http://2013.igem.org/wiki/index.php?title=Special:Contributions/Donna&feed=atom&limit=50&target=Donna&year=&month=2013.igem.org - User contributions [en]2024-03-29T15:46:06ZFrom 2013.igem.orgMediaWiki 1.16.5http://2013.igem.org/Team:SUSTC-Shenzhen-A/Human_PracticeTeam:SUSTC-Shenzhen-A/Human Practice2013-09-27T19:48:44Z<p>Donna: </p>
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<div>[[File:prisonersdilemma1.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety and security]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
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== '''communication''' ==<br />
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|[[Image:humanpractice1.jpg|center|frame|communicate with other teams in HongKong]]<br />
|-<br />
|We introduced sythetic biology and our project to some high school students.<br />
|-<br />
|[[Image:humanpracticesustc2.jpg|left|frame|to high school students]]<br />
[[Image:humanpractice3.jpg|right|frame|to high school students]]<br />
|-<br />
|On Sept.25.2013 Jingyi Liu had a short presentation about synthetic biology and iGem in Wall Street English center at windows of the world in Shen Zhen. Since most of students there are in theri twenties or thirties, we spreaded new ideas in synthetic biology to adults~! They showed big interest in synthetic biology and even came up with their own thoughts during the presentation. What's more, after presentation, though they didn't konw any specialized word, many of them still stayed with Liu discussing about biology with body language till 10 p.m.. It was a amazing moment to make so many people curious in synthetic biology, and it was a even better moment to let them comprehend synthetic biology.<br />
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|[[File:humanpracticesustc3.jpg|left|frame|to adults]]<br />
[[File:humanpracticesustc4.jpg|right|frame|to adults]]<br />
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== '''Sponsors''' ==<br />
[[File:Sponsor-sustc.jpg|center|frame|]]</div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/AttributionsTeam:SUSTC-Shenzhen-A/Attributions2013-09-27T19:48:24Z<p>Donna: </p>
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<div>[[File:prisonersdilemma1.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety and security]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
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== Attributions ==<br />
<ul><br />
<li>Idea:All team members</li><br />
<li>Prepartions:All team members and instructors</li><br />
<li>Finding biobricks to detect:Jingyi Liu and Yan Dai</li><br />
<li>Detecting biobricks:Jingyi Liu、Zi Wang and Jian Cui</li><br />
<li>Constructing biobricks:Jingyi Liu、Zi Wang、Jian Cui、Jingnong Wang and Yan Dai</li><br />
<li>Project instructors:Wei Huang and Yinglan Zhao</li><br />
<li>Experiment instructor(help with plasmid costruction):Lizhong Liu</li><br />
<li>Main experiments:Jingyi Liu、Zi Wang、Jian Cui、Jingnong Wang and Yan Dai</li><br />
<li>Wiki:Dan Chen and Yan He</li><br />
<li>Modeling:Ningyuan Yang</li><br />
<li>Human practice:Jingyi Liu、Zi Wang、Yan He、Jian Cui and Yingzhe Shu</li><br />
<li>Captain:Jian Cui</li><br />
<li>Lab leader:Jingyi Liu</li><br />
<li>Wiki leader:Dan Chen</li><br />
</ul></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/NotebookTeam:SUSTC-Shenzhen-A/Notebook2013-09-27T19:47:57Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety and security]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
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|{{#calendar: title= SUSTC|year=2013 | month=07}}<br />
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|{{#calendar: title= SUSTC|year=2013 | month=08}}<br />
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|{{#calendar: title= SUSTC|year=2013 | month=09}}<br />
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== Notebook ==<br />
<br><br />
<br><br />
<p>&nbsp;&nbsp;&nbsp;&nbsp;We started our project in middle July. You can find every detail by clicking the date.</p><br />
<br><br />
<p>&nbsp;&nbsp;&nbsp;&nbsp;18th July to 10th Aug: Training</p><br />
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<p>&nbsp;&nbsp;&nbsp;&nbsp;12th Aug to 17th Sep: Project and biobricks.<br />
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== Protocol ==<br />
<html><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index.Preparation of LB culture">Preparation of LB culture</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index.Preparation of some antibiotic solution">Preparation of some antibiotic solution</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index.Transformation">Transformation</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index.Preservation of the bacteria">Preservation of the bacteria</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index.Extract the target DNA">Extract the target DNA</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index.The use of spectrometer">The use of spectrometer</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index.Usage of PCR-Cycler">Usage of PCR-Cycler</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index.Usage of ultraviolet spectrophotometer">Usage of ultraviolet spectrophotometer</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index. Preparation for the M9 culture"> Preparation for the M9 culture</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index.Preparation of the nitrate LB culture">Preparation of the nitrate LB culture</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index. Usage of FCM"> Usage of FCM</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index.Preparation of the gel">Preparation of the gel</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index. Recycle of the DNA in the gel and deal with gel"> Recycle of the DNA in the gel and deal with gel</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index.The recycle of the products of the PCR">The recycle of the products of the PCR</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index. check the function of the xylose and the nitrate inducible promote">Check he function of the xylose and the nitrate inducible promote</a><br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="/index.The use of the microplate reader">The use of the microplate reader</a><br><br />
</html></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ModelingTeam:SUSTC-Shenzhen-A/Modeling2013-09-27T19:47:36Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety and security]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
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== Modeling ==<br />
'''Abstract'''<br />
<p>Our model is to simulate a cell-cell mutual help system that is inspired by the classic prisoner's dilemma. We use two kinds of operated cells to act as the two prisoners. Both of them are facing the same problem comes from the environment, if they do not help each other, both of them will get into a terrible situation. Even they choose to collaborate, one may also take the risk that another man would turn traitor to him. So it’s a complex problem that how do our prisoners to choose their strategy to make themselves survive. Here are all equations and variables we have worked out.</p><br />
[[File:modelingsustc5.png]]<br />
<p>'''So, how can our system perform this prisoner’s dilemma? '''</p><br />
<p>We use the growth rate and the concentration of the cells to describe the living status of two prisoners, use Zeocin in our system to represent the punishment on our prisoners, and use the tetA(which will translate companying with the expressing of AHL) to bring Ni into the cells referring to the risk the as telling the lie. And if one receives the shield from another as sufficient AHL, he will start to produce ZeoR protein which can make him survive the Zeocin. </p><br />
'''Here are also some Differences'''<br />
<p>However, our cell-cell mutual help system also do not all obey the classic prisoners’ dilemma, first of all, one prisoner can only have two certain choices in this traditional question, be honest or crafty. But as we have mentioned before, in our system two cells use AHL to help each other, namely the concentration here stands for the attitude of our cell, well it is right the concentration not the existence of AHL makes sense in our system, so our prisoner have a chance to make an elastic choice, they can decide to what level the cooperation will be put into effect. This important difference makes our system more close to the realistic. </p><br />
<p>Then one prisoner will never really die in a classic situation, but in ours there exists some possibility that one cell can actually die out which will result in a big crash. This is what we should put our eyes on.</p><br />
'''Test'''<br />
<p>To confirm whether our simulations can work out a good result, we want to test some important parameters to see whether our subsystem can work properly,</p><br />
'''1.the effect of Zeocin'''<br />
<p>We put our prisoners into a person to see what will happen to this poor man, this will help us understand how powerful the punishment is as well as tell us how much Zeocin we should use to create a temperate environment stress. <br />
As we can see from this figure, this antibiotic leads to a quick death of our prisoner. Without help, one man can hardly get out of this problem.</p><br />
[[File:modelingsustc6.png]]<br />
<p>'''2.separate cell in the environment contain AHL'''</p><br />
<p>To test our relationship between the concentration of AHL and the concentration of our cells, we conduct this test. We put one of our prisoners into AHL concentration gradients to make sure where the efficient concentration of AHL lies, and we get the final cell concentration for each AHL gradients.</p><br />
<p>This EC can tell us some important things such as whether there exists any sensitivity difference of AHL between the two cells, it can help us have a better understanding of the cooperation between these two cells.<br />
As we can see there is a cliffy slope in our data, which give us the idea that the relationship between the AHL and cell concentration is not simply linear, so we should consider twice before we change this influential variable.</p><br />
[[File:modelingsustc7.png]]<br />
<p>'''3.the show begins'''</p><br />
Result 1:Good Cooperation<br />
<p>If both of our prisoners try to help each other things will be much better</p><br />
[[File:modelingsustc11.png]]<br />
Result 2: a Traitor<br />
<p>If one of our prisoners wants to get other help without offering any reward, he may be well benefited at first, but as his partner gets into trouble, he will lose his luck. This though go against the realistic, we can also take well advantage of this flaw in our safety idea. (In the four cases of prisoners’ dilemma there are three cases that the bad man can escape but in our model only if they are well cooperate with each other then they will have chance to run away, but such a good cooperate cannot be easily achieved especially outside the Lab)</p><br />
[[File:modelingsustc8.png]]<br />
<p>'''Result 3: The Egoists'''</p><br />
If both guys are imaginary smart, and have a strong believe that his partner will forswear for him, it’s obvious that they will get deserved penalty.<br />
[[File:modelingsustc9.png]]<br />
<p>'''Some more interesting results'''</p><br />
<p>The results all above are just considering the same situation that both the prisoners have a similar personality, that says our two cells have a very symmetry structure, their physiological parameters are nearly the same. Basing on this, every cell can act the same behavior when meet the same change in the environment.</p><br />
<p>However, two pieces of leaves will never coincide in the world. We can’t adjust everything to meet our plan and this considerable material difference gives us the opportunity to have a sight of the real prisoner’s dilemma.</p><br />
<p>What will happen if we put two people with different sensibility of other’s goodwill into this dilemma? To achieve this, we can simply adjust the Hill coefficient of the differential equation of Zeor, to see what have found.</p><br />
[[File:modelingsustc10.png]]<br />
<p>There appears a clear game between our prisoners, and unlike other results this dynamic equilibrium crashed at last. It’s usually a common sense that the damped oscillation may lead to a stable equilibrium, , but you can hardly tell which people made the mistake. How our prisoners can perform such clumsy play, maybe we can have a further study.</p><br />
<p>This media liked the whole modeling of our project.</p><br />
[[Media:modelingsustc.pdf]]</div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/PartsTeam:SUSTC-Shenzhen-A/Parts2013-09-27T19:47:14Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety and security]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
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<groupparts>iGEM013 SUSTC-Shenzhen-A</groupparts></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ProjectTeam:SUSTC-Shenzhen-A/Project2013-09-27T19:46:52Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety and security]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
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== '''Overall project''' ==<br />
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{|align="justify"<br />
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== '''Abstract''' ==<br />
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<p> <br />
There are many applications of the game theory in some aspects of our life. Each individual has two kinds of choices--to betray or stay silent, and the choice you make would determine your fate. To betray the other side, you may risk being revenged. While staying silent, companion's betrayal may hurt you deeply. As for our project, we work out a new way to imitate the game theory by constructing a community of two E. Coli bacteria. Here we use the growth rate of each species to represent its fate. The effect of one's silent or betrayal on the other species' fate is acted through intercellular signal molecules of two quorum sensing systems. Each signal molecule regulates the expression of toxic genes in the other species and reduces its growth rate. We characterize the consequence of each strategy by quantitatively measure the growth rates of each species in the community.</p><br />
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== '''Background''' ==<br />
<br />
'''Why do we want to do this project?'''<p><br />
We find that most of the researches in synthetic biology aim to study the interaction between parts of a single system. But few focus on the interaction between systems with multi-elements. However, in the real world, there are complex competition and cooperation among the various creatures. And they can work together to achieve a certain function, for example, different kinds of yeast in brewing beer. There is no lack of the ideas of game theory in these processes. So we chose a classical method—prisoner's dilemma as a model to design our project. <br />
</p><br />
'''The importance of our project:'''<p><br />
Our project can simulate the interaction among multiple systems in reality and the final state of them. Through a well-known issue of game theory, we can give synthetic biology and iGem greater publicity from many perspectives. Furthermore, after a slight modification, the project can provide us with an interesting solution to security.<br />
</p><br />
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== '''Project Details'''==<br />
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=== our design ===<br />
[[File:qq1.jpg]]<br />
<p>Parts:</p><br />
<p>Communication: quorum sensing</p><br />
<p>LuxI produces 6HSL, 6HSL cross membrane, 6HSL binds to LuxR, LuxR activate promoter Plux </p><br />
<p>LasI produces 12HSL, 12HSL cross membrane, 12HSL binds to LasR, LasR activate promoter Plas</p><br />
<p>Poissonness genes:</p><br />
<p>tetA: import Nickel into cell, which kills cell</p><br />
<p>Zeo-r: Zeocin damage DNA and kills cell, Zeo-r binds and neutralize Zeocin</p><br />
<p>Truth Table</p><br />
[[File:tablesustc.jpg]]<br />
<p>Tuning gene expression: repressor and inducer</p><br />
<br />
[[File:cella.jpg]]<br />
<p>'''Cell A:'''<br />
Constant expressions:</p><br />
<p>'''LuxR'''(with C6HSL, activate pLux, express Zeo-r): promoter J23100 and rbs B0034</p><br />
<p>'''Pcon''': promoter J23100 to J23107 and rbs B0034</p><br />
<p>'''YFP''' (yellow fluorescent protein labeled cell A): promoter pCon, rbs </p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r,''' adjusted by C6HSL, produced by LuxI from '''cell B''', depends on cell B density </p><br />
<p>'''LasI:''' adjusted by Pcon, LasI produces C12HSL, control cell B</p><br />
<p>'''tetA:''' adjusted by Pcon</p><br />
<br />
<p>'''Zeocin, Nickel''' concentration are controlled by you</p><br />
<p>'''C12SHL '''concentration: controlled by cell A concentration </p><br />
<p>'''Nickel '''either kill cell or slow cell growth: '''tetA''' increase sensitivity of '''cell B '''to''' Nickel''':</p><br />
<p>zeocin either kill cell or slow cell growth:Zeo-r decreases sensitivity of''' cell B''' to''' zeocin'''</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
<p>pMB1 and p15A: control plasmid replication in E coli</p><br />
<p>Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
</p><br />
[[File:cellb.jpg]]<br />
<p>'''Cell B:'''<br />
Constant expressions:</p><br />
<p>'''LasR''' (with C12HSL, activate pLux, express Zeo-r): promoter J23100 to J23107 and rbs B0034</p><br />
<p>'''RFP '''(red fluorescent protein labeled cell B): promoter pCon, rbs</p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r''', adjusted by C12HSL, produced by LasI from cell A, depends on cell A density and Pcon.</p><br />
<p>'''LuxI''': adjusted by Pcon, LuxI produces C6HSL, control cell A</p><br />
<p>'''tetA''': adjusted by Pcon</p><br />
<p>'''Zeocin, Nickel concentration are controlled by you</p><br />
<p>'''C6HSL''' concentration: controlled by cell B concentration and Pcon</p><br />
<p>tetA increase sensitivity of cell B to Nickel: Nickel either kill cell or slow cell growth<br />
Zeo-r decreases sensitivity of cell B to zeocin: zeocin either kill cell or slow cell growth</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli<br />
Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
<br />
=== Experiment process ===<br />
Please refer to our <br />
<html><br />
<a href="/Team:SUSTC-Shenzhen-A/Notebook">protocol and notes</a> <br />
</html> for more details.<br />
<br />
== '''Results''' ==<br />
<br />
=== project results===<br />
<p>What we have done are the plasmid construction and the early experiments ,because of the time limite. Here are some results of our project</p><br />
[[File:projectresult.jpg]]<br />
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=== modeling results ===<br />
<br />
=='''Biobricks checking'''==<br />
=== results ===<br />
<p>We chose four biobricks to detect after search. They are xylose,KNO<sub>3</sub>,glucose and 12HSL.</p><br />
'''BBa_K733018: xylose'''<br />
<br />
[[File:xylose-gfp.jpg|500px]]<br />
<p>First we used the microplate to detect the fluorescence of this part, because we could not see the transition point and we were wondering what it would be look like. The data we got is not so good, for we didn’t see the transition point obviously, and also has some differences comparing to the data from HKUST. According to the detecting from HKUST, fluorescence produced in about 5% xylose is more than that in 10% xylose, however what we got is fluorescence produced in 5% xylose than that in 10% xylose.</p><br />
<br />
[[File:xylosesustc.jpg|xylose|600px]]<br />
<p>Since we didn’t get what we really want using microplate, we tried FCM this time. In 0% xylose culture, we almost got no fluorescence produced and in 0.003% xylose culture we saw obvious fluorescence came out. There was an obvious tendency that the efficiency of the promoter increased as the xylose concentration gathered up. However, with the increase of xylose concentration, the fluorescence increased choppily. What was amazing was that the fluorescence we got was 10 times brighter than the result the HKT got, which appeared to be great.</p><br />
<p>Another interesting thing is most of the cell we detected had no fluorescence produced. Then we guess that may because the xylose molecules taken in the different cell are different, or may because the copy number in each cell is different. Maybe it has some relationship with epigenetics. </p><br />
<br />
'''BBa_K774007: KNO<sub>3</sub>'''<br />
<br />
[[File:kno3sustc.jpg|KNO3]]<br />
<p>In this part we got a similar beginning, but have a different ending. With the increasing of nitrate of potash, the fluorescence produced by single cell increases slowly at the beginning but rapidly later. However, according to the data from NRP-UEA-Norwich, the fluorescence starts to decrease at the 20mM nitrate of potash.</p><br />
<br />
'''BBa_K741002: glucose'''<br />
<br />
[[File:glucosesustc.jpg|glucose]]<br />
<p>Compared with testing result from USTC_China, we’ve got a better data. According to the data from USTC_China, after adding glucose, the fluorescence reduces only about 10% in the most obvious one. However, we got a clear reduce in the production of fluorescence. In about 10-2.4M glucose, the fluorescence has left only a half in one cell. With the increasing of glucose, the fluorescence/OD continuously decreases, and at about 10-1M glucose, the fluorescence/OD remains very low. </p><br />
<br />
<br />
<html><br />
<script><br />
$(document).ready(function(){<br />
$("#toc").css("position","fixed");<br />
$("#toc").css("left","0px;");<br />
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<br />
<b><p>References</p></b><br />
<br />
<br />
<html><br />
<p>Click the <a href="/index.reference">Reference</a> to get more information.<br />
</html></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/TeamTeam:SUSTC-Shenzhen-A/Team2013-09-27T19:46:32Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma1.jpg]]<br />
<br />
<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety and security]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
<br />
<br />
<br />
'''Advisors:'''<br />
<br />
*'''He Jiankui(jiankuihe)''':Gene sequencing<br />
*'''Huang Wei(linghu_y2k)''':Mathematical modeling<br />
*'''Liu Xianggeng(alphasnowzone)''':Major in chemistry<br />
*'''Lv Chenchen(Levia)''':Major in biology<br />
*'''Zhang Mengshi(Cuya)''':Major in biology<br />
<br />
'''Undergrads:'''<br />
<br />
*'''Chen Dan(Donna)''':Datum Collector<br />
*'''Cui Jian(Yohane)''':Biology Database<br />
*'''Dai Yan(DY)''':Datum Collector<br />
*'''He Yan(HY)''':Datum Collector<br />
*'''Liu Jingyi(lisa.deep)''':Datum Collector<br />
*'''Shu Yingzhe(SYZ)''':Datum Collector<br />
*'''Wang Jingnong(WangJingnong)''':Datum Collector<br />
*'''Wang Zi(prince)''':Datum Collector<br />
|<br />
<gallery><br />
Image:yangningyuan.jpg|Ningyuan Yang<br />
Image:Example2_Team_member_2.png|Jingyi Liu<br />
Image:Example2_Team_member_3.png|Dan Chen<br />
Image:Example2_Team_member_4.png|Zi Wang<br />
Image:wangjingnong.jpg|Jingnong Wang<br />
Image:heyan.jpg|Yan He<br />
Image:daiyan.jpg|Yan Dai<br />
Image:shuyingzhe.jpg|Yingzhe Shu<br />
Image:cuijian.jpg|Jian Cui<br />
</gallery><br />
|}<br />
== Brief self-introduction ==<br />
<br />
<br />
<p><br />
<b>Jingyi Liu</b><br />
</p><br />
<p>My name is Liu Jingyi and I'm a Chinese girl with a height of 174 cm and long curly hair.I love shopping like many girls and sports,especially cycling.I love biology very much,for it's amazing to know about ourselves and doing experiments to find out something new is really attractive.I hope we can achieve our idea on prisoner's dilemma.</p><br />
