CA1 pyramidal neuron: synaptic plasticity during theta cycles (Saudargiene et al. 2015)

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Accession:157157
This NEURON code implements a microcircuit of CA1 pyramidal neuron and consists of a detailed model of CA1 pyramidal cell and four types of inhibitory interneurons (basket, bistratified, axoaxonic and oriens lacunosum-moleculare cells). Synaptic plasticity during theta cycles at a synapse in a single spine on the stratum radiatum dendrite of the CA1 pyramidal cell is modeled using a phenomenological model of synaptic plasticity (Graupner and Brunel, PNAS 109(20):3991-3996, 2012). The code is adapted from the Poirazi CA1 pyramidal cell (ModelDB accession number 20212) and the Cutsuridis microcircuit model (ModelDB accession number 123815)
Reference:
1 . Saudargiene A, Cobb S, Graham BP (2015) A computational study on plasticity during theta cycles at Schaffer collateral synapses on CA1 pyramidal cells in the hippocampus. Hippocampus 25:208-18 [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): Hippocampus CA1 pyramidal GLU cell; Hippocampus CA1 basket cell; Hippocampus CA1 bistratified cell; Hippocampus CA1 axo-axonic cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Long-term Synaptic Plasticity; STDP;
Implementer(s): Saudargiene, Ausra [ausra.saudargiene at gmail.com];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell;
/
SaudargieneEtAl2015
readme.html
ANsyn.mod *
bgka.mod *
bistableGB_DOWNUP.mod
burststim2.mod *
cad.mod
cadiffus.mod *
cagk.mod *
cal.mod *
calH.mod *
car.mod *
cat.mod *
ccanl.mod *
d3.mod *
gabaa.mod *
gabab.mod *
glutamate.mod *
gskch.mod *
h.mod
hha_old.mod *
hha2.mod *
hNa.mod *
IA.mod
ichan2.mod
Ih.mod *
kadbru.mod
kadist.mod *
kapbru.mod
kaprox.mod *
Kaxon.mod *
kca.mod *
Kdend.mod *
km.mod *
Ksoma.mod *
LcaMig.mod *
my_exp2syn.mod *
Naaxon.mod *
Nadend.mod *
nap.mod
Nasoma.mod *
nca.mod *
nmda.mod *
nmdaca.mod *
regn_stim.mod *
somacar.mod *
STDPE2Syn.mod *
apical-non-trunk-list.hoc
apical-tip-list.hoc
apical-tip-list-addendum.hoc
apical-trunk-list.hoc
axoaxonic_cell17S.hoc
axon-sec-list.hoc
BasalPath.hoc
basal-paths.hoc
basal-tree-list.hoc
basket_cell17S.hoc
bistratified_cell13S.hoc
burst_cell.hoc
current-balance.hoc *
main.hoc
map-segments-to-3d.hoc *
mod_func.c
mosinit.hoc
ObliquePath.hoc *
oblique-paths.hoc
olm_cell2.hoc
pattsN100S20P5_single.dat
PC.ses
peri-trunk-list.hoc
pyramidalNeuron.hoc
randomLocation.hoc
ranstream.hoc
screenshot.png
soma-list.hoc
stim_cell.hoc *
vector-distance.hoc
                            
// Artificial cells no longer need a default section.
//Network cell templates
//   AACell
// Simplified version (BPG 27-9-08)
//  - geometry and channels from Santhakumar et al 2005
//  - geometry modified to preserve VCUs different dendrites


begintemplate AACell
public is_art
public init, topol, basic_shape, subsets, geom, biophys
public pre_list, connect2target

public soma, radT2, radM2, radt2, lmM2, lmt2, radT1
public radM1, radt1, lmM1, lmt1, oriT1, oriM1, orit1
public oriT2, oriM2, orit2
public all

objref pre_list

proc init() {
  	topol()
  	subsets()
  	geom()
  	biophys()
  	geom_nseg()
  	pre_list = new List()
  	synapses()
}

create soma, radT2, radM2, radt2, lmM2, lmt2, radT1
create radM1, radt1, lmM1, lmt1, oriT1, oriM1, orit1
create oriT2, oriM2, orit2

