Team:Edinburgh/biology(overalldescription)

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<div id=menuitem >  <a href="#"> Overall Description & Design </a> </div>
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<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/biology%28overalldescription%29"> Overall Description & Design </a> </div>
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<div id=menuitem >  <a href="#"> Materials and Methods </a> </div>
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<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/biology%28tntsensing%29"> TNT-Sensing Pathway</a> </div>
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<div id=menuitem >  <a href="#"> Biobricks </a> </div>
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<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/biology%28nitritenitratesensing%29"> Nitrite/Nitrate-Sensing Pathway</a> </div>
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<div id=menuitem >  <a href="#"> Problem Solving and Tips </a> </div>
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                        <div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/biology%28biobricks%29"> Biobrick Parts </a> </div>
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<div id=menuitem >  <a href="#"> Results </a> </div>  
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<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/biology%28results%29"> Results </a> </div>
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<div id=menuitem >  <a href="#"> Future Work </a> </div>
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<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/biology%28solvedproblems%29"> Problem Solving and Tips </a> </div>  
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<div id=menuitem >  <a href="#"> References </a> </div>
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<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/biology%28materialsandmethods%29"> Materials and Methods </a> </div>
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<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/biology%28references%29"> References </a> </div>
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<ul id="nav" class="dropdown dropdown-horizontal">
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  <li><a href="https://2009.igem.org/Team:Edinburgh">Home</a></li>
  <li><a href="https://2009.igem.org/Team:Edinburgh">Home</a></li>
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<li><a href="https://2009.igem.org/Team:Edinburgh/projectmain%28overall%29" class="dir">Top View</a>
 
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  <ul>
 
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  <li><a href="https://2009.igem.org/Team:Edinburgh/projectmain%28overall%29">Overall Description</a></li>
 
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  <li><a href="https://2009.igem.org/Team:Edinburgh/projectmain%28motivationl%29">Motivation</a></li>
 
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  <li><a href="https://2009.igem.org/Team:Edinburgh/projectmain%28whywediffer%29">Why We Differ?</a></li>
 
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  <li><a href="https://2009.igem.org/Team:Edinburgh/projectmain%28glanceatthefuture%29">Glance At The Future</a></li>
 
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  <li><a href="https://2009.igem.org/Team:Edinburgh/projectmain%28references%29">References</a></li>
 
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  </ul>
 
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  </li>
 
   <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28overalldescription%29" class="dir">Biology</a>
   <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28overalldescription%29" class="dir">Biology</a>
   <ul>
   <ul>
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28overalldescription%29">Overall Description and Design</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28overalldescription%29">Overall Description and Design</a></li>
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    <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28tntsensing%29">TNT-Sensing Pathway</a></li>
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    <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28nitritenitratesensing%29">Nitrite/Nitrate-Sensing Pathway</a></li>
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    <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28biobricks%29">Biobrick Parts</a></li>
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    <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28results%29">Results</a></li>
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    <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28solvedproblems%29">Problem Solving and Tips</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28materialsandmethods%29">Materials and Methods</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28materialsandmethods%29">Materials and Methods</a></li>
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    <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28biobricks%29">Biobricks</a></li>
 
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    <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28solvedproblems%29">Problem Solving and Tips</a></li>
 
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    <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28results%29">Results</a></li>
 
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    <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28glanceatthefuture%29">Future Work</a></li>
 
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28references%29">References</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/biology%28references%29">References</a></li>
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     <li><a href="https://2009.igem.org/Team:Edinburgh/reallifeapplication%28scaleup%29">Scale Up</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/reallifeapplication%28scaleup%29">Scale Up</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/modelling%28results%29">Results</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/modelling%28results%29">Results</a></li>
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    <li><a href="https://2009.igem.org/Team:Edinburgh/modelling%28glanceatthefuture%29">Glance At the Future</a></li>
 
