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 19 of 19 for “"quasispecies"”.
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Heterogeneity of hepatitis C-virus in genotype 1 patients treated with the combination therapy of pegylated interferon and ribavirin
… terminal region of E2. Genotypes, subtypes and quasispecies can be distinguished. Quasispecies refer to the genetic diversity of a virus population that can be observed in a single infected individual with individual viral genomes differing 1%-5% in nucleotide sequence. Single stand conformation …
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Contributions of Structural and Non-structural Genes to the Attenuation of the 17D Vaccine
… of genetically related virions, known as quasispecies population, which contributes to the fitness and virulence of a virus. Infectious clone (IC)-derived chimeric viruses will be used to investigate contributions of NS protein genes to the generation of quasispecies population by …
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Molecular characterization of the major envelope protein of porcine reproductive and respiratory syndrome virus (PRRSV) and evaluation of its use for a diagnostic assay, vaccine development, and the examination of quasispecies evolution
… genetic characterization, assay development, and quasispecies evaluation using the PRRSV ORF5 gene while also attempting to develop an improved PRRS vaccine. To explore the possible mechanism for the emergence of acute PRRS, the open reading frame 5 (ORF5) gene encoding the major envelope protein …
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Short interval change in hepatitis C hypervariable region 1 in chronic infection. Are there treatment windows in the envelope?
… fashion resulting in mutant progeny known as quasispecies(QS), thought to form an important mechanism of host immune evasion in the establishment and maintenance of chronic infection, which develops in 50-80% of those acutely infected. HCV has three hypervariable regions (sections of the virus …
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Examination of HIV-1 diversity and evolution by a bioinformatics approach
… genetic diversity of HIV-1 gag genes within quasispecies. The results showed that ultra-deep pyrosequencing of amplified HIV genes is a better method than the traditional Sanger-clone-based method in the comprehensive characterization of genetic diversity of HIV-1 quasispecies, especially in …
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Graph-Based Computational Approaches for Modeling Viral Evolution
… and intra-host diversity. In contrast, quasispecies theory describes viral populations as clouds of closely related mutants evolving within a high-dimensional sequence space, where evolutionary relationships are more naturally captured by graphs than trees. In this dissertation, I …
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Computational Methods for Haplotype-aware De Novo Genome Assembly from Long Reads
… particularly applied in diploid genome, viral quasispecies, polyploid genome and metagenome, respectively. Briefly, these methods firstly perform haplotype-aware sequencing error correction using different strategies, and subsequently construct haplotype-aware sequence graphs to generate …
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Artificial Language Evolution on a Dynamical Interaction Network
… preferential attachment that unifies it with the quasispecies model of molecular evolution. The growing network can now be seen as a process in which the links in the network are undergoing selection, replication, and mutation. We also demonstrate that by varying the mutation rate over time, we …
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Genetic diversity of subtype C HIV-1 env variants in peripheral blood mononuclear cell (PBMC) DNA from infected mother-child pairs : a comparison of Heteroduplex Mobility Assay (HMA) and Base Excision Sequence Scanning (BESS) methods
… present to be representative of the total viral quasispecies. In conclusion, this study compared two methods (HMA and BESS) as cost-effective alternatives to DNA sequencing for HIV-1 diversity studies. in addition, a novel application of the BESS assay was demonstrated. Diversity studies are …
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Diversity in APOBEC3 and CCR5 host genes and HIV-1 in a South African population
… were determined for HIV-1 and env V3 loop quasispecies was analysed for co-receptor usage; in an effort to draw inferences for the subsequent utility of Maraviroc as salvage therapy in South Africa. Results and Discussion Next generation library preparation; Tn5 tagmentation based and …
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Identification of Viral Determinants of Murine Norovirus Pathogenesis
… by this method limits the emergence of viral quasispecies. This makes the analysis of biological phenotypes less complex. We identify four phenotypes in which our cloned viruses behave differently from one another and have chosen two, lethality in STAT1-/- mice and persistent infection in wild …
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Genotypic and Molecular Determinants in the Continued Evolution of West Nile Virus in the United States
… and low genetic diversity in natural WNV quasispecies structure. These in silico results and prior applications of the Harris Co. paradigm identified several natural mutations encoded in the NS4B protein—a protein that has been linked to interferon (IFN)-α/β antagonism. In vitro …
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Engineering resistance to maize lethal necrosis
… variety of mutant genomes, collectively called a quasispecies. To deter the evolution of resistance breaking I devised a novel strategy to include intra-sample variation from NGS data in amiRNA design, and constructs, each containing five of these amiRNAs, were transformed into tropical maize …
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Characterisation of HIV-1 Envelope features of breakthrough infections from the CAPRISA 004 Microbicide Trial
… of in vivo virus but did not reflect the entire quasispecies in plasma. The TFV arm viruses were not more resistant to TFV than those in the placebo arm. A comparison of variable loop characteristics, distance to a consensus representative of viruses circulating in the region, and sensitivity to …
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Epitope mapping of the E2 glycoprotein, including the hypervariable region 1, of the hepatitis C virus genotype 3a, in the context of humoral immune pressure
… The variants of HCV within a host are known as quasispecies. Although the host Ab response is not able to resolve the chronic HCV infection, some Abs can bind to particular HCV variants. These Abs form complexes with virus particles and are known as AAVs (antibody-associated virus). AAVs are …
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Evolution of viral populations in individuals infected with single and multiple HIV subtypes : a study of HIV-1 dual infection in a high risk cohort of female bar workers from Tanzania
… high levels of diversity resulting in numerous quasispecies that form a 'swarm' in the infected individual. HIV diversification is driven by selection pressure exerted by the host. The role of high viral diversity in disease progression in context of infection with more than one subtype (dual …
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An agent-based model to simulate virus-based biocontrol for the soybean cyst nematode, Heterodera glycines
Plant parasitic nematodes are responsible for food losses worth 78 billion dollars worldwide. The damage caused by Heterodera glycines, or soybean cyst nematode (SCN), to the US soybean crop is estimated up to 2 billion dollars annually making it the most destructive soybean pathogen. SCN is a …
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Attenuation of Interferon Responses in the Obese Host and Ramifications for Influenza Virus Evolution
<p>The most insidious pandemic of modern life does not arise from an infectious agent but rather from malnutrition. With its global incidence tripling over the past three decades, obesity is a major public health concern. Obesity’s rising prevalence has also illuminated its impact on communicable …
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Population Structure of Yellow Fever Virus: Influence of Viral Diversity on Vaccine Attenuation
Yellow fever virus (YFV) is the prototype of all arthropod-borne viruses, the study of which encompasses some of the landmark paradigm shifts in modern vaccinology. Recently, studies on the lifecycle of RNA viruses have indicated that population structure of these viruses is in many cases complex, …