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Readme.htm
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<html xmlns:v="urn:schemas-microsoft-com:vml"
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<title>Spiral Ganglion Cell Type-2 Model</title>
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<o:Author>Srdjan Antic</o:Author>
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<o:LastPrinted>2004-12-22T14:10:00Z</o:LastPrinted>
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<div class=Section1>
<p class=MsoNormal>Spiral Ganglion Cell Type-2 Model (<b style='mso-bidi-font-weight:
normal'>Hossain et al., 2005</b>)</p>
<p class=MsoNormal>Author: Srdjan Antic, University Connecticut Health Center, 22-DEC-2004</p>
<p class=MsoNormal><![if !supportEmptyParas]> <![endif]><o:p></o:p></p>
<p class=MsoNormal><u>Instructions for those who had no previous experience
with NEURON!<o:p></o:p></u></p>
<p class=MsoNormal><![if !supportEmptyParas]> <![endif]><o:p></o:p></p>
<p class=MsoNormal>To run the model described in <b style='mso-bidi-font-weight:
normal'><i style='mso-bidi-font-style:normal'>Hossain et al., 2005</i></b>:</p>
<p class=MsoNormal><![if !supportEmptyParas]> <![endif]><o:p></o:p></p>
<ol style='margin-top:0in' start=1 type=1>
<li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list .5in'>Install
NEURON from http://www.neuron.yale.edu/neuron/</li>
<li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list .5in'>Make a
new folder and copy all "<b style='mso-bidi-font-weight:normal'><i
style='mso-bidi-font-style:normal'>Hossain et al., 2005</i></b>" files to it.</li>
<li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list .5in'>Run "<b
style='mso-bidi-font-weight:normal'>mknrndll</b>" to compile "mod" files
in that new folder.</li>
<li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list .5in'>Once
the compiler is finished, go to the folder and double click "mosinit.hoc".</li>
<li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list .5in'>From
the Neuron Main Menu use File --> Load Session.</li>
<li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list .5in'>Pick
any session from the list. The names of the sessions correspond with the
figure panels in Hossain et al., 2005.</li>
<li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list .5in'>For
instance take session "Fig7A".</li>
<li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list .5in'><span
style="mso-spacerun: yes"></span>Once the session is loaded you will see
the following windows:</li>
</ol>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l0 level2 lfo1;
tab-stops:list 1.0in'><![if !supportLists]>a)<span style='font:7.0pt "Times New Roman"'>
</span><![endif]>Neuron Main Menu</p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l0 level2 lfo1;
tab-stops:list 1.0in'><![if !supportLists]>b)<span style='font:7.0pt "Times New Roman"'>
</span><![endif]>4 Voltage-Axis graphs (Graph[1] to Graph[4])</p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l0 level2 lfo1;
tab-stops:list 1.0in'><![if !supportLists]>c)<span style='font:7.0pt "Times New Roman"'>
</span><![endif]>RunControl</p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l0 level2 lfo1;
tab-stops:list 1.0in'><![if !supportLists]>d)<span style='font:7.0pt "Times New Roman"'>
</span><![endif]>PointProcessManager</p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l0 level2 lfo1;
tab-stops:list 1.0in'><![if !supportLists]>e)<span style='font:7.0pt "Times New Roman"'>
</span><![endif]>Temperature</p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l0 level2 lfo1;
tab-stops:list 1.0in'><![if !supportLists]>f)<span style='font:7.0pt "Times New Roman"'>
</span><![endif]>Global Ra,<span style="mso-spacerun: yes"></span><span
style='mso-tab-count:1'></span><i style='mso-bidi-font-style:normal'>and</i></p>
<p class=MsoNormal style='margin-left:1.0in;text-indent:-.25in;mso-list:l0 level2 lfo1;
tab-stops:list 1.0in'><![if !supportLists]>g)<span style='font:7.0pt "Times New Roman"'>
</span><![endif]>Cell Builder (CellBuild[0]</p>
<ol style='margin-top:0in' start=9 type=1>
<li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list .5in'>In the
"RunControl" window click "Init & Run" button.</li>
<li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list .5in'>Graph[3]
shows the membrane potential transients obtained in the receptor-neural
segment (Receptor[5].v(0.5)) and in the cell body (soma). We are now at
"the lower limit of the sensitive range". Both initial segments (ISP and
ISC) are supplied with sodium channels, just enough to pass an action potential
from the peripheral to the central axon via the cell body. To check the
actual density of hh sodium channels, go to CellBuild[0]<span
style="mso-spacerun: yes"></span> window <span style='font-family:Wingdings;
mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
mso-char-type:symbol;mso-symbol-font-family:Wingdings'><span
style='mso-char-type:symbol;mso-symbol-font-family:Wingdings'></span></span>
Biophysics <span style='font-family:Wingdings;mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
Wingdings'><span style='mso-char-type:symbol;mso-symbol-font-family:Wingdings'></span></span>
Init_Seg_Per.</li>
<li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list .5in'>In the
Cell Builder Change gNabar_hh from 929 to 928 in both, <b
style='mso-bidi-font-weight:normal'>Init_Seg_Per </b>(initial segment of
the peripheral axon) and <b style='mso-bidi-font-weight:normal'>Init_Seg_Cen
</b>(initial segment of the central axon).</li>
<li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list .5in'>Run
the simulation again (in "RunControl" window click "Init & Run" button).</li>
<li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list .5in'>Action
potential (AP) now fails to invade the cell body. The only difference
between this and previous trial is the removal of 1 pS/um2 from both
initial segments.</li>
<li class=MsoNormal style='mso-list:l0 level1 lfo1;tab-stops:list .5in'>To
create the graph in Figure 7, panel C you need to find the "lower limits
of the sensitive range" using four different channel mechanisms. Each bar
in the histogram is represented by a session file starting with "<i
style='mso-bidi-font-style:normal'>Fig7C-</i>". If you load any of the
session files starting with "<i style='mso-bidi-font-style:normal'>Fig7C-</i>"
and then decrease the sodium conductance by only 1 pS/um2 from any initial
segment, the AP would fail to invade the cell body. Note that the session
"Fig7C-hh-black_bar.ses" is missing. This session file is identical to
"Fig7A.ses", and therefore is omitted from the download.</li>
</ol>
<p class=MsoNormal style='margin-left:.25in'><![if !supportEmptyParas]> <![endif]><o:p></o:p></p>
<p class=MsoNormal style='margin-left:.25in'>>>the end<<</p>
<p class=MsoNormal style='margin-left:.25in'><![if !supportEmptyParas]> <![endif]><o:p></o:p></p>
</div>
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