Team:Tsinghua/Modeling

From 2014.igem.org

(Difference between revisions)
(Prototype team page)
Line 1: Line 1:
-
<!-- *** What falls between these lines is the Alert Box!  You can remove it from your pages once you have read and understood the alert *** -->
 
-
 
-
 
-
{{CSS/Main}}
 
-
 
<html>
<html>
 +
<body>
 +
<div class="container">
 +
  <header><img src="https://static.igem.org/mediawiki/2014/7/7a/Tsinghua_Header_1.png" width="975" height="119" alt="" usemap="#bannermap"/></header>
 +
  <div class="sidebar1">
 +
<map name="bannermap">
 +
<area shape="rect" coords="40,20,270,100" href="https://2014.igem.org/Team:Tsinghua/Main_page" alt="Team Tsinghua 2014">
 +
<area shape="rect" coords="860,25,950,100" href="https://2014.igem.org/Main_Page" alt="Return to iGEM 2014">
 +
</map>
 +
 +
<div id="sidebarfiller"></div>
 +
  <nav>
 +
    <ul>
 +
      <li><a href="https://2014.igem.org/Team:Tsinghua/Main_page">MAIN PAGE</a></li>
 +
 +
      <li><a href="https://2014.igem.org/Team:Tsinghua/Introduction">INTRODUCTION</a>
 +
<ul>
 +
          <li><a href="https://2014.igem.org/Team:Tsinghua/Introduction">Overview</a></li>     
 +
          <li><a href="https://2014.igem.org/Team:Tsinghua/Introduction/Diabetes">Diabetes Type I</a></li>
 +
          <li><a href="https://2014.igem.org/Team:Tsinghua/Introduction/Gene_therapy">Gene Therapy</a></li>
 +
      </ul>       
 +
      </li>
 +
 +
      <li><a href="https://2014.igem.org/Team:Tsinghua/Project">PROJECT</a>
 +
<ul>
 +
<li><a href="https://2014.igem.org/Team:Tsinghua/Project">Overview</a></li>     
 +
<li><a href="https://2014.igem.org/Team:Tsinghua/Project/Virus">The Virus</a></li>     
 +
<li><a href="https://2014.igem.org/Team:Tsinghua/Project/Drug">The Drug</a></li>
 +
<li><a href="https://2014.igem.org/Team:Tsinghua/Project/Microbe">The Microbe</a></li>
 +
<li><a href="https://2014.igem.org/Team:Tsinghua/Project/Cocktail">The Cocktail</a></li>
 +
</ul>
 +
      </li>
 +
 +
      <li><a href="https://2014.igem.org/Team:Tsinghua/Modeling">Modeling</a></li>
 +
 +
      <li><a href="https://2014.igem.org/Team:Tsinghua/Parts">Parts</a></li>
 +
 +
      <li><a href="https://2014.igem.org/Team:Tsinghua/Safety">SAFETY</a></li>
 +
 +
      <li><a href="https://2014.igem.org/Team:Tsinghua/Notebook">NOTEBOOK</a>
 +
<ul>
 +
        <li><a href="https://2014.igem.org/Team:Tsinghua/Notebook">OVERVIEW</a></li>
 +
        <li><a href="https://2014.igem.org/Team:Tsinghua/Notebook/Protocol">PROTOCOL</a></li>
 +
        <li><a href="https://2014.igem.org/Team:Tsinghua/Notebook/Lablog">LABLOG</a></li>
 +
      </ul>
 +
      </li> 
 +
 +
      <li><a href="https://2014.igem.org/Team:Tsinghua/Human_practice">HUMAN PRACTICE</a>
 +
<ul>
 +
  <li><a href="https://2014.igem.org/Team:Tsinghua/Human_practice">OVERVIEW</a></li>
 +
          <li><a href="https://2014.igem.org/Team:Tsinghua/Human_practice/Gallery">GALLERY</a></li>
 +
          <li><a href="https://2014.igem.org/Team:Tsinghua/Human_practice/Outreach">OUTREACH</a></li>
 +
          <li><a href="https://2014.igem.org/Team:Tsinghua/Human_practice/Video">VIDEO</a></li>         
 +
      </ul>     
 +
      </li>
 +
 +
      <li><a href="https://2014.igem.org/Team:Tsinghua/Team">TEAM</a></li>
 +
 +
    </ul>
 +
  </nav>
 +
<aside style="height: 3300px;"></aside>
 +
  <!-- end .sidebar1 --></div>
 +
 +
  <article class="content">
 +
    <h1>Modeling: Insulin Secretion</h1>
 +
<section>
 +
<h2>Abstract</h2>
 +
<p>In this model, we simulate the insulin  secretion behavior of pancreatic β cells, trying to realize the similar curve in a single β cell, as  that of glucose-insulin secretion which has been shown in literature, according  to the reported insulin secretion mechanisms.</p>
