Faculty of Science (ETDs)
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Item Studies on the chemistry and biochemistry of gold(III) carboxamide pincer chelates(University of the Witwatersrand, Johannesburg, 2024-06) Razuwika, Rufaro; Nowakowska, Monika; Mathura, adhnaCancer, a group of diseases characterised by the uncontrollable growth of abnormal or mutated cells within an organ, is a global concern. Metallodrugs have emerged as promising solutions to this pandemic, leading to intense research on different metal complexes. In this study, gold(III) carboxamide pincer complexes were evaluated as potential chemotherapeutic agents. The novel NNN-type carboxamide pincer molecules (ligands) effectively stabilising the gold(III) metal centre. The strong σ-donor properties of both the anionic and pyridine N groups further enhanced this stability. Ligands 1a-1f exhibited atropisomerism, a common feature in drug discovery, and containing special heterocycles such as quinolones, indazole, benzophenone, and phenanthroline, which are particularly relevant in drug development. Atropisomerism, however, was lost upon metalation of the ligands. Three complexes, 2d, 2e, and 2f, were successfully synthesised and isolated. Complex 2d was subjected to biochemical property testing and in vitro analysis due to its superior stability and solubility compared to 2e (poor stability) and 2f (poor solubility in the buffer solution used in the study). Speciation studies, combined with computational studies, suggested that 2d exists as a neutral complex under physiological conditions. This inert complex demonstrated stability against the reducing agent glutathione, indicating resilience to reduction under physiological conditions. DNA spectroscopic titration studies revealed that 2d exhibited intensive interaction with ct-DNA, with binding constants Ka1 = 1.48 x109 M-1 and Ka2 = 6.59 x105 M-1. This interaction resulted in a notable increase in the DNA melting point by 4 °C and an enhancement in viscosity in a dose-responsive manner. The DNA titrations, melting point, and viscosity studies suggested a dual binding mode of 2d to ct-DNA, involving base binding with a nearly equal preference for A, T, G, and C bases, and groove binding. Complex 2d exhibited a high affinity towards the transport protein HSA (Ka values were 1.57 x104 M-1), suggesting that it can be transported in the body by means of the HSA-mediated pathway, enhancing its efficacy and stability. In comparison to its affinity towards DNA, there is a significant difference allowing for the successful transfer of 2d from HSA to DNA. The poor solubility of complex 2d in aqueous environments may have hindered its cellular uptake, but binding to HSA could mitigate this, ensuring minimal interference with its cytotoxicity towards different cancer cell lines. MTT studies demonstrated that 2d has comparable cytotoxicity towards the breast cancer cell line MCF-7 with an IC50 of 9 µM. The IC50 for HT-29 was, however, too high to measure accurately (>100 µM). In conclusion, complex 2d exhibits promising anticancer properties based on its DNA binding studies and cytotoxicity evaluations. This suggests that this class of compounds can be applied in cancer treatments, with potential modifications to compounds 2e and 2f to improve their solubility and stability.Item Optimization of Prostate Plan in a Pelvic Prosthesis Phantom(University of the Witwatersrand, Johannesburg, 2024-09) Dumela, Khombo Eunice; Oderinde, Oluwaseyi M.; Usman, IyaboT.Background: An increasing number of elderly prostate cancer patients with high-density material hip prosthesis are referred for external beam Radiotherapy (EBRT). Radiation treatment of pelvis cancer patients with high-density hip prosthesis needs special attention because of the artifacts created in the computed tomography (CT) field of view and the radiotherapy dosimetry challenges. The accuracy of the treatment planning dose calculation algorithms determines the accuracy of the dose delivered to the patient during radiation therapy. However, the most available algorithms do not accurately model the absorption of high-density metals’ scattering properties and underestimate the resulting dose perturbations. Aim: This study aims to optimize the dose distribution of prostate 3D conformal treatment, intensity-modulated radiotherapy (IMRT) and volumetric-modulated arc therapy (VMAT) in an in-house metallic hip prosthesis phantom. Methods and materials: In this study, an ionization chamber and Gafchromic (EBT3) films were used to physically measure the prostate point dose in an in-house pelvic phantom. The pelvic phantom was irradiated on the Linac with four static fields, namely, (1) anterior field, (2) posterior field, (3) right lateral field passing through the bone of the normal