Synaptic integration in tuft dendrites of layer 5 pyramidal neurons (Larkum et al. 2009)

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Accession:124043
Simulations used in the paper. Voltage responses to current injections in different tuft locations; NMDA and calcium spike generation. Summation of multiple input distribution.
Reference:
1 . Larkum ME, Nevian T, Sandler M, Polsky A, Schiller J (2009) Synaptic integration in tuft dendrites of layer 5 pyramidal neurons: a new unifying principle. Science 325:756-60 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Synapse; Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell;
Channel(s): I L high threshold; I p,q; I A; I K,leak; I K,Ca; I Sodium;
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Dendritic Action Potentials; Active Dendrites; Detailed Neuronal Models; Synaptic Integration;
Implementer(s): Polsky, Alon [alonpol at tx.technion.ac.il];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; GabaA; AMPA; NMDA; I L high threshold; I p,q; I A; I K,leak; I K,Ca; I Sodium; Gaba; Glutamate;
/
larkumEtAl2009_2
readme.html
ampa.mod
cad2.mod
glutamate.mod *
h.mod *
h2.mod
hh3.mod *
ih.mod
it2.mod *
kap.mod
kca.mod *
kdf.mod
Kdr.mod *
kdr2.mod *
km.mod *
SlowCa.mod *
0.50764
0.55472
070603c2.cll
apic.ses
apical_simulation.hoc
layerV.cll
mosinit.hoc
screenshot1.jpg
screenshot2.jpg
screenshot3.jpg
screenshot4.jpg
screenshot5.jpg
screenshot6.jpg
                            
load_file("070603c2.cll")//the layer 5 cell

axon.L=10
axon.diam=5
create axon1
connect axon1(0),axon(1)
axon1.L=200
axon1.diam=1
objref basal,apical,trunk,hotzone
objref tuft,tuftE,tuftS,temp,tuft1[6]
objref secv,sref
basal = new SectionList()
apical = new SectionList()
trunk = new SectionList()
hotzone = new SectionList()
tuft = new SectionList()
for i=0,5 tuft1[i] = new SectionList()
tuftE = new SectionList()
tuftS = new SectionList()
temp = new SectionList()



apic[45].L=1

apic[30].L=1

apic[74].L=1


access apic[1]
apical.subtree()

access apic 
apical.append()
access apic[10]
tuft.subtree()
for i = 0, 11 apic[i] trunk.append()


for i = 0, 69 dend[i] basal.append()

apic[72] tuft1[4].append()
apic[73] tuft1[4].append()
apic[65] tuft1[4].append()
apic[67] tuft1[4].append()
apic[68] tuft1[4].append()
apic[62] tuft1[4].append()
apic[37] tuft1[4].append()
apic[38] tuft1[4].append()

apic[21] tuft1[4].append()
apic[35] tuft1[4].append()
apic[61] tuft1[4].append()
apic[31] tuft1[4].append()
apic[34] tuft1[4].append()
apic[57] tuft1[4].append()
apic[56] tuft1[4].append()
apic[52] tuft1[4].append()
apic[45] tuft1[4].append()
apic[53] tuft1[4].append()
apic[23] tuft1[4].append()
apic[27] tuft1[4].append()
apic[18] tuft1[4].append()
apic[17] tuft1[4].append()
apic[25] tuft1[4].append()
apic[28] tuft1[4].append()
apic[24] tuft1[4].append()
apic[64] tuft1[4].append()
apic[66] tuft1[4].append()
apic[69] tuft1[4].append()

apic[22] tuft1[3].append()
apic[46] tuft1[3].append()
apic[16] tuft1[3].append()
apic[51] tuft1[3].append()

apic[33] tuft1[3].append()
apic[36] tuft1[3].append()
apic[60] tuft1[3].append()

apic[30] tuft1[3].append()
apic[28] tuft1[3].append()
apic[25] tuft1[3].append()
apic[20] tuft1[3].append()
apic[27] tuft1[3].append()
apic[44] tuft1[3].append()
apic[63] tuft1[3].append()

