MODEL1210260004
type: SBMLModel
species: COPASI9
reaction: COPASI22
parameter: COPASI18
species: COPASI11
reaction: COPASI21
rule: 964406
parameter: COPASI15
substance units: substance
function def: COPASI26
function def: COPASI25
reaction: COPASI23
name: 1 Reactant, 1 inhibitor, 1 activator
rule: 964442
name: Viladomiu2012 - PPARgamma role in C.diff associated disease
volume units: volume
rule: 964430
species: COPASI8
parameter: COPASI16
species: COPASI7
parameter: COPASI14
species: COPASI13
species: COPASI5
parameter: COPASI19
species: COPASI12
area units: area
notes: "Modeling the Role of Peroxisome Proliferator-Activated Receptor γ and MicroRNA-146 in Mucosal Immune Responses to Clostridium difficile" Monica Viladomiu1,2, Raquel Hontecillas1,2, Mireia Pedragosa1,2, Adria Carbo1,2, Stefan Hoops1,2, Pawel Michalak4,5, Katarzyna Michalak4, Richard L. Guerrant2,3, James K. Roche2,3, Cirle A. Warren2,3, Josep Bassaganya-Riera1,2* 1) Nutritional Immunology and Molecular Medicine Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America, 2) Center for Modeling Immunity to Enteric Pathogens, Virginia Tech, Blacksburg, Virginia, United States of America, 3) Division of Infectious Disease and International Health, Center for Global Health, University of Virginia, Charlottesville, Virginia, United States of America, 4) Medical Informatics and Systems Division, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America, 5) Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America E-mail: jbassaga@vt.edu This model represents the interaction between Cdiff, miRNA146b, NCOA4, PPARg, IL10 and IL17. Simulation studies show an aberrant expression of miRNA146b with increasing concentrations of Cdiff over time, which results in decreased PPARg activation due to NCOA4 inhibition. As a final result, PPARg is unable to modulate effector and regulatory responses, since results show an upregulation of IL17 expression and downregulation of IL10 production.
function def: COPASI27
length unit: length
curated: false
reaction: COPASI24
compartment: COPASI2
species: COPASI4
species: COPASI3
is described by: http://identifiers.org/pubmed/23071818
species: COPASI10
rule: 964418
parameter: COPASI17
name: 1 Reactant, 1 inhibitor
reaction: COPASI20
species: COPASI6
name: 1 Reactant, 1 Activator
time units: time

COPASI9
type: Species
notes: Precursor of PPARg
constant: true
boundary condition: true
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: COPASI2
name: pPPARg

COPASI2
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: default

COPASI22
type: Reaction
fast: false
modifier: 102237
name: pPPARg -> PPARg
modifier: 964683
kinetic law: 964695
reactant: 964659
reversible: true
product: 964671
modifier: 102249
modifier: 102261

COPASI6
type: Species
notes: NCOA4, a PPARg co-activator
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.439999130655188
initial amount: NaN
in compartment: COPASI2
name: NCOA4

964743
type: LocalParameter
value: 0.1
name: Vr

964731
type: LocalParameter
value: 4.6671
name: K

964719
type: LocalParameter
value: 0.0270105
name: c1

964707
type: LocalParameter
value: 1.41678E-4
name: c0

964659
type: SpeciesReference
stoichiometry: 1.0
species: COPASI9

964671
type: SpeciesReference
stoichiometry: 1.0
species: COPASI8

COPASI8
type: Species
notes: Peroxisome proliferator receptor gamma
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.00379635306159362
initial amount: NaN
in compartment: COPASI2
name: PPARg

COPASI18
type: Parameter
constant: false
value: 2.29881987622278E-5
name: IL10_ratio

COPASI11
type: Species
notes: Precursor of interleukin 17
constant: true
boundary condition: true
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: COPASI2
name: pIL-17

COPASI21
type: Reaction
modifier: 102201
modifier: 964575
name: pNCOA4 -> NCOA4
modifier: 102213
product: 964563
reversible: true
modifier: 102225
fast: false
reactant: 964550
kinetic law: 964587

