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

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Accession:142104
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).
Reference:
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;
Gene(s):
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 2.2
// Kerstin Menne
// Medical University of Luebeck, 17.12.2001
// cell parameter file for the 1994 Traub CA3 hippocampal cell
// "phi" parameter reduced by e-3
// addition of synaptically activated channels;
// distribution of synapses taken from
// Cellular mechanisms of 4-aminopyridine-induced synchronized after-
// discharge in the rat hippocampal slice, Traub et al., 1995, Journal of
// Physiology, 489.1, pp.127-140

*cartesian
*relative     
*asymmetric

*set_compt_param RM 5.0		// ohm*m^2
*set_compt_param RA 2.0		// ohm*m
*set_compt_param CM 0.0075      // F/m^2

     
// The format for each compartment parameter line is :
// name  parent  x       y       z       d       ch      dens ...
// For channels, "dens" =  maximum conductance per unit area of compartment

// The compartment numbering corresponds to that in the paper, with soma = 4

*spherical
   soma	none	     0    0   25.5  30.0  Ca_concs -24.0e12 Na 1000 Ca 10 K_DR 1350 K_AHPs 8 K_Cs 200 K_A 5     

*set_compt_param RM 2.5 		// ohm*m^2
*set_compt_param CM 0.0150 	        // F/m^2
*cylindrical
ap5	soma	     0    0   50   10.0  Ca_conc -18.0e12 Na   60 Ca 20 K_DR  100 K_AHP 16 K_C  160 K_A 10	        
   
ap6_1   ap5	   -35.36 0     35.36 6.30  Ca_conc -29.0e12 Na   60 Ca 20 K_DR  400 K_AHP 16 K_C  160 K_A 10	       
ap6_2   ap5	     35.36  0    35.36 6.30  Ca_conc -29.0e12 Na   60 Ca 20 K_DR  400 K_AHP 16 K_C  160 K_A 10	       

ap7_1   ap6_1      0    15     68.37   2.78  Ca_conc -47.0e12 Na    0 Ca 40 K_DR    0 K_AHP 16 K_C  80 K_A 0  20 
ap7_4   ap6_2       0  -15     68.37   2.78  Ca_conc -47.0e12 Na    0 Ca 40 K_DR    0 K_AHP 16 K_C  80 K_A 0	 20
ap7_2   ap6_1      0    -20   45.83  5.00  Ca_conc -37.0e12 Na    0 Ca 40 K_DR    0 K_AHP 16 K_C  80 K_A 0	 20
ap7_3   ap6_2        0   20  45.83   5.00  Ca_conc -37.0e12 Na    0 Ca 40 K_DR    0 K_AHP 16 K_C  80 K_A 0	 20

ap8_1   ap7_2      0    -13    58.57   3.14  Ca_conc -13.0e12 Na    0 Ca 60 K_DR    0 K_AHP 16 K_C 240 K_A 0	        
ap8_2   ap7_2        -13   0  58.57   3.14  Ca_conc -13.0e12 Na    0 Ca 60 K_DR    0 K_AHP 16 K_C 240 K_A 0	        
ap8_3   ap7_3      0 13    58.57   3.14  Ca_conc -13.0e12 Na    0 Ca 60 K_DR    0 K_AHP 16 K_C 240 K_A 0	       
ap8_4   ap7_3        13   0     58.57   3.14  Ca_conc -13.0e12 Na    0 Ca 60 K_DR    0 K_AHP 16 K_C 240 K_A 0	          

ap9_1   ap8_1      0    -35.36     35.36   1.40  Ca_conc -34.0e12 Na    0 Ca 60 K_DR    0 K_AHP 16 K_C 240 K_A 0	            
ap9_4   ap8_2        -35.36   0     35.36   1.40  Ca_conc -34.0e12 Na    0 Ca 60 K_DR    0 K_AHP 16 K_C 240 K_A 0	            
ap9_5   ap8_3      0    35.36     35.36   1.40  Ca_conc -34.0e12 Na    0 Ca 60 K_DR    0 K_AHP 16 K_C 240 K_A 0	           
ap9_8   ap8_4     0   35.36        35.36   1.40  Ca_conc -34.0e12 Na    0 Ca 60 K_DR    0 K_AHP 16 K_C 240 K_A 0	           
ap9_2   ap8_1      0    -40   44.72 2.50  Ca_conc -16.0e12 Na    0 Ca 60 K_DR    0 K_AHP 16 K_C 240 K_A 0	          
ap9_3   ap8_2      0    40     44.72   2.50  Ca_conc -16.0e12 Na    0 Ca 60 K_DR    0 K_AHP 16 K_C 240 K_A 0	          
ap9_6   ap8_3        0   0     60   2.50  Ca_conc -16.0e12 Na    0 Ca 60 K_DR    0 K_AHP 16 K_C 240 K_A 0	         
ap9_7   ap8_4        0   -40   44.72 2.50  Ca_conc -16.0e12 Na    0 Ca 60 K_DR    0 K_AHP 16 K_C 240 K_A 0	            

