band2

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000414) Biomodels notes: 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). JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.

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Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.

  • Leah R Band
  • Darren M Wells
  • Antoine Larrieu
  • Jianyong Sun
  • Alistair M Middleton
  • Andrew P French
  • Géraldine Brunoud
  • Ethel Mendocilla Sato
  • Michael H Wilson
  • Benjamin Péret
  • Marina Oliva
  • Ranjan Swarup
  • Ilkka Sairanen
  • Geraint Parry
  • Karin Ljung
  • Tom Beeckman
  • Jonathan M Garibaldi
  • Mark Estelle
  • Markus R Owen
  • Kris Vissenberg
  • T Charlie Hodgman
  • Tony P Pridmore
  • John R King
  • Teva Vernoux
  • Malcolm J Bennett
Proc. Natl. Acad. Sci. U.S.A. 2012; 109 (12): 4668-4673
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.

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
Id Name Spatial dimensions Size
cell 3.0 1.0
Id Name Initial quantity Compartment Fixed
VENUS 1.0 cell

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
VENUSdecayduetoauxin VENUS > ∅

p2 * VENUS / (p1_star * VENUS + qj_star)
VENUSdecayduetophotobleaching VENUS > ∅

lambda_star * p2 * VENUS
VENUSproduction ∅ > VENUS

p2

Global parameters

Id Value
lambda_star 0.52
p1_star 0.056
p2 0.0053
qj_star 0.16

Local parameters

Id Value Reaction

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments