Yes / A new approach is described herein, where neutron reflectivity measurements that probe changes in the density profile of thin films as they absorb material from the gas phase have been combined with a Love wave based gravimetric assay that measures the mass of absorbed material. This combination of techniques not only determines the spatial distribution of absorbed molecules, but also reveals the amount of void space within the thin film (a quantity that can be difficult to assess using neutron reflectivity measurements alone). The uptake of organic solvent vapours into spun cast films of polystyrene has been used as a model system with a view to this method having the potential for extension to the study of other systems. These could include, for example, humidity sensors, hydrogel swelling, biomolecule adsorption or transformations of electroactive and chemically reactive thin films. This is the first ever demonstration of combined neutron reflectivity and Love wave-based gravimetry and the experimental caveats, limitations and scope of the method are explored and discussed in detail.

Arsenic contamination of groundwater remains a serious health concern in many areas of the world. Developing countries such as Bangladesh and Nepal are particularly affected because access to high quality water infrastructure is low. Since the 1970s, most water in these countries is sourced from shallow tube wells installed to reduce the spread of diseases associated with poor water hygiene. In this goal they were successful, however by the mid 1990s it became apparent that many of these wells were contaminated by arsenic and that these countries’ rural poor were being slowly poisoned. No simple, cheap, and reliable test for arsenic exists, and efforts to mitigate arsenic contamination have been severely limited by this over the past two decades. Government backed well-testing efforts using commercially available field kits have many issues with reliability, safety, rigour, and transparency, and have lost their urgency over the past decade, while the expensive field test kits remain out of the reach of most ordinary people in these areas. Synthetic Biology offers the technology to develop a new class of biosensor by exploiting bacteria’s natural ability to sense and respond to levels of arsenic considerably lower than commercially available kits which are based on analytical chemistry. In order to reach this goal, we must first develop our understanding of the natural response to arsenic in our chosen host, B. subtilis. Although we have a reasonably good qualitative understanding of the operon responsible for arsenic sensing, very little quantitative analysis has been carried out, and a robust system for ratiometric characterisation has not been established in the bacteria. In this work, a robust platform for rapid ratiometric characterisation is established in B. subtilis. A rigorous mathematical model of the ars operon is developed and analysed before being verified experimentally. This new knowledge is then used to explore synthetic permutations to the natural system aimed at improving the sensor properties of the system. Finally, a biological architecture for an easily tunable biosensor with good characteristics is recommended.

Embargoed till 18 November 2011 / No abstract available.

Embargoed till 18 November 2011 / No abstract available.

This project is concerned with both the study of different Multiple Quantum Wells (MQWs) structures using the In0.53Ga0.47As/In0.52Al0.48As material system lattice matched to InP and a systematic investigation of the properties of InAs QD systems within GaAs with the aim of achieving enhancements of solar cell performance. The key challenge is the growth of QDs solar cell structures which exhibit sufficient absorption (enhanced infrared absorption) to increase short circuit current density (Jsc) but which can still maintains a high open circuit voltage (Voc). The research consists of epitaxial growth using state-of–the-art MBE, optical absorption, photoluminescence and high resolution x-ray diffraction measurements as well as device fabrication and characterization of novel solar cell structures. Optimization was performed on these novel cells to further improve their efficiency by inserting stacks of QD into different regions of the device. The effect of localized doping of such structures was used in an attempt to maintain and enhance the open-circuit voltage which in turn increases the device efficiency. The fabricated devices were characterized using measurements of the dark/light current-voltage (I-V) characteristics and spectral response (50-480 K). Solar cell external quantum efficiencies under standard air mass (AM) 1.5 spectrum were determined and the suitability of these new cells under solar concentration were assessed. Full physical simulations are performed using SILVACO semiconductors modelling software to generate models of multi-junction solar cells that were crucial in informing iterations to growth and fabrication and help to reconcile theory with experiment. One of the key findings, of this thesis, is the fact that Intermediate band photovoltaic devices using material based on InAs/GaAs vertically stacked quantum dot arrays, can be used in applications according to specific configuration criteria such as high temperature operation conditions. The intermediate band cell, including an inter-dot doped configuration, has been found to be a potential candidate as the inter dot doping profile reduces the efficiency degradation below the GaAs values including an enhancement in the open circuit voltage. It has been proved that these devices not only have a good performance at high temperatures but also by changing the vertical stacking QD layer periodicity can enhance the short circuit current density while keeping a large open circuit voltage. It was confirmed in practical device operation that thermal energy is required to enable the intermediate band in InAs/GaAs QD materials. The impact of this works can help in the future improvements of the intermediate band solar cells based on InAs on GaAs QD. The best overall efficiency of 11.6 % obtained in this work is an excellent value for so simple devices configuration. The Si3N4, tested for the first time on InAs/GaAs QD materials, reduces the reflectance on the device surface to a value of 2% and the operational wavelength can be tuned by controlling the layer thickness. A 100 nm Si3N4 antireflective coating proved to be an excellent coating from 700 to 1000 nm. In terms of short circuit current density a 37% enhancement was achieved.