apic[12] tuft1[0].append()
apic[47] tuft1[0].append()
apic[39] tuft1[0].append()

apic[11] tuft1[0].append()

apic[48] tuft1[0].append()


apic[40] tuft1[1].append()

apic[70] tuft1[1].append()

apic[59] tuft1[1].append()

apic[32] tuft1[1].append()

apic[13] tuft1[1].append()

apic[49] tuft1[1].append()

apic[58] tuft1[1].append()

apic[41] tuft1[1].append()

apic[42] tuft1[1].append()


apic[14] tuft1[2].append()

apic[15] tuft1[2].append()

apic[26] tuft1[2].append()

apic[29] tuft1[2].append()

apic[43] tuft1[2].append()

apic[50] tuft1[2].append()

apic[55] tuft1[2].append()

apic[74] tuft1[2].append()

apic[71] tuft1[2].append()

apic[19] tuft1[2].append()

forall {
	nseg=11
	insert pas
	e_pas=-70
	g_pas=1/20000
	cm=1
}
forsec tuft cm=1.4
forsec apical	diam=diam*1.2
forsec tuft {
	hbar=0.001//0.005
	insert hd
	ghdbar_hd=hbar
}
access soma
apic_it=0.000
apic_il=1
apic_km=0
apic_kdr=0

apic_kca=10
apic_k2=0.0001
apic_k1=0.000
apic_na=0.004
apic_ka=0.003

trunk_it=0.000
trunk_il=1
trunk_km=0
trunk_kca=1
trunk_k2=0.06
trunk_kdr=0
trunk_k1=0.1
trunk_na=0.005
trunk_ka=0.06

soma_na=0.005
soma_k1=0.06
soma_k2=.3
soma_kdr=0
soma_ka=0.06
soma_km=10

axon_na=3
axon_k1=0.8
axon_k2=1
axon_kdr=0
axon_km=0

taun_hh3=1.5
taun2_hh3=10
tauh_hh3=.6
sN_hh3=0

//ca hot zone
hot_dis_dist=300
hot_dis_prox=00

hot_it=0.000
hot_il=10
hot_kca=30

hot_k1=0
hot_k2=0.0001
hot_ka=0.003
hot_km=0
hot_kdr=0
hot_na=0.01

proc ca_hot_zone(){
   forsec all{

	insert kdr
	gbar_kdr=apic_kdr

	insert kca

	gbar_kca=apic_kca
	insert cad2
      // ca diffusion  and kca parameters
      taur_cad2 = 80 
      caix_kca  = 4
      Ra_kca    = 0.05
      Rb_kca    = 0.1

	
	insert it2
	gcabar_it2=apic_it

	vh1_it2=56
	vh2_it2=415
	ah_it2=30				
	v12m_it2=45
	v12h_it2=65  
	am_it2=3
	vshift_it2=-10
	vm1_it2=50
	vm2_it2=125

	insert sca
	gbar_sca=apic_il
	
	insert hh3
	gnabar_hh3=apic_na
	gkbar_hh3=apic_k1
	gl_hh3=0
	gkbar2_hh3=apic_k2
	insert km
	gbar_km=apic_km
	insert kap
	gkabar_kap=apic_ka
  }

	//trunk
	trunk.remove(trunk)
  	
for i = 0, 11 apic[i] trunk.append()

	access apic[10]
	distance()
	forsec tuft {
		if (distance(0)<=hot_dis_prox) trunk.append()	

