Sixteen of the world's 42 species of land tortoises occur in Africa, 10 of which are endemic to southern Africa. South Africa itself, which occupies 0.8% of the earth's total land mass, has the highest tortoise biodiversity in the world, with 13 species. This is the first study to use molecular techniques to investigate the evolutionary history of this group, which displays an unusually high level of speciation on the continent. Four hundred and fifty base pairs of mtDNA cytochrome b sequence were obtained, using direct PCR-based sequencing, from 32 individual tortoise blood samples, comprising 13 different species from 6 genera. PAUP 3. 1.1, and MEGA were used to infer a phylogeny using Chrysemys scripta elegans (an Emydid) an outgroup. Both phenetic and cladistic methods generated similar results. With the exception of Malacochersus, both morphological and molecular work show largely congruent results. When intra-specific relationships, using the molecular results, were compared to the existing morphological data, Psammobates was the only genus with a consistent topology. Proposals for the re-evaluation of Homopus, Kinixys and Geochelone have been made. Suggestions, based on molecular results, include the distinction between Chersobius and Homopus (Hewitt 1937), incorporating Malacochersus tornieri into Kinixys, and the elevation of Geochelone pardalis pardalis and G.p. babcocki to species level. Sequencing a further nine individuals within Homopus areolatus showed a higher than expected sequence variation, suggesting a distinct population structure and possibly cryptic species.

Oesophageal squamous cell carcinoma (OSCC) is a highly malignant tumour that has a poor prognosis and shows marked regional variation in its incidence, implicating environmental factors. South Africa is one of several countries that has areas of high incidence. The exact aetiopathogenesis of OSCC is not well understood. Current environmental risk factors include alcohol, tobacco, human papillomavirus (HPV) infection and nutritional factors including; low intake of Vitamins A, C and riboflavin, lack of fruit and vegetables, ingestion of fungal contaminated foods and consumption of extremely hot beverages. This study was a retrospective immunohistochemical study done on paraffin embedded tissues. The histopathology, grading and staging of all resected squamous cell carcinomas over a twenty one year period from 1982 to 2002, were reviewed. Sixty eight patients were identified; all had an oesophagectomy for OSCC at Groote Schuur Hospital, a tertiary referral centre. Clinical details regarding gender, race, age, smoking or alcohol usage and survival data were collected. Survival data was updated to 23 June 2003. Two paraffin blocks representing OSCC and normal mucosa for each patient were retrieved from the archives in the Division of Anatomical Pathology. In addition, 16 cases of reflux oesophagitis were included for comparison. Initial immunohistochemical staining for HPV (Dako- clone KlH8) was undertaken but the negative results necessitated a shift in the focus of this study to that of cell cycle regulatory proteins. The tissues were evaluated for p53 (Dako - clone D0-7), p2l (Novocastro - clone 4Dl0), cyclin DI (Dako - clone DCS-6) and cyclin E (Novocastro - clone 13A3). Expression was interpreted as positive if 10% or more of the tumour cell population stained. Expression was also stratified into three levels (1, 2 and 3) depending on the percentage positive staining. Normal mucosa did not stain for any of the cell cycle regulators. OSCC stained as follows: 61.8% for p53, 27.9% for p21, 22.1 % for cyclin E and 44.1% for cyclin Dl. Reflux oesophagitis stained as follows: 31.2% for cyclin DI, 12.5% for p21 and 0% for both p53 and cyclin E. Subsequent statistical analysis failed to reveal any prognostic significance to the expression of cell cycle regulators, nor could expression or level of expression be associated with stage, grade, age, gender or alcohol use. There was however a significant relationship between cyclin DI and smoking. In addition, expression of p53 discriminated between malignant and reactive oesophageal lesions. Advancing age proved to be associated with an increased risk of mortality. Lastly, histopathological staging proved to be the most significant prognostic factor in this study.

Hyperammonaemia is not an infrequent presentation in the newborn or neonatal period. While the majority are transitory in nature and due to infective processes or liver pathology/immaturity, a significant number are due to defects in enzymes of the urea cycle. This cycle has evolved to cope with waste nitrogen disposal and the de novo synthesis of arginine. There are five distinct enzymatic steps in the urea cycle, and defects in each, result in a biochemically distinct disease. Four of these diseases, deficiencies of carbamyl phosphate synthetase (CPS), ornithine transcarbamylase (OTC), argininosuccmic acid synthetase (ASS), and argininosuccinate lyase (ASL) can present dramatically within the first 24 to 48 hrs of life with progressive lethargy, hypothermia and apnea, all related to very high plasma ammonia levels. These diseases may also present later in infancy, childhood and adulthood with hyperammonemia and episodic mental status changes. The fifth defect, arginase deficiency presents as progressive spastic quadriplegia and mental retardation but with milder elevation of blood ammonia levels. The molecular genetics of these disorders in South Africans has not been explored and there is thus very little information on phenotype/genotype relationships, specific for citizens of this country. This study aims to correct this imbalance and has concentrated initially on OTC deficiency, which is X-linked and therefore the most common defect encountered. Initial work on this project has concentrated on subjects with a classical X-linked OTC phenotype.

