Difference between revisions of "Team:Fudan/Attributions"
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<!-- Dropdown and List elements in navigation bar --> | <!-- Dropdown and List elements in navigation bar --> | ||
<ul id="dropdown1" class="dropdown-content"> | <ul id="dropdown1" class="dropdown-content"> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Demonstrate">Demonstration</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Antigen_Receptors">Antigen, Receptors</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Results">Transmembrane logic</a></li> |
</ul> | </ul> | ||
<ul id="dropdown2" class="dropdown-content"> | <ul id="dropdown2" class="dropdown-content"> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#ribo">Addon: ribo</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#TALE">Addon: TALE</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#T2">Addon: T2</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Model#Transcriptional_Amplifer">Model: transcriptional amplifer</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Model#NotchLigandKinetics">Model: Notch-ligand kinetics</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Software">Software</a></li> |
</ul> | </ul> | ||
<ul id="dropdown3" class="dropdown-content"> | <ul id="dropdown3" class="dropdown-content"> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/InterLab">iGEM interLab</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Notebook">Our notebook</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Primers">Primers used</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Protocols">Protocols</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Safety">Safety</a></li> |
</ul> | </ul> | ||
<ul id="dropdown4" class="dropdown-content"> | <ul id="dropdown4" class="dropdown-content"> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Basic_Parts">Basic parts</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Composite_Parts">Composite parts</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Optimization">Optimization</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Parts_Collection">Parts collection</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Improve">Parts improvement</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Measurement">Quantification</a></li> |
</ul> | </ul> | ||
<ul id="dropdown5" class="dropdown-content"> | <ul id="dropdown5" class="dropdown-content"> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Bio-Art">Bio-Art display</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Collaborations">Collaborations</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Design_Intention">Design intention</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Human_Practices">Human practices</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Public_Engagement">Public engagement</a></li> |
</ul> | </ul> | ||
<ul id="dropdown6" class="dropdown-content"> | <ul id="dropdown6" class="dropdown-content"> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Acknowledgement">Acknowledgement</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Attributions">Attributions</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Heritage">Heritage</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Team">Members</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Sponsors">Sponsors</a></li> |
</ul> | </ul> | ||
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<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Demonstrate">Demonstration</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Antigen_Receptors">Antigen, Receptors</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Results">Transmembrane logic</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 159: | Line 159: | ||
<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#ribo">Addon: ribo</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#TALE">Addon: TALE</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#T2">Addon: T2</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Model#Transcriptional_Amplifer">Model: transcriptional amplifer</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Model#NotchLigandKinetics">Model: Notch-ligand kinetics</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Software">Software</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
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<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/InterLab">iGEM interLab</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Notebook">Our notebook</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Primers">Primers used</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Protocols">Protocols</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Safety">Safety</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 184: | Line 184: | ||
<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Basic_Parts">Basic parts</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Composite_Parts">Composite parts</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Optimization">Optimization</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Parts_Collection">Parts collection</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Improve">Parts improvement</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Measurement">Quantification</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