Alpacas were first introduced into South Africa during the year 2000. They are valuable because of the fine quality wool they produce which has much better insulation properties than that of merino wool fibres. Alpacas are also used to act as guards of sheep herds against predators. During 2008, blood samples from an alpaca that died acutely with severe lung oedema, respiratory distress and froth exuding from the nose were received at Elsenburg Veterinary Laboratory. The alpaca was from a herd of 23 alpacas of a British veterinarian in the Montagu district in the western Cape. Virus isolation attempts on the blood produced infrequent embryo mortalities. Embryonated chicken egg (ECE) material was send to the Virology Department at the Onderstepoort Veterinary Institute (OVI). A bluetongue virus (BTV) PCR performed at the diagnostic PCR laboratory at OVI on the ECE material was positive. Further intra-venous (IV) inoculations in ECE produced embryo mortalities on two consecutive days, the 8th and 9th November. The dead embryos were harvested separately and named and treated as two separate virus samples, Alp8 and Alp9 which were further passaged on baby hamster kidney (BHK) cells. The BTV virus neutralisation tests (VNT) performed at the Office International des Epizooties (OIE) Laboratory on both Alp8 and Alp9 were negative. Because of the close serological relationship between BTV and epizootic haemorrhagic disease virus (EHDV), an EHDV VNT was also performed and was also negative. In the light of the negative VNT and the positive BTV PCR results, more in-depth molecular analyses were performed. RNA was purified from tissue culture material and agarose gel electrophoresis (AGE) performed. Both Alp8 and Alp9 had a typical orbiviral electrophoretic profile, but their respective profiles were different. A sequence-independent reverse transcriptase PCR amplification method generated ample complementary DNA (cDNA) of both samples for sequencing. Sanger sequencing was used to partially sequence genome segments 5 (NS1) and 2 (VP2). BLAST analysis of the partial information of the genome segments 5 (NS1) of Alp8 confirmed it as being a BTV and Alp9 as being an EHDV. BLAST analysis of the deduced amino acid sequence generated of VP2 of both Alp8 and Alp9 established that these samples were possibly new serotypes of BTV and EHDV respectively. The complete genome of both Alp8 and Alp9 was sequenced with next generation 454 Pyrosequencing. This confirmed the partial sequencing results. BLAST analysis of the complete sequence of S2 (VP2) of Alp8 showed that it has 73 % nucleotide and 77 % deduced amino acid identity to BTV15. In contrast the nucleic acid sequence of genome segment S2 (VP2) of Alp9 had no nucleotide sequence identity to any virus, but its deduced amino acid sequence had 71 % amino acid identity to EHDV2. Hyper immune guinea pig (GP) serum prepared against the putative new BT (Alp8) and EHD (Alp9) virus serotypes were tested for serological cross-reactivity against the 24 OIE reference antigen strains of BTV and the 8 OIE reference antigen strains of EHDV. Alp8 had a neutralising antibody (NAb) titre of > 32 against BTV15. Alp9 did not cross react with any of the OIE BTV and EHDV strains. Six out of the remaining 22 alpacas on the farm had NAbs to a greater or lesser extend against Alp8 (BTV) and Alp9 (EHDV) viruses, which confirmed that the viruses were also present in other alpacas in the herd. Very few cases of EHDV in alpacas have ever been reported in literature. A small scale pilot vector susceptibility study showed that vector competence of C. imicola for both Alp8 and Alp9 was low, below 2 %. The fact that neutralising antibodies to Alp8 and Alp9 were detected in other alpacas in the herd raises the question as to whether there are other Culicoides species circulating in the area that could vector the viruses. In conclusion, the results from the serological and virological analyses as well as the nucleic acid sequence data of the genomes of two virus samples, Alp8 and Alp9, from an alpaca that died in the Montagu district in the western Cape identified Alp9 as a definite new serotype of EHDV and Alp8 as a possible new serotype of BTV most closely related to BTV15. / MSc (Biochemistry), North-West University, Potchefstroom Campus, 2014

