Difference between revisions of "Team:Fudan-TSI/Judging"

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                        <a href="/Team:Fudan-TSI" target="_self"><img alt="2019 team logo" src="https://static.igem.org/mediawiki/2019/3/3c/T--Fudan-TSI--Logo0.gif"></a>
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                    <p style="width: 100%;text-align: center;font-size: 24px"><span class="white-text">Judging</span></p>
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                </div></li>
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                <li>
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                    <ul class="collapsible expandable">
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                        <li>On this page</li>
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                        <li class="onThisPageNav"><a href="#section1">Bronze Requirements</a></li>
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                        <li class="onThisPageNav"><a href="#section2">Silver Requirements</a></li>
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                        <li class="onThisPageNav"><a href="#section3">Gold Requirements</a></li>
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                        <li class="onThisPageNav"><a href="#section4">Special Prizes</a></li>
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                        <li>Team: Fudan-TSI</li>
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<li><div class="collapsible-header">Project</div>
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    <div class="collapsible-body"><ul>
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        <li><a href="/Team:Fudan-TSI/Description">Background</a></li>
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        <li><a href="/Team:Fudan-TSI/Design">Design</a></li>
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        <li><a href="/Team:Fudan-TSI/Applied_Design">Applied Design</a></li>
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        <li><a href="/Team:Fudan-TSI/Experiments">Experiments</a></li>
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        <li><a href="/Team:Fudan-TSI/Judging">Judging</a></li>
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    </ul></div>
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</li>
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<li><div class="collapsible-header">Results</div>
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    <div class="collapsible-body"><ul>
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        <li><a href="/Team:Fudan-TSI/Results#ReverseTranscription">Reverse Transcription</a></li>
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        <li><a href="/Team:Fudan-TSI/Results#Recombination">Recombination</a></li>
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        <li><a href="/Team:Fudan-TSI/Demonstrate">Demonstration</a></li>
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        <li><a href="/Team:Fudan-TSI/Measurement">Measurement</a></li>
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        <li><a href="/Team:Fudan-TSI/Notebook">Notebook</a></li>
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    </ul></div>
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</li>
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<li><div class="collapsible-header">Model</div>
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    <div class="collapsible-body"><ul>
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        <li><a href="/Team:Fudan-TSI/Model">Modeling</a></li>
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        <li><a href="/Team:Fudan-TSI/Software">Software</a></li>
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        <li><a href="/Team:Fudan-TSI/Hardware">Hardware</a></li>
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    </ul></div>
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</li>
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<li><div class="collapsible-header">Parts</div>
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    <div class="collapsible-body"><ul>
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        <li><a href="/Team:Fudan-TSI/Basic_Part">Basic parts</a></li>
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        <li><a href="/Team:Fudan-TSI/Composite_Part">Composite parts</a></li>
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        <li><a href="/Team:Fudan-TSI/Improve">Improved parts</a></li>
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        <li><a href="/Team:Fudan-TSI/Part_Collection">Part collection</a></li>
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    </ul></div>
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</li>
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<li><div class="collapsible-header">Outreach</div>
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    <div class="collapsible-body"><ul>
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        <li><a href="/Team:Fudan-TSI/Public_Engagement">Education &amp; Public engagement</a></li>
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        <li><a href="/Team:Fudan-TSI/Integrated_Human_Practice">Integrated human practice</a></li>
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        <li><a href="/Team:Fudan-TSI/Collaborations">Collaborations</a></li>
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        <li><a href="/Team:Fudan-TSI/Safety">Safety</a></li>
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    </ul></div>
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</li>
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<li><div class="collapsible-header">Team</div>
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    <div class="collapsible-body"><ul>
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        <li><a href="/Team:Fudan-TSI/Team">Members</a></li>
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        <li><a href="/Team:Fudan-TSI/Attributions">Attributions</a></li>
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        <li><a href="https://2018.igem.org/Team:Fudan/Heritage" target=_blank>Heritage</a></li>
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        <li><a href="/Team:Fudan-TSI">&copy; 2019</a></li>
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                         <h2>text from greatbay</h2>
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                         <h2>Bronze Requirements</h2>
 
                         <p>
 
                         <p>
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Judging
 
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GreatBay_China had done so many meaningful and exciting things over the year. To us the significance is far beyond achieving each medal and award criterion, but here is a nice reminder of all the relevant content that proves we fulfilled the necessary requirements.
 