     <li><a href="https://2009.igem.org/Team:Edinburgh/modelling%28references%29">References</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/modelling%28references%29">References</a></li>
   </ul>
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   <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28introduction%29" class="dir">Underlying Philosophy</a>
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   <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28publicperception%29" class="dir">Underlying Philosophy</a>
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     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28introduction%29">Introduction</a></li>
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     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28publicperception%29">Public Perception</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28legislationissues%29">Legislation issues</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28legislationissues%29">Legislation issues</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28biosafety%29">Biosafety</a></li>
     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28biosafety%29">Biosafety</a></li>
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    <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28religiousperception%29">Religious Perception</a></li>
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     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28summary%29">DEMOCS Card Game</a></li>
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    <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28publicperception%29">Public Perception</a></li>
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    <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28surveyandconclusions%29">Survey and Conclusions</a></li>
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     <li><a href="https://2009.igem.org/Team:Edinburgh/ethics%28summary%29">Summary (Synthetic Bilogy Pro and Contras)</a></li>
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     </ul>
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   <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28introduction%29" class="dir">New Informatics</a>
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   <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28introduction%29" class="dir">Informatics</a>
     <ul>
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       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28introduction%29">Introduction</a></li>
       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28introduction%29">Introduction</a></li>
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      <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28conceptsandtechnology%29">Concepts and Technologies</a></li>
 
       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28globetutorial%29">Globe Tutorial</a></li>
       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28globetutorial%29">Globe Tutorial</a></li>
       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28igemwikhacks%29">iGEM WIKI Hacks</a></li>
       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28igemwikhacks%29">iGEM WIKI Hacks</a></li>
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       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28conclusions%29">Conclusions</a></li>
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       <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28conclusions%29">Blog Entry</a></li>
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  <li><a href="https://2009.igem.org/Team:Edinburgh/results">Results</a></li>
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   <li><a href="https://2009.igem.org/Team:Edinburgh/Notebook">Notebook</a></li>
   <li><a href="https://2009.igem.org/Team:Edinburgh/Notebook">Notebook</a></li>
    
    
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   <li><a href="https://2009.igem.org/Team:Edinburgh/team%28teamintroduction%29" class="dir">Team</a>
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   <li><a href="https://2009.igem.org/Team:Edinburgh/team%28teammembers%29" class="dir">Team</a>
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<li><a href="https://2009.igem.org/Team:Edinburgh/team%28teamintroduction%29">Team Introduction</a></li>
 
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<li><a href="https://2009.igem.org/Team:Edinburgh/team%28edinburghuniversity%29">Edinburgh University</a></li>
 
<li><a href="https://2009.igem.org/Team:Edinburgh/team%28teammembers%29">Team Members</a></li>
<li><a href="https://2009.igem.org/Team:Edinburgh/team%28teammembers%29">Team Members</a></li>
<li><a href="https://2009.igem.org/Team:Edinburgh/team%28advisors%29">Advisors</a></li>
<li><a href="https://2009.igem.org/Team:Edinburgh/team%28advisors%29">Advisors</a></li>
<li><a href="https://2009.igem.org/Team:Edinburgh/team%28supervisors%29">Supervisors</a></li>
<li><a href="https://2009.igem.org/Team:Edinburgh/team%28supervisors%29">Supervisors</a></li>
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        <li><a href="https://2009.igem.org/Team:Edinburgh/team%28our message%29">Our Message</a></li>
 
