insert hh

NMODL and the Channel Builder.
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GTR

insert hh

Post by GTR »

I am trying to reproduce rhythmic firing during resting state in the Andrew Gillies' subthalamic nucleus neuron model.
I have constructed the neuron (and network-we had a discussion about this if you remember) based on Gillies-Sterratt tutorial.
I tried to give my model a more subthalamic behaviour by adding more channels guided by Andrew's citation in modelDB about:STh nucleus projection neuron.
My problem is that the only way my neuron achieves rhythmic firing is if I "insert hh" properties in my model along with Gillies' Na and KDR mechanisms.

Code: Select all

// channels
     
     insert Na
     insert NaL
     insert KDR
     insert Kv31
 [b]    insert hh[/b]
      .......................... 
      ena = 71.5
      ek = -89.1
      gnabar_hh=0.25
      gl_hh = .0001666
      el_hh = -60.0
      
in the soma section of the code

If I remove hh I get a straight line response unlike Gillies' RS.
Andrew's model achieves rhythmic firing in rs with its own Na,NaL,KDR...... mechanisms and without 'insert hh' as I can from his hoc code in sthprotocell.hoc
Why this happens?
I don't want to pester you with the codes,just your view.
I don't think I can replace Gillies' Na and KDR mechanisms with standard hh mechanism due to their different formulation.
My model performs the desired behaviour with two different Na and K mechanisms Andrew's and hh.
Is it reasonable?
and something else:
Is there a "cset" statement in NEURON or Andrew named it like ,What its function and syntax form?
In sample.hoc he uses this to load the levels of conductances he has into a seperate folder.

Code: Select all

// linear conductances (loaded from files)...
   printf("loading linear+uniform conductances\n")
   
   // KDR
   cset(0,"gk_KDR","")
   // Kv3.1   
   cset(0,"gk_Kv31","")
   // Ih
   cset(0,"gk_Ih","")
   // sKCa
   cset(0,"gk_sKCa","")
   // CaT   
   cset(0,"gcaT_CaT","")
   // CaN
   cset(0,"gcaN_HVA","")
   // CaL
   cset(0,"gcaL_HVA","")
   
and the same question about ion_style:

Code: Select all

// set the ion styles  
   
   forall ion_style("na_ion",1,2,1,0,1)
   forall ion_style("k_ion",1,2,1,0,1)
   forall ion_style("ca_ion",3,2,1,1,1)   
   
I failed in finding them in the reference manual.

ted
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Re: insert hh

Post by ted »

GTR wrote:I am trying to reproduce rhythmic firing during resting state in the Andrew Gillies' subthalamic nucleus neuron model.
A neuron's firing pattern depends on its intrinsic properties, synaptic inputs, and applied
stimuli. If your model does not fire rhythmically but the Gillies-Sterratt model does, there
must be some difference between the models in one or more of those three factors.
What that difference might be, and how to change your model so that it too fires
rhythmically is a research question. Many minimal spike mechanisms (fast, inactivating
inward current plus slower, delayed outward current) are capable of producing rhythmic
firing in a single compartment model, if a steady depolarizing current is applied or if
the conductance densities preclude a resting potential below spike threshold. You may
find some theoretical analyses informative--see
Ermentrout, B. Type I membranes, phase resetting curves, and synchrony.
Neural Computation 8:979-1001, 1966
Rinzel, J. and Ermentrout, G. B.
Analysis of neuronal excitability and oscillations.
Chapter 7 in Koch, C. and Segev, I., editors, Methods in neuronal modeling, 2nd edition,
MIT Press, Cambridge, MA 1998
http://www.math.pitt.edu/~bard/xpp/xpp.html
I don't think I can replace Gillies' Na and KDR mechanisms with standard hh mechanism due to their different formulation.
My model performs the desired behaviour with two different Na and K mechanisms Andrew's and hh.
Is it reasonable?
Who knows? Sometimes it seems that the definition of reasonable is "what you can
sneak past journal referees." By that standard, the answer is probably "no."
Is there a "cset" statement in NEURON
If you can't find something in the alphabetical index of the Programmer's Reference, try
this:
Start nrngui
At the oc> prompt type cset().
What do you see?
the same question about ion_style
Did you look in the alphabetical index for that?
http://www.neuron.yale.edu/neuron/stati ... index.html

GTR

Post by GTR »

Excuse me for the late reply and for not probably stating my problem correctly.

my STN network model produces rhythmic firing but with hh mechanism inserted in the soma section while Gillies-Willshaw STN projection neuron model performs the same behaviour with its own Na,KDR and Kv3.1(fast rectifier).
I am impressed because 'hh mechanism' made the same work for me as their own mechs did!
Many minimal spike mechanisms (fast, inactivating
inward current plus slower, delayed outward current) are capable of producing rhythmic
firing in a single compartment model, if a steady depolarizing current is applied or if
the conductance densities preclude a resting potential below spike threshold
In my case,I have a very excitatory neuron (subthalamic nucleus) that performs something remarkable (at least it is my view so) it produces rhythmic firing in its RS without external stimuli or synaptic events!

In his paper, Gillies attributes this behaviour to the presence of a persistent sodium channel that he has added to the neuron ,
so can I assume that the hh mechanism I applied plays also the role of this Na persistent that he uses?

So the STN neurons fall into this category-condition you are referring to about the conductance densities.Although they are 'below threshold value' they fire rhythmically!
But what's the point of speaking about threshold in a neuron which already produces spikes in its RS ?
What are the mechanisms that makes these "resting" channels produce spiking?Is it the levels of conductances that play role?

I find extremely interesting your citation for "analysis of neural excitability" as a senior applied mathematics undergraduate,
but as far as I know John Rinzel and Bard Ermentrout are more mathematical neuroscientists than computational so you suggest me to study firing and bursting activity from a dynamical perspective (with XPP).

By the way ,does computational neuroscience as a field include mathematical neuroscience?
I understand that there is an interplay between them,no doubt!
where are the boundaries of computational neuroscience and where these of mathematical?
Let's think about bursting for example, from what point of view does XPP deal with bursting and from what does NEURON?
To what deductions as a tool can the first package lead us and to what the second?
Judging from your experience as a computational neuroscientist,are there cases that these computational tools (like Neuron and Genesis ) fail and there is need for a more mathematical and dynamical analysis(XPP etc.)?

Sorry for the host of questions but I would like your view and also to become aware of the current trends underlying these two fields in the US.

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