An ion-based model for swelling of neurons and astrocytes (Hubel & Ullah 2016)

 Download zip file 
Help downloading and running models
Accession:187599
The programs describe ion dynamics and osmosis-driven cellular swelling. “code_fig3.ode” shows a scenario of permanent cessation of energy supply / Na/K-pump activity, and the induced transition from normal conditions to the Donnan equilibrium for an isolated neuron and its extracellular space. “code_Fig7.ode” shows spreading depolarization induced by an interruption of energy supply in a model consisting of a neuron, a glia cell and the extracellular space. The simulations show the evolution of ion concentrations, Nernst potentials, the membrane potential, gating variables and cellular volumes.
Reference:
1 . Hubel N, Ullah G (2016) Anions Govern Cell Volume: A Case Study of Relative Astrocytic and Neuronal Swelling in Spreading Depolarization. PLoS One 11:e0147060 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Glia;
Brain Region(s)/Organism:
Cell Type(s): Astrocyte; Abstract single compartment conductance based cell;
Channel(s): I Chloride; I Na,t; I p,q; I K; I K,leak; I h; I Sodium; I_K,Na; Na/K pump; I Cl, leak; I Na, leak; Osmosis-driven water flux;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s): Ions;
Simulation Environment: XPP;
Model Concept(s): Depolarization block; Anoxic depolarization; Spreading depression; Volume transmission;
Implementer(s):
Search NeuronDB for information about:  I Chloride; I Na,t; I p,q; I K; I K,leak; I h; I Sodium; I_K,Na; Na/K pump; I Cl, leak; I Na, leak; Osmosis-driven water flux; Ions;
/
Anions_Govern_Cell_Volume
README
code_Fig3.ode
code_Fig7.ode
                            
The code files "code_Fig3.ode" and "code_Fig4.ode" were used for the
respective simulations of Fig. 3 and 7 in
***********************************************************************
Hübel, N. and Ullah, G., "Anions Govern Cell Volume: a Case Study of 
Relative Astrocytic and Neuronal Swelling in Spreading Depolarization",
PLoS ONE, 10.1371/journal.pone.0147060 (2016).
***********************************************************************
The code is written for XPP/XPPAUT.


Running "code_Fig3.ode" yields the time series shown in the main parts
of Fig. 3. Changing "par s=0" to "par s=1" in line 45 (or equivalently
changing "s=0" to "s=1" in the parameter settings of the XPP/XPPAUT
graphical interface) changes the volume model from "derived" to
"exponential" (see manuscript) and yields the time series shown in the
insets of Fig. 3. The default plot setting in line 198 shows the
potentials. Uncommenting line 199 or 200 will show volumes and ion
concentrations, respectively.
In addition, by changing "par gcl_l=0.05" to "par gcl_l=0" in line 135
(or setting the parameter "gcl_l" to zero in the parameter interface
after opening the file with XPP/XPPAUT) will produce Fig. 4 of the
paper.

Running "code_Fig7.ode" yields the time series shown in Fig 7. The
plot setting in lines 239 (default), 240 and 241 show the potentials
volumes and relative volume changes. Note that the volume plot shows
absolute volumes as the differences between the "vli_line", the
"vle_line" and the "vlg_line".



Loading data, please wait...