Invasive Candida infection is an increasing cause of morbidity and mortality in the immunocompromised patient. Molecular diagnosis based on genomic amplification methods, such as real time PCR, has been reported as an alternative to conventional culture for early detection of invasive candidiasis. The template DNA extraction step has been the major limitation in most reported nucleic acid based assays, due to problems in breaking fungal cell walls and incomplete purification in PCR inhibitor substances. The aim of this study was to compare enzymatic cell wall disruption using recombinant lyticase with mechanical disruption using glass beads. The QIAamp tissue kit was compared with two automated DNA extraction robots, the BioRobot M48 and NucliSens easyMAG, to determine their sensitivity, reliability and duration for DNA release of C. albicans. Mechanical cell wall disruption shortened and facilitated the extraction procedure, but the quantity of released DNA was significantly lower than when enzymatic cell wall disruption was used. Use of robots did not significantly shorten the DNA extraction time, compared with manual DNA extraction. However the NucliSens easyMAG resulted in a higher yield of target DNA compared to the BioRobot M48 and the manual QIAamp tissue kit. / Invasiva svampinfektioner är ett stort problem hos patienter med dåligt immunförsvar. Förekomst av invasiva svampinfektioner har ökat under senare år och medför hög dödlighet. En svampinfektion som inte snabbt diagnostiseras och behandlas kan bli livshotande om patientens kondition är dålig. Candida albicans är den vanligaste orsaken till invasiva svampinfektioner. Med traditionell svampidentifiering kan det ta dagar till veckor att isolera och artbestämma svampen. En snabbare metod att detektera Candida är att använda sig av molekylärbiologiska metoder som påvisar svampens arvsmassa, DNA. Svampar har en cellvägg som är svår att bryta ner och därför är DNA extraktionssteget ett av de mest rapporterade problemen vid DNA svampdiagnostik. Syftet med denna studie var att jämföra enzymatisk och mekanisk cellväggsnedbrytning av C. albicans med hjälp av enzymet lyticase respektive glaskulor. Vi jämförde också en manuell metod med två automatiska robotar för att bestämma deras känslighet, tillförlitlighet och tidsåtgång för DNA-extraktion från C. albicans. De slutsatser som nåtts är att den enzymatiska cellväggsnedbrytningen var känsligare men betydligt mer tidskrävande än den mekaniska cellväggsnedbrytningen. Denna studie visade även att en av de automatiska systemen extraherade signifikant mer DNA än den manuella metoden.

Anaerobe opportunist Clostridium difficile causes the majority of hospital-acquired antibiotic-associated diarrhea. Infections can be severe because of its ability to withstand many antibiotics, to sporulate and to produce toxins (A, B and binary).     In Sundsvall Hospital C. difficile is detected with real-time PCR, which targets the sequences of toxin B, binary toxin and a regulatory gene deletion seen in the virulent ribotype 027. All positive samples are stored frozen for one month, available for further analysis or outbreak investigation. The aim of this study was to investigate if temperature and transportation time may affect the viability of C. difficile, and the PCR-result.     Frozen feces samples were cultivated, identified with MALDI-TOF and analyzed with real-time PCR after at least one month of storage. To simulate the effect of transportation time, samples were stored at 4-8°C for three and seven days before cultivation and identification. Controls were cultivated after freezing for comparison.     Ninety percent of the frozen samples contained viable C. difficile. Discrepancies between PCR-results were found for two of the oldest samples collected (six months), which turned negative. Fresh samples showed lower amount of viable C. difficile after three days (50 %) than after seven days (60 %) of storage, perhaps because of competition with other bacteria and sporulation. The frozen control group contained a higher viable amount, 75 %. The results indicate that C. difficile tolerates to be stored at low temperatures as practiced today at the laboratory. Transportation time seem to affect the outcome of cultivation, but not the PCR-result.

