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BIOMD0000000301 - Friedland2009_Ara_RTC3_counter

 

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Reference Publication
Publication ID: 19478183
Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ.
Synthetic gene networks that count.
Science 2009 May; 324(5931): 1199-1202
Howard Hughes Medical Institute, Department of Biomedical Engineering, Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA.  [more]
Model
Original Model: BIOMD0000000301.xml.origin
Submitter: Lukas Endler
Submission ID: MODEL1012220006
Submission Date: 22 Dec 2010 21:47:01 UTC
Last Modification Date: 08 Apr 2011 12:29:50 UTC
Creation Date: 19 Jan 2011 02:14:29 UTC
Encoders:  Lukas Endler
set #1
bqbiol:occursIn Taxonomy Escherichia coli (strain K12)
set #2
bqbiol:hasVersion Gene Ontology positive regulation of translation, ncRNA-mediated
Gene Ontology regulation of translational initiation
Notes

This is the model of the RTC3 counter described in the article:
Synthetic gene networks that count.
Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. Science. 2009 May 29;324(5931):1199-202. PMID: 19478183 , DOI: 10.1126/science.1172005

Abstract:
Synthetic gene networks can be constructed to emulate digital circuits and devices, giving one the ability to program and design cells with some of the principles of modern computing, such as counting. A cellular counter would enable complex synthetic programming and a variety of biotechnology applications. Here, we report two complementary synthetic genetic counters in Escherichia coli that can count up to three induction events: the first, a riboregulated transcriptional cascade, and the second, a recombinase-based cascade of memory units. These modular devices permit counting of varied user-defined inputs over a range of frequencies and can be expanded to count higher numbers.

The 3 arabinose pulses are implemented using events, one for the start of pulses and one for the end. The variable pulse_flag changes arabinose consumption to fit behaviour during pulses and in between. To simulate two pulses only, set the pulse length of the third pulse to a negative value (though with an absolute value smaller than the pulse intervall length).

Originally created by libAntimony v1.4 (using libSBML 3.4.1)

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 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: 19478183 Submission Date: 22 Dec 2010 21:47:01 UTC Last Modification Date: 08 Apr 2011 12:29:50 UTC Creation Date: 19 Jan 2011 02:14:29 UTC
Mathematical expressions
Reactions
r0 r1a r1b r2a
r2b r3a r3b r6
r7 r8 r9 r10a
r10b r11 r12  
Rules
Assignment Rule (variable: pulse2_start) Assignment Rule (variable: pulse3_start)    
Events
pulse_start1 pulse_start2 pulse_start3 pulse_end1
pulse_end2 pulse_end3    
Physical entities
Compartments Species
cell taRNA mT7cr mGFPcr
pT7 pGFP ara
pT3 mT3cr  
Global parameters
cAra pulse_flag dAra sT
k_ara s0_taRNA d_taRNA s0_mT7cr
d_mT7 s0_mGFPcr k_pT3 n3
km3 d_mGFP s0_pT7 s_pT7k
s0_pGFP s_pGFPk d_pT7 d_pGFP
s0_mT3cr k_pT7 n7 km7
d_mT3 s0_pT3 s_pT3k d_pT3
pulse_interval pulse1_start pulse1_length pulse_conc
pulse2_start pulse2_length pulse3_start pulse3_length
Reactions (15)
 
 r0 [ara] → ;  
 
 r1a  → [taRNA];   {ara}
 
 r1b [taRNA] → ;  
 
 r2a  → [mT7cr];  
 
 r2b [mT7cr] → ;  
 
 r3a  → [mGFPcr];   {pT3}
 
 r3b [mGFPcr] → ;  
 
 r6  → [pT7];   {taRNA} , {mT7cr}
 
 r7  → [pGFP];   {taRNA} , {mGFPcr}
 
 r8 [pT7] → ;  
 
 r9 [pGFP] → ;  
 
 r10a  → [mT3cr];   {pT7}
 
 r10b [mT3cr] → ;  
 
 r11  → [pT3];   {taRNA} , {mT3cr}
 
 r12 [pT3] → ;  
 
