as 52 % mentioned them at national level and 59 % at global level. This study also assessed if there is concern for biodiversity loss. The results showed that there is concern for biodiversity with 71 % of the respondents in support for conservation and 60 % of the respondents willing to donate towards conservation. This study found that reasons for conservation related to the level of products consumed directly from the environment. Those that supported conservation for use values consumed more products from the environment than those who were in support for non-use values. Furtherly, this study found that women were more concerned about biodiversity loss than men. Highly educated respondents were more concerned and the youth was not. Furtherly, this study found that knowledge about biodiversity loss corelated with concern. For example, women had more knowledge and were more concerned about biodiversity loss. Overall, this study has shown that there is some knowledge and concern that people have about biodiversity and its loss. This can assist the relevant policy makers and researchers to know where intervention is needed to increase the knowledge that people have of biodiversity loss and which aspects of biodiversity people are most concerned about. This is so that new policies and conservation measures can include what is appealing to the local people so that support for conservation can be built and accepted by local people. , Thesis (MSc) -- Faculty of Science, Environmental Science, 2022
- Full Text:
- Authors: Toyisi, Zanele Jacqueline
- Date: 2022-10-14
- Subjects: Biodiversity Public opinion , Biodiversity conservation South Africa , Maputaland-Pondoland-Albany Hotspot , Biodiversity loss , Local knowledge
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/365025 , vital:65671
- Description: Biodiversity forms the basis of the ecosystem services that society depends on. However, humanity has caused an increase in the extinction rates up to 100 times higher than that of evolutionary background levels. Recent studies found that biodiversity conservation becomes successful when it is grounded in local support. Support for conservation of biodiversity depends on peoples’ knowledge of biodiversity, their attitudes and awareness of the number of species that are present and that are threatened with extinction. However, some studies have shown that the public has little knowledge about the concept of biodiversity and have poor biodiversity identification skills. There is growing concern that people know and are more concerned about global biodiversity loss than what is happening around them locally. The notion that people know and are more concerned about global biodiversity loss rather than local, has not been deeply studied. Most studies have been in developed countries, with limited studies in developing countries and countries that have high diversity such as South Africa. Having accurate knowledge about biodiversity and the environment is said to be the key predictor of intention to change behaviour in relation to biodiversity. Therefore, the purpose of this study was to understand the knowledge and concern (if any) people have of biodiversity at global and local scales. More so, it set out to determine how familiar people are with the term biodiversity, what they consider as forces leading to biodiversity decline, the level of concern that they have for biodiversity loss and if knowledge and concern is influenced by demographic profiles. To achieve this aim, a total of 220 random interviews were conducted in three towns within the Maputaland-Pondoland-Albany Hotspot in South Africa. The results show that respondents are familiar with the term biodiversity. There was a strong relationship between having heard of the term and the ability to define it with 55 % of the respondents aware of it and able to define it. Respondents had moderate knowledge general knowledge related to biodiversity. Gender, education and childhood background did play a role in the knowledge of biodiversity. Women had more knowledge about biodiversity than men, highly educated respondents knew more and the youth knew more than older respondents. The results of this study found that there were no respondents who could not name any local species from South Africa. However, things changed at global level with 32 % of the participants unable to name species at global level. Endangered species are still relatively unknown, as the majority of respondents could not name any at district (84 %) or at global level (61 %). Charismatic species were known the most by respondents as 52 % mentioned them at national level and 59 % at global level. This study also assessed if there is concern for biodiversity loss. The results showed that there is concern for biodiversity with 71 % of the respondents in support for conservation and 60 % of the respondents willing to donate towards conservation. This study found that reasons for conservation related to the level of products consumed directly from the environment. Those that supported conservation for use values consumed more products from the environment than those who were in support for non-use values. Furtherly, this study found that women were more concerned about biodiversity loss than men. Highly educated respondents were more concerned and the youth was not. Furtherly, this study found that knowledge about biodiversity loss corelated with concern. For example, women had more knowledge and were more concerned about biodiversity loss. Overall, this study has shown that there is some knowledge and concern that people have about biodiversity and its loss. This can assist the relevant policy makers and researchers to know where intervention is needed to increase the knowledge that people have of biodiversity loss and which aspects of biodiversity people are most concerned about. This is so that new policies and conservation measures can include what is appealing to the local people so that support for conservation can be built and accepted by local people. , Thesis (MSc) -- Faculty of Science, Environmental Science, 2022
- Full Text:
Land degradation and livelihood strategies in rural Zimbabwe: the case of two A1 farms in Shurugwi District
- Authors: Nciizah, Tendai
- Date: 2022-10-14
- Subjects: Land degradation Zimbabwe , Sustainable livelihood , Shurugwi District , Conservation of natural resources Zimbabwe , Land reform Zimbabwe
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365989 , vital:65808 , https://doi.org/10.21504/10962/365989
- Description: Land degradation is a global phenomenon which is having serious negative consequences for rural livelihoods, which depend quite fundamentally on land and its resources. At the same time, one of the key conditions contributing to land degradation relates to rural livelihood practices, insofar as these practices fail to protect the land. Hence, there sometimes exists a mutually-reinforcing process of decline, in relation to both land vitality and livelihoods vitality over time. This thesis seeks to investigate and understand this complex land-livelihoods process through a case study of two fast track farms in the Shurugwi District of contemporary Zimbabwe. In the year 2000, the Zimbabwean government introduced the fast track land reform programme which fundamentally reconfigured the rural landscape. In particular, it led to the formation of A1 farms (containing small-scale farming units called A1 plots), onto which people were resettled for purposes of enhancing their livelihoods. The case study focuses on two A1 farms in the district, namely, Selukwe Peak and Adare farms. Through a longitudinal study of land and livelihoods on these A1 farms, this study seeks to identify the multi-faceted character of land degradation on the farms, the multi-layered conditions (or causes) facilitating land degradation (specifically, the farm-based livelihood practices) and the effects of this land degradation on these very livelihood practices. This includes a focus on farmers’ understandings of land degradation and how these understandings may or may not condition livelihood practices on the two farms. Of particular importance is the presence of not only agricultural practices, but also high levels of illegal and legal mining on the farms and in the surrounding areas. In pursuing this study, the thesis draws upon the Sustainable Livelihoods Approach alongside Margaret Archer’s morphogenetic sociological perspective. Combined, they provide an intricate understanding of the relevance of both structure and agency to the analysis. A qualitative methodology was used, and this involved a questionnaire survey, in- depth interviews, life histories, focus group discussions and transect walks. The study concludes that the livelihood strategies undertaken by the villagers of Selukwe Peak and Adare farms are key causes of land degradation, as are the land-degrading activities of illegal and legal miners. The A1 villagers are aware that their activities are causing land degradation but they continue these activities because they are pushed by circumstances beyond their control. Hence, both proximate and underlying causes are of some significance in understanding land degradation and livelihoods on the two farms, and their interrelationships. , Thesis (PhD) -- Faculty of Humanities, Sociology, 2022
