Genetic counselling is an expanding profession, with many services now being offered in multicultural settings. The way in which individuals respond to genetic disorders varies greatly between countries, socio-economic groups, families, communities, religions and cultural groups. Together, these perspectives may influence how people experience genetic counselling with regard to satisfaction of the service, understanding heritability, communication, support and general healthcare provision. To address these issues standardised healthcare and genetic counselling models may need to be adjusted to prevent disparities in healthcare communication for different communities across the globe. South Africa provides a unique setting for genetic counselling because of the rich multicultural and linguistic diversity, as well as the many health and socioeconomic challenges that the country faces. Due to these diversities and challenges, further exploration into individuals‟ experiences of genetic counselling in South Africa is required to gain insight into the service needs for individuals.

MSc (Med), Faculty of Health Sciences, University of the Witwatersrand / Introduction: Systemic sclerosis (SSc) is a complex autoimmune disease characterised by autoantibody release, leading to microvascular injury, fibroblast activation and increased production of collagen. The genetics of SSc is complex with many genes implicated in the development and maintenance of the extracellular matrix (ECM). The main aim of this study was to test for differential expression of matrix metalloproteinase 1 (MMP1), tissue inhibitor of metalloproteinase 1 (TIMP1) and hepatocyte growth factor (HGF) in SSc patients compared to healthy control individuals and to assess whether the differential expression of these genes could have an impact on clinical features of the disease. Methods: Two skin biopsies were analysed for each of 16 black SSc patients, one from clinically involved skin (lateral forearm) and one from clinically uninvolved skin (back). One skin sample was obtained from 15 ethnically matched control individuals. The differential expression of MMP1, TIMP1 and HGF in the clinically involved and uninvolved patient samples would be compared to control individuals using relative quantification polymerase chain reaction (qPCR). The gene expression profiles were then compared to specific clinical features to deduce whether any of the gene expression profiles is correlated with the manifestation of specific clinical features. Results: MMP1 gene expression was significantly decreased in SSc patients for both involved (p=0.0004) and uninvolved skin (p=0.0004) compared to controls. Conversely, TIMP1 gene expression was significantly increased in SSc patients at both sites compared to controls (p=<0.00001 for both comparisons). A trend of significance was observed for the difference in TIMP1 expression between the involved an uninvolved skin within the patients (p=0.05) with a greater increase in involved skin. HGF had increased gene expression in the patients compared to controls for involved and uninvolved skin (p=0.002 and 0.004, respectively). The difference in gene expression between the involved and uninvolved biopsies was not significant for either MMP1 or HGF (p=0.87 and 0.83, respectively). The only correlates that may have a biological significance are HGF in involved skin correlated with disease activity (r=0.60; p=0.013) and HGF in uninvolved skin vi correlated with skin score (MRSS) with r=0.50 and p=0.048. With regards to the categorical data, two marginally significant observations were found, once again with HGF, which was found to be associated with gender in involved skin (p=0.037) and renal disease in uninvolved skin (0.031). Conclusion: The relative under expression of MMP1 and over expression of TIMP1 reflect the pro-fibrotic state of scleroderma skin. The over expression of HGF suggests that HGF may play a compensatory anti-fibrotic role, although this is not sufficient to overcome the pro-fibrotic state of the skin. This study provides supporting evidence to debunk the myth of uninvolved skin in SSc patients. The altered expression of MMP1, TIMP1 and HGF in the clinically uninvolved skin of SSc patients suggests that all subcutaneous tissue is affected, although to a greater extent in the clinically involved skin of the patients.

