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 16 of 16 for “"Metatranscriptome"”.
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Computational analysis of eukaryotic metatranscriptomes from diverse marine environments
… microbes in-situ. This set of transcripts (the metatranscriptome) provides a snapshot of actively transcribed genes at the time of sampling, and can provide insights into microbial metabolism and their relationship with their environment. In this thesis we present the computational analysis of …
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Resolving the molecular ecology of marine microbial eukaryotes with metatranscriptomes
… I leverage poly-A+ selected, deeply sequenced metatranscriptomes to resolve the molecular ecology of in situ marine microbial eukaryote communities. In Chapter 1, I studied a diel-resolved metatranscriptome time series in the North Pacific Subtropical Gyre. I developed a method for assembly, …
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Decoding divergence in marine protistan communities: from strain diversity to basin biogeography
… to physiology. I developed a pipeline for metatranscriptome analysis and taxonomic annotation to address the lack of tools built specifically for microbial eukaryotes, and created mock communities to assess recovery success in protistan metatranscriptome analysis workflows (Chapters 4 and …
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Decoding divergence in marine protistan communities: from strain diversity to basin biogeography
… to physiology. I developed a pipeline for metatranscriptome analysis and taxonomic annotation to address the lack of tools built specifically for microbial eukaryotes, and created mock communities to assess recovery success in protistan metatranscriptome analysis workflows (Chapters 4 and …
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The mucosal microbiome of inflammatory bowel diseases
… pinch biopsies for profiling the metagenome and metatranscriptome of the mucosal associated microbiota. We find that current methodologies are not capable of adequately separating microbial and human DNA or RNA resulting in as few as 1 – 2% of microbial reads after sequencing.
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Defining the ecological and physiological traits of phytoplankton across marine ecosystems
… sequence data for use in RT-qPCR assays or metatranscriptome studies. Using a metatranscriptomic approach, the role of resource partitioning in the coexistence of two closely related diatom species in an estuarine system was examined. This study demonstrated that co-occurring diatoms in a …
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Characterization of microbial primary and secondary metabolism in the marine realm
… increased in abundance and recruitment of metatranscriptome reads towards deeper, hotter sediments, marking a transition to a specialized deep biosphere. In my fifth chapter, I developed MetaPathPredict-E, a deep learningpowered extension of MetaPathPredict for eukaryotic metabolism …
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Characterization of Human Gut Microbiota Dynamics Using Model Communities in Gnotobiotic Mice
… the representation of many functions within the metatranscriptome related to carbohydrate and amino acid metabolism. One prominent community member, Bacteroides cellulosilyticus WH2, was identified as an adaptive forager that tailors its versatile carbohydrate utilization strategy to the dietary …
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Molecular mechanisms of microbial interactions in model systems and natural environments
… transcriptional signatures from environmental metatranscriptome data collected in the North Pacific. Most consistent transcriptional interactions occurred in cross-kingdom pairs especially between diatoms and Proteobacteria, ranging from common functional mechanisms like cross-feeding and …
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Characterization of the prokaryotic community associated with the giant barrel sponge, Xestospongia muta across the Caribbean
… gene specific analyses combined with preliminary metatranscriptome data indicate the presence of genes involved in nitrogen cycling including nifH (nitrogen fixation), amoA (ammonia oxidation), norB (denitrification), and nirK (denitrification). Nitrogen cycling in X. muta appears to be more …
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Defining the ecological and physiological traits of phytoplankton across marine ecosystem
… sequence data for use in RT-qPCR assays or metatranscriptome studies. Using a metatranscriptomic approach, the role of resource partitioning in the coexistence of two closely related diatom species in an estuarine system was examined. This study demonstrated that co-occurring diatoms in a …
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Characterization of Microbial Primary and Secondary Metabolism in the Marine Realm
… increased in abundance and recruitment of metatranscriptome reads towards deeper, hotter sediments, marking a transition to a specialized deep biosphere. In my fifth chapter, I developed MetaPathPredict-E, a deep learning-powered extension of MetaPathPredict for eukaryotic metabolism …
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Structural dynamics of community gene expression In a freshwater cyanobacterial bloom over a day-night cycle
… Illumina sequencing to characterize the metatranscriptome of a tropical eutrophic drinking water reservoir dominated by the toxigenic cyanobacterium Microcystis aeruginosa over a day-night cycle. Cyanobacterial blooms are a major problem in eutrophic lakes and reservoirs, negatively …
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Rewiring anaerobic digestion: production of biofuel intermediates and high-value chemicals from cellulosic wastes
… at the molecular level (metagenome, metatranscriptome, and proteome) are suggested to expand current knowledge and better understand the microbiological factors that dictate the fermentation of cellulosic material within the context of the carboxylate platform. By expanding this …
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Investigating physiological collaborations between a lower termite and its symbionts
<p>This project was completed in an effort to better understand the contributions of symbiotic microbes to the biology of <em>Reticulitermes flavipes,</em> the eastern subterranean termite. Lower-termites, like <em>R. flavipes, </em>house symbionts from all three domains of life within their …