Electronic Theses and Dissertations (PhDs)

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Browsing Electronic Theses and Dissertations (PhDs) by SDG "SDG-3: Good health and well-being"

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    The Impact of different levels of organic plant-based compost on the macro and micro elements, secondary metabolites and water soluble vitamins content of Moringa oleifera leaves
    (University of the Witwatersrand, Johannesburg, 2023) Ngwenya, Nkazimulo; Risenga, Ida M.; Chimuka, Luke
    Moringa oleifera leaves are a high source of phytochemicals and nutrients inclusive of macro and micro elements, secondary metabolites and water-soluble vitamins. All the M. oleifera plant parts inclusive of its leaves have been widely utilised for nutritional and/ medicinal properties because of its high levels of minerals and phytochemicals. Studies have been conducted targeting the improvement of the quantity of M. oleifera nutrient content. However, with increased consumer awareness of high quality organic, consumer and environmentally safe products there is increased need to improve the quality of M. oleifera products. One of the major factors impacting the quality and quantity of M. oleifera leaf nutrients is cultivation practices. Particularly soil amendments applied to improve plant biomass have also been found to significantly improve nutrient content of M. oleifera leaves. However, the popularly used soil amendments which are in the form of synthetic fertilisers or animal based compost have raised environmental and product safety concerns. They contain, among other contaminants, traces of heavy metals and other toxins which are harmful to both the environment and consumers of the produce. Producers of herbal plants such as M. oleifera are looking for sustainable, environmental safe ways of improving the quantity and quality of the produce. Application of organic plant based compost was therefore investigated as a potential soil amendment source in improving M. oleifera nutrients in an organic, clean sustainable way, and thus improving the quality of the produce. The use of plant based compost to improve the nutritional content of M. oleifera grown in South Africa was reported in this thesis. The primary objective of the study was to assess the impact of the plant-based organic compost on the macro and micro elements composition, secondary metabolite accumulation and distribution and water soluble vitamins content in M. oleifera leaves. This work is novel and worth exploring as it seeks to investigate for the first time the correlation between the use of plant-based organic compost and quality improvement in terms of nutrient content of M. oleifera leaf biomass. Furthermore, this research is the first of its kind which looks at the impact of compost on the nutritional content encompassing, macro and micro nutrients, secondary metabolites and water soluble vitamins in M. oleifera grown in South Africa. In addition, the developed and validated high performance liquid chromatography (HPLC) method for the simultaneous quantification of five B vitamins was successfully used in the identification and quantification of the vitamins. Clay soil and M. oleifera seeds used in the study were obtained from the M. oleifera community farm in Hammanskraal, Gauteng, South Africa. The clay soil was amended with plant-based organic compost purchased from the local nursery store. The amendments achieved four treatment levels namely 15 % compost / soil amendment, 30 % compost / soil amendment, 45 % compost / soil amendment and 60 % compost / soil amendment. Moringa oleifera seeds used were obtained from the same farm. Plant samples were grown in the School of Animal, Plant and Environmental Sciences (APES), University of the Witwatersrand, greenhouse under ambient temperatures. Harvesting of the leaf biomass was done after six months and nutrient analysis was carried out. Analytical techniques such as Spectroscopy and Chromatography were used for the nutrient analysis. Presence and quantity of macro and micro elements in the soil and leaves was analysed using the Inductively Coupled Plasma Optical Emission spectroscopy (ICP-OES). Whilst, the Ultra high-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS) was used to determine plant metabolites, and for the quantification of water-soluble vitamins by coupling it with the diode array detector (DAD). The nutrient analysis revealed that the use of organic plant-based compost for the amendment of clay soil improved the quality of the soil and M. oleifera leaves harvested from each soil amendment. The addition of the organic plant-based compost improved the macro and micro nutrients. Comparison of the different compost levels revealed that addition of plant based compost increased the bioavailability of macro and micro nutrients in the soil and increased their accumulation in M. oleifera leaves. Metabolic fingerprinting of M. oleifera leaf samples using UHPLC-ESI-QTOF-MS followed by untargeted compound analysis exposed variation in the identified metabolites. Further use of multivariate analysis in the form of PCA clustered the samples into five distinct clusters indicating diversity in the distribution of secondary metabolite as influenced by the addition of plant-based compost to the soil. The developed HPLC method was suitable for the simultaneous quantification of five B vitamins based on the low LOD and LOQ values, recovery of 97.8- 99.58% and good linearity. Application of the validated method revealed that, the addition of plant based compost significantly improved the quantity of the tested vitamins (Vitamin B1, B2, B3, B6 and B9). The 30% plant-based organic compost and clay soil combination was identified and recommended as the best compost-soil combination in improving nutrients in M. oleifera leaf biomass. It had the highest level of macro and micro nutrients. Leaves harvested from this soil/compost combination had higher concentration of Ca (45 042.5 mg/Kg), Mg (17 430 mg/Kg), P (8802. 5 mg/Kg). In addition leaves, harvested from 30% compost treatment exhibited the highest number of identified secondary metabolites and had the highest concentration of two of the five tested water soluble vitamins. This knowledge will make great contribution in the M. oleifera industry in South Africa and worldwide particularly for farmers who are into organic M. oleifera production.
