Existing optic fibre-bundle based imaging probes have been successfully used to image biological signals from tissue in direct contact with the probe tip (Hirano et al. 1996). These fibre-bundle probe systems employed conventional fluorescence microscopy and thus lacked spatial filtering or a scanned light source, two features used by laser scanning confocal microscopes (LSCMs) to improve signal quality. Improving the methods of imaging tissue in its natural state, deep in-vivo and at cellular resolution is an ever-present goal in biological research. Within this study, a novel (580 μm diameter) optic fibre-bundle direct-contact imaging probe, employing a LSCM, was developed to allow for improved imaging of deep biological tissue in-vivo. The new LSCM/probe system possessed a spatial resolution of 10 μm, and a temporal resolution of 1 msec. The LSCM/probe system was compared to a previously used direct-contact probe system that employed a conventional fluorescence microscope. Quantitative and qualitative data indicated that the LSCM/probe system possessed superior image contrast and quality. Furthermore, the LSCM/probe system was approximately 16 times more effective at filtering unwanted contaminating light from regions below the imaging plane (z-axis). The unique LSCM/probe system was applied to an exploratory investigation of calcium activity of both glial and neuronal cells within the whisker portion of the rat primary somatosensory cortex in-vivo. Fluorescence signals of 106 cells were recorded from 12 female Sprague Dawley rats aged between 7-8 weeks. Fluo-3(AM) fluorophore based calcium fluctuations that coincided with 10 - 14 Hz sinusoidal stimulation of rat whiskers for 0.5-1 second were observed in 8.5% of cells (9 of 106). Both increases and decreases in calcium levels that coincided with whisker stimulation were observed. Of the 8.5 % of cells, 2.8% (3 cells) were categorized as glial and 5.7% (6 cells) as neuronal, based on temporal characteristics of the observed activity. The remaining cells (97 of 106) displayed sufficient calcium-based intensity but no fluctuations that coincided with an applied stimulus. This was partially attributed to electronic noise inherent in the prototype system obscuring potential very weak cell signals. The results indicate that the novel LSCM/probe system is an advancement over previously used systems that employed direct-contact imaging probes. The miniature nature of the probe allows for insertion into soft tissue, like a hypodermic needle, and provides access to a range of depths with minimal invasiveness. Furthermore, when combined with selected dyes, the system allows for imaging of numerous forms of activity at cellular resolution.

Colloidal crystallization in sedimenting systems is an incompletely understood process, where the influence of interparticle forces on the three-dimensional (3-D) microstructure remains to be fully elucidated. This dissertation outlines work that is intended to improve our knowledge of this subject by studying sedimentation equilibrium and phase behavior for electrostatically repulsive systems, as well as the interfacial crystallization of attractive depletion systems. Towards this end, several analytical and experimental tools have been developed to explore the thermodynamic behavior of these systems. For example, the experimental challenges necessitated the development and implementation of the following in this work: (1) core/shell silica particles incorporating molecular fluorophores or semiconductor nanocrystals; (2) modification of silica particle surfaces; (3) the design of specialized sedimentation cells; and (4) the development of a novel fluorescent intensity-based approach to quantifying colloidal sediments. Analysis of the experimental data required the use of the following tools: (1) location of particle centers from images; (2) deconvolution of intensity profiles using a novel Monte Carlo-type algorithm; and (3) prediction of colloidal phase diagrams using perturbation theory. On the basis of this work’s experimental and simulation data, it is concluded that competing orientations of crystal grains may suppress crystallization at grain boundaries, resulting in a non-uniform depth of the fluid/solid transition. Also, it was demonstrated that the grain size in depletion crystals formed from quantum dot-coated silica particles can be increased by localized annealing with the confocal microscope’s laser. Additional findings include the ability of the intensity-based approach to measure interparticle forces in colloidal sediments, as well as the inability to use perturbation theory to predict two-dimensional colloidal fluid/solid transitions. While significant progress has been achieved, work on 3-D imaging of colloidal depletion crystals in a refractive index-match medium is ongoing. This work improves our understanding of 3-D colloidal crystallization at interfaces, as well as provides new tools for future research. Also, this work demonstrates a potential route for zone refining of colloidal crystals, a technique that may be important in the search for low-defect 3-D arrays that can be used as templates for photonic bandgap materials.

Thesis (Ph. D.)--University of Texas at Austin, 2003. / Vita. Includes bibliographical references. Available also from UMI Company.

Thesis (MS)--Montana State University--Bozeman, 2008. / Typescript. Chairperson, Graduate Committee: Jean Starkey. Includes bibliographical references (leaves 70-76).

Thesis (Ph.D.) OGI School of Science & Engineering at OHSU, December 2006. / Abstract: leaves xvii-xviii. Includes bibliographical references (leaves 197-204).

Thesis (Ph. D.)--University of Texas at Austin, 2004. / Supervisor: Michael C. Downer. Vita. Includes bibliographical references.

Thesis (Ph. D.)--Montana State University--Bozeman, 2007. / Typescript. Chairperson, Graduate Committee: Anne Camper. Includes bibliographical references (leaves 104-113).

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

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The filamentous cyanobacteria Nostoc punctiforme ATCC 29133 is a model species fordevelopment of sustainable production methods of numerous compounds. One of its uniquefeatures is the anaerobic environment of the strains nitrogen fixing heterocyst cells. To be ableto properly utilize this environment, more knowledge regarding what regulates cell specificexpression is required. In this study, three motifs of the NsiR I promoter of Anabaena sp.PCC 7120 was studied in this system utilizing YFP-fluorescence as a reporter to determinetheir impact on spatial expression pattern. Investigations were performed on immobilizedcells with the use of confocal microscopy and results point towards sigma factor regulation.