HLA (Human Leukocyte Antigen) molecules provide a framework for T-cell recognition of antigenic peptides and thus play an important role in the immune system and defence against pathogens. HLA molecules are encoded for by genes on the short arm of chromosome six in the human genome, a region of over 4000 kilo bases (kb) known as the human major histocompatibility complex (MHC) or HLA complex. According to structural and functional characteristics, the genes of this region have been classified into three families, namely classes ƒ¹, ƒ¹ƒ¹ and ƒ¹ƒ¹ƒ¹. The HLA genes are highly polymorphic and because of this characteristic, it increases the functional range of recognition of different antigens and contributes to immunological specificity. Previous studies on population groups such as Indians and Cambodians, have identified an association between HLA polymorphisms and susceptibility to TB. A large number of different population groups with diverse gene pools reside in South Africa, of which the Cape Coloured population is one. This anthropologically distinct population group¡¦s diverse gene pool originated from founder individuals of the colonizing population, which came from various nations and cultural backgrounds, including Europe, Africa (such as Khoi, San Xhosa, Sotho and East African populations), Madagascar and the Far East. Unusual MHC allele frequencies and haplotypes have been identified in the Cape Coloured population. The Cape Coloureds are highly susceptible to TB and reside in the Western Cape, which has a TB incidence rate that is higher than that of any other province in South Africa. The recently admixed Coloured population is a valuable candidate population for the identification of genes/mutations underlying complex diseases. This study focussed on polymorphisms of class ƒ¹ƒ¹ genes, specifically HLA-DRB, and their possible contribution to disease susceptibility in populations of South Africa. Two questions have been formulated: 1) What knowledge can we gain from the current literature on HLA variants in the different population groups of South Africa and disease susceptibility? 2) Is there an association between alleles of the most polymorphic class ƒ¹ƒ¹ MHC gene, HLA-DRB, and susceptibility or resistance to TB in the Cape Coloured population? These two primary questions have been addressed by: 1) Reviewing the literature concerning HLA alleles in diverse population groups in South Africa and their contribution to disease susceptibility. Chapter 2 addresses this objective and is written in the format of a review article to facilitate its future publication, 2) Conducting a TB case-control study, typing HLA-DRB in Cape Coloured individuals residing in the Western Cape to investigate the possible association between TB susceptibility or resistance and specific DRB alleles. The HLA-DRB1, DRB3 and DRB4 typing by means of PCR-SSP (polymerase chain reaction ¡V sequence specific primers) was done on DNA isolated from 106 TB patients and 107 controls from the Cape Coloured population. The results obtained for this experimental investigation is presented (also in publication format) in Chapter 3. Summary of main findings: 1) The literature overview of publications describing HLA related disease association in the different population groups in South Africa (Chapter 2), revealed that unique alleles contributing to susceptibility of various diseases have been identified in some South African populations. The large number of ethnic groups in South Africa and unique populations such as the Cape Coloureds provide a genetic resource, which has the potential to be utilized for candidate gene hunting. 2) A weak association between susceptibility for TB and HLA-DRB1*0301-0302 (DR3) and HLA-DRB3*0101-0301 (DR52) exists in the Cape Coloured population (Chapter 3). Since the South African population consists of a large number of different population groups with diverse gene pools, a unique opportunity to study disease predispositions among specific population groups with diverse genetic make-up is presented. With these different populations, often residing in a common environment, the interplay of environmental and genetic factors in disease development could be studied. For example, HLA typing of these populations could clarify the extent to which inter-population HLA variation contributes towards disease susceptibility. The identification of certain HLA-DRB alleles potentially contributing to TB susceptibility, could lead to an understanding of the differential factors involved in disease susceptibility and in turn lead to the understanding of the fundamental mechanisms involved. This could result in therapeutic approaches and treatments that will be advantageous to the population concerned. / Prof. L. Bornman

