Thesis subject

Developmental plasticity in plants

In plant development, regulatory mechanisms involving feedback loops of transcription factors are known to influence cell division [1]. These feedback loops have been modeled and were shown to be remarkably robust to parameter changes. This begs the question how such loops can evolve: what selective advantage does an organism have if the system is robust to small to medium changes?

To investigate this, we intend to investigate the evolvability of (modules of) transcription factor regulatory interactions. One approach would be to mine a large number of genomes of a single species (Arabidopsis thaliana) for transcription factor-coding genes and transcription factor binding sites and investigate their conservation in the light of changes in the overall genome. Once interesting events are found, the presence or absence of such genomic regions in other genomes (tomato, potato etc.) can be investigated. The desired outcome is insight into the evolvability of regulatory feedback loops.

[1] K. ten Tusscher and B. Scheres (2011) Joining forces: feedback and integration in plant development. Curr Opin Genet Dev 21(6):799-805.

Used skills: Programming, systems biology

Requirements: INF-22306 Programming in Python, SSB-30306Molecular systems biology, BIF-30806 Advanced bioinformatics