Paired turbulence and light effect on calcium increase in Hermissenda (Blackwell 2004)

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Accession:53427
The sea slug Hermissenda learns to associate light and hair cell stimulation, but not when the stimuli are temporally uncorrelated...These issues were addressed using a multi-compartmental computer model of phototransduction, calcium dynamics, and ionic currents of the Hermissenda photoreceptor...simulations show that a potassium leak channel, which closes with an increase in calcium, is required to produce both the untrained LLD and the enhanced LLD due to the decrease in voltage dependent potassium currents.
Reference:
1 . Blackwell KT (2004) Paired turbulence and light do not produce a supralinear calcium increase in Hermissenda. J Comput Neurosci 17:81-99 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Electrogenic pump;
Brain Region(s)/Organism:
Cell Type(s): Hermissenda photoreceptor Type B;
Channel(s): I A; I K,leak; I h; I K,Ca; I Sodium; I Calcium; I Potassium;
Gap Junctions:
Receptor(s): GabaA; GabaB; IP3;
Gene(s):
Transmitter(s): Gaba;
Simulation Environment: Chemesis;
Model Concept(s): Temporal Pattern Generation; Invertebrate; Signaling pathways; Calcium dynamics;
Implementer(s): Blackwell, Avrama [avrama at gmu.edu];
Search NeuronDB for information about:  GabaA; GabaB; IP3; I A; I K,leak; I h; I K,Ca; I Sodium; I Calcium; I Potassium; Gaba;
//CHEMESIS2.0
//taperncxcell.g

/****** set clocks, units are milliseconds *********/
setclock 0 0.005	/* Used for Calcium cytosol */
setclock 1 0.01		/* iicr and CaER, Vm, gaba A, serca and leak */
setclock 2 0.02		/* cicr, biochem rxn, gaba B, cytleak and pump */
setclock 3 0.04		/* Used for ip3*/
setclock 4 1.0		/* Used for spike generator, inject current*/
setclock 5 2.0		/* for graphs and plot_out*/
setclock 6 10.0		/* used for spatial output */

create conservepool /extracell
setfield /extracell Cinit 10 Ctot 10 Conc 10 volume 2e-4
useclock /extracell 4

   /************ set up soma *************************/
/* electrical compartment and voltage dependent channels*/
create neutral /soma
Vcomp /soma/vm[1] {somalen} {somarad} {RM} {CM} {RI} {Er} {Vinit}

/* calcium objects */
ca_buf_ip3_taper /soma {somacyls} {somashells} {somarad} {shellsize} {somalen} {ERfactor} {concen} {umole}
/*taper the soma, then make calcium release */
changeradius /soma 24 5.5e-4 2 {shellsize}	
	/* change from 6.0 to 5.5 on 8/16/02 */
changeradius /soma 23 8.0e-4 2 {shellsize}
changeradius /soma 1 4.5e-4 2 {shellsize}
changeradius /soma 2 7e-4 2 {shellsize}
makecyt2er /soma/Cacyt /soma/ip3 /soma/CaER {maxiicr} {iicrpower} {maxcicr} {cicrpower} {somashells} {somacyls} {serca} {pumppower} 1e-3
  useclock /soma/Cacyts#[]/x# 1
  useclock /soma/Cacyts#[]/iicrflux 1
  useclock /soma/Cacyts#[]/x00 2
  useclock /soma/Cacyts#[]/x01 2
  useclock /soma/Cacyts#[]/x10 2
  useclock /soma/Cacyts#[]/x11 2
  useclock /soma/Cacyts#[]/ryanflux 2
  useclock /soma/Cacyts#[]/serca 2
  useclock /soma/Cacyts#[]/leak 2

cytpumpcomp /soma/Cacyts1 /extracell pmca {somacyls} {Vpmca} {kpmca} {pmca_power} {mmole}
ncxcomp /soma/Cacyts1 /soma/vm[1] extracell 1 {somacyls} {Vncx} {kncx}
setsercaleak /soma/Cacyt /soma/CaER {somashells} {somacyls} {serca}

/* channels */
kleak_comp /soma/vm[1] /soma/Cacyts1 1 {somacyls} {gleak}
ica_ghk_comp /soma/vm[1] /soma/Cacyts1 1 {somacyls} {pca_p} {pca_t} /extracell
ih_comp /soma/vm 1 1 {g_ih}
icak_comp /soma/vm[1] /soma/Cacyts1 {somacyls} {gkca}
make_ka /soma/vm[1] {gka}