- Full Text:
- Authors: Nciizah, Tendai
- Date: 2022-10-14
- Subjects: Land degradation Zimbabwe , Sustainable livelihood , Shurugwi District , Conservation of natural resources Zimbabwe , Land reform Zimbabwe
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365989 , vital:65808 , https://doi.org/10.21504/10962/365989
- Description: Land degradation is a global phenomenon which is having serious negative consequences for rural livelihoods, which depend quite fundamentally on land and its resources. At the same time, one of the key conditions contributing to land degradation relates to rural livelihood practices, insofar as these practices fail to protect the land. Hence, there sometimes exists a mutually-reinforcing process of decline, in relation to both land vitality and livelihoods vitality over time. This thesis seeks to investigate and understand this complex land-livelihoods process through a case study of two fast track farms in the Shurugwi District of contemporary Zimbabwe. In the year 2000, the Zimbabwean government introduced the fast track land reform programme which fundamentally reconfigured the rural landscape. In particular, it led to the formation of A1 farms (containing small-scale farming units called A1 plots), onto which people were resettled for purposes of enhancing their livelihoods. The case study focuses on two A1 farms in the district, namely, Selukwe Peak and Adare farms. Through a longitudinal study of land and livelihoods on these A1 farms, this study seeks to identify the multi-faceted character of land degradation on the farms, the multi-layered conditions (or causes) facilitating land degradation (specifically, the farm-based livelihood practices) and the effects of this land degradation on these very livelihood practices. This includes a focus on farmers’ understandings of land degradation and how these understandings may or may not condition livelihood practices on the two farms. Of particular importance is the presence of not only agricultural practices, but also high levels of illegal and legal mining on the farms and in the surrounding areas. In pursuing this study, the thesis draws upon the Sustainable Livelihoods Approach alongside Margaret Archer’s morphogenetic sociological perspective. Combined, they provide an intricate understanding of the relevance of both structure and agency to the analysis. A qualitative methodology was used, and this involved a questionnaire survey, in- depth interviews, life histories, focus group discussions and transect walks. The study concludes that the livelihood strategies undertaken by the villagers of Selukwe Peak and Adare farms are key causes of land degradation, as are the land-degrading activities of illegal and legal miners. The A1 villagers are aware that their activities are causing land degradation but they continue these activities because they are pushed by circumstances beyond their control. Hence, both proximate and underlying causes are of some significance in understanding land degradation and livelihoods on the two farms, and their interrelationships. , Thesis (PhD) -- Faculty of Humanities, Sociology, 2022
- Full Text:
Larval assemblages in intertidal habitats: the use of artificial and natural microhabitats
- Authors: Reddy, Seshnee
- Date: 2022-10-14
- Subjects: Larvae Habitat , Niche (Ecology) , Intertidal ecology South Africa Eastern Cape , Light trap , DNA barcoding , Artificial habitat , Larvae Effect of human beings on South Africa Eastern Cape , Urbanization South Africa Eastern Cape
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/364992 , vital:65668
- Description: Coastal habitats, and more specifically, intertidal habitats, host a unique range of biodiversity and are key areas for many fish and invertebrate species across one or more of their life stages. This is due to the provision of microhabitats which offer an escape from harsh environmental stressors and predation as well as increased food supply, hence increasing chances of survival. Due to the growing human population however, coastal habitats are being replaced by artificial structures (jetties, seawalls, piers, breakwaters) which partially or heavily fragment the natural environment through urbanisation-related expansion processes. These coastal infrastructures also have different physical properties from the natural environment and therefore tend to support different biological assemblages and can potentially alter the existing biodiversity and its functionality. The overall aim of this project was therefore to evaluate the use of artificial and natural intertidal microhabitats by fish and invertebrate larvae along the South African, Eastern Cape coastline. As independent case studies, fieldwork was conducted at an urban (Port Alfred Marina) and rocky shore (Kenton-on-Sea) site. Within each of these study sites, two replicated sheltered subsites were selected, which represented microhabitats. Samples were collected from these replicated microhabitats from September 2019 to February 2020 using light traps which targeted phototactic larval species, as well as a portable pump, for photo-neutral/negative taxa. All samples were preserved onsite in 99% ethanol and specimens were later counted and identified in the laboratory to the lowest possible taxonomic level using a stereomicroscope. Additionally, DNA barcoding was conducted on selected larval taxa for verification of morphological identification as well as contributing to the field of larval taxonomy through development of public database records. The barcoding technique was effective in positively identifying 96% and 58% of fish and invertebrate larvae sampled, respectively (overall identification success of 86%), to either family, genus or species level. Results of microhabitat use indicate higher larval abundances associated with artificial structures as compared to natural structures, with significant differences between the selected microhabitats within the rocky shores and the marina respectively, across months. High numbers of several early stage taxa were observed within the selected microhabitats in the marina, with Pinnotheres sp. (zoea) (Family: Pinnotheridae) being the most abundant invertebrate larval taxon collected at the artificial microhabitats of jetties and vertical walls. Fish larvae of Omobranchus woodi (preflexion) and Etrumeus whiteheadi (postflexion) were the most dominant at the selected artificial microhabitats within the marina. The DNA barcoding tool used in the current study to verify morphological identification proved to be instrumental in the accuracy of the reliable data collection of the early life stages present in these habitats. These results suggest that artificial structures may provide refugia for the vulnerable very early life stages of species and, in turn, play a potential facilitative role in reproductive and population connectivity which could result in replenishment of natural populations. It is therefore possible that these urban habitats could be considered as hubs for maintenance of coastal biodiversity. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2022
- Full Text:
- Authors: Reddy, Seshnee
- Date: 2022-10-14
- Subjects: Larvae Habitat , Niche (Ecology) , Intertidal ecology South Africa Eastern Cape , Light trap , DNA barcoding , Artificial habitat , Larvae Effect of human beings on South Africa Eastern Cape , Urbanization South Africa Eastern Cape
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/364992 , vital:65668
