Probing the binding sites of novel 2-substituted imidazole-4,5-dicarboxylic acids : Towards new imidazole-based drugs
- Authors: Clark, Candyce Raine
- Date: 2021
- Subjects: Heterocyclic compounds Coordination compounds
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/50848 , vital:42957
- Description: A series of benzimidazole and imidazole-4,5-dicarboxylic acids were prepared using known and adapted protocols. Novel ligands synthesised in this study include 2-tert-butyl-benzimidazole, 2-tert-butyl-imidazole-4,5-dicarboxylic acid, an intermediate in the synthesis of 1,2- bis(2-benzimidazyl)-1,2,-dihydroxyethane and 2-(2-hydroxyphenyl)-benzimidazole with a salicylic acid co-crystallisate. All ligands prepared were reacted with metal salt solutions in order to prepare metal coordination compounds. Complexes with Cu(II), Ag(I), Mn(II), Ni(II) and Cd(II) ions and 2-phenyl-imidazole-4,5-dicarboxylic acid were prepared, as well as Cu(II) and Mn(II) with 2-trifluoro-methyl-imidazole-4,5-dicarboxylic acid and Cu(II) ions with 2-(2- hydroxyphenyl)-benzimidazole. The ligands and complexes were characterised by means of single-crystal X-ray diffraction studies, NMR analysis, UV spectrophotometric analysis and IR spectroscopy. DFT studies were carried out for selected ligands in order to provide theoretical values for comparison. Antimicrobial studies were performed on some of the ligands and complexes and these results show promise for the future development of new imidazole-based drugs.
- Full Text:
- Date Issued: 2021
A scheduling model for the charging of electric vehicles in photovoltaic powered smart microgrids
- Authors: Nyumbeka, Dumisani Joshua
- Date: 2020
- Subjects: Electric vehicles , Photovoltaic power generation Photovoltaic power generation -- Developing countries
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/49259 , vital:41615
- Description: Electric vehicles (EVs) have emerged as a viable option to advance sustainable mobility, but adoption is still relatively low. This has been largely due to the limited range one can travel on a single charge, leading to range anxiety, longer charge cycles and long wait times at charging stations. One solution to range anxiety is to erect charging stations on major roads and urban centres. There is also a lack of real-time information regarding the state of charging stations and charging ports in existing charging infrastructure. To increase the benefit of using EVs, using renewable energy sources, such as photovoltaics (PV) to power EVs, can further increase the benefit of reduced carbon footprint. The main research objective was to design a Charge Scheduling Model for charging EVs using a PV-powered smart microgrid (SMG). The model addresses the lack of an integrated platform where EV drivers can schedule when and where to charge their EVs. The model also reduces the negative effects of the adoption of EVs, including range anxiety. The Charge Scheduling Model was developed using the Design Science Research (DSR) methodology and was the main artefact of the study. A literature study was conducted of research related to SMGs, renewable energy, EVs and scheduling, to identify shortcomings that currently exist in EV charge scheduling (EVCS), and to identify the requirements of a potential solution. The literature study also identified the hard and soft constraints that are unique to EVCS, and the available energy in the SMG was identified as one of the hard constraints. Therefore, an Energy Forecasting Model for forecasting energy generated in PV-powered SMGs was required before the Charge Scheduling Model could be designed. During the first iteration of the design and development activities of DSR, four models were designed and implemented to evaluate their effectiveness in forecasting the energy generated in PV-powered SMGs. The models were Support Vector Regression (SVR), K-Nearest Neighbour (KNN), Decision Trees, and Multilayer Perceptron. In the second iteration, the Charge Scheduling Model was designed, consisting of a Four Layered Architecture and the Three-Phase Data Flow Process. The Charge Scheduling Model was then used to design the EVCS prototype. The implementation of the EVCS prototype followed the incremental prototyping approach, which was used to verify the effectiveness of the model. An artificial-summative evaluation was used to evaluate the design of the Charge Scheduling Model, whereas iterative formative evaluations were conducted during the development of the EVCS prototype. The theoretical contribution of this study is the Charge Scheduling Model, and the EVCS prototype is the practical contribution. The results from both evaluations, i.e. the Energy Forecasting Model and the Charge Scheduling Model, also make a contribution to the body of knowledge of EVs.
- Full Text:
- Date Issued: 2020
A trait-based approach to identify indicators for measuring rocky reef ecosystem condition in South Africa
- Authors: Smit, Kaylee
- Date: 2020
- Subjects: Environmental management -- Evaluation , Environmental monitoring -- Methodology Marine ecology -- South Africa
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/49292 , vital:41618
- Description: An important yet challenging task for effective ecosystem-based management of marine ecosystems is the reliable measurement and monitoring of changes in ecosystem condition. In South Africa, the National Biodiversity Assessment (NBA) has relied on cumulative pressure mapping, based on the calculation of cumulative impact scores, as a proxy for measures of marine ecosystem condition. While this method is practical for broad scale assessments where ecological data are lacking, there is a need to groundtruth this approach at local scales using in-situ data. The aim of this thesis was to identify potential indicators that can be used to measure the ecosystem condition of subtidal rocky reefs on the East coast of South Africa to groundtruth national pressure-based condition assessments. This thesis constituted the first attempt to conduct a comprehensive assessment of rocky reef ecosystem condition to validate national pressure-based assessments in South Africa. Based on a comprehensive literature review, a traits-based approach was selected to ensure that ecosystem structure and function were included in condition measurements. Fish and benthic community data were collected using baited remote underwater stereo-video systems (144 video samples) from the Natal Shelf ecoregion. Sampling spanned a gradient of low to high human pressures, which incorporated an effective Marine Protected Area (to define reference conditions), as well as areas exposed to intermediate levels of human pressures and a highly impacted area offshore of a large metropolitan port city. Structural and functional indicators were compared among localities and suitable functional indicators were aggregated into multimetric indices (MMIs) to provide an integrated measurement of ecosystem condition. Approximately 840 benthic biota and 10 400 fish (representing 176 identified fish species) were counted. Results showed that functional indicators, particularly size-based ones, were more effective at detecting changes in ecosystem condition compared with structural indicators based on taxonomy. Reefs in good ecological condition had a higher biomass of target species and a higher proportion of large predatory fish with more adults, compared with impacted areas. Benthic communities, however, appeared less responsive to cumulative pressures. The MMIs, using fish and benthic community data, were used to compare condition categories with those from the NBA. Results showed that the pressure-based assessments provided a reasonable proxy of broad patterns of rocky reef ecosystem condition. However, fine-scale discrepancies between results from the data-driven approach versus the proxy method suggested that broad-scale proxies might overestimate condition in some areas and underestimate it in others. To build on these results, the applicability of structural and functional indicators and MMIs were tested using an independent stereo-BRUVs dataset from the Agulhas Shelf ecoregion. Findings showed that not all MPAs were in good ecological condition compared with adjacent impacted areas, as was estimated by the NBA. However, there is a need to improve the quality of trait data and to test indicators and indices in other ecoregions, ecosystem types and in response to a broader range of improved pressure data. Furthermore, there is a need to apply innovative research to guide the calculation of thresholds for condition categories to advance condition assessments.