/* shunt due to electrode */ 
create leakage /soma/shunt
setfield /soma/shunt Ek 0 Gk {gshunt}
addmsg /soma/shunt /soma/vm[1] CHANNEL Gk Ek
addmsg /soma/vm[1] /soma/shunt VOLTAGE Vm

useclock /soma/vm[1] 1
useclock /soma/Cacyts1[]/pmca 2
useclock /soma/Cacyts1[]/ncx 2
useclock /soma/Cacyts1[]/kleak 3
useclock /soma/Cacyts1[]/cytleak 2
useclock /soma/shunt 3
useclock /soma/vm[1]/ih 2
useclock /soma/Cacyt[]/#ica 1
useclock /soma/Cacyt[]/kca 2
useclock /soma/vm[1]/ka 1

  /************* set up rhabdomere **********************/
        /**voltage compartment **/

create neutral /rhab
Vcomp /rhab/vm {rhablen} {rhabrad} {RM} {CM} {RI} {Er} {Vinit}
//setfield /rhab/vm Rm {RM/rhabSA} Cm {CM*rhabSA} Ra {Rcore}
setfield /rhab/vm Rm {RM/rhabSA} Cm {CM*rhabSA} Ra {RI*rhablen/rhabxarea}
ca_ip3_rhab /rhab {rhabcyls} {rhabshells} {rhabrad} {rhabrad-rhabcorerad} {rhablen} {ERfactor} {quant} {concen} {umole}
cytpumpcomp /rhab/Cacyts1 /extracell pmca {rhabcyls} {Vpmca} {kpmca} {pmca_power} {mmole}
ncxcomp /rhab/Cacyts1 /rhab/vm extracell 1 {rhabcyls} {Vncx} {kncx}
setsercaleak /rhab/Cacyt /rhab/CaER {rhabshells} {rhabcyls} {serca}
kleak_comp /rhab/vm /rhab/Cacyts1 1 {rhabcyls} {gleak}

useclock /rhab/vm 1
useclock /rhab/Cacyts1[]/pmca 2
useclock /rhab/Cacyts1[]/ncx 2
useclock /rhab/Cacyts1[]/cytleak 2
useclock /rhab/Cacyts1[]/kleak 3

  /************* create neck *************/
	/***voltage compartment **/
create neutral /neck
Vcomp /neck/vm {necklen} {neckrad} {RM} {CM} {RI} {Er} {Vinit}
ca_buf_ip3_2D /neck 1 1 {neckrad} {shellsize} {necklen} {ERfactor} {concen} {umole}
cytpumpcomp /neck/Cacyts1 /extracell pmca 1 {Vpmca} {kpmca} {pmca_power} {mmole}
ncxcomp /neck/Cacyts1 /neck/vm extracell 1 1 {Vncx} {kncx}
setsercaleak /neck/Cacyt /neck/CaER 1 1 {serca}

useclock /neck/vm 1
useclock /neck/Cacyts1[]/pmca 2
useclock /neck/Cacyts1[]/ncx 2
useclock /neck/Cacyts1[]/cytleak 2
 
   /************ set up axon *************************/
        /**voltage compartment **/

create neutral /axon
ellipse_vcomp /axon/vm {axonlen} {axonslice} {axondiama} {axondiamb}  {RM} {CM} {RI} {Er} {Vinit}
/* calcium objects */
/* change divide by 2 to divide by 4 because axondiama is diameter */
ca_buf_ip3_taper /axon {axoncyls} 1 {(axondiama+axondiamb)/4} {shellsize} {axonlen} {ERfactor} {concen} {umole}

/*taper the axon, then make calcium release */
changeradius /axon 100 4.0e-4 1 {shellsize}
	/* change from 4.5 to 4.0 on 08/16/02 */
changeradius /axon 99 2.5e-4 1 {shellsize}
	/* change from 3.0 to 2.5 on 08/16/02 */
makecyt2er /axon/Cacyt /axon/ip3 /axon/CaER {maxiicr} {iicrpower} {maxcicr} {cicrpower} 1 {axoncyls} {serca} {pumppower} 1e-3
  useclock /axon/Cacyts#[]/x# 1
  useclock /axon/Cacyts#[]/iicrflux 1
  useclock /axon/Cacyts#[]/x00 2
  useclock /axon/Cacyts#[]/x01 2
  useclock /axon/Cacyts#[]/x10 2
  useclock /axon/Cacyts#[]/x11 2
  useclock /axon/Cacyts#[]/ryanflux 2
  useclock /axon/Cacyts#[]/serca 2
  useclock /axon/Cacyts#[]/leak 2

