published_or_final_version / Microbiology / Master / Master of Philosophy

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A dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the degree of Master of Science in Medicine. Johannesburg, June 2017 / Introduction: Systemic lupus erythematosus (SLE) is a multi-system autoimmune disease of unknown aetiology. There is growing evidence environmental factor(s) trigger the disease in the genetically susceptible host. Fragment crystallisable receptor (FCR) genes encode receptors that recognise the fragment crystallisable (Fc) portion of immunoglobulins (IgG) play an important role in the removal of antigen-antibody complexes from the circulation. Genes that code for these receptors have shown to be associated with susceptibility to SLE in various populations. The aim of the present study is to determine the role of single nucleotide polymorphisms (SNPs), allotypes and copy number variations of FC Gamma receptor genes IIIA and IIIB in susceptibility for the Black South Africans with SLE. Methods: DNA from 162 Black South African SLE patients and 155 matched controls were investigated using Taqman assays to determine SNP genotyping differences (FCGRIIIA) and copy number variation (CNV) number (FCGRIIIB). A PCR was optimised in order to determine the allotype differences (FCGRIIIB) via agarose gel electrophoresis. Statistical analyses were then performed on the data to see if the results displayed significance in susceptibility to SLE. Results: The minor allele of the allotypes (FCGRIIIB) and the rs396991 SNP (FCGRIIIA) were not statistically significant in conferring susceptibility to SLE in cases or controls. The rs10127393 SNP (FCGRIIIA) was shown to be monomorphic within both cases and controls for the T allele and is not associated with SLE. The cumulative percentage of copy numbers (FCGRIIIB) ≤2 copies were 0.6% larger in cases than seen in controls. Although this was not significant, this was what has been previously suggested in the literature. Almost half of the cases (43.8%) had lupus nephritis (LN). Upon investigation the NA1/NA2 alleles were found to confer susceptibility to LN (p=0.018), whereas the rs396991 G allele did not (p=0.643). Conclusion: In this study the allotypes, SNPs and CNV investigated were not found to confer susceptibility to SLE. However, subtle trends suggest that further studies are required with larger sample sizes to acquire more data. Almost half of the cases were diagnosed with LN and the NA2 allele was shown to be a risk factor in developing LN. / MT2017

Faculty of Health Sciencs School of physiology 0010633J bnkeh@uycdc.uninet.m / Blood pressure (BP) is a heritable trait. However, the loci responsible and the mechanisms by which these genes determine BP are uncertain. Based on widely published data regarding frequent phenotypic characteristics that exemplify essential hypertension (EHT) in persons of African ancestry, in the present thesis I explored the role of gene candidates most likely to contribute to BP in this group. In this regard a high frequency of persons of African descent experience increases in BP in response to an enhanced salt intake (salt-sensitive hypertension). In addition, many patients of African origin with EHT fail to respond to inhibition of angiotensin-converting enzyme (ACE) with an appropriate decrease in BP, a factor that cannot be explained entirely on the basis of reduced plasma renin levels in this group. Thus, I evaluated the role of several gene variants that could influence either renal salt handling or the activity and effects of the renin-angiotensin system on BP in subjects of African ancestry. Although the angiotensinogen (AGT) gene has at least 3 variants in the promoter region that influence angiotensinogen expression and which occur with a remarkably high frequency in populations of African ancestry, their role in this group is still controversial. To-date, interactions between these variants have not been considered. Using a casecontrol study design in a sample of 1325 subjects, as well as association analysis with 24 hour ambulatory BP (ABP) values in 626 hypertensives, I confirmed that an independent effect of functional AGT gene variants on the risk for EHT or 24 hour ABP was weak at best. Importantly, however, interactions between the -20A C and -217G A variants were noted to strongly impact on the risk for EHT as well as ABP. Furthermore, interactions between the -20A C and -217G A variants played a major role in iii contributing toward the variability of ABP responses to ACE inhibitors, but not calcium channel blockers in this population group, with genotype determining whether or not ACE inhibitor responses occurred. Although the 825C T polymorphism of the guanosine triphosphate (G) protein 3 subunit (GNB3) gene influences the activity of a substance that modifies renal salt handling, namely the Na+/H+ exchanger, its impact in hypertensives of African descent is controversial. In the present thesis I confirmed in a large sample that the GNB3 variant was not associated with the risk for EHT or ABP values in subjects of African ancestry. However, because the activity of the exchanger is enhanced in obesity I hypothesised that the GNB3 gene variant could mediate a clinically relevant BP effect by modifying the impact of body size on BP (type I or II genetic effect). Indeed, GNB3 genotype proved to be a strong determinant of the impact of body size on systolic BP values, with genotype determining whether or not the effect occurred. The epithelial sodium channel (ENaC) and atrial natriuretic peptide (ANP) have an important influence on renal salt handling. The T594M polymorphism of the -subunit of the ENaC gene only exists with a relatively high frequency in subjects of African ancestry. Previous studies conducted in this population group in relatively small samples have indicated that the ENaC and ANP gene variants determine BP in subjects of African descent. In a larger sample of subjects of African descent I demonstrated that the T594M polymorphism of the ENaC gene has no impact on BP in this population group. However, my results suggest that the ANP gene may be a candidate worthy of further study. In conclusion, the results described in this thesis provide evidence that lends some clarity to the role of likely gene candidates for BP control in people of African descent. iv Importantly, data from this thesis suggest that interactions between functional variants of specific loci (e.g the AGT gene), and clinically relevant type I or II genetic effects (no independent actions, but modifier gene effects, e.g, GNB3) should be considered before excluding loci as playing an important role in BP control. Moreover, this thesis provides the first substantial data to indicate that gene variants determine the variability of BP responses to pharmacological agents in hypertension in this population group.