The process of milling drugs to obtain samples with a desirable particle size range has been widely used in the pharmaceutical industry, especially for the production of drugs for inhalation. However by subjecting materials to milling techniques surfaces may become thermodynamically activated which may in turn lead to formation of amorphous material. Polymorphic conversions have also been noted after milling of certain materials. Salt and cocrystal formation is a good way of enhancing the properties of an API but little or no work has been published which investigates the stability of these entities when subjected to milling. Different milling techniques (ball and jet) and temperatures (ambient and cryogenic) were used to investigate the milling behaviour of polymorphs, salts and cocrystals. All materials were analysed by XRPD and DSC to investigate any physical changes, i.e. changes in melting point and by inverse gas chromatography (IGC) to investigate whether any changes in the surface energetics occurred as a result of milling. Another aim of this thesis was to see if it was possible to predict the milling behaviour of polymorphs by calculating the attachment energies of the different crystal facets using Materials Studio 4.0. These results were compared to the IGC data to see if the predicted surface changes had occurred. The data collected in this study showed that different milling techniques can have a different effect on the same material. For example ball milling at ambient temperature and jet micronisation of the SFZ tosylate salt caused a notable increase in the melting point of the material whereas ball milling at cryogenic temperatures did not cause this to happen. The IGC data collected for this form also showed a contrast between cryomilling and the other two techniques. The study also showed that the formation of salts and cocrystals does not necessarily offer any increased stability in terms of physical properties or surface energetics. Changes in melting point were observed for the SFZ tosylate salt and the IMC:Benzamide cocrystal. Changes in the specific surface energies were also observed indicating that the nature of the surfaces was also changing. The materials which appeared to be affected the least were the two stable polymorphs, gamma IMC and SFZ III. The computational approach used has many limitations. The software does not allow for conversion to the amorphous form or polymorphic conversions. Such conversions were seen to occur, particularly for the metastable polymorphs used, meaning that this computational approach may only be suitable for stable polymorphs.

