Team:Edinburgh/projectmain(overall)

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<div id=menuitem >  <a href="#"> Overall description </a> </div>  
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<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/projectmain%28overall%29"> Overall Description </a> </div>  
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<div id=menuitem >  <a href="#"> Motivation </a> </div>  
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<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/projectmain%28motivationl%29"> Motivation </a> </div>  
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<div id=menuitem >  <a href="#"> Why we differ? </a> </div>
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<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/projectmain%28whywediffer%29"> Why We Differ? </a> </div>
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<div id=menuitem >  <a href="#"> Deliverables </a> </div>
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<div id=menuitem >  <a href="https://2009.igem.org/Team:Edinburgh/projectmain%28glanceatthefuture%29"> Glance At the Future </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/projectmain%28references%29"> References </a> </div>
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   <li class="dir">Introduction
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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%28references%29">References</a></li>
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  <li><a href="./">Submitted parts</a></li>
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    <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%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%28results%29">Results</a></li>
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    <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/modelling%28overalldescription%29" class="dir">Modelling</a>
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     <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/modelling%28overalldescription%29">Overall Description</a></li>
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     <li><a href="https://2009.igem.org/Team:Edinburgh/modelling%28generegulatorynetwork%29">Gene Regulatory Network</a></li>
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     <li><a href="https://2009.igem.org/Team:Edinburgh/modelling%28reallifemodelling%29">Real Life Modelling</a></li>
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    <li><a href="https://2009.igem.org/Team:Edinburgh/reallifeapplication%28scaleup%29">Scale Up</a></li>
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    <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>
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    <li><a href="https://2009.igem.org/Team:Edinburgh/modelling%28references%29">References</a></li>
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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%28legislationissues%29">Legislation issues</a></li>
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    <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%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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   <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">Introduction</a></li>
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      <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28conceptsandtechnology%29">Concepts and Technologies</a></li>
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      <li><a href="https://2009.igem.org/Team:Edinburgh/newinformatics%28globetutorial%29">Globe Tutorial</a></li>
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      <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/results">Results</a></li>
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  <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%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>
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<li><a href="https://2009.igem.org/Team:Edinburgh/team%28teammembers%29">Team Members</a></li>
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<li><a href="https://2009.igem.org/Team:Edinburgh/team%28advisors%29">Advisors</a></li>
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        <li><a href="https://2009.igem.org/Team:Edinburgh/team%28our message%29">Our Message</a></li>
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        <li><a href="https://2009.igem.org/Team:Edinburgh/team%28gallery%29">Gallery</a></li>
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        <li><a href="https://2009.igem.org/Team:Edinburgh/team%28contacts%29">Contacts</a></li>
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        <li><a href="https://2009.igem.org/Team:Edinburgh/team%28acknowledgements%29">Acknowledgements</a></li>
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<font color="#323131" style="font-size:14px;float:left;margin-left:20px;margin-top:20px;"><b>Overall description</b></font>
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<font color="#323131" style="font-size:14px;float:left;margin-left:20px;margin-top:20px;"><b>Top view - Overall description</b></font>
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Our project is concerned with the detection of both the presence of TNT and nitrites/nitrates. We have designed two different pathways, each concerned with the detection of the mentioned substances. These will interconnect to give a different visual signal depending on the presence or absence of our target chemicals. <br /><br /> 
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Before we proceed in a detailed explanation of the biological system it would be useful to demonstrate a simplified explanation of how our system would operate from a practical point of view. The first think to point out is that the bacteria are meant to be spread with an aeroplane over the affected areas and the colour pattern will be viewed over night. An overview of the visual outcome is shown in table 1.
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The first limitation someone might find in this system is that if TNT alone is present then there is not going to be any visual outcome. This problem is solved by adding a TNT degrading enzyme to our chassis, namely a nitroreductase enzyme from Enterobacter cloacae (Pubmed entry:________, Biobrick #:________). This enzyme will be transcribed in the presence of TNT and will produce nitrites in the process of degrading TNT (Christopher E. French 1998). This, along with the fact that TNT is naturally degraded by other soil flora and fauna (Reference) allows us to be confident enough that TNT will always be present with nitrites in the soil overcoming this limitation. <br /><br />
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<th colspan="2"><center>Chemical</center></th>
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<th rowspan="2">Visual outcome</th>
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<th>TNT</th>
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<th>Nitrates/Nitrites</th>
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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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<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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<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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<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>
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<i>Table 1. Visual outcome in different combinations of the detected chemicals</i>
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<b>I am confused, why do you need to have two colours? And if I decide to use your system what colour pattern should I expect?</b>
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The colour pattern to be expected is quite simple, if you imagine that molecules diffuse away from their source of origin in all directions you will realise that you will get concentric circles pinpointing the location of the landmine. 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. So in an idealistic environment you will get two concentric circles, blue on the outside, and yellow on the inside. If you would like more information on that, why don’t you check our modelling page?
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The two colour system allows us to pinpoint the location of a landmine with a higher precision (just 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), and most importantly it not only indicates the position of a landmine but it also creates a so-called “buffer” zone. In this way a person walking through a mine field in which the bacteria are spread, will know that they are possibly approaching a landmine long before they reach it. This is very useful for safety reasons.
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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 biosafety or ethical issues why don’t you visit our ethics and bio-safety pages?
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<b>Detection pathways: in detail</b>
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<br /><br />
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Now that you have understood the general outline of how our system works, why don’t you read further on, for a more detailed approach to our system? If you have any questions please don’t hesitate to contact us.
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<b>Nitrite/nitrate detection system:</b>
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<br /><br />
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As mentioned in the introduction, once in the soil, the landmines often leak (Thomas F. Jenkins 2001). The main chemicals that will leak from TNT filled landmines are 1,3-DNB, 2,4-DNT, and 2,4,6-TNT (Thomas F. Jenkins 2001).
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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 12:15, 6 October 2009