cytpumpcomp /axon/Cacyts1 /extracell pmca {axoncyls} {Vpmca} {kpmca} {pmca_power} {mmole}
ncxcomp /axon/Cacyts1 /axon/vm[1] extracell 1 25 {Vncx} {kncx}
ncxcomp /axon/Cacyts1 /axon/vm[2] extracell 26 50 {Vncx} {kncx}
ncxcomp /axon/Cacyts1 /axon/vm[3] extracell 51 75 {Vncx} {kncx}
ncxcomp /axon/Cacyts1 /axon/vm[4] extracell 76 100 {Vncx} {kncx}
setsercaleak /axon/Cacyt /axon/CaER 1 {axoncyls} {serca}
kleak_comp /axon/vm[1] /axon/Cacyts1 1 25 {gleak}
kleak_comp /axon/vm[2] /axon/Cacyts1 26 50 {gleak}
kleak_comp /axon/vm[3] /axon/Cacyts1 51 75 {gleak}
kleak_comp /axon/vm[4] /axon/Cacyts1 76 100 {gleak}
ih_comp /axon/vm 1 {axonslice}  {g_ih}

useclock /axon/vm[] 1
useclock /axon/Cacyts1[]/pmca 2
useclock /axon/Cacyts1[]/ncx 2
useclock /axon/Cacyts1[]/cytleak 2
useclock /axon/Cacyts1[]/kleak 3
useclock /axon/vm[]/ih 2

   /************ set up terminal branches *************************/
	/* assume 1 of branches has gaba synapse, others don't */

        /**voltage compartment **/
create neutral /branch_syn
Vcomp /branch_syn/vm[1] {branchlen1} {syn_br_rad} {RM} {CM} {RI} {Er} {Vinit}
Vcomp /branch_syn/vm[2] {branchlen2} {syn_br_rad} {RM} {CM} {RI} {Er} {Vinit}

	/**calcium **/
ca_buf_ip3_2D /branch_syn {branchcyls} 1 {syn_br_rad} {shellsize} {(branchlen1+branchlen2)} {ERfactor} {concen} {umole}
cytpumpcomp /branch_syn/Cacyts1 /extracell pmca {branchcyls} {Vpmca} {kpmca} {pmca_power} {mmole}
ncxcomp /branch_syn/Cacyts1 /branch_syn/vm[1] extracell 1 5 {Vncx} {kncx}
ncxcomp /branch_syn/Cacyts1 /branch_syn/vm[2] extracell 6 15 {Vncx} {kncx}
setsercaleak /branch_syn/Cacyt /branch_syn/CaER 1 {branchcyls} {serca}

	/**calcium dependent channels**/
kleak_comp /branch_syn/vm[1] /branch_syn/Cacyts1 1 5 {gleak}
kleak_comp /branch_syn/vm[2] /branch_syn/Cacyts1 6 15 {gleak}
//ih_comp /branch_syn/vm 1 2  {g_ih}

	/**clocks **/
useclock /branch_syn/vm[] 1
useclock /branch_syn/Cacyt[]/pmca 2
useclock /branch_syn/Cacyt[]/ncx 2
useclock /branch_syn/Cacyt[]/cytleak 2
//useclock /branch_syn/vm[]/ih 2
//useclock /branch_syn/Cacyt[]/#ica 1

   /*** Branch without synapse ***/
        /**voltage compartment **/
create neutral /branch
Vcomp /branch/vm[1] {branchlen1} {syn_br_rad} {RM} {CM} {RI} {Er} {Vinit}
Vcomp /branch/vm[2] {branchlen2} {syn_br_rad} {RM} {CM} {RI} {Er} {Vinit}

	/**calcium **/
ca_buf_ip3_2D /branch {branchcyls} 1 {syn_br_rad} {shellsize} {(branchlen1+branchlen2)} {ERfactor} {concen} {umole}
cytpumpcomp /branch/Cacyts1 /extracell pmca {branchcyls} {Vpmca} {kpmca} {pmca_power} {mmole}
ncxcomp /branch/Cacyts1 /branch_syn/vm[1] extracell 1 5 {Vncx} {kncx}
ncxcomp /branch/Cacyts1 /branch_syn/vm[2] extracell 6 15 {Vncx} {kncx}
setsercaleak /branch/Cacyt /branch/CaER 1 {branchcyls} {serca}

	/**calcium dependent channels**/
kleak_comp /branch/vm[1] /branch/Cacyts1 1 5 {gleak}
kleak_comp /branch/vm[2] /branch/Cacyts1 6 15 {gleak}
//ih_comp /branch/vm 1 2  {g_ih}

	/**clocks **/
useclock /branch/vm[] 1
useclock /branch/Cacyt[]/pmca 2
useclock /branch/Cacyt[]/ncx 2
useclock /branch/Cacyt[]/cytleak 2
//useclock /branch/vm[]/ih 2
//useclock /branch/Cacyt[]/#ica 1

