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

Please read the abstract in the section 00front of this document / Dissertation (MSc (Chemical Pathology))--University of Pretoria, 2005. / Chemical Pathology / unrestricted

Genetic polymorphisms can be seen as the occurrence of more than one form of a DNA- or protein sequence at a single locus in a group of organisms, where these different forms occur more frequently than can be attributed to mutation alone. The combination of genetic polymorphisms present in the genome of a particular individual is referred to as its genotype. A wide range of genotyping techniques have been developed to detect and visualize genetic polymorphisms. One such technique examines highly polymorphic repetitive DNA regions called microsatellites, also called “short tandem repeats” (STRs) and sometimes “simple sequence repeats” (SSRs) or “simple-sequence length polymorphisms” (SSLPs). A microsatellite region consists of a DNA sequence of identical units of usually 2-6 base pairs strung together to produce highly variable numbers of tandem repeats among individuals of a population. Microsatellite genotyping is a popular choice for many types of studies including individual identification, paternity testing, germplasm evaluation, genome mapping and diversity studies and can be used in many commercial, academic, social, and agricultural applications. There are, however, many obstacles in effectively managing and analysing microsatellite genotype data. Currently, researchers are struggling to effectively manage and analyse rapidly growing volumes of genotyping data. Management problems range from simply the lack of a secure, easily accessible central data repository to more complex issues like the merging and standardization of data from multiple sources into combined datasets. Due to these issues, genetic fingerprinting applications such as identity matching and relatedness studies can be challenging when data from different experiments or laboratories have to be combined into a central database. The main aim of this M.Sc study in Bioinformatics was to develop a bioinformatics resource for the management and analysis of genetic fingerprinting data from microsatellite marker genotyping studies, and to apply the software to the analysis of microsatellite marker data from ramets of Pinus patula clones with the purpose of analysing clonal identity in pine breeding programmes. The software resource developed here is called GenoSonic. It is a web application that provides users with a secure, easily accessible space where genotyping project data can be managed and analysed as a team. Users can upload and download large amounts of marker genotype data. Once uploaded to the system, DNA fingerprint data needs to be standardised before it can be used in further analyses. To do this, a two-step approach was implemented in GenoSonic. The first step is to assign standardized allele sizes to all of the input allele sizes of the microsatellite fingerprints automatically using a novel automated binning algorithm called CSMerge-1, which was designed specifically to bin data from multiple experiments. The second step is to manually verify the results from the automated binning function and add the verified data to a standardized dataset. Once the genetic fingerprints have been standardized, allele- and genotype frequencies can be viewed for any given marker. GenoSonic also provides functionalities for identity matching. One or more DNA fingerprints from unknown samples can be matched against a standardized dataset to establish identities or infer relatedness. Finally, GenoSonic implements a genetic distance tree construction function, which can be used to visualize relatedness among samples in a selected dataset. The bioinformatics resource developed in this study was applied to a microsatellite DNA fingerprinting project aimed at the re-establishment or confirmation of clonal identity of Pinus patula ramets from pine clonal seed orchards developed by a South African forestry company at one of their new agricultural estates in South Africa. The results from GenoSonic‟s automated binning function (CSMerge-1) and the results from the identity matching and tree construction exercise were compared to results obtained by human experts who have analysed the data manually. It was demonstrated that the results from GenoSonic equalled or surpassed the manual results in terms of accuracy and consistency, and far surpasses the manual effort in terms of the speed at which analyses could be completed. GenoSonic was developed with specific focus on reusability, and the ability to be modified or extended to solve future genotyping-related problems. This study not only provides a solution to current genotype data management and analysis needs of researchers, but is aimed at serving as a basic framework, or component library for future software development projects that may be required to address specific needs of researchers dealing with high-throughput genotyping data. / Dissertation (MSc)--University of Pretoria, 2011. / Biochemistry / unrestricted

