Questions about Traub’s model

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Jaekyung Kim
Posts: 9
Joined: Thu Aug 16, 2012 8:41 pm

Questions about Traub’s model

Post by Jaekyung Kim » Sun Aug 19, 2012 8:53 pm

Hello.

I’m trying to make single cell model for TC neuron based on Traub’s model in the paper of Journal of Neurophysiology, 2005. I want to test my hypotheses in this single TC cell model.

1) In the provided NEURON version simulation, I couldn’t find any function or code to maintain resting membrane voltage. In the other model such as hippocampal CA1 neuron model of Migliore, they adjusted passive membrane properties in order to set resting membrane voltage at start and maintain it over time if there is no other stimulation. However I couldn’t find such effort. Is there any reason? Or didn’t I find that kind of source code?


2) Another question. I see this code like below in the file of ‘oncell.hoc’.

objref fih0_, fih1_
fih0_ = new FInitializeHandler(0, "finit0()")
fih1_ = new FInitializeHandler(1, "finit1()")


proc finit0() { local ix
if (cell != nil) {
ix = cell.type()
forsec cell.all { v = type_vinit.x[ix] }
if (ix == TCRtype) {
forsec cell.all { v = -85 }
}
}
if (cell2 != nil) {
ix = cell2.type()
forsec cell2.all { v = type_vinit.x[ix] }
if (ix == TCRtype) {
forsec cell2.all { v = -85 }
}
}
}

proc finit1() { local ix
if (cell != nil) {
ix = cell.type()
if (ix == TCRtype) {
forsec cell.all { v = type_vinit.x[ix] }
}
}
if (cell2 != nil) {
ix = cell2.type()
forsec cell2.all { v = type_vinit.x[ix] }
if (ix == TCRtype) {
forsec cell2.all { v = type_vinit.x[ix] }
}
}
}

Finit0() and finit1() are done simultaneously. I couldn’t understand why these are done together. Could anyone explain about the purpose of above attached code briefly?

Thank you in advance.

tom_morse
Posts: 40
Joined: Wed May 18, 2005 10:23 pm
Location: Yale University School of Medicine
Contact:

Re: Questions about Traub’s model

Post by tom_morse » Sun Aug 19, 2012 11:22 pm

Regarding your first question on balancing the conductances: Traub set the max conductance values to reproduce electropysiology experiments as seen in the 2005 paper's appendix and previous papers. It is expected that there are ranges of values of max conductances that could also reproduce the experiments so these choices are likely part of what Traub referred to as arbitrary choices. The paper also reported results where ranges of depolarizing currents are injected into some cell types. In these cases balancing the conductances (for an initial equilibrium condition) in these numerical experiments would not be meaningful.

In regards to the second question on the model initialization, we will have to examine the code (I don't recall or know the answer).

Jaekyung Kim
Posts: 9
Joined: Thu Aug 16, 2012 8:41 pm

Re: Questions about Traub’s model

Post by Jaekyung Kim » Mon Aug 20, 2012 4:03 am

Then could you give me some advices to maintain membrane voltage at -65 mV? I tried to some ways such as injecting constant current every time or adjusting passive membrane properites. But I failed to maintain membrane voltage at -65 mV. Do you have any good idea?

tom_morse
Posts: 40
Joined: Wed May 18, 2005 10:23 pm
Location: Yale University School of Medicine
Contact:

Re: Questions about Traub’s model

Post by tom_morse » Mon Aug 20, 2012 1:13 pm

Is -66.5425 close enough? I notice that the TCR model soma settles down to that if run for 10 seconds (10000ms). If this is adequate one could examine all the activation and inactivation variables and voltages in each compartment and initialize the model to them to start with a steady state. Note that the compartments of the model settle to different voltages (run this code to see voltages in each compartment after you have run the model for say 10000ms):

Code: Select all

forall print secname(), ": v = ", v(0.5)

Jaekyung Kim
Posts: 9
Joined: Thu Aug 16, 2012 8:41 pm

Re: Questions about Traub’s model

Post by Jaekyung Kim » Wed Aug 22, 2012 11:09 pm

Thanks. I didn't think each compartment has different steady state, membrane voltage. We decided to test my hypothesis after cell goes to steady state. Thank you for your advice.

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