Mycoplasmas conform most closely with the theoretical concept of 'minimum cells', existing as the smallest, free-living organisms capable of self-replication. They survive as parasites of plants, insects, animals or humans, with the most common human colonising species being Mycoplasma hominis. M. hominis has been characterised as a human pathogen responsible for a variety of infections, which pose a significant threat particularly to immunocompromised patients and neonates. However little has been elucidated about the cell physiology and molecular structure of this organism. Of interest to this study were the investigation of the heat shock response of M. hominis and the diagnostic assays used for its detection. The heat shock response is a ubiquitous physiological feature of all organisms and displays unprecedented conservation. This phenomenon is particularly evident in the 70 kDa family of heat shock proteins (hsp70) which exhibits a high degree of homology between different species. The hsp70 gene from M. hominis was cloned and preliminary partial sequencing indicated the similarity with other hsp70 homologs. The regulation of hsp70 expression at the transcriptional and translational levels was investigated. The level of hsp70 mRNA was found to increase correspondingly in response to heat shock, more visibly than the level of hsp70 protein. However imrnunochemical studies of the M. hominis hsp70 translation product demonstrated further the homology with other species. To facilitate rapid diagnosis of M. hominis infections, a PCR ELISA diagnostic assay was developed and optimised. The amplification of a conserved region of the M. hominis 16S rRNA gene was linked to subsequent hybridisation to an appropriate capture probe in a microtiter plate format. The sensitivity of the assay was comparable to other molecular assays although the PCR ELISA produces more rapid results and is less labour intensive. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 1998.

Integrin-linked kinase (ILK) is an important mechanoreceptor that mediates many cellular signaling pathways. Its dysregulation causes dilated cardiomyopathy and other complications in the heart. Restoration of ILK improves cardiac function and survival, but the exact mechanism is unknown. Recent studies in our lab suggest that the cardioprotective properties of ILK may be related to its regulation of sarco/endoplasmic reticulum calcium ATPase (SERCA2a). The protein expressions of ILK and SERCA2a are positively correlated based on adenoviral transduction of ILK and siRNA targeting ILK in human induced pluripotent stem cell-derived cardiomyocytes. From analysis of their calcium transients, ILK transduction resulted in increased beat rate and faster calcium clearance while siRNA knockdown produced the opposite effect. The use of SERCA-specific inhibitor thapsigargin nullified the observed effects of ILK transduction. Based on these results, we conclude that ILK’s cardioprotective properties are partly related to improving calcium handling in cardiomyocytes through the regulation of SERCA2a.

Integrin-linked kinase (ILK) is an important mechanoreceptor that mediates many cellular signaling pathways. Its dysregulation causes dilated cardiomyopathy and other complications in the heart. Restoration of ILK improves cardiac function and survival, but the exact mechanism is unknown. Recent studies in our lab suggest that the cardioprotective properties of ILK may be related to its regulation of sarco/endoplasmic reticulum calcium ATPase (SERCA2a). The protein expressions of ILK and SERCA2a are positively correlated based on adenoviral transduction of ILK and siRNA targeting ILK in human induced pluripotent stem cell-derived cardiomyocytes. From analysis of their calcium transients, ILK transduction resulted in increased beat rate and faster calcium clearance while siRNA knockdown produced the opposite effect. The use of SERCA-specific inhibitor thapsigargin nullified the observed effects of ILK transduction. Based on these results, we conclude that ILK’s cardioprotective properties are partly related to improving calcium handling in cardiomyocytes through the regulation of SERCA2a.

Several types of antibiotics (roxarsone, virginiamycin, and bacitracin) are widely included in poultry feed to improve animal growth yields. Most of the antibiotics are excreted in manure which is subsequently applied to soils. One concern with this practice is that antibiotics may affect several microbially-mediated nutrient cycling reactions in soils that influence crop productivity and water quality. The main objectives of this study were to determine the effects of livestock antibiotics on nitrification, denitrification, and microbial community composition in soils along a topographic gradient. These objectives were addressed in a series of lab experiments by monitoring changes in inorganic N species and ester-linked fatty acid methyl ester profiles after exposing soil microorganisms collected from different topographic positions to increasing levels of antibiotics. It was discovered that roxarsone and virginiamycin inhibited nitrification and soil microbial growth and also influenced microbial community composition, but only at levels that were much higher than expected in poultry litter-applied soils. Bacitracin did not affect nitrification, microbial growth, or microbial community composition at any concentration tested. None of the antibiotics had a strong affect on denitrification. Thus, it is unlikely that soil, water, or air quality would be significantly impacted by the antibiotics contained in poultry litter.