A) Bariatric surgery for the treatment of obesity has shown much promise. The Roux-en-Y gastric bypass is a procedure that combines both restrictive and malabsorptive elements. Post-operative weight loss and co-morbidity improvements previously achieved are over and above those which are seen during life style modification and drug therapy. 330 patients (2005-2007) with a mean BMI of 45.87 ± 0.63 were characterised pre-operatively with regard to clinical, anthropometric and DEXA scan measurements. 130 were matched for the same parameters post-operatively over a 9-12 month observation period. The data was analysed statistically using paired t-tests and regression analyses. Significant post-operative improvements were observed with regard to patients’ weight loss and co-morbidity improvement. Positive and significant correlations of anthropometric measures to biochemical parameters ensued. Risk factor scoring methodology produced an average total score of 17 points / 36. Average post-op weight loss at 9-12 months follow-up was 20% of initial pre-op weight. Co-morbid diseases and anthropometric measurements illustrated significant changes following surgery. Risk factor scoring is a valuable pre-op tool for assessing eligibility for medical aid re-imbursement for surgery. B) Obesity is a global epidemic and is increasing the worlds’ mortality rate. Genetic predisposition to obesity is recognized as being significant. Polymorphisms within the Melanocortin 4 Receptor (MC4R) gene, which encodes a G-protein coupled receptor responsible for post-prandial satiety signalling, have been associated with monogenic obesity. Obesity prevalence in South Africa is drastically increasing, however there has been no causative investigation done. Thus we sought to perform an initial assessment of the prevalence of MC4R polymorphisms within a South African representative group. Blood was drawn from a mixed Body Mass Index (BMI) cohort of 259 adult individuals and their DNA was extracted. The MC4R gene was PCR amplified from the DNA, the amplicon sequenced and the sequence data was analyzed for polymorphisms. A polymorphism prevalence of 13.51% was found within the patients across a BMI range that spanned from underweight (19.6) to super-obese (126.0). In addition to MC4R polymorphisms that had been identified previously, two new polymorphisms namely R7H and S36T were observed. Four haplotypes were also identified. MC4R mutation frequency was observed to be ethnically dependant; however the hypothesis of differing ethnic backgrounds illustrating varying mutational penetrance was not confirmed. The expected trend regarding MC4R polymorphism functional effect and associated pathogenicity was not followed in light of our results. The question of whether or not MC4R polymorphisms contribute to the development of obesity is indisputable; however the current accepted trend regarding their precise role may be incorrect and must be challenged. / Dissertation (MSc)--University of Pretoria, 2009. / Immunology / unrestricted

Methods to determine genetic diversity and relatedness within populations are essential tools for proper wildlife management. Today the approach of choice is polymerase chain reaction-based microsatellite analysis. Seven new polymorphic loci were isolated from a microsatellite-enriched Caribbean flamingo genomic library and used to characterize survey populations of Caribbean and African greater flamingos. In addition, four of these loci were used to verify parentage relationships within a captive-breeding population of African greater flamingos. Parentage predictions based upon gamekeeper observations of breeding and nesting did not always agree with genetic-based parentage analyses of the nine suggested family groups. Four family groups were supported (groups I, II, III and VI) by there results. However, an analysis of the remaining five suggested groups, with a total of eight offspring/dam and eight offspring/sire suggested relationships, yielded seven exclusions of the suggested dam and six exclusions of the suggested sire. This put the overall suggested dam exclusion rate at 35% and exclusion rate for suggested sires at 29%. Although the keeper observation data for our family groups must be considered a variable of concern at this time, these findings are certainly suggestive that more carefully controlled studies may reveal that flamingos are not monogamous as long accepted, but rather socially monogamous or even promiscuous. Thus we have now been able to both characterize and demonstrate the utility of our polymorphic microsatellite loci. We hope these results will interest additional wildlife facilities in further parentage and behavioral studies that will collectively aid to improve monitoring and maintenance of genetic diversity, and as provide better insight into breeding habits of both wild and captive populations.