         <li><a href="https://2009.igem.org/Team:Edinburgh/team%28gallery%29">Gallery</a></li>
         <li><a href="https://2009.igem.org/Team:Edinburgh/team%28gallery%29">Gallery</a></li>
         <li><a href="https://2009.igem.org/Team:Edinburgh/team%28contacts%29">Contacts</a></li>
         <li><a href="https://2009.igem.org/Team:Edinburgh/team%28contacts%29">Contacts</a></li>
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<b> Abstract </b> <br /><br />
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<b> Personal note </b> <br /><br />
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Participating in the iGEM competition gives the opportunity to people to meet like-minded scientists around the world. The whole structure of the competition promotes the creation of a global scientific community, removing boundaries and making collaboration between different disciplines of science easier. Such a mentality is needed for tackling scientific issues of this era. Science has reached such a level where everyone has become
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so specialised, that sometimes the bigger picture is lost. Hopefully all of us can make a change for the future generations. Participating in iGEM inspired me in looking further into the beneficial prospects of synthetic biology and has motivated me to look further into this branch of science.
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Our project is concerned with the detection of both TNT and nitrites/ nitrates. We have designed two distinct pathways, each detecting the relevant substances. Via signal integration, both pathways interact to give a different visual signals depending on the presence or absence of our target chemicals.
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In this section, we present a simplified explanation of how our system operates from a practical point of view. The first aspect to point out is that we intend for the bacteria to be spread over affected areas with an aeroplane. The resulting colour pattern will be viewed at night. The visual outcome results are summarized in Table 1.
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You will notice that this system has a limitation – When TNT is present in the absence of nitrite, there will be no visual outcome. This is because enhanced yellow fluorescent protein (EYFP) is produced in the presence of TNT and it is not excitable by visible light. However, in the presence of nitrite/ nitrates, luciferase will produce blue light that can excite EYFP. Adding a TNT degrading enzyme to our system solves this problem. The enzyme we have incorporated is PETN reductase, a nitroreductase enzyme from <i>Enterobacter cloacae</i> (Accession #: U68759, BBa_K216006). This enzyme will be produced in the presence of TNT and will degrade TNT to nitrites (French, 1998). Furthermore, TNT is degraded by naturally occurring soil flora and fauna (French, 1998). Hence, we are confident that TNT will always be present with nitrites in the soil.
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<th colspan="2"><center>Chemical</center></th>
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<th rowspan="2"><center>Visual outcome</center></th>
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</tr>
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<tr>
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<th><center>TNT</center></th>
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<th><center>Nitrates/Nitrites</center></th>
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</tr>
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<tr>
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<td><center>Absent</center></td>
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<td><center>Absent</center></td>
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<td><center>No visual outcome</center></td>
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</tr>
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<tr>
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<td><b><center>Present</center></b></td>
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<td><center>Absent</center></td>
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<td><center>No visual outcome</center></td>
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</tr>
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<tr>
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<td><center>Absent</center></td>
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<td><b><center>Present</center></b></td>
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<td><font color="blue"><center>Blue light</center></font></td>
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</tr>
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<tr>
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<td><b><center>Present</center></b></td>
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<td><b><center>Present</center></b></td>
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<td><font color="#f7b60a"><center>Yellow light</center></font></td></tr> </table>
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<i>Table 1. Visual outcome in different combinations of the detected chemicals</i>
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<br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br />
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<b>I am confused, what is the advantage of having two colours?</b> <br /><br />
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The colour pattern to be expected is quite simple- If you imagine TNT molecules diffusing away from their source of origin in all directions, you will realise that a pattern of concentric circles pinpointing the location of the landmine will be formed. As TNT is further away from the point of origin it becomes scarcer, and nitrites will predominate giving rise to a blue colour, whereas nearer the origin TNT will be in higher concentration giving rise to a yellow light. The predicted signal output in the presence of TNT is two concentric circles, blue on the outside, and yellow on the inside (Figure 1). If you would like more information on that, why don’t you check our <a href="https://2009.igem.org/Team:Edinburgh/modelling%28overalldescription%29">modelling page</a>?
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The two-colour system allows us to pinpoint the location of a landmine with a higher precision - imagine trying to pinpoint small areas of light in the night compared to looking for big areas of light with two different colours indicating the actual landmine position. More importantly, this two-colour system boasts a safety feature by creating a “buffer” zone in addition to indicating the exact position of a landmine. In this way, a person walking through a minefield in which the bacteria are spread will know when they are approaching a landmine long before reaching it. This prevents potential explosion of the mine.
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<br /><br />
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<b>Is it safe to spread synthetic bacteria on the soil?</b><br /><br />
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If you have concerns about biosafety or ethical issues, visit our <a href="https://2009.igem.org/Team:Edinburgh/ethics%28introduction%29">ethics</a> and <a href="https://2009.igem.org/Team:Edinburgh/ethics%28biosafety%29">biosafety</a> pages.
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<center><i>Figure 1. Expected visual outcome of our system </i></center>
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<font size=2>Edinburgh University iGem Team 2009</font>
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<font size=2>Edinburgh University iGEM Team 2009</font>
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Latest revision as of 22:55, 21 October 2009