- Full Text:
- Date Issued: 2020
Applied phylogeography : mapping the genetic resource of Honeybush across the Cape Floristic Region
- Authors: Galuszynski, Nicholas C
- Date: 2020
- Subjects: Phylogeography -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/46771 , vital:39655
- Description: Aim: Honeybush tea is a herbal infusion made from members of the Cape Floristic Region (CFR) endemic Cyclopia Vent. Consting of 21 extant species, six are anthropogenically redistributed across the CFR for Honeybush cultivation. However, with no information regarding the distribution and levels of genetic diversity among wild Honeybush populations, anthropogenic translocation of cultivated genotypes may risk disrupting natural genetic diversity patterns. In this thesis, an applied phylogeographic approach is used to provide baseline insights into the spatial structuring of Honeybush genetic diversity. Location: The Cape Floristic Region (CFR), located along the southern Cape of South Africa. Methods: Spatial structuring of evolutionary lineages within Cyclopia are explored at a genus level using data generated from the combination of Anchored Hybrid Enrichment library preparation and high through put sequencing. A High Resolution Melt analysis (HRM) toolkit is then developed to screen haplotype variation across three non-coding chloroplast loci. This HRM toolkit coupled with haplotype confirmation Sanger sequencing is then applied to describe the spatial structuring of genetic diversity in wild populations for two Honeybush species (C. intermedia and C. subternata) and to compare genetic diversity among wild and cultivated populations of three Honeybush species (C. intermedia, C. subternata, and C. longifolia). A reanalysis of published phylogeographic data focusing on CFR plant taxa is used to test if phylogeographic breaks occur across the boundaries among adjacent Centers of Endemism (CoEs). Finally, the low-copy nuclear data set generated via AHE and high throughput sequencing is summarized. Results: Phylogeographic structuring was detected at the inter- and intraspecific levels in Cyclopia. The genus level analysis revealed a strong phylogenetic split between western CFR and eastern CFR endemic species in the nuclear and chloroplast genomes. At the intraspecific level, HRM proved to be a high throughput and accurate tool for haplotype detection, revealing phylogeographic structuring of genetic diversity in C.intermediaand C.subternata. This genetic diversity and structuring was not detected in cultivated Honeybush populations, which appear to have originated from a small number of founding individuals and have experienced a genetic bottleneck. Spatial structuring of genetic lineages is common among CFR plant taxa and the reanalysis of existing data found a significant trend for phylogeographic breaks tooccuracrosstheboundariesamongadjacentCoEs. Finally, over200000baseswere sequenced across 445 low-copy nuclear loci for 14 Cyclopia species. Conclusions: This thesis provides important baseline information on the spatial distribution of wild Honeybush genetic diversity. Phylogeographic structuring is present in wild Honeybush populations. This however is not accounted for in cultivated populations, which may place wild genetic diversity at risk of being disrupted if geneflow among wild and cultivated populations occurs. The results from this thesis should therefore be used to develop precautionary guidelines for the anthropogenic redistribution of Honeybush genetic material for cultivation. Furthermore, the novel insights into regional patterns of phylogeohraphic structuring of plant populations should encourage more efficient and hypothesis driven sampling designs in future phylogeographic work in the CFR. The high throughput sequence data generated in this thesis should transform Cyclopia to a model organism for the study of molecular evolution in the CFR.
- Full Text:
- Date Issued: 2020
Comprehensive characterization of the antidiabetic potential of selected plants and macrofungi from Africa using an in vitro target-directed screening platform and cellomics
- Authors: Pringle, Nadine Alex
- Date: 2020
- Subjects: Hypoglycemic agents
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/46750 , vital:39653
- Description: Several synthetic antidiabetic drugs have been developed to date, however, most are accompanied by adverse side-effects while remaining expensive and largely inaccessible to the vast majority of those who need it. To provide enough scientific evidence to support the inclusion of more affordable African antidiabetic medicinal plants and macrofungi into healthcare programs, this study sought out to develop a comprehensive in vitro antidiabetic target-directed screening platform incorporating high content screening and analysis/ cellomics. To test the success of this model, the potential antidiabetic mechanisms of five plants (Aspalathus linearis, Brachylaena discolor, Carpobrotus deliciosus, Sutherlandia frutescens and Tarchonanthus camphoratus) and two macrofungal species (Ganoderma lucidum and Hericium erinaceus) were explored. The screening model consisted of approximately 22 assays exploring the antidiabetic effects of selected aqueous and ethanolic extracts in five well-characterised antidiabetic targets: the intestine, liver, skeletal muscle, adipose tissue/ obesity and pancreatic β-cells. These targets were further categorised and scored under three mechanistic classes/ therapeutic targets (postprandial hyperglycaemia; insulin resistance and inflammation; pancreatic β-cell function) to elucidate their potential mechanisms of action and select appropriate animal models for future studies. Almost any normal or diabetic rodent model would be suitable to explore the antidiabetic potential of extracts such as A. linearis, B. discolor ethanol, C. deliciosus ethanol or T. camphoratus which obtained high cumulative scores under postprandial hyperglycaemia while high fat diet and genetic models of obesity appear more suited towards extracts such as H. erinaceus aqueous that obtained their highest cumulative score under insulin resistance. In general, a combination of rodent models ranging from non-obese models to models of obesity and β-cell destruction presenting symptoms from all three mechanistic classes should be considered due to the pleiotropic nature of the tested extracts, however, establishing appropriate experimental designs is crucial. To demonstrate the versatility of the screening platform and emphasise the importance of in vitro screening pertaining to diabetic complications, a more detailed biochemical investigation into the potential therapeutic benefits of A. linearis in the treatment of diabetic wounds was conducted. Several properties supporting the therapeutic potential of rooibos were highlighted with the green and fermented extracts presenting distinctly different characteristics. The pro-inflammatory nature of fermented rooibos may have therapeutic value for wounds characterised with a delayed initial inflammatory phase, such as early diabetic wounds while the green extract appears more suited to wounds burdened with excessive inflammation as it attenuated COX-2 levels and effectively protected fibroblasts against oxidative stress. To date, this appears to be the most comprehensive antidiabetic screening platform in existence and consequently provides the only feasible solution that will enable natural product antidiabetic research to progress to the point where natural products can be commercialised and incorporated into meaningful healthcare programs. Future research should be focussed towards further expanding this model by incorporating additional targets, more sophisticated cell culturing techniques, multiplexed high content screening assays and carrying out combination treatments that explore the antidiabetic effects of two or more crude extracts to establish whether they are capable of acting in a synergistic manner.
- Full Text:
- Date Issued: 2020
Conservation biology of an apex predator in the Anthropocene : poaching, pastoralism and lions in multi-use landscapes, South-Eastern Africa
- Authors: Everatt, Kristoffer T
- Date: 2020
- Subjects: Conservation biology -- Africa, Southern
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48290 , vital:40839
- Description: Many of the world’s apex predators are experiencing catastrophic declines as a result of competition with humans. Understanding the mechanisms and ecosystem impacts of apex predator declines is a fundamental ecological question crucial to conserving the Earth’s biodiversity and functioning ecosystems. In this thesis I used the African lion Panthera leo, as a model species to investigate the impacts of anthropogenic pressures on the conservation and ecology of an apex predator. Specifically, I investigated the relative and cumulative influences of pastoralism and poaching on lion occurrence, population connectivity, ecological role, space use, prey selection and viability across a 73 000 km2 multi-use landscape in southern Africa. Using landscape occupancy spoor surveys, I tested the hypotheses that lions were most limited by either interference or by exploitative competition with humans and identified thresholds of lion tolerance to human activities. My results showed that lions occupied only a fraction of the landscape and were limited by a combination of interference and exploitative competition with humans. Interference competition with pastoralism however was the biggest driver limiting lion occupancy, creating a clear disturbance threshold for lions cumulating in their near complete loss from the landscape. I employed call-up surveys, pride monitoring and mortality analysis to investigate the numerical impacts of anthropogenic pressures on the viability of a lion sub-population. I found that persecution by pastoralists was the greatest source of lion mortalities across the landscape. However, the targeted poaching of lions for body parts had emerged as the greatest threat to lions in a nominally protected National Park where I documented a steep population decline and collapse of lion prides. I used GPS tracking and diet analysis of lions at the human-wildlands interface to test if lions foraged optimally or were constrained by competition with humans. I fount that individual lions appeared to select for prey and habitat optimally, while also showing some level of risk avoidance towards anthropogenic pressures. I then considered landscape resistances to test if sink habitats may provide connectivity between sources or act as ecological traps. I found that potential connectivity for lions between the region’s two source populations was limited by a loss of habitat and prey. Furthermore, the impacts of by-catch in snares risked transforming the few remaining potential conservation corridors into ecological traps. Finally, I examined interactions between lions and syntopic mesopredators across gradients of anthropogenic pressures to test if the functional role of lions was affected by human pressures. I found that lions showed limited suppression of mesopredators, however, anthropogenic pressures increased lion’s interactions with syntopic predators. As an apex predator, lions have evolved limited capacity to mitigate top-down competitive pressures, however, like many of the world’s apex predators, they are becoming increasingly limited by anthropogenic pressures. This study provides a predictive understanding of an apex predator’s ecological responses to top-down anthropogenic pressures which can be applied globally to the question of conservation in the Anthropocene.