ABSTRACT Fetal abnormalities are congenital abnormalities that are identified prenatally, which may be structural or functional in nature. Genetic counselling is a non-directive and non-judgmental process of information-giving, at the same time as providing psychosocial support. It is offered to women and their partners who have a fetal abnormality detected during pregnancy. When a fetal abnormality is detected, the patient can sometimes be offered a termination of pregnancy, and the decision of whether or not to continue the pregnancy is made by the patient. The first aim of this research was to conduct an audit of the genetic counselling service provided by the Division of Human Genetics, NHLS and WITS, in order to assess the level of service being offered to patients with diagnosed fetal abnormalities. The second aim of the research was to determine what factors, if any, influenced the decision patients made regarding whether to continue or interrupt their pregnancy. One hundred and seventy one files of women, who received genetic counselling for an identified fetal abnormality during pregnancy from the division between 2002 and 2006, were included in the retrospective clinical audit. The patients seen for genetic counselling represent 1.1 % of the estimated number of women in Johannesburg who could have had abnormalities detected prenatally, based on the prevalence of congenital disorders in the area and an ultrasound prenatal detection rate of 56.2 %. Two thirds of patients who were offered TOP chose to terminate their pregnancy. The most clinically significant predictor of the decision to terminate an affected pregnancy was found to be an earlier gestation at offer of TOP, which suggests that earlier detection and diagnosis of abnormalities is beneficial to patients. Overall, 62 % of patients were not offered genetic counselling follow-up appointments after conclusion of their pregnancy. The genetic counselling service offered to patients thus needs to be improved, in particular, the follow-up service patients receive after TOP or delivery is not adequate.

The potential phenotypic effects of synonymous SNPs (sSNPs) have long been overlooked. Although several sSNPs are no longer thought to be silent, no one has identified which sSNPs may contribute to phenotypic variation on a genome-wide scale. sSNPs that cause a change in codon-usage frequency or mRNA secondary structures may alter translational and protein folding kinetics. In addition, sSNPs that alter splice-site consensus sequences may cause aberrant slicing, which could change the protein product. A sSNP that contributes to any of these molecular mechanisms may thus alter protein structure and function. To computationally identify sSNPs with a potential impact, SynSNP was created. SynSNP is a text-based tool written in Python. All sSNPs published within dbSNP are first identified. SynSNP uses established bioinformatics tools to determine which of the sSNPs may potentially result in a molecular effect. The potentially functional sSNPs are then assessed to determine whether any have previously been associated with a trait or disease in genome-wide association studies (GWAS) and/or occur within genes known to be associated with disease in OMIM (Online Mendelian Inheritance in Man). Of the 90,102 identified sSNPs, 21,086 (23.4%) were predicted to potentially have a functional impact, through one or more of the three molecular mechanisms investigated. Of the sSNPs predicted to potentially have a functional impact, 14 (0.07%) had previously been associated with a trait or disease in GWAS. A subset of 4,057 (19.2%) of the potentially functional sSNPs were within genes known to be associated with disease in OMIM. Only six (0.03%) of the potentially functional sSNPs had previously been associated with a trait or disease in GWAS and occurred within genes known to be associated with disease in OMIM. SynSNP could be developed further to aid the discovery of more sSNPs with a potential functional impact. A significant proportion of sSNPs may have a functional impact and their potential role in disease should therefore not be underestimated or neglected.

