Difference between revisions of "Team:SJTU-BioX-Shanghai/Attributions"

 
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                                 <li class="nav-item active"><a href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Attributions" class="nav-link">Attributions</a></li>
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                                     <a class="nav-link" href="#section1">Summary</a>
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                                     <a class="nav-link" href="#section1">Team Member</a>
 
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                                     <a class="nav-link" href="#section2">Characterize</a>
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                                     <a class="nav-link" href="#section2">Instructor Support </a>
 
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                                     <a class="nav-link" href="#section3">Application Choice</a>
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                                     <a class="nav-link" href="#section3">General support</a>
 
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                                     <a class="nav-link" href="#section4">Problem</a>
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                                     <a class="nav-link" href="#section4">Device Support</a>
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                                    <a class="nav-link" href="#section5">Modify the STAR</a>
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                         <div class="my-title h5-my-responsive" id="section1">Summary</div>
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                         <div class="my-title h5-my-responsive" id="section1">Team Member</div>
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                         <p>This year, we are trying to create a visualized monitor which can detect two or even more factors.</p>
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                         <p class="my-title2">Haowan Chang</p>
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                         <p>To achieve our goal of visualization, we use chromoproteins as our reporter. Chromoproteins, containing different pigmented nonprotein groups, are known that their colors can be easily identified by naked eyes, so that we don’t
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                        <ol type="1" start="1">
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                             need to take certain equipment with us. However, when we were doing experiment to express chromoproteins, we found leaky expression, which means exhibiting colors without inducing. We decided to use small transcription activating
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                            <li>Lab work</li>
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                             RNAs (STAR) to solve the problem. We add specific terminators (STAR target or Target) before RBS to stop transcription, while a small RNA (STAR antisense or Antisense) can control the target to restart transcription.</p>
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                            <li>Help design wiki</li>
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                            <li>Contact to make the team uniforms</li>
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                        </ol>
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                        <p class="my-title2">Zhuoyang Chen</p>
 +
                        <ol type="1" start="1">
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                            <li>PCR</li>
 +
                            <li>Circuits and parts designer</li>
 +
                            <li>STAR 3 system designer</li>
 +
                        </ol>
 +
                         <p class="my-title2">Xueqi Li</p>
 +
                        <ol type="1" start="1">
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                            <li>Wet lab experiment like chromoprotein charcterization,plasmid construction and PCR</li>
 +
                            <li>Help with HP</li>
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                            <li>Some Wiki work</li>
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                        </ol>
 +
                        <p class="my-title2">Haoyu Liu</p>
 +
                        <ol type="1" start="1">
 +
                            <li>Lab worker, doing plasmid construction and identification(like enzyme digestion and ligation, transformation, plasmid extraction, electrophoresis, sequencing)</li>
 +
                            <li>Parts construction</li>
 +
                            <li>Some characterization test design and execution</li>
 +
                            <li>Writing results of wet lab part on wiki</li>
 +
                        </ol>
 +
                        <p class="my-title2">Ruoci Shen</p>
 +
                        <ol type="1" start="1">
 +
                            <li>Human Practice</li>
 +
                            <li>Exploration of the loader</li>
 +
                            <li>Official team contact</li>
 +
                        </ol>
 +
                        <p class="my-title2">Chang Gao</p>
 +
                        <ol type="1" start="1">
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                            <li>Ligase plasmids and identify them(restricted digestion, transformation, plasmid extraction, electrophoresis, sequencing)</li>
 +
                            <li>Characterize chromoproteins and some parts in our project.</li>
 +
                            <li>Write lab notebook and some parts of results on wiki.</li>
 +
                        </ol>
 +
                        <p class="my-title2"></p>
 +
                        <p class="my-title2">Yi Yang</p>
 +
                        <ol type="1" start="1">
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                            <li>A lab worker who works in wet lab and does major construction work</li>
 +
                            <li>An art designer who designs our project logo,our team logo,or wiki art style and our team uniform</li>
 +
                            <li>A schemer who makes plan of our cultural production</li>
 +
                        </ol>
 +
                        <p class="my-title2">Bozitao Zhong</p>
 +
                        <ol type="1" start="1">
 +
                            <li>Team leader. Manage and organize our team.</li>
 +
                            <li>Lab worker. Lay emphasis on expression experiments, also attend transformation, purification and characterization experiments.</li>
 +
                             <li>Helping with other groups. Give advice on the 2048 game design, helping working out the way to use the APP and filter.</li>
 +
                        </ol>
 +
                        <p class="my-title2">Zhengsong Pan</p>
 +
                        <ol type="1" start="1">
 +
                            <li>Integrated Human Practice</li>
 +
                            <li>Safety</li>
 +
                            <li>Education and Public Engagement</li>
 +
                        </ol>
 +
                        <p class="my-title2">Chaowei Wu</p>
 +
                        <ol type="1" start="1">
 +
                            <li>All the modelling work </li>
 +
                            <li>Design&amp;3D print the Box </li>
 +
                            <li>Integrate with Professor Chen</li>
 +
                        </ol>
 +
                        <p class="my-title2">Zhijun Wang</p>
 +
                        <ol type="1" start="1">
 +
                            <li>Website designer, HTML &amp; CSS &amp; Javascript coder </li> 
 +
                            <li>Bring the idea of using S.T.A.R. to our project</li>
 +
                             <li>Poster and PPT maker (work together with team members)</li>
 +
                            <li>Participate in the design of App, Wet Lab and Device.</li>
 +
                        </ol>
 +
                        <p class="my-title2">Haijun Zhang</p>
 +
                        <ol type="1" start="1">
 +
                            <li> I'm mostly responsible for APP development.</li>
 +
                            <li>I participated in many activities and outside communication of our team and played a positive role.</li>
 +
                            <li>In other parts of the hardware design, I have participated in a lot.</li>
 +
                        </ol>
 +
                        <p class="my-title2">Hang Tao</p>
 +
                        <ol type="1" start="1">
 +
                            <li>Assist with HP work</li>
 +
                            <li>Take part in project discussion</li>
 +
                            <li>Help with wet lab experiment</li>
 +
                        </ol>
  