Les virus du genre Begomovirus (famille Geminiviridae) sont fréquemment détectés en association avec des ADN satellites appelées alphasatellite et betasatellite qui font la moitié de la taille du génome viral. L’alphasatellite est autonome pour sa réplication et dépend du virus pour son mouvement et son encapsidation tandis que le betasatellite est dépendant de ces fonctions virales. L’alphasatellite a rarement été montré comme ayant un impact sur le virus assistant, contrairement au betasatellite qui augmente la virulence de son virus assistant. En dehors des bégomovirus tels que le Cotton leaf curl virus (CLCuV) qui ont besoin d’un betasatellite pour initier une infection symptomatique dans leur hôte naturel, la plupart des bégomovirus peuvent causer des symptômes, même sans les satellites avec lesquels ils sont parfois détectés. Le Tomato yellow leaf curl virus (TYLCV), un des virus les plus dommageables dans le monde a rarement été détecté associé à des ADN satellites. Les souches méditerranéennes qui sont aussi les plus invasives, n’ont jamais été détectées avec des ADN satellites, bien qu’elles soient capables en conditions artificielles de les assister avec pour conséquence une considérable augmentation de la virulence en cas de co-inoculation avec un betasatellite. Le risque potentiel d’association de satellites avec le TYLCV-Mld a été évalué en testant divers facteurs potentiellement impliqués dans le maintien de l’association TYLCV-satellite: (i) l'accumulation relative intra-plante du TYLCV et des satellites, (ii) la fréquence de co-infection au niveau cellulaire du TYLCV et des satellites, et (iii) l'efficacité de transmission des satellites par le vecteur Bemisia tabaci. Trois satellites précédemment isolés sur coton au Burkina Faso ont été montrés comme pouvant être assistés par le TYLCV dans des plantes de tomate: Cotton leaf curl Gezira betasatellite (CLCuGB), Cotton leaf curl Gezira alphasatellite (CLCuGA) et Okra leaf curl Burkina Faso alphasatellite (OLCBFA). La quantification par PCR quantitative des ADN du TYLCV et des trois satellites entre 11 et 150 jours après inoculation (dpi) révèle qu’en général, les satellites ont une accumulation supérieure à celle du virus, et que, contrairement aux alphasatellites qui n’ont aucun impact, le betasatellite affecte l’accumulation du TYLCV-Mld. Bien que le rapport des quantités de virus/satellites varie au cours du temps, les satellites sont maintenus avec le TYLCV-Mld au temps tardif de 150 dpi et sont transmis par B. tabaci à 32 et 150 dpi. Le TYLCV-IL interagit différemment avec le CLCuGB car son accumulation n’est pas affectée dans les plantes coinfectées.L’estimation par la technique FISH à 18 et 32 dpi de la fréquence d’association des molécules au niveau cellulaire montre que plus de la moitié des cellules infectées sont coinfectées par le TYLCV et un satellite. Ce résultat est cohérent avec la fréquence observée d’ADN satellite dans les plantes. Cependant, on observe de manière inattendue un nombre important de cellules ne semblant contenir que le betasatellite, ce qui pose des questions sur le fonctionnement des associations virus/satellites. Comme la multiplicité d'infection (MOI) des bégomovirus et des satellites est attendue pour être un facteur déterminant de l’efficacité de la co-infection cellulaire, deux variants équi-competitifs de TYLCV ont été préparés afin de déterminer ce paramètre. Enfin, des amorces PCR permettant la détection générique de betasatellites ont été dessinées pour être utilisées dans le diagnostic par l'Agence française pour l'alimentation, l'environnement et la santé et sécurité au travail (ANSES). Outre les conséquences agronomiques d’un maintien possible des satellites avec le TYLCV, les résultats de cette étude donnent un aperçu novateur sur les interactions entre les bégomovirus et les satellites, au niveau de la plante, au niveau cellulaire et moléculaire. / Begomoviruses (family Geminiviridae) are frequently detected with half genome sized defective virus DNAs, and for some of them with satellite DNAs of similar size, i.e. alphasatellite and betasatellite. Both molecules rely on the virus for maintenance in plant. The alphasatellite was rarely proved to have an impact on the helper virus but the betasatellite was often shown to increase its virulence. Except some begomoviruses, like Cotton leaf curl virus (CLCuV) which rely on a betasatellite for a full symptomatic infection in its natural host plant, most of the