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An investigation on the effects of Afrocentric missense variations on the structure and function of CYP2A6 protein

- Makombe, Chipo Perpetual

Authors: Makombe, Chipo Perpetual
Date: 2025-04-02
Subjects: Missense mutation , Structural dynamics , Enzyme activity , Drugs Metabolism , CYP2A6
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/479119 , vital:78262
Description: Pharmacogenomics, the foundation of personalized medicine distinguishes patients into different categories based on their response to the risk of a disease. Cytochrome P450 (CYPs) proteins are a family of enzymes critical in the metabolism of drugs and other substances. Genetic polymorphisms in CYPs can result in different enzymatic activity in individuals influencing the efficacy and toxicity of drugs. One of the CYPs which primarily metabolizes nicotine and other pharmaceutical drugs such as Artemisinin and Artesunate, Pilocarpine, Valproic Acid and Letrozole is CYP2A6. The gene encoding the protein is highly polymorphic and this can affect the rate of metabolism of drugs in individuals. Previously most studies unveiled connections between CYP2A6 variants and nicotine. Implications concerning the effects of specific missense variations in CYP2A6 drug metabolism have deficiencies. This study aimed to critically examine the structural and functional implications of 13 CYP2A6 allele variations on CYP2A6 protein using Bioinformatics techniques. Methods used were template selection, mutagenesis, parameter assignment and protonation. Molecular Dynamics to get insights regarding protein behavior at an atomic level, clustering to identify conformations during a simulation and DSSP for secondary structure analysis to monitor how secondary structures evolve. Berendsen and Parinello-Rahman barostats at production run were used for comparison. A global analysis was conducted to identify structural transitions (RMSD, RMSF, and Rg), clustering, and secondary structure prediction. Results from Berendsen barostat were inconsistent compared to Parrinello-Rahman barostat implying that CYP2A6 is sensitive to the pressure coupling parameter for precise and accurate results. Our clustering results showed each system in one conformation, fluctuations and shifts on the C-D, H-I loops and F, G, and L helices on variants I149M, F118l, K476R, and E390K_N418D_E419D. This indicated a potential loss of function limiting the protein’s ability to conformational flexibility for catalysis and substrate recognition. Certain regions of CYP2A6 became more rigid due to variations, which could have a negative impact on the catalytic activity, regulatory interactions, and general function of the enzyme in metabolism. Globally the variations did not cause large changes to the protein, there is need for a local analysis using Dynamic Residue Networks to study how residue interactions affect the function of CYP2A6. , Thesis (MSc) -- Faculty of Science, Biochemistry, Microbiology and Bioinformatics, 2025
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Date Issued: 2025-04-02

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Applying human factors and ergonomics to a healthcare clinic record-keeping process using a community-based participatory research approach in Makhanda

- Kingwill, Kirsten Rosemary

Authors: Kingwill, Kirsten Rosemary
Date: 2025-04-02
Subjects: Human engineering , Clinics Records and correspondence , Community-engaged research , Community-based research , Records management
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/479152 , vital:78265
Description: Background: Healthcare record-keeping is an important process. However, several challenges associated with taking, storing and maintaining accurate records have been identified as a barrier to the quality and safety of care globally and locally in primary healthcare clinics in Makhanda, Eastern Cape, South Africa. In this context, local healthcare providers argue that this stems from the hybrid nature of the system (paper and electronic) and the impact of several systemic challenges. Poor records can result in negative outcomes for patients, healthcare workers and the greater public healthcare system. For example, if patient files are not adequately completed, poor patient care and medico-legal litigation costs may emerge. Furthermore, given that HFE promotes the participation of stakeholders in identifying and resolving workplace challenges, this study adopted a participatory research approach, more specifically a Community-Based Participatory Research (CBPR) approach. This research project, therefore, aimed to explore the barriers and facilitators to record-keeping in a primary healthcare clinic in Makhanda, the adequacy of patient file completeness and reasons as to why files may or may not have been adequately completed, following a CBPR approach. Methods: Following a period of pre-data collection embedding in the clinic to become familiar with the system and the staff and to form a relationship with a community collaborator from the clinic, this study was completed in two broad phases. During Phase 1, observations, informal discussions and semi-structured interviews were conducted with 11 clinic staff members to understand the clinic and record-keeping systems through the work system components and barriers of both systems. Phase 1 data was analysed through thematic analysis and presented by work system components, selected SEIPS 101 tools and a Hierarchical Task Analysis to detail the tasks involved in the record-keeping process. During Phase 2, a comparative assessment of a sample of patient files (n=55) was conducted against a local standard checklist, detailing what was to be completed in patient files. This was done to assess the completeness of different file sections which were analysed through a frequency count. This was followed by three interviews with clinicians, which explored their perceptions on why sections of the records may have been better completed than others. The interviews were then thematically analysed. Results: Administrative staff shortages, a lack of file storage space, limited access to technology such as computers, lost files, and the amount of information to complete in files were identified as the major challenges associated with the record-keeping system and influencing the completion of patient files. Through the analysis of patient files, it was found that some patient file sections were completed more adequately than others. For example, administrative details were the most well-completed section, and the Anti-Retroviral Therapy (ART) initiation section was the most poorly completed. The findings also revealed reasons as to why these sections may or may not have been adequately completed. These included the need for the duplication of information, particularly for antenatal care clinicians. Time pressure for clinicians to see and complete patient records and work ethic and accountability were additional emergent themes. Lastly, clinicians argued that having a lack of access to, a shortage of or broken medical and record-keeping equipment that inhibited clinicians from obtaining and recording patient information, were additional reasons for poorly taken records. Conclusions: As the findings revealed, the primary healthcare clinic and its hybrid record-keeping system and process were influenced by a variety of clinic and record-keeping challenges that interacted and ultimately influenced the record-keeping process and completeness of patient files. The system constraints are important considerations as understanding how the clinic functions under them is a starting point for future system improvement. Furthermore, barriers impacting the record-keeping system influence several key steps in the record-keeping process, including the completion of details within patient files. Here it was found that some sections and information details were more adequately completed than others, which impacted the continuity, quality and safety of patient care. Additionally, the discrepancies found between the standard checklist and patient files were highlighted as a point of concern for the Department of Health (DoH) as clinics were being assessed based on a checklist that did not match the patient files, incorrectly representing the completeness of files to the DoH. Throughout the research project, the application and implementation of HFE and CBPR have been shown to be important in the local healthcare record-keeping system in that real-world challenges were identified through the perspective of community members facing the challenges. Therefore, HFE researchers should adopt a CBPR approach and apply these complementary domains in other complex systems and varying contexts to comprehensively understand the barriers, facilitators and opportunities for human-system interaction improvements. , Thesis (MSc) -- Faculty of Science, Human Kinetics and Ergonomics, 2025
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Date Issued: 2025-04-02

