List of Titles

Assessing land degradation and the effectiveness of calcrete bontveld rehabilitation in a grassridge PPC cement mining area using multi-sensor remotely sensed data and machine learning techniques

Authors: Mpisane, Khanyisa
Date: 2023-12
Subjects: Land degradation -- South Africa , Environmental degradation , Mines and mineral resources -- South Africa
Language: English
Type: Master's theses , text
Identifier: http://hdl.handle.net/10948/62527 , vital:72821
Description: This study uses multi-temporal remote sensing data to spatially visualise and quantify land degradation due to mining as well as Calcrete Bontveld rehabilitation at the Grassridge PPC Cement mine, Gqeberha formerly known as Port Elizabeth in the Eastern Cape, South Africa. Botanical field data is also used to verify the suasses of rehabilitation in the area. SPOT-6 and Landsat multi-spectral images were compared, and Support Vector Machine and Random Forest algorithms were used for classification in order to determine which yields more accurate results for a limestone mine. Support Vector Machine analysis using SPOT-6 images yielded the best results. This was due to the high spatial resolution of SPOT-6 compared to Landsat and Support Vector Machine classifier was able to classify images with fewer training points compared to Random Forest. The spatio-temporal land cover change at the mine was then determined between the years 2000, 2015 and 2020. Land cover classification is useful for monitoring land degradation and, in this case, was able to show the extent of rehabilitation success. For the year 2020, a 17% area was rehabilitated; however, the algorithm could not distinguish between unmined Calcrete Bontveld matrix and rehabilitation sites that were older than five years. The performed change detection also showed that 29.50% of unmined Calcrete Bontveld matrix had changed to “mature rehabilitation” (rehabilitation sites older than five years). Again, for this percentage in some areas the algorithm could not distinguish between the unmined Calcrete Bontveld matrix and rehabilitation sites that were older than five years due to high similarities between the two land cover types. Area changes of the different land cover classes could also be used to demonstrate how rehabilitation areas have matured over time and lead to the conclusion that most of the Calcrete Bontveld which was mined, has over the years been successfully rehabilitated. Vegetation analysis was conducted to further validate the rehabilitation success of Calcrete Bontveld matrix. Multivariant Detrended Correspondent Analysis showed that rehabilitation sites which were younger than five years (2–year-old rehabilitation plots that were sampled) had great dissimilarity to the natural unmined Calcrete Bontveld matrix and that rehabilitation sites older than five years, in this case 16–years older, had high similarity and resemblance to natural unmined Calcrete Bontveld matrix and therefore could be considered as being mature. This was a more definitive assessment as it considers all aspects of the vegetation. Species cover and species richness also showed that Calcrete Bontveld matrix rehabilitation sites which have been rehabilitated for more than 5 years had greater similarity to natural unmined vegetation compared to areas that have been rehabilitated for less than five years. This study, therefore, demonstrates that due to the high similarity between mature rehabilitation sites and unmined Calcrete Bontveld, rehabilitation has been successful. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2023
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Date Issued: 2023-12

Assessing the effects of fish stock management on Cape gannet foraging behaviour in South Africa

Authors: Strydom, Zanri , Grémillet, David , Pichegru, Lorien
Date: 2023-12
Subjects: Gannets -- South Africa , Birds of prey -- Behavior -- South Africa , Fish stock assessment
Language: English
Type: Doctoral theses , text
Identifier: http://hdl.handle.net/10948/62622 , vital:72887
Description: Seabirds are one of the most threatened groups of birds under both marine and terrestrial pressures. Among seabirds, the Cape gannet Morus capensis is a southern African endemic species facing several pressures of anthropogenic origin, including competition with industrial fisheries on small pelagic fish stocks. Cape gannets, being a long-lived species that is sensitive to environmental changes, are sentinels of change in oceanic environments granting it important to understand which factors influence their foraging behaviour and breeding outputs. For example, factors like age can result in a loss of physical capabilities which can lead to behavioral compensation and subsequent changes in chick provisioning rates and amounts. With the current fisheries management the fish stocks are continually decreasing, indicating the importance of an updated fine-scale assessment on the spatiotemporal overlap between foraging gannets and fisheries. The first objective of this thesis was to determine the influence of adult Cape gannets’ age and sex on their foraging characteristics and energy expenditure during foraging. I equipped chick-rearing Cape gannets of known age and sex with a 3D accelerometer and GPS device. Foraging effort (trip duration, foraging path and maximum distance to the nest) did not differ between sexes nor with age in Cape gannets. Both sexes rested less on the water with age. Aging females also spent more time in flight than males. The age- and sexual differences in energy expenditure prevalent in our study might reflect niche and/or risk partitioning strategies to ensure adequate provisioning to the chick. The second objective of this thesis was to determine the influence of fisheries catch rates, sardine and anchovy biomass, and adult foraging effort on chick growth rates in Cape gannets, using a long-term dataset collected between 2005 and 2020 on Malgas Island. I equipped chick-rearing adults with a GPS device and I weighed the chicks for between 3 to 6 increments to calculate the average daily mass increment. Of all the variables, foraging trip duration was the main determinant of daily growth rates, with chicks benefitting from parents’ shorter foraging trip durations. Chicks tended to grow slower when fisheries catch of sardine and anchovy were higher, possibly an effect of competition with fisheries. Chicks also grew faster when fish biomass was higher. This long-term monitoring demonstrated the possible effect of food competition between Cape gannets and fisheries, with negative impacts on gannet fitness as determined via chick growth rates. The third objective of this thesis was to determine the influence of both the biomass and fisheries catch rates of sardine and anchovy on Cape gannet foraging effort at a spatial and temporal scale. This was achieved by equipping a total of 668 chick-rearing Cape gannets with a GPS device. With an increase in fisheries catch there was an increase in the birds’ foraging effort. To reduce competition between the gannets and fisheries, the gannets’ core foraging areas seldomly overlapped with the fisheries catch locations, at the cost of the gannets’ increased foraging effort. One method to halt the Cape gannet population decline would be to conserve the fish resources close to the breeding colonies. This would reduce the birds’ foraging whereby increasing their fitness. Safeguarding small pelagic fish to ensure the perseverance of the remaining Benguela seabird populations, would lead to preserving the Benguela marine ecosystem as a whole. My study provided new insight into effects of fish stock management on Cape gannet foraging behaviour in South Africa, and the need for adequate management to ensure population persistence. , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2023
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Date Issued: 2023-12

Case-based research on the fedup model for self-help housing

Authors: Qumbisa, Nolwazi
Date: 2023-12
Subjects: Community participation , Human settlements , Informal settlements
Language: English
Type: doctoral's theses , text
Identifier: http://hdl.handle.net/10948/62199 , vital:72007
Description: In South Africa, the government subsidises the building of starter homes to meet the demand for housing for people with lower incomes. However, it is necessary for the state to revise its efforts to meet the demand for housing in the country. Self-help housing is a model that can be used as an alternative to state housing subsidies. The present research study investigates the essential aspects of sustainable self-help housing in the central region of South Africa. The present study aimed to address the central research topic by eliciting responses from participants: How can self-help provision become sustainable in the central region of South Africa? In response to the question, an effective self-help housing support model was developed, the aim of which is to outline how self-help housing projects could be improved. The literature findings demonstrate the potential of this model as a viable alternative to the existing housing delivery mechanism in South Africa. This assertion is supported by a study of self-help housing trajectories and an examination of relevant South African housing policies. However, there has been a lack of emphasis on the simplification of current models to accommodate the needs of implementers, government entities, and beneficiaries of self-help housing initiatives. This study aimed to address the highlighted gaps by utilising a qualitative methodology and drawing upon the data obtained. The data collection techniques included semi-structured interviews, structured observations, and focus-group discussions. A total of 25 semi-structured interviews were conducted with key stakeholders in human settlements, while the focus-group discussions involved 50 participants. A total of 5 focus group discussions were conducted with each group consisting of 10 participants. Moreover, the researcher conducted a document analysis, observations, and questionnaire survey. The data collected were analysed thematically. The results revealed that there are still challenges with implementing self-help housing. Moreover, the results are attributed mainly to a mismatch of the roles and responsibilities and not understanding the Enhanced People’s Housing Process (EPHP) policy. The principal contribution of the thesis is that housing policies, programmes and sector plans must encourage beneficiaries to play an active role. This study found that weak or unclear project vi specifications lead to contractor misunderstandings or discrepancies in housing project implementation, resulting in poor-quality work or delays. The conventional contractor-driven housing-delivery model also has issues like poor construction, corruption and mismanagement, profit-driven contractors, high contractor rates, project delays/incomplete projects, illegal occupation of incomplete projects, riots and disputes, ineffective project specifications, and beneficiary disengagement. In this study, it is demonstrated how a positive social impact on housing could be the outcome of an improved self-help approach. Consequently, the research suggests the adoption of an effective self-help housing support model, which may effectively address the challenges posed by informal settlements while enhancing the execution of self-help housing projects. The model has the potential to make contemporary contributions to the public housing policy model in South Africa. This study contributes to the broader discourse on sustainable housing alternatives, providing insights into the various obstacles, potential advantages, and recommended strategies within the realm of selfhelp housing. The study's qualitative approach facilitated a comprehensive examination of the lived experiences and viewpoints of diverse stakeholders. This yielded valuable insights that can inform policymakers, practitioners, and communities in their efforts to improve the sustainability of self-help housing solutions in the central region of South Africa. , Thesis (PhD) -- Engineering, Built Environment and Technology, 2023
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Date Issued: 2023-12

