Dr GB Stan, Dr T Ellis
Applications accepted all year round
Funded PhD Project (European/UK Students Only)
About the Project
Synthetic biology is the impact that new genes have on their host cells. Of particular interest to us is to optimise synthetic biology constructs by efficiently allocating cellular resources between native and engineered genes and by quickly recycling wastefully sequestered cellular resources. In this project, the student will develop whole‐cell models to computationally predict how growth is affected by both the (over‐)expression of genes and the controlled recycling of shared cellular resources, for example, through fast enzymatic degradation of misfolded proteins. The project will use this new tool to optimise synthetic biology designs, especially in terms of efficient allocation of shared cellular resources when both consumption and recycling rates of these resources are modulated.
The model will be benchmarked by comparing predicted and real data for thousands of different designs for the production of antibody fragments in E. coli, and further applied to other biosynthetic pathways, e.g. insulin precursors, riboflavin and lycopene. By the end of the PhD this project will deliver a much‐needed platform for forward‐engineering synthetic biology, allowing predictions of yield, genetic stability of different pathway designs and growth rate of engineered cells. This work will benefit from previous and ongoing research on cellular burden carried out by our groups (Nature Methods 2015).
Ideal profile of applicants:
Highly motivated and dynamic with a background in any of the following: (bio)mathematics, (bio)physics, dynamical systems and control, computer science, systems biology, synthetic biology. Other backgrounds might also be considered as long as they are
clearly aligned with the goals of this project.
Information about the groups
• Stan Group (leading group for this project): Stan Group (http://www.bg.ic.ac.uk/research/g.stan/group/), Guy‐Bart Stan’s Webpage (http://www.bg.ic.ac.uk/research/g.stan/)
• Ellis Lab (collaborating group for this project): Ellis Lab (http://tomellislab.com/)
Funding Notes
Competitive PhD Scholarship funding available for outstanding UK/EU students.
Other funding routes can be considered for exceptional overseas students.
References
Ceroni, F., Algar, R., Stan, G.‐B., & Ellis, T. (2015). Quantifying cellular capacity identifies gene
expression designs with reduced burden. Nature Methods, 12(5), 415–418.
http://doi.org/10.1038/nmeth.3339