A thesis submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the Degree of Doctor of Philosophy. / Y chromosome DNA and mitochondrial DNA (mtDNA) variation were examined in Ugandans, Zambians, Biaka Pygmies and non-Pygmies from the Central African Republic. Y chromosome DNA variation was also examined in populations from the Democratic Republic of Congo. Data generated in this study were analysed together with published data to (1) clarify the understanding of the overall patterns of haploid genetic variation in Africa; (2) examine genetic affinities among central African and other African populations; (3) assess the concordance of haploid markers with different mutation rates in assessing population affinities; (4) compare male and female migration rates in African populations; and (5) refine theories regarding the prehistory of central Africa populations based on linguistics and archaeology. Sixteen biallelic and eight microsatellite Y-specific markers were examined in 369 central African individuals. Eleven Y chromosome haplogroups (HGs A, B*, B-M150, B-Ml 12, B- M211, E-M191, E-M2, E-M35, E-M40, FJ and R) and 174 compound haplotypes were identified. The mtDNA 9-bp deletion, 3592 Hpal and 10397 Alul restriction polymorphisms, and two hypervariable regions (HVRs) were examined in 397 individuals. A total of 246 mtDNA types were identified and classified into 19 mtDNA subhaplogroups. Using Y chromosome data, central African populations shared close genetic affinities with each other and with populations from west and southern Africa. Extensive unidirectional Y chromosome gene flow from non-Pygmy populations to Biaka Pygmies was observed. Using mtDNA data, central African non-Pygmy populations shared close genetic affinities with each other and with populations from west, east and southern Africa. MtDNA studies indicated almost complete maternal genetic isolation of Biaka. Overall, using both mtDNA and Y chromosome data, pan-African populations were best grouped by geographic rather than by linguistic criteria. Different mtDNA and Y chromosome data types revealed similar genetic relationships among African populations. Female migration rates appear to have exceeded male migration rates in non-Pygmy central African populations in this study, whilst the opposite was found in Biaka Pygmies. Data types at different levels of resolution suggested that male and female migration rates in Africa may have differed over time, and may not have been significantly different. This research has provided new insights into the complex demographic history that shaped the present-day genetic landscape of central African populations. / WHSLYP2016

Pas de résumé / Nephrotic syndrome (NS) is a kidney disease characterized by disruption of the glomerular filtration barrier and the massive loss of proteins into the urine. Although in the majority of cases treatment with steroids leads to remission of the disease, in 15-20% of cases the disease is not responsive to this therapy and is classified as steroid-resistant nephrotic syndrome (SRNS). SRNS is a clinical condition with high morbidity leading to progressive renal failure as well as multiple metabolic and cardiovascular complications. Extensive research over the last 20 years has identified more than 40 SRNS causing genes that are crucial for function of the podocyte, a highly specialized kidney epithelial cell. However, the mutated gene is still unknown in about half of the familial cases. We have used exome sequencing to identify new genes mutated in SRNS. In order to prove the pathogenicity of the identified mutations we used the Drosophila model, assessing defects of fly viability and the structure and function of nephrocytes, podocyte like-cells. My thesis work consists of two projects. Firstly, we identified biallelic mutations in a new candidate gene, SGPL1, encoding the sphingosine 1- phosphate lyase, in individuals presenting SRNS with facultative adrenal insufficiency, ichthyosis, neurological defects and immunodeficiency. SGPL1 is the main catabolic enzyme of sphingolipids, irreversibly degrading sphingosine 1-phosphate into phosphoethanolamine and hexadecenal. In flies, these mutations were shown to decrease viability, induce nephrocyte defects and lead to the accumulation of sphingoid bases due to the loss of SGPL1 catabolic activity. Together, these results indicate that the identified SGPL1 mutations are pathogenic and cause a new syndromic form of SRNS. Moreover, in a second project, we defined the contribution of homozygous mutations found in two different genes, ADD3 and KAT2B, to a complex phenotype found in affected individuals from one consanguineous family. These individuals presented with neurological defects, cataracts, mild skeletal defects, cardiomyopathy and SRNS. ADD3 encodes adduciny, an F-actin capping protein that also links the actin cytoskeleton to the spectrin based membrane skeleton, while KAT2B encodes the lysine acetyltransferase 2B, mainly known for acetylation of histones and modulation of transcriptional programs. We found additional nonrelated patients carrying only biallelic ADD3 mutations that presented a partially overlapping syndrome but with no cardiac or renal manifestations. In the Drosophila model we found that both ADD3 and KAT2B mutations impaired fly viability and that the ADD3 mutation also impaired fly motor function. However, only the KAT2B mutation induced functional defects in Drosophila heart and nephrocytes. Altogether, these results suggest that ADD3 mutations are responsible for a neurological phenotype with facultative cataracts and skeletal defects while the KAT2B mutation induces heart and kidney defects. These results highlight the Drosophila as a good in vivo model to test the pathogenicity of the mutations found in SRNS candidate genes.