Characterization of the coastal Aquifer of Gqeberha, South Africa : Developing a conceptual understanding

Authors: Vandala, Bamanye
Date: 2023-12
Subjects: Aquifers -- South Africa -- Port Elizabeth , Groundwater ecology , Hydrogeology
Language: English
Type: Master's theses , text
Identifier: http://hdl.handle.net/10948/62710 , vital:72932
Description: The aquifer systems in Gqeberha are poorly understood due to a lack of groundwater studies within the area, and this is particularly the case for the coastal aquifer of Gqeberha. Amidst the water crisis the city is currently facing, groundwater has become crucial, with over 1000 boreholes reportedly drilled in the coastal area, most of which are residential. This has resulted in the need to conduct more groundwater studies in the area and in Nelson Mandela Bay. This study presents a detailed hydrogeological characterization of the coastal aquifer of Gqeberha. This was achieved through the use of different techniques, which include field mapping, geophysics, hydrochemistry, and pumping test analysis. The work was done on the coastal seeps of the Algoa Group Formation and the fractured aquifer of the Peninsula Formation. The results through mapping indicated an abundance of folds, faults, and fractures which all have implications for groundwater flow. The majority of fractures are striking in the NE-SW and NW-SE directions. The pumping test analysis also indicated fractal flow with significant matrix flow resulting in a dual porosity system up to at least 200m in depth. The transmissivity and storativity values range from 6.78 – 44.5 m2/day and 0.0172 – 0.0325, respectively. This is highly dependent on the fracture interconnectivity, which varies across the area and is higher at shallow depths, as suggested by the geophysical profiles. Geophysical profiles indicate that the contact between the Algoa Group Formations and the Peninsula Formation results in coastal seeps due to the difference in hydraulic conductivities. The hydrochemical analysis suggests that the seeps generally have Na-Cl and Ca-Mg-Cl water types. The groundwater in the eastern area has a Ca-HCO3 water type, and the groundwater in the western region has a Ca-Mg-Cl water type, with the Chelsea-Noordhoek Fault system separating the two groundwater signatures. Groundwater at greater depths has a Na-Cl water type with higher TDS values. The chemical signatures seen are due to external factors, which include sea sprays, anthropogenic activities, rock-water processes, and possibly connate water in the Peninsula Formation aquifer. The findings of this study offer valuable insights into the present conditions of the aquifer in Gqeberha. This research serves as a foundational study that can provide a baseline for future hydrogeological investigations in the area. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2023
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Date Issued: 2023-12

Chemical analysis and biological activities of crude extracts and essential oil of selected medicinal plants from the Eastern Cape, South Africa, and Volta Region of Ghana

Authors: Agbo, Irene Adzo
Date: 2023-12
Subjects: Medicinal plants , Lantana camara , Peptic ulcer -- Treatment , Traditional medicine - South Africa -- Eastern Cape , Traditional medicine -- Ghana
Language: English
Type: Master's theses , text
Identifier: http://hdl.handle.net/10948/62431 , vital:72728
Description: Lantana camara and Khaya grandifoliola extracts are among many plants found traditionally effective for the treatment of wounds and ulcers. This study assessed the phytochemical content, isolation and identification of single compounds from methanol and ethyl acetate extracts of Lantana camara and Khaya grandifoliola. Further, the bioactivity testing including antioxidant, antimicrobial and cytoxicity of the extracts was done to confirm the wound healing potential discovered by the traditional healers. Materials and methods: Extraction was done successively using maceration method with 100 % ethyl acetate and 100 % methanol with a biomass-to-solvent ratio of 1:3 (w/v) to obtain L. camara ethyl acetate extracts of berry (ELB), flower (ELF) and leaf (ELL) and methanol extracts of MLB, MLF, MLL and K. grandifoliola ethyl acetate extracts of leaf (EKL), root (EKR) and stem bark (EKSB) and methanol extracts of MKL, MKR, MKSB respectively. L. camara leaf essential oil (EO) was extracted using the hydro-distillation method with a Clevenger apparatus. Total phytochemical content was assessed for each extract using spectrophotometric methods and a calibration curve of standards: bromocresol green method with atropine; Folin–Ciocalteu colorimetric method with gallic acid, aluminium chloride colorimetric method with quercetin and concentrated sulphuric acid chloroform with linalool for total alkaloid, phenolic, flavonoid and terpenoid contents respectively. Single compound isolation and purification was conducted using chromatographic techniques. Elucidation of single compounds was done using spectrometric method, high resolution- mass spectrometry, and one and two-dimensional (1D and 2D)-NMR. Stereochemistry of each compound was confirmed using electronic circular dichroism spectra. A Crystalline compound was identified by single crystal X-ray diffraction using CuKα-radiation. In vitro bioactivities were assessed with methods such as 3-[4,5-dimethylthiazole-2-yl]-2,5-diphenyltetrazolium bromide, free radical scavenging activity of 1,1-diphenyl-2-picrylhydrazyl, inhibitory effect on nitric oxide production in lipopolysaccharide-activated RAW 264.7 macrophages, and 96-well plate micro dilution for cytotoxicity, ant-inflammatory and antimicrobial activity testing. Results: Methanol extracts of both plants retained high phytochemical concentrations of all the phytoconstituents investigated compared with the ethyl acetate extracts which retained lower concentrations. The results of the L. camara methanol extracts include; total alkaloid content (TAC) (2.05±0.18, 1.87±1.54 and 2.60±1.10 mg AEQ/100 mg); total phenolic content (TPC) (14.05±4.04, 34.59±3.01 and 18.58±1.87 mg GAEQ/100 mg); the total flavonoid content(TFC) of flower (12.45±1.87, 20.41±2.69 and mg QEQ/100 mg); total terpenoids (TTC) (20.74±2.34, 20.74±2.34 and 15.97±1.19 mg LIN EQ/100mg) of MLB, MLF and MLL respectively. Whereas that of the K. grandifoliola methanol extracts include; TAC (7.32±0.14,8.49±0.34, 10.67±0.22 mg AEQ/100 mg); TPC (37.49±1.40, 44.41±0.69, 53.57±1.50 mgGAEQ/100 mg); TFC (6.54±0.55, 9.58±0.89 and 10.26±0.92 mg QEQ/100 mg); TTC(10.16±1.41, 35.78±2.14 and 23.45±1.76 mg LIN EQ/100mg) of MKL, MKR and MKSB respectively. The major components of essential oil, out of the 71 constituents identified include Davanone D (32.91 %), Caryophyllene (5.07 %), Nerolidol 2 (3.56 %) and GermacreneD (3.13 %). Compounds 3.47 was isolated from the methanol extract of L. camara flowers. This compound is reported for the first time from the L. camara flower extract. Two compounds, compounds 4.23, and 4.26, were isolated from the methanol extract of K. grandifoliola roots, compound 4.22 was isolated from the ethyl acetate root extract while compounds 4.24 and 4.25 were isolated from the ethyl acetate stem bark extract as isomers in a mixture. Compounds 4.22 and 4.23 are reported from K. grandifoliola root for the first time. The isolated compounds (compounds 3.47 and 4.23) were nontoxic to the Vero cell line and this may contribute to possible stimulation of cell proliferation, promoting wound healing. Cytotoxicity describes extract virulence to Vero cell line. MLF and ELB were found nontoxic even at the highest concentration of 200 μg/mL. The MKSB and MKR, as well as the EKSB were nontoxic. Antioxidant activity results, described by the percentage inhibition in the DPPH assay, showed that MLF and MKSB had the highest antioxidant activities compared with the ascorbic acid standard, with IC50 of 38.68±5.09 and 37.03±11.95 μg/mL for L. camara and K. grandifoliola respectively. ELB exhibited a significant anti-inflammatory activity inhibiting NO• radical generation in the LPS-stimulated RAW 264.7 macrophages at concentration ranging from 50 and 100 μg/mL. EKSB and MKR showed significant anti-inflammatory activity at 100 and 200 μg/ml respectively. ELL and ELF demonstrated potent growth inhibition against S. pyogenes with an MIC value ≤ 0.125 mg/mL, while the MICs of the ELB and MLL were 0.5 mg/mL and 2 mg/mL respectively. MKSB and MKR and EKSB extract exhibited an effective growth inhibition against S. aureus with MIC of 1 mg/mL. The growth of S. pyogenes was supressed by both ethyl acetate and methanol extracts of all plant parts tested with MIC ranging from 0.25–2 mg/mL. Conclusion: The potent bioactivity shown in the results of the cytotoxicity, antioxidant activity, anti-inflammatory and antimicrobial activity testing, and the nontoxic singlecompounds of L. camara and K. grandifoliola extracts led to the conclusion that the two plants had wound healing potential. The study therefore confirmed their traditional uses for treatment of wounds. , Thesis (PhD) -- Faculty of Science, School of Biomolecular and Chemical Sciences, 2023
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Date Issued: 2023-12

