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| − | <p> In the past summer, fifteen members of the iGEM UESTC-Software team worked together to achieve our goal, to develop a biological information storage system. During the process, every one made an effort to go beyond the set goal. Moreover, the team’s success is not only a result of the concerted contribution of all members and but also due to the generous help from many other people.</p> | + | <h2 id="Background">Background</h2> |
| − | <h2 id="Member Attributions">Member Attributions</h2> | + | <p>In our project, the editing protocol of a DNA-based file involves the synthesis of a new DNA fragment encoding the new information and the breakage of the old DNA fragment encod-ing the original information. While the former can be realized easily through the chemical synthesis technique, the latter is not simple until the recent development of CRISPR ge-nome editing method.</p> |
| − | <strong>Projects</strong> | + | <p>Restriction endonuclease can discern special DNA site and cut the particular DNA frag-ments with the endonuclease site, the constraint is that the DNA fragment which needs breakdown must contain the restriction endonuclease recognition site. But for the DNA information storage system, a DNA fragment may contain arbitrary nucleotide sequences.</p> |
| − | <br>
| + | <p>Cas9 (CRISPR associated protein 9) is a RNA-guided DNA endonuclease enzyme. S. py-ogenes utilizes Cas9 to discern and cleave foreign DNA in its immunity system (<italic>Cas9,<a href="https://en.wikipedia.org/wiki/Cas9" target="_blank" style="color: #DB0909;">https://en.wikipedia.org/wiki/Cas9</a></italic>). Cas9 binding site recruits Cas9 form sgRNA-Cas9 complex, the DNA recognition site interrogates dsDNA specifically and inducts sgRNA-Cas9 complex combine with dsDNA so that generate sgRNA-Cas9-dsDNA complex. The combined Cas9 cleaves dsDNA and causes devastating damage to the dsDNA and lead to further hydrolyzation(<italic>Alec AK Nielsen & Christopher A Voigt*. Multi-input CRISPR/Cas genet-ic circuits that interface host regulatory networks</italic>).</p> |
| − | <strong style="color:#3C9CD3;font-size:15px;text-indent:20px;">Bio101 design</strong>
| + | <p>Since Cas9 could cleave any DNA fragment in theory if there is a right sgRNA to guide the recognition process, it is the right tool for DNA information editing. </p> |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Back-end and Webpage Framework: Dongkai Pu, Jianwei Xu</p>
| + | <p class="img-p" style="font-size: 13px;"><img src=""/><br/><B>Fig.1.</B> Guid DNA transcribes sgRNA to guid Cas9.</p> |
| − | <p class="one-line" style="margin:0;text-indent:20px;">Front-end: Jianwei Xu, Jun Li, Meng Liu</p>
| + | <h2 id="Part Design">Part Design</h2> |
| − | <p class="one-line" style="margin:0;text-indent:20px;">Modeling: Dongkai Pu, Meng Liu, Chenxiang Zheng, Hao Xu, Wei Zhao</p>
| + | <p>To degrade a particular DNA fragment, we need to design a part to express the sgRNA tran-script to guide the Cas9 system to cleave the fragment. </p> |
| − | <p class="one-line" style="margin:0;text-indent:20px;">Test and Validation: Zhongtian Ma, Jianwei Xu</p> | + | <p>Inspired by Voigt’s study and the BioBrick parts (BBa_K1723002, BBa_K1723003 and BBa_K1723004) designed by the team of iGEM15_EPFL, we designed our sgRNA express-ing cassette based on the DNA sequence that needs to be modified. The part includes 275 bp and the sequence was biobricked with the pBAD promoter and the S. Pyogenes termina-tor. The sgRNA sequences start right after the promoter and followed by the Cas9 handle sequence which serves the binding purpose with the Cas9 protein.</p> |
| − | <p class="one-line" style="margin:0;text-indent:20px;">Art Design: Xin Ma, Zining Wu</p> | + | <p>In the encoding algorithm, the NGG PAM site is inserted in the middle of the DNA fragment. The sgRNA sequence is generated from the upstream sequence of the PAM site which in-clude the indexing information. Therefore, if the targeted DNA is recognized and cleaved by the Cas9 enzyme, the encoded information will get lost. </p> |
| − | <p class="one-line" style="margin:0;text-indent:20px;">Documentation: Meng Liu, Jun Li, Yuening Yan, Caixi Xi</p>
| + | <p>The Edit page of Bio101 will generate the part automatically based on the editing task. The part is provided as a SBOL format file for users to download.</p> |
