Bacterial infections remain a significant threat to human health. Due to the emergence of widespread antibiotic resistance, development of novel antibiotics is required in order to ensure that effective treatment remains available. The aim of this study was to isolate and identify the fraction responsible for the antimicrobial activity in Tabernaemontana elegans (Stapf.) root extracts. The active fraction was characterised by thin layer chromatography (TLC) and gas chromatography – mass spectrometry (GC-MS). Antibacterial activity was determined using the broth micro-dilution assay and antimycobacterial activity using the BACTEC radiometric assay. Cytotoxicity of the crude extract and fractions was assessed against primary cell cultures; lymphocytes and fibroblasts; as well as a hepatocarcinoma (HepG2) and macrophage (THP-1) cell line using the Neutral Red uptake and MTT assays. The crude root extracts were found to contain a high concentration of alkaloids (1.2% w/w). GC-MS analysis identified the indole alkaloids, voacangine and dregamine, as major components. Antibacterial activity was limited to the Gram-positive bacteria and Mycobacterium species, with MIC values in the range of 64 – 256 ìg/ml. When combined with antibiotics, additive antibacterial effects were observed. Marked cytotoxicity to all cell lines tested was evident in the MTT and Neutral Red uptake assays, with IC50 values ranging between 1.11 – 9.81 ìg/ml. This study confirms the antibacterial activity of T. elegans and supports its potential for being investigated further for the development of a novel antibacterial compound. / Dissertation (MSc)--University of Pretoria, 2011. / Pharmacology / unrestricted

Tuberculosis (TB) remains one of the major public health problems in South Africa. The overall aim of the research project was to evaluate the completeness of TB notification data. A descriptive study design was used. The TB data from the Disease Notification System for the period 1993 to 2003 were analysed to describe 11 year trends by province, sex and population group. The levels of under-reporting of tuberculosis were estimated by comparing the annual numbers and the rates of notified cases and deaths per 100 000 population with the data of registered cases in the electronic TB register and registered TB deaths from the Statistics South Africa’s metadata on causes of deaths in South Africa. A total of 768896 cases and 39052 deaths were recorded in the Disease Notification System for the period 1993 to 2003. The annual case load declined from 42099 cases in 1993 to 36081 in 1996, then peaked to 89111 in 1998. The peak in 1998 resulted mainly from two-fold increases in notified cases in the provinces of Eastern Cape, KwaZulu-Natal and Western Cape. There was also a three-fold increase in Western Cape in 2001 and four-fold increase in Northern Cape in 2002. The lowest numbers of notified cases were for Mpumalanga in the years 1993 to 1996. In Limpopo, a total of 13 cases only were notified between the years 1999 to 2003 inclusively. Nationally and provincially, the annual numbers of notified cases and deaths and rates per 100 000 population were consistently higher among males than females. The Wilcoxon signed rank test comparing the medians between male and female cases showed a p-value of 0.003 indicating that the difference exists between the two medians. Nationally the lowest number of deaths was 1967 notified deaths in 1994 and the highest number of deaths was 6085 notified in 2002. The number of deaths notified varied between the provinces and fluctuated between the years. It was the highest for the years 1993 to 1996 in Western Cape and the highest for the years 1997 to 2003 in Eastern Cape. It was the lowest in Mpumalanga for the years 1993 to 1997 and the lowest in Limpopo for the years 1999 to 2003 and KwaZulu-Natal in the years 2002 to 2003. The Disease Notification System was found to have lesser numbers of notified cases in comparison to registered cases recorded in the TBSYS or electronic TB register. The percent difference between notified and registered cases ranged between 28% in 2001 to 69% in 1996. Comparison of notified and registered TB deaths for the period 1997-2003 showed that the annual numbers and rates of registered deaths in the Statistics South Africa’s metadata were higher for all the years than the notified deaths in the disease surveillance system. It is recommended that the disease surveillance system is evaluated periodically, facility data assessment tools are introduced and capacity for surveillance is strengthened at all levels of the national health systems. Copyright / Dissertation (MSc)--University of Pretoria, 2009. / School of Health Systems and Public Health (SHSPH) / Unrestricted

