No description available.

Robea Balle, Department of Human Genetics, MRC Unit for Skeletal Disorders, UCT Medical School, Observatory, Cape Town, South Africa. Duchenne muscular dystrophy (DMD) is a lethal X-linked neuromuscular disorder, characterised by progressive muscle wasting and weakness. DMD has its onset in early childhood, leading to physical handicap by the mid-teens and usually death by the age of twenty years. Becker muscular dystrophy (BMD) is the allelic form of DMD and is differentiated by its age of onset and milder phenotype. DMD and BMD are incurable and the most effective way of managing affected families is by preventing the recurrence of the di9order. The use of intragenic and closely linked flanking markers facilitates the identification of the defective X chromosome in female carriers and their affected male foetuses. DMD is thought to be the most common of the heritable muscle disorders, having an incidence of l in 3 300. When extrapolated to the large South African population, it presents a significant socioeconomic problem. For this reason, it was decided to develop a molecular genetic service for carrier identification and diagnostic predictions. The first step in the South African study involved the collection of biological material from affected individuals. In so doing, minimum prevalence's in the four major ethnic groups of Black, Caucasian, Indian and Mixed ancestry, were established. Although ascertainment was incomplete for a number of reasons, a markedly increased DMD frequency in the Indian population and a low frequency in the Black population was apparent. In the Caucasian group, an unexpectedly high BMD frequency, compared to DMD, was observed. 110 males affected with DMD and 18 with BMD were screened for deletions using genomic and cDNA probes and multiplex polymerase chain reaction (PCR) technology. Deletions were detected in the dystrophin gene of 47 DMD and 6 BMD patients, occurring predominantly in the 3' region of the gene (65%) and to a lesser extent in the 5' region of the gene (287.). The deletion frequency within individual ethnic groups,

