GitHub - ModelDBRepository/232813: Zebrafish Mauthner-cell model (Watanabe et al 2017)

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Name		Name	Last commit message	Last commit date
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IClamp2.mod		IClamp2.mod
IClamp500.mod		IClamp500.mod
Readme.html		Readme.html
channel analysis.hoc		channel analysis.hoc
channel generator.hoc		channel generator.hoc
firing analysis.hoc		firing analysis.hoc
firing simulator.hoc		firing simulator.hoc
graphs panels.hoc		graphs panels.hoc
ka.mod		ka.mod
kcna.mod		kcna.mod
kcnab2.mod		kcnab2.mod
kcnq.mod		kcnq.mod
kht.mod		kht.mod
leak.mod		leak.mod
mosinit.hoc		mosinit.hoc
na.mod		na.mod
neuron.hoc		neuron.hoc
parameters.hoc		parameters.hoc
screenshot.png		screenshot.png
screenshot0.png		screenshot0.png

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<p>NEURON model files derived from the paper:
</p><p>Takaki Watanabe, Takashi Shimazaki, Yoichi Oda (2017).
Coordinated expression of two types of low-threshold K+ channels establishes
unique single-spiking of Mauthner cells among segmentally homologous neurons
in the zebrafish hindbrain.<br/>
eNeuro 4 October 2017,ENEURO.0249-17.2017; DOI: <a href="https://doi.org/10.1523/ENEURO.0249-17.2017">https://doi.org/10.1523/ENEURO.0249-17.2017</a>  
</p><p>The NEURON model files encode the channel generator and firing simulator for simulating
development and differentiation of the Mauthner cell (M-cell) excitability.
The channel generator consists of "channel generator.hoc" and "channel analysis.hoc",
which enable us to generate arbitrary Na+ and K+ channels by changing parameters of 
a Hodgkin-Huxley model under emulation of two-electrode voltage-clamp recordings
in Xenopus oocyte system for Figure 5. The code and equations of a Hodgkin-Huxley model are
modified from the simulation by Rothman and Manis, 2003.
</p><p>The firing simulator comprising "firing simulator.hoc", "firing analysis.hoc", "graphs panels.hoc",
"neuron.hoc" and "parameters,hoc" simulates current-clamp recordings in the M-cell to
generate firing pattern of the model M-cell, which are implemented with arbitrary determined
basic Na+ and K+ conductances and low-threshold K+ channels Kv7.4/KCNQ4, Kv1.1 or
Kv1.1 coexpressed with Kvbeta2. Default setting is step current injection for 100 ms with 
1pA increment from near threshold current. The Na+ and K+ conductance and current dynamics are
visualized during firing. Threshold current (1T), 1st action potential latency,
number of action potentials at 1.5T and 2T, and interspike interval ratio (ISI(last)/ISI(1st))
at 2T are measured and printed. Run(step) and Run(500Hz) buttons execute firing simulation
showing results for Figures 6, 7, 8 and for Figure 9, respectively.
</p><p>The following .mod files are implemented in a single cylindrical compartment.
<p/>IClamp2.mod:Step  current injection for current-clamp recoding.
<p/>IClamp500.mod:500  Hz current injection for current-clamp recoding.
<p/>kcnq.mod: a low-threshold K+ channel Kv7.4/KCNQ4 encoded in zebrafish kcnq4.
<p/>kcna.mod: a low-threshold K+ channel Kv1.1 encoded in zebrafish kcna1a.
<p/>kcnab2.mod: a low-threshold K+ channel Kv1.1 coexpressed with zebrafish Kvbeta2b subunit.
<p/>kht.mod: a high-threshold voltage-gated K+ channel.
<p/>ka.mod: an A-type voltage-gated K+ channel.
<p/>na.mod: a voltage-gated Na+ channel.
<p/>leak.mod: a leak (passive) channel.
</p>
Example run:
<p/>
Auto-launch from modeldb or download and extract the mod files and start with a command like:
<p/>
nrngui mosinit.hoc
<p/>
If you need more help in starting the model on your platform please consult this web page:
<p/>
<a href="https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.cshtml">https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.cshtml</a>
<p/>
You will see several windows appear, including one that looks like:
<p/>
<img src="./screenshot0.png" width="650" alt="Firing simulator">
<p/>
Clicking on the Run(Step), Fig 6,8 button will show a figure containing some in figure 6 in the paper:
<p/>
<img src="./screenshot.png" width="550" alt="screenshot">

<p>Takaki Watanabe<br/>
<a href="mailto:wtakaki@m.u-tokyo.ac.jp">wtakaki@m.u-tokyo.ac.jp</a>

</p>

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