| − | <strong style="color:#3C9CD3;font-size:15px;text-indent:20px;">Bio2048 design</strong>
| + | <h2 id="Experience">Experience </h2> |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">User Interface: Xin Ma</p> | + | <p>The design scheme and parts remain to be experimentally validated in the future.</p> |
| − | <p class="one-line" style="margin:0;text-indent:20px;">Programming: Xin Ma</p> | + | <h2 id="References">References</h2> |
| − | <p class="one-line" style="margin:0;text-indent:20px;">Icon Degisn：Haobo Zhou</p> | + | <ul> |
| − | <p class="one-line" style="margin:0;text-indent:20px;">Hierarchical Concept: Zhongtian Ma</p> | + | <li>[1] Alec AK Nielsen & Christopher A Voigt*. Multi-input CRISPR/Cas genetic circuits that inter-face host regulatory networks. Mol Syst Biol. 2014 Nov 24;10:763. doi: 10.15252/msb.20145735.</li> |
| − |
| + | <li>[2] Cas9 Targeting and the CRISPR Revolution. SCIENCE VOL 344 2014 MAY 16.</li> |
| − |
| + | </ul> |
| − | <strong>Human Practices and Collaborations</strong> | + | |
| − | <br> | + | |
| − | <strong style="color:#3C9CD3;font-size:15px;text-indent:20px;">Development of Data-Processing Tool for UESTC-China</strong>
| + | |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Programming and Documentation: Jianwei Xu, Dongkai Pu, Xin Ma</p> | + | |
| − | <strong style="color:#3C9CD3;text-indent:20px;">Support for TMMU_China</strong> | + | |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Programming and Documentation: Meng Liu</p> | + | |
| − | <strong style="color:#3C9CD3;text-indent:20px;">Collaboration with AHUT_ China</strong>
| + | |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Video Meeting: Jianwei Xu, Hao Xu</p> | + | |
| | | | |
| − | <strong style="color:#3C9CD3;font-size:15px;text-indent:20px;">iGEM Southwest China Union Meetup</strong>
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| − |
| |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Presentation: Chenxiang Zheng</p>
| |
| − | <p class="one-line" style="margin:0;text-indent:20px;">Poster: Zining Wu</p>
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| − | <p class="one-line" style="margin:0;text-indent:20px;">Brief Introduction: Hui Che</p>
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| − |
| |
| − | <strong style="color:#3C9CD3;font-size:15px;text-indent:20px;">Meet-up with TMMU_China and Nanjing-China</strong>
| |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Presentation: Hui Che, Haobo Zhou</p>
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| − | <p class="one-line" style="margin:0;text-indent:20px;">Poster: Zining Wu</p>
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| − | <p class="one-line" style="margin:0;text-indent:20px;">Brief Introduction: Jianwei Xu</p>
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| − |
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| − | <strong style="color:#3C9CD3;font-size:15px;text-indent:20px;">Science Lecture</strong>
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| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Material Preparation: Caixi Xi, Hao Xu</p>
| |
| − | <p class="one-line" style="margin:0;text-indent:20px;">Presentation: Yuening Yan, Hui Che</p>
| |
| − | <p class="one-line" style="margin:0;text-indent:20px;">PowerPoint Slides Design: Zining Wu</p>
| |
| − | <p class="one-line" style="margin:0;text-indent:20px;">Photo: Haobo Zhou</p>
| |
| − | <p class="one-line" style="margin:0;text-indent:20px;">Documentation: Yuening Yan, Hui Che</p>
| |
| − |
| |
| − | <strong style="color:#3C9CD3;font-size:15px;text-indent:20px;">Lab-Open Day Event</strong>
| |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Design, Planning and Implementation: Hao Xu, Caixi Xi</p>
| |
| − |
| |
| − | <strong style="color:#3C9CD3;font-size:15px;text-indent:20px;">Sina Microblog Public Account</strong>
| |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Management: Zhongtian Ma</p>
| |
| − |
| |
| − | <strong style="color:#3C9CD3;font-size:15px;text-indent:20px;">Community Propaganda</strong>
| |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Design and Plan: Caixi Xi, Haobo Zhou</p>
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| − |
| |
| − | <strong>Art and design</strong>
| |
| − | <br>
| |
| − | <strong style="color:#3C9CD3;font-size:15px;text-indent:20px;">Wiki</strong>
| |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Programming: Meng Liu, Jun Li</p>