	}
	forsec trunk{
		gcabar_it2=trunk_it
		gbar_sca=trunk_il
		gbar_kca=trunk_kca

		gkbar_hh3=trunk_k1

		gkbar2_hh3=trunk_k2

		gkabar_kap=trunk_ka
		gbar_km=trunk_km
		gnabar_hh3=trunk_na
		gbar_kdr=trunk_kdr
	}
	forsec basal{
		gcabar_it2=apic_it
		gbar_sca=apic_il
		gbar_kca=apic_kca

		gkbar_hh3=apic_k1

		gkbar2_hh3=apic_k2

		gkabar_kap=apic_ka
		gbar_km=apic_km
		gnabar_hh3=apic_na

		gbar_kdr=apic_kdr
	}
	//hot zone
	access apic[10]
	distance()
	hotzone.remove(hotzone)
	forsec tuft {
		if ((distance(0)<hot_dis_dist)&&(distance(0)>hot_dis_prox)) hotzone.append()

	}
	forsec hotzone{

		gcabar_it2=hot_it
		gbar_sca=hot_il
		gbar_kca=hot_kca

		gkbar_hh3=hot_k1

		gkbar2_hh3=hot_k2

		gkabar_kap=hot_ka
		gbar_km=hot_km
		gnabar_hh3=hot_na

		gbar_kdr=hot_kdr

	
}

	access soma
	insert hh3
	gnabar_hh3=soma_na
	gkbar_hh3=soma_k1
	gl_hh3=0
	gkbar2_hh3=soma_k2
	insert km
	gbar_km=soma_km
	insert kdr
	gbar_kdr=soma_kdr

	access axon
	insert hh3
	gnabar_hh3=axon_na
	gkbar_hh3=axon_k1
	gl_hh3=0
	gkbar2_hh3=axon_k2
	insert km
	gbar_km=axon_km

	insert kdr
	gbar_kdr=axon_kdr

	access axon1
	insert hh3
	gnabar_hh3=axon_na
	gkbar_hh3=axon_k1
	gl_hh3=0
	gkbar2_hh3=axon_k2
	insert km
	gbar_km=axon_km

	insert kdr
	gbar_kdr=axon_kdr

	access soma
}//proc
ca_hot_zone()


access soma
forsec apical {nseg=11}

objref all
all = new SectionList()
forall all.append()
access axon
all.remove()

access axon1
all.remove()
access soma
all.remove()


print "START OF SIMULATION"
//**********random synapses//
numinputs=1
numS=100
numE=100
numI=30
objref synS[numS]
objref synE[numE]
objref synI[numI]
generation=0//other than 0 will lead to select by bifurcation
pretype=3//1=on one dend;2=2 dends;3=all tuft

gmaxS=0
gmaxE=0
gmaxI=0
DendS=10
DendE=10
delmean=5
nmdaampa=1

dends2=0
subtuftproxS=00
subtuftdistS=1000
subtuftproxE=00
subtuftdistE=1000

objref r,rseg,rdel
r= new Random()
rseg= new Random()
rdel= new Random()
objref stfunc,shape
stfunc=new StringFunctions()
shape=new Shape(0)
shape.view(-200, -200, 400, 2000, 900, 200, 400.48, 600.32) 
shape.show(0)
proc make_shape_plot(){//DRAWS THE POINTS ON THE CELL
	shape.point_mark_remove()

	for i=0,numE-1{
//		shape.point_mark(synE[i], 5, 4, 5)	
	}
	for i=0,numI-1{
//		shape.point_mark(synI[i], 3, 4, 5)	
	}
	for i=0,numS-1{
		shape.point_mark(synS[i], 2, 4, 5)	
	}
	access soma
}//END SHAPE



xpanel("Control")
  xvalue("GmaxS","gmaxS",1,"c_gmax()")
  xvalue("GmaxE","gmaxE",1,"c_gmax()")
  xvalue("GmaxI","gmaxI",1,"c_gmax()")

  xvalue("numS","numS",1,"loclocation()")
  xvalue("numE","numE",1,"loclocation()")
  xvalue("generation","generation",1,"loclocation()")

  xvalue("numI","numI",1,"loclocation()")

  xvalue("NMDA=1;AMPA=2","nmdaampa",1,"loclocation()")
  
