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Evaluation of SNPs of G6PD, with regard to the 3D conformational, structural and stability alterations, in order to investigate the clinical implications and potential applications

  • Authors: Sanabria, Natasha Mary-Anne
  • Date: 2019
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/76500 , vital:30574
  • Description: Expected release date-April 2020
  • Full Text: false
  • Date Issued: 2019

Exploration of challenges in bringing traditional medicine into SA’s healthcare system, using medicinal plants for treatment of waterborne diarrhoeal diseases as a case study

Factors influencing survivorship of Portulacaria afra cuttings in restoration of degraded lands

  • Authors: Sholto-Douglas, Craig
  • Date: 2019
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/92230 , vital:30692
  • Description: Heavy over-browsing, over-grazing, and over-trampling has caused the degradation of vast areas of subtropical thicket, including parts of the Greater Addo Elephant National Park (GAENP). Severe degradation has resulted in the loss of vegetation cover and the deterioration of soils and soil functioning. The South African Department of Environmental Affairs (DEA), and specifically the Natural Resource Management Programme (NRM), have invested in restoration initiatives such as the Subtropical Thicket Restoration Programme (STRP), which has aimed to demonstrate the logistical and practical feasibility of restoring these degraded thickets by planting en masse Portulacaria afra (spekboom) cuttings. However, the planted P. afra cuttings often succumb to various abiotic and biotic stresses. This project aimed to identify various factors which may influence the survival of P. afra cuttings, including i) soil properties, ii) water (rainfall, infiltration, run-off, etc.), iii) browsing by mega-herbivores, iv) topographical features such as slope and aspect, or v) plant species or communities. Biodiversity and carbon baselines were carried out at 50 plots within the Main Camp, Darlington and Kabouga sections of the GAENP, providing pre-planting vegetation and soil data. The en masse planting of P. afra occurred following the completion of the baselines. Following a minimum rest period of three months after planting, survivorship counts were carried out at all plots. Infiltration rate had a significant positive relationship with planted P. afra survivorship across all of the sites. Positive trends between increases in litter and root biomass and planted P. afra cuttings survivorship in Kabouga were also evident. Magnesium, water-holding capacity and increasing soil clay percentage were found to have a significant negative relationship with planted P. afra survivorship in Kabouga. Aluminium, magnesium, and boron all had significant positive relationships with planted P. afra cuttings survivorship in Addo Main Camp. No soil variables had any significant relationship with survivorship of planted P. afra cuttings at Darlington. The presence of elephants (Loxidonta africana) had a significant negative relationship with planted P. afra survivorship. Plant communities in more ‘moderately’ degraded states, characterized by the retention of canopy dominant species, woody vegetation cover, limited bareground and higher cover of litter had higher survivorship of planted P. afra cuttings than those in more severely degraded states. The grass Panicum maximum, and forb Atriplex semibaccata were associated with positive relationships with planted P. afra survivorship across all sites. Future research should aim to develop matrices which plot likely survivorship percentages with parameters of measurable variables, such as infiltration, severity of soil capping, browsing densities, chemical indicators, and degradation severity, to identify suitable biophysical planting conditions for P. afra cuttings. Further research should assess whether the presence of elephants, in high densities, can reduce the economic feasibility of the en masse plantings of P. afra cuttings in attempts to restore degraded landscapes.
  • Full Text:
  • Date Issued: 2019

Foreground simulations for observations of the global 21-cm signal

  • Authors: Klutse, Diana
  • Date: 2019
  • Subjects: Cosmic background radiation , Astronomy -- Observations , Electromagnetic waves , Radiation, Background
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/76398 , vital:30557
  • Description: The sky-averaged (global) spectrum of the redshifted 21-cm line promises to be a direct probe of the Dark Ages, the period before the first luminous sources formed and the Epoch of Reionization during which these sources produced enough ionizing photons to ionize the neutral intergalactic medium. However, observations of this signal are contaminated by both astrophysical foregrounds which are orders of magnitude brighter than the cosmological signal and by non-astrophysical and non-ideal instrumental effects. It is therefore crucial to understand all these data components and their impacts on the cosmological signal, for successful signal extraction. In this view, we investigated the impact that small scale spatial structures of diffuse Galactic foreground has on the foreground spectrum as observed by a global 21-cm observation. We simulated two different sets of observations using a realistic dipole beam model of two synchotron foreground templates that differ from each other in the small scale structure: the original 408 MHz all-sky map by Haslam et al. (1982) and a version where the calibration was improved to remove artifcats and point sources (Remazeilles et al., 2015). We generated simulated foreground spectra and modeled them using a polynomial expansion in frequency. We found that the different foreground templates have a modest impact on the simulated spectra, generate differences up to 2% in the root mean square of residual spectra after the log-polynomial best fit was subtracted out.
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  • Date Issued: 2019

Functional characterization of the nuclear localisation and export signals of the human Hsp70/Hsp90 organising protein (HOP)

  • Authors: Rousseau, Robert
  • Date: 2019
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/97819 , vital:31489
  • Description: Expected release date-April 2021
  • Full Text: false
  • Date Issued: 2019

