Team:Shenzhen SFLS/Project

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<h1 class="hide">Project</h1>
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You are provided with this team page template with which to start the iGEM season. You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki.  You can find some examples <a href="https://2009.igem.org/Help:Template/Examples">HERE</a>.
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You <strong>MUST</strong> have the following information on your wiki:
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<li>a team description</li>  
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<p>This is our project, EcoPi. <br />
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<li>project description</li>
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<img src="https://static.igem.org/mediawiki/2013hs/4/41/Project_img_1.jpg" width="800" height="262" alt="" /> 
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<li>safety information (did your team take a safety training course? were you supervised in the lab?)</li>
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</p>
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<li>team attribution (who did what part of your project?)</li>
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<p>In this page, you can see how it was designed and made.</p>
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</ul>
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<p>Eutrophication can be a very severe problem to the environment. In an effort to solve this problem, we want to build a genetic system which can test and remove the phosphate from water. In our idea, we want to make a product which can automatically detects phosphate and therefore remove it. And it must be a totally environmentally friendly one. And we began our designing.
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Frist we designed a genetic circuit which can test how the work has been done. We wanted to find a promoter which can only be induced by Pi starvation. Then there is a suppressor protein and an <span>rfp</span>. A double terminator is at the end of this device. This device can only work when the concentration of Pi is low. And the water will show red fluorescence. The red can also be a signal of ‘STOP’, which means the work has already finished.<br />
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<li>lab notebook</li>
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<img src="https://static.igem.org/mediawiki/2013hs/e/e2/Project_img_3.jpg" width="800" height="244" alt="" />
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<li>sponsor information</li>
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Next we designed a second device for removing the phosphate. The promoter of this device is repressed by the protein in Device one, which means when the concentration of Pi is low, Device two will be limited and stop working. Then we wanted to find a CDS which can remove phosphate from water. And a <span>gfp</span>+LVA(degradation tag) with a terminator at the end. When this device is working, The CDS will remove the phosphate from water and meanwhile the gfp+LVA will show green fluorescence, just like the green traffic signal. This device is mainly used for removing phosphate.
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<li>other information</li>
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</p>
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</ul>  
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<p>This photo can show you how the two device are linked
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REMEMBER, keep all of your pages within your teams namespace. <br><span style="font-weight:normal; font-style:italic;">Example: 2013hs.igem.org/Team:Shenzhen_SFLS /Our_Pets</span>
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<img src="https://static.igem.org/mediawiki/2013hs/8/87/Project_img_4.jpg" width="800" height="525" alt="" />
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When we put our product into the water which has a very high concentration of phosphate, Device one will be limited and Device two will be activated. Then the water will show green fluorescence which means our product is removing Pi.
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<img src="https://static.igem.org/mediawiki/2013hs/b/bf/Project_img_5.jpg" width="800" height="458" alt="" />
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After a period of time, due to Device two’s work, the concentration of Pi decreases, then Device one will be activated because of Pi starvation. The suppressor protein will repress Device two. Device one will work and show red fluorescence to tell us that the work has been finished.
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</p>
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<p>That’s the idea of our project, we then started searching for files that support our idea. First we searched for a CDS which can digest phosphate. Then after weeks of searching we found Polyphosphate Kinase, also known as PPK. It is a kind of enzyme widely distributed in ecosystem, more importantly, it can be found in E-coli. Here this picture below can show you how it works.
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<img src="https://static.igem.org/mediawiki/2013hs/c/cd/Project_img_6.jpg" width="800" height="298" alt="" />
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</p>
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<p>We found its genetic sequence and we used PCR to made it a standard biobrick. Then we started to find the promoters of our product. Finally we found the Pi Starvation Promoter(BBa_K737023), it’s not on the kits so we again designed its primer and used PCR.</p>
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<p>For the protein we used TetR protein(BBa_C0040)</p>
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<p>Now it’s time for our final genetic circuit. Take a look!
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<img src="https://static.igem.org/mediawiki/2013hs/7/72/Project_img_7.jpg" width="800" height="262" alt="" />
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</p>
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<p>Result</p>
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</p>
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<p>After we finished our project, we started to test it. We test two part of our project. The first one is our Device One. We tested its response to Pi starvation. Here is the results diagram.</p>
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</p>
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<p>In this diagram we can find that Device one can be induced by phosphate starvation. When the concentration of dipotassium phosphate is 0.03μM we can see that our sensor reached a peak because our promoter can be activated by Pi starvation.</p>
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</p>
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<p>Next is our whole Device. We tested when the green fluorescence would vanish and red fluorescence occur. Here is another diagram.</p>
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</p>
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<p>This diagram shows that after several hours the amount of green fluorescence decreases, which means the work has been done and red fluorescence will occur.</p>
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</p>
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<p>This result clearly pointed out that our product can work smoothly. The Pi starvation promoter is working well too. Our experiments have reached a success at last.</p
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{|align="justify"
 
