/* Dentage Gyrus Granule Cell model associated with the papers:
J. Tejada, G.M. Arisi, N. Garcia-Cairasco, A.C. Roque, Morphological alterations in newly born dentate gyrus granule cells that emerge after status epilepticus contribute to make them less excitable, PLoS ONE. 7 (2012) e40726. doi:10.1371/journal.pone.0040726.
J. Tejada, N. Garcia-Cairasco, A.C. Roque, Combined role of seizure-induced dendritic morphology alterations and spine loss in newborn granule cells with mossy fiber sprouting on the hyperexcitability of a computer model of the dentate gyrus, PLoS Comput. Biol. 10 (2014) e1003601. doi:10.1371/journal.pcbi.1003601.
julian.tejada@gmail.com - 2014 */
//Defining granule cell
begintemplate GranuleCell6
// Original name on neuroMorpho.org n06-cont03-sl4.CNG.swc
ndend1=11
public pre_list, connect_pre, subsets, is_art, is_connected
public vbc2gc, vmc2gc, vhc2gc, vgc2bc, vbc2bc, vmc2bc, vhc2bc, vgc2mc, vbc2mc, vmc2mc, vhc2mc, vgc2hc, vmc2hc
public soma, dend
public all, gcldend, pdend, mdend, ddend
nst=10
objectvar stim[nst]
double stimdur[nst], stimdel[nst], stimamp[nst]
public stim, stimdur, stimamp, stimdel
create soma, dend[ndend1]
objref syn, pre_list
proc init() {
pre_list = new List()
subsets()
gctemp()
synapse()
}
objref all, gcldend, pdend, mdend, ddend
proc subsets(){ local i
objref all, gcldend, pdend, mdend, ddend
all = new SectionList()
soma all.append()
for i=0, 10 dend[i] all.append()
gcldend = new SectionList()
dend[0] gcldend.append()
pdend = new SectionList()
for i=1, 2 dend[i] pdend.append()
dend[4] pdend.append()
mdend = new SectionList()
for i=7, 8 dend[i] mdend.append()
ddend = new SectionList()
dend[3] ddend.append()
for i=5, 6 dend[i] ddend.append()
for i=9, 10 dend[i] ddend.append()
}
proc gctemp() {
// soma {nseg=1 L=16.329 diam=11.165} // changed L & diam
//
// dend [0] {nseg=1 L=20.05632 diam=2.6}
// dend [1] {nseg=1 L=80.78021 diam=1.6478}
// dend [2] {nseg=1 L=10.61434 diam=1.1833}
// dend [3] {nseg=1 L=25.82767 diam=1.0346}
// dend [4] {nseg=1 L=30.89202 diam=0.7664}
// dend [5] {nseg=1 L=43.53635 diam=0.9072}
// dend [6] {nseg=1 L=37.46003 diam=0.9215}
// dend [7] {nseg=1 L=85.47885 diam=0.5756}
// dend [8] {nseg=1 L=121.54242 diam=0.6968}
// dend [9] {nseg=1 L=78.91646 diam=0.6705}
// dend [10] {nseg=1 L=97.50034 diam=0.7203}
// dend [11] {nseg=1 L=19.96318 diam=0.8309}
// dend [12] {nseg=1 L=125.23049 diam=0.5746}