Dietary assessment of Cape Gannets (Morus capensis) and African Penguins (Spheniscus demersus) in Algoa Bay using molecular scatology

Authors: Bowmaker - Falconer, Kezia , Von Der Heyden, Sophie
Date: 2023-12
Subjects: Gannets , Gannets -- Food , Sea birds -- South Africa -- Bird Island, Algoa Bay.
Language: English
Type: Master's theses
Identifier: http://hdl.handle.net/10948/62420 , vital:72675
Description: Seabirds are important marine sentinels, providing valuable information about ecosystem health and condition. Dietary studies of seabirds can inform on ecosystem functioning through identifying the condition and changes occurring in their surrounding environment. Dietary studies are also crucial as they can identify threats that seabirds face. Until recently, the diets of southern African endemic and Endangered Cape Gannets Morus capensis and African Penguins Spheniscus demersus were solely investigated through stomach content analyses, which allows for the identification and quantification of prey remains. To overcome some of the limitations associated with stomach content analysis, stable isotope and fatty acid analyses were proposed. However, these methods still require bird handling and thus impose some stress on the birds. DNA metabarcoding of faecal matter shows promise as a completely noninvasive method for seabird dietary studies. This thesis first examined whether DNA metabarcoding could be used to determine the diet of Cape Gannet and African Penguin breeding in Algoa Bay, South Africa. Then, this method was used to investigate the influence of intrinsic (both seabird species) and extrinsic (African Penguins) factors on the diet of the two seabird species. For the first data chapter, stomach content samples and faecal matter were collected concurrently from breeding Cape Gannets and African Penguins on Bird Island. DNA was successfully extracted from most faecal matter samples and the primers (18S_SSU, 16S_Fish) used for group, taxa and fish prey identification allowed amplification of prey DNA for both study species. A similar piscivorous diet was determined by both dietary methods for Cape Gannets with Sardine Sardinops sagax and Atlantic Saury Scomberesox saurus dominating the diet. Sardine also dominated the African Penguin diet in both dietary methods. In addition, DNA metabarcoding in African Penguins revealed a more diverse diet compared to the one determined by stomach content analysis. This was likely due to the limitations on the allowed number of stomach content samples to be collected for that Endangered species. Non-invasive DNA metabarcoding of faecal matter was then used to investigate whether the diet varied with breeding stages (incubation, chick-rearing) and age classes (chick-rearing adults, chicks) in both seabird species, but also breeding colonies (Algoa Bay: Bird Island, St Croix Island) in African Penguins. DNA metabarcoding revealed that breeding stages influenced the diet of Cape Gannets and African Penguins on Bird Island where prey species diversity was greater for incubating adults. On the contrary, the diet of incubating and chick-rearing penguins on St Croix Island was similar. When comparing the diet of African Penguins between Bird Island and St Croix Island, there was an increased overlap in diet composition between incubating and chick-rearing adults on St Croix Island when compared to Bird Island. Importantly, DNA metabarcoding indicated an increase in fishery interactions in Algoa Bay, particularly for Cape Gannets and the hake Merluccius spp. fishery, where the contribution of hake to chick-rearing adults and chick diet was considerably greater than incubating adult diet. In this study, I showed that DNA metabarcoding of faecal matter provides an opportunity for non-invasive dietary studies in two southern African endemic and Endangered seabird species. Incorporating non-invasive methods as a complement to other dietary methods for monitoring seabird trophic ecology is crucial when considering the worsening status of several seabird species. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2023
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Date Issued: 2023-12

Effects of annealing on the structural and optical properties of nanostructured TiO2

Authors: Talla, Assane , Urgessa, Zelalem
Date: 2023-12
Subjects: Titanium dioxide , Nanostructured materials , Nanotubes
Language: English
Type: Doctorial theses , text
Identifier: http://hdl.handle.net/10948/62655 , vital:72907
Description: In this thesis, the structural, morphological and optical properties of titanium dioxide (TiO2) are investigated. Titanium dioxide (TiO2) nanotubes are prepared by anodic oxidation of titanium foil. The as-anodised samples are thermally annealed at various temperatures in nitrogen, air, oxygen and vacuum. The purpose is to study how the annealing conditions affect the properties of the nanostructures, including the anatase to rutile phase transformation. In all annealing atmospheres, except in vacuum, the dominant phase is found to be anatase when annealing is performed up to 600 oC. Above 700 oC the rutile phase becomes dominant. The anatase phase is stable above 600 oC in vacuum and does not evolve significantly up to 900 oC. The morphologies of the tubes tend to deteriorate with increased annealing temperature, in nitrogen, air and oxygen atmospheres, due to sintering effects. However, the integrity of the nanotubes is maintained up to 900 oC in vacuum. The photoluminescence (PL) spectra suggest mainly the presence of oxygen vacancies and self-trapped excitons, with respective emission bands around 2.5 eV and 2.3 eV. The results show that both the annealing temperature and atmosphere strongly influence the crystalline and optical properties of the TiO2 nanotubes. In addition, the phase transformation from anatase to rutile for samples annealed in an oxygen-rich environment is investigated in detail. Complementary structural information obtained from transmission electron microscopy and Raman analysis for oxygen-annealed samples reveals that the nucleation of the rutile phase starts from the titanium substrate and then propagates along the tubes. The results provide suitable annealing conditions to control the phase content and morphology of anodic TiO2 nanotubes. The PL characteristics of bulk crystalline anatase TiO2, namely virgin and hydrogen-annealed at 600 oC for 1 h, are studied. The low temperature PL spectra at 5.5 K shows near band edge (NBE) emissions with two dominant lines ascribed to shallow donor bound exciton and possibly free to bound recombination. The two main transitions are assisted by optical phononmodes. Temperature-dependent PL measurements performed on these anatase crystals reveal that the donor bound exciton is stable below 90 K. Hydrogen trapped in oxygen vacancies is proposed to be the shallow donor. In addition, two activation processes are involved for the thermal quenching of donor bound excitons. The total activation energy is found to correlate well with the localisation energy of the bound exciton. Site-selective PL spectra obtained from anodic TiO2 tubes reveals that the luminescence of the nanostructures depends on the morphology. The result shows unusual near-band edge emission (NBE) for these structures, which is rarely observed in indirect band gap TiO2. , Thesis (PhD) -- Faculty of Science, School of Biomolecular and Chemical Sciences, 2023
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Date Issued: 2023-12

Effects of fire on architecture and composition of canopy shrubs in subtropical dune thicket of the southeastern Cape Floristic Region