- Full Text:
- Date Issued: 2020
Creating Citizen-Science for Groundwater Monitoring prior to potential Shale Gas Development in Cradock (South-Eastern Karoo, South Africa)
- Authors: Dhliwayo, Nyaradzo
- Date: 2020
- Subjects: Natural gas -- Prospecting -- Environmental aspects -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48224 , vital:40526
- Description: Citizen Science is an integral tool for community engagement in scientific project design, implementation, data interpretation and reporting, in the quest to promote local capacity development as well as scientific knowledge. Based on the relevance of public engagement in aspects of the natural environment and associated scientific issues associated with the risks and opportunities of potential Shale Gas Development (SGD), a Citizen-Science (CS) study was designed in the Eastern Karoo region of South Africa linked to a Shale Gas Baseline Study initiated by the Africa Earth Observatory Network (AEON). As the pilot area of the baseline study, the town of Cradock was chosen to be the study area for this research; and CS was used to facilitate the identification of the Cradock community’s abilities to monitor the effects of potential SGD in this region. The development of new knowledge, skills and support, as well as a deeper understanding of the community’s role in Citizen Science studies, was also facilitated by this process. This study demonstrates the feasibility of integrating Citizen Science into existing community structures in Africa, thereby encouraging community engagement in the developmental programmes through participatory methods. Using a collaborative Action-Research Approach, consistent community roundtable meetings and key informant interviews served as invaluable platforms for the establishment of a 7-member community working group, that played the liaison role between the researcher and the Cradock community in the CS implementation process. Coupled with this was the recruitment and the training of eight young citizens in conducting a hydro-census and groundwater sampling for six boreholes within the identified Cradock commonage farms, as well as two boreholes on the farm of an identified emergent farmer. The engagements between the researcher, AEON scientists, the community working group and the community at large, enabled the successful implementation of CS training in two groundwater monitoring aspects and the testing of eleven water quality parameters. The training process was combined with the design and the development of a customised ‘Xoras’ Online Application, which was used to capture and share the hydro-census data recorded. Experiential learning in hydro-census and groundwater sampling resulted subsequently in an increased understanding and awareness of these aspects (Figure A). Even if SGD does not materialise in the South-Eastern Karoo, CS training will enable communities in the Shale-Gas Development precincts to participate in local decision-making forums on ground water, health, or on any related regional development projects. It is anticipated that the adoption of CS will ix promote future community engagements, especially about water across this water-scarce region, allowing for greater community-voice representation in resource-policy decisions related to potential Shale-Gas and related natural resource industries in the Karoo.
- Full Text:
- Date Issued: 2020
Data transport over optical fibre for ska using advanced modulation flexible spectrum technology
- Authors: Dlamini, Phumla Patience
- Date: 2020
- Subjects: Fiber optics
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/50666 , vital:42329
- Description: Flexible Spectrum Dense Wavelength Division Multiplexed (DWDM) optical fibre networks are next-generation technology for handling extremely high data rates of the kind produced by MeerKAT and SKA.We optimise the flexible spectrum for real-time dynamic channel wavelength assignment, to ensure optimum network performance. We needed to identify and develop novel hardware and dynamic algorithms for these networks to function optimally to perform critical tasks. Such tasks include wavelength assignment, signal routing, network restoration and network protection. The antennas of the Square Kilometre Array (SKA) network connect to the correlator and data processor in a simple point-to-point fixed configuration. The connection of the astronomer users to the data processor, however, requires a more complex network architecture. This is because the network has users scattered around South Africa, Africa and the whole world. This calls for upgrade of the classical fixed wavelength spectrum grids, to flexible spectrum grid that has improved capacity, reliable, simple and cost-effectiveness through sharing of network infrastructure. The exponential growth of data traffic in current optical communication networks requires higher capacity for the bandwidth demands at a reduced cost per bit. All-optical signal processing is a promising technique to improve network resource utilisation and resolve wavelength contention associated with the flexible spectrum. Flexible Spectrum Dense Wavelength Division Multiplexed (DWDM) optical fibre networks are next-generation technology for handling extremely high data rates of the kind produced by MeerKAT and SKA. Each DWDM channel is capable of 10 Gbps transmission rate, which is sliceable into finer flexible grid 12.5 GHz granularity to offer the network elastic spectrum and channel spacing capable of signal routing and wavelength switching for the scalability of aggregate bandwidth. The variable-sized portions of the flexible spectrum assignment to end users at different speeds depend on bandwidth demand, allowing efficient utilisation of the spectrum resources. The entire bandwidth of dynamic optical connections must be contiguously allocated. However, there is an introduction of spectrum fragmentation due to spectrum contiguity related to the optical channels having different width. Thus large traffic demands are likely to experience blocking regardless of available bandwidth. To minimise the congestion and cost-effectively obtain high performance, the optical network must be reconfigurable, achievable by adding wavelength as an extra degree of freedom for effectiveness. This can introduce colourless, directionless and contentionless reconfigurability to route individual wavelengths from fibre to fibre across multiple nodes to avoid wavelength blocking/collisions, increasing the flexibility and capacity of a network. For these networks to function optimally, novel hardware and dynamic algorithms identification and development is a critical task. Such tasks include wavelength assignment, signal routing, network restoration and network protection. In this work, we for the first time to our knowledge proposed a spectrum defragmentation technique through reallocation of the central frequency of the optical transmitter, to increase the probability of finding a sufficient continuous spectrum. This is to improve network resource utilisation, capacity and resolve wavelength contention associated with a flexible spectrum in optical communication networks. The following chapter provides details on a flexible spectrum in optical fibre networks utilising DWDM, optimising transmitter-receivers, advanced modulation formats, coherent detection, reconfigurable optical add and drop multiplexer (ROADM) technology to implement hardware and middleware platforms which address growing bandwidth demands for scalability, flexibility and cost-efficiency. A major attribute is tunable lasers, an essential component for future flexible spectrum with application to wavelength switching, routing, wavelength conversion and ROADM for the multi-node optical network through spectrum flexibility and cost-effective sharing of fibre links, transmitters and receivers. Spectrum slicing into fine granular sub-carriers and assigning several frequency slots to accommodate diverse traffic demands is a viable approach. This work experimentally presents a spectral efficient technique for bandwidth variability, wavelength allocation, routing, defragmentation and wavelength selective switches in the nodes of a network, capable of removing the fixed grid spacing using low cost, high bandwidth, power-efficient and wavelength-tunable vertical-cavity surface-emitting laser (VCSEL) transmitter directly modulated with 10 Gbps data. This to ensure that majority of the spectrum utilisation at finer channel spacing, wastage of the spectrum resource as caused by the wavelength continuity constraint reduction and it improves bandwidth utilisation. The technique is flexible in terms of modulation formats and accommodates various formats with spectrally continuous channels, fulfilling the future bandwidth demands with transmissions beyond 100 Gbps per channel while maintaining spectral efficiency.
- Full Text:
- Date Issued: 2020
Database and guide for Lesotho wool and mohair production and quality
- Authors: Maqalika, Papali Elizabeth
- Date: 2020
- Subjects: Mohair -- Dissertations -- Lesotho , Wool -- Dissertations -- Lesotho Textile fabrics -- Lesotho Textile industry -- Lesotho
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/49148 , vital:41605
- Description: Lesotho produces significant quantities of Merino apparel wool and mohair, both of a quality that allows them to compete on the global market and to make a significant contribution to the economy of the country. Nevertheless, very little production and quality data and trends of these fibres have been documented. This is a serious disadvantage in terms of international trading and benchmarking as well as attempts to improve the production and quality of Lesotho wool and mohair. In the light of the aforementioned, the available production and quality data of the past 10 years have been captured and analysed for trends and also benchmarking, where considered applicable. The main focus is on fibre diameter (fineness), staple length, and yield since they largely determine fibre quality, application and price. Some quality related tests were undertaken to fill certain important gaps in the available data. In addition, prickle and medullation were evaluated on representative wool and mohair samples, respectively, because they represent important quality measures for apparel wool and mohair, respectively. It was found that Lesotho wool and mohair are of a fairly good and internationally competitive quality, with the wool having an average fibre diameter (MFD) of ≈20μm, an average staple length of about 64mm, an average VM level of about 4%, an average yield of about 57%, and the annual production being about 4 million kilograms greasy. The average staple length of the mohair was about 140mm, average MFD about 29μm and the average medullation, which unless otherwise specified, refers to the objectionable medullated fibres (kemp type) including the flat medullated fibre, relatively high at about 5.7%. The latter is certainly an area of concern which needs attention and improvement. It was found that the prickle level (Comfort Factor), of some of the wools tested was of such a level as to make the wool suitable for wearing against the skin. With respect to mohair, there is considerable scope to substantially reduce the level of objectionable medullated (kemp style) fibre level through the appropriate breeding interventions. Production of both wool and mohair has increased slightly over the ten years covered by this study. It also became apparent that Lesotho wool and mohair quality and production are greatly influenced by the farming practices and climatic conditions. Greater adoption of the merino sheep breed, sheds/barns and sheep coats are suggested as ways to reduce mortality rate (due to extremely cold temperatures), improve quality and increase yield and production. Some farming practices such as the lack of barns, supplementary feeding and veterinary care present constraints in terms of production of both wool and mohair. The districts in the Highlands region had the highest production of mostly wool, this being ascribed to better pastures, climatic and other conditions conducive to wool and mohair production. Both wool and mohair are considered to have potential for improved quality and production, which could be affected by appropriate interventions by the Small Agricultural and Development Project (SADP) and others through National Wool and Mohair Growers Association (NWMGA). Nevertheless, since the wool and mohair growers (farmers) do not form part of these and other interventions, they do not readily adopt the various strategies and decisions and do not receive the associated benefits immediately. It is therefore advised that local farmers, relevant educators and researchers be represented in policy and other decision making forums. In this way, educational campaigns will be demand driven with greater chance of adoption and success.