  //xvalue("Change dends","dends2",1,"loclocation()")
  
  xvalue("DendS","DendS",1,"loclocation()")
  xvalue("DendE","DendE",1,"loclocation()")

  xvalue("SubTuftProxS","subtuftproxS",1,"loclocation()")

  xvalue("SubTuftDistS","subtuftdistS",1,"loclocation()")

  xvalue("SubTuftProxE","subtuftproxE",1,"loclocation()")

  xvalue("SubTuftDistE","subtuftdistE",1,"loclocation()")

xpanel()
xpanel("Apicals")
  xvalue("Hbar","hbar",1,"forsec tuft ghdbar_hd=hbar")
  xvalue("Na","apic_na",1,"ca_hot_zone()")
  xvalue("it","apic_it",1,"ca_hot_zone()")
  xvalue("il","apic_il",1,"ca_hot_zone()")
  xvalue("kca","apic_kca",1,"ca_hot_zone()")
  xvalue("km","apic_km",1,"ca_hot_zone()")

  xvalue("ka","apic_ka",1,"ca_hot_zone()")
  xvalue("k1","apic_k1",1,"ca_hot_zone()")
  xvalue("k2","apic_k2",1,"ca_hot_zone()")
  xvalue("kdr","apic_kdr",1,"ca_hot_zone()")
  xlabel("Hot zone")

  xvalue("prox","hot_dis_prox",1,"ca_hot_zone()")
  xvalue("dist","hot_dis_dist",1,"ca_hot_zone()")
  xvalue("Na","hot_na",1,"ca_hot_zone()")
  xvalue("it","hot_it",1,"ca_hot_zone()")
  xvalue("il","hot_il",1,"ca_hot_zone()")
  xvalue("kca","hot_kca",1,"ca_hot_zone()")
  xvalue("km","hot_km",1,"ca_hot_zone()")
  xvalue("ka","hot_ka",1,"ca_hot_zone()")
  xvalue("k1","hot_k1",1,"ca_hot_zone()")
  xvalue("k2","hot_k2",1,"ca_hot_zone()")
  xvalue("kdr","hot_kdr",1,"ca_hot_zone()")
xpanel()
xpanel("Soma&Trunk")

  xvalue("Na","axon_na",1,"ca_hot_zone()")
  xvalue("k1","axon_k1",1,"ca_hot_zone()")
  xvalue("k2","axon_k2",1,"ca_hot_zone()")
  xvalue("km","axon_km",1,"ca_hot_zone()")

  xvalue("kdr","axon_kdr",1,"ca_hot_zone()")

  xlabel("Soma")
  xvalue("Na","soma_na",1,"ca_hot_zone()")
  xvalue("k1","soma_k1",1,"ca_hot_zone()")
  xvalue("k2","soma_k2",1,"ca_hot_zone()")
  xvalue("km","soma_km",1,"ca_hot_zone()")
  xvalue("ka","soma_ka",1,"ca_hot_zone()")

  xvalue("kdr","soma_kdr",1,"ca_hot_zone()")

  xlabel("Trunk")
  xvalue("Na","trunk_na",1,"ca_hot_zone()")
  xvalue("it","trunk_it",1,"ca_hot_zone()")
  xvalue("il","trunk_il",1,"ca_hot_zone()")
  xvalue("kca","trunk_kca",1,"ca_hot_zone()")
  xvalue("km","trunk_km",1,"ca_hot_zone()")
  xvalue("ka","trunk_ka",1,"ca_hot_zone()")
  xvalue("k1","trunk_k1",1,"ca_hot_zone()")
  xvalue("k2","trunk_k2",1,"ca_hot_zone()")
  xvalue("kdr","trunk_kdr",1,"ca_hot_zone()")
xpanel()

