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BIOMD0000000414 - Band2012_DII-Venus_ReducedModel

 

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Reference Publication
Publication ID: 22393022
Band LR, Wells DM, Larrieu A, Sun J, Middleton AM, French AP, Brunoud G, Sato EM, Wilson MH, Péret B, Oliva M, Swarup R, Sairanen I, Parry G, Ljung K, Beeckman T, Garibaldi JM, Estelle M, Owen MR, Vissenberg K, Hodgman TC, Pridmore TP, King JR, Vernoux T, Bennett MJ.
Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.
Proc. Natl. Acad. Sci. U.S.A. 2012 Mar; 109(12): 4668-4673
Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom.  [more]
Model
Original Model: BIOMD0000000414.xml.origin
Submitter: Leah Band
Submission ID: MODEL1203230001
Submission Date: 23 Mar 2012 14:45:23 UTC
Last Modification Date: 02 Apr 2014 00:26:52 UTC
Creation Date: 05 Apr 2012 14:39:10 UTC
Encoders:  Vijayalakshmi Chelliah
   Leah Band
set #1
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #2
bqbiol:isVersionOf Gene Ontology positive gravitropism
Gene Ontology regulation of auxin metabolic process
set #3
bqbiol:hasTaxon Taxonomy Arabidopsis
Notes

This model is from the article:
Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.
Band LR, Wells DM, Larrieu A, Sun J, Middleton AM, French AP, Brunoud G, Sato EM, Wilson MH, Péret B, Oliva M, Swarup R, Sairanen I, Parry G, Ljung K, Beeckman T, Garibaldi JM, Estelle M, Owen MR, Vissenberg K, Hodgman TC, Pridmore TP, King JR, Vernoux T, Bennett MJ. Proc Natl Acad Sci U S A.2012 Mar 20;109(12):4668-73 22393022,
Abstract:
Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a "tipping point" mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.

This model corresponds to the simplified model described in the article. It is assumed that, on the timescale of DII-VENUS degradation, the concentrations of auxin, TIR1/AFB, and their complexes can be approximated by quasi-steady-state expressions. This reduced the full model to a single ODE that describes how the DII-VENUS dynamics depend on the auxin influx and four parameter groupings.

Model
Publication ID: 22393022 Submission Date: 23 Mar 2012 14:45:23 UTC Last Modification Date: 02 Apr 2014 00:26:52 UTC Creation Date: 05 Apr 2012 14:39:10 UTC
Mathematical expressions
Reactions
VENUSproduction VENUSdecayduetophotobleaching VENUSdecayduetoauxin  
Physical entities
Compartments Species
cell VENUS    
Global parameters
p1_star p2 lambda_star qj_star
Reactions (3)
 
 VENUSproduction  → [VENUS];  
 
 VENUSdecayduetophotobleaching [VENUS] → ;  
 
 VENUSdecayduetoauxin [VENUS] → ;  
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 VENUS
Compartment: cell
Initial concentration: 1.0
 
Global Parameters (4)
 
   p1_star
Value: 0.056
Constant
 
   p2
Value: 0.0053
Constant
 
   lambda_star
Value: 0.52
Constant
 
   qj_star
Value: 0.16
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000414

Curator's comment: (updated: 05 Apr 2012 15:38:25 BST)

Figure s19 in the supplementary material of the reference publication has been reproduced here. The model as such corresponds to the auxin dose of 10nM (cyan line in the plot). Different auxin doses are incorporated in the model using the parameter, qj_star.
qj_star = 1.00 (no auxin)
qj_star = 0.68 (1nM)
qj_star = 0.23 (5nM)
qj_star = 0.16 (10nM)
qj_star = 0.05 (100nM)
qj_star = 0.03(1000nM).

The model was simulated using Copasi v4.8 (Build 35).

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