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Assessing how bird diversity of urban golf courses is influenced by course and landscape connectivity

- Benjamin, Jonathan

Authors: Benjamin, Jonathan
Date: 2025-04-02
Subjects: Birds , Biodiversity , Connectivity , Golf courses South Africa , Green space , Urban ecology (Biology)
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/478969 , vital:78245
Description: With increasing urbanisation and corresponding environmental impacts, urban green infrastructure (UGI) and the services it provides are of high importance. However, the degree to which these spaces are beneficial and provide ecological services are influenced by the extent to which patches of UGI are connected to each other. Varying levels of connectivity may enhance or lower the resilience of the UGI and the biodiversity it houses. Although not considered as UGI, golf courses are prominent green spaces in many urban landscapes occupying vast areas of land, and therefore hold potential to aid biodiversity and facilitate species movement. However, the extent which golf courses are able to do so is a function of both the structure and availability of resources on the golf courses, as well as in the surroundings areas or landscape in which they are situated. This notion of connectivity of golf courses to their surroundings UGI (in its many forms) and landscapes has not been adequately explored in the literature as much of the present literature has addressed golf courses’ biodiversity in isolation of other UGI, or where it has been considered, only the context in which golf courses were situated has been acknowledged (i.e. urban or rural landscapes). Moreover, as golf courses occupy large areas of lands forms of UGI, they may also be able to enhance the connectivity of the landscapes in which they are situated through increasing land cover, and lowering fragmentation through connecting patches. This however, is also context specific, as seen in natural settings were golf courses would in fact fragment the landscape. This study therefore sought to assess the extent to which urban golf courses are connected to other forms of UGI in the South African context, and illustrate the importance of paying attention to connectivity in an avifaunal diversity study. It also aimed to investigate the potential of urban golf courses to foster avifaunal diversity in comparison to a reference landscape, the direct surrounding urban and residential areas. To analyse the extent to which golf courses in three South African cities were connected to the wider landscape a connectivity analysis was undertaken using GIS software. This analysis indicated that all golf courses were to some extent connected to a range of different UGI. Whilst the level of connectivity fluctuated between golf courses and cities, there was however no significant difference noted. Urban golf courses in the South African context are thus not isolated habitats but connected to other land uses and therefore potentially provide valuable resources that aid biodiversity. Despite being physically connected to surrounding UGI illustrating that both the golf courses benefit from the surrounding UGI and vice versa, at a larger landscape there was not sufficient evidence of the ability of golf courses to enhance connectivity. Although there was little evidence of golf courses’ ability to aid connectivity at the larger landscape scale, the observed extent to which golf courses were connected to their directly surrounding landscape and the high presence UGI within the larger landscape, informed the more refined investigation of avian biodiversity of golf courses in comparison to surrounding urban areas in the city of Cape Town. This biodiversity analysis indicated that there was significantly higher bird diversity on golf courses in comparison to the surrounding urban areas. However, the high level of connectivity to directly surrounding UGI that was obtained in the former part of the study proved to have no impact on the diversity noted. In contrast, the connectivity at the landscape scale, a scale addressing the broader landscape, provided valuable insight into factors determining the levels of avifaunal diversity noted. This dissertation therefore provides evidence of the biodiversity supporting function of urban golf courses and highlights the importance of landscape context in ecological assessment. These findings are a starting point for future research about the capacity of golf courses to support biodiversity in conjunction with other UGI. In the Global South context, which is complex and dynamic in nature, this information is vital, as these dynamic and changing landscapes provide opportunities to incorporate, and preserve already existing biodiversity. , Thesis (MSc) -- Faculty of Science, Environmental Science, 2025
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Date Issued: 2025-04-02

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Assessing land use and land cover change dynamics of wildlife ranches in South Africa

