Calcium influx during striatal upstates (Evans et al. 2013)

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Accession:150912
"... To investigate the mechanisms that underlie the relationship between calcium and AP timing, we have developed a realistic biophysical model of a medium spiny neuron (MSN). ... Using this model, we found that either the slow inactivation of dendritic sodium channels (NaSI) or the calcium inactivation of voltage-gated calcium channels (CDI) can cause high calcium corresponding to early APs and lower calcium corresponding to later APs. We found that only CDI can account for the experimental observation that sensitivity to AP timing is dependent on NMDA receptors. Additional simulations demonstrated a mechanism by which MSNs can dynamically modulate their sensitivity to AP timing and show that sensitivity to specifically timed pre- and postsynaptic pairings (as in spike timing-dependent plasticity protocols) is altered by the timing of the pairing within the upstate. …"
Reference:
1 . Evans RC, Maniar YM, Blackwell KT (2013) Dynamic modulation of spike timing-dependent calcium influx during corticostriatal upstates. J Neurophysiol 110:1631-45 [PubMed]
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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: Striatum;
Cell Type(s): Neostriatum medium spiny direct pathway GABA cell;
Channel(s): I Na,t; I L high threshold; I N; I A; I K; I K,Ca; I A, slow; I Krp; I R;
Gap Junctions:
Receptor(s): AMPA; NMDA; Gaba;
Gene(s): Cav1.3 CACNA1D; Cav1.2 CACNA1C; Cav2.2 CACNA1B;
Transmitter(s):
Simulation Environment: GENESIS;
Model Concept(s): Oscillations; STDP; Calcium dynamics;
Implementer(s): Evans, Rebekah [Rebekah.Evans at nih.gov];
Search NeuronDB for information about:  Neostriatum medium spiny direct pathway GABA cell; AMPA; NMDA; Gaba; I Na,t; I L high threshold; I N; I A; I K; I K,Ca; I A, slow; I Krp; I R;
//genesis

/***************************		MS Model, Version 9	*********************
**************************** 	      Ca_constants.g 	*********************
	Avrama Blackwell 	kblackw1@gmu.edu
	Wonryull Koh		wkoh1@gmu.edu
	Rebekah Evans 		rcolema2@gmu.edu
	Sriram 			dsriraman@gmail.com	
******************************************************************************

*****************************************************************************/
    str  CalciumName = "Ca_difshell_"
    str  CA_BUFF_1 = "Ca_difshell_1"     // L and T type channels
    str  CA_BUFF_2 = "Ca_difshell_2"     // coupled to the other channels (N and R)
    str  CA_BUFF_3 = "Ca_difshell_3"     // all calcium channels
  
	int calciumdye = 0  //  flags for calcium dye. "0" means NO calcium dyes.
                     // 1= Fura-2 (default conc 100 uM, can change below)
                     // 2= Fluo-5F (300uM for Shindou, 100uM for Sabatini (check) and Lovinger)
	int calciumtype = 0     // we  have two shell-modes:
                     //  mode = 0 : detailed multi-shell model, using "difshell" object
                     //  mode = 1 : simple calcium pool adopted from  Sabatini's work(Sabatini, 2001, 2004)
	int calciuminact = 0 //calcium dependent inactivation of calcium channels, CaL1.2 and 1.3
		//0 = no CDI
		//1 = CDI for 1.3 and 1.2 N and R
	float cdiqfact = 1
	int NMDABufferMode = 0       // 1, connect both NMDA and AMPA calcium to NMDA_buffer
                                     // 0, connect only NMDA currents to NMDA_buffer


float base = 50e-6 //50nM

float outershell_thickness = 0.1e-6 //outermostshell thickness
float thicknessincrease=2 //perhaps only 1.5		

float dca = 200.0e-12 //200 (um^2)(s^(-1))
//dca = 0.1*dca

//buffer variables [Kim et al 2010 (J Neurosci)]
str bname1 = "calbindin"
float btotal1 = 80.0e-3 	//4 * 40 uM total
float kf1 =  0.028e6 //0.028 (nM^(-1))(s^(-1))  
float kb1 = 19.6 //19.6 (s^(-1))
float d1 = 0 

str bname2 = "CaMC"
if (calciumdye == 0)
	float btotal2 = 15.0e-3 	//was 30.0e-3, but Rodrigo's paper seems to have about half the CaM as Myungs.
else
	float btotal2 = 0.0e-3		//CaM is 'dialyzed' when there is a calcium dye present
end
float kf2 =  0.006e6 //0.006 (nM^(-1))(s^(-1))  
float kb2 = 9.1 //9.1 (s^(-1))
float d2 = 11.0e-12// 11 ((um)^2)(s^(-1)) 

str bname4 = "CaMN" //Ca4? in Kim et al. 2011
if (calciumdye == 0)
	float btotal4 = 15.0e-3 	//was 30.0e-3, but Rodrigo's paper seems to have about half the CaM as Myungs.
else
	float btotal4 = 0.0e-3		//CaM is 'dialyzed' when there is a calcium dye present
end		
float kf4 =  0.1e6 //0.1 (nM^-1)(s^-1)
float kb4 = 1000 // (s^(-1))
float d4 = 11.0e-12 

str bname3 = "Fura-2"  //parameters fall within ranges given in  deshutter's book chapter in Methods in Neuronal Modeling 
float btotal3 = 100e-3 	//100uM?  Kerr uses 100? others use 10? 
float kf3 =  100e3 //1000e3  // 1e5(mM^(-1))(s^(-1))  (deschutter range: 0.25-6e8 M-1sec-1) (25e3 to 6e5 mM-1sec-1) kb kf ratio 185nM (0.000185) 
float kb3 = 18.5 //185 //(s^(-1))  17-380 s^-1 range given in deShutter's chapter(methods in neuronal modeling)
float d3 = 6e-11 //((m)^2)(s^(-1)) (deschutter range: 0.4e-11 m^2sec-1 to 2e-10 m^2sec-1) 6e-11 based on Young's eqn and a viscossity of 4.1, eqn is in Rodrigo's EPAC paper

str bname5 = "Fluo5F" 
float btotal5 = 100.0e-3 //Shindou and Wickens use 300uM Lovinger will use 100uM
float kf5 = 236e3 //236,000 (mM^(-1))(s^(-1)) (2.36e8 M-1sec-1, from Zenisek et al., 2003 kd=2.3uM) 
float kb5 = 5.428e3 //5,428(s^(-1)) for kb/kf=0.023 (for Kd=2.3uM from Shindou 2011)
float d5 = 6e-11 //mol weight similar to Fura2, using same dif constants.  

//kcat & km for MMPump
float km = 0.3e-3
float kcat =  75.0e-8 //75 pmol ((cm)^(-2)) (s^(-1)) //Markram et al 1998

float kcatsoma = 85e-8
float kcatdend = 12e-8 //12e-8