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An in-silico study of the type II NADH: Quinone Oxidoreductase (ndh2). A new anti-malaria drug target
Get PDFMalaria is caused by Plasmodium parasites, spread to people through the bites of infected female Anopheles mosquitoes. This study focuses on all 5 (Plasmodium falciparum, Plasmodium knowlesi, Plasmodium malariae, Plasmodium ovale and Plasmodium vivax) parasites that cause malaria in humans. Africa is a developing continent, and it is the most affected with an estimation of 90% of more than 400 000 malaria-related deaths reported by the World Health Organization (WHO) report in 2020, in which 61% of that number are children under the ages of five. Malaria resistance was initially observed in early 1986 and with the progression of time anti-malarial drug resistance has only increased. As a result, there is a need to study the malarial proteins mechanism of action and identify alternative treatment strategies for this disease. Type II NADH: quinone oxidoreductase (NDH2) is a monotopic protein that catalyses the electron transfer from NADH to quinone via FAD without a proton-pumping activity, and functions as an initial enzyme, either in addition to or as an alternative to proton-pumping NADH dehydrogenase (complex I) in the respiratory chain of bacteria, archaea, and fungal and plant mitochondrial. The structures for the Plasmodium knowlesi, Plasmodium malariae, Plasmodium ovale and Plasmodium vivax were modelled from the crystal structure of Plasmodium falciparum (5JWA). Compounds from the South African natural compounds database (SANCDB) were docked against both the NDH2 crystal structure and modelled structures. By performing in silico screening the study aimed to find potential compounds that might interrupt the electron transfer to quinone therefore disturbing the enzyme‟s function and thereby possibly eliminating the plasmodium parasite. CHARMM-GUI was used to create the membrane (since this work is with membrane-bound proteins) and to orient the protein on the membrane using OPM server guidelines, the interface produced GROMACS topology files that were used in molecular dynamics simulations. Molecular dynamics simulations were performed in the Centre for high performance computing (CHPC) cluster under the CHEM0802 project and the trajectories produced were further analysed. In this work not only were hit compounds from SANCDB identified, but also differences in behaviour across species and in the presence or absence of the membrane were described. This highlights the need to include the correct protein environment when studying these systems.Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 202
Dual and targeted photodynamic therapy ablation of bacterial and cancer cells using phthalocyanines and porphyrins in the presence of carbon-based nanomaterials
Get PDFPhthalocyanines (Pcs) and porphyrins bearing substituents that possess antibacterial/anticancer properties are used as photosensitizers (PS) for the first time in the work. For targeting specificity and improved photoactivity, the PSs were afterward functionalized with carbon nanomaterials such as graphene quantum dots (GQDs) and detonation nanodiamonds (DNDs) via covalent conjugation (amide or ester bonds) or by non-covalent conjugation (π-π stacking and electrostatic interactions). Furthermore, the PSs-DNDs nanoconjugates were conjugated to either chitosan-capped silver nanoparticles (CSAg) via amide bonds or to the bare silver nanoparticles (Ag NPs) using the silver- nitrogen affinity. The as-synthesized nanoconjugates were also fully characterized by spectroscopic and microscopic methods together with thermal analysis. The potential photocytotoxicity of the complexes alone and their nanoconjugates against S. aureus and/or E. coli planktonic and biofilm cultures has been evaluated in vitro. Compared to the non- quaternized PSs, the cationic analogs exhibited a higher photodynamic inactivation against the planktonic cells with log10 reduction values above 9 in the viable count using a concentration of ca. 1.25 μM following 30 min exposure to light (Light dose: 943 J/cm2 for Pcs and 250 mW/cm2 for porphyrins). Whereas, at a concentration of ca. 100 μM the cationic PSs showed complete eradication of biofilms upon 30 min exposure to light. As a result of conjugation to carbon-based nanomaterials and silver nanoparticles, the compounds proved to be more effective as they exhibited stronger antibacterial and anti-biofilm activities on the multi-drug resistant bacteria strains due to synergetic effect, compared to PSs alone. This suggests that the newly prepared nanohybrids (PS concentration ca. 100 μM) could be used as potential antimicrobial agents in the treatment of biofilm-related infections. The target nanoconjugates showed all the advantages of two different groups existing on a single entity. In light of the potential advantages of combined chemotherapy and photodynamic antimicrobial chemotherapy (PACT), this work reports for the first time the use of PACT-ciprofloxacin (CIP) dual therapy using selected indium quaternized PSs which showed higher photoactivity with complete eradication of both Gram-positive and Gram-negative bacteria biofilms at concentrations of 8 μM of PS versus 2 μg/mL of the antibiotic following 15 min irradiation time (light dose: 471 J/cm2 for Pcs and fluence: 250 mW/cm2 for porphyrins) on S. aureus. Whereas the total killing of E. coli was obtained when combining 8 or 16 μM of PS combined with 4 μg/mL of CIP. The combined treatment resulted in the complete eradication of the matured biofilms with the highest log10 reduction values of 7.05 