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Bronze Requirements
 
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1. Registration and Giant Jamboree Attendance
 
1. Registration and Giant Jamboree Attendance
 
2. Competition Deliverables
 
2. Competition Deliverables
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4.(b) Characterization in Parts
 
4.(b) Characterization in Parts
 
We have added new, high quality, experimental characterization data to an existing BioBrick Part from the Registry: J23101
 
We have added new, high quality, experimental characterization data to an existing BioBrick Part from the Registry: J23101
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                    </p></div>
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Silver Requirements
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                    <div class="section container" id="section2">
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                        <h2>Silver Requirements</h2>
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                        <p>
 
1. Validated Part
 
1. Validated Part
 
We have designed three new parts related to our project works and documented the characterization on Part's Registry. We followed by successful DNA shippments of these parts.
 
We have designed three new parts related to our project works and documented the characterization on Part's Registry. We followed by successful DNA shippments of these parts.
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3. Human Practices
 
3. Human Practices
 
Check our HP overview to see what approaches we used to investigate street cats issue and connect with our communities, and our work is socially responsibile for a better world.
 
Check our HP overview to see what approaches we used to investigate street cats issue and connect with our communities, and our work is socially responsibile for a better world.
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                    </p></div>
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Gold Requirements
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                    <div class="section container" id="section3">
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                        <h2>Gold Requirements</h2>
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                        <p>
 
1. Integrated Human Practices
 
1. Integrated Human Practices
 
Our human practice is a mirror to our project, as we were constantly improving our project, applied design and hardware, based on others feedback.
 
Our human practice is a mirror to our project, as we were constantly improving our project, applied design and hardware, based on others feedback.
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4. Demonstration
 
4. Demonstration
 
Check how our project is repeatable and realistic, and how it is followed by requirements of iGEM Safety Committee.
 
Check how our project is repeatable and realistic, and how it is followed by requirements of iGEM Safety Committee.
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                    </p></div>
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                        <h2>Special Prizes</h2>
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                        <p>
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<h4>Integrated Human Practices</h4>
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<p>
 +
Stray cats is a thorny problem, but we proposed an innovative solution coherent to our project. Through a number of online and field research, we perceived the severity of this problem and broadened our perspective. We thoughtfully incorporated ‘value sensitive design’ throughout our human practice, connecting different stakeholders from the society. In practice, we communicated with stray cat rescue teams for advice, and collaborated with organisations like Maker Space and environmental NGOs to get more information, and furthermore, raise public awareness on this issue. We interviewed many citizens to collect comprehensive opinions and suggestions, which make our design more viable. Moreover, we inquired laws and regulations from relevant governmental departments to community level in order to ensure smooth implementation of our applied design. Above all, we have made a series of documentary about our human practice and the process of conceiving, building and improving our applied design: “Kitty Wonderland”.</p>
  
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<h4>Education and Public Engagement</h4>
 +
<p>
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We hosted a workshop on synbio and its application, and hold an exhibition of our project in the international Maker Faire. We discussed with audiences including artists, students, investors and engineers who inquired about the safety and potential of synbio eagerly. And engineers and artists established long-term collaboration with us on applied design. We closely engaged with neighbourhood, urban management agencies and animal welfare groups, presenting how microbial factory can integrate with cat shelter we built to solve the problem of feral cats. Through direct interviews, in-depth conversations, presentations or polls, we learnt their concerns and how synbio-related design can be better accepted by the public. Innovatively, we connect with people in art field by holding activities which allow the public to draw and design the cat shelter. Moreover, we filmed a series of documentaries to reach even further, by uploading them on popular media platforms.</p>
  
