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Transcriptional response to stressors in arabidopsis thaliana
Stress is defined as any external force that can trigger a defensive response from an organism. In plants, stress is something that has been shown to affect plant reproduction and productivity by activating a defensive response. It can be caused by various things including but not limited to biotic...
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2017
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| access_status_str | Open Access |
| author | Galal, Aya Abd Elsalam |
| author_browse | Galal, Aya Abd Elsalam |
| author_facet | Galal, Aya Abd Elsalam |
| author_sort | Galal, Aya Abd Elsalam |
| collection | Thesis |
| dc_rights_str_mv | The author retains all rights with regard to copyright. The author certifies that written permission from the owner(s) of third-party copyrighted matter included in the thesis, dissertation, paper, or record of study has been obtained. The author further certifies that IRB approval has been obtained for this thesis, or that IRB approval is not necessary for this thesis. Insofar as this thesis, dissertation, paper, or record of study is an educational record as defined in the Family Educational Rights and Privacy Act (FERPA) (20 USC 1232g), the author has granted consent to disclosure of it to anyone who requests a copy. |
| description | Stress is defined as any external force that can trigger a defensive response from an organism. In plants, stress is something that has been shown to affect plant reproduction and productivity by activating a defensive response. It can be caused by various things including but not limited to biotic or abiotic conditions such as temperature, drought or salt stress. Exposure to stress leads to the production of various transcriptomes that are governed by signals released as a result of the exposed stress. Arabidopsis thaliana is characterized by its inability to tolerate any form of extreme stress and given its status as a model organism it is an ideal candidate to investigate the various effects of stress on plants. By studying the transcriptomes produced by Arabidopsis thaliana under different stress conditions, a more well-rounded profile of how plant systems react to different stress conditions is produced. Experiments were carried out in KAUST by exposing the stress intolerant plant to Pladienolide B; a drug that is known to affect the slicing mechanism, RNA sequencing was used in order to produce the transcriptome profile of the plant in response to the stress over a series of time points. The classic tuxedo protocol for RNA sequencing analysis was used to assemble the transcripts and following differential gene expression analysis by CuffDiff, the R package CummeRbund was used to visualize the results. Functional analysis of the significant differentially expressed genes was carried out using PANTHER. PANTHER was able to classify 12,646 genes; expressed at after exposure to the treatment for 6 hours, and 10,649 genes; expressed after exposure to the treatment for 24 hours, into functional classes. With around 50% of the differentially expressed gene having catalytic activity and around 25% having binding activity. Further investigation revealed that the alternatively spliced differentially expressed genes were heavily involved in various development and regulatory process that are essential for plant maturation. While a few functionally uncharacterized genes were expressed, some of which may hold valuable information in understanding plant stress response. This research offers a deeper understanding of how plants are effected by stress through the characterization of the differentially expressed genes. Future investigation of the uncharacterized genes expressed is needed as it may provide deeper insights to the plant stress response. |
| format | Thesis |
| id | oai:fount.aucegypt.edu:etds-1370 |
| institution | American University in Cairo (Egypt) |
| last_indexed | 2026-06-10T12:35:41.195Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from AUC Knowledge Fountain — bepress |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| publisher | AUC Knowledge Fountain |
| publisherStr | AUC Knowledge Fountain |
| record_format | dspace |
| source_str | AUC Knowledge Fountain — bepress |
| spelling | oai:fount.aucegypt.edu:etds-1370 Transcriptional response to stressors in arabidopsis thaliana Galal, Aya Abd Elsalam Stress is defined as any external force that can trigger a defensive response from an organism. In plants, stress is something that has been shown to affect plant reproduction and productivity by activating a defensive response. It can be caused by various things including but not limited to biotic or abiotic conditions such as temperature, drought or salt stress. Exposure to stress leads to the production of various transcriptomes that are governed by signals released as a result of the exposed stress. Arabidopsis thaliana is characterized by its inability to tolerate any form of extreme stress and given its status as a model organism it is an ideal candidate to investigate the various effects of stress on plants. By studying the transcriptomes produced by Arabidopsis thaliana under different stress conditions, a more well-rounded profile of how plant systems react to different stress conditions is produced. Experiments were carried out in KAUST by exposing the stress intolerant plant to Pladienolide B; a drug that is known to affect the slicing mechanism, RNA sequencing was used in order to produce the transcriptome profile of the plant in response to the stress over a series of time points. The classic tuxedo protocol for RNA sequencing analysis was used to assemble the transcripts and following differential gene expression analysis by CuffDiff, the R package CummeRbund was used to visualize the results. Functional analysis of the significant differentially expressed genes was carried out using PANTHER. PANTHER was able to classify 12,646 genes; expressed at after exposure to the treatment for 6 hours, and 10,649 genes; expressed after exposure to the treatment for 24 hours, into functional classes. With around 50% of the differentially expressed gene having catalytic activity and around 25% having binding activity. Further investigation revealed that the alternatively spliced differentially expressed genes were heavily involved in various development and regulatory process that are essential for plant maturation. While a few functionally uncharacterized genes were expressed, some of which may hold valuable information in understanding plant stress response. This research offers a deeper understanding of how plants are effected by stress through the characterization of the differentially expressed genes. Future investigation of the uncharacterized genes expressed is needed as it may provide deeper insights to the plant stress response. 2017-06-01T07:00:00Z thesis application/pdf https://fount.aucegypt.edu/etds/371 https://fount.aucegypt.edu/context/etds/article/1370/viewcontent/Aya_20Galal_20Thesis_201_2002_202017.pdf The author retains all rights with regard to copyright. The author certifies that written permission from the owner(s) of third-party copyrighted matter included in the thesis, dissertation, paper, or record of study has been obtained. The author further certifies that IRB approval has been obtained for this thesis, or that IRB approval is not necessary for this thesis. Insofar as this thesis, dissertation, paper, or record of study is an educational record as defined in the Family Educational Rights and Privacy Act (FERPA) (20 USC 1232g), the author has granted consent to disclosure of it to anyone who requests a copy. Theses and Dissertations AUC Knowledge Fountain RNA-seq Stress |
| spellingShingle | RNA-seq Stress Galal, Aya Abd Elsalam Transcriptional response to stressors in arabidopsis thaliana |
| title | Transcriptional response to stressors in arabidopsis thaliana |
| title_full | Transcriptional response to stressors in arabidopsis thaliana |
| title_fullStr | Transcriptional response to stressors in arabidopsis thaliana |
| title_full_unstemmed | Transcriptional response to stressors in arabidopsis thaliana |
| title_short | Transcriptional response to stressors in arabidopsis thaliana |
| title_sort | transcriptional response to stressors in arabidopsis thaliana |
| topic | RNA-seq Stress |
| url | https://fount.aucegypt.edu/etds/371 https://fount.aucegypt.edu/context/etds/article/1370/viewcontent/Aya_20Galal_20Thesis_201_2002_202017.pdf |
| work_keys_str_mv | AT galalayaabdelsalam transcriptionalresponsetostressorsinarabidopsisthaliana |