Cloutier2009 - Brain Energy Metabolism

View the 2015-08 Model of the Month entry for this model
  public model
Short description
Cloutier2009 - Brain Energy Metabolism


This model was taken from the  CellML repository  and automatically converted to SBML.  Following the submission the parameters are manually encoded and annotated as spices and global quantities by BioModels curators. 
 
The original model was:  Cloutier M, Bolger FB, Lowry JP, Wellstead P. (2009) - version=1.0 
The original CellML model was created by: 
Catherine Lloyd  
c.lloyd@auckland.ac.nz 
The University of Auckland 

This model is described in the article:

Cloutier M, Bolger FB, Lowry JP, Wellstead P.
J Comput Neurosci 2009 Dec; 27(3): 391-414

Abstract:

An integrative, systems approach to the modelling of brain energy metabolism is presented. Mechanisms such as glutamate cycling between neurons and astrocytes and glycogen storage in astrocytes have been implemented. A unique feature of the model is its calibration using in vivo data of brain glucose and lactate from freely moving rats under various stimuli. The model has been used to perform simulated perturbation experiments that show that glycogen breakdown in astrocytes is significantly activated during sensory (tail pinch) stimulation. This mechanism provides an additional input of energy substrate during high consumption phases. By way of validation, data from the perfusion of 50 microM propranolol in the rat brain was compared with the model outputs. Propranolol affects the glucose dynamics during stimulation, and this was accurately reproduced in the model by a reduction in the glycogen breakdown in astrocytes. The model's predictive capacity was verified by using data from a sensory stimulation (restraint) that was not used for model calibration. Finally, a sensitivity analysis was conducted on the model parameters, this showed that the control of energy metabolism and transport processes are critical in the metabolic behaviour of cerebral tissue.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Format
SBML (L2V4)
Related Publication
  • An integrative dynamic model of brain energy metabolism using in vivo neurochemical measurements.
  • Cloutier M, Bolger FB, Lowry JP, Wellstead P
  • Journal of computational neuroscience , 12/ 2009 , Volume 27 , pages: 391-414
  • Hamilton Institute, National University of Ireland Maynooth, Maynooth, Ireland.
  • An integrative, systems approach to the modelling of brain energy metabolism is presented. Mechanisms such as glutamate cycling between neurons and astrocytes and glycogen storage in astrocytes have been implemented. A unique feature of the model is its calibration using in vivo data of brain glucose and lactate from freely moving rats under various stimuli. The model has been used to perform simulated perturbation experiments that show that glycogen breakdown in astrocytes is significantly activated during sensory (tail pinch) stimulation. This mechanism provides an additional input of energy substrate during high consumption phases. By way of validation, data from the perfusion of 50 microM propranolol in the rat brain was compared with the model outputs. Propranolol affects the glucose dynamics during stimulation, and this was accurately reproduced in the model by a reduction in the glycogen breakdown in astrocytes. The model's predictive capacity was verified by using data from a sensory stimulation (restraint) that was not used for model calibration. Finally, a sensitivity analysis was conducted on the model parameters, this showed that the control of energy metabolism and transport processes are critical in the metabolic behaviour of cerebral tissue.
Contributors
administrator, Camille Laibe

Metadata information

is
BioModels Database MODEL1006230041
BioModels Database BIOMD0000000554
isDescribedBy
PubMed 19396534
isDerivedFrom
PubMed 16260743
BioModels Database MODEL1411210000
hasTaxon
Taxonomy Homo sapiens
Taxonomy Rattus norvegicus
occursIn
Brenda Tissue Ontology brain
Curation status
Curated
Name Description Size Actions

Model files

BIOMD0000000554_url.xml SBML L2V4 representation of Cloutier2009 - Brain Energy Metabolism 172.14 KB Preview | Download

Additional files

BIOMD0000000554.vcml Auto-generated VCML file 900.00 bytes Preview | Download
Cloutier2009(final).cps Copasi file of the model 207.18 KB Preview | Download
BIOMD0000000554.m Auto-generated Octave file 32.56 KB Preview | Download
BIOMD0000000554.xpp Auto-generated XPP file 25.60 KB Preview | Download
BIOMD0000000554.pdf Auto-generated PDF file 281.99 KB Preview | Download
BIOMD0000000554_urn.xml Auto-generated SBML file with URNs 167.84 KB Preview | Download
BIOMD0000000554.png Auto-generated Reaction graph (PNG) 5.04 KB Preview | Download
BIOMD0000000554-biopax3.owl Auto-generated BioPAX (Level 3) 22.78 KB Preview | Download
BIOMD0000000554.sci Auto-generated Scilab file 1.14 KB Preview | Download
BIOMD0000000554.svg Auto-generated Reaction graph (SVG) 851.00 bytes Preview | Download
BIOMD0000000554-biopax2.owl Auto-generated BioPAX (Level 2) 17.82 KB Preview | Download

  • Model originally submitted by : administrator
  • Submitted: Jun 23, 2010 10:12:09 AM
  • Last Modified: Dec 21, 2018 5:39:15 PM
Revisions
  • Version: 3 public model Download this version
    • Submitted on: Dec 21, 2018 5:39:15 PM
    • Submitted by: administrator
    • With comment: Include the additional files provided by the submitter in the original submission: Cloutier2009(final).cps
  • Version: 2 public model Download this version
    • Submitted on: Apr 20, 2015 4:57:22 PM
    • Submitted by: Camille Laibe
    • With comment: Current version of Cloutier2009 - Brain Energy Metabolism
  • Version: 1 public model Download this version
    • Submitted on: Jun 23, 2010 10:12:09 AM
    • Submitted by: Camille Laibe
    • With comment: Original import of Cloutier2009_BrainEnergyMetabolism
Curator's comment:
(added: 22 Oct 2014, 18:38:51, updated: 22 Oct 2014, 18:38:51)
Figures 2f and 2i of the reference publication have been reproduced here. Concentration of extracellular glucose and lactate are plotted over time. The profile moves along the x-axis depending on the neuronal stimulation start, strength and duration. The simulation was done using Copasi v4.12 (Build 81) and the plots were generated using Gnuplot. The Copasi file of the model with simulation settings can be downloaded from the below link: