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| − | <h2>Biosafety</h2> | + | <h1>Description</h1> |
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| | + | <h2><strong>ShanghaiTech 2018</strong></h2> |
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| + | <h3><strong>Project introduction</strong></h3> |
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| − | <a href="#background" data-toggle="collapse">
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| − | <h3>Background</h3>
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| − | <p><strong>Retrospect</strong></p>
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| − | <p>In 2017, during the 4th Conference of China iGEMer Community, professor OYE who concerns the biosafety issues as one of the Headquarters of iGEM mentioned that the guidelines of biology laboratory in China hasn’t been as complete as the international and US version. Finding out this is true, we led a big team consist of 11 Chinese iGEM teams to make some teleplay like episodes covering important topics about safety guidelines of biology laboratory with a handbook including the core information of these topics. As a result, we were nominated for safety commendation in 2017 iGEM jamboree. Professor OYE praised us during the post section for our achievement in less than 3 months.</p>
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| − | <p><strong>Further attempt</strong></p>
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| − | <p>These awards and praise encouraged us to go further. We took the advice from professor OYE about getting the governments support. However, after a series of investigation and contacting the education, science research, environment and medical department from district level to national ones, we found that only the bio-labs over P3 level have regular exam and training by government’s team. All the other institutions have to solve biosafety problems themselves. </p>
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| − | <p>Considering this as a huge market, we decided to begin a 2.0 bio-lab safety project for some reasons. Firstly, though we will always acknowledge those teams without whom we could not complete the first years’ work, most of them are dissolved so we can’t get the copy rights of their works. In this situation, we have to make a new one and form a clear and integrated teaching outline at the same time.</p>
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| − | <p>Secondly, instead of conventional teaching, those chapters, which are full of entertainment materials, are aiming to arouse student’s interest of biosafety. Accordingly, we will write a deliverable handbook, and film videos to teach standard operation instruction to cover whole spectrum of biological experiments. </p>
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| − | <p>Finally, even the international and US version of guidelines are consist of pictures and words requiring examination to verify the students’ ability. We will make a VR video game to find a way to simulate the interest of learning biosafety.We will use this method, instead of traditional written exam, to increase student’s lab skills. </p>
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| − | <p><a href="https://2017.igem.org/Team:Shanghaitech/BioSafety">https://2017.igem.org/Team:Shanghaitech/BioSafety</a></p>
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| − | <a href="#design" data-toggle="collapse">
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| − | <h3>Design</h3>
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| − | <div class="card-body collapse" id="design">
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| − | <p><strong>Handbook</strong></p>
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| − | <p>After going through lots of biosafety handbooks, we found there are onlyfew biosafety handbooks with detail operations in Chinese. So we try our best to fill this gap. We had designed our biosafety handbooks since last year, and already got many insightful feedbacks. We began this year’s biosafety handbook based on last year’s work, especially focusing on the feedbacks.</p>
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| − | <p>Traditional biosafety handbooks are usually too boring to read for learners. To overcome it, we designed some cute cartoon painting related to the content. We divide the handbook into two parts, the first part talks about fundamental laboratory safety，while the second part focuses on biological laboratory safety. We organized the main content of the book with the reference from piles of safety materials all over the world.</p>
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| − | <p>We also wrote a matched workbook for biosafety handbook users to help them to master all the key points. Although there are several problem sets for biosafety on the market, most of them are existed alone,with no assorted instruction book. To meet this need, we screened out all important points from each chapter, and design matched practice and/or exam accordingly. We are very confident that this newly designed set of handbook will become a popular and important guide book for all new beginners studing biology.</p>
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| − | <p><img class="img-fluid mx-auto d-block" alt="Biosafety_1" src="https://static.igem.org/mediawiki/2018/9/9b/T--ShanghaiTech--biosafety_1.jpg"/></p>
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| − | <p><strong>Video and cartoon</strong></p>
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| − | <p>To make the learning process more interesting and enjoyable, we use courseware to present the biosafety work. Two forms of courseware are designed, videos and cartoon.</p>
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| − | <p>We shot biosafety videos last year together with some iGEM teams in China and it was a huge success.. Considering those episodes are more like entertainment materials to arouse people’s awareness of biosafety rather than actually teach them the standard way, we want to make more professional and systematic episodes this year. Considering effective learning time, every episode lasts for 2-3 minutes.</p>