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<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Bio-Art">Bio-Art display</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Collaborations">Collaborations</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Design_Intention">Design intention</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Human_Practices">Human practices</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Public_Engagement">Public engagement</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
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<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Acknowledgement">Acknowledgement</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Attributions">Attributions</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Heritage">Heritage</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Team">Members</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Sponsors">Sponsors</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
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<h2>Project design</h2> | <h2>Project design</h2> | ||
<p> | <p> | ||
| − | Zijie Yang and Dr. Cai, through discussions, came up with the first draft of <a href=" | + | Zijie Yang and Dr. Cai, through discussions, came up with the first draft of <a href="/Team:Fudan/Results" target="_blank">3-layer</a> transmembrane logic gates with mutual effort, Ziyan Yu, through literal reading, designed the experiments to <a href="/Team:Fudan/Optimization" target="_blank">optimize</a> <a href="/Team:Fudan/Basic_Parts" target="_blank">the Notch core</a>. Everyone on the team contributed to the improvement of the project. |
</p> | </p> | ||
<h2>Experiment</h2> | <h2>Experiment</h2> | ||
<p>Based on <a href="https://2017.igem.org/Team:Fudan" target="_blank">previous experience</a> designing genetic circuits response to different input densities, Zijie Yang and Ziyan Yu came up with the genetic circuits for the project. Dr. Cai gave comments and provided several references aiding the improvement. | <p>Based on <a href="https://2017.igem.org/Team:Fudan" target="_blank">previous experience</a> designing genetic circuits response to different input densities, Zijie Yang and Ziyan Yu came up with the genetic circuits for the project. Dr. Cai gave comments and provided several references aiding the improvement. | ||
</p> | </p> | ||
| − | <p>Ziyan Yu, Chuyue Zhang, Yuyan Zeng, and Rongrong Du were responsible for the majority of <a href=" | + | <p>Ziyan Yu, Chuyue Zhang, Yuyan Zeng, and Rongrong Du were responsible for the majority of <a href="/Team:Fudan/Protocols" target="_blank">molecular cloning</a>. Fangfei Ye, Mitchell Wan, and Jingbo Fu assisted in some molecular cloning. |
</p> | </p> | ||
<p> | <p> | ||
| − | Zijie and Ziyan conducted cell culture, transient transfection, and <a href=" | + | Zijie and Ziyan conducted cell culture, transient transfection, and <a href="/Team:Fudan/Measurement" target="_blank">flow cytometry analysis</a>. Zijie constructed the stable cell lines using retroviral infection and cell sorting. |
</p> | </p> | ||
<p> | <p> | ||
| Line 291: | Line 291: | ||
</p> | </p> | ||
<p> | <p> | ||
| − | Mitchell conducted the Addon thought experiments (<a href=" | + | Mitchell conducted the Addon thought experiments (<a href="/Team:Fudan/Addon#ribo" target="_blank">ribo</a>, <a href="/Team:Fudan/Addon#TALE" target="_blank">TALE</a>, and <a href="/Team:Fudan/Addon#T2" target="_blank">T2</a>) with advice from Dr. Cai. |
</p> | </p> | ||
<h2>InterLab</h2> | <h2>InterLab</h2> | ||
<p> | <p> | ||
| − | Mitchell Wan completed <a href=" | + | Mitchell Wan completed <a href="/Team:Fudan/InterLab" target="_blank">the experiments</a> with help from Zijie Yang and people from iGEM team <a href="https://2018.igem.org/Team:Fudan-CHINA" target="_blank">Fudan-CHINA</a>. |
</p> | </p> | ||
<h2>Model</h2> | <h2>Model</h2> | ||
| − | <p>Yiheng Wang came up with the model on <a href=" | + | <p>Yiheng Wang came up with the model on <a href="/Team:Fudan/Model#Transcriptional_Amplifer" target=_blank>transcriptional amplifier</a>.</p> |
<p> | <p> | ||
| − | Lingwei Zhang simulated <a href=" | + | Lingwei Zhang simulated <a href="/Team:Fudan/Model#NotchLigandkinetics" target="_blank">multi-cell interactions and evolution</a> with a population perspective. Lingwei also built our <a href="/Team:Fudan/Software" target="_blank">software</a> based on his modeling results. |
</p> | </p> | ||
<p> | <p> | ||
| Line 307: | Line 307: | ||
<h2>Software</h2> | <h2>Software</h2> | ||
<p> | <p> | ||
| − | Lingwei Zhang wrote up our <a href=" | + | Lingwei Zhang wrote up our <a href="/Team:Fudan/Software" target="_blank">software</a>. |
</p> | </p> | ||
<h2>Integrated HP</h2> | <h2>Integrated HP</h2> | ||
<p> | <p> | ||
| − | Jingbo Fu, Yuyan Zeng, Fangfei Ye, and Rongrong Du made huge efforts in advertising our project and <a href=" | + | Jingbo Fu, Yuyan Zeng, Fangfei Ye, and Rongrong Du made huge efforts in advertising our project and <a href="/Team:Fudan/Human_Practices" target="_blank">human practice activities</a> to the public. |
</p> | </p> | ||
<p> | <p> | ||
| − | Jingbo led the surveys, organized the <a href=" | + | Jingbo led the surveys, organized the <a href="/Team:Fudan/Human_Practices#section1" target="_blank">interviews</a> with researchers and doctors. Everyone on the team heartily helped and participated in various HP events. |
</p> | </p> | ||
<p> | <p> | ||
| Line 320: | Line 320: | ||
</p> | </p> | ||
<p> | <p> | ||
| − | Jingbo and Yuyan kept in contact with <a href=" | + | Jingbo and Yuyan kept in contact with <a href="/Team:Fudan/Public_Engagement#section1" target="_blank">high schools</a>, organizers responsible for the summer camp, and other undergraduate students. They led our presentations for them, and everyone on the team participated actively. |
</p> | </p> | ||
<p> | <p> | ||
| − | Jingbo designed and trained high school students from Qibao Dwight High School during this summer, also organized the multi-disciplinary <a href=" | + | Jingbo designed and trained high school students from Qibao Dwight High School during this summer, also organized the multi-disciplinary <a href="/Team:Fudan/Public_Engagement#section4" target="_blank">debate</a> on project safety and ethical topics. |
</p> | </p> | ||
<p> | <p> | ||
| − | Fangfei planned and assembled the <a href=" | + | Fangfei planned and assembled the <a href="/Team:Fudan/Bio-Art" target="_blank">Bio-Art Display</a> and everyone on the team took part in making the Display come true. |
</p> | </p> | ||
<h2>Art design</h2> | <h2>Art design</h2> | ||
<p> | <p> | ||
| − | Fangfei Ye is responsible for all <a href=" | + | Fangfei Ye is responsible for all <a href="/Team:Fudan/Design_Intention" target="_blank">art design</a>, which includes our team logo, team flag, team uniform (Dr. Cai gave comments), team name card, brochures, our posters, as well as materials related to our human practice events. |
</p> | </p> | ||
<h2>Wiki</h2> | <h2>Wiki</h2> | ||
| Line 396: | Line 396: | ||
<span>Project</span> | <span>Project</span> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Demonstrate">Demonstration</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Antigen_Receptors">Antigen, Receptors</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Results">Transmembrane logic</a></li> |
<li><a href="https://2017.igem.org/Team:Fudan">2017.iGEM</a></li> | <li><a href="https://2017.igem.org/Team:Fudan">2017.iGEM</a></li> | ||
</ul> | </ul> | ||
| Line 405: | Line 405: | ||
<span>Dry lab</span> | <span>Dry lab</span> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#ribo">Addon: ribo</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#TALE">Addon: TALE</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Addon#T2">Addon: T2</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Model#Transcriptional_Amplifer">Model: transcriptional amplifer</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Model#NotchLigandKinetics">Model: Notch-ligand kinetics</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Software">Software</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 416: | Line 416: | ||
<span>Wet lab</span> | <span>Wet lab</span> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/InterLab">iGEM interLab</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Notebook">Our notebook</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Primers">Primers used</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Protocols">Protocols</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Safety">Safety</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 428: | Line 428: | ||
<span>Toolbox</span> | <span>Toolbox</span> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Basic_Parts">Basic parts</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Composite_Parts">Composite parts</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Optimization">Optimization</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Parts_Collection">Parts collection</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Improve">Parts improvement</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Measurement">Quantification</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 439: | Line 439: | ||
<span>Outreach</span> | <span>Outreach</span> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Bio-Art">Bio-Art display</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Collaborations">Collaborations</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Design_Intention">Design intention</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Human_Practices">Human practices</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Public_Engagement">Public engagement</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
| Line 449: | Line 449: | ||
<span>Team</span> | <span>Team</span> | ||
<ul> | <ul> | ||
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Acknowledgement">Acknowledgement</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Attributions">Attributions</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Heritage">Heritage</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Team">Members</a></li> |
| − | <li><a href=" | + | <li><a href="/Team:Fudan/Sponsors">Sponsors</a></li> |
</ul> | </ul> | ||
</div> | </div> | ||
Latest revision as of 15:09, 7 November 2018
- Addon: ribo
- Addon: TALE
- Addon: T2
- Model: transcriptional amplifer
- Model: Notch-ligand kinetics
- Software
Attributions
Project design
Zijie Yang and Dr. Cai, through discussions, came up with the first draft of 3-layer transmembrane logic gates with mutual effort, Ziyan Yu, through literal reading, designed the experiments to optimize the Notch core. Everyone on the team contributed to the improvement of the project.
