/********************** GRANULE CELL ****************************************
// extracted from
// Dentate gyrus network model
// Santhakumar V, Aradi I, Soltesz I (2005) J Neurophysiol 93:437-53
// https://senselab.med.yale.edu/ModelDB/showModel.cshtml?model=51781&file=\dentategyrusnet2005\DG500_M7.hoc
// ModelDB file along with publication:
// Yim MY, Hanuschkin A, Wolfart J (2015) Hippocampus 25:297-308.
// http://onlinelibrary.wiley.com/doi/10.1002/hipo.22373/abstract
// modified and augmented by
// Abraham Nunes / 2022
// Man Yi Yim / 2015
// Alexander Hanuschkin / 2011
TODO:
- Pass ndend1/2 as arguments
- Allow for creation of more than just 2 dendrites
*/
begintemplate GranuleCell
ndend1=4
ndend2=4
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, gcdend1, gcdend2
public all, gcldend, pdend, mdend, ddend
objref all, gcldend, pdend, mdend, ddend
create soma, gcdend1[ndend1], gcdend2[ndend2]
objref syn, pre_list
//to include steady state current injection
nst=1
objectvar stim[nst]
public stim
// double stimdur[nst], stimdel[nst], stimamp[nst]
// public stim, stimdur, stimamp, stimdel
proc init() {
// Process input arguments
// This is ridiculous. There must be a cleaner way. [ TODO ]
narg = numarg()
cell_index = $1
scale_ka_conductances = 1
scale_km_conductances = 1
gbar_ht_ = 0
gbar_lt_ = 0
scale_size_ = 1
scale_gabaa_ = 1
scale_kir_ = 0
if (narg > 1) { scale_ka_conductances = $2 }
if (narg > 2) { scale_km_conductances = $3 }
if (narg > 3) { gbar_ht_ = $4 }
if (narg > 4) { gbar_lt_ = $5 }
if (narg > 5) { scale_size_ = $6 }
if (narg > 6) { scale_gabaa_ = $7 }
if (narg > 7) { scale_kir_ = $8 }
// Run actual initialization
pre_list = new List()
subsets()
gctemp()
synapse()
}
proc subsets(){ local i
all = new SectionList()
soma all.append()
for i=0, 3 gcdend1 [i] all.append()
for i=0, 3 gcdend2 [i] all.append()
gcldend = new SectionList()
gcdend1 [0] gcldend.append()
gcdend2 [0] gcldend.append()
pdend = new SectionList()
gcdend1 [1] pdend.append()
gcdend2 [1] pdend.append()
mdend = new SectionList()
gcdend1 [2] mdend.append()
gcdend2 [2] mdend.append()
ddend = new SectionList()
gcdend1 [3] ddend.append()
gcdend2 [3] ddend.append()
}
proc gctemp() {
scale_area = 1./1.13 * scale_size_
// ********** Parameters for reversal potentials (assigned below) *********
e_gabaa_ = -70. // reversal potential GABAA
// ***************** Parameters
g_pas_fit_ = 1.44e-05
gkbar_kir_fit_ = 1.44e-05 * scale_kir_
ggabaabar_fit_ = 0.722e-05 * scale_gabaa_
// *********************** PAS ******************************************
cm_fit_ = 1.
Ra_fit_ = 184. // fitted
// *********************** KIR *****************************************
vhalfl_kir_fit_ = -98.923594 // for Botzman I/V curve, fitted
kl_kir_fit_ = 10.888538 // for Botzman I/V curve, fitted
q10_kir_fit_ = 1. // temperature factor, set to 1
vhalft_kir_fit_ = 67.0828 // 3 values for tau func from Stegen et al. 2011
at_kir_fit_ = 0.00610779
bt_kir_fit_ = 0.0817741
// ********************* Neuron Morphology etc ***************************
LJP_ = -10. // Liquid junction potential [mV]
V_rest = -68.16+LJP_ // resting potential [mV]
V_init = -68.16+LJP_ // initial potential [mV]
// ******************** GABAA ********************
e_pas_fit_ = -83.8
e_pas_fit_Dend = -81.74
soma {nseg=1 L=16.8*scale_area diam=16.8*scale_area} // changed L & diam
gcdend1 [0] {nseg=1 L=50*scale_area diam=3*scale_area}
for i = 1, 3 gcdend1 [i] {nseg=1 L=150*scale_area diam=3*scale_area}
gcdend2 [0] {nseg=1 L=50*scale_area diam=3*scale_area}
for i = 1, 3 gcdend2 [i] {nseg=1 L=150*scale_area diam=3*scale_area}
forsec all {
insert ccanl
catau_ccanl = 10
caiinf_ccanl = 5.e-6
insert HT
gbar_HT = gbar_ht_
kan_HT = 0.5
kbn_HT = 0.3
insert LT
gbar_LT = gbar_lt_
Ra=Ra_fit_
}
soma {insert bk