// dend [13] {nseg=1 L=117.23326 diam=0.6059}
// dend [14] {nseg=1 L=31.96199 diam=0.6411}
// dend [15] {nseg=1 L=45.48879 diam=0.6389}
// dend [16] {nseg=1 L=22.50602 diam=0.5591}
// dend [17] {nseg=1 L=37.40208 diam=0.6970}
// dend [18] {nseg=1 L=20.88699 diam=0.6050}
// dend [19] {nseg=1 L=10.10732 diam=0.5985}
// for i = 1, 20 dend [i] {nseg=1 L=150 diam=3}
// gcdend2 [0] {nseg=1 L=50 diam=3}
// for i = 1, 3 gcdend2 [i] {nseg=1 L=150 diam=3}
forsec all {
insert ccanl
catau_ccanl = 10
caiinf_ccanl = 0.000005
Ra=210
}
soma {insert ichan2 //ildikos ichan
gnatbar_ichan2=0.12 //original 0.030 to .055
gkfbar_ichan2=0.016 //original 0.015
gksbar_ichan2=0.006
insert borgka
gkabar_borgka=0.012
insert nca // HAV-N- Ca channel
gncabar_nca=0.002 // check to modify- original 0.004
insert lca
glcabar_lca=0.005
insert cat
gcatbar_cat=0.000037
insert gskch
gskbar_gskch=0.001
insert cagk
gkbar_cagk=0.0006
gl_ichan2 = 0.00004
cm=1
}
forsec gcldend {insert ichan2
gnatbar_ichan2=0.018 //original 0.015
gkfbar_ichan2=0.004
gksbar_ichan2=0.006
insert nca // HAV-N- Ca channel
gncabar_nca=0.003 // check to modify- original 0.004
insert lca
glcabar_lca=0.0075
insert cat
gcatbar_cat=0.000075
insert gskch
gskbar_gskch=0.0004
insert cagk
gkbar_cagk=0.0006
gl_ichan2 = 0.00004
cm=1}
forsec pdend {insert ichan2
gnatbar_ichan2=0.013
gkfbar_ichan2=0.004
gksbar_ichan2=0.006
insert nca // HAV-N- Ca channel
gncabar_nca=0.001 // check to modify- original 0.004
insert lca
glcabar_lca=0.0075
insert cat
gcatbar_cat=0.00025
insert gskch
gskbar_gskch=0.0002
insert cagk
gkbar_cagk=0.001
gl_ichan2 = 0.000063
cm=1.0
insert pas
g_pas = 4e-05
}
forsec mdend {insert ichan2
gnatbar_ichan2=0.008
gkfbar_ichan2=0.001
gksbar_ichan2=0.006
insert nca // HAV-N- Ca channel
gncabar_nca=0.001 // check to modify- original 0.004
insert lca
glcabar_lca=0.0005
insert cat
gcatbar_cat=0.0005
insert gskch
gskbar_gskch=0.0
insert cagk
gkbar_cagk=0.0024
gl_ichan2 = 0.000063
cm=1.0
insert pas
g_pas = 4e-05}
forsec ddend {insert ichan2
gnatbar_ichan2=0.008
gkfbar_ichan2=0.001
gksbar_ichan2=0.008
insert nca // HAV-N- Ca channel
gncabar_nca=0.001 // check to modify- original 0.004
insert lca
glcabar_lca=0.0
insert cat
gcatbar_cat=0.001
insert gskch
gskbar_gskch=0.0
insert cagk
gkbar_cagk=0.0024
gl_ichan2 = 0.000063
cm=1.0
insert pas
g_pas = 4e-05}
// connect dend[0](0), soma(1)
// connect gcdend2[0](0), soma(1)
