unit of the recorded current measured at the soma

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manyi
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Joined: Mon Apr 02, 2012 6:48 am

unit of the recorded current measured at the soma

Post by manyi »

Hi! I want to fit some data from voltage clamp experiments. Now I have a multi-compartment model and use VClamp(0.5) as the stimulation. Somewhere in the mod files, ik is 'assigned'

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ASSIGNED {
        ik                              (mA/cm2)
...}
In my code,

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vector_current.record(&soma.ik(.5))
I got a reasonable trace of the recorded current, but what is the unit of the values in vector_current? Actually I expect to obtain something with current unit ampere, not per unit area, in order to compare the current that the soma electrode see in experiments. Am I doing it right? Many thanks!
ted
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Re: unit of the recorded current measured at the soma

Post by ted »

Suggest you read the FAQ entry What units does NEURON use for current, concentration, etc.?. There's a link to the FAQ list at NEURON's Documentation page http://www.neuron.yale.edu/neuron/docs.
manyi wrote:I want to fit some data from voltage clamp experiments. Now I have a multi-compartment model
Then your voltage clamp will only control membrane potential in the near vicinity of the clamp electrode, and the current that the clamp collects will be contaminated with cable charging artifact, and confounded by the facts that membrane is not isopotential, and the clamp won't be capturing all of the membrane current. But maybe you're not interested in the current recorded by the clamp.
and use VClamp(0.5)
Use SEClamp, not VClamp. See
What is the difference between SEClamp and VClamp, and which should I use?
in the FAQ list. This won't eliminate the problems related to the extended architecture of your model, but at least you won't be piling additional artifacts on top of others.
In my code,

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vector_current.record(&soma.ik(.5))
So you are recording the potassium current density associated with the node at the middle of soma--something that can't be done in real life. OK, that's one of the strengths of computational modeling.
I got a reasonable trace of the recorded current, but what is the unit of the values in vector_current?
mA/cm2, as you will discover from the first FAQ list item that I mentioned.
Actually I expect to obtain something with current unit ampere, not per unit area, in order to compare the current that the soma electrode see in experiments.
Sorry to dash your expectations, but
1. In real experiments, the clamp electrode will capture current from more than just the soma. As I pointed out above, experiments on cells with extended architectures produce "dirty" results because of cable filtering and imperfect space clamp.
2. In NEURON, transmembrane ionic currents have units of current density. From this I infer that there may be additional items that need clarification, so let me suggest that you read chapters 5 and 6 of The NEURON Book, or this article
Hines, M.L. and Carnevale, N.T.
The NEURON simulation environment.
Neural Computation 9:1179-1209, 1997
(available for download from http://www.neuron.yale.edu/neuron/nrnpubs)

The most convenient way to study a voltage gated channel in NEURON is to insert it into a single compartment model that has no other ionic currents, attach an SEClamp to the model, and record the SEClamp's i variable, which has units of nA. Also, set the SEClamp's rs (series resistance) parameter to a very small value, e.g. 1e-3. The current record will then have a brief brief capacitive artifact at every abrupt change of command potential, but it will be free of electrode series resistance artifact. Final tip: it is convenient to make the surface area of the model 100 um2, since this ensures that total current in nA is numerically equal to current density in mA/cm2.
manyi
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Re: unit of the recorded current measured at the soma

Post by manyi »

Thanks for the detailed reply. In fact, we already have a neuron model with topology reconstructed from experimental data, and want to further compare its neuronal dynamics with physiological data.

Adding only one channel and then recording the SEC i is not a good option as we want a realistic model with multiple channels and their interactions. We want the "dirty" current with all the artifacts of the experiment. Is it possible to get the current in nA of ion x at the soma with all accumulated artefacts of space clamp errors, like doing a real recording of what the electrode actually see?
ted
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Re: unit of the recorded current measured at the soma

Post by ted »

manyi wrote:we want a realistic model with multiple channels and their interactions
. . .
Is it possible to get the current in nA of ion x at the soma with all accumulated artefacts of space clamp errors, like doing a real recording of what the electrode actually see?
Given any patch of membrane, NEURON can tell you the current carried by any named ion through that patch of membrane. It is simply
secname.ina(x)
where
secname is the name of the section that contains the patch of membrane
x is the "range" that corresponds to the patch of membrane (the relative distance of the patch from the 0 end of secname).
The units of secname.ina(x) will be mA/cm2. To convert them to nA, multiply by the area of the patch in cm2.