Thesis (MScMedSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Please see fulltext for abstract / AFRIKAANSE OPSOMMING: Parkinson se siekte ( PD ) is 'n toenemend algemene neurodegeneratiewe siekte wat die progressiewe verlies van dopaminergiese neurone in die substantia nigra pars compacta behels, wat lei tot die ontwrigting van die motororiese senuweestelsel. ’n Neuronale verlies van meer as 50% van die normale vlakke is nodig vir die ontwikkeling van die kliniese simptome, insluitende bewing, spier rigiditeit, bradykinesia, en posturale onstabiliteit. Alhoewel beskikbare medikasies vir PD wel simptome onderdruk, is dit nie in staat om die siekte te voorkom of vordering daarvan te verhoed nie. Een van die mees bedeidende risikofaktore vir PD is toenemende ouderdom. Huidige epidemiologiese studies voorspel ‘n toename in populasie ouderdom wat belangrike implikasies vir die voorkoms van PD kan inhou. Die molekulere meganismes onderliggend aan die neurale agteruitgang in PD is steeds onbekend, maar dit blyk dat ‘n aantal genetiese faktore (in kombinasie met omgewingsfaktore) bydra tot die komplekse patogeniese agteruitgang van die siekte. Agt bevestigde gene is gevind om direk betrokke te wees by die etiologie van PD, naamlik: parkin, PINK1, DJ-1, ATP13A2, SNCA, LRRK2, VPS35, en EIF4G1. Hierdie gene is oorwegend geïdentifiseer en bestudeer in die Europese, Noord-Amerikaanse en Asiatiese bevolkings; terwyl die bestudering van Sub -Sahara- Afrika (SSA) bevolkings, veral dié van Swart Afrika afkoms, onderverteenwoordig bly in genetiese studies. Siende dat resultate verkry vanaf ander bevolkings nie verwant is aan die SSA bevolking nie, en ook nie ‘n voorspelling van wereldwye toename van die siekte kan verteenwoordig nie, is dit van belang dat omvattende genetiese studies uitgevoer word op hierdie onderbestudeerde bevolkings van SSA. Desnieteenstaande, die doel van die studie was om die molekulere etiologie van PD in ‘n groep Swart Suid-Afrikaanse (SA) PD pasiente te ondersoek. ‘n Totaal van 47 pasiente is gewerf vir die studie waarvan 26% ‘n famielie geskiedenis het vir die afwyking. Die gemiddelde ouderdom van aanvang vir die pasiente was 55.3 ± 11.2 jaar. Mutasie volgorderbepaling vir alle bekende PD gene is uitgevoer. Addisionele mutasie volgorderbepaling vir die GBA is ook uitgevoer siende dat heterosigotiese mutasies in die geen dien as ‘n sterk risikofaktor vir die ontwikkeling van PD. ‘n Verskeidenheid mutasie volgordebepalingstegnieke is geinkorporeer vir die studie, naamlik: Sanger volgordebepaling en hoë resolusie smelt tegniek (vir die identifisering van missense mutasies asook kleinskaalse invoegings of weglatings), en multiplex-afbinding afhanklike ondersoek versterkingstoets (vir die opsporing van veranderinge in kopiegetal). Verder is volgende generasie volgordebepaling gebruik vir die sistematiese ondersoek van die bekende PD gene, asook vir 160 kandidaat gene wat vooraf bepaal is. Fluoreserend-geetiketeerde polymerase ketting reaksie primers is gebruik vir genotipering van CAG herhalings uitbreidings in die ataxin-2 (SCA2) en die ataxin-7 (SCA7) gene, gevolg deur elektroforese met behulp van die “ABI 3130x1 Genetic Analyzer”. Mutasie volgordebepaling het voor die lig gebring dat die bekende PD gene klaarblyklik nie ‘n beduidende oorsaaklike rol speel in die patogenese van die siekte in die huidige groep Swart SA pasiente nie, want slegs 2 uit die 47 (43%) pasiente koester mutasies in parkin. Een van die pasiente besit ‘n heterosigotiese duplikasie van ekson 2 en ‘n heterosigotiese weglating van ekson 9; in die ander pasient is ‘n heterosigotiese ekson 4 weglating en ‘n heterosigotiese G430D mutasie geïdentifiseer. Verder is ‘n Q311K verandering in parkin gevind asook vier nuwe variante (I610T, H1758P, N2133S en T2423S) in die LRRK2 geen. Die patogenisiteit van hierdie variante moet egter nog bepaal word. Geen patogeniese herhaalings uitbreidings is gevind in die SCA2 en SCA7 lokusse nie, en die moontlikheid van die twee spinocerebellar ataksie subtipes as genetiese bepalers vir PD is uitgekanselleer. Geen patogeniese mutasies is gevind in enige van die oorblywende bekende PD gene nie, dit is dus waarskeinlik dat die pasiente wel mutasies in nuwe PD-geassosieerde gene besit. Hierdie is die eerste molekulere genetiese studie uitgevoer op uitsluitlik Swart SA PD pasiente, en ook die eerste omvattende ondersoek van al die bekende PD gene in ‘n SSA bevolking. Die algemene patogeniese mutasies in gene, wat voorheen bewys is as siekte veroorsakend in ‘n aantal Europese bevolkings, is nie bespeur in die huidige studie nie en kan dus nie verantwoordelik gehou word vir die voorkoms van PD in hierdie pasiente nie. Maar, siende dat die steekproefgrootte in hierdie studie relatief klein was, kan addisionele volgordebepaling van ‘n groter pasient groep voordelig wees in die bepaal van nuwe siekte-veroorsakende gene wat die potensiaal het om huidige hipoteses, dat die genetiese etiologie van PD duidelik verskil oor verskeie etniese groepe wereldwyd, te weerlê of bevestig. Die voortsetting van genetiese ondersoeke onder hierdie groep pasiente kan bydra tot insig met betrekking tot bevolking-spesifieke genetiese bepalers, en uiteindelik tot die identifisering van nuwe teikens vir medikasies teen die siekte.