gkbar_bk = 0.00036609754167888492 // fitted to iPSC [SS]
insert ichan2
gnatbar_ichan2 = 0.30382538214974524893 // fitted to iPSC [SS]
el_ichan2 = e_pas_fit_ // set leak reversal poti to gain Vrest of cell <ah>
vshiftma_ichan2 = 67.29851063919572595751 // fitted to iPSC [SS]
vshiftmb_ichan2 = 23.47095335846364605459 // fitted to iPSC [SS]
vshiftha_ichan2 = 118.87882140094222904736 // fitted to iPSC [SS]
vshifthb_ichan2 = 22.72663207632274762204 // fitted to iPSC [SS]
vshiftnfa_ichan2 = 33.30911097464424841519 // fitted to iPSC [SS]
vshiftnfb_ichan2 = 76.56629644409436252772 // fitted to iPSC [SS]
vshiftnsa_ichan2 = 43.38534894819657949938 // fitted to iPSC [SS]
vshiftnsb_ichan2 = 107.92862157059448691143 // fitted to iPSC [SS]
gkfbar_ichan2 = 0.02959266830902676504 // fitted to iPSC [SS]
gksbar_ichan2 = 0.00089829523855913590 // fitted to iPSC [SS]
gl_ichan2 = 0.00001482952021232379 // fitted to iPSC [SS]
insert lca
glcabar_lca = 0.00255351892233713837 // fitted to iPSC [SS]
insert nca
gncabar_nca = 0.00019822407216141575 // fitted to iPSC [SS]
insert sk
gskbar_sk = 0.00051118925530526131 // fitted to iPSC [SS]
insert tca
gcatbar_tca = 0.00000193161941306084 // fitted to iPSC [SS]
insert ka
gkabar_ka = 0.012 * scale_ka_conductances // Yim et al.
insert km
gbar_km = 0.001 * scale_km_conductances // Yim et al.
cm=cm_fit_
}
forsec gcldend {
// all values fitted to iPSC except cm [SS]
insert bk
gkbar_bk = 0.00043569687585868756
insert ichan2
gnatbar_ichan2 = 0.00587566700903554423
el_ichan2 = e_pas_fit_ // set leak reversal poti to gain Vrest of cell <ah>
vshiftma_ichan2 = 72.00908352837669212931
vshiftmb_ichan2 = 10.05866287297631878062
vshiftha_ichan2 = 105.82526035660306718000
vshifthb_ichan2 = 16.07700513630057770342
vshiftnfa_ichan2 = 26.69303619146630168757
vshiftnfb_ichan2 = 20.32044322166495575743
vshiftnsa_ichan2 = 36.39794892716360408258
vshiftnsb_ichan2 = 55.50669569855109841683
gkfbar_ichan2 = 0.00604530884973730146
gksbar_ichan2 = 0.00722289049440019357
gl_ichan2 = 0.00002443855292375595
insert lca
glcabar_lca = 0.00238773027021453111
insert nca
gncabar_nca = 0.00107884546982767800
insert sk
gskbar_sk = 0.00012346487525245479
insert tca
gcatbar_tca = 0.00002366405892739300
cm=cm_fit_
}
forsec pdend {
// all values fitted to iPSC except cm [SS]
insert bk
gkbar_bk = 0.00190061289795323031
insert ichan2
gnatbar_ichan2 = 0.02417375891213749753
el_ichan2 = e_pas_fit_ // set leak reversal poti to gain Vrest of cell <ah>
vshiftma_ichan2 = 35.73928645034203555042
vshiftmb_ichan2 = 8.64376377434796161481
vshiftha_ichan2 = 116.92605508197789276892
vshifthb_ichan2 = 5.98516212833397798221
vshiftnfa_ichan2 = 33.04698698782424060028
vshiftnfb_ichan2 = 44.25661422225875440972
vshiftnsa_ichan2 = 50.93545152479049420435
vshiftnsb_ichan2 = 61.79259722382041530864
gkfbar_ichan2 = 0.00331335014246558453
gksbar_ichan2 = 0.00821248429069832732
gl_ichan2 = 0.00004203000622739663
insert lca
glcabar_lca = 0.00268616527884109162
insert nca
gncabar_nca = 0.00099715092192572351
insert sk
gskbar_sk = 0.00009965352319819307
insert tca
gcatbar_tca = 0.00045442618393490557
cm=cm_fit_*1.6
}
forsec mdend {
// all values fitted to iPSC except cm [SS]
insert bk
gkbar_bk = 0.00155438620883594880
insert ichan2
gnatbar_ichan2 = 0.01092949038241916061
el_ichan2 = e_pas_fit_ // set leak reversal poti to gain Vrest of cell <ah>
vshiftma_ichan2 = 53.42393602450565737172
vshiftmb_ichan2 = 26.31602077683473694947
vshiftha_ichan2 = 71.56344028728052819588
vshifthb_ichan2 = 5.10487127392129202974
vshiftnfa_ichan2 = 23.30935492611515869044
vshiftnfb_ichan2 = 81.83265112336158608741
vshiftnsa_ichan2 = 19.76201462459690461060
vshiftnsb_ichan2 = 83.33946866528904706684
gkfbar_ichan2 = 0.00117364421069368272
gksbar_ichan2 = 0.00588083391646980393
