Background
Plant cells are encapsulated by cell walls, structures that are essential for maintaining the plant's shape, and for its interaction with environmental signals and during various growth stages. These walls play a pivotal role in development, defence, and adaptation. Cell Wall Integrity (CWI) refers to maintaining the functional and structural integrity of the plant cell wall. The CWI system adapts to environmental and growth changes by modifying the cell wall's structure and composition. With the challenges posed by climate change and the increasing demand for sustainable feedstocks, a deeper understanding of CWI is crucial. Although significant progress has been made in model organisms like Arabidopsis, there is a need to expand this knowledge by identifying more genes involved in CWI, including transcription factors and kinases, and by exploring genes in other organisms that face diverse environmental challenges.
Project Overview
This project offers a unique opportunity for a computational biology student to merge computational and experimental approaches to uncover new genes involved in CWI. By employing text mining, gene co-expression networks, and phylogenetics, this project aims to broaden our understanding of CWI across different organisms. This comprehensive approach will not only identify new candidate genes but also enhance our understanding of how plants adapt to their environment.
Tasks Involved
- Text Mining: You will sift through vast amounts of scientific literature to identify potential genes involved in CWI. This involves using software tools to scan articles for keywords related to cell wall integrity and gene functions.
- Co-expression Network: By analysing gene expression data, you will construct networks that reveal how genes involved in CWI are co-expressed under various conditions. This will help in identifying new genes that play a role in maintaining cell wall integrity.
- Finding Orthologous Genes in Other Organisms: This task involves using phylogenetic tools to identify genes similar to those known to be involved in CWI in other organisms, such as unicellular green algae. This will help in understanding how CWI mechanisms are conserved across different species.
- Functional Analysis: Through experimental biology approaches, you will validate the function of the identified genes in maintaining cell wall integrity. This might involve analysing mutants for defects in cell wall integrity or other related phenotypes.
Opportunity
This project is an exciting blend of computational and experimental biology, ideal for students passionate about plant biology, genetics, and bioinformatics. Participants will gain valuable experience in data analysis, gene network construction, and functional genomics. This research will contribute to our understanding of plant adaptation and resilience, paving the way for the development of crops better suited to changing environmental conditions.
Supervisor: Assistant Professor Laura Bacete, Dept of Plant Physiology, UMU
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