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| − | <p>Beside this, we use Storyline to produce cartoon for biosafety. Our courseware displays content from the handbook concisely, leaving learners a deep impression. Meanwhile, this is also a courseware with effective interactivity，when every single operation is finished, learners could only continue their studying by correcting the mistakes made in the previous experiment.</p>
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| − | <p><strong>VR game platform</strong></p>
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| − | <p>The core mechanism of this game is that if one cannot identify a wrong action in a key step of virtual experiment, there is high possibility that he/she will make similar mistake in the future. Players should find the wrong action immediately when ‘operating’ experiments and ‘walking’ along the bench.</p>
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| − | <p>Video teaching has long history been used in the sports field. Professional players can’t train all the time. However, watching huge amounts of videos can take place of the training purpose to some degree by increasing their experience and sub consciousness of right action. Similar to the sports, potential bio-lab users have few laboratory resources. That’s why we want to film the videos with first personal view for players to interaction. Watching themselves ‘doing’ the experiment closely is much clearer about every detailed finger movement than watching cartoons.</p>
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| − | <p>Simulation of the bio-lab environment is another problem. 3D model requires a lot of time while still cannot reflect the real complexity of countless interaction possibility in the lab. We found a solution to give each viewpoint and moving route a panoramic scene, by developing a special technique introduced in the method section, to simulate the reality as much as we can as well as the possibility of missing the answer interaction.</p>
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| − | <p>The game is also called a platform due to the DIY function. With our developing interaction helper, teachers can film their tasks and add interaction point easily to expand ultimate tasks through this game. The game can be ran on android or PC for widely use and opening source.</p>
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| − | <h3>Highlight</h3>
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| − | <div class="card-body collapse" id="highlight">
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| − | <p><strong>Handbook</strong></p>
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| − | <p><img class="img-fluid rounded mx-auto d-block" alt="biosafety_1" src="https://static.igem.org/mediawiki/2018/1/12/T--ShanghaiTech--biosafety_1.5.png"/></p>
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| − | <p class="text-center"><small>Figure 1. Cover of Laboratory biosafety handbook</small></p>
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| − | <p><img class="img-fluid mx-auto d-block" alt="biosafty_2" src="https://static.igem.org/mediawiki/2018/a/a2/T--ShanghaiTech--biosafety_2.png"/></p>
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| − | <p class="text-center"><small>Figure 2. Table of content: Part Ⅰ. The basic laboratory safety; Part Ⅱ. Biological laboratory safety</small></p>
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| − | <p><img class="img-fluid mx-auto d-block" alt="biosafety_3" src="https://static.igem.org/mediawiki/2018/2/28/T--ShanghaiTech--biosafety_3.png"/></p>
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| − | <p class="text-center"><small>Figure 3. Example: Risk assessment: Ⅰ. Microorganism; Ⅱ. Instrument</small></p>
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| − | <p><strong>Video</strong></p>
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| − | <p>Example: Biological laboratory equipment</p>
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| − | <p>How to use cabinet and refrigerator</p>
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| − | <div class="embed-responsive embed-responsive-16by9">
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| − | <p><video controls src="https://static.igem.org/mediawiki/2018/8/8d/T--ShanghaiTech--lab_equipment.mp4"></video></p>
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| − | </div>
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| − | <br>
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| − | <p><strong>VR game platform</strong></p>
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| − | <div class="embed-responsive embed-responsive-16by9">
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| − | <p><video controls src="https://static.igem.org/mediawiki/2018/f/f6/T--ShanghaiTech--biosafety_1.mp4"></video></p>
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| − | </div>
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| − | <p>Through the example of finding the mistake that player isn’t wearing gloves, the tutorial part enables the players to get used to the operation of control and method to finish tasks.</p>
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| − | <p>Task1:</p>
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| − | <p><img class="img-fluid mx-auto d-block" alt="biosafety_4" src="https://static.igem.org/mediawiki/2018/c/cc/T--ShanghaiTech--biosafety_4.png"/></p>
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| − | <p>The players should find ‘themselves’ touching the orifice of the EP tube when picking up it.</p>
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| − | <p>Task 2:</p>
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| − | <p><img class="img-fluid mx-auto d-block" alt="biosafety_5" src="https://static.igem.org/mediawiki/2018/e/ed/T--ShanghaiTech--biosafety_5.png"/></p>
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| − | <p>The players should find ‘themselves’ touching the orifice of the EP tube when picking up it.</p>
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| − | <div class="card">
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| − | <a href="#method" data-toggle="collapse">
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| − | <h3>Method</h3>
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| − | </a>
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| − | <div class="card-body collapse" id="method">
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| − | <p><strong>Handbook</strong></p>