Ground thermal regimes in Western Dronning Maud Land, Antarctica in 2016

  • Authors: Masebe, Consliah Tebogo
  • Date: 2019
  • Subjects: Climatic changes -- Antarctica , Frozen ground -- Research -- Antarctica , Frozen ground -- Thermal properties -- Antarctica , Queen Maud Land , Earth temperature -- Antarctica , Soil temperature -- Antarctica -- Measurement
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/95581 , vital:31173
  • Description: Research shows that the climate of Antarctica is changing and, it is vital that the change is monitored to understand how it will affect global ecosystems. Since the International Polar Year (IPY) 2007-2008, research in permafrost studies has grown. However, there are still existing gaps that impede complete understanding of Antarctic cold environments and landscape processes. Permafrost has been noted as one of the major controlling factors of the terrestrial ecosystem dynamics in Antarctica. However, the understanding of Antarctic permafrost, when compared to other cryospheric components, is limited, especially its thermal and physical properties, evolution, as well as links to pedogenesis, hydrology, geomorphic dynamics, and responses to global change. This project provided an understanding and insight to over-arching research that evaluates the state and status of permafrost and the active layer in Dronning Maud Land (DML) through examining short-term variations on ground thermal regimes. The main focus is on understanding the influence of synoptic, diurnal and seasonal events on the active layer in 2016. Analysis of available data shows that ground thermal regimes are influenced by variations in air temperature, pressure, wind speed and to some extent, relative humidity. Subsequently, ground thermal regimes also depend on soil physical characteristics including sediment particle size and bulk density. Furthermore, sediment particle size and bulk density have been found to have a great influence on thermal propagation rates as well as active layer depth; the higher the bulk density, the higher the thermal propagation rate and the lower the bulk density, the lower the thermal propagation rate. Conversely, a large proportion of bigger sediment particle size in soil corresponds with a higher thermal propagation rate and a large proportion of smaller sediment particle size in soil corresponds with a lower thermal propagation rate. Also, ground thermal regimes vary according to seasons. Ground temperatures are more variable in summer, while air temperatures are more variable in winter. The variability according to different seasons shows that the active layer responds to seasonal climatic variations. Additionally, the active layer also responds to synoptic and diurnal weather events.
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  • Date Issued: 2019

How do urban dwellers identify with features within urban green spaces in the Eastern Cape?

  • Authors: Manyani, Amanda
  • Date: 2019
  • Subjects: Land use, Urban -- South Africa , Greenbelts -- South Africa , City planning -- South Africa
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/95596 , vital:31174
  • Description: Public urban green spaces contain natural and artificial features which play crucial roles in supporting urban social-ecological systems, a fact now recognized globally. The various natural and artificial features contained in public urban green spaces are said to be key contributors to the quality of life and well-being of urban dwellers. Nevertheless, this has been largely ignored in urban design in South Africa, especially in the poorer township and Reconstruction Development Program (RDP) areas. At the individual household and community levels within the poorer communities, the provision of green spaces and trees, as well as recreation facilities, is well below world standards, and much less than what is available in the more affluent areas of South African towns. Additionally, most research on the links between nature and human well-being in urban contexts comes from developed world contexts which adopt a westernized view of the relationship. Yet, in many societies of the Global South, including South Africa, worldviews and experiences of nature in green spaces and use of other recreational features takes on different meanings to those of the Global North. To show these differences, a combination of methods was used in this study, different types of green spaces were assessed and evaluated by structured observations so as to record the features present within the spaces. A survey of 360 households was conducted by targeting green space users and households within 100 metres from a green space. Results indicated that, across all the green space types, formal green spaces had a low cover of shrubs, trees and herbs whilst having high lawn cover. Furthermore, vegetation had poor rating across all the green spaces since the vegetation was either overgrown herbs, dense thickets of shrubs and mostly alien trees that were either diseased or forked. Similar to the disparity in the composition and structure of vegetation within the green spaces, there was a wide variability in the composition of recreational features and amenities across the green spaces. The formal green spaces had the most amenities like play equipment, shelter and seating. Informal green spaces and commonages had little or no recreational features available. The attributes of these spaces therefore influenced the reasons for visiting as more than 90 % of the respondents simply used the spaces for transit. With regards to attitudes and preferences towards particular features, they were emerging sense of strong negative feelings towards natural features. Most respondents emphasized the need for green spaces that are well laid out with maintained lawns, recreational facilities and open vegetation. Thus, the current design and available features within the studied urban green spaces do not meet local needs and aspirations and thus do not contribute to better well-being and quality of life as much as they could. Specifically, the various health benefits linked with being in contact with nature in the public green spaces were not evident in this study. The South African specific context in green space use, perception and people’s preferences is thus crucial for urban planning and sustainability.
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  • Date Issued: 2019

Identification of possible natural compounds as potential inhibitors against Plasmodium M1 alanyl aminopeptidase

