pyramidal spine-neck EPSPs

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davidhubbardmd
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Re: pyramidal spine-neck EPSPs

Post by davidhubbardmd »

Thank you Ted. Wiley wants $59 for a copy of:

Selective activation of BK channels in small-headed dendritic spines suppresses excitatory postsynaptic potentials.
Tazerart S, Blanchard MG, Miranda-Rottmann S, Mitchell DE, Navea Pina B, Thomas CI, Kamasawa N, Araya R.
J Physiol. 2022 May;600(9):2165-2187. doi: 10.1113/JP282303. Epub 2022 Mar 9.
PMID: 35194785

Could you share your copy with me?
ted
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Re: pyramidal spine-neck EPSPs

Post by ted »

The senior author's lab has a web site at which you can request a copy--see https://www.arayalab.org/about-8
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Re: pyramidal spine-neck EPSPs

Post by davidhubbardmd »

thx, I got the preprint from the list of publications on the Araya lab website.
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Re: pyramidal spine-neck EPSPs

Post by davidhubbardmd »

I browsered modeldb.science/135787 :
Title:
Intracortical synaptic potential modulation by presynaptic somatic potential (Shu et al. 2006, 2007)
References:
Shu Y, Duque A, Yu YG, McCormick DA. Properties of action potential
initiation in neocortical pyramidal cells: evidence from whole cell
axon recordings. Journal of Neurophysiology. 97: 746-760, (2007).
Shu Y, Hasenstaub A, Duque A, Yu Y, McCormick DA (2006) Modulation of
intracortical synaptic potentials by presynaptic somatic membrane
potential. Nature 441: 761-765.
I opened the Files tab which showed many mod files including:
ca.mod, cad.mod. caL3d.mod, capump.mod
I clicked on only the ca.mod file, then the small gray download arrow and downloaded it directly into desktop/ted/initspineneckcalcium folder.
I browsered modeldb.science/3670
Title:
Thalamic Reticular Network (Destexhe et al 1994)
Reference:
Destexhe A, Contreras D, Sejnowski TJ, Steriade M. (1994). A model of spindle rhythmicity in the isolated thalamic reticular nucleus. J Neurophysiol 72 [PubMed]
I opened the Files tab which showed only one calcium mod file:
capump.mod
I clicked on capump.mod file, and as above put it in the initspineneckcalcium folder.
I confirmed that ca.mod and capump.mod were in the folder.
In the hoc file initspineneckcalcium I looked in vain for a statement that inserts the cad calcium accumulation mechanism (cad), so that I could insert a statement changing the depth parameter to diam/2. I wonder if I am missing an objref statement. I decide to wait for class to garner more details on how to change mod file parameters.
I left clicked on Windows Terminal
at prompt I typed cd initspineneckcalcium, then nrnivmodl, and got:
nrnmech.dll was built successfully.
PS C:\Users\david\Desktop\ted\initspineneckcalcium>
I double-clicked on the folder, then double-clicked on the GUI icon
The familiar graphs and windows opened.
In Biophysics I inserted ca and cad (I saw cad but not capump as Ted had warned me)
into both the spine_head (kopf) and spine_neck.
I made current graphs of cai for both the spine_head and the neck
I Init&Run’d it. I checked View = plot.

https://docs.google.com/document/d/1K-M ... sp=sharing

I expected a baseline calcium concentration of .5-1 x10-4 mM until the first synaptic transmission at 5 ms, then a rapid peak, possibly 10-100 times higher, then a plateau for the 4 synaptic transmissions in the spine_head (kopf), then a return to baseline.

Instead I got a reasonable starting concentration of 1x10-4, but then it decays to zero even before the synaptic transmissions begin.

I am doubtful my failure to change the depth parameter of the calcium accumulation on the inner membrane explains this finding. How much calcium ion is diffused out into the dendrite and how much is pumped out channels along the neck membrane is uncertain. My spine_neck diameter is 0.3 mm, default for the mechanism is 2 mm.

I tried adding an AMPA.mod and an NMDA.mod to the spine_head (kopf) in case the ExpSyn and NetStim mechanisms do not include the ion concentration changes in the standard glutamatergic synaptic transmission parameters. But that made no difference.
ted
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Re: pyramidal spine-neck EPSPs

Post by ted »

OK, this is where it starts to get complicated. If one starts building a model from scratch, one is responsible for all the decisions about the model's anatomical and biophysical properties. That includes, but is not limited to, what ion channels, buffers, pumps etc. it should include. AND the values of those mechanisms' parameters. And it also means justifying those decisions to skeptical reviewers (excuse the tautology). The alternative is to build on and/or borrow from something that already exists. The model by Tazerart et al. seemed like a good starting point. They didn't provide their own source code, but at least they said where they got key mechanisms: an HVA calcium channel (which generates a transmembrane calcium current), and a calcium accumulation mechanism (which deals with mass balance--i.e. relating intracellular calcium concentration to transmembrane calcium flux).

