Fragile X Syndrome (FXS) is a prevalent monogenic disease, often presenting with cognitive and neurological disorders including autism and epilepsy. The Fmr1 gene - transcriptionally silenced in FXS - normally encodes the Fragile X Mental Retardation Protein (FMRP), which acts as an activity dependent translational regulator at the base of dendritic spines. In an attempt to understand its role, dendritic spines in the dentate gyrus (DG) and cornu ammonis 1 (CA1) hippocampal regions of three-week old Fmr1- mice were analyzed and compared to wildtype (WT) littermate controls using electron microscopy. Dendritic spines with a continuous profile of the parent dendrite, spine neck, and spine head complete with synaptic components (presynaptic vesicles and postsynaptic densities) were included in our morphological analyses. We observed no changes in postsynaptic density length (DG: 5.69±0.30/6.18±0.85; SR: 7.55±0.87/6,96±0.33 µm/100 µm2; p=0.627/0.620), synapse density (DG: 32.3±3.8/30.3±1.9; SR: 34.4±1.8/30.7±0.5 synapses/100 µm2; p=0.655/0.270), spine head diameters (DG: 0.524±0.016/0.529±0.014; SR: 0.524±0.014/0.515±0.014 µm; p=0.098/0.20) or spine neck lengths (DG: 0.457±0.016/0.485±0.019; SR: 0.421 ± 0.015/0.425±0.017 µm; p=0.14/0.26), but found that in the DG spine necks were significantly narrower in the Fmr1- mice (0.193±0.0062/0.167±0.0064 µm; p=0.0002), whereas there were no changes in CA1 spine neck widths (0.162±0.0049/0.161±0.0061 µm; p=0.073). Estimated resistance calculated from spine necks morphologies revealed a ~1.7 fold increase in the Fmr1- DG compared to WT DG. These findings support that FMRP plays a role in granule cell spine neck structure and may influence synaptic signal compartmentalization and propagation in a regionally dependent manner. / Graduate

Philosophiae Doctor - PhD / Transition metal oxides magneli phases present crystallographic shear structure which is of great interest in multiple applications because of their wide range of valence, which is exhibited by the transition metals. The latter affect chemical and physical properties of the oxides. Amongst them we have nanostructures VO2 system of V and O components which are studied including chemical and physical reactions based on non-equilibrium thermodynamics. Due to their structural classes of corundum, rocksalt, wurtzite, spinel, perovskite, rutile, and layer structure, these oxides are generally used as catalytic materials which are prepared by common methods under mild conditions presenting distortion or defects in the case of VO2. Existence of an intermediate phase is proved using an x-ray thermodiffraction experiment providing structural information as the nanoparticles are heated. Potential application as gas sensing device has been the first time obtained due to the high surface to volume ratio, and good crystallinity, purity of the material and presence of suitable nucleating defects sites due to its n-type semiconductor behavior. In addition, annealing effect on nanostructures VO2 nanobelts shows a preferential gas reductant of Ar comparing to the N2 gas. Also, the hysteresis loop shows that there is strong size dependence to annealing treatment on our samples. This is of great interest in the need of obtaining high stable and durable material for Mott insulator transistor and Gas sensor device at room temperature.