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<h4>Model</h4>
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<p>
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Special Prizes
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Integrated Human Practices
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Stray cats is a thorny problem, but we proposed an innovative solution coherent to our project. Through a number of online and field research, we perceived the severity of this problem and broadened our perspective. We thoughtfully incorporated ‘value sensitive design’ throughout our human practice, connecting different stakeholders from the society. In practice, we communicated with stray cat rescue teams for advice, and collaborated with organisations like Maker Space and environmental NGOs to get more information, and furthermore, raise public awareness on this issue. We interviewed many citizens to collect comprehensive opinions and suggestions, which make our design more viable. Moreover, we inquired laws and regulations from relevant governmental departments to community level in order to ensure smooth implementation of our applied design. Above all, we have made a series of documentary about our human practice and the process of conceiving, building and improving our applied design: “Kitty Wonderland”.
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Education and Public Engagement
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We hosted a workshop on synbio and its application, and hold an exhibition of our project in the international Maker Faire. We discussed with audiences including artists, students, investors and engineers who inquired about the safety and potential of synbio eagerly. And engineers and artists established long-term collaboration with us on applied design. We closely engaged with neighbourhood, urban management agencies and animal welfare groups, presenting how microbial factory can integrate with cat shelter we built to solve the problem of feral cats. Through direct interviews, in-depth conversations, presentations or polls, we learnt their concerns and how synbio-related design can be better accepted by the public. Innovatively, we connect with people in art field by holding activities which allow the public to draw and design the cat shelter. Moreover, we filmed a series of documentaries to reach even further, by uploading them on popular media platforms.
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Model
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We built an ODE kinetics framework to model the mutualistic co-culture system of E.coli and S.cerevisiae we intended to use in our project, taking into account substrate utilization, product inhibitions and product formation involved in two species’ interactions. By recording the growth of the two engineered strains in co-culture and performing parameter sensitivity analyses, we were able to better interpret the behavior of the system.
 
We built an ODE kinetics framework to model the mutualistic co-culture system of E.coli and S.cerevisiae we intended to use in our project, taking into account substrate utilization, product inhibitions and product formation involved in two species’ interactions. By recording the growth of the two engineered strains in co-culture and performing parameter sensitivity analyses, we were able to better interpret the behavior of the system.
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In addition, we have also devised a model to analyze the relationship between E.coli’s geraniol production level and the copy number of the plasmid containing the two key enzymes for production, GES and GPPS, under the stabilization of different transcription activator-like effectors stabilized promoters(TALEsp) from our promoter library, so as to choose the desired combination for optimal geraniol production. The model can also be applied to choosing TALEsp for other situations involving tuning expressions of genes or maximizing down-stream production stabilized by TALEsp.
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In addition, we have also devised a model to analyze the relationship between E.coli’s geraniol production level and the copy number of the plasmid containing the two key enzymes for production, GES and GPPS, under the stabilization of different transcription activator-like effectors stabilized promoters(TALEsp) from our promoter library, so as to choose the desired combination for optimal geraniol production. The model can also be applied to choosing TALEsp for other situations involving tuning expressions of genes or maximizing down-stream production stabilized by TALEsp.</p>
  
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Product Design
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<h4>Product Design</h4>
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Free-roaming feral cats have posed a serious threat to public health and biodiversity. The current solution to manage feral cats called Trap&Neuter&Release often fail to control cats’ population due to the difficulties in capturing them. Aiming at the microbial production of nepetalactol, an ingredient in the cat-attracting plant catnip, we proposed the use of microorganism-derived nepetalactol for capturing feral cats and have devised a cat shelter, “Kitty Wonderland” as an implement tool of this idea. Through active communication with animal rescue NGOs, government, and hardware specialists, we optimised the design of Kitty Wonderland overtime, ensuring it’s safe and practical. Nonetheless, the cat shelter may be subjected to vandalism if our society didn’t realise the importance of respecting animals’ life and welfare. Thus, we employed public education as a complimentary component to the Kitty Wonderland.
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<p>
 +
Free-roaming feral cats have posed a serious threat to public health and biodiversity. The current solution to manage feral cats called Trap&Neuter&Release often fail to control cats’ population due to the difficulties in capturing them. Aiming at the microbial production of nepetalactol, an ingredient in the cat-attracting plant catnip, we proposed the use of microorganism-derived nepetalactol for capturing feral cats and have devised a cat shelter, “Kitty Wonderland” as an implement tool of this idea. Through active communication with animal rescue NGOs, government, and hardware specialists, we optimised the design of Kitty Wonderland overtime, ensuring it’s safe and practical. Nonetheless, the cat shelter may be subjected to vandalism if our society didn’t realise the importance of respecting animals’ life and welfare. Thus, we employed public education as a complimentary component to the Kitty Wonderland.</p>
  
