Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California
Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008.
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| Format: | Thesis |
| Language: | eng |
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Massachusetts Institute of Technology
2009
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| Online Access: | http://hdl.handle.net/1721.1/45149 |
| _version_ | 1826191976544862208 |
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| author | Rich, Virginia Isabel |
| author2 | Edward F. DeLong and George Somero. |
| author_facet | Edward F. DeLong and George Somero. Rich, Virginia Isabel |
| author_sort | Rich, Virginia Isabel |
| collection | MIT |
| description | Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. |
| first_indexed | 2024-09-23T09:04:15Z |
| format | Thesis |
| id | mit-1721.1/45149 |
| institution | Massachusetts Institute of Technology |
| language | eng |
| last_indexed | 2024-09-23T09:04:15Z |
| publishDate | 2009 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/451492019-04-10T20:32:37Z Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California Rich, Virginia Isabel Edward F. DeLong and George Somero. Woods Hole Oceanographic Institution. Massachusetts Institute of Technology. Dept. of Biology. Joint Program in Biological Oceanography. Woods Hole Oceanographic Institution. Biology. Joint Program in Biological Oceanography. Woods Hole Oceanographic Institution. Microbial genomes Marine microbial ecology Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. Includes bibliographical references (p. 155-181). This thesis describes the development and application of a new tool for profiling marine microbial communities. Chapter 1 places the tool in the context of the range of methods used currently. Chapter 2 describes the development and validation of the "genome proxy" microarray, which targeted marine microbial genomes and genome fragments using sets of 70-mer oligonucleotide probes. In a natural community background, array signal was highly linearly correlated to target cell abundance (R² of 1.0), with a dynamic range from 10²-10⁶ cells/ml. Genotypes with >/=~80% average nucleotide identity to those targeted crosshybridized to target probesets but produced distinct, diagnostic patterns of hybridization. Chapter 3 describes the development an expanded array, targeting 268 microbial genotypes, and its use in profiling 57 samples from Monterey Bay. Comparison of array and pyrosequence data for three samples showed a strong linear correlation between target abundance using the two methods (R²=0.85- 0.91). Array profiles clustered into shallow versus deep, and the majority of targets showed depth-specific distributions consistent with previous observations. Although no correlation was observed to oceanographic season, bloom signatures were evident. Array-based insights into population structure suggested the existence of ecotypes among uncultured clades. Chapter 4 summarizes the work and discusses future directions. by Virginia Rich. Ph.D. 2009-04-29T14:46:26Z 2009-04-29T14:46:26Z 2008 2008 Thesis http://hdl.handle.net/1721.1/45149 313787720 eng M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 282 p. application/pdf Massachusetts Institute of Technology |
| spellingShingle | Biology. Joint Program in Biological Oceanography. Woods Hole Oceanographic Institution. Microbial genomes Marine microbial ecology Rich, Virginia Isabel Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California |
| title | Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California |
| title_full | Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California |
| title_fullStr | Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California |
| title_full_unstemmed | Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California |
| title_short | Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California |
| title_sort | development of a genome proxy microarray for profiling marine microbial communities and its application to a time series in monterey bay california |
| topic | Biology. Joint Program in Biological Oceanography. Woods Hole Oceanographic Institution. Microbial genomes Marine microbial ecology |
| url | http://hdl.handle.net/1721.1/45149 |
| work_keys_str_mv | AT richvirginiaisabel developmentofagenomeproxymicroarrayforprofilingmarinemicrobialcommunitiesanditsapplicationtoatimeseriesinmontereybaycalifornia |