Team:Fudan-Shanghai/Project

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<title>2011 iGEM Fudan_Project</title>
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You are provided with this team page template with which to start the iGEM season.  You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki.  You can find some examples <a href="https://2008.igem.org/Help:Template/Examples">HERE</a>.
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<td colspan=2><h1><img src="https://static.igem.org/mediawiki/2011/e/ee/Fudan_Etree.jpg  " alt="E.tree" width=100 align=center hspace=20><b> Part I: E.Tree </b></h1></td>
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<td rowspan=2 bgcolor=#FFFFCE width=400  ><h1>Detail:</h1><font size=3>
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<b>E.trunk bacteria</b> detect nitrates in the medium and release either LasI or RhlI directed signals. It includes two circuits: the first pathway is controlled by a nitrate sensitive promoter (pYeaR), so that if the medium contains nitrates, the entire pathway will be on, RhlI (produces AHL C4-homoserine lactone), tetR and GFP will be produced. TetR then binds with pTet in the second pathway and blocks it. <br>
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If the medium contains no nitrates, the first pathway is repressed while the second one is unblocked, so LasI (produces 3OC12-homoserine lactone) and RFP will be synthesized. <br>
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<b>E.leaf bacteria </b>change color according to the signal molecules released by E.trunk. LasR and RhlR are constitutive synthesized in E.leaf; they bind to the LasI and RhlI directed signals, respectively. <br>
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<br><b>Overall effect:</b>
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  If the medium contains nitrates, E.trunk releases C4-homoserine lactone (the product of RhlI); the signal molecules enter E.leaf bacteria and bind to RhlR. This RhlI/R complex then interact with pRhl promoter and green fluorescence is emitted. Meanwhile, RhlI molecules further synthesized in E.leaf bacteria, so that not only bacteria grow along the border but all E.leaf bacteria on the plate will turn green. <br>
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  Similarly, if the medium lacks nitrates, E.trunk bacteria release 3OC12-homoserine lactone  (the products of LasI) and the “leaves” turn yellow.
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<td bgcolor=#CEFFCE align=center><a href="https://static.igem.org/mediawiki/2011/a/a9/E.tree_detail.JPG"><img src="https://static.igem.org/mediawiki/2011/a/a9/E.tree_detail.JPG" height=300></a></td>
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<td><a href="https://static.igem.org/mediawiki/2011/e/e8/Fudan_Testall.JPG"><img src="https://static.igem.org/mediawiki/2011/a/aa/Fudan_exam.JPG" width=500></a></td>
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<td colspan=2><h1><img src="https://static.igem.org/mediawiki/2011/9/96/DINER_SERVICE.jpg" alt="E.DinnerService" width=100  align=center hspace=20><b> Part II: Dinner Service </b></h1></td>
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<td rowspan=2 bgcolor=#FFE6D9 width=400  ><h1>Detail:</h1><font size=3>
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<b>The "customer" E.coli </b>is consisted of two pathways.
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The first pathway codes IsrR, a siganl that activates the second pathway, and aiiA, which degrades IsrR. The promoter for IsrR is stronger than that of aiiA. In that case, part of the IsrR will be degraded, but still some will be able to activate the second pathway. When the second pathway is activated, LuxI is produced and CFP emitted.<br>
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<b>The "chef" E.coli</b> also includes two pathways. The first synthesize LuxR, in the presence of AHL( the product of LuxI), it binds to the promoter LuxR and LuxS( the meal) is served, YFP is emited to show this process.<br><br>
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In sum, the hungry customer orders the meal by giving out signal "luxI". The "chef" containing luxR, senses the "order" signal and prepares for the meal-LuxS. The dinner service is accompanied with yellow fluorescent.
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When the customer is full, IsrR synthesis is inhibited, the aiiA degrades the remaining IsrR in the cell, thus the production of LuxI is stopped. And meal is no longer served.
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<td bgcolor=#E2C2DE align=center><a href="https://static.igem.org/mediawiki/2011/a/a4/DinnerService.JPG"><img src="https://static.igem.org/mediawiki/2011/a/a4/DinnerService.JPG" height=300 alt="dinner service"></a></td>
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<td><a href="https://static.igem.org/mediawiki/2011/b/bc/Dinner2.jpg"><img src="https://static.igem.org/mediawiki/2011/b/bc/Dinner2.jpg" width=500 height=150></a></td>
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<td colspan=2><h1><img src="https://static.igem.org/mediawiki/2011/1/11/Fudan_neonLights.jpg" alt="E.Lights" width=100 align=center hspace=20><b> Part III: Neon Lights </b></h1></td>
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
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!align="center"|[[Team:Fudan-Shanghai|Home]]
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!align="center"|[[Team:Fudan-Shanghai/Team|Team]]
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<td  bgcolor= #FFECF5 width=600  ><h1>Detail:</h1><font size=3>
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!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=Fudan-Shanghai Official Team Profile]
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In the project of neon lights, we intended to have E.coli engineered for emitting one color of luminescence during exponential phase and another color during stationary phase, so that it is convenient to identify the growth phase and may also be utilized for other purposes.<br>
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!align="center"|[[Team:Fudan-Shanghai/Project|Project]]
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To achieve this goal, we chose BBa_J45992, a stationary phase promoter, and BBa_J45996, a promoter that is only active during exponential phase and assemble different luciferase under the control of the promoters. Parts of various luciferases have been obtained from the registry submitted by the team of Cambridge in 2010, for example, BBa_K325210, BBa_K325229, etc. System of degradation, such as ClpXP, can be used to optimize the project by degrading the previous luciferase when the latter is being produced, to make the latter color purer and the process of color changing faster. In addition, the fluctuation of the lusiferase activity due to the growth should be taken into consideration.  
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!align="center"|[[Team:Fudan-Shanghai/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:Fudan-Shanghai/Modeling|Modeling]]
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<td bgcolor=#F1E1FF align=center><a href="https://static.igem.org/mediawiki/2011/d/d1/Neonlights.JPG"><img src="https://static.igem.org/mediawiki/2011/d/d1/Neonlights.JPG" width=300></a></td>
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!align="center"|[[Team:Fudan-Shanghai/Notebook|Notebook]]
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!align="center"|[[Team:Fudan-Shanghai/Safety|Safety]]
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!align="center"|[[Team:Fudan-Shanghai/Attributions|Attributions]]
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== '''Overall project''' ==
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Your abstract
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What is the first thing that comes to your mind when you see these three words: tree, neon lights and dinner service?  Christmas. Well, exactly, and that is what our project is all about.
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Our synthetic biology project will modify several E.coli to perform different jobs:
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(1)'''Part I: E.tree'''
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The tree includes the leaf part and the trunk part. The “leaves” will change color according to the nutrients in the “soil”: if the soil is rich in nitrates, the “leaves” are green and healthy; otherwise, the leaves will turn yellow.
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(2) '''Part II: neon lights'''
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Each engineered E.coli can emit one light at first (such as red); after a while, the red light fades and another light is emitted. The different combination of such E.coli could therefore achieve the effect of neon lights.
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(3)'''Part III: dinner service'''
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The genetically modified bacteria involve a certain self-feedback system. When the “customer” is starving, it orders dinner from the “chef”; and the chef serves meals. While the “customer” is full, it releases a signal molecule and tells the “chef” that no more food is wanted, so the “chef” stops cooking.
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== Project Details==
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=== Part 2 ===
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=== The Experiments ===
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=== Part 3 ===
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== Results ==
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Latest revision as of 19:50, 5 October 2011