- Description: Coastal habitats, and more specifically, intertidal habitats, host a unique range of biodiversity and are key areas for many fish and invertebrate species across one or more of their life stages. This is due to the provision of microhabitats which offer an escape from harsh environmental stressors and predation as well as increased food supply, hence increasing chances of survival. Due to the growing human population however, coastal habitats are being replaced by artificial structures (jetties, seawalls, piers, breakwaters) which partially or heavily fragment the natural environment through urbanisation-related expansion processes. These coastal infrastructures also have different physical properties from the natural environment and therefore tend to support different biological assemblages and can potentially alter the existing biodiversity and its functionality. The overall aim of this project was therefore to evaluate the use of artificial and natural intertidal microhabitats by fish and invertebrate larvae along the South African, Eastern Cape coastline. As independent case studies, fieldwork was conducted at an urban (Port Alfred Marina) and rocky shore (Kenton-on-Sea) site. Within each of these study sites, two replicated sheltered subsites were selected, which represented microhabitats. Samples were collected from these replicated microhabitats from September 2019 to February 2020 using light traps which targeted phototactic larval species, as well as a portable pump, for photo-neutral/negative taxa. All samples were preserved onsite in 99% ethanol and specimens were later counted and identified in the laboratory to the lowest possible taxonomic level using a stereomicroscope. Additionally, DNA barcoding was conducted on selected larval taxa for verification of morphological identification as well as contributing to the field of larval taxonomy through development of public database records. The barcoding technique was effective in positively identifying 96% and 58% of fish and invertebrate larvae sampled, respectively (overall identification success of 86%), to either family, genus or species level. Results of microhabitat use indicate higher larval abundances associated with artificial structures as compared to natural structures, with significant differences between the selected microhabitats within the rocky shores and the marina respectively, across months. High numbers of several early stage taxa were observed within the selected microhabitats in the marina, with Pinnotheres sp. (zoea) (Family: Pinnotheridae) being the most abundant invertebrate larval taxon collected at the artificial microhabitats of jetties and vertical walls. Fish larvae of Omobranchus woodi (preflexion) and Etrumeus whiteheadi (postflexion) were the most dominant at the selected artificial microhabitats within the marina. The DNA barcoding tool used in the current study to verify morphological identification proved to be instrumental in the accuracy of the reliable data collection of the early life stages present in these habitats. These results suggest that artificial structures may provide refugia for the vulnerable very early life stages of species and, in turn, play a potential facilitative role in reproductive and population connectivity which could result in replenishment of natural populations. It is therefore possible that these urban habitats could be considered as hubs for maintenance of coastal biodiversity. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2022
- Full Text:
Lateral and vertical mineral-chemical variation in high-grade ores of the Kalahari Manganese Field, and implications for ore genesis and geometallurgy
- Authors: Motilaodi, Donald
- Date: 2022-10-14
- Subjects: Manganese ores , Geometallurgy , Hydrothermal alteration , Petrology , Mineralogy , Geochemistry
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362972 , vital:65379
- Description: The Kalahari Manganese Field (KMF) is a world-class resource of manganese ore hosted by the Paleoproterozoic Hotazel banded iron formation. KMF ores are categorised into two main types, i.e., low-grade, carbonate rich, braunitic ore (Mn≤40wt%) and carbonate-free, high-grade, Ca-braunite+hausmannite ore (Mn≥44wt%). High-grade ores, also known as Wessels type from the homonymous mine in the northernmost KMF, are thought to have formed from variable degrees of hydrothermal carbonate and silica leaching from a low-grade ore precursor, termed Mamatwan-type after the homonymous mine in the southernmost KMF. This project aims to conduct a mineralogical and mineral-chemical study of representative manganese ore samples from a suite of drillcores intersecting both the upper and the lower layers in the northern KMF, covering the areas of Wessels, N’chwaning and Gloria mines. Petrographically, the high-grade Mn ore displays great variability in three-dimensional space. Texturally, the ores exhibit a great variety of textures which may or may not show preservation of the laminated and ovoidal textures that typify the postulated low-grade protore. There is also significant variation in the mineralogical and geochemical characteristics of the high-grade Mn ores both vertically and laterally. Vertical variation includes, probably for the first time, variability between the upper and lower ore layers within individual drillcores of the Hotazel sequence. Mineralogically, the ores contain variable modal abundances of the ore-forming minerals braunite (I, II, “new”) and hausmannite, and much less so of bixbyite, marokite and manganite. Common accessories include andradite, barite and low-Mn carbonate minerals. Chemically, the dominant ore minerals braunite and hausmannite, contain Fe up to 22 and 15wt% respectively, which accounts for the bulk of the iron contained in the ores. Braunite compositions also exhibit a large range with respect to their ratio of Ca/Si. Mineral-specific trace element concentrations for the same minerals measured by LA-ICP-MS, reveal generally large variations from one element to the other. When normalized against the trace element composition of bulk low-grade precursor ore, strong enrichments are recorded for both hausmannite and braunite in selected alkali/alkali earth elements, transition metals and lanthanides, such as Sc, Co, Zn, Cu, Pb, La, and Ce. These are akin to enrichments recorded in average high-grade ore. Although there is also no obvious relationship between Fe content in both hausmannite and braunite and their trace element abundances, the drillcore that captures high-grade ore with the highest trace element concentrations appears to be located most proximal to a major fault. Results collectively suggest that high-grade Mn ores of the KMF have undergone a complex hydrothermal history with a clear and significant metasomatic addition of trace elements into ore-forming minerals. First order trends in the mineralogical and mineral-chemical distribution of the ores in space, suggest hausmannite-dominated ores near the Hotazel suboutcrop, and an apparent decline in ore quality with braunite II-andradite-barite-calcite ores as the major graben fault is approached in a southwesterly direction. The latter trend appears to be at odds with prevailing fault-controlled alteration models. Elucidating that hydrothermal history of the Wessels-type high grade Mn ores of the KMF, will be crucial to understanding the compositional controls of these ores in space, and the potential impact thereof in terms of geometallurgy. , Thesis (MSc) -- Faculty of Science, Geology, 2022
- Full Text:
- Authors: Motilaodi, Donald
- Date: 2022-10-14
- Subjects: Manganese ores , Geometallurgy , Hydrothermal alteration , Petrology , Mineralogy , Geochemistry
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362972 , vital:65379
- Description: The Kalahari Manganese Field (KMF) is a world-class resource of manganese ore hosted by the Paleoproterozoic Hotazel banded iron formation. KMF ores are categorised into two main types, i.e., low-grade, carbonate rich, braunitic ore (Mn≤40wt%) and carbonate-free, high-grade, Ca-braunite+hausmannite ore (Mn≥44wt%). High-grade ores, also known as Wessels type from the homonymous mine in the northernmost KMF, are thought to have formed from variable degrees of hydrothermal carbonate and silica leaching from a low-grade ore precursor, termed Mamatwan-type after the homonymous mine in the southernmost KMF. This project aims to conduct a mineralogical and mineral-chemical study of representative manganese ore samples from a suite of drillcores intersecting both the upper and the lower layers in the northern KMF, covering the areas of Wessels, N’chwaning and Gloria mines. Petrographically, the high-grade Mn ore displays great variability in three-dimensional space. Texturally, the ores exhibit a great variety of textures which may or may not show preservation of the laminated and ovoidal textures that typify the postulated low-grade protore. There is also significant variation in the mineralogical and geochemical characteristics of the high-grade Mn ores both vertically and laterally. Vertical variation includes, probably for the first time, variability between the upper and lower ore layers within individual drillcores of the