<p><br />
<b>Jingnong Wang</b><br />
</p><br />
<p>My name is Wang Jingnong and I am a sophomore at SUSTC. Fascinated by the vitality and mystery of plants and animals, I fell in love with biology when I was at a young age. I was introduced to synthetic biology by IGEM, which gives me a precious chance to do research in relevant area.So far, I have been learning a lot about synthetic biology, biological process lab work and teamwork skills with my friends. It was quite a big challenge to comprehend so much material in such a short time, but I am having a wonderful time since I am able to get in depth with something I truly enjoy!</p><br />
<p><br />
<b>Jian Cui</b><br />
</p><br />
<p>My name is Cui Jian .I'm now the team leader of this iGEM team .I am 19 years old ,and was born in Jiangsu Province ,China .Generally speaking ,I am hardworking when doing the things that I am interested in .But what puzzles me most is my poor English .It's a great honor for me to have the chance join this year's iGEM Jamboree.</p><br />
<p><br />
<b>Zi Wang</b><br />
</p><br />
<p>I am from the Igem 2013 SUSTC-Shenzhen-A team and you can call me WangZi.<br />
I am fond of designs of various synthetic biology accompyed by many interesting experiments.<br />
As for my characters,I am active but a little shy,which I desire to overcome through this competiton.<br />
I am glad that I have this chance to know more friends and attend the jamboree with you guys<br />
from all over the world </p><br />
<p><br />
<b>Ningyuan Yang</b><br />
</p><br />
<p>Hey friends! Who you are staring at is a happy guy from SUSTC, he likes almost everything comes into his life and wants to have a well comprehension of them. So he joins the Igem to try to have some fresh things as well as make some difference. Who knows what he will meet there. Maybe at last someone would remember there was once a guy named Ningyuan Yang.</p><br />
<p><br />
<b>Dan Chen</b><br />
</p><br />
<p>Hi ! I’m Dan Chen . You can call me Donna too . I’m outgoing and easygoing , and I love making new friends . Biology will be my major course in the next two years . I think biology is very interesting . We could explore nature 、ourselves and almost everything . And I think what igemers have done is amazing . I feel so lucky that I could join in our project.</p><br />
<p><br />
<b>Yan Dai</b><br />
</p><br />
<p>My name is Yan DAI. I am interested in molecular biology and organic chemistry. I got lots of experience and knowledge in iGEM, which were hard to get in class. The process is tough but meaningful. We met some difficulties in the lab, but dealing with them is quite fun. And I really enjoy the time with my teammates.</p><br />
<p><br />
<b>Yan He</b><br />
</p><br />
<p>Hi everyone! I am Yan He who always smile. I am interested in Synthetic biology and it is my great honor to take part in this competition, this summer in the lab was so unforgettable. In my spare time, I enjoy watching movie and listen to the music, and I also like reading some books about psychology.</p><br />
<p><br />
<b>Yingzhe Shu</b><br />
</p><br />
<p>My name is Yingzhe Shu, and you can also call me Vincent Shu. I’m a sophomore from the South University of Science and Technology of China. And I feel so excited that I can take part in iGEM this summer.<br />
<br />
I’m a sports’ fan. So in my spare time, I like to go outsides and do all kinds of sports. But soccer is my favourite. I’m also the top player in our school soccer team. I also enjoy the time when I listen to the music, especially the American and European pop music.<br />
<br />
I learned so much during this summer with iGEM. And I hope you all enjoy it too!</p></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-ATeam:SUSTC-Shenzhen-A2013-09-27T19:45:58Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma1.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety and security]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== '''Welcome~''' ==<br />
<br />
<br><br />
<br />
[[File:welcome3.jpg|center|frame]]<br />
<b><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This is SUSTC-Shenzhen-A.</p><br />
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;We are sophomores from South University of Science and Technology of China (SUSTC).</p><br />
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Our main project is about quorum sensing. </p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;You can get more information about our project by clicking other pages. </b><br />
<br><br />
[[File:sustc group photo.jpg|center|frame]]<br />
<br><br />
<br><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[File:wangzishiyan.JPG]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[[File:liujingyishiyan.JPG]]<br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br><br />
<br></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/SafetyTeam:SUSTC-Shenzhen-A/Safety2013-09-27T19:45:34Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocl and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety and security]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== '''Security''' ==<br />
<p>One of the most essential problem urgent to solve in synthetic biology is the security problem. It has been a troublesome part whether we can pursue that the constructed bacteria cannot survive in the circumstance with some target genes imported by us. As for our project, though there is no safety worry, we come up with an original way to synthesis one kind of standard constructed bacteria, if slightly simplified by our project. In our previous project there are three cases when criminal can survive, but based on the safety consideration, we cannot let any bacteria alive in the wild, so we refer to this design because there is nearly no possibility for them to survive in the wild, for the living conditions have to reach several high levels, which is hard to achieve in the natural circumstance. What’s more, we have made mathematic model of it, which offers the theoretic evidence of it and make it more feasible. The design is like the figure below.</p><br />
[[File:safetysustc.png]]<br />
<p>Just as the graph has shown, we make some modifications in our previous design. We remain the communication pair genes as the message access between them-LuxR and LasR, the products of which-6HSL and 12HSL still function as the signals between the two bacteria communities. It’s apparent that reporter genes are unrelated to the safety problem. So just leave them out. In the meantime, we cut off the tetA gene directly and import the cl gene exactly the same place of the zeo-R. The function of the cl gene is to reduce the expression of the ccdB gene. What is an obvious change is that we replace zeo-r gene that is resistant to the antibiotic zeocin in the culture with the toxin gene ccdB, whose product is a kind of poisonous protein and ccdB can express continuously and by itself. This requires us to switch the gene circuit, which means we change the poisonous protein gene and the mechanism of the toxin principle.</p><br />
<p>On the one hand, when the two types of bacteria are culture separately, each of them cannot survive because the ccdB gene expresses continuously and the toxin would result the death of the bacteria, what’s more, they cannot get the signal molecular from the partener-6HSL and 12HSL, so even though they are let out, they have no safety risk to our environment. On the other hand, when they are cultured together, they cannot survive as well, only when the concentration of the products of the cl gene reach a relative high level would the degree of the toxin ccdB product decease, but this kind of situation only occur in the laboratory circumstance because of human control. In the natural environment, due to the lack of products of the cl genes, the poisonous protein produced by the ccdB cannot disappear, which would lead to the death of the both sides.</p><br />
<p>Eventually, in order that the target genes we import would not lose efficacy for the sake of the loss of the plasmid by the bacteria. We proposal that all the target genes can be connected to the genome of the bacteria, then the condition would not happen.</p><br />
<p>Our model have imitated this idea, and there are the figures showing below:</p><br />
[[File:safetysustc2.png|figure 1]]<br />
<p>Figure 1:When the concentration of these two bacteria are all very low (in nature)</p><br />
[[File:safetysustc4.png|figure 2]]<br />
<p>Figure 2:When the concentration of these two bacteria are all very high (in lab)</P><br />
[[File:safetysustc5.png|figure 3]]<br />
<p>Figure 3:Model for the mentioned figures</p><br />
== '''Safety''' ==<br />
Our project is safe for the following reasons :<br />
<ul><li><br />
The ''E-coli'' strains and genes we usd are already existed and are commercially available for years.</li><br />
<br />
<li>We would not release the bacteria to the environment</li> <br />
Please click the pdf linked to get more details .<br />
<br />
[[Media:saftysustc.pdf]]</div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ProjectTeam:SUSTC-Shenzhen-A/Project2013-09-27T19:37:27Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== '''Overall project''' ==<br />
<br />
{|align="justify"<br />
|<br />
== '''Abstract''' ==<br />
<br />
<p> <br />
There are many applications of the game theory in some aspects of our life. Each individual has two kinds of choices--to betray or stay silent, and the choice you make would determine your fate. To betray the other side, you may risk being revenged. While staying silent, companion's betrayal may hurt you deeply. As for our project, we work out a new way to imitate the game theory by constructing a community of two E. Coli bacteria. Here we use the growth rate of each species to represent its fate. The effect of one's silent or betrayal on the other species' fate is acted through intercellular signal molecules of two quorum sensing systems. Each signal molecule regulates the expression of toxic genes in the other species and reduces its growth rate. We characterize the consequence of each strategy by quantitatively measure the growth rates of each species in the community.</p><br />
<br />
== '''Background''' ==<br />
<br />
'''Why do we want to do this project?'''<p><br />
We find that most of the researches in synthetic biology aim to study the interaction between parts of a single system. But few focus on the interaction between systems with multi-elements. However, in the real world, there are complex competition and cooperation among the various creatures. And they can work together to achieve a certain function, for example, different kinds of yeast in brewing beer. There is no lack of the ideas of game theory in these processes. So we chose a classical method—prisoner's dilemma as a model to design our project. <br />
</p><br />
'''The importance of our project:'''<p><br />
Our project can simulate the interaction among multiple systems in reality and the final state of them. Through a well-known issue of game theory, we can give synthetic biology and iGem greater publicity from many perspectives. Furthermore, after a slight modification, the project can provide us with an interesting solution to security.<br />
</p><br />
<br />
== '''Project Details'''==<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== our design ===<br />
[[File:qq1.jpg]]<br />
<p>Parts:</p><br />
<p>Communication: quorum sensing</p><br />
<p>LuxI produces 6HSL, 6HSL cross membrane, 6HSL binds to LuxR, LuxR activate promoter Plux </p><br />
<p>LasI produces 12HSL, 12HSL cross membrane, 12HSL binds to LasR, LasR activate promoter Plas</p><br />
<p>Poissonness genes:</p><br />
<p>tetA: import Nickel into cell, which kills cell</p><br />
<p>Zeo-r: Zeocin damage DNA and kills cell, Zeo-r binds and neutralize Zeocin</p><br />
<p>Truth Table</p><br />
[[File:tablesustc.jpg]]<br />
<p>Tuning gene expression: repressor and inducer</p><br />
<br />
[[File:cella.jpg]]<br />
<p>'''Cell A:'''<br />
Constant expressions:</p><br />
<p>'''LuxR'''(with C6HSL, activate pLux, express Zeo-r): promoter J23100 and rbs B0034</p><br />
<p>'''Pcon''': promoter J23100 to J23107 and rbs B0034</p><br />
<p>'''YFP''' (yellow fluorescent protein labeled cell A): promoter pCon, rbs </p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r,''' adjusted by C6HSL, produced by LuxI from '''cell B''', depends on cell B density </p><br />
<p>'''LasI:''' adjusted by Pcon, LasI produces C12HSL, control cell B</p><br />
<p>'''tetA:''' adjusted by Pcon</p><br />
<br />
<p>'''Zeocin, Nickel''' concentration are controlled by you</p><br />
<p>'''C12SHL '''concentration: controlled by cell A concentration </p><br />
<p>'''Nickel '''either kill cell or slow cell growth: '''tetA''' increase sensitivity of '''cell B '''to''' Nickel''':</p><br />
<p>zeocin either kill cell or slow cell growth:Zeo-r decreases sensitivity of''' cell B''' to''' zeocin'''</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
<p>pMB1 and p15A: control plasmid replication in E coli</p><br />
<p>Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
</p><br />
[[File:cellb.jpg]]<br />
<p>'''Cell B:'''<br />
Constant expressions:</p><br />
<p>'''LasR''' (with C12HSL, activate pLux, express Zeo-r): promoter J23100 to J23107 and rbs B0034</p><br />
<p>'''RFP '''(red fluorescent protein labeled cell B): promoter pCon, rbs</p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r''', adjusted by C12HSL, produced by LasI from cell A, depends on cell A density and Pcon.</p><br />
<p>'''LuxI''': adjusted by Pcon, LuxI produces C6HSL, control cell A</p><br />
<p>'''tetA''': adjusted by Pcon</p><br />
<p>'''Zeocin, Nickel concentration are controlled by you</p><br />
<p>'''C6HSL''' concentration: controlled by cell B concentration and Pcon</p><br />
<p>tetA increase sensitivity of cell B to Nickel: Nickel either kill cell or slow cell growth<br />
Zeo-r decreases sensitivity of cell B to zeocin: zeocin either kill cell or slow cell growth</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli<br />
Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
<br />
=== Experiment process ===<br />
Please refer to our <br />
<html><br />
<a href="/Team:SUSTC-Shenzhen-A/Notebook">protocol and notes</a> <br />
</html> for more details.<br />
<br />
== '''Results''' ==<br />
<br />
=== project results===<br />
<p>What we have done are the plasmid construction and the early experiments ,because of the time limite. Here are some results of our project</p><br />
[[File:projectresult.jpg]]<br />
<br />
=== modeling results ===<br />
<br />
=='''Biobricks checking'''==<br />
=== results ===<br />
<p>We chose four biobricks to detect after search. They are xylose,KNO<sub>3</sub>,glucose and 12HSL.</p><br />
'''BBa_K733018: xylose'''<br />
<br />
[[File:xylose-gfp.jpg|500px]]<br />
<p>First we used the microplate to detect the fluorescence of this part, because we could not see the transition point and we were wondering what it would be look like. The data we got is not so good, for we didn’t see the transition point obviously, and also has some differences comparing to the data from HKUST. According to the detecting from HKUST, fluorescence produced in about 5% xylose is more than that in 10% xylose, however what we got is fluorescence produced in 5% xylose than that in 10% xylose.</p><br />
<br />
[[File:xylosesustc.jpg|xylose|600px]]<br />
<p>Since we didn’t get what we really want using microplate, we tried FCM this time. In 0% xylose culture, we almost got no fluorescence produced and in 0.003% xylose culture we saw obvious fluorescence came out. There was an obvious tendency that the efficiency of the promoter increased as the xylose concentration gathered up. However, with the increase of xylose concentration, the fluorescence increased choppily. What was amazing was that the fluorescence we got was 10 times brighter than the result the HKT got, which appeared to be great.</p><br />
<p>Another interesting thing is most of the cell we detected had no fluorescence produced. Then we guess that may because the xylose molecules taken in the different cell are different, or may because the copy number in each cell is different. Maybe it has some relationship with epigenetics. </p><br />
<br />
'''BBa_K774007: KNO<sub>3</sub>'''<br />
<br />
[[File:kno3sustc.jpg|KNO3]]<br />
<p>In this part we got a similar beginning, but have a different ending. With the increasing of nitrate of potash, the fluorescence produced by single cell increases slowly at the beginning but rapidly later. However, according to the data from NRP-UEA-Norwich, the fluorescence starts to decrease at the 20mM nitrate of potash.</p><br />
<br />
'''BBa_K741002: glucose'''<br />
<br />
[[File:glucosesustc.jpg|glucose]]<br />
<p>Compared with testing result from USTC_China, we’ve got a better data. According to the data from USTC_China, after adding glucose, the fluorescence reduces only about 10% in the most obvious one. However, we got a clear reduce in the production of fluorescence. In about 10-2.4M glucose, the fluorescence has left only a half in one cell. With the increasing of glucose, the fluorescence/OD continuously decreases, and at about 10-1M glucose, the fluorescence/OD remains very low. </p><br />
<br />
<br />
<html><br />
<script><br />
$(document).ready(function(){<br />
$("#toc").css("position","fixed");<br />
$("#toc").css("left","0px;");<br />
$("#toc").css("top","140px");<br />
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<br />
<b><p>References</p></b><br />
<br />
<br />
<html><br />
<p>Click the <a href="/index.reference">Reference</a> to get more information.<br />
</html></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ProjectTeam:SUSTC-Shenzhen-A/Project2013-09-27T19:36:27Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== '''Overall project''' ==<br />
<br />
{|align="justify"<br />
|<br />
== '''Abstract''' ==<br />
<br />
<p> <br />
There are many applications of the game theory in some aspects of our life. Each individual has two kinds of choices--to betray or stay silent, and the choice you make would determine your fate. To betray the other side, you may risk being revenged. While staying silent, companion's betrayal may hurt you deeply. As for our project, we work out a new way to imitate the game theory by constructing a community of two E. Coli bacteria. Here we use the growth rate of each species to represent its fate. The effect of one's silent or betrayal on the other species' fate is acted through intercellular signal molecules of two quorum sensing systems. Each signal molecule regulates the expression of toxic genes in the other species and reduces its growth rate. We characterize the consequence of each strategy by quantitatively measure the growth rates of each species in the community.</p><br />
<br />
== '''Background''' ==<br />
<br />
'''Why do we want to do this project?'''<p><br />
We find that most of the researches in synthetic biology aim to study the interaction between parts of a single system. But few focus on the interaction between systems with multi-elements. However, in the real world, there are complex competition and cooperation among the various creatures. And they can work together to achieve a certain function, for example, different kinds of yeast in brewing beer. There is no lack of the ideas of game theory in these processes. So we chose a classical method—prisoner's dilemma as a model to design our project. <br />
</p><br />
'''The importance of our project:'''<p><br />
Our project can simulate the interaction among multiple systems in reality and the final state of them. Through a well-known issue of game theory, we can give synthetic biology and iGem greater publicity from many perspectives. Furthermore, after a slight modification, the project can provide us with an interesting solution to security.<br />
</p><br />
<br />
== '''Project Details'''==<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== our design ===<br />
[[File:qq1.jpg]]<br />
<p>Parts:</p><br />
<p>Communication: quorum sensing</p><br />
<p>LuxI produces 6HSL, 6HSL cross membrane, 6HSL binds to LuxR, LuxR activate promoter Plux </p><br />
<p>LasI produces 12HSL, 12HSL cross membrane, 12HSL binds to LasR, LasR activate promoter Plas</p><br />
<p>Poissonness genes:</p><br />
<p>tetA: import Nickel into cell, which kills cell</p><br />
<p>Zeo-r: Zeocin damage DNA and kills cell, Zeo-r binds and neutralize Zeocin</p><br />
<p>Truth Table</p><br />
[[File:tablesustc.jpg]]<br />
<p>Tuning gene expression: repressor and inducer</p><br />
<br />
[[File:cella.jpg]]<br />
<p>'''Cell A:'''<br />
Constant expressions:</p><br />
<p>'''LuxR'''(with C6HSL, activate pLux, express Zeo-r): promoter J23100 and rbs B0034</p><br />
<p>'''Pcon''': promoter J23100 to J23107 and rbs B0034</p><br />
<p>'''YFP''' (yellow fluorescent protein labeled cell A): promoter pCon, rbs </p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r,''' adjusted by C6HSL, produced by LuxI from '''cell B''', depends on cell B density </p><br />
<p>'''LasI:''' adjusted by Pcon, LasI produces C12HSL, control cell B</p><br />
<p>'''tetA:''' adjusted by Pcon</p><br />
<br />
<p>'''Zeocin, Nickel''' concentration are controlled by you</p><br />
<p>'''C12SHL '''concentration: controlled by cell A concentration </p><br />
<p>'''Nickel '''either kill cell or slow cell growth: '''tetA''' increase sensitivity of '''cell B '''to''' Nickel''':</p><br />
<p>zeocin either kill cell or slow cell growth:Zeo-r decreases sensitivity of''' cell B''' to''' zeocin'''</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
<p>pMB1 and p15A: control plasmid replication in E coli</p><br />
<p>Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
</p><br />
[[File:cellb.jpg]]<br />
<p>'''Cell B:'''<br />
Constant expressions:</p><br />
<p>'''LasR''' (with C12HSL, activate pLux, express Zeo-r): promoter J23100 to J23107 and rbs B0034</p><br />
<p>'''RFP '''(red fluorescent protein labeled cell B): promoter pCon, rbs</p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r''', adjusted by C12HSL, produced by LasI from cell A, depends on cell A density and Pcon.</p><br />
<p>'''LuxI''': adjusted by Pcon, LuxI produces C6HSL, control cell A</p><br />
<p>'''tetA''': adjusted by Pcon</p><br />
<p>'''Zeocin, Nickel concentration are controlled by you</p><br />
<p>'''C6HSL''' concentration: controlled by cell B concentration and Pcon</p><br />
<p>tetA increase sensitivity of cell B to Nickel: Nickel either kill cell or slow cell growth<br />
Zeo-r decreases sensitivity of cell B to zeocin: zeocin either kill cell or slow cell growth</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli<br />
Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
<br />
=== Experiment process ===<br />
Please refer to our <br />
<html><br />
<a href="/Team:SUSTC-Shenzhen-A/Notebook">protocol and notes</a> <br />
</html> for more details.<br />
<br />
== '''Results''' ==<br />
<br />
=== project results===<br />
<p>What we have done are the plasmid construction and the early experiments ,because of the time limite. Here are some results of our project</p><br />
[[File:projectresult.jpg]]<br />
<br />
=== modeling results ===<br />
<br />
=='''Biobricks checking'''==<br />
=== results ===<br />
<p>We chose four biobricks to detect after search. They are xylose,KNO<sub>3</sub>,glucose and 12HSL.</p><br />
'''BBa_K733018: xylose'''<br />
<br />
[[File:xylose-gfp.jpg|500px]]<br />
<p>First we used the microplate to detect the fluorescence of this part, because we could not see the transition point and we were wondering what it would be look like. The data we got is not so good, for we didn’t see the transition point obviously, and also has some differences comparing to the data from HKUST. According to the detecting from HKUST, fluorescence produced in about 5% xylose is more than that in 10% xylose, however what we got is fluorescence produced in 5% xylose than that in 10% xylose.</p><br />
