The exploration of a quantum dot fluorescence resonance energy transfer (QD-FRET) based bioassay for label-free target nucleic acid detection is reported herein. This work explores the potential for developing a displacement assay for detection of nucleic acid sequences of various lengths, including one of 484 bases. Short probe oligonucleotides conjugated to QDs were allowed to hybridize to short partially mismatched dye-labelled oligonucleotide targets. The non-labelled target of interest, a 484-base segment of heat shock protein 70 (HSP 70), contained a portion that was fully complementary to the probe. Thermodynamic parameters suggested that HSP 70 would displace dye-labelled targets; however, detection was not observed. Modifications were made to this assay to reduce sterics and increase the stability of hybrids. The results obtained using this modified assay indicated that detection of non-labelled, long oligonucleotide sequences was possible using a displacement assay that relied on a short probe oligonucleotide.

Lab-on-a-chip (LOC) biological assays have the potential to fundamentally reform healthcare. The move away from centralized facilities to Point-of-Care (POC) testing of biological assays would improve the speed and accuracy of these, thereby improving patient care. Before LOC can be realized, a number of challenges must be addressed: the need for expert users must be abstracted away; the manufacturing cost of $5 per test threshold must be met; and the supporting infrastructure must be integrated down to an easily portable size. These challenges can be addressed with the deposition of microfluidics on CMOS chips. By designing application specific integrated circuits (ASICs) much of the automation and the supporting infrastructure needed to run these assays can be integrated into the chip. Additionally, CMOS fabrication is some of the most optimized manufacturing in industry today. One of the central challenges with LOC on ASIC is the signal acquisition from the microfluidics into the CMOS. Optical sensing of fluorescence is one form of sensing used for LOC assays. Despite a large literature, there has not been a strong demonstration of monolithic LOC fluorescence detection (FD) for low concentration samples. This work explores the limit-of-detection (LOD) for LOC FD through analysis of the signal and noise of a proposed acquisition channel. The proposed signal acquisition channel consists of an on chip photodiode and integrator based amplification circuits. A hand analysis of the signal propagation through the channel and the noise sources introduced by the circuitry, is performed. This analysis is used to establish relationships between different circuit parameters and the LOD of a hypothetical LOC device. The hand analysis is verified through simulation and the acquisition channel is implemented in: (i) the Austrian Microsystems 350nm CMOS process, (ii) discrete components. Testing of the CMOS chip revealed several issues not identified in extracted simulation; however, the discrete integrator demonstrated many of the trends predicted by the hand analysis and simulations and achieved a LOD of 7.2$\mu M$. This analysis provides insight into the engineering trade-offs required to improve the LOD, to enable more wide spread application of LOC FD.

In this study, we describe the use of different silica materials to separate vanadium compounds from Asphaltenes. We used high performance flash chromatography separation method to separate asphaltenes at different solvent strengths on sea sand. The separation conditions were optimized for flow rate and the strength of the solvent. The selectivity of separation was determined based on asphaltene and metal recovery. With separation on sea sand as the solvent strength increased, the recovery percentage of the asphaltenes also increased. Similarly, stronger solvent blends give poor selectivity based on peak shifts in fluorescence spectra. The separation conditions were then used to compare the performance of a series of silica materials treated with alkaline earth metals. These samples were treated with the same molar concentration of reactant at the same temperature. Treatment of silica materials resulted in an increase in metals recovery and asphaltene recovery by providing less active sites for adsorption. / Chemical Engineering

