Magister Scientiae - MSc / Sexual assault is a significant problem facing the South African society. In this context, efficient but also affordable genotyping systems are needed for positive identification of criminals in incidences of sexual violence. The aim of this study was therefore to develop non-commercial Y-STR genotyping systems suitable for sexual assault cases in South Africa. Y-chromosome STR loci constituting the minimal haplotype are still the most widely used loci in investigating sexual assault cases despite the fact that DYS391 and DYS392 have shown low levels of polymorphism in Xhosa populations in Cape Town. The minimal haplotype was, therefore, further investigated in the Cape Muslim population. The Cape Muslim population generally exhibited high GD values among all the South African populations. These values were higher than 0.5 for most loci, and ranged from 0.447 for DYS391 to 0.957 for DYS385. The highest number of alleles in most loci was also recorded in this population. The overall assessment of the minimal haplotype has shown that this system is still a useful in investigating sexual assault case in many South African subpopulations. Therefore the exercise of internal validation of the minimal haplotype system was successfully carried out in the laboratory. The properties of additional novel and widely used STRs were also investigated in this study. Loci were successfully sequenced and allele nomenclature was assigned to them according to the ISFG guidelines. / South Africa

Magister Scientiae - MSc / The objective of this study was to develop and validate a six Non-CODIS miniSTR genotyping system and to determine its suitability for forensic casework in South Africa. In Non-CODIS miniSTR genotyping systems, smaller PCR products are amplified and the primers are positioned as close as possible to the repeat region. For this reason, these systems can be valuable in a variety of scenarios including complex paternity cases, missing persons work, and mass fatality disasters. / South Africa

Magister Scientiae - MSc / The aim of the present study was to evaluate the power of discrimination and genetic (diversity) parameters in the Y chromosome extended haploytpe markers in populations of Tanzania for forensic and populations studies. Eleven Y chromosome extended haplotype markers were selected for this study, these includes Minimal haplotypes markers i.e. DYS19, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS389I/II and two additional markers DYS438 and DYS439. Six populations of Tanzania were investigated under this study. These populations were selected based on the language family categories; Niger Congo (Kuria and Sukuma), Nilo Saharan (Luo and Maasai) and Afro Asiatic (Iraqw and Alagwa). / South Africa

Magister Scientiae - MSc / The aim of this study was to investigate the genetic diversity of the SLC22A1 gene and to deduce its possible pharmacogenetic implications within the Cape Coloured population of South Africa; a uniquely admixed population of immigrant Europeans, Asians and the indigenous populations. Recent studies have reported an abundance of polymorphic variants within this solute carrier transporter gene encoding for the organic cation transporter 1, as well as evidence linking these variants to an effect on metformin uptake. This study included establishing baseline frequency distribution of previously reported alleles for 20 SNP variants within the SLC22A1 gene, as well as the development of SNaPshot® and Multiplex AS-PCR genotyping assays, and also exploring the possibility of using High-resolution melt (HRM) analysis as a costeffective alternative for SNP genotyping. Ethics clearance was obtained from the Ethics Committee of the University of the Western Cape. Biological samples in the form of buccal (oral) swabs were collected from 132 unrelated voluntary donors from the Cape Coloured population residing in the Cape Metropolitan area. Two SNaPshot® Multiplex Systems were specifically designed for the study,successfully optimized and used for genotyping. Hundred genetic profiles were then generated for a total of 20 SNP variants on SLC22A1 gene, using this primer extension-based genotyping method that enables multiplexing up 10 SNPs. Population genetics data obtained for the investigated SNPs were analysed using various statistical analysis software. Important population genetic parameters were calculated, and possible pharmacogenetics implications were then discussed. Among others, allelic and genotypic frequencies, as well as linkage disequilibrium were determined and compared with world populations. Minor deviation from Hardy- Weinberg equilibrium was observed in the Cape Coloured population. No significantLinkage Disequilibrium between the investigated SNPs was observed in this population. A Multiplex allele specific – PCR (MAS-PCR) genotyping system was successfully designed and optimized for the genotyping of 10 SNPs from the SLC22A1. This system, also developed specifically for this study, was made of 2 multiplexes each covering 5 SNPs. It is an inexpensive genotyping assay that allows for efficient discrimination of SNP polymorphisms in one reaction tube with standard PCR conditions. A pilot study was conducted to explore the possibility of using High-resolution melt (HRM) analysis as a cost-effective alternative for SNP genotyping. In addition to genotyping, HRM analysis can be used to scan large numbers of samples for novel genetic variations. / South Africa