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    Uncovering genetic changes underlying adaptation in southern African dwarf chameleons (Bradypodion)
    (University of the Witwatersrand, Johannesburg, 2024) Taft, Jody M.; Alexander, Graham J.
    Natural selection acting on the available range of phenotypes in a population will favour alleles beneficial to an organism’s fitness, resulting in adaptation. Characterizing patterns of adaptive genetic variation in wild populations is a fundamental first step toward understanding the potential for adaptation in response to selection. With recent advances in sequencing technology, the increased availability of high-quality genomic resources has made efforts to identify loci under selection across the genome more tractable. As a result, there is a growing body of research challenging the notion that adaption takes place over deep evolutionary timescales, with evidence of rapid adaptation occurring in a range of taxa. Examples of rapid adaptation are rife within reptiles, particularly in response to contemporary environmental changes such as urbanization. Despite this, insights into the genetic architecture of adaptation in reptiles remain limited as appropriate genomic resources are currently lacking. The southern African dwarf chameleons, Bradypodion, are the most recently diverged lineage in Chamaeleonidae. These arboreal lizards are well known for their high capacity for adaptation, especially in response to environmental change. Bradypodion are known to have undergone rapid diversification linked to habitat specialization resulting in the emergence of few convergent phenotypes, or ecomorphs, across the genus. These lizards occupy a variety of habitat types, from closed-canopy forests to open-canopy habitats such as grasslands, but are also known to occur within urban environments. As ecomorphs of various Bradypodion species display phenotypic convergence in similar habitat types, populations may also converge phenotypically in urban habitats. However, the underlying genetic architecture of these phenotypes remains unknown for Bradypodion, further constrained given the absence of appropriate genomic resources for these lizards. To facilitate insights into the genetic architecture underlying adaptation in Bradypodion, two de novo assembled whole genomes were produced using Pacific Biosciences long-read sequencing data. These assemblies are among the highest-quality squamate genomes published to date. In addition, coalescent analyses of these assemblies indicated that historical changes in effective population size correspond to notable shifts in the southern African environment. Furthermore, the high-quality annotations of both Bradypodion genome assemblies were generated and used to describe the genetic feature landscapes and evaluate the gene family evolution of Bradypodion. Findings indicated that expanded gene families within this genus are likely the result of responses to changing environmental conditions, facilitating the diversification of Bradypodion. In addition, differences in gene family composition at the species level provide insights into underlying genetic pathways resulting in adaptive traits possibly promoting ecomorph divergence across the genus. Lastly, to detect loci under selection, population structure and genetic diversity were assessed in five species of Bradypodion known to have populations in natural and urban habitats using a pairwise comparative approach. While there is evidence of allele frequency differentiation between urban and natural populations, it is uncertain that this is due to selection pressures experienced by the urban population. While links between genes containing outlier loci and the phenotypic traits known to be associated with adaptation in urban habitats are made, it is recommended that these genes be used as candidates for targeted gene modification to evaluate the phenotypes generated by those modifications and contrasted with phenotypes present in urban populations. This thesis provides insights into the mechanistic genomic basis of adaption in Bradypodion. The high-quality genomes and annotations produced here will hopefully serve as a resource for further assessments of genetic adaptation in chameleons and reptiles more broadly. Furthermore, these findings present a framework from which to formulate robust hypotheses to assess candidate genes presented here as likely underlying adaptive phenotypes in urban populations