begomoviruses which were frequently detected with satellites do not rely on them for infectivity. Tomato yellow leaf curl virus (TYLCV) is one of the most damaging begomovirus worldwide. The Mediterranean IL and Mld strains, the most invasive ones, were never detected in association with satellites, although they were experimentally proved to readily assist them for replication and movement in plant. This was particularly true for betasatellites and resulted in a dramatic increase in the virulence of TYLCV.The potential of a TYLCV-satellite association was assessed by testing various factors involved in the maintenance of both molecules in tomato plants: (i) the relative intra-plant accumulation of TYLCV and satellites, (ii) the frequency of host cells co-infected with TYLCV and satellites, and (iii) the transmission efficiency of satellites by the natural whitefly vector of TYLCV, Bemisia tabaci. Three satellites previously isolated from okra in Burkina Faso, were shown here to be assisted by TYLCV in tomato plants: Cotton leaf curl Gezira betasatellite (CLCuGB), Cotton leaf curl Gezira alphasatellite (CLCuGA) and Okra leaf curl Burkina Faso alphasatellite (OLCBFA). The dynamic of TYLCV and satellite DNAs monitored between 11 and 150 days post-inoculation (dpi) by quantitative PCR revealed that satellites accumulated at a higher level than the virus, and that, in contrast with alphasatellites which have no impact, betasatellites affected TYLCV-Mld accumulation. Although the ratio of virus/satellite amounts varies over time, satellites were maintained in all test plants up to 150 dpi and were readily transmitted at 32 and 150 dpi. TYLCV-IL interacts differentially with CLCuGB as its accumulation was not affected in the coinfected plants.At 32 dpi, the TYLCV/satellite infection status of plant cells was determined by FISH and more than 50% of the monitored infected cells were co-infected with TYLCV and a satellite. The infection status was consistent with the frequency of satellite DNA in plants. Unexpectedly a substantial number of cells were positive only for betasatellite, suggesting that the coinfection with the virus could be dispensable for replication. This observation raises question on the functioning of virus/satellite association or multipartite viruses. As the multiplicity of infection (MOI) of begomoviruses and satellites is expected to be a determinant of the efficiency of virus/satellite cell coinfection, two equi-competitive TYLCV variants were prepared to determine this parameter for TYLCV. Finally, PCR primers designed for the generic detection of betasatellites were designed to be used as a diagnostic tool by the French Agency for Food, Environmental and Occupational Health & Safety (ANSES).Besides the agronomic concern of the possible maintenance of DNA satellites with TYLCV, the results of our study are expected to provide a new insight on the interactions between begomovirus and satellites, at the plant, cellular and molecular levels.

L’objectif était la caractérisation moléculaire de la vaginose bactérienne (VB) et l’identification d’une relation entre anomalies moléculaires de la flore vaginale et prématurité. Nous avons élaboré un outil de quantification par PCR spécifique en temps réel ciblant 8 microorganismes impliqués dans la VB. Seule la combinaison de la quantification d’Atopobium vaginae (108 copies/mL) à celle de Gardnerella vaginalis (109 copies/mL) présentait une sensibilité (95%) et une spécificité (99%) élevées pour le diagnostic de VB. La classification des flores selon la présence d’une VB, d’après les 2 méthodes de référence (critères d’Amsel et score de Nugent), et d’après notre outil moléculaire était concordante dans 94.5% des cas (kappa=0.81, intervalle de confiance [IC] 95%: 0.70-0.81). La discordance portait sur 9 flores intermédiaires (5.5%) dont les concentrations en G. vaginalis et en A. vaginae étaient élevées. De plus, nous avons démontré une étroite corrélation entre l’auto-prélèvement vaginal et le prélèvement réalisé par le médecin pour la quantification microbienne. Cette méthode alternative semble utile pour le suivi des anomalies de la flore vaginale. Nous avons enfin établi un lien entre la composition de la flore vaginale et le risque de prématurité parmi 90 patientes hospitalisées pour une menace d’accouchement prématuré (MAP). L’analyse par courbe de survie montrait un délai raccourci entre le diagnostic de MAP et le terme de l’accouchement en présence de concentrations