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Hardware
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<h4>Hardware</h4>
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In order to solve the stray cats problem, we devise this hardware, the Kitty Wonderland, to provide homeless stray cats with shelters which could offer them a safe, comfortable and permanent living environment. Through the interviews and discussions we made with specialists, officials and residence, we improve our hardware to combine the merits of existing methods like Trap&Neuter&Release. The hardware assists volunteered caregivers by attracting stray cats and capturing them if necessary, so the difficulties and costs in tracking and taking care of stray cats are greatly reduced. Besides, we apply nepetalactol, which is the focus of our project, to our hardware to make it more effective in attracting cats and emphasize the significance of our project. Finally, our hardware can be easily deployed on various locations in the community where it stresses the stray cats problem to a broad population in an original approach.
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<p>
 +
In order to solve the stray cats problem, we devise this hardware, the Kitty Wonderland, to provide homeless stray cats with shelters which could offer them a safe, comfortable and permanent living environment. Through the interviews and discussions we made with specialists, officials and residence, we improve our hardware to combine the merits of existing methods like Trap&Neuter&Release. The hardware assists volunteered caregivers by attracting stray cats and capturing them if necessary, so the difficulties and costs in tracking and taking care of stray cats are greatly reduced. Besides, we apply nepetalactol, which is the focus of our project, to our hardware to make it more effective in attracting cats and emphasize the significance of our project. Finally, our hardware can be easily deployed on various locations in the community where it stresses the stray cats problem to a broad population in an original approach.</p>
  
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Best Part Collection
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<h4>Best Part Collection</h4>
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We created a novel, well-characterized, and well-documented transcription-activator-like effector (TALE) stabilized promoter (TALEsp) collection as well as two parts enabling future teams to create more stabilized promoters. The TALEsp makes gene expression independent of copy number, maintaining a constant and constitutive expression level at any copy. They were cloned on vectors of different copy and were inserted to the genome to be characterized with not only green fluorescence but also with a metabolic engineering setting -- geraniol synthesis. Our results have proven the stabilization effect of the promoters. As building a synthetic biological system requires the correct proportion of each component, but in reality, the cellular environment is usually dynamic and complex, making the engineering process sometimes difficult, this promoter library provides a reliable tool which allows teams to construct predictable and robust synthetic systems.
+
<p>
 +
We created a novel, well-characterized, and well-documented transcription-activator-like effector (TALE) stabilized promoter (TALEsp) collection as well as two parts enabling future teams to create more stabilized promoters. The TALEsp makes gene expression independent of copy number, maintaining a constant and constitutive expression level at any copy. They were cloned on vectors of different copy and were inserted to the genome to be characterized with not only green fluorescence but also with a metabolic engineering setting -- geraniol synthesis. Our results have proven the stabilization effect of the promoters. As building a synthetic biological system requires the correct proportion of each component, but in reality, the cellular environment is usually dynamic and complex, making the engineering process sometimes difficult, this promoter library provides a reliable tool which allows teams to construct predictable and robust synthetic systems.</p>
  