proc topol() { local i
  	connect radT2(0), soma(1)
  	connect radM2(0), radT2(1)
  	connect radt2(0), radM2(1)
  	connect lmM2(0), radt2(1)
  	connect lmt2(0), lmM2(1)
  	connect radT1(0), soma(0)
  	connect radM1(0), radT1(1)
  	connect radt1(0), radM1(1)
  	connect lmM1(0), radt1(1)
  	connect lmt1(0), lmM1(1)
  	connect oriT1(0), soma(0)
  	connect oriM1(0), oriT1(1)
  	connect orit1(0), oriM1(1)
  	connect oriT2(0), soma(1)
  	connect oriM2(0), oriT2(1)
  	connect orit2(0), oriM2(1)
  	//basic_shape()
}

proc basic_shape() {
  	soma {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(15, 0, 0, 1)}
  	radT2 {pt3dclear() pt3dadd(15, 0, 0, 1) pt3dadd(45, 30, 0, 1)}
  	radM2 {pt3dclear() pt3dadd(45, 30, 0, 1) pt3dadd(75, 60, 0, 1)}
  	radt2 {pt3dclear() pt3dadd(75, 60, 0, 1) pt3dadd(90, 75, 0, 1)}
  	lmM2 {pt3dclear() pt3dadd(90, 75, 0, 1) pt3dadd(105, 90, 0, 1)}
  	lmt2 {pt3dclear() pt3dadd(105, 90, 0, 1) pt3dadd(120, 105, 0, 1)}
  	radT1 {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(-14, 15, 0, 1)}
  	radM1 {pt3dclear() pt3dadd(-14, 15, 0, 1) pt3dadd(-29, 30, 0, 1)}
  	radt1 {pt3dclear() pt3dadd(-29, 30, 0, 1) pt3dadd(-44, 45, 0, 1)}
  	lmM1 {pt3dclear() pt3dadd(-44, 45, 0, 1) pt3dadd(-59, 60, 0, 1)}
  	lmt1 {pt3dclear() pt3dadd(-59, 60, 0, 1) pt3dadd(-89, 90, 0, 1)}
  	oriT1 {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(-29, -29, 0, 1)}
  	oriM1 {pt3dclear() pt3dadd(-29, -29, 0, 1) pt3dadd(-59, -59, 0, 1)}
  	orit1 {pt3dclear() pt3dadd(-59, -59, 0, 1) pt3dadd(-89, -89, 0, 1)}
  	oriT2 {pt3dclear() pt3dadd(15, 0, 0, 1) pt3dadd(45, -29, 0, 1)}
  	oriM2 {pt3dclear() pt3dadd(45, -29, 0, 1) pt3dadd(75, -59, 0, 1)}
  	orit2 {pt3dclear() pt3dadd(75, -59, 0, 1) pt3dadd(105, -89, 0, 1)}
}

objref all
proc subsets() { local i
  	objref all
  	all = new SectionList()
    	soma all.append()
    	radT2 all.append()
    	radM2 all.append()
    	radt2 all.append()
    	lmM2 all.append()
    	lmt2 all.append()
    	radT1 all.append()
    	radM1 all.append()
    	radt1 all.append()
    	lmM1 all.append()
    	lmt1 all.append()
    	oriT1 all.append()
    	oriM1 all.append()
    	orit1 all.append()
    	oriT2 all.append()
    	oriM2 all.append()
    	orit2 all.append()

}

proc geom() {
  	forsec all {  }
  	soma {  L = 20  diam = 10  }
  	radT2 {  L = 100  diam = 4  }
  	radM2 {  L = 100  diam = 3  }
  	radt2 {  L = 200  diam = 2  }
  	lmM2 {  L = 100  diam = 1.5  }
  	lmt2 {  L = 100  diam = 1  }
  	radT1 {  L = 100  diam = 4  }
  	radM1 {  L = 100  diam = 3  }
  	radt1 {  L = 200  diam = 2  }
  	lmM1 {  L = 100  diam = 1.5  }
  	lmt1 {  L = 100  diam = 1  }
  	oriT1 {  L = 100  diam = 2  }
  	oriM1 {  L = 100  diam = 1.5  }
  	orit1 {  L = 100  diam = 1  }
  	oriT2 {  L = 100  diam = 2  }
  	oriM2 {  L = 100  diam = 1.5  }
  	orit2 {  L = 100  diam = 1  }
}

external lambda_f
proc geom_nseg() {
  	forsec all { nseg = int((L/(0.1*lambda_f(100))+.9)/2)*2 + 1  }
}

proc biophys() {

	gna = 0.15

	soma {
		insert ichan2  		
		gnatbar_ichan2 = gna  		// 0.12 //original 0.030 to .055 
		gkfbar_ichan2 = 0.013  		//original 0.015
		gl_ichan2 = 0.00018
		cm=1.4
	} 