This dissertation focuses on the modelling, identification and the parameter estimation for the co-infection of HIV-1 and M. tuberculosis. Many research papers in this field focus primarily on HIV, but multiple infections are explored here, as it is common in many individuals infected by HIV. Tuberculosis is also responsible for the highest number of casualties per year in the group of HIV-infected individuals. A model is proposed to indicate the populations of both pathogen as well as key information factors, such as the overall infected cell population and antigen-presenting cells. Simulations are made to indicate the growth and decline in cell-type numbers for a specific individual. Such simulations would provide a means for further, well-founded investigation into appropriate treatment strategies. One previous such model developed by Kirschner is used to obtain a nominal parameter set. Furthermore, the nominal set is then used in conjunction with real-world samples provided by the National Institute for Communicable Diseases in South Africa, to solidify the credibility of the model in the practical case. This is achieved via simulations and employs parameter estimation techniques, namely the Nelder-Mead cost-function method. An identifiability study of the model is also done. Conclusions drawn from this study include the result that the treatment of M. tuberculosis does not affect the course of HIV-1 progression in a notable way, and that the model can indeed be used in the process of better understanding the disease profile over time of infected individuals. / Dissertation (MEng)--University of Pretoria, 2008. / Electrical, Electronic and Computer Engineering / MEng / unrestricted

Ingeniero Civil / En el presente trabajo se compara la respuesta experimental de muros rectangulares de diferentes configuraciones de hormigón armado (H.A.), con modelos de elementos finitos generados con elementos cuadriláteros con capa tipo membrana. Se utiliza la plataforma SAFE-TB, de F. Rojas [11], desarrollada en Matlab, la cual realiza un análisis numérico no lineal de elementos finitos ante cargas verticales estáticas y ante cargas laterales por medio del método pushover cíclico, con el fin de validar la plataforma y verificar las leyes constitutivas de los materiales asumidas. Cada uno de los muros modelados representan muros experimentales ensayados por otros investigadores, los cuales serán usados como validación de los resultados, replicando sus condiciones de ensayo, cargas dispuestas y ciclos de desplazamiento utilizados. Para el análisis de los resultados, se comparan las respuestas experimentales con los mo- delos, utilizando envolventes en ambos casos y comparando la rigidez. Los desplazamientos producto del corte y flexión se estudia de igual forma que en las investigaciones de los muros ensayados. Se valida la capacidad de la plataforma de modelar muros de H.A., prediciendo correcta- mente su comportamiento ante desplazamientos impuestos, con distribuciones de esfuerzos y deformaciones, rigidez durante los ciclos por medio de una envolvente, además de lograr analizar los desplazamientos por flexión y corte por separado.

Thesis (MSc. (Medical Sciences)) -- University of Limpopo, 2015 / Introduction: Multidrug-resistant tuberculosis (MDR-TB) caused by resistance to at least rifampicin (RIF) and isoniazid (INH) drugs is a growing public health concern in South Africa. The detection of MDR-TB still relies on culture despite advancement in molecular diagnostic technology. Currently MTBDRplus and GeneXpert are the only available assays used in rapid diagnosis of MDR-TB using chromosomal mutations in drug target regions. Some strains are missed by these assays due to their limitation in mutational detection profile. Novel Seegene Anyplex assays simultaneously detect TB and resistance to RIF and INH using fifteen and six mutational probes, respectively within 3 hours. Limpopo Province has limited information on the circulating strains of TB. Aim: To determine drug-resistant Mycobacterium tuberculosis (M. tuberculosis) mutations using Anyplex™ MTB/NTM/MDR-TB real time assay and characterise the drug-resistant strains. Methods: We prospectively collected 204 clinical samples at Modimolle MDR-TB unit and retrospectively used 104 culture isolates from MRC laboratory in Pretoria. The MTBDRplus assay was used to screen for M. tuberculosis and drug resistant mutations to RIF and INH drugs. Anyplex™ MTB/NTM/MDR-TB assay was used for rapid detection of M. tuberculosis and drug resistance to RIF and INH within 3 hours. The discordance between phenotypic and genotypic assays was resolved by sequencing and the Anyplex™ resistant profiles were spoligotyped. Diagnostic data was collected from NHLS and MRC databases and analysed using the Microsoft excel and Epi Info version 3.5. Descriptive statistics (percentages and frequencies) were used to explain proportions. Results: The Anyplex™ MTB/NTM assay detected M. tuberculosis in 69/111(62%) and 100/104 (96%) of clinical and culture samples respectively. The sensitivities, specificity, PPV and NPV obtained for both RIF and INH resistance by Anyplex™ MDR-TB assay were 67%, 59%, 67%, 55% and 15%, 100%, 100% and 17%, respectively. Anyplex™ MTB/NTM/MDR-TB resolved 23/45 (51%) of discordant vi samples. Sequencing of remaining discordant isolates revealed L511P, L533P and D516Y mutations within rpoB gene. A novel R385W mutation within katG was also detected. Spoligotyping of Anyplex™ MDR-TB resistant clinical isolates revealed Euro American clade with 20% followed by 15% Manu2, 5% East African Indian, 5% H37Rv, 5% atypical and 50% were orphans. Conclusion: The novel Anyplex™ MTB/NTM/MDR-TB assay is a rapid and valid technique for detecting M. tuberculosis and most common mutations conferring resistance to RIF and INH. However further investigations are required, as the assay has a lower sensitivity as compared to already endorsed techniques. / National Research Foundation (NRF) and University of Limpopo TB Grant