// for i=1,3 {
// connect dend[i](0), dend[i-1](1)
// }
// for i=1,3 {
// connect gcdend2[i](0), gcdend2[i-1](1)
// }
connect dend(0), soma(1)
for i = 1, 2 connect dend[i](0), dend(1)
for i = 3, 4 connect dend[i](0), dend[1](1)
for i = 5, 6 connect dend[i](0), dend[3](1)
for i = 7, 8 connect dend[i](0), dend[4](1)
for i = 9, 10 connect dend[i](0), dend[5](1)
basic_shape()
// connect axon(1), soma(0)
forsec all {enat = 45 ekf = -90 eks = -90 ek=-90 elca=130 etca=130 esk=-90
el_ichan2 =-70
cao_ccanl=2 } // make catau slower70e-3 cao=2 cai=50.e-6
// current injection
//for i=0,0 {
//stimdel[i]=500
//stimdur[i]=200
//stimamp[i]=0.2
//soma stim[i] = new IClamp(0.5)
//stim.del[i]=stimdel[i]
//stim.dur[i]=stimdur[i]
//stim.amp[i]=stimamp[i]
//}
}
proc shape3d_1() {
// axon {pt3dclear()
// pt3dadd(-0.1761, -38, 0, 0.2)
// pt3dadd(-0.1761, -18, 0, 10)
// }
//
soma {pt3dclear()
// pt3dadd(-0.121, -0.4145, 0.01, 10.45)
pt3dadd(-0.1761, -18, 0, 10)
pt3dadd(-0.1761, -0.445, 0, 7.283)
}
dend {pt3dclear()
pt3dadd(-0.1761, -0.445, 0, 7.283)
pt3dadd(0.09, -5.7, 0, 2.13)
pt3dadd(0.19, -8.09, -0.59, 1.95)
pt3dadd(-0.09, -10.02, -1.49, 1.76)
pt3dadd(-0.74, -11.49, -1.51, 1.86)
pt3dadd(-1.39, -12.59, -1.51, 2.23)
}
dend[1] {pt3dclear()
pt3dadd(-1.39, -12.59, -1.51, 2.23)
pt3dadd(-0.95, -14.24, -1.81, 1.48)
pt3dadd(0.16, -15.34, -2.09, 1.3)
pt3dadd(0.81, -16.63, -2.33, 1.11)
pt3dadd(1.09, -17.73, -1.95, 1.11)
pt3dadd(1.55, -19.93, -2.31, 1.11)
pt3dadd(1.83, -21.5, -2.59, 1.11)
pt3dadd(2.11, -22.69, -2.64, 1.3)
pt3dadd(2.67, -23.61, -4.13, 1.76)
pt3dadd(3.04, -24.71, -4.13, 1.86)
pt3dadd(3.13, -25.45, -4.47, 2.04)
}
dend[2] {pt3dclear()
pt3dadd(-1.39, -12.59, -1.51, 2.23)
pt3dadd(-2.78, -12.41, -0.66, 1.48)
pt3dadd(-3.99, -11.77, -0.75, 0.74)
pt3dadd(-6.31, -11.31, -1.05, 0.65)
pt3dadd(-8.53, -10.94, -1.54, 0.65)
pt3dadd(-10.57, -11.21, -1.66, 0.65)
pt3dadd(-13.08, -10.48, -2.27, 0.65)
pt3dadd(-15.21, -10.39, -2.19, 0.65)
pt3dadd(-16.7, -9.65, -2.85, 0.56)
pt3dadd(-17.62, -9.08, -3.43, 0.56)
pt3dadd(-19.2, -8.07, -4.57, 0.56)
pt3dadd(-20.78, -7.79, -4.81, 0.56)
pt3dadd(-22.82, -7.89, -4.88, 0.56)
pt3dadd(-24.86, -7.43, -4.88, 0.56)
pt3dadd(-26.25, -6.97, -5.05, 0.56)
pt3dadd(-27.73, -6.51, -4.56, 0.56)
pt3dadd(-29.59, -5.5, -4.56, 0.56)
pt3dadd(-31.07, -4.94, -5.38, 0.56)
pt3dadd(-32.46, -3.84, -5.38, 0.56)
}
dend[3] {pt3dclear()
pt3dadd(3.13, -25.45, -4.47, 2.04)