−
                         <div class="figure-intro">
+
                         <p class="my-title2">Yuchen Wang</p>
−
                            <img src="https://static.igem.org/mediawiki/2017/7/70/T--SJTU-BioX-Shanghai--pttb.png" class="img-fluid">
+
                        <ol type="1" start="1">
−
                            <div class="figure-text"><strong>Figure1 | Mechanism of STAR system. </strong>In the absence of antisense, sense target RNA will form a stem-loop structure, functioning as a terminator and stop the following transcription. When antisense RNA, a mRNA
+
                            <li>Give assistance to HP</li>
−
                                fragment which is the antisense of part of the target RNA, is transcribed, the terminator structure will be disrupted and switch on the inhibited transcription. </div>
+
                            <li>Help with paperwork</li>
−
                         </div>
+
                           
−
                         <div class="my-title h5-my-responsive" id="section2">Characterize</div>
+
                        </ol>
−
                         <p>To characterize our STAR system, we use sfGFP (superfolder green fluorescent protein) as the reporter gene. Here are the plasmids we constructed. Plasmids pETDuet1 and pCDF-Duet1 are used for both of them have two multiple cloning
+
                        <div class="my-title h5-my-responsive" id="section2">Instructor Support</div>
−
                            sites (MCS), which can perfectly suit insertion of target and antisense fragments.</p>
+
                        <p class="my-title2">Lin He</p>
 +
                        <p>The supervisor of our team and the direct of Bio-X, who gives us funding and university-related support. He initiated the first team and support us since then.</p>
 +
                        <p class="my-title2">Gang Ma</p>
 +
                        <p>The supervisor of our team and the professor of Bio-X, who gives us advice and instruction. We fought together dealing with all of the hard problems.</p>
 +
                         <p class="my-title2">Yushu Wang</p>
 +
                        <p> She spent a lot of time and energy on us, helping all kinds of problems, and she especially do us a favor in providing support for part submission.</p>
 +
                         <div class="my-title h5-my-responsive" id="section3">General support</div>
 +
                         <p class="my-title2">Research institute of Bio-X</p>
 +
                        <p>During the whole preparation procedure of the iGEM competition, Bio-X offered us a great support in all aspects. Thanks to their providing of experimental funds and drugs.
  
