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n24.hoc
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/* 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 GranuleCell24
// Original name on neuroMorpho.org n24-r01-02-sl2.CNG.swc
ndend1=9
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, 8 dend[i] all.append()
gcldend = new SectionList()
dend[0] gcldend.append()
pdend = new SectionList()
for i= 1, 2 dend[i] pdend.append()
for i= 4, 6 dend[i] pdend.append()
dend[8] pdend.append()
mdend = new SectionList()
dend[3] mdend.append()
ddend = new SectionList()
dend[7] 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[2](1)
for i = 7, 8 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(0.6784, -38, 0.01, 0.2)
// pt3dadd(0.6784, -18, 0.01, 10)
// }
soma {pt3dclear()
pt3dadd(0.6784, -18, 0.01, 10)
pt3dadd(0.6784, -0.3921, 0, 10)
}
dend {pt3dclear()
pt3dadd(0.6784, -0.3921, 0, 9.935)
pt3dadd(4.08, -4.69, 0, 2.6)
pt3dadd(4.17, -5.97, 0, 2.04)
pt3dadd(3.99, -7.35, -0.23, 1.76)
pt3dadd(3.62, -8.92, -0.12, 1.58)
pt3dadd(3.25, -10.02, 0, 1.58)
pt3dadd(3.06, -11.31, -0.28, 1.58)
pt3dadd(2.88, -12.59, -0.01, 1.76)
pt3dadd(2.78, -13.79, 0.3, 2.04)
pt3dadd(2.97, -15.26, 0.3, 2.23)
pt3dadd(3.15, -16.54, 0.3, 2.5)
pt3dadd(3.15, -17.56, 0.3, 3.15)
pt3dadd(3.37, -18.83, 0.3, 3.62)
}
dend[1] {pt3dclear()
pt3dadd(3.37, -18.83, 0.3, 3.62)
pt3dadd(2.08, -20.81, 0.31, 1.48)
pt3dadd(1.62, -22.09, 0.28, 1.48)
pt3dadd(1.06, -23.01, 0.9, 1.67)
pt3dadd(0.87, -23.66, 0.9, 1.67)
}
dend[2] {pt3dclear()
pt3dadd(3.37, -18.83, 0.3, 3.62)
pt3dadd(5.23, -20.58, 0.3, 1.48)
pt3dadd(5.97, -21.68, 0.3, 1.48)
pt3dadd(6.62, -22.97, 0.3, 1.95)
pt3dadd(6.99, -24.07, 0.65, 2.32)
}
dend[3] {pt3dclear()
pt3dadd(0.87, -23.66, 0.9, 1.67)
pt3dadd(-0.16, -24.55, 0.31, 1.02)
pt3dadd(-0.9, -25.83, 0.31, 1.11)
pt3dadd(-1.92, -26.94, 1.16, 1.21)
pt3dadd(-2.39, -28.04, 1.16, 1.48)
pt3dadd(-2.57, -28.87, 0.55, 1.39)
pt3dadd(-3.32, -30.71, 0.54, 0.74)
pt3dadd(-3.41, -32.36, 0.44, 0.74)
pt3dadd(-3.78, -33.92, 0.33, 0.74)
pt3dadd(-4.06, -35.49, -0.22, 0.74)
pt3dadd(-4.98, -36.68, 0.69, 0.74)
pt3dadd(-5.08, -38.15, 0.77, 0.74)
pt3dadd(-5.45, -39.25, 0.23, 0.74)
pt3dadd(-6.19, -40.63, 0.38, 0.74)
pt3dadd(-6.75, -42.84, 0.46, 0.74)
pt3dadd(-7.12, -44.4, 0.52, 0.65)
