MODEL1004010001
type: SBMLModel
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notes: This the detailed model for 37°C from the article: Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli : Quantitative Analysis via Automated Model Abstraction. Hiroyuki Kuwahara, Chris J. Myers and Michael S. Samoilov PLoS Comput Biol. 2010 6(3): e1000723. doi: 10.1371/journal.pcbi.1000723 , Abstract: Uropathogenic Escherichia coli (UPEC) represent the predominant cause of urinary tract infections (UTIs). A key UPEC molecular virulence mechanism is type 1 fimbriae, whose expression is controlled by the orientation of an invertible chromosomal DNA element—the fim switch. Temperature has been shown to act as a major regulator of fim switching behavior and is overall an important indicator as well as functional feature of many urologic diseases, including UPEC host-pathogen interaction dynamics. Given this panoptic physiological role of temperature during UTI progression and notable empirical challenges to its direct in vivo studies, in silico modeling of corresponding biochemical and biophysical mechanisms essential to UPEC pathogenicity may significantly aid our understanding of the underlying disease processes. However, rigorous computational analysis of biological systems, such as fim switch temperature control circuit, has hereto presented a notoriously demanding problem due to both the substantial complexity of the gene regulatory networks involved as well as their often characteristically discrete and stochastic dynamics. To address these issues, we have developed an approach that enables automated multiscale abstraction of biological system descriptions based on reaction kinetics. Implemented as a computational tool, this method has allowed us to efficiently analyze the modular organization and behavior of the E. coli fimbriation switch circuit at different temperature settings, thus facilitating new insights into this mode of UPEC molecular virulence regulation. In particular, our results suggest that, with respect to its role i…
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reaction: 517803
reaction: 517814
reaction: 517801
reaction: 517812
reaction: 517787
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is described by: http://identifiers.org/pubmed/20361050
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517888
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type: Reaction
kinetic law: 160607
product: 160594
reactant: 160582
reactant: 160569
fast: false
reversible: true
name: r17

160594
type: SpeciesReference
stoichiometry: 1.0
species: 517767

160582
type: SpeciesReference
stoichiometry: 1.0
species: 517755

160569
type: SpeciesReference
stoichiometry: 1.0
species: 517740

517858
type: Parameter
constant: true
value: 0.001625

517859
type: Parameter
constant: true
value: 1.0

517856
type: Parameter
constant: true
value: 10.0

517879
type: Parameter
constant: true
value: 8.62637E-4

517875
type: Parameter
constant: true
value: 5.58342E-4

517892
type: Parameter
constant: true
value: 1.0

517846
type: Parameter
constant: true
value: 10.0

517794
type: Reaction
kinetic law: 160994
product: 160982
reactant: 160970
reactant: 160958
reactant: 160946
fast: false
reversible: true
name: r3

160982
type: SpeciesReference
stoichiometry: 1.0
species: 517775

160970
type: SpeciesReference
stoichiometry: 1.0
species: 517755

160958
type: SpeciesReference
stoichiometry: 1.0
species: 517744

160946
type: SpeciesReference
stoichiometry: 1.0
species: 517740