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|Shenzhen_SFLS is the first time to take part in iGEM High School Competition and 2013 is the first year there are 4 chinese teams entered the lists. SFLS is one of the top high schools in Shenzhen and there are all the best students in Shenzhen, China. With the guidance from BGI-Shenzhen, we aim to build fantastic and useful genetic circuits.
 
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|[[Image:Shenzhen_SFLS_logo.png|200px|right|frame]]
 
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Shenzhen_SFLS iGEM team was set up in October 2012, after the iGEM Collegiate Division in Asia. The team leader watched the jamboree and he was deeply attracted by the great game. He found 7 students who followed him overcame the difficulties and obstacles. In october 2013, they went to BGI to study how to make a gene circuit。
 
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|[[Image:Shenzhen_SFLS.png|right|frame|Your team picture]]
 
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|align="center"|[[Team:Shenzhen_SFLS | Team Shenzhen_SFLS]]
 
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<!--- Team Information Link --->
 
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
 
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!align="center"|[https://igem.org/Team.cgi?year=2013&division=high_school&team_name=Shenzhen_SFLS Official Team Profile]
 
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|}
 
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===Team===
 
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Peilin Li:Teacher of SFLS and the instructor of SFLS students.
 
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Kang Kang: the advisor of SFLS students. In BGI, K2 is veeeeery famous for lurking on BBS and sarcasm! As a former champion in a national robot contest, a hacker, a web engineer, a designer, a magazine editor, a citizen reporter, a filmmaker and a drama actor, he has always too many wonderings, including how life works on its core database - genome. Cracking and hacking the code of life, making actors in cell perform on his scripts, has become the primary task of this young scientist.
 
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Hekang Jia: the captain of SFLS students, set his sights on get the only grand prize. The boy who set up the team by himself，has strong desire to make everthing best. He is often very serious in team's seminar and made others under pressure. He is also the leader of team's students working on theoretical derivation.
 
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Biwei Zheng: the associate captain of SFLS students.The boy has the sense of responsibility for his team and the program. He has a great enthusiasm in Molecular biology and  he really enjoy learning it.Besides these,the boy has many hobits and very popular among his friends.
 
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Ruping Liu: Conscientious and careful to anything. She’s interested in biology, not only because of its diversity but also its mystery. Her dream is to do something which is useful to the world in the future. The girl is working on reading paper and do some experiments in SFLS iGEM team.
 
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Kang Li: Eric Lee is a senior one student in SFLS and is responsible for the team’s communication group. He has a strong desire in biology and is very good at communicating with people. He is in charge of contacting with the headquaters and other teams. He is a good speaker too. Eric is looking forward to helping the team more.
 
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Ziying Tan: Tina is studying in SFLS Class 7 Grade 10. Aside from spending time before the computer or in the lab, she enjoys rubber sculpture and reading.She is now one of the leaders of vacation club. She couldn`t think of a better way to enjoy her summer in school than joining Shenzhen SFLS IGEM team!
 
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Jeffrey Sanders: Jeff is a conversational English teacher at SFLS. A recent college graduate, he earned a BS in molecular biology and will soon be studying for an MPH in epidemiology. He serves as an adviser for the SFLS iGEM team and helps the team bounce ideas.
 
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Jessica Landoll: Jess is a conversational English teacher at SFLS as well. A recent college graduate, she earned a BS in chemistry and will soon be studying for a PhD in neuroscience. She serves as an adviser for the SFLS iGEM team, helps the team bounce ideas, and designed the team's logo.
 