Alpacas were first introduced into South Africa during the year 2000. They are valuable because of the fine quality wool they produce which has much better insulation properties than that of merino wool fibres. Alpacas are also used to act as guards of sheep herds against predators. During 2008, blood samples from an alpaca that died acutely with severe lung oedema, respiratory distress and froth exuding from the nose were received at Elsenburg Veterinary Laboratory. The alpaca was from a herd of 23 alpacas of a British veterinarian in the Montagu district in the western Cape. Virus isolation attempts on the blood produced infrequent embryo mortalities. Embryonated chicken egg (ECE) material was send to the Virology Department at the Onderstepoort Veterinary Institute (OVI). A bluetongue virus (BTV) PCR performed at the diagnostic PCR laboratory at OVI on the ECE material was positive. Further intra-venous (IV) inoculations in ECE produced embryo mortalities on two consecutive days, the 8th and 9th November. The dead embryos were harvested separately and named and treated as two separate virus samples, Alp8 and Alp9 which were further passaged on baby hamster kidney (BHK) cells. The BTV virus neutralisation tests (VNT) performed at the Office International des Epizooties (OIE) Laboratory on both Alp8 and Alp9 were negative. Because of the close serological relationship between BTV and epizootic haemorrhagic disease virus (EHDV), an EHDV VNT was also performed and was also negative. In the light of the negative VNT and the positive BTV PCR results, more in-depth molecular analyses were performed. RNA was purified from tissue culture material and agarose gel electrophoresis (AGE) performed. Both Alp8 and Alp9 had a typical orbiviral electrophoretic profile, but their respective profiles were different. A sequence-independent reverse transcriptase PCR amplification method generated ample complementary DNA (cDNA) of both samples for sequencing. Sanger sequencing was used to partially sequence genome segments 5 (NS1) and 2 (VP2). BLAST analysis of the partial information of the genome segments 5 (NS1) of Alp8 confirmed it as being a BTV and Alp9 as being an EHDV. BLAST analysis of the deduced amino acid sequence generated of VP2 of both Alp8 and Alp9 established that these samples were possibly new serotypes of BTV and EHDV respectively. The complete genome of both Alp8 and Alp9 was sequenced with next generation 454 Pyrosequencing. This confirmed the partial sequencing results. BLAST analysis of the complete sequence of S2 (VP2) of Alp8 showed that it has 73 % nucleotide and 77 % deduced amino acid identity to BTV15. In contrast the nucleic acid sequence of genome segment S2 (VP2) of Alp9 had no nucleotide sequence identity to any virus, but its deduced amino acid sequence had 71 % amino acid identity to EHDV2. Hyper immune guinea pig (GP) serum prepared against the putative new BT (Alp8) and EHD (Alp9) virus serotypes were tested for serological cross-reactivity against the 24 OIE reference antigen strains of BTV and the 8 OIE reference antigen strains of EHDV. Alp8 had a neutralising antibody (NAb) titre of > 32 against BTV15. Alp9 did not cross react with any of the OIE BTV and EHDV strains. Six out of the remaining 22 alpacas on the farm had NAbs to a greater or lesser extend against Alp8 (BTV) and Alp9 (EHDV) viruses, which confirmed that the viruses were also present in other alpacas in the herd. Very few cases of EHDV in alpacas have ever been reported in literature. A small scale pilot vector susceptibility study showed that vector competence of C. imicola for both Alp8 and Alp9 was low, below 2 %. The fact that neutralising antibodies to Alp8 and Alp9 were detected in other alpacas in the herd raises the question as to whether there are other Culicoides species circulating in the area that could vector the viruses. In conclusion, the results from the serological and virological analyses as well as the nucleic acid sequence data of the genomes of two virus samples, Alp8 and Alp9, from an alpaca that died in the Montagu district in the western Cape identified Alp9 as a definite new serotype of EHDV and Alp8 as a possible new serotype of BTV most closely related to BTV15. / MSc (Biochemistry), North-West University, Potchefstroom Campus, 2014

