List of Titles

Feminist simulations: deep in the dream of a game

Authors: Mackintosh, Tayla
Date: 2023-10-13
Subjects: Video games in art , Crocheting , Minecraft (Game) , Feminism in art , Simulation games , Handicraft in art , Autoethnography , Intersectionality (Sociology)
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/425333 , vital:72230
Description: This study delves into how the worlds of computer gaming and fine art intersect, employing DIY feminism to reflect on the gendered world of gaming and the links between simulation, reality, and fantasy within the game of Minecraft. I argue for a feminine craft (crochet) to challenge masculine gaming oppressions and the lack of representation, acceptance, and visibility for women in gaming culture. My research question is taken from the End Poem seen when the player has beaten the game's main boss. There is a line within the poem that asks, “But what true structure did this player create, in the reality behind the screen?” (End Poem, 2022). This is the question I have sought to answer within this study, by exploring a methodological approach that combines autoethnography and phenomenology to create a reflexive personal narrative. , Thesis (MFA) -- Faculty of Humanities, Fine Art, 2023
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Field facilitation in open and distance learning in resource-constrained environments: a case of Mzuzu University, Malawi

- Kalima, Robert Chagwamtsoka

Authors: Kalima, Robert Chagwamtsoka
Date: 2023-10-13
Subjects: Uncatalogued
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/431554 , vital:72785 , DOI 10.21504/10962/431554
Description: As part of the drive to enhance students’ learning experiences and success for students pursuing the B.Ed Science programme through distance education at Mzuzu University (Mzuni), the Open and Distance Learning (ODL) Steering Committee of Mzuni introduced the field facilitation strategy in 2014 to provide additional academic support to such students off campus. There have been questions, though, regarding the effectiveness of this strategy in terms of enhancement of student learning and success. This study, therefore, sought to examine the current field facilitation strategy in the B.Ed Science programme under the ODL mode of delivery, with a view to proposing improvements that would be made to the field facilitation strategy so that it enables enhanced learning and success in Science and Mathematics at Mzuni. Efforts to improve the current field facilitation strategy have been informed by an empirically based understanding of the shortfalls and strengths of the existing field facilitation strategy for ODL students in the B.Ed Science programme. To enhance students’ learning and success for ODL students in resource-constrained contexts such as Mzuni and similar contexts, the study adopted a qualitative case study design guided by tools from the second generation of the Cultural Historical Activity Theory. Qualitative data was obtained in two phases, a contextual profiling phase and a modified Change Laboratory Workshop phase. The modified Change Laboratory Workshops were conducted through the social media application ‘WhatsApp’ rather than in person as is usually done. Qualitative data in the contextual profiling phase was obtained from three categories of participants, namely, Science and Mathematics lecturers, Science and Mathematics field facilitators, and Science and Mathematics students. The contextual profiling phase included surveys, focus group interviews, individual interviews with lecturers at Mzuni and the field facilitators from the five satellite learning centres of Mzuni, and document analysis. The contextual profiling data acted as the mirror data for the next phase of data generation (Change Laboratory Workshop phase). The findings indicated that the support currently rendered by field facilitators to ODL Science and Mathematics students was inadequate and consisted of a shallow mode of instruction focusing on v traditional ways of teaching and learning. This meant that the field facilitators focused on lecturing as a pedagogical strategy for supporting the learning of Science and Mathematics. This was largely because the support offered to field facilitators by Mzuni was inadequate and did not empower them to generate their own strategies of conducting field facilitation innovatively and creatively, which would in turn empower the students to engage actively and reflectively in their own learning activities. This was due to structural, historical and cultural tensions that existed in the larger system (the university system). The implementation of the field facilitation strategy was challenged by such conflicts in the university structure which manifested themselves in the smaller activity system (the field facilitation activity system) which is the focus of this study. Thematically, such conflicts included students’ attributes, institutional policies, institutional pedagogy and the material and digital divide which Mzuni has not harnessed to support field facilitation. The study further established that institutional sensitivity to the conflicts raised above would result in an improved field facilitation strategy as the conflicts at the higher level (university level) have an impact on what happens in the smaller systems, for example the ODL in general and the field facilitation activity system in particular. The improved field facilitation strategy was supposed to recognise ODL students as students in transit from the traditional face-to-face learning context to the novel ODL learning context. As such, the transitional period of study from secondary school to university, particularly to year one, required an intensive field facilitation support strategy, and thus greater institutional support for both field facilitators and students for enhanced learning experiences and success that would eventually result in improved students’ retention and throughput. The findings of this study will therefore inform all those involved in ODL, particularly those in resource-constrained contexts, to be conscious when implementing ODL innovations. Serious consideration of the contexts in which the innovations are to be implemented is critical. , Thesis (PhD) -- Faculty of Education, Primary and Early Childhood Education, 2023
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Framing VBS: a textual analysis of Daily Maverick’s coverage of the VBS Mutual Bank heist in the years 2018-2020