  • Authors: Soliman, Omar Samir Abdel Ghaffar
  • Date: 2019
  • Subjects: Plasmodium , Malaria -- Chemotherapy , Plasmodium -- Inhibitors , Drug resistance in microorganisms , Aminopeptidases
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/72284 , vital:30026
  • Description: Malaria is a major tropical health problem with a 29% mortality rate among people of all ages; it also affects 35% of the children. Despite the decrease in mortality rate in recent years, malaria still results in around 2000 deaths per day. Malaria is caused by Plasmodium parasites and is transmitted to humans via the bites from infected female Anopheles mosquitoes during blood meals. There are five different Plasmodium species that can cause human malaria, which include Plasmodium falciparum, Plasmodium vivax, Plasmodium malariae, Plasmodium ovale and Plasmodium knowlesi. Among these five species, the most pathogenic ones are Plasmodium falciparum and Plasmodium vivax. Malaria is usually hard to diagnose because the symptoms are not exclusive to malaria and very similar to flu, e.g., fever, muscle pain, and chills, which lead to the misdiagnosis of malaria cases. Malaria is lethal if not treated because it can cause severe complications in the respiratory tract, liver, metabolic acidosis, and hypoglycemia. The malaria parasite life cycle includes two types of hosts, i.e., a human host and female Anopheles mosquito host. Malaria continuously develops resistance to the available drugs, which is one of the major challenges in disease control. This situation confirms the need to develop new drugs that target virulence factors of malaria. The malarial parasite has three main life cycle stages, which include the host liver stage, host blood stage and vector stage. In the blood stage, parasites degrade hemoglobin to amino acids, which is important as these parasites cannot produce their own amino acids. Different proteases are involved in this hemoglobin degradation process. M1 alanyl aminopeptidase is one of these proteases involved at the end of hemoglobin degradation. This study focused on M1 alanyl aminopeptidase as a potential drug target. M1 alanyl aminopeptidase consists of four domains: N-terminal domain, catalytic domain, middle domain and C-terminal domain. The catalytic domain remains conserved among different Plasmodium species. Inhibition of this enzyme might prevent Plasmodium growth as it can’t produce its own amino acids. In this study, sequence analysis was carried out in both human and Plasmodium M1 alanyl aminopeptidase to identify conserved and divergent regions between them. 3D protein models of the M1 alanyl aminopeptidase from Plasmodium species were built and validated. Then the generated models were used for virtual screening against 623 compounds retrieved from the South African Natural Compounds Database (SANCDB, https://sancdb.rubi.ru.ac.za/). Virtual screening was done using blind and targeted docking methods. Docking was used to identify compounds with selective high binding affinity to the active site of the parasite protein. In this study, one SANCDB compound was selected for each protein: SANC00531 was selected against P. falciparum M1 alanyl aminopeptidase, SANC00469 against P. knowlesi, SANC00660 against P. vivax, SANC00144 against P. ovale and SANC00109 against P. malariae. It was found that Plamsodium M1 alanyl aminopeptidase can be used as a potential drug target as it showed selective binding against different inhibitor compounds. This result will be investigated in future work though molecular dynamic analysis to investigate the stability of protein-ligand complexes.
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  • Date Issued: 2019

Interaction between the root-feeding beetle, Longitarsus bethae (Coleoptera: Chrysomelidae) and the root-knot nematode, Meloidogyne javanica (Nematoda: Heteroderidae): Implications for the biological control of Lantana camara L. (Verbenaceae) in South Africa

  • Authors: Musedeli, Jufter
  • Date: 2019
  • Subjects: Insect-plant relationships , Insects -- Host plants , Flea beetles , Symbiosis , Longitarsus , Chrysomelidae , Lantana camara -- Biological control -- South Africa , Heteroderidae , Root-knot nematodes , Weeds -- Biological control -- South Africa
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/71130 , vital:29788
  • Description: Plants often are simultaneously attacked by several herbivores that can affect each other’s performance, and their interaction may affect their host plant fitness. The current study was conducted to determine the interaction between the root-feeding beetle, Longitarsus bethae Savini & Escalona (Coleoptera: Chrysomelidae) and a root-knot nematode, Meloidogyne javanica (Treub) Chitwood (Tylenchida: Heteroderidae), with implications for the biological control of Lantana camara L. (Verbenaceae) in South Africa. The studies were conducted under quarantine conditions at the Agricultural Research Council-PHP, Roodeplaat, Pretoria, South Africa. Specifically, the study determined; (i) whether root damage by the flea beetle enhanced infection by M. javanica, (ii) whether L. camara roots infected with the nematode enhanced the performance of the beetle, (iii) whether single or combined effect of the two organisms (i.e. L. bethae and M. javanica) had an overall effect on the growth and biomass of their shared host, L. camara, and (iv) the susceptibility of 10 L. camara varieties that are commonly found in South Africa to M. javanica. The study found that galling on the roots of L. camara by the nematode occurs at the highest inoculation of 300 eggs of L. bethae per plant, and no galling occurred at inoculation of 200 eggs per plant and below. The findings also showed that L. bethae performed better on M. javanica-infected than on healthy L. camara roots, and that more L. bethae adult progeny with slightly bigger body size emerged from M. javanica-infected, than from healthy plants. Fresh weight (galls) of plant roots from treatments where both species (i.e., L. bethae and M. javanica) were combined was significantly higher than that from plants infected with the nematode only, suggesting that the combination of both species induces more galling than the nematode does alone. The above-ground dry biomass was significantly lower both in combined and M. javanica only treatments, than in L. bethae only treatment. The study also found that selected L. camara varieties were infected with M. javanica, albeit at varying degrees of infection. Among the 10 L. camara varieties, Orange Red OR 015 was the most susceptible. Other susceptible varieties included Light Pink 009 LP, Total Pink 021 TP and Dark Pink 018 DP, and these, together with variety Orange Red OR 015, constituted 40% of the L. camara varieties evaluated in the current study. Fifty percent of the varieties displayed slight to moderate susceptibility to M. javanica, while 10% displayed lack of susceptibility. The study concluded that the symbiotic relationship between L. bethae and M. javanica was mutual, resulting in increase in the fitness of the beetle. The combined herbivory by L. bethae and M. javanica was also found to be additive on one of the most common varieties of L. camara in South Africa, and therefore co-infestation by both species might enhance the biological control of this weed in South Africa. The study further concluded that the suitability of some invasive L. camara cultivars such as Light Pink 009 LP and Orange Red 015 OR for M. javanica, might also contribute towards biological control of this weed in South Africa, particularly in areas where the two herbivores species co-exist.
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  • Date Issued: 2019

Investigating assay formats for screening malaria Hsp90-Hop interaction inhibitors

