Random Access Memory (RRAM) has emerged as a leading candidate for nonvolatile memory storage. RRAM devices typically consist of a metal/insulator/metal (MIM) structure and exhibit switching of the device resistivity state (low-to-high, highto- low) by application of electrical bias. It is now widely accepted that shunting and rupturing of local conductive paths (filaments) directly determines the resistance state. The size and composition of these filaments are very much an open question, but are usually attributed to high local concentrations of oxygen vacancies. Although there has been a huge body of research conducted in this field, the fundamental nature of the conductive path and basic switching/failure mechanisms are still under debate. This is largely due to a lack of structural analysis of existing filament size and composition in actual devices. Since the non-volatile nature and device reliability issues (i.e. retention and endurance) are directly related to the irreversible structural transformations in the device, microstructural characterization is essential for eventual commercialization of RRAM. In this study, I investigated oxygen vacancy defect dynamics under electric filed essential for resistive switching and aim to identify size, location, and chemical nature of the conductive filaments in RRAM devices by using a variety of devices and materials characterization methods: in situ transmission electron microscopy (TEM), highresolution TEM (HRTEM), scanning TEM (STEM)-electron energy loss spectroscopy (EELS), electron holography, rapid thermal annealing (RTA), transient thermometry, and electro-thermal simulation. I adopt an in situ electrical biasing TEM technique to study microstructural changes occurring during resistive switching using a model TiO2-based RRAM device, and confirmed the device is switchable inside of the TEM column. I observed extension and contraction of {011} and {121}-type Wadsley defects, crystallographic shear faults, associated with resistive switching. More specifically, emission and adsorption of oxygen vacancies under different polarity of electrical biases at the fault bounding dislocations were identified. The motion of Wadsley defects was used to track oxygen vacancy migration under electric field. Also, the microstructural changes that occur when the device experiences low electric field (~104 V/cm) was reported, akin to read disturb. Crossbar type RRAM device stacks consisting of TiN/a-HfAlOx/Hf/TiN were investigated to estimate filament size, filament temperature, and its chemical footprint using HRTEM, transient thermometry and numerical simulation. In each of the switched devices, a single crystallite ~ 8-16 nm in size embedded in an amorphous HfAlOx matrix was found. The HfAlOx crystallization temperature (Tc) of 850 K was determined by combining RTA and HRTEM imaging. In parallel, the filament size has been determined by transient thermometry. The temperature profile extracted from these measurements suggested that the peak filament temperature was > 1500 K at the center, with the hot zone (T > Tc = 850 K) extending to a radius of 7 nm around the filament. These results were consistent with the HRTEM observations of the crystallite size. The potential filament location (crystallite) in the switching devices was analyzed by STEM-EELS and identification of the filament chemical nature identification has been attempted.

Sambucus Nigra belongs to the most favourite plants of our national folk medicine. It has important place in pharmacy and food industry. It is know in our environment mainly in wild form however increasing interest and demand for qualitative balanced drug contributed to cultivation of cultural varieties in plantations. Flower of Sambucus Nigra contains mostly flavonoids. For receiving of the most quality drug is necessary to follow the rules of harvesting and drying. Currently is drug obtained only just from the plants in wild nature. The goal of thesis was valorising of all characteristic features of flowers Sambacus Nigra and differentiation between cultural varieties and wild forms with using microscopic test of identity stated in Czech Pharmacopoeia 2009. Characteristic flower features of Albida, Alleső, Aurea, Bohatka, Dana, Haschberg, Juicy, Kőrsőr, Madona, Pregarten, Riese aus Vobloch, Tulbing and wild form of Sambuca Nigra were examined. All samples were brightened in solution of chloral hydrate and afterwards microscopic preparations were created. Results were photographically documented. Among the observed features belongs: cells containing sand of calcium oxalate, stomata and epidermal cells of crown leaf. Besides were observed pollen grains, flowers venation or cuticle corrugation of...