pt3dadd(1.82, -26.28, -0.13, 1.21)
pt3dadd(0.98, -27.57, 0.06, 0.93)
pt3dadd(0.24, -29.04, 0.06, 0.74)
pt3dadd(-0.32, -30.24, -0.02, 0.74)
pt3dadd(-0.6, -32.53, -0.02, 0.93)
pt3dadd(-1.15, -33.82, 0.51, 0.93)
pt3dadd(-1.43, -35.38, 0.51, 0.83)
pt3dadd(-1.9, -36.76, 0.23, 1.02)
pt3dadd(-1.99, -37.77, 0.99, 0.83)
pt3dadd(-1.34, -39.24, 0.99, 0.74)
pt3dadd(-1.15, -40.81, 0.88, 0.83)
pt3dadd(-1.06, -42.28, 1.28, 0.83)
pt3dadd(-1.52, -43.84, 1.28, 0.83)
pt3dadd(-1.59, -45.03, 1.08, 0.83)
pt3dadd(-2.24, -46.87, 1.03, 0.83)
pt3dadd(-2.98, -48.8, 1.28, 0.83)
pt3dadd(-3.53, -50.27, 1.01, 1.02)
pt3dadd(-3.91, -51.65, 1.51, 0.93)
pt3dadd(-4.28, -53.03, 1.61, 0.83)
pt3dadd(-5.2, -55.05, 1.7, 0.83)
pt3dadd(-5.76, -55.97, 2.61, 0.65)
pt3dadd(-6.22, -57.72, 2.18, 0.65)
pt3dadd(-5.95, -59.19, 3.05, 0.65)
pt3dadd(-6.04, -60.94, 3.43, 0.74)
pt3dadd(-6.13, -62.13, 3.43, 0.74)
pt3dadd(-6, -63.69, 3.43, 0.83)
pt3dadd(-6, -65.9, 3.95, 0.74)
pt3dadd(-5.91, -67.55, 3.95, 0.74)
pt3dadd(-6, -69.39, 3.95, 0.83)
pt3dadd(-6.09, -70.77, 3.36, 0.74)
pt3dadd(-6, -72.15, 3.36, 0.74)
pt3dadd(-6.28, -73.9, 3.81, 0.74)
pt3dadd(-6, -75.37, 3.81, 0.65)
pt3dadd(-6.37, -76.56, 3.81, 0.83)
pt3dadd(-6.19, -77.76, 3.92, 0.74)
pt3dadd(-6.09, -78.95, 3.7, 0.74)
pt3dadd(-6.28, -80.33, 3.7, 0.74)
pt3dadd(-6.42, -81.72, 4.24, 0.74)
pt3dadd(-6.69, -83.74, 4.47, 0.74)
pt3dadd(-7.34, -85.3, 4.47, 0.74)
pt3dadd(-7.62, -86.77, 4.47, 0.74)
pt3dadd(-7.81, -88.52, 4.47, 0.74)
pt3dadd(-7.99, -90.63, 4.3, 0.74)
pt3dadd(-8.27, -92.66, 4.43, 0.74)
pt3dadd(-8.08, -94.68, 4.41, 0.74)
pt3dadd(-8.64, -96.15, 4.41, 0.74)
pt3dadd(-9.2, -97.25, 4.28, 0.93)
pt3dadd(-9.66, -98.72, 4.28, 0.74)
pt3dadd(-10.44, -100.1, 3.96, 0.74)
pt3dadd(-10.81, -101.7, 3.96, 0.83)
pt3dadd(-10.62, -103.3, 3.96, 0.83)
pt3dadd(-10.53, -105.2, 3.63, 0.74)
pt3dadd(-11.27, -106.9, 3.78, 0.74)
pt3dadd(-11.92, -108.4, 3.57, 0.74)
pt3dadd(-12.29, -109.4, 3.36, 0.65)
pt3dadd(-12.48, -111.1, 3.36, 0.56)
pt3dadd(-12.57, -112.7, 3.3, 0.56)
pt3dadd(-13.22, -115, 4.13, 0.56)
pt3dadd(-14.15, -116.8, 3.79, 0.56)
pt3dadd(-13.38, -118.3, 4.57, 0.56)
pt3dadd(-12.82, -119.1, 5.04, 0.56)
pt3dadd(-13.1, -120.3, 5.04, 0.56)
}
dend[4] {pt3dclear()
pt3dadd(3.13, -25.45, -4.47, 2.04)
pt3dadd(4.8, -26.55, -5.26, 0.74)
pt3dadd(6.1, -27.47, -5.26, 0.74)
pt3dadd(6.75, -28.67, -5.26, 0.74)
pt3dadd(7.03, -29.31, -5.26, 0.74)
pt3dadd(7.82, -30.02, -5.76, 0.65)