M.Sc. / Tuberculosis, of which the causative agent is Mycobacterium tuberculosis, presents itself as a serious health problem globally, especially in Africa. Susceptibility to this infectious disease is influenced by the virulence of the strain of mycobacteria, environmental factors, and genetic variation within the host. The Vitamin D Receptor gene or VDR has been identified as a candidate gene for TB susceptibility. This gene codes for the VDR protein that mediates the biological actions of the active form of vitamin D. Vitamin D has been shown to impair growth of Mycobacterium tuberculosis in human monocytes and macrophages. Vitamin D also provides a link between Toll-like receptor activation and the antibacterial responses of innate immunity in its production of cathelicidin. The VDR protein is a transcription factor that mediates the effects of the active form of vitamin D. Vitamin D has an immunomodulatory role and variations in the VDR gene may result in variations in the functioning of the VDR protein, and hence variations in response to infection. The VDR gene includes the largely non-coding 5’ regulatory region exons 1a-1f and the coding exons 2-9. As a result of increased awareness of the heritability of gene expression and reports of disease associations with VDR promoter region variants, the focus of the research described in this dissertation was the regulatory region of the VDR gene. Polymorphisms that occur within the regulatory region were viii investigated, as were the effects these polymorphisms may have on gene expression, influencing host susceptibility to tuberculosis, with an emphasis on African populations. VDR polymorphisms have been shown to be involved in susceptibility to tuberculosis, particularly the FokI SNP in exon 2, BsmI and ApaI in intron 8 and the synonomous TaqI in exon 9. However, results have been inconsistent. SNPs shown to be associated with TB may serve as markers of truly functional SNP with which they are in linkage disequilibrium (LD). The majority of these association studies involve single nucleotide polymorphisms (SNPs) found in the introns or are silent mutations in the coding exons. Variations in the 5’ regulatory region have been shown to affect gene expression, in particular if they influence the binding sites of transcription factors.

The global prevalence of type 2 diabetes (T2DM) and obesity is increasing, with obesity the most important predisposing factor contributing to the development of T2DM. Epidemiological and genetic evidence supports a major genetic component in both multifactorial and heterogeneous disorders. The identification of disease susceptibility genes in humans could greatly assist in the elucidation of underlying pathophysiological mechanisms and allow the development of more effective preventative and therapeutic strategies for these conditions. Three candidate genes, uncoupling proteins 2 and 3 (UCP2; UCP3) and calpain 10 (CAPN10), are proposed and the rationale for their selection discussed. Gene variants were identified in UCP2 and UCP3. These variants were tested for association with T2DM, obesity and intermediate quantitative traits in a South Indian population and family collection, and also a cohort of British obese case/control subjects. No variant was associated with T2DM. However, investigations revealed positive associations with a UCP2 3'UTR 45bp Ins/Del and a novel UCP3 promoter variant (-55C/T) with variation in body mass (BMI) and fat distribution (WHR) respectively. The results support the view that uncoupling proteins may influence weight gain and hence progression to obesity/T2DM. A significant correlation with plasma leptin levels and the UCP2 Ins/Del variant might indicate one potential mechanism whereby weight could be modulated by uncoupling proteins. A linkage study in affected sibling pairs of North European descent, was negative for the putative T2DM susceptibility gene region, NIDDMI. In contrast, haplotypes of four sequence variants of a T2DM susceptibility gene (CAPN10) identified in this region positively associated with T2DM in a South Indian population. In conclusion, these investigations provide evidence that the three genes studied may contribute to susceptibility for development of T2DM or obesity. However, the findings are in agreement with the most likely genetic model for non-Mendelian complex diseases, that many genes are involved in determining susceptibility to disease with no single gene capable of determining the overall disease phenotype.

No description available.

Thesis (Ph. D. in Human Genetics)--Vanderbilt University, May 2009. / Title from title screen. Includes bibliographical references.