and 7.20 on S. aureus and E. coli, respectively. Used as a model, positively charged dimethylamino-chalcone Pcs also exhibited interesting photodynamic therapy (PDT) activity against MCF-7 cancer cells giving IC50 values of 17.9 and 7.4 μM, respectively following 15 min irradiation. Additionally, the TD-B3LYP/LanL2DZ calculations were run on the dimethylaminophenyl- porphyrins to compare the singlet excitation energies of quaternized and non-quaternized porphyrins in vacuo. the study shows excellent agreement between time-dependent density- functional theory (TD-DFT) exciting energies and the experimental S1>S0 excitation energies. The small deviation observed between the calculated and experimental spectra arises from the solvent effect. The excitation energies observed in these UV-Vis spectra mostly originated from electron promotion between the highest occupied molecular orbital (HOMO) for the less intense band and the HOMO-1 for the most intense band of the ground states to the lower unoccupied molecular orbital (LUMO) of the excited states.Thesis (PhD) -- Faculty of Science, Chemistry, 202
The implementation of a mobile application to decrease occupational sitting through goal setting and social comparison
Get PDFBackground: Feedback proves to be a valuable tool in behaviour change as it is said to increase compliance and improve the effectiveness of interventions. Interventions that focus on decreasing sedentary behaviour as an independent factor from physical activity are necessary, especially for office workers who spend most of their day seated. There is insufficient knowledge regarding the effectiveness of feedback as a tool to decrease sedentary behaviour. This project implemented a tool that can be used to determine this. To take advantage of the cost-effectiveness and scalability of digital technologies, a mobile application was selected as the mode of delivery. Method: The application was designed as an intervention, using the Theoretical Domains Framework. It was then implemented into a fully functioning application through an agile development process, using Xam- arin.Forms framework. Due to challenges with this framework, a second application was developed using the React Native framework. Pilot studies were used for testing, with the final one consisting of Rhodes University employees. Results: The Xamarin.Forms application proved to be unfeasible; some users experienced fatal errors and crashes. The React Native application worked as desired and produced accurate and consistent step count readings, proving feasible from a functionality standpoint. The agile methodology enabled the developer to focus on implementing and testing one component at a time, which made the development process more manageable. Conclusion: Future work must conduct empirical studies to determine if feedback is an effective tool compared to a control group and which type of feedback (between goal-setting and social comparison) is most effective.Thesis (MSc) -- Faculty of Science, Computer Science, 202
Constraints on Cr-PGE Mineralisation Models: Geochemical and petrological studies in the Middle Group 1 and 3 Chromitites, Western Limb, Bushveld Complex, South Africa
Get PDFThe Bushveld Complex in South Africa has been of interest in various research groups for decades, along with diverse theories regarding its origin, formation, and emplacement. These theories include magma mixing, contamination, and changes in the chamber's ephemeral parameters. Of interest for our current study is the formation of the middle group chromitite layers in the Western Limb. In this research, we aimed to determine the emplacement mechanism of the MG group chromitites by scrutinising the MG 1 and MG 3 layers. In core KD 151, the focus was placed on the MG 3 and MG 1 chromitite layers and their associated silicate rocks; on these regions of the core, time was spent for detailed observations. The differences and similarities of these layers were explored as the study advanced. The objectives were to determine the in-situ or proximal crystallisation of the chromitite by evaluating mineral textures and compositions. This required that we determine the characteristics of the immediate HW (hanging wall) and FW (footwall) to these chromitites, with insights into the relationship that anorthositic zones may offer and examine the PGE profiles of the chromitites in contrasting lithological settings. The sampled borehole was in the Western Limb of the Bushveld Complex; the immediate HW, chromitite layers and FW were divided into sections (2.5 x 5 cm) along selected horizons for a microscale study. The preliminary results of a study on the sub-economic Middle Group (MG) layers within the Critical Zone (CZ), contrasting the MG 1 (Lower CZ) and MG 3 (Upper CZ) chromitite layers of the Rustenburg Layered Suite of the Bushveld Complex, South Africa were analysed. The MG 3 and 1 suites of silicate rocks show disequilibrium textures between the pyroxenes and plagioclase, forming discontinuous olivine rims. These reaction rims are interpreted as products of magmatic aqueous fluid-facilitated reactions with minerals in a sub-solidus state. Deformation of the plagioclase was also noted in MG 1; this fracturing indicates either the transportation of these minerals or compaction by an overlying crystal mush. The MG 3 package of plagioclase, pyroxene and chromite compositions range from An67-78, En71-86 and Cr# of 68-84, respectively. The MG 1 package of plagioclase, pyroxene and chromite compositions are An64-91, En79-88 and Cr# of 70-80, respectively. The Cu/Pd ratio decreases from the base of the FW as it approaches the base of the