	lmt1 {
		insert ichan2
		gnatbar_ichan2 = gna		//0.5  	//original 0.015
		gkfbar_ichan2 = 0.013
		gl_ichan2 = 0.00018
		cm=1.4
	}		

	lmt2 {
		insert ichan2
		gnatbar_ichan2 = gna		//0.5  	//original 0.015
		gkfbar_ichan2 = 0.013
		gl_ichan2 = 0.00018
		cm=1.4
	}		

	lmM1 {
		insert ichan2
		gnatbar_ichan2 = gna		//0.45  	//original 0.015
		gkfbar_ichan2 = 0.013
		gl_ichan2 = 0.00018
		cm=1.4
	}		

	lmM2 {
		insert ichan2
		gnatbar_ichan2 = gna		//0.45  	//original 0.015
		gkfbar_ichan2 = 0.013
		gl_ichan2 = 0.00018
		cm=1.4
	}		
	
	radt1 {
		insert ichan2
		gnatbar_ichan2 = gna		//0.4  	//original 0.015
		gkfbar_ichan2 = 0.013
		gl_ichan2 = 0.00018
		cm=1.4
	}		

	radt2 {
		insert ichan2
		gnatbar_ichan2 = gna		//0.4  	//original 0.015
		gkfbar_ichan2 = 0.013
		gl_ichan2 = 0.00018
		cm=1.4
	}		

	radM1 {
		insert ichan2
		gnatbar_ichan2 = gna		//0.3  	//original 0.015
		gkfbar_ichan2 = 0.013
		gl_ichan2 = 0.00018
		cm=1.4
	}		

	radM2 {
		insert ichan2
		gnatbar_ichan2 = gna		//0.3  	//original 0.015
		gkfbar_ichan2 = 0.013
		gl_ichan2 = 0.00018
		cm=1.4
	}		

	radT1 {
		insert ichan2
		gnatbar_ichan2 = gna		//0.2  	//original 0.015
		gkfbar_ichan2 = 0.013
		gl_ichan2 = 0.00018
		cm=1.4
	}		

	radT2 {
		insert ichan2
		gnatbar_ichan2 = gna		//0.2  	//original 0.015
		gkfbar_ichan2 = 0.013
		gl_ichan2 = 0.00018
		cm=1.4
	}			

	oriT1 {
		insert ichan2
		gnatbar_ichan2 = gna  		//original 0.015
		gkfbar_ichan2 = 0.013
		gl_ichan2 = 0.00018
		cm=1.4
	}		

	oriT2 {
		insert ichan2
		gnatbar_ichan2 = gna  		//original 0.015
		gkfbar_ichan2 = 0.013
		gl_ichan2 = 0.00018
		cm=1.4
	}		

	oriM1 {
		insert ichan2
		gnatbar_ichan2 = gna  		//original 0.015
		gkfbar_ichan2 = 0.013
		gl_ichan2 = 0.00018
		cm=1.4
	}		

	oriM2 {
		insert ichan2
		gnatbar_ichan2 = gna  		//original 0.015
		gkfbar_ichan2 = 0.013
		gl_ichan2 = 0.00018
		cm=1.4
	}		
	
	orit1 {
		insert ichan2
		gnatbar_ichan2 = gna  		// Sodium conductance (original 0.015)
		gkfbar_ichan2 = 0.013		// Delayed K+ rectifier (fast)
		gl_ichan2 = 0.00018		// Leak conductance
		cm=1.4
	}		

	orit2 {
		insert ichan2
		gnatbar_ichan2 = gna  		// Sodium conductance (original 0.015)
		gkfbar_ichan2 = 0.013		// Delayed K+ rectifier (fast)
		gl_ichan2 = 0.00018		// Leak conductance
		cm=1.4
	}		

	forsec all {
		insert ccanl
		catau_ccanl = 10		// Time constant for decay of intracellular Ca2+
		caiinf_ccanl = 5.e-6		// Steady-state intracellular Ca2+ concentration
		
		insert borgka
		gkabar_borgka = 0.00015		// A-type K+ conductance
		
		insert nca  			// N-type Ca2+ conductance
		gncabar_nca = 0.0008   		// check to modify- original 0.004
		
		insert lca 
		glcabar_lca = 0.005		// L-type Ca2+ conductance
		
		insert gskch
		gskbar_gskch = 0.000002		// Ca2+-dependent K (SK) conductance
		
		insert mykca
		gkbar = 0.0002			// Ca2+ and Voltage-dependent K+ (BK) conductance

