Thesis (MScMedSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Context: Excessive exposure to ultraviolet radiation (UV) results in the risk of acquiring long-term harmful effects such as photoaging, which is characterised by deep wrinkles, roughness, dyspigmentation and an increased loss in elasticity. As a result, the detection of photoaging at an early stage is crucial to improving morbidity, whilst preventing the advancement of skin cancer. Aim: The aim of the study was to develop and to validate a diagnostic real-time PCR method in order to establish the gene expression profiles of potential biomarkers in the skin so as to quantify the degree of photoaging: this was conducted by retrieving total RNA from cells adherent to tape strips from sun exposed and non-exposed skin areas. Materials and methods: Twenty healthy volunteers consisting of seven males and thirteen females aged 25 to 67 years were included in this study. Tape stripping was performed using pre-cut D-Squame® 22 mm adhesive discs. Samples were collected on the right medial thigh area 20 cm above the patella and 2 cm below the lateral canthus of the right eye. Total RNA was extracted and relative standard curve method of gene expression was performed. TGF-β, MMP 9, TNF-α and IL-6 mRNA transcripts were selected as representative cytokines to determine the relative fold-change in sun exposed and non-exposed areas of the skin so as to determine extent of photoaging. Results: Repeatability and reproducibility was determined by the coefficient of variation (CV) was within an acceptable range. Thirty five percent (n=7) samples displayed down-regulatory effects for TGF-β. Down regulation of MMP 9 was observed within 30% (n=6) of samples, while 15% (n=3) showed marked up regulation. Only two samples showed measurable levels of TNF-α in the assay, of which one showed significant up regulation. Furthermore, we were unable to detect any IL-6 expression in any of the samples prepared. Conclusion: we have shown that epidermal cytokines can be retrieved from tape stripped samples and can be quantified via real-time PCR. However, the choices of cytokine biomarkers reveal that they are as important as the concentration of starting material. In this study cytokines such as IL-6 is not as informative in determining the extent of photoaging without high doses of ultraviolet radiation before sample collection as opposed to the other explored cytokines. / AFRIKAANSE OPSOMMING: Konteks: Oormatige blootstelling aan ultraviolet (UV) bestraling kan tot ‘n risiko van skadelike en lantermynse nagevolge lei wat gekenmerk word deur foto-veroudering. Dit sluit in diep plooie, growwe vel en ‘n toenemende verlies in elastisiteit. Die ontdekking van foto-veroudering op ‘n vroeë stadium is van kardinale belang vir die verbetering van morbiditeit en die voorkoming van velkanker bevordering. Doelstelling: Die doel van hierdie studie was om ‘n diagnostiese polimerase kettings reaksie (PKR) metode te ontwikkel om geen uitdrukkings profiele van potensiële bio-merkers te vestig in die vel, om so die graad van foto-veroudering in areas van vel wat blootgestel word aan die son en beskermde van die son te bepaal deur totale RNS te versamel van kleeflintskyfies. Materiale en metodes: Twintig gesonde vrywilligers (sewe mans en dertien vroue), tussen die ouderdom van 25 en 67 jaar, was ingesluit in hiedie studie. Vel monsters was versamel deur gebruik te maak van Dsquame® 22 mm kleeflintskyfies 20 cm bokant die patella van die regterkanste mediale heup en 2 cm onder die regter oog. Totale RNS was geisoleer en die relatiewe vlak van geen uitdrukking was bepaal deur gebruik te maak van die kurwe model. Die boodskapper ribonukleiosier transkripsies van die sitokiene TGF- β, MMP 9, TNF-α en IL-6 was gekies as verteenwoordigers van foto-veroudering om die relatiewe verandering van foto-veroudering in die vel te bepaal. Resultate: Validering metodes was aanvaarbaar. ‘n Afwaarts reguleringseffek in TGF-β en MMP 9 merker uitdrukking is gevind in vyf en dertig persent (n=7) en dertig persent (n=6) van monsters, onderskuidelik. In vyftien persent (n=3) van monsters is ‘n opwaarts reguleringseffek in die laasgenoemde gevind. Slegs twee monsters het meetbare vlakke van TNF-α getoon in die eksperiment, waarvan slegs een ‘n noemenswaardige opwaartse regulering getoon het. IL-6 uitdrukking is nie gevind in enige van die monsters. Gevolgtrekkings: Hierdie studie het bepaal dat sitokiene van die vel geisoleer van kleeflint monsters en gekwantifiseer deer relatiewe PKR uitdrukking bepaal kan word. Die keuse van bio-merkers is egter net so belangrik as konsentrasie bepaling van die monsters. Die IL-6 sitokien, in vergelyking met ander, is slegs informaliet tydens hoë ultraviolet bestraling aan die vel blootgestel is.

