Microsporidia are unicellular fungi that are intracellular parasites of animals, including humans. They are both complex and simple, armed with a sophisticated infection apparatus and possessing the smallest eukaryotic nuclear genomes. The microsporidian Encephalitozoon cuniculi has a genome size of 2.9 Mb, which is smaller than many bacterial genomes. Genome reduction and compaction in size, content, and form has been interpreted as an adaptation to parasitism. One of the effects of genome size reduction concerns intron evolution — E. cuniculi has retained only a few extremely short spliceosomal introns. This thesis examines the splicing of introns in the spore stage. The introns were retained in spores, suggesting life-stage specific splicing and splicing inhibition. How the short introns are recognized was also examined. Unique splicing signal motifs were predicted, and were used to find additional introns. The intron density was doubled for this species, and I also obtained data that counter current views about intron evolution in compacted genomes with low intron densities. I also predict that E. cuniculi introns are recognized in a unique way by the spliceosome.

We propose a PCF-based interferometer by the misaligned splicing method. The PCF-based interferometers are composed of a photonic crystal fiber (PCF) and single-mode fibers (SMFs) which are spliced with lateral offsets. As the wave propagates at the first splicing point, the lateral offset will excite the cladding mode and the core mode simultaneously. As the two modes reach the other splicing point, they are recombined and coupled into another SMF. Thus, we can observe the interference pattern resulted from the phase difference between the two modes. In addition, as the length of PCF is increased, the average splicing of the interference fringes become smaller in the same measured range. We demonstrate the applications of the PCF-based interferometer as temperature, bending, and the surrounding refractive index sensors. The temperature sensitivity for the 2-cm and 4-cm PCF-based-interferometer is 3.9.~4.3pm/¢XC and 3.5~4.3pm/¢XC, respectively. As we increase the surrounding refractive index, the curves move toward longer wavelengths. Besides, the measured bending sensitivity of the PCF-based interferometer is 3.8~4.2nm/m-1. We also fabricated the liquid-filled-PCF-based interferometers by using the vacuum filling method. The measured bending sensitivity of the liquid-filled-PCF-based interferometer is 8.5nm/m-1 which is higher than that of the PCF-based interferometer. The measured surrounding refractive index sensitivity is insensitive. Thus, this liquid-filled-PCF-based interferometer can also be utilized as a sensor.

Thesis (Ph. D.)--University of Chicago, Dept. of Biochemistry and Molecular Biology, August 2001. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--University of Texas at Austin, 2002. / Vita. Includes bibliographical references. Available also from UMI Company.

Thesis (Ph. D.)--University of Oregon, 2003. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 111-124). Also available for download via the World Wide Web; free to University of Oregon users.

Thesis (M.S.)--Florida State University, 2003. / Dr. Nancy L. Greenbaum, Florida State University, College of Arts and Sciences, Dept. of Chemistry and Biochemistry. A Title and description from dissertation home page (viewed Mar. 12, 2004). Includes bibliographical references.

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Microsporidia are unicellular fungi that are intracellular parasites of animals, including humans. They are both complex and simple, armed with a sophisticated infection apparatus and possessing the smallest eukaryotic nuclear genomes. The microsporidian Encephalitozoon cuniculi has a genome size of 2.9 Mb, which is smaller than many bacterial genomes. Genome reduction and compaction in size, content, and form has been interpreted as an adaptation to parasitism. One of the effects of genome size reduction concerns intron evolution — E. cuniculi has retained only a few extremely short spliceosomal introns. This thesis examines the splicing of introns in the spore stage. The introns were retained in spores, suggesting life-stage specific splicing and splicing inhibition. How the short introns are recognized was also examined. Unique splicing signal motifs were predicted, and were used to find additional introns. The intron density was doubled for this species, and I also obtained data that counter current views about intron evolution in compacted genomes with low intron densities. I also predict that E. cuniculi introns are recognized in a unique way by the spliceosome.

No description available.