  • Authors: Derry, Leigh-Anne Tracy Kim
  • Date: 2019
  • Subjects: Antimalarials , Heat shock proteins , Drug interactions , Drug resistance , Plasmodium falciparum , High throughput screening (Drug development) , Bioluminescence resonance energy transfer (BRET) , Fluorescence resonance energy transfer (FRET)
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/63345 , vital:28395
  • Description: Although significant gains have been made in the combat against malaria in the last decade, the persistent threat of drug and insecticide resistance continues to motivate the search for new classes of antimalarial drug compounds and targets. Due to their predominance in cellular reactions, protein-protein interactions (P-PIs) are emerging as a promising general target class for therapeutic development. The P-PI which is the focus of this project is the interaction between the chaperone heat shock protein 90 (Hsp90) and its co-chaperone Hsp70/Hsp90 organising protein (Hop). Hop binds to Hsp70 and Hsp90 and facilitates the transfer of client proteins (proteins undergoing folding) from the former to the latter and also regulates nucleotide exchange on Hsp90. Due to its role in correcting protein misfolding during cell stress, Hsp90 is being pursued as a cancer drug target and compounds that inhibit its ATPase activity have entered clinical trials. However, it has been proposed that inhibiting the interaction between Hsp90 and Hop may be alternative approach for inhibiting Hsp90 function for cancer therapy. The malaria parasite Plasmodium falciparum experiences temperature fluctuations during vector-host transitions and febrile episodes and cell stress due to rapid growth and immune responses. Hence, it also depends on chaperones, including PfHsp90, to maintain protein functionality and pathogenesis, demonstrated inter alia by the sensitivity of parasites to Hsp90 inhibitors. In addition, PfHsp90 exists as a complex with the malarial Hop homologue, PfHop, in parasite lysates. Consequently, the purpose of this study was to explore P-PI assay formats that can confirm the interaction of PfHsp90 and PfHop and can be used to identify inhibitors of the interaction, preferably in a medium- to high-throughput screening mode. As a first approach, cell-based bioluminescence and fluorescence resonance energy transfer (BRET and FRET) assays were performed in HeLa cells. To facilitate this, expression plasmid constructs containing coding sequences of P. falciparum and mammalian Hsp90 and Hop and their interacting domains (Hsp90 C-domain and Hop TPR2A domain) fused to the BRET and FRET reporter proteins – yellow fluorescent protein (YFP), cyan fluorescent protein (CFP) and Renilla luciferase (Rluc) - were prepared and used for HeLa cell transient transfections. The FRET assay produced positive interaction signals for the full-length P. falciparum and mammalian Hsp90-Hop interactions. However, C-domain-TPR2A domain interactions were not detected, no interactions could be demonstrated with the BRET assay and western blotting experiments failed to detect expression of all the interaction partners in transiently transfected HeLa cells. Consequently, an alternative in vitro FRET assay format using recombinant proteins was investigated. Expression constructs for the P. falciparum and mammalian C-domains and TPR2A domains fused respectively to YFP and CFP were prepared and the corresponding fusion proteins expressed and purified from E. coli. No interaction was found with the mammalian interaction partners, but interaction of the P. falciparum C-domain and TPR2A domain was consistently detected with a robust Z’ factor value of 0.54. A peptide corresponding to the PfTPR2A domain sequence primarily responsible for Hsp90 binding (based on a human TPR2A peptide described by Horibe et al., 2011) was designed and showed dose-dependent inhibition of the interaction, with 53.7% inhibition at 100 μM. The components of the assay are limited to the purified recombinant proteins, requires minimal liquid steps and may thus be a useful primary screening format for identifying inhibitors of P. falciparum Hsp90-Hop interaction.
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  • Date Issued: 2019

Investigating epistemic justice in an adaptive planning process: towards developing a local catchment management strategy

  • Authors: Ralekhetla, Mateboho Mary
  • Date: 2019
  • Subjects: Watershed management -- South Africa , Watershed management -- South Africa -- Moral and ethical aspects , Water resources development -- South Africa -- Eastern Cape , Water-supply -- South Africa -- Makhanda , Makana Water Forum (Makhanda, South Africa) , Makana Municipality (Makhanda, South Africa)
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/95980 , vital:31220
  • Description: In South Africa, Integrated Water Resource Management (IWRM) is being put into practice in a way that incorporates the belief that all stakeholders should be given a voice in decisions that affect them. Catchment Management Forums (CMFs) are the first place for stakeholder participation, supported by Catchment Management Agencies (CMAs). A key first task of a CMA is to develop of their Catchment Management Strategy (CMS). In this research, I consulted and worked with stakeholders in the Makana Water Forum (Makana Local Municipality, Eastern Cape, South Africa) throughout the process as they worked towards formulating their local CMS. Importantly, this study used insights from the community to focus on the inter- and intra-group interactions among the stakeholders who participated in the first step of Strategic Adaptive Planning. In the process, I explored epistemic contestations that occurred between different epistemic agents (participants) who may have held identity prejudices. The research aimed to allow voices, which could otherwise have been marginalised, to come out in ways that were not stigmatised through the written and personal reflective process. In doing this, the study tried to hear the voice of the oppressed speaker whose knowledge and lived experiences have been overlooked by the hearer’s prejudice. Findings show that participants who were part of the CMS development process experienced epistemic justice. These findings further established that the addition of participant reflections enhanced the level of epistemic justice promoted by the Adaptive Planning Process (APP).
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  • Date Issued: 2019

Investigating household energy conservation behaviours in Johannesburg, South Africa