Thesis (PhD (Food Science))--University of Stellenbosch, 2006. / High-rate anaerobic bioreactors are used for the treatment of various wastewaters, of which the upflow anaerobic sludge blanket (UASB) bioreactor has the widest application, especially in the food and beverage industries. In an UASB bioreactor sludge develops in a particular granular or flocculent form and the success of the anaerobic process relies on the formation of active and settable granules. These granules are formed by self-aggregation of bacteria that can be divided into different trophic groups that are responsible for the metabolic breakdown of organic substrates. The successful performance of a bioreactor is influenced by the composition of the substrate which subsequently may have an impact on the microbial consortium present in the UASB granules. In order to determine if a change in the structure of the non-methanogenic microbial community takes place, UASB brewery granules were subjected to the sudden addition of different carbon sources at different concentrations. A shift in the microbial community did occur when the granules were subjected to lactate medium (5 g.l-1). No changes in the microbial community were observed when the granules were stressed with glucose medium as carbon source, regardless of an increase in the glucose concentration. In order to better understand the effect that different wastewaters may have on the microbial consortium present in different UASB granules, the polymerase chain reaction (PCR) based denaturing gradient gel electrophoresis (DGGE) technique and sequence analysis were used to fingerprint and identify the Bacteria and Archaea present in either, winery, brewery, distillery or peach-lye canning UASB granules. Each granule type showed distinct PCR-based DGGE fingerprints with unique bands, while other bands were found to be present in all the granules regardless of the wastewater being treated. Bacillus, Pseudomonas, Bacteroides, Enterococcus, Alcaligenes, Clostridium, Shewanella, Microbacterium, Leuconostoc, Sulfurospirillum, Acidaminococcus, Vibrio, Aeromonas, Nitrospira, Synergistes, Rhodococcus, Rhodocyclus, Syntrophobacter and uncultured bacteria were identified, representing different acidogenic, acetogenic and homoacetogenic Bacteria.Different methanogenic bacteria such as Methanosaeta, Methanosarcina, Methanobacterium and uncultured bacteria belonging to the group Archaea were also fingerprinted and identified from different UASB granules. In both these studies a DGGE marker was constructed that may be used to assist in the identification of bacteria. The DGGE marker can also be used to monitor the presence of bacteria over a time period during anaerobic digestion. Bioaugmentation or the enrichment of granules results in tailor-made granules that may be used for the treatment of specific wastewaters. One of the most important contributions to the maintenance and enhancement of UASB granule formation is the inclusion of suitable microbes in the granule structure. Enterobacter sakazakii was isolated from raw winery wastewater and was found to produce sufficient amounts of desired fatty acids. This bacteria was, therefore, incorporated into batch cultured granular sludge. In order to identify and monitor the presence of the incorporated E. sakazakii in the tailor-made granules, 16S rRNA gene sequence primers and PCR conditions were developed. The use of molecular techniques such as PCR-based DGGE and sequence analysis proved to be successful methods to fingerprint and identify the microbial consortium present in the different UASB granules.

