Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 43 for “"Viral genomes"”.
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Identification of evolutionarily conserved nucleic acid secondary structures within viral genomes
… sequences such as certain DNA and RNA virus genomes form complex secondary structures through Watson-Crick base-pairing interactions between bases on the same DNA or RNA strand. Both computational and experimental methods are available for determining the secondary structure conformations of …
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Gene expression from unintegrated HIV-1 is restricted by the SMC5/6 complex
Integration of viral DNA into the host genome is the hallmark of human immunodeficiency virus 1 (HIV-1) infections. However, in early infection, the most abundant viral DNA species are extrachromosomal unintegrated viral genomes, which despite being competent for gene expression, are poorly …
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Computational investigation of pathogen evolution
Pathogen genomes, especially those of viruses, often change rapidly. Changes in pathogen genomes may have important functional implications, for example by altering adaptation to the host or conferring drug resistance. Accumulated genomic changes, many of which are functionally neutral, also serve …
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Metagenomic approaches for examining the diversity of large DNA viruses in the biosphere
… has challenged the traditional perception of viral complexity due to their enormous genome size and physical dimensions. Previously, viruses were considered small, filterable agents until the discovery of large DNA viruses. Among large DNA viruses, the phylum Nucleocytoviricota and its …
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The development and use of cutting edge next generation sequencing methodologies to study RNA viruses
… viruses and host transcriptomes (in response to viral infection) has expanded – driving virology forward. Here we show the development and use of novel methodologies to study RNA viruses from their impact on the host, to variations in viral genomes, to how context of an infection may alter …
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Molecular investigations of subgroup I geminiviruses
… fragment length polymorphisms (RFLPs) between viral genomes in individual infected plants; DNA cross-hybridization between virus isolates; restriction endonuclease mapping of whole virus genomes; and nucleic acid sequencing. The complete genome of the Natal sugarcane streak virus isolate was …
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Cooperative Assembly of Terminase and Integration Host Factor at the Packaging Initiation Site of Bacteriophage Lambda
Packaging of viral genomes into procapsids by terminase enzymes is conserved in many DNA viruses. Terminases bind to linear concatemers of replicated viral genomes and concomitantly excise (mature) and package a single genome per procapsid. In this thesis, I interrogate the role of E. coli …
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Platforms for exploring host-pathogen interactions in hepatitis C virus infection
… enables visualization and enumeration of single viral genomes in individual cells. We demonstrate that single-cell, multiplexed quantification of viral genomes and host gene transcripts can be used to dissect host-virus interactions, yielding an unexpected positive correlation between stage of …
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Integrative analysis of transcriptional activity and genome architecture changes upon viral infections
… architecture and transcriptional activity during viral infections, I employed a genome-wide chromosome conformation capture approach (Hi-C) on infected murine and human cells and further enriched those libraries for genomic loci of interest and the viral genomes with biotinylated RNA baits. In …
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Pan-Cancer Genomic Characterization of Human Papillomavirus Associated Tumors
… DNA (dsDNA) viruses capable of integrating their genomes into host chromosomes, a phenomenon known to promote HPV-associated cancer formation. HPV integration rates vary by HPV genotype and anatomic site, and some studies have suggested that viral integration, viral load, and HPV type influence …
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MINING SARS-COV-2 PHYLOGENETIC TREES TO ESTIMATE CIRCULATING INFECTIONS AND PATTERNS OF MIGRATION
… the formation of very large databases of genomic viral data. These databases contain information on transmission dynamics, emergence and evolution of SARS-CoV-2. However, extracting this information from sequences is difficult, as most methods of analyzing viral genomes were developed for smaller …
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Genome Organization And Expression Of Selected Potexviruses
… as their respective coat proteins. All viral RNAs tested in vitro produced high molecular weight polypeptides. Peptide mapping of these high molecular weight polypeptides for PMV and CYMV has indicated that they are related to each other but not to their respective coat proteins. The …
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Molecular Evolution of Viruses
… of a methodology to study phylogeny of viral protein sequences based on a technique called chaos game representation. Here we present a method for using CGR to explore evolutionary relationships of protein sequences based on amino acid properties and illustrate the approach with complete …
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Computational Analysis of Viruses in Metagenomic Data
… different strains of known phages. Analysis of viral assemblies from metagenomic data reveals that viral assemblies often contain assembly errors like chimeric sequences which means more than one viral genomes are incorrectly assembled together. In order to identify and fix these types of …
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The evolution and genetics of virus resistance in Drosophila
… the genetic basis of infection between different viral and Drosophila genotypes, I investigated two classic models, gene-for-gene and matching-allele models. These models consider that the outcome of the infection depends on the specific compatibility between host and parasite genotypes. Here, I …
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Characterization of the anti-viral effects inhibited by the vaccinia virus K1 protein
… strategies to evade the host immune and anti-viral response. One such host anti-viral response, activation of the double-stranded RNA activated protein kinase (PKR) pathway, is important in sensing the presence of intracellular viral genomes and their products. PKR is activated by dsRNA, a …
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Demographics of lytic viral infection of coastal ocean Vibrio
Viral predation on bacteria in the ocean liberates carbon from the particulate fraction, where it is accessible to higher trophic levels, and redirects it to the dissolved fraction, where it supports microbial growth. Although viruses are highly abundant in the ocean little is known about how their …
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Chlorellavirus-Proteine: I. Die Hüllprotein-Genfamilie II. Ein primitiver Kaliumkanal
… family Coat proteins play a decisive role in viral host recognition. They interact specifically with structures of the cell surface and mediate viral adherence. Chlorella virus isolates are highly host specific and are grouped accordingly: Pbi viruses infect Chlorella strain Pbi (isolated from …
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Heterogeneity of hepatitis C-virus in genotype 1 patients treated with the combination therapy of pegylated interferon and ribavirin
… in a single infected individual with individual viral genomes differing 1%-5% in nucleotide sequence. Single stand conformation polymorphism (SSCP) is an accurate and reproducible method to study the complexity of HCV quasispecies. <br>This study investigated the degree of complexity of HCV by …
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