In this research we consider two different approaches for microfabricating physical templates to be used in template directed colloidal self-assembly experiments. Fabrication of templates, usable with confocal microscopy, forms an essential part of observation and analysis of template directed colloidal self-assembly studies. We use existing laboratory based microfabrication methods for patterning thin glass coverslips and polymeric films. These templates when used for directing colloidal self-assembly along with confocal microscopy analysis provide us with relevant information on the effect of confined geometries of the template on particle packing and order. The first method of template fabrication involves ultraviolet photolithography, thin film deposition, and glass micro machining. Various stages of the process were optimized while selecting reactive ion etch (RIE) and nickel etch mask with a suitable etch recipe for microfabrication of patterns on thin multi-component glass coverslips. Pattern dimensions were shown to be nearly commensurate with patterns on the microfiche, which was used as a field mask. In another approach, mechanical machining for fabricating polymeric templates was attempted on poly(methyl methacrylate) films spin coated on thin glass cover slips. The mechanical machining was implemented using computer numerical control (CNC) machines with the pattern dimensions in the range of 50 Mu m-150 Mu m. The glass and polymeric templates were used in template directed colloidal self-assembly experiments us ing polystyrene or silica particles. Confocal microscopy was used to obtain images of particle packing in template geometries. Imaging of the particles confined in the template geometries show increased particle concentration along pattern walls and corners. Inherent pattern irregularities and roughness possibly resulted in limited order in particle. Using a simple fortran program, image stack generated from confocal microscopy is used for obtaining images of particle packing in four different view planes which includes top, side, cross sectional and diagonal view of the image stack. The results from this research show the application of simple microfabrication processes for creating physical templates for template directed colloidal self-assembly. Confocal microscopy imaging combined with fortran image processing program can provide images of particle packing in different view planes. These images of the particles confined in various pattern geometries illustrate greater possibility of packing order in straight and regular pattern geometries or profiles.

Thesis (Ph. D.)--University of Missouri-Columbia, 1999. / Typescript. Vita. Includes bibliographical references (leaves 99-102). Also available on the Internet.

Thesis (M.S.)--California Polytechnic State University, 2009. / Title from PDF title page; viewed on January 5, 2010. Major professor: Lily Laiho, Ph.D. "Presented to the faculty of California Polytechnic State University, San Luis Obispo." "In partial fulfillment of the requirements for the degree [of] Master of Science in Engineering." "December 2009." Includes bibliographical references (p. 79-83). Also available on microfiche.

Thesis (Ph. D.)--University of California, San Diego and San Diego State University, 2003. / Vita. Includes bibliographical references.

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Chemotaxis is a process whereby single- and multi-cellular organisms migrate in response to external chemical stimuli. This directed cell movement is regulated by complex signaling pathways and is implicated in embryonic development, immune response, and the metastasis of cancer cells. Dictyostelium discoideum, social amoebae with the ability to migrate and aggregate in response to chemoattractants such as cAMP, have been used as a model system to study chemotaxis. Preliminary research suggests that protein kinase (PKA) is involved in some of the signaling pathways that regulate chemotaxis. The role of PKA in chemotaxis was investigated, first, by characterizing the phenotype of PKA null cells using established cell biological and biochemical assays. Furthermore, spatiotemporal regulation of critical cytoskeletal proteins was probed in wild-type and PKA null cells using confocal fluorescence microscopy, indicating misregulation of both F-actin and Myosin II in pkaC- and pkaR- cells. Finally, preliminary work was done to lay the groundwork for experiments exploring possible PKA targets mediating TORC2 function in chemotaxis.

Ovarian cancer is the fifth leading cause of cancer related deaths among women. Early detection improves the chances of survival following diagnosis, and new imaging modalities have the potential to reduce deaths due to this disease. The confocal microendoscope (CME) is a non-destructive in-vivo imaging device for visualization of the ovaries that operates in real-time. Two components of the CME system are evaluated in this paper, and initial results from an ongoing clinical trial are presented.Fiber-optic imaging bundles are used in the CME imaging catheter to relay images over distances of up to 20 feet. When detecting fluorescent signals from investigated tissue, any fluorescence in the system can potentially reduce contrast in images. The emission and transmission properties of three commercially available fiber optic imaging bundles were evaluated. Emission maps of fluorescence from bundles were generated at multiple excitation wavelengths to determine the profile and amount of fluorescence present in bundles manufactured by Sumitomo, Fujikura, and Schott. Results are also presented that show the variation of transmittance as a function of illumination angle in these bundles. Users of high-resolution fiber-optic imaging bundles should be aware of these properties and take them into account during system design.Contrast is improved in images obtained with the CME through the application of topical dyes. Acridine orange (AO) and SYTO 16 are two fluorescent stains that are used to show the size, shape, and distribution of cell nuclei. Unfortunately, little is known about the effects of these dyes on living tissues. This study was undertaken to evaluate the effects of dye treatment on peritoneal tissues in mice. Seventy-five Balb/c mice were split into five groups of fifteen and given peritoneal injections of dye or saline. The proportions of negative outcomes for the control and test groups were compared using confidence intervals and the Fisher's exact test. No significant difference was determined between the groups. These data provide preliminary results on determining the effect of these dyes on living tissues.Preliminary results of a clinical trial are presented showing in-vivo use of the CME for imaging of the ovaries. This is the first portion of a two part study to demonstrate the clinical diagnosis potential of the CME system. A mobile version of the bench-top CME was modified to be used in the clinic. Fluorescein sodium is used as an initial contrast agent in these studies to demonstrate fluorescence imaging. Twenty patients were successfully imaged, and results of this study have allowed progression to a clinical validation study showing the diagnostic capabilities of the CME.

This dissertation presents the design of a miniature injection-molded objective lens for a fiber-optic confocal reflectance microscope. This is part of an effort to demonstrate the ability to fabricate low cost, high performance biomedical optics for high resolution in vivo imaging. Disposable endoscopic microscope objectives could help in vivo confocal microscopy technology mature to enable large-scale clinical screening and detection of early cancers and pre-cancerous lesions. This five lens plastic objective has been tested as a stand-alone optical system and has been coupled to a confocal microscope for in vivo imaging of cells and tissue. Changing the spacing and rotation of the individual optical elements can compensate for fabrication inaccuracies and improve performance. An optical-bench testing system was constructed to allow interactive alignment during testing. The modulation transfer function (MTF) of the miniature objective lens is determined using the slanted-edge method. A custom MATLAB program, edgeMTF, was written to collect, analyize, and record test data. An estimated Strehl ratio of 0.64 and an MTF value of 0.70, at the fiber-optic bundle Nyquist frequency, have been obtained. The main performance limitations of the miniature objective are mechanical alignment and flow-induced birefringence. Annealing and experimental injection molding runs were conducted in effort to reduce birefringence.