- Nyulu, Siyamthanda Natascha

Authors: Nyulu, Siyamthanda Natascha
Date: 2023-10-13
Subjects: VBS Mutual Bank (South Africa) , Banks and banking Corrupt practices South Africa , Journalism, Commercial South Africa , Journalistic ethics South Africa , Frames (Sociology) , Journalism Social aspects South Africa , Daily Maverick
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/425256 , vital:72223
Description: This study investigates how Daily Maverick framed the VBS Mutual Bank scandal for its readers in the years 2018-2020. It utilises framing theory as the guiding theoretical framework in trying to understand how Daily Maverick portrayed the corruption case for its readers. This study also leans on social responsibility and normative theories of the press to analyse whether Daily Maverick fulfilled its role of facilitating dialogue between the elite and ordinary citizens of Limpopo affected by the corruption at the bank. Using a qualitative textual analysis, the thesis discusses how elite sources were quoted more than ordinary citizens who are affected the most by the corruption scandal. This allowed the elite to turn the VBS matter into a political spectacle whereas, because it is an example of failure in the financial sector, the heist caused further failures in municipalities already failing in Limpopo, North-West and Gauteng. , Thesis (MA) -- Faculty of Humanities, Journalism and Media Studies, 2023
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Freshwater invasive alien crayfish species in South Africa: testing eDNA assessment and DNA barcoding

- Mdidimba, Nonkazimulo Dorothea

Authors: Mdidimba, Nonkazimulo Dorothea
Date: 2023-10-13
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/424413 , vital:72151
Description: The expansion of the wild populations of the two invasive alien crayfish species, i.e., Cherax quadricarinatus and Procambarus clarkii in South Africa is of high concern. Given this, innovative and improved monitoring methods are required to be explored in order to effectively detect and manage their spread. Environmental DNA (eDNA) has shown promising and reliable results to detect and monitor alien crayfish in freshwater systems even at low densities. This research study aimed to field-test the application of eDNA for detecting and monitoring invasive alien freshwater crayfish species (IAFCs) in South African freshwater systems (Chapter 2). Further, this study also aimed to confirm the true taxonomic identity of the IAFCs in South African freshwater systems by using DNA barcoding to avoid potential misidentifications with morphological identification alone (Chapter 3). Also, ectocommensal temnocephalans and leeches attached to the crayfishes were also identified with DNA barcoding. The mitochondrial COI gene fragment of the crayfishes and the ectocommensal temnocephalans and leeches was amplified, sequenced, and used for species identification. For eDNA monitoring of C. cainii, C. quadricarinatus and P. clarkii, water samples were collected from Eastern Cape, Free State and KwaZulu Natal sites that are known to house these species. The current study did not detect the eDNA of the wild populations of both C. quadricarinatus and P. clarkii. This failure was encountered despite employing several methods, such as, end-point polymerase chain reaction (PCR), quantitative PCR (qPCR) and next-generation sequencing (NGS). The eDNA assessment to detect IAFCs in the wild populations is discussed in detail, and corrective measures suggested (Chapter 2). However, only C. cainii was able to be detected by eDNA. Cherax cainii is housed/farmed in an aquaculture facility (Vaughn Bursey’s Stock Farm in Eastern Cape) with large number of individuals per pond. For this, NGS was able to detect C. cainii but the other two methods, end-point PCR and qPCR were not able to detect the species. Based on the results, refinement of eDNA monitoring methods for the South African freshwater systems is recommended. Evaluation of different DNA collection methods, preservation, DNA extraction kits and primer design to obtain effective eDNA detection is discussed as possible sources of error. Interestingly, the newly established population of P. clarkii in Mimosa Dam in Free State was infested with alien leeches, that were confirmed by DNA barcoding to be Helobdella europaea and Helobdella octatestica. Consequently, this study reports for the first time in South Africa the presence of this alien freshwater leeches. The presence of alien leeches and P. clarkii suggests a double invasion in Mimosa Dam, P. clarkii seems to continue expanding its range in the country. However, the long-established population of P. clarkii in Driehoek Farm in Mpumalanga, which has been in the country for over 30 years did not have any leech or temnocephalan infestation. This could suggest several interesting ecological phenomena, including environmental filtering over time of the co-invaders, differential source populations, and post-introduction adaptation. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
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From more sustainable isocyanide-based multicomponent reactions to spiro-heterocyclic compound syntheses

- Salami, Sodeeq Aderotimi

Authors: Salami, Sodeeq Aderotimi
Date: 2023-10-13
Subjects: Uncatalogued
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/432229 , vital:72853 , DOI 10.21504/10962/432229
Description: The global pharmaceutical industry has undergone profound transformations in the past two decades in the search for new drugs. For this reason, most pharmaceutical companies made significant investments not only in the development of new drugs but new methodologies. Modern drug development is confronted with the challenge of developing chemical reactions that are highly capable of providing most of the elements of structural complexity and diversity with the fewest possible synthetic steps for the specific target with the most intriguing properties. The discovery of more sustainable, environmentally friendly reactions capable of forming multiple bonds in a single step has been a challenge in organic synthesis over the years. Many organic chemists have recently started focusing on creative ways of reducing environmental pollution. The use of hazardous solvents has been reduced or eliminated in research to limit harm to both people and the environment. The pursuit of this goal has drawn many organic chemists to the study of various sustainable synthetic techniques including catalysis, aqueous organic reactions and mechanochemistry. The scope of this thesis was to apply sustainable techniques to design multicomponent synthetic protocols for the Passerini reaction and further apply these new protocols to construct spiro-heterocyclic compounds, all based on green chemistry principles. There is a need to develop rapid, efficient, and versatile strategies for the synthesis of bioactive molecules via multicomponent reactions. This project tried to avoid some of the pitfalls of traditional approaches, such as toxicity, low yield, long reaction times, harsh conditions, experimental complexity, and limited functionalization scope. This was achieved by focussing on the use of isonitriles and isothiocyanates as key reactive intermediates, and making extensive use of aqueous reaction conditions, mechanochemistry and microwave activation. , Thesis (PhD) -- Faculty of Science, Chemistry, 2023
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Gender and the COVID-19 pandemic: exploring female vendors’ coping strategies in Lichtenburg during the lockdown