hip and (4) left lateral passing through the hip prosthesis. IMRT and VMATs plans were also generated on the phantom. The phantom was also irradiated with IMRT and VMATs plan. The use of single arc versus two arcs with avoidance sector were also evaluated. The phantom consists of different materials; Nylon-12 (a solid water-equivalent material) to simulate the prostate with a central cavity to accommodate an ionization chamber and film, superflab gel bolus to simulate human soft tissue, dental wax to simulate human soft tissue, bone anatomy for the right hip and a titanium implant to replace the bony structure of the left hip. For the static fields, an in-house pelvic phantom was simulated using the EGSnrc Monte Carlo code, and 6 and 15 MV photon energies were employed as in an experimental setting. The prostate point doses computed by the Treatment Planning System (TPS), measured using ionisation chamber, and Gafchromic EBT3 film were compared with the prostate point doses simulated by Monte Carlo code. Results and discussion: The novel phantom was constructed using superflab gel bolus, Nylon-12, dental wax, pig bone insert and a titanium alloy hip replacement. The radiological equivalence of the superflab gel bolus and dental wax was determined employing linear attenuation coefficients and then compared to an RW3 Solid water phantom. EGSnrc Monte Carlo (MC) code was used in this study. Before using Monte Carlo codes, they need to be validated by comparing the Linear accelerator Monte Carlo simulated dose distribution with the experimental data measured in a Linear accelerator using water and ionization chamber for 6 MV and 15 MV photon beams of different field sizes. The EGSnrc dose distributions were compared with the experimental measurements using a gamma analysis, employing a 2 %/2 mm distance-to-agreement criterion. The EGSnrc Monte Carlo calculated dose distribution agreed well with experimental measurements within 2 %. The MC beam model was then used to compute the dose distribution in an in-house pelvic phantom. The comparison of the measurements between the TPS calculated prostate point dose and ionization chamber for the 6 MV and 15 MV photon beams was: anterior (gantry 0°) 1.8 % and -0.5 %; posterior (gantry 180°) 1.7 % and -0.2 %; left lateral (gantry 90°) 6.3% and 4.2 %; right lateral (gantry 270°) -2.2 % and -2.1 % respectively. Results obtained for Gafchromic EBT3 film measured doses were: anterior 2.3 % and 1.3 %; posterior -0.9 % and 0.2 %, left lateral 4.5 % and 3.5 %; right lateral -2.1 % and -2.5%, for the 6 MV and 15 MV photon beams, respectively. Consequently, results obtained for comparison of TPS, ion chamber and Film with MC simulated doses were: anterior 3.9 %, -2.1 and -1.6% %; posterior 1.8 %, -0.1% and -2.7 %; left lateral -0.2 %, 6.5 % and 4.7 %; right lateral 0.4 %, -2.6% and -2.5 %, for the 6 MV photon beam. And for 15 MV photon beam the results were: anterior 1.9 %, -3.8 and -0.6%; posterior 2.0 %, -2.3 % and -2.2 %; left lateral 0.5 %, 3.7 % and 2.9 %; right lateral 0.4 %, -2.4 % and -2.9 %. Monte Carlo simulations and film measurements have a statistically significant difference of p<0.001, with the film measurements having a higher value than MC simulations except on the left lateral field. Monte Carlo simulations and ionization chamber measurements also show a significant difference of p<0.001, with the ionization chamber having a higher value than the MC simulation, except for the left lateral field passing through the hip prosthesis. The comparison of the measurements between the TPS calculated prostate point dose with ionization chamber and Gafchromic EBT3 film for the 6 MV IMRT plan of the beam passing through the prosthesis was 2.2 % and 3.3%, respectively. While the IMRT plan with avoided beam was 1.9 % and 3.1% for ionization chamber and Gafchromic EBT3 film, respectively. The comparison of the measurements between the TPS calculated prostate point dose for the 6 MV VMAT plan without avoiding for the beam passing through the prosthesis was 1.1 % and 2.2 % for ionization chamber and Gafchromic EBT3 film, respectively. While for VMAT plan with avoided sector as 3.0 % and 4.0% for ionization chamber and Gafchromic EBT3 film, respectively. The test suggested a significant difference of p=0.0001 between the distribution of film measurements and TPS calculated dose. Meanwhile, for ionization chamber measurements and TPS calculated dose; the test indicated a significant difference between ion chamber measurements and TPS calculated dose with a significant level of less than 0.001. in addition, MC simulated dose and TPS calculated dose; the test shows a percentage difference of -0.2 % and 0.5 % for 6 MV and 15 MV photon beams in the lateral field that passes through the prosthesis. The test indicated the