Magister Scientiae (Medical Bioscience) - MSc(MBS) / The aim of this study was to determine and evaluate the prevalence of TB infection, active TB cases and the risk factors associated with TB infection in Macassar Camp in Macassar (about 40 km from Cape Town on the False Bay coast, with a population of 369). The study design of this epidemiological study was a cross sectional study with a descriptive and an analytic component A comparison between the Mantoux, TB ELISA and X-ray screening tests was performed first. A description of the origin, discovery, characteristics and pathology associated with Mycobacterium tuberculosis as well as the development of the TB epidemic on a global, national and local level, is given. TB was first described to give a South African perspective of the TB epidemic and both the "Virgin Soil" and "Non-Virgin Soil" theory of TB was reviewed. Secondly, ~he TB infection rate in Macassar Camp and the risk factors as well as the determinants of TB infection with regards to overcrowding, ventilation, primary food subsistence level rating (PFSL), social class and employment status were evaluated The third aspect of the study compares prevalence/incidence rates of TB to clinical diagnosis with regards to the symptomatology, radiographs, sputum microscopy, bacteriology and Mantoux test. Lastly the Mantoux test was compared with the TB ELISA test with regards to diagnosis of infection, in new and past confirmed TB cases. The first part of the survey involved the measurement of openable window area and the floor area of each Camp dwelling (to determine if ventilation was within required limits), during the administration of a household questionnaire which was designed to determine the number of occupants, rooms, income, food expenditure per household in the Camp. A personal questionnaire was administered to all Macassar Camp residents to elicit information on demography, knowledge and attitudes to TB, history of past TB, TB contacts, alcohol intake and smoking habits, occupation and BCG status. The Mantoux test were performed on consenting Camp residents in addition to the collection of 5 ml of blood for the TB ELISA tests. The Camp residents heights and weights were recorded prior to the miniature mass chest radiographs being taken. The 'TB suspects' sputa were collected for the microscopy and bacteriological examination. A review of the clinical records of TB patients in the Macassar/Stellenbosch area was also undertaken. The response rate to the household questionnaire was 60 from 63 (95,2%) dwelling units. Whereas the response rate to the personal questionnaire was 296 (80,2%). As for the Mantoux and TB ELISA tests the response rate was 209 (56,6%). Of the 60 dwelling units, 43 (71,7%) were calculated (according to . Batsons Index) to be crowded and 16 (26,7%) dwelling units had an overall ventilation of less than 5% (below the required regulation). There were significantly (p<0,005) more male than female smokers and only 78 (34,2%) of the residents regarded themselves as non-smokers. A similar trend was noted with regards to the alcohol intake of the residents, where only 86 (37,7%) regarded themselves as teetotallers, with significantly more (p=0,003) male than female alcohol consumers. Females sc6red significantly (p=0,002) better than the males with regards to TB knowledge and awareness. Only 199 (67,2%), residents indicated that they had had BeG vaccination. Of the 296 residents responding to the survey, there were 83 children aged 14 years or less. And only 74 of these children were confirmed to have been vaccinated with BeG, resulting in a 89,2% BeG coverage. Two (4,7%) of the 43 children aged 14 years or less were determined to be malnourished on the basis of Z-scores (below -2SD) taking into account height for age as well as weight for height.

