BIOMD0000000296
type: SBMLModel
species: 566102
units def: 348152
parameter: 071325
reaction: 071301
area units: area
parameter: 071313
creator:
  ORG:
    orgname: Department of Biomedical Engineering and Institute for Genome Sciences and Policy, Duke University
  n:
    given: Hao
    family: Song
rule: 566121
parameter: 071333
time units: 348152
reaction: 071305
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
reaction: 071299
species: 071283
is described by: http://identifiers.org/pubmed/18414488
parameter: 071319
parameter: 071331
reaction: 071309
notes: This is the reduced model described in the article: A synthetic Escherichia coli predator–prey ecosystem Balagaddé FK, Song H, Ozaki J, Collins CH, Barnet M, Arnold FH, Quake SR, You L. Mol Syst Biol. 2008;4:187. Epub 2008 Apr 15. PMID: 18414488 ; DOI: 10.1038/msb.2008.24 Abstract: We have constructed a synthetic ecosystem consisting of two Escherichia coli populations, which communicate bi-directionally through quorum sensing and regulate each other's gene expression and survival via engineered gene circuits. Our synthetic ecosystem resembles canonical predator–prey systems in terms of logic and dynamics. The predator cells kill the prey by inducing expression of a killer protein in the prey, while the prey rescue the predators by eliciting expression of an antidote protein in the predator. Extinction, coexistence and oscillatory dynamics of the predator and prey populations are possible depending on the operating conditions as experimentally validated by long-term culturing of the system in microchemostats. A simple mathematical model is developed to capture these system dynamics. Coherent interplay between experiments and mathematical analysis enables exploration of the dynamics of interacting populations in a predictable manner. In the article the cell density is given in per 10 3 cells per microlitre. To evade a conversion factor in the SBML implementation, the unit for the cell densities was just left the same as for the AHLs A and A2 (nM). This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 The BioModels.net Team. For more information see the terms of use . To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4…
name: Balagaddé2008_E_coli_Predator_Prey
parameter: 071323
length unit: length
species: 071275
species: 071279
occurs in: http://identifiers.org/taxonomy/562
reaction: 071297
parameter: 071329
parameter: 071317
modified:
  W3 CDTF: Thu Apr 19 18:14:53 BST 2012
is: MODEL8305195207
compartment: 071270
volume units: volume
has version: GO:0009372
parameter: 071327
reaction: 071303
parameter: 071315
parameter: 071335
reaction: 071311
parameter: 071321
curated: true
species: 071273
species: 071281
rule: 566123
species: 071277
substance units: 348127
units def: 348127
reaction: 071307
created:
  W3 CDTF: Wed Jan 12 02:16:09 GMT 2011

566102
type: Species
initial concentration: 5.0
constant: true
notes: IPTG default 5 nM
is: SBO:0000247
is: CHEBI:61448
in compartment: 071270
boundary condition: false
is: http://identifiers.org/pubchem.compound/656894
initial amount: NaN
has only substance units: false

071270
type: Compartment
is: GO:0005576
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0

348152
type: SBMLUnitsDef
unit: 348164
name: hours

348164
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 3600.0
kind: SECOND

071325
type: Parameter
notes: prey cell death rate constant
is: SBO:0000356
constant: true
value: 0.3

071301
type: Reaction
modifier: 348298
reversible: false
fast: false
is: GO:0008283
name: prey growth
is: SBO:0000375
reactant: 348273
kinetic law: 348310
product: 348285

071273
type: Species
initial concentration: 20.0
constant: false
notes: predator cells (MG1655) (per 103 cells per microlitre)
initial amount: NaN
boundary condition: false
has only substance units: false
is version of: http://identifiers.org/taxonomy/562
in compartment: 071270
is: SBO:0000240

348273
type: SpeciesReference
stoichiometry: 1.0
species: 071283

071283
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 071270

348285
type: SpeciesReference
stoichiometry: 1.0
species: 071275

071275
type: Species
initial concentration: 20.0
initial amount: NaN
notes: prey cells (Top10F) (per 103 cells per microlitre)
boundary condition: false
is: SBO:0000240
has only substance units: false
is version of: http://identifiers.org/taxonomy/562
constant: false
in compartment: 071270

071313
type: Parameter
notes: predator cell growth rate constant
is: SBO:0000035
constant: true
value: 0.8

071333
type: Parameter
notes: cellular A1 (3OC12HSL) decay rate constant
is: SBO:0000356
constant: true
value: 0.017

