Developing Aiptasia pallida as a tractable model system for cnidarian-dinoflagellate symbiosis : identifying transferred metabolites and designing tools for analysis of ultra-high-throughput-sequencing data
Abstract/Contents
- Abstract
- This dissertation describes a general method for identifying and roughly quantifying the metabolites that are produced by symbiotic dinoflagellates and transferred to cnidarian hosts. I developed a system of rapid filtration and gas chromatography-mass spectrometry (GC-MS) to identify these compounds in the anemone tissue and dinoflagellates separately. I used 13C-sodium bicarbonate to label compounds produced from newly-fixed carbon; the principal compound detected in the animal was glucose. I developed a way to visualize these and other large GC-MS datasets using open-source software. I also built tools for analyzing Ultra-High-Throughput-Sequencing (UHTS) data, and these were useful in the de novo assembly of the Aiptasia pallida transcriptome. One tool I developed compares each read to each other read using a MapReduce framework to merge near-duplicate reads and reduce redundancy in the dataset. In addition, our lab sequenced symbiotic animals and therefore often worked with pools of sequences from multiple organisms. I developed a tool for identifying which transcript sequence was produced by which organism in a symbiotic ecosystem: it was 99% accurate on high-quality validation data.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2011 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Burriesci, Matthew Strecker | |
|---|---|---|
| Associated with | Stanford University, Department of Genetics | |
| Primary advisor | Pringle, John | |
| Thesis advisor | Pringle, John | |
| Thesis advisor | Altman, Russ | |
| Thesis advisor | Long, Sharon | |
| Thesis advisor | Sherlock, Gavin | |
| Advisor | Altman, Russ | |
| Advisor | Long, Sharon | |
| Advisor | Sherlock, Gavin |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Matthew Strecker Burriesci. |
|---|---|
| Note | Submitted to the Department of Genetics. |
| Thesis | Thesis (Ph. D.)--Stanford University, 2011. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2011 by Matthew Strecker Burriesci
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