Difference between revisions of "Team:Shanghaitech/Demonstrate"

 
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<h1>Our Project</h1>
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<h1>Demonstrate our work</h1>
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<h2>Huge Gap between the public &amp; synthetic biology</h2>
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<p>Public participation is a powerful booster for science advancement. The game, FoldIT, had encouraged thousands of people contribute to the structural biology research using their three-dimensional pattern matching and spatial-temporal reasoning ability. Folding@Home, another protein folding program based on public participation, had accumulated the computing efficiency that overrun all other super-computers during 2007-2012.</p>
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<p>This year, our project is focused on the distance between the public attention and the frontiers of Biology. We are committed to reducing the barriers for amateurs’ participation into the work related to biology, synthetic biology and biological designs, so that people who don’t have the background of biological researching could fulfill their creative ideas and take participation into the innovative work related to biology, through which we could make a little contribution to the promotion of the development of synthetic biology and the overall biology.</p>
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<p>We image a future of synthetic biology like
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<p><strong>To fulfill the perspectives above, we build a comprehensive platform named MAGICBLOCK, consisting of an interactive software interface, bacteria and hardware. Furthermore, our integrated human practice constitutively guides our project in many ways:</strong></p>
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this, when people in different field can contribute their intelligence to
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advance synthetic biology. However, it is not easy for non-biologists to start
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working on gene blocks since it requires a complex understanding of molecular
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cloning, sufficient biosafety training as well as an actual lab. In this
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project, we tried to build a public platform for synthetic biology with two
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attempts. </p>
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<p>First, we simplified the “block” concept to the public.Instead of using gene blocks, we consider a group of functionally definedbacteria as a “block”. Quorum sensing (QS) system in synthetic biology is greatexamples to show that bacteria cells can communicate to achieve differentfunction. Thus, we use QS system as the executioners to achieve synthetic aim inour project.</p>
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<p> </p>
 
<p> </p>
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<p>Secondly, we built an interactive platform that combinessoftware control with an automatic liquid handling system. With this platform,most people, even elementary school students, can design their syntheticbiology experiment online and have the robot perform their experiments. </p>
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<p><img src=https://static.igem.org/mediawiki/2017/0/0b/T--Shanghaitech--Home-Homepage-story.png
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<h2>Pack the difficulties in the box: how can our project narrow the gap</h2>
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' alt='img' /></p>
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<p>We aim to build a platform named MagicBlock,
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<p> </p>
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consisting of an interactive software interface, bacteria and robots. Designers
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<ol start='' >
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can use the software interface to design gene circuits of a bio-product. Several
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<h2>1. Hardware</h2>
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MagicBlocks, the bacteria, are cultured according to the gene circuits
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retrieved from the cloud server and these blocks are interacted by liquid
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handling robot for supernatant transfer. </p>
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<h2>What’s Lux-like Quorum Sensing system?</h2>
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</ol>
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<p>In Gram Negative bacteria, Acyl Homoserine Lactones (AHLs) are used to communicate among their community. A family of AHL-synthetases keep synthesize AHLs in a relative low level. When the bacteria population increases and the synthesized AHLs reach a critical concentration, AHLs bind and induce the dimerization of LuxR-like receiver proteins, which in turn allow the protein to bind specific promoters to initiate gene expression. We&#39;ve used this feature of communicating between bacteria to connect our MagicBlocks together.</p>
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<p>We’ve established a platform consist of a hardware for block assembly and software for the public to operate it. We’ve made a special tube to catch pure chemical signal liquid from bacterium culture solutions. By reconfiguring a 3D printer and plus a syringe pump, we can control the transfer of chemical signals among tubes of functional bacteria. With this robot, we’ve realized the assembly of modular bio-systems. It can be easily programmed to significantly reduce the laboratory and time cost during molecular cloning. As a prototype of cloud bio-lab, this robot is able to be controlled remotely. For the public’s friendly usage, this robot can automatically assemble the blocks only base on the logic rules set according to an idea. </p>
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<p>Details: <a href='https://2017.igem.org/Team:Shanghaitech/Hardware'>https://2017.igem.org/Team:Shanghaitech/Hardware</a></p>
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<p> </p>
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<ol start='2' >
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<h2>2. Software</h2>
  