/******************messages between compartments ***************/
/* messages between voltage compartments */
addmsg /rhab/vm /neck/vm RAXIAL Ra previous_state
addmsg /neck/vm /rhab/vm AXIAL previous_state
addmsg /neck/vm /soma/vm[1] RAXIAL Ra previous_state
addmsg /soma/vm[1] /neck/vm AXIAL  previous_state
addmsg /soma/vm[1] /axon/vm[1] RAXIAL Ra previous_state
addmsg /axon/vm[1] /soma/vm[1]  AXIAL  previous_state
addmsg /axon/vm[{axonslice}] /branch_syn/vm[1] RAXIAL Ra previous_state
addmsg /branch_syn/vm[1] /axon/vm[{axonslice}] AXIAL previous_state
addmsg /branch_syn/vm[1] /branch_syn/vm[2] RAXIAL Ra previous_state
addmsg /branch_syn/vm[2] /branch_syn/vm[1] AXIAL previous_state
addmsg /axon/vm[{axonslice}] /branch/vm[1] RAXIAL Ra previous_state
addmsg /branch/vm[1] /axon/vm[{axonslice}] AXIAL previous_state
addmsg /branch/vm[1] /branch/vm[2] RAXIAL Ra previous_state
addmsg /branch/vm[2] /branch/vm[1] AXIAL previous_state

/* messages between rxnpool compartments */
difcyl /rhab/ip3s2[{rhabcyls}] /neck/ip3s1[1] /rhab/neck_ip3dif {ip3dif} {umole}
difcyl /neck/ip3s1[1] /soma/ip3s2[1] /neck/soma_ip3dif {ip3dif} {umole}
difcyl /soma/ip3s2[{somacyls}] /axon/ip3s1[1] /soma/axon_ip3dif {ip3dif} {umole}
difcyl /axon/ip3s1[{axoncyls}] /branch_syn/ip3s1[1] /axon/brsyn_ip3dif {ip3dif} {umole}
difcyl /axon/ip3s1[{axoncyls}] /branch/ip3s1[1] /axon/branch_ip3dif {ip3dif} {umole}

useclock /neck/soma_ip3dif 3
useclock /rhab/neck_ip3dif 3
useclock /soma/axon_ip3dif 3
useclock /axon/brsyn_ip3dif 3
useclock /axon/branch_ip3dif 3

difcyl /rhab/Cacyts2[{rhabcyls}] /neck/Cacyts1[1] /rhab/neck_Cacytdif {Cadif} {mmole}
difcyl /neck/Cacyts1[1] /soma/Cacyts2[1] /neck/soma_Cacytdif {Cadif} {mmole}
difcyl /soma/Cacyts2[{somacyls}] /axon/Cacyts1[1] /soma/axon_Cacytdif {Cadif} {mmole}
difcyl /axon/Cacyts1[{axoncyls}] /branch_syn/Cacyts1[1] /axon/brsyn_Cacytdif {Cadif} {mmole}
difcyl /axon/Cacyts1[{axoncyls}] /branch/Cacyts1[1] /axon/branch_Cacytdif {Cadif} {mmole}

/***************************************************/
/* set up statocyst as a spiker with adapting rate */

create neutral /stat
create randomspike /stat/spike
setfield /stat/spike min_amp 1.0 max_amp 1.0 rate 0.2 abs_refract 4.0
create transmitter /stat/spike_rate
setfield /stat/spike_rate peak 0.15 tau_fall 1000 decay_type 0 delay 100
addmsg /stat/spike_rate /stat/spike RATE trans_conc

useclock /stat/spike 4

/************************GABA synapse*******************/
str vpath="/branch_syn/vm[2]"
str ip3path="/branch_syn/ip3s1"

/**** make gabaa channel in the synaptic branch ****/
makegabaa {vpath} /stat/spike {g_gabaa}

echo {plctype}
/* make gabab receptor, biochem reactions */
gabab_synapse {vpath} {branchlen2/2} {syn_br_rad} {ip3path} {plctype}

/* make gabab channel */
makegabab {vpath} {vpath}/Gbg {g_gabab}

/***use clock 2 for biochemical reactions and GABA B conductance***/
useclock /branch_syn/vm[2]/# 2
useclock /branch_syn/gabaa 1
useclock /branch_syn/gabab 2
 

/* Add pulse current injection to measure input resistance before and 
	during IPSP*/
/*create pulsegen /soma/inject
setfield /soma/inject width1 200 level1 -0.5 baselevel 0 delay1 600 trig_mode 0
addmsg /soma/inject /soma/vm[1] INJECT output
useclock /soma/inject 4
*/




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