2011 iGEM Fudan-Shanghai Template

2011 iGEM Fudan_Project


E.tree Part I: E.Tree

Detail:

E.trunk bacteria detect nitrates in the medium and release either LasI or RhlI directed signals. It includes two circuits: the first pathway is controlled by a nitrate sensitive promoter (pYeaR), so that if the medium contains nitrates, the entire pathway will be on, RhlI (produces AHL C4-homoserine lactone), tetR and GFP will be produced. TetR then binds with pTet in the second pathway and blocks it.
If the medium contains no nitrates, the first pathway is repressed while the second one is unblocked, so LasI (produces 3OC12-homoserine lactone) and RFP will be synthesized.
E.leaf bacteria change color according to the signal molecules released by E.trunk. LasR and RhlR are constitutive synthesized in E.leaf; they bind to the LasI and RhlI directed signals, respectively.

Overall effect: If the medium contains nitrates, E.trunk releases C4-homoserine lactone (the product of RhlI); the signal molecules enter E.leaf bacteria and bind to RhlR. This RhlI/R complex then interact with pRhl promoter and green fluorescence is emitted. Meanwhile, RhlI molecules further synthesized in E.leaf bacteria, so that not only bacteria grow along the border but all E.leaf bacteria on the plate will turn green.
Similarly, if the medium lacks nitrates, E.trunk bacteria release 3OC12-homoserine lactone (the products of LasI) and the “leaves” turn yellow.

E.DinnerService Part II: Dinner Service

Detail:

The "customer" E.coli is consisted of two pathways. The first pathway codes IsrR, a siganl that activates the second pathway, and aiiA, which degrades IsrR. The promoter for IsrR is stronger than that of aiiA. In that case, part of the IsrR will be degraded, but still some will be able to activate the second pathway. When the second pathway is activated, LuxI is produced and CFP emitted.
The "chef" E.coli also includes two pathways. The first synthesize LuxR, in the presence of AHL( the product of LuxI), it binds to the promoter LuxR and LuxS( the meal) is served, YFP is emited to show this process.

In sum, the hungry customer orders the meal by giving out signal "luxI". The "chef" containing luxR, senses the "order" signal and prepares for the meal-LuxS. The dinner service is accompanied with yellow fluorescent. When the customer is full, IsrR synthesis is inhibited, the aiiA degrades the remaining IsrR in the cell, thus the production of LuxI is stopped. And meal is no longer served. 		dinner service

E.Lights Part III: Neon Lights

Detail:

In the project of neon lights, we intended to have E.coli engineered for emitting one color of luminescence during exponential phase and another color during stationary phase, so that it is convenient to identify the growth phase and may also be utilized for other purposes.
To achieve this goal, we chose BBa_J45992, a stationary phase promoter, and BBa_J45996, a promoter that is only active during exponential phase and assemble different luciferase under the control of the promoters. Parts of various luciferases have been obtained from the registry submitted by the team of Cambridge in 2010, for example, BBa_K325210, BBa_K325229, etc. System of degradation, such as ClpXP, can be used to optimize the project by degrading the previous luciferase when the latter is being produced, to make the latter color purer and the process of color changing faster. In addition, the fluctuation of the lusiferase activity due to the growth should be taken into consideration.

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