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479287
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154838
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MODEL1004010000
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length unit: 335510
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reaction: 479214
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parameter: 479317
is described by: http://identifiers.org/pubmed/20361050
parameter: 479273
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curated: false
notes: This the detailed model for 28°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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parameter: 479265
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time units: 950070

155251
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155604
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479198
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154559
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479251
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479168
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155433
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479284
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154814
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479211
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479226
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479264
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479188
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155482
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154511
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154377
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479312
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155335
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479156
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155494
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154389
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479313
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479250
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154317
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479157
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479261
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155165
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154875
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479275
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155628
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154583
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479177
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479256
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154595
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479165
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479320
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154655
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479155
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479267
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154716
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479215
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479222
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479280
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479277
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479194
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154704
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154365
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155105
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479164
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479255
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154740
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154401
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154619
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479268
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155445
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479216
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479321
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479202
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155580
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479195
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155189
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155263
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155371
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479265
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155907
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479153
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479224
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479192
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479279
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479167
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479203
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479301
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479292
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154692
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155530
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154353
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155081
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479152
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479214
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155724
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154426
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479223
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479204
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479253
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479291
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155568
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479300
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155359
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479151
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479219
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479303
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154997
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154293
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479190
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154948
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155299
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479307
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155214
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155506
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479181
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155871
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155736
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155408
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479259
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479160
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479171
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155822
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155652
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155798
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479191
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154487
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155749
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479220
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479289
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479163
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479143
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479207
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479305
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479319
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155287
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155555
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155895
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155202
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479309
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479269
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479183
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154850
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479257
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154607
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155033
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479304
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type: Parameter

479308
constant: true
value: 1.0
type: Parameter

154752
stoichiometry: 1.0
species: 479161
type: SpeciesReference

154499
stoichiometry: 1.0
species: 479147
type: SpeciesReference

155640
stoichiometry: 1.0
species: 479151
type: SpeciesReference

479218
kinetic law: 155664
product: 155652
reactant: 155640
reactant: 155628
fast: false
reversible: true
name: r_PfimB_HNS
type: Reaction

155117
stoichiometry: 1.0
species: 479164
type: SpeciesReference

479208
kinetic law: 155275
product: 155263
product: 155251
reactant: 155238
fast: false
reversible: false
name: prod8
type: Reaction