pt3dadd(-7.77, -45.78, 0.48, 0.65)
pt3dadd(-8.32, -46.88, 0.15, 0.65)
pt3dadd(-8.88, -47.25, 0.15, 0.65)
pt3dadd(-9.16, -48.54, 0.15, 0.83)
pt3dadd(-9.62, -49.46, 0.82, 1.11)
pt3dadd(-10.09, -50.28, 0.82, 1.11)
pt3dadd(-10.64, -50.74, 0.19, 0.74)
pt3dadd(-11.76, -51.85, 0.62, 0.74)
pt3dadd(-12.41, -53.04, 0.8, 0.74)
pt3dadd(-12.96, -53.87, 0.89, 0.74)
pt3dadd(-13.33, -54.79, 1.09, 0.74)
pt3dadd(-14.17, -56.07, 0.52, 0.74)
pt3dadd(-14.35, -57.27, 0.52, 0.74)
pt3dadd(-13.94, -58.25, 1.66, 0.74)
pt3dadd(-13.84, -60, 1.23, 0.56)
pt3dadd(-13.75, -61.2, 1.37, 0.56)
pt3dadd(-13.57, -62.39, 1.25, 0.56)
pt3dadd(-13.38, -63.49, 0.76, 0.56)
pt3dadd(-12.64, -65.33, 0.76, 0.56)
pt3dadd(-13.01, -66.25, 0.73, 0.56)
pt3dadd(-13.66, -67.91, 0.35, 0.56)
pt3dadd(-14.22, -69.28, 0.61, 0.56)
pt3dadd(-14.77, -70.85, 0.2, 0.74)
pt3dadd(-15.51, -72.13, 0.2, 0.74)
pt3dadd(-16.07, -73.88, 0.2, 0.74)
pt3dadd(-16.18, -75.02, -0.85, 0.56)
pt3dadd(-16.46, -76.22, -0.59, 0.56)
pt3dadd(-17.2, -77.41, -0.2, 0.56)
pt3dadd(-17.38, -78.88, -1.04, 0.56)
pt3dadd(-17.94, -80.45, -0.57, 0.56)
pt3dadd(-18.96, -82.1, -0.94, 0.56)
pt3dadd(-19.24, -83.57, -0.35, 0.56)
pt3dadd(-20.26, -84.68, -1.15, 0.56)
pt3dadd(-20.35, -85.87, -1.6, 0.56)
pt3dadd(-20.54, -86.7, -1.6, 0.56)
pt3dadd(-20.35, -87.71, -1.7, 0.56)
pt3dadd(-20.26, -88.44, -1.24, 0.56)
}
dend[4] {pt3dclear()
pt3dadd(0.87, -23.66, 0.9, 1.67)
pt3dadd(1.8, -25.03, 0.89, 1.02)
pt3dadd(2.08, -26.87, 0.71, 1.02)
pt3dadd(1.71, -28.53, 0.69, 1.02)
pt3dadd(1.43, -29.91, 0.83, 0.74)
pt3dadd(1.06, -31.1, 0.6, 0.74)
pt3dadd(0.59, -32.57, 1.09, 0.74)
pt3dadd(-0.33, -33.31, 1.09, 0.74)
pt3dadd(-1.08, -34.5, 0.87, 0.83)
pt3dadd(-1.63, -35.33, 0.6, 0.83)
pt3dadd(-2.47, -36.62, 0.46, 1.02)
pt3dadd(-3.21, -37.35, 0.46, 0.83)
pt3dadd(-3.49, -37.9, 0.46, 0.83)
pt3dadd(-3.87, -39.16, 0.73, 0.56)
pt3dadd(-3.5, -40.27, 1.22, 0.56)
}
dend[5] {pt3dclear()
pt3dadd(6.99, -24.07, 0.65, 2.32)
pt3dadd(6.09, -26.34, 0.96, 0.83)
pt3dadd(6.09, -28.18, 0.62, 0.83)
pt3dadd(6, -29.1, 1.45, 0.83)
pt3dadd(5.53, -30.48, 1.11, 0.83)
pt3dadd(4.88, -32.32, 0.82, 1.11)
pt3dadd(4.23, -33.05, 1.02, 1.21)
}
dend[6] {pt3dclear()
pt3dadd(6.99, -24.07, 0.65, 2.32)
pt3dadd(8.38, -25.63, 0.27, 0.83)
pt3dadd(8.66, -26.73, -0.08, 0.74)