The overall aim of this project was to investigate HIV-1 genetic diversity in South Afri ca and to characterise the immune response in mice to a South African subtype C gp120. To investigate the relationship between subtype and mode of transmission, samples were collected from individuals infected by heterosexual and male homosexual transmission from patients attending local HIV/AIDS clinics in Cape Town (n=49) and Bloemfontein (n=4). Isolates were subtyped using heteroduplex mobility assay (HMA) based on the V3-V5 region of the env geneusing reference plasmids (2 B, 2 C and 1 D) representative of local subtypes. HMA identified four env subtypes: A, B, C and D. Subtype B viruses were found in 92.9% (26/28) of the male homosexual/bisexual group and subtype C viruses in 77.2% (17 /22) of the heterosexual group. Subtype B viruses were also identified in two heterosexual patients, one patient infected by blood transfusion and in two patients with. unknown mode of transmission. Subtype D viruses were found in one male homosexual patient and one heterosexual patient and a husband and wife couple were infected with subtype A viruses. A significant association between subtype and mode of transmission (p=<0.0001) was identified, confirming two independent epidemics. To determine the subtype distribution of HIV within urban heterosexual populations throughout South Africa, samples were collected from women attending antenatal clinics in Johannesburg (n=34), Pretoria (n=S) and Durban (n=20). Samples from Bloemfontein (n=24) were taken from individuals attending an HIV/AIDS clinic. All eighty-three samples were subtyped by HMA in the env region as before. The predominant subtype circulating within the urban heterosexual population throughout South Africa was identified as subtype C (92.8%) although subtype B was also detected (7.2%). It may thus be beneficial if a HIV vaccine for South Africa is based on a subtype C model. In addition, a rapid method for identification of HIV-1 gag subtypes was developed based on restriction fragment length polymorphism (RFLP) analysis of 400bp (p17) or 650bp (p17 and 5' p24) long PCR fragments. This strategy was appl i ed to eighty-six samples (Cape Town n=47, Johannesburg n=20, Bloemfontein n=17 and Durban n=2) previously subtyped by either sequence analysis of the gag p17 region (n=31), heteroduplex mobility assay (HMA) based on the env gene (n=76), or both (n=21). RFLP analysis identified two subtype A, twenty-five subtype B, fifty-eight subtype C and one subtype D isolates. There were no discrepancies between RFLP and sequence gag subtypes, demonstrating the reliability of this method and no discordance between gag RFLP subtypes and env HMA subtypes, indicating no recombinant viruses in the genomic regions analysed.

No description available.

The HLA complex is the most polymorphic genetic system known in man. The frequency of the HLA class II antigens have been well studied in Caucasoids but little data is available concerning HLA antigen frequencies in Negroes. In this thesis the class II antigens, excluding HLA-DP, were studied in South African (SA) Negroes (Xhosa), Cape Coloureds ( a group of mixed racial origin) and SA Caucasoids using serological, cellular ( HTC typing) and Southern blot techniques. The results obtained for the SA Negroes were compared with those previously found in Nigerians and American Negroes. Marked differences in HLA distribution occurred between these groups, which in part may be explained by Khoisan admixture in the SA Negroes. In addition, striking frequency differences were observed between the three SA populations. For example, in the Xhosa the HLA-DR1, DR4, DR7, DRw8, DQw2, DQw3, Dw1 and Dw3 specificities were found at a significantly lower frequency, whereas HLA-DR3, DRw6 and Dw' RSH' were found at a significantly higher frequency compared with the SA Caucasoids. The frequency in the Cape Coloureds was intermediate between those of the Xhosa and Caucasoids. In the SA Negroes and Cape Coloureds, several new specificities were detected such as HLA-DRw18, DR2 LUM(CT), DRwl2x6, DRw8x14, Dw' RSH', Dw' JOH' and Dw' BME'. The HLA-DR and DQ haplotypes in significant linkage disequilibrium were similar in the three groups. However, several haplotypes with unusual DR and DQ combinations such as HLA-DRw17,DQw7; DR9, DQw2 and DR4, DQw5 were present in the SA Negroes and Cape Coloured families. Al though some of these unusual haplotypes could be explained in terms of recombination between the common haplotypes, none could be typed using a panel of well defined homozygous typing cells, suggesting that the response observed in mixed lymphocyte culture arises from separate molecular determinants. The data on HLA class II antigen frequencies presented in this thesis is essential for future studies on HLA and disease associations and for establishing population relationships. Knowledge of new HLA class II antigens in the various population groups is also important in renal transplantation as matching for HLA-DR antigens is known to improve graft survival.