Thesis (PhD (Pathology. Medical Microbiology))--University of Stellenbosch, 2005. / Pneumocystis jirovecii is a significant contributor to the burden of disease in immunocompromised patients. The polymerase chain reaction (PCR) is more sensitive and specific than microscopy. Cotrimoxazole prophylactic breakthrough and treatment failures have been reported, and associated with mutations at codons 55 and 57 of P. jirovecii dihydropteroate synthase (DHPS). No phylogenetic or population genetic models have been successful in elucidating P. jirovecii intraspecies strain relatedness. Aims: 1) Compare detection rates of nine PCR techniques and immunofluorescence microscopy (IF); 2) Determine the extent of co-infecting pathogens associated with Pneumocystis Pneumonia (PcP); 3) Determine local P. jirovecii ITS1-5.8S-ITS2 rDNA strain types, and model lineage evolution employing a coalescent-theory based statistical parsimony network analysis; 4) Investigate the possible emergence of cotrimoxazole-resistant strains Methods: PCR was evaluated on clinical specimens employing: ITS nested; DHPS single and nested; DHFR nested; major surface glycoprotein (MSG) heminested; mitochondrial large subunit rRNA (mtLSUrRNA) single and nested; 18S rRNA onetube nested, and real-time 5S rRNA PCR. Retrospective analysis of co-infecting pathogens seen in PcP patients was conducted. ITS regions were amplified, cloned and sequenced. Statistical parsimony was applied for coalescence based network genotype analysis. DHPS genome walking was attempted and DHPS and DHFR primer annealing sites explored. Amplified DHPS and DHFR genes were cloned and sequenced. Results: Most sensitive PCR technique was mtLSUrRNA nested followed by 5S realtime PCR. A poor correlation exist between mtLSUrRNA PCR and IF. Review of clinical records suggested a high rate of false-positive IF results. P. jirovecii was detected in 4.3% M. tuberculosis-positive HIV-positive, and 2.5% M. tuberculosispositive HIV-negative patients. P. jirovecii was detected in 45% HIV-negative patients. The most prevalent ITS type was Eg. Four new combinations: Eo, Je, Ge, No; 11 new ITS1 and 13 new ITS2 sequences were identified. A new ITS2 type was detected in three patients and designated u. More than one strain type was detected in 15/19 patients. Analysis of 5.8SrDNA region revealed 13 clones containing 1-2 nucleotide polymorphisms. Of 85 mtLSUrRNA PCR-positive specimens, currently employed primers amplified DHPS and DHFR genes from 53 and 27 specimens, respectively. Newly designed DHPS primers increased detection in 3 / 28 previously DHPS-negative mtLSUrRNA-positive specimens. Of 56 DHPS genes amplified and sequenced, one contained the double mutation (Thr55Aa; Pro57Ser). DHFR Ala67Val was detected in three specimens and a new DHFR genotype (Arg59Gly; C278T) was demonstrated. Conclusions: The study emphasises the need to evaluate PCR primers against local strains. It is recommended that mtLSUrRNA PCR be performed in parallel to IF and discordant results resolved with clinical evaluation. Co-infection with P. jirovecii and M. tuberculosis occurs in South Africa, and treatment for both pathogens is recommended when demonstrated by the laboratory. ITS genotyping employing statistical parsimony network analysis suggests type Eg as major ancestral haplotype, and supports recombination contributing to strain diversity worldwide. DHPS mutations may signal emergence of resistance to cotrimoxazole in South Africa, however, low sensitivity of primers limits surveillance efforts.