- Full Text:
- Date Issued: 2020
Decision analysis to inform invasive alien plant management in the Garden Route Biosphere Reserve
- Authors: Masunungure, Current
- Date: 2020
- Subjects: Invasive plants -- South Africa , Alien plants -- South Africa , Biodiversity -- South Africa -- Management , Ecosystem management -- South Africa
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/49159 , vital:41606
- Description: Invasive alien plants (IAP) pose significant threats to global economies and biodiversity and are often considered as wicked problems. With an increasing number of IAP and limited resources, their management and decision-making processes are becoming difficult because of uncertainty, multiple and conflicting objectives, and diverse stakeholder views, facts and values. This is particularly challenging given the complex interactions between economic, ecological, and social elements that exist in invaded areas. Consequently, it is important to incorporate new ways of thinking and novel methodologies to improve our understanding of IAP management and the decision-making processes around them, which are currently inadequate. Decision analysis can help with dealing with these challenges and support decision-making under uncertainty. Drawing on the systems thinking approach and the concepts of leverage points, transition management and transformational change, the aim of this thesis was to explore the effectiveness of IAP management and the decision-making process in the Garden Route Biosphere Reserve (GRBR). This was achieved using a mixed methods approach involving: social-ecological inventory (identifying relevant stakeholders); review of literature on the available decision support tools; key informant interviews (stakeholder perspectives on the current decision-making process); and stakeholder workshop and expert consultation (casual loop modelling). The results of this thesis provide evidence that application of the proposed principles of robust decision-making has the potential to overcome the weaknesses of the current decision-making process and as such, enables decision-makers to efficiently allocate resources towards IAS management. A novel causal loop diagram (CLD) was developed to highlight the interconnections between key variables in IAP management and decision-making. This revealed that to transcend ‘policy resistance’ and ‘quickfixes that fail’ archetypes, and improve IAP management, the stakeholders need to consider deep leverage points, for example, fostering trust and shared understanding among different stakeholder groups. These can be realistically maintained over the long-term and can cause a fundamental change in IAP management, rather than focusing on shallow leverage points that are relatively easy to implement but do not result in significant systemic change. The findings of this thesis are flexible and could guide various stakeholder groups at local, national, and international scales in improving the effectiveness of IAP management and decision-making.
- Full Text:
- Date Issued: 2020
Development of a UV-tolerant strain of the South African isolate of Cryptophlebia leucotreta granulovirus for use as an enhanced biopesticide for Thaumatotibia leucotreta control on citrus
- Authors: Mwanza, Patrick
- Date: 2020
- Subjects: Baculoviruses -- South Africa , Ultraviolet astronomy
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48533 , vital:40885
- Description: Baculoviruses are pathogenic to insects in the orders Diptera, Hymenoptera, and Lepidoptera. As a result of this natural relationship with insects they provide an environmentally friendly method to combat crop and forest pests. As such, a number of baculoviruses have been formulated into biopesticides. The use of baculovirus biopesticides is gaining popularity as the use of chemical pesticides has come under stringent regulatory conditions imposed by governments and continental blocks such as the European Union. Baculoviruses have a narrow host range and therefore do not harm non-pests or humans who consume the crops. One such baculovirus is Cryptophlebia leucotreta granulovirus (CrleGV), which is pathogenic to the citrus pest Thaumatotibia leucotreta, commonly referred to as the false codling moth (FCM). CrleGV has an occlusion body (OB) that encloses a single virion. Several CrleGV biopesticides have been registered in South Africa for use on citrus, avocadoes, macadamias, grapes and other crops by two commercial producers, River Bioscience (SA) and Andermatt (Switzerland). These biopesticides are used as part of the FCM integrated pest management (IPM) programme, a multifacetted approach to controlling FCM. However, baculoviruses are susceptible to the ultraviolet (UV) radiation component of sunlight and lose their activity within hours to a few days, after exposure to UV. Several substances have been tested as UV protectants to improve the persistence of baculovirus biopesticides in the field. These include optical brighteners, UV absorbers and anti-oxidants. While very promising in the laboratory, UV-protectants have not been as successful in the field. A few published reports have reported, that UV-tolerant baculoviruses could be isolated from a population by repeatedly exposing and re-exposing the virus to UV irradiation with a propagation step in insect host fourth or fifth instars between each exposure cycle. In this study, the South African isolate of Cryptophlebia leucotreta (CrleGV-SA) was exposed to UV irradiation for 5 exposure cycles in a Q-Sun Xe-3 HC test chamber (Qlab, USA) with parameters set to mimic a typical summer day in the Sundays River Valley, Eastern Cape Province, in South Africa. In between exposures the virus survivors were allowed to multiply in FCM fifth instars. Surface dose bioassays were also conducted to determine the LC50 of the virus after each exposure cycle. Samples from exposure cycle 1 and cycle 5 (UV-tolerant) irradiated for 72 h were prepared for Next Generation Sequencing (NGS) of DNA. The resultant sequence data were analysed using the Geneious R11 software (New Zealand) and compared with the unexposed CrleGV-SA sequence. In-silico restriction enzyme analsysis (REN) with several enzymes was also carried on both the cycle 1 and cycle 5 exposed samples and the resulting digestion patterns were compared with the original CrleGV-SA digestion patterns. The same samples were also analysed by transmission electron microscopy (TEM) and Attenuated Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR) to evaluate the effect of UV irradiation on the structure of the CrleGV-SA OB. In addition, three UV protectants, lignin sulphate (Sappi, SA), BREAK-THRU®OE446 (OE446) (Evonik Industries, Germany) and Uvinul Easy (BASF, Germany) were prepared with CrleGV-SA to give final protectant concentrations of 0.09 %, 0.9 % and 9 %. The protectant-virus suspensions were exposed to UV for 24 h in the Q-Sun test chamber and bioassays conducted to determine the protective effect of each protectant concentration. The most successful protectants were then combined with the UV-tolerant CrleGV-SA and exposed to UV for 24 h in the Q-Sun test chamber and surface dose bioassays conducted afterwards. Samples exposed to UV in cycle 5 had lower LC50 values compared to samples in the early cycles. With each re-exposure cycle the LC50 values moved closer to that of the unexposed control. The LC50 of virus samples decreased from 2.89 x 108 OBs/ml after 24 h UV-exposure in cycle 1 to 2.16 x 105 OBs/ml after the same duration of exposure in cycle 5; and from 2.11 x 109 OBs/ml in cycle 1 after 72 h UV-exposure to 1.73 x 106 OBs/ml after the same duration of exposure. This represented a 1338-fold difference and a 1220-fold difference, respectively. When the UV-tolerant samples were sequenced seven SNPs were identified in cycle 1, which were thought to help establish UV tolerance, while a further seven SNPs were identified in cycle 5 samples; these were thought to further establish and maintain the UV-tolerance. Additionally, REN analysis with EcoR1 for both test samples yielded digestion patterns that were different from those of the original CrleGV-SA. TEM data showed that UV damages the virion as well as the crystalline structure of the OB. This is the first time visual evidence for UV damage to baculoviruses has been published. Comparison of cycle 1 and cycle 5 UV exposed OBs revealed that the cycle 5 OBs were significantly larger than the cycle 1 OBs (P<0.05). In addition, several peaks in the fingerprint region were shown to have either appeared or disapeered from the ATR-FTIR spectra after UV irradiation. However, there was no difference in the spectra of the Cycle 1 and Cycle 5 virus samples. The tests with potential UV-protectants revealed that the 0.9 % lignin, 9 % OE446 and 9 % Uvinul Easy were the most effective in protecting the virus from UV. However, there was no significant difference in their protection of UV tolerant CrleGV-SA and wild type CrleGV-SA. Going forward, it is recommended that the 0.9 % lignin, 9 % OE446 and 9 % Uvinul Easy combinations be explored further in future studies, particulary in the field. This study therefore forms an important foundation for the development of UV-tolerant baculovirus that will last longer in the field.