<br />
[[File:xylosesustc.jpg|xylose|600px]]<br />
<p>Since we didn’t get what we really want using microplate, we tried FCM this time. In 0% xylose culture, we almost got no fluorescence produced and in 0.003% xylose culture we saw obvious fluorescence came out. There was an obvious tendency that the efficiency of the promoter increased as the xylose concentration gathered up. However, with the increase of xylose concentration, the fluorescence increased choppily. What was amazing was that the fluorescence we got was 10 times brighter than the result the HKT got, which appeared to be great.</p><br />
<p>Another interesting thing is most of the cell we detected had no fluorescence produced. Then we guess that may because the xylose molecules taken in the different cell are different, or may because the copy number in each cell is different. Maybe it has some relationship with epigenetics. </p><br />
<br />
'''BBa_K774007: KNO<sub>3</sub>'''<br />
<br />
[[File:kno3sustc.jpg|KNO3]]<br />
<p>In this part we got a similar beginning, but have a different ending. With the increasing of nitrate of potash, the fluorescence produced by single cell increases slowly at the beginning but rapidly later. However, according to the data from NRP-UEA-Norwich, the fluorescence starts to decrease at the 20mM nitrate of potash.</p><br />
<br />
'''BBa_K741002: glucose'''<br />
<br />
[[File:glucosesustc.jpg|glucose]]<br />
<p>Compared with testing result from USTC_China, we’ve got a better data. According to the data from USTC_China, after adding glucose, the fluorescence reduces only about 10% in the most obvious one. However, we got a clear reduce in the production of fluorescence. In about 10-2.4M glucose, the fluorescence has left only a half in one cell. With the increasing of glucose, the fluorescence/OD continuously decreases, and at about 10-1M glucose, the fluorescence/OD remains very low. </p><br />
<br />
<br />
<html><br />
<script><br />
$(document).ready(function(){<br />
$("#toc").css("position","fixed");<br />
$("#toc").css("left","0px;");<br />
$("#toc").css("top","140px");<br />
});<br />
</script><br />
<br />
<b><p>references</p></b><br />
<br />
<br />
<html><br />
<p>Click the <a href="/index.reference">Reference</a> to get more information.<br />
</html></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ProjectTeam:SUSTC-Shenzhen-A/Project2013-09-27T19:34:41Z<p>Donna: /* Experiment process */</p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== '''Overall project''' ==<br />
<br />
{|align="justify"<br />
|<br />
== '''Abstract''' ==<br />
<br />
<p> <br />
There are many applications of the game theory in some aspects of our life. Each individual has two kinds of choices--to betray or stay silent, and the choice you make would determine your fate. To betray the other side, you may risk being revenged. While staying silent, companion's betrayal may hurt you deeply. As for our project, we work out a new way to imitate the game theory by constructing a community of two E. Coli bacteria. Here we use the growth rate of each species to represent its fate. The effect of one's silent or betrayal on the other species' fate is acted through intercellular signal molecules of two quorum sensing systems. Each signal molecule regulates the expression of toxic genes in the other species and reduces its growth rate. We characterize the consequence of each strategy by quantitatively measure the growth rates of each species in the community.</p><br />
<br />
== '''Background''' ==<br />
<br />
'''Why do we want to do this project?'''<p><br />
We find that most of the researches in synthetic biology aim to study the interaction between parts of a single system. But few focus on the interaction between systems with multi-elements. However, in the real world, there are complex competition and cooperation among the various creatures. And they can work together to achieve a certain function, for example, different kinds of yeast in brewing beer. There is no lack of the ideas of game theory in these processes. So we chose a classical method—prisoner's dilemma as a model to design our project. <br />
</p><br />
'''The importance of our project:'''<p><br />
Our project can simulate the interaction among multiple systems in reality and the final state of them. Through a well-known issue of game theory, we can give synthetic biology and iGem greater publicity from many perspectives. Furthermore, after a slight modification, the project can provide us with an interesting solution to security.<br />
</p><br />
<br />
== '''Project Details'''==<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== our design ===<br />
[[File:qq1.jpg]]<br />
<p>Parts:</p><br />
<p>Communication: quorum sensing</p><br />
<p>LuxI produces 6HSL, 6HSL cross membrane, 6HSL binds to LuxR, LuxR activate promoter Plux </p><br />
<p>LasI produces 12HSL, 12HSL cross membrane, 12HSL binds to LasR, LasR activate promoter Plas</p><br />
<p>Poissonness genes:</p><br />
<p>tetA: import Nickel into cell, which kills cell</p><br />
<p>Zeo-r: Zeocin damage DNA and kills cell, Zeo-r binds and neutralize Zeocin</p><br />
<p>Truth Table</p><br />
[[File:tablesustc.jpg]]<br />
<p>Tuning gene expression: repressor and inducer</p><br />
<br />
[[File:cella.jpg]]<br />
<p>'''Cell A:'''<br />
Constant expressions:</p><br />
<p>'''LuxR'''(with C6HSL, activate pLux, express Zeo-r): promoter J23100 and rbs B0034</p><br />
<p>'''Pcon''': promoter J23100 to J23107 and rbs B0034</p><br />
<p>'''YFP''' (yellow fluorescent protein labeled cell B): promoter pCon, rbs </p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r,''' adjusted by C6HSL, produced by LuxI from '''cell B''', depends on cell B density </p><br />
<p>'''LasI:''' adjusted by Pcon, LasI produces C12HSL, control cell B</p><br />
<p>'''tetA:''' adjusted by Pcon</p><br />
<br />
<p>'''Zeocin, Nickel''' concentration are controlled by you</p><br />
<p>'''C12SHL '''concentration: controlled by cell A concentration </p><br />
<p>'''Nickel '''either kill cell or slow cell growth: '''tetA''' increase sensitivity of '''cell B '''to''' Nickel''':</p><br />
<p>zeocin either kill cell or slow cell growth:Zeo-r decreases sensitivity of''' cell B''' to''' zeocin'''</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
<p>pMB1 and p15A: control plasmid replication in E coli</p><br />
<p>Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
</p><br />
[[File:cellb.jpg]]<br />
<p>'''Cell B:'''<br />
Constant expressions:</p><br />
<p>'''LasR''' (with C12HSL, activate pLux, express Zeo-r): promoter J23100 to J23107 and rbs B0034</p><br />
<p>'''RFP '''(red fluorescent protein labeled cell A): promoter pCon, rbs</p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r''', adjusted by C12HSL, produced by LasI from cell A, depends on cell A density and Pcon.</p><br />
<p>'''LuxI''': adjusted by Pcon, LuxI produces C6HSL, control cell A</p><br />
<p>'''tetA''': adjusted by Pcon</p><br />
<p>'''Zeocin, Nickel concentration are controlled by you</p><br />
<p>'''C6HSL''' concentration: controlled by cell B concentration and Pcon</p><br />
<p>tetA increase sensitivity of cell B to Nickel: Nickel either kill cell or slow cell growth<br />
Zeo-r decreases sensitivity of cell B to zeocin: zeocin either kill cell or slow cell growth</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli<br />
Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
<br />
=== Experiment process ===<br />
Please refer to our <br />
<html><br />
<a href="/">protocol and notes</a> <br />
</html> for more details.<br />
<br />
== '''Results''' ==<br />
<br />
=== project results===<br />
<p>What we have done are the plasmid construction and the early experiments ,because of the time limite. Here are some results of our project</p><br />
[[File:projectresult.jpg]]<br />
<br />
=== modeling results ===<br />
<br />
=='''Biobricks checking'''==<br />
=== results ===<br />
<p>We chose four biobricks to detect after search. They are xylose,KNO<sub>3</sub>,glucose and 12HSL.</p><br />
'''BBa_K733018: xylose'''<br />
<br />
[[File:xylose-gfp.jpg|500px]]<br />
<p>First we used the microplate to detect the fluorescence of this part, because we could not see the transition point and we were wondering what it would be look like. The data we got is not so good, for we didn’t see the transition point obviously, and also has some differences comparing to the data from HKUST. According to the detecting from HKUST, fluorescence produced in about 5% xylose is more than that in 10% xylose, however what we got is fluorescence produced in 5% xylose than that in 10% xylose.</p><br />
<br />
[[File:xylosesustc.jpg|xylose|600px]]<br />
<p>Since we didn’t get what we really want using microplate, we tried FCM this time. In 0% xylose culture, we almost got no fluorescence produced and in 0.003% xylose culture we saw obvious fluorescence came out. There was an obvious tendency that the efficiency of the promoter increased as the xylose concentration gathered up. However, with the increase of xylose concentration, the fluorescence increased choppily. What was amazing was that the fluorescence we got was 10 times brighter than the result the HKT got, which appeared to be great.</p><br />
<p>Another interesting thing is most of the cell we detected had no fluorescence produced. Then we guess that may because the xylose molecules taken in the different cell are different, or may because the copy number in each cell is different. Maybe it has some relationship with epigenetics. </p><br />
<br />
'''BBa_K774007: KNO<sub>3</sub>'''<br />
<br />
[[File:kno3sustc.jpg|KNO3]]<br />
<p>In this part we got a similar beginning, but have a different ending. With the increasing of nitrate of potash, the fluorescence produced by single cell increases slowly at the beginning but rapidly later. However, according to the data from NRP-UEA-Norwich, the fluorescence starts to decrease at the 20mM nitrate of potash.</p><br />
<br />
'''BBa_K741002: glucose'''<br />
<br />
[[File:glucosesustc.jpg|glucose]]<br />
<p>Compared with testing result from USTC_China, we’ve got a better data. According to the data from USTC_China, after adding glucose, the fluorescence reduces only about 10% in the most obvious one. However, we got a clear reduce in the production of fluorescence. In about 10-2.4M glucose, the fluorescence has left only a half in one cell. With the increasing of glucose, the fluorescence/OD continuously decreases, and at about 10-1M glucose, the fluorescence/OD remains very low. </p><br />
<br />
<br />
<html><br />
<script><br />
$(document).ready(function(){<br />
$("#toc").css("position","fixed");<br />
$("#toc").css("left","0px;");<br />
$("#toc").css("top","140px");<br />
});<br />
</script><br />
<br />
<b><p>references</p></b><br />
<br />
<br />
<html><br />
<p>Click the <a href="/index.reference">Reference</a> to get more information.<br />
</html></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ProjectTeam:SUSTC-Shenzhen-A/Project2013-09-27T19:33:48Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== '''Overall project''' ==<br />
<br />
{|align="justify"<br />
|<br />
== '''Abstract''' ==<br />
<br />
<p> <br />
There are many applications of the game theory in some aspects of our life. Each individual has two kinds of choices--to betray or stay silent, and the choice you make would determine your fate. To betray the other side, you may risk being revenged. While staying silent, companion's betrayal may hurt you deeply. As for our project, we work out a new way to imitate the game theory by constructing a community of two E. Coli bacteria. Here we use the growth rate of each species to represent its fate. The effect of one's silent or betrayal on the other species' fate is acted through intercellular signal molecules of two quorum sensing systems. Each signal molecule regulates the expression of toxic genes in the other species and reduces its growth rate. We characterize the consequence of each strategy by quantitatively measure the growth rates of each species in the community.</p><br />
<br />
== '''Background''' ==<br />
<br />
'''Why do we want to do this project?'''<p><br />
We find that most of the researches in synthetic biology aim to study the interaction between parts of a single system. But few focus on the interaction between systems with multi-elements. However, in the real world, there are complex competition and cooperation among the various creatures. And they can work together to achieve a certain function, for example, different kinds of yeast in brewing beer. There is no lack of the ideas of game theory in these processes. So we chose a classical method—prisoner's dilemma as a model to design our project. <br />
</p><br />
'''The importance of our project:'''<p><br />
Our project can simulate the interaction among multiple systems in reality and the final state of them. Through a well-known issue of game theory, we can give synthetic biology and iGem greater publicity from many perspectives. Furthermore, after a slight modification, the project can provide us with an interesting solution to security.<br />
</p><br />
<br />
== '''Project Details'''==<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== our design ===<br />
[[File:qq1.jpg]]<br />
<p>Parts:</p><br />
<p>Communication: quorum sensing</p><br />
<p>LuxI produces 6HSL, 6HSL cross membrane, 6HSL binds to LuxR, LuxR activate promoter Plux </p><br />
<p>LasI produces 12HSL, 12HSL cross membrane, 12HSL binds to LasR, LasR activate promoter Plas</p><br />
<p>Poissonness genes:</p><br />
<p>tetA: import Nickel into cell, which kills cell</p><br />
<p>Zeo-r: Zeocin damage DNA and kills cell, Zeo-r binds and neutralize Zeocin</p><br />
<p>Truth Table</p><br />
[[File:tablesustc.jpg]]<br />
<p>Tuning gene expression: repressor and inducer</p><br />
<br />
[[File:cella.jpg]]<br />
<p>'''Cell A:'''<br />
Constant expressions:</p><br />
<p>'''LuxR'''(with C6HSL, activate pLux, express Zeo-r): promoter J23100 and rbs B0034</p><br />
<p>'''Pcon''': promoter J23100 to J23107 and rbs B0034</p><br />
<p>'''YFP''' (yellow fluorescent protein labeled cell B): promoter pCon, rbs </p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r,''' adjusted by C6HSL, produced by LuxI from '''cell B''', depends on cell B density </p><br />
<p>'''LasI:''' adjusted by Pcon, LasI produces C12HSL, control cell B</p><br />
<p>'''tetA:''' adjusted by Pcon</p><br />
<br />
<p>'''Zeocin, Nickel''' concentration are controlled by you</p><br />
<p>'''C12SHL '''concentration: controlled by cell A concentration </p><br />
<p>'''Nickel '''either kill cell or slow cell growth: '''tetA''' increase sensitivity of '''cell B '''to''' Nickel''':</p><br />
<p>zeocin either kill cell or slow cell growth:Zeo-r decreases sensitivity of''' cell B''' to''' zeocin'''</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
<p>pMB1 and p15A: control plasmid replication in E coli</p><br />
<p>Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
</p><br />
[[File:cellb.jpg]]<br />
<p>'''Cell B:'''<br />
Constant expressions:</p><br />
<p>'''LasR''' (with C12HSL, activate pLux, express Zeo-r): promoter J23100 to J23107 and rbs B0034</p><br />
<p>'''RFP '''(red fluorescent protein labeled cell A): promoter pCon, rbs</p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r''', adjusted by C12HSL, produced by LasI from cell A, depends on cell A density and Pcon.</p><br />
<p>'''LuxI''': adjusted by Pcon, LuxI produces C6HSL, control cell A</p><br />
<p>'''tetA''': adjusted by Pcon</p><br />
<p>'''Zeocin, Nickel concentration are controlled by you</p><br />
<p>'''C6HSL''' concentration: controlled by cell B concentration and Pcon</p><br />
<p>tetA increase sensitivity of cell B to Nickel: Nickel either kill cell or slow cell growth<br />
Zeo-r decreases sensitivity of cell B to zeocin: zeocin either kill cell or slow cell growth</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli<br />
Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
<br />
=== Experiment process ===<br />
Please refer to our <br />
<html><br />
<a href="/index.html">protocol and notes</a> <br />
</html> for more details.<br />
<br />
== '''Results''' ==<br />
<br />
=== project results===<br />
<p>What we have done are the plasmid construction and the early experiments ,because of the time limite. Here are some results of our project</p><br />
[[File:projectresult.jpg]]<br />
<br />
=== modeling results ===<br />
<br />
=='''Biobricks checking'''==<br />
=== results ===<br />
<p>We chose four biobricks to detect after search. They are xylose,KNO<sub>3</sub>,glucose and 12HSL.</p><br />
'''BBa_K733018: xylose'''<br />
<br />
[[File:xylose-gfp.jpg|500px]]<br />
<p>First we used the microplate to detect the fluorescence of this part, because we could not see the transition point and we were wondering what it would be look like. The data we got is not so good, for we didn’t see the transition point obviously, and also has some differences comparing to the data from HKUST. According to the detecting from HKUST, fluorescence produced in about 5% xylose is more than that in 10% xylose, however what we got is fluorescence produced in 5% xylose than that in 10% xylose.</p><br />
<br />
[[File:xylosesustc.jpg|xylose|600px]]<br />
<p>Since we didn’t get what we really want using microplate, we tried FCM this time. In 0% xylose culture, we almost got no fluorescence produced and in 0.003% xylose culture we saw obvious fluorescence came out. There was an obvious tendency that the efficiency of the promoter increased as the xylose concentration gathered up. However, with the increase of xylose concentration, the fluorescence increased choppily. What was amazing was that the fluorescence we got was 10 times brighter than the result the HKT got, which appeared to be great.</p><br />
<p>Another interesting thing is most of the cell we detected had no fluorescence produced. Then we guess that may because the xylose molecules taken in the different cell are different, or may because the copy number in each cell is different. Maybe it has some relationship with epigenetics. </p><br />
<br />
'''BBa_K774007: KNO<sub>3</sub>'''<br />
<br />
[[File:kno3sustc.jpg|KNO3]]<br />
<p>In this part we got a similar beginning, but have a different ending. With the increasing of nitrate of potash, the fluorescence produced by single cell increases slowly at the beginning but rapidly later. However, according to the data from NRP-UEA-Norwich, the fluorescence starts to decrease at the 20mM nitrate of potash.</p><br />
<br />
'''BBa_K741002: glucose'''<br />
<br />
[[File:glucosesustc.jpg|glucose]]<br />
<p>Compared with testing result from USTC_China, we’ve got a better data. According to the data from USTC_China, after adding glucose, the fluorescence reduces only about 10% in the most obvious one. However, we got a clear reduce in the production of fluorescence. In about 10-2.4M glucose, the fluorescence has left only a half in one cell. With the increasing of glucose, the fluorescence/OD continuously decreases, and at about 10-1M glucose, the fluorescence/OD remains very low. </p><br />
<br />
<br />
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<br />
<b><p>references</p></b><br />
<br />
<br />
<html><br />
<p>Click the <a href="/index.reference">Reference</a> to get more information.<br />
</html></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ProjectTeam:SUSTC-Shenzhen-A/Project2013-09-27T19:32:11Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== '''Overall project''' ==<br />
<br />
{|align="justify"<br />
|<br />
== '''Abstract''' ==<br />
<br />
<p> <br />
There are many applications of the game theory in some aspects of our life. Each individual has two kinds of choices--to betray or stay silent, and the choice you make would determine your fate. To betray the other side, you may risk being revenged. While staying silent, companion's betrayal may hurt you deeply. As for our project, we work out a new way to imitate the game theory by constructing a community of two E. Coli bacteria. Here we use the growth rate of each species to represent its fate. The effect of one's silent or betrayal on the other species' fate is acted through intercellular signal molecules of two quorum sensing systems. Each signal molecule regulates the expression of toxic genes in the other species and reduces its growth rate. We characterize the consequence of each strategy by quantitatively measure the growth rates of each species in the community.</p><br />
<br />
== '''Background''' ==<br />
<br />
'''Why do we want to do this project?'''<p><br />
We find that most of the researches in synthetic biology aim to study the interaction between parts of a single system. But few focus on the interaction between systems with multi-elements. However, in the real world, there are complex competition and cooperation among the various creatures. And they can work together to achieve a certain function, for example, different kinds of yeast in brewing beer. There is no lack of the ideas of game theory in these processes. So we chose a classical method—prisoner's dilemma as a model to design our project. <br />
</p><br />
'''The importance of our project:'''<p><br />
Our project can simulate the interaction among multiple systems in reality and the final state of them. Through a well-known issue of game theory, we can give synthetic biology and iGem greater publicity from many perspectives. Furthermore, after a slight modification, the project can provide us with an interesting solution to security.<br />
</p><br />
<br />
== '''Project Details'''==<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== our design ===<br />
[[File:qq1.jpg]]<br />
<p>Parts:</p><br />
<p>Communication: quorum sensing</p><br />
<p>LuxI produces 6HSL, 6HSL cross membrane, 6HSL binds to LuxR, LuxR activate promoter Plux </p><br />
<p>LasI produces 12HSL, 12HSL cross membrane, 12HSL binds to LasR, LasR activate promoter Plas</p><br />
<p>Poissonness genes:</p><br />
<p>tetA: import Nickel into cell, which kills cell</p><br />
<p>Zeo-r: Zeocin damage DNA and kills cell, Zeo-r binds and neutralize Zeocin</p><br />
<p>Truth Table</p><br />
[[File:tablesustc.jpg]]<br />
<p>Tuning gene expression: repressor and inducer</p><br />
<br />
[[File:cella.jpg]]<br />
<p>'''Cell A:'''<br />
Constant expressions:</p><br />
<p>'''LuxR'''(with C6HSL, activate pLux, express Zeo-r): promoter J23100 and rbs B0034</p><br />
<p>'''Pcon''': promoter J23100 to J23107 and rbs B0034</p><br />
<p>'''YFP''' (yellow fluorescent protein labeled cell B): promoter pCon, rbs </p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r,''' adjusted by C6HSL, produced by LuxI from '''cell B''', depends on cell B density </p><br />
<p>'''LasI:''' adjusted by Pcon, LasI produces C12HSL, control cell B</p><br />
<p>'''tetA:''' adjusted by Pcon</p><br />
<br />
<p>'''Zeocin, Nickel''' concentration are controlled by you</p><br />
<p>'''C12SHL '''concentration: controlled by cell A concentration </p><br />
<p>'''Nickel '''either kill cell or slow cell growth: '''tetA''' increase sensitivity of '''cell B '''to''' Nickel''':</p><br />
<p>zeocin either kill cell or slow cell growth:Zeo-r decreases sensitivity of''' cell B''' to''' zeocin'''</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli</p><br />
<p>Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
</p><br />
[[File:cellb.jpg]]<br />
<p>'''Cell B:'''<br />
Constant expressions:</p><br />
<p>'''LasR''' (with C12HSL, activate pLux, express Zeo-r): promoter J23100 to J23107 and rbs B0034</p><br />
<p>'''RFP '''(red fluorescent protein labeled cell A): promoter pCon, rbs</p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r''', adjusted by C12HSL, produced by LasI from cell A, depends on cell A density and Pcon.</p><br />