−
                        <div class="figure-intro">
 
−
                            <img src="https://static.igem.org/mediawiki/2017/7/70/T--SJTU-BioX-Shanghai--pttb.png" class="img-fluid">
 
−
                            <div class="figure-text"><strong>Figure 2 | Map of plamid pETDuet-1. </strong></div>
 
−
                        </div>
 
−
 
−
                        <p>And by mixing two types of chromoproteins, we can create a third color with a series of different chromaticity, which can be taken as the characterization of the relative abundance of two signal molecules.
 
 
                         </p>
 
                         </p>
−
                         <div class="my-title h5-my-responsive" id="section3">Application Choice</div>
+
                         <p class="my-title2">Shanghai Jiao Tong University</p>
−
                         <p>
+
                        <p> Our university gives us logistics support for the whole project. Thanks for the substantial support given by our university.</p>
−
                            We believe our monitor can be applied in various situations. To demontrate its feasibility, we choose heavy metal ion detection as an application. We plan to use cjBlue and eforRed to indicate Co and Hg. Not only can we determine whether Co or Hg exists,
+
                        <p class="my-title2">School of Life Sciences and Biotechnology, SJTU</p>
−
                            but also can get their rough concentrations by analyzing mixed color. What makes it special is that we can get information about two factors at the same time only by working on one indication.
+
                         <p>During the whole experimentation, School of Life Science and Biotechnology provided us with experimental funds, laboratory and experimental apparatus.</p>
−
                        </p>
+
                         <div class="my-title h5-my-responsive" id="section4">Device Support</div>
−
                         <div class="my-title h5-my-responsive" id="section4">Problem</div>
+
                         <p class="my-title2">Xiang Chen </p>
−
                         <p>During our experiments, we found that the Star2 system didn’t function well as we expected, with leakage at a non-neglectable level. So we decided to go further to improve the STAR system according to a few strategies. </p>
+
                         <p> He provided us the lab to do the experiment of loaders. Thanks for the advice on choosing loader, writing app and designing the box.</p>
−
                         <p>However, while basic expression in OFF state decreases, the activated expression in ON state also decreases too and we were quite worried that chromoprotein was expressed too little for us to see in naked eyes. Given above, we
+
                         <p class="my-title2">Shikun Zhao</p>
−
                            intended to add a hairpin to the 5’ end and a scaffold to the 3’ end of Antisense to stable it so that more Antisense will bind to target and lead to a higher level of activated expression.</p>
+
                         <p>A graduated PhD in Micro Nano Research Institute of SJTU who used to be the team leader of SJTU-BioX-Shanghai in 2009. He gave us much suggestion to improve our device design and instructed us in various aspects.</p>
−
                         <div class="my-title h5-my-responsive" id="section5">Modify the STAR</div>
+
                         <p class="my-title2">Yang Yu</p>
−
                         <p>Finally, we wanted to modify the STAR2 system at primary structure and secondary structure according to STAR1 system which had been proved functioned extremely well.</p>
+
                        <p>A PhD in Micro Nano Research Institute of SJTU. He offered much help in chip experiment and gave advice in our device design.</p>
−
                         <p>We noticed that although target of STAR1 (denotes Target1) is shorter than that of STAR2 (denote Target2), it still worked better. So before we stepped further, we used RNAstructure to predict the structure of both Target1 and
+
                       
−
                            Target2. The result is shown below.</p>
+
                         <p class="my-title2">Mengjia Cao</p>
−
                         <p>Given the fact that Target2 couldn’t stop transcription effectively as Target1, we assumed that the two stem-loops together contributed to the high activation fold. So we retained the first stem-loop of Target2 and use the sequence
+
                        <p>A master in Micro Nano Research Institute of SJTU. She helped us a lot in doing chip experiment.</p>
−
                            upstream to make a second stem-loop, with downstream of poly T discarded. A little modification was done on order to make sure the length of the stem and length of the loop consistent with Target1. The new STAR system we design
+
                       
−
                            from STAR2 was denoted as STAR3 system. Noticed that STAR3 system in fact was design from part of STAR2 system, although we named it a new STAR system, it wasn’t the case when talking of its orthogonality with STAR2 system
+
                       