- Marumo, Mmaki Lesego

Authors: Marumo, Mmaki Lesego
Date: 2023-10-13
Subjects: COVID-19 Pandemic, 2020- South Africa , Street vendors South Africa Lichtenburg , Adjustment , Informal economy , COVID-19 pandemic lockdown , Self-employed women South Africa Lichtenburg
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/425141 , vital:72214
Description: The 2019 outbreak of the Coronavirus (COVID-19) in Wuhan, China, and its subsequent spread around the world caused uncertainty in the economy and other aspects of life. Most governments around the world took drastic measures to stop the spread of the virus and save lives. The most common of these measures were restrictions on people’s movement and trade. As a result, the world of work in South Africa changed dramatically, with over a million workers losing their jobs. That said, South Africa acutely felt the negative income effects of the COVID-19 pandemic. For those working in the informal economy, the five-week lockdown between March and May 2020 was a period of unprecedented insecurity and hunger, without work, income, or benefits. In light of the above, the study aimed to explore how female street vendors in Lichtenburg survived the impact of the COVID-19 national lockdown restrictions on trading activities between March 2020 and May 2020. The study sought to contribute to the understanding of the gendered impacts of the pandemic, particularly in relation to women in the informal economy, by examining the strategies and coping mechanisms adopted by them. Drawing on the sustainable livelihoods framework, this study examined the experiences of female street traders in Lichtenburg who were subjected to COVID-19 trade restrictions, assessed their coping strategies, and examined their support systems. The study was exploratory in nature, followed a qualitative approach, and adopted a case study design. Depending on the needs of the study, a purposive and convenience sampling techniques were chosen to address the research problem and questions. In order to explore women’s experiences on a specific topic, qualitative, semi-structured individual interviews were conducted with a sample of six female street vendors in Lichtenburg. The collected data were analysed using the thematic analysis technique. In this regard, the findings show that the perception upheld that the informal economy is an employment shock absorber during economic crises has been proven otherwise by the COVID-19 pandemic. The loss of profits led to a reduction in trading activities, which in turn increased the hardships of women street vendors. These vulnerability and hardships were made worse by the absence of government support structures since they were unable to navigate the procedures and had no one to turn to in times of need. As a result of the lack of formal channels of support and appropriate policy interventions, street vendors were particularly vulnerable to the financial consequences of the pandemic, resulting in an unpleasant reality of unsustainable livelihoods in the face of COVID-19. , Thesis (MA) -- Faculty of Humanities, Sociology, 2023
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Gender, informality and urban livelihoods: eamining the livelihood strategies adopted by Black female street vendors in Makhanda, Eastern Cape

- Khoele, Lineo

Authors: Khoele, Lineo
Date: 2023-10-13
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/431474 , vital:72775
Description: This study sought to examine livelihood strategies adopted by black female street vendors in Makhanda, Eastern Cape. The street vending activities that were undertaken by the research participants included selling: cooked foods, fresh fruit and vegetables, eggs, and beauty products. This study used the Sustainable Livelihood Approach (SLA) to examine the livelihood strategies of black female street vendors in Makhanda. The SL approach was chosen as an ideal framework for a study of this nature as it holistically and traditionally focuses on vulnerable population groups around the world. More importantly, the SLA gives agency to these vulnerable groups, as it prioritizes their innovative techniques in mobilizing diverse assets at their disposal in order to survive. The study is, therefore, ideal as it also gives agency to selected black female street vendors by examining how they utilized diverse assets at their disposal to sustain their livelihoods. This study seeks to contribute to the ongoing debate on urban livelihoods and the informal economy in South Africa, focusing particularly on the different methods or strategies employed by black female street vendors to enhance the sustainability of street vending as a livelihood. Due to the nature of this study, which seeks to capture the lived experiences of the selected black female street vendors in Makhanda, qualitative research methodologies were used to collect and analyse data. This study proved street vending to be a survival strategy that is used by black unskilled women in pursuit of livelihoods. It argues that, faced with the socio-economic realities associated with high unemployment, street vending can be used by many to best support their households. When it comes to livelihood strategies, this study found that, livelihood diversification is the most common livelihood strategy adopted by street vendors in Makhanda, with the only difference being the type of diversification adopted. Two forms of livelihood diversification strategies were identified in this study, and these included: product diversification and income diversification. The conclusion drawn from the findings argues that the selected street vendors in Makhanda strategically used different assets accessible to them to enhance and sustain their livelihoods. The study found that despite the different structural challenges faced by street vendors in Makhanda, the selected black female street vendors are able to meet their livelihood outcomes and support their families through engaging in street vending. , Thesis (MSocSci) -- Faculty of Humanities, Sociology, 2023
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Giving a voice and holding to account: a critical civic and democratic discourse analysis of The Big Debate South Africa TV show’s opportunities for ‘Political Listening’