by Tam Yan Kit. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1992. / Includes bibliographical references (leaves 102-114). / Abstract --- p.1 / Acknowledgement --- p.3 / Table of Contents --- p.5 / List of Tables --- p.7 / List of Figures --- p.8 / List of Plates --- p.8 / Chapter Chapter1 --- Introduction --- p.9 / Chapter Chapter2 --- Literature Review / Chapter 2.1 --- The study of enzyme polymorphism --- p.11 / Chapter 2.2 --- The zymogram technique --- p.20 / Chapter 2.3 --- Molecular approaches to systematic studies --- p.24 / Chapter 2.4 --- Genetic variation and systematic studies of decapod Crustacea --- p.29 / Chapter 2.5 --- Taxonomy of Penaeus and Metapenaeus --- p.33 / Chapter Chapter3 --- Materials and Methods / Chapter 3.1 --- Sample collection and storage --- p.43 / Chapter 3.2 --- Extract preparation --- p.44 / Chapter 3.3 --- Starch gel preparation --- p.45 / Chapter 3.4 --- Starch gel electrophoresis --- p.46 / Chapter 3.5 --- Gel slicing --- p.47 / Chapter 3.6 --- Enzyme staining --- p.47 / Chapter 3.7 --- Data collection --- p.48 / Chapter 3.8 --- Data analysis --- p.49 / Chapter Chapter4 --- Results / Chapter 4.1 --- Genetic interpretation of zymograms --- p.65 / Chapter 4.2 --- Conformity to Hardy-Weinberg equilibrium distribution --- p.67 / Chapter 4.3 --- Level of genetic variability --- p.67 / Chapter 4.4 --- Interspecific and intergeneric genetic differentiation --- p.68 / Chapter Chapter5 --- Discussion / Chapter 5.1 --- Enzyme polymorphism in Penaeus and Metapenaeus --- p.84 / Chapter 5.2 --- Level of genetic variability --- p.85 / Chapter 5.3 --- Phylogenetic relationships --- p.91 / Chapter 5.4 --- Biochemical and molecular systematic studies of Penaeus and Metapenaeus --- p.96 / Chapter Chapter6 --- General Conclusions --- p.99 / References --- p.102

