Difference between revisions of "Team:NAU-CHINA/Description"

Line 1: Line 1:
−
{{NAU-CHINA}}
 
 
<html>
 
<html>
 +
<head>
 +
<meta charset="UTF-8" />
 +
<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
 +
<meta name="viewport" content="width=device-width, initial-scale=1.0">
 +
<link rel="stylesheet" type="text/css"
 +
href="https://2016.igem.org/Template:NAU-CHINA/texiao?action=raw&ctype=text/css" />
 +
<link rel="stylesheet" type="text/css"
 +
href="https://2016.igem.org/Template:NAU-CHINA/component?action=raw&ctype=text/css" />
 +
<style type="text/css">
 +
/* Hide top title */
 +
#top_title, #sideMenu {
 +
display: none;
 +
}
 +
 +
/* Hide first heading */
 +
.firstHeading {
 +
display: none;
 +
}
  
  
−
<p>The project is aiming to design an engineered bacteria that can degrade 3-PBA thoroughly <b>(as shown in picture1)</b> and efficiently in about 3 days.</p>
+
/*-- Remove borders, float content left and remove padding/margin */
 +
#globalWrapper, #content{
 +
background-color: transparent;
 +
border: none;
 +
float: center;
 +
width: auto;
 +
margin-left: 0px;
 +
margin-top: -8px;
 +
padding: auto;
 +
}
  
−
<p><b>3-PBA</b>, the main metabolite in the degradation of insecticide pyrethroids (widely used for insect control in agriculture industry), is typically detected as a vital environmental contaminant and half-life of 3-phenoxybenzoate (3-PBA) in soil is 180 days (conventional pesticides is 30 days).</p>
+
/*left align Black Menu Bar */
 +
#top_menu_inside {
 +
margin-left: 0px;
 +
}
 +
.centerImage
 +
{
 +
text-align:center;
 +
display:block;
 +
}
 +
.wraptocenter {
 +
  display: table-cell;
 +
  text-align: center;
 +
  vertical-align: middle;
 +
  width: 200px;
 +
  height: 200px;
 +
  background-color: #999;
 +
}
 +
.wraptocenter * {
 +
  vertical-align: middle;
 +
}
  
−
<p>Microbial biodegradation is valued for its environment-friendly method to eliminate pollution. It is noted that <i>sphingobium wenxiniae JZ-1</i> is able to degrade 3-PBA into 3-hydroxybenzoate(3-HBA) in 3 days and Klebsiella pneumoniae M5a1 can convert 3—HBA to pyruvate and fumarate via gentisate. </p>
+
.qunidehongzi{
 +
color: red;
 +
}
 +
.qunidelanzi{
 +
color: blue;
 +
}
 +
h3{
 +
padding-left: 12px;
 +
}
 +
h4{
 +
padding-left: 24px;
 +
}
 +
.saner{
 +
padding-left: 48px;
 +
}
 +
                        #maintext{
 +
padding-top: 900px;
 +
}
 +
@media screen and (max-width: 1220px) {
  
−
<p>Employing microbial biodegradation techniques to degrade 3-PBA is both feasible and worthy of research.</p>
+
    .menu{
−
</br>
+
        display: none;
−
<img src="https://static.igem.org/mediawiki/2016/7/71/NAU_China_description_pic01.gif" width="1000px">
+
        opacity: 0;
 +
    }
  
−
</br>
+
    .container {
−
<b>Picture 1</b> Process of 3-PBA Degradation
+
        display: block;
 +
    }
  