Hotazel sequence. Mineralogically, the ores contain variable modal abundances of the ore-forming minerals braunite (I, II, “new”) and hausmannite, and much less so of bixbyite, marokite and manganite. Common accessories include andradite, barite and low-Mn carbonate minerals. Chemically, the dominant ore minerals braunite and hausmannite, contain Fe up to 22 and 15wt% respectively, which accounts for the bulk of the iron contained in the ores. Braunite compositions also exhibit a large range with respect to their ratio of Ca/Si. Mineral-specific trace element concentrations for the same minerals measured by LA-ICP-MS, reveal generally large variations from one element to the other. When normalized against the trace element composition of bulk low-grade precursor ore, strong enrichments are recorded for both hausmannite and braunite in selected alkali/alkali earth elements, transition metals and lanthanides, such as Sc, Co, Zn, Cu, Pb, La, and Ce. These are akin to enrichments recorded in average high-grade ore. Although there is also no obvious relationship between Fe content in both hausmannite and braunite and their trace element abundances, the drillcore that captures high-grade ore with the highest trace element concentrations appears to be located most proximal to a major fault. Results collectively suggest that high-grade Mn ores of the KMF have undergone a complex hydrothermal history with a clear and significant metasomatic addition of trace elements into ore-forming minerals. First order trends in the mineralogical and mineral-chemical distribution of the ores in space, suggest hausmannite-dominated ores near the Hotazel suboutcrop, and an apparent decline in ore quality with braunite II-andradite-barite-calcite ores as the major graben fault is approached in a southwesterly direction. The latter trend appears to be at odds with prevailing fault-controlled alteration models. Elucidating that hydrothermal history of the Wessels-type high grade Mn ores of the KMF, will be crucial to understanding the compositional controls of these ores in space, and the potential impact thereof in terms of geometallurgy. , Thesis (MSc) -- Faculty of Science, Geology, 2022
- Full Text:
Leveraging LTSP to deploy a sustainable e-infrastructure for poor communities in South Africa
- Authors: Zvidzayi, Tichaona Manyara
- Date: 2022-10-14
- Subjects: Linux Terminal Server Project , Network computers , Thin client , Fat client , Cyberinfrastructure , Poverty reduction
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/365577 , vital:65761
- Description: Poverty alleviation is one of the main challenges the South African government is facing. Information and knowledge are key strategic resources for both social and economic development, and nowadays they most often rely on Information and Communication Technologies (ICTs). Poor communities have limited or no access to functioning e-infrastructure, which underpins ICT. The Siyakhula Living Lab (SLL) is a joint project between the universities of Rhodes and Fort Hare that has been running for over 15 years now. The SLL solution is currently implemented in schools in the Eastern Cape’s Dwesa-Mbhashe municipality as well as schools in Makhanda (formerly Grahamstown). Over the years, a number of blueprints for the meaningful connection of poor communities was developed. The research reported in this thesis sought to review and improve the Siyakhula Living Lab (SLL) blueprint regarding fixed computing infrastructure (as opposed to networking and applications). The review confirmed the viability of the GNU/Linux Terminal Server Project (LTSP) based computing infrastructure deployed in schools to serve the surrounding community. In 2019 LTSP was redesigned and rewritten to improve on the previous version. Amongst other improvements, LTSP19+ has a smaller memory footprint and supports a graphical way to prepare and maintain the client’s image using virtual machines. These improvements increase the potential life of ICT projects implementing the SLL solution, increasing the participation of members of the community (especially teachers) to the maintenance of the computing installations. The review recommends the switching from thin clients deployments to full ("thick") clients deployments, still booting from the network and mounting their file systems on a central server. The switch is motivated by reasons that go from cost-effectiveness to the ability to survive the sudden unavailability of the central server. From experience in the previous deployment, electrical power surge protection should be mandatory. Also, UPS to protect the file system of the central server should be configured to start the shutdown immediately on electrical power loss in order to protect the life of the UPS battery (and make it possible to use cheaper UPS that report only on network power loss). The research study contributed to one real-life computing infrastructure deployment in the Ntsika school in Makhanda and one re-deployment in the Ngwane school in the Dwesa-Mbhashe area. For about two years, the research also supported continuous maintenance for the Ntsika, Ngwane and Mpume schools. , Thesis (MSc) -- Faculty of Science, Computer Science, 2022
- Full Text:
- Authors: Zvidzayi, Tichaona Manyara
- Date: 2022-10-14
- Subjects: Linux Terminal Server Project , Network computers , Thin client , Fat client , Cyberinfrastructure , Poverty reduction
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/365577 , vital:65761
- Description: Poverty alleviation is one of the main challenges the South African government is facing. Information and knowledge are key strategic resources for both social and economic development, and nowadays they most often rely on Information and Communication Technologies (ICTs). Poor communities have limited or no access to functioning e-infrastructure, which underpins ICT. The Siyakhula Living Lab (SLL) is a joint project between the universities of Rhodes and Fort Hare that has been running for over 15 years now. The SLL solution is currently implemented in schools in the Eastern Cape’s Dwesa-Mbhashe municipality as well as schools in Makhanda (formerly Grahamstown). Over the years, a number of blueprints for the meaningful connection of poor communities was developed. The research reported in this thesis sought to review and improve the Siyakhula Living Lab (SLL) blueprint regarding fixed computing infrastructure (as opposed to networking and applications). The review confirmed the viability of the GNU/Linux Terminal Server Project (LTSP) based computing infrastructure deployed in schools to serve the surrounding community. In 2019 LTSP was redesigned and rewritten to improve on the previous version. Amongst other improvements, LTSP19+ has a smaller memory footprint and supports a graphical way to prepare and maintain the client’s image using virtual machines. These improvements increase the potential life of ICT projects implementing the SLL solution, increasing the participation of members of the community (especially teachers) to the maintenance of the computing installations. The review recommends the switching from thin clients deployments to full ("thick") clients deployments, still booting from the network and mounting their file systems on a central server. The switch is motivated by reasons that go from cost-effectiveness to the ability to survive the sudden unavailability of the central server. From experience in the previous deployment, electrical power surge protection should be mandatory. Also, UPS to protect the file system of the central server should be configured to start the shutdown immediately on electrical power loss in order to protect the life of the UPS battery (and make it possible to use cheaper UPS that report only on network power loss). The research study contributed to one real-life computing infrastructure deployment in the Ntsika school in Makhanda and one re-deployment in the Ngwane school in the Dwesa-Mbhashe area. For about two years, the research also supported continuous maintenance for the Ntsika, Ngwane and Mpume schools. , Thesis (MSc) -- Faculty of Science, Computer Science, 2022
- Full Text:
Linking Hop and LANA1 in the KSHV life cycle
- Authors: Ruck, Jamie-Lee
- Date: 2022-10-14
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/365291 , vital:65724
- Description: Thesis embargoed. Possible release date set for early 2025. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Authors: Ruck, Jamie-Lee
- Date: 2022-10-14
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/365291 , vital:65724
- Description: Thesis embargoed. Possible release date set for early 2025. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