Includes bibliographical references (leaves 49-55). / Beta-catenin is normally complexed with adenomatous polyposis coli (APC) protein and E-cadherin adhesion molecule, and localized on the cell membrane. If APC/beta-catenin is disrupted, beta-catenin transfers into the nucleus, where it functions as a transcriptional activator, causing unregulated cell proliferation. The localisation of beta-catenin in H NPCC adenomas has not been studied but a shift in beta-catenin to the nucleus has been previously demonstrated in a range of col 0 recta I cancers, including those in HNPCC. The aim of the first part of the study was to determine whether there is a beta-catenin shift occurring as an early event in HNPCC tumours. Coded sections of tumours were immunohistochemically stained with antibody against beta-catenin and counterstained in haematoxylin. 14 HNPCC adenomas, 13 HNPCC carcinomas, 10 FAP adenomas, 10 FAP carcinomas, 10 sporadic adenomas and carcinomas and 10 juvenile polyps -three with dysplasia and seven without- were studied. A score was given for loss of membrane staining (0-1), presence of cytoplasmic staining (0-2) or nuclear staining (0- 2) and a total out of five obtained. An shift in beta-catenin was demonstrated at the adenoma phase in HNPCC. HNPCC, tumours were compared with sporadic tumours and a statistically significant similarity in prevalence of beta-catenin shift found in adenomas and carcinomas. The early shift in beta-catenin in HNPCC led to the second part of the study evaluating the "down-stream" effects of this shift in HNPCC tumours. TheHNPCC sections were immunohistochemically stained with E-cadherin, cmyc and cyclin 01. The results showed a positive correlation between Ecadherin loss, increased cyclin 01 and a shift in beta-catenin. No significant change in c-myc or correlation between c-myc and a shift of beta-catenin was found. In conclusion the study indicates that disruption of the APC/beta-catenin pathway plays a similar role in HNPCC tumours to that in sporadic tumours. A notable exeption is the effect on c-myc and further study is needed in this regard.

Includes bibliographical references.

Breast cancer management continues to be a challenge due to the heterogeneity of the disease and the fact that individuals with the same stage and pathological diagnosis may respond differently to treatment as a result of differences in gene expression. Several components of the Her-2/PI3K/Akt pathway were evaluated for their relevance as potential prognostic markers or indicators for treatment. A secondary objective was to evaluate the CISH technique for its suitability for analysis of Her-2 gene amplification on archived, Papanicolaou-stained fine needle aspiration (FNA) samples. Tissue blocks from a retrospective series of 93 primary breast carcinoma cases were selected, based on their Her-2 status. Twenty six of these cases received trastuzumab treatment while 67 did not. Expression of Her-2, ER, PI3K, PTEN, p-Akt, BCL2, NFκB, MDM2 and p53 were analysed and compared with various clinicopathological features. The CISH technique was evaluated for its suitability for analysis of Her-2 gene amplification on archived, Papanicolaou-stained FNA samples.

Hyperhomocysteinaemia is a recently established risk factor for the development of vascular disease and is caused by a variety of defects in the metabolism of methionine as well as dietary deficiencies of the vitamin cofactors (B6, B12 and folate) of the enzymes involved in methionine metabolism. Cystathionine β-synthase (CBS) is the most common genetic cause of homocystinuria, the severe form of the disease. The incidence of CBS deficiency in a group of 12 young patients of varied ethnic origin, who had peripheral vascular disease (PVD) that could not be ascribed to any of the conventional risk factors and were selected for having hyperhomocysteinaemia, either in the fasting state or after methionine load, was investigated. Nine out of the ten patients tested, showed abnormally elevated plasma homocysteine levels after methionine load, indicating a high incidence of deficient transsulfuration, which may have been caused by defects in CBS. Very wide variation in the CBS assay has hampered efforts to establish the contribution of CBS deficiency to the hyperhomocysteinaemia observed in this population. Therefore, a major part of this work has focussed on the source of this variation and the data suggests that between experiment variation as a result of changes in enzyme activity during the culture of the fibroblasts makes the biggest contribution. The most appropriate criterion to identify heterozygotes for CBS deficiency under these circumstances is to measure reduced CBS activity on several separate occasions compared to a control group. Only one of the group of 12 PVD patients (patient 1000) was identified as a heterozygote for CBS deficiency using this standard. Heterozygosity for CBS deficiency therefore seems to make only a minor contribution to the observed hyperhomocysteinaemia in this group of patients. Molecular genetic investigations were performed on selected individuals. Patient 1000 was confirmed to be a heterozygote for CBS deficiency. An A to G transition at nucleotide 695 leading to histidine to arginine substitution at amino acid 232 was found in one allele of this patient. A young homocystinuric female (patient 960) was confirmed to be compound heterozygote for CBS deficiency, with the common Celtic G₉₁₉A transition on the one allele and a novel duplication of the 7 bases between position 1553 and 1559 on the other allele. This 7bp insertion was identified as coming from the mother (patient 961). In an attempt to find an alternative or perhaps more sensitive method for the detection of defects in methionine metabolism, dual metabolic labelling of cultured fibroblasts with L-[methyl-³H]-methionine and L-[³⁵S]-methionine was developed to investigate these pathways in homozygotes and heterozygotes for CBS deficiency compared to controls. Although, no differences in the ratio of ³H/³⁵S were found that could be used to identify the zygosity of the patient for CBS deficiency, changes in the ratio of ³H/³⁵S over time in certain cellular compartments suggest that further development of this approach may prove to be useful.