赤黴素有多種生物學功能，包括促進莖的伸長、種子萌發以及花的發育。玉米赤黴素缺陷型突變體dwarf1 (d1) 表現出植株矮壯和雌雄兩性花，即原為雌花部位發育出雙性花。但是該突變的分子基礎尚不清楚。通過分析多個d1等位基因突變體的分子組成特征，我們證明d1突變體是由能催化赤黴素中間代謝物轉變為活性赤黴素的赤黴素3-氧化酶（ZmGA3ox2） 突變引起的。重組D1 蛋白能於體外催化至少4個反應，包括GA20 轉變為GA3，GA5轉變為GA3，GA20轉變為GA1 以及GA9轉變為GA4等。煙草細胞中D1-GFP 的瞬時表達和細胞組分蛋白質印染分析等兩個獨立的方法，揭示了D1 蛋白是雙定位於細胞核和細胞質中。此結果暗示活性赤黴素能夠在此兩種細胞器中合成。這個雙定位的結果與赤黴素受體GID1蛋白的定位壹致。在早期的玉米雌花發育的過程中，D1 蛋白特異且大量地表達在雌花中的雄花原基細胞，揭示了赤黴素發揮其抑制雄花原基發育的功能需要在該組織大量合成。 / DELLA 蛋白是赤黴素信號傳導的壹個阻遏物。玉米包含僅壹個DELLA蛋白命為DWARF8（D8）。發生在D8 蛋白N端的突變產生了赤黴素非敏感型突變體dwarf8 （d8）。d8突變體與d1突變體有很多共同特征，包括侏儒植株，深綠色的葉片以及雌雄兩性花。這些特點都表明玉米對赤黴素的響應是被DELLA蛋白所抑制的。DELLA蛋白是通過蛋白互作的方式來限制其互作蛋白功能，以達到抑制赤黴素下遊信號傳導的目的。多樣的赤黴素響應必然需要多樣的DELLA互作蛋白。基於赤黴素在調控玉米性別決定過程當中的獨特功能，我們提出假設：玉米當中存在未知的D8互作蛋白。通過酵母雙雜交方法篩選玉米雌花的cDNA文庫，找到14個在酵母系統與D8互作的蛋白。ZmSPX1是這些蛋白中的壹個但不清楚功能。通過雙分子熒光互補實驗和蛋白質體外結合實驗，D8和ZmSPX1之間的互作被進壹步確定。基于此，我们找到数个候选的D8互作蛋白以及证明了ZmSPX1是D8真正的互作蛋白；这些工作都为进一步研究ZmSPX1蛋白在调控性别分化、细胞分裂和分化等赤霉素响应中的作用提供了基础。 / Gibberellins (GA) have multiple biological functions including promoting stem elongation, seed germination and flower development. The GA deficient dwarf1 (d1) mutant in maize displays plant dwarfism and andromonoecy, i.e. forming anthers in the female flower. However, the molecular basis is not clear. Through molecular characterization of multiple d1 alleles, I prove that the d1 is caused by mutations in the GA 3-oxidase (ZmGA3ox2) that converts the inactive GA intermediates to bioactive GAs. The recombinant D1 protein catalyzes at least four reactions in vitro, converting GA20 to GA3, GA5 to GA3, GA20 to GA1 and GA9 to GA4. Subcellular localization analysis by two independent approaches which are in vivo D1-GFP analysis and western blot analysis of organelle fractions revealed that the D1 protein is dual-localized in the nucleus and the cytosol. ZmGA20ox was also localized in both the cytosol and the nucleus by the in vivo GFP fusion analysis. Interestingly, the dual-localization of D1 and ZmGA20ox coincides with the localization of the GA receptor GID1. In early phase of maize female flower development, the D1 protein was found specifically and highly expressed in the stamen primordia within the female florets. These results indicate that bioactive GAs can be synthesized in both the cytosol and the nucleus, and that the suppression of stamen in female florets is mediated by locally synthesized GAs. This finding provides new insights to the understanding of GA biosynthesis and signal transduction in plants. / DELLA proteins are repressors of GA signal transduction. DWARF8 (D8) is a DELLA protein in maize, Mutations in the N-terminal of D8 resulted in dominant GA insensitive dwarf8 (d8) phenotype. d8 displayed similar phenotypes as the d1mutants; i.e. plant dwarfism, dark green leaves and andromonoecy, indicating that D8 is a master repressor mediating these GA functions. DELLA proteins suppressed the downstream signal transduction of GA by restricting their interacting protein functions through protein-protein interaction. Diverse GA responses require numerous DELLA interacting proteins. Based on the unique function of GA in regulating sex determination in maize, I hypothesize that D8 mediates the GA responses by interacting with yet unknown proteins in maize. Through yeast two hybrid screening of the maize ear cDNA library, I identified 14 proteins that showed genuine interaction in yeast system. Among these, a SPX domain containing protein named as ZmSPX1 was present. SPX domain containing proteins in yeast are implicated in cell cycle regulation; however, their functions in plants are unknown. GFP fusion analysis indicated that ZmSPX1 co-localizes with D8 in the nucleus and their interaction was confirmed by bimolecular fluorescence complementation (BiFC) and in vitro pull-down assay. To this point, I have identified several candidates for D8 interacting proteins and provided strong evidence that ZmSPX1 is a bona fide D8 interacting protein which set a foundation for further analysis of its function in mediating GA responses including sex determination, cell division and elongation. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Chen, Yi. / Thesis (Ph.D.) Chinese University of Hong Kong, 2015. / Includes bibliographical references (leaves 60-67). / Abstracts also in Chinese. / Chen, Yi.