Long-term trends in fish length-at-age, catch-at-length and condition of the Namibian and South African commercially exploited species
- Authors: Iyambo, Elago Martha
- Date: 2022-10-14
- Subjects: Fishery management South Africa , Fishery management Namibia , Fishes Growth , Fisheries Fishing effort , Climatic changes , Fishes Climatic factors
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362872 , vital:65370
- Description: Fish growth rate is a flexible trait that can evolve in response to fishing or environmental change. Therefore, knowledge of fish growth rate patterns, long-term and short-term responses to fishing effort and environmental change is important for fisheries management in the Benguela. Historical and current age length keys have been used as indicators of annual fish growth in the Benguela, the growth rate study on Merluccius paradoxus demonstrated long-term changes in growth over three decades as a response to fishing. However, the fish growth rate patterns, in relation to fishing effort and environmental change patterns are still not known for the many commercially important stocks in the Benguela. The specific objectives of the project were to determine the annual variability and long-term trends, in annual mean lengths-at-age, catch-at-length and fish condition of 17 commercially exploited resources, targeted and bycatch in Namibia and South Africa in relation to environmental changes (sea surface temperature). The results showed that there was a significant decrease in mean length at age 7 for Merluccius capensis (Namibian stock), a significant decrease in mean length at ages 3 to 7 for South African M. capensis and a significant increase in mean length at ages 2 to 6 for South African M. paradoxus Fishery-induced evolution may be the reason for the increase in mean length in the early stages of hake. A regime shift was detected in the mean length at age 1 for Etrumeus whiteheadi (South African stock) caused by changes in water temperatures. A decrease in mean length of the catch was observed for Namibian M. capensis and the reason for this could have been the stock being overexploited during the years of the observed trend (1968 to 1987). Historically both the Namibian Lophius vomerinus and Helicolenus dactylopterus were bycatch of the hake fishery, therefore, the decrease in their mean length of the catch may be due to increased bycatch mortalities due to increased hake catches. The improvement in the management measures of the Jasus lalandii fishery and possible favourable oxygen fluctuation might have caused the stock to increase in mean length of the catch between 1977 and 1982. Fish condition showed a significant difference in stocks between years. Fish condition of M. capensis, M. paradoxus and T. capensis were analysed. The rest of the commercial stocks were omitted because there was limited length-weight data. For Namibian M. capensis the spawning season may have caused fish to have the best condition in 1987 and while higher temperatures in 1983 may have led to the worst condition in 1983. Higher prey availability in 1979 for Namibian M. paradoxus could have been the reason for fish with best condition being found in 1979. T. capensis had the highest condition index in 1986 when cooler summer SST prevailed that may have been more favourable for T. capensis to live in. July, September and January SSTs were significantly negatively correlated with the mean length of M. capensis at age 3. This was perhaps due to upwelling intensity and plankton productivity which increases in winter and decreases in summer. A separate study of the impacts of fishery-induced changes and density-dependence on fish growth rate, as well as the effects of other environmental variables is recommended. Since data for some species was outdated, it is suggested to update biological variables and assessment for future work. This study can be used to understand the key life history characteristics of Namibian and South African exploited resources, targeted and bycatch. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2022
- Full Text:
- Authors: Iyambo, Elago Martha
- Date: 2022-10-14
- Subjects: Fishery management South Africa , Fishery management Namibia , Fishes Growth , Fisheries Fishing effort , Climatic changes , Fishes Climatic factors
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/362872 , vital:65370
- Description: Fish growth rate is a flexible trait that can evolve in response to fishing or environmental change. Therefore, knowledge of fish growth rate patterns, long-term and short-term responses to fishing effort and environmental change is important for fisheries management in the Benguela. Historical and current age length keys have been used as indicators of annual fish growth in the Benguela, the growth rate study on Merluccius paradoxus demonstrated long-term changes in growth over three decades as a response to fishing. However, the fish growth rate patterns, in relation to fishing effort and environmental change patterns are still not known for the many commercially important stocks in the Benguela. The specific objectives of the project were to determine the annual variability and long-term trends, in annual mean lengths-at-age, catch-at-length and fish condition of 17 commercially exploited resources, targeted and bycatch in Namibia and South Africa in relation to environmental changes (sea surface temperature). The results showed that there was a significant decrease in mean length at age 7 for Merluccius capensis (Namibian stock), a significant decrease in mean length at ages 3 to 7 for South African M. capensis and a significant increase in mean length at ages 2 to 6 for South African M. paradoxus Fishery-induced evolution may be the reason for the increase in mean length in the early stages of hake. A regime shift was detected in the mean length at age 1 for Etrumeus whiteheadi (South African stock) caused by changes in water temperatures. A decrease in mean length of the catch was observed for Namibian M. capensis and the reason for this could have been the stock being overexploited during the years of the observed trend (1968 to 1987). Historically both the Namibian Lophius vomerinus and Helicolenus dactylopterus were bycatch of the hake fishery, therefore, the decrease in their mean length of the catch may be due to increased bycatch mortalities due to increased hake catches. The improvement in the management measures of the Jasus lalandii fishery and possible favourable oxygen fluctuation might have caused the stock to increase in mean length of the catch between 1977 and 1982. Fish condition showed a significant difference in stocks between years. Fish condition of M. capensis, M. paradoxus and T. capensis were analysed. The rest of the commercial stocks were omitted because there was limited length-weight data. For Namibian M. capensis the spawning season may have caused fish to have the best condition in 1987 and while higher temperatures in 1983 may have led to the worst condition in 1983. Higher prey availability in 1979 for Namibian M. paradoxus could have been the reason for fish with best condition being found in 1979. T. capensis had the highest condition index in 1986 when cooler summer SST prevailed that may have been more favourable for T. capensis to live in. July, September and January SSTs were significantly negatively correlated with the mean length of M. capensis at age 3. This was perhaps due to upwelling intensity and plankton productivity which increases in winter and decreases in summer. A separate study of the impacts of fishery-induced changes and density-dependence on fish growth rate, as well as the effects of other environmental variables is recommended. Since data for some species was outdated, it is suggested to update biological variables and assessment for future work. This study can be used to understand the key life history characteristics of Namibian and South African exploited resources, targeted and bycatch. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2022
- Full Text:
M.M. Hala: Memoirs of an Umkhonto WeSizwe Cadre
- Authors: Hala, Mzimasi Mike
- Date: 2022-10-14
- Subjects: African National Congress , Umkhonto we Sizwe (South Africa) , Anti-apartheid movements South Africa , Anti-apartheid activists South Africa , South Africa Politics and government 1948-1994 , Hani, Chris, 1942-1993 , Holomisa, Bantu, 1955- , Bisho massacre
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/406785 , vital:70307