Thesis (Masters Diploma (Medical Technology))-- Cape Peninsula University of Technology, 1992 / Studies that document the higher incidence of tuberculosis as well as the variable efficacy of the BCG vaccine in Black, compared to White, populations have alluded to resistance or susceptibility to tuberculosis being genetically controlled.The HIA system has been associated with many diseases involving an immune aetiology. It has been shown that T cell receptor genes have limited restriction fragment length polymorphisrns, serving to create a variation in the repertoire of expressed T cell receptor genes. These repertoire differences may play a fundamental role in disease susceptibility.A study was therefore undertaken to establish whether linkage exists between the HIA system or the T cell receptor genes and a putative susceptibility gene for tuberculosis.Polymorphisrns of these genetic markers were examined in three Cape Coloured multiplex families, affected individuals having culture-positive pulmonary tuberculosis.HLA haplotypes were derived from serological typing of peripheral leucocytes from each individual. B-Iymphoblastoid cell lines were established from each family member. DNA was then extracted and digested with a variety of restriction endonucleases. After gel electrophoresis and Southern blotting, the DNA fragments were probed with a panel of T cell receptor cDNA probes, revealing the allelic polymorphisms.Linkage analysis was done using the Liped computer programme and Lad scores were determined for each marker locus using various genetic models. Haplotypes were also established for the T cell receptor genes and used in the linkage analysis.Although most of the Lad scores fell within the indeterminate range, a cumulative Lod score of 1.79 was obtained from the allele generated by the EcoRV/a2 enzyme/probe combination under a recessive model with 50% penetrance. This represents odds of about 52: 1 in favour of linkage between the T cell receptor a gene and a putative susceptibility gene to tuberculosis.

South Africa is at present encountering one of the worst Tuberculosis (TB) epidemics in the world, accentuating the need for intervention to eradicate TB. Various studies have established that certain population groups are at risk for increased susceptibility to infection with Mycobacterium tuberculosis (M. tuberculosis). This predominantly occurs in populations, like the native African population groups, who were not exposed to TB until the disease arrived in their country with European settlers, colonialists and missionaries. These population groups consequently lack the natural resistance to infection, which other populations developed through years of exposure to the pathogen. Several susceptibility-associated genetic polymorphisms have been proposed to explain differential susceptibility to TB. HLA class II molecules play a pivotal role in the activation of the host immune response against M. tuberculosis. Consequently numerous HLA class II genes have been found to be associated with TB. Among the most commonly observed associations is that of HLA-DR2 with TB, which has been observed in various population groups. Although this association has been observed to transcend ethnic barriers, inter-population variation has also been established regarding HLA-TB associations. In this study, the possible association of HLA class II polymorphisms, specifically of the HLA-DRB1, DQB1, DRB3, DRB4 and DRB5 loci, with TB susceptibility was investigated in the Venda population of South Africa. This was achieved by conducting both a case-control and family-based association study. The results obtained in this study established a unique association between HLA-DRB1*1302, DQ7 and TB susceptibility. A marginally significant association was also observed with DRB1*1301 and DQ6d and possible TB resistance. The above-mentioned results, which were observed in the case-control group, could not be replicated in the family-based study. It was therefore concluded from the results obtained in this study that employing both a case-control and family-based analysis when undertaking an association study is the most beneficial option. / Prof. Liza Bornman

M.Sc. / Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis). TB is a multifactorial disease, influenced by both environmental and genetic factors. Susceptibility varies among individuals and is likely explained by differential environmental exposures and genetic factors. For example, Africans are more susceptible to TB than non-Africans, likely attributed to their generally lower socioeconomic status and possible higher frequencies of ‘susceptible’ genetic variants. Similarly, males are more susceptible to TB than females, presumably as a consequence of gender-based sociocultural differences as well as biological and/or genetic differences. From a host genetic perspective, TB is a complex disease associated with variants from several genes. The Vitamin D Receptor (VDR) gene, coding for the VDR protein, has received much attention as a candidate gene; the VDR mediates vitamin D functions, of which one is to restrict M. tuberculosis survival in macrophages. Several studies attempting to associate VDR single nucleotide polymorphisms (SNPs) with TB susceptibility have given inconsistent results. Factors suggested to contribute to these inconsistencies include confounding environmental factors as well as higher VDR genetic/haplotypic diversity and less linkage disequilibrium (LD) in African populations compared to non-African populations. However, epigenetic variation has not yet been considered as an additional confounding factor leading to inconsistencies in genetic association studies for TB and VDR. vi Epigenetic factors are heritable and pivotal to regulate gene transcription. Moreover, epigenetic factors are highly susceptible to environmental influences and have been shown to be the underlying factor in certain disease aetiologies. Not only are epigenetic factors susceptible to environmental influences, but also to genetic factors acting in cis or in trans. An example is the formation or elimination of a methylatable CpG by a SNP. On the other hand, epigenetic factors may influence the genotype through formation of methylation-induced SNPs. The synergistic effect of genetic variants, epigenetic variants and the environment on disease is known as the common disease genetic epigenetic (CDGE) hypothesis. The CDGE hypothesis supports the study of both genetic and epigenetic variants to provide a better understanding of disease aetiologies and to increase the power of association studies.