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<h2>&quot;Primary Bio-Blocks&quot; are Bio-Blocks containing single quorum sensing system.</h2>
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</ol>
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<p>We&#39;ve named simple Bio-Blocks containing only one quorumsensing system &quot;Primary Bio-Blocks&quot;. These simple bio-blocks are mainly used as input/output (I/O) units, response to physical or chemicalstimulations, send input signals to the whole MagicBlock system, or express highlevel of a reporter protein as the output.</p>
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<p>* we established a simple database. The users can submit their parts, add descriptions, retrieve and comment on others’ parts.</p>
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<p>We generated a collection of these bacteria sensors andreporters. Since they are sharing the similar design, one can easily switchbetween these bio-blocks to change the function for different purpose.</p>
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<p>* we wrote a Python crawler which can crawl the relevant parts information on the iGEM website.</p>
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<p>To validate thefunction of these primary bio-blocks, experimental tests have been combinedwith mathematic modeling to better characterize each QS system.</p>
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<p>* we designed and improved a circuit game. The users can retrieve parts and use them to design their own synthetic genetic circuits, through an intuitive graphical user interface.</p>
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<p>* user’s design will be passed to our 3D printing program to automatically perform the experiments to realize the circuit.</p>
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<p>* the users will get theexperimental data feedback.</p>
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<p>Details: <a href='https://2017.igem.org/Team:Shanghaitech/Software' target='_blank' >https://2017.igem.org/Team:Shanghaitech/Software</a></p>
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<p> </p>
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<ol start='3' >
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<h2>3. Wet lab </h2>
  
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<h2>&quot;Advanced Bio-Blocks&quot; are Bio-Blocks containing more than one quorum sensing systems.</h2>
 
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<p>"Advanced Bio-Blocks" refer to bio-blockscontaining more than one quorum sensing systems. Applying multiple quorumsensing systems is not a straightforward thing. We've examined the cross-talkbetween AHLs and their receiver proteins.  Las quorum sensing system from Pseudomonas aeruginosa and Rpa systemfrom Rhodopseudomonas palustris demonstratedgreat orthogonal function in our experiments, thus we used them to construct theadvanced bio-blocks.</p>
 
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<p>Mainly used as the intermediatelayers carrying out logic processing, the Advanced Bio-Blocks often produce onekind of AHLs in response to another. However, it is hard to measure the actuallevel of each AHL. We have generated an indirect method to determine theefficiency of Advanced Bio-Blocks by mathematic modelling.</p>
 
  
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<h2>Dynamical model of a typical bio-block</h2>
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</ol>
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<h3>Indicate the main factor affecting the growth of E.coli from both theoretical simulation and experiment.</h3>
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<p>*We&#39;ve constructed six Quorum sensing fluorescent receivers with its cognate promoter. Besides, 22 vectors of Quorum sensing receivers and non-cognate promotor are built for testing of receiver protein -- promotor orthogonality.</p>
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<p>*We&#39;ve conducted AHLs to Receiverorthogonality test for LasR and RpaR.</p>
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<p>*We&#39;ve conducted the AHL induced Fluorescent expression experiment for LasR-GFP, RhlR-GFP and RpaR-GFP.</p>
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<p>*We&#39;ve characterized the AHL production of RpaR-LasI and pCon-LasI</p>
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<p>*We&#39;ve modeled expression efficiency &amp; speed to characterized parameters for hardware experiment and AHLs&#39; effect on bacteria population and compared these model with experimental data, refined the model from experimental data and guided following experiment.</p>
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<p>Details:</p>
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<p> <a href='https://2017.igem.org/Team:Shanghaitech/Parts' target='_blank' >https://2017.igem.org/Team:Shanghaitech/Parts</a></p>
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<p><a href='http://parts.igem.org/Part:BBa_K2315046' target='_blank' >http://parts.igem.org/Part:BBa_K2315046</a></p>
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<p><a href='http://parts.igem.org/Part:BBa_K2315034' target='_blank' >http://parts.igem.org/Part:BBa_K2315034</a></p>
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<p><a href='http://parts.igem.org/Part:BBa_K2315033' target='_blank' >http://parts.igem.org/Part:BBa_K2315033</a></p>
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<p><a href='http://parts.igem.org/Part:BBa_C0179' target='_blank' >http://parts.igem.org/Part:BBa_C0179</a></p>
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<p><a href='http://parts.igem.org/Part:BBa_C0178' target='_blank' >http://parts.igem.org/Part:BBa_C0178</a></p>
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<p><a href='https://2017.igem.org/Team:Shanghaitech/Model' target='_blank' >https://2017.igem.org/Team:Shanghaitech/Model</a></p>
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<p><a href='https://2017.igem.org/Team:Shanghaitech/Experiment_and_Modeling' target='_blank' >https://2017.igem.org/Team:Shanghaitech/Experiment_and_Modeling</a></p>
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<p> </p>
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<p> </p>
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<ol start='4' >
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<h2>4. Model</h2>
  
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<h2>Automated devices helps to realize bio-block concept.</h2>
 
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<p> Figure: How the whole system works?</p>
 
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<p>Automated devices are used to transfer culture supernatant and connect different MagicBlocks together. Users could design genetic circuits through our software with easy to use user interface, then their design will automatically be translated as machine code controlling the robotic liquid handling system, transferring supernatant between bacteria cultures and connecting bio-blocks. </p>
 
