DNA fingerprinting of Mycobacterium tuberculosis strain has been used in combination with conventional epidemiologic investigation, which has improved the understanding of tuberculosis transmission. Restriction Fragment Length Polymorphism (RFLP) based on IS6110 probe has become a standard method of fingerprinting of M tuberculosis. Since the technique is labour intensive and the discriminatory power of IS611 0 fingerprinting method for strains habouring only one to five copies is poor, other typing methods for typing M tuberculosis should be evaluated. In this regard, Amplified Fragment Length Polymorphism (AFLP) has the potential to overcome many of the RFLP problems. The first objective was to determine the suitability of the RFLP and AFLP techniques and to study the extent of transmission of tuberculosis in a referral hospital in South Africa. A total of 47 M tuberculosis isolates were differentiated using RFLP technique. The same samples were typed using the PCR- based AFLP technique and results were compared. The second objective was to determine the prevalence of isoniazid (INH) resistance and estimate the incidence of recent transmission of the disease in the Eastern-Cape (EC) and North-West province (NW) by using the best suited technique. RFLP grouped the 47 typed M. tuberculosis isolates into five families and four clusters. AFLP grouped the analyzed isolates (previously typed by RFLP) into two groups based on the banding patterns observed. As a result of the low degree of genotypic variation among the AFLP band pattern of M tuberculosis isolates, AFLP seemed less promising for individual strain differentiation of M tuberculosis. This technique can be used in future for differentiation of Mycobacterial species and The prevalence of INH resistance was found to be 6.7% in the EC and 8.4% in the NW province. The magnitude of recent transmission in the Eastern Cape studied by RFLP method, was found to be at 22% among the positive tuberculosis isolates identified. Transmission of TB in NW province was associated with reactivation rather than recent transmission due to lack of clustering of strains in that region. / Dissertation (MSc(Microbiology))--University of Pretoria, 2006. / Microbiology and Plant Pathology / unrestricted

Les accidents nucléaires des centrales de Tchernobyl et de Fukushima rendent primordial la compréhension des transferts de la contamination radioactive dans l'environnement et de ses conséquences écologiques. Bien que certaines études aient été réalisées sur les organismes supérieurs, trop peu ont étudié les communautés bactériennes telluriques, qui jouent pourtant un rôle essentiel dans la mobilité des contaminants dans les sols en diminuant ou en améliorant leur transfert vers d'autres compartiments (eau, végétaux, animaux). Cependant, les radionucléides (RNs) peuvent avoir des effets toxiques sur les bactéries, entrainant une inhibition de leur rôle dans ce transfert. Les objectifs de cette étude étaient (1) d'évaluer l'impact d’une contamination radioactive sur les communautés bactériennes d’un sol de la zone d’exclusion de Tchernobyl (sol de la tranchée n°22) et (2) d’étudier les interactions bactérie-uranium pour une souche résistante, isolée à partir de ce sol. / The nuclear power plants accidents of Chernobyl and Fukushima demonstrate the importance of the understanding of the transfers of the radioactive contamination in the environment and their ecological consequences. Although certain studies have been realized on superior organisms of the food chain, studies on telluric bacterial communities are scarce. The later play nevertheless an essential role in the mobility of contaminants in soils by decreasing or by improving their transfer towards other compartments (water, vegetables, and animals). Moreover, radionuclides (RNs) can have toxic effects on bacteria, leading to an inhibition of their participation in such transfer. The objectives of this study were (1) to estimate the impact of radioactive contamination on bacterial communities belonging to a soil of a Chernobyl exclusion zone (trench n°22) and (2) to study the uranium-bacteria interactions of a resistant strain, isolated from this soil.