- Full Text:
- Date Issued: 2020
Development of bio-based xylan composites for food packaging applications
- Authors: Naidu, Darrel Sarvesh
- Date: 2020
- Subjects: Xylanases
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48544 , vital:40886
- Description: Currently a large number of chemicals and plastics are produced from petroleum-based resources. However, due to the concerns surrounding the depletion of petroleum resources and growing carbon emissions, there is a desire to produce chemicals and plastics from renewable and carbon natural sources. Lignocellulosic biomass (biomass consisting of cellulose, lignin and hemicellulose) is the most common biomass on earth and is renewable and carbon neutral. Of the three main constituents of lignocellulosic biomass, hemicellulose is composed of a mixture of sugars which can be converted into chemicals and plastics. The most common form of hemicellulose found in nature is xylan. This study is aimed at extracting xylan from maize stalk waste residues and the development of xylan films with properties that are suitable for food packaging applications. Xylan was extracted from maize stalk waste residues using an alkaline pre-treatment method. The effects of bleaching conditions (time, temperature and bleach concentration) prior to alkaline treatment on the yield and purity of xylan extracted was studied using a Box-Behnken experimental design. It was observed that the experimental conditions tested had no effect on the yield of the xylan extracted but the bleach concentration had a significant effect on the purity of the xylan extracted. The samples with the lowest lignin content were found to be the samples treated with 3wt% bleach prior to alkaline pre-treatment. One of the main disadvantages of xylan is that it has poor film forming properties, a method of overcoming this is to combine it with another abundantly available biopolymer that has good film forming properties, such as alginate. The effect of xylan, alginate and glycerol content on the mechanical, thermal, moisture uptake and water barrier properties of the films were investigated. It was observed that with an increase in the alginate content there was an increase in the tensile strength and Young’s modulus of the films, whereas the water vapour permeability (WVP) of the films decreased. This was attributed to the greater cohesion between alginate polymer chains compared to the cohesion between xylan polymer chains. The xylanalginate films exhibited better optical and water sorption properties at higher xylan content. In order to improve the inherently poor mechanical and barrier properties of the xylan-alginate films, bentonite and halloysite were incorporated into the films. It was found that 5wt% incorporation of either bentonite or halloysite resulted in a 49% decrease of the WVP, which was attributed to water vapour impermeable nature of the silicate layers that make up both clays. The incorporation of the clays into the xylan-alginate matrix resulted in a significant
- Full Text:
- Date Issued: 2020
Development of MOVPE-grown InAsSb for barrier diode applications
- Authors: Dobson, Stephen R
- Date: 2020
- Subjects: Gallium arsenide semiconductors , Electronics
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/49071 , vital:41598
- Description: In this study, layers of GaSb, InAs and InAsSb are grown by metalorganic vapour phase epitaxy and characterised. Growth is conducted using the precursors of trimethylgallium, trimethylindium, trimethylantimony and tertiarybutylarsine. Focus is then placed on the characterisation of the materials, carried out by the techniques of X-ray diffraction, photoluminescence spectroscopy, Hall measurements and photocurrent spectroscopy. It is observed that V/III ratio plays a vital role in the growth of the GaSb and InAsSb layers. Epilayers of GaSb showed best crystalline quality when a V/III ratio of 1.2 was used at a growth temperature of 600 °C and a cell pressure of 600 Torr. Resultant Hall measurements indicated p-type GaSb. The Hall carrier concentrations of the p-type GaSb samples were analyzed considering electrical neutrality conditions and found to be highly compensated with evidence of band impurity conduction at low measurement temperatures. Both the donor and acceptor concentrations were determined to be of the order of 1016 cm−3 for all samples. For low temperature (< 150 K) a monovalent acceptor concentration is calculated to have an activation energy at approximately 20 meV. At high temperature (> 150 K) a divalent acceptor is extracted with an activation energy varying between samples based on compensation in a range of 90 meV to 70 meV. Photoluminescence measurements show four peaks with recombination mechanisms linked to the native acceptor identified in literature as either the gallium antisite and/or vacant gallium site. A fifth peak observed is attributed to the longitudinal phonon of the native acceptor. InAs and InAsSb epilayer are all grown at a temperature of 600 °C and cell pressure of 600 Torr. InAs is grown at a V/III ratio of 9.5 on GaAs substrate. Photoluminescence of the InAs layer shows two distinct peaks, one of which is an extrinsic band to band recombination. The other is attributed to free electron to acceptor or a donor-acceptor pair transition. An additional weak peak is also observed which is assigned to the longitudinal phonon of the band to band. InAsSb growth was conducted under a range of V/III ratios of 4.8 to 5, with a vapour phase composition of 0.4 to 0.435. Structural analysis via X-ray diffraction showed a 6 % to 12 % solid antimony content. Photoluminescence exhibited a single broad peak for all samples, with extended band tails. Temperature and power dependant analysis of luminescence indicated a convolution of extrinsic band to tail and band to band recombinations. Hall measurements indicated the InAsSb was n-type material with an apparent measured maximum mobility at 120 K of 9.5 × 103 cm2/V.s. and a room temperature apparent mobility of 7.5 × 103 cm2/V.s. Analysis of hall results using a two-layer model calculated a true bulk mobility of the epilayer at room temperature with an increased value of 15.4 × 103 cm2/V.s. The two-layer model details the effects of the surface conduction. From photoconductivity measurements and further analysis a resultant effective lifetime, at room temperature, was found to be on same order of magnitude as that of InAs materials. Application of a single Einstein oscillator extrapolated 0 K energy gaps for two samples of solid Sb contents of 6 % and 12 %, of 354 meV and 332 meV, respectively. Finally consideration was given to the growth of aluminium containing compounds, particularly AlGaSb. Multiple phases were observed under scanning electron microscope showing growth of GaSb regions surrounded by amorphous solid aluminium and/or aluminium oxide phases. The failure of the aluminium to incorporate into the desired crystal structure is speculated to be due to impure precursor introducing oxygen into the films. Additionally, the effectiveness of the gallium precursor compared to the aluminium precursor in helping the removal of the methyl groups at the growth surface, could also promote a preference for GaSb growth.
