Thesis (M.Phil.)--Hong Kong University of Science and Technology, 2007. / Includes bibliographical references (leaves 81-86). Also available in electronic version.

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Diversity in excitatory synaptic transmission by cortical pyramidal neurons give rise to the possibility of different neuronal networks that mediate distinct cortical function. Understanding heterogeneity of excitatory input to pyramidal neurons across distinct cortical areas and species will provide insight into cortical specialization and, ultimately, selective vulnerability of cortical areas to neuropathology in humans. In a previous study in our laboratory (Medalla and Luebke, 2015), significant differences in the ultrastructural features of excitatory asymmetric synapses in layers 2-3 (L2-3) neuropil were found between two distinct cortical areas in the rhesus monkey – primary sensory visual (V1) versus higher-order lateral prefrontal (LPFC) cortices. Here, we used serial sectioning electron microscopy to determine whether these differences in synaptic elements also exist in the corresponding visual (V1) and frontal (FC) cortices in the mouse. Multiple analyses of L2-3 neuropil of FC and V1 in mouse revealed three fundamental principles. First, in contrast to the diverse synapses in monkey LPFC and V1, asymmetric axospinous synapses in L2-3 neuropil of mouse FC and V1 are remarkably homogenous with regard to presynaptic and postsynaptic entities. Second, asymmetric axospinous synapses in L2-3 neuropil of mouse V1 resemble that of monkey V1 in postsynaptic entities, but differ in presynaptic entity. Third, asymmetric axospinous synapses in L2-3 neuropil of mouse FC and monkey LPFC differ substantially in both presynaptic and postsynaptic entities. These findings have broad implications for extrapolation of excitatory synaptic transmission data from one cortical area to another, and also from one species to another.

Chronic kidney disease (CKD) and end stage renal disease (ESRD) are significant causes of adult morbidity and mortality worldwide. Though these conditions are common, the mechanisms of pathogenesis in kidney disease are poorly understood. Genetic predisposition has been established in the African American population; however this does not explain the ubiquity of CKD in the United States and abroad. Diabetes and hypertension are the two most frequently occurring co-morbidities in kidney disease and both have been identified as putative sources of injury to the delicate filtering structures of the kidney. Furthermore, the intrinsic functional relationship between the cardiovascular and renal organ systems adds to the plausibility of a hemodynamic cause. In light of this knowledge, we aim to explore the roles of genetic predisposition and hypertension in the pathogenesis and progression of CKD. The filtering apparatus of the kidney, the glomerulus, is a looping tuft of capillaries specialized to allow the passage of water and certain substances from the blood while restricting others. Glomeruli at the corticomedullary boundary of the kidney experience blood pressures closer to those in systemic arterioles and are subject to similar hemodynamic stresses. To evaluate the role of hypertension in CKD, we employed a well-known model of hypertensive kidney disease in mice involving uninephrectomy (UNX), subcutaneous implantation of a timed-release pellet containing the active aldosterone precursor deoxycorticosterone acetate (DOCA), and a high-salt diet. Given the role of heritability in human CKD pathogenesis, we applied the DOCA-UNX model in two strains of mice with differing susceptibility to kidney damage, the 129S6 and C57BL/6 strains, to evaluate the effects of genetic predisposition. Mice were subjected to varying lengths of hypertension exposure and their kidneys were subsequently examined by transmission electron microscopy (TEM). Ultrastructural lesions of glomeruli were evaluated by a renal pathologist and assigned subjective pathology scores based on the extent and severity of involvement. We hypothesized that certain glomerular lesions, particularly those involving the podocytes of the visceral epithelium, would increase in severity in mice with heritable susceptibility (129S6) as well as those with longer exposure to glomerular hypertension. Our observations demonstrate these hypotheses are partially correct. By TEM histopathology, mouse strain was found to have a significant effect on the severity of certain epithelial lesions while duration of hypertension had a significant effect on the overall morphological pathology of the podocytes, glomerular basement membrane, and glomerulus as a whole. These results provide a promising foundation for further investigation of the pathogenesis of CKD in mice.

