BIOMD0000000413
type: SBMLModel
reaction: 119126
curated: true
reaction: 119114
substance units: substance
parameter: 119151
is described by: http://identifiers.org/pubmed/22393022
species: 119104
parameter: 119147
compartment: 119099
area units: area
modified:
  W3 CDTF: Fri May 18 10:44:57 BST 2012
reaction: 119122
species: 119101
parameter: 119138
reaction: 119110
species: 119102
is version of: GO:0090354
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
time units: time
reaction: 119116
created:
  W3 CDTF: Thu Apr 05 15:38:40 BST 2012
name: Band2012_DII-Venus_FullModel
parameter: 119153
species: 119106
volume units: volume
parameter: 119149
parameter: 119141
is: MODEL1203230002
reaction: 119124
reaction: 119112
length unit: length
occurs in: http://identifiers.org/taxonomy/3701
species: 119108
parameter: 119145
reaction: 119120
reaction: 119118
creator:
  ORG:
    orgname: Centre for Plant Integrative Biology, University of Nottingham
  n:
    given: Leah
    family: Band
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 full model described in the article.
parameter: 119155
parameter: 119143
parameter: 119139

119126
type: Reaction
kinetic law: 658831
reactant: 658819
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false

658819
type: SpeciesReference
stoichiometry: 1.0
species: 119108

119108
type: Species
is: SBO:0000297
has only substance units: false
has part: Q940U6
has part: Q9XFM0
initial amount: NaN
initial concentration: 40.4
boundary condition: false
constant: false
in compartment: 119099

119099
type: Compartment
is version of: GO:0005623
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0

119114
type: Reaction
is: SBO:0000526
product: 658637
reactant: 658625
kinetic law: 658649
reversible: false
reactant: 658613
fast: false
is version of: GO:0006461

658637
type: SpeciesReference
stoichiometry: 1.0
species: 119106

119106
type: Species
is: SBO:0000297
has part: Q570C0
has part: Q940U6
constant: false
has only substance units: false
in compartment: 119099
initial concentration: 2.78
has part: Q9XFM0
initial amount: NaN
has part: P49677
boundary condition: false

658625
type: SpeciesReference
stoichiometry: 1.0
species: 119108

658613
type: SpeciesReference
stoichiometry: 1.0
species: 119104

119104
type: Species
has part: Q570C0
is: SBO:0000297
has only substance units: false
in compartment: 119099
has part: P49677
constant: false
initial concentration: 0.28
initial amount: NaN
boundary condition: false

119151
type: Parameter
constant: true
value: 0.00316

119147
type: Parameter
constant: true
value: 1.15

119122
type: Reaction
kinetic law: 658781
reactant: 658769
is version of: GO:0030163
is: SBO:0000179
fast: false
reversible: false

658769
type: SpeciesReference
stoichiometry: 1.0
species: 119101

119101
type: Species
is version of: P49677
is: SBO:0000252
constant: false
boundary condition: false
has only substance units: false
initial concentration: 7.38
initial amount: NaN
in compartment: 119099

119138
type: Parameter
constant: true
value: 0.334

119110
type: Reaction
product: 658540
reactant: 658528
fast: false
is version of: GO:0006461
reactant: 658516
reversible: false
is: SBO:0000526
kinetic law: 658552

658540
type: SpeciesReference
stoichiometry: 1.0
species: 119104

658528
type: SpeciesReference
stoichiometry: 1.0
species: 119102

119102
type: Species
is version of: Q9LPW7
is: SBO:0000252
boundary condition: false
is version of: Q9ZR12
is version of: Q9LW29
in compartment: 119099
is version of: Q570C0
initial amount: NaN
initial concentration: 15.4
has only substance units: false
constant: false

658516
type: SpeciesReference
stoichiometry: 1.0
species: 119101

119116
type: Reaction
is version of: GO:0043241
product: 658685
fast: false
reversible: false
reactant: 658661
product: 658673
kinetic law: 658697
is: SBO:0000180

658685
type: SpeciesReference
stoichiometry: 1.0
species: 119108

658661
type: SpeciesReference
stoichiometry: 1.0
species: 119106

658673
type: SpeciesReference
stoichiometry: 1.0
species: 119104

119153
type: Parameter
constant: true
value: 18.5

119149
type: Parameter
constant: true
value: 0.486

119141
type: Parameter
constant: true
value: 0.79

119124
type: Reaction
kinetic law: 658807
product: 658794
is version of: GO:0006412
is: SBO:0000393
fast: false
reversible: false

658794
type: SpeciesReference
stoichiometry: 1.0
species: 119108

119112
type: Reaction
kinetic law: 658601
product: 658576
reversible: false
product: 658589
is: SBO:0000180
is version of: GO:0043241
fast: false
reactant: 658564

658576
type: SpeciesReference
stoichiometry: 1.0
species: 119101

658589
type: SpeciesReference
stoichiometry: 1.0
species: 119102

658564
type: SpeciesReference
stoichiometry: 1.0
species: 119104

119145
type: Parameter
constant: true
value: 0.175

119120
type: Reaction
kinetic law: 658757
product: 658745
is version of: GO:0006412
is: SBO:0000393
fast: false
reversible: false

658745
type: SpeciesReference
stoichiometry: 1.0
species: 119101

119118
type: Reaction
kinetic law: 658733
product: 658721
reactant: 658709
is version of: GO:0043241
is: SBO:0000180
fast: false
reversible: false

658721
type: SpeciesReference
stoichiometry: 1.0
species: 119104

658709
type: SpeciesReference
stoichiometry: 1.0
species: 119106

119155
type: Parameter
constant: true
value: 30.5

119143
type: Parameter
constant: true
value: 4.49

119139
type: Parameter
constant: true
value: 8.22E-4