Shaping NMDA spikes by timed synaptic inhibition on L5PC (Doron et al. 2017)

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Accession:231427
This work (published in "Timed synaptic inhibition shapes NMDA spikes, influencing local dendritic processing and global I/O properties of cortical neurons", Doron et al, Cell Reports, 2017), examines the effect of timed inhibition over dendritic NMDA spikes on L5PC (Based on Hay et al., 2011) and CA1 cell (Based on Grunditz et al. 2008 and Golding et al. 2001).
Reference:
1 . Doron M, Chindemi G, Muller E, Markram H, Segev I (2017) Timed Synaptic Inhibition Shapes NMDA Spikes, Influencing Local Dendritic Processing and Global I/O Properties of Cortical Neurons. Cell Rep 21:1550-1561 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex V1 L6 pyramidal corticothalamic cell;
Channel(s): I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I M; I h; I K,Ca; I Calcium; I A, slow;
Gap Junctions:
Receptor(s): NMDA; GabaA; AMPA;
Gene(s):
Transmitter(s): Glutamate; Gaba;
Simulation Environment: NEURON;
Model Concept(s): Active Dendrites; Detailed Neuronal Models;
Implementer(s): Doron, Michael [michael.doron at mail.huji.ac.il];
Search NeuronDB for information about:  Neocortex V1 L6 pyramidal corticothalamic cell; GabaA; AMPA; NMDA; I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I M; I h; I K,Ca; I Calcium; I A, slow; Gaba; Glutamate;
/
reproduction
readme.txt
ampa.mod
Ca_HVA.mod
Ca_LVAst.mod *
cad.mod *
cadiffus.mod
CaDynamics_E2.mod *
canmda.mod *
car.mod *
gabaa.mod *
gabab.mod *
Ih.mod *
Im.mod *
K_Pst.mod *
K_Tst.mod *
Nap_Et2.mod *
NaTa_t.mod *
NaTs2_t.mod *
nmda.mod *
ProbAMPA.mod
ProbAMPANMDA2_ratio.mod
ProbUDFsyn2_lark.mod
SK_E2.mod *
SKv3_1.mod *
SynExp5NMDA.mod *
cell1.asc *
cellmorphology.hoc *
create_data_for_figure_01.py
create_data_for_figure_02.py
create_data_for_figure_03.py *
create_data_for_figure_03_control.py
create_data_for_figure_03_Dt_10.py *
create_data_for_figure_03_Dt_40.py *
data_same_excitation.pickle
iniparameter.hoc
L5PCbiophys3.hoc
L5PCbiophys3_noActive.hoc
mosinit.hoc
plot_figure_01.py
plot_figure_02.py
plot_figure_03.py
plot_figure_04.py
plot_figure_05.py
plot_figure_06.py
spikes_num.pickle
spine.hoc
TTC.hoc
                            
TITLE Calcium ion accumulation with longitudinal and radial diffusion

COMMENT
PROCEDURE factors_cadiffus() sets up the scale factors 
needed to model radial diffusion.
These scale factors do not have to be recomputed
when diam is changed.
The amount of calcium in an annulus is ca[i]*diam^2*vol[i] 
with ca[0] being the 2nd order correct concentration at the exact edge
and ca[NANN-1] being the concentration at the exact center.

ENDCOMMENT

NEURON {
	SUFFIX cadiffus
	USEION ca READ cai, ica WRITE cai
	GLOBAL vrat
}

DEFINE Nannuli  4

UNITS {
	(molar) =	(1/liter)
	(mM) =	(millimolar)
	(um) =	(micron)
	(mA) =	(milliamp)
	FARADAY =	(faraday)	(10000 coulomb)
	PI = (pi)	(1)
}

PARAMETER {
	DCa = 	0.23		(um2/ms) 
}

ASSIGNED {
	diam	(um)
	ica		(mA/cm2)
	cai		(mM)
	vrat[Nannuli]		: numeric value of vrat[i] equals the volume
                        : of annulis i of a 1um diameter cylinder
                        : multiply by diam^2 to get volume per um length
	B0		(mM)
}

CONSTANT { volo = 1e10 (um2)}

STATE {
	ca[Nannuli]		(mM) <1e-6>	: ca[0] is equivalent to cai
}

BREAKPOINT {
	SOLVE state METHOD sparse
}

LOCAL factors_done

INITIAL {
	if (factors_done == 0) {
		factors_done = 1
		factors()
	}

	FROM i=0 TO Nannuli-1 {
		ca[i] = cai
	}
}

LOCAL frat[Nannuli]

PROCEDURE factors() {
	LOCAL r, dr2
	r = 1/2			:starts at edge (half diam)
	dr2 = r/(Nannuli-1)/2	:half thickness of annulus
	vrat[0] = 0
	frat[0] = 2*r
	FROM i=0 TO Nannuli-2 {
		vrat[i] = vrat[i] + PI*(r-dr2/2)*2*dr2	:interior half
		r = r - dr2
		frat[i+1] = 2*PI*r/(2*dr2)	:exterior edge of annulus
					: divided by distance between centers
		r = r - dr2
		vrat[i+1] = PI*(r+dr2/2)*2*dr2	:outer half of annulus
	}
}

LOCAL dsq, dsqvol	: can't define local variable in KINETIC block 
			: or use in COMPARTMENT

KINETIC state {
	COMPARTMENT i, diam*diam*vrat[i] {ca CaBuffer Buffer}
	LONGITUDINAL_DIFFUSION i, DCa*diam*diam*vrat[i] {ca}
	~ ca[0] << (-ica*PI*diam/(2*FARADAY))
	FROM i=0 TO Nannuli-2 {
		~ ca[i] <-> ca[i+1] (DCa*frat[i+1], DCa*frat[i+1])
	}
cai = ca[0]
}

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