Abstract As the defects in DNA repair and cell cycle control are known to promote tumorigenesis, a proportion of inherited breast cancers might be attributable to mutations in the genes involved in these functions. In the present study, three such genes, TP53, CHK2 and ATM, which are also associated with known cancer syndromes, were screened for germline mutations in Finnish breast cancer patients. In combination with our previous results, three TP53 germline mutations, Tyr220Cys, Asn235Ser and Arg248Gln, were detected in 2.6% (3/108) of the breast cancer families. The only observed CHK2 alteration with a putative effect on cancer susceptibility, Ile157Thr, segregated ambiguously with the disease, and was also present in cancer-free controls. The available functional data, however, suggests that the altered CHK2 in some way promote tumorigenesis. Furthermore, compared to the other studied populations, Ile157Thr seems to be markedly enriched in Finland. Thus, the clinical significance of Ile157Thr requires further investigation among Finnish cancer patients. ATM germline mutations appear to contribute to a small proportion of the hereditary breast cancer risk, as two distinct ATM mutations, Ala2524Pro and 6903insA, were found among three families (1.9%, 3/162) displaying breast cancer. They all originated from the same geographical region as the AT families with the corresponding mutations, possibly referring to a founder effect concerning the distribution of these mutations in the Finnish population. The genes important for tumorigenesis in sporadic disease might also contribute to familial breast cancer. Therefore, four putative LOH targets genes in chromosome 11q21-q24 were screened for intragenic mutations, and five were analyzed for epigenetic inactivation in sporadic breast tumors. The lack of somatic intragenic mutations in MRE11A, PPP2R1B, CHK1 and TSLC1 led us next to investigate promoter region hypermethylation as a mechanism capable of silencing these genes, as well as the ATM gene. Only TSLC1 demonstrated involvement of CpG island methylation, which was especially prominent in three tumors. This suggests that together with LOH, methylation could result in biallelic inactivation of the TSLC1 gene in breast cancer.

Abstract Eddy currents and susceptibility differences are the most important sources that interfere with the quality of MR images in the presence of an artificial macroscopic object in the volume to be imaged. In this study, both of these factors have been examined. The findings show that the RF field is the most important cause of induced eddy currents when gradients with relatively slow slew rates are used. The induced eddy currents amplify or dampen the RF field with the result that the flip angle changes. At the proximal end in the vicinity of the hip prosthesis surface, there have been areas where the flip angle is nearly threefold compared to the reference flip angle. Areas with decreased flip angles have also been found near the surface of the prosthesis top. The incompleteness of the image due to eddy currents manifests as signal loss areas. Two different methods based on MRI were developed to estimate the susceptibility of a cylindrical object. One of them is based on geometrical distortions in SE magnitude images, while the other takes advantage of phase differences in GRE phase images. The estimate value of the Profile™ test hip prosthesis is χ = (170 ± 13) 10-6. A remapping method was selected to correct susceptibility image distortions. Correction was accomplished with pixel shifts in the frequency domain. The magnetic field distortions were measured using GRE phase images. The method was tested by simulations and by imaging a hip prosthesis in a water tank and in a human pelvis. The main limitations of the method described here are the loss of a single-valued correction map with higher susceptibility differences and the problems with phase unwrapping in phase images. Modulation transfer functions (MTF) were exploited to assess the effect of correction procedure. The corrected image of a prosthesis in a human hip after total hip arthroplasty appears to be equally sharp or slightly sharper than the corresponding original images. The computer programs written for this study are presented in an appendix.

The susceptibilities of C.dubliniensis fluconazol-resistant (FR), C. dublinienis fluconazole-susceptible (FS) and C. albicans from oral candidiasis were tested to antiseptics chlorhexidine gluconate (CHX), cetylpiridinium chloride (CPC), triclosan (TCS) and natural compounds carvacrol, eugenol and thymol. In general C. dubliniensis FS was more sensitive to antiseptics than C. dublinienis FR and C. albicans. However to CHX the group FR was significantly less susceptible than the others. To fungicidal activity, the three groups did not show susceptibilities differences to CHX and TCS and the group FR was as sensitive as C. albicans to CPC. In general a similar profile of susceptibility was observed to natural products. The susceptibilities of the three groups of Candida spp to antiseptics confirmed the good antifungal activity of them. The authors discuss the importance of monitoring the susceptibility of Candida to antifungal agents as well as to antiseptics widely used in order to detect emergence of antiseptics resistance. / As suscetibilidades in vitro de C. dubliniensis resistentes ao fluconazol (RF), C. dublinienis sensíveis ao fluconazol (SF) e C. albicans sensíveis ao fluconazol foram testadas para os antissépticos gluconato de clorexidina (CHX), cloreto de cetilpiridineo (CPC), triclosan (TCS) e para os compostos naturais carvacrol, eugenol e timol. Em geral as cepas de C. dubliniensis SF apresentaram maior suscetibilidade aos agentes antissépticos do que as cepas C. dublinienis RF e C. albicans SF. No entanto, para o antisséptico CHX as cepas de C. dubliniensis RF foram significativamente menos susceptíveis quando comparadas as demais. A atividade fungicida dos três grupos de isolados não mostrou diferença quanto a susceptibilidades para a CHX e o TCS, e o grupo RF foi tão sensível quanto C. albicans ao CPC. Em geral, foi observado um perfil semelhante de susceptibilidade aos produtos naturais. As suscetibilidades dos três grupos de Candida spp aos antissépticos confirmou boa atividade antifúngica. Os autores discutem a importância de controlar a susceptibilidade de Candida aos agentes antifúngicos, bem como antissépticos utilizados a fim de detectar o aparecimento de resistência aos antissépticos.