As knowledge of the human genome has accelerated, various diseases and individuals’ responses to drugs have been pinpointed to specific DNA variations in one’s genome. Among many different types of variants, the most common and simplest is the single nucleotide polymorphism (SNP) in which a single base substitution occurs. Although there have been considerable improvements in technologies that can reveal a single base difference in a DNA strand, simple and affordable methods that have high detection sensitivity and require small sample volume are expected to facilitate widespread adoption of routine SNP analysis in clinical settings. One such method that meets these requirements is to use nanopore as a single molecule detector, an emerging analytic system that detects changes in current related to molecules occupying a nanometer aperture. This dissertation thus chronicles our endeavors in developing a nanopore-based SNP assay using polymer tagged dideoxynucleotides (ddNTPs). The fundamental principles of this method rely on single base extension (SBE) of a primer by DNA polymerase using polymer tagged ddNTP analogs for allele discrimination and simple electronic readout of an alpha hemolysin (αHL) nanopore current for allele detection at the single molecule level. Using four uniquely tagged ddNTPs, a characteristic current level that is specific to each base is produced, thus identifying the SNP alleles present and the genotype at the site. To demonstrate the feasibility of this approach, four polymer attached ddNTPs, each with a different tag that generates a characteristic current blockade level in the αHL nanopore, were designed and synthesized. To search for a DNA polymerase that can accept these tagged ddNTP analogs as substrates, several candidate DNA polymerases were surveyed and their relative efficiencies for incorporation of the analogs were compared (Chapter 2). To generate a steady and stable blockade event for accurate SNP analysis, two different means of positioning a tag molecule in the αHL nanopore after the SBE reaction have been explored: covalent conjugation of DNA primer to the pore and immobilization of biotinylated primer within the pore by streptavidin. To find a suitable position for primer attachment on the pore, three αHL mutants, each with a different single conjugation point, were constructed. Using these mutants, different DNA-pore conjugates were produced and purified via various chromatography systems (Chapter 3). In the nanopore system, charged molecules such as DNA are electrophoretically driven through the pore under an applied voltage, thereby modulating the ionic current through the nanopore. This current reveals useful information about the structure and dynamic motion of the molecule at the single molecule level. Before performing SNP analysis, we first studied single molecule behaviors of oligonucleotides of different lengths and structures in the αHL pore and their ensuing current signatures in the system (Chapter 4). Finally, harnessed with tools and insights from the nanopore single molecule studies, actual SNP assays were performed in our nanopore system using the polymer tagged ddNTPs and SBE. Chapter 5 discusses the integrated approach where SBE is achieved on a primer-conjugated αHL nanopore and Chapter 6 presents the results using a biotin-streptavidin complex for immobilization of tag molecules in the pore. Overall, this thesis validates adaptation of the nanopore detection system for SNP analysis using the polymer tagged ddNTPs.

