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dc.contributor.advisor Moustafa, Ahmed Abou El Hassan, Diana 2016-05-23T11:37:19Z 2016-05-23T22:00:20Z Spring 2016 en_US 2016-05-23
dc.description.abstract Plants are sessile organisms that are constantly exposed to a variety of abiotic and biotic environmental stresses. Some plants are known to be more tolerant to those environmental stressors than others; those are the extremophilic plants. Studying the stress response pathways in such plants is extremely important in developing transgenic crop plants with enhanced tolerance to environmental stresses. Eutrema salsugineum is an extremophilic plant that is known to be resistant to many abiotic stress factors such as drought, cold, salt, and nitrogen deficiency. Experiments were carried out in KAUST by exposing the extremophilic plant to heat stress and exogenous ABA stress. RNA sequencing was done in order to get the transcriptome profile of the plant in response to the stresses. De novo transcriptome assembly was done followed by transcript abundance quantification and normalization using Kallisto. Differential expression analaysis was done to identify the differentially expressed transcripts in response to the different treatments in the shoot and root using the R bioconductor package EdgeR. The transcripts were annotated using EggNOG. The protein coding transcripts were identified by aligning them to the nr protein database using tblastx. Functional analysis of the DE transcripts to get the enriched terms was carried out using DAVID. Trinity de novo assembly produced 49857 genes and 134493 transcripts. Out of the 134493 transcripts, 114692 (85.28%) transcripts had tblastx hits (protein coding). Thus, 19801 potentially non coding or novel transcripts have been identified. A large variety of proteins were found to be differentially expressed depending on the pair-wise comparison. The genes were mainly involved in plant heat and ABA stress, ROS signaling pathway, ROS scavenging, secondary metabolite production, and lipid transfer. Further investigation of the role of secondary metabolites such as flavonoids, and nitrogen and sulfur containing compounds in the abiotic stress response of E. salsugineum is needed since it appears to be a major mechanism used by the plant. The results of this research offer a wide variety of stress related protein in E.salsugineum. Investigation of the over-expression of some of these genes in stress sensitive plants will help in further understanding their functions and mechanisms of action. en_US
dc.description.sponsorship I thank my supervisor, Dr. Ahmed Moustafa, for introducing me to my newly found passion, bioinformatics. I thank him for his support and care throughout my undergraduate and graduate years at AUC. I thank him for being there for me through my last year in the biotechnology program even though he was in another continent. I thank the American University in Cairo for awarding me the lab instruction fellowship for my three years as an undergraduate student; without it, I would not have been able to finish the MSc degree. I thank all my professors from the biology department at AUC; Dr. Rania Siam, Dr. Hamza El Dory, Dr. Suher Zada, and Dr. Walid Fouad. Thank you for providing guidance through my undergraduate and graduate years at AUC. I thank my one and only true love, Yousef Hamed, for supporting me and pushing me forward whenever I was ready to quit. I thank him for believing in me and forcing me to believe in myself. I thank my parents for believing in me and encouraging me to pursue my dreams. I thank my best friends and work collegues Yara El Shorafa and Rafif Kassab for providing me with emotional and physical support whenever I needed it. I thank my friend Omar Sheikha for his endless help with this project, and for offering his office and headphones when I needed a quiet place to write. I thank my friend Mohamed Ibrahim for his endless help with this project. Excel was a piece of cake because of you. en_US
dc.format.extent 109 p. en_US
dc.format.medium theses en_US
dc.language.iso en en_US
dc.rights Author retains all rights with regard to copyright. en
dc.subject Eutrema en_US
dc.subject Stress en_US
dc.subject Heat en_US
dc.subject ABA en_US
dc.subject thermotolerance en_US
dc.subject.lcsh Thesis (M.S.)--American University in Cairo en_US
dc.title Transcriptomic profiling of the extremophile eutrema salsugineum response to environmental stressors en_US
dc.type Text en_US
dc.subject.discipline Biotechnology en_US
dc.rights.access This item is available en_US
dc.contributor.department American University in Cairo. Graduate School of Education en_US
dc.description.irb American University in Cairo Institutional Review Board approval is not necessary for this item, since the research is not concerned with living human beings or bodily tissue samples. en_US
dc.contributor.committeeMember Fouad, Walid
dc.contributor.committeeMember Assem, Shireen
dc.contributor.committeeMember Abd Ellatif, Ahmed
dc.contributor.committeeMember Moustafa, Ahmed
dc.contributor.committeeMember Mahfouz, Magdy

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    This collection includes presentations, research findings, publications, and projects authored by AUC students

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