pt3dadd(8.84, -31.12, -5.76, 0.65)
pt3dadd(9.21, -32.04, -5.76, 0.56)
}
dend[5] {pt3dclear()
pt3dadd(-13.1, -120.3, 5.04, 0.56)
pt3dadd(-14.11, -121.4, 4.72, 0.56)
pt3dadd(-14.21, -122.6, 4.72, 0.56)
pt3dadd(-14.76, -123.4, 4.72, 0.65)
pt3dadd(-15.41, -123.7, 4.21, 0.65)
pt3dadd(-15.78, -124.5, 4.21, 0.83)
}
dend[6] {pt3dclear()
pt3dadd(-13.1, -120.3, 5.04, 0.56)
pt3dadd(-12.17, -121.9, 4.02, 0.56)
pt3dadd(-11.62, -123.7, 3.65, 0.56)
pt3dadd(-10.41, -125.8, 3.54, 0.56)
pt3dadd(-9.11, -128.1, 2.94, 0.56)
pt3dadd(-8.46, -130.2, 2.94, 0.56)
pt3dadd(-8.09, -132.2, 2.26, 0.56)
pt3dadd(-8.37, -133.7, 2.23, 0.65)
pt3dadd(-8.46, -134.9, 2.23, 0.56)
pt3dadd(-7.97, -136.2, 2.62, 0.56)
pt3dadd(-7.32, -137.7, 2.62, 0.56)
}
dend[7] {pt3dclear()
pt3dadd(9.21, -32.04, -5.76, 0.56)
pt3dadd(9.39, -33.61, -1.55, 0.56)
pt3dadd(9.39, -35.45, -1.56, 0.56)
pt3dadd(9.21, -37.56, -1.56, 0.56)
pt3dadd(8.84, -39.95, -0.95, 0.56)
pt3dadd(8.93, -41.7, -0.95, 0.56)
pt3dadd(10.32, -42.99, -0.95, 0.56)
pt3dadd(10.88, -44.55, -0.7, 0.56)
pt3dadd(11.62, -46.48, -1.07, 0.56)
pt3dadd(11.9, -48.59, -1.07, 0.56)
pt3dadd(12.36, -50.25, -0.44, 0.56)
pt3dadd(13.12, -52.35, -0.81, 0.65)
pt3dadd(13.68, -53.82, -0.81, 0.56)
pt3dadd(14.42, -55.11, -0.8, 0.56)
pt3dadd(15.07, -55.94, -0.8, 0.65)
pt3dadd(15.16, -56.58, -0.8, 0.74)
pt3dadd(15.53, -57.68, -0.47, 0.56)
pt3dadd(15.72, -59.43, -0.74, 0.56)
pt3dadd(16.09, -60.44, -0.82, 0.56)
pt3dadd(16.83, -61.82, -1.04, 0.56)
pt3dadd(17.2, -62.46, -1.73, 0.56)
}
dend[8] {pt3dclear()
pt3dadd(9.21, -32.04, -5.76, 0.56)
pt3dadd(11.27, -33.39, -0.4, 0.65)
pt3dadd(11.73, -35.69, -0.6, 0.65)
pt3dadd(12.85, -37.25, -0.6, 0.65)
pt3dadd(13.68, -38.26, 0.1, 0.56)
pt3dadd(14.05, -40.47, 0.78, 0.56)
pt3dadd(14.89, -42.31, 0.64, 0.56)
pt3dadd(16.09, -44.24, 0.64, 0.56)
pt3dadd(16.84, -46.72, 1.37, 0.56)
pt3dadd(18.32, -49.11, 2.13, 0.56)
pt3dadd(19.71, -50.58, 2.13, 0.56)
pt3dadd(20.81, -51.64, 1.69, 0.56)
pt3dadd(21.74, -52.38, 1.69, 0.56)
}
dend[9] {pt3dclear()
pt3dadd(-15.78, -124.5, 4.21, 0.83)
pt3dadd(-16.73, -125.7, 3.83, 0.46)
pt3dadd(-17.38, -126.8, 3.44, 0.46)
pt3dadd(-18.86, -128, 2.77, 0.46)
pt3dadd(-20.25, -129, 2.47, 0.46)
pt3dadd(-21.46, -130, 2.47, 0.46)
pt3dadd(-22.48, -131.6, 2.55, 0.46)
pt3dadd(-23.04, -132.4, 2.55, 0.65)
pt3dadd(-23.59, -133, 2.55, 0.56)
pt3dadd(-24.89, -134.2, 1.84, 0.56)
pt3dadd(-26.38, -135.7, 2.22, 0.56)