- Moon, Lisa

Authors: Moon, Lisa
Date: 2025-04-02
Subjects: Wildlife refuges South Africa , Biodiversity conservation South Africa , Land use Planning , Social ecology , Business model , Land cover
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/478980 , vital:78246
Description: With increasing urbanisation and corresponding environmental impacts, urban green infrastructure (UGI) and the services it provides are of high importance. However, the degree to which these spaces are beneficial and provide ecological services are influenced by the extent to which patches of UGI are connected to each other. Varying levels of connectivity may enhance or lower the resilience of the UGI and the biodiversity it houses. Although not considered as UGI, golf courses are prominent green spaces in many urban landscapes occupying vast areas of land, and therefore hold potential to aid biodiversity and facilitate species movement. However, the extent which golf courses are able to do so is a function of both the structure and availability of resources on the golf courses, as well as in the surroundings areas or landscape in which they are situated. This notion of connectivity of golf courses to their surroundings UGI (in its many forms) and landscapes has not been adequately explored in the literature as much of the present literature has addressed golf courses’ biodiversity in isolation of other UGI, or where it has been considered, only the context in which golf courses were situated has been acknowledged (i.e. urban or rural landscapes). Moreover, as golf courses occupy large areas of lands forms of UGI, they may also be able to enhance the connectivity of the landscapes in which they are situated through increasing land cover, and lowering fragmentation through connecting patches. This however, is also context specific, as seen in natural settings were golf courses would in fact fragment the landscape. This study therefore sought to assess the extent to which urban golf courses are connected to other forms of UGI in the South African context, and illustrate the importance of paying attention to connectivity in an avifaunal diversity study. It also aimed to investigate the potential of urban golf courses to foster avifaunal diversity in comparison to a reference landscape, the direct surrounding urban and residential areas. To analyse the extent to which golf courses in three South African cities were connected to the wider landscape a connectivity analysis was undertaken using GIS software. This analysis indicated that all golf courses were to some extent connected to a range of different UGI. Whilst the level of connectivity fluctuated between golf courses and cities, there was however no significant difference noted. Urban golf courses in the South African context are thus not isolated habitats but connected to other land uses and therefore potentially provide valuable resources that aid biodiversity. Despite being physically connected to surrounding UGI illustrating that both the golf courses benefit from the surrounding UGI and vice versa, at a larger landscape there was not sufficient evidence of the ability of golf courses to enhance connectivity. Although there was little evidence of golf courses’ ability to aid connectivity at the larger landscape scale, the observed extent to which golf courses were connected to their directly surrounding landscape and the high presence UGI within the larger landscape, informed the more refined investigation of avian biodiversity of golf courses in comparison to surrounding urban areas in the city of Cape Town. This biodiversity analysis indicated that there was significantly higher bird diversity on golf courses in comparison to the surrounding urban areas. However, the high level of connectivity to directly surrounding UGI that was obtained in the former part of the study proved to have no impact on the diversity noted. In contrast, the connectivity at the landscape scale, a scale addressing the broader landscape, provided valuable insight into factors determining the levels of avifaunal diversity noted. This dissertation therefore provides evidence of the biodiversity supporting function of urban golf courses and highlights the importance of landscape context in ecological assessment. These findings are a starting point for future research about the capacity of golf courses to support biodiversity in conjunction with other UGI. In the Global South context, which is complex and dynamic in nature, this information is vital, as these dynamic and changing landscapes provide opportunities to incorporate, and preserve already existing biodiversity. , Thesis (MSc) -- Faculty of Science, Environmental Science, 2025
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Date Issued: 2025-04-02

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Bioprospecting for entomopathogenic fungi against a foliar citrus pest

- Boon, Erin Ashley

Authors: Boon, Erin Ashley
Date: 2025-04-02
Subjects: Citrus Diseases and pests South Africa , Entomopathogenic fungi , Pests Integrated control , Biological assay , Cryptophlebia leucotreta , Ultraviolet radiation Physiological effect
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/478991 , vital:78247
Description: Historically, pest management was highly dependent on the use of chemical insecticides for the control of agriculturally important pests. However, more recently, key export markets have imposed stringent chemical residue restrictions for citrus export. This deterring factor for chemical use has been coupled with the fact that these economically important pests are experiencing insecticidal resistance. As a result, the use of entomopathogenic fungi (EPF) has been explored as a complementary control option in integrated pest management (IPM) regimes. Previous research in South Africa identified several strains of Beauveria bassiana and Metarhizium spp. (including isolate M. pinghaense FCM Ar 23 B3). Laboratory bioassays evaluating the virulence of these isolates against major pests such as the false codling moth (FCM) (Thaumatotibia leucotreta, Lepidoptera: Tortricidae), citrus thrips (Scirtothrips aurantii, Thysanoptera: Thripidae), and citrus mealybugs (Planococcus citri, Hemiptera: Pseudococcidae) highlighted the potential of these EPF. While field trials targeting FCM with soil-applied treatments yielded encouraging results, foliar applications aimed at controlling citrus thrips and mealybugs showed limited success. These findings highlighted the need to assess the biological traits of the recovered isolates. Varying temperature ranges and humidity levels were found to not hinder the isolates' efficacy in the field. Conidial inactivation induced by ultraviolet (UV) radiation however, was. As these strains were recovered from the soil environment, it stood to reason that EPF isolates recovered from the foliar environment may be more suited for foliar application. Thus, bioprospecting for isolates from the aboveground environment was initiated and was the focal point of this thesis. Following the isolation and identification, the pathogenic ability and virulence, as well as the UV tolerance of these novel strains were established. Of the isolates recovered from the aboveground environment and identified using morphological and molecular techniques, four were B. bassiana (Px LM 4, Ha LM 11, Ha LM 12, Coe 18), one M. anisopliae (Hu LM 14), one Fusarium oxysporum (Pc HV 9), and one Geotrichum candidum yeast (Ha LM 2). The majority were isolated from insect cadavers, but one (Coe 18) was isolated as a foliar endophyte from an organically managed citrus farm in the Eastern Cape. Using standard protocols and conidial doses, the virulence of the recovered isolates was established against a common foliar pest of citrus, citrus mealybug. Isolate FCM Ar 23 B3 was included as a comparative control in this study as the virulence against citrus mealybug has previously been established. The initial screening of the isolates ranged between 15 and 90 % mortality. Isolates Px LM 4 and FCM Ar 23 B3 both induced an average mortality of 90 %. Isolates Ha LM 11, Ha LM 12, Hu LM 14, and Coe 18 caused mortalities greater than 60 % and were further investigated under dose-response assays. Of the six isolates measured for LC50, FCM Ar 23 B3 was the most virulent (5.25 × 105 conidia/ml), followed by Px LM 4 (1.09 × 106 conidia/ml) and Hu LM 14 (1.32 × 106 conidia/ml). The UV susceptibility to simulated sunlight of the six most virulent isolates was investigated. Whilst UV radiation certainly delayed the conidial germination of all the isolates, all the strains isolated from the aboveground environment demonstrated significant initial tolerance to UV radiation compared to the most virulent M. pinghaense FCM Ar 23 B3, which was recovered from the soil environment. Even though the B. bassiana Coe 18, which was recovered as an endophytic EPF, was not the most virulent, it stood out with strong initial UV tolerance and sustained a relatively high germination rate over time, establishing it as the most UV-tolerant isolate. Although formulation for development as a microbial biocontrol programme should not be overlooked for these isolates, the initial UV and sustained tolerance demonstrated by these aboveground isolates warrants further investigation under field conditions. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2025
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Date Issued: 2025-04-02

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Enculturation and adaptation: a practice-led investigation into the history and contemporary transformation of the Bahananwa harepa