Authors: Strydom, Tiaan , Grobler, Adriaan
Date: 2023-12
Subjects: Plant ecology -- Research , Plant communities -- South Africa , Browsing (Animal behavior)
Language: English
Type: Doctorial theses , text
Identifier: http://hdl.handle.net/10948/62632 , vital:72899
Description: Disturbance, such as fire and megaherbivory, is a pervasive phenomenon globally and has different effects on the flora and vegetation of different ecosystems. The Cape Floristic Region (CFR) of South Africa includes the distinctive Subtropical Thicket biome, which occurs as interrupted blocks that are not exposed to fire, but also as mosaics with the fire-prone vegetation of the Fynbos biome, especially on coastal dunes where thicket species are exposed to fire. Subtropical Dune Thicket (hereafter thicket) thus co-occurs with Fynbos, capable of supporting intense fires that can lead to thicket shrub defoliation and mortality. Thicket also experiences disturbance from meso- and megaherbivores that causes defoliation and mortality of shrubs. The aim of this study was to investigate the resilience of thicket shrub species to varying disturbance levels from fire and browsing to understand what drives thicket persistence in a fire-prone landscape. Firstly, I established the architectural traits of thicket species in long unburnt and post-fire contexts and investigated the relationships between these traits and the survival, resprouting ability and persistence of thicket shrubs. In mature thicket, I identified three distinct architectural guilds, namely hedge formers, lateral spreaders, and vertical growers. In post-fire thicket I identified three resprouting architectures, namely weak resprouters, moderate resprouters and strong resprouters. There was no strong relationship between the unburnt and post-fire resprouting architectures. Secondly, I compared thicket species and architectural composition in patches of landscape that experience different levels of fire exposure to assess the potential effect of fire frequency on determining thicket structure. I recognised three thicket vegetation units, each with a distinct structure and each corresponding to the level of fire exposure in the landscape. The first unit, forest-thicket, is exposed to low levels of fire frequency (> 100 years) and harbours forest species, many of which were vertical growers. The second unit, thicket, is exposed to moderate levels of fire frequency (50-100 years) and is dominated by lateral spreaders. The last unit, fynbos-thicket, is exposed to high levels of fire frequency (10-50 years) and here hedge-forming shrubs dominate the canopy cover. Forest-thicket and fynbos-thicket had a diverse set of shrub species with many being restricted to their respective vegetation type, whereas thicket had a lower diversity with no unique shrub species. , Thesis (DPhil) -- Faculty of Science, School of Natural Resource Management, 2023
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Date Issued: 2023-12

Establishment of a high-content neurodegenerative disease model screening platform

Authors: Swanepoel, Bresler
Date: 2023-12
Subjects: Molecular neurobiology , Nervous system -- Diseases , Nervous system -- Degeneration
Language: English
Type: Doctorial theses , text
Identifier: http://hdl.handle.net/10948/62644 , vital:72906
Description: The identification of viable therapeutic targets and new treatments for central nervous system disorders, especially neurodegenerative diseases, remain major challenges in the field of drug discovery. Over the past few years there has been a steady decline in the turnaround time of current screening processes to yield viable drugs. Therefore, an increasing need exists for better technologies, protocols, and the screening of larger libraries. High-throughput screening provides the best solution to this problem and has become a key part in the drug discovery and development process. Likewise, high-content analysis has gained popularity over the past few years and is suitable for high-throughput screening. The aim of this study was to establish a comprehensive in vitro neuroprotective screening platform incorporating high throughput screening, using Parkinson’s disease as the neurodegenerative disease of interest. To evaluate the success of this platform, the neuroprotective potential of two mushrooms (Hericium erinaceus and Phlebopus sudanicus), two plants (Lippia javanica and Myrothamnus flabellifolia) and two seaweeds (Eucheuma denticulatum and Kappaphycus alvarezii) were investigated. Aqueous and ethanolic extracts of the selected natural products were evaluated across 21 parameters associated with four hallmarks of neurodegeneration: acquiring senescence, acquiring cell death, neuroinflammation and altered metabolism/cell survival. Based on the effects of these selected natural products on the 21 parameters, their potential mechanisms of action were elucidated. In addition to this, the natural products were scored under each of these therapeutic targets in an attempt to identify the most suitable animal models for future studies. The scoring system indicated that animal models investigating anti-senescence ability would be more suited for extracts of H. erinaceus, P. sudanicus and E. denticulatum whereas studies investigating the prevention of cell death would be more suited for extracts of E. denticulatum, L. javanica and K. alvarezii. Likewise, models based on neuroinflammation would be best suited for extracts of H. erinaceus, E. denticulatum and L. javanica while studies examining altered metabolism/cell survival would be best suited to extracts of H. erinaceus, E. denticulatum, K. alvarezii and M. flabellifolia. Considering the pleiotropic nature of the selected natural products, models that can combine these therapeutic targets could be of great interest. 6-OHDA proved to be capable of inducing favourable effects, in all the parameters investigated, with regard to a neurodegenerative state. However, it is known to have some disadvantages when it comes to pathological features such as the lack of the ability to induce Lewy body formation. Choosing the correct inducer remains a daunting task and no model, whether cell-based or animal-based, exists yet in which all the features of neurodegenerative diseases have been successfully replicated. The limitations of the current models, however, does not mean that they do not produce valuable insights. This is especially true if the mechanism of action for a specific compound or natural product is unknown. Animal models are still indispensable for the validation and interpretation of the results obtained from cell models with particular importance to toxicity. Therefore, this study assessed the best studied extract with the highest overall score for its toxicity using a zebrafish larvae-based model. Assessment of the toxicity of H. erinaceus revealed that both aqueous and ethanolic extracts resulted in death at the highest concentrations. This was supported by the results obtained in the in vitro cytotoxicity screening. In conclusion, this highlighted the importance of using physiologically relevant concentrations and supported the translational value of the current cell-based screening model to animal models and possibly humans. The findings of the present study suggest that a scoring system, which categorizes the different activities of selected natural products into distinct groups, can be a useful tool to improve the translatability of in vitro results to animal models. Furthermore, the current study arguably provides the most comprehensive neuroprotective screening platform in existence. Future research can look at expanding the platform through incorporation of additional parameters based on other hallmarks of neurodegeneration, not covered in this study, including protein folding and aggregation, altered epigenetics and the examination of other neuronal markers such as the involvement of astrocytes, oligodendrocytes, and microglia. In addition to this, future research can make use of more sophisticated cell models such as differentiated, human induced pluripotent stem cells and three-dimensional cultures. , Thesis (PhD) -- Faculty of Science, School of Biomolecular and Chemical Sciences, 2023
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Date Issued: 2023-12

Evaluating antidiabetic properties of selected African medicinal plants in a cell-based model

Authors: Sirkhotte, Saeedah , Reddy, Shanika
Date: 2023-12
Subjects: Medicinal plants -- South Africa , Insulin resistance , Gluconeogenesis
Language: English
Type: Master's theses , text
Identifier: http://hdl.handle.net/10948/62600 , vital:72827
Description: The World Health Organisation lists diabetes as one of the major non-communicable diseases affecting the world, and its prevalence is expected to increase rapidly. Type II diabetes mellitus (T2DM) is characterised by insulin resistance and impaired blood glucose control. T2DM is of growing concern within South Africa, with 10.8% of the population currently diagnosed. The popularity, as well as availability, of traditional plant-based medicine in South Africa, might provide a solution. Antidiabetic potential is commonly tested by in vitro assays, however the methods to test this potential via gluconeogenesis are limited. This project aimed to optimise an in vitro hepatic gluconeogenesis model. In addition, this project aimed to determine the antidiabetic properties of Prunus africana, Hypoxis stellipilis, and Eriocephalus africanus by in vitro analysis. These properties were examined in human hepatoma cells (C3A cell line) and rat pancreatic cells (INS1 cell line) and methods included: cytotoxicity analysis, Amplex® red glucose oxidase assay, antibody staining, gene expression analysis by RT-qPCR, oxidative stress analysis, and calcium signaling for insulin release. Insulin resistance was successfully induced by exposing C3A hepatocarcinoma cells to a combination treatment of 50 μM dexamethasone, 1.25 mM fructose and 0.125 mM palmitic acid for a period of three days. Thereafter, gluconeogenesis was assessed using the Amplex® red glucose oxidase assay. The established model was effective in inducing insulin resistance and upregulating gluconeogenesis. Of the tested plant extracts, H. stellipilis showed the most potential as an antidiabetic treatment. It had low toxicity, significantly decreased hepatic glucose production and reduced the amount of phosphoenolpyruvate carboxykinase (PCK) and well as PCK gene expression, and reduced lipid content and reactive oxygen species (ROS) in the C3A cell line. H. stellipilis increased calcium signalling in INS1 rat insulinoma cells, however there was a decrease in expression of genes for insulin and glucose transporter 2 after 6 hr exposure. H. stellipilis appears be beneficial as an antidiabetic treatment. Although antidiabetic studies have been done on other Hypoxis species, this is the first study on the effects of H. stellipilis on gluconeogenesis and diabetes. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2023
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Date Issued: 2023-12