A doença de Alzheimer (DA) é complexa e de etiologia desconhecida. Provavelmente componentes multifatoriais influenciam no desencadeamento dessa patologia, sendo que o único fator genético de risco bem estabelecido até o momento para a doença é a variante alélica APOE*E4. Nos últimos anos, descobriu-se uma série de polimorfismos em genes diferentes sugerindo que essas alterações possam ter participação discreta na patologia. O presente estudo avaliou vinte e um polimorfismos distribuídos em treze genes, sendo estes APOE, ACE, APP, BDNF, CALHM1, CST3, GAB2, GAPDH, GSK3B, GSTP1, IL1A, IL1B e SORL1 , em pacientes, controles idosos e indivíduos com comprometimento cognitivo leve, na tentativa de verificar se existe algum tipo de associação entre os polimorfismos investigados como fatores de risco para DA. Nossos resultados mostraram associações positivas entre cinco polimorfismos conferindo risco elevado para o desenvolvimento de DA (rs429358 e rs7412 de APOE, rs2373115 de GAB2, rs6438552 de GSK3B e rs641120 de SORL1). Outro achado consistente de nosso estudo foi que 20/21 polimorfismos estudados apresentaram ao menos um genótipo associado com risco elevado para DA na presença de um alelo APOE*E4. Com nosso trabalho contribuímos para aumentar o conhecimento sobre a etiologia da DA, identificando possíveis marcadores moleculares de suscetibilidadenessa patologia. / Alzheimers disease (AD) is complex, and its ethiology is not completely understood yet. It is likely that multifactorial components do account for this pathology development, being the allelic variant APOE*E4 is the only well-established genetic risk factor so far. Recently, a series of polymorphisms located at different genes were related to AD, suggesting that those variations might have a modest participation in this pathology. The present study evaluated twenty-one polymorphisms distributed in thirteen genes, being them APOE, ACE, APP, BDNF, CALHM1, CST3, GAB2, GAPDH, GSK3B, GSTP1, IL1A, IL1B and SORL1, in elderly controls, AD and mild cognitive impairment patients, attempting to verify if there is any kind of association between the selected polymorphisms as risk factors for AD. Our results show positive associations between five polymorphisms and AD (APOE rs429358 and rs7412, GAB2 rs2373115, GSK3B rs6438552 and SORL1 rs641120). Another consistent finding was that 20/21 polymorphisms analyzed showed at least one genotype associated with increased risk for AD at the presence of at least one APOE*E4 allele. We intend that our research might contribute to increase what is known about AD ethiology, by deciphering possible molecular susceptibility markers evolved with this pathology.

Orientador: Mary Massumi Itoyama / Resumo: Dentro da subordem Heteroptera algumas espécies pertencentes a família Pentatomidae apresentam espermátides polimórficas em seus lobos testiculares que são oriundas de dois fenômenos: a polimegalia e o lobo harlequin. Para a investigação dessas espermátides polimórficas e de seu desenvolvimento comparadas às espermátides não polimórficas, foram coletadas em São José do Rio Preto as espécies Antiteuchus tripterus, Edessa meditabunda, Loxa deducta e Proxys albopunctulatus (Pentatomidae, Heteroptera). Os machos tiveram seus testículos extraídos, fixados e incluídos em parafina ou resina. O material incluído em parafina foi cortado e corado com hematoxilina/eosina (HE) e analisados em microscopia de luz, outros testículos, destas quatro espécies, foram incluídos em resina e analisados em microscópio eletrônico de transmissão (MET). Os testículos A. tripterus são alongados e divididos em 6 lobos, sendo 1 a 3 sem alterações, 4 e 6 com polimegalia e o 5 o lobo harlequin. Foi possível observar, também, que os lobos 4 e 6 possuem espermátides grandes enquanto o 5 apresenta espermátides pequenas. Em MET foi possível observar em todos os lobos a formação da cauda da espermátide onde ocorre a formação dos derivados mitocondriais e a posterior formação do axonema entre os derivados. Além disso, foi detectada a presença de três tipos de espermatozoides no ducto eferente, sendo estes oriundos dos diferentes lobos. Há o espermatozoide maior com morfologia alongada com pequenas protuberâncias... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Within the suborder Heteroptera, some species belonging to the Pentatomidae family show alterations in some of their testicular lobes, where we can show the polymegaly and the harlequin lobe. For the investigation of these polymorphic cells and their development compared to non-polymorphic cells, the species Antiteuchus tripterus, Edessa meditabunda, Loxa deducta and Proxys albopunctulatus (Pentatomidae, Heteroptera) were collected in São José do Rio Preto. The males had their testicles extracted, fixed and included in paraffin or resin. The material included in paraffin was cut and stained with hematoxylin / eosin (HE) and analyzed under light microscopy, other testicles, of these four species, were included in resin and analyzed using a transmission electron microscope (TEM). The testicles A. tripterus are elongated and divided into 6 lobes, 1 to 3 without changes, 4 and 6 with polymegaly and the 5 the harlequin lobe. It was also possible to observe that lobes 4 and 6 have large cells while 5 has small cells. In TEM, it was possible to observe the formation of the sperm tail in all lobes where the formation of the mitochondrial complex occurs, which divides into two mitochondrial derivatives and the subsequent formation of the axoneme between the derivatives. In addition, the presence of three types of sperm in the efferent duct was detected, these coming from different lobes. There is the larger sperm with elongated morphology with small protuberances at its ends; the inte... (Complete abstract click electronic access below) / Doutor