published_or_final_version / abstract / Chemistry / Doctoral / Doctor of Philosophy

Salmonella enteritidis (S. enteritidis) is a bacterial pathogen of chickens, and is currently one of the leading causes of human food poisoning in the world. It is believed that contaminated poultry products, especially eggs and egg products, have been responsible for the dramatic increase in the incidence of this Salmonella serotype. Detection of S. entertidis has conventionally involved bacteriological examination of samples, yet these procedures are time-consuming which could lead to the rapid spread of S. enteritidis through commercial flocks and potentially cause a human health risk. A number of alternative detection techniques, mostly based on serological methods, have been reported as effective diagnostic assays. However, some of these reports have not been supported by representations of SDS-PAGE gels or Western blots. The objective of this study was the evaluation of these serological techniques as well as a PCR amplification technique, which has been reported to show promising results as a diagnostic method. The techniques discussed in these reports were evaluated with regards to how rapid they were, their specificity and their potential for use in local diagnostic laboratories. Antigens from the outer surface of S. enteritidis were purified by several methods and their antigenicity was tested by separating the antigens by means of SDS-PAGE, followed by Western blotting using sera of chickens infected with S. enteritidis. A high degree of cross reactivity was observed with many of the antigens tested, especially the lipopolysaccharides (LPSs) and outer membrane proteins (OMPs) which had previously been reported as containing antigens which could be used for specific detection of S. enteritidis. This cross-reactivity could be explained by the conserved nature of many of the LPS and OMP antigens among the Salmonella serotypes tested. A fimbrial antigen, SEF14, which has been reported as a novel antigen, was seen as a prominent band at 14.3 kDa and was found to react with antibodies against S. enteritidis, yet not to the specificity levels described in previous reports. PCR amplification of the sefA gene sequence, which encodes for the SEF14 fimbrial antigen, was found to give a predicted product of 310 bp when using a previously described oligonucleotide primer pair. This amplified product was found to be specific for S. enteritidis and other serogroup D Salmonella serotypes that are not poultry pathogens The cross-reactivity observed with many of the serological techniques used in this study, meant that detection of S. enteritidis infection in chickens was considerably hindered. However, the identification of further novel antigens by serological means, could result in the development of new vaccines. The specificity and speed afforded by PCR amplification indicated that this technique showed excellent potential for use in local diagnostic laboratories. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 2003.

Bacillus cereus is traditionally thought to be the only member of its genus accepted as a pathogen in foods like grains, fruits, vegetables and milk due to the presence of the nonhemolytic (Nhe) operon. However, many other Bacillus spp. may also harbor the Nhe operon and be pathogenic. Real-time PCR targeted the nheA gene in 37 samples obtained from food, soil, and reference cultures by analyzing the standard deviations of melt peaks. Rep-PCR was used to compare the banding patterns of each sample against B. cereus ATCC14579 and three B. thuringiensis strains to “fingerprint” each isolate. Of the original 43 isolated tested, 37 were Gram-positive rods. The remaining six samples were Gram-positive cocci. Twenty-five of the 37 Gram-positive Bacillus spp. were nheA positive, while twelve were negative. Many of the nheA positive strains were species not previously known to contain Nhe, and were capable of causing gastroenteritis in consumers. / Department of Biology

Technological and methodological advances in the fields of medical and life-sciences have, over the last 25 years, revolutionised the way in which cellular activity is measured at the molecular level. Three such advances have provided a means of accurately and rapidly quantifying mRNA, from the development of quantitative Polymerase Chain Reaction (qPCR), to DNA microarrays, and second-generation RNA-sequencing (RNA-seq). Despite consistent improvements in measurement precision and sample throughput, the data generated continue to be a ffected by high levels of variability due to the use of biologically distinct experimental subjects, practical restrictions necessitating the use of small sample sizes, and technical noise introduced during frequently complex sample preparation and analysis procedures. A series of experiments were performed during this project to pro le sources of technical noise in each of these three techniques, with the aim of using the information to produce more accurate and more reliable results. The mechanisms for the introduction of confounding noise in these experiments are highly unpredictable. The variance structure of a qPCR experiment, for example, depends on the particular tissue-type and gene under assessment while expression data obtained by microarray can be greatly influenced by the day on which each array was processed and scanned. RNA-seq, on the other hand, produces data that appear very consistent in terms of differences between technical replicates, however there exist large differences when results are compared against those reported by microarray, which require careful interpretation. It is demonstrated in this thesis that by quantifying some of the major sources of noise in an experiment and utilising compensation mechanisms, either pre- or post-hoc, researchers are better equipped to perform experiments that are more robust, more accurate, and more consistent.