- Mgqoboka, Banathi

Authors: Mgqoboka, Banathi
Date: 2023-10-13
Subjects: Big Debate South Africa , Television talk shows South Africa , Citizenship in journalism South Africa , Democracy South Africa , Mass media and public opinion South Africa , Listening Political aspects South Africa
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/425245 , vital:72222
Description: The television studio debate genre was initially inspired by the 1960s television news coverage that captured the zeitgeist of American political campaigns and elections, which featured prominent political figures. The genre has since been adapted by broadcast networks around the world to facilitate politically-charged public discussions that allow ordinary people to pose significant questions and express their concerns or cynicism to the political elites in power. The Big Debate South Africa is a popular televised town hall debate show that began airing in 2009 on eMedia Investment’s eNCA and later on the SABC. During its ninth-season run, the show attracted an audience of up to 12 million. The programme is formatted to give South African citizens a voice to hold state leaders to account. Anthea Garman and Herman Wasserman’s (2014) research on citizenship and media in a democratic society, asserts that the media’s contribution to citizenship is often a way to encourage citizens to exercise their influence over political decisions and dialogue in an overt manner. Through observations and qualitative in-depth interviews, this tightly focused study analysed the third episode of The Big Debate South Africa’s ninth season, hosted by journalist and broadcaster Redi Tlhabi. It explored the show’s format and discourse to investigate how it creates opportunities for the practice of Susan Bickford’s (1996) conception of ‘political listening’ within the confines of hierarchical binary oppositions (‘Us and Them’ and ‘lay’/‘expert’). By deconstructing how civil society organisations, activists and citizens (‘lay’) interact with the political elites (‘experts’), this study chronicled how the show mediates these binary oppositions with an anticipation for them to collectively hear each other out. In examining the show’s structure as a participative civic political broadcast talk platform that promotes democratic deliberation, this study ultimately demonstrated the capacity of The Big Debate South Africa to pluralise democratic life in its practice of ‘political listening’. While the show advances equality and amplifies marginalised voices, this research also found that these significant practices seemingly only held temporary effects once the cameras shut down. , Thesis (MA) -- Faculty of Humanities, Journalism and Media Studies, 2023
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Halogenated Aza-BODIPY dyes for photodynamic anticancer and antimicrobial activity studies

- Magwaza, Temlandvo Matshidiso

Authors: Magwaza, Temlandvo Matshidiso
Date: 2023-10-13
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/424514 , vital:72160
Description: This thesis reports on the synthesis and characterisation of differently substituted aza-BODIPY dyes for use in photodynamic antimicrobial chemotherapy (PACT) and photodynamic therapy (PDT) activity studies. The aza-BODIPY dyes were synthesised by adding phenyl and naphthyl rings at the 3,5-positions of the aza-BODIPY core, with methylthiolphenyl (9a and 9b, respectively) or thien-2-yl rings (9c and 9d, respectively) at the 1,7-positions. 9a-c were iodinated at the 2-position to form 10a-c, respectively, while 9d was diiodinated at the 2,6-positions to form 10d. The methylthiolphenyl-substituted dyes (10a and 10b) were successfully conjugated to gold nanoparticles (AuNPs) to form nanoparticles conjugates (10a-AuNPs and 10b-AuNPs), while attempts to conjugate the thien-2-yl-substituted dyes were unsuccessful. The photophysicochemical properties of 9a-d, 10a-d and nanoconjugates 10a-AuNPs and 10b-AuNPs were investigated to determine their suitability for use in the applications. Adding heavy atoms such as iodine at the 2,6-positions of the aza-BODIPY led to enhanced singlet oxygen generation since these dyes displayed moderate to high singlet oxygen quantum yields. None of the dyes exhibited any fluorescence. The PACT activity studies for 9c-d, 10a-d, and the 10a-AuNPs and 10b-AuNPs were carried out against Staphylococcus aureus and Escherichia coli with a Thorlabs M660L3 light-emitting diode (LED) with an irradiance of 280 mW/cm2 for all dyes other than 10d. A Thorlabs M730L4 LED with an irradiance of 160 mW/cm2 was used for 10d. Time dependence studies were only carried out against Staphylococcus aureus, so very low log reductions were observed against Escherichia coli in initial concentration studies. The 10a-AuNP and 10b-AuNP nanoconjugates exhibited high antimicrobial activity with a log reduction of 9.41 and 0.00% viable colonies, while the iodinated aza-BODIPY had a log reduction of 8.94. The in vitro photodynamic therapy activities and dark cytotoxicity were investigated against human MCF-7 breast cancer cells for dyes 9c-d and 10c-d with a Thorlabs M660L3 LED (280 mW/cm2) for all dyes. The dark cytotoxicity was minimal in each case with IC50 > 50. Iodinated dyes 10c and 10d had IC50 values of 11.6 and 8.2 μM, respectively, and non-iodinated dyes 9c and 9d had IC50 values of 12.5 and 19.2 μM. The heavy atom effect associated with the iodine atoms increases the singlet oxygen quantum yield and enhances the suitability of the dyes for photodynamic therapy. , Thesis (MSc) -- Faculty of Science, Chemistry, 2023
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HI View of the Norma Galaxy Cluster with MeerKAT