Developments in scanning transmission electron microscopy (STEM) have opened up new possibilities for time-resolved imaging at the atomic scale. However, rapid imaging of single atom dynamics brings with it a new set of challenges, particularly regarding noise and the interaction between the electron beam and the specimen. This thesis develops a set of analytical tools for capturing atomic motion and analyzing the dynamic behaviour of materials at the atomic scale. Machine learning is increasingly playing an important role in the analysis of electron microscopy data. In this light, new unsupervised learning tools are developed here for noise removal under low-dose imaging conditions and for identifying the motion of surface atoms. The scope for real-time processing and analysis is also explored, which is of rising importance as electron microscopy datasets grow in size and complexity. These advances in image processing and analysis are combined with computational modelling to uncover new chemical and physical insights into the motion of atoms adsorbed onto surfaces. Of particular interest are systems for heterogeneous catalysis, where the catalytic activity can depend intimately on the atomic environment. The study of Cu atoms on a graphene oxide support reveals that the atoms undergo anomalous diffusion as a result of spatial and energetic disorder present in the substrate. The investigation is extended to examine the structure and stability of small Cu clusters on graphene oxide, with atomistic modelling used to understand the significant role played by the substrate. Finally, the analytical methods are used to study the surface reconstruction of silicon alongside the electron beam-induced motion of adatoms on the surface. Taken together, these studies demonstrate the materials insights that can be obtained with time-resolved STEM imaging, and highlight the importance of combining state-ofthe- art imaging with computational analysis and atomistic modelling to quantitatively characterize the behaviour of materials with atomic resolution.

>Magister Scientiae - MSc / One-dimensional silicon nanowires (SiNWs) are promising building blocks for solar cells as they provide a controlled, vectorial transport route for photo-generated charge carriers in the device as well as providing anti-reflection for incoming light. Two major approaches are followed to synthesise SiNWs, namely the bottom-up approach during vapour-liquid-solid mechanism which employs chemical vapour deposition techniques. The other method is the top-down approach via metal assisted chemical etching (MaCE). MaCE provides a simple, inexpensive and repeatable process that yields radially and vertically aligned SiNWs in which the structure is easily controlled by changing the etching time or chemical concentrations. During MaCE synthesis, a crystalline silicon (c-Si) substrate covered with metal nanoparticles (catalyst) is etched in a diluted hydrofluoric acid solution containing oxidising agents. Since the first report on SiNWs synthesised via MaCE, various publications have described the growth during the MaCE process. However lingering questions around the role of the catalyst during formation, dispersion and the eventual diameter of the nanowires remain. In addition, very little information pertaining to the changes in crystallinity and atomic bonding properties of the nanowires post synthesis is known. As such, this study investigates the evolution of vertical SiNWs from deposited silver nanoparticles by means of in-depth electron microscopy analyses. Changes in crystallinity during synthesis of the nanowires are probed using x-ray diffraction (XRD) and transmission electron microscopy (TEM). Deviations in the optical properties are quantified using optical reflectivity measurements by employing ultraviolet-visible (UV-Vis) spectroscopy, whereas the bonding configurations of the nanowires are probed by Raman and Fourier transforms infrared spectroscopy. Diameters of 50 – 200 nm vertical SiNWs were obtained from scanning electron micrographs and nanowires lengths linearly increased with etching time duration from about 130 nm after 30 seconds to over 15 μm after 80 minutes. No diameter modulations along nanowires axial direction and rough nanowires apexes were observed for nanowires obtained at longer etching times. These SiNWs remained crystalline as their bulk single crystalline Si wafers but had a thin amorphous layer on the surface, findings confirmed by TEM, XRD and Raman analysis. Nanowires were found to be partially passivated with oxygen with small traces of hydrogen termination, confirmed with infrared absorption studies. Finally, low optical reflection of less than 10% over visible range compared to an average of 30% for bulk Si were measured depicting an antireflective ability required in silicon solar cells.