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Biology - Overall description
Personal note

Participating in the iGEM competition gives the opportunity to people to meet like-minded scientists around the world. The whole structure of the competition promotes the creation of a global scientific community, removing boundaries and making collaboration between different disciplines of science easier. Such a mentality is needed for tackling scientific issues of this era. Science has reached such a level where everyone has become so specialised, that sometimes the bigger picture is lost. Hopefully all of us can make a change for the future generations. Participating in iGEM inspired me in looking further into the beneficial prospects of synthetic biology and has motivated me to look further into this branch of science.
Vasilis
Our project is concerned with the detection of both TNT and nitrites/ nitrates. We have designed two distinct pathways, each detecting the relevant substances. Via signal integration, both pathways interact to give a different visual signals depending on the presence or absence of our target chemicals.

In this section, we present a simplified explanation of how our system operates from a practical point of view. The first aspect to point out is that we intend for the bacteria to be spread over affected areas with an aeroplane. The resulting colour pattern will be viewed at night. The visual outcome results are summarized in Table 1.

You will notice that this system has a limitation – When TNT is present in the absence of nitrite, there will be no visual outcome. This is because enhanced yellow fluorescent protein (EYFP) is produced in the presence of TNT and it is not excitable by visible light. However, in the presence of nitrite/ nitrates, luciferase will produce blue light that can excite EYFP. Adding a TNT degrading enzyme to our system solves this problem. The enzyme we have incorporated is PETN reductase, a nitroreductase enzyme from Enterobacter cloacae (Accession #: U68759, BBa_K216006). This enzyme will be produced in the presence of TNT and will degrade TNT to nitrites (French, 1998). Furthermore, TNT is degraded by naturally occurring soil flora and fauna (French, 1998). Hence, we are confident that TNT will always be present with nitrites in the soil.














I am confused, what is the advantage of having two colours?

The colour pattern to be expected is quite simple- If you imagine TNT molecules diffusing away from their source of origin in all directions, you will realise that a pattern of concentric circles pinpointing the location of the landmine will be formed. As TNT is further away from the point of origin it becomes scarcer, and nitrites will predominate giving rise to a blue colour, whereas nearer the origin TNT will be in higher concentration giving rise to a yellow light. The predicted signal output in the presence of TNT is two concentric circles, blue on the outside, and yellow on the inside (Figure 1). If you would like more information on that, why don’t you check our modelling page?

The two-colour system allows us to pinpoint the location of a landmine with a higher precision - imagine trying to pinpoint small areas of light in the night compared to looking for big areas of light with two different colours indicating the actual landmine position. More importantly, this two-colour system boasts a safety feature by creating a “buffer” zone in addition to indicating the exact position of a landmine. In this way, a person walking through a minefield in which the bacteria are spread will know when they are approaching a landmine long before reaching it. This prevents potential explosion of the mine.

Is it safe to spread synthetic bacteria on the soil?

If you have concerns about biosafety or ethical issues, visit our ethics and biosafety pages.
Edinburgh University iGEM Team 2009

Retrieved from "http://2009.igem.org/Team:Edinburgh/biology(overalldescription)"