pt3dadd(8.01, -28.57, -0.08, 0.74)
pt3dadd(8.19, -30.04, -1.07, 0.74)
pt3dadd(8.94, -31.51, -0.87, 0.74)
pt3dadd(9.59, -32.53, -1.19, 0.74)
pt3dadd(9.49, -33.54, -0.94, 0.74)
pt3dadd(9.77, -34.73, -0.27, 0.74)
pt3dadd(10.61, -35.47, -0.27, 0.74)
pt3dadd(11.16, -36.57, 0.16, 0.74)
}
dend[7] {pt3dclear()
pt3dadd(4.23, -33.05, 1.02, 1.21)
pt3dadd(3.68, -33.79, 1.02, 1.21)
pt3dadd(2.84, -34.98, 0.68, 1.21)
pt3dadd(2.57, -35.9, 0.68, 1.21)
pt3dadd(2.29, -37.09, 0.49, 0.93)
pt3dadd(1.92, -38.38, 0.93, 0.74)
pt3dadd(0.99, -39.85, 0.78, 0.74)
pt3dadd(0.15, -41.87, 0.7, 0.65)
pt3dadd(-0.5, -43.25, 0.77, 0.65)
pt3dadd(-1.42, -44.36, 1.43, 0.65)
pt3dadd(-2.26, -45.83, 0.92, 0.65)
pt3dadd(-2.91, -46.93, 0.45, 0.56)
pt3dadd(-3.93, -48.03, 0.45, 0.56)
pt3dadd(-4.67, -49.23, 0.93, 0.56)
pt3dadd(-5.23, -50.33, 0.93, 0.74)
pt3dadd(-6.15, -51.43, 0.05, 0.56)
pt3dadd(-6.71, -52.63, -0.04, 0.56)
pt3dadd(-7.73, -53.82, 0.39, 0.56)
pt3dadd(-8.66, -54.65, -0.15, 0.74)
pt3dadd(-9.31, -55.39, -0.15, 0.74)
pt3dadd(-10.34, -56.54, -0.15, 0.65)
pt3dadd(-11.08, -57.64, 0.35, 0.65)
pt3dadd(-11.08, -58.93, 0.35, 0.56)
pt3dadd(-10.71, -59.48, -0.03, 0.56)
pt3dadd(-11.82, -60.49, -0.46, 0.74)
pt3dadd(-12.1, -61.5, 0.73, 0.74)
pt3dadd(-12.01, -62.15, -0.18, 0.74)
pt3dadd(-13.12, -63.06, -0.02, 0.56)
pt3dadd(-13.21, -64.17, 0.38, 0.56)
pt3dadd(-13.95, -65.36, -0.18, 0.56)
pt3dadd(-14.79, -66.65, -0.51, 0.74)
pt3dadd(-15.44, -67.75, 0.29, 0.74)
pt3dadd(-15.99, -68.95, 0.4, 0.74)
pt3dadd(-16.18, -69.87, 0.57, 0.83)
pt3dadd(-16.27, -70.88, -0.15, 0.65)
pt3dadd(-16.55, -72.26, -0.11, 0.56)
pt3dadd(-17.2, -73.36, 0.38, 0.56)
pt3dadd(-17.39, -74.55, -0.01, 0.56)
pt3dadd(-17.29, -75.28, -0.01, 0.56)
pt3dadd(-17.57, -76.38, 0.14, 0.56)
pt3dadd(-18.13, -77.48, 0.38, 0.74)
pt3dadd(-18.78, -78.4, 0.38, 0.56)
pt3dadd(-19.15, -79.23, 0.42, 0.56)
pt3dadd(-19.89, -80.24, 0.41, 0.56)
pt3dadd(-20.82, -80.98, 0.41, 0.65)
pt3dadd(-21.28, -82.08, -0.09, 0.56)
pt3dadd(-21.47, -82.63, -0.09, 0.65)
pt3dadd(-22.21, -83.37, 0.07, 0.56)
pt3dadd(-22.58, -84.29, 0.08, 0.56)
pt3dadd(-23.23, -84.84, 0.13, 0.56)
pt3dadd(-23.88, -85.94, -0.23, 0.56)
pt3dadd(-24.62, -86.86, 0.16, 0.74)
pt3dadd(-24.71, -88.42, 0.24, 0.56)
pt3dadd(-25.36, -89.8, -0.64, 0.56)
pt3dadd(-25.46, -90.81, -0.64, 0.56)