 +
            <p>In general, we divide the process from  glucose sensation to insulin secretion into three sessions. The first session  covers the metabolic process from glucose intake to production of ATP. The  second session covers the behavior of ion channels after the change in [ATP]/[ADP] ratio. The last session depicts the insulin secretion activated by  cellular [Ca<sup>2+</sup>] rise.</p>
 +
            <p>This single-cell model is key to the overall insulin secretion curve due to the synchronization of the cells in the  same pancreas islet.</p>
 +
        </section>
 +
<section>
 +
<h2>Introduction</h2>
 +
<p>In physiology, the secretion of insulin is  tightly regulated. After food intake and rising of blood glucose concentration, insulin is quickly secreted to down tune the blood glucose. Lack of insulin as  well as its overproduction causes harm to human bodies. Thus it is really a  need to determine the physiological parameters during insulin secretion. Of the  first priority is the [glucose]-insulin secretion curve.</p>
 +
<p><img class="center" src="https://static.igem.org/mediawiki/2014/c/c1/Tsinghua_Modeling_Image002.jpg" /></p>
 +
</section>
 +
<section>
 +
<h2>Task Analysis</h2>
 +
<p>Our model is in fact a time-amount model addressing the total insulin secretion amount with time under given glucose concentration. </p>
 +
<p>The secretion of insulin is considered as the result of a series of regulation, which includes acceleration of metabolism, opening of ATP-sensitive K<sup>+</sup> channel, depolarization of membrane, influx of Ca<sup>2+</sup>, etc. While this is not the whole picture, there is another pathway leading to the secretion of insulin, as is shown in the graph above, but due to its complexity and lack of studies, we focus on the major and clearer part of the pathway.</p>
 +
<p>There are two phases of insulin secretion. First of them comes from the drastic reaction to glucose of β cells in all islets, and the second comes from the difference of secretion paces of different islets.</p>
 +
<p>The main events are shown in the following chart:</p>
 +
<p class="center">[Glc] rising &#8594; [ATP]/[ADP] change &#8594; K<sub>ATP</sub> Ch closure</p>
 +
<p class="center">&#8594; Ca<sup>2+</sup> Ch opening &#8594; [Ca<sup>2+</sup>]<sub>c</sub> rising &#8594; insulin secretion</p>
 +
<p>As the insulin secretion-[Ca<sup>2+</sup>] is quite expectable, we focus mainly on the [Ca<sup>2+</sup>]-time curve.</p>
 +
</section>
 +
<section>
 +
<h2>Modeling</h2>
 +
<p>We make the following assumptions:</p>
 +
<ol type="1">
 +
<li>The reactions in metabolic process obey the M-M equations;</li>
 +
<li>There is a time interval between [ATP[/[ADP] ratio reaches the threshold and closure of K+ ch;</li>
 +
<li>The infux of Ca2+ is only subject to the chemical and electrical gradient, and cellular retrieval of Ca2+ is constant.</li>
 +
</ol>
 +
<h3>Stage I</h3>
 +
<div class="indent">
 +
<p>Michaelis-Menten equation:</p>
 +
<p>Normally [ATP]/[ADP]= x<sub>0</sub> (during fast)</p>
 +
<p class="center">X<sub>1</sub>(t) = <img src="https://static.igem.org/mediawiki/2014/1/1a/Tsinghua_ModelImage003.png" /></p>
 +
<p>Where δx(t) = <img src="https://static.igem.org/mediawiki/2014/c/c6/Tsinghua_ModelImage007.png" /> ∈(0,1), p is the concentration of ATP, and [G] is that of the glucose.</p>
 +
<p>We assume that under discrete time intervals reactions conduct in packet <img class="vcenter" src="https://static.igem.org/mediawiki/2014/6/64/Tsinghua_ModelImage009.png" />.</p>
 +
</div>
 +
<h3>Stage II</h3>
 +
<div class="indent">
 +
