Attempts to produce an effective vaccine against group B meningococcal disease have been unsuccessful due to poor immunogenicity of the capsular polysaccharide, and high variability in the currently identified outer membrane proteins. There is therefore a need to find other vaccine candidates. It is clear from studies of bacteria such as Salmonella typhimurium, that successful pathogens have the ability to specifically express genes in response to an in vivo environment. Many of these in vivo-expressed gene products will contribute to virulence of the organism and may therefore be target antigens for development of new vaccines. An in vivo promoter-probe strategy was developed using the Cre/lox recombination system to identify meningococcal promoters that are specifically expressed in vivo. The strategy employs the cre gene, which encodes a site-specific recombinase that targets two 34-base pair directly repeated lox sites. A vector, pUS1604, was constructed which contains two lox sites flanking a transcriptional terminator that separates the aph (encoding kanamycin resistance) coding sequence from its promoter. A promoterless ere gene was placed on a low copy number vector to limit the number of Cre molecules within each host bacterial cell. Expression of Cre is detected by its ability to recombine the two lox sites and reconstitute a functional kanamycin resistance gene. The system was initially tested in E. coli by cloning a known regulated promoter from the araBAD operon that is induced by L-arabinose and repressed by D-glucose. However, the promoter failed to tightly control the regulation of cre gene expression, resulting in partial loxP recombination, which produced a mixed population of streptomycin and kanamycin resistant cells within each colony. Also, attempts to place the system into the meningococcus were unsuccessful. Efforts were made to tighten the regulation of the cre gene by placing the system into a different E. coli strain and test the system using a library of meningococcal genomic DNA fragments, as a compromise to show the experiments intended to isolate promoters. A vector, pUS1623, was constructed that would place the cre gene under the control of external promoters. A group B meningococccal genomic library was cloned upstream of the promoterless cre gene, with the inserted DNA fragments ranging from 0.1-1kb in size. The library was introduced into the E.coli XLl-Blue strain carrying pUS1604, and the Cre/lox recombination event has been shown to behave as expected, yielding a proportion of kanamycin-resistant clones. This indicates that promoter-like sequences are driving Cre, which is seen through the kanamycin-resistant phenotype of the clone. Conversely, clones that remain streptomycin-resistant do not have promoterlike sequences driving the expression of Cre. This streptomycin-resistant pool of clones was used to inoculate 50% serum/50% PBS liquid medium to identify group B strain meningococcal promoter sequences that drive Cre expression in this environment. Several sequences found to induce Cre expression from the initial screen, and during the serum experiment were sequenced. The sequence data was next analysed for homology against the sequences on the group B meningococcal genome sequence database (http://www.tigr.org). to identify the function of the contig from which the isolated sequence is found within the meningococcal genome. Finally, the sequences were analysed for prokaryote -35 and -10 consensus regions and orientated to determine the direction of transcription relative to the cre gene and also to genomic open reading frames, to determine the likelihood of isolating actual promoters. Although the experiments carried out in E. coli do not give an accurate picture of the regulatory gene pathways in the meningococcus, the results give an insight into the suitability of the system as regards to its use in an IVET strategy.

The development of two original Monte Carlo models of solvent diffusion into a polymer is described. Employing a coarse grained model of a polymer solution on a regular lattice, the dynamic properties of both the solvent and polymer molecules can be observed. The "Simple" Monte Carlo model reliably reproduces Case I dynamics, but no departure from this is seen for any reasonable model parameters. This "Simple" Monte Carlo model is unable to reproduce Case II diffusion dynamics. One reason for this is that in this Monte Carlo model the processes of solvent diffusion and polymer relaxation are entirely independent processes. In this thesis it is suggested that a simple Monte Carlo model of this type will always produce Case I diffusion dynamics. The dynamic algorithm described in this work relies on simple instantaneous molecular motions between neighbouring lattice sites. It is shown that a diffusion process based on these motions is purely concentration dependent, relying only on the current state of the system. To use the Monte Carlo method to simulate Case II diffusion dynamics, the diffusion process is made time dependent by incorporating a history dependent model of diffusion first proposed by Crank (CRANK 1953). In this "History Dependent" Monte Carlo model the motions of both the solvent and the polymer are no longer instantaneous, but occur at a rate that approaches equilibrium by a first order process governed by a relaxation time characteristic of the viscoelastic relaxation of the polymer. This "History Dependent" Monte Carlo model successfully simulates most of the features of Case II diffusion and also demonstrates a return to Case I diffusion in the limit of long times. Unlike many models of Case II diffusion, this Monte Carlo model is able to simultaneously model the microscopic motions of both the solvent and the polymer molecules. This novel feature demonstrates the formation of a discontinuous moving boundary between the rubbery polymer and the glassy polymer that is typical of Case II diffusion dynamics.