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In this thesis, I present three microscopy studies of surface growing Escherichia coli (E. coli ) microcolonies. All experiments were carried out by growing microcolonies on agarose pads, and imaging their growth using phase contrast, fluorescence and confocal microscopy. In the first project, the importance of spatial structure and growth strategies between competing populations of E. coli was studied. An agarose pad was seeded with bacterial cells and their colonisation success tracked. Cell lag-times and local cell density were found to play important roles in determining the eventual success of a colony. Arrangements of neighbouring cells were found to be partially responsible at high cell densities. These results were reproduced using a simple simulation, which also highlighted the importance of exponential expansion in determining colonisation success. The second project investigates the effect of confinement on growing microcolonies restricted to one plane (2d growth). Colonies were grown in agarose microchannels with different aspect ratios, and in unconfined environments. In particular internal physical colony structure and genealogical structure was studied by using single-cell tracking. Results showed that relatedness between cells was directionally biased (cells tended to be more closely related to cells at their poles, than to their side) regardless of the amount of spatial restriction. Furthermore, confinement caused cells to align with each other more, and induced high cell velocities at the colony edges driven by cell expansion. In the final project, growth of secondary layers in growing colonies of E. coli was studied. Cells initially grew as a monolayer, before invading the agarose bulk, producing a secondary layer. By analysing time-lapse movies, this layer was found to initially expand rapidly well in excess of cell growth rates and initial colony expansion rates, before slowing down. The initial secondary growth rate likely depends on the colony area at agarose invasion. Furthermore, the colony area when colonies invaded the agarose depended on their rate of growth, suggesting a complex interplay between forces exerted by the agarose, and by the colony.

The actin cytoskeleton plays a vital role in various biological processes such as cell migration, morphogenesis, and intracellular trafficking. The polymerization of actin filaments at membranes provides the force for generating dynamic actin structures such as protrusions and invaginations that drive these processes. In filopodia, which are finger-like protrusions comprised of bundled actin filaments, actin regulatory proteins are believed to assemble a distal 'tip complex' which stimulates actin nucleation at the membrane. However how these regulators collectively behave in a macromolecular complex still remains poorly understood. To understand the macromolecular nature of these complexes, I investigated the dynamic properties and spatial organization of actin regulatory factors, using an in vitro reconstitution assay for filopodia-like structures (FLS) utilizing artificial lipid bilayers and Xenopus laevis egg extracts. FRAP analysis of seven actin regulatory factors (Toca-1, N-WASP, GTPase-binding domain, Ena, VASP, Diaph3, Fascin) revealed that the FLS tip complex has both dynamic and stable properties, with different proteins displaying distinct dynamics. Further analyses on the membrane-binding protein Toca-1 showed that its dynamic turnover is controlled by interactions with actin and exchange of molecules with solution. Single-molecule localization microscopy resolved the nanoscale organization of Toca-1, showing its arrangement into flat plaque-like and narrowly elevated tubular substructures. Plaque-like structures showed similarities to phase-transition patterns, while tubule-like structures closely resembled those previously found to decorate membrane tubules in vitro, which are thought to be involved in endocytic membrane remodeling. Endocytic accessory proteins such as SNX9 and Dynamin2 were also found to localize to FLS tips. This work provides new insights into the dynamics and organization of protein ensembles at actin nucleation sites, and proposes a novel link between endocytosis and filopodia formation, which is relevant to understanding how cells decide when and where to assemble actin at the membrane.

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by Chen Yunjie. / Thesis (Ph.D.)--Chinese University of Hong Kong, 1997. / Includes bibliographical references (p. 141). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web.

The validity of corneal confocal microscopy (CCM) in assessing peripheral neuropathy has been studied extensively in several studies with a large cohort of subjects with diabetes and in a handful of studies with small sample sizes in subjects with other systemic conditions. The non-invasive nature of this technique as well as its high reproducibility, moderate to high sensitivity and specificity, and ease of use make it an ideal biomarker for diagnosing onset, severity and progression of peripheral neuropathy. This thesis aims to further investigate the potential of CCM by evaluating abnormalities in the corneal sub-basal nerve plexus, Langerhans Cells (LCs) and epithelial cells in neuropathy related to diabetes and cancer. This thesis has established that evaluating the sub-basal nerve plexus in the centre and at the inferior whorl increases the diagnostic performance of CCM. In addition to diagnosing clinical and subclinical neuropathy in children and adults with diabetes CCM can also identify sub-clinical nerve damage in patients with upper gastrointestinal cancer and assess the effects of chemotherapy. CCM also identifies differences in small fibre pathology between diabetic patients with and without painful neuropathy. Although there was an increased prevalence and severity of dry eye and LCs' density, this was not related to an abnormality of corneal nerves in diabetic patients with no or mild neuropathy. Epithelial cell morphology was not associated with corneal nerve damage and did not alter in patients with Type 1 diabetes. In conclusion, CCM has been shown to be an ideal marker for quantifying early small fibre pathology and assessing peripheral neuropathies.