- Description: Born in Komani (Queenstown) in 1959 and detained for Congress of South African Students (COSAS) activities while still at school, Mzimasi Mike Hala departed South Africa via Swaziland in 1981 and joined uMkhonto WeSizwe (MK). Trained in Angola, Cuba and East Germany, he commanded Cacuso camp in Angola, until redeployed to South Africa in 1987 to work underground in Venda and Cape Town. Following the unbanning of the liberation movements in 1990, he was appointed Commander of MK’s Transkei Region, where he was in charge of Chris Hani’s personal security. For reasons of space, the memoir does not proceed beyond his integration into the South African National Defence Force (SANDF) with the rank of Lieutenant-Colonel and second-in-command of SANDF Group 46 in Mthatha. Besides its value as a primary source of previously undocumented information, the thesis seeks to bridge the gap between the academic literature on MK and the lived experience of MK soldiers. Having considered both the academic literature and the published MK memoirs in Chapter One, the thesis refers back to the literature in narrative chapters Two to Five. Consolidating its findings in its conclusion, the final chapter is divided into three sections: the political culture of MK, MK gender dynamics and the consequences of the political merger of the “exiles,” including MK, and the “inziles” who subsequently came to dominate the ANC. , Thesis (MA) -- Faculty of Humanities, Institute of Social and Economic Research, 2022
- Full Text:
- Authors: Hala, Mzimasi Mike
- Date: 2022-10-14
- Subjects: African National Congress , Umkhonto we Sizwe (South Africa) , Anti-apartheid movements South Africa , Anti-apartheid activists South Africa , South Africa Politics and government 1948-1994 , Hani, Chris, 1942-1993 , Holomisa, Bantu, 1955- , Bisho massacre
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/406785 , vital:70307
- Description: Born in Komani (Queenstown) in 1959 and detained for Congress of South African Students (COSAS) activities while still at school, Mzimasi Mike Hala departed South Africa via Swaziland in 1981 and joined uMkhonto WeSizwe (MK). Trained in Angola, Cuba and East Germany, he commanded Cacuso camp in Angola, until redeployed to South Africa in 1987 to work underground in Venda and Cape Town. Following the unbanning of the liberation movements in 1990, he was appointed Commander of MK’s Transkei Region, where he was in charge of Chris Hani’s personal security. For reasons of space, the memoir does not proceed beyond his integration into the South African National Defence Force (SANDF) with the rank of Lieutenant-Colonel and second-in-command of SANDF Group 46 in Mthatha. Besides its value as a primary source of previously undocumented information, the thesis seeks to bridge the gap between the academic literature on MK and the lived experience of MK soldiers. Having considered both the academic literature and the published MK memoirs in Chapter One, the thesis refers back to the literature in narrative chapters Two to Five. Consolidating its findings in its conclusion, the final chapter is divided into three sections: the political culture of MK, MK gender dynamics and the consequences of the political merger of the “exiles,” including MK, and the “inziles” who subsequently came to dominate the ANC. , Thesis (MA) -- Faculty of Humanities, Institute of Social and Economic Research, 2022
- Full Text:
Mechanistic analysis of two cytotoxic thiazolidinones as novel inhibitors of Triple-Negative Breast Cancer
- Authors: Vukea, Nyeleti
- Date: 2022-10-14
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365734 , vital:65780
- Description: Thesis embargoes. Expected release date early 2025. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Authors: Vukea, Nyeleti
- Date: 2022-10-14
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365734 , vital:65780
- Description: Thesis embargoes. Expected release date early 2025. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
Mentoring as social learning value creation in two South African environmental organisations: a social realist analysis
- Authors: Hiestermann, Michelle
- Date: 2022-10-14
- Subjects: Social realism , Social learning , Mentoring , Environmental education South Africa
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/366248 , vital:65846 , https://doi.org/10.21504/10962/366248
- Description: South Africa is facing overwhelming crises of educational quality, record rates of unemployment (especially amongst youth) and environmental issues and risks, further exacerbated by the Covid-19 pandemic. Environmental education research that addresses these challenges is critical to ensuring that future generations thrive in a warming climate. South Africa needs environmental leaders; we therefore need to understand and explore the possibilities of mentoring young professionals in environmental organisations in South Africa. Several initiatives have been developed to contribute to the mentoring of young professionals in South African environmental organisations. This study drew on a critical realist ontology, social realist meta-theory and domain specific theory on mentoring and evaluation to explore mentoring as a value creating proposition in two environmental organisations in South Africa that were part of the national Groen Sebenza youth employment creation programme which had a strong focus on mentoring. To strengthen conceptual analytical tools on mentoring, I undertook an immanent critique of domain specific mentoring theory to develop a more appropriate foundation for mentoring theory in the environmental sector that was not subject to the historical influence of human capital theory only (which has tended to dominate the field’s literature). I then developed in-depth understanding of mentoring in two case study contexts, namely a non-profit environmental organisation and an environmental consulting company, using qualitative research approaches that included contextual profiling, case study research and mirror data workshops. Analytically, I considered the case data drawing on the value creation evaluation framework of Wenger-Trayner and Wenger-Trayner (2014) which itself was developing as an analytical framework as the study developed. I strengthened the analytical framework with social realist interpretations drawing on Archer (1995). This offered me a way of developing an in-depth understanding of the factors which constrain or enable the value creation possibilities of mentoring, with a view to inform human capacity development initiatives that support mentoring in the environment sector. It was possible to explain the value creation possibilities of mentoring within two case study environmental organisations through considering mentoring as a social learning process of value creation and this overcame some of the shortfalls identified in other early learning theories as well as theories of mentoring. The research revealed how mentoring can provide a value creation social learning trajectory for unemployed youth. A social realist perspective explained how young professionals expanded their primary agency, through full participation in workplace communities of practice, to find their identity as corporate agents in the workplace with their mentors. In this research, Social Realist ontology, theory and methodology was able to achieve what Human Capital Theory could not and provided an account of the interplay of structure, culture and agency over time, through emergent properties and the separation of structure and agency. Thus, it was possible to avoid conflation and the limitation of theory of the present tense, with a deeper, ontologically robust explanation of mentoring as social learning and social change and a social realist orientation to human capacity development. South Africa has a history of oppression, inequality and injustice and requires social processes that are reflexive, critical, emancipatory and transformative. Therefore, this research required theory and approaches that could explain mentoring of unemployed youth, as a common good initiative for a more just and sustainable society. As shown in this study, a Social Realist approach can uncover the underlying generative mechanisms and make the implicit more explicit in research, policy and strategy, offering a robust alternative to the tenets of Human Capital Theory that have driven much mentoring research in South Africa and elsewhere to date. , Thesis (PhD) -- Faculty of Education, Education, 2022
- Full Text:
- Authors: Hiestermann, Michelle
- Date: 2022-10-14
- Subjects: Social realism , Social learning , Mentoring , Environmental education South Africa
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/366248 , vital:65846 , https://doi.org/10.21504/10962/366248