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Best New Basic Part
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<h4>Best New Basic Part</h4>
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Have a look on our favourite basic part: BBa_K2753003.
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<p>
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Best New Composite Part
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Please have a look on our favourite basic part: BBa_K2753003.</p>
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Have a look on our favourite composite part: BBa_K2753018.
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<h4>Best New Composite Part</h4>
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To iGEMers who read this page,
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<p>
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Hi iGEMers! This is Alexis Zeng writing to you. And as you can see on the home page: we actually did pretty well this year! Therefore I also want to share some tips which helped us a great deal, and high school teams especially might find them useful.
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Have a look on our favourite composite part: BBa_K2753018.</p>
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1. Don’t miss any important deadlines. Deadlines of Part submission, judging form freeze, and the final wiki freeze are soooo vital if you want to win medals. Although it doesn’t affect how good your project is, it’s still better to keep an eye on them. Shared calendar is a helpful tool to make sure everyone in the team is aware of the deadlines.
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2. Actively reach out for help. Obstacles and mysteries are inevitable, but you are not alone. Be brave to seek assistance from your advisors, PIs, other PIs, and literally anyone is relevant or is able to connect you with more resources. And when in doubt about rules or safety issues, it’s a good idea to write to the HQ. Active communication is an excellent solution for everything.
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3. Start early. We began the project in March, which gave us more abundant time compared to those who start in the summer and allowed us to complete this huge project.
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4. Read the judging handbook ahead. In my opinion, the judging handbook provides clear guidance to design a good project: it includes good examples from previous years; some aspects likely to be neglected when designing; how would the judges assess your project.
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Charles would like to agree every points Alexis mentioned above. In addition, documentation of your project, HP, and labwork is also important. It will make life easier when you comes to the end of the project. Engaging in meetups and talking to other teams can give you some valuable and unexpected advices.
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Hallo! This is Lucinda Lin with something else to add:
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5. Communication is important! When you feel that iGEM has negatively impacted your academics or relationships with your family, do tell your teammates and see whether they can help you by sharing some of your tasks. Don't take up more tasks than you can finish and then overwork yourself, because the result is often not satisfying for both you and the team.
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6. Checking on previous teams' wikis is a good way to get to know iGEM better and find inspiration. However, you should know that some of the contents have been revised after the competition. For example, we use external links to share our presentation powerpoints and merge the hardware and public engagement pages based on judging feedbacks..
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7. Keep in touch with the HQ and safety commitee! They kindly answered our questions on criteria and biosafety & ethics throughout the competition.
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You can find our team email at the bottom of this page. Feel free to contact us through email or twitter!
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                        <h2>title</h2>
 
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                            Fangfei Ye is responsible for all <a href="/Team:Fudan-TSI/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.
 
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                          <p>PCR and subcloning were performed using standard methods. Detailed primer sequences are <a href="/Team:Fudan-TSI/Primers">provided</a>. All constructs were verified by Sanger sequencing.
 
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                          </p>
 
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                          <p>Cells were cultured in DMEM supplemented with 10% FBS (HyClone), 100 U/ml penicillin, 100 μg/ml streptomycin and 1x GlutaMax (Gibco). Transient transfections were performed using Lipofectamine 2000 (Invitrogen) and Opti-MEM (Gibco). Viral packaging, infection and fluorescence-activated cell sorting were performed using standard methods.
 
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                          </p>
 
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                          <p>Images, unless otherwise indicated, were captured using an inverted epifluorescence microscope (IX-81, Olympus) and a sCMOS camera (pixel size = 0.3222 &mu;m; Zyla 5.5, Andor; 20x objective N.A.  0.75) and were controlled by <a href="http://www.micro-manager.org/" target=_blank>Micro-Manager software</a>.
 
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                          </p>
 
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                          <p>All statistical analysis was performed using Prism (Graphpad) and <a href="http://rsbweb.nih.gov/ij/developer/macro/macros.html" target=_blank>ImageJ</a>. All experiments were independently performed in triplicates; unless otherwise indicated. Images were combined and annotated in Powerpoint for presentation. Representative images are shown.
 
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                                  <th>Our protocols as PDF files</th><th>&nbsp;</th>
 
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                                  <th>Download</th>
 
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                                  <td>Be a Good Lab Member</td><td><i>GoodLabPractices.pdf</i></td>
 
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                                  <td><a href="https://2018.igem.org/File:T--Fudan--GoodLabPractices.pdf" target="_blank"><i class="fa fa-download"></i></a></td>
 
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                                  <td>Molecular Cloning</td><td><i>MolecularCloning.pdf</i></td>
 
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                                  <td><a href="https://2018.igem.org/File:T--Fudan--MolecularCloning.pdf" target="_blank"><i class="fa fa-download"></i></a></td>
 
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                                  <td>Tissue Culture</td><td><i>CellCulture.pdf</i></td>
 
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                                  <td><a href="https://2018.igem.org/File:T--Fudan--CellCulture.pdf" target="_blank"><i class="fa fa-download"></i></a></td>
 