- Mophahlane, Koketso Vincent

Authors: Mophahlane, Koketso Vincent
Date: 2023-10-13
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/432530 , vital:72878
Description: Studies reveal that galaxies assemble into clusters as gas-rich, active star-forming disks and eventually settle in the virialized core as quenched early-type galaxies with depleted gas. To examine environmental effects responsible for the quenched population in the cluster core, we exploit the higher sensitivity of the MeerKAT telescope to probe Hi properties of galaxies in the Norma cluster. The Norma cluster is an ideal laboratory for this study since it is a rich and massive cluster of nearby galaxies. The Hi data cube used covers a velocity range of 483 − 11, 113 km/s, with a noise rms sensitivity of 0.09 mJy/beam and an angular resolution of ∼ 14.65′′ × 9.28′′. A total of 25 reliable Hi sources were detected over the entire velocity range. The Hi detections reveal two major galaxy overdensities located at vrad ∼ 2096 − 7646 km/s and vrad ∼ 10, 000 km/s. The first is associated with the Norma cluster gravitational potential and indicates a substructure in its velocity distribution; the other is a population of background galaxies. In this work, the Norma cluster has 13 cluster members detected in Hi and 130 galaxies from optical surveys. The spatial distribution of cluster members covers a field that is 2/3 × RA, where RA = 2.02 Mpc at cz = 4871 km/s. From the spatial distribution, optical galaxies are densely populated in the central regions, while most galaxies in Hi were detected on the outskirts. From the phase-space diagram, 6 galaxies detected in Hi are found in the virialised region, while the rest of the detections are infalling for the first time. Hi detections that are not yet virialised have asymmetrical morphologies, while virialised detections have truncated gas disks. Most cluster members that were found to have asymmetrical gas disks are also Hi deficient by 0.8 − 1.2 dex but show excess SFR efficiency for the amount of Hi detected. The results demonstrate that the initial phase of galaxy-ICM interactions might be responsible for morphological transformation and enhancement of star formation activity. , Thesis (MSc) -- Faculty of Science, Physics and Electronics, 2023
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High-resolution hydraulic modelling as an approach to planning rehabilitation interventions in unchanneled valley-bottom palmiet wetlands: a case study of the Kromme River

- Langner, Wiebke

Authors: Langner, Wiebke
Date: 2023-10-13
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/424610 , vital:72168
Description: This study employs high-resolution hydraulic modelling techniques to inform the planning of rehabilitation interventions in unchanneled valley-bottom palmiet wetlands, using the upper Kromme River wetlands as a case study. It investigates the impact of geomorphic processes on the morphology of the valley, how changes in valley morphology affect the flow characteristics (velocity, stream power, depth) of the river, and how these changes affect the geomorphic dynamics of the wetlands. An aerial LiDAR survey was conducted for a 23km-long reach of the upper Kromme River where the wetlands are situated. A high-resolution (5 m) DTM was created from the LiDAR data to examine the valley morphology. Focusing on three major wetland basins, the relationship between valley morphology and geomorphic processes was examined using high-resolution imagery that accompanied the LiDAR survey and Google Satellite imagery. The hydraulic modelling software HEC-RAS was used to investigate the spatial variation in velocity, stream power, and water depth down the surveyed length of the river. The model outputs provide insight into the effect of valley morphology on flow characteristics. The river appears to have a graded longitudinal profile, such that there is a systematic reduction in slope down its length. Water flowing down the river works, through the processes of erosion and deposition, to control the longitudinal slope, channel planform, and geometry to create a valley with a gentle longitudinal slope (approximately 1%) and a broad, near-horizontal valley-bottom in the mountainous landscape of the Cape Fold Mountains. The overall form of the Kromme River valley and wetlands is primarily a consequence of repeated cycles of cutting and filling. Tributary alluvial fans control the initiation of gully erosion in the wetlands, but their effect is diminished in a downstream direction. Despite a 10-fold increase in discharge down the 23km length of river for a given flood magnitude, there is no significant increase in flow velocity, stream power, or depth in a downstream direction. Consequently, the kinetic energy of the water in the lower wetland basin is surprisingly low. These conditions favour the establishment of palmiet. Flows in eroded reaches are much higher than in non-eroded reaches where discharge is spread across a broad valley bottom. In terms of palmiet establishment and regeneration, this means that areas dominated by depositional processes are best suited to the establishment of palmiet. Based on this information, optimal sites to trial new wetland rehabilitation strategies that employ palmiet were selected. This work supports the importance of understanding the role of geomorphology in wetland structure and dynamics when approaching wetland rehabilitation and is likely to be more sympathetic to natural processes than current interventions. , Thesis (MSc) -- Faculty of Science, Geography, 2023
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Identification of novel Arf1 GTPase inhibitors for cancer target validation