国立情報学研究所で電子化したコンテンツを使用している。

Bacteria are implicated in endodontic infections. They not only infect the root canal lumen but also invade the dentinal tubules where they may remain untouched by contemporary chemomechanical preparation during root canal therapy. The contentious issue is whether the bacteria within these tubules contribute to secondary infections. Many studies have shown that clinicians fail to completely eradicate them during root canal therapy. At present there are no techniques available to detect the effectiveness of the current chemomechanical treatment regime within dentinal tubules. It is difficult to detect bacteria within the dentinal tubules. Culturing techniques have been used routinely as they are versatile and easy to use. However, they are unable to show the distribution of the bacteria within the dentinal tubules. Scanning electron microscopy, on the other hand, shows detailed surface structure in association with bacteria. Histological examination of root dentine specimens under the light microscope also shows the distribution of bacteria within the specimen but not viability. The dilemma posed by these existing techniques is that the results offer limited information; either demonstrating bacterial viability or bacterial distribution within specimens. No techniques able to show both the viability and the distribution of bacteria within the dentinal tubules have been reported to date. Fluorescent stains, in particular SYTO�9 and propidium iodide (LIVE/DEAD� Baclight[TM] viability kit, Molecular Probes Inc., Eugene, Oregon), have made it possible not only to stain bacteria but to differentiate live and dead bacteria. The combination of these two stains has yet to be applied to dental hard tissue in situ and they provide the basis for this investigation. The aim of this study was to evaluate the potential of the LIVE/DEAD� Baclight[TM] stains in conjuction with confocal laser scanning microscopy in the development of a technique to evaluate the viability and distribution of bacteria within dentinal tubules. This was extended to demonstrate the application of this technique by examining three different means of root canal disinfection both qualitatively and quantitatively. An important aspect of this study was to maintain bacterial viability, as well as to get maximum bacterial invasion into dentinal tubules. Results indicated that when the root canals were instrumented with Protaper� files and then irrigated with sodium hypochlorite (NaOCl) and ethylene diaminetetraacetic acid with cetrimide (EDTAC), there was more bacterial invasion into the dentinal tubules than when the root canals were only irrigated with NaOCl and EDTAC. Daily replenishments of nutrients resulted in deeper bacterial invasion into the dentinal tubules. Bacteria colonized the dentinal tubules up to a distance of 594 � 133 [mu]m from the canal. In the untreated tubules, 96 � 4 % of bacteria remained viable (green-fluorescent), whereas the Amoxicillin-treated tubules contained 94 � 6 % dead (red-fluorescent) bacteria. The calcium hydroxide-treated tubules resulted in 92 � 7 % bacterial death while the laser-treated tubules contained 81 � 12 % dead cells, frequently displaying an inner zone of dead cells surrounded by an outer zone of viable cells. The application of the fluorescent stains combined with confocal microscopy offers a new method for assessing the in vitro efficacy of root canal disinfection regimens.

This thesis describes several aspects of cosmic ray composition studies using the Utah Fly's Eye and High Resolution Fly's Eye (HiRes) detectors. The Fly's Eye detector utilises the atmospheric fluorescence technique to measure the development of cosmic ray cascades as they pass through the atmosphere. This is complementary to the surface array technique, as used by the Akeno experiment in Japan, which measures the electromagnetic and muon content of air showers at a single observation level. For some time it was thought that Fly's Eye and Akeno gave inconsistent composition results. In Chapter 4 I show that the inconsistency is due, for the most part, to a difference in the assumptions made about hadronic interactions. In Chapter 5 I present analysis of the composition between 10^17 and 10^18 eV using the prototype High Resolution Fly's Eye (HiRes) detector in coincidence with the Michigan Muon Array (MIA). The hybrid nature of these measurements gives us more information about cosmic ray showers than either technique on its own. The consistency or otherwise of the composition measured by the two detectors is discussed. Finally, in Chapter 6, I discuss a method of extracting the total proton-proton cross section from the cosmic ray data. This information is of interest because it is derived at centre of mass energies much higher (by at least an order of magnitude) than those currently accessible by collider experiments. I present a preliminary calculation of the cross section using the HiRes/MIA hybrid data set. / Thesis (Ph.D.)--Department of Physics and Mathematical Physics, 2001.

Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.

Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.

Thesis (Ph. D.)--University of Wyoming, 2005. / Title from PDF title page (viewed on Feb. 22, 2008). Includes bibliographical references (p. 110-118).

Thesis (M.S.)--University of Missouri-Columbia, 2007. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on January 11, 2008) Includes bibliographical references.