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                                  <td>Make a Stable Cell Line</td><td><i>MakeStableCellLine.pdf</i></td>
 
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                                  <td><a href="https://2018.igem.org/File:T--Fudan--MakeStableCellLine.pdf" target="_blank"><i class="fa fa-download"></i></a></td>
 
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                                  <td>Cell Sorting</td><td><i>FACS.pdf</i></td>
 
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                                  <td><a href="https://2018.igem.org/File:T--Fudan--FACS.pdf" target="_blank"><i class="fa fa-download"></i></a></td>
 
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                                  <td>Cell Staining</td><td><i>FixStain.pdf</i></td>
 
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                                  <td><a href="https://2018.igem.org/File:T--Fudan--FixStain.pdf" target="_blank"><i class="fa fa-download"></i></a></td>
 
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                                  <td>Time-lapse Live-cell Imaging</td><td><i>TimeLapseImaging.pdf</i></td>
 
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                                  <td><a href="https://2018.igem.org/File:T--Fudan--TimeLapseImaging.pdf" target="_blank"><i class="fa fa-download"></i></a></td>
 
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                      <p style="color:grey">
 
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                          For practical reasons, all full-length protocols are in Chinese.
 
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                     <h2 style="margin: 0;padding: 10px 0;">Project Summary</h2>
 
                     <h2 style="margin: 0;padding: 10px 0;">Project Summary</h2>
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                     <p style="margin: 0">abstract abstract abstract abstract abstract abstract abstract abstract abstract abstract abstract abstract abstract abstract abstract abstract due sep 5 due sep 5 due sep 5 due sep 5 due sep 5 due sep 5 due sep 5 due sep 5 due sep 5 due sep 5 due sep 5 due sep 5
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                     <p style="margin: 0">Mutation library generation is critical for biological and medical research, but current methods cannot mutate a specific sequence continuously without manual intervention. Here we present a toolbox for <i>in vivo</i> continuous mutation library construction. First, the target DNA is transcribed into RNA. Next, our reverse transcriptase reverts RNA into cDNA, during which the target is randomly mutated by enhanced error-prone reverse transcription. Finally, the mutated version replaces the original sequence through recombination. These steps will be carried out iteratively, generating a random mutation library of the target with high efficiency as mutations accumulate along with bacterial growth. Our toolbox is orthogonal and provides a wide range of applications among various species. R-Evolution could mutate coding sequences and regulatory sequences, which enables the <i>in vivo</i> evolution of individual proteins or multiple targets at a time, promotes high-throughput research, and serves as a foundational advance to synthetic biology.
 
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                             <a href="https://2019.igem.org/Team:Fudan-TSI"><img alt="2018 Team:Fudan logo white" class="col s3 m6 l3" style="position:relative; padding: 0.5em 0.3rem; margin:-0.15rem 0; left: -0.45rem;" src="https://static.igem.org/mediawiki/2019/7/7f/T--Fudan-TSI--Logo0-crop-grey.png">
 
                             </a><a href="http://www.fudan.edu.cn/en/" target="_blank"><img class="col s3 m6 l3" alt="Fudan University" src="https://static.igem.org/mediawiki/2018/f/f7/T--Fudan--schoolLogo.png">
 
                             </a><a href="http://www.fudan.edu.cn/en/" target="_blank"><img class="col s3 m6 l3" alt="Fudan University" src="https://static.igem.org/mediawiki/2018/f/f7/T--Fudan--schoolLogo.png">
 
                         </a><a href="http://life.fudan.edu.cn/" target="_blank"><img class="col s3 m6 l3" style="margin-bottom: 4%;/* 该图比其他小一点，排版需要 */" alt="School of Life Sciences, Fudan University" src="https://static.igem.org/mediawiki/2018/1/1d/T--Fudan--schoolOfLifeSciencesIcon.png">
 
                         </a><a href="http://life.fudan.edu.cn/" target="_blank"><img class="col s3 m6 l3" style="margin-bottom: 4%;/* 该图比其他小一点，排版需要 */" alt="School of Life Sciences, Fudan University" src="https://static.igem.org/mediawiki/2018/1/1d/T--Fudan--schoolOfLifeSciencesIcon.png">
 