−
                            but it also had great orthogonality with STAR1 system as STAR2 system does. The prediction of Target3 using the same parameters is shown below.</p>
+
−
 
+
 
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                             <span class="direction">Wet Lab</span>
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                             <span class="direction">Back To</span>
 
                             <div>
 
                             <div>
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                                 Protocol
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                                 Home Page
 
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Latest revision as of 16:33, 15 December 2017

Attributions
Team Member

Haowan Chang

  1. Lab work
  2. Help design wiki
  3. Contact to make the team uniforms

Zhuoyang Chen

  1. PCR
  2. Circuits and parts designer
  3. STAR 3 system designer

Xueqi Li

  1. Wet lab experiment like chromoprotein charcterization,plasmid construction and PCR
  2. Help with HP
  3. Some Wiki work

Haoyu Liu

  1. Lab worker, doing plasmid construction and identification(like enzyme digestion and ligation, transformation, plasmid extraction, electrophoresis, sequencing)
  2. Parts construction
  3. Some characterization test design and execution
  4. Writing results of wet lab part on wiki

Ruoci Shen

  1. Human Practice
  2. Exploration of the loader
  3. Official team contact

Chang Gao

  1. Ligase plasmids and identify them(restricted digestion, transformation, plasmid extraction, electrophoresis, sequencing)
  2. Characterize chromoproteins and some parts in our project.
  3. Write lab notebook and some parts of results on wiki.

Yi Yang

  1. A lab worker who works in wet lab and does major construction work
  2. An art designer who designs our project logo,our team logo,or wiki art style and our team uniform
  3. A schemer who makes plan of our cultural production

Bozitao Zhong

  1. Team leader. Manage and organize our team.
  2. Lab worker. Lay emphasis on expression experiments, also attend transformation, purification and characterization experiments.
  3. Helping with other groups. Give advice on the 2048 game design, helping working out the way to use the APP and filter.

Zhengsong Pan

  1. Integrated Human Practice
  2. Safety
  3. Education and Public Engagement

Chaowei Wu

  1. All the modelling work
  2. Design&3D print the Box
  3. Integrate with Professor Chen

Zhijun Wang

  1. Website designer, HTML & CSS & Javascript coder
  2. Bring the idea of using S.T.A.R. to our project
  3. Poster and PPT maker (work together with team members)
  4. Participate in the design of App, Wet Lab and Device.

Haijun Zhang

  1. I'm mostly responsible for APP development.
  2. I participated in many activities and outside communication of our team and played a positive role.
  3. In other parts of the hardware design, I have participated in a lot.

Hang Tao

  1. Assist with HP work
  2. Take part in project discussion
  3. Help with wet lab experiment

Yuchen Wang

  1. Give assistance to HP
  2. Help with paperwork
Instructor Support

Lin He

The supervisor of our team and the direct of Bio-X, who gives us funding and university-related support. He initiated the first team and support us since then.

Gang Ma

The supervisor of our team and the professor of Bio-X, who gives us advice and instruction. We fought together dealing with all of the hard problems.

Yushu Wang

She spent a lot of time and energy on us, helping all kinds of problems, and she especially do us a favor in providing support for part submission.

General support

Research institute of Bio-X

During the whole preparation procedure of the iGEM competition, Bio-X offered us a great support in all aspects. Thanks to their providing of experimental funds and drugs.

Shanghai Jiao Tong University

Our university gives us logistics support for the whole project. Thanks for the substantial support given by our university.

School of Life Sciences and Biotechnology, SJTU

During the whole experimentation, School of Life Science and Biotechnology provided us with experimental funds, laboratory and experimental apparatus.

Device Support

Xiang Chen

He provided us the lab to do the experiment of loaders. Thanks for the advice on choosing loader, writing app and designing the box.

Shikun Zhao

A graduated PhD in Micro Nano Research Institute of SJTU who used to be the team leader of SJTU-BioX-Shanghai in 2009. He gave us much suggestion to improve our device design and instructed us in various aspects.

Yang Yu

A PhD in Micro Nano Research Institute of SJTU. He offered much help in chip experiment and gave advice in our device design.

Mengjia Cao

A master in Micro Nano Research Institute of SJTU. She helped us a lot in doing chip experiment.

Team
Members
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