Rules (2)
 
 Assignment Rule (name: pulse2_start) pulse2_start = pulse1_start+pulse1_length+pulse_interval
 
 Assignment Rule (name: pulse3_start) pulse3_start = pulse2_start+pulse2_length+pulse_interval
 
Events (6)
 
 pulse_start1
pulse_flag = 1
ara = pulse_conc
 
 pulse_start2
pulse_flag = 1
ara = pulse_conc
 
 pulse_start3
pulse_flag = 1
ara = pulse_conc
 
 pulse_end1
pulse_flag = 0
 
 pulse_end2
pulse_flag = 0
 
 pulse_end3
pulse_flag = 0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 taRNA
Compartment: cell
Initial concentration: 0.006796941377
 
 mT7cr
Compartment: cell
Initial concentration: 0.3569405099
 
 mGFPcr
Compartment: cell
Initial concentration: 0.176991329
 
 pT7
Compartment: cell
Initial concentration: 0.05230744612
 
 pGFP
Compartment: cell
Initial concentration: 6.338921181
 
 ara
Compartment: cell
Initial concentration: 0.0
 
 pT3
Compartment: cell
Initial concentration: 6.41674E-5
 
 mT3cr
Compartment: cell
Initial concentration: 0.00566438
 
Global Parameters (36)
 
   cAra
Value: 3.0E-4
Constant
 
   pulse_flag  
 
   dAra
Value: 0.1201
Constant
 
   sT
Value: 0.8467
Constant
 
   k_ara
Value: 0.0571
Constant
 
   s0_taRNA
Value: 8.0E-4
Constant
 
   d_taRNA
Value: 0.1177
Constant
 
   s0_mT7cr
Value: 0.0252
Constant
 
   d_mT7
Value: 0.0706
Constant
 
   s0_mGFPcr
Value: 0.0123
Constant
 
   k_pT3
Value: 3.006
Constant
 
   n3
Value: 0.8892
Constant
 
   km3
Value: 7.9075
Constant
 
   d_mGFP
Value: 0.07
Constant
 
   s0_pT7
Value: 3.0E-4
Constant
 
   s_pT7k
Value: 0.0766
Constant
 
   s0_pGFP
Value: 0.1007
Constant
 
   s_pGFPk
Value: 0.9923
Constant
 
   d_pT7
Value: 0.0056
Constant
 
   d_pGFP
Value: 0.0030
Constant
 
   s0_mT3cr
Value: 3.0E-4
Constant
 
   k_pT7
Value: 3.8009
Constant
 
   n7
Value: 2.602
Constant
 
   km7
Value: 3.0455
Constant
 
   d_mT3
Value: 0.0701
Constant
 
   s0_pT3
Constant
 
   s_pT3k
Value: 0.0115
Constant
 
   d_pT3
Value: 0.0069
Constant
 
   pulse_interval
Value: 20.0
Constant
 
   pulse1_start
Value: 0.01
Constant
 
   pulse1_length
Value: 11.0
Constant
 
   pulse_conc
Value: 0.01
Constant
 
   pulse2_start
Value: NaN
 
   pulse2_length
Value: 11.0
Constant
 
   pulse3_start
Value: NaN
 
   pulse3_length
Value: 22.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000301

Curator's comment: (updated: 19 Jan 2011 02:14:09 GMT)

Reproduction of fig S5 in the supplement of the reference publication. The simulation was performed with Copasi 4.6. The curves display the pGFP concentration at each time point minus the steady state concentration of pGFP. To simulate to pulses the length of the third pulse was set to -1. The values for the pulses were:

pulse1_start = 0.01, pulse_interval = 20

three pulses: pulse1_length = pulse2_length = 11, pulse3_length = 22

two pulses: pulse1_length = pulse2_length = 22, pulse3_length = -1

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