Evaluation of the antidiabetic potential, safety and efficacy of selected natural products using zebrafish larvae and in vitro bioassays

Authors: Reddy, Shanika , Dambuza, Ntokozo
Date: 2023-12
Subjects: Traditional medicine -- Research -- South Africa , Medicinal plants -- South Africa -- Research , Insulin resistance
Language: English
Type: Doctoral theses , text
Identifier: http://hdl.handle.net/10948/62575 , vital:72825
Description: Abstract. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2023
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Date Issued: 2023-12

Evidence of Late Holocene extreme marine wave event (tsunami) deposits along the South African coast and implications for coastal zone management

Authors: Mfikili, Athi Nkosibonile
Date: 2023-12
Subjects: Tsunamis -- South Africa , Coasts -- Risk assessment , Sediments (Geology)
Language: English
Type: Doctoral theses , text
Identifier: http://hdl.handle.net/10948/62517 , vital:72811
Description: Although extreme marine wave events such as tsunamis and storm surges have always been part of human existence, their impact on ever-growing coastal population of the world’s coast was highlighted by the recent catastrophic events over the past three decades. Although in situ observations and eyewitness accounts have improved our ability to record and interpret wave inundation by modern extreme marine events, records documenting inundation by pre-historic and historical events are relatively sparse to provide reasonable information on their distribution, magnitude and frequency intervals in most parts of the world. Owing to consequences these natural coastal hazards have on coastal population and infrastructure of the world’s coast, onshore sedimentary deposits preserved in the geological records have been extensively utilized by scientists worldwide to reconstruct the record of pre-historic and historical events and establish the recurrence interval of future events. Although studies investigating inundation of past tsunami has increased worldwide over the past two decades, research on extreme marine inundation has received little attention along the South African coast, despite known inundation by recent events and potential source mechanisms. Therefore, the aim of this study is to investigate sedimentary evidence of past tsunamis and related extreme marine wave events (i.e., storm surges) preserved in the recent geological archive of several coastal environments along the South African coast. The Swartkops, Kabeljous, Kromme and Keurbooms estuaries located in log-spiral bays along the south-east coast and sheltered coastal systems of the Berg Estuary and Verlorenvlei as well as coastal lowlands of the Dwarskersbos on the west coast were selected as the study sites. The sediment cores were collected from these coastal environments and identification of extreme marine wave inundation was based on the recognition of distinct anomalous sand layers. To characterise sediment transport and reconstruct provenance source origin of the deposits, a combination of sedimentological (i.e., grain size distribution), exoscopy (i.e., quartz grain surface microtextures) and micropaleontological (i.e., foraminiferal assemblages) proxies were utilized. Furthermore, age estimation of the deposits was determined using a combination of radiocarbon (14C) and radiometric (137Cs and 210Pb) dating methods.Evidence of coastal flooding by high-energy marine wave events is found preserved in the stratigraphic records of Swartkops and Kabeljous estuaries along the south-east coast and lowlands of Dwarskersbos on the west coast in the form of anomalous sand deposits (layers). The anomalous deposits of Swartkops and Kabeljous estuaries generally consist of gravel-sized shell fragments often with a sharp erosive contact suggesting deposition by a highly energetic marine wave event. Although the preservation varies between cores, a maximum of three anomalous sand depositional layers are preserved in the Swartkops whereas only a single layer in the Kabeljous Estuary with a basal layer of calcrete deposits. 210Pb and 14C dating, constrain the ages of the younger deposits (i.e., the uppermost layer) at Swartkops between 1770-1804 AD and 339-3 cal. BP (1611-1947 cal. AD), respectively. Although these ages span over a wide period, they are interpreted to represent evidence of one of the historical tsunamis generated in the subduction zones of the Indian Ocean e.g., 1762 AD and 1797 AD events generated by 8.8 and 8.0 Mw earthquakes in the Arakan and Sunda Subduction Zones, respectively. Furthermore, the deposits could also represent geological evidence of the 1833 Mentawai events whereas evidence of 1883 Krakatau tsunami is not disregarded, since this event reportedly inundated Algoa Bay. On the other hand, the 14C dating constrain the ages of the second anomalous deposits between 1526-1253 cal. BP (424-697 cal. AD), whereas the older anomalous deposits preserved in the deeper sections of the Swartkops cores as well as the backwater channel of the Kabeljous Estuary are constrained to have been deposited around 4000 cal. BP. Although there is no known locally documented extreme marine wave event during this period, these deposits are interpreted to represent late and mid-Holocene tsunamis associated with mega-thrust subduction zones of the Indian Ocean whereas local submarine landslide generated event are also not disregarded entirely. On the west coast, three anomalous deposits representing extreme marine wave inundation are preserved in the coastal lowlands of the Dwarskersbos. Although the general sedimentary features and thickness vary between the deposits, the first anomalous deposits in the uppermost section of the cores consist of medium sand with scattered shell fragments whereas, the third anomalous deposits in the deeper section of the cores are generally coarser with gravel-sized shell fragments and sharp erosive basal contacts. By contrast, the second anomalous deposits consist of three successive sub-layers of yellow sand with variable sedimentary features and these layers represent successive wave inundation events. Although the sedimentary characteristics of these sub-layers varies, it was noted that the lowermost layers consist of coarser and less well sorted sediments often with basal erosive contact, suggesting that the first wave was more energetic than the two-succeeding waves. Furthermore, calibrated 14C dated shell fragments from the first and second anomalous deposits yielded ‘post-bomb’ ages suggesting deposition after 1950 AD. Given their position within the stratigraphic records, the two deposits are interpreted to represent first geological evidence of the 2008 west coast and 1969 Dwarskersbos events, respectively. On the other hand, the 14C dated shell fragments constrain the deposition of the third anomalous deposits between 315-0 cal. BP (1635-11950 cal. AD) and 358-0 cal. BP (1592-1950 cal. AD), respectively. The third anomalous deposits are interpreted to the 07 April 1620 event, which was described as ‘Two startling thunderclaps’ near Robben Island. Although initially associated to earthquakes, there are no records of an earthquake during this period, therefore, we postulate that the 1620 event could have been a similar event to that of 2008 that inundated the west coast region and/or an unknown event. While it is acknowledged that the absence of reliable source mechanisms poses a great challenge in the reconstruction of extreme marine wave events inundation along the south-east coast, the findings of exoscopy and micropaleontological analyses suggest that the deposits were transported to their depositional environments, although resultant microtextural features and occurrence of individual foraminiferal species and their taphonomical conditions is dependent on coastal setting. The south-east coast deposits consist of highly diverse foraminiferal assemblages, which are dominated by marine and marginal-marine taxa with relatively low abundances of estuarine-brackish species and variable taphonomical conditions. Furthermore, the mechanical-induced features such as percussion marks, fresh surfaces with sharp edges were still preserved on quartz grain surface of the Swartkops deposits, despite dominance by chemical-induced features such as dissolution. By contrast, grain surface microtextural signatures of the Dwarskersbos deposits are dominated by mechanical features such as fresh surfaces and v-percussion marks. Furthermore, the foraminiferal assemblages of the Dwarskersbos deposits consist of exclusively marine and marginal-marine species, suggesting that the sediments were sourced from shallow water environments as well as the adjacent beach. It was further noted that the foraminiferal tests of these deposits consist of higher abundance of corroded and fragmented tests indicating deposition by high-energy conditions. , Thesis (D.Phil) -- Faculty of Science, School of Environmental Sciences, 2023
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Date Issued: 2023-12

Field mapping and geochemistry of lower Jurassic sediments and volcanics of the upper Karoo supergroup near Ha Mosi, Lesotho mountains