//		Ra = 10.3			// 31.3 +/- 10.9
		Ra = 100			// 31.3 +/- 10.9
		enat = 55
		ekf = -90
		ek = -90
		elca = 130
		esk = -90
		el_ichan2 = -60			//-60.06
		cao_ccanl = 2
	
	} 					// make catau slower70e-3 	cao=2 cai=50.e-6

}

obfunc connect2target() { localobj nc //$o1 target point process, optional $o2 returned NetCon
  	soma nc = new NetCon(&v(1), $o1)
  	nc.threshold = -10
  	if (numarg() == 2) { $o2 = nc } // for backward compatibility
  	return nc
}

objref syn_
proc synapses() {
  	/* E0 */   lmM1 syn_ = new MyExp2Syn(0.5)  pre_list.append(syn_)	// AMPA		EC
    	syn_.tau1 = 0.5
    	syn_.tau2 = 3
    	syn_.e = 0
  	/* E1 */   lmM2 syn_ = new MyExp2Syn(0.5)  pre_list.append(syn_)	// AMPA		EC
    	syn_.tau1 = 0.5
    	syn_.tau2 = 3
    	syn_.e = 0
  	/* E2 */   radM1 syn_ = new MyExp2Syn(0.5)  pre_list.append(syn_)	// AMPA		CA3 Shaffer collateral
    	syn_.tau1 = 0.5
    	syn_.tau2 = 3
    	syn_.e = 0
  	/* E3 */   radM2 syn_ = new MyExp2Syn(0.5)  pre_list.append(syn_)	// AMPA		CA3 Shaffer collateral
    	syn_.tau1 = 0.5
    	syn_.tau2 = 3
    	syn_.e = 0
  	/* E4 */   radT1 syn_ = new MyExp2Syn(0.5)  pre_list.append(syn_)	// AMPA		CA3 Shaffer collateral
    	syn_.tau1 = 0.5
    	syn_.tau2 = 3
    	syn_.e = 0
  	/* E5 */   radT2 syn_ = new MyExp2Syn(0.5)  pre_list.append(syn_)	// AMPA		CA3 Shaffer collateral
    	syn_.tau1 = 0.5
    	syn_.tau2 = 3
    	syn_.e = 0
  	/* E6 */   oriT1 syn_ = new MyExp2Syn(0.5)  pre_list.append(syn_)	// AMPA		PC
    	syn_.tau1 = 0.5
    	syn_.tau2 = 3
    	syn_.e = 0
  	/* E7 */   oriT2 syn_ = new MyExp2Syn(0.5)  pre_list.append(syn_)	// AMPA		PC
    	syn_.tau1 = 0.5
    	syn_.tau2 = 3
    	syn_.e = 0
  	/* I8 */   soma syn_ = new MyExp2Syn(0.5)  pre_list.append(syn_)	// GABA-A	Neighboring basket cell
    	syn_.tau1 = 1
    	syn_.tau2 = 8
    	syn_.e = -75
  	/* I9 */   soma syn_ = new MyExp2Syn(0.6)  pre_list.append(syn_)	// GABA-A	Bistratified cell
    	syn_.tau1 = 1
    	syn_.tau2 = 8
    	syn_.e = -75
  	/* I10 */   oriT1 syn_ = new MyExp2Syn(0.6)  pre_list.append(syn_)	// GABA-A	Septum
    	syn_.tau1 = 1
    	syn_.tau2 = 8
    	syn_.e = -75
  	/* I11 */   oriT2 syn_ = new MyExp2Syn(0.6)  pre_list.append(syn_)	// GABA-A	Septum
    	syn_.tau1 = 1
    	syn_.tau2 = 8
    	syn_.e = -75
  	/* I12 */   oriT1 syn_ = new MyExp2Syn(0.6)  pre_list.append(syn_)	// GABA-B	Septum
    	syn_.tau1 = 35
    	syn_.tau2 = 100
    	syn_.e = -75
  	/* I13 */   oriT2 syn_ = new MyExp2Syn(0.6)  pre_list.append(syn_)	// GABA-B	Septum
    	syn_.tau1 = 35
    	syn_.tau2 = 100
    	syn_.e = -75
}

func is_art() { return 0 }

endtemplate AACell

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