Magister Scientiae (Medical Bioscience) - MSc(MBS) / The blood brain barrier (BBB) is a signaling interface between the blood and the central nervous system (CNS), which prohibits the entry of harmful blood-borne substances into the brain micro-environment, thus maintaining brain homeostasis. The crucial role of the BBB is protecting the CNS, which may adversely be affected by alcohol. The central component of the BBB, endothelial cells (ECs), regulates BBB transport by regulating the permeability both transcellularly and through their paracellular junctions, by structures called tight junctions (TJs) that are composed of proteins. The aim of this study was to investigate the in vitro effects of ethanol (EtOH) and fermented rooibos (Rf) on a monolayer of bEnd5 mouse brain ECs, by determining the effects of EtOH and Rf on bEnd5 (i) cell viability (ii) cell proliferation (iii) rate of cell division (iv) cell toxicity (v) claudin-5 transcription (vi) permeability across a monolayer of bEnd5 ECs and (vii) morphology, for a selected experimental timeline of 24, 48, 72, and 96hrs. We then investigated if the simultaneous exposure of Rf and EtOH could reverse or alleviate the EtOHinduced effects on the bEnd5 ECs. EtOH metabolism induces oxidative stress and results in a range of adverse physiological effects. Aspathalus linearis (rooibos) contains many phenolic compounds, of which the main antioxidant activity is attributed to aspalathin. Our underlining hypothesis is that the antioxidants in an aqueous rooibos extract may therefore protect against the potential oxidant damaging effects of alcohol on the BBB. Cells were exposed for 24hrs to selected concentrations of EtOH (25mM and 100mM), a concentration of Rf containing equivalent of 1.9nM aspalathin, and the combinations of EtOH and Rf. Cell viability and cell toxicity was determined, while cell proliferation and rate of cell division was estimated using the trypan blue exclusion assay. Real time quantitative PCR was implemented to quantify claudin-5 transcription, normalized against housekeeping genes, GAPDH and HPRT. Transepithelial electrical resistance (TEER) was measured using the Ohm Millicell-electrical resistance system, while bEnd5 monolayer morphology was analysed using the Zeiss scanning electron microscope. Both concentrations of EtOH led to an overall decrease in cell viability, and a decreased number of live cells across 72hrs. Consistent with this, EtOH resulted in increased cell toxicity across the 96hr experimental timeframe and a diminished rate of cell division. The transcription of claudin-5 in bEnd5 ECs exposed to 25mM and 100mM EtOH varied dramatically across the 96hr timeframe. While 25mM EtOH resulted in an overall decrease in TEER, cells exposed to 100mM EtOH only decreased TEER between 48 and 96hrs. Morphologically, both concentrations of EtOH led to compromised paracellular spaces as endorsed by high definition SEM analysis. The administration of Rf on its own resulted in an initial decrease in viability, followed by recovery between 72 and 96hrs. Exposure to Rf diminished live cell numbers at 72 and 96hrs, accompanied by a compromised rate of cell division and an overall increase in cell toxicity. In addition, Rf down-regulated claudin-5 transcription across the course of the experiment, particularly between 24 and 48hrs. In alignment with this, Rf also led to an increase in BBB permeability from 24 to 96hrs. However, SEM studies were not able to discriminate any differences between control and Rf treated cells. Our study showed that the BBB could be protected against the adverse effects of EtOH, and this at the plasma concentration induced by 500ml’s of Rooibos tea. The simultaneous exposure of Rf and EtOH was able to negate the effects of EtOH on cell viability, cell proliferation, and cell toxicity but exacerbated the effects of EtOH on claudin-5 transcription and paracellular permeability. Morphologically, co-exposure with Rf only reversed the effects of 25mM EtOH while exacerbating the effects of 100mM EtOH at 96hrs. In conclusion, EtOH was shown to be detrimental to the integrity of bEnd5 ECs, and the addition of a minuscule quantity of the Rf extract was able to partially alleviate excess ROS-induced effects.

The burgeoning field of nanotechnology motivates comprehensive elucidation of nanoscale materials. This thesis addresses transmission electron microscope characterisation of nanoparticle morphology, concerning specifically the crystal- lographic status of novel intermetallic GaPd2 nanocatalysts and advancement of electron tomographic methods for high-fidelity three-dimensional analysis. Going beyond preceding analyses, high-resolution annular dark-field imaging is used to verify successful nano-sizing of the intermetallic compound GaPd2. It also reveals catalytically significant and crystallographically intriguing deviations from the bulk crystal structure. So-called ‘non-crystallographic’ five-fold twinned nanoparticles are observed, adding a new perspective in the long standing debate over how such morphologies may be achieved. The morphological complexity of the GaPd2 nanocatalysts, and many cognate nanoparticle systems, demands fully three-dimensional analysis. It is illustrated how image processing techniques applied to electron tomography reconstructions can facilitate more facile and objective quantitative analysis (‘nano-metrology’). However, the fidelity of the analysis is limited ultimately by artefacts in the tomographic reconstruction. Compressed sensing, a new sampling theory, asserts that many signals can be recovered from far fewer measurements than traditional theories dictate are necessary. Compressed sensing is applied here to electron tomographic reconstruction, and is shown to yield far higher fidelity reconstructions than conventional algorithms. Reconstruction from extremely limited data, more robust quantitative analysis and novel three-dimensional imaging are demon- strated, including the first three-dimensional imaging of localised surface plasmon resonances. Many aspects of transmission electron microscopy characterisation may be enhanced using a compressed sensing approach.

