Distance-dependent synaptic strength in CA1 pyramidal neurons (Menon et al. 2013)

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Accession:222726
Menon et al. (2013) describes the experimentally-observed variation in synaptic AMPA and NMDA conductance as a function of distance from the soma. This model explores the effect of this variation on somatic EPSPs and dendritic spike initiation, as compared to the case of uniform AMPA and NMDA conductance.
Reference:
1 . Menon V, Musial TF, Liu A, Katz Y, Kath WL, Spruston N, Nicholson DA (2013) Balanced synaptic impact via distance-dependent synapse distribution and complementary expression of AMPARs and NMDARs in hippocampal dendrites. Neuron 80:1451-63 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Synapse;
Brain Region(s)/Organism: Hippocampus;
Cell Type(s): Hippocampus CA1 pyramidal cell;
Channel(s): I A; I K; I Na, slow inactivation;
Gap Junctions:
Receptor(s): AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Synaptic Integration;
Implementer(s): Menon, Vilas [vilasmenon2008 at u dot northwestern dot edu];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal cell; AMPA; NMDA; I A; I K; I Na, slow inactivation;
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MenonEtAl2013
README.txt
dv.mod
ih_new.mod
kadist.mod *
kaprox.mod *
kdrca1.mod *
leakcond.mod *
nafast2.mod
naslowcond2.mod
nmda.mod
spines.mod *
synampa.mod *
vmax.mod
vmax2.mod
vmaxlast.mod
vms.mod
code_membrane.hoc
code_objects.hoc
code_point_processes.hoc
code_routine_for_runs.hoc
code_run_multiple_spines_on_branch.hoc
code_run_single_spine.hoc
code_synapse_array_setup.hoc
code_synapse_setup.hoc
mosinit.hoc
ri06.nrn *
simulated_axon.nrn *
spinearraygeom.nrn
spinegeom.nrn
                            
Code to run simulations outlined in Menon, Musial, Liu, Katz, Kath, Spruston, Nicholson (2013)

This code can be used to run two sets of simulations, each corresponding to a master .hoc file:
1. code_run_single_spine.hoc
This run places a synapse on a spine at every location along the basal dendritic tree (using 10-micron segments), and calculates the maximum deflection in voltage in the spine, local dendritic segment, and soma, as well as the peak inward current and total charge flowing through the synapse. 
The code cycles through placing a single nonperforated synapse and a single perforated synapse. The latter are run with and without the experimentally observed AMPA and NMDA scaling, in all combinations. 

2. code_run_multiple_spines_on_branch.hoc
This run sequentially places 1-20 synapses on a single basal branch, and calculates the maximum voltage deflection locally and at the soma. Because the location of these synapses is chosen stochastically, the simulation runs 50 times. The code runs multiple flavors of simulations, reflecting either uniform synapse location and strength, or experimentally observed synapse location distributions (for nonperforated synapses) and strength (for perforated synapses). Triggering of local dendritic spikes is clearly observable as a nonlinear change in the maximum voltage deflection in the dendrite of interest.

Both sets of simulations use the parallel context in NEURON, and can be run specifying the number of parallel processes to use. Since this is trivially parallelizable (each simulation runs separately), there are no concerns with optimal distribution of tasks to processers. The code will also run as-is on a single processor.

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