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 90 for “"amplicon sequencing"”.
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High-throughput Amplicon Sequencing Optimization for Downstream Prediction Purposes
… involves the optimization of a high-throughput amplicon sequencing assay targeting ~2,000 SNPs associated with pigmentation, facial morphology, and ancestry. Over 400 samples were processed through a genotyping pipeline involving DNA extraction, library preparation with a modified version of a …
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Metagenomic amplicon sequencing as a rapid and high-throughput tool for aquatic biodiversity surveys
… system management. In particular, metagenomics amplicon sequencing of environmental DNA (eDNA) can characterize hundreds to thousands of species within a single sample in a timely and cost effective manner, and allow hundreds of samples to be sequenced in a single reaction. This PhD thesis aims …
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Microbial transformation of arsenic in Bengal floodplain
… in Bangladesh. In the present study, 16S rRNA amplicon sequencing and metagenomics (Illumina), alongside chemical analysis in paddy and nonpaddy soils, from Holocene and Pleistocene regions, of Bangladesh to investigate microbial composition and functional diversity of arsenic metabolism genes …
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Seafloor Sediment Bacterial Community Profiling for Baselines and Environmental Effects Monitoring at a Deep-Sea Oil Production Site Offshore Nova Scotia, Canada
… were used to generate 51 bacterial 16S rRNA gene amplicon libraries (V3-V4 region) to form a DNA baseline. A 300-day-long mock oil spill experiment using Scotian Slope sediment identified potential bacterial bioindicators of pristine and contaminated conditions, relative to baseline, underpinning …
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THE BROWN BEAR GUT MICROBIOME: A NOVEL TOOL FOR CONSERVATION & MANAGEMENT
… and extracted microbial DNA for 16S rRNA amplicon sequencing and microbial taxonomic classification. My results indicate that location and diet drive GMB variation and GMB composition reflects diverse foraging strategies while allowing brown bears to achieve similar body condition …
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Environmental DNA (eDNA) Metabarcoding: Analysis of Freshwater Macroinvertebrate Community Structure and Diversity
… and I targeted cytochrome c oxidase I (COI) for amplicon sequencing. I analyzed the resulting alpha and beta biodiversity indexes to assess the ecological distribution of freshwater macroinvertebrates and found that freshwater macroinvertebrate community composition was significantly different …
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The Impacts of Disruptive Environmental Change on Vital Microbial Ecosystems
… of high-throughput fluid imaging and 18S amplicon sequencing, we demonstrate a taxonomic convergence but a functional divergence of microbes in response to warming and elevated CO<sub>2</sub> ; we find novel evidence that warming effects on functional composition are reversed by elevated …
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Linking sequence to function in microbial genomics
… communities still rely on bulk, single-gene amplicon sequencing. In this thesis, I present methods that interrogate the gene content of single cells derived from complex natural communities. In the first project, I present a novel molecular biology method to link a bacterial functional gene …
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Profiling Bacterial Community Dynamics For Wildlife Ecology and Geological Mineral Exploration
… environments. Bacterial community 16S rRNA gene amplicon sequencing is an approach to microbiome exploration that profiles community composition, structure, and dynamics across environmental conditions. In this thesis, 16S rRNA gene amplicon sequencing is used to investigate the bacterial …
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EPIDEMIOLOGY AND POPULATION GENETICS OF THE GRAPE POWDERY MILDEW CAUSAL FUNGUS, ERYSIPHE NECATOR, AND ITS RELATION TO COMMERCIAL DISEASE MANAGEMENT
… a couple years of deployment. For this study, Amplicon Sequencing (AmpSeq) was performed on 3,170 field samples of E. necator collected between 2015 and 2020 with multiple timepoints per season investigated starting in 2018. This dissertation addresses the following questions: i) How accurately …
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Quantitative modeling for microbial ecology and clinical trials
… and increased quality of next-generation DNA sequencing. In general, studies that use DNA sequencing are no longer limited by the sequencing itself but instead by the acquisition of the samples and by methods for analyzing and interpreting the resulting sequence data. In this thesis, I …
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Assessment of a Passive Sampler for Aquifer Microbial Community Profiling and Comparison of Porous Media
… and laboratory-grade silica sand. 16S rRNA gene amplicon sequencing was applied to profile microbial communities and revealed that native aquifer sediment from the aquifer of study best reflected influent microbial composition and temporal shifts, particularly among the dominant bacterial phyla …
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Effects of the antibiotic tetracycline on the honey bee gut microbiome
… gut microbiome as determined with 16S rRNA gene amplicon sequencing, as fecal and whole gut samples did not differ significantly for individual bees. The fecal sampling technique was then used to examine changes to individual honey bee gut bacterial communities before and after tetracycline …
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Nitrification inhibitors have minimal impact on microbial and Collembola communities in Danish arable soil
… identification, quantitative PCR (qPCR) and amplicon sequencing. Our results revealed that neither ammonia-oxidizing microorganisms nor non-target bacterial and fungal communities, as well as collembola, were not significantly affected by short-term NI application, even at tenfold dosages …
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Effect of Soil Type, Composting, and Antibiotic Use on Fate of Antibiotic Resistance Genes and Microbial Community Composition in Dairy and Beef Manure Applied Soils
… composition was determined via 16S rRNA amplicon sequencing. The results indicated that while prior antibiotic administration elevated the relative abundance of ARGs and changed the microbial community of raw manure applied soils, composting reduced this effect. However, compost applied …
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What Drives Gut Microbial Diversity and Community Structure Among Closely-Related Host Species?
… microbial DNA from fecal samples for 16S rRNA amplicon sequencing. I identified “core” bacterial taxa within herbivore species based on abundance and occurrence within samples. I discovered that certain bacterial taxa serve as environmental and physiological indicators in hosts. I found that …
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THE GUT MICROBIOTA OF A WILD AMERICAN BLACK BEAR (Ursus americanus) POPULATION
… legally harvested black bears, 16S rRNA gene amplicon sequencing to identify microbial taxa, and stable isotope analysis of black bear hair to estimate diet. My results suggest that the jejunum and colon of black bears do not harbor significantly different GMB communities, but that increased …
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Effect of Soil Amendments from Antibiotic Treated Cows on Antibiotic Resistant Bacteria and Genes Recovered from the Surfaces of Lettuce and Radishes: Field Study
… (12 plots, n=3). Culture-based methods, 16SrDNA amplicon sequencing, qPCR and shot-gun metagenomics were utilized to profile bacteria and characterize the different gene markers for antibiotic resistance. Culture-based methodologies revealed that lettuce grown in soils amended with BSAs had …
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Deciphering the contribution of root hairs in barley to the structure and function of the rhizosphere bacterial microbiota
… were developed:<br/><br/>By using 16S rRNA gene amplicon sequencing, it was demonstrated that the presence and development of root hairs are a determinant of nearly one fifth of the barley rhizosphere microbiota, with a bias for members of the order Actinomycetales, Burkholderiales, Rhizobiales, …
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