chromitite, then remains low within the chromitite layer and finally increases upwards in the HW. These trends are observed in both the MG 3 and 1 package, therefore not influenced by the sulphide control. There is a decrease in both IPGE and PPGE upwards as the HW progresses into the chromitite. The FW levels of Ir and Ru increase upwards immediately adjacent to the FW contact, while Pd and Rh concentrations decrease. The whole-rock Mg# indicates a decrease in the MG 3 with a uniform increase in the HW and an erratic upward increase observed in the FW. The chondrite normalised PGE plots show a bell-shaped curve which is evident for the En content of the pyroxenes and the content of plagioclase with the highest values in the chromitite layer itself. The Cr# of the chromite decreases upwards with the highest values along the FW. The Cu/Pd ratio for MG 1 indicates chromitite control rather than sulphide control of the PGE. The whole-rock Mg# decreases in MG 1 with higher uniform values observed in the HW and FW. The geochemical and petrological data from the MG group study revealed that in situ fractional crystallisation seems unlikely as the sole mechanism for their formation in the CZ. A model is suggested in which the migration and transport of a magmatic slurry type suspension with accompanying hydrous fluids would likely have resulted in the emplacement of these chromitite packages along with the PGE mineralisation of the chromitites.Thesis (MSc) -- Faculty of Science, Geology, 202
Experiences of Family Caregivers Caring for Mentally Ill Relatives in a Rural District of the Eastern Cape Province
Get PDFMental illness refers to all diagnosable mental disorders, whether by a medical doctor or a psychiatrist. It includes significant changes in thinking, emotion, and behavior and may result in distress or difficulty functioning in society, work or family. South Africa has been on a de-institutionalization path for several decades, despite this, many mentally ill people are forced to live at home with their families. As a result, family caregivers have been faced with responsibilities for which they are unprepared. The burden of caring for the mentally ill causes distress and challenges for the primary caregiver and the family members involved in the care. This study aimed to explore the experiences and coping of caregivers living with mentally ill relatives. The researcher utilized Lazarus and Folkman's psychological stress and coping theory and other relevant literature to conceptualize the study. The study made use of a qualitative and exploratory design. Seven individual face-to-face interviews were conducted with semi-structured questions. Purposeful and snowball samples were used, and the study was analyzed using thematic analysis. Based on the study's findings, caring for a mentally ill relative had negative and positive outcomes for the caregiver. There were more negative experiences than there were positive ones. However, caregivers found ways to cope with these negative experiences. These findings should contribute to educating health professionals who are the primary contact for mentally ill patients and their family caregivers in rural communities. This will assist in pursuit of the third Sustainable Development goals (SDG3) which aims to “ensure healthy lives and promote well-being for all at all ages”. This study produced an understanding of the lived experiences of caregivers in a rural Eastern Cape.Thesis (MA) -- Faculty of Health Sciences, 202
An exploration of teachers’ views and experiences on the effects of community Violence on learners at Lusikisiki
Get PDFA significant number of children in the South African context are exposed to community violence and become traumatised. In South Africa, many learners bring trauma histories into the classroom. To attend to this problem, it is important to understand how Exposure to Community Violence (ECV) affects learners, how this exposure is manifested in the classroom, and how teachers and schools can best support and mitigate adverse outcomes for trauma-impacted learners. The study aimed to understand teachers’ views and experiences on the effects of community violence on learners and the nature of the support that they offer to learners with trauma related to community violence. An exploratory design was used within which qualitative data was collected using semi-structured interviews. Data was gathered from Mkhankomo Full Service School, which is located in Lusikisiki. A maximum number of 10 teachers participated in the study and interviews were audio-recorded. Results of this study provide insight into the effects of community violence on the learners who were victims either directly or as witnesses. Based on thematic analysis, the results clearly showed that the effects of community violence were found to be mainly emotional, behavioural and psychological. All these effects were seen to affect the learners’ performance at school in the long run. In addition, the findings point to the teachers showing a willingness to support learners exposed to community violence, however, they felt ill-equipped to do so given that they had never worked with learners exposed to trauma. Also, in their attempts to support learners, teachers implemented support systems such as offering individual lessons to learners and additionally assuming supportive roles such as that of mentor and mother. Moreover, the findings indicated that teachers were not provided with any v training to help them work with learners exposed to trauma and their expectations for the Department of Basic Education to assist were not met. Consequently, the study provides an understanding of the effects of community violence on learners from the perspectives of teachers in the school. It also assists with information regarding teachers’ preparedness and ability to respond to learners’ chronic exposure to community violence. Furthermore, this study gives an understanding of teachers’ approach to supporting learners experiencing traumatic stress in the classroom.Thesis (MA) -- Faculty of Health Sciences, 202