- Full Text:
- Date Issued: 2020
Development of Tio 2 nanostructure arrays for photonic extraction of hydrogen gas
- Authors: Suliali, Nyasha Joseph
- Date: 2020
- Subjects: Nanostructures , Nanostructured materials Hydrogen
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/49314 , vital:41620
- Description: Amid the energy crisis of the 21st century, renewable energy is a thriving field of study, light harvesting materials being a central theme due to the abundance of solar energy. Nanostructured TiO2 is the most studied photocatalysis material, since the discovery of its energy harvesting properties by Fujishima and Honda in 1972. Environmentally friendly products such as hydrogen fuel, can be produced using TiO2 due to its non-toxicity, chemical stability and photocatalytic activity. The surprising aspect of this important material is that it can be prepared using cost-effective methods such as hydrothermal synthesis, solution gelation and anodic oxidation. This research focused on the three key elements required to develop TiO2 photoelectrodes i.e. the deposition of Ti films on transparent substrates, a thorough analysis of the chemistry of the anodic oxidation process and the development of the TiO2 thin films. Glass substrates that have Ti films are the base component for TiO2 photoelectrode production. Ti films with thicknesses up to 4 μm, were developed on commercial F-doped SnO2 (FTO) glass substrates using high-power impulse magnetron sputtering (HiPIMS). The sputter deposition experiments were performed in the 1 to 8 kW range at a substrate temperature of 500 °C and Ar pressure of 400 mPa. At higher powers, thicker films were deposited, resulting in increased intensity of Xray-diffraction peaks. However, on comparing the XRD patterns, the (001) peak outgrew the rest regardless of thickness of the film. The deposition process therefore favoured orientation of most of the α-Ti phase crystallites with the [001] axis perpendicular to the substrate surface. Surface roughness results were interesting, showing a non-linear dependence of the surface roughness on HiPIMS pulse energy in the 1 to 8 kW range. The surface roughness is highest at the starting deposition power of 1450 W and reduces to a minimum at 4500 W. From this minimum, it increases to its second highest value at 7900 W. From this data, the parameters required to produce Ti films of lowest surface roughness, for deposition on commercial Technistro® FTO glass, were deduced at the inflection point, where the deposition power was 4500 W. The surface roughness obtained is a critical result for the anodic production of quality TiO2 photoelectrodes, which if high, leads to uneven etching, thus irregular and inefficient photoelectrodes. Direct current magnetron sputtering was also carried out in the 1 to 5 kW range to obtain ratios of power-normalised growth rates of the Ti films. This investigation provided the Ti films on FTO glass, the transparent, conductive substrates which were used to develop TiO2 photoelectrodes. To elucidate the chemistry of anodic oxidation of Ti, a mathematical model of the anodic current density, which had not been reported at the time of its publication, was developed. The technique, a highlight of this research, is a predictive numerical computation of the instantaneous quantities of species that participate in the anodization process. From eleven chemical reactions, 14 first order ordinary differential equations were compiled using the principles of chemical reaction kinetics. The pattern, transient behaviour and response to anodization parameters of the current density signal, were successfully predicted. Strong agreement between the model and measurements was demonstrated in seven experiments. The results confirm that the current density signal is a numerical integral of the kinetics of redox reactions of water. The bulk of this research was on the development of TiO2 nanotubular arrays on Ti foil substrates and Ti films on FTO glass. TiO2 films with well-defined tubular structures were synthesised. The films were developed in anhydrous, polar organic hosts with water and etching agents in the range of 10 V to 70 V. The control of geometrical properties of the tubes such as the length, pore diameter, wall thickness, tube separation and number of nanotubes per unit area was demonstrated. Anatase only and mixed anatase-rutile phase compositions were obtained at different annealing temperatures. Nanotubes with diameters as small as 20 nm and thickness as high as 29 μm were produced. Apart from an increase in nanotube thickness, a decrease in distance between nanotubes grown in diethylene glycol was observed at longer anodization times. Studies of the effects of anodization parameters on the current density measured, morphological and crystallographic properties of the nanotube films were conducted in three main investigations. The first was the study of the effect of anodization parameters on current density. Besides the obvious increase of current density with anodic voltage, the first steady state of the growth process was found to depend on the NH4F concentration. The second investigation focused on the effect of accelerated growth of TiO2 nanotubular films. In the study, 9 μm-thick nanotube films were synthesised at twice the growth rate of a 9 μm-thick control sample. The array obtained by accelerated growth had distinguishable nanotubes, however, the morphological quality was reduced. The third investigation demonstrates the control of the number of nanotubes per unit area. By varying the etchant content, the anodic voltage and the viscosity of the electrolyte host, various distributions were obtained. The research ends with a photoelectrochemical application: measurement on photocurrents generated in a two-electrode setup. The photocurrent densities measured in the off and on conditions were 30 nA/cm2 and 2.57 μA/cm2, respectively, demonstrating photoactivity of the developed films.
- Full Text:
- Date Issued: 2020
Foraging in a dynamic environment: movement and stable isotope ecology of marine top predators breeding at the Prince Edward Archipelago
- Authors: Carpenter-Kling, Tegan
- Date: 2020
- Subjects: Marine ecology , Stable isotope tracers , Estuarine ecology
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/49049 , vital:41596
- Description: Marine ecosystems are experiencing rapid changes due to climate change. The associated temporal and spatial changes in resource distribution impacts on the foraging behaviour of marine top predators. If these changes negatively affect the ability of marine predators to forage efficiently, there may be dire consequences for their populations. However, evidence of foraging plasticity during adverse conditions, or generalist foraging behaviour, can allow inference about the resilience of species to environmental change and provide essential knowledge towards effective and proactive conservation measures. I examined plasticity in the trophic ecology of 12 marine predator species breeding on Marion Island, southern Indian Ocean, over three years (2015 – 2018), a period characterized by pronounced environmental variability. Firstly, I correlated behavioural states inferred along the GPS tracks of incubating wandering, grey-headed, sooty and light-mantled albatrosses to environmental variables that are indicative of biologically productive oceanographic features. Secondly, I analysed δ13C and δ15N blood values in 12 marine predator species (the afore-mentioned albatrosses as well as king, gentoo, macaroni and eastern rockhopper penguins, northern and southern giant petrels and Antarctic and sub-Antarctic fur seals) over two seasons: summer and autumn. My results revealed that the foraging behaviour of all the species is, to some degree, either plastic (temporally variable isotopic niche) or general (large isotopic niche which remained similar over time), except for the king penguin (small isotopic niche which remained similar over time), a known foraging specialist. Furthermore, despite their dynamic foraging behaviour, resource partitioning among the predators was maintained over time. Due to the ease and relatively low cost of collecting tissues for stable isotope analysis it has the potential to be a powerful tool to monitor the trophic ecology of marine predators. I thus used my simultaneously collected dataset of GPS tracks with the stable isotope blood compositions to investigate some of the assumptions underlying the inferences made from marine predator δ13C and δ15N blood values. I reconstructed species- and guild- specific δ13C and δ15N isoscapes for eight seabird species. Following this, I coupled individual-based movement models of northern giant petrels with global marine isotope models to explore the sensitivity of tissue δ13C values to a range of extrinsic (environmental) and intrinsic (behavioural, physiological) drivers. My results demonstrate the strong influence of reference isoscapes on the inference of stable isotope compositions of marine predators. Furthermore, I show that caution should be used when using non-species-specific or temporally inaccurate isoscapes. I furthermore demonstrate that biological interactions, such as competition for food resources, either past or present, as well as spatio-temporal distribution of food patches strongly influence the foraging behaviour of marine predators. These findings highlight the importance of integrating biological interactions in species distribution models which are used to predict possible distributional shifts of marine predators in the context of global changes. My thesis further developed previously available methods and presents a novel approach to investigate sources of variance in the stable isotopic composition of animals’ tissues.
- Full Text:
- Date Issued: 2020
Genetic connectivity in sandy beach macroinfauna with contrasting life histories and zonation patterns
- Authors: Bezuidenhout, Karien
- Date: 2020
- Subjects: Fishes -- Genetics , Seashore ecology -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/45944 , vital:39380
- Description: Open-ocean sandy beaches are highly dynamic ecosystems that continuously respond to waves, tides and storms. These beaches support a suite of uniquely adapted fauna that exhibits a high degree of endemism. This diversity, which also includes some economically important resource species, contributes to the great socio-economic and ecological value of sandy beach systems, which provide ecosystem services such as nutrient recycling and water purification, fish nursery habitat (surf zone), and natural buffering against storms. Despite their broad global distribution comprising ~70 % of the world’s ice-free coastline, beaches are naturally fragmented by other intertidal marine habitats and extensive coastal development. Sea-level rise is now threatening beaches, particularly along developed coasts through coastal squeeze, with an increased risk of habitat loss and exacerbated fragmentation. Such habitat loss has important implications for population and species persistence, depending on the level of connectivity among populations. While sandy beach macroinfauna tend to be highly mobile across and along shore, they also show a strong bias towards direct, or aplanktonic, development; the latter could reduce opportunities for dispersal and sustained population connectivity. However, comparatively little is known about population connectivity on sandy beaches, limiting scientifically sound management of much of the world’s coastline. This study aims to address this knowledge gap by working towards a conceptual model quantifying population connectivity, and by investigating the specific roles of life history, across-shore zonation, and geographic range as putative indicators and possibly drivers of genetic differentiation (ΦST) and connectivity (gene flow) among beach macroinvertebrate populations. The main hypotheses are that 1) species with a pelagic larval stage will display lower genetic differentiation with higher rates of gene flow among populations than species with a benthic lecithotrophic larval stage or direct development; and 2) genetic differentiation among populations will decrease along an across-shore axis, from the supratidal to the low water mark. Two opposing hypotheses were tested concerning the relationship between genetic structure and distributional range: 3a) Species with a large range (measured as distance and number of latitudes) will show less genetic differentiation than those with a narrow range, because they are more able to disperse; or 3b) more widely distributed species may occur across more phylogenetic | v breaks, and thus show higher genetic differentiation than species restricted to a smaller ranges and single biogeographic provinces. First, the extent and likely drivers of population connectivity were investigated for a suite of temperate South African macroinfauna. Very low, non-significant genetic differentiation was demonstrated for the beach clam Donax serra, thus supporting the hypothesis that pelagic larval dispersers display low/no genetic differentiation among populations (Chapter 2). Statistical power of the COI locus was, however, low in this species, due to reduced genetic variability which could be attributed to an expansion from a small source population into extant habitats. The results highlighted the need for caution when interpreting a lack of genetic differentiation as evidence for population connectivity. Nevertheless, COI sequences verified that D. serra occupying the cool and warm-temperate regions of the South African coast, constitute a single species, despite morphological and behavioural differences between inhabitants of these two bioregions. D. sordidus, a congener of D. serra, and endemic to the warm-temperate (Agulhas) bioregion of South Africa, was investigated to test two opposing hypotheses (Chapter 3): 1) this pelagic larval disperser lack genetic differentiation with high rates of gene flow across its range, or alternatively 2) these clams are genetically structured across their range due to the influence of freshwater input (measured as distance to nearest estuary), and morphodynamics of the surf zone (represented by surf-zone width). Significant global ΦST was estimated for D. sordidus, with differentiation predominantly driven by haplotype frequencies at a single study site and estimates of gene flow among most sample locations generally high. Tentative evidence suggested that natural selection driven by differences in water salinity due to estuarine runoff and surf-zone width, might be maintaining two dominant haplotypes across the range of this species. Beach clams from the Southern Hemisphere, occupying different distributional ranges, were compared to test the hypothesis that genetic structure decreases with an increase in range. This hypothesis was poorly supported by the results; opposite (yet mostly non-significant) trends demonstrated for ΦST and haplotype diversity, thus providing some support for the alternative hypothesis that more phylogeographic breaks in broad-ranging species results in higher estimates of genetic structure in these species.