pt3dadd(-27.67, -137.2, 2.22, 0.56)
pt3dadd(-29.07, -139, 2.11, 0.56)
pt3dadd(-30.27, -140.5, 1.59, 0.56)
pt3dadd(-31.01, -141.4, 1.69, 0.56)
pt3dadd(-31.94, -142.6, 2.35, 0.56)
pt3dadd(-33.19, -144.3, 1.89, 0.56)
pt3dadd(-34.58, -146.5, 1.89, 0.56)
pt3dadd(-35.88, -148.8, 1.89, 0.56)
pt3dadd(-38.02, -150.5, 1.89, 0.56)
pt3dadd(-39.59, -152.3, 1.89, 0.56)
pt3dadd(-41.17, -154, 2.19, 0.56)
pt3dadd(-41.82, -155.9, 2.47, 0.56)
pt3dadd(-43.4, -157.3, 1.74, 0.56)
pt3dadd(-45.25, -158.7, 1.74, 0.56)
pt3dadd(-46.55, -159.6, 2.04, 0.56)
pt3dadd(-47.29, -160.4, 2.04, 0.56)
}
dend[10] {pt3dclear()
pt3dadd(-15.78, -124.5, 4.21, 0.83)
pt3dadd(-16.15, -126.2, 5.29, 0.46)
pt3dadd(-16.53, -127.6, 5.32, 0.46)
pt3dadd(-17.08, -128.3, 5.1, 0.46)
pt3dadd(-16.9, -129.7, 5.1, 0.46)
pt3dadd(-16.62, -131.3, 3.99, 0.46)
pt3dadd(-16.71, -133.4, 4.47, 0.46)
pt3dadd(-16.8, -135.1, 3.69, 0.46)
pt3dadd(-16.99, -137.4, 3.69, 0.46)
pt3dadd(-16.99, -139, 3.69, 0.46)
pt3dadd(-17.26, -141.4, 3.65, 0.46)
pt3dadd(-17.54, -143, 4.22, 0.46)
pt3dadd(-17.54, -144.1, 3.3, 0.46)
}
}
proc basic_shape() {
shape3d_1()
// shape3d_2()
}
proc connect_pre() { // $o1 target point process, $o2 returned NetCon
soma $o2 = new NetCon (&v(1), $o1)
//alternative statement $o1.soma pre_list.append(new NetCon(soma.v(1),syn,0,Delsyn,0))
}
objref syn
// objref DistalSynapses
// objref DistalSynapsePositions
objref ProximalSynapses
objref ProximalSynapsePositions
proc synapse() {
// //***** PP syn
// //***** MC syn
ProximalSynapses = new Vector(0,0)
ProximalSynapses .append(0, 1, 2 , 3, 4, 7 , 8)
ProximalSynapsePositions = new Vector(0,0)
ProximalSynapsePositions .append(0.5 , 0.5 , 0.5 , 0.11298 , 0.5 , 0.19709 , 0.24732)
for i= 0 , 6 {
dend[ProximalSynapses .x[i]] syn = new Exp2Syn(ProximalSynapsePositions .x[i]) // // MC syn *** Estimated
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn) // #
}
// //***** HIPP
// //***** BC syn
soma syn = new Exp2Syn(0.5) // BC syn syn based on Bartos
syn.tau1 = 0.26 syn.tau2 = 5.5 syn.e = -70
pre_list.append(syn) // # 0
// //***** Sprout
for i= 0 , 6 {
dend[ProximalSynapses .x[i]] syn = new Exp2Syn(ProximalSynapsePositions .x[i]) // // MC syn *** Estimated
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn) // # 0
}
}
func is_art() { return 0 }
endtemplate GranuleCell6
//************************************************************************************************************