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.

Background: Psoriasis is a complex disease with a genetic component contributing to disease pathogenesis. Chronic plaque psoriasis can be dichotomised into two subtypes according to age of onset; type 1 (early-onset; <40 years) and type 2 (late-onset; ≥40 years). Despite clinical and biological differences between the two subtypes, the genetics underpinning late-onset psoriasis remains poorly characterised compared to early-onset psoriasis. Aims: The aim of this project was to identify genetic loci associated with late-onset psoriasis, to assess the overlap of loci with early-onset psoriasis and to elucidate the functional role of the identified variants. Methods: The study had three parts; the first was a candidate-gene association study of the IL1B gene. A total of 16 SNPs from the region were genotyped in 595 late-onset and 1,137 early-onset psoriasis samples and compared to 4,770 controls from the European population. The second was a large-scale study conducted in 543 late-onset psoriasis and 4,373 controls using the Immunochip array. The third was a functional study using bioinformatics data mining, chromatin immunoprecipitation and electrophoretic mobility shift assay techniques to analyse the role of a disease-associated variant at the biological level. Results: The candidate-gene study replicated a previously reported association at a promoter polymorphism, rs16944 (P<0.05), within the IL1B gene and discovered a novel association at a second variant, rs11687624 (P<3.12x10-3), in late-onset psoriasis. None of the variants analysed were significantly associated with early-onset psoriasis. Bioinformatic eQTL data suggests the two variants and their proxies are associated with the expression of IL1A, IL1B, IL38 and PAX8. The Immunochip study identified 6 non-HLA loci (P<2.3x10-5) previously associated with early-onset psoriasis to also be associated with late-onset psoriasis (IFIH1, IL12B, IL23A, IL23R, TRAF3IP2 and ZNF313). Conditional analysis of the MHC region also identified two loci (HLA-C and HLA-A). A novel locus, IL1R1, was associated with late-onset psoriasis, but not early-onset psoriasis. Bioinformatic data mining found no role for the IL1R1 variants as eQTLs and prioritised the IL1B variant rs2708914 for functional analysis. The transcription factor STAT3 was found to be enriched at rs2708914 in keratinocyte and CD8+ T-lymphocyte cell lines. Allele-specific binding could not be established. Conclusions: This project is the largest genetic study of late-onset psoriasis to date and provides evidence that it shares susceptibility loci with early-onset psoriasis as well as having specific susceptibility loci. These findings provide further evidence for the dichotomisation of chronic plaque psoriasis, firstly to facilitate better understanding of the pathogenesis of the two subtypes and secondly to enable tailored therapy to be developed. Both have potential benefits for patients in the future. The genetic and functional studies conducted have provided a platform from which further studies can be carried out.

To test the hypothesis that a metaphorical technique would be more effective than a direct technique to induce hypnosis, 60 volunteers from students at North Texas State University were divided into high- and low-susceptible subjects by the Harvard Group Scale of Hypnotic Susceptibility. They were randomly assigned to direct and metaphorical induction groups and to a control group, with 10 high- and 10 low-susceptible subjects in each group. After hypnosis they completed the Field Inventory of Hypnotic Depth, and their mean scores were subjected to an analysis of variance and a Newman-Keuls test. Neither method of hypnotic induction was found more effective than the other, although both were effective when compared to a control group. It was also found that subjects who expected to be able to experience hypnosis were no more likely to be hypnotized than those who expected not to be able to experience hypnosis. Finally, it was found that low-susceptible subjects were as likely to respond to a post-hypnotic suggestion as high-susceptible subjects.