Background The lack of an effective diagnostic tool for Carrion’s disease leads to misdiagnosis, wrong treatments and perpetuation of asymptomatic carriers living in endemic areas. Conventional PCR approaches have been reported as a diagnostic technique. However, the detection limit of these techniques is not clear as well as if its usefulness in low bacteriemia cases. The aim of this study was to evaluate the detection limit of 3 PCR approaches. Methodology/Principal Findings We determined the detection limit of 3 different PCR approaches: Bartonella-specific 16S rRNA, fla and its genes. We also evaluated the viability of dry blood spots to be used as a sample transport system. Our results show that 16S rRNA PCR is the approach with a lowest detection limit, 5 CFU/μL, and thus, the best diagnostic PCR tool studied. Dry blood spots diminish the sensitivity of the assay. Methodology/Principal Findings We determined the detection limit of 3 different PCR approaches: Bartonella-specific 16S rRNA, fla and its genes. We also evaluated the viability of dry blood spots to be used as a sample transport system. Our results show that 16S rRNA PCR is the approach with a lowest detection limit, 5 CFU/μL, and thus, the best diagnostic PCR tool studied. Dry blood spots diminish the sensitivity of the assay. Conclusions/Significance From the tested PCRs, the 16S rRNA PCR-approach is the best to be used in the direct blood detection of acute cases of Carrion’s disease. However its use in samples from dry blood spots results in easier management of transport samples in rural areas, a slight decrease in the sensitivity was observed. The usefulness to detect by PCR the presence of low-bacteriemic or asymptomatic carriers is doubtful, showing the need to search for new more sensible techniques.

Philosophiae Doctor - PhD / DNA profiling the male specific region on the Y-chromosome is fundamental to forensic practise. Its recognised as a powerful analytical tool for investigation of sexual assault when the DNA evidence is highly admixed. Standard practises for processing sexual assault evidence include physically separate the sperm cell from the female fraction using differential extraction followed by autosomal DNA profiling. However, under specific scenarios of assault physical separation may not be possible due to the nature of the evidence. The research presented in this thesis was focused on the development and validation of the UniQTyper™ Y-10 prototype for male specific DNA profiling. The prototype which contains 10 Y-STR markers was developed and validated to deliver a rapid and cost-effective system while maintaining a forensic applicable level of performance. An allelic ladder is produced with an allele cloning approach for which an overview of the workflow and technicalities presented herein is aimed to assists an efficient bulk production process. In a second component novel sequence variation was reported across 153 sequenced alleles and submitted to Genbank. In this output the Y-STR panel was perused beyond the scope of length polymorphisms. In a proof of concept, its potential to discriminate between shared allele sizes by characterizing sequence structure variations is discussed. In a final component we generate the largest Y-STR survey across South Africa to establish reference data and to comprehensively assess the forensic genetics parameters for the UniQTyper™ Y-10.

