Hippocampal CA3 network and circadian regulation (Stanley et al. 2013)

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This model produces the hippocampal CA3 neural network model used in the paper below. It has two modes of operation, a default mode and a circadian mode. In the circadian mode, parameters are swept through a range of values. This model can be quite easily adapted to produce theta and gamma oscillations, as certain parameter sweeps will reveal (see Figures). BASH scripts interact with GENESIS 2.3 to implement parameter sweeps. The model contains four cell types derived from prior papers. CA3 pyramidal are derived from Traub et al (1991); Basket, stratum oriens (O-LM), and Medial Septal GABAergic (MSG) interneurons are taken from Hajos et al (2004).
1 . Stanley DA, Talathi SS, Parekh MB, Cordiner DJ, Zhou J, Mareci TH, Ditto WL, Carney PR (2013) Phase shift in the 24-hour rhythm of hippocampal EEG spiking activity in a rat model of temporal lobe epilepsy. J Neurophysiol 110:1070-86 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Hippocampus; Medial Septum;
Cell Type(s): Hippocampus CA3 pyramidal GLU cell; Hippocampus CA3 interneuron basket GABA cell; Hippocampus CA3 stratum oriens lacunosum-moleculare interneuron; Hippocampus septum medial GABAergic neuron;
Channel(s): I Na,t; I A; I K; I h; I K,Ca; I Calcium;
Gap Junctions:
Receptor(s): GabaA; AMPA;
Transmitter(s): Gaba; Glutamate;
Simulation Environment: GENESIS; MATLAB;
Model Concept(s): Epilepsy; Brain Rhythms; Circadian Rhythms;
Implementer(s): Stanley, David A ;
Search NeuronDB for information about:  Hippocampus CA3 pyramidal GLU cell; Hippocampus CA3 interneuron basket GABA cell; GabaA; AMPA; I Na,t; I A; I K; I h; I K,Ca; I Calcium; Gaba; Glutamate;
// genesis
include kons_b.g

/*****This script creates a prototype for the basket interenuron which 
******selectively terminates on soma and proximal dendrites of pyramidal cells 
******controlling action potential geneartion and passive propagation

create neutral /prot_b

//*****Somatic compartment
create	compartment 	/prot_b/soma
setfield 		/prot_b/soma \
	Cm		{CM_B * SOMA_A_B} \			// F
	Ra		{RA_B * SOMA_L_B /SOMA_XA_B}\ // ohm (felesleges)
	Em  		{EREST_ACT_B} \				// V
	Rm		{RM_B/SOMA_A_B} \  			// ohm
	inject		{1.4 * {SOMA_A_B} * 1e-2} \
	initVm		-0.065

//*****Active sodium channel a la Wang & Buzsaki '96 with fast m gate
create	vdep_channel	/prot_b/soma/Na_channel
setfield 	/prot_b/soma/Na_channel \
	Ek 		55e-3 \					// V
	gbar		{ 350 * {SOMA_A_B} }			// S

//*****the m gate of the sodium channel
create table /prot_b/soma/Na_channel/m_gate

ce /prot_b/soma/Na_channel/m_gate

int i
float y
float alpham
float betam
float x
for (i = 0; i<= VRES; i = i + 1)
   x = (i * (VMAX - VMIN) / VRES) + VMIN
   alpham= -0.1e+6 * ( x  + 0.035) / ({ exp {-0.1e+3 * ( x + 0.035 )} } - 1)
   betam= 4e+3 * { exp { -1 * ( x + 0.060 ) / 0.018 } }
   y = alpham / ( alpham + betam )
   if (x == -0.035)
      y = 0.9970947
   setfield . table->table[{i}] {y}
setfield . table->calc_mode 0

ce /

//*****the h gate of the sodium channel
create tabgate /prot_b/soma/Na_channel/h_gate

/*****tobb dolog is megkavarja a nagysagrandeket es elojeleket: atteres mV->V;
******atteres ms->s; az exponencialis szamlaloban, vagy nevezoben van-e

setupgate ^ alpha {Phi*70} 0 0 58e-3 20e-3 -size {VRES} -range {VMIN} {VMAX}
setupgate ^ beta {Phi*1e+3} 0 1 28e-3 -10e-3 -size {VRES} -range {VMIN} {VMAX}

//*****Connecting gates to the channel
ce /prot_b/soma/Na_channel
addmsg m_gate . MULTGATE output 3
addmsg h_gate . MULTGATE m 1
ce /

//*****Active potassium channel (deleyed rectifier)

create vdep_channel /prot_b/soma/K_channel
setfield ^  Ek -90e-3 gbar {90*{SOMA_A_B}}

create tabgate /prot_b/soma/K_channel/nv_gate

setupgate ^ alpha {-0.01e+6*Phi*0.034} {-0.01e+6*Phi} -1 0.034 -10e-3 -size {VRES} -range {VMIN} {VMAX}
setupgate ^ beta {0.125e+3*Phi} 0 0 0.044 0.080 -size {VRES} -range {VMIN} {VMAX}

//*****Connecting gates to the channel
ce /prot_b/soma/K_channel
addmsg nv_gate . MULTGATE m 4
ce /

//*****Copying constituents to a prototype cell

ce /prot_b/soma

addmsg . 		K_channel/nv_gate 	VOLTAGE	Vm
addmsg K_channel	. 			CHANNEL Gk Ek
addmsg . 		K_channel 		VOLTAGE Vm

addmsg . 		Na_channel/m_gate	INPUT	Vm
addmsg . 		Na_channel/h_gate	VOLTAGE Vm
addmsg Na_channel	.			CHANNEL	Gk Ek
addmsg . 		Na_channel		VOLTAGE	Vm

ce /

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