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| − | <ol><li>Read piles of biosafety handbooks worldwide</li><li>Decide the table of content</li><li>Organize materials for each part</li><li>Design cartoon pictures all by ourselves with Photo shop</li><li>Select error-prone points to make quiz</li><li>Ask experts in this area for advice and correct the error</li></ol>
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| − | <p><strong>Video</strong></p>
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| − | <ol><li>Choose the error-prone chapter from our biosafety handbook </li><li>Write script for the selected chapter </li><li>Shoot video with our camera in a suitable laboratory</li><li>Edit the original video clip together</li><li>Ask experts in this area for advice and correct the error</li></ol>
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| − | <p><strong>Cartoon</strong> </p>
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| − | <p>How to make Script and narrator</p>
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| − | <ol><li>Summarize the main content of the chapter and write the script</li><li>Make the audio for the script with voice dubber or use the artificial voice synthetized by Xfyun.</li><li>Edit the audio file with Adobe Audition.</li><li>Use storyline to make slices </li><li>Insert audio files into the slices and make the subtitle for it</li></ol>
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| − | <p>How to make Graphics and animation</p>
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| − | <ol><li>Insert pictures according to the content of each slice</li><li>Add interaction buttons and triggers</li><li>Adjust the time line</li><li>Preview the chapter and make final modification.</li></ol>
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| − | <p><strong>Panorama & First personal view</strong></p>
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| − | <p>How to build a virtual reality environment for this game:</p>
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| − | <ol><li>Get a panoramic camera.</li><li>Join it stably to a robot vehicle. The less vibration the better.</li><li>Take a video with peaceful and slow movement along the bench.</li><li>Program the ‘walking’ forward or backward action as playing the video forward or backward.</li></ol>
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| − | <div class="embed-responsive embed-responsive-16by9">
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| − | <p><video controls src="https://static.igem.org/mediawiki/2018/1/15/T--ShanghaiTech--biosafety_2.mp4"></video></p>
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| − | </div>
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| − | <div class="embed-responsive embed-responsive-16by9">
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| − | <p><video controls src="https://static.igem.org/mediawiki/2018/f/f7/T--ShanghaiTech--biosafety_3.mp4" type="video/mp4"></video></p>
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| − | </div>
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| − | <br>
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| − | <p>How to make a task for this game:</p>
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| − | <ol><li>Film a first personal view or panoramic video.</li><li>Import the video by the Interaction Helper.</li><li>Click to add the interaction area around the chosen point.</li><li>Press A and D to change the frame and S to save.</li><li>Code for interaction rules will be saved. Pressing PAUSE button during the video playing will skip to the next edited frame for interaction.</li></ol>
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| − | <div class="embed-responsive embed-responsive-16by9">
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| − | <p><video controls src="https://static.igem.org/mediawiki/2018/5/55/T--ShanghaiTech--biosafety_4.mp4"></video></p>
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| − | </div>
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| − | <div class="card">
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| − | <a href="#achievement" data-toggle="collapse">
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| − | <h3>Achievement</h3>
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| − | </a>
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| − | <div class="card-body collapse" id="achievement">
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| − | <p><strong>Effect verification</strong></p>
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| − | <p>To find out the effect of the game, we designed and implemented a behavioral experiment. First of all, we figured out whether students know that they shouldn’t touch the orifice of the EP tube when picking it up. To conceal our goal, we delivered a questionnaire investigation as an exam with several biology experiment behavior questions including the most important one: which part you should hold when picking up an EP tube? The result came out that 100% of the student know they should grab the outside instead of the orifice. However, they actually did that in a wrong way. </p>
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| − | <p>In our university, biology experiment courses are divided into groups with two students in each group. To keep subject’s behavior as usual, we ask one student of each group to observe whether or nothis/her partner pick up the EP tubes in the right way.</p>
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| − | <p>The result is that 26% of the student caught EP tube in a wrong way. This means students actually pick up EP tubes in random way. Furthermore, this proved that examination in a traditional way does not reflect the reality of students’ behavior. </p>
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| − | <p>Then we asked the students to finish the task1 in the game till they can find the mistake correctly. At the first time, they missed the mistake. But they can find that mistake on time after learning from the failure feedback and testing through the interaction of task1. The same convert observation discovered an obvious decrease of 16% of wrong gesture picking up the EP tube.</p>
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| − | <p><img class="img-fluid mx-auto d-block" alt="biosafety_game" src="https://static.igem.org/mediawiki/2018/3/31/T--ShanghaiTech--biosafety_game.png"/></p>
