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
//phototrans.g
//stochastic activation of rhodopsin in individual microvilli

function phototrans (ip3path)
 
create neutral /rhabmemb
ce /rhabmemb

int cyl, i
float value, cumvalue
float slice_volume, vil_volume, vil_xarea, vil_sa

/******* light stimulus **********/
create pulsegen shutter
setfield shutter      \
  baselevel 0  \ 
  level1 {intensity} \ /* photon rate (msec-1) during light on */
  width1 {duration} \ /* specify in units of time, not steps */
  delay1 {lightdelay} \ /* specify in units of time, not steps */
  delay2 99999  \
  trig_mode 0 \
  trig_time 0

create randomspike light
setfield light min_amp 0 max_amp 1.0 rate 0
addmsg shutter light RATE output

/****setup phototransduction in ncyls membrane compartments of rhabdomere **/ 
            /* outerrad*outerrad - innerrad*innerrad */
slice_volume=PI*(rhabrad*rhabrad-(rhabcorerad*rhabcorerad))*(rhablen/rhabcyls)/1000
vil_xarea=PI*rhabvilrad*rhabvilrad
vil_volume=vil_xarea*rhabvillen/1000
vil_sa=PI*rhabvilrad*2*rhabvillen
int slice_vil = numvilli/rhabcyls
echo {slice_vil}

for (cyl = 1; cyl <= rhabcyls; cyl=cyl+1)

/*******rhodopsin activation and inactivation***********/

	create rhodopsin mrhod[{cyl}]
	setfield mrhod[{cyl}] \
		slice {cyl} \
		total_villi {numvilli} \
		slice_villi {slice_vil} \
		villus_vol {vil_volume} \
		villus_xarea {vil_xarea} \
		villus_sa {vil_sa} \
		inact_const {Krkcat*Krkf*RKArrtot/(Krkcat+Krkb)} \
		len {rhabvillen} \
		radius {rhabvilrad} \
		depletion {deplete_power} \
		factor[1] 1 factor[2] 1.9 factor[3] 2.7 factor[4] 3.4 factor[5] 4.02 \
		factor[6] 4.56 factor[7] 5.0 factor[8] 5.4 factor[9] 5.74 factor[0] 0 \
		units {umole}
	cumvalue=0
	for (i=1; i<10; i=i+1)
		value=1/{sqrt {i}}
		cumvalue=cumvalue+value
		setfield mrhod[{cyl}] factor[{i}] {cumvalue}
	end
	addmsg light mrhod[{cyl}] ISOM state

	create randomspike inact[{cyl}]
	setfield inact[{cyl}]  min_amp 0 max_amp 1.0 rate 0
	addmsg mrhod[{cyl}] inact[{cyl}] RATE inact_rate
	addmsg inact[{cyl}] mrhod[{cyl}] INACT state

        /*** calcium feedback to arrestin activity ***/
/*   setfield RKcomplex[{cyl}] form {RKform} pow 1 thresh {RKthresh} halfmax {RKhalf} sign 1
   addmsg {capath}[{cyl}] RKcomplex[{cyl}] FEEDBACK Conc {RKwhich}
*/
 
/********* G protein *******************************/
        /*** Gprotein pools ***/
   create enzyme mrhoGprot[{cyl}]
   setfield mrhoGprot[{cyl}] kf {Kgf} kb {Kgb} kcat {Kgcat} type {quant} units {umole}
   pool2D Ga[{cyl}] {rhabrad} {rhabrad-rhabvillen} {rhablen/rhabcyls} 0 {quant} {umole}
   conservepool Gprot[{cyl}] {Gtot} {slice_volume} {quant} {umole}
   pool2D Ginact[{cyl}] {rhabrad} {rhabrad-rhabvillen} {rhablen/rhabcyls} 0 {quant} {umole}

        /*** messages to set up reaction ***/
   addmsg mrhod[{cyl}] mrhoGprot[{cyl}] RHODOPSIN effective slice_vol slice_xarea slice_sa
   addmsg mrhod[{cyl}] Gprot[{cyl}] VOLUME slice_vol
   addmsg Gprot[{cyl}] mrhoGprot[{cyl}] SUBSTRATE Conc

   addmsg mrhoGprot[{cyl}] Ga[{cyl}] RXN0MOLES deltacat
   addmsg mrhoGprot[{cyl}] Ga[{cyl}] VOLUME vol SAin SAout

	/*** decrement Gprot conservepool by Ga and mrhoGprot amount ***/
   addmsg mrhoGprot[{cyl}] Gprot[{cyl}] MOLES complex_quant
   addmsg Ga[{cyl}] Gprot[{cyl}] MOLES quantity

        /*** degradation of active Ga & production of Ginact ***/
   create reaction gadeg[{cyl}]
   setfield gadeg[{cyl}] kf {Khyd}
   addmsg Ga[{cyl}] gadeg[{cyl}] SUBSTRATE quantity
   addmsg gadeg[{cyl}] Ga[{cyl}] RXN1 kf
   addmsg gadeg[{cyl}] Ginact[{cyl}] RXN0MOLES kfsubs
   addmsg Ga[{cyl}] Ginact[{cyl}] VOLUME vol SAin SAout
   addmsg Ginact[{cyl}] Gprot[{cyl}] MOLES quantity
  
