Difference between revisions of "Team:Imperial College/SingleCell"

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Revision as of 20:42, 19 October 2016

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Single Cell Modelling Overview

The first stage of our modelling process was to construct a single cell in silico model of our circuit. Our model was built using mass action kinetics in Simbiology (Matlab toolbox) and built up reaction by reaction.

Once, the models were built they were first used to test and compare the time taken for four different growth regulators (GP0.4, GP2, Leucine B Auxotrophy and Chloramphenicol acetyl transferase antibiotic resistance) that we shortlisted in order to determine which of them would work the fastest.

This allowed us to optimize our assembly experiments allowing us to achieve a faster route to a working prototype circuit. We decided to focus our attention on the GP2 and GP0.4 systems as they were predicted by our single cell model to work the fastest.

We performed sensitivity analysis on each of our circuit designs. We only analysed the parameters that we can change in lab (transcriptions rates via promoter strength, translation rates via RBS strength, copy numbers and degradation rates via the inclusion of degradation tags). This allows us to identify which parameters should be tweaked in order to balance our system in order to set the population ratios that we want.

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Works Cited

Chen, Y., Kim, J., Hirning, A., Josi, K. and Bennett, M. (2015). Emergent genetic oscillations in a synthetic microbial consortium. Science, 349(6251), pp.986-989.

Zhang, D. and Winfree, E. (2009). Control of DNA Strand Displacement Kinetics Using Toehold Exchange. J. Am. Chem. Soc., 131(47), pp.17303-17314.