- Full Text:
- Date Issued: 2020
Ichthyofaunal and isotope changes along the rivere-stuarine continuum in a fluvially dominated Southern African coastal system
- Authors: Nashima, Festus Panduleni
- Date: 2020
- Subjects: Fishes -- Ecology
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48555 , vital:40890
- Description: Catchment to coast and the continuum concept recognize linkages and make it imperative to take an ecosystem approach to catchment management, water allocation, fisheries management and environmental management as a whole. Fishes that utilise estuarine environments are influenced by physical and chemical conditions as well as biological interactions. Community structure, drivers and trophic linkages between species of different origin, utilising the low salinity waters along the riverestuarine continuum remain poorly understood in the lower Orange River and estuary. This body of work investigated the spatio-temporal dynamics structuring fishes in the lower Orange River Estuary Continuum (OREC) within the context of River Continuum (Vannote et al., 1980). Eight years (2004 - 2018) of seasonal sampling at 18 sites comprised of multi-species catches were analysed, including three years (2016 - 2018) exploring trophic linkages between the dominant species of marine, estuarine and freshwater fishes in the system. In total, 30 species belonging to 16 families were collected in the lower OREC. The Family Mugilidae dominated all catches. Fish species composition was comprised mostly of freshwater (47%), followed by the marine (33%) and estuarine species (20%). Numerically, the marine euryhaline Chelon richardsonii and solely estuarine Gilchristella aestuaria were the dominant species in the estuary region (site 1 - 11) with 95% and 4% contribution, respectively. Chelon richardsonii also dominated all catches (67%) upstream into the river (site 12 - 18), followed by freshwater Labeobarbus aeneus (13%) and Pseudocrenilabrus philander (8%). This highlights the point that besides the marine Chelon richardsonii, other species albeit marine, estuarine and freshwater are utilising unique areas within the OREC. Temporal differentiation in fish abundance (catch-per-unit-effort, CPUE), diversity, richness and evenness were higher in the high-flow season than the low-flow season. Mean CPUE was higher at the mouth of the estuary and declined upstream into the river, whilst species diversity (including richness and evenness) increased upstream. High catches but low species diversity observed close to the mouth of the estuary were attributed to the domination of Chelon richardsonii. However, species diversity increased upstream in the river due to the dominance of freshwater fishes coupled with several marine and estuarine species. This diversity patterns were inconsistent with the general Remane and revised model for estuaries, hence a new RiverEstuarine Continuum concept suitable for OREC was developed. With the exception of Chelon richardsonii, spatial variability in the length-frequency distribution of most fishes was observed. Physico-chemical drivers provided valuable information on adaptation limits of species movement and distribution. Fishes were structured along a salinity gradient and interaction between temperature and salinity influenced community structure and diversity patterns in the OREC. Fish species utilising the lower OREC are predominantly zoobenthivores but a few detritivores/planktivores dominate numerically. Trophic inferences from stable isotope analysis showed increased carbon isotope values (δ 13C) with salinity toward the mouth of the estuary, whilst nitrogen isotope values (δ 15N) increased upstream into the river. Ontogenetic shifts in the SI ratios of all five fish species (marine Chelon richardsonii; estuarine Gilchristella aestuaria; freshwater Labeobarbus aeneus, Pseudocrenilabrus philander and Mesobola brevianalis) were observed in the OREC. Variability in seasons and salinity gradient influenced the SI ratios of several fish species. Seasonal changes influenced the δ 13C ratios of all species, except for Labeobarbus aeneus and Pseudocrenilabrus philander whereas the δ 15N ratios of all species (except for Mesobola brevianalis) differed significantly between the high-flow and low-flow season. This can be due to their feeding on specific life-history stages, such as eggs, larvae, gametophytes, sporophytes or zoospores of prey. Stable isotope ratios revealed that Mesobola brevianalis fed at a higher trophic level than Chelon richardsonii and Gilchristella aestuaria. Mesobola brevianalis feed on planktonic crustacean and insects. Chelon richardsonii feed on a wide range of prey, with prey switching between planktonic and detritivore food resources, whilst Gilchristella aestuaria feed selectively on zooplankton but switched to filter feeding modes in turbid water. Generally, δ 15N SI ratios increase with growth, however, for Labeobarbus aeneus, it was significantly higher in small size length than in large size individuals, probably because most of the juveniles assessed were caught upstream where δ 15N increases. Juveniles of Labeobarbus aeneus mainly feed on zoobenthos whilst in larger fish phytoplankton becomes increasingly important, suggesting the possibility that zoobenthos was more 15N enriched than plant materials. The trophic niches of Mesobola brevianalis were isotopically distinguishable from Chelon richardsonii and Gilchristella aestuaria during the low-flow season, revealing that these species are probably accessing carbon sources from different food chains. During high-flow season, the isotopic niche overlapped among several species, indicating that these species are probably deriving carbon sources from the same or similar food chains. Results from Layman isotope-based metrics revealed that Chelon richardsonii, Pseudocrenilabrus philander and Labeobarbus aeneus occupied the widest isotopic niche in the lower OREC, suggesting that these species are utilising food sources which may be derived from a wide variety of carbon sources. Mesobola brevianalis had the narrowest isotopic niche, however this does not imply "a narrow range of food sources’’ for the species. Overall, the potential carbon sources for selected fish species revealed that they are supported by a variety of food sources (mainly phyto-and zooplanktonic) or their food items constituted different basal sources which enable them to coexist. This study represents the first, integrated investigation of trophic relations among fishes of different origin using δ 13C and δ15N SI analyses. The current study provides a broader understanding of fish ecology within the River-Estuarine Continuum in the lower Orange River and estuary. By filling research gaps identified in the lower OREC, this synthesis of work also supports and informs management, conservation and responsible utilisation of estuarine fishery resources, in particular within the OREC.