<p>K<sup>+</sup> Channel opening state:</p>
 +
<p class="center">K(t) = <img src="https://static.igem.org/mediawiki/2014/9/9b/Tsinghua_ModelImage011.png" /></p>
 +
<p>K(t) limiting conditions:</p>
 +
<span class="center">
 +
<p>K(0) = 0;</p>
 +
<p>K(t) = 1, when X1(t) ≥ Ra;</p>
 +
<p>K(t) = 0, when X1(t) ≤ Ra;</p>
 +
<span>
 +
<p>Amount of imported Ca<sup>2+</sup>:</p>
 +
<p class="center"><img src="https://static.igem.org/mediawiki/2014/4/4a/Tsinghua_ModelImage017.png" /></p>
 +
<p>Suppose the intracellular Ca2+ concentration is:</p>
 +
<p class="center"><img src="https://static.igem.org/mediawiki/2014/6/61/Tsinghua_ModelImage019.png" />&nbsp;&nbsp;&nbsp;&nbsp;(*)</p>
 +
<p class="center">Note 1 for the successful application of iteration, we introduce F(t) and C(t) with relationship as:</p>
 +
<p class="center">F(i) = exp(-c1)*(F(i-1)-1) + 1;</p>
 +
<p class="center">C(i) = c*(F(i) - F(i-1)) - c2 + C(i-1);</p>
 +
<p>These two functions in fact realize the behavior of the above C(t). </p>
 +
<p>Note 2 we assume that there should be a time period after [ATP]/[ADP] reaches the threshold before the K+ channel closes, resulting in a time delay:</p>
 +
<div style="text-indent: 150px; line-height: 10px;">
 +
<p>if i > 150</p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;for j = 1:150</p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;if K(i-j) == 1</p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;q = 1;</p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;end</p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;end</p>
 +
<p>end</p>
 +
</div>
 +
<h3>Stage III: Ca<sup>2+</sup>-induced insulin secretion</h3>
 +
<p>With the increase in cellular [Ca2+] concentration, insulin secretion comes into a steady state concerned with [Ca2+] after an intense release.</p>
 +
<p class="center">I(t) = <img src="https://static.igem.org/mediawiki/2014/5/56/Tsinghua_ModelImage021.png" /></p>
 +
<p>Thus we are able to get an insulin secretion curve.</p>
 +
</div>
 +
</section>
 +
<section>
 +
<h2>Results and Analysis</h2>
 +
<p>Our program gives the following [Ca2+]-t graph:</p>
 +
<p class="center"><img src="https://static.igem.org/mediawiki/2014/3/3d/Tsinghua_ModelImage023.png" /></p>
 +
<p class="center">Fig. 2 simulated [Ca2+]-t curve (x-axis in unit of 0.01min)</p>
 +
<p>Physiological curve as follows:</p>
 +
<p class="center"><img src="https://static.igem.org/mediawiki/2014/6/6a/Tsinghua_ModelImage025.png" /></p>
 +
<p class="center">Fig. 3 physiological insulin secretion curve</p>
 +
</section>
 +
<section>
 +
<h2>Reference</h2>
 +
<p>[1] J. C. Henquin, Regulation of insulin secretion: a matter  of phase control and amplitude modulation,<em> Diabetologia</em> (2009) 52:739–751.<br>
 +
  [2] Evren U. Azeloglu, et al., Interconnected Network Motifs, Control Podocyte  Morphology and Kidney Function, <em>Science  Signaling</em> (311), ra12.<br>
 +
  [3] <em>Lehninger Principles of Biochemistry </em>5th  ed., David L. Nelson, Michael M. Cox, W. H. Freeman and Company, New York,  2007.<br>
 +
  [4] <em>Physiology</em> first edition, Yao  Tai, et al., People&rsquo;s Hygiene Press, 2008.11.<br>
 +
  [5] Philippe D.et al., Interplay between cytoplasmic Ca2+ and the ATP/ADP  ratio: a feedback control mechanism in mouse pancreatic islets. <em>Biochem. J.</em> (1998)333,  269–274.<br>
 +
    [6]  Barbara  E. et al., Regulation of Steady-state Free Ca2+ Levels by the  ATP/ADP Ratio and Orthophosphate in Permeabilized RINm5F Insulinoma Cells, <em>The Journal of Biological Chemistry</em>.  1988, Vol 263, No.9:4247-4253.</p>
-
<!--main content -->
+
<!-- end .content --></article>
-
<table width="70%" align="center">
+
-
 