But few things are as simple as they may seem.

In Tazerart et al., the first paragraph under "Modeling" has a sentence that ends with " . . . Ca2+ buffering /removal [mechanism] (resting concentration of 1 nM; Destexhe et al. 1993) [was] inserted in the spine head." That would be a mechanism called cad, which is defined in the file capump.mod that I referred to in a previous post. But put that mechanism, and the HVA calcium channel model, with their default parameter values into a single compartment model cell that has diam = L = 10 um and a resting potential of -65 mV (a reasonable value), and run a simulation . . . and you'll see that cai starts out at 1e-4 mM ( = 0.1 uM = 100 nM), then plummets over the next 10 ms to about 1.4e-8 mM (0.014 pM), then slowly settles to 1.06e-12 mM (1.06 fM, but who's counting . . .) over the next few hundred ms.

So the model description in Tazerart et al. is not as complete as we would like. In their model, what were the values of the calcium channel and accumulation mechanisms' parameters? Did their model involve other calcium currents? And was the steady state value of cai really 1 pM? The usual estimate of resting cai in neurons, based on experimental observations, is about 100 nM. Would you like to contact them privately and gently ask these questions?

The alternative would be to tinker with one or more parameters with the aim of getting cai to rest at 1e-4 mM; my first guess would be to reduce cad's taur to something in the range of 1e2 to 1e3, but it would be better to find out exactly what Tazerart et al. did.
How much calcium ion is diffused out into the dendrite and how much is pumped out channels along the neck membrane is uncertain.
Good question, especially in a real cell. The cad mechanism does not include a representation of longitudinal diffusion, so all changes of cai are due to transmembrane fluxes.

An aside: longitudinal diffusion of calcium is often ignored in models that do not include "hot spots" (compact region in which cai is much higher than adjacent areas). The reason is that most models include the unspoken assumption that calcium channel density, membrane potential, and neurite diameter all change gradually with distance. Consequently the gating state of calcium channels will also vary gradually with distance, and so will v - eca (the driving force for calcium current), and so will the product
gca * (v - eca)
which of course is the formula for calcium current. So transmembrane calcium current is relatively uniform along the length of any branch, and if diameter is also relatively uniform, then the concentration of calcium will also be relatively uniform along any branch. Result: small longitudinal concentration gradient means little longitudinal diffusion of cai.

The one notable exception, of course, is the junction between a spine neck and its parent dendrite. The much smaller diameter of the neck means that, even if transmembrane ica is relatively uniform, cai in the spine neck will rise much more than it will in the dendritic shaft. So at some point it may be useful to represent longitudinal diffusion. But for now, it's best to KISS.
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Re: pyramidal spine-neck EPSPs

Post by davidhubbardmd »

Good plan. A good model of calcium in sensory spine_necks needs a good launch with a model that's recently published. I am reaching out to the team that created it.
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Re: pyramidal spine-neck EPSPs

Post by davidhubbardmd »

Thank you. I'm waiting to hear back from Dr. Tazerart.
ted
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Re: pyramidal spine-neck EPSPs

Post by ted »

The first author is not necessarily the "corresponding author" i.e. the one who takes primary responsibility for communications. Depending on the journal, the corresponding author's identity is usually indicated at the beginning of the paper e.g. near the author list or Abstract, or at the end of the paper e.g. just before or after the References section, or in the "Author contributions" or "Acknowledgements" sections etc.. This paper has a "Data availability statement" right after the References which says "All primary data reported here are available upon reasonable request to the corresponding author (R.A.).". Presumably "primary data" includes the source code for the model, with the parameter values that were used to generate the published results.

By the way, Journal of Physiology (which published this article) has specific policies about papers that report work done with models. Quoting from their "Information for Authors" document at https://jp.msubmit.net/cgi-bin/main.ple ... quirements:
The model should be described in such a way that the results can be reproduced, i.e. all parameters are listed and any computation codes made available.
As it stands, the modeling results published by Tazerart et al. cannot be reproduced, and all parameters were not listed (not surprising--most journals don't like to print detailed parameter lists for reasons that include space limitations; even when such lists are published, they are often incomplete and/or contain typographical errors). The work reported in this paper was probably completed in 2020 or maybe early 2021. Let us hope that the authors can still find the code that was actually used, with the parameters that generated the reported results, and that any necessary usage instructions are included.
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Re: pyramidal spine-neck EPSPs

Post by ted »

Aha--Araya's lab just published another article that combines experimentation with modeling that involved the same model cell, so it is quite likely that they will be able to find the source code.