Thesis (MSc (Genetics))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: The South African abalone, Haliotis midae, is the only endemic species of commercial value. Aquaculture remains the only avenue for expanding the industry, since the closure of the fishery. The current focus is on implementing a molecular breeding programme; thus the development of molecular markers for linkage mapping and QTL analysis is a priority. Various markers, mainly anonymous, have been developed for H. midae; however emphasis is being placed on the development of gene-linked type I molecular markers. The present study investigates and demonstrates the use of public sequence collections to develop type I markers for a species with limited genomic resources, via three strategies: Surveying anonymous H. midae microsatellite markers’ flanking regions to find homology to gene sequences in public databases, cross-species marker transfer of anonymous markers from H. rubra and H. discus hannai demonstrating putative gene associations and lastly EST marker mining (SNP and microsatellites) from various Haliotids and testing transfer to the target species. Approximately 17% of H. midae anonymous markers showed significant similarity to genes. The current study also reports higher cross-species transferability from both H. rubra and H. discus hannai to H. midae (39% and 20.5%, respectively) than previously demonstrated and 15 EST-microsatellites and 16 EST-SNPs were successfully mined. Furthermore, the non-random distribution of microsatellites and high nucleotide diversity in the H. midae genome was confirmed. This is a low cost and time effective method for marker development and presents a continuous and dynamic resource that could be used for future marker development and characterisation as sequence information in public databases grow exponentially. / AFRIKAANSE OPSOMMING: Die Suid-Afrikaanse perlemoen, Haliotis midae, is die enigste van vyf inheemse spesies van kommersiële waarde. Na die noodgedwonge sluiting van die vissery, is akwakultuur die mees praktiese oplossing om die perlemoen industrie uit te brei. Die huidige fokus is gerig op die implementering van ‘n molekulêre teel-program en dus is die ontwikkeling van molekulêre merkers vir genetiese kartering en kwantitatiewe kenmerk lokus analise, van uiterste belang. Tipe II merkers is voorheen vir die perlemoen ontwikkel, maar huidige tendense lê klem op die ontwikkeling van geen-gekoppelde tipe I merkers. Die huidige studie ondersoek die gebruik van publieke databasisse vir die ontwikkeling van tipe I molekulêre merkers vir ‘n spesie met beperkte genomiese bronne. Drie strategieë is geïmplementeer: Eerstens is ‘n opname gemaak van die homologie van perlemoen tipe II merker-vleuelende volgordes met geen volgordes in databasisse. Verder is die oordraagbaarheid van tipe II merkers vanaf H. rubra en H. discus hannai wat assosiasie met gene toon ondersoek. Laastens is ‘n Uitgedrukte Volgorde Merk (UVM) (Expressed Sequence Tag, EST) merker-ontginnings metode vanaf verskeie Haliotis spesies en toetsing van oordraagbaarheid na die teiken spesie uitgevoer. Ongeveer 17% van die tipe II H. midae merkers het geniese assosiasie getoon. ‘n Hoër tussen-spesie oordraagbaarheid vanaf beide H. rubra en H. discus hannai na H. midae (39% en 20.5%, onderskeidelik) word gerapporteer in vergelyking met vorige studies en 15 UVM-mikrosatelliete en 16 UVM-enkel nukleotied polimorfismes (single nucleotide polimorphism, SNP) is ontwikkel. Verder bevestig die studie die nie-lukrake verspreiding van mikrosatelliete en hoë nukleotied diversiteit in die perlemoen genoom. Die gebruik van publieke databasise vir die ontwikkeling en karakterisering van tipe I molekulêre merkers is tyd- en koste-besparend en bied ‘n volgehoue en dinamiese bron vir toekomstige gebruik.

A pig genetic resources study was conducted in five municipalities of Sekhukhune with the aim of characterising pig genetic resources in communal farming systems. A total of 52 pig farmers were interviewed using a structured questionnaire instrument. Of the 52 farmers 65 percent were subsistence, 27 percent back-yard and 8 percent emerging farmers. The primary data collected included demography, production practices, herd structure, feeds and feeding, breeding practices, marketing, and conservation methods. Two indigenous pig farmers and one exotic pig farmers were selected for purpose of measuring growth and other linear traits of piglets over a period of two months. Four hundred and nine (409) pigs were used for body measurements of which 124 were from emerging farms, 71 from subsistence and 206 from back-yard farms. Data was analysed using SAS Package (SAS, Version 9.3). Demographic representation of farmers showed 79 percent of farmers being males, 85 percent married. With 50 percent between the ages of 55-64; 60 percent owning the farms and 83 percent Northern Sotho speaking farms. The majority of farmers (39 percent) had secondary education with 81 percent trained in production and over eight years of farming experience. The objective of farmers raising pigs was mainly for selling at a frequency of 60 percent. Over 70 percent of the farmers had a good grasp of controlling internal and external parasites. However, over 80 percent of the farmers did not vaccinate or get advice from extension officers. When comparing the production systems, there was no variation in the number of young pigs produced. Only 13 percent of the emerging farmers and eight percent in back-yard had proper housing. Only 10 percent of the farmers had financial assistance. That led to only 10 percent of the farmers able to feed complete rations to their animals. Cross breeding has been practiced within communal areas by over 75 percent of the farmers. Over 15 percent bought boars from commercial farmers. This practice enabled them to sell their piglets to private buyers at 50-60 kg at an average price of R500 – R1000. Though the value of indigenous breeds was rated high by over 63 percent the size and price compelled them to cross-breed. An establishment of an indigenous breeding program is highly recommended. / Agriculture, Animal Health and Human Ecology / M. Sc. (Agriculture)