Experiment
Based on previous experience designing genetic circuits response to different input densities, Zijie Yang and Ziyan Yu came up with the genetic circuits for the project. Dr. Cai gave comments and provided several references aiding the improvement.
Ziyan Yu, Chuyue Zhang, Yuyan Zeng, and Rongrong Du were responsible for the majority of molecular cloning. Fangfei Ye, Mitchell Wan, and Jingbo Fu assisted in some molecular cloning.
Zijie and Ziyan conducted cell culture, transient transfection, and flow cytometry analysis. Zijie constructed the stable cell lines using retroviral infection and cell sorting.
Rongrong purified EGFP protein, attached the protein to beads, which were used in our shaking test for SynNotch activation.
Dr. Cai provided numerous suggestions and advice on experimental design and data analysis.
Mitchell conducted the Addon thought experiments (ribo, TALE, and T2) with advice from Dr. Cai.
InterLab
Mitchell Wan completed the experiments with help from Zijie Yang and people from iGEM team Fudan-CHINA.
Model
Yiheng Wang came up with the model on transcriptional amplifier.
Lingwei Zhang simulated multi-cell interactions and evolution with a population perspective. Lingwei also built our software based on his modeling results.
Zijie Yang and Yijie Pan provided suggestions to different details in our modeling.
Software
Lingwei Zhang wrote up our software.
Integrated HP
Jingbo Fu, Yuyan Zeng, Fangfei Ye, and Rongrong Du made huge efforts in advertising our project and human practice activities to the public.
Jingbo led the surveys, organized the interviews with researchers and doctors. Everyone on the team heartily helped and participated in various HP events.
Zijie Yang and Ziyan Yu invited Prof. Blacklow to Fudan University, and accompany his visit.
Jingbo and Yuyan kept in contact with high schools, organizers responsible for the summer camp, and other undergraduate students. They led our presentations for them, and everyone on the team participated actively.
Jingbo designed and trained high school students from Qibao Dwight High School during this summer, also organized the multi-disciplinary debate on project safety and ethical topics.
Fangfei planned and assembled the Bio-Art Display and everyone on the team took part in making the Display come true.
Art design
Fangfei Ye is responsible for all art design, which includes our team logo, team flag, team uniform (Dr. Cai gave comments), team name card, brochures, our posters, as well as materials related to our human practice events.
Wiki
Tian Huang built the wiki template with Materialize framework. Fangfei Ye and Tian coded the site, while rest of the team worked on content write-up. Dr. Cai gave comments on the coding and writeup.
Support
Dr. Lu and Dr. Cai secured the primary funding for the team. Dr. Cai provided the lab space. All team members participated in the crowdfunding campaign.
Abstract
Contact-dependent signaling is critical for multicellular biological events, yet customizing contact-dependent signal transduction between cells remains challenging. Here we have developed the ENABLE toolbox, a complete set of transmembrane binary logic gates. Each gate consists of 3 layers: Receptor, Amplifier, and Combiner. We first optimized synthetic Notch receptors to enable cells to respond to different signals across the membrane reliably. These signals, individually amplified intracellularly by transcription, are further combined for computing. Our engineered zinc finger-based transcription factors perform binary computation and output designed products. In summary, we have combined spatially different signals in mammalian cells, and revealed new potentials for biological oscillators, tissue engineering, cancer treatments, bio-computing, etc. ENABLE is a toolbox for constructing contact-dependent signaling networks in mammals. The 3-layer design principle underlying ENABLE empowers any future development of transmembrane logic circuits, thus contributes a foundational advance to Synthetic Biology.