Isolation of plant DNA is complicated due to the presence of polyphenols, polysaccharides and other metabolites, that are isolated together with DNA. These compounds can affect the yield and quality of DNA and can inhibit a polymerase chain reaction (PCR). A modern, simple, and fast method of DNA isolation in molecular biology laboratories is magnetic separation based on reversible DNA immobilization on magnetic particles. These methods allow to obtain DNA of high quality and purity. In the experimental part, magnetic microparticles PGMA 2 mg/ml and magnetic nanoparticles functionalized by polylysine (PLL) 0,2 mg/ml were used for isolation of plant DNA from vegetables (carrots), fruits (pear, apple, lemon, mango) and heat treated food products for children (Hami first carrot, Nestlé fruit pocket, dmBIO pear carrot apple, Hello fruit snack with apples and Hello fruity snack with mango). The efficiency of separation of magnetic particles with bound DNA using a magnetic needle and a magnetic separator were compared. The quality and quantity of isolated DNA were verified by spectrophotometric analysis. The amplificability of isolated DNA was tested in a conventional PCR using primers specific for plant ribosomal DNA (rDNA). PCR products were analyzed by agarose gel electrophoresis. Major fluorescent bands were of 700, 350 and 220 bp corresponding to three different rDNA amplicons. DNA was isolated from heat treated food products for children in a PCR-ready quality. Only 220 bp long PCR products were detected, that indicated DNA degradation. The identity of PCR products was determined by restriction fragment lenght analysis (RFLP) using NlaIII enzyme cutting the rDNA subregion (ITS1) of Daucus carota (carrot). The digestion profiles were in a good agreement with those predicted from bioinformatic analysis confirming, thus, the specificity of the developed PCR method.

Polymerase chain reaction (PCR) is molecular diagnostic method which allows the identification of lactic acid bacteria used in food industry. In this work species-specific PCR primers (targeted on highly conserved 16S rDNA region) were used for identification of bacteria of species Streptoccocus thermophilus in 10 randomly commercially accessible fermented milk products and for identification of species Streptococcus thermophilus in 25 lyophilisates collected in Culture Collection of Dairy Microorganisms Laktoflora (CCDM, Tábor, Czech Republic). The PCR products (968 bp) were detected using electrophoresis in 1,2 % agarose gel. Bacterial DNA was isolated from crude cell lysates by magnetic carriers P(HEMA co GMA) containing carboxyl groups. DNA was reversibly bind on their surface in the presence of high concentrations of poly(ethylene glycol) (PEG 6000) and sodium chloride. Phenol extraction of DNA was used as control. Streptococcus thermophilus strains were identificated using PCR in all analysed samples.

The aim of this study was focused on the study of conditions of growth of strains Lbc. paracasei subsp. paracasei CCDM 211, Lbc. paracasei CCDM 212, Lbc. paracasei subsp. paracasei CCDM 213 and Lbc. salivarius CCDM 216 in media with different amount of carbon-source (glucose, lactose and whey). Next part of the experiment was dealed with study of conditions of bacteria growth at stress conditions (lower pH). The purity od bacterial culture was verified with help of streaking. Purity DNA isolated from bacteria was tested using agarose gel electrophoresis, DNA concentration was estimated spectrophotometricaly. The presence of bacteria of genus Lactobacillus was proved using polymerase chain reaction (PCR) with genus specific primers.

Extraction of nucleic acids is an important step for all molecular biological studies. The process of isolation of plant DNA is complicated due to the presence of polyphenols, polysaccharides and other metabolites. They can be co-isolated with DNA and act as PCR inhibitors. The aim of this study was to compare CTAB extraction procedure, Qiagen DNA easy kit, direct homogenization, carboxyl-functionalised magnetic non-porous HEMA based microspheres and combination of the above mentioned methods for DNA isolation from different plants. The DNA was evaluated regarding concentration, purity and amplification in PCR. All methods provided DNA that could be used in downstream PCR applications. However, there were differences regarding yield, purity, labour intensiveness and cost. Combination of direct homogenization and magnetic microspheres coated by carboxyl groups was isolated DNA from various plants and plant foods in a quality suitable for convectional PCR, real time PCR and restriction analysis. This method is fast, simple and does not require work with harmful substances.

This thesis is interested in isolation and identification of probiotic bacteria in three different probiotic products using polymerase chain reaction (PCR). DNA in quality suitable for PCR was isolated from crude lysates using three different types of magnetic microparticles and phenol extraction. Identification genera and species of probiotic bacteria was proven using genus and species specific PCRs. Results were in accordance with data presented by manufacturers.

Magnetically driven separation techniques using magnetic solid carriers are one of modern methods to speed up and facilitate the previously used separation and purification procedures. The use of magnetic particles in biology imposes strict requirements on physical, and chemical properties of the particles, including low toxicity, biocompatibility and non-interference with the chemical environment in diagnostics. The aim of this study was to evaluate carboxyl-functionalised magnetic non-porous P(HEMA-co-GMA), P(HEMA-co-EDMA), PGMA, silica-coated lanthanum manganese peroskvite La0.75Sr0.25MnO3 and thermosensitive poly(N-isopropylacrylamide) microspheres – P(NIPAAm) for DNA isolation from different types of complex food and environmental samples containing PCR inhibitors. The solid-phase reversible immobilisation (SPRI) of nucleid acids on microsphere surface and the release of adsorbed DNA were optimised. DNA from real samples (milk products and probiotic food suplements, mouse faeces) was apparently adsorbed on solid particles from the aqueous phase system composed of 16% PEG 6000 and 2M NaCl. The conditions of the subsequent release absorbed DNA to the elution buffer (pH of elution buffer, temperature and time of elution) were optimized. The quality of eluted DNA and the presence of target DNA were examined by PCR and q-PCR using domain-specific Bacteria and genus-specific Lactobacillus primer set. Real-time PCR was used for an estimation of the PCR interference by comparing the amplification efficiencies of purified DNA containing solid nanoparticles with the DNA standards free of any nanoparticles