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.
Results
Showing 1 to 20 of 93 for “"deep-sequencing"”.
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A survey of fly and nematode small RNAs by deep sequencing
… to generate a miRNA:miRNA* duplex. Large-scale sequencing of cDNAs derived from endogenously expressed small RNAs is used here to examine the small RNAs of the nematode Caenorhabditis elegans and the fly Drosophila melanogaster, revealing a number of previously unidentified miRNA genes from each …
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Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissues as Revealed by Deep Sequencing
Drought is a major environmental stress factor that poses a serious threat to food security. The effects of drought on early reproductive tissue at 1-2 DAP (days after pollination) is irreversible in nature and leads to embryo abortion, directly affecting the grain yield production. We developed a …
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Population Structure of Yellow Fever Virus: Influence of Viral Diversity on Vaccine Attenuation
… passaged and attenuated vaccine strains. Using deep sequencing techniques, a comparison was made between the prototype West African YFV strain Asibi, and a commercial aliquot of the YFV 17D-204 vaccine. In silico methods revealed the vaccine to be of lower diversity than the parental strain, …
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An investigation Into the genetic variation of hepatitis C virus in patients coinfected with HIV
… completed with the UK and European cohort. A deep sequencing approach was utilised to two effects. The first focussed on a specific notable polymorphism – Q80K in the NS3 gene – to determine whether deep sequencing would benefit the clinic in the detection of this polymorphism at low …
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Implementation, adaptation and evaluation of statistical analysis techniques for next generation sequencing data
Deep sequencing is a new high‐throughput sequencing technology intended to lower the cost of DNA sequencing further than what was previously thought possible using standard methods. Analysis of sequencing data such as SAGE (serial analysis of gene expression) and microarray data has been a popular …
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Investigating the role of germline RNA helicase-1 in Caenorhabditis elegans
… as compared to wild type worms. We utilized deep sequencing on an Illumina platform to analyze differences in miRNA abundance between glh-1(gk100) mutant and wild type worms. In addition, to ascertain whether any miRNAs are germline specific, we also analyzed differences in miRNA expression …
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Influenza C : a pilot study investigating the prevalence in Lancaster of a neglected respiratory virus
… influenza C following PCR and so were sent for deep sequencing. A further seven mixed cDNA samples were also sent for deep sequencing to allow for comparison between different population groups etc. Overall, it was found that influenza C is prevalent in the Lancaster area, with the entire study …
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Tsyn-Seq: A T Cell Synapse-Based Antigen Identification Platform
… followed by antigen identification quantified by deep sequencing (Tsyn-seq). When applied to a previously characterized TCR specific for the E7 antigen derived from human papillomavirus type 16 (HPV16), Tsyn-seq successfully enriched the correct cognate antigen from a cDNA library derived from an …
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FUNCTIONAL ANALYSIS OF THE UPSTREAM PSEUDOKNOT DOMAIN AND ITS SUBSTITUTION WITH A POLY(A) TRACT IN TOBACCO MOSAIC VIRUS (TMV)
… MOSAIC SYMPTOMS IN NICOTIANA BENTHAMIANA. DEEP SEQUENCING RESULTS SHOWED THAT SMALL RNA PROFILES DIFFERED BETWEEN TMV- AND TMV-43A-INFECTED PLANTS. SEVERAL VIRAL SMALL INTERFERING RNAS DERIVED FROM TMV-UPD WERE PREDICTED TO TARGET HOST GENES. RNA STRUCTURES WERE ANALYZED USING SELECTIVE …
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Investigation of Genetic Alterations In Emt Suppressor, Dear1, Through Pan-Cancer Analysis and Ultra-Deep Targeted Sequencing In Ductal Carcinoma In Situ
… of DCIS to IDC. Therefore, targeted ultra-deep sequencing of <em>DEAR1</em> was completed in FFPE samples of 17 Pure DCIS and 17 DCIS samples associated with invasive lesions. Deep sequencing of DCIS indicate <em>DEAR1</em> is mutated in 71% of DCIS. Within these samples, multiple mutations …
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Genetic Characterization of Pediatric T-cell Acute Lymphoblastic Leukemia
… single nucleotide polymorphism (SNP) array, and deep sequencing of 75 selected candidate genes – to characterize co-operative genetic aberrations in a consecutive series of paediatric T-ALL (Article V). One common change identified by SNP array was segemtal uniparental isodisomy (sUPID). This …
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The impact of neutralizing antibody and ADCC responses on HIV-1 envelope evolution in early infection
… cells, may also be protective. This thesis uses deep sequencing, together with immune assays, to characterise HIV-1 Envelope evolution associated with both nAb and ADCC responses in early infection, and investigates broadly neutralizing and non-neutralizing monoclonal antibody ADCC activity …
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Molecular targets of chromatin marks H3K4ME3, H3K9ME3 and H3K27ME3 in an adult germinal niche
… (chromatin immuneprecipitation followed by deep sequencing) to determine genome wide gene targets of three histone modifications: H3K4me3, H3K9me3 and H3K27me3. Our data suggest these chromatin marks are associated with genes responsible for cellular organization and morphology, …
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Discovery and Elucidation of The Fgfr3-Tacc3 Recurrent Fusion In Glioblastoma
… however, with the advent of more powerful sequencing technologies, fusions have recently been reported in several solid tumors. Using next-generation deep sequencing approaches, we discovered a fusion gene connecting the <em>fibroblast growth factor receptor 3</em> (<em>FGFR3</em>) gene to …
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Detecting Changes in Alternative mRNA Processing From Microarray Expression Data
… engine of complexity in higher organisms. Recent deep sequencing studies have indicated that essentially all human genes containing more than a single exon generate multiple RNA transcripts. Functional roles of alternative processing have been established in virtually all areas of biological …
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Genetic circuits for functional screens of Cas12a guide RNA libraries
… libraries with scaffold permutations. Subsequent deep-sequencing of these sorted pools reveals enrichment for a diverse set of highly active, novel functional scaffold sequences. These variants hugely expand the toolbox of Cas12a components available to synthetic biologists, eliminating many of …
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Hypoxia Mediated Downregulation of Mirna Biogenesis Leads to Increased Tumor Progression
… Drosha downregulation under hypoxia. Data from deep sequencing of normoxia and hypoxia treated cells demonstrate clear effect of this downregulation on miRNA maturation. Collectively, we show substantial functional effects of this downregulation on cancer progression under <em>in vivo</em> …
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A molecular characterization of the fungal endophytes within the needles of ponderosa pine (Pinus ponderosa)
… that emerged in 2014. Although more data from a deep sequencing project will be required to confirm this, the results presented here suggests that fungal endophyte communities in ponderosa pine are fairly diverse geographically, and that communities in the same tree differ depending on the age of …
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Host and pathogen genomics: the molecular repertoire of soybean and Sclerotinia interactions
… the RNA samples used in the microarrays to deep sequencing using the Illumina/Solexa SBS platform. These studies allowed for the identification of a set of genes that may play important roles during pathogenicity, including several known defense-related genes. The data also suggested the …
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Evolvability of a viral protease: experimental evolution of catalysis, robustness and specificity
… nucleophile. High-throughput screening and sequencing revealed how the array of possible beneficial mutations changes as the enzyme evolves. Potential adaptive mutations are abundant at each step along the evolutionary trajectory, enriched around the active site periphery. It is currently …
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