A manutenção da morfologia normal do endotélio da córnea é um importante indicador da integridade funcional. A reparação endotelial frente a um trauma, em coelhos, ocorre por migração, hipertrofia e mitose celular. Objetivou-se comparar a morfologia das células do endotélio, da região periférica perincisional à região central, da córnea de coelhos (Oryctolagus cuniculus) em diferentes períodos pós-operatórios. Foram designados três grupos, com 5 animais cada, para avaliação pós-operatória, sendo G1 (7 dias); G2 (15 dias) e G3 (45 dias). Trinta bulbos dos olhos de coelhos, da raça Nova Zelândia, foram submetidos à incisão de córnea clara uniplanar com 3,2 mm. Ao fim dos períodos determinados, procedeu-se a avaliação da morfologia endotelial valendose da microscopia eletrônica de varredura. Realizaram-se seis eletromicrografias de varredura, de cada região da córnea, com aumento de 1000 vezes. Para análise do percentual do número de lados celular, foram analisadas 100 células endoteliais. Na região periférica perincisional, avaliada ao 7° dia de pós-operatório, foram encontradas células com 6 lados (47,8%), 5 lados (31,3%), 7 lados (13,9%), 3 lados (0,1%), 4 lados (4,9%), 8 lados (1,8%) e 9 lados (0,2%). Na avaliação ao 15° dia de pós-operatório, observaram-se células com 6 lados (45,6%), 5 lados (32,6%), 7 lados (17,4%), 4 lados (1,7%) e 8 lados (2,7%). No 45° dia de pós-operatório, verificou-se a presença de células com 6 lados (57%), 5 lados (24%), 7 lados (17,2%), 4 lados (0,1%), 8 lados (1,6%) e 9 lados (0,1%). Na área central, ao 7° dia de pós-operatório, detectaram-se células com 6 lados (75,6%), 5 lados (13,3%), 7 lados (10,8%) e 8 lados (0,3%). Na avaliação, ao 15° dia de pós-operatório, foi possível observar células com 6 lados (78,9%), 5 lados (11,5%) e 7 lados (9,6%). No 45° dia de pós-operatório identificaram-se células com 6 lados (74,8%), 5 lados (13,6%) e 7 lados (11,6%). Os resultados demonstraram que na região periférica perincisional ocorreu diminuição das células com seis lados e aumento do número de células com cinco e sete lados. Na região central manteve-se o padrão regular de hexagonalidade das células endoteliais nos diferentes períodos pós-operatórios. Conclui-se que houve alteração na morfologia das células endoteliais, da região periférica perincisional comparada à região central, da córnea de coelhos nos diferentes períodos pós-operatórios. / The maintenance of the normal corneal endothelium morphology is an important indicator of its functional integrity. In rabbits, endothelial repair in the event of traumas is made through cell migration, hypertrophy and mitosis. The purpose of this study was to compare the morphology of endothelial cells of the perincisional area with the central area of the cornea of rabbits (Oryctolagus cuniculus), in different post-operative periods. Three groups containing 5 animals each were designed for post-operative evaluation: G1 (7 days); G2 (15 days) and G3 (45 days). The clear cornea of thirty New Zealand rabbits was subjected to a single-planed incision of 3.2 mm. At the end of the established periods, a morphological evaluation of the endothelium was carried out using scanning electron microscopy. Six scanning electron micrographs of each corneal area were performed using a magnification of 1000 x. One hundred endothelial cells were analyzed to obtain the cell side count percentage. In the perincisional peripheral area, which was evaluated at the 7 post-operative day, 6-sided (47.8%), 5-sided (31.3%) and 7-sided (13.9%) cells were found, in addition to, 3-sided cells (0.1%), 4-sided cells (4.9%), 8-sided cells (1.8%) and 9-sided cells (0.2%). In the evaluation made on the 15th post-operative day, 6-sided (45.6%), 5-sided (32.6%) and 7-sided (17.4%) cells were observed, as well as 4-sided (1.7%) and 8-sided cells (2.7%). On the 45th postoperative day, the presence of 6-sided (57%), 5-sided (24%), 7-sided (17.2%), 4-sided (0,1%), 8-sided (1.6%) and 9-sided cells (0.1%) was verified. On the 7th post-operative day, 6-sided (75.6%), 5-sided (13.3%), 7-sided (10.8%) and 8-sided cells (0.3%) were observed in the central area .Upon evaluation made on the 15th post-operative day, it was possible to observe 6-sided (78.9%), 5-sided (11.5%) and 7-sided (9.6%) cells. Results have shown that there was a reduction of six-sided cells and an increase in the number of five and seven-sided cells in the perincisional peripheral area. The regular hexagonal standard of the endothelial cells was maintained in the central area in different post-operative periods. In comparison to the central area, there was a morphological alteration of the endothelial cells of the peripheral perincisional area in different post-operative periods of the cornea of rabbits.