| |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Design: Haobo Zhou</p>
| |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Copywriting: Hui Che, Yuening Yan, Meng Liu, Caixi Xi, Wei Zhao, Zhongtian Ma, Chenxiang Zheng</p>
| |
| − | <strong style="color:#3C9CD3;font-size:15px;text-indent:20px;">Team sign and uniform</strong>
| |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Inspiration: Haobo Zhou</p>
| |
| − | <p class="one-line" style="margin-bottom:0;text-indent:20px;">Design and Draw: Zining Wu, Xin Ma</p>
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| − |
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| − |
| |
| − | <h2 id="Special Thanks" >Special Thanks</h2>
| |
| − | <strong>Professor Xianlong Wang, Primary PI</strong>
| |
| − |
| |
| − | <p>Helping the team design and plan the project. His guidance to all 15 members is greatly appreciated. </p>
| |
| − |
| |
| − | <strong>Professor Fengbiao Guo, Secondary PI</strong>
| |
| − | <p>Giving the team precious advice on the presentation and wiki design. </p>
| |
| − |
| |
| − | <strong>Ling Quan and Qiong Zhang, Instructors</strong>
| |
| − |
| |
| − | <p>Their leadership and directions on how to build a successful team is worth mentioning. They taught us how to become more friendly and united. Also, they gave us advice on issues regarding travelling to Boston and the contents of our presentation.</p>
| |
| − |
| |
| − | <strong>Kaiyue Zhang, the team leader of 2015 UESTC-China, and Yaocong Duan, the team leader of 2015 UESTC-Software.</strong>
| |
| − | <p>For giving us advice on building our team and disciplines, providing support outside of training, which encouraged us to be focused and produce a perfect project.</p>
| |
| − |
| |
| − | <strong>Xu Wang, System Administrator at Xingchen Studio</strong>
| |
| − | <p>For building the server and helping us set up backstage when we had problem during visualization design.</p>
| |
| − |
| |
| − | <strong>Bohan Li, Ziyun Guan, Jingyi Wang, Huanghao Yang, Wei Liu, the Preliminary Team Members (sophomores of UESTC).</strong>
| |
| − | <p>For helping us with human practices including the implementation of the open-day visiting activity “To Be Scientists Tomorrow” and Community Advocacy. Their help is especially appreciated for taking photos, shooting videos and preparing materials. </p>
| |
| − |
| |
| − | <div style="line-height:30px">
| |
| − | <strong>Other teams taking part in the competition</strong>
| |
| − |
| |
| − | <strong><a href="https://2016.igem.org/Team:SCU-China" style="color:#3C9CD3;text-indent:28px;font-size:15px;" target="_blank"> ·SCU-China</a>,<a href="https://2016.igem.org/Team:Nanjing-China" style="color:#3C9CD3;text-indent:28px;font-size:15px;" target="_blank">Nanjing-China</a>,<a href="https://2016.igem.org/Team:TMMU_China" style="color:#3C9CD3;text-indent:28px;font-size:15px;" target="_blank"> TMMU_China</a>,<a href="https://2016.igem.org/Team:UESTC-China" style="color:#3C9CD3;text-indent:28px;font-size:15px;" target="_blank"> UESTC-China</a>,<a href="https://2016.igem.org/Team:AHUT_China" style="color:#3C9CD3;text-indent:28px;font-size:15px;" target="_blank">AHUT_China</a></strong>
| |
| − | <p>For discussing our projects with us and putting forward some views and suggestions to improve our task. </p>
| |
| − | <strong><a href="https://2016.igem.org/Team:UESTC-China" style="color:#3C9CD3;text-indent:28px;font-size:15px;" target="_blank"> ·UESTC-China</a></strong>
| |
| − | <p>For mentoring us to do wet-lab experiment and assisting us with two human practices, the lab-open day “To Be Scientists Tomorrow” and the science lecture in Puyang Middle School. </p>
| |
| − | <strong><a href="https://2016.igem.org/Team:AHUT_China" target="_blank" style="color:#3C9CD3;text-indent:28px;font-size:15px;" target="_blank"> ·AHUT_China</a></strong>
| |
| − | <p>For doing dry-lab testing and offering testing report for our project. </p>
| |
| − | </div>
| |
| − | <strong>Developers of the Following Open-Source Libraries and Packages</strong>
| |
| − | <p>Django, Owl-Carousel, Bootstrap, JQuery and ISAAC.</p>
| |
| − |
| |
| − | <strong>Dean’s Office of University of Electronic Science and Technology of China</strong>
| |
| − | <p>It’s a great deal for us that the Dean’s Office provided our funds during the competition. The Dean’s Office covered the flight fees, accommodation, also Team Registration Fees and the Jamboree Attendance Fee, which greatly reduced our financial burden and motivated us to focus on the competition.</p>