Authors: Valashiya, Khaya
Date: 2023-12
Subjects: Sediments (Geology) -- South Africa -- karoo basin , Geochemistry , Geological mapping
Language: English
Type: Master's theses , text
Identifier: http://hdl.handle.net/10948/62687 , vital:72925
Description: Geological mapping in the Lesotho-Drakensberg Mountains spans over 100 years with du Toit and Stockley being the major contributors to the published maps and to the understanding of emplacement of the Karoo Large Igneous Province (KLIP) in the countries of South Africa and Lesotho. Despite the detailed previous work, there remains limited data on paleoenvironmental changes at the contact between the sedimentary and volcanic sequences of the upper Karoo Supergroup. This study aims to map the lithostratigraphic boundaries, volcano-sedimentary facies and faults near Ha Mosi in southern Lesotho. A total 48 rock samples were collected for petrography, XRF and ICP-MS analyses. The new results were used to characterize the local chemostratigraphy and to propose new regional correlations across Lesotho and South Africa. In this thesis, eight lithostratigraphic units were defined with a total thickness of 550 m. The first two units (Units 1 and 2) comprise massive and bedded sandstones, interpreted as possible floodplain and ephemeral lacustrine deposits; these are ascribed to the upper Stormberg Group. These units are unconformably overlain by locally preserved thin basaltic (Unit 3) flows that are characterised by high Zr/Nb and Zr/Y ratios; and low Ti/Zr and P/Zr ratios similar to the Golden Gate Unit of the Drakensberg Group. The lava flows are overlain by bedded sandstone ascribed to Unit 4 and volcaniclastic breccia ascribed to Units 5 and 6. Unit 6 consists of a monolithic breccia that is composed of angular sandstone clasts similar to those of the underlying Stormberg Group. The monolithic breccia transitions upwards into a massive megaclastic clast-supported volcanic breccia, which consists of angular to sub-rounded basaltic and doleritic boulders. Petrified wood fragments are found within the megaclastic breccia, indicating the presence of vegetation during deposition and enhanced preservation. Unit 6 laterally grades into Unit 5, which is characterised by poorly bedded breccia composed of angular sandstone, mudstone clasts with minor basaltic and doleritic clasts and, breccia intraclasts. The breccia units are often associated with reworked sediments interpreted to be deposited by fluvial systems. The breccia is conformably overlain by basaltic lava flows (Unit 8) characterised by high Ti/Zr and P/Zr ratios and moderate to low Zr/Y and Zr/Nb ratios compared to the Unit 3 lavas and is similar to that of the Sani Pass Unit of the Drakensberg Group. The basaltic sequences in the Ha Mosi studied area preserve both pahoehoe textures and pillow lavas, indicating subaerial and subaqueous volcanism. The studied lithologies are intruded by gabbro and dolerites of the Karoo Dolerite Suite at 183 Ma. This stratigraphy records the transition from sedimentation in the Karoo Basin through to a dominantly volcanic succession, which has importance in terms of the Toarcian extinction at ca. 182 Ma. Mapped faults and associated fractures are orientated predominantly NW-SE with the hanging walls moved maximum 80 m to the south. The different dykes and fault structures possibly relate to the Weddel Triple Junction that developed during the Early Jurassic break up of Gondwana, between 200 and 180 Ma. The mapped lavas show that the magma source was a chemically heterogenous mantle that was subjected to different degrees of partial melting, with the introduction of small-scale chemical heterogeneities. The geodynamic setting is comparable to the Afar Triangle of north-east Africa where active tectonics created a large-scale NW-SE orientated fault system in response to crustal thinning and rifting. In both the Afar and Lesotho, vertical movements created lowlands that allow for the preservation of volcanic breccia and basalts with pillow lavas. These findings show that existing geological models in the Drakensberg-Lesotho Mountains can be improved upon detailed field mapping and geochemistry. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2023
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Date Issued: 2023-12

Finite difference methods for Burgers-Huxley equation and biofilm formation

Authors: Tijani, Yusuf Olatunji
Date: 2023-12
Subjects: Burgers equation , Terrestrial heat flow , Applied mathematics
Language: English
Type: Doctorial theses , text
Identifier: http://hdl.handle.net/10948/62732 , vital:72934
Description: In this thesis, we constructed some versions of finite difference scheme for the Burgers-Huxley equation and for a set of partial differential equations (PDEs) arising in biofilm formation. The Burgers-Huxley equation serves as a fundamental model that describes the interaction between reaction mechanisms, convection effects, and diffusion transport. It has applications in the study of wave mechanics, population dynamics, physiology, fluid mechanics to list but a few. The study of biofilm formation is becoming increasingly important due to micro-organisms (i.e. bacteria) forming a protected mode from the host defense mechanism which may result in alteration in the host gene transcription and growth rate. Applications can be found useful in the treatment of bacterial infections, contamination of foods and water quality. We designed two nonstandard finite difference and two exponential finite difference schemes for the Burgers-Huxley equation. Numerical experiments with six cases and in three different regimes were studied. We show that the nonstandard scheme preserves the properties of the continuous equation which include positivity and boundedness. The stability region of the explicit exponential scheme was obtained and we outlined the algorithm for the implicit exponential scheme. The performance of the four schemes are compared in regard to absolute error, relative error, L1 and L∞ norms. For a singularly perturbed Burgers-Huxley equation, a novel nonstandard finite difference technique is constructed. It is demonstrated numerically that the NSFD scheme outperforms the classical scheme by comparing maximum pointwise errors and rate of convergence. We then solved the 2D Burgers-Huxley equation using four novel nonstandard finite difference schemes (NSFD1, NSFD2, NSFD3 and NSFD4). The numerical profiles from NSFD1 and NSFD2 exhibit some deviation from the exact profile. Our quest for a better performing scheme led to the modification of NSFD1 using the remainder effect technique. NSFD4 was designed by employing the time splitting approach. All the schemes preserve the properties of the continuous model (positivity and boundedness). The performance of all the schemes are analysed. We construct three nonstandard finite difference schemes for the equations modelling biomass equation and coupled substrate-biomass system of equations respectively. We checked the accuracy of our scheme by the conservation of physical properties (positivity, boundedness, biofilm formation and annihilation) since an analytical solution is not available. We show the instability, lack of conservation of physical properties by the classical scheme. Our proposed scheme shows good performance when compared with other results in the literature. The results here give more insight into the benefits of the nonstandard finite difference approximations. , Thesis (DPhil) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics , 2023
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Date Issued: 2023-12

Functional traits and potential physical drivers of offshore benthic epifauna on the west and south coast of South Africa

Authors: Van Stavel, Jordan , Morris, Tamaryn
Date: 2023-12
Subjects: Marine ecology , Marine biology -- South Africa , Oceanography -- South Africa
Language: English
Type: Master's theses , text
Identifier: http://hdl.handle.net/10948/62698 , vital:72931
Description: Offshore benthic ecosystems (> 200 m depth) are challenging to access and remain poorly studied globally. Epifaunal invertebrates comprise a critical trophic level in benthic ecosystems and can serve as indicators of the overall health and functioning. There is limited knowledge of South Africa’s offshore marine environment and benthic ecosystem functioning due to limitations in funding, resources, and the lack of suitable science-based monitoring tools which are vital for sustainable management into the future. The aim of this research was to improve the understanding of epifaunal functioning as well as their potential physical drivers in 13 South African offshore biogeographic ecotypes. The objectives of this study were threefold: 1) to investigate the functional composition of benthic epifauna from 13 biogeographic ecotypes, 2) to quantify the Functional Diversity (FD) associated with epifaunal traits between the different assemblages (i.e. biogeographic ecotypes), and 3) to evaluate the relationship between physical variables and epifaunal functional traits at the biogeographic ecotype level. Biological trait-based approaches were applied to a subset of 80 benthic epifaunal species collected from 909 offshore stations along the west and south coasts of South Africa. Nine biological traits (associated with life history, morphology and behavioural characteristics exhibited by each species) were classified into 39 modalities and weighted with biomass. Community Weighted Means (CWMs) were used to evaluate the benthic epifaunal functional trait composition of the 13 biogeographic ecotypes. Functional composition across the 13 ecotype assemblages on the west and south coast appeared to be dominated by species with similar trait compositions, such as large, long-lived, surface crawling/burrowing/filter-feeding epifauna with medium to no mobility, however, their percentage of contribution to trait expression (CWMs) was higher on the west coast. Functional diversity indices (alpha and beta) showed higher overall FD for west coast ecotypes, with most ecotypes on the continental shelf (except slopes and canyons) being significantly different (p<0.05) from ecotypes on the south coast. The global RLQ (three-table co-inertia) test did not reveal a significant relationship between biomass and physical variables or between biomass and traits (p>0.05). The fourth-corner method was used to test the significance of individual traitenvironment relationships. The fourth-corner results were similar overall to the RLQ analysis, revealing that three physical variables (temperature, depth, and fluorescence) were significantly correlated to two trait modalities belonging to the feeding mode filter-feeders (FM1) and scavengers (FM5). Scavengers were positively correlated with depth and negatively with temperature, while filter-feeders were positively correlated with fluorescence levels. This indicated that the presence of scavenging epifauna increased with a decrease in temperature and an increase in depth. While a positive significant correlation between filter-feeders and fluorescence suggested their potential tolerance or preference for environmental conditions with high levels of fluorescence. This research was the first such study to explore the functional composition and diversity of benthic epifauna and their relationship with potential physical drivers in offshore west and south coast benthic biogeographic ecotypes of South Africa. The application of new tools to quantify the functional diversity of epifauna as indicators of ecosystem health, and their potential physical drivers. This provided a platform on which to advance our understanding of benthic communities and the roles they play in ecosystem functioning under changing environments. Functional trait-based approaches such as those applied in this study can provide us with vital information on the relationship between biodiversity, ecosystem functioning, and physical drivers. Environmental stressors and changing climate patterns threaten to impact marine ecosystems and their functioning. Benthic epifauna are especially sensitive to changes in their environment and these fluctuations could potentially lead to the loss of certain benthic functionality, altering the thresholds these ecosystems have to response to disturbances. This undermines the stability of these ecosystems which can have ripple effects on the health of these ecosystems and their ability to provide the ecosystem services humans dependent on. Having suitable tools to track current and predict future changes will therefore be vital to inform management and conservation strategies for sustainable ocean utilisation. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2023
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Date Issued: 2023-12