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.

To investigate the bacterial composition of infected and non-infected dog bite wounds (DBW), a prospective study was performed on dogs with various grades of bite wounds presenting at the Onderstepoort Veterinary Academic Hospital, University of Pretoria, and a nearby animal shelter. Fifty dogs with bite wounds inflicted within the previous 72 hours were selected. This represented 104 wounds. Wounds were clinically graded according to severity. Swabs were collected from all wounds for bacterial culture and cytology. Infection was diagnosed if 2 of the following 3 criteria were met: macroscopic purulence, microscopic presence of phagocytosed bacteria, or pyrexia. Non-infected wounds were either classed as sterile (established by culture) or contaminated (culture positive but bacteria not phagocytosed on cytology). To determine the origin of the bacteria, swabs were collected from the skin near the wounds and gingiva of 15 bite victims. All swabs were cultured aerobically and anaerobically and all aerobic cultures were evaluated for antimicrobial susceptibility using the Kirby Bauer disk diffusion test. The victims were predominately male, uncastrated, small-breed dogs. Of the 104 wounds studied, 21 were judged to be infected and 83 non-infected. Infected wounds were significantly more likely to culture positive (Fisher's exact test: p = 0.02). Sixteen per cent of wounds did not culture bacteria, 67% grew aerobes only, 1% anaerobes only and 67% a mixture of aerobes and anaerobes. A total of 213 isolates were cultured representing a mean of 2 isolates per wound. Of the aerobe species cultured, 22%, 19% and 17% belonged to the genera of Pasteurella, Streptococcus and Staphylococcus respectively. The species of Pasteurella multocida (66%) and Staphylococcus intermedius (70%) were predominant. Pasteurella canis and pyogenic streptococci were common in infected wounds, whereas Bacillus spp., Actinomyces spp. and oral streptococci were usually found in contaminated wounds. Three anaerobic genera were cultured, namely, Prevotella, Clostridium and Peptostreptococcus, and were usually associated with wounds with dead space. This study also describes the first documented case of Capnocytophaga canimorsus in an infected dog bite wound. Notably clinical and cytological assessment was capable of establishing whether antimicrobials were required or not. Although no single antimicrobials was considered to be effective against all the bacteria, amoxycillin plus clavulanic acid, 1st and 3rd generation cephalosporins, ampicillin or amoxycillin and potentiated sulphonamides gave the best in vitro sensitivity results. / Dissertation (MMedVet(Surgery) Small Animal Surgery)--University of Pretoria, 2007. / Companion Animal Clinical Studies / unrestricted

MENVSC (Geography) / Department of Geography and Geo-Information Sciences / The Limpopo lowveld is at risk of floods from tropical storms from the South West Indian Ocean. The flood risk is particularly high in low altitude areas with poor infrastructure and limited resources. This study assessed flood vulnerability and adaptation at Lenyenye, Ga-Kgapane Masakaneng and Nkowankowa Section B and C within the Mopani District in the Limpopo Province of South Africa. The research objectives were to establish the determinants of flood vulnerability, assess the levels of flood vulnerability and the community‟s coping strategies. A quantitative survey approach was employed using questionnaires which were administered to affected households to identify determinants of flood vulnerability, indicators and coping strategies by communities. A qualitative survey was also undertaken to supplement the information obtained from the quantitative survey. Key informant interviews were conducted with disaster management authorities in the study area to provide information on indicators, flood experience, adaptation and mitigation measures. Field observations were undertaken to observe the physical landscape and flood impacts. Secondary data were acquired through records, maps, Census 2011 and from the South African Weather Service. Collected data were imputed into the flood vulnerability index to measure the level of flood vulnerability. The results of this study will contribute to flood disaster risk reduction in the lowveld. The results indicate that flood vulnerability in the study areas is determined by dwelling quality, poor or lack of drainage, education levels, employment status, rainfall amount and topography. The calculated flood vulnerability levels in the three case study villages indicate that Ga-Kgapane Masakaneng, Lenyenye and Nkowankowa Section B and C have a „vulnerability to floods‟ level. However, the FVI also showed that the economic aspect scored a high vulnerability to floods in Ga-Kgapane. In Nkowankowa Section B and C; physical component obtained a „high vulnerability to floods.‟ Major coping strategies in the three case villages were: making „Le-guba‟ around houses; sand-bags; making a furrow and channel around houses and on roads; temporary relocation and lastly relocating to a safer area. Key recommendations are public awareness; integrating modern mitigations with local knowledge; development of programs to ensure resilience through incorporation of (Integrated Development Planning) IDP and flood management and flood early warning system.