- Full Text:
- Date Issued: 2020
Investigating the fitness of sea turtles nesting in South Africa
- Authors: Le Gouvello du Timat, Diane Z M
- Date: 2020
- Subjects: Sea turtles -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48445 , vital:40877
- Description: The South African rookeries of the South Western Indian Ocean (SWIO) loggerhead and leatherback regional management units have been continuously monitored for more than 5 decades, representing one of the longest-running sea turtle beach protection and monitoring programmes in the world. Although such conservation has been successful in protecting adults on land when they come to nest, it might not be enough to ensure population recovery if survival is not ensured across all life stages. Sea turtles are particularly vulnerable to direct threats and changing environmental conditions because they are long-lived, slow maturing, and have low survival rates at early life stages, making them conservation-dependent. These characteristics also render them difficult to conserve as a consequence of their wide geographic distributions, spanning multiple jurisdictions and legislative systems with different conservation targets, and a complex life cycle with changes in habitats and diets at different life stages. Sea turtle populations have been severely depleted as a result of historical over-exploitation and current threats including fisheries bycatch, direct harvest, habitat loss, pollution and pathogens, and climate change. In many cases however, population declines have been reversed by a variety of effective conservation measures such as beach protection programs, and marine protected areas, enabling successful population recovery around the world. Despite protection and apparent increase in abundance, indirect pressures can still affect turtle populations. Therefore, it is fundamental to evaluate the effectiveness of conservation measures (using fitness traits such as female and hatchling sizes) and examine underlying trends. The aim of this thesis was thus to evaluate the fitness of loggerhead and leatherback sea turtles nesting in South Africa. Long-term female size trends over time were evaluated and the populations were split between first-time nesters and experienced nesters. As sea turtle reproductive output (clutch size only) is correlated with female size and evidence is showing that in some populations individual female size is decreasing, the effects of maternal body size on reproductive output and hatchling fitness were investigated for both species. Crawling and swimming speeds were used as proxies of hatchling fitness, because these two traits positively influence their survival. An oceanic model was further used in combination with a particle tracking framework to estimate, for the first time, post-hatchling dispersal of loggerhead and leatherback turtles in the SWIO. I investigated whether the trend in female size for loggerhead turtles nesting in South Africa is a result of their foraging strategy to determine if there is a foraging dichotomy (neritic and oceanic). Despite an apparent increasing population, a significant 3.7 and 3.6 cm decrease in the size of both recruit and remingrant female loggerhead turtles, but a stable mean size of leatherbacks for both age groups was observed. I hypothesise that these contradictory effects are attributable to the very distinct foraging ecologies of the two turtle species and speculate that these variations in carapace length may be driven by environmental change. The reproductive strategy of both loggerhead and leatherback turtles nesting in South Africa supports the optimal egg size theory with larger turtles producing larger clutches but not larger eggs. Egg size was thus constant irrespective of maternal length. Hatchlings with longer carapaces and flippers had higher swimming speed, suggesting that larger hatchlings are fitter (potentially higher survival) than smaller ones by spending less time in high predation risk areas (i.e. beach and nearshore). The model revealed that dispersal trajectories of both loggerhead and leatherback sea turtle hatchlings were very similar and simulations indicated that initial active swimming (frenzy) as well as variability in oceanic conditions strongly influenced dispersal of virtual hatchlings. The trends observed in this study emphasize the importance of long-term monitoring, examining not only abundance but also individual size, to understand population dynamics, support recovery planning and prioritize future conservation practices. Furthermore, the findings of this study have important implications for overall population growth if smaller hatchlings of lower fitness are produced as a result of climate change and thus have decreased dispersal abilities and lower likelihood of survival.
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- Date Issued: 2020
Investigation of potential induced degradation as a performance limiting defect in photovoltaic modules
- Authors: Kwembur, Isaac Morko
- Date: 2020
- Subjects: Photovoltaic cells
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10948/48423 , vital:40875
- Description: Potential Induced Degradation (PID) impacts negatively on photovoltaic (PV) module durability because it significantly affects the output of PV modules and systems. Unless detected at infancy, PID progression can be catastrophic. This study involved systematic PID stressing of PV modules using a custom-built environmental chamber that can achieve suitable environmental conditions, viz., of the 35 °C ± 1 °C and relative humidity of 75 % ± 5 %. The first part of this work was to induce PID using three approaches: climate chamber testing, inducing PID using a conductive aluminium plate on the surface of the module without touching the frame and a localised PID induction on one cell in a module. The second part is to detect induced PID using Electroluminescence (EL) images taken at current corresponding to 10% Isc, EL histograms analysis and Voc ratio taken at 1000 W/m2 to 200 W/m2 . The third part is to study module regeneration after PID shunting degradation in two ways, viz., forced reverse polarization and natural recovery. The PID detection tools used in this work are well known module characterization techniques such as EL imaging, Infrared imaging, and light and dark current-voltage measurements. These characterisation tools are used in combination to detect defects such as optical losses, cracks, breakage, electric circuit degradation and PID. Under normal testing PID was detected and in some cases, modules were able to recover, while for advanced stage PID regeneration or PID reversal was difficult. This thesis focuses on PID detection at infancy using three approaches; EL imaging at current corresponding to 10% of Isc. Light and dark current – voltage measurements (L-IV & D-IV) and open circuit voltage (Voc) ratios at low irradiance. The early detection procedures are essential in reversing the degradation caused by PID which is reversible. The time taken to reverse the PID degradation will depend on the extent of the degradation. If detected early, it will take a short period of time to completely reverse lost power. Infrared thermography is a non-contact characteristic tool that can be deployed in large scale plants using drones to detect the presence of PID in PV plants. Module performance and device parameters extracted from the L-IV curves on a module before and after PID stress, such as Pmpp, Voc, Isc Fill Factor (FF), shunt resistance (Rsh) and series resistance (Rs) and ideality (n) are sensitive to PID shunting. Voc and Rsh drop significantly with the onset of PID, while Rs increases. The decrease in Voc and Rsh is due to heavy shunting on the module resulting in increased carrier recombination, while the increase in Rs is due to increased shunting paths leading to decreased photocurrent. When substantial degradation on a module occurs Pmpp, FF and n will drop and at very advanced stage of PID degradation Isc may drop excessively.
- Full Text:
- Date Issued: 2020
Ocean dynamics of the shelf and bays of the eastern Agulhas bank: a process-oriented numerical modelling study
- Authors: Bailey, Dylan Francis
- Date: 2020
- Subjects: Oceanography -- Research , Marine biology , Marine meteorology , Hydrography
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/49038 , vital:41595
- Description: There is a general need for a broader base of information on the finer detail of ocean processes in the Eastern Agulhas Bank region. In this thesis, the Regional Ocean Modelling System (ROMS) was applied to resolve high resolution (~1km) bay and shelf scale ocean processes along the south eastern coastline of South Africa using an offline multi-nested approach. Experimental and reference ocean model runs were used with in situ instrument mooring data to investigate how currents and temperature in the bays and the adjacent shelf are affected by the bathymetry, Agulhas Current (AC), regional winds, and coastal trapped waves (CTW). Focus was given to temperature, circulation, and coastal trapped waves, given the abundance of hourly in situ mooring data for these variables, making them suitable for comparison with the ocean model. SST variability trends were seasonally and spatially predictable, being greatest in the summer months and smallest in the winter months. A region of high SST variability extended from Port Alfred toward the south-west, indicating entrainment of nearshore upwelled water and instabilities in the inshore front of the AC. Shelf bottom temperature variability had a more spatially diverse seasonal trend, with coastal variability the highest (lowest) and offshore variability the lowest (highest) during the summer (winter) months. A distinct asymmetry in mean seasonal shelf bottom temperatures evident to the south of Algoa Bay and St Francis Bay was shown to be dependent on the profile of the shelf margin in relation to the inshore front of the AC using an experimental model run. Bay-scale anti-cyclonic circulation patterns dominate the bays throughout the year, with regions of strong mean surface currents occurring south of Cape Recife and Cape St Francis. General circulation patterns over the shelf are strongly governed by regional wind regimes, with the strongest flows being south-westward occurring during north-easterly wind events. Shelf bottom flows typically follow the expected Ekman-veering response, apart from near coastal flows that are topographically steered. A region of consistently strong south-westward shelf bottom flow extends from the east of Port Alfred to the shelf margin south of Bird Island. This flow is predominantly driven by the AC, although its velocity is strongly governed by regional winds. Circulation patterns during powerful eastward moving wind systems are strongly governed by the passage of associated CTW. Comparisons with an experimental model run where surface winds were removed revealed that the shelf wave was responsible for 61% of water volume displacement during a CTW event, and that the coastal shear turbulence caused by this displacement has a direct effect on the mixed layer depth. The links made between the complex shelf and bay ocean processes indicate that subtle changes to the ocean state will have far reaching effects on the regional ocean environment and its biota. Given the challenges of climate change, this is of paramount importance if we are to quantify these effects and mitigate their impacts, particularly with respect to the socio-economic dependency of those who rely on the ocean for its living resources.
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- Date Issued: 2020