+
  <footer>
-
 
+
<div id="logoContainer">
-
<!--welcome box -->
+
<a href="http://www.tsinghua.edu.cn/"><img src="https://static.igem.org/mediawiki/2014/3/30/Tsinghua_Logo_thu.png" /></a>
-
<tr>
+
<a href="http://life.tsinghua.edu.cn/"><img src="https://static.igem.org/mediawiki/2014/2/22/Tsinghua_Logo_thulife_full.png" /></a>
-
<td style="border:1px solid black;" colspan="3" align="center" height="150px" bgColor=#FF404B>
+
<a href="http://xuetangban.life.tsinghua.edu.cn/"><img src="https://static.igem.org/mediawiki/2014/b/bf/Tsinghua_Logo_xtb_full.png" /></a>
-
<h1 >WELCOME TO iGEM 2014! </h1>
+
</div>
-
<p>Your team has been approved and you are ready to start the iGEM season!
+
    <address>
-
<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
+
    </address>
-
<br>
+
  </footer>
-
<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:Tsinghua/Modeling&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
+
  <!-- end .container --></div>
-
</td>
+
<div id="preload">
-
</tr>
+
<img src="https://static.igem.org/mediawiki/2014/1/10/Tsinghua_Icon_Intro_Diabetes_active.gif" width="1" height="1" alt="" />
-
 
+
<img src="https://static.igem.org/mediawiki/2014/4/4b/Tsinghua_Icon_Intro_GeneTherapy_active.gif" width="1" height="1" alt="" />
-
<tr> <td colspan="3"  height="5px"> </td></tr>
+
</div>
-
<!-- end welcome box -->
+
</body>
-
<tr>
+
-
 
+
-
<!--navigation menu -->
+
-
<td align="center" colspan="3">
+
-
 
+
-
<table  width="100%">
+
-
<tr heigth="15px"></tr>
+
-
<tr heigth="75px">
+
-
 
+
-
 
+
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7> 
+
-
<a href="https://2014.igem.org/Team:Tsinghua"style="color:#000000">Home </a> </td>
+
-
 
+
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
-
<a href="https://2014.igem.org/Team:Tsinghua/Team"style="color:#000000"> Team </a> </td>
+
-
 
+
-
<td style="border:1px solid black;" align="center"  height ="45px"  onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
+
-
<a href="https://igem.org/Team.cgi?year=2014&team_name=Tsinghua"style="color:#000000"> Official Team Profile </a></td>
+
-
 
+
-
<td style="border:1px solid black" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
-
<a href="https://2014.igem.org/Team:Tsinghua/Project"style="color:#000000"> Project</a></td>
+
-
 
+
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
+
-
<a href="https://2014.igem.org/Team:Tsinghua/Parts"style="color:#000000"> Parts</a></td>
+
-
 
+
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
+
-
<a href="https://2014.igem.org/Team:Tsinghua/Modeling"style="color:#000000"> Modeling</a></td>
+
-
 
+
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
-
<a href="https://2014.igem.org/Team:Tsinghua/Notebook"style="color:#000000"> Notebook</a></td>
+
-
 
+
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
+
-
<a href="https://2014.igem.org/Team:Tsinghua/Safety"style=" color:#000000"> Safety </a></td>
+
-
 
+
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
-
<a href="https://2014.igem.org/Team:Tsinghua/Attributions"style="color:#000000"> Attributions </a></td>
+
-
 
+
-
 
+
-
<td align ="center"> <a href="https://2014.igem.org/Main_Page"> <img src="https://static.igem.org/mediawiki/igem.org/6/60/Igemlogo_300px.png" width="55px"></a> </td>
+
-
</tr>
+
-
</table>
+
-
</tr>
+
-
</tr>
+
-
</td>
+
-
 
+
-
 
+
-
<tr> <td colspan="3"  height="15px"> </td></tr>
+
-
<tr><td bgColor="#e7e7e7" colspan="3" height="1px"> </tr>
+
-
<tr> <td colspan="3"  height="5px"> </td></tr>
+
-
 
+
-
 
+
-
<!--modeling content -->
+
-
<tr><td colspan="3"> <h3>Modeling</h3></td></tr>
+
-
</tr>
+
-
 
+
-
 
+
-
<tr>
+
-
<td width="45%"  valign="top">
+
-
<p>If you choose to create a model during your project, please write about it here. Modeling is not an essential part of iGEM, but we encourage any and all teams to model some aspect of their project. See previous "Best Model" awards for more information.</p>
+
-
</td>
+
-
 
+
-
<td></td>
+
-
<td></td>
+
-
</tr>
+
-
 
+
-
 
+
-
</table>
+
</html>
</html>

Revision as of 03:45, 16 October 2014

Modeling: Insulin Secretion

Abstract

In this model, we simulate the insulin secretion behavior of pancreatic β cells, trying to realize the similar curve in a single β cell, as that of glucose-insulin secretion which has been shown in literature, according to the reported insulin secretion mechanisms.