| |
| − |
| |
| − | <strong>Thanks again to all the people who helped us during the summer. With your support, we become a successful iGEM team. </strong>
| |
| − | <br>
| |
| − | <br>
| |
| − | <img src="https://static.igem.org/mediawiki/2016/7/7d/Uestc_software-mingxie1.PNG" style="width:50%;margin-left:200px;"></img>
| |
| | </div> | | </div> |
| | <footer class="footer"> | | <footer class="footer"> |
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| | <ul> | | <ul> |
| | <li> | | <li> |
| − | <a href="#Member Attributions"> | + | <a href="#Background"> |
| | <span></span> | | <span></span> |
| − | Member Attributions | + | Background |
| | </a> | | </a> |
| | </li> | | </li> |
| | <li> | | <li> |
| − | <a href="#Special Thanks"> | + | <a href="#Part Design"> |
| | + | <span></span> |
| | + | Part Design |
| | + | </a> |
| | + | </li> |
| | + | <li> |
| | + | <a href="#Experience"> |
| | + | <span></span> |
| | + | Experience |
| | + | </a> |
| | + | </li> |
| | + | <li> |
| | + | <a href="#References"> |
| | <span></span> | | <span></span> |
| − | Special Thanks | + | References |
| | </a> | | </a> |
| | </li> | | </li> |
Background
In our project, the editing protocol of a DNA-based file involves the synthesis of a new DNA fragment encoding the new information and the breakage of the old DNA fragment encod-ing the original information. While the former can be realized easily through the chemical synthesis technique, the latter is not simple until the recent development of CRISPR ge-nome editing method.
Restriction endonuclease can discern special DNA site and cut the particular DNA frag-ments with the endonuclease site, the constraint is that the DNA fragment which needs breakdown must contain the restriction endonuclease recognition site. But for the DNA information storage system, a DNA fragment may contain arbitrary nucleotide sequences.
Cas9 (CRISPR associated protein 9) is a RNA-guided DNA endonuclease enzyme. S. py-ogenes utilizes Cas9 to discern and cleave foreign DNA in its immunity system (Cas9,https://en.wikipedia.org/wiki/Cas9). Cas9 binding site recruits Cas9 form sgRNA-Cas9 complex, the DNA recognition site interrogates dsDNA specifically and inducts sgRNA-Cas9 complex combine with dsDNA so that generate sgRNA-Cas9-dsDNA complex. The combined Cas9 cleaves dsDNA and causes devastating damage to the dsDNA and lead to further hydrolyzation(Alec AK Nielsen & Christopher A Voigt*. Multi-input CRISPR/Cas genet-ic circuits that interface host regulatory networks).
Since Cas9 could cleave any DNA fragment in theory if there is a right sgRNA to guide the recognition process, it is the right tool for DNA information editing.
![]()
Fig.1. Guid DNA transcribes sgRNA to guid Cas9.
Part Design
To degrade a particular DNA fragment, we need to design a part to express the sgRNA tran-script to guide the Cas9 system to cleave the fragment.
Inspired by Voigt’s study and the BioBrick parts (BBa_K1723002, BBa_K1723003 and BBa_K1723004) designed by the team of iGEM15_EPFL, we designed our sgRNA express-ing cassette based on the DNA sequence that needs to be modified. The part includes 275 bp and the sequence was biobricked with the pBAD promoter and the S. Pyogenes termina-tor. The sgRNA sequences start right after the promoter and followed by the Cas9 handle sequence which serves the binding purpose with the Cas9 protein.
In the encoding algorithm, the NGG PAM site is inserted in the middle of the DNA fragment. The sgRNA sequence is generated from the upstream sequence of the PAM site which in-clude the indexing information. Therefore, if the targeted DNA is recognized and cleaved by the Cas9 enzyme, the encoded information will get lost.
The Edit page of Bio101 will generate the part automatically based on the editing task. The part is provided as a SBOL format file for users to download.
Experience
The design scheme and parts remain to be experimentally validated in the future.
References
- [1] Alec AK Nielsen & Christopher A Voigt*. Multi-input CRISPR/Cas genetic circuits that inter-face host regulatory networks. Mol Syst Biol. 2014 Nov 24;10:763. doi: 10.15252/msb.20145735.
- [2] Cas9 Targeting and the CRISPR Revolution. SCIENCE VOL 344 2014 MAY 16.
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