                         </a><a href="http://www.yfc.cn/en/" target="_blank"><img class="col s3 m6 l3" style="padding: 0.15rem 0.9rem;" alt="Yunfeng Capital" src="https://static.igem.org/mediawiki/2018/e/e2/T--Fudan--yunfengLogo.png">
 
                         </a><a href="http://www.yfc.cn/en/" target="_blank"><img class="col s3 m6 l3" style="padding: 0.15rem 0.9rem;" alt="Yunfeng Capital" src="https://static.igem.org/mediawiki/2018/e/e2/T--Fudan--yunfengLogo.png">
 
                         </a>
 
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                             <h3 class="col s12" style="text-align: left; color: rgba(255, 255, 255, 0.8); font-size: 18px">Repeated Evolution in vivo</h3>
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                             <h3 class="col s12" style="text-align: left; color: rgba(255, 255, 255, 0.8); font-size:12px">R-Evolution: an <i>in vivo</i> sequence-specific toolbox for continuous mutagenesis</h3>
 
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                                   <span><a href="/Team:Fudan-TSI/Description">Project</a></span>
 
                                   <span><a href="/Team:Fudan-TSI/Description">Project</a></span>
 
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Revision as of 05:01, 15 September 2019

2019 Team:Fudan-TSI Judging

Judging

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Judging

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2018 team Fudan title attributions

Bronze Requirements

1. Registration and Giant Jamboree Attendance 2. Competition Deliverables Apart from this wiki your are looking, posters and presentations will come to you at Jamboree. Here is our judging form. 3. Attributions See each member's contribution and help from others. 4.(a) Characterization in Interlab We have successfully completed the InterLab Measurement Study and submitted high-quality data. 4.(b) Characterization in Parts We have added new, high quality, experimental characterization data to an existing BioBrick Part from the Registry: J23101

Silver Requirements

1. Validated Part We have designed three new parts related to our project works and documented the characterization on Part's Registry. We followed by successful DNA shippments of these parts. 2. Collaboration See how we established meaningful collaborations with teams all over the world. 3. Human Practices Check our HP overview to see what approaches we used to investigate street cats issue and connect with our communities, and our work is socially responsibile for a better world.

Gold Requirements

1. Integrated Human Practices Our human practice is a mirror to our project, as we were constantly improving our project, applied design and hardware, based on others feedback. 2. Improve a Previous Part We have improved existing part, Part:BBa_J23119, to a new part, Part:BBa_K2753023, and produced experimental data of both parts in comparison. We also followed by successful DNA shippments. 3. Model Modeling tools aid in the rational design and make the engineered system predictable. Visit our Model page to take a closer look. 4. Demonstration Check how our project is repeatable and realistic, and how it is followed by requirements of iGEM Safety Committee.

Special Prizes

Integrated Human Practices

Stray cats is a thorny problem, but we proposed an innovative solution coherent to our project. Through a number of online and field research, we perceived the severity of this problem and broadened our perspective. We thoughtfully incorporated ‘value sensitive design’ throughout our human practice, connecting different stakeholders from the society. In practice, we communicated with stray cat rescue teams for advice, and collaborated with organisations like Maker Space and environmental NGOs to get more information, and furthermore, raise public awareness on this issue. We interviewed many citizens to collect comprehensive opinions and suggestions, which make our design more viable. Moreover, we inquired laws and regulations from relevant governmental departments to community level in order to ensure smooth implementation of our applied design. Above all, we have made a series of documentary about our human practice and the process of conceiving, building and improving our applied design: “Kitty Wonderland”.

Education and Public Engagement

We hosted a workshop on synbio and its application, and hold an exhibition of our project in the international Maker Faire. We discussed with audiences including artists, students, investors and engineers who inquired about the safety and potential of synbio eagerly. And engineers and artists established long-term collaboration with us on applied design. We closely engaged with neighbourhood, urban management agencies and animal welfare groups, presenting how microbial factory can integrate with cat shelter we built to solve the problem of feral cats. Through direct interviews, in-depth conversations, presentations or polls, we learnt their concerns and how synbio-related design can be better accepted by the public. Innovatively, we connect with people in art field by holding activities which allow the public to draw and design the cat shelter. Moreover, we filmed a series of documentaries to reach even further, by uploading them on popular media platforms.