The SR Ca²⁺-ATPase is an ATP driven pump that removes calcium from the sarcoplasm and myofibrils to allow muscle relaxation. The sulfhydryl crosslinker, 1,4- phenylenebismaleimide, reacts with Ca²⁺-ATPase (110 kD) to form a species with an apparent molecular weight of 125 kD, as well as dimers and high order oligomers, on SDS-P AGE. During the course of this study we have optimised and characterised the reaction of 1,4-phenylenebismaleimide with SR Ca²⁺-ATPase to produce the 125 kD species that is reminiscent of an E 125 species formed by intramolecular crosslink with glutaraldehyde. The glutaraldehyde crosslink involves the active site Lys 492 and Arg 678, in a zero distance link that overlaps with the ATP binding pocket, since it can be inhibited by nucleotides. It has been previously shown that the putative intramolecular crosslink with 1,4-phenylenebismaleimide is also sensitive to nucleotide binding. We show that the formation of the putative intramolecular crosslink of SR vesicles ( approximately 20 % of ATPase) with 1,4-phenylenebismaleimide is optimum at alkaline pH with micromolar concentrations of the crosslinker. The formation of ATPase dimers and high order oligomers, which were prominent in the reaction with SR vesicles, were eliminated by solubilising in Triton X-100. Under these conditions and in the presence of calcium, two intramolecular crosslinks are formed as seen in the formation of 125 and 130 kD species. The former seems to be in proximity of the y-phosphate and the latter in the β-phosphate region of the ATP binding site according to nucleotide protection studies. In the presence of detergent (Triton X-100) and absence of calcium, only the 125 kD species is formed and requires stabilisation by thapsigargin, a sesquiterpene lactone that binds the transmembrane α-helices. These conditions yield up to 60 % intramolecularly crosslinked ATPase. Trypsin digestion altered the apparent molecular weight of the 125 kD species to 135 kD, suggesting, in accordance with the results of glutaraldehyde crosslink, that the putative intramolecular crosslink 1s between tryptic fragments A and B. [¹⁴C]1,4-phenylenebismaleimide was synthesised to further characterise the reaction and to elucidate crosslinked amino acid residue following protein digestion, radioactive peptide purification, and sequencing. From filtration studies it was evident that a number of sulfhydryl residues were derivatized in both SR vesicles and solubilised Ca²⁺-ATPase. The results suggests that there is very fast reacting set of sulfhydryl groups, which could comprise of sulthydryls from Ca²⁺-ATPase and/or a minor contaminant protein as previous studies have indicated. Only this fast set was reduced by nucleotide binding. In Triton X-100, the total reactive residues increased two-fold and the biphasic nature of the curve showed that the intramolecular crosslink possibly involves a fast reacting sulfhydryl residue and a slow reacting one. Derivatization with [¹⁴C]1,4-phenylenebismaleimide followed by digestion and HPLC analysis revealed radio labelled peaks. Purification and sequencing of the adducts identified 8 reactive cysteines, namely Cys 12, Cys 344, Cys 364, Cys 471, Cys 498, Cys 636, Cys 670 and Cys 674. The cysteines involved in the putative intramolecular crosslink could not be identified but it is proposed that either Cys 471 or Cys 498 crosslink with Cys 670 or Cys 674.

Includes abstract. / Includes bibliographical references. / Breast carcinoma is a common cancer in South African women. In the Republic of South Africa, 41 new cases of breast cancer are diagnosed per 100 000 population and the mortality rate is 21 per 100 000 population. Many risk factors have been implicated in the carcinogenesis of this disease; including smoking, family history and hormones, however, this only accounts for about 1/3 of the cases diagnosed. Some studies have implicated Human papillomavirus (HPV) as a possible aetiologic agent in the pathogenesis of breast carcinoma however the results have been inconsistent and sometimes controversial. This study was designed to determine the presence of HPV in breast cancer in a South African cohort and to investigate its influence on the cell cycle. A retrospective and prospective cell block study was undertaken.

Includes bibliographical references (leaves 40-44). / The aims of this study were to determine the age at presentation and the racial distribution of prostatic adenocarcinoma in the Western Cape region and correlate this with histological grade; to correlate the expression of androgen receptor, bcl-2, p53 and Cox-2 with the Gleason grade of disease and patient demographic data and to establish a method to determine androgen receptor (AR) gene amplification in formalin fixed prostatic carcinoma tissue.