COPASI7
type: Species
notes: Precursor of NCOA4
constant: true
boundary condition: true
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: COPASI2
name: pNCOA4

COPASI4
type: Species
notes: miRNA 146b
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.568
initial amount: NaN
in compartment: COPASI2
name: miR-146b

964563
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

964550
type: SpeciesReference
stoichiometry: 1.0
species: COPASI7

964647
type: LocalParameter
value: 47.9736
name: c1

964635
type: LocalParameter
value: 5.9841E-4
name: c0

964623
type: LocalParameter
value: 0.1
name: Vr

964611
type: LocalParameter
value: 18.0
name: n

964599
type: LocalParameter
value: 0.384846
name: K

COPASI15
type: Parameter
constant: true
value: 1.0
name: Bactin

COPASI23
type: Reaction
modifier: 964779
modifier: 102273
kinetic law: 964803
reactant: 964755
fast: false
reversible: true
name: pIL-10 -> IL-10
modifier: 964791
modifier: 102309
product: 964767
modifier: 102297
modifier: 102285

COPASI3
type: Species
notes: Clostridium difficile
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: COPASI2
name: Cdiff

COPASI10
type: Species
notes: Precursor of interleukin 10
constant: true
boundary condition: true
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: COPASI2
name: pIL-10

964867
type: LocalParameter
value: 0.1
name: Vr

964854
type: LocalParameter
value: 1.0E-6
name: K1

964842
type: LocalParameter
value: 0.1
name: n1

964830
type: LocalParameter
value: 1000.0
name: K

964818
type: LocalParameter
value: 3.30707E-6
name: Vf

964755
type: SpeciesReference
stoichiometry: 1.0
species: COPASI10

COPASI12
type: Species
notes: Interleukin 10
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.29881987622278E-5
initial amount: NaN
in compartment: COPASI2
name: IL-10

964767
type: SpeciesReference
stoichiometry: 1.0
species: COPASI12

COPASI16
type: Parameter
constant: false
value: 0.439999130655188
name: NCOA4_ratio

COPASI14
type: Parameter
constant: true
value: 2.0
name: HillCoeff

COPASI13
type: Species
notes: Interleukin 17
constant: false
boundary condition: false
has only substance units: false
initial concentration: -1.96342127958466E-34
initial amount: NaN
in compartment: COPASI2
name: IL-17

COPASI5
type: Species
notes: Precursor of miRNA 146b
constant: true
boundary condition: true
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: COPASI2
name: p-miR-146b

COPASI19
type: Parameter
constant: false
value: -1.96342127958466E-34
name: IL17_ratio

COPASI24
type: Reaction
modifier: 102357
modifier: 102345
modifier: 102321
kinetic law: 964927
reactant: 964879
product: 964891
modifier: 102333
name: pIL-17 -> IL-17
reversible: true
modifier: 964915
modifier: 964903
fast: false

964987
type: LocalParameter
value: 0.06
name: Vr

964976
type: LocalParameter
value: 7.80698E-6
name: K1

964963
type: LocalParameter
value: 0.1
name: n1

964951
type: LocalParameter
value: 996.619
name: K

964939
type: LocalParameter
value: 0.06
name: Vf

964879
type: SpeciesReference
stoichiometry: 1.0
species: COPASI11

964891
type: SpeciesReference
stoichiometry: 1.0
species: COPASI13

COPASI17
type: Parameter
constant: false
value: 0.00379635306159362
name: PPARg_ratio

COPASI20
type: Reaction
modifier: 102189
product: 964466
modifier: 102165
name: pmiR-146b -> miR-146b
fast: false
reactant: 964455
modifier: 102177
modifier: 964478
kinetic law: 964490
reversible: true

964466
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

964455
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

964538
type: LocalParameter
value: 0.1
name: Vr

964526
type: LocalParameter
value: 89.763
name: K

964514
type: LocalParameter
value: 20.9518
name: c1

964502
type: LocalParameter
value: 0.0568
name: c0