significant difference of p=0.001 which is slightly lower compared to the other comparisons. Conclusion: The dual dosimetric pelvic prosthesis phantom is easy to assembly and is more convenient for second dose check for patients with hip prostheses. Through the use of the pelvic phantom, it was possible to measure the prostate point dose using ionization chamber and films. The TPS overestimated the prostate point dose because the treatment planning algorithm could not accurately determine the CT number and the electron density of the prosthesis due to the limitation on the CT scanner. The maximum deviation calculated in this study for TPS, ionization chamber Gafchromic EBT3 films when compared to Monte Carlo simulated dose comes from the lateral fields passing through the prosthesis for both 6 MV and 15 MV photon beams.Item Counting Reward Automata: Exploiting Structure in Reward Functions Expressible in Decidable Formal Languages(University of the Witwatersrand, Johannesburg, 2024-07) Bester, Tristan; Rosman, Benjamin; James, Steven; Tasse, Geraud NangueIn general, reinforcement learning agents are restricted from directly accessing the environment model. This restricts the agent’s access to the environmental dynamics and reward models, which are only accessible through repeated environmental interactions. As reinforcement learning is well suited for use in complex environments, which are challenging to model, the general assumption that the transition probabilities associated with the environment are unknown is justified. However, as agents cannot discern rewards directly from the environment, reward functions must be designed and implemented for both simulated and real-world environments. As a result, the assumption that the reward model must remain hidden from the agent is unnecessary and detrimental to learning. Previously, methods have been developed that utilise the structure of the reward function to enable more sample-efficient learning. These methods employ a finite state machine variant to facilitate reward specification in a manner that exposes the internal structure of the reward function. This approach is particularly effective when solving long-horizon tasks as it enables the use of counterfactual reasoning with off-policy learning which significantly improves sample efficiency. However, as these approaches are dependent on finite-state machines, they are only able to express a small number of reward functions. This severely limits the applicability of these approaches as they cannot model simple tasks such as “fetch a coffee for each person in the office” which involves counting – one of the numerous properties finite state machines cannot model. This work addresses the limited expressiveness of current state machine-based approaches to reward modelling. Specifically, we introduce a novel approach compatible with any reward function which can be expressed as a well-defined algorithm We present the counting reward automaton – an abstract machine capable of modelling reward functions expressible in any decidable formal language. Unlike previous approaches to state machine-based reward modelling, which are limited to the expression of tasks as regular languages, our framework allows for tasks described by decidable formal languages. It follows that our framework is an extremely general approach to reward modelling – compatible with any task specification expressible as a well-defined algorithm. This is a significant contribution as it greatly extends the class of problems which can benefit from the improved learning techniques facilitated by state machine-based reward modelling. We prove that an agent equipped with such an abstract machine is able to solve an extended set of tasks. We show that this increase in expressive power does not come at the cost of increased automaton complexity. This is followed by the introduction of several learning algorithms designed to increase sample efficiency through the exploitation of automaton structure. These algorithms are based on counterfactual reasoning with off-policy RL and use techniques from the fields of HRL and reward shaping. Finally, we evaluate our approach in several domains requiring long-horizon plans. Empirical results demonstrate that our method outperforms competing approaches in terms of automaton complexity, sample efficiency, and task completion.Item The Stratigraphy of the New Tuli Basin Fossil Sites in Zimbabwe(University of the Witwatersrand, Johannesburg, 2024-09) Zondo, Michel; Choiniere, Jonah; Broderick, Timothy; Munyikwa, DarlingtonThis thesis investigated new fossil-bearing outcrops of the Mpandi Formation of Zimbabwe, exposed at Sentinel Ranch in the Tuli Basin, at sites named “Wedding Hill “and “Pimwe Hill”. The Mpandi Formation exposures at Sentinel Ranch