<p>'''LuxI''': adjusted by Pcon, LuxI produces C6HSL, control cell A</p><br />
<p>'''tetA''': adjusted by Pcon</p><br />
<p>'''Zeocin, Nickel concentration are controlled by you</p><br />
<p>'''C6HSL''' concentration: controlled by cell B concentration and Pcon</p><br />
<p>tetA increase sensitivity of cell B to Nickel: Nickel either kill cell or slow cell growth<br />
Zeo-r decreases sensitivity of cell B to zeocin: zeocin either kill cell or slow cell growth</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli<br />
Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
<br />
=== Experiment process ===<br />
Please refer to our notebook.<br />
<html><br />
<a href="/index.html">protocol and notes</a> <br />
</html><br />
<br />
== '''Results''' ==<br />
<br />
=== project results===<br />
<p>What we have done are the plasmid construction and the early experiments ,because of the time limite. Here are some results of our project</p><br />
[[File:projectresult.jpg]]<br />
<br />
=== modeling results ===<br />
<br />
=='''Biobricks checking'''==<br />
=== results ===<br />
<p>We chose four biobricks to detect after search. They are xylose,KNO<sub>3</sub>,glucose and 12HSL.</p><br />
'''BBa_K733018: xylose'''<br />
<br />
[[File:xylose-gfp.jpg|500px]]<br />
<p>First we used the microplate to detect the fluorescence of this part, because we could not see the transition point and we were wondering what it would be look like. The data we got is not so good, for we didn’t see the transition point obviously, and also has some differences comparing to the data from HKUST. According to the detecting from HKUST, fluorescence produced in about 5% xylose is more than that in 10% xylose, however what we got is fluorescence produced in 5% xylose than that in 10% xylose.</p><br />
<br />
[[File:xylosesustc.jpg|xylose|600px]]<br />
<p>Since we didn’t get what we really want using microplate, we tried FCM this time. In 0% xylose culture, we almost got no fluorescence produced and in 0.003% xylose culture we saw obvious fluorescence came out. There was an obvious tendency that the efficiency of the promoter increased as the xylose concentration gathered up. However, with the increase of xylose concentration, the fluorescence increased choppily. What was amazing was that the fluorescence we got was 10 times brighter than the result the HKT got, which appeared to be great.</p><br />
<p>Another interesting thing is most of the cell we detected had no fluorescence produced. Then we guess that may because the xylose molecules taken in the different cell are different, or may because the copy number in each cell is different. Maybe it has some relationship with epigenetics. </p><br />
<br />
'''BBa_K774007: KNO<sub>3</sub>'''<br />
<br />
[[File:kno3sustc.jpg|KNO3]]<br />
<p>In this part we got a similar beginning, but have a different ending. With the increasing of nitrate of potash, the fluorescence produced by single cell increases slowly at the beginning but rapidly later. However, according to the data from NRP-UEA-Norwich, the fluorescence starts to decrease at the 20mM nitrate of potash.</p><br />
<br />
'''BBa_K741002: glucose'''<br />
<br />
[[File:glucosesustc.jpg|glucose]]<br />
<p>Compared with testing result from USTC_China, we’ve got a better data. According to the data from USTC_China, after adding glucose, the fluorescence reduces only about 10% in the most obvious one. However, we got a clear reduce in the production of fluorescence. In about 10-2.4M glucose, the fluorescence has left only a half in one cell. With the increasing of glucose, the fluorescence/OD continuously decreases, and at about 10-1M glucose, the fluorescence/OD remains very low. </p><br />
<br />
<br />
<html><br />
<script><br />
$(document).ready(function(){<br />
$("#toc").css("position","fixed");<br />
$("#toc").css("left","0px;");<br />
$("#toc").css("top","140px");<br />
});<br />
</script><br />
<br />
<b><p>references</p></b><br />
<br />
<br />
<html><br />
<p>Click the <a href="/index.reference">Reference</a> to get more information.<br />
</html></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ProjectTeam:SUSTC-Shenzhen-A/Project2013-09-27T19:23:10Z<p>Donna: /* Experiment process */</p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== '''Overall project''' ==<br />
<br />
{|align="justify"<br />
|<br />
== '''Abstract''' ==<br />
<br />
<p> <br />
There are many applications of the game theory in some aspects of our life. Each individual has two kinds of choices--to betray or stay silent, and the choice you make would determine your fate. To betray the other side, you may risk being revenged. While staying silent, companion's betrayal may hurt you deeply. As for our project, we work out a new way to imitate the game theory by constructing a community of two E. Coli bacteria. Here we use the growth rate of each species to represent its fate. The effect of one's silent or betrayal on the other species' fate is acted through intercellular signal molecules of two quorum sensing systems. Each signal molecule regulates the expression of toxic genes in the other species and reduces its growth rate. We characterize the consequence of each strategy by quantitatively measure the growth rates of each species in the community.</p><br />
<br />
== '''Background''' ==<br />
<br />
'''Why do we want to do this project?'''<p><br />
We find that most of the researches in synthetic biology aim to study the interaction between parts of a single system. But few focus on the interaction between systems with multi-elements. However, in the real world, there are complex competition and cooperation among the various creatures. And they can work together to achieve a certain function, for example, different kinds of yeast in brewing beer. There is no lack of the ideas of game theory in these processes. So we chose a classical method—prisoner's dilemma as a model to design our project. <br />
</p><br />
'''The importance of our project:'''<p><br />
Our project can simulate the interaction among multiple systems in reality and the final state of them. Through a well-known issue of game theory, we can give synthetic biology and iGem greater publicity from many perspectives. Furthermore, after a slight modification, the project can provide us with an interesting solution to security.<br />
</p><br />
<br />
== '''Project Details'''==<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== our design ===<br />
[[File:qq.jpg]]<br />
<p>Parts:</p><br />
<p>Communication: quorum sensing</p><br />
<p>LuxI produces 6HSL, 6HSL cross membrane, 6HSL binds to LuxR, LuxR activate promoter Plux </p><br />
<p>LasI produces 12HSL, 12HSL cross membrane, 12HSL binds to LasR, LasR activate promoter Plas</p><br />
<p>Poissonness genes:</p><br />
<p>tetA: import Nickel into cell, which kills cell</p><br />
<p>Zeo-r: Zeocin damage DNA and kills cell, Zeo-r binds and neutralize Zeocin</p><br />
<p>Truth Table</p><br />
[[File:tablesustc.jpg]]<br />
<p>Tuning gene expression: repressor and inducer</p><br />
<br />
[[File:cella.jpg]]<br />
<p>'''Cell A:'''<br />
Constant expressions:</p><br />
<p>'''LuxR'''(with C6HSL, activate pLux, express Zeo-r): promoter J23100 and rbs B0034</p><br />
<p>'''Pcon''': promoter J23100 to J23107 and rbs B0034</p><br />
<p>'''RFP '''(red fluorescent protein labeled cell A): promoter pCon, rbs </p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r,''' adjusted by C6HSL, produced by LuxI from '''cell B''', depends on cell B density and IPTG concentration</p><br />
<p>'''LasI:''' adjusted by arabinose, LasI produces C12HSL, control cell B</p><br />
<p>'''tetA:''' adjusted by arabinose</p><br />
<br />
<p>'''Zeocin, Nickel''' concentration are controlled by you</p><br />
<p>'''C12SHL '''concentration: controlled by cell A concentration and arabinose</p><br />
<p>'''Nickel '''either kill cell or slow cell growth: '''tetA''' increase sensitivity of '''cell B '''to''' Nickel''':</p><br />
<p>zeocin either kill cell or slow cell growth:Zeo-r decreases sensitivity of''' cell B''' to''' zeocin'''</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli</p><br />
<p>Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
</p><br />
[[File:cellb.jpg]]<br />
<br />
=== Experiment process ===<br />
Please refer to our notebook.<br />
<br />
== '''Results''' ==<br />
<br />
=== project results===<br />
<p>What we have done are the plasmid construction and the early experiments ,because of the time limite. Here are some results of our project</p><br />
[[File:projectresult.jpg]]<br />
<br />
=== modeling results ===<br />
<br />
=='''Biobricks checking'''==<br />
=== results ===<br />
<p>We chose four biobricks to detect after search. They are xylose,KNO<sub>3</sub>,glucose and 12HSL.</p><br />
'''BBa_K733018: xylose'''<br />
<br />
[[File:xylose-gfp.jpg|500px]]<br />
<p>First we used the microplate to detect the fluorescence of this part, because we could not see the transition point and we were wondering what it would be look like. The data we got is not so good, for we didn’t see the transition point obviously, and also has some differences comparing to the data from HKUST. According to the detecting from HKUST, fluorescence produced in about 5% xylose is more than that in 10% xylose, however what we got is fluorescence produced in 5% xylose than that in 10% xylose.</p><br />
<br />
[[File:xylosesustc.jpg|xylose]]<br />
<p>Since we didn’t get what we really want using microplate, we tried FCM this time. In 0% xylose culture, we almost got no fluorescence produced and in 0.003% xylose culture we saw obvious fluorescence came out. There was an obvious tendency that the efficiency of the promoter increased as the xylose concentration gathered up. However, with the increase of xylose concentration, the fluorescence increased choppily. What was amazing was that the fluorescence we got was 10 times brighter than the result the HKT got, which appeared to be great.</p><br />
<p>Another interesting thing is most of the cell we detected had no fluorescence produced. Then we guess that may because the xylose molecules taken in the different cell are different, or may because the copy number in each cell is different. Maybe it has some relationship with epigenetics. </p><br />
<br />
'''BBa_K774007: KNO<sub>3</sub>'''<br />
<br />
[[File:kno3sustc.jpg|KNO3]]<br />
<p>In this part we got a similar beginning, but have a different ending. With the increasing of nitrate of potash, the fluorescence produced by single cell increases slowly at the beginning but rapidly later. However, according to the data from NRP-UEA-Norwich, the fluorescence starts to decrease at the 20mM nitrate of potash.</p><br />
<br />
'''BBa_K741002: glucose'''<br />
<br />
[[File:glucosesustc.jpg|glucose]]<br />
<p>Compared with testing result from USTC_China, we’ve got a better data. According to the data from USTC_China, after adding glucose, the fluorescence reduces only about 10% in the most obvious one. However, we got a clear reduce in the production of fluorescence. In about 10-2.4M glucose, the fluorescence has left only a half in one cell. With the increasing of glucose, the fluorescence/OD continuously decreases, and at about 10-1M glucose, the fluorescence/OD remains very low. </p><br />
<br />
<br />
<html><br />
<script><br />
$(document).ready(function(){<br />
$("#toc").css("position","fixed");<br />
$("#toc").css("left","0px;");<br />
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<br />
<b><p>references</p></b><br />
<br />
<br />
<html><br />
<p>Click the <a href="/index.reference">Reference</a> to get more information.<br />
</html></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/Human_PracticeTeam:SUSTC-Shenzhen-A/Human Practice2013-09-27T19:21:42Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma1.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
<br />
|}<br />
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{|align="justify"<br />
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== '''communication''' ==<br />
<br />
|[[Image:humanpractice1.jpg|center|frame|communicate with other teams in HongKong]]<br />
|-<br />
|We introduced sythetic biology and our project to some high school students.<br />
|-<br />
|[[Image:humanpracticesustc2.jpg|left|frame|to high school students]]<br />
[[Image:humanpractice3.jpg|right|frame|to high school students]]<br />
|-<br />
|On Sept.25.2013 Jingyi Liu had a short presentation about synthetic biology and iGem in Wall Street English center at windows of the world in Shen Zhen. Since most of students there are in theri twenties or thirties, we spreaded new ideas in synthetic biology to adults~! They showed big interest in synthetic biology and even came up with their own thoughts during the presentation. What's more, after presentation, though they didn't konw any specialized word, many of them still stayed with Liu discussing about biology with body language till 10 p.m.. It was a amazing moment to make so many people curious in synthetic biology, and it was a even better moment to let them comprehend synthetic biology.<br />
<br />
|-<br />
|[[File:humanpracticesustc3.jpg|left|frame|to adults]]<br />
[[File:humanpracticesustc4.jpg|right|frame|to adults]]<br />
|-<br />
|}<br />
<br />
== '''Sponsors''' ==<br />
[[File:Sponsor-sustc.jpg|center|frame|]]</div>Donnahttp://2013.igem.org/File:Humanpractice3.jpgFile:Humanpractice3.jpg2013-09-27T19:16:35Z<p>Donna: uploaded a new version of &quot;File:Humanpractice3.jpg&quot;</p>
<hr />
<div></div>Donnahttp://2013.igem.org/File:Humanpracticesustc4.jpgFile:Humanpracticesustc4.jpg2013-09-27T19:12:46Z<p>Donna: uploaded a new version of &quot;File:Humanpracticesustc4.jpg&quot;</p>
<hr />
<div></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/SafetyTeam:SUSTC-Shenzhen-A/Safety2013-09-27T19:09:32Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocl and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== '''Security''' ==<br />
<p>One of the most essential problem urgent to solve in synthetic biology is the security problem. It has been a troublesome part whether we can pursue that the constructed bacteria cannot survive in the circumstance with some target genes imported by us. As for our project, though there is no safety worry, we come up with an original way to synthesis one kind of standard constructed bacteria, if slightly simplified by our project. In our previous project there are three cases when criminal can survive, but based on the safety consideration, we cannot let any bacteria alive in the wild, so we refer to this design because there is nearly no possibility for them to survive in the wild, for the living conditions have to reach several high levels, which is hard to achieve in the natural circumstance. What’s more, we have made mathematic model of it, which offers the theoretic evidence of it and make it more feasible. The design is like the figure below.</p><br />
[[File:safetysustc.png]]<br />
<p>Just as the graph has shown, we make some modifications in our previous design. We remain the communication pair genes as the message access between them-LuxR and LasR, the products of which-6HSL and 12HSL still function as the signals between the two bacteria communities. It’s apparent that reporter genes are unrelated to the safety problem. So just leave them out. In the meantime, we cut off the tetA gene directly and import the cl gene exactly the same place of the zeo-R. The function of the cl gene is to reduce the expression of the ccdB gene. What is an obvious change is that we replace zeo-r gene that is resistant to the antibiotic zeocin in the culture with the toxin gene ccdB, whose product is a kind of poisonous protein and ccdB can express continuously and by itself. This requires us to switch the gene circuit, which means we change the poisonous protein gene and the mechanism of the toxin principle.</p><br />
<p>On the one hand, when the two types of bacteria are culture separately, each of them cannot survive because the ccdB gene expresses continuously and the toxin would result the death of the bacteria, what’s more, they cannot get the signal molecular from the partener-6HSL and 12HSL, so even though they are let out, they have no safety risk to our environment. On the other hand, when they are cultured together, they cannot survive as well, only when the concentration of the products of the cl gene reach a relative high level would the degree of the toxin ccdB product decease, but this kind of situation only occur in the laboratory circumstance because of human control. In the natural environment, due to the lack of products of the cl genes, the poisonous protein produced by the ccdB cannot disappear, which would lead to the death of the both sides.</p><br />
<p>Eventually, in order that the target genes we import would not lose efficacy for the sake of the loss of the plasmid by the bacteria. We proposal that all the target genes can be connected to the genome of the bacteria, then the condition would not happen.</p><br />
<p>Our model have imitated this idea, and there are the figures showing below:</p><br />
[[File:safetysustc2.png|figure 1]]<br />
<p>Figure 1:When the concentration of these two bacteria are all very low (in nature)</p><br />
[[File:safetysustc4.png|figure 2]]<br />
<p>Figure 2:When the concentration of these two bacteria are all very high (in lab)</P><br />
[[File:safetysustc5.png|figure 3]]<br />
<p>Figure 3:Model for the mentioned figures</p><br />
== '''Safety''' ==<br />
Our project is safe for the following reasons :<br />
<ul><li><br />
The ''E-coli'' strains and genes we usd are already existed and are commercially available for years.</li><br />
<br />
<li>We would not release the bacteria to the environment</li> <br />
Please click the pdf linked to get more details .<br />
<br />
[[Media:saftysustc.pdf]]</div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/SafetyTeam:SUSTC-Shenzhen-A/Safety2013-09-27T19:08:40Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocl and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== '''Security''' ==<br />
<p>One of the most essential problem urgent to solve in synthetic biology is the security problem. It has been a troublesome part whether we can pursue that the constructed bacteria cannot survive in the circumstance with some target genes imported by us. As for our project, though there is no safety worry, we come up with an original way to synthesis one kind of standard constructed bacteria, if slightly simplified by our project. In our previous project there are three cases when criminal can survive, but based on the safety consideration, we cannot let any bacteria alive in the wild, so we refer to this design because there is nearly no possibility for them to survive in the wild, for the living conditions have to reach several high levels, which is hard to achieve in the natural circumstance. What’s more, we have made mathematic model of it, which offers the theoretic evidence of it and make it more feasible. The design is like the figure below.</p><br />
[[File:safetysustc.png]]<br />
<p>Just as the graph has shown, we make some modifications in our previous design. We remain the communication pair genes as the message access between them-LuxR and LasR, the products of which-6HSL and 12HSL still function as the signals between the two bacteria communities. It’s apparent that reporter genes are unrelated to the safety problem. So just leave them out. In the meantime, we cut off the tetA gene directly and import the cl gene exactly the same place of the zeo-R. The function of the cl gene is to reduce the expression of the ccdB gene. What is an obvious change is that we replace zeo-r gene that is resistant to the antibiotic zeocin in the culture with the toxin gene ccdB, whose product is a kind of poisonous protein and ccdB can express continuously and by itself. This requires us to switch the gene circuit, which means we change the poisonous protein gene and the mechanism of the toxin principle.</p><br />
<p>On the one hand, when the two types of bacteria are culture separately, each of them cannot survive because the ccdB gene expresses continuously and the toxin would result the death of the bacteria, what’s more, they cannot get the signal molecular from the partener-6HSL and 12HSL, so even though they are let out, they have no safety risk to our environment. On the other hand, when they are cultured together, they cannot survive as well, only when the concentration of the products of the cl gene reach a relative high level would the degree of the toxin ccdB product decease, but this kind of situation only occur in the laboratory circumstance because of human control. In the natural environment, due to the lack of products of the cl genes, the poisonous protein produced by the ccdB cannot disappear, which would lead to the death of the both sides.</p><br />
<p>Eventually, in order that the target genes we import would not lose efficacy for the sake of the loss of the plasmid by the bacteria. We proposal that all the target genes can be connected to the genome of the bacteria, then the condition would not happen.</p><br />
<p>Our model have imitated this idea, and there are the figures showing below:</p><br />
[[File:safetysustc2.png|figure 1]]<br />
<p>Figure 1When the concentration of these two bacteria are all very low (in nature)</p><br />
[[File:safetysustc4.png|figure 2]]<br />
<p>Figure 2When the concentration of these two bacteria are all very high (in lab)</P><br />
[[File:safetysustc5.png|figure 3]]<br />
<p>Figure 3Model for the mentioned figures</p><br />
== '''Safety''' ==<br />
Our project is safe for the following reasons :<br />
<ul><li><br />
The ''E-coli'' strains and genes we usd are already existed and are commercially available for years.</li><br />
<br />
<li>We would not release the bacteria to the environment</li> <br />
Please click the pdf linked to get more details .<br />
<br />
[[Media:saftysustc.pdf]]</div>Donnahttp://2013.igem.org/File:Safetysustc5.pngFile:Safetysustc5.png2013-09-27T19:03:56Z<p>Donna: </p>
<hr />
<div></div>Donnahttp://2013.igem.org/File:Safetysustc4.pngFile:Safetysustc4.png2013-09-27T19:03:20Z<p>Donna: </p>
<hr />
<div></div>Donnahttp://2013.igem.org/File:Safetysustc2.pngFile:Safetysustc2.png2013-09-27T19:02:48Z<p>Donna: </p>
<hr />
<div></div>Donnahttp://2013.igem.org/File:Safetysustc.pngFile:Safetysustc.png2013-09-27T19:02:15Z<p>Donna: </p>
<hr />
<div></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/SafetyTeam:SUSTC-Shenzhen-A/Safety2013-09-27T19:01:29Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocl and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== '''Security''' ==<br />
<p>One of the most essential problem urgent to solve in synthetic biology is the security problem. It has been a troublesome part whether we can pursue that the constructed bacteria cannot survive in the circumstance with some target genes imported by us. As for our project, though there is no safety worry, we come up with an original way to synthesis one kind of standard constructed bacteria, if slightly simplified by our project. In our previous project there are three cases when criminal can survive, but based on the safety consideration, we cannot let any bacteria alive in the wild, so we refer to this design because there is nearly no possibility for them to survive in the wild, for the living conditions have to reach several high levels, which is hard to achieve in the natural circumstance. What’s more, we have made mathematic model of it, which offers the theoretic evidence of it and make it more feasible. The design is like the figure below.</p><br />
[[File:safetysustc.png]]<br />