by Lee Wing Kin. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2000. / Includes bibliographical references (leaves 81-90). / Abstracts in English and Chinese. / Abstract --- p.i / Acknowledgments --- p.iii / List of Figures --- p.vii / List of Tables --- p.viii / Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Clustering --- p.1 / Chapter 1.1.1 --- Hierarchical Classification --- p.2 / Chapter 1.1.2 --- Partitional Classification --- p.3 / Chapter 1.1.3 --- Comparative Analysis --- p.4 / Chapter 1.2 --- Cluster Analysis and Traveling Salesman Problem --- p.5 / Chapter 1.3 --- Solving Clustering Problem --- p.7 / Chapter 1.4 --- Genetic Algorithms --- p.9 / Chapter 1.5 --- Outline of Work --- p.11 / Chapter 2 --- The Clustering Algorithms and Applications --- p.13 / Chapter 2.1 --- Introduction --- p.13 / Chapter 2.2 --- Traveling Salesman Problem --- p.14 / Chapter 2.2.1 --- Related Work on TSP --- p.14 / Chapter 2.2.2 --- Solving TSP using Genetic Algorithm --- p.15 / Chapter 2.3 --- Applications --- p.22 / Chapter 2.3.1 --- Clustering for Vertical Partitioning Design --- p.22 / Chapter 2.3.2 --- Horizontal Partitioning a Relational Database --- p.36 / Chapter 2.3.3 --- Object-Oriented Database Design --- p.42 / Chapter 2.3.4 --- Document Database Design --- p.49 / Chapter 2.4 --- Conclusions --- p.53 / Chapter 3 --- The Experiments for Vertical Partitioning Problem --- p.55 / Chapter 3.1 --- Introduction --- p.55 / Chapter 3.2 --- Comparative Study --- p.56 / Chapter 3.3 --- Experimental Results --- p.59 / Chapter 3.4 --- Conclusions --- p.61 / Chapter 4 --- Three New Operators for TSP --- p.62 / Chapter 4.1 --- Introduction --- p.62 / Chapter 4.2 --- Enhanced Cost Edge Recombination Operator --- p.63 / Chapter 4.3 --- Shortest Path Operator --- p.66 / Chapter 4.4 --- Shortest Edge Operator --- p.69 / Chapter 4.5 --- The Experiments --- p.71 / Chapter 4.5.1 --- Experimental Results for a 48-city TSP --- p.71 / Chapter 4.5.2 --- Experimental Results for Problems in TSPLIB --- p.73 / Chapter 4.6 --- Conclusions --- p.77 / Chapter 5 --- Conclusions --- p.78 / Chapter 5.1 --- Summary of Achievements --- p.78 / Chapter 5.2 --- Future Development --- p.80 / Bibliography --- p.81

"Concepts in manufacturing such as CIMS (Computer Integrated Manufacturing Systems), JIT (Just In Time), Lean Production, Virtual Manufacturing, and Flexible Fixturing have been proposed to meet the fundamental requirements of manufacturing - decrease the cost and satisfy the needs of customers. Fast fixture generation and fixture reusability are essential in the current manufacturing environment. The dissertation focuses on the models, methods, and algorithms for fixture synthesis and variation that satisfy the functional requirements specified by on-site industrial engineers. With the reusability of a fixture base combined with variation of other fixture components, fixture configuration can be rapidly adapted and accommodated to the new workpiece. The dissertation presents methods and algorithms for fixture base synthesis, which directly result in fixture reusability. Optimization functions are derived based on engineering requirements due to the mass production nature of automotive parts. Specific optimization algorithms are developed and their complexities, compared to other alternatives, are comprehensively evaluated according to different optimization functions. The fixture variation and reusability provide an engineering tool to rapidly generate and validate fixtures in production planning stage. It applies scientific reasoning methodology in combination with best knowledge of fixture designs, which heavily relies on designers' manufacturing knowledge and experience. It also provides means to bridge the gap between CAD and CAM integration and therefore reduces the new product and production development cycle time and cost while maintaining the quality of fixtures."

