Chemical and Biomolecular Engineering, Department of
First Advisor
Rajib Saha
Date of this Version
8-2024
Document Type
Thesis
Citation
A thesis presented to the faculty of the Graduate College at the University of Nebraska in partial fulfilment of requirements for the degree of Master of Science
Major: Chemical Engineering
Under the supervision of Professor Rajib Saha
Lincoln, Nebraska. August 2024
Abstract
Arabidopsis thaliana (Arabidopsis) is the most well-established model plant to date. Being the first plant to have its genome mapped, studies on Arabidopsis have provided insurmountable insights into the physiological and biochemical nature of plants. Methods that allow us to computationally study the metabolism of organisms include the use of genome-scale metabolic models (GEMs). Despite its popularity, no GEM currently maps the metabolic activity in the root system of Arabidopsis, which is the first organ to face and respond to stress conditions in the soil. This work aims to develop and implement a comprehensive GEM of the Arabidopsis root system named AraRoot. The final model comprises of 2,682 reactions, 2,748 metabolites, and 1,310 genes. Analyzing the metabolic pathways in the model identified 158 possible bottleneck genes that impact biomass production. Further insights conclude that the cortex layer in the roots is conceivably responsible for root growth under prolonged exposure to high salt growth conditions, while the endodermis and epidermis are responsible for producing metabolites responsible for increased cell wall biosynthesis.
The open-access AraRoot model is available at: https://github.com/ssbio/AraRoot
Advisor: Rajib Saha
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