NMDAR & GABAB/KIR Give Bistable Dendrites: Working Memory & Sequence Readout (Sanders et al., 2013)

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Accession:169985
" ...Here, we show that the voltage dependence of the inwardly rectifying potassium (KIR) conductance activated by GABA(B) receptors adds substantial robustness to network simulations of bistability and the persistent firing that it underlies. The hyperpolarized state is robust because, at hyperpolarized potentials, the GABA(B)/KIR conductance is high and the NMDA conductance is low; the depolarized state is robust because, at depolarized potentials, the NMDA conductance is high and the GABA(B)/KIR conductance is low. Our results suggest that this complementary voltage dependence of GABA(B)/KIR and NMDA conductances makes them a "perfect couple" for producing voltage bistability."
References:
1 . Sanders H, Berends M, Major G, Goldman MS, Lisman JE (2013) NMDA and GABAB (KIR) conductances: the "perfect couple" for bistability J Neurosci 33:424-9 [PubMed]
2 . Sanders H, Kolterman BE, Shusterman R, Rinberg D, Koulakov A, Lisman J (2014) A network that performs brute-force conversion of a temporal sequence to a spatial pattern: relevance to odor recognition. Front Comput Neurosci 8:108 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s): Hodgkin-Huxley neuron;
Channel(s): I K; I Na, leak; Kir;
Gap Junctions:
Receptor(s): GabaA; GabaB; AMPA; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: C or C++ program;
Model Concept(s): Working memory; Dendritic Bistability;
Implementer(s): Sanders, Honi [honi at brandeis.edu];
Search NeuronDB for information about:  GabaA; GabaB; AMPA; NMDA; I K; I Na, leak; Kir; Gaba; Glutamate;
/
NMDA_network_modelDB
NMDA-GABAB_2013
Temporal-Spatial_2014
ReadMe.txt
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These files go with two papers:

Sanders H, Berends M, Major G, Goldman MS, Lisman JE (2013) NMDA and
GABAB (KIR) Conductances: The "Perfect Couple" for Bistability. J
Neurosci 33:424-429.  doi: 10.1523/JNEUROSCI.1854-12.2013
http://www.jneurosci.org/cgi/doi/10.1523/JNEUROSCI.1854-12.2013

Sanders H, Kolterman BE, Shusterman R, Rinberg D, Koulakov A, Lisman J
(2014) A network that performs brute-force conversion of a temporal
sequence to a spatial pattern: relevance to odor recognition. Front
Comput Neurosci 8:1-11.  doi: 10.3389/fncom.2014.00108
http://journal.frontiersin.org/Journal/10.3389/fncom.2014.00108/


The simulations are written in C++, requiring no external libraries.
The plotting is written in gnuplot (http://gnuplot.info).  The wrapper
functions for compiling, running, submitting jobs to cluster, and
plotting are written in BASH.  My condolences to Windows users, you
are on your own.


**** NMDA and GABAB (KIR) Conductances: The "Perfect Couple" for
     Bistability ***

The files necessary for producing the figures from the 2013 paper are
in the folder "NMDA-GABAB_2013".  network.h is a header file
containing constants and function declarations.  It is identical for
both papers.  functions.cpp contains function definitions.  It has two
points of difference between the two papers, pointed out at the top of
the file.  main.cpp contains the simulation loop.  It is obviously
fairly different between the two papers, as they are different
simulations.


To compile and run the simulation with the default parameter values,
type
./crnewnetwork
at the command line.  This will save the results of the simulation to
results/.  It will additionally plot the results if you have gnuplot
installed at /usr/local/bin/gnuplot.

If the crnewnetwork script fails due to platform differences/package
dependencies you can likely compile and run the model with

g++ -g main.cpp functions.cpp -o newnetwork
./newnetwork

You can add up to four command line arguments after ./crnewnetwork.
These command line arguments are the eeNMDAscale (NMDA conductance at
excitatory-excitatory synapses), GABAAscale (the GABAA conductance at
inhibitory-excitatory synapses), N_prf (the fraction of excitatory
cells activated by external input, expressed as a decimal).  The
conductances at each synapse are scaled by number of active cells so
that the total conductance seen by each cell is approximately the same
as the conductance passed as a command line argument.  Also of note is
that the conductances in the model are expressed in uS/mm^2, whereas
in the paper conductances are expressed in mS/cm^2, which leads to the
numbers in the simulation being 10 times larger than the numbers in
the paper (1000/10^2=10).

clusterscripts/ contains scripts for submitting jobs to the Brandeis
HPCC cluster.  For questions about this or about anything else,
contact Honi Sanders at honi@brandeis.edu.

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