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Modelling fim expression in Escherichia coli K12

de Vries, Patrick, Johnson, Colin G., Blomfield, Ian C. (2010) Modelling fim expression in Escherichia coli K12. In: International Conference on Computational Systems-Biology and Bioinformatics. Communications in Computer and Information Science . pp. 14-25. Springer, Heidelberg ISBN 978-3-642-16749-2. E-ISBN 978-3-642-16750-8. (doi:10.1007/978-3-642-16750-8_2)

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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. How- ever, 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.

Item Type: Conference or workshop item (Paper)
DOI/Identification number: 10.1007/978-3-642-16750-8_2
Subjects: Q Science > QA Mathematics (inc Computing science) > QA 76 Software, computer programming,
Q Science > QH Natural history > QH301 Biology
Q Science > QH Natural history > QH324.2 Computational biology
Divisions: Faculties > Sciences > School of Biosciences
Faculties > Sciences > School of Computing
Depositing User: Colin Johnson
Date Deposited: 12 Dec 2018 14:08 UTC
Last Modified: 30 May 2019 08:33 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/70973 (The current URI for this page, for reference purposes)
Johnson, Colin G.: https://orcid.org/0000-0002-9236-6581
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