3. Electronic Theses and Dissertations (ETDs) - All submissions
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Item Genetic diversity of tamarix lineages in South Africa and heavy metal tolerance of the indigenous species(2018) Mayonde, Samalesu GuelorThree species of saltcedar (Tamarix L.; Tamaricaceae) occur in South Africa, although only T. usneoides is indigenous and is effectively used in southern Africa mines for phytoremediation. Tamarix ramosissima and T. chinensis were reportedly introduced into South Africa from Eurasia also for phytoremediation, but have since invaded riparian zones. Tamarix species are morphologically similar and hybridization adds to their taxonomic confusion. Biological invasions of Tamarix species have serious negative impacts in most riparian zones from changing the ecosystem function to altering the river flow system, to depositing salt crystals on the top soil and displacing native biodiversity. Mechanical and chemical control of the invasive Tamarix has been reported ineffective, leaving biocontrol as an alternative option to suppress Tamarix infestations thereby reducing its negative impacts. However, for the biocontrol programme of Tamarix in South Africa, hybridization and introgression events, and the presence of the indigenous species poses a challenge of host shifts for non-target effects to the indigenous species. Assessing the levels of genetic diversity and differentiation in invasive species and their closely related indigenous species is essential to better understand the invasion process and population genetic relations for an effective biocontrol programme. Molecular techniques are widely used during the initial phase of biocontrol programmes before the release of agents to accurately identify the invading species, assess the genetic diversity and compare the genetic structure between and within species. In South Africa, the indigenous Tamarix usneoides is used for phytoremediation in rehabilitation efforts of mine lands contaminated with acid mine drainage. Although the plant has been planted on tailing storage facilities, its ability to tolerate the highly acidic conditions and heavy metals has not been fully investigated. Plants suitable for phytoremediation should have the ability to tolerate high concentrations of heavy metals and accumulate them in their above ground biomass. Therefore, this study investigated the physiological responses of T. usneoides to metal toxicity by assessing growth parameters. Profiles of gene expression patterns of T. usneoides for heavy metal tolerance were also investigated to assess the ability of the plant in activating its genome for tolerance against environmental stress conditions. Nine microsatellite loci were used to assess the genetic diversity and differentiation of 150 Tamarix samples (117 individuals from South Africa and 33 from the U.S.). In South Africa, samples were collected from four Tamarix taxa viz. T. usneoides, T. chinensis, T. ramosissima and Tamarix hybrids with 30 samples per taxon; while from the U.S. we collected Tamarix hybrids to compare against those from South Africa. This study showed that the indigenous T. usneoides is genetically more diverse than the invasive T. chinensis but is less diverse than T. ramosissima, another invasive species. There was great genetic differentiation between the indigenous and the invasive Tamarix species in South Africa. In addition, private alleles unique to T. usneoides were obtained in some remote places in the north-western part of the Northern Cape Province suggesting unpolluted populations of the indigenous T. usneoides germplasm. The low genetic diversity in T. chinensis seems to be as a result of its autogamous nature other than caused by founder effects. Higher genetic diversity was observed in the South Africa Tamarix hybrids compared to their U.S. counterparts and there is substantial genetic differentiation between the two hybridization incidences. The high genetic differentiation suggests that there might be minimal or no non-target effects on the indigenous species from biocontrol control agents against the invasive genotypes. This study also suggests that exploration of biocontrol agents should be done in the place of origin of the invasive plants other than in the U.S. where species of the Diorhabda beetles are effectively controlling Tamarix infestations. Three different concentrations of cadmium (Cd) – 6 ppm, 12 ppm, 18 ppm, were applied to 240 individuals of indigenous T. usneoides propagated from 20 trees from different localities. The plants were exposed to Cd for eight weeks where plant height, shoot growth and chlorophyll content were measured weekly to assess the physiological responses against Cd toxicity. Of the 240 individuals, 80 samples were randomly selected for gene expression profiling using cDNAAFLP analysis. Height, shoot growth and chlorophyll content of T. usneoides were all found to decrease with an increase in Cd concentrations over time as there were significant differences between the Cd treated groups and the controls. Chlorophyll content was found to be the most sensitive to Cd toxicity followed by shoot growth with plant height the least affected parameter. Although Cd toxicity affected the physiology and growth of T. usneoides, the plants were observed to be tolerant to the low (6 ppm) and medium (12 ppm) Cd concentrations as the measured parameters were not significantly reduced compared to the controls. Additionally, no visible signs of metal toxicity were observed at low and high concentrations. However, phenotypic signs such as leaf chlorosis, drying of branch bottoms, even the death of some plants were observed at the high (18 ppm) Cd concentration. The high Cd concentration level resulted in a significant reduction in the growth of T. usneoides. cDNA-AFLP analysis of T. usneoides showed different profiles in expression patterns where high numbers of AFLP bands were obtained with an increase in Cd concentrations over time. The medium concentration was observed to generate the highest transcript derived fragments (TDFs) associated with heavy metal tolerance. The ability of T. usneoides to tolerate heavy metal concentrations < 12 ppm and the wide regions of the genome being expressed with an increase in metal concentration suggest that T. usneoides is a good candidate for phytoremediation. To sum up, the indigenous Tamarix usneoides is moderately diverse genetically and is greatly differentiated from the exotic and invasive T. chinensis, T. ramosissima and their hybrids. The invasive Tamarix genotypes can be considered for biocontrol with suggested minimum non-target effects on the native species which is considered for conservation and presents a good candidate for use in phytoremediation because it can tolerate more than usual concentrations of heavy metals in contaminated soils.Item Human red