- Madiba, Elijah Moleseng

Authors: Madiba, Elijah Moleseng
Date: 2025-04-02
Subjects: Enculturation , Gananwa (African people) , Gananwa dialect , Northern Sotho language , Stringed instruments South Africa Limpopo , Cultural identity , Pedi (African people)
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/479607 , vital:78328 , DOI 10.21504/10962/479607
Description: This thesis investigates the cultural and musical transformations of the harepa, a stringed instrument initially introduced as the autoharp by Christian missionaries in the late nineteenth century, now deeply embedded within the Basotho ba Lebowa community in Limpopo, South Africa. Through an interdisciplinary approach that blends historical ethnography with practice-led research, this thesis explores the harepa's negotiation of identity amidst the cultural shifts and modernisation affecting the community. The musical output of the harepa showcases a unique hybridity that fuses Basotho ba Lebowa traditions with Western musical influences. The aim of this research is to document the harepa instrument, analyse its music and transformation processes, highlight the musical history of research partners and emphasise the unique tunings which are distinct from Western standards. Employing methodologies that integrate participant observation, ethnographic interviews, and direct musical practice, the research engages with local musicians to understand the contemporary relevance of the harepa and its role in sustaining cultural heritage. It examines shifts in musical practices, the decline of traditional uses of the harepa, and efforts towards its revitalisation, including documenting musical repertoires and analysing performance practices. The findings highlight a complex narrative of enculturation, adaptation, and resistance, revealing the resilience of cultural identity through unique tuning systems that contrast sharply with Western musical paradigms. African tuning practices, characterised by their flexibility and reliance on auditory perception, challenge the adequacy of Western tuning methodologies. This study also investigates the potential of sampling as a method for the sonic representation of African music, advocating for a more culturally sensitive framework that respects the diversity of global musical traditions. By focusing on this localised musical phenomenon, the study illustrates broader cultural preservation and innovation dynamics within Limpopo's Basotho ba Lebowa community. It calls for ongoing dialogue and research to develop methodologies that reflect the unique cultural contexts of musical traditions worldwide. Ultimately, this work underscores the importance of engaged, practice-led research in documenting and revitalising endangered musical cultures in the face of globalisation and cultural homogenisation. , Thesis (PhD) -- Faculty of Humanities, Music and Musicology, 2025
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Date Issued: 2025-04-02

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Examining the effects of small molecule tyrosine kinase inhibitors on glucose metabolism in skeletal muscle and liver cell lines in vitro

- Mugiya, Takudzwa Cleophas

Authors: Mugiya, Takudzwa Cleophas
Date: 2025-04-02
Subjects: Diabetes , Blood glucose , Cancer , Insulin , Protein kinase B , Glucose transporters
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/478829 , vital:78227
Description: Diabetes mellitus is rising due to aging, sedentary lifestyles, obesity, and unhealthy diets, posing a global health threat. Due to increase in prevalence together with shortfalls associated with current treatment options, there is still a necessity for a continuous search of new pharmacotherapies. Small molecule tyrosine kinase inhibitors are drugs, used in cancer chemotherapy and have been shown to affect glycaemic control and metabolism variably. Studies have shown that tyrosine kinase inhibitors can alter glycaemic control and glucose metabolism, with some demonstrating hypoglycaemic activities whilst others showing hyperglycaemic properties. The mechanism by which tyrosine kinase inhibitors cause glycaemic dysregulation is not well understood, therefore, the clinical significance of these chemotherapeutic agents on glucose handling is also poorly documented. Aims and objectives: This study aims to elucidate how small molecule tyrosine kinase inhibitors affect glucose metabolism in C2C12 and HepG2 cells in vitro, including their impact on glucose uptake, AKT, GLUT-4, and IL-6 expression, GLUT-4 translocation, and alpha-amylase and alpha-glucosidase activity. Methods: In this study, C2C12 and HepG2 cells were seeded in well plates and the initial media glucose concentration was recorded. Cells were then treated with small molecule tyrosine kinase inhibitors; imatinib, dasatinib, axitinib, and erlotinib for 24 hours. Thereafter, the effect of the test drugs was assessed on cell viability, glucose uptake, expression of AKT GLUT-4 and IL-6, and translocation of GLUT-4. Furthermore, effects of the drugs were assessed on the activities of alpha amylase and glucosidase using calometric assays. Results and Discussion: Cells treated with small molecule tyrosine kinase inhibitors were viable after 24 hours. A concentration-dependent increase in glucose uptake in C2C12 cells treated with imatinib was observed as the concentration of imatinib increased. Axitinib, dasatinib, and erlotinib demonstrated glucose uptake levels comparable to the control across all concentrations. Small molecule tyrosine kinase inhibitors demonstrated an increase in GLUT4 translocation in the absence of insulin. GLUT4 expression was comparable in cells treated with small molecule tyrosine kinase inhibitors and the control. Small molecule tyrosine kinase inhibitors showed an increase in AKT expression. C2C12 cells treated with small molecule tyrosine kinase inhibitors were observed to have elevated IL-6 expression compared to the control. The HepG2 cells treated with erlotinib and imatinib demonstrated elevated glucose uptake while cells treated with axitinib and dasatinib were observed to have a lower glucose uptake. Treatment with dasatinib led to a decrease in Akt expression as concentration increased. Small molecule tyrosine kinase inhibitors demonstrated inhibition of alpha-amylase, while only dasatinib and axitinib showed inhibition of alpha-glucosidase. Conclusion: The results show that small molecule tyrosine kinase inhibitors impact glucose metabolism in C2C12 and HepG2 cells via their effect on GLUT-4 translocation and expression and AKT expression. Dasatinib showed promising potential with regard to antidiabetic capabilities. Further research is needed to better understand these mechanisms' effects on metabolic homeostasis and inform future therapeutic strategies. , Thesis (MSc (Pharm)) -- Faculty of Pharmacy, Pharmacy, 2025
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Date Issued: 2025-04-02

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Exploring the impact of sub-ambient CO2 concentrations on Oxalis growth: implications for food sustainability among Pleistocene human foragers in the Greater Cape Floristic Region