<p>Just as the graph has shown, we make some modifications in our previous design. We remain the communication pair genes as the message access between them-LuxR and LasR, the products of which-6HSL and 12HSL still function as the signals between the two bacteria communities. It’s apparent that reporter genes are unrelated to the safety problem. So just leave them out. In the meantime, we cut off the tetA gene directly and import the cl gene exactly the same place of the zeo-R. The function of the cl gene is to reduce the expression of the ccdB gene. What is an obvious change is that we replace zeo-r gene that is resistant to the antibiotic zeocin in the culture with the toxin gene ccdB, whose product is a kind of poisonous protein and ccdB can express continuously and by itself. This requires us to switch the gene circuit, which means we change the poisonous protein gene and the mechanism of the toxin principle.</p><br />
<p>On the one hand, when the two types of bacteria are culture separately, each of them cannot survive because the ccdB gene expresses continuously and the toxin would result the death of the bacteria, what’s more, they cannot get the signal molecular from the partener-6HSL and 12HSL, so even though they are let out, they have no safety risk to our environment. On the other hand, when they are cultured together, they cannot survive as well, only when the concentration of the products of the cl gene reach a relative high level would the degree of the toxin ccdB product decease, but this kind of situation only occur in the laboratory circumstance because of human control. In the natural environment, due to the lack of products of the cl genes, the poisonous protein produced by the ccdB cannot disappear, which would lead to the death of the both sides.</p><br />
<p>Eventually, in order that the target genes we import would not lose efficacy for the sake of the loss of the plasmid by the bacteria. We proposal that all the target genes can be connected to the genome of the bacteria, then the condition would not happen.</p><br />
<p>Our model have imitated this idea, and there are the figures showing below:</p><br />
[[File:safetysustc2.png]]<br />
[[File:safetysustc4.png]]<br />
[[File:safetysustc5.png]]<br />
== '''Safety''' ==<br />
Our project is safe for the following reasons :<br />
<ul><li><br />
The ''E-coli'' strains and genes we usd are already existed and are commercially available for years.</li><br />
<br />
<li>We would not release the bacteria to the environment</li> <br />
Please click the pdf linked to get more details .<br />
<br />
[[Media:saftysustc.pdf]]</div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/SafetyTeam:SUSTC-Shenzhen-A/Safety2013-09-27T19:00:01Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocl and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== '''Security''' ==<br />
<p>One of the most essential problem urgent to solve in synthetic biology is the security problem. It has been a troublesome part whether we can pursue that the constructed bacteria cannot survive in the circumstance with some target genes imported by us. As for our project, though there is no safety worry, we come up with an original way to synthesis one kind of standard constructed bacteria, if slightly simplified by our project. In our previous project there are three cases when criminal can survive, but based on the safety consideration, we cannot let any bacteria alive in the wild, so we refer to this design because there is nearly no possibility for them to survive in the wild, for the living conditions have to reach several high levels, which is hard to achieve in the natural circumstance. What’s more, we have made mathematic model of it, which offers the theoretic evidence of it and make it more feasible. The design is like the figure below.</p><br />
[[File:safetysustc.png]]<br />
<p>Just as the graph has shown, we make some modifications in our previous design. We remain the communication pair genes as the message access between them-LuxR and LasR, the products of which-6HSL and 12HSL still function as the signals between the two bacteria communities. It’s apparent that reporter genes are unrelated to the safety problem. So just leave them out. In the meantime, we cut off the tetA gene directly and import the cl gene exactly the same place of the zeo-R. The function of the cl gene is to reduce the expression of the ccdB gene. What is an obvious change is that we replace zeo-r gene that is resistant to the antibiotic zeocin in the culture with the toxin gene ccdB, whose product is a kind of poisonous protein and ccdB can express continuously and by itself. This requires us to switch the gene circuit, which means we change the poisonous protein gene and the mechanism of the toxin principle.</p><br />
<p>On the one hand, when the two types of bacteria are culture separately, each of them cannot survive because the ccdB gene expresses continuously and the toxin would result the death of the bacteria, what’s more, they cannot get the signal molecular from the partener-6HSL and 12HSL, so even though they are let out, they have no safety risk to our environment. On the other hand, when they are cultured together, they cannot survive as well, only when the concentration of the products of the cl gene reach a relative high level would the degree of the toxin ccdB product decease, but this kind of situation only occur in the laboratory circumstance because of human control. In the natural environment, due to the lack of products of the cl genes, the poisonous protein produced by the ccdB cannot disappear, which would lead to the death of the both sides.</p><br />
<p>Eventually, in order that the target genes we import would not lose efficacy for the sake of the loss of the plasmid by the bacteria. We proposal that all the target genes can be connected to the genome of the bacteria, then the condition would not happen.</p><br />
<p>Our model have imitated this idea, and there are the figures showing below:</p><br />
[[File:safetysustc2.png]]<br />
<br />
== '''Safety''' ==<br />
Our project is safe for the following reasons :<br />
<ul><li><br />
The ''E-coli'' strains and genes we usd are already existed and are commercially available for years.</li><br />
<br />
<li>We would not release the bacteria to the environment</li> <br />
Please click the pdf linked to get more details .<br />
<br />
[[Media:saftysustc.pdf]]</div>Donnahttp://2013.igem.org/File:Modelingsustc10.pngFile:Modelingsustc10.png2013-09-27T15:07:14Z<p>Donna: </p>
<hr />
<div></div>Donnahttp://2013.igem.org/File:Modelingsustc9.pngFile:Modelingsustc9.png2013-09-27T15:06:33Z<p>Donna: </p>
<hr />
<div></div>Donnahttp://2013.igem.org/File:Modelingsustc11.pngFile:Modelingsustc11.png2013-09-27T15:05:45Z<p>Donna: </p>
<hr />
<div></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ModelingTeam:SUSTC-Shenzhen-A/Modeling2013-09-27T15:05:01Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="80%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
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== Modeling ==<br />
'''Abstract'''<br />
<p>Our model is to simulate a cell-cell mutual help system that is inspired by the classic prisoner's dilemma. we use two kinds of operated cells to act as the two prisoners. Both of them are facing the same problem comes from the environment, if they do not help each other, both of them will get into a terrible situation. Even they choose to collaborate, one may also take the risk that another man would turn traitor to him. So it’s a complex problem that how do our prisoners to choose their strategy to make themselves survival. Here are all equations and variables we have worked out.</p><br />
[[File:modelingsustc5.png]]<br />
<p>'''So, how can our system perform this prisoner’s dilemma? '''</p><br />
<p>We use the growth rate and the concentration of the cells to describe the living status of two prisoners, use Zeocin in our system to represent the punishment on our prisoners, and use the tetA(which will translate companying with the expressing of AHL) to bring Ni into the cells referring to the risk the as telling the lie. And if one receive the shield from another as sufficient AHL, he will start to produce ZeoR protein which can make him survive the Zeocin. </p><br />
'''Here are also some Differences'''<br />
<p>However our cell-cell mutual help system also do not all obey the classic prisoners’ dilemma, first of all, one prisoner can only have two certain choices in this traditional question, be honest or crafty. But as we have mentioned before, in our system two cells use AHL to help each other, namely the concentration here stands for the attitude of our cell, well it is right the concentration not the existence of AHL makes sense in our system, so our prisoner have a chance to make an elastic choice, they can decide to what level the cooperation will be put into effect. This important difference make our system more close to the realistic. </p><br />
<p>Then one prisoner will never really die in a classic situation, but in ours there exist some possibility that one cell can actually die out which will result in a big crash. This is what we should put our eyes on.</p><br />
'''Test'''<br />
<p>To confirm whether our simulations can work out a good result, we want test some important parameters to see whether our subsystem can work properly,</p><br />
'''1.the effect of Zeocin'''<br />
<p>We put our prisoners into a person to see what will happen to this pool man, this will help us understand how powerful the punishment is as well as tell us how much Zeocin we should use to create a temperate environment stress. <br />
As we can see from this figure, this antibiotic leads to a quick death of our prisoner. Without help one man can hardly get out of this problem.</p><br />
[[File:modelingsustc6.png]]<br />
<p>'''2.separate cell in the environment contain AHL'''</p><br />
<p>To test our relationship between the concentration of AHL and the concentration of our cells, we conduct this test. We put one of our prisoner into AHL concentration gradients to make sure where the efficient concentration of AHL lies, and we get the final cell concentration for each AHL gradients.</p><br />
<p>This EC can tell us some important things such as whether there exists any sensitivity difference of AHL between the two cells, it can help us have a better understading of the coporation between these two cells.<br />
As we can see there is a cliffy slope in our data, which give us the idea that the relationship between the AHL and cell concentration is not simply linear, so we should concider twise before we change this influential variable.</p><br />
[[File:modelingsustc7.png]]<br />
<p>'''3.the show begins'''</p><br />
Result 1:Good Cooperation<br />
<p>If both of our prisoners try to help each other things will be much better</p><br />
[[File:modelingsustc11.png]]<br />
Result 2: a Traitor<br />
<p>If one of our prisoner wants to get others help without offering any reward, he may be well benefit at first, but as his partner get into the trouble, he will lose his lucky. This though go against the realistic, we can also take well advantage of this flaw in our safety idea. (In the four cases of prisoners’ dilemma there are three cases that the bad man can escape but in our model only if they are well cooperate with each other then they will have chance to run away, but such a good cooperate cannot be easily achieved especially outside the Lab)</p><br />
[[File:modelingsustc8.png]]<br />
<p>'''Result 3: The Egoists'''</p><br />
If the both guy are imaginary smart, and have a strong believe that his partner will forswear for him, it’s obviously that they will get deserved penalty.<br />
[[File:modelingsustc9.png]]<br />
<p>'''Some more interesting results'''</p><br />
<p>The results all above are just considering the same situation that both the prisoners have a similar personality, that says our two cells have a very symmetry structure, their physiological parameter are nearly the same. Basing on this, every cell can act the same behavior when meet the same change in the environment.</p><br />
<p>However, two pieces of leaves will never coincide in the world. We can’t adjust everything to meet our plan and this considerable material difference gives us the opportunity to have a sight of the real prisoner’s dilemma.</p><br />
<p>What will happen if we put two people with different sensibility of other’s goodwill into this dilemma? To achieve this we can simply adjust the Hill coefficient of the differential equation of Zeor, to see what have found.</p><br />
[[File:modelingsustc10.png]]<br />
<p>There appears a clear game between our prisoners, and unlike other result this dynamic equilibrium crashed at last. It’s usually a common sense that the damped oscillation may lead to a stable equilibrium, , but you can hardly tell which people made the mistake. How our prisoners can performed such clumsy play, maybe we can have a farther study.</p><br />
<p>This media liked the whole modeling of our project.</p><br />
[[Media:modelingsustc.pdf]]</div>Donnahttp://2013.igem.org/File:Modelingsustc8.pngFile:Modelingsustc8.png2013-09-27T15:00:27Z<p>Donna: uploaded a new version of &quot;File:Modelingsustc8.png&quot;</p>
<hr />
<div></div>Donnahttp://2013.igem.org/File:Modelingsustc8.pngFile:Modelingsustc8.png2013-09-27T14:59:31Z<p>Donna: </p>
<hr />
<div></div>Donnahttp://2013.igem.org/File:Modelingsustc7.pngFile:Modelingsustc7.png2013-09-27T14:58:31Z<p>Donna: </p>
<hr />
<div></div>Donnahttp://2013.igem.org/File:Modelingsustc6.pngFile:Modelingsustc6.png2013-09-27T14:56:18Z<p>Donna: </p>
<hr />
<div></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ModelingTeam:SUSTC-Shenzhen-A/Modeling2013-09-27T14:54:50Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="80%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
== Modeling ==<br />
'''Abstract'''<br />
<p>Our model is to simulate a cell-cell mutual help system that is inspired by the classic prisoner's dilemma. we use two kinds of operated cells to act as the two prisoners. Both of them are facing the same problem comes from the environment, if they do not help each other, both of them will get into a terrible situation. Even they choose to collaborate, one may also take the risk that another man would turn traitor to him. So it’s a complex problem that how do our prisoners to choose their strategy to make themselves survival. Here are all equations and variables we have worked out.</p><br />
[[File:modelingsustc5.png]]<br />
<p>'''So, how can our system perform this prisoner’s dilemma? '''</p><br />
<p>We use the growth rate and the concentration of the cells to describe the living status of two prisoners, use Zeocin in our system to represent the punishment on our prisoners, and use the tetA(which will translate companying with the expressing of AHL) to bring Ni into the cells referring to the risk the as telling the lie. And if one receive the shield from another as sufficient AHL, he will start to produce ZeoR protein which can make him survive the Zeocin. </p><br />
'''Here are also some Differences'''<br />
<p>However our cell-cell mutual help system also do not all obey the classic prisoners’ dilemma, first of all, one prisoner can only have two certain choices in this traditional question, be honest or crafty. But as we have mentioned before, in our system two cells use AHL to help each other, namely the concentration here stands for the attitude of our cell, well it is right the concentration not the existence of AHL makes sense in our system, so our prisoner have a chance to make an elastic choice, they can decide to what level the cooperation will be put into effect. This important difference make our system more close to the realistic. </p><br />
<p>Then one prisoner will never really die in a classic situation, but in ours there exist some possibility that one cell can actually die out which will result in a big crash. This is what we should put our eyes on.</p><br />
'''Test'''<br />
<p>To confirm whether our simulations can work out a good result, we want test some important parameters to see whether our subsystem can work properly,</p><br />
'''1.the effect of Zeocin'''<br />
<p>We put our prisoners into a person to see what will happen to this pool man, this will help us understand how powerful the punishment is as well as tell us how much Zeocin we should use to create a temperate environment stress. <br />
As we can see from this figure, this antibiotic leads to a quick death of our prisoner. Without help one man can hardly get out of this problem.</p><br />
[[File:modelingsustc6.png]]<br />
<p>'''2.separate cell in the environment contain AHL'''</p><br />
<p>To test our relationship between the concentration of AHL and the concentration of our cells, we conduct this test. We put one of our prisoner into AHL concentration gradients to make sure where the efficient concentration of AHL lies, and we get the final cell concentration for each AHL gradients.</p><br />
<p>This EC can tell us some important things such as whether there exists any sensitivity difference of AHL between the two cells, it can help us have a better understading of the coporation between these two cells.<br />
As we can see there is a cliffy slope in our data, which give us the idea that the relationship between the AHL and cell concentration is not simply linear, so we should concider twise before we change this influential variable.</p><br />
[[File:modelingsustc7.png]]<br />
<p>'''3.the show begins'''</p><br />
Result 1:Good Cooperation<br />
<p>If both of our prisoners try to help each other things will be much better</p><br />
[[File:modelingsustc8.png]]<br />
Result 2: a Traitor<br />
<p>If one of our prisoner wants to get others help without offering any reward, he may be well benefit at first, but as his partner get into the trouble, he will lose his lucky. This though go against the realistic, we can also take well advantage of this flaw in our safety idea. (In the four cases of prisoners’ dilemma there are three cases that the bad man can escape but in our model only if they are well cooperate with each other then they will have chance to run away, but such a good cooperate cannot be easily achieved especially outside the Lab)</p><br />
[[File:modelingsustc8.png]]<br />
<p>'''Result 3: The Egoists'''</p><br />
If the both guy are imaginary smart, and have a strong believe that his partner will forswear for him, it’s obviously that they will get deserved penalty.<br />
[[File:modelingsustc9.png]]<br />
<p>'''Some more interesting results'''</p><br />
<p>The results all above are just considering the same situation that both the prisoners have a similar personality, that says our two cells have a very symmetry structure, their physiological parameter are nearly the same. Basing on this, every cell can act the same behavior when meet the same change in the environment.</p><br />
<p>However, two pieces of leaves will never coincide in the world. We can’t adjust everything to meet our plan and this considerable material difference gives us the opportunity to have a sight of the real prisoner’s dilemma.</p><br />
<p>What will happen if we put two people with different sensibility of other’s goodwill into this dilemma? To achieve this we can simply adjust the Hill coefficient of the differential equation of Zeor, to see what have found.</p><br />
[[File:modelingsustc10.png]]<br />
<p>There appears a clear game between our prisoners, and unlike other result this dynamic equilibrium crashed at last. It’s usually a common sense that the damped oscillation may lead to a stable equilibrium, , but you can hardly tell which people made the mistake. How our prisoners can performed such clumsy play, maybe we can have a farther study.</p><br />
<p>This media liked the whole modeling of our project.</p><br />
[[Media:modelingsustc.pdf]]</div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ModelingTeam:SUSTC-Shenzhen-A/Modeling2013-09-27T14:51:04Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="80%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
== Modeling ==<br />
'''Abstract'''<br />
<p>Our model is to simulate a cell-cell mutual help system that is inspired by the classic prisoner's dilemma. we use two kinds of operated cells to act as the two prisoners. Both of them are facing the same problem comes from the environment, if they do not help each other, both of them will get into a terrible situation. Even they choose to collaborate, one may also take the risk that another man would turn traitor to him. So it’s a complex problem that how do our prisoners to choose their strategy to make themselves survival. Here are all equations and variables we have worked out.</p><br />
[[File:modelingsustc5.png]]<br />
<p>'''So, how can our system perform this prisoner’s dilemma? '''</p><br />
<p>We use the growth rate and the concentration of the cells to describe the living status of two prisoners, use Zeocin in our system to represent the punishment on our prisoners, and use the tetA(which will translate companying with the expressing of AHL) to bring Ni into the cells referring to the risk the as telling the lie. And if one receive the shield from another as sufficient AHL, he will start to produce ZeoR protein which can make him survive the Zeocin. </p><br />
'''Here are also some Differences'''<br />
<p>However our cell-cell mutual help system also do not all obey the classic prisoners’ dilemma, first of all, one prisoner can only have two certain choices in this traditional question, be honest or crafty. But as we have mentioned before, in our system two cells use AHL to help each other, namely the concentration here stands for the attitude of our cell, well it is right the concentration not the existence of AHL makes sense in our system, so our prisoner have a chance to make an elastic choice, they can decide to what level the cooperation will be put into effect. This important difference make our system more close to the realistic. </p><br />
<p>Then one prisoner will never really die in a classic situation, but in ours there exist some possibility that one cell can actually die out which will result in a big crash. This is what we should put our eyes on.</p><br />
'''Test'''<br />
<p>To confirm whether our simulations can work out a good result, we want test some important parameters to see whether our subsystem can work properly,</p><br />
'''1.the effect of Zeocin'''<br />
<p>We put our prisoners into a person to see what will happen to this pool man, this will help us understand how powerful the punishment is as well as tell us how much Zeocin we should use to create a temperate environment stress. <br />
As we can see from this figure, this antibiotic leads to a quick death of our prisoner. Without help one man can hardly get out of this problem.</p><br />
[[File:modelingsustc6.jpg]]<br />
'''2.separate cell in the environment contain AHL'''<br />
<p>To test our relationship between the concentration of AHL and the concentration of our cells, we conduct this test. We put one of our prisoner into AHL concentration gradients to make sure where the efficient concentration of AHL lies, and we get the final cell concentration for each AHL gradients.</p><br />
<p>This EC can tell us some important things such as whether there exists any sensitivity difference of AHL between the two cells, it can help us have a better understading of the coporation between these two cells.<br />
As we can see there is a cliffy slope in our data, which give us the idea that the relationship between the AHL and cell concentration is not simply linear, so we should concider twise before we change this influential variable.</p><br />
[[File:modelingsustc7.jpg]]<br />
'''3.the show begins'''<br />
Result 1:Good Cooperation<br />
<p>If both of our prisoners try to help each other things will be much better</p><br />
[[File:modelingsustc8.jpg]]<br />
Result 2: a Traitor<br />