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===Project===
 
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Pollution caused by development and expansion of human society is an enormous problem that has been discussed for centuries. The negative effects of ruining the environment can be seen readily all around the world, especially in nations growing as rapidly as China. One common type of pollution that has been increasing with the advent of large-scale industrialization is known as eutrophication. In eutrophication, water supplies experience a heightened concentration of phosphorus and nitrogen due to human activity. One consequence of such a shift in balance is an increase in the biomass of phytoplankton, resulting in a higher incidence of toxic mutants and a lower concentration of oxygen in the water, killing other life present in the pond and severely changing local ecosystems and fishing economies.　
 
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One clear example of eutrophication can be the 2008 Beijing Olympic games.The enormous growth of China’s industrialization somehow created sharp problems for the environment. Waste water from factories contains high concentration of phosphate and nitrogen. These elements gathered in water and finally created water-blooms that caused a huge catastrophe. The windsurfing games, however, were terribly affected by the water-blooms , costing huge amount of money of the China Official.
 
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Our home city of Shenzhen, China, is a relatively new city undergoing large amounts of growth due to its status as a special economic zone. As the population increases, pollution worsens, especially in locations deemed desireable by families. In Dameisha, one subdistrict of Shenzhen, the eutrophication seen in the water at the beach has driven tourists away, effectively limiting the economic growth the area could otherwise be experiencing. At SFLS, we therefore decided that our project should concern itself with eutrophication. Finally we've decided to use bioengineering as a tool to limit the damage humans will inevitably cause to their own water supplies.
 
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Our project involves the creation of two connecting devices, Devices 1 and 2. Device 1 contains a promoter which will be induced by phosphate starvation, supressors lac or tetR, and an RFP system. This device is activated in the absence of phosphate and acts as a sensor. It serves to let us know phosphate levels are safe by prompting host bacteria to emit a red fluorescence.
 
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Device 2, on the other hand, includes a promoter which is limited by the suppressor protein featured in Device 1, which means that Device 2 is not active while Device 1 operates. Most importantly, it includes a coding sequence called PPK that is key in digesting phosphate and a GFP player that allows the bacteria to emit a green fluorescence while it is doing so. We've also included an LVA element that quickly dampens green fluorescence production once Device 2 has successfully cleared the surrounding water of sufficient amounts of phosphate and begins to shut down, allowing the red fluorescence produced by Device 1 to shine uninhibited and making it easy for us to know we've successfully purified the water.
 
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In a nutshell, when there is too much phosphorus in the water, Device 1 won't be active. This allows Device 2 to operate unsuppressed, and our bacteria will produce PPK, which allows the bacteria to digest phosphate and emit a green fluorescence. When the concentration of phosphate decreases, Device 1 will be activated, stopping Device 2's activities via a suppressor protein and allowing the bacteria to glow red via RFP. Our product is automatic and environmentally friendly!
 
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===Notebook===
 
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Show us how you spent your days.
 
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===Results/Conclusions===
 
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What did you achieve over the course of your semester?
 
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===Safety===
 
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What safety precautions did your team take? Did you take a safety training course? Were you supervised at all times in the lab?
 
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Safety Questions
 
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1. Would any of your project ideas raise safety issues in terms of: researcher safety, public safety, or environmental safety?
 
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No. Before doing the experiments, all of our team members have already listened to the laboratory safety talk given by advisor. Our design is based on the commonly used nonpathogenic E. coli K.12strain and genes we manipulated are original genes in E. coli. .To guarantee the safety of our researchers and lab personnel, we especially emphasized protection while doing experiments related to bacteria, toxic reagents, fire or electricity. All of us were required to clean up the experiment area to ensure that there was no harmful things left.
 
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===Attributions===
 
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Who worked on what?
 
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===Backgrounds===
 
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Too much phosphorus in the body can be just as harmful as having too little. Likewise, too much phosphorus in lakes and streams can have negative side effects on the surrounding environment, it will make the water eutrophication.
 