- Description: South Africa is facing overwhelming crises of educational quality, record rates of unemployment (especially amongst youth) and environmental issues and risks, further exacerbated by the Covid-19 pandemic. Environmental education research that addresses these challenges is critical to ensuring that future generations thrive in a warming climate. South Africa needs environmental leaders; we therefore need to understand and explore the possibilities of mentoring young professionals in environmental organisations in South Africa. Several initiatives have been developed to contribute to the mentoring of young professionals in South African environmental organisations. This study drew on a critical realist ontology, social realist meta-theory and domain specific theory on mentoring and evaluation to explore mentoring as a value creating proposition in two environmental organisations in South Africa that were part of the national Groen Sebenza youth employment creation programme which had a strong focus on mentoring. To strengthen conceptual analytical tools on mentoring, I undertook an immanent critique of domain specific mentoring theory to develop a more appropriate foundation for mentoring theory in the environmental sector that was not subject to the historical influence of human capital theory only (which has tended to dominate the field’s literature). I then developed in-depth understanding of mentoring in two case study contexts, namely a non-profit environmental organisation and an environmental consulting company, using qualitative research approaches that included contextual profiling, case study research and mirror data workshops. Analytically, I considered the case data drawing on the value creation evaluation framework of Wenger-Trayner and Wenger-Trayner (2014) which itself was developing as an analytical framework as the study developed. I strengthened the analytical framework with social realist interpretations drawing on Archer (1995). This offered me a way of developing an in-depth understanding of the factors which constrain or enable the value creation possibilities of mentoring, with a view to inform human capacity development initiatives that support mentoring in the environment sector. It was possible to explain the value creation possibilities of mentoring within two case study environmental organisations through considering mentoring as a social learning process of value creation and this overcame some of the shortfalls identified in other early learning theories as well as theories of mentoring. The research revealed how mentoring can provide a value creation social learning trajectory for unemployed youth. A social realist perspective explained how young professionals expanded their primary agency, through full participation in workplace communities of practice, to find their identity as corporate agents in the workplace with their mentors. In this research, Social Realist ontology, theory and methodology was able to achieve what Human Capital Theory could not and provided an account of the interplay of structure, culture and agency over time, through emergent properties and the separation of structure and agency. Thus, it was possible to avoid conflation and the limitation of theory of the present tense, with a deeper, ontologically robust explanation of mentoring as social learning and social change and a social realist orientation to human capacity development. South Africa has a history of oppression, inequality and injustice and requires social processes that are reflexive, critical, emancipatory and transformative. Therefore, this research required theory and approaches that could explain mentoring of unemployed youth, as a common good initiative for a more just and sustainable society. As shown in this study, a Social Realist approach can uncover the underlying generative mechanisms and make the implicit more explicit in research, policy and strategy, offering a robust alternative to the tenets of Human Capital Theory that have driven much mentoring research in South Africa and elsewhere to date. , Thesis (PhD) -- Faculty of Education, Education, 2022
- Full Text:
Mobilising indigenous technologies of making oshikundu and uumboloto to motivate and enable sense making of the topic carbon dioxide by grade 8 rural school learners
- Nandjedi, Fredinard Nghinaounditala
- Authors: Nandjedi, Fredinard Nghinaounditala
- Date: 2022-10-14
- Subjects: Science Study and teaching (Secondary) Social aspects Namibia , Culturally relevant pedagogy Namibia , Ethnoscience Namibia , Carbon dioxide
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/405357 , vital:70164
- Description: Poor performance in Science has been noted in most rural schools and this has become a concern to education planners and implementers. Part of the failure is said to be caused by inadequate school resources, under-preparedness of teachers to teach Science, poor command of the Language of Learning and Teaching, negative attitudes that are accompanied by lack of insights into the value of Science, low self-efficacy, and poor-quality environments for learning Science. In this regard, literature has revealed that many Science teachers in Namibia do not consider learners’ local indigenous knowledge (IK) also known as indigenous technology to mediate learning. Yet, it is a requirement of the Namibian Science curriculum. I assume that this could be due in part to the fact that the Science curriculum is not explicit on how IK should be integrated into Science teaching. It is against this backdrop that this study sought to explore the opportunities IK integration into Science may offer in mediating learning and sense-making on the topic of carbon dioxide (CO2). Learners’ indigenous technological practices of making oshikundu and uumboloto were used as vehicles of learning. This qualitative case study is underpinned by the interpretive and indigenous research paradigms. Within the indigenous research paradigm, I focused on the Ubuntu perspective. This study was conducted at a rural under-resourced school in the Ohangwena region in Namibia. Thirty Grade 8 learners, one science teacher and two expert community members were involved as participants. Data were gathered using focus group interviews (sharing circles), group activities, participatory observations, and journal reflections. Data interpretation and analysis were done using Vygotsky’s sociocultural theory and Ogunniyi’s contiguity argumentative theory. A thematic approach to data analysis was adopted. That is, an inductive approach was employed whereby sub-themes were identified, and thereafter common sub-themes were combined into themes. The findings of this study revealed that the process of making oshikundu and uumboloto can be used to enable learners to make sense of the topic of CO2 and other related concepts. Furthermore, the study revealed that hands-on practical activities done with easily accessible resources which are related to learners’ indigenous technologies help learners learn Science easily. The study thus recommends that educators should use oshikundu and/or uumboloto to mediate learning of topics such as CO2. Science teachers should always try to tap into learners’ socio-cultural backgrounds in their lessons to enhance better understanding of Science concepts. , Thesis (MEd) -- Faculty of Education, Education, 2022
- Full Text:
- Authors: Nandjedi, Fredinard Nghinaounditala
- Date: 2022-10-14
- Subjects: Science Study and teaching (Secondary) Social aspects Namibia , Culturally relevant pedagogy Namibia , Ethnoscience Namibia , Carbon dioxide
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/405357 , vital:70164