<p>If one of our prisoner wants to get others help without offering any reward, he may be well benefit at first, but as his partner get into the trouble, he will lose his lucky. This though go against the realistic, we can also take well advantage of this flaw in our safety idea. (In the four cases of prisoners’ dilemma there are three cases that the bad man can escape but in our model only if they are well cooperate with each other then they will have chance to run away, but such a good cooperate cannot be easily achieved especially outside the Lab)</p><br />
[[File:modelingsustc8.jpg]]<br />
'''Result 3: The Egoists'''<br />
If the both guy are imaginary smart, and have a strong believe that his partner will forswear for him, it’s obviously that they will get deserved penalty.<br />
[[File:modelingsustc9.jpg]]<br />
'''Some more interesting results'''<br />
<p>The results all above are just considering the same situation that both the prisoners have a similar personality, that says our two cells have a very symmetry structure, their physiological parameter are nearly the same. Basing on this, every cell can act the same behavior when meet the same change in the environment.</p><br />
<p>However, two pieces of leaves will never coincide in the world. We can’t adjust everything to meet our plan and this considerable material difference gives us the opportunity to have a sight of the real prisoner’s dilemma.</p><br />
<p>What will happen if we put two people with different sensibility of other’s goodwill into this dilemma? To achieve this we can simply adjust the Hill coefficient of the differential equation of Zeor, to see what have found.</p><br />
[[File:modelingsustc10.jpg]]<br />
<p>There appears a clear game between our prisoners, and unlike other result this dynamic equilibrium crashed at last. It’s usually a common sense that the damped oscillation may lead to a stable equilibrium, , but you can hardly tell which people made the mistake. How our prisoners can performed such clumsy play, maybe we can have a farther study.</p><br />
<p>This media liked the whole modeling of our project.</p><br />
[[Media:modelingsustc.pdf]]</div>Donnahttp://2013.igem.org/File:Modelingsustc5.pngFile:Modelingsustc5.png2013-09-27T14:49:45Z<p>Donna: </p>
<hr />
<div></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ModelingTeam:SUSTC-Shenzhen-A/Modeling2013-09-27T14:33:39Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="80%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
== Modeling ==<br />
'''Abstract'''<br />
<p>Our model is to simulate a cell-cell mutual help system that is inspired by the classic prisoner's dilemma. we use two kinds of operated cells to act as the two prisoners. Both of them are facing the same problem comes from the environment, if they do not help each other, both of them will get into a terrible situation. Even they choose to collaborate, one may also take the risk that another man would turn traitor to him. So it’s a complex problem that how do our prisoners to choose their strategy to make themselves survival. Here are all equations and variables we have worked out.</p><br />
[[File:modelingsustc5.jpg]]<br />
'''So, how can our system perform this prisoner’s dilemma? '''<br />
<p>We use the growth rate and the concentration of the cells to describe the living status of two prisoners, use Zeocin in our system to represent the punishment on our prisoners, and use the tetA(which will translate companying with the expressing of AHL) to bring Ni into the cells referring to the risk the as telling the lie. And if one receive the shield from another as sufficient AHL, he will start to produce ZeoR protein which can make him survive the Zeocin. </p><br />
'''Here are also some Differences'''<br />
<p>However our cell-cell mutual help system also do not all obey the classic prisoners’ dilemma, first of all, one prisoner can only have two certain choices in this traditional question, be honest or crafty. But as we have mentioned before, in our system two cells use AHL to help each other, namely the concentration here stands for the attitude of our cell, well it is right the concentration not the existence of AHL makes sense in our system, so our prisoner have a chance to make an elastic choice, they can decide to what level the cooperation will be put into effect. This important difference make our system more close to the realistic. </p><br />
<p>Then one prisoner will never really die in a classic situation, but in ours there exist some possibility that one cell can actually die out which will result in a big crash. This is what we should put our eyes on.</p><br />
'''Test'''<br />
<p>To confirm whether our simulations can work out a good result, we want test some important parameters to see whether our subsystem can work properly,</p><br />
'''1.the effect of Zeocin'''<br />
<p>We put our prisoners into a person to see what will happen to this pool man, this will help us understand how powerful the punishment is as well as tell us how much Zeocin we should use to create a temperate environment stress. <br />
As we can see from this figure, this antibiotic leads to a quick death of our prisoner. Without help one man can hardly get out of this problem.</p><br />
[[File:modelingsustc6.jpg]]<br />
'''2.separate cell in the environment contain AHL'''<br />
<p>To test our relationship between the concentration of AHL and the concentration of our cells, we conduct this test. We put one of our prisoner into AHL concentration gradients to make sure where the efficient concentration of AHL lies, and we get the final cell concentration for each AHL gradients.</p><br />
<p>This EC can tell us some important things such as whether there exists any sensitivity difference of AHL between the two cells, it can help us have a better understading of the coporation between these two cells.<br />
As we can see there is a cliffy slope in our data, which give us the idea that the relationship between the AHL and cell concentration is not simply linear, so we should concider twise before we change this influential variable.</p><br />
[[File:modelingsustc7.jpg]]<br />
'''3.the show begins'''<br />
Result 1:Good Cooperation<br />
<p>If both of our prisoners try to help each other things will be much better</p><br />
[[File:modelingsustc8.jpg]]<br />
Result 2: a Traitor<br />
<p>If one of our prisoner wants to get others help without offering any reward, he may be well benefit at first, but as his partner get into the trouble, he will lose his lucky. This though go against the realistic, we can also take well advantage of this flaw in our safety idea. (In the four cases of prisoners’ dilemma there are three cases that the bad man can escape but in our model only if they are well cooperate with each other then they will have chance to run away, but such a good cooperate cannot be easily achieved especially outside the Lab)</p><br />
[[File:modelingsustc8.jpg]]<br />
'''Result 3: The Egoists'''<br />
If the both guy are imaginary smart, and have a strong believe that his partner will forswear for him, it’s obviously that they will get deserved penalty.<br />
[[File:modelingsustc9.jpg]]<br />
'''Some more interesting results'''<br />
<p>The results all above are just considering the same situation that both the prisoners have a similar personality, that says our two cells have a very symmetry structure, their physiological parameter are nearly the same. Basing on this, every cell can act the same behavior when meet the same change in the environment.</p><br />
<p>However, two pieces of leaves will never coincide in the world. We can’t adjust everything to meet our plan and this considerable material difference gives us the opportunity to have a sight of the real prisoner’s dilemma.</p><br />
<p>What will happen if we put two people with different sensibility of other’s goodwill into this dilemma? To achieve this we can simply adjust the Hill coefficient of the differential equation of Zeor, to see what have found.</p><br />
[[File:modelingsustc10.jpg]]<br />
<p>There appears a clear game between our prisoners, and unlike other result this dynamic equilibrium crashed at last. It’s usually a common sense that the damped oscillation may lead to a stable equilibrium, , but you can hardly tell which people made the mistake. How our prisoners can performed such clumsy play, maybe we can have a farther study.</p><br />
<p>This media liked the whole modeling of our project.</p><br />
[[Media:modelingsustc.pdf]]</div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ProjectTeam:SUSTC-Shenzhen-A/Project2013-09-27T09:34:32Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="80%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
<br />
<br />
== '''Overall project''' ==<br />
<br />
{|align="justify"<br />
|'''Abstract'''<br />
<p> <br />
There are many applications of the game theory in some aspects of our life. Each individual has two kinds of choices--to betray or stay silent, and the choice you make would determine your fate. To betray the other side, you may risk being revenged. While staying silent, companion's betrayal may hurt you deeply. As for our project, we work out a new way to imitate the game theory by constructing a community of two E. Coli bacteria. Here we use the growth rate of each species to represent its fate. The effect of one's silent or betrayal on the other species' fate is acted through intercellular signal molecules of two quorum sensing systems. Each signal molecule regulates the expression of toxic genes in the other species and reduces its growth rate. We characterize the consequence of each strategy by quantitatively measure the growth rates of each species in the community</p><br />
'''Background'''<br />
<br />
<br />
<br />
== Project Details==<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== our design ===<br />
[[File:designsustc.png]]<br />
<p>Parts:</p><br />
<p>Communication: quorum sensing</p><br />
<p>LuxI produces 6HSL, 6HSL cross membrane, 6HSL binds to LuxR, LuxR activate promoter Plux </p><br />
<p>LasI produces 12HSL, 12HSL cross membrane, 12HSL binds to LasR, LasR activate promoter Plas</p><br />
<p>Poissonness genes:</p><br />
<p>tetA: import Nickel into cell, which kills cell</p><br />
<p>Zeo-r: Zeocin damage DNA and kills cell, Zeo-r binds and neutralize Zeocin</p><br />
<p>Truth Table</p><br />
[[File:tablesustc.jpg]]<br />
<p>Tuning gene expression: repressor and inducer</p><br />
<p>lacI repress gene expression (LuxI); IPTG binds to tetR and release the repression </p><br />
<p>araC repress gene expression (LasI or LuxI); arabinose binds to araC and release the repression </p><br />
[[File:designasustc.jpg]]<br />
[[File:designbsustc.jpg]]<br />
'''Cell A:'''<br />
Constant expressions:<br />
'''LuxR'''(with C6HSL, activate pLux, express Zeo-r): promoter J23100 and rbs B0034</p><br />
<p>'''araC'''(with arabinose, activate LasI, tetA): promoter J23100 and rbs B0034</p><br />
<p>'''mCherry '''(red fluorescent protein labeled cell A): promoter pCon, rbs </p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r,''' adjusted by C6HSL, produced by LuxI from '''cell B''', depends on cell B density and IPTG concentration</p><br />
<p>'''LasI:''' adjusted by arabinose, LasI produces C12HSL, control cell B</p><br />
<p>'''tetA:''' adjusted by arabinose</p><br />
<br />
<p>'''Arabinose, Zeocin, Nickel''' concentration are controlled by you</p><br />
<p>'''C12SHL '''concentration: controlled by cell A concentration and arabinose</p><br />
<p>'''Nickel '''either kill cell or slow cell growth: '''tetA''' increase sensitivity of '''cell B '''to''' Nickel''':</p><br />
<p>zeocin either kill cell or slow cell growth:Zeo-r decreases sensitivity of''' cell B''' to''' zeocin'''</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli</p><br />
<p>Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
</p><br />
<br />
=== Experiment process ===<br />
<br />
<br />
== Results ==<br />
<br />
=== project results===<br />
<p>What we have done are the plasmid construction and the early experiments ,because of the time limite. Here are some results of our project</p><br />
[[File:projectresult.jpg]]<br />
<br />
=== modeling results ===<br />
<br />
<br />
==Biobricks checking==<br />
=== process ===<br />
<br />
=== results ===<br />
<p>We chose four biobricks to detect after search . They are xylose、KNO<sub>3</sub>、glucose and 12HSL.</p><br />
'''xylose'''<br />
[[File:xylosesustc.jpg|xylose]]<br />
<p>Compared with the results of the efficiency of the xylose inducible promoter detected by the HKT, our consequence differed from them in some aspects, or better. We had used the FCM to detect it. There was an obvious tendency that the efficiency of the promoter increased as the xylose concentration gathered up. What was amazing was that the fluorescence we got was 10 times brighter than the result the HKT got, which appeared to be great.</p><br />
<p>But when the concentration of the xylose was 0.03% and 0.3%, we got an unexpected result that the expression of the GFP fell after rise. What’s more. While the concentration of the xylose was 10%, the expression of the GFP decreased, which corresponded with the result of the HKT.</p><br />
<br />
'''KNO<sub>3</sub>'''<br />
<br />
[[File:kno3sustc.jpg|KNO3]]<br />
<p>BBa_K774007 KNO3: This part we got a similar beginning, but have a different ending. With the increasing of nitrate of potash, the fluorescence produced by single cell increases slowly at the beginning but rapidly later. However, according to the data from NRP-UEA-Norwich, the fluorescence starts to decrease at the 20mM nitrate of potash.</p><br />
<br />
[[File:glucosesustc.jpg|glucose]]<br />
<p>BBa_K741002 glucose: Compared with testing result from USTC_China, we’ve got a better data. According to the data from USTC_China, after adding glucose, the fluorescence reduces only about 10% in the most obvious one. However, we got a clear reduce in the production of fluorescence. In about 10-2.4M glucose, the fluorescence has left only a half in one cell. With the increasing of glucose, the fluorescence/OD continuously decreases, and at about 10-1M glucose, the fluorescence/OD remains very low. </p><br />
[[File:12hslsustc.jpg|12HSL]]<br />
<p>lalala</p><br />
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<br />
<b><p>references</p></b><br />
<br />
<br />
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</html></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ProjectTeam:SUSTC-Shenzhen-A/Project2013-09-27T09:33:25Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="80%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
<br />
<br />
== '''Overall project''' ==<br />
<br />
{|align="justify"<br />
|'''Abstract'''<br />
<p> <br />
There are many applications of the game theory in some aspects of our life. Each individual has two kinds of choices--to betray or stay silent, and the choice you make would determine your fate. To betray the other side, you may risk being revenged. While staying silent, companion's betrayal may hurt you deeply. As for our project, we work out a new way to imitate the game theory by constructing a community of two E. Coli bacteria. Here we use the growth rate of each species to represent its fate. The effect of one's silent or betrayal on the other species' fate is acted through intercellular signal molecules of two quorum sensing systems. Each signal molecule regulates the expression of toxic genes in the other species and reduces its growth rate. We characterize the consequence of each strategy by quantitatively measure the growth rates of each species in the community</p><br />
'''Background'''<br />
<br />
<br />
<br />
== Project Details==<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== our design ===<br />
[[File:designsustc.png]]<br />
<p>Parts:</p><br />
<p>Communication: quorum sensing</p><br />
<p>LuxI produces 6HSL, 6HSL cross membrane, 6HSL binds to LuxR, LuxR activate promoter Plux </p><br />
<p>LasI produces 12HSL, 12HSL cross membrane, 12HSL binds to LasR, LasR activate promoter Plas</p><br />
<p>Poissonness genes:</p><br />
<p>tetA: import Nickel into cell, which kills cell</p><br />
<p>Zeo-r: Zeocin damage DNA and kills cell, Zeo-r binds and neutralize Zeocin</p><br />
<p>Truth Table</p><br />
[[File:tablesustc.jpg]]<br />
<p>Tuning gene expression: repressor and inducer</p><br />
<p>lacI repress gene expression (LuxI); IPTG binds to tetR and release the repression </p><br />
<p>araC repress gene expression (LasI or LuxI); arabinose binds to araC and release the repression </p><br />
[[File:designasustc.jpg]]<br />
[[File:designbsustc.jpg]]<br />
'''Cell A:'''<br />
Constant expressions:<br />
'''LuxR'''(with C6HSL, activate pLux, express Zeo-r): promoter J23100 and rbs B0034</p><br />
<p>'''araC'''(with arabinose, activate LasI, tetA): promoter J23100 and rbs B0034</p><br />
<p>'''mCherry '''(red fluorescent protein labeled cell A): promoter pCon, rbs </p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r,''' adjusted by C6HSL, produced by LuxI from '''cell B''', depends on cell B density and IPTG concentration</p><br />
<p>'''LasI:''' adjusted by arabinose, LasI produces C12HSL, control cell B</p><br />
<p>'''tetA:''' adjusted by arabinose</p><br />
<br />
<p>'''Arabinose, Zeocin, Nickel''' concentration are controlled by you</p><br />
<p>'''C12SHL '''concentration: controlled by cell A concentration and arabinose</p><br />
<p>'''Nickel '''either kill cell or slow cell growth: '''tetA''' increase sensitivity of '''cell B '''to''' Nickel''':</p><br />
<p>zeocin either kill cell or slow cell growth:Zeo-r decreases sensitivity of''' cell B''' to''' zeocin'''</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli</p><br />
<p>Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
</p><br />
<br />
=== Experiment process ===<br />
<br />
<br />
== Results ==<br />
<br />
=== project results===<br />
<p>What we have done are the plasmid construction and the early experiments ,because of the time limite. Here are some results of our project</p><br />
[[File:projectresult.jpg]]<br />
<br />
=== modeling results ===<br />
<br />
<br />
==Biobricks checking==<br />
=== process ===<br />
<br />
=== results ===<br />
<p>We chose four biobricks to detect after search . They are xylose、KNO<sub>3</sub>、glucose and 12HSL.</p><br />
'''xylose'''<br />
[[File:xylosesustc.jpg|xylose]]<br />
<p>Compared with the results of the efficiency of the xylose inducible promoter detected by the HKT, our consequence differed from them in some aspects, or better. We had used the FCM to detect it. There was an obvious tendency that the efficiency of the promoter increased as the xylose concentration gathered up. What was amazing was that the fluorescence we got was 10 times brighter than the result the HKT got, which appeared to be great.</p><br />
<p>But when the concentration of the xylose was 0.03% and 0.3%, we got an unexpected result that the expression of the GFP fell after rise. What’s more. While the concentration of the xylose was 10%, the expression of the GFP decreased, which corresponded with the result of the HKT.</p><br />
<br />
'''KNO<sub>3</sub>'''<br />
<br />
[[File:kno3sustc.jpg|KNO3]]<br />
<p>BBa_K774007 KNO3: This part we got a similar beginning, but have a different ending. With the increasing of nitrate of potash, the fluorescence produced by single cell increases slowly at the beginning but rapidly later. However, according to the data from NRP-UEA-Norwich, the fluorescence starts to decrease at the 20mM nitrate of potash.</p><br />
<br />
[[File:glucosesustc.jpg|glucose]]<br />
<p>BBa_K741002 glucose: Compared with testing result from USTC_China, we’ve got a better data. According to the data from USTC_China, after adding glucose, the fluorescence reduces only about 10% in the most obvious one. However, we got a clear reduce in the production of fluorescence. In about 10-2.4M glucose, the fluorescence has left only a half in one cell. With the increasing of glucose, the fluorescence/OD continuously decreases, and at about 10-1M glucose, the fluorescence/OD remains very low. </p><br />
[[File:12hslsustc.jpg|12HSL]]<br />
<p>lalala</p><br />
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=== references ===<br />
<br />
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</html></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ProjectTeam:SUSTC-Shenzhen-A/Project2013-09-27T09:32:23Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="80%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
<br />
<br />
== '''Overall project''' ==<br />
<br />
{|align="justify"<br />
|'''Abstract'''<br />
<p> <br />
There are many applications of the game theory in some aspects of our life. Each individual has two kinds of choices--to betray or stay silent, and the choice you make would determine your fate. To betray the other side, you may risk being revenged. While staying silent, companion's betrayal may hurt you deeply. As for our project, we work out a new way to imitate the game theory by constructing a community of two E. Coli bacteria. Here we use the growth rate of each species to represent its fate. The effect of one's silent or betrayal on the other species' fate is acted through intercellular signal molecules of two quorum sensing systems. Each signal molecule regulates the expression of toxic genes in the other species and reduces its growth rate. We characterize the consequence of each strategy by quantitatively measure the growth rates of each species in the community</p><br />
'''Background'''<br />
<br />
<br />
<br />
== Project Details==<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== our design ===<br />
[[File:designsustc.png]]<br />
<p>Parts:</p><br />
<p>Communication: quorum sensing</p><br />
<p>LuxI produces 6HSL, 6HSL cross membrane, 6HSL binds to LuxR, LuxR activate promoter Plux </p><br />
<p>LasI produces 12HSL, 12HSL cross membrane, 12HSL binds to LasR, LasR activate promoter Plas</p><br />
<p>Poissonness genes:</p><br />
<p>tetA: import Nickel into cell, which kills cell</p><br />
<p>Zeo-r: Zeocin damage DNA and kills cell, Zeo-r binds and neutralize Zeocin</p><br />
<p>Truth Table</p><br />
[[File:tablesustc.jpg]]<br />
<p>Tuning gene expression: repressor and inducer</p><br />
<p>lacI repress gene expression (LuxI); IPTG binds to tetR and release the repression </p><br />
<p>araC repress gene expression (LasI or LuxI); arabinose binds to araC and release the repression </p><br />
[[File:designasustc.jpg]]<br />
[[File:designbsustc.jpg]]<br />
'''Cell A:'''<br />
Constant expressions:<br />
'''LuxR'''(with C6HSL, activate pLux, express Zeo-r): promoter J23100 and rbs B0034</p><br />
<p>'''araC'''(with arabinose, activate LasI, tetA): promoter J23100 and rbs B0034</p><br />
<p>'''mCherry '''(red fluorescent protein labeled cell A): promoter pCon, rbs </p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r,''' adjusted by C6HSL, produced by LuxI from '''cell B''', depends on cell B density and IPTG concentration</p><br />
<p>'''LasI:''' adjusted by arabinose, LasI produces C12HSL, control cell B</p><br />
<p>'''tetA:''' adjusted by arabinose</p><br />
<br />
<p>'''Arabinose, Zeocin, Nickel''' concentration are controlled by you</p><br />
<p>'''C12SHL '''concentration: controlled by cell A concentration and arabinose</p><br />
<p>'''Nickel '''either kill cell or slow cell growth: '''tetA''' increase sensitivity of '''cell B '''to''' Nickel''':</p><br />
<p>zeocin either kill cell or slow cell growth:Zeo-r decreases sensitivity of''' cell B''' to''' zeocin'''</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli</p><br />
<p>Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
</p><br />
<br />
=== Experiment process ===<br />
<br />
<br />
== Results ==<br />
<br />
=== project results===<br />
<p>What we have done are the plasmid construction and the early experiments ,because of the time limite. Here are some results of our project</p><br />
[[File:projectresult.jpg]]<br />
<br />
=== modeling results ===<br />