ap10_1  ap9_2      -42.43    0     42.43   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	          
ap10_2  ap9_2        42.43   0     42.43   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	         
ap10_3  ap9_3      -42.43    0     42.43   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	          
ap10_4  ap9_3        42.43   0     42.43   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	          
ap10_5  ap9_6      0    -42.43     42.43   1.60  Ca_conc -25.0e12 Na 0    Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	          
ap10_6  ap9_6        0   42.43     42.43   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	       
ap10_7  ap9_7      -42.43    0     42.43   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	         
ap10_8  ap9_7        42.43   0     42.43   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	        
                                                            
ap11_1  ap10_1       0    0    60   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	 
ap11_2  ap10_2       0    0    60   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	 
ap11_3  ap10_3       0    0    60   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	 
ap11_4  ap10_4       0    0    60   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	 
ap11_5  ap10_5       0    0    60   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	 
ap11_6  ap10_6       0    0    60   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	 
ap11_7  ap10_7       0    0    60   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	 
ap11_8  ap10_8       0    0    60   1.60  Ca_conc -25.0e12 Na    0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	 

bas3_1  soma         -15  0      0   5.00  Ca_conc -123.0e12 Na  20 Ca 20 K_DR  300 K_AHP 16 K_C  160 K_A 10	        
bas3_2  soma         0  -11.18 -10   5.00  Ca_conc -123.0e12 Na  20 Ca 20 K_DR  300 K_AHP 16 K_C  160 K_A 10	         
bas3_3  soma       0  11.18    -10   5.00  Ca_conc -123.0e12 Na  20 Ca 20 K_DR  300 K_AHP 16 K_C  160 K_A 10	             
bas3_4  soma        15    0      0   5.00  Ca_conc -123.0e12 Na  20 Ca 20  K_DR  300 K_AHP 16 K_C  160 K_A 10	          

bas2_1  bas3_1      0   -19.37      -35   3.14  Ca_conc -164.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 10	   
bas2_2  bas3_1      0   35  -19.37  3.14  Ca_conc -164.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 1	   
bas2_3  bas3_2      0 -19.37   -35   3.14  Ca_conc -164.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 10	   
bas2_4  bas3_2      0     0    -40   3.14  Ca_conc -164.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 10	    
bas2_5  bas3_3      0     0    -40   3.14  Ca_conc -164.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 10	    
bas2_6  bas3_3  0     19.37    -35   3.14  Ca_conc -164.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 10	   
bas2_7  bas3_4     0     35  -19.37  3.14  Ca_conc -164.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 10	   
bas2_8  bas3_4     0     -35 -19.37   3.14  Ca_conc -164.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 10	   

bas1_1   bas2_1   -36.06 0      -60   2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
bas1_2   bas2_1      0   0      -70   2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
bas1_3   bas2_2      0   0      -70   2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
bas1_4   bas2_2      0   -60 -36.06   2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
bas1_5   bas2_3      0   60 -36.06   2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
   bas1_6   bas2_3      0   0    -43.6   2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
bas1_7   bas2_4      0   26    -35   2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
   bas1_8   bas2_4      0     0    -70   2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
   bas1_9   bas2_5      0     36.06    -60   2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
bas1_10  bas2_5     -26     0    -35   2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
bas1_11  bas2_6     -26     0    -35   2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
bas1_12  bas2_6     60     0  -36.06  2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
bas1_13  bas2_7     60     0  -36.06  2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
bas1_14  bas2_7     0     0      -70   2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
bas1_15  bas2_8     0     0      -70   2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  
bas1_16  bas2_8     0   -36.06    -60   2.00  Ca_conc -148.0e12 Na   0 Ca 20 K_DR    0 K_AHP 16 K_C  80 K_A 0	  

*set_compt_param  CM 0.0075     //F/m^2
*set_compt_param  RM 0.1       	//ohm*m^2
*set_compt_param  RA 1.0
   axonIS   soma  0      53         53   4.00      NaA  5000 K_DRA 2500  

*set_compt_param  CM 0.0075     //F/m^2
*set_compt_param  RM 0.1 	//ohm*m^2
*set_compt_param  RA 1.0
   ax       axonIS     40     0     63.44   1.00      NaA  5000 K_DRA 2500	pyr_spikegen -0.03


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