The inter- and intraspecific taxonomy of the genus Lepus is highly controversial. Since these animals play an important ecological role as prey species, their conservation is of high priority. A prerequisite for adequate management strategies is the precise knowledge of taxonomic borders and geographic distributions of the taxa in question. Especially in African hares the clear delimitations of the species and subspecies are still unresolved. In an attempt to obtain a clearer understanding of the evolutionary history, the phylogenetic relationships and the detection of conservation relevant units in African hares, a molecular investigation using mitochondrial DNA sequence data and information from six microsatellite loci was initiated. In this study, the phylogenetic analyses of DNA sequence data of the mitochondrial control region and the cytochrome b gene identified 2 major maternal lineages within South African hares that were further subdivided into two clusters each. The nuclear genetic structure revealed by six dedicated microsatellite loci confirmed this subdivision. While the mitochondrial diversity was characterized by high sequence divergences and haplotype diversities, the nuclear variation seemed more moderate with relatively low FST and RST values. Using the information content of the six microsatellite loci developed for this project, the results of assignment tests strongly supported the validity of the four genetic lineages. The levels of of cytochrome b sequence divergences among the four clusters suggested that they may warrant distinct species status (applying the phylogenetic species concept). The data are suggestive of two species groups consisting of two sister species each: A "saxatilis" group with Lepus saxatilis sensu stricto and another species (possibly L. victoriae), and a "capensis" group with L. capensis s. str. and another, yet to be described species. Applying a molecular clock for cytochrome b, the historical dates for the separation of the South African hares from European outgroup species and the split between the two South African species groups were calculated as 4.84 and 3.45 million years ago, respectively. The divergence dates between the sister species was 1.09-1.45 million years ago. Following the biological species concept, the two major clades represent two species: L. saxatilis sensu lata and L. capensis s. I. , that are both subdivided into two geographically separated phylogroups, one in the southern parts of the country and one in the northern. These intraspecific lineages meet the criteria of evolutionarily significant units and should be considered separately in conservation actions. The evolutionary history of scrub and Cape hares in South Africa has been influenced mainly by contiguous range expansions and sudden population size expansions during the Pleistocene climate changes. / Thesis (PhD (Zoology))--University of Pretoria, 2002. / Zoology and Entomology / unrestricted

The International Commission on Radiological Protection (ICRP) determines the policy regarding radiation safety internationally. To the ICRP, hereditary changes as a result of either high or low doses, are of a major concern. The SA Forum for Radiation Protection recommended that a research project to determine the genetically-significant dose (GSD) for the South African population should be done as such a project has never been undertaken to date. This term was at first defined by UNSCEAR in 1958. The National Radiological Protection Board derived a formula from this definition as shown in the NRPB Report, NRPB-R106 (1980). This formula was implemented in the project. It combines the frequency of radiological examinations obtained during the country-wide survey and estimates of gonadal doses for different examination types, together with population and child expectancy data. New procedures, techniques and data processing that were relevant to this project had to be developed because the available information and conditions are unique to South Africa. The task was set to find a model in order to draw the best representative sample of the population and it was determined in a unique way, namely the so-called Dollar Unit Sampling method. A sample of 27 institutions out of a possible 292 (9%) was drawn in comparison, e.g., with the 8% of France and 8% in Great Britain. It was necessary to rely mainly on the calculation of gonad doses due to a shortage of manpower, contrary to other countries that were able to physically measure doses. Information obtained in the survey was used in this regard. The "RADCOMP Entrance Skin Exposure Software Program " of Nuclear Associates was used to produce parametric Free Air Exposure tables based on doses from Table B.3, NCRP Report No. 102. After the skin entrance doses were calculated, it was possible to calculate the gonad doses. A computer program was obtained from the Food and Drug Administration in the USA for this purpose. Data analysis was performed by means of the software package Microsoft Excel version 4.0. The above-mentioned formula was used in order to obtain the final results. The GSD for the total SA-population was calculated as 94.6 μGy. The breakdown of the GSD for the various South African race groups was Asian - 229.0 μGy, Black - 66.5 μGy, Coloured - 112.2 μGy and White - 463.4 μGy.