<br />
<br />
==Biobricks checking==<br />
=== process ===<br />
<br />
=== results ===<br />
<br />
=== references ===<br />
<br />
<p>We chose four biobricks to detect after search . They are xylose、KNO<sub>3</sub>、glucose and 12HSL.</p><br />
'''xylose'''<br />
[[File:xylosesustc.jpg|xylose]]<br />
<p>Compared with the results of the efficiency of the xylose inducible promoter detected by the HKT, our consequence differed from them in some aspects, or better. We had used the FCM to detect it. There was an obvious tendency that the efficiency of the promoter increased as the xylose concentration gathered up. What was amazing was that the fluorescence we got was 10 times brighter than the result the HKT got, which appeared to be great.</p><br />
<p>But when the concentration of the xylose was 0.03% and 0.3%, we got an unexpected result that the expression of the GFP fell after rise. What’s more. While the concentration of the xylose was 10%, the expression of the GFP decreased, which corresponded with the result of the HKT.</p><br />
<br />
'''KNO<sub>3</sub>'''<br />
<br />
[[File:kno3sustc.jpg|KNO3]]<br />
<p>BBa_K774007 KNO3: This part we got a similar beginning, but have a different ending. With the increasing of nitrate of potash, the fluorescence produced by single cell increases slowly at the beginning but rapidly later. However, according to the data from NRP-UEA-Norwich, the fluorescence starts to decrease at the 20mM nitrate of potash.</p><br />
<br />
[[File:glucosesustc.jpg|glucose]]<br />
<p>BBa_K741002 glucose: Compared with testing result from USTC_China, we’ve got a better data. According to the data from USTC_China, after adding glucose, the fluorescence reduces only about 10% in the most obvious one. However, we got a clear reduce in the production of fluorescence. In about 10-2.4M glucose, the fluorescence has left only a half in one cell. With the increasing of glucose, the fluorescence/OD continuously decreases, and at about 10-1M glucose, the fluorescence/OD remains very low. </p><br />
[[File:12hslsustc.jpg|12HSL]]<br />
<p>lalala</p><br />
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<br />
=== References===<br />
<br />
<html><br />
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</html></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ProjectTeam:SUSTC-Shenzhen-A/Project2013-09-27T09:30:19Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="80%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
<br />
<br />
== '''Overall project''' ==<br />
<br />
{|align="justify"<br />
|'''Abstract'''<br />
<p> <br />
There are many applications of the game theory in some aspects of our life. Each individual has two kinds of choices--to betray or stay silent, and the choice you make would determine your fate. To betray the other side, you may risk being revenged. While staying silent, companion's betrayal may hurt you deeply. As for our project, we work out a new way to imitate the game theory by constructing a community of two E. Coli bacteria. Here we use the growth rate of each species to represent its fate. The effect of one's silent or betrayal on the other species' fate is acted through intercellular signal molecules of two quorum sensing systems. Each signal molecule regulates the expression of toxic genes in the other species and reduces its growth rate. We characterize the consequence of each strategy by quantitatively measure the growth rates of each species in the community</p><br />
'''Background'''<br />
<br />
<br />
<br />
== Project Details==<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== our design ===<br />
[[File:designsustc.png]]<br />
<p>Parts:</p><br />
<p>Communication: quorum sensing</p><br />
<p>LuxI produces 6HSL, 6HSL cross membrane, 6HSL binds to LuxR, LuxR activate promoter Plux </p><br />
<p>LasI produces 12HSL, 12HSL cross membrane, 12HSL binds to LasR, LasR activate promoter Plas</p><br />
<p>Poissonness genes:</p><br />
<p>tetA: import Nickel into cell, which kills cell</p><br />
<p>Zeo-r: Zeocin damage DNA and kills cell, Zeo-r binds and neutralize Zeocin</p><br />
<p>Truth Table</p><br />
[[File:tablesustc.jpg]]<br />
<p>Tuning gene expression: repressor and inducer</p><br />
<p>lacI repress gene expression (LuxI); IPTG binds to tetR and release the repression </p><br />
<p>araC repress gene expression (LasI or LuxI); arabinose binds to araC and release the repression </p><br />
[[File:designasustc.jpg]]<br />
[[File:designbsustc.jpg]]<br />
'''Cell A:'''<br />
Constant expressions:<br />
'''LuxR'''(with C6HSL, activate pLux, express Zeo-r): promoter J23100 and rbs B0034</p><br />
<p>'''araC'''(with arabinose, activate LasI, tetA): promoter J23100 and rbs B0034</p><br />
<p>'''mCherry '''(red fluorescent protein labeled cell A): promoter pCon, rbs </p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r,''' adjusted by C6HSL, produced by LuxI from '''cell B''', depends on cell B density and IPTG concentration</p><br />
<p>'''LasI:''' adjusted by arabinose, LasI produces C12HSL, control cell B</p><br />
<p>'''tetA:''' adjusted by arabinose</p><br />
<br />
<p>'''Arabinose, Zeocin, Nickel''' concentration are controlled by you</p><br />
<p>'''C12SHL '''concentration: controlled by cell A concentration and arabinose</p><br />
<p>'''Nickel '''either kill cell or slow cell growth: '''tetA''' increase sensitivity of '''cell B '''to''' Nickel''':</p><br />
<p>zeocin either kill cell or slow cell growth:Zeo-r decreases sensitivity of''' cell B''' to''' zeocin'''</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli</p><br />
<p>Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
</p><br />
<br />
=== Experiment process ===<br />
<br />
<br />
== Results ==<br />
<br />
=== project results===<br />
<p>What we have done are the plasmid construction and the early experiments ,because of the time limite. Here are some results of our project</p><br />
[[File:projectresult.jpg]]<br />
<br />
=== modeling results ===<br />
<br />
<br />
==Biobricks checking==<br />
=== process ===<br />
<br />
=== results ===<br />
<br />
<p>We chose four biobricks to detect after search . They are xylose、KNO<sub>3</sub>、glucose and 12HSL.</p><br />
'''xylose'''<br />
[[File:xylosesustc.jpg|xylose]]<br />
<p>Compared with the results of the efficiency of the xylose inducible promoter detected by the HKT, our consequence differed from them in some aspects, or better. We had used the FCM to detect it. There was an obvious tendency that the efficiency of the promoter increased as the xylose concentration gathered up. What was amazing was that the fluorescence we got was 10 times brighter than the result the HKT got, which appeared to be great.</p><br />
<p>But when the concentration of the xylose was 0.03% and 0.3%, we got an unexpected result that the expression of the GFP fell after rise. What’s more. While the concentration of the xylose was 10%, the expression of the GFP decreased, which corresponded with the result of the HKT.</p><br />
<br />
'''KNO<sub>3</sub>'''<br />
<br />
[[File:kno3sustc.jpg|KNO3]]<br />
<p>BBa_K774007 KNO3: This part we got a similar beginning, but have a different ending. With the increasing of nitrate of potash, the fluorescence produced by single cell increases slowly at the beginning but rapidly later. However, according to the data from NRP-UEA-Norwich, the fluorescence starts to decrease at the 20mM nitrate of potash.</p><br />
<br />
[[File:glucosesustc.jpg|glucose]]<br />
<p>BBa_K741002 glucose: Compared with testing result from USTC_China, we’ve got a better data. According to the data from USTC_China, after adding glucose, the fluorescence reduces only about 10% in the most obvious one. However, we got a clear reduce in the production of fluorescence. In about 10-2.4M glucose, the fluorescence has left only a half in one cell. With the increasing of glucose, the fluorescence/OD continuously decreases, and at about 10-1M glucose, the fluorescence/OD remains very low. </p><br />
[[File:12hslsustc.jpg|12HSL]]<br />
<p>lalala</p><br />
<html><br />
<script><br />
$(document).ready(function(){<br />
$("#toc").css("position","fixed");<br />
$("#toc").css("left","0px;");<br />
$("#toc").css("top","140px");<br />
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</script><br />
<br />
=== References===<br />
<br />
<html><br />
<p>Click the <a href="/index.reference">Reference</a> to get more information.<br />
</html></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/Human_PracticeTeam:SUSTC-Shenzhen-A/Human Practice2013-09-27T04:41:29Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma1.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="90%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
{|align="justify"<br />
|[[Image:humanpractice1.jpg|center|frame|to new students]]<br />
|-<br />
<br />
|We introduced sythetic biology and our project to some high school students.<br />
[[Image:humanpracticesustc2.jpg|left|frame|to high school students]]<br />
[[Image:humanpractice3.jpg|right|frame|to high school students]]<br />
|-<br />
|We introduced sythetic biology and our project to some adults.<br />
[[File:humanpracticesustc3.jpg|left|frame|to adults]]<br />
[[File:humanpracticesustc4.jpg|right|frame|to adults]]<br />
<br />
<br />
|}<br />
|<br />
<br />
<br />
<br />
<br />
<br />
== Sponsor ==</div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/SafetyTeam:SUSTC-Shenzhen-A/Safety2013-09-27T04:40:24Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocl and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== Security ==<br />
<p>One of the most essential problem urgent to solve in synthetic biology is the system safety problem. It has been a troublesome part whether we can pursue that the constructed bacteria cannot survive in the circumstance with some target genes imported by us. As for our project, though there is no safety worry, we come up with an original way to synthesis one kind of standard constructed bacteria, if slightly simplified by our project. In our previous project there are three cases when criminal can survive, but based on the safety consideration, we cannot let any bacteria alive in the wild, so we refer to this design because there is nearly no possibility for them to survive in the wild, for the living conditions have to reach several high levels, which is hard to achieve in the natural circumstance. What’s more, we have made mathematic model of it, which offers the theoretic evidence of it and make it more feasible. The design is like the figure below.</p><br />
[[File:Examp.jpg]]<br />
<p>Just as the graph has showed, we make some modifications in our previous design. We remain the communication pair genes as the message access between them-LuxR and LasR, the products of which-6HSL and 12HSL still function as the signals between the two bacteria communities. It’s apparent that reporter genes are unrelated to the safety problem, so just leave them out. In the meantime, we cut off the tetA gene directly and import the cl gene exactly the same place of the zeo-R. The function of the cl gene is to reduce the expression of the ccdB gene. What is an obvious change is that we replace zeo-r gene that is resistant to the antibiotic zeocin in the culture with the toxin gene ccdB, whose product is a kind of poisonous protein and ccdB can express continuously and by itself. This requires us to switch the gene circuit, which means we change the poisonous protein gene and the mechanism of the toxin principle.</p><br />
<p>On the one hand, when the two types of bacteria are culture separately, each of them cannot survive because the ccdB gene expresses continuously and the toxin would result the death of the bacteria, what’s more, they cannot get the signal molecular from the partener-6HSL and 12HSL, so even though they are let out, they have no safety risk to our environment. On the other hand, when they are cultured together, they cannot survive as well, only when the concentration of the products of the cl gene reach a relative high level would the degree of the toxin ccdB product decease, but this kind of situation only occur in the laboratory circumstance because of human control. In the natural environment, due to the lack of the products of the cl genes, the poisonous protein produced by the ccdB cannot disappear, which would lead to the death of the both sides.</p><br />
<p>Eventually, in order that the target genes we import would not lose efficacy for the sake of the loss of the plasmid by the bacteria. We proposal that all the target genes can be connected to the genome of the bacteria, then the condition would not happen.</p><br />
<p>Our model have imitated this idea, and there are the figures showing below:</p><br />
[[File:Examp.jpg]]<br />
<br />
== Safety ==<br />
Our project is safe for the following reasons :<br />
<ul><li><br />
The ''E-coli'' strains and genes we usd are already existed and are commercially available for years.</li><br />
<br />
<li>We would not release the bacteria to the environment</li> <br />
Please click the pdf linked to get more details .<br />
<br />
[[Media:saftysustc.pdf]]</div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/SafetyTeam:SUSTC-Shenzhen-A/Safety2013-09-27T04:36:58Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="100%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocl and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
== Safety ==<br />
Our project is safe for the following reasons :<br />
<ul><li><br />
The ''E-coli'' strains and genes we usd are already existed and are commercially available for years.</li><br />
<br />
<li>We would not release the bacteria to the environment</li> <br />
Please click the pdf linked to get more details .<br />
<br />
[[Media:saftysustc.pdf]]<br />
<br />
<br />
== Security ==</div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ModelingTeam:SUSTC-Shenzhen-A/Modeling2013-09-27T04:17:27Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="80%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
== Modeling ==<br />
'''Abstract'''<br />
<p>Our model is to simulate a cell-cell mutual help system that is inspired by the classic prisoner's dilemma. we use two kinds of operated cells to act as the two prisoners. Both of them are facing the same problem comes from the environment, if they do not help each other, both of them will get into a terrible situation. Even they choose to collaborate, one may also take the risk that another man would turn traitor to him. So it’s a complex problem that how do our prisoners to choose their strategy to make themselves survival. Here are all equations and variables we have worked out.</p><br />
[[File:Examp.jpg]]<br />
'''So, how can our system perform this prisoner’s dilemma? '''<br />
<p>We use the growth rate and the concentration of the cells to describe the living status of two prisoners, use Zeocin in our system to represent the punishment on our prisoners, and use the tetA(which will translate companying with the expressing of AHL) to bring Ni into the cells referring to the risk the as telling the lie. And if one receive the shield from another as sufficient AHL, he will start to produce ZeoR protein which can make him survive the Zeocin. </p><br />
'''Here are also some Differences'''<br />
<p>However our cell-cell mutual help system also do not all obey the classic prisoners’ dilemma, first of all, one prisoner can only have two certain choices in this traditional question, be honest or crafty. But as we have mentioned before, in our system two cells use AHL to help each other, namely the concentration here stands for the attitude of our cell, well it is right the concentration not the existence of AHL makes sense in our system, so our prisoner have a chance to make an elastic choice, they can decide to what level the cooperation will be put into effect. This important difference make our system more close to the realistic. </p><br />
<p>Then one prisoner will never really die in a classic situation, but in ours there exist some possibility that one cell can actually die out which will result in a big crash. This is what we should put our eyes on.</p><br />
'''Test'''<br />
<p>To confirm whether our simulations can work out a good result, we want test some important parameters to see whether our subsystem can work properly,</p><br />
'''1.the effect of Zeocin'''<br />
<p>We put our prisoners into a person to see what will happen to this pool man, this will help us understand how powerful the punishment is as well as tell us how much Zeocin we should use to create a temperate environment stress. <br />
As we can see from this figure, this antibiotic leads to a quick death of our prisoner. Without help one man can hardly get out of this problem.</p><br />
[[File:Examp.jpg]]<br />
<p>This media liked the whole modeling of our project.</p><br />
[[Media:modelingsustc.pdf]]<br />
'''2.separate cell in the environment contain AHL'''<br />
<p>To test our relationship between the concentration of AHL and the concentration of our cells, we conduct this test. We put one of our prisoner into AHL concentration gradients to make sure where the efficient concentration of AHL lies, and we get the final cell concentration for each AHL gradients.</p><br />
<p>This EC can tell us some important things such as whether there exists any sensitivity difference of AHL between the two cells, it can help us have a better understading of the coporation between these two cells.<br />
As we can see there is a cliffy slope in our data, which give us the idea that the relationship between the AHL and cell concentration is not simply linear, so we should concider twise before we change this influential variable.</p><br />
[[File:Examp.jpg]]<br />
'''3.the show begins'''<br />
Result 1:Good Cooperation<br />
<p>If both of our prisoners try to help each other things will be much better</p><br />
[[File:Examp.jpg]]<br />
Result 2: a Traitor<br />
<p>If one of our prisoner wants to get others help without offering any reward, he may be well benefit at first, but as his partner get into the trouble, he will lose his lucky. This though go against the realistic, we can also take well advantage of this flaw in our safety idea. (In the four cases of prisoners’ dilemma there are three cases that the bad man can escape but in our model only if they are well cooperate with each other then they will have chance to run away, but such a good cooperate cannot be easily achieved especially outside the Lab)</p><br />
[[File:Examp.jpg]]<br />
'''Result 3: The Egoists'''<br />
If the both guy are imaginary smart, and have a strong believe that his partner will forswear for him, it’s obviously that they will get deserved penalty.<br />
[[File:Examp.jpg]]<br />
'''Some more interesting results'''<br />
<p>The results all above are just considering the same situation that both the prisoners have a similar personality, that says our two cells have a very symmetry structure, their physiological parameter are nearly the same. Basing on this, every cell can act the same behavior when meet the same change in the environment.</p><br />
<p>However, two pieces of leaves will never coincide in the world. We can’t adjust everything to meet our plan and this considerable material difference gives us the opportunity to have a sight of the real prisoner’s dilemma.</p><br />
<p>What will happen if we put two people with different sensibility of other’s goodwill into this dilemma? To achieve this we can simply adjust the Hill coefficient of the differential equation of Zeor, to see what have found.</p><br />
[[File:Examp.jpg]]<br />
<p>There appears a clear game between our prisoners, and unlike other result this dynamic equilibrium crashed at last. It’s usually a common sense that the damped oscillation may lead to a stable equilibrium, , but you can hardly tell which people made the mistake. How our prisoners can performed such clumsy play, maybe we can have a farther study.</p></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ModelingTeam:SUSTC-Shenzhen-A/Modeling2013-09-27T04:15:15Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="80%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
== Modeling ==<br />
'''Abstract'''<br />
<p>Our model is to simulate a cell-cell mutual help system that is inspired by the classic prisoner's dilemma. we use two kinds of operated cells to act as the two prisoners. Both of them are facing the same problem comes from the environment, if they do not help each other, both of them will get into a terrible situation. Even they choose to collaborate, one may also take the risk that another man would turn traitor to him. So it’s a complex problem that how do our prisoners to choose their strategy to make themselves survival. Here are all equations and variables we have worked out.</p><br />
[[File:Example.jpg]]<br />
'''So, how can our system perform this prisoner’s dilemma? '''<br />
<p>We use the growth rate and the concentration of the cells to describe the living status of two prisoners, use Zeocin in our system to represent the punishment on our prisoners, and use the tetA(which will translate companying with the expressing of AHL) to bring Ni into the cells referring to the risk the as telling the lie. And if one receive the shield from another as sufficient AHL, he will start to produce ZeoR protein which can make him survive the Zeocin. </p><br />
'''Here are also some Differences'''<br />
<p>However our cell-cell mutual help system also do not all obey the classic prisoners’ dilemma, first of all, one prisoner can only have two certain choices in this traditional question, be honest or crafty. But as we have mentioned before, in our system two cells use AHL to help each other, namely the concentration here stands for the attitude of our cell, well it is right the concentration not the existence of AHL makes sense in our system, so our prisoner have a chance to make an elastic choice, they can decide to what level the cooperation will be put into effect. This important difference make our system more close to the realistic. </p><br />
<p>Then one prisoner will never really die in a classic situation, but in ours there exist some possibility that one cell can actually die out which will result in a big crash. This is what we should put our eyes on.</p><br />
'''Test'''<br />
<p>To confirm whether our simulations can work out a good result, we want test some important parameters to see whether our subsystem can work properly,</p><br />
'''1.the effect of Zeocin'''<br />
<p>We put our prisoners into a person to see what will happen to this pool man, this will help us understand how powerful the punishment is as well as tell us how much Zeocin we should use to create a temperate environment stress. <br />
As we can see from this figure, this antibiotic leads to a quick death of our prisoner. Without help one man can hardly get out of this problem.</p><br />
[[File:Example.jpg]]<br />
<p>This media liked the whole modeling of our project.</p><br />
[[Media:modelingsustc.pdf]]<br />
'''2.separate cell in the environment contain AHL'''<br />
<p>To test our relationship between the concentration of AHL and the concentration of our cells, we conduct this test. We put one of our prisoner into AHL concentration gradients to make sure where the efficient concentration of AHL lies, and we get the final cell concentration for each AHL gradients.</p><br />
<p>This EC can tell us some important things such as whether there exists any sensitivity difference of AHL between the two cells, it can help us have a better understading of the coporation between these two cells.<br />
As we can see there is a cliffy slope in our data, which give us the idea that the relationship between the AHL and cell concentration is not simply linear, so we should concider twise before we change this influential variable.</p><br />
[[File:Example.jpg]]<br />
'''3.the show begins'''<br />