Doctorat en Sciences / info:eu-repo/semantics/nonPublished

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No description available.

No description available.

Organic-inorganic hybrid materials of divalent transition metal halides and simple organic molecules are known to exhibit interesting properties, with both the organic and the inorganic metal halide components contributing to the overall properties of the material (Aakeroy, Champness and Janaik, 2010) (Alexandre et al., 2007) (Aruta et al., 2004) (Criado et al., 1999) (Chondroudis and Mitzi, 1999) (Mitzi, Chondroudis and Kagan, 2001) (Robin and Fromm, 2006). The benzamide molecule was chosen as the primary organic component in this study, due to its potential to form aromatic interactions, and the fact that it possesses two potential sites for hydrogen bonding or protonation or coordination, via the amide group. In addition, the 4-aminobenzamide molecule was investigated due to its similarity to the benzamide molecule, except for an additional functional group on the opposite side of the amide group. A range of inorganic, divalent transition metal chlorides and bromides were selected as inorganic components, including CuX2, CdX2, CoX2, MnX2, HgX2 and ZnX2, where X = Cl or Br. Both ionic and neutral coordination type materials can be formed through the combination of the organic components and inorganic components described above, and the outcome of the reaction is controlled by the presence or absence of acid in the reaction medium. In acidic medium protonation of the organic component results in the formation of an ionic material, and in the absence of an acid a neutral coordination material results from the coordination of the organic component to the metal atom of the metal halide component. The stoichiometry and concentration of the acid will also have an influence on the structure as some of the organic ligand may remain unprotonated. In this study seven novel neutral coordination type structures and one ionic material were characterised by single crystal X-ray diffraction. Four isostructural, neutral, one-dimensional coordination polymer structures were observed for the combination of benzamide with CuCl2, CuBr2, CdCl2 and CdBr2 respectively. In this isostructural series the metal ions adopt an octahedral geometry in the case of the Cd analogues, and a tetragonal geometry, due to Jahn-Teller distorsion, for the Cu members of the series. The combination of ZnCl2 with benzamide yielded an isolated, zero-dimensional, neutral coordination compound in which the zinc(II) ion displays a tetrahedral geometry. An octahedral, paddle wheel-type, isolated, zero-dimensional coordination molecule formed from the combination of MnBr2 and benzamide. In all the coordination compounds of benzamide, coordination was found to occur through the oxygen atom of the amide group, while the NH2 group participates in intra- and intermolecular hydrogen bonding interactions. Due to the poor basicity of benzamide, only one ionic compound of this organic component was characterised structurally. In this compound, formed in combination with HgBr2, half of the benzamide molecules are protonated, and a unique, novel, one-dimensional perhalometallate anion was observed in this structure. The combination of 4-aminobenzamide with CoBr2 yielded an isolated, zero-dimensional, neutral coordination structure, in which the cobalt(II) ion adopts an octahedral geometry. The neutral, coordination compound formed between 4-aminobenzamide and CuBr2 has a trigonal bipyramidal geometry, and in addition to the organic and halogeno ligands, aqua ligands are also coordinated to the metal ion in both of the 4-aminobenzamide-containing molecules. Hydrogen bonding and aromatic interactions occur in all of the structures, and these interaction geometries were analysed in detail. It was found that these interactions play an important role in the cohesion of the units in the structure, with exception of the ionic compound of benzamide, which displays strong hydrogen bonding interactions but long aromatic centroid-to-centroid distances. Diffuse reflectance spectroscopy (DRS) was employed to measure the band gaps of the series of isostructural, one-dimensional coordination polymers. These measurements indicated that the Cd analogues in this series have band gaps that place them in the category of electronic insulators. The Cu members of this series were found to be two-band gap materials, with the lower of the two band gaps falling within the conductor range, while the higher band gap falls in the semi-conductor range for the structure containing CuBr2 and benzamide and the structure containing CuCl2 and benzamide. The suitability of Density Functional Theory (DFT) calculations to theoretically calculate the electronic structures and band gap values of the isostructural series of one-dimensional coordination polymers was tested in this study. The plane-wave cut off energy and k-point grid were optimised for the structures, and a range of functionals were tested. The best performing functional was used to calculate the band gap energies, the band structures and the density of states for the four isostructural materials. DFT calculations are known to underestimate band gap energies, and even though the calculated band gaps differ from the experimentally measured band gaps, this difference is smaller than expected. In addition, the DFT calculations were successful in predicting and providing insight into the electronic characteristics of the materials. Copyright / Dissertation (MSc)--University of Pretoria, 2012. / Chemistry / unrestricted

