Difference between revisions of "Team:UST Beijing/Model"

 
(6 intermediate revisions by 3 users not shown)
Line 75: Line 75:
 
<body>
 
<body>
 
        
 
        
 +
<!-- BEGIN HEADER -->
 
<!-- BEGIN HEADER -->
 
<!-- BEGIN HEADER -->
 
<header id="fh5co-header" role="banner">
 
<header id="fh5co-header" role="banner">
Line 92: Line 93:
 
                   <li><a href="https://2016.igem.org/Team:UST_Beijing/EnzymaticActivity">Enzymatic Activity</a></li>
 
                   <li><a href="https://2016.igem.org/Team:UST_Beijing/EnzymaticActivity">Enzymatic Activity</a></li>
 
                     <li class="divider"></li>
 
                     <li class="divider"></li>
                     <li><a href="https://2016.igem.org/Team:UST_Beijing/Model">Recombination</a></li>
+
                     <li><a href="https://2016.igem.org/Team:UST_Beijing/Description">Recombination</a></li>
 
                     <li class="divider"></li>
 
                     <li class="divider"></li>
 
                     <li><a href="https://2016.igem.org/Team:UST_Beijing/Demonstrate">Mixed Fermentation</a></li>
 
                     <li><a href="https://2016.igem.org/Team:UST_Beijing/Demonstrate">Mixed Fermentation</a></li>
Line 99: Line 100:
 
               </ul>
 
               </ul>
 
                                                 </li>
 
                                                 </li>
          <li class="dropdown">
+
          <li><a href="https://2016.igem.org/Team:UST_Beijing/Model">Modeling</a></li>
              <a href="#" class="dropdown-toggle" data-toggle="dropdown">Modeling <b class="caret"></b>
+
              </a>
+
                <ul class="dropdown-menu">
+
                  <li><a href="https://2016.igem.org/Team:UST_Beijing/Model">Mathematic Model</a></li>
+
                    <li class="divider"></li>
+
                    <li><a href="https://2016.igem.org/Team:UST_Beijing/AnimalModel">Animal Model</a></li>
+
              </ul>
+
                                                </li>
+
 
           <li><a href="https://2016.igem.org/Team:UST_Beijing/Parts">Parts</a></li>
 
           <li><a href="https://2016.igem.org/Team:UST_Beijing/Parts">Parts</a></li>
 +
 
           <li class="dropdown">
 
           <li class="dropdown">
 
               <a href="#" class="dropdown-toggle" data-toggle="dropdown">Human Practices <b class="caret"></b>
 
               <a href="#" class="dropdown-toggle" data-toggle="dropdown">Human Practices <b class="caret"></b>
Line 144: Line 139:
 
<div class="row">
 
<div class="row">
 
<div class="col-md-8 col-md-offset-2">
 
<div class="col-md-8 col-md-offset-2">
<h1 class="intro-lead">Model</h1>
+
<h1 class="intro-lead">Modeling</h1>
<p>β-galactosidase is used to deglycosylate saponin of notoginseng. Our Lab have a PET-28a plasmid withβ-galactosidase gene and LacI gene. The transcription of β-galactosidase is repressed by LacI protein. But lactose and IPTG can induce the expression of LacI protein. We used a 3L fermentation tank to conduct preliminary experiments, then the enzyme was extracted from bacteria solution using glycine buffer.</p>
+
<p>We analyzed the pet28a-β-glucosidase plasmid and pSB1C3-pBAD-T7RNAp plasmid in double-transformed E. coli, and using JDesigner software we set up the model of β-glucosidase expression. This model displayed the process of pNPG’ decomposition in wells. </p>
 
</div>
 
</div>
 
</div>
 
</div>
Line 160: Line 155:
 
<div class="row">
 
<div class="row">
 
<div id="sidebar" class="col-md-3 animate-box">
 
<div id="sidebar" class="col-md-3 animate-box">
<h3>Model</h3>
+
<h3>Modeling</h3>
 
<ul class="fh5co-list-check">
 
<ul class="fh5co-list-check">
<li><a href="#part1">Enzyme activity</a></li>
+
<li><a href="#part1">Double Plasmids</a></li>
 
+
<li><a href="#part2">Enzymatic Activity</a></li>
 
</ul>
 
</ul>
 
</div>
 
</div>
Line 169: Line 164:
  
  
<div id="part1"><h2>Enzyme activity</h2>
+
<div id="part1"><h2>Double Plasmids</h2>
 +
<img src="https://static.igem.org/mediawiki/2016/5/52/T--UST_Beijing--recobination02.png" style="width:700px;"></br>
 +
<p></p>
  