- Description: Poor performance in Science has been noted in most rural schools and this has become a concern to education planners and implementers. Part of the failure is said to be caused by inadequate school resources, under-preparedness of teachers to teach Science, poor command of the Language of Learning and Teaching, negative attitudes that are accompanied by lack of insights into the value of Science, low self-efficacy, and poor-quality environments for learning Science. In this regard, literature has revealed that many Science teachers in Namibia do not consider learners’ local indigenous knowledge (IK) also known as indigenous technology to mediate learning. Yet, it is a requirement of the Namibian Science curriculum. I assume that this could be due in part to the fact that the Science curriculum is not explicit on how IK should be integrated into Science teaching. It is against this backdrop that this study sought to explore the opportunities IK integration into Science may offer in mediating learning and sense-making on the topic of carbon dioxide (CO2). Learners’ indigenous technological practices of making oshikundu and uumboloto were used as vehicles of learning. This qualitative case study is underpinned by the interpretive and indigenous research paradigms. Within the indigenous research paradigm, I focused on the Ubuntu perspective. This study was conducted at a rural under-resourced school in the Ohangwena region in Namibia. Thirty Grade 8 learners, one science teacher and two expert community members were involved as participants. Data were gathered using focus group interviews (sharing circles), group activities, participatory observations, and journal reflections. Data interpretation and analysis were done using Vygotsky’s sociocultural theory and Ogunniyi’s contiguity argumentative theory. A thematic approach to data analysis was adopted. That is, an inductive approach was employed whereby sub-themes were identified, and thereafter common sub-themes were combined into themes. The findings of this study revealed that the process of making oshikundu and uumboloto can be used to enable learners to make sense of the topic of CO2 and other related concepts. Furthermore, the study revealed that hands-on practical activities done with easily accessible resources which are related to learners’ indigenous technologies help learners learn Science easily. The study thus recommends that educators should use oshikundu and/or uumboloto to mediate learning of topics such as CO2. Science teachers should always try to tap into learners’ socio-cultural backgrounds in their lessons to enhance better understanding of Science concepts. , Thesis (MEd) -- Faculty of Education, Education, 2022
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Mobilising the indigenous technology of making soap to mediate learning of saponification in organic chemistry
- Authors: Neporo, Johannes Kanyetu
- Date: 2022-10-14
- Subjects: Chemistry Study and teaching (Secondary) Social aspects Namibia , Culturally relevant pedagogy Namibia , Ethnoscience Namibia , Saponification , Ubuntu (Philosophy) , Pedagogical content knowledge
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/405368 , vital:70165
- Description: Scholars across the world are advocating for culturally responsive pedagogies that allow for the integration of indigenous knowledge (IK) in science teaching. This is in the hope of making science accessibleand relevant to learners from different social, economic and cultural backgrounds. Although the Namibian curriculum welcomes the integration of IK in teaching, it, however, does not stipulate how it should be implemented. It is against this backdrop that this interventionist study aimed to mobilise the indigenous technology of making soap to mediate the learning of saponification in organic chemistry. This study is underpinned by the interpretive and indigenous research paradigms. Within these paradigms, it employed a qualitative case study research design. The study was conducted in Walvis Bay in Namibia with four Grade 11 chemistry teachers, two expert community members and a critical friend who were purposively and conveniently sampled. Data were gathered using semi-structured interviews, semi-structured questionnaires, workshop discussions, participatory observation, stimulated recall interviews and journal reflections. Vygotsky’s Socio-Cultural Theory (SCT) and Shulman’s Pedagogical Content Knowledge (PCK) were used as theoretical frameworks. Within PCK, Mavhunga and Rollnick’s Topic-Specific Pedagogical Content Knowledge (TSPCK) served as an analytical framework. A thematic approach to data analysis was employed. That is, data were analysed inductively to come up with sub-themes. Thereafter, common sub-themes were combined to form themes. The findings of the study revealed that the Grade 11 chemistry teachers demonstrated positive attitudes toward the integration of IK in their teaching. However, they seemed not tohave pedagogical insights on how to do it. Despite this, they learnt, interacted and participated actively during the two expert community members’ presentation workshops on making soap. That subsequently enabled them to co-developan exemplar lesson plan on saponification that integrated IK. This study implies that there is a need for Chemistry teachers to be empowered on how to make science accessible and relevant to learners’ socio-cultural backgrounds. The study thus recommends that higher education institutions and educational authorities reform and amend the curriculum to cater for the integration of IK. The study further recommends that Chemistry teachers should tap into the cultural heritage of expert community members in mediating the learning of science concepts. Lastly, Chemistry teachers are encouraged to form professional learning communities to develop themselves professionally. , Thesis (MEd) -- Faculty of Education, Education, 2022
- Full Text:
- Authors: Neporo, Johannes Kanyetu
- Date: 2022-10-14
- Subjects: Chemistry Study and teaching (Secondary) Social aspects Namibia , Culturally relevant pedagogy Namibia , Ethnoscience Namibia , Saponification , Ubuntu (Philosophy) , Pedagogical content knowledge
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/405368 , vital:70165
- Description: Scholars across the world are advocating for culturally responsive pedagogies that allow for the integration of indigenous knowledge (IK) in science teaching. This is in the hope of making science accessibleand relevant to learners from different social, economic and cultural backgrounds. Although the Namibian curriculum welcomes the integration of IK in teaching, it, however, does not stipulate how it should be implemented. It is against this backdrop that this interventionist study aimed to mobilise the indigenous technology of making soap to mediate the learning of saponification in organic chemistry. This study is underpinned by the interpretive and indigenous research paradigms. Within these paradigms, it employed a qualitative case study research design. The study was conducted in Walvis Bay in Namibia with four Grade 11 chemistry teachers, two expert community members and a critical friend who were purposively and conveniently sampled. Data were gathered using semi-structured interviews, semi-structured questionnaires, workshop discussions, participatory observation, stimulated recall interviews and journal reflections. Vygotsky’s Socio-Cultural Theory (SCT) and Shulman’s Pedagogical Content Knowledge (PCK) were used as theoretical frameworks. Within PCK, Mavhunga and Rollnick’s Topic-Specific Pedagogical Content Knowledge (TSPCK) served as an analytical framework. A thematic approach to data analysis was employed. That is, data were analysed inductively to come up with sub-themes. Thereafter, common sub-themes were combined to form themes. The findings of the study revealed that the Grade 11 chemistry teachers demonstrated positive attitudes toward the integration of IK in their teaching. However, they seemed not tohave pedagogical insights on how to do it. Despite this, they learnt, interacted and participated actively during the two expert community members’ presentation workshops on making soap. That subsequently enabled them to co-developan exemplar lesson plan on saponification that integrated IK. This study implies that there is a need for Chemistry teachers to be empowered on how to make science accessible and relevant to learners’ socio-cultural backgrounds. The study thus recommends that higher education institutions and educational authorities reform and amend the curriculum to cater for the integration of IK. The study further recommends that Chemistry teachers should tap into the cultural heritage of expert community members in mediating the learning of science concepts. Lastly, Chemistry teachers are encouraged to form professional learning communities to develop themselves professionally. , Thesis (MEd) -- Faculty of Education, Education, 2022
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Molecular identification of potential ciprofloxacin degrading bacteria and determination of its possible breakdown intermediates in rivers, Eastern Cape
- Authors: Ncgauzele, Zenande Rose
- Date: 2022-10-14
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/403003 , vital:69913
- Description: Thesis embargoed. To be released early 2026. , Thesis (MSc) -- Faculty of Pharmacy, Pharmacy, 2023
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- Authors: Ncgauzele, Zenande Rose
- Date: 2022-10-14
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/403003 , vital:69913
- Description: Thesis embargoed. To be released early 2026. , Thesis (MSc) -- Faculty of Pharmacy, Pharmacy, 2023
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