In the mammalian seminiferous epithelium, the cytoplasm of Sertoli cells adjacent to sites of intercellular attachment exhibits unique structural attributes. In each of these regions, a layer of hexagonally packed actin filaments lies situated between a cistern of endoplasmic reticulum and the plasma membrane. The filament layer together with the reticulum and adjacent plasma membrane are collectively termed an "ectoplasmic specialization". Ectoplasmic specializations occur in apical Sertoli cell regions at sites of attachment to spermatids and basally at sites of attachment to adjacent Sertoli cells. Ectoplasmic specializations have been hypothesized to be actin associated intercellular adhesion junctions. If this is true, molecular components that characterize actin associated adhesion junctions in general should be present in ectoplasmic specializations. In this study, I tested this prediction in two ways. First, I investigated whether or not the protein vinculin is co-distributed with actin filament bundles in ectoplasmic specializations of the ground squirrel. Second, I immunologically probed ectoplasmic specializations for three cell adhesion molecules (CAMs) that are commonly found in regions of intercellular adhesion in other tissues. My results indicate that vinculin is co-distributed with actin in Sertoli cell regions attached to spermatids. These data are consistent with the conclusion that vinculin is a component of ectoplasmic specializations and, therefore, with the hypothesis that the latter structures are a form of actin associated adhesion junction. Experiments using probes for the CAMs indicate that E-cadherin, A-CAM and N-CAM are probably not present in ectoplasmic specializations. The adhesion molecule at these sites may be a different member of the known CAMs or an as yet unidentified CAM. Based on data presented here and elsewhere indicating that ectoplasmic specializations are a form of actin associated adhesion junction, I describe the elaborate changes that occur in constituent filament bundles at sites of attachment to spermatids of the ground squirrel and interprete them in the context of the adhesion hypothesis. During the course of the co-localization studies described above, I observed that vinculin and actin are co-distributed at certain sites of intercellular attachment between interstitial cells of Leydig in the ground squirrel testis. Moreover, at the ultrastructural level I found these sites correspond to microfilament rich junction regions. These observations are consistent with the conclusion that actin associated intercellular adhesion junctions exist between interstitial cells of Leydig in the ground squirrel testis. / Medicine, Faculty of / Graduate

Molluscan shells show great diversity in colour, which is due to many different classes of chemical compounds. The identification of the pigments found in the molluscan shells of a diverse group of marine species was done in situ using Resonance Raman spectroscopy, and found to be unsubstituted polyacetylenes. Two South African species (D. serra and J. janthina) were chosen for extraction of the pigment-containing organic component, and it was found that the vibrational bands in the Raman spectra of the extracted component shifted relative to that obtained in the molluscan matrix, indicating structural changes in the pigmentary molecules upon extraction. Published correlations were used to evaluate the possible length of the conjugated chain, and a new correlation was established using previous reported data. The conjugated chain length predicted from the new correlation of the studied pigmentary molecules ranges between ten and twelve double bonds. Copyright 2011, University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. Please cite as follows: Barnard, W 2006, A spectroscopic investigation of polyacetylenic molecules in the molluskan biogenic matrix, MSc dissertation, University of Pretoria, Pretoria, viewed yymmdd < http://upetd.up.ac.za/thesis/available/etd-06262008-114600 / > E216/ag / Dissertation (MSc (Chemistry))--University of Pretoria, 2008. / Chemistry / unrestricted

Display technology has become a vital and ubiquitous part of our daily life. Undoubtedly, today’s technologically minded society is living in the era of the digital image. After high resolution and efficiency could successfully be realized, the major trends in display technology now aim towards achieving high color purity for natural looking display colors. Organic light-emitting diodes (OLEDs), as one strong contender for high performance displays and lighting, have been undergoing tremendous industrial and commercial development. Despite the great progress, though, there is still space for improvement, especially in the case of blue light emitting devices. Blue OLEDs are always challenging, since they traditionally suffer from low efficiencies and lifetimes. Both, novel materials and device architectures, are driving ongoing developments while still always aiming to lower the overall costs. In a continual effort to search for robust materials for blue devices, small molecules (SMs) and polymers, are shown to be promising candidates. In this thesis is presented the results of the detailed study of photophysical and electroluminescence (EL) properties in the case of thin films based on blends of the conjugated polymer Poly(9,9-di-n-octylfluorenyl-2,7-diyl) (PFO) and the of novel SMs; 4,4'-(anthracene-9,10-diyl)bis(N,N-bis(4-methoxyphenyl)aniline) (TPAA) and 4,4'-(pyrene-1,6-diyl)bis(N,N-bis(4-methoxyphenyl)aniline) (TPAP). Finally, devices based on these systems are optimized step by step as a solution processable emissive layer (EML), for applications in sky blue OLEDs.