- Faltein-Maqubela, Zintle

Authors: Faltein-Maqubela, Zintle
Date: 2025-04-02
Subjects: Carbon dioxide Thermal properties , Geophyte , Hunting and gathering societies Pleistocene , Paleobotany Pleistocene , Oxalis , Prehistoric peoples Food , Cape Floristic Kingdom
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/479097 , vital:78260
Description: Humans inhabiting the glacial refugia of the Cape Floristic Region during the Middle Pleistocene are believed to have relied on underground storage organs (USOs) as a crucial carbohydrate source. While previous research has highlighted the nutritional potential of these plants for early human gatherers, such studies are typically conducted under modern climatic conditions and do not account for the reduced plant productivity and USO yields associated with the lower atmospheric CO₂ concentrations characteristic of Pleistocene glacial periods. To evaluate the impact of CO₂ availability on plant productivity, I cultivated two Oxalis species—O. pes-caprae and O. punctata, both known to have been harvested by early foragers—under CO₂ concentrations ranging from 180 ppm to 400 ppm. Results showed that glacial-level CO₂ concentrations significantly reduced bulb production in O. pes-caprae and photosynthetic rates in both species. Using these findings to model Pleistocene foraging behaviour, I estimate that human foragers would have needed to spend an additional 8 hours gathering food to meet their daily dietary requirements of 2000 calories, suggesting the need for alternative food sources to supplement their diet. These findings emphasise the importance of considering historical plant growth conditions, particularly atmospheric CO₂ levels, when reconstructing past human diets. Failure to account for these factors may represent a significant gap in our understanding of human subsistence strategies during glacial periods. , Thesis (MSc) -- Faculty of Science, Botany, 2025
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Date Issued: 2025-04-02

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Filling the language gap: the feasibility of communication resources used in the provision of healthcare for HIV/AIDS and tuberculosis in the Eastern Cape, South Africa

- Lourenço, Nathalia Jane

Authors: Lourenço, Nathalia Jane
Date: 2025-04-02
Subjects: Uncatalogued
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/478504 , vital:78192 , DOI 10.21504/10962/478504
Description: South Africa has the largest number of Human Immunodeficiency Virus (HIV)-positive people in the world, the third-highest rate of Tuberculosis (TB) infections, and the second-highest rate of Multi-Drug Resistant TB (MDR-TB) globally, with up to 60% of HIV-positive healthcare users (HCUs) infected with TB as a co-infection. Both HIV/AIDS and TB require strict medicines adherence for disease management or treatment respectively; however, this is often not attained, and as such these statistics also represent lives affected by or lives lost to these diseases. Moreover, in South Africa, up to 80% of healthcare consultations are conducted through a second language. Despite language policies suggesting the contrary, African languages are neglected in healthcare provision in South Africa. This perpetuates inequalities within the South African healthcare system by limiting HCUs understanding of and agency in their own healthcare and maintaining a barrier to more effective treatment. Such language barriers may also result in HCUs defaulting on treatment. Added to this, the fear and mistrust arising from language power dynamics contributes to high rates of avoidance behaviour. This research therefore aimed to (a) explore how healthcare professionals (HCPs) and HCUs communicate when they are not fluent in the same language in care for HIV/AIDS and TB patients; (b) develop practical and feasible strategies that would enable HCPs to address language barriers in their consultations for HIV and TB and (c) to empirically evaluate these strategies in a pilot feasibility trial in the Eastern Cape. The first aim (a) concerning the problem of language barriers in healthcare consultations was addressed through identifying communication barriers experienced by HCPs in South Africa, exploring the strategies used to navigate or alleviate these barriers, creating and implementing communication resources, and analysing the effects of these resources on HCPs’ communication. A selective narrative review was conducted (Chapter 2) to identify the main communication problems experienced by HCPs and HCUs, as well as the main communication strategies and resources used by HCPs to reduce these communication problems. This was further explored by conducting two needs analyses with HCPs (n=31) in South Africa, and specifically in the Eastern Cape, which revealed differing perspectives on health communication and confirmed HCPs’ need for communication resources. For the second aim (b), existing communication resources were reviewed and selected or further developed following a Participatory Action Research approach, and then (c) empirically evaluated in a pilot feasibility trial with six healthcare sites in the Eastern Cape. Both the needs analyses and the pilot feasibility trial were adapted to employ an online or blended approach due to COVID-19-related limitations. The feasibility and acceptability of both the study protocol and the proposed communication resources were evaluated. Three major findings emerged from this research. First, this research echoed existing literature confirming that HCPs do not have the support they need at a structural level. Second, while it was found that there is no one-size-fits-all solution for resources and training to improve HCP-HCU communication, it was noted that the most appropriate resources are those that are flexible, and those that support HCPs’ language learning. HCPs who were already sensitive to communication barriers and were already taking steps to improve their second language (L2) proficiency also took initiative to use the resources in ways other than those suggested in order to best support the communication needs of them and the HCUs they consulted. Third, and linked to the second finding, it was found that communication resources that covered conditions including, but not limited to, HIV and TB were more appropriate. HCPs who used the resources showed a small, although not statistically significant, increase in communication satisfaction, satisfaction with resource support, and trust after using the resources for one month. Although implementation problems were encountered in some settings of the intervention, it was found that this intervention has the potential to be further evaluated in a larger, multi-site randomised controlled trial (RCT). These findings inform recommendations which are made to improve the feasibility of such a study in order to conduct an RCT; to further develop the resources in order to enhance communication between HCPs and HCUs both in HIV and TB consultations and in other fields of healthcare; and to implement a similar intervention at the university level and as Continuing Medical Education. The insights gained into HCPs’ support for language support resources, which resources were used, and particularly how they were used, are significant for taking actionable steps in supporting HCPs’ provision of more equitable healthcare in multilingual South Africa. , Thesis (PhD) -- Faculty of Humanities, Languages and Literatures, 2025
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Date Issued: 2025-04-02

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Geological, petrological and geochemical investigation of the c. 3.45 Ga Stolzburg TTG Pluton at Crushers’ Quarry, Barberton greenstone belt, South Africa

