Thesis (Ph. D.)--Biomedical Engineering, Georgia Institute of Technology, 2006. / Tannenbaum, Allen, Committee Member ; Choi, Jung, Committee Member ; Borodovsky, Mark, Committee Chair ; Voit, Eberhard, Committee Member ; Lee, Eva, Committee Member.

Thesis (Ph.D.)--University of Nebraska-Lincoln, 2006. / Title from title screen (site viewed on Oct. 6, 2006). PDF text: xiv, 307 p. : ill. (some col.) ; 4.75Mb. UMI publication number: AAT 3213861. Includes bibliographical references. Also available in microfilm, microfiche and paper format.

No description available.

published_or_final_version / Microbiology / Master / Master of Philosophy

Whether certain Epstein-Barr virus (EBV) strains are associated with pathogenesis of nasopharyngeal carcinoma (NPC) is still an unresolved question. In the present study, we aimed to sequence the complete EBV genomes harbored in NPC tumor biopsies and compare against the non-NPC EBV strains to identify NPC-specific EBV variations. In the first part of the study, EBV genome contained in one primary NPC tumor biopsy was PCR-amplified and sequenced using next-generation and dideoxy-DNA sequencing. The EBV genome, designated HKNPC1 (Accession number JQ009376), was generated by reference mapping and it appears to be a uniform strain in general despite minor heterogeneity. Phylogenetic analysis with the four published EBV strains, B95-8, AG876, GD1, and GD2, indicated HKNPC1 was more closely related to the Chinese NPC strains. HKNPC1 contains 1,589 single nucleotide variations (SNVs) and 132 insertions or deletions (indels). We found 76 non-synonymous SNVs shared amongst the Chinese GD1, GD2 and HKNPC1 isolates, while another 88 nonsynonymous SNVs were shared only by the two NPC tumor-derived strains HKNPC1 and GD2. In the second part of the study, SureSelect target enrichment technology was used instead of PCR to capture EBV DNA from total DNA. The study was scaled-up to sequence EBV strains in cell lines, saliva and NPC tumor, using the MiSeq Personal Sequencer and the Genome Analyzer IIx platforms. The reads were de novo assembled to generate 17 complete EBV genomes, out of which 9 were NPC-EBV strains. Phylogenetic analysis of all available EBV strains has demonstrated that all NPC strains were type 1 EBV. Phylogeny predicted by LMP-1 gene showed clear geographical pattern of where the EBV strains were isolated. A total of 5,011 variations were identified by comparing every EBV strain against the reference. MicroRNAs and EBERs are generally well conserved across all genomes. Comparative analysis of variations between NPC and non-NPC EBV strains discovered 904 NPC-specific variations, out of which 112 appeared in more than one NPC strains. Among these recurrent variations, 39 non-synonymous substitutions and seven deletions in coding region were found. About half of these recurrent variations were located in EBNA-3A, -3B and -3C, while the rest was found in latent, tegument, capsid and packaging-related proteins and transcription factors. There were two NPC EBV strains isolated from the primary tumors which later diagnosed to have distant metastasis. Unique variations were shared in these two EBV strains in regions between IR2 and IR3, where genes such as BPLF1, BOLF1 and EBNA-3A, -3B and -3C were located, and leftward of IR3, where BBLF2/3 and BBRF1 were found. In conclusion, we have demonstrated the feasibility of target capture and next-generation sequencing in whole genome sequencing of EBV. Comparison of reference mapping and de novo assembly of EBV sequences illustrated that both are feasible approaches, though de novo assembly is preferred since the method is less dependent on the reference genome. Large-scale sequencing of NPC and non-NPC EBV strains may facilitate the discovery of previously unknown variations of biological significance and reveal the diverse role of EBV in NPC pathogenesis. words) / published_or_final_version / Paediatrics and Adolescent Medicine / Doctoral / Doctor of Philosophy

Thesis (M.S.)--University of Texas at El Paso, 2009. / Title from title screen. Vita. CD-ROM. Includes bibliographical references. Also available online.

No description available.

This thesis presents novel methods for analysis of short viral sequences and identifying biologically significant regions based on their statistical properties. The first section of this thesis describes the ab initio method for identifying genes in viral genomes of varying type, shape and size. This method uses statistical models of the viral protein-coding and non-coding regions. We have created an interactive database summarizing the results of the application of this method to viral genomes currently available in GenBank. This database, called VIOLIN, provides an access to the genes identified for each viral genome, allows for further analysis of these gene sequences and the translated proteins, and displays graphically the distribution of protein-coding potential in a viral genome. The next two sections of this thesis describe individual projects for two specific viral genomes analyzed with the new method. The first project was devoted to the recently sequenced Herpes B virus from Rhesus macaque. This genome was initially thought to lack an ortholog of the gamma-34.5 gene encoding for a neurovirulence factor necessary for viability of the two close relatives, human herpes simplex viruses 1 and 2. The genome of Rhesus macaque Herpes B virus was annotated using the new gene finding procedure and an in-depth analysis was conducted to find a gamma-34.5 ortholog using a variety of tools for a similarity search. A profound similarity in codon usage between B virus and its host was also identified, despite the large difference in their GC contents (74% and 51%, respectively). The last thesis section describes the analysis of the Mouse Cytomegalovirus (MCMV) genome by the combination of methods such as sequence segmentation, gene finding and protein identification by mass spectrometry. The MCMV genome is a challenging subject for statistical sequence analysis due to the heterogeneity of its protein coding regions. Therefore the MCMV genome was segmented based on its nucleotide composition and then each segment was considered independently. A thorough analysis was conducted to identify previously unnoticed genes, incorrectly annotated genes and potential sequence errors causing frameshifts. All the findings were then corroborated by the mass spectrometry analysis.

Viral metagenomics of feces collected from 58 Peruvian children with unexplained diarrhea revealed several small circular ssDNA genomes. Two genomes related to sequences previously reported in feces from chimpanzees and other mammals and recently named smacoviruses were characterized and then detected by PCR in 1.7 % (1/58) and 19 % (11/58) of diarrheal samples, respectively. Another three genomes from a distinct small circular ssDNA viral group provisionally called pecoviruses encoded Cap and Rep proteins with <35 % identity to those in related genomes reported in human, seal, porcine and dromedary feces. Pecovirus DNA was detected in 15.5 % (9/58), 5.9 % (3/51) and 3 % (3/100) of fecal samples from unexplained diarrhea in Peru, Nicaragua and Chile, respectively. Feces containing these ssDNA genomes also contained known human enteric viral pathogens. The cellular origins of these circular ssDNA viruses, whether human cells, ingested plants, animals or fungal foods, or residents of the gut microbiome, are currently unknown.

Thesis (M.S.)--University of Delaware, 2006. / Principal faculty advisor: Calvin L. Keeler, Dept. of Animal & Food Sciences. Includes bibliographical references.