Top view - Overall description
Personal note

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Our project is concerned with the detection of both the presence of TNT and nitrites/nitrates. We have designed two different pathways, each concerned with the detection of the mentioned substances. These will interconnect to give a different visual signal depending on the presence or absence of our target chemicals.

Before we proceed in a detailed explanation of the biological system it would be useful to demonstrate a simplified explanation of how our system would operate from a practical point of view. The first think to point out is that the bacteria are meant to be spread with an aeroplane over the affected areas and the colour pattern will be viewed over night. An overview of the visual outcome is shown in table 1.
The first limitation someone might find in this system is that if TNT alone is present then there is not going to be any visual outcome. This problem is solved by adding a TNT degrading enzyme to our chassis, namely a nitroreductase enzyme from Enterobacter cloacae (Pubmed entry:________, Biobrick #:________). This enzyme will be transcribed in the presence of TNT and will produce nitrites in the process of degrading TNT (Christopher E. French 1998). This, along with the fact that TNT is naturally degraded by other soil flora and fauna (Reference) allows us to be confident enough that TNT will always be present with nitrites in the soil overcoming this limitation.

I am confused, why do you need to have two colours? And if I decide to use your system what colour pattern should I expect?

The colour pattern to be expected is quite simple, if you imagine that molecules diffuse away from their source of origin in all directions you will realise that you will get concentric circles pinpointing the location of the landmine. 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. So in an idealistic environment you will get two concentric circles, blue on the outside, and yellow on the inside. 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 (just 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), and most importantly it not only indicates the position of a landmine but it also creates a so-called “buffer” zone. In this way a person walking through a mine field in which the bacteria are spread, will know that they are possibly approaching a landmine long before they reach it. This is very useful for safety reasons.

Is it safe to spread synthetic bacteria on the soil?

If you have biosafety or ethical issues why don’t you visit our ethics and bio-safety pages?

Detection pathways: in detail

Now that you have understood the general outline of how our system works, why don’t you read further on, for a more detailed approach to our system? If you have any questions please don’t hesitate to contact us.

Nitrite/nitrate detection system:

As mentioned in the introduction, once in the soil, the landmines often leak (Thomas F. Jenkins 2001). The main chemicals that will leak from TNT filled landmines are 1,3-DNB, 2,4-DNT, and 2,4,6-TNT (Thomas F. Jenkins 2001).
Edinburgh University iGEM Team 2009

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