Result 1:Good Cooperation<br />
<p>If both of our prisoners try to help each other things will be much better</p><br />
[[File:Example.jpg]]<br />
Result 2: a Traitor<br />
<p>If one of our prisoner wants to get others help without offering any reward, he may be well benefit at first, but as his partner get into the trouble, he will lose his lucky. This though go against the realistic, we can also take well advantage of this flaw in our safety idea. (In the four cases of prisoners’ dilemma there are three cases that the bad man can escape but in our model only if they are well cooperate with each other then they will have chance to run away, but such a good cooperate cannot be easily achieved especially outside the Lab)</p><br />
[[File:Example.jpg]]<br />
'''Result 3: The Egoists'''<br />
If the both guy are imaginary smart, and have a strong believe that his partner will forswear for him, it’s obviously that they will get deserved penalty.<br />
[[File:Example.jpg]]<br />
'''Some more interesting results'''<br />
<p>The results all above are just considering the same situation that both the prisoners have a similar personality, that says our two cells have a very symmetry structure, their physiological parameter are nearly the same. Basing on this, every cell can act the same behavior when meet the same change in the environment.</p><br />
<p>However, two pieces of leaves will never coincide in the world. We can’t adjust everything to meet our plan and this considerable material difference gives us the opportunity to have a sight of the real prisoner’s dilemma.</p><br />
<p>What will happen if we put two people with different sensibility of other’s goodwill into this dilemma? To achieve this we can simply adjust the Hill coefficient of the differential equation of Zeor, to see what have found.</p><br />
[[File:Example.jpg]]<br />
<p>There appears a clear game between our prisoners, and unlike other result this dynamic equilibrium crashed at last. It’s usually a common sense that the damped oscillation may lead to a stable equilibrium, , but you can hardly tell which people made the mistake. How our prisoners can performed such clumsy play, maybe we can have a farther study.</p></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ProjectTeam:SUSTC-Shenzhen-A/Project2013-09-27T03:51:23Z<p>Donna: /* results */</p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="80%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
<br />
<br />
== '''Overall project''' ==<br />
<br />
{|align="justify"<br />
|'''Abstract'''<br />
<p> <br />
There are many applications of the game theory in some aspects of our life. Each individual has two kinds of choices--to betray or stay silent, and the choice you make would determine your fate. To betray the other side, you may risk being revenged. While staying silent, companion's betrayal may hurt you deeply. As for our project, we work out a new way to imitate the game theory by constructing a community of two E. Coli bacteria. Here we use the growth rate of each species to represent its fate. The effect of one's silent or betrayal on the other species' fate is acted through intercellular signal molecules of two quorum sensing systems. Each signal molecule regulates the expression of toxic genes in the other species and reduces its growth rate. We characterize the consequence of each strategy by quantitatively measure the growth rates of each species in the community</p><br />
'''Background'''<br />
<br />
<br />
<br />
== Project Details==<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== our design ===<br />
[[File:designsustc.png]]<br />
<p>Parts:</p><br />
<p>Communication: quorum sensing</p><br />
<p>LuxI produces 6HSL, 6HSL cross membrane, 6HSL binds to LuxR, LuxR activate promoter Plux </p><br />
<p>LasI produces 12HSL, 12HSL cross membrane, 12HSL binds to LasR, LasR activate promoter Plas</p><br />
<p>Poissonness genes:</p><br />
<p>tetA: import Nickel into cell, which kills cell</p><br />
<p>Zeo-r: Zeocin damage DNA and kills cell, Zeo-r binds and neutralize Zeocin</p><br />
<p>Truth Table</p><br />
[[File:tablesustc.jpg]]<br />
<p>Tuning gene expression: repressor and inducer</p><br />
<p>lacI repress gene expression (LuxI); IPTG binds to tetR and release the repression </p><br />
<p>araC repress gene expression (LasI or LuxI); arabinose binds to araC and release the repression </p><br />
[[File:designasustc.jpg]]<br />
[[File:designbsustc.jpg]]<br />
'''Cell A:'''<br />
Constant expressions:<br />
'''LuxR'''(with C6HSL, activate pLux, express Zeo-r): promoter J23100 and rbs B0034</p><br />
<p>'''araC'''(with arabinose, activate LasI, tetA): promoter J23100 and rbs B0034</p><br />
<p>'''mCherry '''(red fluorescent protein labeled cell A): promoter pCon, rbs </p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r,''' adjusted by C6HSL, produced by LuxI from '''cell B''', depends on cell B density and IPTG concentration</p><br />
<p>'''LasI:''' adjusted by arabinose, LasI produces C12HSL, control cell B</p><br />
<p>'''tetA:''' adjusted by arabinose</p><br />
<br />
<p>'''Arabinose, Zeocin, Nickel''' concentration are controlled by you</p><br />
<p>'''C12SHL '''concentration: controlled by cell A concentration and arabinose</p><br />
<p>'''Nickel '''either kill cell or slow cell growth: '''tetA''' increase sensitivity of '''cell B '''to''' Nickel''':</p><br />
<p>zeocin either kill cell or slow cell growth:Zeo-r decreases sensitivity of''' cell B''' to''' zeocin'''</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli</p><br />
<p>Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
</p><br />
<br />
=== Experiment process ===<br />
<br />
<br />
== Results ==<br />
<br />
=== project results===<br />
<p>What we have done are the plasmid construction and the early experiments ,because of the time limite. Here are some results of our project</p><br />
[[File:projectresult.jpg]]<br />
<br />
=== modeling results ===<br />
<br />
<br />
==Biobricks checking==<br />
=== process ===<br />
<br />
=== results ===<br />
<br />
<p>We chose four biobricks to detect after search . They are xylose、KNO<sub>3</sub>、glucose and 12HSL.</p><br />
'''xylose'''<br />
[[File:xylosesustc.jpg|xylose]]<br />
<p>Compared with the results of the efficiency of the xylose inducible promoter detected by the HKT, our consequence differed from them in some aspects, or better. We had used the FCM to detect it. There was an obvious tendency that the efficiency of the promoter increased as the xylose concentration gathered up. What was amazing was that the fluorescence we got was 10 times brighter than the result the HKT got, which appeared to be great.</p><br />
<p>But when the concentration of the xylose was 0.03% and 0.3%, we got an unexpected result that the expression of the GFP fell after rise. What’s more. While the concentration of the xylose was 10%, the expression of the GFP decreased, which corresponded with the result of the HKT.</p><br />
<br />
'''KNO<sub>3</sub>'''<br />
<br />
[[File:kno3sustc.jpg|KNO3]]<br />
<p>BBa_K774007 KNO3: This part we got a similar beginning, but have a different ending. With the increasing of nitrate of potash, the fluorescence produced by single cell increases slowly at the beginning but rapidly later. However, according to the data from NRP-UEA-Norwich, the fluorescence starts to decrease at the 20mM nitrate of potash.</p><br />
<br />
[[File:glucosesustc.jpg|glucose]]<br />
<p>BBa_K741002 glucose: Compared with testing result from USTC_China, we’ve got a better data. According to the data from USTC_China, after adding glucose, the fluorescence reduces only about 10% in the most obvious one. However, we got a clear reduce in the production of fluorescence. In about 10-2.4M glucose, the fluorescence has left only a half in one cell. With the increasing of glucose, the fluorescence/OD continuously decreases, and at about 10-1M glucose, the fluorescence/OD remains very low. </p><br />
[[File:12hslsustc.jpg|12HSL]]<br />
<p>lalala</p><br />
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'''References'''<br />
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<p>Click the <a href="/index.reference">Reference</a> to get more information.<br />
</html></div>Donnahttp://2013.igem.org/Index.referenceIndex.reference2013-09-27T03:43:59Z<p>Donna: Created page with "1.Axelrod, Robert: The Evolution of Cooperation, 1985. <br> 2.Axelrod, Robert: The Complexity of Cooperation - Agent-Based Models of Competition and Collaboration, 1997. <br> 3.A..."</p>
<hr />
<div>1.Axelrod, Robert: The Evolution of Cooperation, 1985. <br><br />
2.Axelrod, Robert: The Complexity of Cooperation - Agent-Based Models of Competition and Collaboration, 1997. <br><br />
3.Axelrod R Effective Choice in the Prisoner's Dilemma 1980(03) <br><br />
4.Grim Patrick Spatialization and Greater Generosity in The Stochastic Prisoner's Dilemma . 1996(1-2) doi:10.1016/0303-2647(95)01541-8 <br><br />
5.Nowak M A;Sigmund K Oscillations in the Evolution of Reciprocity . 1989(11) doi:10.1016/S0022-5193(89)80146-8 <br> <br />
6.Maynard Smith J. Evolution and the Theory Games. Cambridge University Press, Cambridge. 1982 <br><br />
7.Dawkins R. The Selfish Gene. Oxford University Press. 1989 <br><br />
8.Fudenberg D, Eric Maskin. Evolution and Cooperation in Noisy Repeated Games. American Economic Review. 1990, May, 80, pp. 274-279 <br><br />
9.Harsanyi John C, Rein Selten. A General Theory of Equilibrium Selection in Games. Cambridge:MIT Press, 1998.<br> <br />
<br />
10.Selten R. Reexamination of the Perfectness Concept for Equilibrium Points in Extensive Games. International Journal of Game Theory, 1975, 4:25-55.<br><br />
<br />
11.Crowley P H. Hawks, doves, and mixed-symmetry games. J. Theor. Biol. 2000, 204:543-563.<br><br />
<br />
12.Enquist M, Leimar 0. Evolution of fighting behaviour: the effect of variation in resource value,J. theor. Biol. 1987, 127, 187-205.<br><br />
<br />
13.Mesterton-Gibbons M, Dugatkin L A. Toward a theory of dominance hierarchies:effects of assessment, group size, and variation in fighting ability. Behav. Ecol. 1995, 6, 416-423.<br><br />
<br />
14.Grafen A. The logic of divisively asymmetric contests:respect for ownership and desperado effect. Anim. Behav. 1987, 35, 462-467.<br><br />
<br />
15.Dixit, Avinash K./ Skeath, Susan: Games of Strategy, 1999.<br><br />
<br />
16. Axelrod R The complexity of cooperation:agent-based models of competition and collaboration,princeton 1997.<br><br />
<br />
17. Boyd R;Lorberbaum J P No pure strategy is evolutionary stable in the repeated prisoner's dilemma . 1987 doi:10.1038/327058a0 <br><br />
<br />
18.Fogel D Evolving behaviours in the iterated prisoners dilemma 1993(01) doi:10.1162/evco.1993.1.1.77 <br><br />
<br />
19. Palomino F;Vega-edondo F Convergence of aspirations and(partial) cooperation in the prisoner's dilemma .1999(04) doi:10.1007/s001820050120<br><br />
<br />
20.Janssen M A Evolution of cooperation in a one-shot prisoner' s dilemma based on recognition of trustworthy and untrustworthy agents . 2008 doi:10.1016/j.jebo.2006.02.004 <br></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ProjectTeam:SUSTC-Shenzhen-A/Project2013-09-27T03:20:29Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="80%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
<br />
<br />
== '''Overall project''' ==<br />
<br />
{|align="justify"<br />
|'''Abstract'''<br />
<p> <br />
There are many applications of the game theory in some aspects of our life. Each individual has two kinds of choices--to betray or stay silent, and the choice you make would determine your fate. To betray the other side, you may risk being revenged. While staying silent, companion's betrayal may hurt you deeply. As for our project, we work out a new way to imitate the game theory by constructing a community of two E. Coli bacteria. Here we use the growth rate of each species to represent its fate. The effect of one's silent or betrayal on the other species' fate is acted through intercellular signal molecules of two quorum sensing systems. Each signal molecule regulates the expression of toxic genes in the other species and reduces its growth rate. We characterize the consequence of each strategy by quantitatively measure the growth rates of each species in the community</p><br />
'''Background'''<br />
<br />
<br />
<br />
== Project Details==<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== our design ===<br />
[[File:designsustc.png]]<br />
<p>Parts:</p><br />
<p>Communication: quorum sensing</p><br />
<p>LuxI produces 6HSL, 6HSL cross membrane, 6HSL binds to LuxR, LuxR activate promoter Plux </p><br />
<p>LasI produces 12HSL, 12HSL cross membrane, 12HSL binds to LasR, LasR activate promoter Plas</p><br />
<p>Poissonness genes:</p><br />
<p>tetA: import Nickel into cell, which kills cell</p><br />
<p>Zeo-r: Zeocin damage DNA and kills cell, Zeo-r binds and neutralize Zeocin</p><br />
<p>Truth Table</p><br />
[[File:tablesustc.jpg]]<br />
<p>Tuning gene expression: repressor and inducer</p><br />
<p>lacI repress gene expression (LuxI); IPTG binds to tetR and release the repression </p><br />
<p>araC repress gene expression (LasI or LuxI); arabinose binds to araC and release the repression </p><br />
[[File:designasustc.jpg]]<br />
[[File:designbsustc.jpg]]<br />
'''Cell A:'''<br />
Constant expressions:<br />
'''LuxR'''(with C6HSL, activate pLux, express Zeo-r): promoter J23100 and rbs B0034</p><br />
<p>'''araC'''(with arabinose, activate LasI, tetA): promoter J23100 and rbs B0034</p><br />
<p>'''mCherry '''(red fluorescent protein labeled cell A): promoter pCon, rbs </p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r,''' adjusted by C6HSL, produced by LuxI from '''cell B''', depends on cell B density and IPTG concentration</p><br />
<p>'''LasI:''' adjusted by arabinose, LasI produces C12HSL, control cell B</p><br />
<p>'''tetA:''' adjusted by arabinose</p><br />
<br />
<p>'''Arabinose, Zeocin, Nickel''' concentration are controlled by you</p><br />
<p>'''C12SHL '''concentration: controlled by cell A concentration and arabinose</p><br />
<p>'''Nickel '''either kill cell or slow cell growth: '''tetA''' increase sensitivity of '''cell B '''to''' Nickel''':</p><br />
<p>zeocin either kill cell or slow cell growth:Zeo-r decreases sensitivity of''' cell B''' to''' zeocin'''</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli</p><br />
<p>Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
</p><br />
<br />
=== Experiment process ===<br />
<br />
<br />
== Results ==<br />
<br />
=== project results===<br />
<p>What we have done are the plasmid construction and the early experiments ,because of the time limite. Here are some results of our project</p><br />
[[File:projectresult.jpg]]<br />
<br />
=== modeling results ===<br />
<br />
<br />
==Biobricks checking==<br />
=== process ===<br />
<br />
=== results ===<br />
<br />
<p>We chose four biobricks to detect after search . They are xylose、KNO<sub>3</sub>、glucose and 12HSL.</p><br />
'''xylose'''<br />
[[File:xylosesustc.jpg|xylose]]<br />
<p>Compared with the results of the efficiency of the xylose inducible promoter detected by the HKT, our consequence differed from them in some aspects, or better. We had used the FCM to detect it. There was an obvious tendency that the efficiency of the promoter increased as the xylose concentration gathered up. What was amazing was that the fluorescence we got was 10 times brighter than the result the HKT got, which appeared to be great.</p><br />
<p>But when the concentration of the xylose was 0.03% and 0.3%, we got an unexpected result that the expression of the GFP fell after rise. What’s more. While the concentration of the xylose was 10%, the expression of the GFP decreased, which corresponded with the result of the HKT.</p><br />
<br />
'''KNO<sub>3</sub>'''<br />
<br />
[[File:kno3sustc.jpg|KNO3]]<br />
<p>BBa_K774007 KNO3: This part we got a similar beginning, but have a different ending. With the increasing of nitrate of potash, the fluorescence produced by single cell increases slowly at the beginning but rapidly later. However, according to the data from NRP-UEA-Norwich, the fluorescence starts to decrease at the 20mM nitrate of potash.</p><br />
<br />
[[File:glucosesustc.jpg|glucose]]<br />
<p>BBa_K741002 glucose: Compared with testing result from USTC_China, we’ve got a better data. According to the data from USTC_China, after adding glucose, the fluorescence reduces only about 10% in the most obvious one. However, we got a clear reduce in the production of fluorescence. In about 10-2.4M glucose, the fluorescence has left only a half in one cell. With the increasing of glucose, the fluorescence/OD continuously decreases, and at about 10-1M glucose, the fluorescence/OD remains very low. </p><br />
[[File:12hslsustc.jpg|12HSL]]<br />
<p>lalala</p><br />
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== Reference ==<br />
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<p>Click the <a href="/index.reference">'''Reference'''</a> to get more information.<br />
</html></div>Donnahttp://2013.igem.org/Team:SUSTC-Shenzhen-A/ProjectTeam:SUSTC-Shenzhen-A/Project2013-09-27T03:19:35Z<p>Donna: </p>
<hr />
<div>[[File:prisonersdilemma.jpg]]<br />
{| style="color:#ff9900;background-color:#ffffff;" cellpadding="3" cellspacing="0" border="0" bordercolor="#000000" width="80%" align="center"<br />
!align="center"|[[Team:SUSTC-Shenzhen-A|Home]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=SUSTC-Shenzhen-A Official Team Profile]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Project|Project]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Modeling|Modeling]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Notebook|Protocol and notes]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Safety|Safety]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Attributions|Attributions]]<br />
!align="center"|[[Team:SUSTC-Shenzhen-A/Human Practice|Human Practice]]<br />
|}<br />
<HR style="border:3 double #ff9900" width="100%" color=#ff9900 SIZE=3><br />
<br />
<br />
<br />
<br />
== '''Overall project''' ==<br />
<br />
{|align="justify"<br />
|'''Abstract'''<br />
<p> <br />
There are many applications of the game theory in some aspects of our life. Each individual has two kinds of choices--to betray or stay silent, and the choice you make would determine your fate. To betray the other side, you may risk being revenged. While staying silent, companion's betrayal may hurt you deeply. As for our project, we work out a new way to imitate the game theory by constructing a community of two E. Coli bacteria. Here we use the growth rate of each species to represent its fate. The effect of one's silent or betrayal on the other species' fate is acted through intercellular signal molecules of two quorum sensing systems. Each signal molecule regulates the expression of toxic genes in the other species and reduces its growth rate. We characterize the consequence of each strategy by quantitatively measure the growth rates of each species in the community</p><br />
'''Background'''<br />
<br />
<br />
<br />
== Project Details==<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== our design ===<br />
[[File:designsustc.png]]<br />
<p>Parts:</p><br />
<p>Communication: quorum sensing</p><br />
<p>LuxI produces 6HSL, 6HSL cross membrane, 6HSL binds to LuxR, LuxR activate promoter Plux </p><br />
<p>LasI produces 12HSL, 12HSL cross membrane, 12HSL binds to LasR, LasR activate promoter Plas</p><br />
<p>Poissonness genes:</p><br />
<p>tetA: import Nickel into cell, which kills cell</p><br />
<p>Zeo-r: Zeocin damage DNA and kills cell, Zeo-r binds and neutralize Zeocin</p><br />
<p>Truth Table</p><br />
[[File:tablesustc.jpg]]<br />
<p>Tuning gene expression: repressor and inducer</p><br />
<p>lacI repress gene expression (LuxI); IPTG binds to tetR and release the repression </p><br />
<p>araC repress gene expression (LasI or LuxI); arabinose binds to araC and release the repression </p><br />
[[File:designasustc.jpg]]<br />
[[File:designbsustc.jpg]]<br />
'''Cell A:'''<br />
Constant expressions:<br />
'''LuxR'''(with C6HSL, activate pLux, express Zeo-r): promoter J23100 and rbs B0034</p><br />
<p>'''araC'''(with arabinose, activate LasI, tetA): promoter J23100 and rbs B0034</p><br />
<p>'''mCherry '''(red fluorescent protein labeled cell A): promoter pCon, rbs </p><br />
<p>Adjustable expressions:</p><br />
<p>'''Zeo-r,''' adjusted by C6HSL, produced by LuxI from '''cell B''', depends on cell B density and IPTG concentration</p><br />
<p>'''LasI:''' adjusted by arabinose, LasI produces C12HSL, control cell B</p><br />
<p>'''tetA:''' adjusted by arabinose</p><br />
<br />
<p>'''Arabinose, Zeocin, Nickel''' concentration are controlled by you</p><br />
<p>'''C12SHL '''concentration: controlled by cell A concentration and arabinose</p><br />
<p>'''Nickel '''either kill cell or slow cell growth: '''tetA''' increase sensitivity of '''cell B '''to''' Nickel''':</p><br />
<p>zeocin either kill cell or slow cell growth:Zeo-r decreases sensitivity of''' cell B''' to''' zeocin'''</p><br />
<p>'''-asv''': amino acid sequence that increase response time of LuxI, tetA and Zeo-r to regulation</p><br />
pMB1 and p15A: control plasmid replication in E coli</p><br />
<p>Kan and Cam(r): with antibiotics Kanamycin and chloramphenicol, prevent lost of plasmids<br />
</p><br />
<br />
=== Experiment process ===<br />
<br />
<br />
== Results ==<br />
<br />
=== project results===<br />
<p>What we have done are the plasmid construction and the early experiments ,because of the time limite. Here are some results of our project</p><br />
[[File:projectresult.jpg]]<br />
<br />
=== modeling results ===<br />
<br />
<br />
==Biobricks checking==<br />
=== process ===<br />
<br />
=== results ===<br />
<br />
<p>We chose four biobricks to detect after search . They are xylose、KNO<sub>3</sub>、glucose and 12HSL.</p><br />
'''xylose'''<br />
[[File:xylosesustc.jpg|xylose]]<br />
<p>Compared with the results of the efficiency of the xylose inducible promoter detected by the HKT, our consequence differed from them in some aspects, or better. We had used the FCM to detect it. There was an obvious tendency that the efficiency of the promoter increased as the xylose concentration gathered up. What was amazing was that the fluorescence we got was 10 times brighter than the result the HKT got, which appeared to be great.</p><br />
<p>But when the concentration of the xylose was 0.03% and 0.3%, we got an unexpected result that the expression of the GFP fell after rise. What’s more. While the concentration of the xylose was 10%, the expression of the GFP decreased, which corresponded with the result of the HKT.</p><br />
<br />
'''KNO<sub>3</sub>'''<br />
<br />
[[File:kno3sustc.jpg|KNO3]]<br />
<p>BBa_K774007 KNO3: This part we got a similar beginning, but have a different ending. With the increasing of nitrate of potash, the fluorescence produced by single cell increases slowly at the beginning but rapidly later. However, according to the data from NRP-UEA-Norwich, the fluorescence starts to decrease at the 20mM nitrate of potash.</p><br />
<br />
[[File:glucosesustc.jpg|glucose]]<br />
<p>BBa_K741002 glucose: Compared with testing result from USTC_China, we’ve got a better data. According to the data from USTC_China, after adding glucose, the fluorescence reduces only about 10% in the most obvious one. However, we got a clear reduce in the production of fluorescence. In about 10-2.4M glucose, the fluorescence has left only a half in one cell. With the increasing of glucose, the fluorescence/OD continuously decreases, and at about 10-1M glucose, the fluorescence/OD remains very low. </p><br />
[[File:12hslsustc.jpg|12HSL]]<br />
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== Reference ==<br />
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