Insights into the relative abundance, demographics and behaviour of sea turtles along the east coast of South Africa

Authors: dos Santos, Natalie Aida
Date: 2023-12
Subjects: Sea turtles -- Conservation -- South Africa , Sea turtles -- South Africa , Photogrammetry
Language: English
Type: Master's theses , text
Identifier: http://hdl.handle.net/10948/62495 , vital:72778
Description: Sea turtles are ecologically important species that have endured a history of overexploitation. Combined with their long, complex life cycles and ongoing anthropogenic pressures, they remain conservation-dependent. Conservation efforts worldwide focus on sea turtle nesting beach protection, however, comprehensive management strategies require an understanding of their lives at sea which are often spent in distant waters. This understanding is hindered by the relative challenges of in-water studies. South Africa has also focused research and conservation efforts on nesting adult female loggerheads (Caretta caretta) and leatherbacks (Dermochelys coriacea), largely overlooking the species or age classes remaining at sea. Green turtles (Chelonia mydas), hawksbills (Eretmochelys imbricata) and non-breeding loggerheads are frequently stranded and rehabilitated by aquaria, and observed by recreational divers on reefs, suggesting year-round residency along the country’s entire seaboard. Recent technological advancements in photo-identification methods for sea turtles, underwater photography and internet connectivity allowing even recreational divers to become citizen scientists now place us on the verge of an exciting opportunity to unravel the cryptic in-water ecology of these species. The overall aim of this study was to conduct the first assessment of relative abundance, demographics, distribution, and behaviour of sea turtles on reefs within the iSimangaliso and Aliwal Shoal Marine Protected Areas (MPAs) on the east coast of South Africa. A robust photo-identification database was established from research dives, voluntourism and citizen science contributions over a two-year period. From 1057 sightings in the two MPAs, a total of 227 individual sea turtles were identified constituting three species (green turtles: n = 120; hawksbills: n = 46; loggerheads: n = 61). Their relative abundance was proportional to the overall sizes of the South West Indian Ocean (SWIO) populations (green turtles > hawksbills > loggerheads > leatherbacks). However, sightings per unit effort (SPUE) showed that loggerheads were more prevalent than hawksbills in iSimangaliso, likely due to its proximity to this loggerhead rookery. Reefs supported mixed size aggregations with juvenile to adult-sized green turtles (straight carapace lengths, SCLs of 44.9–99.2 cm), whilst hawksbills were mostly juveniles or subadults (SCL range: 37.4–73.4 cm) and loggerheads were mostly adult-sized (SCL range: 66.9–81 cm). Adult sex ratios were slightly female-biased but not significantly different from 1:1. The longest minimum residence periods recorded for individual subadult green and hawksbill turtles (676 and 675 days respectively) and adult-sized loggerheads (621 days) were suggestive of residency. Resident sea turtle activities were typical; they wereobserved foraging, resting, cleaning and interacting year-round, whilst only loggerheads and leatherbacks were observed in breeding behaviour (e.g., patrolling and mating) just after the seasonal arrival of transient individuals. This study thus reveals that the east coast of South Africa hosts regionally important resident and transient sea turtle aggregations with some of the highest SPUE results recorded for the region. This first attempt at monitoring foraging grounds using a variety of techniques and stakeholder groups can serve as the baseline assessment for future work and the foundation for a long-term in-water monitoring programme, allowing for expansion along the entire coastline. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2023
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Date Issued: 2023-12

Integrating state-space modelling and systematic conservation planning to recommend penguin-fishery management zones in Algoa Bay, South Africa

Authors: Stockdale, Victoria , Goodall, Victoria , Clifford-Holmes, Jia
Date: 2023-12
Subjects: Biodiversity conservation -- South Africa -- Port Elizabeth , Natural resource conservation , Marine ecology
Language: English
Type: Master's theses , text
Identifier: http://hdl.handle.net/10948/62611 , vital:72828
Description: Direct anthropogenic impacts on vulnerable marine ecosystems are growing and require effective conservation measures. Integrating the cost impacts of conservation interventions and optimising the spatiotemporal scale of management interventions may improve cohesion between opposing marine users. This study aimed to integrate spatial and temporal models to advise dynamic penguin-fishery management plans in Algoa Bay, off Gqeberha, South Africa, that would maximise penguin foraging success while minimising the impact on the fishing industry. Determining the foraging locations important to breeding penguins is fundamental when understanding the relationship between fisheries and prey availability. Using Global Positioning System (GPS) data gathered from feeding trips of breeding African penguins between 2012 and 2017, and a hidden Markov model, three behavioural states (foraging, commuting, transitioning) were inferred and used as conservation targets in spatial prioritisation using the prioritizr package in R. The cost to the fishery was estimated using the catch of pelagic fish by the fishing industry between 2012 and 2015 as the proxy. The energetic cost to penguins was the distance they travelled from their breeding colony. Nine prioritisation scenarios, varying in levels of conservation for penguins, spatial cohesion and costs to fisheries, were developed using all year’s combined data to explore an ‘optimal’ closure configuration. The optimal closure was determined as an area which met the targets for penguin conservation, with a low cost to the fishery, close to the breeding colony and spatially clumped. The best solution from each scenario was isolated and the solution for the conservation target of 20% foraging habitat, 10% commuting habitat and 10% transitioning habitat and a boundary penalty of 0.01 (a dimensionless value that is used to reduce spatial fragmentation – increasing the value of the parameter signals that it is important to minimise the total exposed boundary of the prioritisation by favouring solutions where units are clumped together) was chosen as the optimal closure. This configuration was used as a static closure and applied to individual fishing seasons to estimate how the cost of a static closure design to the fishery would vary between seasons. Subsequently, a dynamic closure was designed using the same optimal configuration criteria every year, and the cost to the fishing industry was compared seasonally with the cost of a static closure. The cost to fisheries of dynamic closures was consistently lower than that of a static closure and the area required to meet the penguin feeding targets was drastically reduced. While dynamic closure scenarios show promise to minimise costs to the industry while meeting penguin conservation targets, these configurations were designed retrospectively with data collected after the end of the fishery seasons. For efficient management, the closures need to be designed by using data collected at an appropriate temporal scale. For that, the critical missing dimension to this study is the addition of real-time data on pelagic fish positions, areas of fishing intensity and sites of penguin foraging to create appropriate recommendations for up-to-date fishery exclusion zones. Therefore, the priority now is to explore methods of collecting real-time data on pelagic fish abundance, feeding behaviour of penguins at sea, site and mass of pelagic fishery catch, and using these data to delineate real-time, dynamic closures, coupled with a governance and management strategy that can implement dynamic closures. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2023
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Date Issued: 2023-12

Investigating the effect of peptide-functionalized gold nanoparticles on colon cancer cells