 +
}
 +
 +
@media screen and (min-width: 1220px) {
 +
 +
    .menu{
 +
        display: block;
 +
    }
 +
 +
    .container {
 +
        display: none;
 +
    }
 +
 +
}
 +
</style>
 +
<script type="text/javascript">
 +
 +
function ChangeImg(ThisPic)
 +
{
 +
var size=document.body.clientWidth;
 +
var TrueWidth=ThisPic.width;
 +
var TrueHeight=ThisPic.height;
 +
var Multiple=TrueWidth/size;
 +
 +
ThisPic.width=size;
 +
ThisPic.height=TrueHeight/Multiple;
 +
}
 +
 +
</script>
 +
</head>
 +
 +
<body>
 +
 +
<!-- small screen menu -->
 +
<nav>
 +
<div class="container" >
 +
<ul id="gn-menu" class="gn-menu-main" >
 +
<li class="gn-trigger">
 +
<a class="gn-icon gn-icon-menu">
 +
</a>
 +
<nav class="gn-menu-wrapper">
 +
<div class="gn-scroller">
 +
<ul class="gn-menu">
 +
<li>
 +
<a href="https://2016.igem.org/Team:NAU-CHINA"><span> HOME</span></a>
 +
</li>
 +
<li>
 +
<a href="https://2016.igem.org/Team:NAU-CHINA/Participator"> TEAM</a>
 +
</li>
 +
<li>
 +
<a href="https://2016.igem.org/Team:NAU-CHINA/Description"> PROJECT</a>
 +
</li>
 +
<li>
 +
<a href="https://2016.igem.org/Team:NAU-CHINA/Parts_list"> PARTS</a>
 +
</li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Safety"> SAFETY</a></li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Attribution"> ATTRIBUTION</a></li>
 +
<li>
 +
<a href="https://2016.igem.org/Team:NAU-CHINA/Human_Practices"> HP</a>
 +
</li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Conclusion">CONCLUSION</a></li>
 +
</ul>
 +
</div><!-- /gn-scroller -->
 +
</nav>
 +
</li>
 +
</ul>
 +
 +
</div><!-- /container -->
 +
 +
 +
 +
 +
<!-- big screen menu-->
 +
<div class="nav" id="main" role="main">
 +
<ul class="menu">
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA">HOME</a></li>
 +
<li><a>TEAM</a>
 +
<ul class="submenu">
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Participator">Participator</a></li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Collaboration">Collaboration</a></li>
 +
</ul>
 +
</li>
 +
<li><a>PROJECT</a>
 +
<ul class="submenu">
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Description">Description</a></li>
 +
                                <li><a href="https://2016.igem.org/Team:NAU-CHINA/Applied Design">Applied Design</a></li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Experiment">Experiment</a></li>
 +
                                <li><a href="https://2016.igem.org/Team:NAU-CHINA/Proof_of_Concept">Proof of Concept</a></li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Demonstrate">Demonstrate </a></li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Model">Model </a></li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Result">Result </a></li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Notebook">Notebook </a></li>
 +
</ul>
 +
</li>
 +
<li><a>PARTS</a>
 +
<ul class="submenu">
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Parts_list">Parts list</a></li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Collection">Collection</a></li>
 +
 +
</ul>
 +
</li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Safety">SAFETY</a></li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Attribution">ATTRIBUTION</a></li>
 +
<li><a>HUMAN PRACTICE</a>
 +
<ul class="submenu">
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Human_Practices">Human Practices</a></li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Silver">Silver</a></li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Gold">Gold</a></li>
 +
</ul>
 +
</li>
 +
<li><a href="https://2016.igem.org/Team:NAU-CHINA/Conclusion">CONCLUSION</a></li>
 +
</ul>
 +
</div>
 +
</nav>
 +
<div id="maintext">
 +
<h1>Description</h1>
 +
<p>We are aiming to <b class="qunidehongzi">degrade 3-phenoxybenzoate acid (3-PBA) thoroughly</b> through employing Synthetic Biology concept and microbial biodegradation techniques. Also we are eager to take the first steps to <b class="qunidehongzi">make our project real</b>.</p>
 +
 +
<h2>Outline</h2>
 +
<ol >
 +
<li>Background - Why we need to degrade 3-PBA thoroughly?</li>
 +
<li>Method - How to degrade 3-PBA thoroughly?</li>
 +
<li>Practice - How to make our project real?</li>
 +
</ol>
 +
 +
<h3>1.Background - Why we need to degrade 3-PBA thoroughly?</h3>
 +
<ol type="A" class="saner">
 +
<li>Harm to the enviroment and human</li>
 +
<li>Drosophila toxicological experiment</li>
 +
<li>Cost-benefit analysis for engineered bacteria</li>
 +
</ol>
 +
 +