élevées en A. vaginae ou en G. vaginalis (hasard ratio: 3.3; IC 95%: 1.1-9.5). Notre travail a contribué à améliorer l’analyse de la flore vaginale et à l’évaluation de son lien avec la prématurité. / The aim was the molecular characterization of bacterial vaginosis (BV) and the estimation of the relationship between molecular abnormalities and preterm delivery. A quantitative molecular tool targeting 8 bacterial vaginosis-related microorganisms was developed using specific real-time PCR. Only the combination of the quantification of Atopobium vaginae (108 copies/mL) and Gardnerella vaginalis (109 copies/ml) had an excellent sensitivity (95%) and specificity (99%) for the diagnosis of BV. The categorization of the vaginal flora according to the presence of BV based on the 2 reference methods (Amsel criteria and Nugent score), and our molecular tool was agree in 94.5% of the cases (kappa=0.81, 95% confidence interval [CI] 0.70-0.81). There was disagreement for 9 intermediate floras (5.5%) for which vaginal concentrations of A. vaginae and G. vaginalis were high. We also reported a good agreement for bacterial quantification in self-collected compared with practitioner-collected vaginal swabs. This method provides an alternative to practitioner-collected swabs especially for follow-up. We finally demonstrated a relationship between the high vaginal concentrations of A. vaginae and G. vaginalis and the risk of preterm delivery among 90 women with preterm labor. Survival curves analysis for preterm labor-to-delivery interval showed a significantly shorter interval for high vaginal concentrations of both A. vaginae or G. vaginalis (hazard ratio: 3.3; IC 95%: 1.1-9.5). Our work improved vaginal flora analysis and investigated the relationship with preterm delivery.

ABSTRACT The aim of this study is develop and test an inexpensive molecular tool kit to be used for diagnostic PCR for diseases such as Leber hereditary optic neuropathy (LHON) and Cystic fibrosis(CF). By developing and optimizing recombinant Taq polymerase and making a DNA size ladder from plasmids pPSU1 and pPSU2 the financial cost for the tool kit would be reduced significantly compared to the commercial components. With an inhouse method both the recombinant Taq polymerase and the pPSU1 and pPSU2 plasmids were purified from the E.coil strain DH5-α. Thereafter to analyse the components of the tool kit both conventional PCR and Real-time PCR to make sure that the tool kit would work for both types of PCRs.     The homemade Taq polymerase proved to be able to sustain in room temperature for at least 24 h and the polymerase also showed that it works with different primers such as LHON, CF and Beta-globin in both endpoint and probe base real-time PCR. The homemade size marker produced a reliable in agarose gel electrophoresis but requires optimization for continued usage for smaller PCR products.     In conclusion the homemade Taq polymerase will be used in future PCR analysis in the laboratory and the recombinant production process as well. Meanwhile the homemade size marker did not work sufficiency enough to be continuously used with gel electrophoresis in the laboratory without being further modified.

The thesis has optimized DNA isolation from pure yoghurt cultures and yoghurt products. The isolated DNA was than subjected to RT-PCR analysis. In the first part of the thesis, DNA isolation from pure yoghurt cultures using a commercial kit was evaluated as more effective than isolation by phenol extraction and magnetic microparticles. To assess the quality and quantity of DNA obtained the spectrophotometric determination of concentration and purity and qPCR were used. DNA of a total of ten pure yoghurt cultures in a quality suitable for PCR was obtained using the commercial kit. In the second part of the thesis, bacterial DNA was isolated from yoghurt products using the same commercial kit with a previous sample washing by lysation solution. DNA of six yoghurt products was isolated this way. Furthermore, two packages of homemade yoghurt were mad of each product, of which DNA was isolated in the same way. DNA obtained from yoghurts was subjected to RT-PCR using six pairs of primers (V3_F a V3_R, V6_F a V6_R, V1_F a V1_R, GroHRM_F a GroHRM_R, UPF a UPR, P1V1 a P2V1) and using the pure cultures DNA as a positive controls. The results confirmed the presence of cultures declared in each yoghurt and their ability to multiply after inoculation into a new medium (milk).