- Mqwathi, Nomxolisi Vuyokasi

Authors: Mqwathi, Nomxolisi Vuyokasi
Date: 2023-10-13
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/424666 , vital:72173
Description: The key regulators of both anterograde and retrograde vesicular traffic, adenosine diphosphate-ribosylation factors (Arfs), also coordinate various signalling pathways and regulate cellular processes required for cell survival and function. In addition to its role in mediating secretory trafficking in the Golgi apparatus, the involvement of Arf1 in signalling pathways that contribute to the formation and progression of cancer has become apparent, and the overexpression and deregulation of Arf1 activity has been associated with cancer cell invasion, proliferation and metastasis. As with other small GTPases, Arf1 must cycle back and forth between an inactive (GDP-bound) and active (GTP-bound) conformation to carry out its function. However, the cycle of Arf1 inactivation and activation is controlled by Arf GTPase activating proteins (Arf-GAPs) that stimulate Arf1 to hydrolyse the bound GTP to GDP and Arf guanine nucleotide exchange factors (Arf-GEFs) that facilitate GDP for GTP exchange on Arf1, respectively. The identification of Arf1 inhibitors that indirectly disrupt Arf1 function by blocking its interaction with Arf-GAPs or Arf-GEFs has generated interest in their use as possible anti-cancer agents. The suppression of Arf1 activation (by targeting Arf-GEFs) has been investigated as a potential cancer therapeutic target and resulted in inhibitor compounds that have micromolar-range activity against cancer cells and targets and promising results in mouse models, but experience problems with bioavailability when used in vivo. This motivates the search for novel Arf1 inhibitors for validation purposes to question whether Arf1 is a viable target for cancer therapy. The purpose of the study was to employ a recently developed colourimetric screening assay to identify inhibitors of Arf1 activation (Arf-GEF inhibitors) and deactivation (Arf-GAP inhibitors), with a focus on evaluating the potential of Arf1 deactivation as an entirely novel anti-cancer target. The proteins required for the assay (Arf1, Arf-GEF and -GAP domains and a reporter protein, GST-GGA3) were expressed in E. coli. and purified using affinity chromatography. The assay could detect the activation of Arf1 by the catalytic Sec7 domain of the three Arf-GEFs chosen for this study, but reproducibility was compromised by the occasional spontaneous activation of Arf1 in the absence of the Arf-GEFs. By contrast, the assay could reproducibly detect Arf1 deactivation by an Arf-GAP domain (Arf-GAP1GAP) and was subsequently used to screen a library of α-helix mimetics. Thirteen hit compounds with IC50 values ranging from 0.53 to 20.95 μM were found to inhibit Arf-GAP1GAP-mediated stimulation of GTP hydrolysis by Arf1-GTP in this assay format, however, they did not effectively suppress the proliferation of three tested cell lines (HeLa, MCF-7 and MCF-12A). Interestingly, the results obtained from fluorescence microscopy studies suggested that the compounds disrupt Golgi structure and Arf1 localisation, presumably by keeping Arf1 in its active conformation by blocking Arf-GAP1 function. This suggests that the compounds affect Arf1 function in cells, and may be used to explore the feasibility of targeting Arf1 deactivation for anti-cancer purposes in a wider range of cell lines and experiments. It has been reported that Arf-GAP1 inhibition is associated with the suppression of cell migration, and the potential of the compounds as metastasis inhibitors may also be explored. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2023
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Implementing a sexual and reproductive citizenship intervention refinement instrument for youth sexuality education: a formative evaluation

- Mthethwa, Thobile

Authors: Mthethwa, Thobile
Date: 2023-10-13
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/425008 , vital:72201
Description: While Out of School sexuality education (SE) programmes in South Africa have attempted to bridge the gap in the number of young people who receive SE, there is still a large number of youth between the age groups of 15 to 24 years who lack adequate sexual knowledge. The manner in which sex education is taught and its accessibility is accompanied by challenges, in particular in relation to empowerment. To better understand the effectiveness of sexual education programmes, evaluations of their content is needed. Therefore, the purpose of this study was to investigate whether and how an Out of school SE programme run by Partners in Sexual Health (PSH) promotes understandings of sexual and reproductive citizenship. A formative evaluation of their sexual and reproductive health and rights (SRHR) facilitator’s manual was conducted (owing to COVID the actual programme was not run in the year data for this thesis were collected). To help perform the formative evaluation, the feminist sexual and reproductive citizenship (SRC) framework as conceptualized by Macleod and Vincent (2014) was used. The SRC framework consists of five key principles that, it is suggested, need to be adopted for SE programmes to be inclusive, namely, citizenship as status and practice, differentiated citizenship, private and public interstice, and politics of recognition, redistribution and reparation. An additional principle of inclusive and process-based educational practices was added into the five key principles. To analyse data, template analysis was used which enabled the researcher to create a priori of themes using the Masizixhobise toolkit which is informed by the SRC framework. Findings from this study reveal the interconnectedness between the different citizenship principles. Moreover, while the PSH SRHR programme promotes principles of the SRC framework, there are aspects of the SRC that are lacking from the programme. Therefore, the SRHR manual needs to take into account a spectrum of issues which include but are not limited to the incorporation of sexually diverse differently-abled individuals' sexual experiences and challenges when it comes to accessing SE. This means for SE programmes to achieve inclusivity and to be empowering, they need to encourage individuals to be agentic beings, engage in informed decision-making and encourage young people to take up their rights. , Thesis (MA) -- Faculty of Humanities, Psychology, 2023
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In silico characterization of missense mutations in infectious diseases: case studies of tuberculosis and COVID-19