Strawberry powdery mildew, caused by Podosphaera aphanis, has the potential to cause over 20% yield loss, particularly where strawberries are grown under cover. A holistic approach to the control of strawberry powdery mildew (P. aphanis) is important, since the disease is never absent from the crop. The new disease assessment key was developed to assess strawberry powdery mildew (the old one is for assessing red blotches on leaves, See appendix 8). The results (Chapter 3) showed that the disease is present in the crop when new plants are bought in from a propagator, with 14% of strawberry crowns were infected by P. aphanis in July 2013 and 4% of the strawberry plants had symptoms of powdery mildew in pre-assessment of plants for the 2013 Si nutrient fertigation field experiment. Control measures used in one growing season reduced the disease carry-over, thus reducing the initial inoculum in the following season. The use of a late autumn fungicide spray and a fungicide spray before the plants were covered by fleece in spring reduced the number and maturity of overwintering chasmothecia, thus contributing to a reduction in initial inoculum. The use of silicon (Si) nutrient (foliar spray and root treatment) also suppressed strawberry powdery mildew development (Chapter 4). The results of Area Under Disease Progress Curve (AUDPC) and the rate of epidemic growth curve (r) in 2012 indicated that the high concentration of Si nutrient foliar spray inhibited (r = 0.002, AUDPC = 44) the epidemic build-up of P. aphanis better than the low concentration of Si nutrient (r = 0.012, AUDPC = 51) and untreated (r = 0.018, AUDPC = 70). The Si nutrient root treatment (AUDPC = 12.8) was better in inhibiting strawberry powdery mildew development than the Si nutrient foliar spray treatment. Moreover, the high concentration of Si nutrient foliar spray resulted in fewer chasmothecia compared to the untreated. Si nutrient foliar spray and root treatments increased the concentration of Si in the plants and produced physiological changes in the plants, including wax formation on the adaxial leaf surface, greater leaf thickness and cuticle layer and increased Brix0 value in plants, which all were associated with reduced disease incidence. The integrated use of all these control strategies suppresses disease development so that control is achieved with less use of conventional fungicides.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Bovine tuberculosis (BTB) is a chronic, infectious disease found in domestic livestock and wildlife, and has serious biodiversity, economic and public health implications. African buffalo act as a wildlife reservoir of BTB, maintaining and transmitting the disease within the environment. The research presented in this thesis addresses the role of host genetic variation in resistance to BTB infection in African buffalo, and reviews the possible practical application of such information. Annual BTB prevalence within the African buffalo population in Hluhluwe iMfolozi Park, South Africa, was evaluated over a seven year period in order to define the extent of M. bovis infection. Prevalence changes over time suggest that the test and cull operation currently in place is performing successfully with respect to the original aims of the programme. A review of genetic studies of BTB in livestock and wildlife collated previous findings in this field and provided a collection of possible candidate genes and variants. It also highlighted a lack of research in wildlife, and the limitations of working with species with insufficient genetic data. To overcome the absence of whole-genome data, next-generation sequencing was performed on nine African buffalo, in order to identify novel genetic variants in this species. Upwards of 76 000 novel SNPs within gene regions were identified, and subsequent fluorescent genotyping of 173 SNPs showed a 57% validation rate. From the validated set, 69 SNPs located in genes related to the immune system were selected for association testing with BTB status in African buffalo, and were fluorescently genotyped in 868 individuals. Three SNPs, in the Solute Carrier family 7, member A13 (SLC7A13), Deleted in Malignant Brain Tumour-1 (DMBT1) and Interleukin 1 alpha (IL1α) genes, were identified as significantly associated with BTB