Model

We built an ODE kinetics framework to model the mutualistic co-culture system of E.coli and S.cerevisiae we intended to use in our project, taking into account substrate utilization, product inhibitions and product formation involved in two species’ interactions. By recording the growth of the two engineered strains in co-culture and performing parameter sensitivity analyses, we were able to better interpret the behavior of the system. In addition, we have also devised a model to analyze the relationship between E.coli’s geraniol production level and the copy number of the plasmid containing the two key enzymes for production, GES and GPPS, under the stabilization of different transcription activator-like effectors stabilized promoters(TALEsp) from our promoter library, so as to choose the desired combination for optimal geraniol production. The model can also be applied to choosing TALEsp for other situations involving tuning expressions of genes or maximizing down-stream production stabilized by TALEsp.

Product Design

Free-roaming feral cats have posed a serious threat to public health and biodiversity. The current solution to manage feral cats called Trap&Neuter&Release often fail to control cats’ population due to the difficulties in capturing them. Aiming at the microbial production of nepetalactol, an ingredient in the cat-attracting plant catnip, we proposed the use of microorganism-derived nepetalactol for capturing feral cats and have devised a cat shelter, “Kitty Wonderland” as an implement tool of this idea. Through active communication with animal rescue NGOs, government, and hardware specialists, we optimised the design of Kitty Wonderland overtime, ensuring it’s safe and practical. Nonetheless, the cat shelter may be subjected to vandalism if our society didn’t realise the importance of respecting animals’ life and welfare. Thus, we employed public education as a complimentary component to the Kitty Wonderland.

Hardware

In order to solve the stray cats problem, we devise this hardware, the Kitty Wonderland, to provide homeless stray cats with shelters which could offer them a safe, comfortable and permanent living environment. Through the interviews and discussions we made with specialists, officials and residence, we improve our hardware to combine the merits of existing methods like Trap&Neuter&Release. The hardware assists volunteered caregivers by attracting stray cats and capturing them if necessary, so the difficulties and costs in tracking and taking care of stray cats are greatly reduced. Besides, we apply nepetalactol, which is the focus of our project, to our hardware to make it more effective in attracting cats and emphasize the significance of our project. Finally, our hardware can be easily deployed on various locations in the community where it stresses the stray cats problem to a broad population in an original approach.

Best Part Collection

We created a novel, well-characterized, and well-documented transcription-activator-like effector (TALE) stabilized promoter (TALEsp) collection as well as two parts enabling future teams to create more stabilized promoters. The TALEsp makes gene expression independent of copy number, maintaining a constant and constitutive expression level at any copy. They were cloned on vectors of different copy and were inserted to the genome to be characterized with not only green fluorescence but also with a metabolic engineering setting -- geraniol synthesis. Our results have proven the stabilization effect of the promoters. As building a synthetic biological system requires the correct proportion of each component, but in reality, the cellular environment is usually dynamic and complex, making the engineering process sometimes difficult, this promoter library provides a reliable tool which allows teams to construct predictable and robust synthetic systems.

Best New Basic Part

Please have a look on our favourite basic part: BBa_K2753003.

Best New Composite Part

Have a look on our favourite composite part: BBa_K2753018.

project summary

Project Summary

Mutation library generation is critical for biological and medical research, but current methods cannot mutate a specific sequence continuously without manual intervention. Here we present a toolbox for in vivo continuous mutation library construction. First, the target DNA is transcribed into RNA. Next, our reverse transcriptase reverts RNA into cDNA, during which the target is randomly mutated by enhanced error-prone reverse transcription. Finally, the mutated version replaces the original sequence through recombination. These steps will be carried out iteratively, generating a random mutation library of the target with high efficiency as mutations accumulate along with bacterial growth. Our toolbox is orthogonal and provides a wide range of applications among various species. R-Evolution could mutate coding sequences and regulatory sequences, which enables the in vivo evolution of individual proteins or multiple targets at a time, promotes high-throughput research, and serves as a foundational advance to synthetic biology.