Tomography of crystal defects in the electron microscope was first attempted in 2005 by the author and colleagues. This thesis further develops the technique, using a variety of samples and methods. Use of a more optimised, commercial tomographic reconstruction program on the original GaN weak beam dark-field (WBDF) tilt series gave a finer reconstruction with lower background, line width 10-20 nm. Four WBDF tilt series were obtained of a microcrack surrounded by dislocations in a sample of indented silicon, tilt axes parallel to g = 220, 220, 400 and 040. Moiré fringes in the defect impaired alignment and reconstruction. The effect on reconstruction of moiré fringe motion with tilt was simulated, resulting in an array of rods, not a flat plane. Dislocations in a TiAl alloy were reconstructed from WBDF images with no thickness contours, giving an exceptionally clear reconstruction. The effect of misalignment of the tilt axis with systematic row g(ng) was assessed by simulating tilt series with diffraction condition variation across the tilt range of Δn = 0, 1 and 2. Misalignment changed the inclination of the reconstructed dislocation with the foil surfaces, and elongated the reconstruction in the foil normal direction; this may explain elongation additional to the missing wedge effect in experiments. Tomography from annular dark-field (ADF) STEM dislocation images was also attempted. A tilt series was obtained from the GaN sample; the reconstructed dislocations had a core of bright intensity of comparable width to WBDF reconstructions, with a surrounding region of low intensity to 60 nm width. An ADF STEM reconstruction was obtained from the Si sample at the same microcrack as for WBDF; here automatic specimen drift correction in tomography acquisition software succeeded, a significant improvement. The microcrack surfaces in Si reconstructed as faint planes and dislocations were recovered as less fragmented lines than from the WBDF reconstruction. ADF STEM tomography was also carried out on the TiAl sample, using a detector inner angle (βin) that included the first order Bragg spots (in other series βin had been 4-6θ B). Extinctions occurred which were dependent on tilt; this produced only weak lines in the reconstruction. Bragg scattering in the ADF STEM image was estimated by summing simulated dark-field dislocation images from all Bragg beams at a zone axis; a double line was produced. It was hypothised that choosing the inner detector angle to omit these first Bragg peaks may preclude most dynamical image features. Additional thermal diffuse scattering (TDS) intensity due to dilatation around an edge dislocation was estimated and found to be insignificant. The Huang scattering cross section was estimated and found to be 9Å, ten times thinner than experimental ADF STEM dislocation images. The remaining intensity may be from changes to TDS from Bloch wave transitions at the dislocation; assessing this as a function of tilt is for further work. On simple assessment, only three possible axial channeling orientations were found over the tilt range for GaN; if this is typical, dechanneling contrast probably does not apply to defect tomography.

Optoelectronic devices fabricated from nitride semiconductors include blue and green light emitting diodes (LEDs) and laser diodes (LDs). To design efficient devices, the structure and composition of the constituent materials must be well-characterised. Traditional microscopy techniques used to examine nitride semiconductors include transmission electron microscopy (TEM), and atomic force microscopy (AFM). This thesis describes the study of nitride semiconductor materials using these traditional methods, as well as atom probe tomography (APT), a technique more usually applied to metals that provides three-dimensional (3D) compositional information at the atomic scale. By using both APT and correlative microscopy techniques, a more complete understanding of the material can be gained, which can potentially lead to higher-efficiency, longer-lasting devices. Defects, such as threading dislocations (TDs), can harm device performance. An AFM-based technique was used to show that TDs affect the local electrical properties of nitride materials. To investigate any compositional changes around the TD, APT studies of TDs were attempted, and evidence for oxygen enrichment near the TD was observed. The dopant level in nitride devices also affects their optoelectronic properties, and the combination of APT and TEM was used to show that Mg dopants were preferentially incorporated into pyramidal inversion domains, with a Mg content two orders of magnitude above the background level. Much debate has been focused on the microstructural origin of charge carrier localisation in InGaN. Alloy inhomogeneities have often been suggested to provide this localisation, yet APT has revealed InGaN quantum wells to be a statistically random alloy. Electron beam irradiation in the TEM caused damage to the InGaN, however, and a statistically significant deviation from a random alloy distribution was then observed by APT. The alloy homogeneity of InAlN was also studied, and this alloy system provided a unique opportunity to study gallium implantation damage to the APT sample caused during sample preparation by the focused ion beam (FIB). The combination of APT with traditional microscopy techniques made it possible to achieve a thorough understanding of a wide variety of nitride semiconductor materials.

Electron microscopy was first conducted in the 1930s with the advent of theTEM and later the STEM. In 1969, the first commercial SEM was released,with the possibility of retrofitting it to behave like a STEM following soonafterwards. In 1979, Danilatos and Robinson advanced electron microscopyby creating a new type of SEM which allowed a controlled quantity of gasinto the sample chamber, termed ESEM. The most recent evolution in thisline was the combination of ESEM and STEM in 2005, a procedure termedWet STEM.The focus of this work is on investigating applications of this new technique,along with the contrast mechanisms involved in forming an image. Tothat end, a wide variety of samples will be imaged. Clay and paint suspensions(colloids) are used to test Wet STEM’s capacity to image submergedobjects, as well as thin objects which are stacked together. Diblock copolymerfilms are used to test Wet STEM’s ability to distinguish chemically similarmaterials without staining, the physical effects of heavy metal staining andto demonstrate the necessity of gas for the purpose of charge neutralisation. Single cell biological samples are also investigated. Internal contrast inmammalian cells is visible without recourse to staining, but chemical fixationis required despite maintaining a high relative humidity. Bacteria are moreresilient and as such are easier to image than animal cells, requiring no priortreatment. When exposed to low relative humidity, bacteria are found tocollapse. The collapse pattern is observed to differ between wild-type andcytoskeletal-deficient bacteria of the same species and strain, so it is likelythat dehydration-induced collapse offers information about the position andshape of the bacterial cytoskeleton.