 +
<p class="animate-box">We tested the affection of β-glucosidase induced by IPTG(1000uM) and Ara(1000uM) in 96-well plates and measuring the A450(pNPG decomposed as substrate to pNP which can be detected at 450nm) every hour. After collected data, we output a graph of A450-time.</p>
 +
 +
<img src="https://static.igem.org/mediawiki/2016/9/96/T--UST_Beijing--Model_1.png" style="width:700px;"></br>
 +
<p></p>
 +
 +
<p class="animate-box">We analyzed the pET28a-β-glucosidase plasmid and pSB1C3-pBAD-T7RNAp plasmid in double-transformed E. coli, and using JDesigner we set up the model of the expression toβ-glucosidase . This model displayed the process of pNPG’ decomposition in wells.</p>
 +
 +
<img src="https://static.igem.org/mediawiki/2016/5/50/T--UST_Beijing--Model_2.jpeg" style="width:700px;"></br>
 +
<p></p>
 +
 +
<p class="animate-box">Set parameters as:Lac=1000, Ara=1000, pNPG=13 and export the graph to pNPG-time. Modify the parameters(k1, k2_Vmax, k2_Km, k2_Ki, k3_1, k3_2,k4, k5) until the curve fit to the graph output from origin data.</p>
 +
 +
<img src="https://static.igem.org/mediawiki/2016/a/ae/T--UST_Beijing--Model_3.png" style="width:700px;"></br>
 +
<p></p>
 +
<p class="animate-box">In this result, the parameter (k1, k2_Vmax, k2_Km, k2_Ki, k3_1, k3_2, k4, k5) is 1, 3.4, 2.9, 0.4, 1, 96000, 1, 1. </p>
 +
</div>
 +
 +
 +
 +
 +
<div id="part2"><h2>Enzyme activity</h2>
 
<img src="https://static.igem.org/mediawiki/2016/5/57/T--UST_Beijing--model01.png" style="width:700px;"></br>
 
<img src="https://static.igem.org/mediawiki/2016/5/57/T--UST_Beijing--model01.png" style="width:700px;"></br>
 
<img src="https://static.igem.org/mediawiki/2016/3/39/T--UST_Beijing--model02.png" style="width:700px;"></br>
 
<img src="https://static.igem.org/mediawiki/2016/3/39/T--UST_Beijing--model02.png" style="width:700px;"></br>
 
+
<p></p>
<p class="animate-box">As Chinese traditional medicinal materials, notoginseng has been widely recognized on its efficacy by Chinese people during thousands of years. With the developing of modern medicine, other characteristics of notoginseng have been utilizing. Now it’s been proved that notoginsenoside has therapeutic effect on hyperlipidemia and cardiovascular diseases. However, the bioavailability of saponin of notoginseng in human body can reach only 4%. Based on this premise, we hope to hydrolyze glycosyl on saponin of notoginseng molecule out of body, so that deglycosylated saponin of notoginseng can be easy for human to absorb.</p>
+
<p class="animate-box">β-glucosidase is used to hydrolyze sugars from saponins of notoginseng. Our Lab has a pET-28a plasmid with β-glucosidase gene. The transcription of β-glucosidase is repressed by LacI protein. But lactose and IPTG can induce the expression of LacI protein. We used a 3L fermentation tank to conduct preliminary experiments, then the enzyme was extracted from bacteria solution using glycine buffer. The result showed us that extracted solution has strong ability to hydrolyze saponins. However, there’s no lactose in notoginseng solid fermentation medium. In order to reduce costs, another plasmid pSB1C3 which contains T7 RNA Polymerase gene under the control of pBAD promoter was transformed into E.coli. This double-plasmid system is expected to be regulated by arabinose, and expresses a large number of T7RNA polymerase to overcome the effect of LacI repression, switch on the expression of β-glucosidase. It’s been reported in scientific literature that the cell wall of notoginseng root cells contains a certain concentration of arabinose. Our ultimate goal is to use notoginseng root to provide nutrients for E.coli in solid state fermentation, where E.coli can hydrolyze saponin of notoginseng as well.</p>
  
  
Line 191: Line 209:
  
  
<footer id="fh5co-footer">
+
<footer id="fh5co-footer">
 
<div class="container">
 
<div class="container">
 
<div class="row">
 
<div class="row">
<div class="col-md-10 col-md-offset-1 text-center">
+
      <div class="col-md-10 col-md-offset-1 text-center" style="text-align: left;">
<p>北京科技大学</p>
+
<div class="col-xs-3">
 +
                <ul class="list-unstyled" style="margin:0; font-family:'Gotham5dbe91ec4165f3';font-weight:bold ">
 +
  <a href="#"><h4 style="font-weight:bold">Project</h4></a>
 +
                  <li><a href="https://2016.igem.org/Team:UST_Beijing/HP/Gold">Background</a></li>
 +
                  <li><a href="https://2016.igem.org/Team:UST_Beijing/EnzymaticActivity">Enzymatic activity</a></li>
 +
                  <li><a href="https://2016.igem.org/Team:UST_Beijing/Description">Recombination</a></li>
 +
                  <li><a href="https://2016.igem.org/Team:UST_Beijing/Demonstrate">Mixed Fermentation</a></li>
 +
                  <li><a href="https://2016.igem.org/Team:UST_Beijing/Description">Animal Experiment</a></li>
 +
                </ul>
 +
              </div>
 +
 +
 