pt3dadd(-25.55, -92.1, -0.89, 0.56)
pt3dadd(-25.46, -92.65, -0.89, 0.65)
pt3dadd(-25.46, -93.39, -0.89, 0.65)
pt3dadd(-25.58, -94.54, -0.89, 0.65)
pt3dadd(-25.76, -95.73, 0.04, 1.21)
pt3dadd(-26.41, -96.28, 0.04, 0.74)
pt3dadd(-26.88, -96.84, 0.04, 0.74)
pt3dadd(-27.25, -98.03, -0.37, 0.74)
pt3dadd(-27.06, -98.86, -0.37, 0.83)
pt3dadd(-26.78, -99.5, -0.14, 0.65)
pt3dadd(-27.06, -100.9, -0.46, 0.46)
pt3dadd(-27.16, -102.6, -0.33, 0.46)
pt3dadd(-27.16, -104.2, -0.3, 0.46)
pt3dadd(-27.34, -105.8, 0.07, 0.46)
pt3dadd(-27.43, -107.4, -0.44, 0.46)
pt3dadd(-27.9, -107.9, -0.44, 0.46)
pt3dadd(-27.9, -108.9, -0.44, 0.46)
pt3dadd(-28.27, -110.1, 0.05, 0.46)
pt3dadd(-28.64, -111, -0.58, 0.46)
pt3dadd(-29.01, -112, -0.26, 0.46)
pt3dadd(-28.72, -113.1, -0.45, 0.46)
pt3dadd(-28.81, -114.1, -0.02, 0.46)
pt3dadd(-28.72, -115.2, -0.02, 0.46)
pt3dadd(-28.72, -116.6, -0.56, 0.46)
pt3dadd(-28.34, -117.9, -0.23, 0.46)
pt3dadd(-28.25, -119.1, -0.05, 0.46)
pt3dadd(-28.53, -119.8, -0.61, 0.74)
pt3dadd(-28.62, -120.5, -0.61, 0.74)
pt3dadd(-29.09, -121.1, -0.26, 0.56)
pt3dadd(-29.55, -121.4, -0.26, 0.56)
}
dend[8] {pt3dclear()
pt3dadd(4.23, -33.05, 1.02, 1.21)
pt3dadd(4.79, -34.52, 1.02, 0.74)
pt3dadd(4.88, -35.44, 1.02, 0.56)
pt3dadd(4.42, -36.64, 0.76, 0.56)
}
}
proc shape3d_2() {
dend[8] { pt3dadd(4.61, -37.65, 1.2, 0.56)
pt3dadd(4.33, -38.93, 1.2, 0.56)
pt3dadd(4.33, -39.94, 1.47, 0.83)
pt3dadd(4.33, -40.96, 1.16, 0.83)
pt3dadd(4.23, -42.06, 1.12, 0.93)
pt3dadd(4.14, -43.35, 1.98, 0.93)
pt3dadd(4.42, -44.26, 1.98, 0.56)
pt3dadd(4.7, -45.37, 1.42, 0.56)
pt3dadd(5.35, -45.73, 0.95, 0.74)
pt3dadd(5.9, -45.92, 0.95, 0.74)
}
}
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 ProximalSynapses
objref ProximalSynapsePositions
proc synapse() {
// //***** PP syn
// //***** MC syn
ProximalSynapses = new Vector(0,0)
ProximalSynapses .append(0 , 1, 2, 3, 4 , 5 , 6 , 7, 8)
ProximalSynapsePositions = new Vector(0,0)
ProximalSynapsePositions .append(0.5 , 0.5 , 0.5 , 0.17147 , 0.5 , 0.5 , 0.5 , 0.070731 , 0.5)
for i= 0 , 8 {
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 , 8 {
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 GranuleCell24
//************************************************************************************************************