Thesis (Ph. D.)--Oklahoma State University, 2006. / Vita. Includes bibliographical references (p. 90-100).

Thesis (M.S.)--Oklahoma State University, 2006. / Vita. Includes bibliographical references.

Thesis (M. S.)--Oklahoma State University, 2006. / Vita. Includes bibliographical references.

The aim of this project was to produce some principles that would assist software developers (SD's) in the design of software for South African general medical practitioners (GP's). The author wanted to give SD's a cognitive model of general medical practice in the hope that this will improve the relevancy of future medical software. This cognitive model is in the form of a set of principles that SD's can keep in mind when developing software for GP's. An evaluation was done of the attitudes and competence of GP's towards information technology. This was done via detailed telephonic interviews, which were analyzed in order to deduce these principles.

Thesis (MScMedSc (Biomedical Sciences. Human Biology and Human Genetics))--University of Stellenbosch, 2010. / Thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Medical Biochemistry at the Faculty of Health Sciences, University of Stellenbosch. / ENGLISH ABSTRACT: Mycobacterium tuberculosis is the causative agent of tuberculosis, a disease which causes approximately 2 million deaths each year. Despite extensive research on tuberculosis and M. tuberculosis, little is understood of the mechanisms of pathogenicity of the organism. The genome of M. tuberculosis contains five ESAT-6 gene cluster regions, each of which contains genes encoding proteins involved in the formation of a dedicated protein secretion system. Included in these regions are genes encoding exported T-cell antigens, serine proteases, ATP-binding proteins and other membrane-associated proteins. Although it is known that some of these secretion systems are involved in virulence and phagosomal escape of M. tuberculosis, and that deletion thereof causes attenuation of the organism, the structure, substrates and functions of the systems are largely unknown. Understanding the structure of the ESX secretion systems will advance our understanding of the mechanisms of mycobacterial pathogenicity and provide clues to ways in which to interfere with these virulence mechanisms. The ESAT-6 gene cluster region 3, encoding the ESX-3 secretion machinery, is the only ESAT-6 gene cluster region which is essential for the in vitro growth of M. tuberculosis. It is however not required for the growth of the saprophytic mycobacterium M. smegmatis. In this study we have identified proteinprotein interactions within the ESX-3 secretion system, using the Mycobacterial – Protein Fragment Complementation (M-PFC) mycobacterial two-hybrid system, and created a model of the M. tuberculosis ESX-3 secretion system. According to this model, the EsxG-EsxH and PE5-PPE4 substrate protein complexes bind to the same components of the ESX-3 secretion machinery and are secreted via the same mechanism. A knock-out of the ESX-3 secretion system in M. smegmatis was generated by homologous recombination to allow further research into the functions and properties of this secretion system. This knock-out was used, together with wild-type M. smegmatis, to investigate the secretion of the M. tuberculosis EsxH protein by the M. smegmatis ESX-3 secretion system. The ESX-3 secretion system interactome may serve as a model for the ESX secretion systems and assist in our understanding of this secretion machinery which is key to the virulence and survival of M. tuberculosis and other pathogenic mycobacteria. Improved understanding of these mechanisms and their role in pathogenicity and survival may provide means of interfering with the secretion machinery, potentially leading to developments in the prevention and treatment of tuberculosis disease. / AFRIKAANSE OPSOMMING: Tuberkulose, wat veroorsaak word deur Mycobacterium tuberculosis, eis jaarliks ongeveer 2 miljoen lewens. Ten spyte van uitgebreide navorsing oor tuberkulose en M. tuberculosis is min bekend oor die meganismes van patogenisiteit van díe organisme. Die genoom van M. tuberculosis bevat vyf ESAT-6 geen groep gebiede wat elk proteïene kodeer wat ‘n toegewyde sekresie sisteem vorm. Ingesluit in elk van díe geen groep gebiede is gene wat T-sel antigene, serien proteases, ATP-bindingsproteïene en ander membraan-geassosieërde proteïene kodeer. Alhoewel dit bekend is dat sekere van hierdie sekresie sisteme betrokke is by virulensie en fagosoom-ontsnapping, en dat delesie daarvan die organisme attenueer, is die struktuur, substrate en funksies van die sisteme grootliks onbekend. Kennis van die struktuur van die ESX sekresie sisteme sal ons verstaan van die meganismes van mikobakteriele patogenisiteit verbeter en leidrade verskaf na maniere om in te meng by díe meganismes van virulensie. Die ESAT-6 geen groep gebied 3, wat die ESX-3 sekresie sisteem kodeer, is die enigste ESAT-6 geen groep gebied wat noodsaaklik is vir die in vitro groei van M. tuberculosis. Dit is egter nie nodig vir die groei van die saprofitiese mikobakterium M. smegmatis nie. In hierdie studie het ons proteïenproteïen interaksies van die ESX-3 sekresie sisteem geïdentifiseer, deur middel van die Mikobakteriële - Proteïen Fragment Komplementasie (M-PFC) mikobacteriële twee-hibriede stelsel. Die interaksies is gebruik om ‘n model van die M. tuberculosis ESX-3 sekresie sisteem te skep. Volgens díe model bind die EsxG-EsxH en PE5-PPE4 substraat proteïen komplekse aan dieselfde komponente van die ESX-3 sekresie apparaat en word deur dieselfde meganisme uitgevoer. ‘n uitklopmutant van die ESX-3 sekresie sisteem word deur homoloë rekombinasie in M. smegmatis gegenereer om verdere ondersoeke na die funksies en eienskappe van hierdie sekresie sisteem in staat te stel. Hierdie uitklopmutant is tesame met die wilde-tipe M. smegmatis gebruik om die sekresie van die M. tuberculosis EsxH proteïen deur die M. smegmatis ESX-3 sekresie sisteem te ondersoek. Die ESX-3 sekresie sisteem interaktoom kan dien as ‘n model vir die ESX sekresie sisteme om te help om ons kennis van hierdie sekresie apparaat, wat belangrik is vir die virulensie en oorlewing van M. tuberculosis en ander patogeniese mikobakterieë, te verbeter. Kennis van hierdie meganismes en hul rol in patogenisiteit en oorlewing mag maniere verskaf om by díe sekresie sisteme in te meng, wat moontlik kan lei tot ontwikkelings in die voorkoming en behandeling van tuberkulose.