- Mofammere, Thato Constance

Authors: Mofammere, Thato Constance
Date: 2025-04-02
Subjects: Geology Barberton Greenstone Belt (Eswatini and South Africa) , Petrology Barberton Greenstone Belt (Eswatini and South Africa) , Geochemistry Barberton Greenstone Belt (Eswatini and South Africa) , Intrusions (Geology) Barberton Greenstone Belt (Eswatini and South Africa) , Tonalite-Trondhjemite-Granodiorite
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/479163 , vital:78266
Description: This study investigates the tonalite-trondhjemite-granodiorite (TTG) suite and associated amphibolite xenoliths of the Stolzburg pluton at Crushers’ Quarry in the Barberton Granitoid-Greenstone Terrain, South Africa. Through detailed field mapping, petrography, geochemical analysis, δ¹⁸O investigation of quartz, and U-Pb zircon geochronology, the petrogenesis and geodynamic context of these Archean rocks were explored. Five major lithologies were identified: Coarse-grained trondhjemites, medium-grained tonalites, fine-grained tonalites, granodiorite sheets, and amphibolite xenoliths. Field evidence, including cross-cutting relationships, indicates that the coarse-grained trondhjemites intruded as the earliest phase, followed by medium-grained tonalites, which were then followed by fine-grained tonalites, and finally, granodiorite sheets, which represent the latest intrusive phase. Petrographic analysis reveals mineralogical differences between the trondhjemites and tonalites, with trondhjemites lacking hornblende and having lower mafic mineral content. Geochemical data support the interpretation that the TTGs formed through partial melting of variably hydrated metabasaltic sources (possibly at depth in the garnet stability field). The metabasaltic melt incorporated varying proportions of older, intermediate trondhjemite crust and volcaniclastic sediments during ascent and emplacement to form the Stolzburg pluton TTG suite of rocks. Elevated (above mantle) δ¹⁸O quartz values of the Stolzburg pluton TTG rocks ranging between 8.72 to 9.71‰ combined with it’s strongly peraluminous geochemical composition indicate the presence of an ancient crustal component that was assimilated into the metabasaltic melt source(s). It is proposed that a number of petrogenetic factors controlled the composition of the Stolzburg TTG rocks, including composition of the metabasalt source, degree of hydration of the metabasalt source and the extent of crustal contamination with older, pre-existing intermediate composition rocks. A possible candidate for the crustal contamination component could be the older 3.509 Ga Steynsdorp trondhjemite as well as ancient volcaniclastic sediments in the greenstone belt. The protolith to the amphibolite xenoliths occurring within the TTG suite are geochemically characterized as komatiitic basalt, recording either a subduction zone or crustal contamination geochemical signature. U-Pb zircon dating of the coarse-grained trondhjemites and medium-grained tonalites yield Concordia ages of 3429.9 ± 12 Ma (2σ) and 3414.0 ± 14 Ma (2σ), respectively. These Concordia ages represent an estimate of the igneous crystallization ages of the zircons and confirm that these TTGs were emplaced in close temporal succession. The U-Pb zircon ages are comparable to those in the published literature, although one sample with a significantly younger age is attributed to zircon open-system Pb-loss in complex early Archean zircons and also challenges with the LA-ICP-MS analytical technique used. The depth of metabasalt melting is not constrained in this study, similar to recent studies on early Archean TTGs. Various TTG geodynamic settings are explored ranging from melting at the base of a thick oceanic plateau to generation at depth in a subduction zone. In light of recent regional field observations, metamorphic constraints, apatite thermochronological data, U-Pb detrital zircon data and greenstone belt metabasalt geochemistry, a model of TTG crust generation in an episodic proto-subduction zone, involving subcretion and tectonic imbrication of oceanic lithosphere at c. 3.45 Ga, is considered. , Thesis (MSc) -- Faculty of Science, Geology, 2025
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Date Issued: 2025-04-02

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Leveraging visualizations with systems for operational and strategic decision-making

- Cuthbert, Carol Elaine

Authors: Cuthbert, Carol Elaine
Date: 2025-04-02
Subjects: Information visualization , Subject-matter expert , Automated decision-making , Strategic planning , Knowledge sharing , Practice management system
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/479570 , vital:78325 , DOI 10.21504/10962/479570
Description: Dynamic capability-enhancing technology, Subject Matter Experts (SMEs), System Experts (SEs) in planning and forecasting, and big data used for sensemaking combine to enable knowledge-based management decisions in interdisciplinary teams, increasing competitive advantage. This research extended Contingent Resource-based Theory CRBT by focusing on visualization’s role in this process. SMEs and SEs configure assumptions, with visualizations, in an interdisciplinary team to enable planning within the context of legal practice management systems. The study employed a mixed-method sequential explanatory design. An initial quantitative component determining which types of decision-making information technology contribute to the competitiveness of a firm was undertaken. Niche systems were found to increase technological dynamic capability through their highly configurable workflow tools, which provide customization capabilities and the ability to react to a changing environment quickly. Niche systems differentiated through process automation were found to be the aspect to focus on in a qualitative research study. A knowledge-sharing process model was developed from the literature, and this was overlayed with visualization as the new knowledge-sharing enabler. Then, a thematic qualitative study of interviews focusing on SMEs' and SEs' use of visualization in legal and financial system implementation was employed to establish the extent to which this process occurs in legal financial transformation projects. Seven subject matter experts and four system experts in legal transformation implementations were interviewed regarding using visualization to facilitate communication, verification, and process configuration during the knowledge-sharing process. The research illustrated how (1) low code systems data, (2) people, and (3) data enable the creation, sharing, and configuration of knowledge in practice in the legal practice management context. Recommendations for further research were made to automate refining budgeting and forecasting assumptions. This enables management to arrive at more accurate forecasts by refining assumptions and producing the resultant profit and loss reports visually in heat maps depicting variance between the forecast and actual profit and loss reports. The SMEs provide feedback, and the system cycles between multiple assumption iterations, reducing the variance and enhancing management decision-making. Visualization was found to assist the knowledge-sharing process through (1) verification, (2) process enablement, and (3) communication for decision-making. This research highlighted the value of variance heat maps and other visualizations and workflows in making planning assumptions explicit, thereby enhancing forecasting accuracy. , Thesis (PhD) -- Faculty of Commerce, Rhodes Business School, 2025
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Date Issued: 2025-04-02