  • Authors: Williams, Stephanie
  • Date: 2019
  • Subjects: Environmental behavior -- South Africa , Energy conservation -- Psychological aspects -- South Africa , Energy consumption -- Psychological aspects -- South Africa , South Africans -- Energy consumption
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/94101 , vital:31000
  • Description: Behavioural change is increasingly anticipated as an important pathway towards the reduction of the human footprint on the environment. Monitoring resource consumption at the household scale is essential as a basis for evaluating current performance and supports the understanding of how behaviour change interventions can be implemented. Yet, there are comparatively fewer studies on pro-environmental behaviour (PEB) in developing country contexts than in developed countries. Further, where research efforts have been made in developing countries, these have mainly focussed on low-income households. This means the extant literature on PEB is limited across a geographic and economic gradient, making generalisations about PEB problematic and limiting the scope for thinking about interventions for promoting pro-environmental behaviour in developing countries. In response to this, the study focuses on high-income households in Johannesburg, South Africa. Overall, the findings show a high level of heterogeneity in reported pro-environmental energy use behaviour, attributed to a suit of socio-demographic and value factors. Mainly, age, number of dependents, household size. Valuing leisure time were negatively correlated to energy use behaviours, while valuing environmental quality positively correlated to energy use behaviours. The provision of information energy-saving interventions yielded positive behavioural change as shown by reduced energy consumption of up to 12% in the Treatment group. However, no significant correlations were found between energy reduction and socio-demographic and personal value factors, which can be attributed to a different cultural context. The study discusses the implications of the findings on debates around pro-environmental behaviour and factors influencing pro-environmental behaviour, and provides further recommendations for future energy policies related to the household sector.
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  • Date Issued: 2019

Machine learning methods for calibrating radio interferometric data

  • Authors: Zitha, Simphiwe Nhlanhla
  • Date: 2019
  • Subjects: Calibration , Radio astronomy -- Data processing , Radio astronomy -- South Africa , Karoo Array Telescope (South Africa) , Radio telescopes -- South Africa , Common Astronomy Software Application (Computer software)
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/97096 , vital:31398
  • Description: The applications of machine learning have created an opportunity to deal with complex problems currently encountered in radio astronomy data processing. Calibration is one of the most important data processing steps required to produce high dynamic range images. This process involves the determination of calibration parameters, both instrumental and astronomical, to correct the collected data. Typically, astronomers use a package such as Common Astronomy Software Applications (CASA) to compute the gain solutions based on regular observations of a known calibrator source. In this work we present applications of machine learning to first generation calibration (1GC), using the KAT-7 telescope environmental and pointing sensor data recorded during observations. Applying machine learning to 1GC, as opposed to calculating the gain solutions in CASA, has shown evidence of reducing computation, as well as accurately predict the 1GC gain solutions representing the behaviour of the antenna during an observation. These methods are computationally less expensive, however they have not fully learned to generalise in predicting accurate 1GC solutions by looking at environmental and pointing sensors. We call this multi-output regression model ZCal, which is based on random forest, decision trees, extremely randomized trees and K-nearest neighbor algorithms. The prediction error obtained during the testing of our model on testing data is ≈ 0.01 < rmse < 0.09 for gain amplitude per antenna, and 0.2 rad < rmse <0.5 rad for gain phase. This shows that the instrumental parameters used to train our model more strongly correlate with gain amplitude effects than phase.
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  • Date Issued: 2019

Mapping and predicting potential distribution patterns of free-range livestock in the rural communal rangelands of Mgwalana, Eastern Cape, South Africa

  • Authors: Mkabile, Qawekazi
  • Date: 2019
  • Subjects: Range management -- South Africa , Grazing -- South Africa , Livestock -- South Africa , Livestock -- Monitoring -- South Africa , Livestock -- Remote sensing -- South Africa , Communal rangelands -- South Africa
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/96000 , vital:31223
  • Description: Communal rangelands provide habitat to many plants and animals. However, there is evidence that livestock cause range degradation. Range degradation occurs because livestock select grazing based on the availability of resources such as water and forage material, their use of the landscape is non-uniform, consequently causing resource deterioration. Range management is thus necessary because communities depend on range condition for livestock productivity. However, precise quantification of livestock distribution within communal rangelands is lacking. In developed countries, Global Positioning Systems (GPS) collars have been used to monitor wildlife and domestic livestock in pastures and seem to have worked efficiently. However, in a developing country like South Africa, GPS technology to monitor animal behaviour has been used only for wildlife on privately owned land. The high costs of monitoring livestock herds in large open areas such as communal rangelands have resulted in little or no monitoring of domestic livestock using GPS technology. This study links monitored livestock distribution to physical landscape variables in Mgwalana, and uses the modelled relationship to predict livestock distribution in quaternary catchments, T12A and T35A-E. The research addresses the questions (1) where do livestock spend time in the wet and dry seasons? And (2) how can areas of potential livestock distribution be identified in other catchments where actual distribution is unknown? Livestock were tracked during the wet and dry seasons using GPS collars. The resulting distribution data is combined with selected physical landscape variables to identify selectivity. The GPS location data and the physical landscape variables are used to predict potential livestock distribution where distribution is unknown in quaternary catchments (T12A and T35A-E). The ArcGIS Predictive Analysis Tool (PAT) was used to extract the selected landscape variable ranges based on the GPS location data and identify areas with the same conditions in the quaternary catchments were subsequently selected. The key findings are that livestock prefer accessible areas with gentle terrain near water sources, avoiding south-facing slopes which receive less solar radiation and tend to be cooler. Livestock are attracted to vegetation in riparian zones. Rural communal lands are dominated by poverty, and land-based livelihood strategies can potentially contribute to the well-being of the community. Therefore, understanding livestock distribution can contribute to a rangeland management strategy aimed at improving range condition which could increase livestock productivity and contribute to the livelihoods of local people.
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  • Date Issued: 2019