 +
    <div class="col-xs-3">
 +
 
 +
<a href="https://2016.igem.org/Team:UST_Beijing/Model"><h4 style="font-weight:bold">Modeling</h4></a>
 +
</div>
 +
 
 +
  <div class="col-xs-3">       
 +
  <a href="https://2016.igem.org/Team:UST_Beijing/Parts"><h4 style="font-weight:bold">Parts</h4></a>
 +
               
 +
              </div>
 +
  <div class="col-xs-3">
 +
                <ul class="list-unstyled" style="margin:0; font-family:'Gotham5dbe91ec4165f3';font-weight:bold ">
 +
  <a href="#"><h4 style="font-weight:bold">Human practice</h4></a>
 +
                  <li><a href="https://2016.igem.org/Team:UST_Beijing/Collaborations">Collaboration</a></li>
 +
                  <li><a href="https://2016.igem.org/Team:UST_Beijing/HP/Silver">Public engagement</a></li>
 +
                </ul>
 +
              </div>
 +
    <div class="col-xs-3">
 +
                <ul class="list-unstyled" style="margin:0; font-family:'Gotham5dbe91ec4165f3';font-weight:bold ">
 +
  <a href="#"><h4 style="font-weight:bold">Team</h4></a>
 +
                  <li><a href="https://2016.igem.org/Team:UST_Beijing/HP/Silver">Member</a></li>
 +
                  <li><a href="https://2016.igem.org/Team:UST_Beijing/Notebook">Notebook</a></li>
 +
                  <li><a href="https://2016.igem.org/Team:UST_Beijing/Attributions">Attribution</a></li>
 +
                  <li><a href="https://2016.igem.org/Team:UST_Beijing/Satety">Safety</a></li>
 +
                </ul>
 +
              </div><img src="https://static.igem.org/mediawiki/2016/b/b8/T--UST_Beijing--logo.png" style="width:400px;margin-top: 3em;">
 +
 
 +
 
 
</div>
 
</div>
 
</div>
 
</div>

Latest revision as of 03:55, 20 October 2016

iGEM team wiki of UST_Beijing

Modeling

We analyzed the pet28a-β-glucosidase plasmid and pSB1C3-pBAD-T7RNAp plasmid in double-transformed E. coli, and using JDesigner software we set up the model of β-glucosidase expression. This model displayed the process of pNPG’ decomposition in wells.

Double Plasmids


We tested the affection of β-glucosidase induced by IPTG(1000uM) and Ara(1000uM) in 96-well plates and measuring the A450(pNPG decomposed as substrate to pNP which can be detected at 450nm) every hour. After collected data, we output a graph of A450-time.


We analyzed the pET28a-β-glucosidase plasmid and pSB1C3-pBAD-T7RNAp plasmid in double-transformed E. coli, and using JDesigner we set up the model of the expression toβ-glucosidase . This model displayed the process of pNPG’ decomposition in wells.


Set parameters as:Lac=1000, Ara=1000, pNPG=13 and export the graph to pNPG-time. Modify the parameters(k1, k2_Vmax, k2_Km, k2_Ki, k3_1, k3_2,k4, k5) until the curve fit to the graph output from origin data.


In this result, the parameter (k1, k2_Vmax, k2_Km, k2_Ki, k3_1, k3_2, k4, k5) is 1, 3.4, 2.9, 0.4, 1, 96000, 1, 1.

Enzyme activity



β-glucosidase is used to hydrolyze sugars from saponins of notoginseng. Our Lab has a pET-28a plasmid with β-glucosidase gene. The transcription of β-glucosidase is repressed by LacI protein. But lactose and IPTG can induce the expression of LacI protein. We used a 3L fermentation tank to conduct preliminary experiments, then the enzyme was extracted from bacteria solution using glycine buffer. The result showed us that extracted solution has strong ability to hydrolyze saponins. However, there’s no lactose in notoginseng solid fermentation medium. In order to reduce costs, another plasmid pSB1C3 which contains T7 RNA Polymerase gene under the control of pBAD promoter was transformed into E.coli. This double-plasmid system is expected to be regulated by arabinose, and expresses a large number of T7RNA polymerase to overcome the effect of LacI repression, switch on the expression of β-glucosidase. It’s been reported in scientific literature that the cell wall of notoginseng root cells contains a certain concentration of arabinose. Our ultimate goal is to use notoginseng root to provide nutrients for E.coli in solid state fermentation, where E.coli can hydrolyze saponin of notoginseng as well.