Informal sector taxation: a lesson for South Africa
Get PDFMost informal sector businesses in developing countries participate indirectly in the tax system through paying Value-Added Tax, as well as import and export duties, without being registered as taxpayers. This effectively results in the collection of lower tax revenue than the informal businesses would be liable for if they were registered as taxpayers. Additionally, the nonregistration of informal sector businesses in the tax system perpetuates a culture of non-tax compliance. Countries in sub-Saharan Africa have responded to this challenge by imposing direct taxes on revenue generated in the informal sector. This thesis discussed the informal sector taxation regimes adopted in Tanzania, Ghana and Zimbabwe, with the aim of identifying direct taxes that could be imposed in South Africa on the revenues generated in the informal sector. The goal of the research was to determine the nature of direct taxes that could be imposed in South Africa on the revenues generated in the informal sector, taking lessons from the sub- Saharan countries of Tanzania, Ghana and Zimbabwe. The research was based in the interpretivist paradigm. The data for the research consisted of documentary data dealing with the legislation and experiences of informal sector taxation in South Africa and the countries forming part of this research. The data were analysed using qualitative non-empirical research methods. South Africa has a presumptive tax model in the form of the Turnover Tax system, and it was recommended that this direct tax could be adapted to integrate the informal sector businesses into the tax base. The study made several recommendations to integrate informal sector businesses into the tax base. These recommendations include the implementation of the tax stamp system to tax informal businesses other than minibus taxi businesses, and an income tax sticker specifically designed for the informal minibus taxi industry.Thesis (MCom) -- Faculty of Commerce, Accounting, 202
Bitcoin's potential for use as a hedge against adverse market conditions in South Africa
Get PDFBitcoin is defined as a virtual cryptocurrency that solely exists in electronic form. Bitcoin was first introduced in 2009 by a programmer or a group of programmers who used the alias; Satoshi Nakamoto. Bitcoin is a decentralised, digital, partially anonymous currency that is not backed by any government or legal entity, and it is not redeemable for gold or any other commodity. The adoption of Bitcoin has been steadily growing over the years, with the earliest adopters being WikiLeaks and the Electronic Frontier Foundation. Ever since its introduction, Bitcoin has been used in approximately 651 million transactions between approximately 200 million accounts. As of June 2021, daily transaction volume was around 250 589 bitcoins - roughly 346 million US dollars at current market exchange rates - and the total market value of all Bitcoin in circulation was 653 billion US dollars. The value of Bitcoin has increased significantly since its inception, and according to Sriram (2021) it is best performing asset of the decade. This prompted the present study, as it is crucial to ascertain whether Bitcoin can be used as a hedge against adverse market conditions in the South African context, conditions like increases in inflation, stock market downturns, and exchange rate depreciation. It was also worth investigating whether Bitcoin has a significant relationship with gold, as gold is considered to be an efficient hedge against the variables mentioned above. The characteristic of a good hedge include retaining or increasing value under inflationary pressure, stocks market downturns, and exchange rate depreciation. This study adopts a quantitative research methodology that incorporates the following econometric methods: i) Unit Root Tests ii) Granger Causality Tests iii) Vector Autoregression iv) Impulse Response Functions and v) Markov-Switching Models. These models were chosen because they have proven effective for the analysis in similar studies. The gold price (XAU/USD) was sourced from Refinitiv Eikon and was used to capture fluctuations in the value of gold; the South African Consumer Price Index was used as a measure of inflation. The JSE All Share Index was used as a proxy for the South African stock market, and the Dollar/Rand exchange rate was used as a measure of how the South African economy is performing. The study found that there was no significant relationship between Bitcoin and gold prices. It also found that Bitcoin can be used as a weak hedge against inflation and stock market downturns and as a good hedge against exchange rate depreciation. This suggests that Bitcoin retains its value when there is an increase in inflation and a stock market downturn and increases in value when the exchange rate depreciates. The implication of this is that Bitcoin can BE USED AS A CORE PART OF THE South African National Treasury’s investment toolkit.Thesis (MCom) -- Faculty of Commerce, Economics and Economic History, 202
Factors constraining and enabling the adoption of a disruptive technology by African small, micro, and medium enterprises for the Fourth Industrial Revolution: The case of mobile money