Epstein-Barr virus (EBV) is a gammaherpes virus that infects >90% of the adult population worldwide. During childhood infection is generally sub-clinical, however if delayed until adolescence infectious mononucleosis (IM) may develop. The virus has also been aetiologically linked with a number of tumours including B-cell lymphoma following organ transplantation: post-transplant lymphoproliferative disease (PTLD). The symptoms of IM are caused by an expansion of immune cells in response to infection whilst in the transplant situation immunosuppressive drug therapy allows the outgrowth of the tumour. Understanding the immuno-regulatory mechanisms involved in such EBV-associated diseases is crucial for devising new treatment strategies. We undertook 3 separate studies (1-3) investigating different aspects of the immune response to EBV. In a recently reported phase II trial using allogenic, EBV-specific cytotoxic T-cell (CTL) to treat PTLD, tumour response was significantly increased with a high degree of donor/recipient HLA-allele matching suggesting that further refinement of the matching procedure may be important. In study 1 we investigated the epitope specificity and T-cell receptor (TCR) clonality of the infused CTL to identify potential areas for refinement. We found the protein specificity of the CTL to be polyclonal with dominant recognition of Epstein-Barr nuclear antigen-3 proteins and sub-dominant recognition of Latent membrane protein (LMP)-1 and LMP-2 proteins. Where possible, specificity was confirmed at the peptide level. No single TCR family was preferentially used by CTLs. The CTL epitope specificity did not differ between treatment responders and non-responders however the response was improved in those with several CTL HLA-restricted epitope matches and those infused with CTL containing polyclonal TCR families as opposed to monoclonal. CTL/recipient matching based on HLA matching alone was improved when also matched via HLA- restricted epitiope specificity. Therefore mapping CTL peptide epitope specificity prior to CTL infusions may enhance patient responses. In recent years, interest has developed in genetic variation within components of the immune system. Of particular interest are cytokine/cytokine receptor genes and genes of the human leukocyte antigen (HLA), both of which act to regulate the immune response. Variation within these genes could potentially alter the immune response leading to disease. In study 2 we investigated single nucleotide polymorphisms (SNPs) in several cytokine genes (TNF, IL-1, -6, -10) in both IM and PTLD cases and compared with relevant control groups. We found that the frequency of two TNF promoter alleles was significantly increased in PTLD patients compared to controls whilst the frequency of a TNF receptor II allele was increased in IM and EBV seropositive individuals, suggesting a role for this allele in susceptibility to EBV infection. The frequency of a second TNF receptor II allele was increased in both PTLD and IM subjects compared to controls highlighting the possible significance of TNF and its receptor in the development of EBV associated disease. In study 3 we analyzed two microsatellite markers and two SNPs located near the HLA class I locus in IM, PTLD and control subjects to further determine whether the HLA genes may affect development of EBV-associated diseases. Alleles of both microsatellite markers were significantly associated with development of IM. Specific alleles of the two SNPs were also more frequent in IM patients. Moreover IM cases possessing the associated microsatellite allele had significantly fewer lymphocytes, increased neutrophils, and displayed higher EBV titres and milder IM symptoms relative to IM cases lacking the allele. The results indicate that HLA class I polymorphisms may predispose patients to development of IM upon primary EBV infection and suggest that genetic variation in T cell responses can influence the course of EBV infection.