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Listening otherwise in the face of gender-based violence in South Africa: a critical exploration of the listening deficiencies in public narratives and a listening-based framework for healing and social change

- Bombi, Thandi

Authors: Bombi, Thandi
Date: 2025-04-02
Subjects: Gender-based violence , Rhetoric Social aspects , Interviewing in journalism , Facilitation , Social change
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/478515 , vital:78193 , DOI 10.21504/10962/478515
Description: South Africa has one of the highest rates of gender-based violence (GBV) in the world. This includes femicide, rape and intimate partner violence. Scholars and activists in the space of GBV have challenged society to alter the way we have been taught to engage with rape and gender-based violence. Despite many interventions, gender-based violence remains an intractable social problem. This study uses Lipari’s (2014) concept of “listening otherwise” to respond to the challenge. By interrogating how South Africa’s violent history and patriarchal society has been normalised, the study attempts to see beyond the narrow ideas prescribed by the country’s history and violent cultures. This study uses the grounded theory approach (Glaser & Strauss 1967) to investigate the relationship between listening and gender-based violence in South Africa. The concept of “listening otherwise” is explored alongside the concepts “voice”, “speak out” and “break the silence” that are the most visible and codified strategies in the fight against gender-based violence. Following the exploration, the study then develops a theoretical and methodological framework for “listening otherwise” in the spaces, fields, and engagements that deal with gender-based violence in South Africa. The two central questions of the study ask; how do we reshape the collective emotional response to patriarchal structural violence? And furthermore, how do we listen otherwise when faced with experiences of gender-based violence in South Africa? The data used to construct the framework includes in-depth interviews, studies of actual cases, academic literature, news interviews and newspaper articles. There are a multitude of ways in which people are talking about gender-based violence, exposing perpetrators and “breaking the silence”. There is, in fact, no silence around rape, gender-based violence and femicide. The silence exists around engagements about gender, misogyny and patriarchy when discussing the causes of gendered violence in the country. This research found that the public’s listening practices around gender-based violence are shaped by patriarchal cultures and rape myths which are endemic in media discourses, legal discourses and in general social talk. Building a caring society, in which people play and use restorative justice practices, may alter the communal listening practices and have an impact on the public response to gender-based violence. The framework for listening otherwise, that emerged as a result of the research, is a contribution to listening scholarship and the activism against gender-based violence. The framework considered various aspects of listening and the field of gender-based violence and arrived at six conceptual considerations and six actions for listening otherwise. , Thesis (PhD) -- Faculty of Humanities, Journalism and Media Studies, 2025
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Date Issued: 2025-04-02

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Managing operational uncertainty in manufacturing with industry 4.0 and 5.0 technologies: a modified neo-configurational perspective

- Mtotywa, Matolwandile Mzuvukile

Authors: Mtotywa, Matolwandile Mzuvukile
Date: 2025-04-02
Subjects: Industry 4.0 , Industry 5.0 , Operational risk , Organizational learning , Qualitative comparative analysis , Configurational analysis
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/479584 , vital:78326 , DOI 10.21504/10962/479584
Description: The manufacturing sector is a significant economic multiplier due to its strong connections to the economy's downstream and upstream output sectors. It supports the notion that manufacturing drives industrialisation and can serve as the primary engine for growth and employment creation. Despite its importance, the manufacturing sector has challenges associated with diminishing size and lack of competitiveness, especially in countries such as South Africa. These challenges are exacerbated by prevailing operational uncertainties that negatively impact manufacturing firms. Literature on operational uncertainty, fourth and fifth industrial revolution technologies and organisational learning show several interrelated theoretical and methodological gaps, highlighting three empirical and theoretical gaps as well as two methodological gaps. Six propositions were developed to investigate the research objectives. This was done using a multi-method quantitative design based on the post-positivist paradigm, with data collected from 22 experts (expert survey) and 262 firm representatives (firm survey). The results of the study confirmed that operational uncertainty is a multi-dimensional construct with a reflective model for dimensions and reflective-reflective for higher-order construct. This means that for the dimensions, the indicators can be added or excluded in the formation of the dimension. The same is also true for construct, operational uncertainty. The results of the present study also confirm that operational uncertainty is a norm in the manufacturing industry with a Manufacturing Operational Uncertainty Index (MOUI) = 0.752, indicating the range of futures. This posits that it is difficult to divide these futures into a discrete and exhaustive set of possibilities due to the complexity of conditions (variables) at play. Industry 4.0 and 5.0 technologies and their capabilities can manage the operational uncertainty dimensions with these technologies capable of scenario planning and supply chain integration (SPSI), flexible production and mass customisation (FPMC), real-time system and process monitoring and response (RPMR), root cause analysis and sustainable solutions (RCAS). These technologies are mainly artificial intelligence (AI), Internet of Things (IoT), big data analytics (BDA) and to a less extent advanced robotics (ARB), blockchain and augmented and virtual reality (ARVR). Organisation learning is also an effective causal condition to incorporate in managing operational uncertainty with Industry 4.0 and 5.0 technologies. The study has both theoretical and methodological contributions. In theory, it advanced the modified neo-configuration theory, while the methodology provided an Manufacturing Operational Uncertainty Index and integrated fsQCA with fuzzy decision-making trial and evaluation laboratory (DEMATEL), and structural equation modelling partial least square (PLS-SEM). This research study is important since the recognition and dissemination of subjects within the field of operations management hold great significance for firms, which is contingent upon their sector of operation. This research offers valuable insights for academia, policymakers, and the manufacturing sector. It helps with their activities to effect meaningful change in day-to-day business operations, allowing for more effective progress in the subject area, and promoting practical, real-world issue-solving. , Thesis (PhD) -- Faculty of Commerce, Rhodes Business School, 2025
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Date Issued: 2025-04-02