Mesoscale alongshore and cross-shore transport and settlement of invertebrate larvae on the south east coast of South Africa

  • Authors: Dyantyi, Siphelele Buntu
  • Date: 2019
  • Subjects: Marine invertebrates -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Benthic animals -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Mexilhao mussel -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Mytilus galloprovincialis -- Larvae -- Dispersal -- South Africa -- Eastern Cape , Oysters -- Larvae -- Dispersal -- South Africa -- Eastern Cape
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/97007 , vital:31386
  • Description: Pelagic larval stages of most marine benthic species are important in maintaining coastal populations of adults. Several physio-chemical factors such as currents, winds, larval behaviour and time have an influence on the dispersal and transport of larvae to the adult habitat but their role is however still poorly understood. The aim of this study was to investigate the alongshore and cross-shore transport and temporal delivery of invertebrate larvae at four sites (Kenton on Sea, Cannon Rocks, Schoenmakerskop and Cape St Francis) along the south east coast of Eastern Cape, South Africa. Larval distribution of several taxa was determined during two sampling periods, by collecting water samples at nearshore line transects (3 distances: 900m, 1500m and 2400m – perpendicular to the shore) and at three depths (surface, thermocline/middle, bottom), which ranged from 15m (inshore) to 50m (offshore). Physical properties (current speed and direction, dissolved oxygen, fluorescence, turbidity, temperature, salinity, pH, pressure, density and conductivity) were measured and coupled in order to further understand larval distribution. The larvae were analysed as both total abundance and separately as the abundances of a variety of taxa which were: Perna perna, Mytilus galloprovincialis, oysters, early and late nauplii and cyprids. Larval settlement and recruitment on the rocky shores were measured by monthly deployment and collection of 20 (10 each for barnacles and mussels) artificial collectors at each site, which were preserved in ethanol or frozen for further processing. Multiple Permutational Multivariate Analysis of Variance (PERMANOVA) analyses were used to test the effects of site, depth and distance from the shore for the nearshore larvae (taxa analysed separately). In addition, a distance based linear model (distLM) was performed to analyse the relationship between the total larval abundance and the above mentioned physical variables. Multiple two-way analyses of variance (ANOVA) were performed to test the effects of months and sites on the settlement and recruitment of the larvae (P. perna, M. galloprovincialis, other bivalves, cyprids and juvenile barnacles) arriving on the shore. For the nearshore larval distribution, results from the PERMANOVAs revealed that most taxa showed a significant site and depth interactions with the exception of ‘early nauplii’ taxon. Also nearly all taxa were found within the thermocline, besides ‘oyster’ and ‘cyprids’ which were located at thermocline or bottom. Larvae were also located at variable distances from the shore, with most occurring at the offshore stations. Furthermore, there was a geographical separation of larval abundance according to sites, with most larvae located at Cannon Rocks and Kenton on Sea and least at Schoenmakerskop and Cape St Francis. For the settlement and recruitment, most taxa showed a seasonal trend, with the highest abundance of settlers and recruits expectedly appearing during the summer months of the sampling period. Additionally there was a site effect for most taxa (P. perna, M. galloprovincialis, other bivalves and juvenile barnacles), where settlers and recruits were mostly found at Cannon Rocks. Significant differences in abundance of settlers and recruits amongst the four sites indicate spatial and temporal variability for the targeted 180km stretch of coast. Overall for this study, taxon and ontogenetic stage of larvae were important in the distribution and abundance of larvae. Throughout the time frame of nearshore and intertidal sampling, Cannon Rocks consistently resulted as a ‘hot spot’ for larval abundance, settlement and recruitment, while a broad west to east separation was also observed. These results hence highlight that within this stretch of c.180km coast, time, taxon, ontogeny and post-settlement factors influence early dynamics of benthic populations.
  • Full Text:
  • Date Issued: 2019

Mineralogical, geochemical and lead isotopic analysis of the lead mineralization of the Skorpion Deposit, south western Namibia