Fluorescence microscopy is a popular biological technique because it allows the study of cells in great detail. However, the resolution achievable is limited by the diffraction properties of light, meaning that fine detail cannot be resolved. Various super-resolution microscopy methods have been developed to break this resolution limit. This thesis focuses on the single molecule localisation microscopy techniques. My host laboratory focuses on DNA replication and repair pathways using the model organism Schizosaccharomyces pombe (fission yeast). The aim of this thesis is thus to apply the technique of photo-activatable localisation microscopy (PALM) to specific biological questions in order to establish its benefits and limitations. In theory, in PALM every molecule will be imaged once and, as such, could be counted. So far this has been largely limited to membrane proteins. Using a combination of artificially created fluorescent oligomers, endogenous ribonucleotide reductase proteins tagged with mEos and computer simulations I studied the feasibility of counting highly expressed cytoplasmic proteins and assigning them to complexes of known or unknown stoichiometry. I established that density of expression is a significant limiting factor when using PALM to resolve complex stoichiometry. I thus went on to develop a variation of fluorescence correlation spectrometry to study the same protein complexes to see if we could determine their stoichiometry by diffusion speed. I established that the technique could differentiate between quite small changes in size. However the endogenous complex did not respond well to the fluorophore used so I was not able to establish its size. Using the PALM system I also studied a biological molecule, Rrp2, which was expressed at such low levels it was not possible to observe with conventional fluorescence microscopy. I established that we were able to observe this protein at endogenous levels and characterised its behaviour in response to stress.

With the wide-spread adoption of exogenous fluorescent indicators – and more recently genetically encoded fluorescent proteins – over the past two decades, there exists a diverse chemical toolkit with which to probe biological systems. Individual cell types and sub-cellular compartments can be targeted in an increasingly wide range of model organisms. However, imaging these samples is often an exercise in balancing the needs of any given experiment against the constraints of the chosen imaging technology. For example, a volume of brain tissue is host to neurons, glia, vascular compartments and red blood cells that all occupy discrete locations in 3D space, but must work together to support healthy organ function. Single-cell activity on the order of milliseconds can trigger downstream processes that unfold over the course of multiple seconds or even minutes. The development of a technique capable of providing depth-resolved, volumetric imaging with scalable spatiotemporal resolution is crucial to developing a proper understanding of such biological systems. Bottlenecks in the throughput of existing technologies stem from a combination of inefficient illumination and volume acquisition strategies, and insufficient sensor read-out speeds. Light sheet microscopy is a promising solution, but individual designs tend to be highly specialized to specific types of samples and do not easily adapt to a wide range of experimental settings. In this thesis, I detail my work in developing swept, confocally-aligned planar excitation (SCAPE) microscopy from a first-generation prototype into a versatile, easy-to-reproduce, easy-to-use system for high-speed, 3D imaging. The first chapter introduces the challenges of designing optical systems capable of high-speed, volumetric imaging. An introduction to design choices faced in the construction of fluorescence microscopes, and current approaches to 3D imaging are discussed. The second chapter describes the progression from the 1st to 2nd generation SCAPE system. Improvements made through ray-tracing models and an enhanced optomechanical design are described, and results from this system in a number of model organisms are presented. The third chapter presents results from a range of biological applications to which SCAPE microscopy has been applied. Work in imaging the zebrafish heart to demonstrate the system’s improved imaging speed, the C. elegans to show the system’s resolution, and finally a number of examples of large field-of-view and high-resolution structural imaging are all described. Finally, the fourth chapter concludes with an overview of the work that lies ahead to both further develop of SCAPE microscopy, as well as to bring the existing system’s strengths to bear in a wider range of environments.