Tuberculosis (TB) is primarily a pulmonary disease caused by Mycobacterium tuberculosis (Mtb). Mtb is highly infectious, but studies have shown that only 5–15% of Mtb-infected individuals develop TB disease. The Bacille Calmette-Gu.rin (BCG) vaccine is the only commercially available Mtb vaccine, but its efficacy varies based on the strain used. The Mtb PhoPR-mutant variant, MTBVAC, has been tested as a possible attenuated live vaccine against Mtb. Although it has successfully conferred durable CD4+ T-cell responses in infants, it has also resulted in adverse effects. Our goal is to identify PhoPR-regulated gene(s) that mediate Mtb-induced burst size necrosis in infected cells. PhoPR is a two-component system in mycobacteria. PhoR responds to environmental cues, such as changes in pH, and phosphorylates the PhoP transcription factor, which then activates or suppresses the expression of approximately 40 Mtb genes. The Mtb PhoPR-mutant strain is able to replicate in infected macrophages, but it does not induce the horizontal spread of Mtb to other immune cells. Our lab has previously shown that virulent, cytopathic strains of Mtb, such as H37Rv, suppress early apoptosis, have faster replication rates in macrophages, and trigger cell death at a lethal load threshold of approximately 25 bacteria. Cell death of infected macrophages primarily occurs via necrosis, which involves nuclear pyknosis without DNA fragmentation and general disruption of lipid bilayer membranes. Viable bacilli are released to infect other macrophages and neutrophils recruited to the developing TB lesion. Here, we show that PhoP contributes to burst size necrosis in macrophages and that the PhoP-regulated genes, fadD21 and pks3, are potential drivers of this necrosis. FadD21 and pks3 are involved in the generation of diacyl trehalose/penta-acyl trehalose (DAT/PAT) for cell wall synthesis, suggesting that Mtb cell wall composition may determine virulence. Therefore, we have uncovered potential targets for early intervention or vaccinations to avoid granuloma formation or tissue damage in response to Mtb-induced macrophage necrosis.

Introduction: Tuberculosis (TB) pericarditis is a relatively rare form of tuberculosis which has been on the decline. However, the advent of the human immunodeficiency virus (HIV) pandemic has brought about the resurgence of tuberculosis pericarditis and an even poorer prognosis for patients with HIV co-infection. Objectives: The aim is to describe the baseline characteristics of tuberculous pericarditis patients and to assess the impact of HIV on the clinical presentation of this disease. Methods: The study describes baseline data from a randomised clinical trial which explored the use of adjunctive corticosteroids in management of TB pericarditis then went on to compare HIV co-infected patients versus those without HIV co-infection using logistic regression. Results: There were 1394 patients enrolled into the study, 64% were HIV positive, 19% were HIV negative and 17% had an unknown HIV status. Forty four percent of the participants were female and age had a positively skewed distribution with median 36 years (IQR: of 29-46). HIV co-infected patients were younger with OR 0.97(95% CI: 0.96-0.98), more likely to have previously had TB with OR 2.15(95% CI: 1.25-3.72), had a more acute illness with OR 0.99(95% CI: 0.99-1.00), had lower hemoglobin with OR 0.72(95% CI: 0.67-0.78), lower White Cell Count, (WCC) with OR 0.90(95% CI: 0.86-0.96) and higher globulin with OR 1.07(95% CI: 1.05-1.09). Conclusion: HIV co-infected participants are younger, more likely to have been previously diagnosed with TB, have a more acute illness, lower haemoglobin, lower WCC and higher globulin. / Dissertation (MSc)--University of Pretoria, 2013. / School of Health Systems and Public Health (SHSPH) / unrestricted

MCur / Department of Advanced Nursing Science

In this work we studied properties of garnet scintillator layers (RxLu3-xAl5O12, RxY3-xAl5O12) doped by rare earth ions (Ce, Pr, Tb), orthosilicates (Y2SiO5; R = Ce, Tb) and influence of Sc codoping on Pr3+ and Tb3+ emissions. The Zr codoping on Ce3+ emission in orthosilicates was also studied. The samples were prepared by liquid phase epitaxy. The studied materials show high quantum efficiency and good chemical and mechanical stability. They represent ideal materials for 2D imaging devices. We studied optical absorption, excitation and emission spectra and scintillation properties (radiolunescence and photoelectron yield). The aim was to determine the properties of grown layers and their comparison to Czochralski grown single crystals. We looked for the impact of melt and growth conditions on measured layer properties. We also tried to determine optimal amount of dopants in layer. We used PbO - B2O3 and BaO - BaF2 - B2O3 fluxes. Using these fluxes, we succeeded in growing layers with less intrinsic defects in crystal lattice in comparison to single crystals. In grown layers of thickness from 1 to 30 µm higher dopant concentration was achieved than in single crystals.