Fire is a natural component of most terrestrial ecosystems and can act as a local wound stimulus to plants. The ultimate goal of this work was to characterize the array of transcripts which systemically accumulate in plants after fire damage. Before this could be accomplished, substantial development of methods for gene expression analysis using sequence data was necessary. This involved developing methods for identifying contamination in DNA sequence data (Chapter 2), identifying over 78,000 false sequences in GenBank and several thousand more in the indica rice genome (Chapter 2), developing a novel method for identifying housekeeping controls using sequence data (Chapter 3), performing relative expression analyses for 127 potential housekeeping control transcripts (Chapter 3), and characterizing 23 transcripts which encode all 13 subunits of vacuolar H+-ATPases in tomato plants (Chapter 4). A subtractive cDNA library served as a starting point to identify and characterize 9 novel tomato transcripts systemically up-regulated in leaves in the first hour after a distant leaf is flame wounded (Chapters 5). Real-time RT-PCR using leaf RNA isolated at different times after flaming showed that the most common pattern of transcript accumulation was an increase within 30 to 60 minutes, followed by a return to basal levels within 3 hours. Expression analyses also showed that most up-regulated transcripts were already present in unwounded tissues. A total of 46 different transcripts were identified from the subtractive cDNA library (Chapters 6). Compared with the entire tomato transcriptome, these 46 transcripts are very highly conserved in plants. The vast majority fell into 5 classes: enzymes of general metabolism; protein synthesis, modification, and transport; transcription; membrane transport; and photosynthesis and respiration. At least half of the transcripts have been previously associated with wounding or stress, suggesting that the systemic response to fire damage has components similar to those of other wound and stress responses. On the other hand, 30% of transcripts were associated with photosynthesis and respiration, suggesting that part of the response to fire damage is notably different from other wound and stress responses. Conclusions and future directions are included in Chapter 7.
| Identifer | oai:union.ndltd.org:NCSU/oai:NCSU:etd-05072004-132534 |
| Date | 10 May 2004 |
| Creators | Coker, Jeffrey Scott |
| Contributors | Dr. Judy Thomas, Dr. Eric Davies, Dr. Jack Wheatley, Dr. Chris Brown, Dr. Dominique Robertson |
| Publisher | NCSU |
| Source Sets | North Carolina State University |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://www.lib.ncsu.edu/theses/available/etd-05072004-132534/ |
| Rights | unrestricted, I hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to NC State University or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. |
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