Mitchell DE, Miranda-Rottmann S, Blanchard M, Araya R.
Altered integration of excitatory inputs onto the basal dendrites of layer 5 pyramidal neurons in a mouse model of Fragile X syndrome.
Proc Natl Acad Sci U S A. 2023 Jan 10;120(2):e2208963120. doi: 10.1073/pnas.2208963120. Epub 2023 Jan 3.
PMID: 36595706; PMCID: PMC9926222.

Here's the preprint https://www.biorxiv.org/content/10.1101 ... 1.full.pdf
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Re: pyramidal spine-neck EPSPs

Post by davidhubbardmd »

Sensory Spine model-Araya
Mitchell et al 2023, and Tazerart et al 2022 (referenced in link) describe the following mechanisms and parameters:
spine-neck length 1 um.
spine axial resistance, neck, head 500, 150 MΩ.
spine-head volume 0.18 um3. V = ℼ* D3/6 diam = 0.7 um
connected to basilar dendrite 170 um from soma
channels in spine head:
AMPA. Already in my spine head
NMDA. Already in my spine head
HVA (voltage gated calcium channel modeldb 135787). Already in my head and neck.
Nav1.6 sodium channel (3 S/cm2). Since this is the standard sodium ch., I didn’t add an extra one.
Calcium buffering mechanism (Destexhe ‘93, capump.mod, cad). Already added as a distributed mechanism.
BK calcium activated K+ influx. I believe this is included in the Destexhe module.
Stimulation: Polsky et al (2009) modified the glutamate synapse to obtain AMPA and NMDA conductances of 10 nS and 0.086 nS, respectively. This is a study of NMDA spikes using their own parameters, which I did not incorporate.
I did not find any parameters or mechanisms to add or change.
Last edited by davidhubbardmd on Wed Apr 12, 2023 9:32 am, edited 1 time in total.
ted
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Re: pyramidal spine-neck EPSPs

Post by ted »

I did not find any parameters or mechanisms to add or change.
That's why you need to see the actual source code that those authors used in their simulations. Where did the first figure in your most recent Forum post come from? A simulation on your PC or Mac? If yes, then what you're looking at shows you can't replicate their results. What is that evidence? First and foremost, cai (intracellular calcium concentration) was clearly not initialized to steady state. It starts at 100 nM and then rapidly plummets to a much lower concentration, even before the model's synapse was activated. And it settles to a level that is many orders of magnitude smaller what the models' authors report as steady state cai in their simulations. That's a big problem. Either their reported results are incorrect, or the model code that was executed to generate your first figure is using the wrong mechanisms and/or the wrong parameters. And if their papers don't provide the numerical values of the parameters that govern cai, then you need to see the source code that they actually used to generate their results. Or you could spend your time playing around with your own model while you try to guess what the parameter values should be, with no guarantee of outcome.

Of course there's also another issue: your first figure shows that none of the excitatory synaptic events has a visible effect on cai. Maybe the epsp isn't big enough to open the ca channels in the spine neck or head, but resolving that issue should wait until the first problem has been resolved.
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Re: pyramidal spine-neck EPSPs

Post by davidhubbardmd »

Just to be sure, I ran a longer train of synaptic transmissions
https://docs.google.com/document/d/1Iu9 ... sp=sharing
But I still got no response in the intracellular calcium concentration.
I wonder if I need voltage-gated calcium channels distributed in the head and neck. I also haven’t varied the dendrite or calcium pump parameters. I emailed both first authors and the corresponding author/lab director. I look forward to their input.
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Re: pyramidal spine-neck EPSPs

Post by ted »

You are experiencing why "available upon reasonable request" is no substitute for requiring model authors to make source code available through a publically accessible online resource, in close temporal proximity to the date of acceptance for publication.
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Re: pyramidal spine-neck EPSPs

Post by davidhubbardmd »

I am looking forward to the research group’s input on their model.
In the meantime, I note another group has reported that a single action potential generates a calcium influx into the spine of about 20 uM,
Higley, M. J., & Sabatini, B. L. (2008). Calcium signaling in dendrites and spines: practical and functional considerations. Neuron, 59(6), 902-913.
Another paper by this group, Compartmentalization of GABAergic inhibition by dendritic spines (Chiu et al Science. 2013) included their NEURON model in the Method section which unfortunately was in the supplemental material I was unable to download. I will initiate a request.
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Re: pyramidal spine-neck EPSPs

Post by ted »

The source code for Chiu et al is in ModelDB. Search for Chiu or, if that generates too many hits, Higley.

Note that two of the co-authors are involved with ModelDB's development. We eat our own dog food.
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