<h4>A.Harm to the enviroment and human</h4>
 +
<p>3-PBA is the main metabolite in the degradation of pyrethroids(widely used for insect control in agriculture industry). For being a metabolite, it is easy to be ignored. Through loads of information handling we list the main <b class="qunidehongzi">harm</b>.</p>
 +
<ol>
 +
<li>Long natural degradation half-life(180 days)</li>
 +
<li>Hindering the mineralization of pyrethroids</li>
 +
<li>Widespread occurrence in surface water, sediment, and soil</li>
 +
<li>Potential reproductive toxicity</li>
 +
</ol>
 +
<h4><a href="">B.Drosophila toxicological experiment</a></h4>
 +
 +
<h4>C.Cost-benefit analysis for engineered bacteria</h4>
 +
<p>Degradation comes at a price.3-PBA thorough biodegradation is a series of enzymatic reactions. Protein synthesis and enzyme reactions needs materials、ATP and NADH. Catechol,the intermediate metabolite of 3-PBA, is toxic to the Escherichia coli. 3-pba as the carbon source can be degradated and absored entering the TCA circle to produce energy. Based on these facts we can get a formula Net proceeds(N)=Benefit(B)-Cost(C).</p>
 +
<img src="https://static.igem.org/mediawiki/2016/5/5b/NAU_CHINA_DESCRIPTION_IMG01.jpeg">
 +
 +
<h3>2.Method - How to degrade 3-PBA thoroughly?</h3>
 +
<ol type="A" class="saner">
 +
<li>Gene circut design</li>
 +
<li>Experimental test & previous parts improvement & analysis</li>
 +
<li>Gene circut redesign</li>
 +
</ol>
 +
 +
<h4>A.Gene circut design</h4>
 +
<img src="https://static.igem.org/mediawiki/2016/6/60/NAU_CHINA_DESCRIPTION_IMG02.jpeg">
 +
<p>ptA: promoterA</p>
 +
<p>ptB: promoterB</p>
 +
<p>ptR: promoterRight</p>
 +
<p>ptL: promoterLight</p>
 +
 +
 +
<p>Before gene circut design, knowing the biodegradation process is necessary.</p>
 +
<img src="https://static.igem.org/mediawiki/2016/3/35/NAU_CHINA_DESCRIPTION_IMG03.jpeg">
 +
<p>Thorough 3-PBA biodegradation means put 3-PBA into fumarate, pyruvate and HMS.</p>
 +
<p><b class="qunidelanzi">pbaA1A2B & pbaC</b> gene cluster: coding degrading-enzyme to put 3-PBA into 3-hydroxybenzoate(3-HBA) and catechol</p>
 +
<p><b class="qunidelanzi">mhbDHIM</b> gene cluster:coding degrading-enzyme to put 3-HBA into fumarate and pyruvate, carbon source</p>
 +
<p><b>c230</b> gene fragment:coding degrading-enzyme to put catechol into HMS,ring opening product</p>
 +
<img src="1234asdf.jpg">
 +
<p><b class="qunidelanzi">mhbR</b> gene fragment: coding operon mhbR</p>
 +
<p>3-HBA is a kind of intermediate metabolite of 3-PBA but inducer. The promoterR expression  strength is depend on the operon mhbR. Without the inducer 3-HBA the expression strength is of low level but when the inducer combines with mhbR, the expression strength is of high level. This makes that the degradation product is ued as an inducer for the expression of downsream genes.</p>
 +
<p>To sum up, pba gene cluster codes degrading-enzyme to put 3-PBA into 3-HBA and catechol. 3-HBA works as an inducer making the high expression level of downsream genes real to put 3-HBA into fumarate and pyruvate used as carbon source. But at design stage the degradation of catechol was ignored.</p>
 +
 +
<h4>B.Experimental test & previous parts improvement & analysis</h4>
 +
<p>To push the theory into the real, experimental test was demanded. During the experimental period some points put questions to us. After researching we decided to improve previous parts, CopA and RiboJ. For more details please read the Experiment section.</p>
 +
 +
<a href=""><h4>C.Gene circut redesign</h4></a>
 +
 +
<br>
 +
 +
<h3>3.Practice - How to make our project real?</h3>
 +
<ul>
 +
<li>Social investigation</li>
 +
<li>Applied design</li>
 +
<li>Concept & achievement sharing</li>
 +
</ul>
 +
<p>The project came from life and finally will go back to life. For more details please read the Applied Design and Human Practice sections.</p>
 +
 +
                </div>
 +
 +
<img src="https://static.igem.org/mediawiki/2016/b/b9/NAU_CHINA_DESCRIPTION_BG.jpeg"  onload="ChangeImg(this)" style="z-index:-60;position:absolute;left:0;top:0px"><!--backgroundimg-->
 +
<script type="text/javascript" src="https://2016.igem.org/Template:NAU-CHINA/gnmenu?
 +
action=raw&ctype=text/javascript"></script>
 +
<script type="text/javascript" src="https://2016.igem.org/Template:NAU-CHINA/classie?
 +
action=raw&ctype=text/javascript"></script>
 +
<script>
 +
new gnMenu( document.getElementById( 'gn-menu' ) );
 +
</script>
 +
</body>
 