Leishmanioses são doenças classificadas pela Organização Mundial da Saúde (OMS) como negligenciadas, o que as caracterizam como aquelas que prevalecem em condições de pobreza e representam significativo entrave ao desenvolvimento por contribuírem para desigualdade. Cerca de 350 milhões de pessoas vivem sob o risco de infecção em 98 países da África, Eurásia e Américas. Acometem o homem e outros animais sob um espectro clínico amplo, que varia de discretas lesões, de cura espontânea, a quadros de comprometimento sistêmico, potencialmente fatais. A manutenção do ciclo de transmissão está inserida em um sistema biológico complexo, com a participação de mais de 20 espécies de Leishmania e uma grande variedade de reservatórios e vetores, e o diagnóstico está entre as estratégias empregadas para o controle dessas doenças. A precisa identificação das espécies envolvidas no ciclo de transmissão permite a geração de dados importantes para mapeamentos ecoepidemiológicos e para o delineamento de estratégias terapêuticas e de controle. O material genético do parasita como alvo de detecção e identificação desses organismos é descrito na literatura científica em trabalhos que abordam diversas estratégias metodológicas. Entre as técnicas mais recentes estão as análises de dissociação em alta resolução (HRM- High Resolution Melting), descrita como uma estratégia eficiente para a discriminação de polimorfismos em fragmentos específicos de DNA gerados por PCR (Polymerase Chain Reaction). O presente trabalho teve como principal objetivo padronizar um protocolo de detecção e identificação de Leishmania capaz de discriminar o maior número possível de espécies com base em polimorfismos do gene hsp70, utilizando HRM como ferramenta metodológica. Sequências nucleotídicas de hsp70 disponíveis em banco de dados e obtidas no laboratório foram analisadas in silico e regiões polimórficas foram delimitadas. Das regiões delimitadas, três foram escolhidas por conterem polimorfismos que geraram fragmentos cujas temperaturas de dissociação simuladas são distintas entre espécies ou grupo de espécies. A exploração de perfis de dissociação dos três amplicons de hsp70 obtidos por PCR em tempo real revelou diferenças que permitiram a discriminação das espécies de Leishmania responsáveis por doenças nas Américas, África e Eurásia. Os testes foram padronizados com a utilização de DNA de cepas-referência de Leishmania e então aplicados a amostras de DNA obtidas de amostras clínicas, de campo ou experimentais, como isolados, biópsias humanas frescas ou fixadas, flebotomíneos e cães naturalmente infectados e camundongos experimentalmente infectados. Os resultados obtidos por HRM foram comparados aos obtidos previamente por outras metodologias como PCR convencional, RFLP (Restriction Fragment Length Polymorphism) ou sequenciamento, com confirmação da identidade do parasita nas amostras testadas. O protocolo descrito é relativamente barato, tecnicamente simples, passível de automatização, podendo ser uma alternativa para a detecção e identificação de Leishmania em amostras, em estudos diagnósticos e ecoepidemiológicos. / According to the World Health Organization (WHO), the leishmaniases are classified as neglected diseases, since they are related to poverty and contribute to inequality. Approximately 350 million people are at risk of infection in 98 countries in Africa, Eurasia and Americas. They affect humans and other animals that, depending on the species, causes a wide spectrum of clinical manifestations, that range from discrete lesions of spontaneous healing to potentially fatal systemic disease. The maintenance of the transmission cycle is part of a complex biological system, in which there is the participation of more than 20 species of Leishmania and a large variety of reservoirs and vectors. Diagnosis is important for early control of the disease. A precise identification of the species involved in the transmission cycle allows the generation of important data for eco-epidemiological mapping and for therapeutic measures and control strategies. Several genes have been used as diagnostic targets and several molecular strategies have been used in diagnosis. High resolution melting (HRM) analysis is among the most recent techniques and it is described as an efficient strategy for discriminating polymorphisms in specific DNA fragments generated by PCR (Polymerase Chain Reaction). The main objective of this work was to standardize a protocol for detection and identification of Leishmania spp, capable of discriminating the largest possible number of species based on hsp70 gene polymorphisms through HRM methodological tool. Available nucleotide sequences of hsp70 in databases as well as the ones obtained in the laboratory were analyzed in silico and polymorphic regions were delimited. Three regions were chosen since they contained polymorphisms that generated distinct simulated dissociation temperatures among species or group of species. The analysis of dissociation profiles of the three amplicons of hsp70 obtained by real-time PCR revealed differences that allowed the discrimination of Leishmania species responsible for diseases in the Americas, Africa and Eurasia. The tests were standardized using DNA from Leishmania reference strains and then applied to DNA samples obtained from clinical or from field samples, such as isolates, fresh or fixed human biopsies, phlebotomines and dogs naturally infected, and experimentally infected mice. The results obtained by HRM were compared to those obtained previously by other methodologies such as conventional PCR, RFLP (Restriction Fragment Length Polymorphism) or sequencing, confirming the parasite identity in the samples tested. The described protocol is relatively inexpensive, technically simple, potentially automated, and may be an alternative for the detection and identification of Leishmania in biological samples, in diagnostic and eco-epidemiological studies.