In general, we divide the process from glucose sensation to insulin secretion into three sessions. The first session covers the metabolic process from glucose intake to production of ATP. The second session covers the behavior of ion channels after the change in [ATP]/[ADP] ratio. The last session depicts the insulin secretion activated by cellular [Ca2+] rise.

This single-cell model is key to the overall insulin secretion curve due to the synchronization of the cells in the same pancreas islet.

Introduction

In physiology, the secretion of insulin is tightly regulated. After food intake and rising of blood glucose concentration, insulin is quickly secreted to down tune the blood glucose. Lack of insulin as well as its overproduction causes harm to human bodies. Thus it is really a need to determine the physiological parameters during insulin secretion. Of the first priority is the [glucose]-insulin secretion curve.

Task Analysis

Our model is in fact a time-amount model addressing the total insulin secretion amount with time under given glucose concentration.

The secretion of insulin is considered as the result of a series of regulation, which includes acceleration of metabolism, opening of ATP-sensitive K+ channel, depolarization of membrane, influx of Ca2+, etc. While this is not the whole picture, there is another pathway leading to the secretion of insulin, as is shown in the graph above, but due to its complexity and lack of studies, we focus on the major and clearer part of the pathway.

There are two phases of insulin secretion. First of them comes from the drastic reaction to glucose of β cells in all islets, and the second comes from the difference of secretion paces of different islets.

The main events are shown in the following chart:

[Glc] rising → [ATP]/[ADP] change → KATP Ch closure

→ Ca2+ Ch opening → [Ca2+]c rising → insulin secretion

As the insulin secretion-[Ca2+] is quite expectable, we focus mainly on the [Ca2+]-time curve.

Modeling

We make the following assumptions:

  1. The reactions in metabolic process obey the M-M equations;
  2. There is a time interval between [ATP[/[ADP] ratio reaches the threshold and closure of K+ ch;
  3. The infux of Ca2+ is only subject to the chemical and electrical gradient, and cellular retrieval of Ca2+ is constant.

Stage I

Michaelis-Menten equation:

Normally [ATP]/[ADP]= x0 (during fast)

X1(t) =

Where δx(t) = ∈(0,1), p is the concentration of ATP, and [G] is that of the glucose.

We assume that under discrete time intervals reactions conduct in packet .

Stage II

K+ Channel opening state:

K(t) =

K(t) limiting conditions:

K(0) = 0;

K(t) = 1, when X1(t) ≥ Ra;

K(t) = 0, when X1(t) ≤ Ra;

Amount of imported Ca2+:

Suppose the intracellular Ca2+ concentration is:

    (*)

Note 1 for the successful application of iteration, we introduce F(t) and C(t) with relationship as:

F(i) = exp(-c1)*(F(i-1)-1) + 1;

C(i) = c*(F(i) - F(i-1)) - c2 + C(i-1);

These two functions in fact realize the behavior of the above C(t).

Note 2 we assume that there should be a time period after [ATP]/[ADP] reaches the threshold before the K+ channel closes, resulting in a time delay:

if i > 150

    for j = 1:150

        if K(i-j) == 1

            q = 1;

        end

    end

end

Stage III: Ca2+-induced insulin secretion

With the increase in cellular [Ca2+] concentration, insulin secretion comes into a steady state concerned with [Ca2+] after an intense release.

I(t) =

Thus we are able to get an insulin secretion curve.

Results and Analysis

Our program gives the following [Ca2+]-t graph:

Fig. 2 simulated [Ca2+]-t curve (x-axis in unit of 0.01min)

Physiological curve as follows:

Fig. 3 physiological insulin secretion curve

Reference

[1] J. C. Henquin, Regulation of insulin secretion: a matter of phase control and amplitude modulation, Diabetologia (2009) 52:739–751.
[2] Evren U. Azeloglu, et al., Interconnected Network Motifs, Control Podocyte Morphology and Kidney Function, Science Signaling (311), ra12.
[3] Lehninger Principles of Biochemistry 5th ed., David L. Nelson, Michael M. Cox, W. H. Freeman and Company, New York, 2007.
[4] Physiology first edition, Yao Tai, et al., People’s Hygiene Press, 2008.11.
[5] Philippe D.et al., Interplay between cytoplasmic Ca2+ and the ATP/ADP ratio: a feedback control mechanism in mouse pancreatic islets. Biochem. J. (1998)333, 269–274.
[6] Barbara E. et al., Regulation of Steady-state Free Ca2+ Levels by the ATP/ADP Ratio and Orthophosphate in Permeabilized RINm5F Insulinoma Cells, The Journal of Biological Chemistry. 1988, Vol 263, No.9:4247-4253.