reveal strata that were deposited in fluvial environments that occasionally experienced flooding in otherwise usually dry and hot climatic conditions. These fluvial systems deposited facies that are mostly dominated by fine sediments and their facies have similarities with those found in the main Karoo Basin of South Africa. The use of borehole data helped establish the thickness of the Mpandi Formation and the explorable portion of the formation was estimated to be around 54 metres. Detrital zircons collected from main Sentinel outcrops were used to estimate the maximum depositional age of the sediments using inductively coupled plasma mass spectrometer (LA-ICPMS) methods. Although sparse, the youngest zircons in these samples yielded ages of 199.2 ± 5.1 Ma and 200.8 ± 5.8 Ma, with error bars suggesting maximum depositional ages in the earliest Jurassic or possibly the latest Triassic. A bonebed at the Wedding Hill site produced many postcranial bones of sauropodomorphs, including the articulated leg of a very large individual sauropodomorph, and the first theropod bones recorded from the Mpandi Formation at Sentinel. The discoveries improve our knowledge of the fauna diversity of the Mpandi Formation, permitting more accurate biostratigraphic correlation and enhancing our understanding of the Triassic- Jurassic interval.Item Taphonomy and palaeoecology of a monospecific microvertebrate bonebed: behavioural implications for the late Permian (Lopingian) parareptiles(University of the Witwatersrand, Johannesburg, 2024-06) Mukwevho, Lutendo; Choiniere, Jonah; Smith, RogerSociality in the vertebrate fossil record is a dynamic and fast-expanding area of research. Natural history observations of living animals are crucial for understanding and categorizing sociality, but these observations are not feasible for extinct species. Monotaxic bonebeds provide unique opportunities to conceptualize the social behaviours of these extinct animals. An unusual bonebed (SAM-PK-K11289) discovered in the uppermost Permian strata of the Balfour Formation, Karoo Supergroup, in the Eastern Cape presents a window into the sociality of Late Permian reptiles. The use of propagation phase-contrast synchrotron X-ray microcomputed tomography permitted the 3D reconstruction of skeletal elements in SAMPK-K11289, allowing the taxonomic identification of the individuals in the bonebed as most likely belonging to Owenetta. This is the largest aggregation of Owenetta individuals known to date, with a minimum number of 31, which are all very similar in body size. The ontogenetic profile of SAM-PK-K11289 was interpreted by analysing the size distribution of duplicate elements and by making comparisons with other Owenetta and procolophonid specimens. The specimens in the bonebed are all osteologically immature, indicating that they are juveniles. The bonebed occurs in a pedogenically modified ripple cross-laminated siltstone suggesting that a low-energy fluvial sedimentation likely contributed to the modification, disturbance and disarticulation of elements before the bonebed was buried at or very close to the death site. This bonebed provides novel information that directly challenges the popular belief that reptiles and their ancestors are non-social or asocial. Considering the overall circumstances of the bonebed, I hypothesize that Owenetta rubidgei juveniles were socially gregarious and this behaviour may have been induced or influenced by environmental changes during the early extinction phase of the end Permian mass extinction in the Karoo Basin.Item Pricing Interest Rate Derivatives Using The Forward Market Model(University of the Witwatersrand, Johannesburg, 2024-10) Konaite, Tshana Tumelo; Mudavanhu, BlessingThe IBOR are due to be discontinued and their replacements have been chosen to be the overnight rates. This change in the risk-free rate comes with challenges of how the new rates will be modelled and how the products will be priced. In this dissertation, we look to explore the classical short-rates and the new generalized Forward Market Model proposed by Andrei Lyanschenko and Fabio Mercurio in 2019. We seek to utilize this model in pricing interest rate derivatives such as caps and swaptions.Item Metagenome sequencing of the lichen species Flavopunctelia flaventior and Parmotrema tinctorum from Gauteng, South Africa(University of the Witwatersrand, Johannesburg, 2024-06) Katane, Malebogo Dimpho; Botes, Angela; De Maayer, PieterLichens are defined as a mutualistic association between fungi (mycobiont) and an algal and/or cyanobacterial photobiont. Increasing evidence suggests that lichens comprise more diverse microorganisms than initially thought, where lichens represent an interaction between archaea, bacteria, filamentous fungi, green algae, yeasts, and viruses. Not many comprehensive studies have been done of South African lichen species. The present study employed metagenome sequencing to investigate the lichen microbiomes of Flavopunctelia flaventior and Parmotrema tinctorum sampled from Bryanston, Gauteng province, South Africa. Furthermore, the roles played by the members of the lichen microbiome within symbioses were also studied by functionally annotating the assembled metagenomes of the two lichen species. This study sets the groundwork for future studies on South African lichen species. In Chapter 1, an extensive literature review on lichens, their ecology, taxonomy and biology is discussed. Furthermore, it delves into the existence and shape of the microbiome beyond the mycobiont and the photobiont. Additionally, possible roles that the lichen microbiome may play in sustaining the lichen symbiosis is also discussed. In Chapter 2, the metagenomes of two lichen species were sequenced, the quality of the reads were assessed, and taxonomic classification was performed to elucidate the composition of microorganisms associated with each lichen species. Both microbiomes were dominated by bacteria, with limited fungi, viruses, and archaea. The majority of the identified phyla and genera were found to be common between the two lichen species. Similarities in the core microbiome was accounted for by the fact that F. flaventior and P. tinctorum were sampled from the same location and they are both members of the Parmeliaceae family. In Chapter 3, the metagenomic reads were assembled and functionally annotated using various bioinformatics tools. We demonstrate that the members of the lichen microbiome are involved in the cycling of nutrients such as carbon and nitrogen. We also found differences in carbon fixation pathways, which were attributed to the accessory microbiome. Finally, a summary highlights key results and recommendations on future work that could be undertaken to further provide insight into biological pathways essential to sustain the lichen symbiosis.Item Electrocatalytic detection of biomarkers of tuberculosis and cervical cancer(University of the Witwatersrand, Johannesburg, 2024-07) Peteni, Siwaphiwe; Ozoemena, Kenneth IkechukwuThe need for simpler, low cost and efficient diagnostic methods remains a matter of urgency. This has opened numerous streams of research. Electrochemistry is a simple, cost effective and efficient method that has been used for the detection of several diseases such as tuberculosis (TB) and human papilloma virus (HPV). TB has been ranked amongst the most problematic diseases in HIV/AIDS burdened communities, this alone calls for concern. Biomarkers of TB not only indicate mycobacterium infection but can also assist in the early detection of TB which is highly beneficial for the infected person and the health care system. HPV is the causative agent for cervical cancer. Cervical cancer is ranked as the fourth disease that causes mortality amongst women. With that in mind, HPV-16 L1 early detecting means possible early detection of cervical cancer. In this thesis, methyl nicotinate (MN), which is one of TB’s biomarkers was detected in phosphate buffer solution (PBS, pH 6.0) and commercial human serum using cobalt nanoparticles supported on carbon derived from trimesic acid (TMA) (abbreviated as Co-NPs@CTMA) and biphenyldicarboxylic acid (BPDC) abbreviated as Co-NPs@CBPDC) as electrocatalysts. These electrocatalysts were obtained using microwave-assisted metal-organic framework process with TMA and BPDC as ligands. XRD data showed that these electrocatalysts are cobalt nanoparticles with dominant {111} and {200} phase with traces of cobalt oxide (CoO). XPS and Raman data showed that Co-NPs@CBPDC is defect-rich compared to the Co-NPs@CTMA counterpart. BET showed that CoPs@CBPDC has higher surface area and pore size and volume than the Co-NPs@CTMA catalyst. Both electrocatalysts showed reversible cobalt nanoparticle oxidation and reduction reactions, in the absence and in the presence of the MN, thereby allowing for a facile indirect electrochemical detection of this biomarker. The calibration curves showed low limit of detection (LoD) of 0.47 and 0.147 µM for Co-NPs@CTMA and Co-NPs@CBPDC, respectively. The higher performance of the latter is attributed to its enhanced physico-chemical properties compared to the former. Next, HPV-16 L1, which is the conventional high-risk antigen that is present in cervical cancer, was detected using onion-like carbon (OLC) and polyacrylonitrile fibre integrated with OLC (OLC-PAN) as electrode platforms. Two electrode platforms were used; onion-like carbon (OLC) and its polyacrylonitrile (OLC-PAN) composites. Both platforms led to the detection in a wide linear concentration range (1.95 fg/ml to 50 µg/ml), excellent sensitivity (>5.2 µA/log([HPV-16 L1, fg/mL]) and ultra-low detection of ca. 1.0 and 1.4 fg/ml for OLC-PAN and OLC-based immunosensors, respectively. The high specificity of detection was proven by experimenting with an anti-Ovalbumin antibody (anti-Ova) and native Ovalbumin protein (Ova). An immobilized antigenic HPV-16-L1 peptide showed insignificant interaction with anti-OVA in contrast with the excellent interaction with anti-HPV-16 LI antibody. The immunosensors showed satisfactory stability of ~ 3 days of re-usability. The application of the immunosensor as a potential point-of-care diagnostic (PoC) device was investigated with the screen printed carbon electrode which showed the ability to detect ultra-low (~ 0.7 fg/ml) and high (~ 12 µg/ml) concentrations. This study opens the door of opportunity for further investigation with other electrode platforms and realization of PoC diagnostic devicesfor screening and testing of HPV biomarker for cervical cancer.Item Exploring the Structure, Function and Stability of Glutathione Transferases Engineered from Intra- and Inter-class Consensus Sequences: How Forgiving is Nature?(University of the Witwatersrand, Johannesburg, 2024-10) Mulenga, Thabelo; Achilonu, Ikechukwu; Sayed, YasienProtein folding is an enigmatic biochemical process that is foundational to the structural and functional requirements of a cell. The problem of protein folding, in a nutshell, concerns itself with the rate of protein folding as well as the conversion of amino acids from a linear sequence to a fully folded structure. This problem is partly answered by the existence of folding pathways. The folding funnel was conceptualised as a depiction of folding pathways, and it is a framework that illustrates that native proteins naturally favour the lowest energy state, encountering kinetic and thermodynamic barriers as they fold. Consensus protein design, based on this understanding, aims to: (1) enhance stability and (2) navigate the pitfalls of folding by modifying the folding funnel of a protein. This approach can also shed light on the significance of evolutionarily conserved residues. In this study, consensus protein mutants were generated for the Alpha and Mu glutathione transferases (GSTs) classes. The consensus proteins were then benchmarked against the parental proteins that were chosen (hGSTA1-1 and hGSTM1-1). The Alpha consensus mutant had 11 consensus mutations, including a notable M50L mutation, which affects the dynamic behaviour of helices α2 and α9, while the Mu consensus mutant had 13 unique mutations. Protein production and purification showed that the Mu consensus mutant had larger and purer yields. Data from far-UV circular dichroism studies and root-mean-squared-fluctuation (RMSF) from molecular dynamics (MD) simulations showed that the secondary structural components of the Alpha and Mu proteins remained largely the same, although the Alpha consensus mutant displayed a far lower molar residue ellipticity reading than its wildtype counterpart, indicating the disruption of secondary structural elements, likely caused by the M50L mutation. The ANS binding results showed that the M50L mutation in the Alpha consensus protein caused an increase in exposure of the surface area of the H-site, while the Mu consensus protein had a decrease in the solvent accessibility of its H-site. Thermal shift assay results indicated the consensus proteins had increased thermal stability. Enzyme kinetics results showed that the functionality of the proteins was severely diminished in the consensus mutants, particularly the Alpha consensus mutant. MD simulation results showed that there was an overall increase in the rigidity and compactness of the consensus mutant proteins, further affirming the improvement of thermal stability, while signalling the loss in functionality. The results produced herein have the potential to facilitate the proliferation of engineered GSTs for biotechnological applications that require proteins with an increased half-life and greater stability.Item Natural resource use and environmental perceptions in different types of rural villages in Bushbuckridge, South Africa(University of the Witwatersrand, Johannesburg, 2024-09) Mbedzi, Mary Emma; Twine, WayneHouseholds in rural communities in developing countries rely on natural resources that contribute to income generation, food, medicine, cooking energy, and act as livelihood safety nets. Levels of dependency vary between households within communities due to factors such as wealth status and household size. However, less is known about differences in household resource use between communities within an area. Environmental awareness, values, and preferences are shaped by various factors including, local context. Thus, perceptions of the environment and natural