Klotho (KL), an anti-aging protein, attracted interest in the aging field because of the dramatic phenotype of KL deficient mice and its connection to signaling pathways implicated in aging. The KLVS variant consists of the F352V (KLV) and C370S (KLS) substitutions. It was detected in genome wide association studies (GWAS) that linked it to alterations in longevity and disease risk. The molecular mechanism(s) underlying these associations are unknown. To understand how KL increases the risk of age-related diseases, the studies in this dissertation investigated whether expression of the KLVS variant, when compared to wildtype (KLWT), displays differences in processing, protein-protein interactions and enzymatic activity. Differences in processing were evaluated by studying changes in shedding, half-life and plasma membrane localization of KL variants. The decrease in KLV shedding, as measured by the intracellular: extracellular ratio, were explained by a decreased half-life. This decreased half-life is potentially due to decreased KLV plasma membrane localization, which is attenuated by co-expression of dominant negative dynamin, suggesting a role of endocytosis in these differences. To assess whether there are changes in KLVS protein-protein interactions, differences in dimerization were measured by Blue Native gel electrophoresis and cross-linking. KLV dimerization was increased while KLS and KLVS variants decreased dimerization. Co-immunoprecipitation of tagged KL assessed whether these changes were due to alterations in homodimerization. The presence of KLVS in dimers decreased the levels of immunoprecipitated KL suggesting KLVS decreases homodimerization. Changes in heterodimerization of KLVS with fibroblast growth factor receptor (FGFR) 1c were also investigated through co-immunoprecipitation. KLVS increased heterodimerization with FGFR1c. Addition of FGF23, for which KL is a co-receptor, showed that KLVS increases FGF signaling downstream of FGFR1c. To determine differences in enzymatic activity of KLVS, 4-metylumbelliferyl-beta-D-glucuronide was used to measure alterations in glucuronidase activity. Results showed that KLVS had decreased enzymatic activity compared to KLWT. These findings are the first to show that KLVS leads to differences in function as demonstrated by decreased homodimerization and enzymatic activity and increased heterodimerization with FGFR1c. Given the association of KLVS with disease and longevity, these results suggest that these functions are integral in KL's anti-aging role in humans.

Silver nitrate staining, a rapid and efficient method, has proven to be excellent for nucleolar organizing region (NOR) studies in fish. Some fish appear to have only two NOR-bearing chromosomes in their karyo-type, whereas others probably have several. In the present study we analyzed the NORs of Leporinus friderici, a species that, on the basis of previous studies, has been considered as representative of species with NORs carried by a single chromosome pair. The analyses were performed by a combination of three methods, i.e. silver nitrate staining, staining with the GC-specific fluorochrome chromomycin A3, and in situ hybridization with digoxigenin-labeled probes. The results showed that, although more frequent and conspicuous in a single chromosome pair, the NORs of this species are present in multiple chromosomes. Intra- and inter-individual variations observed by the three methods strongly suggest the occurrence of post-zygotic modifications involving NORs. NOR identification in fish, almost exclusively performed by the silver nitrate method, is currently being re-evaluated by methods such as chromomycin A3 staining and in situ hybridization, which may provide important information leading to a better understanding of chromosome evolution in these animals.

No description available.