On sait que les sols et les populations bactériennes indigènes ont une influence sur la mobilité des métaux, donc sur leur toxicité. Cette étude a été menée sur des sols uranifères et contrôles collectés dans le Limousin (régions naturellement riches en uranium ). une analyse physico-chimique et minéralogique des échantillons de sol a été réalisée. La structure des communautés bactériennes a été étudiée par électrophorèse en gradient de dénaturant (DGGE). La structure des communautés est remarquablement stable dans les sols uranifères, ce qui indique que l'uranium exerce une forte pression de sélection. D'autre part, une collection de bactéries cultivables à été réalisée à partir des sols, puis criblée pour la résistance à l'uranium, dans le but d'étudier les interactions entre bactéries et uranium. Des observations en Microscopie Électronique à Balayage ont mis en évidence différents mécanismes de chélation de l'uranium à la surface cellulaire / It is well known that soils play a key role in controlling the mobility of toxic metals and this property is greatly influenced by indigeous bacterial communities. This study has been conducted on radioactive and controls soils, collected in natural uraniferous areas (Limousin). A physico-chemical and mineralogical analysis of soils samples was carried out.The structure of bacterial communities was etimated by Denaturing Gradient Gel Electrophoresis (DGGE). The community structure is remarkably more stable in the uranium-rich soils than in the control ones, indicating that uranium exerts a high selection from the soils was constructed and screened for uranium resistance in order to study basteria-uranium interactions. Scanning electron microscopy revealed that a phylogenetically diverse set of uranium-resistant species ware able to chelate uranium at the cell surface.

No description available.

Thesis (M.Sc. (Microbiology)) -- University of Limpopo, 2019 / Schkuhria pinnata was selected for this study based on its use in traditional medicine. This study was aimed at isolating and charactserising antimycobacterial compounds from S. pinnata. Different extraction procedures coupled with solvents of varying polarities were used in extraction of the plant materials. Solvents of intermediate polarity had the highest mass of the extracts and serial exhaustive extraction was the best extraction procedure which extracted high amounts of plant material obtained with dichloromethane solvent. The chromatograms were developed in three solvent systems (BEA, CEF and EMW) and sprayed with vanillin-sulphuric acid reagent for colour development. Different colours on the chromatograms indicated various phytochemical constituents. Standard chemical tests confirmed the presence of tannins, flavonoids, alkaloids, phlabotannins, terpenes, steroids, cardiac glycosides and saponins. It was discovered that S. pinnata possesses high phenolic and tannin content which could be behind the antioxidant and anti-inflammatory activities observed. Antioxidant activity was analysed using 2, 2–diphenyl-1-picrylhydrazyl (DPPH) qualitative and quantitative experiments. Chromatograms were sprayed with 0.2% DPPH solution, yellow bands or spot against the purple background indicated the presence of antioxidant compounds. On quantitative analysis methanol extracts had a good scavenging activity at various concentrations. Ferric ion reducing power of antioxidants from plant extracts was determined using FRAP assay. S. pinnata extracts had high ferric reducing power which was in a concentration-dependent manner. Antimycobacterial activity was evaluated using Bioautography and broth microdilution assays. Plant extracts indicated antimycobacterial activity observed on bioautograms with low MIC values ranging from 0.27 mg/ml to 2.5 mg/ml. African green monkey Vero kidney cells were used to evaluate the toxicity of crude extracts. The plant extract had cytotoxic value of 25 µg/ml with a selectivity index of 0.02 SI. It was observed that S. pinnata had anti-inflammatory activity on LPS-induced Raw 246.7 macrophage cells in a concentration-dependent manner. Bioassay guided fractionation on column chromatography managed to isolate two compounds which were characterised using nuclear magnetic resonance techniques. The compounds were elucidated to be helaingolide and eucannabinolide sesquiterpene lactones. Biological assays indicated that the compounds were active against Mycobacterium smegmatis. The compounds were toxic to Vero monkey kidney cells with less than 30 µg/ml LC50 value and <1 selectivity index. These compounds had a good anti- inflammatory activity on LPS-induced Raw 246.7 macrophage cells which was in a concentration dependent manner. The compounds can be used as new leads in the development of anti-inflammatory and antimycobacterial drugs. The crude extracts and the isolated compounds from S. pinnata should be evaluated for their cytotoxicity and anti-inflammatory effects in in vivo experiments. / National Research Foundation (NRF)