Os tumores do sistema nervoso central representam aproximadamente 2% de todos os tipos de cânceres. Embora a incidência dos tumores do SNC seja pequena, comparada com outras neoplasias, estes tumores estão entre as mais graves malignidades humanas, pois afetam o órgão responsável pela coordenação e integração de todas as atividades orgânicas. Os gliomas são os tumores mais comuns do SNC. Apesar do progresso marcante na caracterização da patogênese molecular dos gliomas, esses tumores permanecem incuráveis e, na maioria dos casos, refratários aos tratamentos, devido à sua heterogeneidade molecular. O aparecimento desses tumores ocorrem a partir do acúmulo de alterações genéticas nas células. Para entender o mecanismo molecular de formação e progressão tumoral é indispensável identificar os genes que acumulam essas alterações. Um polimorfismo de base única (SNP Single Nucleotide Polymorphism) é geralmente definido como uma substituição estável de apenas uma base na molécula de DNA com frequência maior que 1%, em pelo menos uma população Os SNPs são reconhecidos como importantes ferramentas na genética humana e médica e têm sido amplamente utilizados nos estudos de associação genética de várias doenças complexas, como por exemplo: distúrbios cardiovasculares, psiquiátricos e autoimunes, obesidade, osteoporose, diabetes e câncer Sendo assim, este trabalho teve como objetivo analisar polimorfismos entre populações caso e controle na intenção de identificar associações destes genótipos na suscetibilidade aos tumores. A técnica utilizada para a análise de polimorfismos foi de PCR-RFLP onde observamos diferenças nas distribuições genotípicas entre pacientes e controles nos SNPs EGF+61, GSTP-1Ile 105 Val, XRCC1 Arg 194 Trp, Pro 206 Pro, Arg 280 His, Arg 399 Gln, Gln 632 Gln, XRCC2 Arg 188 His, XRCC3 Thr 241 Met e XRCC4 G1394T, onde as variantes EGF G61, Trp194, Val105, Pro206, His280, Gln632, His188, Met241 e XRCC4 T1394 foram observados com maior freqüência entre os portadores de gliomas. Dessa forma, estas variantes podem ser fatores de susceptibilidade para o desenvolvimento dos tumores. / The Central nervous system tumors represent about 2% of all cancers. Although the incidence of CNS tumors is small compared with other cancers, these tumors are among the most serious human malignancies, because they affect the body responsible for coordination and integration of all organic activities. Gliomas are the most common tumors of the CNS. Despite remarkable progress in characterizing the molecular pathogenesis of gliomas, these tumors remain incurable and, in most cases, refractory to treatment, due to its molecular heterogeneity. The appearance of these tumors occurs from the accumulation of genetic changes in cells. To understand the molecular mechanism of tumor formation and progression is essential to identify genes that accumulate these changes. A single base polymorphism (SNP Single Nucleotide Polymorphism) is generally defined as a stable replacement of only one base in the DNA molecule often greater than 1% in at least one population SNPs are recognized as important tools in human genetics and medical and have been widely used in genetic association studies of various complex diseases, such as: cardiovascular, psychiatric and autoimmune diseases, obesity, osteoporosis, diabetes and cancer. Thereby, the objective of this study was to analyze the polymorphisms between cases and control the intention to identify associations of these genotypes in susceptibility to tumors. The technique used for the analysis of polymorphisms were PCR-RFLP where we observe differences in genotype between patients and controls in the EGF +61, GSTP-1 Ile105Val, XRCC1 Arg 194 Trp, Pro 206 Pro, Arg 280 His, Arg 399 Gln, Gln 632 Gln, XRCC2 Arg 188 His, XRCC3 Thr 241 Met and XRCC4 G1394T, where the variants EGF G61, Trp194, val105, Pro206, His280, Gln632, His188, Met241 and XRCC4 T1394 were observed more frequently among patients with gliomas. Thus, these variants can be important factors of susceptibility to the tumor development.

The paraoxonase gene family consists of three members (PON1, PON2, and PON3) with both distinct and overlapping roles in human health. These enzymes influence oxidative stress, inflammation, and bacterial infections, along with a large number of diseases and disorders, such as atherosclerosis. The wide-reaching effects of the PON gene family make them an important and highly advantageous subject of study. Their ability to be modified by diet, lifestyle, and environmental exposures, as well as various polymorphisms and genetic influences, provide for a complex, highly modifiable internal form of individual protection. The overall goal of this project was to determine what factors affect individual variations in paraoxonase activity, as well as the influence of individual PON members on health and exposure outcomes. The initial study in this project provided the first data about intra-individual PON1 variations over a time of about 15 years, showing levels remain relatively stable in an agricultural population. This study also contributed data regarding the polymorphic distributions of influential PON SNPs and the influence of lifestyle factors on PON1 activity. The use of a twin population for the next study allowed for examination of the heritability of PON1 activity and antioxidant capacity, and provided novel data regarding the influence of genetic variations on PON1 activity. To further attempt to eliminate the complexity of influences on these genes and individual polymorphisms, the third study in this project characterized an innovative transgenic Drosophila melanogaster model with the goal of analyzing the influence of individual PON family members on exposure and disease outcomes without the effects of compensation from other PONs. By further elucidating the effects of the PONs at the individual level, human populations will be able to be advised regarding the most at-risk individuals and modifiable changes to improve PON levels, and therefore overall health.

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