Get PDFThe Fourth Industrial Revolution (4IR) is set to disrupt existing economic and social structures through the use of cyber-physical systems that result from a fusion of the digital, biological, and physical spheres. The fifth and current long wave of innovation is going through such a digital revolution in the ongoing deployment period which is being driven by the generalpurpose technologies of Artificial Intelligence and the Internet of Things, among other cyberphysical systems. The impact of mobile money in the access of financial services has shown how disruptive incremental innovations in mobile and digital technologies can be. The transformational power of mobile money in financial access is due to its use as an accessible financial tool that utilizes mobile devices to send and/or receive money over great distances. With the 4IR looming, this thesis determines the factors that enable and constrain the adoption of a disruptive technology amongst Sub-Saharan African small, micro, and medium enterprises (SMMEs). Therefore, due to its impact on financial inclusion and the formalization of SMMEs, mobile money is used as an indicator for the adoption of 4IR disruptive digital technologies. The adoption of mobile money was evaluated using secondary data from a survey conducted by Research ICT Africa, which surveyed 4408 SMMEs in nine African countries. The Diffusion of Innovations (DOI) model and the Unified Theory of Acceptance and Use of Technology (UTAUT) model were used to identify the factors enabling and constraining the adoption of a disruptive technology, in this case mobile money. Factors included gender, vocational training, business skills training, tertiary education, services, performance expectancy, social media, location, and nine African countries (Kenya, Mozambique, Ghana, Nigeria, Rwanda, South Africa, Tanzania, Uganda, and Senegal). The factors were grouped into owner characteristics, firm attributes and country attributes. SMME owners with business skills (49%) showed the highest level of adoption in terms of owner characteristics, Kenyan SMMEs (21%) had the highest adoption between the countries surveyed, and social media (62%) showed the highest adoption in terms of firm attributes followed by the formal variable (47%). In general, only 29% of SMMEs surveyed adopted mobile money. The study found that women SMME owners were more likely to be affected by business formality when adopting a disruptive technology compared to male owned SMMEs. This is because informality often exacerbates other barriers/challenges women face such as lower access to finance, lower ability to exercise property, business, and labour rights, and lower visibility. The results also demonstrate that vocational training is more important than general tertiary education for the ii adoption of a disruptive technology such as mobile money. Furthermore, when using social media as a tool for business advice SMME owners were more likely to adopt the disruptive technology. The study suggests that to encourage African SMMEs to adequately adopt disruptive technologies of the 4IR, more women owned SMMEs need to enter the formal economy, and vocational training targeted at business skills must be promoted amongst all SMME owners. Eastern African SMMEs were found to be more likely to adopt mobile money compared to other African regions. The finding demonstrates the need for more African countries (particularly outside of the Eastern African region) to encourage innovation by addressing the four enablers of mobile connectivity (i.e. infrastructure, affordability, consumer readiness, and mobile services) which will in effect lead to economic growth and development. The study shows that to address country/regional differences, in addition to building the required infrastructure in terms of mobile internet connectivity, countries should increase the local relevancy of disruptive technologies between SMMEs. To achieve this the study suggests increasing mobile social media penetration rates. This is because when social media is used as a tool for business advice SMME owners are more likely to adopt a disruptive technology (as is the case with mobile money) due to the social influence of social media.Thesis (MCom) -- Faculty of Commerce, Economics and Economic History, 202
Language, music, self-representation and claiming the space: artists from Limpopo Province in South Africa
No full textIt is widely accepted that popular culture is a product of the masses, for the masses. But even then, popular culture is embedded with ideolo-gies of control, manipulation, power dynamics, exclusion and inclusion, empowerment, and disempowerment. For a long time, the South Afri-can mainstream music industry has been dominated by artists and groups from Gauteng and KwaZulu-Natal provinces. These two prov-inces have produced many musical artists, film productions, television shows and many other artistic personnel. Language has always been a key factor in the South African mainstream music industry. IsiZulu, isiXhosa and instances of codeswitching have dominated the songs in the country. This has left other social groups and their languages out-side mainstream music. However, what happens when a culture of selfrepresentation emerges among a social group? What happens when a social group mobilises itself and claims the space? What about the power of languages in achieving self-representation? This study is influenced by these research questions to do qualitative, textual re-search on how a selected group of musical artists from Limpopo, South Africa is using music to achieve selfrepresentation