gl_ichan2 = 0.00001327627437971709
insert lca
glcabar_lca = 0.00016453535694872594
insert nca
gncabar_nca = 0.00140331052932918601
insert sk
gskbar_sk = 0.00000000000000000000
insert tca
gcatbar_tca = 0.00045539566021616032
cm=cm_fit_*1.6
}
forsec ddend {
// all values fitted to iPSC except cm [SS]
insert bk
gkbar_bk = 0.00416445454329038029
insert ichan2
gnatbar_ichan2 = 0.00000000000000000000
el_ichan2 = e_pas_fit_ // set leak reversal poti to gain Vrest of cell <ah>
vshiftma_ichan2 = 62.09792868319234315777
vshiftmb_ichan2 = 23.33265723737859431708
vshiftha_ichan2 = 82.64902797714709947741
vshifthb_ichan2 = 11.90267377608926580024
vshiftnfa_ichan2 = 10.17372302817697971022
vshiftnfb_ichan2 = 20.52908377932466521543
vshiftnsa_ichan2 = 27.76758550795040747516
vshiftnsb_ichan2 = 65.82531822034421509215
gkfbar_ichan2 = 0.00036926305629303115
gksbar_ichan2 = 0.00620601662772069223
gl_ichan2 = 0.00004338333500614437
insert lca
glcabar_lca = 0.00000000000000000000
insert nca
gncabar_nca = 0.00033063009592414682
insert sk
gskbar_sk = 0.00000000000000000000
insert tca
gcatbar_tca = 0.00185425322596450442
cm=cm_fit_*1.6
}
connect gcdend1[0](0), soma(1)
connect gcdend2[0](0), soma(1)
for i=1,3 {
connect gcdend1[i](0), gcdend1[i-1](1)
}
for i=1,3 {
connect gcdend2[i](0), gcdend2[i-1](1)
}
forsec all {
insert kir // kir conductance added in Yim et al. 2015, note that eK=-90mV is used instead of -105mV as reported in the paper <ah>
gkbar_kir = gkbar_kir_fit_
vhalfl_kir = vhalfl_kir_fit_
kl_kir = kl_kir_fit_
vhalft_kir = vhalft_kir_fit_
at_kir = at_kir_fit_
bt_kir = bt_kir_fit_
ggabaa_ichan2 = ggabaabar_fit_ // added GabaA in Yim et al. 2015 <ah>
egabaa_ichan2 = e_gabaa_ // reversal potential GABAA added in Yim et al. 2015 <ah>
ena = 50 // ena was unified from enat=55 (BC, HIPP, MC) and enat=45 (GC) in Santhakumar et al. (2005) <ah>
ek = -90 // simplified ekf=eks=ek=esk; note the eK was erroneously reported as -105mV in the Yim et al. 2015 <ah>
cao_ccanl = 2 }
} // end of gctemp()
// Retrieval of objref arguments uses the syntax: $o1, $o2, ..., $oi.
// http://web.mit.edu/neuron_v7.1/doc/help/neuron/general/ocsyntax.html#arguments
proc connect_pre() {
soma $o2 = new NetCon (&v(1), $o1)
}
// Define synapses on to GCs using
//- an Exp2Syn object (parameters tau1 -rise, tau2 -decay,
// time constant [ms] and e - rev potential [mV]
// delay [ms] and weight -variable betw 0 and 1 [1 corresponding to 1 'S]
proc synapse() {
gcdend1[3] syn = new Exp2Syn(0.5) // PP syn based on data from Greg Hollrigel and Kevin Staley <AH> NOTE: both synapses are identical!
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend2[3] syn = new Exp2Syn(0.5) // PP syn based on Greg and Staley
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend1[1] syn = new Exp2Syn(0.5) // MC syn *** Estimated
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend2[1] syn = new Exp2Syn(0.5) // MC syn *** Estimated
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend1[3] syn = new Exp2Syn(0.5) // HIPP syn based on Harney and Jones corrected for temp
syn.tau1 = 0.5 syn.tau2 = 6 syn.e = -70
pre_list.append(syn)
gcdend2[3] syn = new Exp2Syn(0.5) // HIPP syn based on Harney and Jones corrected for temp
syn.tau1 = 0.5 syn.tau2 = 6 syn.e = -70
pre_list.append(syn)
soma syn = new Exp2Syn(0.5) // BC syn based on Bartos
syn.tau1 = 0.26 syn.tau2 = 5.5 syn.e = -70
pre_list.append(syn)
gcdend1[1] syn = new Exp2Syn(0.5) // NOTE: SPROUTED SYNAPSE based on Molnar and Nadler
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend2[1] syn = new Exp2Syn(0.5) // NOTE: SPROUTED SYNAPSE
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
// Total of 7 synapses per GC 0,1 PP; 2,3 MC; 4,5 HIPP and 6 BC 7,8 Sprout
}
func is_art() { return 0 }
endtemplate GranuleCell