Abstract
Fimbriae are structures in Escherichia coli, the expression of which is controlled by the fim operon. Understanding this expression is important because the fimbriae are important virulence factors.
This expression can be studied using targeted mutations to the DNA, which can be used to disable binding or transcription of a protein. However, this can be problematic as only the net effect is observed. Turning off expression of a protein may enhance fim expression, but deactivating this protein may also repress another protein that functions as an activator of fim expression. The net result may be that fim expression goes down, so it would seem at first glance that the disabled protein was an activator of fim expression and not a repressor.
In order to understand this complex network of interactions, an agent based model of fim expression has been created. The subject of this paper is to introduce this model and to use it to disambiguate between a number of hypotheses about this system. Parameters such as binding probability will be optimised using a genetic algorithm. The final model and parameters show a good match to experimental data.
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de Vries, P., Johnson, C.G., Blomfield, I.C. (2010). Modelling fim Expression in Escherichia Coli K12. In: Chan, J.H., Ong, YS., Cho, SB. (eds) Computational Systems-Biology and Bioinformatics. CSBio 2010. Communications in Computer and Information Science, vol 115. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16750-8_2
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DOI: https://doi.org/10.1007/978-3-642-16750-8_2
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