cell NADP-dependent xylitol dehydrogenase: kinetic and genetic studies(1984) Lane, Anthony BruceA deficiency of the enzyme NADP dependent xylitol dehydrogenase (L-xylulose reductase) has previously been found to be the cause of chronic essential pentosuria. Essential pentosuria is a recessively inherited condition which is marked by the continual excretion of relatively large amounts of the enzymes substrate, L-xylulose. The major objective of the study described was to find a simple method for the identification of individuals who are heterozygous for the "pentosuria" and normal alleles. The pentosuria allele could then be used as a gene marker in linkage studies aimed at mapping the L-xylulose reductase locus. A L-xylulose reductase assay suitable for the identification of carriers of essential pentosuria was developed and tested on members of a South African Lebanese family in which the inheritance of pentosuria had previously been suggested to be dominant. It was found that family members could, on the basis of their L-xylulose reductase activities, be classified as either normal, heterozygous or homozygous for the pentosuria allele. Measurements of serum L-xylulose concentrations revealed that pentosuria is, contrary to the previous report, . recessively inherited in this family. A sample of the local Ashkenazi Jewish population was screened for pentosuria carriers. Six out of the 237 individuals screened were found (on the basis of their L-xylulose reductase activities and from the results of a loading test), to carry the pentosuria allele. The frequency of the pentosuria allele in this population was estimated from the apparent heterozygote frequency to be 0.0127. Linkage analyses were carried out on the families of the identified heterozygotes and on members of the Lebanese family mentioned above. No evidence of tight linkage was found between the pentosuria allele's locus and those coding for various red cell antigens, red cell enzymes and serum proteins. Kinetic, chromatographic and electrophoretic studies revealed that the red cells of normal individuals contain two distinct L-xylulose reductases, a minor and a major isozyme. Pentosurics lack the major isozyme but appear to have approximately normal amounts of the minor isozyme. The minor isozyme is e1ectrophoretica 1 1 y distinct from the major isozyme, has markedly higher Michael is constants for the substrates L-xylulose and xylitol and shows a lower pH optimum when catalysing the oxidation of xylitol. Electrophoresis also revealed that liver tissue contains two L-xylulose reductases which occur in similar proportions to those of red cells but which migrate at slightly different rates.Item Variation in ABCB1 and its effect on immune recovery with antiretrovirals(2012-02-03) Du Plooy, Ingrid MarieThe ABCB1 gene encodes P-glycoprotein, a transmembrane protein that regulates the efflux of drugs in the cells and may affect the response to antiretroviral drugs. ABCB1 polymorphisms affect the function or expression of P-gp. The 3435T allele has been associated with decreased protein production, but is in linkage disequilibrium with other polymorphisms. HIV is prevalent in Southern Africa, and characterization of ABCB1 variation may provide insight into its role in antiretroviral immune response. The aim was to determine if there was any association between ABCB1 variation, relative mRNA levels and immune response. Seven known polymorphisms were characterized for linkage disequilibrium and haplotype analysis, regions upstream of the gene were sequenced for bioinformatic analysis, the relative amounts of mRNA were determined, and CD4+ and viral load data was analyzed for association. Sequencing revealed six novel variations: T-137G, C-233T and G-298A upstream of exon 1, T108G and G153A in exon 2, and A111G in intron 26. The frequencies of the -129T (0.85), 1236T (0.70), 2677G (0.77), IVS 25+3050G (0.86), IVS 25+5231T (0.51), 3435C (0.88) and IVS 26+80T (0.89) polymorphisms were different and LD was lower compared to other populations. The haplotype frequencies were different to other populations and the genetic structure was probably a result of multiple recombination or mutation events. The viral load counts at the second measurement after baseline (time point 2) were significantly different from baseline for the 2677GG and 2677GA genotypes, and the -129T allele was associated with a lower proportional decrease in viral load at 8 the second measurement. The IVS 25+3050GG, 3435CC and IVS 26+80TT genotypes have been associated with lower mean relative mRNA levels. In conclusion, the genetic structure of the southern African populations is different from other populations and that genetic association and functional studies derived from other populations would be irrelevant in this population. A larger sample size and functional studies would be required to attempt to resolve the molecular mechanisms of the ABCB1 gene and to confirm the findings of association between ABCB1 polymorphisms and immune response.Item A reflection on the morality of ownership of genetic material(2011-11-23) De Carvalho, Candice LeeThe question of ownership of genetic material is highly relevant to medical ethics at this point in our history. What has become a major debate is how DNA can, and if it ought to be commoditised; and how and if individuals can keep their genetic information private, or whether it ought to be shared with all. In this research report I question whether genetic information is exceptional when compared with other medical or health-related information. The Kantian view of commoditisation of the body and human dignity is given along with some of the most prominent views on self-ownership. Patenting and genetic biobanking have received much attention in recent years, I focus on these issues and moral questions that surround these practices. The idea of genetic information as a common and natural 'resource' is discussed. If it is indeed a common heritage for all, how ought individuals, populations, researchers and funders to relate to genetic information? I briefly examine what some communities and cultures may have to say about genetic information and I attempt to tie all these varying perspectives together. I find that it is not ownership per se that is often the subject of dispute, but how those who happen to have control over that information share it. I present a possible maxim to guide the sharing of genetic information with others; that patenting does not necessarily amount to an affront to human dignity in the Kantian sense and that inter-cultural perspectives on genetic information may differ significantly. I conclude that how genetic material is shared, or not shared and why seems to depend more on the population in question at any given time and its social, political and economic structures than on the question of ownership per se.