The crotoxin complex protein is the major neurotoxic component in the venom of the Brazilian rattlesnake, Crotalus durissus terrificus. The purified protein can be crystallized in the form of thin platelets (less than 500 Å thick) suitable for electron crystallography and image processing techniques. The unit cell dimensions of the crystal are a = 38.8 Å, b = 38.8 Å, c = 256 Å, and α = β = γ = 90°. These crystals can grow in layers. For a three-dimensional image reconstruction this necessitates the determination of the crystal thickness in order to combine information from low dose images of crystals of the same thickness. In the past, the highest resolution image (to 3.9 Å) recorded from a crotoxin complex crystal on the electron microscope was from a crystal embedded in glucose. However, since glucose cannot be removed in order to accurately determine the crystal thickness, a different embedding technique (amorphous ice embedding) and tried. It was determined that high resolution image information (to 3.9 Å) can be recorded from crotoxin complex crystals embedded in amorphous ice. Five images of crystals preserved in amorphous ice, all exhibiting resolution to at least 9 Å, were first processed by a global averaging method from which two-dimensional projection maps were calculated. These maps were not interpretable due to variations in the images as demonstrated by a second processing method. In the second processing method the images were divided into smaller areas, or patches, and these patches were averaged. The patchwork images produced from the second process indicate that there is variation across the original images. The most likely explanation for the variation is the bending, or lack of flatness, of the crystals on the grid. The determination of mass thickness of the crystals from optical density differences between the crystals and the carbon support in images of freeze-dried crystals was explored. It was found that this method could not determine the mass thickness of crotoxin complex crystals to within one layer (64 Å), but could clearly distinguish between one and three overlapping layers of freeze-dried purple membrane which was used as a test specimen.

>Magister Scientiae - MSc / There are limited reports on virus population in haloalkaline environments; therefore the aim of this study was to investigate the genetic diversity and biology of bacteriophage communities in these environments. Bacteria were isolated to be used as phage hosts. One bacterium from Lake Magadi and four bacteria from Lake Shala were successfully isolated from sediment samples. A further two Lake Shala bacterial hosts from the IMBM culture collection were also used to isolate bacteriophages. Bacterial isolates were identified to be most closely related to Bacillius halodurans, Halomonas axialensis, Virgibacillus salarius, Bacillus licheniformis, Halomonas venusta, Bacillus pseudofirmus and Paracoccus aminovorans. Bacteriophages were screened using all bacteria against sediment samples from both Lake Shala and Lake Magadi. One phage was identified from Lake Magadi sediments (MGBH1) and two phages from Lake Shala sediments (SHBH1 and SHPA). TEM analysis showed that these phages belong to three different dsDNA phage families; Siphoviridae (MGBH1), Myoviridae (SHBH1) and Podoviridae (SHPA). All phages showed different genome sizes on agarose gel. Due to the small genome size, phage SHPA was chosen for further investigation. Partial, genome sequence analysis showed homology to both bacterial and phage proteins. A further investigation of phage diversity in this environment is essential using metagenomic approaches to understand these unique communities.

>Magister Scientiae - MSc / Magnetic luminescent nanoparticles of an iron oxide (Fe₃O₄) superparamagnetic core and an indium phosphide/zinc selenide (InP/ZnSe) quantum dot shell are reported. The magnetic nanoparticles (MNP’s) and quantum dots (QD’s) were each synthesized separately before conjugation. The MNP’s were functionalized with a thiol-group allowing the QD shell to bind to the surface of the MNP by the formation of a thiol-metal bond. The nanocomposite was capped with 3-mercaptopropionic acid, 1-propanethiol, 2-methyl-1-propanethiol and their properties investigated using the characterization techniques: high- resolution transmission electron microscopy (HR-TEM), energy-dispersive spectroscopy (EDS), UV-vis, scanning electron microscopy (SEM), superconducting quantum interference device (SQUID), and photoluminescence. These techniques yielded significant information on particle size, morphology, dispersion, and chemical composition including luminescence and florescence.