071305
type: Reaction
reversible: false
kinetic law: 348407
reactant: 348371
has version: http://identifiers.org/ec-code/2.3.1.184
modifier: 348395
is: SBO:0000205
name: 3OC12HSL synthesis
fast: false
product: 348383
is: GO:0009058

348371
type: SpeciesReference
stoichiometry: 1.0
species: 071283

348383
type: SpeciesReference
stoichiometry: 1.0
species: 071277

071277
type: Species
boundary condition: false
notes: 3OC12HSL
initial concentration: 0.1
is: CHEBI:56080
initial amount: NaN
has only substance units: false
constant: false
in compartment: 071270
is: SBO:0000247

071299
type: Reaction
modifier: 348248
is: SBO:0000179
reversible: false
kinetic law: 348261
fast: false
product: 348236
name: predator death
is version of: GO:0008219
reactant: 348224

071279
type: Species
boundary condition: false
is: CHEBI:55474
notes: 3OC6HSL
initial amount: NaN
constant: false
initial concentration: 0.1
is: SBO:0000247
has only substance units: false
in compartment: 071270
is: C18049

348236
type: SpeciesReference
stoichiometry: 1.0
species: 071281

071281
type: Species
is: SBO:0000291
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 071270

348224
type: SpeciesReference
stoichiometry: 1.0
species: 071273

071319
type: Parameter
notes: Dilution rate
is: SBO:0000356
constant: true
value: 0.1125

071331
type: Parameter
notes: A2 (3OC6HSL) concentration for half-maximal inhibition of PluxI promoter
is: SBO:0000191
constant: true
value: 10.0

071309
type: Reaction
kinetic law: 348492
reactant: 348455
fast: false
name: 3OC6HSL synthesis
modifier: 348480
is: GO:0009058
product: 348467
reversible: false
has version: http://identifiers.org/ec-code/2.3.1.184
is: SBO:0000205

348455
type: SpeciesReference
stoichiometry: 1.0
species: 071283

348467
type: SpeciesReference
stoichiometry: 1.0
species: 071279

071323
type: Parameter
notes: prey cell A2 (3OC6HSL) synthesis rate costant
is: SBO:0000035
constant: false
value: NaN

071297
type: Reaction
fast: false
modifier: 348200
is version of: GO:0008283
reversible: false
kinetic law: 348212
name: predator growth
reactant: 348176
is: SBO:0000375
product: 348188

348176
type: SpeciesReference
stoichiometry: 1.0
species: 071283

348188
type: SpeciesReference
stoichiometry: 1.0
species: 071273

071329
type: Parameter
notes: predator cell death rate constant
is: SBO:0000356
constant: false
value: NaN

071317
type: Parameter
notes: Cell carrying capacity
is: SBO:0000196
constant: true
value: 100.0

071327
type: Parameter
notes: A1 (3OC12HSL) concentration for half-maximal activation of PluxI promoter
is: SBO:0000191
constant: true
value: 10.0

071303
type: Reaction
is version of: GO:0008219
is: SBO:0000179
name: prey death
product: 348334
reactant: 348322
modifier: 348346
reversible: false
fast: false
kinetic law: 348359

348334
type: SpeciesReference
stoichiometry: 1.0
species: 071281

348322
type: SpeciesReference
stoichiometry: 1.0
species: 071275

071315
type: Parameter
notes: prey cell growth rate constant
is: SBO:0000035
constant: true
value: 0.4

071335
type: Parameter
notes: cellular A2 (3OC6HSL) decay rate constant
is: SBO:0000356
constant: true
value: 0.11

071311
type: Reaction
kinetic law: 348528
product: 348516
reactant: 348504
is version of: GO:0009056
is: SBO:0000179
fast: false
reversible: false
name: 3OC6HSL removal

348516
type: SpeciesReference
stoichiometry: 1.0
species: 071281

348504
type: SpeciesReference
stoichiometry: 1.0
species: 071279

071321
type: Parameter
notes: predator cell A1 (3OC12HSL) synthesis rate costant
is: SBO:0000035
constant: true
value: 0.1

348127
type: SBMLUnitsDef
unit: 348139
name: nanomole

348139
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

071307
type: Reaction
kinetic law: 348443
product: 348431
reactant: 348419
is version of: GO:0009056
is: SBO:0000179
fast: false
reversible: false
name: 3OC12HSL removal

348431
type: SpeciesReference
stoichiometry: 1.0
species: 071281

348419
type: SpeciesReference
stoichiometry: 1.0
species: 071277