status. Very little sequence information of the NRAMP1 (SLC11A1) gene was obtained from the next-generation sequencing performed, and this gene has been associated with brucellosis, salmonella and paratuberculosis in other animal species, making it an excellent candidate for BTB resistance. To characterise this gene in African buffalo, Sanger sequencing was performed to generate the complete coding region, and partially sequence the 5’UTR, intronic and 3’UTR regions. Fifteen novel polymorphisms and three microsatellites were identified within the gene. Finally, a review was prepared to assess the applicability of genetic information on BTB resistance to selective breeding programmes for African buffalo. Phenotypic, marker-assisted and genomic breeding strategies were discussed, with particular emphasis on their suitability to African buffalo. Identifying genes and variants involved in BTB resistance in African buffalo provides potential targets for drug or vaccine development, as well as information that could be incorporated into selective breeding programmes. This may support new management options for controlling the BTB epidemic in the game parks of South Africa, as an alternative to, or in conjunction with, lethal control / AFRIKAANSE OPSOMMING: Beestuberkulose (BTB) is ‘n chroniese, aansteeklike siekte wat in vee en wild voorkom en wat ernstige gevolge vir die ekonomie, biodiversiteit en openbare gesondheid inhou. Die Kaap-buffel is ‘n wild reservoir vir BTB wat die siekte onderhou en versprei in die omgewing. Die navorsing wat in hierdie tesis aangebied word fokus op die rol van gasheer genetiese variasie in die weerstand teen BTB infeksie in Kaap-buffels en gee ‘n oorsig van die moontlike praktiese toepassing van die resultate. Die jaarlikse BTB voorkomsyfer in die Kaap-buffel bevolking in die Hluhluwe iMfolozi Park in Suid-Afrika is oor ‘n tydperk van sewe jaar geëvalueer om die omvang van M. bovis infeksie te bepaal. Die verandering in voorkomsyfer oor tyd dui daarop dat die toets-en-slag operasie wat tans gebruik word die oorspronklike doelwitte van die program suksesvol bereik. ‘n Oorsig en vergelyking van vorige genetiese studies van BTB in vee en wild het ‘n versameling van moontlike kandidaatgene en –variante verskaf. Dit het ook die gebrek aan navorsing in wildediere uitgewys en die navorsingsbeperkinge wanneer ‘n spesie met onvoldoende genetiese data bestudeer word benadruk. Aangesien daar nie heel genoom data beskikbaar is nie, is volgende-generasie volgordebepaling van 9 Kaap-buffels gedoen om nuwe genetiese variasies in hierdie spesie te identifiseer. Meer as 76 000 nuwe enkel-nukleotied polimorfismes (ENPs) binne geen-areas is geïdentifiseer en die daaropvolgende genotipering van 173 ENPs het ‘n bevestigingskoers van 57% gehad. Vanuit die bevestigde stel ENPs is 69 gekies vir assosiasietoetse met BTB status in die Kaap-buffel en genotipering van 868 individue is gedoen. Drie ENPs, in die Solute Carrier family 7, member A13 (SLC7A13), Deleted in Malignant Brain Tumour-1 (DMBT1) en Interleukin 1 alpha (IL1α) gene, was beduidend geassosieer met BTB status. Baie min volgorde inligting van die NRAMP1 (SLC11A1) geen is verkry uit die volgende-generasie volgordebepaling. Aangesien hierdie geen voorheen met brucellose, salmonella en paratuberkulose in ander dierespesies geassosieer is, is dit ‘n uitstekende kandidaat vir BTB weerstand. Hierdie geen is in Kaap-buffels gekarakteriseer deur Sanger volgordebepaling van die volledige koderende, gedeeltelike 5’UTR, introniese en 3’UTR areas te doen. Vyftien nuwe polimorfismes en drie mikrosatelliete is geïdentifiseer. Ten slotte is ‘n oorsigstudie gedoen om die toepaslikheid van BTB genetiese weerstandsdata in selektiewe telingsprogramme van Kaap-buffels te evalueer. Fenotipiese, merkerbemiddelde en genomiese teling strategieë is bespreek, met spesifieke klem op die geskiktheid van die metodes vir Kaap-buffels. Identifisering van gene en variante wat betrokke is by BTB weerstand in die Kaap-buffel bied potensiële teikens vir medikasie of entstof ontwikkeling, sowel as inligting wat in selektiewe telingsprogramme gebruik kan word. Dit kan nuwe bestuursopsies vir die beheer van die BTB-epidemie in die parke van Suid-Afrika bied as 'n alternatief vir, of in samewerking met, dodelike beheermetodes.