L’essor de la demande actuelle pour des matériaux architecturés, en microélectronique par exemple, ou pour des matériaux de structure, nécessite le développement d’outils de caractérisation toujours plus performants. Dans cette optique, un instrument de caractérisation multifonctionnel basé sur un couplage mécanique / électrique, a été développé au laboratoire SIMaP. Le cœur de ce dispositif est un nanoindenteur in situ FEG-SEM (Field Emission Gun Scanning Electron Microscope) couplé à des mesures électriques. Ce travail est porté par trois principales motivations: (1) L’étude du comportement mécanique d’objets petites échelles, (2) L’apport des données électriques à l’analyse quantitative du comportement mécanique pendant l’indentation, en particulier pour obtenir une meilleur estimation de l’aire de contact, (3) L’étude locale des propriétés électroniques d’empilements de films minces. L’intégration in situ SEM a été validée et permet un positionnement des indents avec une précision meilleure que 100 nm, autorisant ainsi l’étude des propriétés mécaniques à l’échelle submicrométrique. La rapidité des essais permet également des mesures statistiques. Des caractérisations mécaniques ont été menées aussi bien sur des échantillons composites massifs que sur des ilots d’or submicrométriques. Pour ce dernier cas, malgré la nature stochastique de leur comportement mécanique, une loi déterministe a pu être extraite des données mécaniques. Des mesures 3D-BCDI (Bragg Coherent Diffraction Imaging) au synchrotron ont été réalisées sur certains ilots avant et après chargement mécanique, révélant une germination de dislocations avant l’avalanche de grandes déformations plastiques. En parallèle de cette étude, des mesures électriques ont été réalisées pendant l’indentation de divers échantillons. Des mesures de nanoindentation résistive ont ainsi été effectuées sur des métaux nobles (Au) ou recouverts de leur oxyde natif (Cu, Al), soit à l’état de monocristal massif ou de film polycristallin. Les résultats quantitatifs soulignent l’importance de la présence d’une couche d’oxyde sur la réponse électrique. En présence d’un oxyde, l’interface pointe / échantillon semble être le lieu d’importantes réactions électrochimiques. En l’absence d’oxyde, la résistance mesurée peut être entièrement décrite par un modèle analytique. Dans ce cas, l’aire de contact électrique peut être prédite à partir des mesures de résistance. Enfin, des mesures capacitives ont été réalisées sur des structures MOS avec différentes épaisseurs d’oxyde. Les résultats expérimentaux sont parfaitement décrits par un modèle analytique, ce qui ouvre la voie à des mesures locales de permittivité diélectrique sous contrainte mécanique. / The increasing demand for multifunctional materials has become a recurrent challenge for a wide panel of application fields such as microelectronics and structural applications. Within the frame of this project, a multifunctional characterisation set-up has been developed at SIMaP lab, mainly based on the electrical / mechanical coupling. The heart of this device is an in situ FEG-SEM (Field Emission Gun Scanning Electron Microscope) nanoindenter coupled with an electrical measurement apparatus. This work has threefold objectives: (1) The investigation of mechanical behavior of small scale systems, (2) The input of electrical data to the quantitative analysis of mechanical behavior during indentation, in particular to obtain a better estimation of the contact area (3) The local study of electronic properties of thin film stacks. SEM integration of the device has been validated and indent positioning with a precision better than 100 nm is successfully obtained. This performance allows the studies of mechanical properties at submicrometric length scale, with a high throughput allowing statistical measurements. Various bulk composite materials have been characterized as well as submicrometric gold islands on sapphire. In the latter case, despite the stochastic nature of their mechanical behavior, a deterministic law has been extracted. 3D-BCDI (Bragg Coherent Diffraction Imaging) experiments have been performed on a few islands at synchrotron facility to investigate the crystal state before and after mechanical loading. These experiments reveal initial dislocation nucleation prior to large deformation bursts. In parallel to this study, electrical measurements have been performed during indentation on various cases. Resistive-nanoindentations have been performed on noble metals (Au) and natively oxidized metals (Cu, Al), either as bulk single crystals or as polycrystalline thin films. Qualitative results emphasize the importance of the oxide layer on the electrical response. In the presence of an oxide layer, strong electrochemical reactions seem to occur at the tip-to-sample interface. When no oxide is involved, the measured resistance can be fully described by an analytical model and the computed electrical contact area is successfully validated with residual areas measurements. Finally, capacitive measurements have been performed on MOS structures with various oxide thicknesses. Experimental results have been well described by analytical modelling, which paves the way for quantitative local dielectric permittivity measurements under mechanical loading.

Cassava (Manihot esculenta Crantz) is a basic staple food crop in Tanzania. Cassava mosaic disease (CMD) caused by cassava mosaic geminiviruses (CMGs) constitutes a major limiting factor to cassava production in the country. This study was undertaken to characterize the CMGs occurring in Tanzania using molecular techniques and to map their geographical distribution to generate information on which the formulation of control measures can be based. Using Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism (RFLP) for analysis of CMGs DNA-A genomes, different CMGs were found to be associated with CMD. Higher molecular diversity was observed among East African cassava mosaic viruses (EACMVs) than African cassava mosaic viruses (ACMVs), which was confirmed later by complete nucleotide sequence analysis. In addition to EACMV and ACMV isolates, two isolates of EACMV Cameroon virus (EACMCV) were found in Tanzania. These were confirmed to be strains of EACMCV Cameroon, originally described in Cameroon, West Africa and here named EACMCV- [TZ1] and EACMCV-[TZ7]. They had high (92%) overall DNA-A nucleotide sequence identity and EACMCV-[TZ1] was widespread in the southern part of the country. A subgenomic DNA form of CMG that appeared to be truncated was identified in a CMD-infected cassava plant. It was confirmed upon sequence analysis to be a defect of EACMV DNA-A and had a capacity of attenuating symptoms when coinoculated with wild-type EACMV. In addition, this study revealed for the first time the presence of two novel non-geminivirus single-stranded DNA (ssDNA) sub-genomic molecules associated with CMG infection. They were shown to be dependent on CMG for replication and movement within the plants, confirming their status as satellite molecules named here as satDNA-II and satDNA-III. When present in coinfection with CMGs, they enhance symptoms and can break high levels of resistance in a cassava landrace. Finally a simple, inexpensive technique is described of archiving, transporting and recovering plant DNA for downstream geminivirus characterisation. / Thesis (PhD)--University of Pretoria, 2007. / Microbiology and Plant Pathology / Unrestricted