Thesis (M.S.)--University of Tennessee, Knoxville, 2009. / Title from title page screen (viewed on Oct. 23, 2009). Thesis advisor: Reza Hajimorad. Vita. Includes bibliographical references.

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Some positive-strand RNA plant viruses possess a transfer RNA-like structure (TLS) at the 3'-terminus of their genomic RNAs. The closest mimicry to tRNA is exhibited by the valylatable TLSs from tymoviruses and furo-like viruses, which are able to interact with key cellular tRNA enzymes: [CTP, ATP]:tRNA nucleotidyltransferase (CCA NTase), valyl-tRNA synthetase (ValRS), and translation elongation factor 1A (eEF1A). In this thesis, I report the discovery of two new roles of the Turnip yellow mosaic tymovirus TLS, in translation enhancement (Chapter 2) and repression of minus strand initiation (Chapter 4). Placement of the 3'-terminal 109 nts of TYMV RNA in a luciferase reporter RNA with a generic 5'-UTR enhanced translation by about 20-fold in cowpea protoplasts. Exhibiting a synergistic relationship with the 5'-cap, the 3'-translation enhancement was largely dependent on the aminoacylatability of the TLS and apparently on eEF1A interaction. In the presence of the 5'-UTR from genomic TYMV RNA, translation of both the overlapping proteins p69 and p206 was strongly dependent on a 5'-cap structure, and was enhanced by the 3'-enhancer. These in vivo results contradict the proposed model in which translation initiation of p206, but not p69, is cap-independent and TLS-dependent (Barends et al. Cell 112(2003):123-9). In vitro experiments with a partially purified preparation of TYMV replicase have investigated the phenomenon of minus strand repression. Interaction of purified eEF1A���GTP specifically with the valylated TLS decreased the template activity for minus strand to near-background levels. eEF1A���GTP acts by making the 3'-CCA minus strand initiation site unavailable to the replicase. The influence of eEF1A in simultaneously enhancing translation and repressing minus strand synthesis can be considered a regulation that ensures robust translation early in the infection and that offers a coordinated transition from translation to replication. Previously shown to be critical for TYMV infectivity, a valylatable TLS was investigated for its role in the replication and infectivity of the bipartite Peanut clump pecluvirus. A valylatable TLS provided a small competitive advantage in protoplasts and whole plants. The advantage was more apparent in protoplasts than in whole plants, and more so in the replication protein-encoding RNA1 than in the trans-replicating RNA2. / Graduation date: 2004

The genomic diversity of viral quasispecies is a subject of great interest, especially for chronic infections. Characterization of viral diversity can be addressed by high-throughput sequencing technology (454 Life Sciences, Illumina, SOLiD, Ion Torrent, etc.). Standard assembly software was originally designed for single genome assembly and cannot be used to assemble and estimate the frequency of closely related quasispecies sequences. This work focuses on parsimonious and maximum likelihood models for assembling viral quasispecies and estimating their frequencies from 454 sequencing data. Our methods have been applied to several RNA viruses (HCV, IBV) as well as DNA viruses (HBV), genotyped using 454 Life Sciences amplicon and shotgun methods.

The genomic diversity of viral quasispecies is a subject of great interest, especially for chronic infections. Characterization of viral diversity can be addressed by high-throughput sequencing technology (454 Life Sciences, Illumina, SOLiD, Ion Torrent, etc.). Standard assembly software was originally designed for single genome assembly and cannot be used to assemble and estimate the frequency of closely related quasispecies sequences. This work focuses on parsimonious and maximum likelihood models for assembling viral quasispecies and estimating their frequencies from 454 sequencing data. Our methods have been applied to several RNA viruses (HCV, IBV) as well as DNA viruses (HBV), genotyped using 454 Life Sciences amplicon and shotgun methods.

Thesis (Ph. D.)--University of Texas at Austin, 2000. / Vita. Includes bibliographical references (leaves 105-129). Available also in a digital version from Dissertation Abstracts.

Thesis (M.Sc.)--York University, 2008. Graduate Programme in Biology. / Typescript. Includes bibliographical references (leaves 94-99). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:MR38791

Thesis (Ph. D.) in Biochemistry and Molecular Biology--University of Maine, 2001. / Includes vita. Includes bibliographical references (leaves 71-83).

No description available.

Copy of author's previously published work, inserted. / Bibliography: leaves 83-99. / ix, 99, [43] leaves, [29] leaves of plates : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Investigates an improved method with high efficiency for reassembly of CMV (Cucumber mosaic virus) and TAV (Tomato aspermy virus). Physico-chemical, serological and biological analyses show that the reassembled particles are indistinguishable from the native viruses. / Thesis (Ph.D.)--University of Adelaide, Dept. of Crop Protection, 1992