/******** plc reaction and GAP activity ***************/
	/*** pool of PLCtot and plcGa ***/
   pool2D plcGqa[{cyl}] {rhabrad} {rhabrad-rhabvillen} {rhablen/rhabcyls} 0 {quant} {umole}
   conservepool PLC[{cyl}] {plctot} {slice_volume} {quant} {umole}

	/*** volume and SA messages */
   addmsg Ga[{cyl}] plcGqa[{cyl}] VOLUME vol SAin SAout
   addmsg Ga[{cyl}] PLC[{cyl}] VOLUME vol

	/*** reaction between PLC and Ga ***/
   create reaction Ga_plc[{cyl}]
   setfield Ga_plc[{cyl}] kf {Kplcf} kb {Kplcb}

   addmsg Ga[{cyl}] Ga_plc[{cyl}] SUBSTRATE quantity
   addmsg PLC[{cyl}] Ga_plc[{cyl}] SUBSTRATE Conc
   addmsg plcGqa[{cyl}] Ga_plc[{cyl}] PRODUCT quantity
   addmsg Ga_plc[{cyl}] Ga[{cyl}] RXN2MOLES kbprod kfsubs
   addmsg Ga_plc[{cyl}] plcGqa[{cyl}] RXN2MOLES kfsubs kbprod

	/*** decrement PLC and Gprot conservepools by plcGa amount ***/
   addmsg plcGqa[{cyl}] PLC[{cyl}] MOLES quantity
   addmsg plcGqa[{cyl}] Gprot[{cyl}] MOLES quantity

	/*** degradation of plcGa via GAP activity ***/
   create reaction GAP[{cyl}]
   setfield GAP[{cyl}] kf {Kgap}
   addmsg plcGqa[{cyl}] GAP[{cyl}] SUBSTRATE quantity
   addmsg GAP[{cyl}] plcGqa[{cyl}] RXN1 kf
   addmsg GAP[{cyl}] Ginact[{cyl}] RXN0MOLES kfsubs

/*****************IP3 production by PLC action on PIP2 ************/
	/*** pool of PIP2 (IP3 already created) ***/
	/*** don't use conserve pool because IP3 diffuses and degrads in multiple  compartments ***/
   pool2D pip2[{cyl}] {rhabrad} {rhabrad-rhabvillen} {rhablen/rhabcyls} {piptot} {quant} {umole}
   pool2D plcPI[{cyl}] {rhabrad} {rhabrad-rhabvillen} {rhablen/rhabcyls} 0 {quant} {umole}
   create reaction plc_pip[{cyl}]
   setfield plc_pip[{cyl}] kf {Kpif} kb {Kpib}

	/*** messages to compute enzyme complex ***/
   addmsg pip2[{cyl}] plc_pip[{cyl}] SUBSTRATE Conc
   addmsg plcGqa[{cyl}] plc_pip[{cyl}] SUBSTRATE quantity
   addmsg plcPI[{cyl}] plc_pip[{cyl}] PRODUCT quantity

   addmsg plc_pip[{cyl}] plcGqa[{cyl}] RXN2MOLES kbprod kfsubs
   addmsg plc_pip[{cyl}] pip2[{cyl}] RXN2MOLES kbprod kfsubs
   addmsg plc_pip[{cyl}] plcPI[{cyl}] RXN2MOLES kfsubs kbprod

	/* volume messages from enzyme to substrate and product pools */
   addmsg plcGqa[{cyl}] plcPI[{cyl}] VOLUME vol SAin SAout
   addmsg plcGqa[{cyl}] pip2[{cyl}] VOLUME vol SAin SAout
   addmsg plcGqa[{cyl}] {ip3path}[{cyl}] VOLUME vol SAin SAout

	/*** reaction to create ip3 and produce plc and Ginact***/
   create reaction plcPIgap[{cyl}]
   setfield plcPIgap[{cyl}] kf {Kpicat2}

   addmsg plcPI[{cyl}] plcPIgap[{cyl}] SUBSTRATE quantity
   addmsg plcPIgap[{cyl}] plcPI[{cyl}] RXN1 kf
   addmsg plcPIgap[{cyl}] {ip3path}[{cyl}] RXN0MOLES kfsubs
   addmsg plcPIgap[{cyl}] Ginact[{cyl}] RXN0MOLES kfsubs

	/*** reaction to create ip3 and regenerate plcGqa***/
   create reaction plcPIenz[{cyl}]
   setfield plcPIenz[{cyl}] kf {Kpicat1} 

   addmsg plcPI[{cyl}] plcPIenz[{cyl}] SUBSTRATE quantity
   addmsg plcPIenz[{cyl}] plcPI[{cyl}] RXN1 kf
   addmsg plcPIenz[{cyl}] {ip3path}[{cyl}] RXN0MOLES kfsubs
   addmsg plcPIenz[{cyl}] plcGqa[{cyl}] RXN0MOLES kfsubs

   addmsg plcPI[{cyl}] Gprot[{cyl}] MOLES quantity
   addmsg plcPI[{cyl}] PLC[{cyl}] MOLES quantity
end

useclock /rhabmemb/#[] 2

ce /

end


function step2isom
float isom
    while (isom == 0)
        showfield /rhabmemb/light state
        showfield /rhabmemb/mrhod[1] total_time
        step
        isom={getfield /rhabmemb/mrhod[1] last_isom}
    end
    isom=0
    showfield /rhabmemb/light state
end

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