resources, and changes in these are likely to vary between communities. This study aimed to compare the levels of natural resource use and environmental perceptions across village types and determine if there is any relationship between the level of natural resource use and environmental perceptions across village types in the Bushbuckridge Local Municipality in the Mpumalanga province, South Africa. Village types were defined and categorised based on their size, socio-economic factors, access to basic services, connectedness, and remoteness. The level of natural resource use was analysed using existing data from a survey of 491 households across 12 villages located in the Agincourt Health and Demographic Surveillance System (AHDSS) site. This included data on the use, collection, buying, and selling of a range of natural resources used locally (e.g., wild foods, firewood, and medicinal plants), annual consumptions, ownership of resources made from natural resources, and livestock (cattle) ownership. The survey included questions on respondents’ perception of the change in the supply of natural resources over the past 5 years (2016-2021) before the survey. Focus group discussions were conducted in 10 of the study villages asking participants their perception of the changes in the environment and the causes thereof, the importance of the natural environment, natural resources used for their daily needs, income generation, their culture, as well as the changes in availability of natural resources and impacts on their livelihoods. The study villages were classified according to a village typology that had been developed for the AHDSS study site, based on factors such as connectedness, access to amenities and services, and the proportion of Mozambican refugee households. ANOVA and Kruskal Wallis tests were used for continual data, while the Chi-squared test was used for categorical data to test for significant differences across village types in the quantitative part of the study. For qualitative, responses of participants from each village were recorded and grouped into village types, and an overall picture of the perception of natural resources that participants used was developed using the focus group schedule. Similarities and differences in natural resources between villages were assessed by grouping widely and less used resources by villages and village types. There was no significant difference (p>0.05) in the mean prevalence of use, collection, buying, and selling of natural resources, or annual consumption of natural resources across villages and village types. Households in better-serviced villages owned more products from natural resources and were to greater extent, likely to own livestock than poorly-serviced villages. As to environmental perceptions, more respondents in the poorly serviced village types (refugee settlements (RS) and underdeveloped communities (UC)) perceived a decrease in the supply of natural resources than better-serviced village types (established communities (EC) and central communities (CC)). Participants in focus group discussions also noted a decrease in the supply of natural resources across all villages and village types. There was a relationship between village types, natural resource use, and perceptions of change in natural resource availability. Established communities correlated with a higher number of resources perceived as decreasing and central communities were associated with higher cattle ownership. Underdeveloped communities and refugee settlements were associated with a higher number of resources used/owned, a higher number of resources used often (more than 4 times a month), and a higher number of resources sold, and buying firewood. Natural resources were more highly used in, better-serviced village types (central communities, and established communities), than in poorly-serviced village types (underdeveloped communities, and refugee settlements), which was unexpected. However, there were quite a few proxies such as the collection and selling of resources, which were used that did not help back up these findings which could explain the unexpected results. Most respondents in remote and poorly-serviced village types perceived a change in the supply of natural resources, the greatest decrease being in the supply of natural resources. This is associated with awareness of the value of the environment and high reliance on natural resources for these poorly-serviced village types. This study suggests that differences exist in resource use patterns between villages, even in the same area. However, village characteristics were not a good predictor of all aspects of resource use. Changes in proxies of resource utilization and re-evaluating the existing village typology would be useful for further studies.