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Water eutrophication can be human-caused or natural. Untreated sewage effluent and agricultural run-off carrying fertilizers are examples of human-caused eutrophication. However, it also occurs naturally in situations where nutrients accumulate (e.g. depositional environments), or where they flow into systems on an ephemeral basis. Eutrophication generally promotes excessive plant growth and decay, favouring simple algae and plankton over other more complicated plants, and causes a severe reduction in water quality. Phosphorus is a necessary nutrient for plants to live, and is the limiting factor for plant growth in many freshwater ecosystems. The addition of phosphorus increases algal growth, but not all phosphates actually feed algae.[2] These algae assimilate the other necessary nutrients needed for plants and animals. When algae die they sink to the bottom where they are decomposed and the nutrients contained in organic matter are converted into inorganic form by bacteria. The decomposition process uses oxygen and deprives the deeper waters of oxygen which can kill fish and other organisms. Also the necessary nutrients are all at the bottom of the aquatic ecosystem and if they are not brought up closer to the surface, where there is more available light allowing for photosynthesis for aquatic plants, a serious strain is placed on algae populations. Enhanced growth of aquatic vegetation or phytoplankton and algal blooms disrupts normal functioning of the ecosystem, causing a variety of problems such as a lack of oxygen needed for fish and shellfish to survive. The water becomes cloudy, typically coloured a shade of green, yellow, brown, or red. Eutrophication also decreases the value of rivers, lakes, and estuaries for recreation, fishing, hunting, and aesthetic enjoyment. Health problems can occur where eutrophic conditions interfere with drinking water treatment.
 
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===Human Practices===
 
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Even though our human practises have just started. We have already done something.
 
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We invited the school's TV&Broadcast Center to shoot an advertising video for our team.
 
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This can make contribution to us and let more people know iGEM, as well as Synthetic Biology.
 
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More human practises are preparing. Please do look forward to it.
 
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===Fun!===
 
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What was your favorite team snack?? Have a picture of your team mascot?
 
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<forum_subtle />
 

Latest revision as of 02:35, 22 June 2013

Project

This is our project, EcoPi.

In this page, you can see how it was designed and made.

Eutrophication can be a very severe problem to the environment. In an effort to solve this problem, we want to build a genetic system which can test and remove the phosphate from water. In our idea, we want to make a product which can automatically detects phosphate and therefore remove it. And it must be a totally environmentally friendly one. And we began our designing. Frist we designed a genetic circuit which can test how the work has been done. We wanted to find a promoter which can only be induced by Pi starvation. Then there is a suppressor protein and an rfp. A double terminator is at the end of this device. This device can only work when the concentration of Pi is low. And the water will show red fluorescence. The red can also be a signal of ‘STOP’, which means the work has already finished.
Next we designed a second device for removing the phosphate. The promoter of this device is repressed by the protein in Device one, which means when the concentration of Pi is low, Device two will be limited and stop working. Then we wanted to find a CDS which can remove phosphate from water. And a gfp+LVA(degradation tag) with a terminator at the end. When this device is working, The CDS will remove the phosphate from water and meanwhile the gfp+LVA will show green fluorescence, just like the green traffic signal. This device is mainly used for removing phosphate.

This photo can show you how the two device are linked When we put our product into the water which has a very high concentration of phosphate, Device one will be limited and Device two will be activated. Then the water will show green fluorescence which means our product is removing Pi.

After a period of time, due to Device two’s work, the concentration of Pi decreases, then Device one will be activated because of Pi starvation. The suppressor protein will repress Device two. Device one will work and show red fluorescence to tell us that the work has been finished.

That’s the idea of our project, we then started searching for files that support our idea. First we searched for a CDS which can digest phosphate. Then after weeks of searching we found Polyphosphate Kinase, also known as PPK. It is a kind of enzyme widely distributed in ecosystem, more importantly, it can be found in E-coli. Here this picture below can show you how it works.

We found its genetic sequence and we used PCR to made it a standard biobrick. Then we started to find the promoters of our product. Finally we found the Pi Starvation Promoter(BBa_K737023), it’s not on the kits so we again designed its primer and used PCR.

For the protein we used TetR protein(BBa_C0040)

Now it’s time for our final genetic circuit. Take a look!

Result

After we finished our project, we started to test it. We test two part of our project. The first one is our Device One. We tested its response to Pi starvation. Here is the results diagram.

In this diagram we can find that Device one can be induced by phosphate starvation. When the concentration of dipotassium phosphate is 0.03μM we can see that our sensor reached a peak because our promoter can be activated by Pi starvation.

Next is our whole Device. We tested when the green fluorescence would vanish and red fluorescence occur. Here is another diagram.

This diagram shows that after several hours the amount of green fluorescence decreases, which means the work has been done and red fluorescence will occur.

This result clearly pointed out that our product can work smoothly. The Pi starvation promoter is working well too. Our experiments have reached a success at last.

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