Thesis (Ph. D.)--Ohio State University, 2005. / Title from first page of PDF file. Includes bibliographical references (p. 196-235).

Thesis (Ph. D.)--University of Texas at Austin, 2006. / Vita. Includes bibliographical references.

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.

This thesis discusses various large multi-dimensional dataset analysis methods and their applications. Particular attention is paid to non-linear optimization analyses and general processing algorithms and frameworks when the datasets are significantly larger than the available computer memory. All new presented algorithms and frameworks were implemented in the HyperSpy analysis toolbox. A novel Smart Adaptive Multi-dimensional Fitting (SAMFire) algorithm is presented and applied across a range of scanning transmission electron microscope (STEM) experiments. As a result, the Stark effect in quantum disks was mapped in a cathodoluminescence STEM experiment, and fully quantifiable 3D atomic distributions of a complex boron nitride core-shell nanoparticle were reconstructed from an electron energy loss spectrum (EELS) tilt-series. The EELS analysis also led to the development of two new algorithms to extract EELS near-edge structure fingerprints from the original dataset. Both approaches do not rely on standards, are not limited to thin or constant thickness particles and do not require atomic resolution. A combination of the aforementioned fingerprinting techniques and SAMFire allows robust quantifiable EELS analysis of very large regions of interest. A very large dataset loading and processing framework, “LazySignal”, was developed and tested on scanning precession electron diffraction (SPED) data. A combination of SAMFire and LazySignal allowed efficient analysis of large diffraction datasets, successfully mapping strain across an extended (ca. 1 μm × 1 μm) region and classifying the strain fields around precipitate needles in an aluminium alloy.

>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.