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On β-Normal Spaces

- Ngcamphalala, Thobile

Authors: Ngcamphalala, Thobile
Date: 2025-04-02
Subjects: Beta normal form , Open set , Bitopological space , Topology
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/479186 , vital:78268
Description: This thesis revisits some types of normal spaces, namely, β-normal spaces and α-normal spaces, which were introduced by Arkhangel’skii and Ludwig in 2001. We study some properties of these spaces with a focus on improving some of the already existing properties and exploring new properties that are not available in the literature. Under β-normal spaces, among other things, we characterize these spaces using some types of open sets. We use the ultrafilter space to answer Murtinova’s question about the existence of a β-normal and regular space which is not Tychonoff. α-normal spaces are described in terms of countable open sets, a result imitating that of normality. It turns out that continuous functions which are onto, open and closed preserve β-normality, while those which are injective, open and closed reflect α-normality. The notion of β-normal spaces is extended to the category of bitopological spaces where we characterize these bitopological spaces simultaneously in terms of i-open sets, (i, j)-preopen and (i, j)-α-open sets. We study the interrelations of these spaces with other bitopological spaces. , Thesis (MSc) -- Faculty of Science, Mathematics, 2025
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Date Issued: 2025-04-02

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Pre-release evaluation of stem-galling and seed-feeding midges (Diptera: Cecidomyiidae) from South Africa as biological control agents for Guinea grass (Megathyrsus maximus) in Texas, United States

- De la Fontaine, Benjamin

Authors: De la Fontaine, Benjamin
Date: 2025-04-02
Subjects: Guinea grass Biological control Texas , Gall midges , Invasive plants Biological control Texas , Maxent , Phylogeny , Grasses Texas
Language: English
Type: Academic theses , Master's theses , text
Identifier: http://hdl.handle.net/10962/479002 , vital:78248
Description: Guinea grass (Megathyrsus maximus) is a tall-statured C4 grass with a native range spanning sub-Saharan Africa. Intentionally exported for centuries for its grazing value, it has become a near-global invasive. Texas, USA is the first territory to initiate a biological control program for Guinea grass, targeting an invasive population with genetic origins that have been traced to South Africa. This study focuses on the identification and evaluation of biological control agents for Guinea grass. Native-range natural enemy surveys were performed in South Africa, resulting in the identification of several undescribed species of phytophagous midges (Diptera: Cecidomyiidae) on Guinea grass, including stem-galling taxa (gall midges) and seed-feeding taxa (seed midges). These taxa are expected to be highly host-specific based on the known biology of this family of insects, but the difficulty of rearing them in the laboratory necessitated field-based assessments. Field host range assessments of stem gall midges resulted in the rejection of one candidate (the horn gall midge, undescribed sp.) due to feeding on a relative of the target plant, Batochloa deusta, and the prioritization of another candidate (the blister gall midge, Arabukodiplosis vesicaria) that feeds only on Megathyrsus maximus. Combined field host range evaluations and phylogenetic analysis of a cryptic species complex of seed midges resolved this as a new genus containing up to seven species, with five species that are likely to be specific to their respective Panicoideae grass hosts, including Megathyrsus maximus and Cenchrus ciliaris (buffelgrass – also invasive in the USA). Climate matching models for the blister gall midge and seed midge on Guinea grass predicted high likelihood of establishment and nearly complete coverage of invaded sites in Texas, and identified northern KwaZulu-Natal, South Africa as an ideal source region for Guinea grass biocontrol agents. The nascent sub-field of grass biocontrol research has developed slowly because of inaccurate perceptions that grasses lack host-specific herbivores, and faces a severe taxonomic impediment given the large number of undescribed insect species feeding on grasses, especially in Africa. This study has contributed to resolving both challenges by identifying several new host-specific insect species, showing that the prospects for future success and discovery in grass biological control are promising. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2025
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Date Issued: 2025-04-02

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Productive piano pedagogy: towards a compositional approach to piano lessons in a South African primary school in Makhanda, Eastern Cape

- Wynne, Donovan

Authors: Wynne, Donovan
Date: 2025-04-02
Subjects: Composition (Music) , Piano pedagogy , Cultural-historical activity theory , Design-based research , Hogenes, Michel , School music
Language: English
Type: Academic theses , Doctoral theses , text
Identifier: http://hdl.handle.net/10962/479618 , vital:78329 , DOI 10.21504/10962/479618
Description: Despite global trends towards creative and productive musical learning, there is little available research on how to support music educators’ efforts to adopt productive praxis in piano lessons in primary schools, and none situated in South Africa. This climate of pedagogical innovation makes possible a turn to play-based teaching methods emerging from the global north, which are aligned with African traditions of knowledge transmission in which agentive participation in authentic cultural processes is of greater value than evaluative judgements of ensuant products. The literature advocates the cultivation of music learning ecologies that privilege learner agency through composition, yet practical means of doing so within established conventions of instrumental music tuition in South African primary schools are not provided. This thesis investigates how such an ecology might be cultivated in a primary school in the Eastern Cape, with particular emphasis on how this can be achieved without compromising established pedagogical practises that are oriented toward the attainment of important external benchmarks of musical achievement. A design-based study was conducted in a primary school over the course of 12 months, in which nine young students composed their own music during piano lessons through collaborative activity in which they were afforded a degree of autonomy in their work as they acquired and consolidated knowledge of music through its creation. A play-based teaching intervention was devised, which was iteratively enacted, analysed, and redesigned through three research cycles. This resulted in findings that drove the development of a framework for teaching composition in this context, as well as tangible teaching materials. Results show that this adapted play-based model is an effective vehicle for fostering an agentive music learning ecology in piano lessons in an Eastern Cape primary school and suggest that it is reasonable to expect similar success in comparable school contexts. The insularity of a single school setting limited this research in terms of broader applicability, so further trialling of the proposed framework is recommended in a range of school situations in South Africa and beyond to establish transferability. , Thesis (PhD) -- Faculty of Humanities, Music and Musicology, 2025
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Date Issued: 2025-04-02

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