De nombreuses fonctions cellulaires sont réalisées grâce à l'interaction coordonnée de plusieurs gènes. Identifier le graphe de ces interactions, appelé réseau de régulation génétique, à partir de données d'expression de gènes est l'un des objectifs majeurs de la biologie des systèmes. Dans cette thèse, nous abordons ce problème en choisissant de modéliser les relations entre gènes par un réseau bayésien. Se pose alors la question de l'apprentissage de la structure de ce type de modèle à partir de données qui sont en général peu nombreuses. Pour résoudre ce problème, nous recherchons parmi tous les modèles possibles le modèle le plus simple, expliquant le mieux les données. Pour cela, nous introduisons et étudions différents types d'algorithmes génétiques permettant d'explorer l'espace des modèles. Nous nous intéressons plus particulièrement aux méthodes de spéciation. ces dernières, en favorisant la diversité des solutions candidates considérées, empêchent l'algorithme de converger trop rapidement vers des optima locaux. Ces algorithmes génétiques sont comparés avec différentes méthodes d'apprentissage de structure de réseaux bayésiens, classiquement utilisées dans la littérature. Nous mettons ainsi en avant la pertinence des approches evolutionnaires pour l'apprentissage de ces graphes d'interactions. Enfin, nous les comparons à une classe alternative d'algorithmes évolutionnaires qui s'avère particulièrement prometteuse : les algorithmes à estimation de distribution. Tous ces algorithmes sont testés et comparés sur un modèle du réseau de régulation de l'insuline de 35 noeuds dont nous tirons des jeux de données synthétiques de taille modeste. / Inferring gene regulatory networks from data requires the development of algorithms devoted to structure extraction. When only static data are available, gene interactions may be modelled by a bayesian network that represents the presence of direct interactions from regulators to regulees by conditional probability distributions. In this work, we used enhanced evolutionary algorithms to stochastically evolve a set of candidate bayesian network structures and found the model that best fits data without prior knowledge. We proposed various evolutionary strategies suitable for the task and tested our choices using simulated data drawn from a given bio-realistic network of 35 nodes, the so-called insulin network, which has been used in the literature for benchmarking. We introduced a niching strategy that reinforces diversity through the population and avoided trapping of the algorithm in one local minimum in the early steps of learning. We compared our best evolutionary approach with various well known learning algorithms (mcmc, k2, greedy search, tpda, mmhc) devoted to bayesian network structure learning. Then, we compared our best genetic algorithm with another class of evolutionary algorithms : estimation of distribution algorithms. We show that an evolutionary approach enhanced by niching outperforms classical structure learning methods in elucidating the original model. Finally, it appears that estimation of distribution algorithms are a promising approach to extend this work. These results were obtained for the learning of a bio-realistic network and, more importantly, on various small datasets.