Determinants of fast calcium dynamics in dendritic spines and dendrites (Cornelisse et al. 2007)

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Accession:97903
"... Calcium influx time course and calcium extrusion rate were both in the same range for spines and dendrites when fitted with a dynamic multi-compartment model that included calcium binding kinetics and diffusion. In a subsequent analysis we used this model to investigate which parameters are critical determinants in spine calcium dynamics. The model confirmed the experimental findings: a higher SVR (surface-to-volume ratio) is not sufficient by itself to explain the faster rise time kinetics in spines, but only when paired with a lower buffer capacity in spines. Simulations at zero calcium-dye conditions show that calmodulin is more efficiently activated in spines, which indicates that spine morphology and buffering conditions in neocortical spines favor synaptic plasticity. ..."
Reference:
1 . Cornelisse LN, van Elburg RAJ, Meredith RM, Yuste R, Mansvelder HD (2007) High Speed Two-Photon Imaging of Calcium Dynamics in Dendritic Spines: Consequences for Spine Calcium Kinetics and Buffer Capacity. PLoS ONE 2(10):e1073 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Synapse; Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Neocortex U1 pyramidal intratelencephalic L2-5 cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: CalC Calcium Calculator;
Model Concept(s): Calcium dynamics;
Implementer(s): van Elburg, Ronald A.J. [R.van.Elburg at ai.rug.nl];
Search NeuronDB for information about:  Neocortex U1 pyramidal intratelencephalic L2-5 cell;
Author: Ronald van Elburg  (RonaldAJ at vanElburg eu)

This software contains all the code used in the modelling and subsequent analysis 
of calcium dynamics as described in the paper:
   Cornelisse LN, van Elburg RAJ, Meredith RM, Yuste R, Mansvelder HD (2007) 
   High Speed Two-Photon Imaging of Calcium Dynamics in Dendritic Spines: 
   Consequences for Spine Calcium Kinetics and Buffer Capacity. 
   PLoS ONE 2(10): e1073 doi:10.1371/journal.pone.0001073

This software is released under the GNU GPL version 3: 
http://www.gnu.org/copyleft/gpl.html

Purpose:        
 To show how the Calcium signal changes in time after an actionpotential and how
 these timecourses depend on the distance to the membrane and the membrane 
 morphology which can be spherical (spine) or cylindrical (dendrite).  

Background:  
 
The model code organized in par-files is developed for CalC 5.0.3, available from:
http://web.njit.edu/~matveev/calc.html.
Analysis was done using Matlab (The Mathworks,Natick, MA):
http://www.mathworks.com/.

The model can be found in the main file CaSignal_Main.par which describes
the core model. The other *.par files specify the experiments carried out with the 
model and which model variables are exported to file for analysis. The files 
runcalcscripts.sh and CaSignal_Master.m describe which files are needed for which
paper figures, and can also be used for generating all model figures albeit in a
slightly different organization then found in the paper. The shell script 
runcalcscripts.sh was developed under windows using the bash from cygwin.

The recommendation for code reuse is to focus on the calc scripts specifying the model 
and write new matlab analysis code. The matlab code is merely provided to make it 
possible to check the results in our paper and is not ment for reuse. 

General organization of the code:
    
    For 2D parameter scans 
        Output\*_CombinedFigures.pdf  where * is KdEndo, SVREndo, SVREndoCalmod,
        DtGamma or  KOnKOff.
            Steps:
            1. Ensure the existence of the folder Exp* in the Output folder
            2.  Run CaSignal_*Sphere.par    (Simulations for the spine.)
                Run CaSignal_*Disc.par      (Simulations for the dendrite.)
            3.  Run CaSignal_*.m            (Process data and generate figures.)
            4.  Run *_MergedAtomics.m       (Gather main figures into one combined figure.)
                                     
    For individual traces
        Output\FreeAndDyeInShells.pdf 
        Output\EndoBufs_CombinedFigures.pdf 
             1. Ensure the existence of the Exp3 ExpB8A, ExpB8B, ExpB8E, ExpB8F,
                ExpB8G, ExpB8H folders in the Output folder.                            
             2. Run CaSignal*Sphere.par                 (Simulations for the spine.)  
                Run CaSignal*Disc.par                   (Simulations for the dendrite.)
                where * corresponds to elements from the lsit in step 1.
             3. Run CaSignal_Exp3.m, CaSignal_Exp8.m    (Process data and generate figures.) 
             4. Adjust paths in and then run: Python\DoRenameFiles.py 
                Run FreeCalcium4EndoBufs_MergedAtomics.m  
                (Gather main figures into one combined figure.)
                     
    and also for individual traces                        
        For Output\Exp4DCSE4DBoundDyeAverageRisePhase_Time_Plot_Combi.pdf 
             1. Ensure the existence of the Exp4D  in the Output folder                  
             2. Run CaSignal*Sphere.par     (Simulations for the spine.) 
                Run CaSignal*Disc.par       (Simulations for the dendrite.)
                where * corresponds to elements from the list in step 1.
             3. Run CaSignal_Exp4D.m        (Process data and generate figures.) 

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