  • Authors: Uazeua, Kakunauua
  • Date: 2019
  • Subjects: Zinc ores -- Namibia , Formations (Geology) -- Namibia , Mineralogy -- Namibia , Lead -- Metallurgy -- Namibia , Lead -- Isotopes -- Namibia
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/68391 , vital:29250
  • Description: The Skorpion none-sulphide Zinc Deposit is located in the para-autochtonous Port Nolloth Zone of the Gariep Belt, which overlays the Lower-Proterozoic Orange River Group basement rocks (Corrans et al., 1993). Situated in close proximity to the larger Rosh Pinah Zn-Pb deposit, the Skorpion Deposit contained a resource of 24.6 Mt at 10.6 % Zn and unquantified Cu and Pb prior to mining. To date, zinc has been the only metal exploited, with minor amounts of copper as a by-product. This study aims at understanding the mineralogical composition of the Skorpion lead mineralization and understanding the relationship between lead and the major metals such as zinc and copper in order to form a basis for further work that could determine the potential of processing lead as a by-product. As part of the study, work was also done on lead isotopes mainly with the aim of understanding the mineralization genesis and to determine the differences between the Skorpion and Rosh Pinah deposit which rationalize the inferior economic potential of the Skorpion lead mineralization. Results of the study have shown that majority of the lead mineralization is hosted by the felsic metavolcanics as galena and subordinately in the metasiliciclastics as pyromorphite, a lead manganese phosphate. In terms of the mineral textures, the lead minerals appear to be mainly secondary phases that have been remobilized and reprecipitated around pyrite, within pyrite cracks and intergrown with minerals such as chalcocite and greenockite. Lead has been mainly concentrated along fault zones. The elevated pyromorphite concentrations tend to occur within gossanous zones in close association with iron and manganese oxides. These textures represent supergene enrichment of a sulphide proto ore. However, contrary to copper and zinc mineralization, lead was not remobilized far from the proto ore merely as a function of its poor mobility in acidic fluids (Reddy et al., 1995). This substantiates the concentration of secondary lead in the felsic metavolcanics and to a much lesser extent, in the metasiliciclastics. Both secondary zinc and copper were reprecipitated in the metasiliciclastics, further away from the sulphide proto ore, hosted mainly by the felsic metavolcanics. The average lead isotope ratios of 206Pb/204Pb (17.26), 207Pb/204Pb (15.60) and 208Pb/204Pb (37.42) resemble results provided by Frimmel (2004) for both the Skorpion and Rosh Pinah deposits. For the Skorpion samples from Frimmel (2004) had the following average ratios: 206Pb/204Pb (17.29), 207Pb/204Pb (15.59) and 208Pb/204Pb (37.51). The Rosh Pinah samples had the following average ratios: 206Pb/204Pb (17.17), 207Pb/204Pb (15.61) and 208Pb/204Pb (37.45). These results indicate lead derivation from the lower 2.0 Ga Eburnean pre-Gariep basement in agreement with and Frimmel et al. (2004). The host felsic metavolcanics might have been derived from melting of the basement rocks during the formation of the Adamastor Ocean. In comparison to the Rosh Pinah deposit lead isotope signatures, the Skorpion lead isotopes overlap with the Rosh Pinah deposit isotopes, but have a much narrower range. This is an indication of a much shorter lived and potentially faster mineralization event contrary to the SEDEX type Rosh Pinah deposit. The smaller tonnage of the Skorpion deposit, its inferior lead concentrations and the elevated radiogenic lead isotopes point toward a VMS deposit which was formed in a small graben fed by shallow conduits during a short lived mineralization event. Sedimentary rocks covered the forming deposit at a fast rate and impaired the deposit advancement. The interaction between the upper crustal rocks and the mineralizing fluids is what may have resulted in the elevated radiogenic lead signature. In contrast to this, SEDEX deposits such as the Rosh Pinah Deposit, are generally fed by deep seated conduits that allow more longer lived leaching of metals from the underlying basement rocks and generally allow minor influence from upper crustal rocks.
  • Full Text:
  • Date Issued: 2019

Modernisation and extension of InetVis: a network security data visualisation tool

  • Authors: Johnson, Yestin
  • Date: 2019
  • Subjects: Data visualization , InetVis (Application software)
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/69223 , vital:29447
  • Description: This research undertook an investigation in digital archaeology, modernisation, and revitalisation of the InetVis software application, developed at Rhodes University in 2007. InetVis allows users to visualise network traffic in an interactive 3D scatter plot. This software is based on the idea of the Spinning Cube of Potential Doom, introduced by Stephen Lau. The original InetVis research project aimed to extend this concept and implementation, specifically for use in analysing network telescope traffic. The InetVis source code was examined and ported to run on modern operating systems. The porting process involved updating the UI framework, Qt, from version 3 to 5, as well as adding support for 64-bit compilation. This research extended its usefulness with the implementation of new, high-value, features and improvements. The most notable new features include the addition of a general settings framework, improved screenshot generation, automated visualisation modes, new keyboard shortcuts, and support for building and running InetVis on macOS. Additional features and improvements were identified for future work. These consist of support for a plug-in architecture and an extended heads-up display. A user survey was then conducted, determining that respondents found InetVis to be easy to use and useful. The user survey also allowed the identification of new and proposed features that the respondents found to be most useful. At this point, no other tool offers the simplicity and user-friendliness of InetVis when it comes to the analysis of network packet captures, especially those from network telescopes.
  • Full Text:
  • Date Issued: 2019

Petrography and geochemistry of the Masoke Iron Formation and its associated ferruginous counterparts, kanye basin Botswana

  • Authors: Nkabelane, Ndifelani Oriel
  • Date: 2019
  • Subjects: Petrology -- South Africa , Geochemistry -- South Africa
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/115221 , vital:34101
  • Description: A sequence of Transvaal Supergroup sediments extends into southern Botswana beneath Kalahari cover as the Kanye basin, these are known to host billions of tons @ 60>Fe. Masoke Iron Formation (Kanye Basin) which is stratigraphic correlative of The Ghaap Group and Chuniespoort Group of the Griqualand West basin and Transvaal basin, respectively. The Palaeoproterozoic Transvaal Supergroup in the Northern Cape Province of South Africa hosts high grade (>60% Fe) hematitic and specularitic iron and manganese mineralisation. It is therefore important to study and record the petrographic, mineralogy and geochemistry of Masoke Iron Formation, compare the results to the much known Kuruman and Griquatown Iron Formations. This study systematically investigate and record the petrography, mineralogy and geochemistry of all Masoke Iron Formation of Taupone Group in the Kanye Basin, which is stratigraphic correlative of The Ghaap Group and Chuniespoort Group of the Griqualand West basin and Transvaal basin, respectively. The further objective is to compare Masoke Iron Formation to the equivalent units in the Transvaal basin and Griqualand basin. In contrast to both Transvaal and Griqualand West Basin the Masoke iron Formation (Kanye Basin) has not been the subject of systematic scientific investigations. The study covers three main areas in the Kanye Basin: Keng Pan Area, Ukwi/Moretlwa hill and Janeng Hill Area. The mineralogy and geochemistry of these areas are presented in this study. Kanye Basin has a potential to host a large iron ore deposit, the geological setting in this area incorporates many of the elements necessary for iron ore formation. These include: banded iron formation (BIF), major unconformities with prolonged periods of weathering, carbonate sequences etc. In addition, several large deposits and mines are known from this area. This area can potentially have both hypogene and supergene enrichment of BIF. In this model, prospectively for new deposits is a function of the following: presence of iron formation units, proximity of mapped Asbestos Hills and Voëlwater BIF, thrust faulting (as indicated by the aero-magnetic interpretation), duplication of the ore horizon by folding, intersection of the BIF by major extensional fault, proximity of Olifantshoek/Waterberg outcrop, Gamagara unconformity, presence of carbonates (dolomites) and thin Kalahari sand cover. Major BIF units in the area of study include: the Masoke Iron Formation, equivalent to Kuruman Formation of the Asbestos Hills Subgroup, the Rooinekke iron formation of the Koegas Subgroup and the Hotazel Formation of the Voëlwater Subgroup. Supergene enrichment of these BIFs may occur wherever they are overlain by a major regional unconformity. The base of the Waterberg and the OlifantshoekSupergroups represent major unconformities in this regional target area. Potential for hypogene deposits is indicated by faulting (preferably extensional) proximal to BIF.
  • Full Text:
  • Date Issued: 2019