proc c_gmax(){

	for i=0,numS-1{
		synS[i].gmax=gmaxS
	}

	for i=0,numE-1{
		synE[i].gmax=gmaxE
	}

	for i=0,numI-1{
		synI[i].gmax=gmaxI
	}

}


//LOCAL SYNAPSES

proc loclocation(){
	objref synS[numS]
	objref synE[numE]
	objref synI[numI]
	dendnumE=0
	dendnumS=0
	dendnum=0
	dendnum1=0
	strdef st
	count=0
	groupc=0
	groupd=0	
	st=""

	found=0
	tuftE = new SectionList()	
	access apic[DendE]
	temp = new SectionList()
	temp.subtree()
	distance()
	forsec temp {
		if ( (distance(0.5)<subtuftdistE) && ( distance(0.5)>subtuftproxE) ){
			tuftE.append()
		}
	}
	numbranchesE=0
	forsec tuftE{
		numbranchesE=numbranchesE+1
	}


	tuftS = new SectionList()
	temp = new SectionList()	
	access apic[DendS]
	if ((generation==0)||(generation>=6)){
		temp.subtree()
		distance()
		forsec temp {
			if ( (distance(0.5)<subtuftdistS) && ( distance(0.5)>subtuftproxS) ){
				tuftS.append()
			}
		}
	}else{
		tuftS=tuft1[generation-1]
	}//generation
	numbranchesS=0
	forsec tuftS{
		numbranchesS=numbranchesS+1
	}

	rdel.uniform(0, 1000)
	r.uniform(0, numbranchesS-1)
	for i=0,numS-1{

		loc=int(r.repick())
		count=0
		forsec tuftS{
			if (count==loc){
				sprint(st,"%s",secname())
				stfunc.right(st,5)
				stfunc.left(st,stfunc.len(st)-1)
				sscanf(st,"%d",&dendnum)

			}//if
			count=count+1
		}//forsec
		access apic[dendnum]

		rseg.uniform(.1,.9)
		if (nmdaampa==1){
			synS[i]=new glutamate(rseg.repick)
		  	synS[i].ntar=1
		}else{
	      	synS[i]=new ampa(rseg.repick)
		}
		
		synS[i].gmax=gmaxS
		synS[i].del=50
		synS[i].Nspike=3
		synS[i].Tspike=20
	}//numS
	r.uniform(0, numbranchesE-1)
	for i=0,numE-1{

		loc=int(r.repick())
		count=0
		forsec tuftE{
			if (count==loc){
				sprint(st,"%s",secname())
				stfunc.right(st,5)
				stfunc.left(st,stfunc.len(st)-1)
				sscanf(st,"%d",&dendnum)
			}//if
			count=count+1
		}//forsec
		access apic[dendnum]
		rseg.uniform(.1,.9)
		if (nmdaampa==1){
			synE[i]=new glutamate(rseg.repick)
		  	synE[i].ntar=1
		}else{
	      	synE[i]=new ampa(rseg.repick)
		}
		
		synE[i].gmax=gmaxE
		synE[i].del=rdel.repick()
		synE[i].Nspike=1
		synE[i].Tspike=20
	}//numE
	for i=0,numI-1{

		loc=int(r.repick())
		count=0
		forsec tuftE{
			if (count==loc){
				sprint(st,"%s",secname())
				stfunc.right(st,5)
				stfunc.left(st,stfunc.len(st)-1)
				sscanf(st,"%d",&dendnum)
			}//if
			count=count+1
		}//forsec
		access apic[dendnum]
		rseg.uniform(.1,.9)
		synI[i]=new AlphaSynapse(rseg.repick)
		synI[i].gmax=gmaxI/1000
		synI[i].onset=rdel.repick()
		synI[i].tau=3
		synI[i].e=-70
	}//numE	
	make_shape_plot()
}//LOCAL SYNAPSES

loclocation()
c_gmax()
load_file("apic.ses")//the cell
access soma

vshift_sca=-10
forsec apical vshift_hh3=-10

tau1_glutamate=70
tau2_glutamate=3
gama_glutamate=0.08
n_glutamate=0.3
tau_ampa_glutamate=1
tau_ampa_ampa=1
global_ra = 80
celsius = 34