Lyme disease is the most common vector-borne infection in the Western world with an annual incidence usually in excess of 100 cases per 100 000 people in temperate areas of the United States and Europe. Same as other infectious diseases, Lyme borreliosis wreaks havoc on the host they have invaded. B. burgdorferi, the causative agent of this disease, circulates among wildlife vertebrate hosts and Ixodes tick vectors but may sometimes infect humans. Its natural enzootic cycle usually occurs as follows: The larval/nymphal stage tick feeds on an infected host. During this engorgement, the spirochetes reach the tick gut and stay confined to it. After the tick molts into the next developmental stage, it finds a second host. The new bloodmeal triggers the spirochetes to multiply within the gut and traverse the gut endothelium in a highly organized manner. They finally disseminate through the hemocoel up to the tick salivary glands and into the new host. We studied whether B. burgdorferi is capable of reaching the tick salivary glands during the first infective feeding period in uninfected ticks.

Over the last five years hybrid organic-inorganic metal halide perovskites have attracted strong interest in the solar cell community as a result of their high power conversion efficiency and the solid opportunity to realise a low-cost as well as industry-scalable technology. Nevertheless, several aspects of this novel class of materials still need to be explored and the level of our understanding is rapidly and constantly evolving, from month to month. This dissertation reports investigations of perovskite solar cells with a particular focus on their local chemical composition. The analytical characterisation of such devices is very challenging due to the intrinsic instability of the organic component in the nanostructured compounds building up the cell. STEM-EDX (Scanning Transmission Electron Microscopy - Energy Dispersive X-ray spectroscopy) was employed to resolve at the nanoscale the morphology and the elemental composition of the devices. Firstly, a powerful procedure, involving FIB (Focus Ion Beam) sample preparation, the acquisition of STEM-EDX maps and the application of cutting edge post-processing data techniques based on multivariate analysis was developed and tested. The application of this method has drastically improved the quality of the signal that can be extracted from perovskite thin films before the onset of beam-induced transformations. Morphology, composition and interfaces in devices deposited by using different methodologies and external conditions were then explored in detail by combining multiple complementary advanced characterisation tools. The observed variations in the nanostructure of the cells were related to different photovoltaic performance, providing instructive indications for the synthesis and fabrication routes of the devices. Finally, the main degradation processes that affect perovskite solar cells were probed. STEM-EDX was used in conjunction with the application of in situ heating, leading to the direct observation of elemental species migration within the device, reported here for the first time with nanometric spatial resolution. Further analyses, involving a set of experiments aimed to study the effects of air exposure and light soaking on the cells, were designed and performed, providing evidence of the main pathways leading to the drastic drop in the device performance.

Four negative stains, hafnium chloride and europium, samarium and gadolinium nitrates, were tested in single particle electron microscopy as potential alternatives to uranyl acetate, which is recently being widely restricted for its toxicity. The new stains were applied to a structurally well-described plant photosystem I, visualized by a transmission electron microscope and classified in a single particle analysis. The quality of the stains was evaluated by the obtained resolution and ability to provide reliable structural information.