Photocatalytic treatment of organic and inorganic water pollutants using zinc phthalocyanine-cobalt ferrite magnetic nanoparticle conjugates

  • Authors: Mapukata, Sivuyisiwe
  • Date: 2019
  • Subjects: Phthalocyanines , Cobalt ferrite , Zinc , Nanoparticles
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/67603 , vital:29119
  • Description: This work explores the synthesis and photophysicochemical properties of zinc phthalocyanines when conjugated to cobalt ferrite magnetic nanoparticles. Phthalocyanines with amine and carboxylic acid functional groups were synthesised so as to covalently link them via amide bonds to cobalt ferrite magnetic nanoparticles with carboxylic acid and amine groups, respectively. Spectroscopic and microscopic studies confirmed the formation and purity of the phthalocyanine-cobalt ferrite magnetic nanoparticle conjugates which exhibited enhanced triplet and singlet quantum yields compared to the phthalocyanines alone. The studies showed that the presence of cobalt ferrite nanoparticles significantly lowered fluorescence quantum yields and lifetimes. The conjugates not only showed much higher singlet oxygen quantum yields compared to the phthalocyanines alone but were also attractive because of their magnetic regeneration and hence reusability properties, making them appealing for photocatalytic applications. The photocatalytic ability of some of the phthalocyanines and their conjugates were then tested based on their photooxidation and photoreduction abilities on Methyl Orange and hexavalent chromium, respectively. For catalyst support, some of the zinc phthalocyanines, cobalt ferrite magnetic nanoparticles and their respective conjugates were successfully incorporated into electrospun polystyrene and polyamide-6 fibers. Spectral characteristics of the functionalized electrospun fibers confirmed the incorporation of the photocatalysts and indicated that the phthalocyanines and their respective conjuagates remained intact with their integrity maintained within the polymeric fiber matrices. The photochemical properties of the complexes were equally maintained within the electrospun fibers hence they were applied in the photooxidation of azo dyes using Orange G and Methyl Orange as model organic compounds.
  • Full Text:
  • Date Issued: 2019

Photophysicochemical properties and surface-enhanced Raman scattering of phthalocyanine-nanoparticle conjugates

  • Authors: Nwahara, Nnamdi
  • Date: 2019
  • Subjects: Boron compounds , Electrochemistry , Phthalocyanines , Nanoparticles , Bioconjugates , Raman effect
  • Language: English
  • Type: text , Thesis , Masters , MSc
  • Identifier: http://hdl.handle.net/10962/71647 , vital:29928
  • Description: This work presents the synthesis, photophysical and photochemical characterization of a series of metallophthalocyanines (MPcs) and boron dipyrromethene (BODIPY) and their conjugates with either gold or silver nanoparticles (AuNPs or AgNPs) or graphene quantum dots (GQDs). The rich π-electron systems of GQDs and MPcs employed in this work enabled the coordination of MPcs to GQDs (either as pristine or modified) via the non-covalent (π-π stacking) method. GQDs, AuNPs and AgNPs were also functionalized with L-glutathione (GSH) in order to assist coupling to the Pcs or BODIPY dye. Spectroscopic and microscopic studies confirmed the formation of the respective nanoparticles (NPs) as well as the conjugates which exhibited enhanced photophysicochemical properties in comparison to the phthalocyanines (Pcs) or BODIPY alone. This work also shows that the incorporation of folic acid (FA) into Pcs-NPs composites leads to further enhancements in the singlet oxygen generation capabilities of the resulting conjugates, and so experimentally demonstrates for the first time, a synergy between FA and the respective nanoparticles (GQDs, AuNPs and AgNPs) in affecting the photophysical properties of Pcs complexes. GQDs and Pcs/GQDs hybrids were also herein decorated with AuNPs – metallic nanostructures that employ localized surface plasmon resonances to capture or radiate electromagnetic waves at optical frequencies. These nanostructures herein reported, have been shown to possess enhanced light-matter properties, enabling unique surface-enhanced Raman scattering (SERS) behaviours, with unprecedented enhancement factors of up to 30-fold. This work therefore, reports on the fabrication of Pc/GQDs/AuNPs hybrids and experimentally demonstrates their incredible potential as novel Raman-active PDT agents.
  • Full Text:
  • Date Issued: 2019
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