One approach to manage collections is to create data about the things in it. This descriptive data is called metadata, and this term is in this thesis used as a collective noun, i.e no plural form exists. A library is a typical example of an organization that uses metadata, to manage a collection of books. The metadata about a book describes certain attributes of it, for example who the author is. Metadata also provides possibilities for a person to judge if a book is interesting without having to deal with the book itself. The metadata of the things in a collection is a representation of the collection that is easier to deal with than the collection itself. Nowadays metadata is often managed in computer-based systems that enable search possibilities and sorting of search results according to different principles. Metadata can be created both by computers and humans. This thesis will deal with certain aspects of the human activity of creating metadata and includes an explorative study of this activity. The increased amount of public information that is produced is also required to be easily accessible and therefore the situation when metadata is a part of the Semantic Web has been considered an important part of this thesis. This situation is also referred to as the Web of Data or Linked Data. With the Web of Data, metadata records living in isolation from each other can now be linked together over the web. This will probably change what kind of metadata that is being created, but also how it is being created. This thesis describes the construction and use of a framework called Annotation Profiles, a set of artifacts developed to enable an adaptable metadata creation environment with respect to what metadata that can be created. The main artifact is the Annotation Profile Model (APM), a model that holds enough information for a software application to generate a customized metadata editor from it. An instance of this model is called an annotation profile, that can be seen as a configuration for metadata editors. Changes to what metadata can be edited in a metadata editor can be done without modifying the code of the application. Two code libraries that implement the APM have been developed and have been evaluated both internally within the research group where they were developed, but also externally via interviews with software developers that have used one of the code-libraries. Another artifact presented is a protocol for how RDF metadata can be remotely updated when metadata is edited through a metadata editor. It is also described how the APM opens up possibilities for end user development and this is one of the avenues of pursuit in future research related to the APM. / <p>QC 20141028</p>

No description available.

At the interface of quantum information and condensed matter physics, the study of entanglement in quantum many-body systems requires a new toolset which combines concepts from each. This thesis introduces a set of computational methods to study phases and phase transitions in lattice models of quantum systems, using the Renyi entropies as a means of quantifying entanglement. The scaling of entanglement entropy can give valuable insight into the phase of a condensed matter system. It can be used to detect exotic types of phases, to pinpoint transitions between phases, and can give us universal information about a system. The first approach in this thesis is a technique to measure entanglement in finite size lattice systems using zero-temperature quantum Monte Carlo simulations. The algorithm is developed, implemented, and used to explore anomalous entanglement scaling terms in the spin-1/2 Heisenberg antiferromagnet. In the second part of this thesis, a new and complementary numerical technique is introduced to study entanglement not just in finite size systems, but as we approach the thermodynamic limit. This “numerical linked-cluster expansion” is used to study two different systems at their quantum critical points — continuous phase transitions occurring at zero temperature, at which these systems exhibit universal properties. Remarkably, these universal properties can be reflected in the scaling of entanglement. Entanglement offers a new perspective on condensed matter systems, one which takes us closer to genuinely understanding what goes on in these materials at the quantum mechanical level. This thesis demonstrates the first steps in developing an extensive list of computational tools that can be used to study entanglement over a wide range of interacting quantum many-body systems. With the ever increasing computational power available, it may be only a matter of time before these tools are used to create a comprehensive framework for the characterization of condensed matter phases and phase transitions.

Increased reactive oxygen species (ROS) have been reported to be at the centre of various diseases. Although several reports have implicated elevated levels of ROS in the pathogenesis of diabetes mellitus, the early detection of ROS is still not attainable. This limitation causes difficulty in the early diagnosis of ROS related disorders. The presence of high levels of ROS was reported to result in differential expression of antioxidant genes involved in protecting cells from their deleterious effects. Among the antioxidant genes that are expressed, it was postulated that expression of metallothioneins (MTs) are also induced. MTs are low molecular weight, cysteine-rich proteins involved in metal homeostasis and reported to harbour antioxidant function. The aim of this investigation was to explore MTs as biomarkers for elevated levels of ROS in whole blood of type 2 diabetic (T2D) individuals. The level of ROS in diabetic, non-diabetic as well as individuals at risk of developing T2D was determined via the use of biochemical assays. Real-Time PCR was utilised to analyse the expression of MTs and the presence of MT proteins was analysed via the ELISA. In this study it was observed that diabetic individuals had elevated levels of ROS. However, no significant difference in the expression of MTs and the presence of MT proteins between the diabetic and non-diabetic individuals was observed. In vitro experimental conditions indicated that MT expression is induced by elevated levels of ROS. In pathological conditions the ROS-dependent induction of MT expression needs to be elucidated further. It therefore can be suggested that MTs can not yet be utilised as biomarkers for the detection of elevated levels of ROS in pathological conditions with ROS aetiology. This investigation also highlights the fact that blood is not an optimal medium in which this objective can be attained. / Thesis (Ph.D. (Biochemistry))--North-West University, Potchefstroom Campus, 2005.