Philosophiae Doctor - PhD / This thesis was informed by what I perceived to be a tense relationship between Western biomedical science and, for example, “traditional” or “indigenous” ways of producing knowledge about medicinal plants used to manage a pervasive condition like Tuberculosis (TB) in South Africa. Hoping to reimagine this relationship and its possibilities, I follow medicinal plants collected from Genadendal through three research spaces with disparate but intertwined knowledge heritages to investigate these tensions but also to tease out how knowledge about locally used medicinal plants is generated and “done” in practice. The first space was at the South African Herbal Science and Medicines Institute (SAHMI) as part of an experiential science project led by scientists who were interested in studying medicinal plants which could potentially provide new sources of safe, affordable, and sustainable medicine for communicable conditions such as TB.

Modern intelligent monitoring systems use digital computer technology to analyze and evaluate physiological vital signs. This analytical and evaluative process is performed by algorithms developed for this purpose. The degree of 'intelligence' of the monitoring system is dependent on the 'sensitivity' and 'specificity' of these algorithms. In order to develop robust and clinically valid algorithms, a database of representative waveforms is required. The aim of this thesis was to create a neonatal vital signs database to be used for this purpose, by means of a computer-based central station. The computer was interfaced to a number of neonatal monitors (Neonatal ICU, Groote Schuur Hospital). The monitors were interrogated to obtain patient condition, ECG waveforms and respiration waveforms using the impedance technique. When possible, percentage oxygen saturation was also captured. The database contains 509 documented clinical records obtained from 35 patients and 20 records containing examples of technical alarm conditions and high frequency noise. Additional patient record data is included. Clinical events recorded include apnoea, bradycardia, periodic breathing tachycardia, tachypnoea and normal traces. These events were recorded against a variety of signal quality conditions that have been characterized in Appendix C. A prototype rate detection algorithm was checked using samples from the database.

Parkinson’s disease is associated with reduced coordination between respiration and locomotion. For the neurological rehabilitation research, it requires a long-time monitoring system, which enables the online analysis of the patient’s vegetative locomotor coordination. In this work a real time step detector using three-dimensional accelerometer signal for the patients with Parkinson‘s disease is developed. This step detector is a complement for a recently developed system included of intelligent, wirelessly communicating sensors. The system helps to focus on the scientific questions whether this coordination may serve as a measure for the rehabilitation progress of PD patients. / +46-762453110 +46-462886970

The recent rise of multidrug resistant microorganisms has grown from an isolated concern to a massive public health crisis. It has become imperative that scientists look for new ways to combat this issue. Due to the selective pressures of competition, bacteria and other microbes possess a host of defenses and weapons designed to exploit vulnerabilities in other microorganisms. Consequently, the study of these systems and microbial interactions has much to reveal in the search for novel antimicrobial treatments. Previous research from our laboratory has discovered that both Alcaligenes faecalis and Alcaligenes viscolactis, two rarely studied and generally non-virulent bacteria, exert a microbicidal effect on Candida albicans and Staphylococcus aureus, two pathogenic and frequently drug-resistant organisms. In this study, we confirmed that these effects are via a live-cell, contact-dependent mechanism and showed that both Alcaligenes species inhibit S. aureus at the attachment phase of biofilm growth. Additionally, we found that A. faecalis and A. viscolactis target Gram-positive bacteria outside the genus Staphylococcus and certain Gram-negative species as well as Candida glabrata. This study also provides novel evidence of a putative Type VI Secretion System in both Alcaligenes species, which may explain their antimicrobial phenotype. Despite efforts to identify the genetic elements involved via mutagenesis, the mechanism of these interactions remain elusive due to the difficulty of gene transfer in these organisms. We hope these results will increase current knowledge of Alcaligenes’ capabilities and genetic composition as well as establish the groundwork for future efforts to discover its inhibitory system and mechanisms.