Or are you asking for something else? The current recorded by a voltage clamp attached to the soma reflects contributions from all membrane currents throughout the entire cell, subject to filtering (signal loss) due to the properties of the membrane and cytoplasm that separates the clamp electrode from any given patch of membrane. Do you want to know what portion of that clamp current is attributable to sodium current throughout the cell? Is that what you're asking?
manyi
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Re: unit of the recorded current measured at the soma

Post by manyi »

The current recorded by a voltage clamp attached to the soma reflects contributions from all membrane currents throughout the entire cell, subject to filtering (signal loss) due to the properties of the membrane and cytoplasm that separates the clamp electrode from any given patch of membrane. Do you want to know what portion of that clamp current is attributable to sodium current throughout the cell? Is that what you're asking?
Yes! Do you have any reference or suggestion for me?
I am still wondering whether I shall use VClamp or SEClamp.
Shall I measure the current soma.i(0.5) or stim.i? (Here, stim is either VClamp or SEClamp)
In "Units used in NEURON", two units are used for current - [mA/cm2] (distributed) and [nA] (point process). How can I know what the unit is when I perform a current measurement?
ted
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Re: unit of the recorded current measured at the soma

Post by ted »

manyi wrote:
Do you want to know what portion of that clamp current is attributable to sodium current throughout the cell? Is that what you're asking?
Yes! Do you have any reference or suggestion for me?
Can't be done. Period. Not by NEURON, not by any pharmacological manipulation, not by any experimental or theoretical or computational approach.
manyi
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Re: unit of the recorded current measured at the soma

Post by manyi »

Let me clarify. We have some voltage clamp data in presence of step depolarizations and ion channel blockers. Our data are current recorded at the soma with unit Ampere. We have built a model using NEURON with topology and multiple ion channels.
Next goal: reproduce the experimental result in the NEURON model, and fit the channel parameters.

Can this be done?
ted
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Re: unit of the recorded current measured at the soma

Post by ted »

People do it all the time; you'll find many examples in NEURON's bibliography http://www.neuron.yale.edu/neuron/stati ... ednrn.html.
manyi
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Re: unit of the recorded current measured at the soma

Post by manyi »

Thanks for your patient reply. And we have further inquiries.

I think we understand different things by "... what portion of that clamp current is attributable to sodium current..."

I understand that in a typical experimental voltage-clamp characterization of an ion channel, the current is isolated by applying a specific drug and subtracting current post-drug from current pre-drug.

In an (slice) experiment you cannot block all ion channels of a neuron and record only one specific remaining ion channel (you may be able to record a subset of K+ currents, but it is not possible to really block all other conductances).

Therefore the difference between the model and the experiment is that you can insert only on ion channel in the model and read the variable i of a SEClamp object at the soma (in unit of nA, right?). Alternatively we can read the variable of any sub-compartment by e.g. soma.ix (in mA/cm2), which is also difficult experimentally (because the area is only determined with large errors).

Hence, to have a situation we can compare model to experiment, we would need to read the variable i of the SEClamp, but for selected ion
channel mechanisms (stim.ix). This is possible experimentally by drug-subtraction, is it really not possible in NEURON?
ted
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Re: unit of the recorded current measured at the soma

Post by ted »

manyi wrote:I think we understand different things by "... what portion of that clamp current is attributable to sodium current..."
I agree.
I understand that in a typical experimental voltage-clamp characterization of an ion channel, the current is isolated by applying a specific drug and subtracting current post-drug from current pre-drug.
And this assumes good space clamp.
In an (slice) experiment you cannot block all ion channels of a neuron and record only one specific remaining ion channel (you may be able to record a subset of K+ currents, but it is not possible to really block all other conductances).
True of any wet-lab (i.e. real) experiment.
Therefore the difference between the model and the experiment is that you can insert only on ion channel in the model and read the variable i of a SEClamp object at the soma (in unit of nA, right?).
That is a difference between what is possible in a computational experiment on a model and what is possible in a wet-lab experiment.
Alternatively we can read the variable of any sub-compartment by e.g. soma.ix (in mA/cm2), which is also difficult experimentally (because the area is only determined with large errors).
soma.ix would be the density of the current carried by the "x ion" in the compartment that contains the middle of the soma. For example, soma.ina would be the density of the transmembrane sodium current at the middle of the soma. This is discoverable in NEURON, but not in a real experiment unless na is the only charge carrier (and you'd still have to subtract the capacitive membrane current).
Hence, to have a situation we can compare model to experiment, we would need to read the variable i of the SEClamp, but for selected ion
channel mechanisms (stim.ix). This is possible experimentally by drug-subtraction, is it really not possible in NEURON?
The procedure would be identical for wet-lab or computational experiment:
Record clamp current under control condtions. Call this icontrol(t).
Record clamp current after blocking a particular ion channel. Call this itest(t).
Current attributable to the blocked ion channel is icontrol(t) - itest(t)
However, unless the cell is electrically compact, you have to be concerned about space clamp regardless of whether the experiment is computational or wet-lab.
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