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Find ion channels that relate to motor neurons AS01, AS02, DA01, DA02, DB01, DD01, SMDDL, SMDDR #31

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Interintel opened this Issue Jan 9, 2013 · 15 comments

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Interintel commented Jan 9, 2013

Define the specific types of Ion Channels and how they work within the cell.

Here's a powerpoint presentation that explains what ion channels are and some of the math behind simulating them.

Here's a book explaining what ion channels are, and how they relate to neurons.

This spreadsheet contains a very early documenting of ion channels in muscle cells, but begins to lay out the way in which we should start describing them.

Gene expression patterns that can be used to infer the location of ion channels are in another sheet in that same spreadsheet.

Here's a list of neurotransmitter receptors and what neurotransmitters they receive.

A wealth of neurotransmitter receptors are described on [https://docs.google.com/spreadsheet/ccc?key=0ArNOKkIblIRadE5lVkN4WGMzNUZLdVROUEZVTUlUVGc#gid=0](this spreadsheet), maintained by Z.F. Altun.

Textpresso for c elegans provides full text search of c. elegans journal articles and can be used to find papers that talk about specific ion channel types.

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slarson commented May 11, 2013

including @Crystinjoni on this.

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slarson commented Sep 28, 2013

Updated this with a bunch of links to resources

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slarson commented Sep 30, 2013

@Neurophile thought I'd add this comment here and make you a watcher on this. Cheers!

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slarson commented Oct 20, 2013

@ArjunSub check this out

@Interintel Interintel removed their assignment Mar 5, 2014

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slarson commented Mar 5, 2014

@VahidGh has been helping out with this. The ion channels spreadsheet is moving again.

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slarson commented Jan 10, 2015

@Linuxese --thanks for agreeing to look into c. elegans RNASeq data. We also talked about looking into c. elegans ion channel mutants -- maybe we can try this as a next step. Could you update us here on any progress that you make?

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slarson commented Jan 10, 2015

@VahidGh is working on the following:

Right now, I'm working on studies related to ion channels underlying current in NMJ, studies are more related to body wall muscle than motor neurons.
In brief, important genes from the spread sheet are: egl-19, SHK-1, SLO-1, SHL-1, and CCA-1, and UNC-36 in muscle cells, and UNC-2, SLO-1, SLO-2, and SHK-1 for motor neurons.
(I'm working on a document with detailed info and refs)

@slarson slarson changed the title from Document Neuron Ion Channels: Types to Find ion channels that relate to motor neurons AS01, AS02, DA01, DA02, DB01, DD01, SMDDL, SMDDR Jan 10, 2015

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slarson commented Jan 10, 2015

Adding my update I typed up earlier:

As many channels as we can infer that are in the motor neurons (AS01, AS02, DA01, DA02, DB01, DD01, SMDDL, SMDDR), models for the synapses between these and our muscle cell, and the muscle cell itself. So @ahrasheed -- your efforts to get the motor neurons LEMS files generated then creates a rallying point for these ion channels to be attached. @VahidGh and @wilzh40 if we can start sorting the ion channel spreadsheet for those ion channels that either reference those neurons by name or has the word "motor" or possibly "ventral cord" or "dorsal cord" neurons since those neurons go through there, then we can start to build up a better list of ion channels to pursue. Make sense, all?

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slarson commented Jan 10, 2015

I've added columns L-T to the spreadsheet to sort out specifically which ion channels we can infer are in which cells. If I've marked YES, the cell has been called out by name in a specific paper as having that ion channel expressed. In the case of the body wall muscle cell, I don't use the standard of called out by name for a YES, instead just if it says it is expressed in "body wall muscle" without qualifications. If I've marked Maybe, the cell is called out as being a member of either the ventral cord neurons or the ring neurons. If I've marked Maybe-weak, it is a member of the class but someone said expression was weak.

Here are the ion channels of most interest for the motor neurons (marked YES for at least some):

LGC-46, TRP-1, LGC-55, GLR-1, UNC-8, ACC-4

Next priority, those marked Maybe or Maybe-Weak for at least some:

CLH-2, SLO-1, SLO-2, UNC-36, SHL-1, TWK-20, CCA-1, AVR-14, EGL-2, EXP-2, GLC-3, GLC-4, TAX-4, AVR-15, KVS-1, MOD-1

Although the spreadsheet was focused on looking for ion channels for neurons, not muscles, the following came out as YES for body wall muscle:

CLH-2, SLO-1, SLO-2, UNC-36, LGC-46, SHL-1, SUP-9, SHK-1, LGC-34

and these as Maybe for body wall muscle:

TWK-20, CCA-1, DEG-1

@slarson slarson added the in progress label Jan 10, 2015

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VahidGh commented Jan 12, 2015

@slarson, according to this new study, this is the only study with voltage/current clamp data available for motor neurons (the study is based-on VA5, VB6 and VD5 motor neurons):

  • "To our knowledge, there has been no report on whole-cell voltage- and current-clamp recordings from C. elegans motor neurons. In the present study, we successfully performed electrophysiological recordings of motor neurons, and combined the electrophysiological data with PSCs recorded from body-wall muscle cells to assess physiological roles of SLO-2 in motor neurons. Our results suggest that SLO-2 is a major contributor to delayed outward current in motor neurons with its activity dependent on Ca2+ entry through a L-type voltage-gated Ca2+ channel (VGCC), and that SLO-2 controls the strength of synaptic transmission by regulating the duration and charge transfer rate of PSC bursts, which are used by motor neurons to control body-wall muscle."
  • "Observations suggest that delayed outward current of VA5 and VB6 results primarily from SLO-2 with a small contribution from an unidentified channel(s), whereas that of VD5 results almost completely from SHK-1 and SLO-2"
  • "While SLO-1 is localized at the presynaptic site and is likely regulated by Ca2+ entry through UNC-2, which is also localized at the presynaptic site, SLO-2 might be localized to other subcellular domains and coupled to Ca2+ entry through EGL-19."

going to start modeling the above ion channels...

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slarson commented Jan 18, 2015

@VahidGh This is a great find! It looks like the Wang Lab has many relevant publications for us.

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VahidGh commented Jan 18, 2015

@slarson, unfortunately, the paper is more focused on the genetic part and lacking data related to their patch clamp experiment.
It would be great if we could have their raw data.

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slarson commented Jan 18, 2015

What about the I/V curves in Figures 1 & 5. What additional data would we
want? We can always email the authors, but we should figure out
specifically what we would want.

On Sun, Jan 18, 2015 at 10:15 AM, Vahid Ghayoomi notifications@github.com
wrote:

@slarson https://github.com/slarson, unfortunately, the paper is more
focused on the genetic part and lacking data related to their patch clamp
experiment.
It would be great if we could have their raw data.


Reply to this email directly or view it on GitHub
#31 (comment).

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VahidGh commented Jan 18, 2015

yes, but it's not enough for the fitting (especially activation/inactivation expressions).
according to the paper: "Current- and voltage-clamp experiments were performed with a Multiclamp 700B amplifier (Molecular Devices, Sunnyvale, CA, USA) and the Clampex software (version 10, Molecular Devices)."
So if we could have Axon abf/atf files, we could simulate and analyze the experiment more accurate and easier.

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slarson commented Jun 7, 2016

This effort has spun off into the https://github.com/openworm/channelworm repository

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