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| − | <p> <strong>Application</strong></p>
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| − | <p>Our biosafety work is used as training process for the classmates preparing to enter the lab. After communicating with our school’s lab teacher, we used our biosafety videos and handbook in the first experimental class for sophomore to give them some basic biosafety knowledge. What we have done is very popular among these students and our schools’ lab teacher. Some students took the initiative to keep these handbooks and asked for the resource of our videos. They thought our biosafety work was very interesting and were willing to learn it by themselves in their spare time. The student’s response met our goal, making the biosafety learning process more interesting. </p>
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| − | <p><img class="img-fluid mx-auto d-block" alt="Biosafety_3" src="https://static.igem.org/mediawiki/2018/5/5d/T--ShanghaiTech--biosafety_5.jpg"/></p>
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| − | <p><strong>Future plan</strong></p>
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| − | <p>Although our biosafety work received praise from school teachers and classmates, there is still room to improve. We will show our biosafety work to more people and collect their feedback to do some adjustment, which will make the biosafety work better and better. </p>
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| − | <p>The goal that is making the biosafety learning process more interesting has already achieved. The distance to our initial dream filling up the biosafety gap in Chinese market is shorter. We would hope to commercialize our work in biosafety and popularize it into more universities, enterprises as a training course for experimental safety.</p>
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| − | <a href="#download_resource" data-toggle="collapse">
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| − | <h3>Download resource</h3>
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| − | </a>
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| − | <div class="card-body collapse" id="download_resource">
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| − | <p><strong>Handbook</strong></p>
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| − | <p><a href="https://static.igem.org/mediawiki/2018/9/93/T--ShanghaiTech--handbook.pdf">Handbook.pdf</a></p>
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| − | <p><strong>Videos</strong></p>
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| − | <p>[请制作网页的同学创建一个链接，放共计6集video，去声音]</p>
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| − | <p><strong>Cartoon</strong></p>
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| − | <p><strong>VR game</strong></p> | + | <p>The construction of increasingly complex genetic networks in engineered bacteria has been particularly susceptible to circuit failure, due to undesirable expressions of proteins involved. Many influencing factors have been identified, including the recombinant plasmid copy number and the competition of translational resources between foreign genes and the bacterial genome. In order to minimize the unpredictable disturbances and stabilize the expression of genetic circuits, a system employing feedforward control and orthogonal ribosomes is devised.</p> |
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| − | <p> Link of: game.apk, game.exe, demonstration video.mp4, interaction helper.exe, game construction file.rar.</p> | + | <h3><strong>The feedforward control circuit</strong></h3> |
| | + | <p>Inspired by the control theory that developed into the system biology, we decide to integrate the typical control model with three nodes into our circuit. This three-module feedforward loop would act as the core foundation of our system, in which, orthogonal 16s rRNA will be a constant output through repressive and stimulative interactions. The first module is the LuxR, which is a commonly-utilized part in synthetic biology from the quorum sensing in origin. It stimulates the second module, the STAR RNA and meanwhile the output, orthogonal ribosome. The STAR RNA would continue to trigger the third module, the negative RNA transcriptional regulator pT181, which then suppresses the LuxR expression and complete the negative feedback loop.</p> |
| | + | <p>The three modules are orthogonal to each other and the host itself, which is important in artificial design of gene circuits.</p> |
| | + | <h3><strong>The orthogonal ribosome</strong></h3> |
| | + | <p>When expressed in genetically engineered bacteria, foreign proteins compete with the native proteins of the host for ribosomes, affecting the stability of the expression system (Known as Resource Competition). Therefore, an additional set of ribosome systems that are orthogonal to the natural ribosomes from the host is particularly critical. </p> |
| | + | <p>The basic principles of the artificial ribosome design are mutations in the SD region of the 16s rRNA so that it can only read and translate the specific mRNA. Several exciting outcomes have been achieved by the scientists working on this theme. We have tried to apply two editions of the orthogonal ribosome design so far. One design originates from Jason Chin's lab (<a href="https://www2.mrc-lmb.cam.ac.uk/ccsb/">https://www2.mrc-lmb.cam.ac.uk/ccsb/</a>), the other one comes from the iGEM team of Tianjin University in 2012(<a href="https://2012.igem.org/Team:Tianjin">https://2012.igem.org/Team:Tianjin</a>).</p> |
| | + | <h3>Project Summary</h3> |
| | + | <p>By separating the ribosome pool from host reserves, expression of proteins under correspondent orthogonal ribosome binding sites would ideally minimize the inevitable translational resource competition. The specific output(desired protein expression level) could further be controlled by the feedforward loop upon the binding of external AHL molecules, the input limit for LuxR protein. The complex formed accordingly activates the downstream gene expression in a predictable manner, which may hopefully boost the success rate of intricate circuit designs and propel the overall development of synthetic biology.</p> |
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