</html>
 
</html>

Revision as of 10:48, 6 October 2016

Description

We are aiming to degrade 3-phenoxybenzoate acid (3-PBA) thoroughly through employing Synthetic Biology concept and microbial biodegradation techniques. Also we are eager to take the first steps to make our project real.

Outline

  1. Background - Why we need to degrade 3-PBA thoroughly?
  2. Method - How to degrade 3-PBA thoroughly?
  3. Practice - How to make our project real?

1.Background - Why we need to degrade 3-PBA thoroughly?

  1. Harm to the enviroment and human
  2. Drosophila toxicological experiment
  3. Cost-benefit analysis for engineered bacteria

A.Harm to the enviroment and human

3-PBA is the main metabolite in the degradation of pyrethroids(widely used for insect control in agriculture industry). For being a metabolite, it is easy to be ignored. Through loads of information handling we list the main harm.

  1. Long natural degradation half-life(180 days)
  2. Hindering the mineralization of pyrethroids
  3. Widespread occurrence in surface water, sediment, and soil
  4. Potential reproductive toxicity

B.Drosophila toxicological experiment

C.Cost-benefit analysis for engineered bacteria

Degradation comes at a price.3-PBA thorough biodegradation is a series of enzymatic reactions. Protein synthesis and enzyme reactions needs materials、ATP and NADH. Catechol,the intermediate metabolite of 3-PBA, is toxic to the Escherichia coli. 3-pba as the carbon source can be degradated and absored entering the TCA circle to produce energy. Based on these facts we can get a formula Net proceeds(N)=Benefit(B)-Cost(C).

2.Method - How to degrade 3-PBA thoroughly?

  1. Gene circut design
  2. Experimental test & previous parts improvement & analysis
  3. Gene circut redesign

A.Gene circut design

ptA: promoterA

ptB: promoterB

ptR: promoterRight

ptL: promoterLight

Before gene circut design, knowing the biodegradation process is necessary.

Thorough 3-PBA biodegradation means put 3-PBA into fumarate, pyruvate and HMS.

pbaA1A2B & pbaC gene cluster: coding degrading-enzyme to put 3-PBA into 3-hydroxybenzoate(3-HBA) and catechol

mhbDHIM gene cluster:coding degrading-enzyme to put 3-HBA into fumarate and pyruvate, carbon source

c230 gene fragment:coding degrading-enzyme to put catechol into HMS,ring opening product

mhbR gene fragment: coding operon mhbR

3-HBA is a kind of intermediate metabolite of 3-PBA but inducer. The promoterR expression strength is depend on the operon mhbR. Without the inducer 3-HBA the expression strength is of low level but when the inducer combines with mhbR, the expression strength is of high level. This makes that the degradation product is ued as an inducer for the expression of downsream genes.

To sum up, pba gene cluster codes degrading-enzyme to put 3-PBA into 3-HBA and catechol. 3-HBA works as an inducer making the high expression level of downsream genes real to put 3-HBA into fumarate and pyruvate used as carbon source. But at design stage the degradation of catechol was ignored.

B.Experimental test & previous parts improvement & analysis

To push the theory into the real, experimental test was demanded. During the experimental period some points put questions to us. After researching we decided to improve previous parts, CopA and RiboJ. For more details please read the Experiment section.

C.Gene circut redesign

3.Practice - How to make our project real?

  • Social investigation
  • Applied design
  • Concept & achievement sharing

The project came from life and finally will go back to life. For more details please read the Applied Design and Human Practice sections.