>Magister Scientiae - MSc / As the global human population grows, so does the demand for faster food production rates. Owing to this, agricultural practices have had to expand and move into semi-arid and arid regions, too, where frequent irrigation is essential. However, irrigated ground water contains many salt ions (mainly Na+ and Cl-) which contribute to soil salinization on croplands. Soil salinity negatively impacts crop growth and yield and thus, strategies for the alleviation of salt stress on crop plants have had to be developed. This study assessed the use of plant growth promoting bacteria (PGPB). The aim of this study was to isolate, identify and characterize bacterial endophytes isolated from the halophyte, Arctotheca calendula. Endophytes were identified using 16S rDNA and were screened for plant growth promoting properties including nitrogen fixation, phosphate and zinc solubilization, siderophore, ammonia and indole-3-acetic acid (IAA) when exposed to 0 mM, 300 mM and 600 mM NaCl. The endophytes had been identified as Erwinia persicina NBRC 102418T, Bacillus marisflavi JCM 11544T, Ochrobactrum rhizosphaerae PR17T, Microbacterium gubbeenense DSM 15944T and Bacillus zhangzhouensis DW5-4T and all of which had demonstrated some plant growth promoting characteristics. Thereafter, we aimed to demonstrate plant growth promotion of P. vulgaris cv. Star 2000 inoculated with PGPB under salinity stress. P. vulgaris cv. Star 2000 seeds were inoculated with the PGPB and exposed to 0 mM and 100 mM NaCl. Post-harvest, plants were assessed for their dry mass, cell death, superoxide concentration and nutrient content. It was discovered that salinity negatively impacted P. vulgaris cv. Star 2000’s dry mass, NaCl-induced cell death, and differentially influenced superoxide concentration, nutrient uptake and content of the leaf and root material in the inoculated and control treatments. However, the isolated PGPB had been able to mitigate the negative effects of soil salinity on P. vulgaris cv. Star 2000.

Systems biology adopts an integrated approach to study and understand the function of biological systems, particularly, the response of such systems to perturbations, such as the inhibition of a reaction in a pathway, or the administration of a drug. The complexity and large scale of biological systems make modelling and simulation an essential and critical part of systems-level studies. Systems-level modelling of pathogenic organisms has the potential to significantly enhance drug discovery programmes. In this thesis, we show how systems--level models can positively impact anti-tubercular drug target identification. *Mycobacterium tuberculosis*, the principal aetiological agent of tuberculosis in humans, is estimated to cause two million deaths every year. The existing drugs, although of immense value in controlling the disease to some extent, have several shortcomings, the most important of them being the emergence of drug resistance rendering even the front-line drugs inactive. As drug discovery efforts are increasingly becoming rational, focussing at a molecular level, the identification of appropriate targets becomes a fundamental pre-requisite. We have constructed many system-level models, to identify drug targets for tuberculosis. We construct a constraint-based stoichiometric model of mycolic acid biosynthesis, and simulate it using flux balance analysis, to identify critical points in mycobacterial metabolism for targeting drugs. We then analyse protein--protein functional linkage networks to identify influential hubs, which can be targeted to disrupt bacterial metabolism. An important aspect of tuberculosis is the emergence of drug resistance. A network analysis of potential information pathways in the cell helps to identify important proteins as co-targets, targeting which could counter the emergence of resistance. We integrate analyses of metabolism, protein--protein interactions and protein structures to develop a generic drug target identification pipeline, for identifying most suitable drug targets. Finally, we model the interplay between the pathogen and the human immune system, using Boolean networks, to elucidate critical factors influencing the outcome of infection. The strategies described can be applied to understand various pathogens and can impact many drug discovery programmes.