BioModels Database logo

BioModels Database

spacer

BIOMD0000000179 - Kim2007_CellularMemory_AsymmetricModel

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 17892872
Kim TH, Jung SH, Cho KH.
Interlinked mutual inhibitory positive feedbacks induce robust cellular memory effects.
FEBS Lett. 2007 Oct; 581(25): 4899-4904
Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul 151-747, Republic of Korea.  [more]
Model
Original Model: BIOMD0000000179.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL8716051482
Submission Date: 14 Aug 2008 12:43:30 UTC
Last Modification Date: 07 Apr 2014 00:31:47 UTC
Creation Date: 14 Aug 2008 03:16:36 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:hasTaxon Taxonomy cellular organisms
bqbiol:isVersionOf Gene Ontology regulation of cellular component movement
Notes

This model is from the article:
Interlinked mutual inhibitory positive feedbacks induce robust cellular memory effects.
Kim TH, Jung SH, Cho KH FEBS Lett.2007 Oct; 581(25) 17892872,
Abstract:
Mutual inhibitory positive feedback (MIPF), or double-negative feedback, is a key regulatory motif of cellular memory with the capability of maintaining switched states for transient stimuli. Such MIPFs are found in various biological systems where they are interlinked in many cases despite a single MIPF can still realize such a memory effect. An intriguing question then arises about the advantage of interlinking MIPFs instead of exploiting an isolated single MIPF to realize the memory effect. We have investigated the advantages of interlinked MIPF systems through mathematical modeling and computer simulations. Our results revealed that interlinking MIPFs expands the parameter range of achieving the memory effect, or the memory region, thereby making the system more robust to parameter perturbations. Moreover, the minimal duration and amplitude of an external stimulus required for off-to-on state transition are increased and, as a result, external noises can more effectively be filtered out. Hence, interlinked MIPF systems can realize more robust cellular memories with respect to both parameter perturbations and external noises. Our study suggests that interlinked MIPF systems might be an evolutionary consequence acquired for a more reliable memory effect by enhancing robustness against noisy cellular environments.

Note: The model reproduces the simulation result for an asymmetric model as depicted in Fig 3G of the paper. Model successfully tested on MathSBML

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: 17892872 Submission Date: 14 Aug 2008 12:43:30 UTC Last Modification Date: 07 Apr 2014 00:31:47 UTC Creation Date: 14 Aug 2008 03:16:36 UTC
Mathematical expressions
Reactions
React1 React2 React3 React4
React5 React6 React7 React8
React9 React10 React11 React12
React13 React14 React15 React16
React17      
Rules
Assignment Rule (variable: i2)      
Physical entities
Compartments Species
compartment R1 P1 P1_prime
R2 P2 P2_prime
P3_prime    
Global parameters
i1 d_R1 sP1R1 d_P1
sP1_prime_P1 s1 n s3
d_P1_prime i2 d_R2 sP2R2
d_P2 sP2_prime_P2 s2 d_P2_prime
sP3_prime_P2_prime d_P3_prime    
Reactions (17)
 
 React1  → [R1];  
 
 React2 [R1] → ;  
 
 React3  → [P1];   {R1}
 
 React4 [P1] → ;  
 
 React5  → [P1_prime];   {P1}
 
 React6  → [P1_prime];   {P2_prime}
 
 React7  → [P1_prime];   {P3_prime}
 
 React8 [P1_prime] → ;  
 
 React9  → [R2];  
 
 React10 [R2] → ;  
 
 React11  → [P2];   {R2}
 
 React12 [P2] → ;  
 
 React13  → [P2_prime];   {P2}
 
 React14  → [P2_prime];   {P1_prime}
 
 React15 [P2_prime] → ;  
 
 React16  → [P3_prime];   {P2_prime}
 
 React17 [P3_prime] → ;  
 
Rules (1)
 
 Assignment Rule (name: i2) i2 = piecewise(1, (t >= 50) && (t <= 100), 0)
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 R1
Compartment: compartment
Initial amount: 0.01
 
 P1
Compartment: compartment
Initial amount: 0.1
 
 P1_prime
Compartment: compartment
Initial amount: 0.1
 
 R2
Compartment: compartment
Initial amount: 0.1
 
 P2
Compartment: compartment
Initial amount: 1.0
 
 P2_prime
Compartment: compartment
Initial amount: 1.0
 
 P3_prime
Compartment: compartment
Initial amount: 0.1
 
Global Parameters (18)
 
   i1  
 
   d_R1
Value: 0.23521
Constant
 
   sP1R1
Value: 0.47305
Constant
 
   d_P1
Value: 0.22367
Constant
 
   sP1_prime_P1
Value: 0.28687
Constant
 
   s1
Value: 0.4
Constant
 
   n
Value: 9.0
Constant
 
   s3
Value: 0.2
Constant
 
   d_P1_prime
Value: 0.37048
Constant
 
   i2
Value: 1.0
 
   d_R2
Value: 0.23521
Constant
 
   sP2R2
Value: 0.47305
Constant
 
   d_P2
Value: 0.22367
Constant
 
   sP2_prime_P2
Value: 0.28687
Constant
 
   s2
Value: 0.3
Constant
 
   d_P2_prime
Value: 0.37048
Constant
 
   sP3_prime_P2_prime
Value: 0.5
Constant
 
   d_P3_prime
Value: 0.37048
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000179

Curator's comment: (updated: 14 Aug 2008 13:41:44 BST)

The plot corresponds to the asymmetric model as depicted in Fig 3G of the paper. Result obtained using MathSBML.

spacer
spacer