Compartmentalization of GABAergic inhibition by dendritic spines (Chiu et al. 2013)

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Accession:143604
A spiny dendrite model supports the hypothesis that only inhibitory inputs on spine heads, not shafts, compartmentalizes inhibition of calcium signals to spine heads as seen in paired inhibition with back-propagating action potential experiments on prefrontal cortex layer 2/3 pyramidal neurons in mouse (Chiu et al. 2013).
Reference:
1 . Chiu CQ, Lur G, Morse TM, Carnevale NT, Ellis-Davies GC, Higley MJ (2013) Compartmentalization of GABAergic inhibition by dendritic spines. Science 340:759-62 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Synapse; Dendrite;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex L2/3 pyramidal GLU cell;
Channel(s): I Na,t; I L high threshold; I K;
Gap Junctions:
Receptor(s): GabaA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Dendritic Action Potentials; Influence of Dendritic Geometry;
Implementer(s): Carnevale, Ted [Ted.Carnevale at Yale.edu]; Morse, Tom [Tom.Morse at Yale.edu];
Search NeuronDB for information about:  Neocortex L2/3 pyramidal GLU cell; GabaA; I Na,t; I L high threshold; I K;
20130317

I need to focus on "cleaning" up the model code to make a public
version for the Science magazine article.

I stored an as-is version as a private model in ModelDB if ever needed
for future reference.

I want to do two things with the public version.

1) make button pushes to create the basic results
a) spine inhibition results in a compartmentalized Ca signal inhibition.
b) dendritic inhibition results in less inhibition amplitude which is
more widespread.

2) make another button push come up with the research panel which
includes instructions on how to recreate the figures from the paper
with button pushes

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Include two readme's

1) the readme.html includes the basic instructions to do 1 above.

2) a readme_research.html includes directions on how to generate the
paper figures and additional "control" simulations (the sealed end
effects and the dendritic inhibition combination with spine neck
resistances that mimic the case where spine inhibition is present (a
result is that the spine neck resistance would have to be ~24 GOhm,
more than a factor of 10 greater than the highest neck resistances
measured (1.2 GOhm) under experimental protocols designed to make the
resistances as large as possible (Grunditz et al. (2008) (in a
different cell type, the hippocampal CA1 pyramidal neuron).

The readme.html can state that: Ca signals were compared between
protocols. The case of bAP alone produces Ca signals in the model
spine heads and dendritic shaft.  The main simulations that support
the paper's hypothesis comes about comparing the bAP alone Ca signals
with two cases 1) inhibition in a spine head combined with a bAP which
showed that the Ca signal in the spine head was reduced but not in the
dendritic shaft nor neighboring spines and 2) 10 times the inhibiton
that was used in the spine head being applied to the dendritic shaft
adjacent to the spine head (with no spine inhibiton) in combination
with the bAP produces Ca signals that are slightly reduced in spine
heads and shaft.  This shows that dendritic inhibition is less
effective at reducing the Ca signal and that the reduced Ca signal is
present in nearby spine heads and shaft.

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Button layout

xpanel("Chiu et al. 2013")
  xlabel("Demonstrations of main result:")
  xbutton("spine inhibiton with bAP (compartmentalized inhibition)","spineinhib_bAP_demo()")
  xbutton("10x dend inhib with bAP (widespread inhib with less amplitude","dend10x_bAP_demo()")
  xbutton("open research panels instead","open_research_panels()")
xpanel()

Actually the most ideal way to run the model would be to have the
model start the same except postpone all the gui creations until the
end that way, the model doesn't have to be restarted.

Process: go through the code and collect all the window creations into
an open_research_panels() proc. Use the notation "// shadow X" near
where the old code is and "// view X" where the new code is.  That way
if there is some kind of dependence it can be traced back.

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