- Barozi, Victor

Authors: Barozi, Victor
Date: 2023-10-13
Subjects: Microbial mutation , COVID-19 (Disease) , Drug resistance in microorganisms , Antitubercular agents , Tuberculosis , Molecular dynamics , Single nucleotide polymorphisms
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/431626 , vital:72791 , DOI 10.21504/10962/431626
Description: One of the greatest challenges facing modern medicine and the global public health today is antimicrobial drug resistance (AMR). This “silent pandemic,” as coined by the world health organization (WHO), is steadily increasing with an estimated 4.95 million mortalities attributed to AMR in 2019, 1.27 million of which were directly linked to AMR. Some of the contributors to AMR include self-prescription, drug overuse, sub-optimal drug prescriptions by health workers, and inaccessibility to drugs, especially in remote areas, which leads to poor adherence. The situation is aggravated by the upsurge of new zoonotic infections like the coronavirus disease 2019, which present unique challenges and take the bulk of resources hence stunting the fight against AMR. Quite alarming still is our current antimicrobial arsenal, which hasn’t had any novel antimicrobial drug discovery/addition, of a new class, since the 1980s. This puts a burden on the existing broad-spectrum antimicrobial drugs which are already struggling against multi-drug resistant strains like multi-drug resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB). Besides the search for new antimicrobial agents, the other avenue for addressing AMR is studying drug resistance mechanisms, especially single nucleotide polymorphisms (SNPs), that change drug target characteristics. With the advancement of computational power and data storage resources, computational approaches can be applied in mutational studies to provide insight into the drug resistance mechanisms with an aim to inform future drug design and development. Therefore, in the first part of this thesis, we employ integrative in silico approaches, including 3D structure modeling, molecular dynamic (MD) simulations, comparative essential dynamics (ED), and protein network analysis approaches i.e., dynamic residue network (DRN) analysis to decipher drug resistance mechanisms in tuberculosis (TB). This involved an investigation of the drug resistance mutations in the catalase-peroxidase (KatG) and pyrazinamidase (MtPncA) enzymes which are responsible for activation of TB first-line drugs; Isoniazid (INH) and Pyrazinamide (PZA), respectively. In the case of KatG, eleven high confidence (HC) KatG mutations associated with a high prevalence of phenotypic INH resistance were identified and their 3D structures modeled before subjecting them to MD simulations. Global analysis showed an unstable KatG structure and active site environment in the mutants compared to the wildtype. Active site dynamics in the mutants compromised cofactor (heme) interactions resulting in less bonds/interactions compared to the wildtype. Given the importance of the heme, reduced interactions affect enzyme function. Trajectory analysis also showed asymmetric protomer behavior both in the wildtype and mutant systems. DRN analysis identified the KatG dimerization domain and C-terminal domain as functionally important and influential in the enzyme function as per betweenness centrality and eigenvector centrality distribution. In the case of the MtPncA enzyme, our main focus was on understanding the MtPncA binding ability of Nicotinamide (an analogue of PZA) in comparison to PZA, especially in the presence of 82 resistance conferring MtPncA mutations. Like in KatG, the mutant structures were modeled and subjected to MD simulations and analysis. Interestingly, more MtPncA mutants favored NAM interactions compared to PZA i.e., 34 MtPncA mutants steadily coordinated NAM compared to 21 in the case of PZA. Trajectory and ligand interaction analysis showed how increased active site lid loop dynamics affect the NAM binding, especially in the systems with the active site mutations i.e., H51Y, W68R, C72R, L82R, K96N, L159N, and L159R. This led to fewer protein-ligand interactions and eventually ligand ejection. Network analysis further identified the protein core, metal binding site (MBS), and substrate binding site as the most important regions of the enzyme. Furthermore, the degree of centrality analysis showed how specific MtPncA mutations i.e., C14H, F17D, and T412P, interrupt intra-protein communication from the MtPncA core to the MBS, affecting enzyme activity. The analysis of KatG and MtPncA enzyme mutations not only identified the effects of mutations on enzyme behaviour and communication, but also established a framework of computational approaches that can be used for mutational studies in any protein. Besides AMR, the continued encroachment of wildlife habitats due to population growth has exposed humans to wildlife pathogens leading to zoonotic diseases, a recent example being coronavirus disease 2019 (COVID-19). In the second part of the thesis, the established computational approaches in Part 1, were employed to investigate the changes in inter-protein interactions and communication patterns between the severe acute respiratory coronavirus 2 (SARS-CoV-2) with the human host receptor protein (ACE2: angiotensin-converting enzyme 2) consequent to mutations in the SARS-CoV-2 receptor binding domain (RBD). Here, the focus was on RBD mutations of the Omicron sub-lineages. We identified four Omicron-sub lineages with RBD mutations i.e., BA.1, BA.2, BA.3 and BA.4. Each sub-lineage mutations were modeled into RBD structure in complex with the hACE2. MD analysis of the RBD-hACE2 complex highlighted how the RBD mutations change the conformational flexibility of both the RBD and hACE2 compared to the wildtype (WT). Furthermore, DRN analysis identified novel allosteric paths composed of residues with high betweenness and eigenvector centralities linking the RBD to the hACE2 in both the wildtype and mutant systems. Interestingly, these paths were modified with the progression of Omicron sub-lineages, highlighting how the virus evolution affects protein interaction. Lastly, the effect of mutations on S RBD and hACE2 interaction was investigated from the hACE2 perspective by focusing on mutations in the hACE2 protein. Here, naturally occurring hACE2 polymorphisms in African populations i.e., S19P, K26R, M82I, K341R, N546D, and D597Q, were identified and their effects on RBD-hACE2 interactions investigated in presence of the Omicron BA.4/5 RBD mutations. The hACE2 polymorphisms subtly affected the complex dynamics; however, RBD-hACE2 interaction analysis showed that hACE2 mutations effect the complex formation and interaction. Here, the K26R mutation favored RBD-hACE2 interactions, whereas S19P resulted in fewer inter-protein interactions than the reference system. The M82I mutation resulted in a higher RBD-hACE2 binding energy compared to the wildtype meaning that the mutation might not favor RBD binding to the hACE2. On the other hand, K341R had the most RBD-hACE2 interactions suggesting that it probably favors RBD binding to the hACE2. N546D and D597Q had diminutive differences to the reference system. Interestingly, the network of high betweenness centrality residues linking the two proteins, as seen in the previous paragraph, were maintained/modified in presence of hACE2 mutations. HACE2 mutations also changed the enzyme network patterns resulting in a concentration of high eigenvector centrality residues around the zinc-binding and active site region, ultimately influencing the enzyme functionality. Altogether, the thesis highlights fundamental structural and network changes consequent to mutations both in TB and COVID-19 proteins of interest using in silico approaches. These approaches not only provide a new context on impact of mutations in TB and COVID target proteins, but also presents a framework that be implemented in other protein mutation studies. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2023
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In-silico investigation of the effects of genetic mutations on the structural dynamics of thiopurine s-methyltransferase and their implications on the metabolism of 6-mercaptopurine

- Mwaniki, Rehema Mukami

Authors: Mwaniki, Rehema Mukami
Date: 2023-10-13
Subjects: Uncatalogued
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/432553 , vital:72880
Description: Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme that catalyzes the S-methylation of aromatic and heterocyclic sulfhydryl compounds such as 6-mercaptopurine (6MP), 6-thioguanine (6TG) and azathioprine (AZA) which is first converted to 6MP through reduction by glutathione S- transferases (GST). The compounds, generally referred to as thiopurines, are immunosuppressants used to treat childhood acute lymphoblastic leukemia (ALL), autoimmune disorders and transplant rejection. Thiopurines are prodrugs which require metabolic activation to give thioguanine nucleotides that exert their cytotoxic effects by incorporation into DNA or inhibiting purine synthesis. The methylation reaction by TPMT utilizing S-adenosylmethionine (SAM) as the methyl donor prevents their conversion to these toxic compounds. The catalytic activity of TPMT in metabolising these compounds has been associated with occurrence of genetic variations. The variations that result to missense mutations cause amino-acid changes and in turn alter the polypeptide sequence of the protein. This could alter functionality and structural dynamics of the enzyme. This study sought to understand the underlying mechanism by which 7 specially selected mutations impede metabolic activity of the enzyme on 6-MP using in silico techniques. VAPOR and PredictSNP were used to predict the effects of single nucleotide polymorphisms (SNPs) on the stability and function of the enzyme. Of the 7 mutations, only H227Q was predicted to be functionally benign while the rest (L49S, L69V, A80P, R163H, R163C and R163P) were predicted to be deleterious or associated with disease. All the SNPs were predicted to destabilize the enzyme. Molecular dynamics (MD) simulations were preformed to mimic the behaviour of the apo, holo and drug-bound WT and mutant enzymes in vivo. This was followed by post-MD analysis to identify changes in the local and global motions of the protein in the presence of mutations and changes in intra-protein communication networks through contact map and centrality metrics calculations. RMSD and Rg analyses were performed to assess changes in global motions and compactness of the enzyme in the apo, holo and drug-bound states and in the presence of mutations. These revealed that binding of the ligand had a stabilizing effect on the WT enzyme evident from more steady trends from the analyses across trajectories in the holo and drug-bound enzymes compared to the apoenzyme. The occurrence of mutations had an effect on the global motions and compactness of the enzyme across the trajectories. Most mutations resulted in destabilized systems and less compact structures shown by unsteady RMSD and Rg across trajectories respectively. The drugbound systems appeared to be more stable in most of the systems meaning that the binding of 6MP stabilized the enzyme regardless of the presence of a mutation. RMSF analysis recorded local changes in residue flexibility due to the presence of mutations in all the systems. All the drug-bound mutant systems lost flexibility on the αAhelix which caps the active site. This could have an effect on drug binding and result to defective drug metabolism. The A80P mutation resulted to a more rigid structure from both global and local motions compared to the WT enzyme which could be associated with its nearly loss of function in vivo and in vitro. Dynamic cross correlation calculations were performed to assess how the atoms moved together. Correlated, anti-correlated and areas of no correlations were recorded in all the systems and in similar places when compared to each other. This meant that occurrence of mutations had no effect on how the atoms moved together. Contact map analysis showed that occurrence of mutations caused changes in interactions around the positions where the mutations occurred, which could have an effect on protein structural dynamics. The A80P substitution which occurred on the surface away from the binding site was identified as an allosteric mutation that resulted to changes in the catalytic site. Contact maps for the drug-cofactor complex in the mutant systems in comparison with the WT protein revealed changes that could suggest reorientation of the drug at the catalytic site. This could be an implication to altered drug metabolism. Eigenvector centrality (EC) and betweenness centrality (BC) for the most equilibrated portions of the trajectories were calculated for all the studied systems to identify residues connected to the most important residues and those that were spanned the most in shortest paths connecting other residues. Areas that scored highest in these metrics where mostly found in regions surrounding the catalytic site. Top 5% centrality hubs calculations showed loss of major hubs due to mutations with gaining of new ones. This means that mutations affected communication networks within the protein. The gained hubs were in areas close-by the lost ones which could have been an attempt of the protein to accommodate the mutations. Persistent top 5% BC hubs were identified at positions 90 and 151 while one persistent top 5% EC hub was identified at position 70. This positions play important roles in shaping the catalytic site and are in direct contact with the ligands. It was concluded that in silico techniques and analysis applied in this study revealed possible mechanisms in which genetic variations affected the structural dynamics of TMPT enzyme an affecte 6MP metabolism. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2023
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