Authors: Ramagoma, Rolivhuwa Bishop
Date: 2023-12
Subjects: Colon (Anatomy) -- Cancer -- Research , Colon (Anatomy) -- Cancer -- Treatment , Nanoparticles
Language: English
Type: Master's theses , text
Identifier: http://hdl.handle.net/10948/62564 , vital:72824
Description: Colon cancer like any other cancer is a condition in which cells grow uncontrollably and may even spread to other regions of the body through metastasis. Colon cancer was ranked the second leading cause of cancer related deaths worldwide in 2018. Research to advance treatment of cancer keeps advancing daily, However, a big challenge is drug-induced side effects due to toxicity against normal body cells. Therefore, the development of controlled release technologies in conjunction with targeted drug delivery may provide a more efficient and less dangerous approach to overcome the limits of traditional chemotherapy. Including the creation of nanoscale delivery vehicles capable of directing the release of chemotherapeutic drugs into cancer cells only. This study aims to investigate p14 peptide that would specifically target colorectal cancer cells and not normal body cells to develop a targeted drug delivery system using gold nanoparticles. This study serves as a pilot study of the primary aim. To achieve this, the effect of the peptide p14 and peptide functionalized gold nanoparticles (p14-AuNP) on colon cancer cells (HT-29) and normal epithelial cells (KMST-6) was determined. Firstly, gold nanoparticles were chemically synthesised and then functionalized with p14 peptide through Polyethylene glycol. Then assessment of their effect through in vitro cytotoxicity assay (MTT) and gene expression analysis (RT-qPCR) was conducted. Nanoparticles’ synthesis and functionalization was performed and confirmed: In vitro cytotoxicity through MTT assay was successfully conducted and p14-AuNP showed toxicity against colon cancer cells and lesser toxicity towards normal cells as compared to 5-Flourouracil (commercially approved drug for colon cancer treatment). Gene expression analysis revealed that apoptosis was induced in both cell lines by p14-AuNP either through upregulation of caspase 3, 7 and/or BCL2. A cell survival gene, AKT1, also had significant effect on this. CDC42 was downregulated which indicates that cell proliferation was inhibited. , Thesis (MSc) -- Faculty of Science, School of Biomolecular & Chemical Sciences, 2023
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Date Issued: 2023-12

Investigating the interannual variability of the Benguela coastal upwelling system using a ROMS numerical model from 1993-2014

Authors: Silima, Rudzani Faith , Roagosha, Moagabo
Date: 2023-12
Subjects: Oceanography , Coasts , Marine sciences
Language: English
Type: Master's theses , text
Identifier: http://hdl.handle.net/10948/62586 , vital:72826
Description: The seasonal and interannual variability of the coastal Benguela upwelling system is described using 22 years (September 1993 - December 2014) of a regional Ocean model (ROMS) output. The model-derived SSTs are evaluated against satellite SSTs (GHRSST) and biases between the datasets investigated, allowing for confidence in using the ROMS data to investigate details of spatial and temporal variability over the Benguela System. Variability of coastal SSTs are investigated together with alongshore winds (from the ERA-Interim Reanalysis product). The driver of the seasonality in upwelling in the Benguela region is the seasonal shift of the South Atlantic High pressure system, leading to an enhanced seasonal signal in the southern Benguela (with strongest upwelling favourable winds in austral spring and summer). In the northern Benguela, the seasonal signal reduces with the peak of upwelling favourable winds shifting to late winter and spring. Interannual variability is evident in the model and is investigated with respect to various modes of climate variability. Though the direct relationship of the Benguela upwelling system to large-scale climate modes such as SAM and ENSO is not clear in most places, some evidence was found for their connection. For instance, in the southernmost cell of the southern Benguela a significant positive and negative correlation exists between SST and wind respectively with ENSO during summer months. This relates to increased (decreased) winds and decreased (increased) SST during La Niña (El Niño) events. Although there was no direct correlation with either SST or alongshore wind anywhere in the Benguela system, there was some indication of its importance. A trend toward a positive SAM (i.e a more poleward position of the South Atlantic High-Pressure system) was consistent with a trend toward enhanced winds and reduced SSTs in the southernmost upwelling cell. In addition to this, there was evidence to suggest that when SAM and ENSO are out-of-phase, which occurred primarily during summer months, the wind and SST response is amplified. This seemed to be particularly true in the first 10 years of the timeseries when the anomalies were strongly alternating. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2023
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Date Issued: 2023-12

Marine benthic (epilithic) diatom communities along the coast of South Africa: A contribution to their diversity, spatio-temporal variations, and ecology

Authors: Cotiyane-Pondo, Phumlile
Date: 2023-12
Subjects: Marine ecology , Marine biodiversity , Coastal ecology
Language: English
Type: Doctorate Dissertation , text
Identifier: http://hdl.handle.net/10948/62453 , vital:72754
Description: Diatoms remain one of the most diverse and ecologically important microorganisms within microphytobenthos. The highly variable South African coastline, comprised of heterogeneous rocky intertidal habitats provides the ideal study area to investigate epilithic microphytobenthos and their associated influential drivers. In South Africa, in-depth taxonomic research on marine littoral diatoms exists, however, quantitative research and knowledge on their abundance, diversity, community composition and distribution remain limited. Thus, the main aim of this research was to explore the spatial and temporal variability of marine benthic (epilithic) diatoms, in relation to the variable physico-chemical conditions in the nearshore intertidal environments along the coastline of South Africa. To achieve this, field-based observational (natural substrata) and experimental (artificial substrata) studies were conducted on selected locations around the coastline, with a large focus on south coast localities. For the Spatial studies, large (i.e., encompassing all three biogeographical regions) and small-scale (i.e., coastal island in the warm temperate region) surveys of epilithic diatom assemblages from natural rocky substrata were conducted. Large-scale investigation results revealed highly variable diatom assemblages, diversity and distribution, with compositional differences observed between the coastal sections (around the coastline). A total of 85 diatom taxa from 31 genera were observed at 15 sites, and the number of taxa varied un-systematically along coastline. Genera with noticeable contribution included Nitzschia, Cocconeis and Achnanthes. On the coastal Bird Island (small-scale), similar variability was observed, but with a much higher diatom diversity and number of rarely observed species (e.g. Actinoptychus senarius (Ehrenberg) Ehrenberg, Cocconeis capensis (Cholnoky) Witkowski, Fragilariopsis kerguelensis (O’Meara) Hustedt, Striatella unipunctata (Lyngbye) Agardh. Seventy-two (72) species from 35 genera were recorded with a varied abundance and diversity around the island. The study also revealed a high contribution of typical benthic diatom species to the surf zone environment around the island. To study temporal variations, medium-term compositional differences on natural substrata were assessed monthly over an annual cycle at a single site. A paucity of diatom material was evident during this study and observations indicated a trend of presence and absence of diatom taxa from the study site. Nineteen (19) diatom genera were identified and those observed, albeit as one or two individual valves, included taxa from several genera including Biddulphia, Diploneis, Campyloneis, Trachyneis and Triceratium. Noteworthy was a seasonal increase in the number of diatom valves encountered, with the highest diatom abundance observed during spring (September) and the genera Cocconeis, Grammatophora and Navicula appearing regularly. To complement the sparse data from the long-term temporal study, a short-term experimental study on artificial substrata (Plexiglass) revealed rapid temporal variations of benthic diatom assemblages. The composition differed spatio-temporally during the experimental period, with fluctuating species occurrences and abundances between the two study sites. The experimental study also revealed the highest number of diatom species observed during this research (134 species belonging to 44 genera). While Cocconeis (13 species) and Nitzschia (9 species) were the dominant genera, 48% of the diatomcomposition was composed of rarely observed taxa that included Cocconeis testudo Giffen, Donkinia sp., Paralia sulcata (Ehrenberg) Cleve. Regarding environmental drivers, the findings indicated the importance of temperature and nutrients in driving diatom spatial abundance and composition along the coastline, as well as the island. However, the potential influence of the interplay between measured variables and unexplored coastal oceanographic processes (e.g., wave action) was noted. Temporally, from the annual study, the nature of the rocky substrate (rock type) rather than environmental conditions was postulated to have been the influential factor that resulted in the low diatom abundance data, however this requires further in-depth investigations on the influence of rock microtopography on microphytobenthos in this region. Contrastingly, the experimental study results indicated environmental variables having varying influences on the diatom diversity indices, however, study site and sampling occasion were revealed as the most important predictors of the observed variability. Further, site-specific biofilm processes, including biological interaction (e.g. grazing), were shown to alter biofilm succession, thus influencing the observed diatom assemblages. Overall, this research provided new and relevant knowledge on the variability of benthic (epilithic) diatom composition, biodiversity and distribution along the coastline, further contributing to our understanding of marine benthic diatoms ecology, their ecological role in the context of intertidal food web and their potential as bioindicators of change in the coastal ecosystems in Southern Africa. , Thesis (PhD) -- Faculty of Science, School of Environmental Sciences, 2023
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Date Issued: 2023-12

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