Thesis (M. Phil.)--University of Hong Kong, 2006. / Title proper from title frame. Also available in printed format.

Thesis (M. Phil.)--University of Hong Kong, 2006. / Also available online.

Thesis (Ph. D.)--Cornell University, May, 2008. / Vita. Includes bibliographical references (leaves 125-133).

Thesis (Ph. D.)--Oregon State University, 2009. / Printout. Titles called 1 and 2. Includes bibliographical references (leaves 174-197). Also available on the World Wide Web.

Thesis (Ph. D.)--Case Western Reserve University, 2007. / [School of Medicine] Department of Molecular Virology. Includes bibliographical references. Available online via OhioLINK's ETD Center.

No description available.

Molecular typing of strains among the highly diverse population of Helicobacter pylori (H. pylori) is an important approach for both basic and clinical studies. Genomic DNAs prepared from 18 gastric biopsy specimens, 21 H. pylori clinical isolates obtained from gastric biopsy specimens, and five isolates collected from a single patient at weekly intervals, were subjected to a combined single- and double-stranded conformational polymorphism (SDSCP) assay. The results showed that 19 of 21 isolates tested were discriminated by SDSCP analysis. SDSCP analysis of five H. pylori isolates collected from the same patient at different times resulted in five identical profiles, suggesting the reproducibility of the method. When DNA preparations from 18 gastric biopsy specimens were subjected to SDSCP analysis, 18 unique profiles were generated that matched those of their corresponding cultured H. pylori isolates from each patient. For comparison, polymerase chain reaction (PCR)-based restriction fragment length polymorphism analysis yielded only nine profiles for 20 strains. The data suggest that SDSCP analysis may be an effective and reliable method for differentiation of H. pylori strains directly from gastric biopsy specimens without requiring isolation of the organisms by culture.

Recognition of non-self, pathogen-associated molecular patterns is a central component of host immune response to pathogens like viruses. Intracellular detection of viral nucleic acids leads to the production of type I interferons (IFN-I) and subsequent establishment of an antiviral state in infected and neighboring cells. Viruses have evolved multiple mechanisms to counteract IFN-I responses in infected cells, however, viral nucleic acids released from dying cells can stimulate IFN-I production in surrounding or distal uninfected cells. This thesis examines the mechanisms by which cells recognize extracellular viral nucleic acids and the subsequent downstream antiviral signaling. Class A scavenger receptors (SR-As) internalize extracellular viral double-stranded RNA (dsRNA) to mediate IFN-I responses, but little is known about extracellular viral DNA. We observed that extracellular DNA is recognized and internalized by SR-As in a manner like extracellular dsRNA. Furthermore, we established that SR-A1 is sufficient in mediating extracellular dsRNA-induced cellular responses and other nucleic acid receptors like SR-J1 and DEC-205 are dispensable. Finally, a direct interaction of RNA and DNA species was demonstrated with the coiled-coil collagenous domain of SR-A1, but not the scavenger receptor cysteine rich domain of SR-A6.We elaborated the role of SR-A1 by identifying the cellular processes activated through SR-A1 following uptake of extracellular dsRNA. Cytosolic sensors are essential in mediating an antiviral response to the endocytosed dsRNA, but the mechanism of endoplasmic release and cytoplasmic entry of dsRNA remains an enigma. We demonstrated that the lack of a dsRNA-channel, SIDT2, impaired the ability of the cells to mediate an antiviral response to extracellular dsRNA. Understanding host responses to extracellular viral nucleic acids will enable the development of novel vaccines and antiviral therapeutics against RNA and DNA viruses that efficiently counteract these responses in infected cells. / Thesis / Doctor of Philosophy (PhD) / Viral infections remain a threat to global health as new diseases continue to emerge. To develop effective vaccines and antivirals to combat viruses and alleviate human disease require a deeper understanding of virus-host interactions. Host cells identify virus-associated molecules to detect viruses and eliminate them whereas, viruses employ tactics to prevent the activation of the immune system. However, virus-induced cell lysis releases viral molecules that can stimulate immune responses in neighbouring uninfected cells. This thesis examines the mechanism by which cells respond to extracellular viral nucleic acids. We showed that a protein present at the cell surface called ‘class A scavenger receptor 1’ is sufficient to internalize extracellular viral nucleic acids, leading to immune responses. The response is impaired when a channel protein, SIDT2, is absent in the cells. Further work is necessary to understand how this knowledge can be harnessed to develop vaccines and antiviral therapeutics.

<p> An improved method for the synthesis of oligoribonucleotides of defined sequence was developed. The general phosphotriester synthesis of Neilson and co-workers was modified by the introduction of a new condensing agent, mesitylenesulfonyl-1,2,4-triazole, and by the replacement of the bis(cyclohexylammonium) salt of mono-2,2,2-trichloroethyl phosphate with its acid salt. These modifications provided significant increases in the yields for the condensation of protected nucleosides - especially in the case of purine residues. Finally, modification of the three-step procedure for the deprotection of protected oligoribonucleotides resulted in the isolation of oligomers of exceptional purity and biological activity.</p> <p> Oligomers corresponding to natural sequences in transfer RNA molecules were obtained by this improved method of synthesis. These oligomers were then used to study: 1. The formation of short double-stranded RNA helices and 2. The interactions of aminoacyl-tRNA ligases with tRNA fragments.</p> / Thesis / Doctor of Philosophy (PhD)

No description available.