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BIOMD0000000296 - Balagaddé2008_E_coli_Predator_Prey

 

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Reference Publication
Publication ID: 18414488
Balagaddé FK, Song H, Ozaki J, Collins CH, Barnet M, Arnold FH, Quake SR, You L.
A synthetic Escherichia coli predator-prey ecosystem.
Mol. Syst. Biol. 2008; 4: 187
Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA.  [more]
Model
Original Model: http://www.nature.com/msb/...
Submitter: Lukas Endler
Submission ID: MODEL8305195207
Submission Date: 03 Dec 2008 12:41:11 UTC
Last Modification Date: 01 Apr 2014 14:29:34 UTC
Creation Date: 12 Jan 2011 02:16:09 UTC
Encoders:  Lukas Endler
   Hao Song
set #1
bqbiol:hasTaxon Taxonomy Escherichia coli
bqbiol:hasVersion Gene Ontology quorum sensing
set #2
bqbiol:isVersionOf Gene Ontology predatory behavior
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 103 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., 4:92.

Model
Publication ID: 18414488 Submission Date: 03 Dec 2008 12:41:11 UTC Last Modification Date: 01 Apr 2014 14:29:34 UTC Creation Date: 12 Jan 2011 02:16:09 UTC
Mathematical expressions
Reactions
predator growth predator death prey growth prey death
3OC12HSL synthesis 3OC12HSL removal 3OC6HSL synthesis 3OC6HSL removal
Rules
Assignment Rule (variable: d1) Assignment Rule (variable: kA2)    
Physical entities
Compartments Species
environment IPTG C1 C2
A1 A2 sink
source    
Global parameters
kc1 kc2 Cm D
kA1 kA2 d2 K2
d1 K1 dAA1 dAA2
Reactions (8)
 
 predator growth [source] → [C1];   {C2}
 
 predator death [C1] → [sink];   {A2}
 
 prey growth [source] → [C2];   {C1}
 
 prey death [C2] → [sink];   {A1}
 
 3OC12HSL synthesis [source] → [A1];   {C1}
 
 3OC12HSL removal [A1] → [sink];  
 
 3OC6HSL synthesis [source] → [A2];   {C2}
 
 3OC6HSL removal [A2] → [sink];  
 
Rules (2)
 
 Assignment Rule (name: d1) d1 = 0.5+IPTG^2/(5^2+IPTG^2)
 
 Assignment Rule (name: kA2) kA2 = 0.02+0.03*IPTG^2/(5^2+IPTG^2)
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 IPTG
Compartment: environment
Initial concentration: 5.0
Constant
 
 C1
Compartment: environment
Initial concentration: 20.0
 
 C2
Compartment: environment
Initial concentration: 20.0
 
 A1
Compartment: environment
Initial concentration: 0.1
 
 A2
Compartment: environment
Initial concentration: 0.1
 
 sink
Compartment: environment
Initial concentration: 0.0
 
 source
Compartment: environment
Initial concentration: 0.0
 
Global Parameters (12)
 
 kc1
Value: 0.8
Constant
 
 kc2
Value: 0.4
Constant
 
 Cm
Value: 100.0
Constant
 
 D
Value: 0.1125
Constant
 
 kA1
Value: 0.1
Constant
 
  kA2
Value: NaN
 
 d2
Value: 0.3
Constant
 
 K2
Value: 10.0
Constant
 
  d1
Value: NaN
 
 K1
Value: 10.0
Constant
 
 dAA1
Value: 0.017
Constant
 
 dAA2
Value: 0.11
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000296

Curator's comment: (updated: 12 Jan 2011 02:15:44 GMT)

Reproduction of parts of figure 2 of the original publication using Copasi 4.6.

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