This Diploma thesis deals with probiotic bacterias for children nutrition. It proposes a probiotic food supplement with a probiotic blend composed of a strain of the genus Lactobacillus and of the genus Bifidobacterium, which would be most suitable for infant consumers. The theoretical part is focused on probiotics, constitution of the children´s ganstrointestinal tract and screening of probiotic and gelatine supplements which are already sold on the market. In the experimental part, probiotic bacteria were subjected to model digestion, whereby mixtures of strains having the lowest reduction in viability after digestion were blend based on the results. The blend of Bifidobacterium breve CCM 7825T, Bifidobacterium longum CCM 4990 and Lactobacillus casei CCM 4798 was chosen as the most suitable blend of the lowest viability reduction. PCR in real time was demonstrated the presence of all strains added to the blend after model digestion. Finally, from the data was suggested a more comprehensive probiotic food supplement in the form of an alginate-agar gummy-bear for children over three years of age. The probiotic food supplement was subjected to sensory analysis too. The proposed probiotic food supplement also contained Chlorella and Spirulina active compounds and higher content of omega 3 and 6 fatty acids in hemp oil.

Onemocnění z potravin (alimentární onemocnění) vyvolaná bakteriemi jsou stále aktuálním tématem v celosvětovém měřítku. Abychom zajistili výrobu zdravotně nezávadných potravin, je potřeba nových poznatků o virulenci patogenů, které by doplnily již známé skutečnosti o jejich růstu a přeživání v potravinách. Také potřebujeme vyvíjet rychlé a citlivé metody na detekci těchto patogenů. Dizertační práce popisuje metodu na detekci S. aureus v potravinách, která je založená na PCR v reálném čase ve spojení s namnožením v selektivním médium. Dále pojednává o vlivu environmentálních faktorů na růst S. aureus a tvorbu enterotoxinů v mléce a sýrech. Vyvinuli jsme rychlou a citlivou metodu na detekci S. aureus v potravinách s použitím selektivního namnožení a PCR v reálném čase. Nově vyvinutá metoda umožnila detekci S. aureus na druhý den od přijetí vzorku. Tato metoda může být použita jako rychlejší, citlivějsí a vysoce specifická alternativní metoda ke konvenční mikrobiologické metodě. Zkoumali jsme vliv tří různých teplot, 8°C, 12°C a 20°C na růst S. aureus a tvorbu enterotoxinu D v pasterizovaném mléce a na růst, expresi genu sed a tvorbu enterotoxinu D v tekutém médiu s extraktem z mozku a srdce (BHI). Experimenty byly prováděny v malých skleněných fermentorech po 6 dní. Genová exprese byla sledována pomocí qRT-PCR a tvorba enterotoxinu D byla měřena pomocí imunologické metody ELISA. Růstová křivka v BHI měla stejný průběh při 20°C a 12°C, ale v při 12°C začal růst se spožděním. Při 8°C nebyl pozorován žádný růst. Růst S. aureus v mléce byl ve srovnání s BHI menší. sed mRNA byla detekována při 20°C po 4 hodinách a při 12°C po 7 hodinách a produkce enterotoxinu se objevila v exponenciální fázi růstu. V mléce se produkce SED při 20°C a při 12°C objevila dříve, ale celkové množství vyprodukovaného SED bylo nižší než v BHI. Při 8°C nebyla pozorována žádná produkce SED stejně jako v BHI. Dále byl zkoumán společný vliv nízké teploty 12°C a přítomnosti kompetitivní doprovodné mikroflóry pocházející ze surového mléka na růst S. aureus a produkci enterotoxinu v pasterizovaném mléce. Byl pozorován inhibiční účinek na růst a produkci enterotoxinů a vliv kompetice byl výraznější než vliv nízké teploty. Produkce enterotoxinu byla nízká a odpovídala růstu. Snížením množství doprovodné mikroflóry a zvýšením inokula došlo pouze k nepatrnému zvýšení produkce enterotoxinu. V další fázi byly dva různé typy sýrů zaočkovány S. aureus za účelem simulace sekundární kontaminace při výrobě sýrů. Vzorky byly odebírány v průběhu 4 týdnů. Kritické faktory jako jsou kompetitivní mikrofóra nebo pH, které jsou zodpovědné za regulaci virulence S. aureus byly sledovány. Snažili jsem se rozlišit situace při kterých: (i) není pozorován růst, ale objevuje se produkce enterotoxinu a (ii) dochází k růstu ale bez produkce enterotoxinu.