This thesis is driven by the motivation to explore a way of working collaboratively that closely reflects the World Wide Web (WWW), more specifically the potential of the Web architecture built on Semantic Web technologies and Linked Data. The goal is to describe a generic approach and architecture that satisfies the needs for loose collaboration and collective knowledge construction as exemplified by the applications described in this thesis. This thesis focuses on a contribution-centric architecture which allows for flexible applications that support loose forms of collaboration. The first research question deals with how Web-based collective knowledge construction can be supported. The second research question explores the characteristics of collective knowledge construction with respect to the Open World Assumption (OWA). The OWA implies that complete knowledge about a subject cannot be assumed at any time, which is one of the most fundamental properties of the WWW. The third research question investigates how Semantic Web technologies be used in order to support such a contribution-centric architecture. The thesis and its underlying publications are of a technical character and are always grounded in theoretical models and considerations that have led to functional implementations. The research has evolved in iterative development processes and was explicitly directed at building applications that can be used in collaborative settings and that are based on standardized Web technologies. One of the main outcomes, an information model, was developed together with such an application and provides a number of novel approaches in the context in which it was designed. The validity of the presented research is supported by evaluations from different perspectives: a list of implemented applications and showcases, results from structured interviews that have investigated the suitability for various resource annotation processes, as well as scalability aspects. The thesis concludes that it is ultimately up to the application how "loose" the collaboration should be and to which extent the OWA is incorporated. The presented architecture provides a toolkit to support the development of loosely collaborative applications. The showcased applications allow the construction of collaborative conceptual models and to collaboratively annotate educational resources. They show the potential of the used technology stack and the introduced contribution-centric architecture that sits on top if it. / <p>QC 20140417</p>

Programmed cell death (apoptosis) is the most common mechanism of cell death in eukaryotes. The ability of cancer cells to evade and inhibit apoptosis has become a hallmark feature of cancer. This is accomplished through a family of proteins known as the inhibitor of apoptosis proteins (IAPs). X-Linked inhibitor of apoptosis protein (XIAP) is one of the best characterized IAPs. XIAP suppresses apoptosis by forming complexes with cysteine-aspartic proteases (caspase), through one of its baculovirus IAP repeat (BIR) domains. Its activity is endogenously antagonized by a second mitochondria derived activator of caspase (Smac). The anti-apoptotic behaviour of XIAP and the critical role it plays in the apoptotic program makes the Smac-XIAP interaction an important drug target. To this end, our laboratory is interested in synthesizing biologically related Smac mimetics which can induce apoptosis in a MDA-MB-231 cell line. Efforts have focused on (1) understanding BIR domain binding sites which allow for this interaction, and (2) the design and synthesis of molecules which are much more effective at inducing apoptosis compared to other well known analogues. Through the synthesis and evaluation of various divalent Smac mimetics we have been able to support the hypothesis that the likely binding site on XIAP is the BIR3 domain. As well, through the synthesis of a library of novel compounds, as described in the thesis, we have been able to assess the nature of the linker which joins the two tetrapeptide units. In our effort to understand which domains Smac binds with, various divalent analogues were synthesized containing MeAVPI-linker-IPVMeA (forward-reverse) and MeAVPI-linker-MeAVPI (forward-forward) sequence, which incorporated linkers with varying degrees of flexibility. We hypothesized that the forward-forward divalent mimetics would have decreased activity compared to the peptides synthesized in a forward-reverse fashion. Lastly, information gathered from structure activity relationship (SAR) studies have shown that substituting the lysine (P2) and isoleucine residues (P4) in the AVPI protein can create more potent inducers of apoptosis than its native AVPI sequence. As one of the most potent Smac mimetic that has been previously made known contains an alkyne bridge at P2 and a large hydrophobic moiety at P4, we hypothesized that similar Smac mimetics containing a propargyl glycine residue at P2 and a bulky hydrophobic moiety at P4 will be much more potent in inducing apoptosis.