Organometallic chemotherapeutic agents, many of which target DNA, have been shown to be effective in the treatment of cancer. With that said though, these compounds have a number of side affects such as nephrotoxicity. Two novel compounds, Ferrocene [ferrocenoyltrichloroacetone] and Rhodium-ferrocene [(1.5 cyclooctadiene)(1-ferrocenyl- 4,4,4-trichloro-1,3-butanedionate], synthesised by the research group of J Swarts (University of the Free State) were evaluated to determine their mechanism of action and their potential use as novel therapeutic agents. It is hypothesized, by merit of their chemical structures, that these compounds’ anti-cancer activity is due to their interaction with DNA. Both drugs were evaluated from a cellular to a molecular level, in vitro, to validate this hypothesis. Linearised DNA was exposed to both drugs and digested with a variety of restriction enzymes. It was found that the compounds bind to the PstI restriction site; thereby inhibiting the enzyme’s restriction activity. From this point it was necessary to show that the compounds are able to interact with DNA in a cellular system. By exposing a transformed breast epithelial cell line (MCF-12A) and a cancerous breast epithelial cell line (MCF-7) to the compounds, for various times, followed by flow cytometric analyses, it was found that both affect progression through the cell cycle. Cells accumulated at various phases of the cell cycle, as a result of checkpoint gene activation. Further flow cytometric analyses showed that both drugs induce necrosis in MCF-7 cells. The “normal” cell line however did not show this response as it is believed that cell cycle arrest and repair mechanisms were initiated, which would delay cell death. Gene expression analyses were performed by reverse transcriptase real-time PCR in which panels of cell cycle related genes as well as DNA damage associated genes were probed in two separate array formats. These studies revealed that a number of DNA damage and repair genes are activated; specifically those associated with excision repair and free-radical induced DNA damage. Members of the RAD family as well as the genes GADD45A, XPC and OGG1 were found to be upregulated as a result of Ferrocene treatment. This could be expected as it was shown that ferrocene binds to DNA, and it logically then follows that this would lead to excision repair being attempted by the cell. Similar gene expression patterns were found following Rhodium-ferrocene treatment with the up-regulation of genes such as OGG1, ATM and GADD45G, albeit to a lesser extent. It is hypothesised that the larger molecule may not interact as effectively with DNA, due to steric hinderance. Arrest mechanisms, for both drugs, were more pronounced in the “normal” cell line and it is believed that this is due to the fact that many of these genes have been inactivated in the cancerous cell line. We have shown, on multiple levels, that both compounds’ therapeutic action is as a result of their interaction with the cell’s DNA. This interaction leads to cell death in both the transformed and the cancerous cell line. In order to clarify these mechanisms it is suggested that proteomic and metabolomic studies should be performed. / Dissertation (MSc)--University of Pretoria, 2012. / Genetics / unrestricted

While the presence of ≥1% of an undeclared species in ground meat generally used as an indicator of intentional mislabeling as opposed to cross-contamination, the actual percent of undeclared species resulting from cross-contamination has not been experimentally determined. The objective of this study was to quantify the effect of sanitation procedures on the crosscontamination of animal species in ground meat products, using undeclared pork in ground beef. Pork (13.6 kg) was processed using a commercial grinder, then one of three sanitation treatments was completed (“no cleaning”, “partial cleaning”, or “complete cleaning”). Next, beef (13.6 kg) was ground using the same equipment. For “no cleaning,” beef was ground immediately after pork without any cleaning step; for “partial cleaning,” the hopper tray was wiped, and excess meat was taken out from the auger; for “complete cleaning,” all parts of the grinder were disassembled and thoroughly cleaned with water and soap. A 100-g sample was collected for each 0.91 kg (2 lb) of beef processed with the grinder and each sanitation treatment was tested twice. Real-time polymerase chain reaction (PCR) was used to quantify pork in ground beef. For “no cleaning,” the first 100-g sample of ground beef run through the grinder contained 24.42 ± 10.41% pork, while subsequent samples contained