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<h3>Hardware</h3>
 
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<p>Common liquid handling robots are far too expensive for a project aiming at public engagement. We&#39;ve built a Low-cost Robotic Liquid handling system to assemble our MagicBlocks. For a cost of only $150, our improvise liquid handling robot had been proved competent to complete the task of assembling Bio-Blocks. </p>
 
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<p> Figure: Low-cost Robotic liquid handling system.</p>
 
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<h3>Software</h3>
 
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<p>Our controlling software is one of the essential parts to allow people to design a synthetic gene circuit. We&#39;ve created an user-friendly software for this purpose. Anyone could use it to assemble MagicBlocks with the function of their desire, but no need for any wet-lab training.</p>
 
  
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<h2>HP</h2>
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</ol>
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<p>In the Human Practice part, we found the problem,designed a product, tested it and received evaluation.</p>
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<p>*Our Models helps to explain the phenomenon in experiments.</p>
 +
<p>*Measuring working efficiency of Bioblocks.</p>
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<p>*Predicting best working parameters for Bioblocks.</p>
 +
<p>*Modeling bacteria population inside a MagicBlock.</p>
 +
<p>Details: <a href='https://2017.igem.org/Team:Shanghaitech/Model' target='_blank' >https://2017.igem.org/Team:Shanghaitech/Model</a></p>
 +
<p> </p>
 +
<p> </p>
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<ol start='5' >
  
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<p>After interviewing people at different ages and withdifferent occupations, we encountered many person with fascinating ideas, yethave little biological knowledge or lab experience. Hence we inventedMagicBlock, an integrated platform for users to design and modify theirbio-product simply by programming. The public were invited to the workshops,where they were guided to use MagicBlock to design their own bio-products andcreated various thought-provoking designs. We got feedback and improved theMagicBlock accordingly. In the end, it is rewarding to find out that ourMagicBlock can really inspire people’s creativity and help them to realize it.</p>
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<h2>5. Human Practice</h2>
  
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<p>We’ve also got experts’ opinions by interviewing, seeking advices on building the MagicBlockas well as the related mathematic modeling.</p>
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</ol>
−
</div></div></div>
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<p>This year, our project focused on the distance between the public attention and the frontiers of Biology. We are committed to reducing the barriers for amateurs’ participation into the work related to biology, synthetic biology and biological designs, so that people who don’t have the background of biological researching could fulfill their creative ideas and take participation into the innovative work related to biology, through which we could make a little contribution to the promotion of the development of synthetic biology and the overall biology.</p>
 +
<p>To fulfill the perspectives above, we build a comprehensive platform named MAGICBLOCK, consisting of an interactive software interface, bacteria and hardware. </p>
 +
<p>Furthermore, our integrated human practice constitutively guides our project in various ways:</p>
 +
<p>From one hand, inspired by the creativity and enthusiasm of non-biologists through interviews and questionnaires, we have found that many people are very enthusiastic and imaginative about bio-designs, yet have little knowledge in synthetic biology and little lab experience. </p>
 +
<p>
 +
<a href='https://2017.igem.org/Team:Shanghaitech/Background' target='_blank' >https://2017.igem.org/Team:Shanghaitech/Background</a></p>
 +
<p>During the invention of MagicBlock, we maintain contact with the public, to test MagicBlock as well as receiving suggestions. we held two workshops, guiding participants to use MagicBlock to design their own bio-products. We received various thought-provoking designs using MagicBlock elements, such as water pollution alarm, synthetic music, and bacteria painting panel .et al, all originated from non-biologists. </p>
 +
<p><a href='https://2017.igem.org/Team:Shanghaitech/Workshop' target='_blank' >https://2017.igem.org/Team:Shanghaitech/Workshop</a></p>
 +
<p>During this practice, we received valuable suggestions to improve MagicBlock . <a href='https://2017.igem.org/Team:Shanghaitech/Feedback' target='_blank' >https://2017.igem.org/Team:Shanghaitech/Feedback</a></p>
 +
<p>From the other hand, Professional Insights we’ve received by professors, provide guidelines for our follow-up works including human practice, hardware and software design, and modeling.</p>
 +
<p><a href='https://2017.igem.org/Team:Shanghaitech/ScientificInsights' target='_blank' >https://2017.igem.org/Team:Shanghaitech/ScientificInsights</a></p>
 +
</div>
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Latest revision as of 01:46, 2 November 2017

Demonstrate our work

This year, our project is focused on the distance between the public attention and the frontiers of Biology. We are committed to reducing the barriers for amateurs’ participation into the work related to biology, synthetic biology and biological designs, so that people who don’t have the background of biological researching could fulfill their creative ideas and take participation into the innovative work related to biology, through which we could make a little contribution to the promotion of the development of synthetic biology and the overall biology.

To fulfill the perspectives above, we build a comprehensive platform named MAGICBLOCK, consisting of an interactive software interface, bacteria and hardware. Furthermore, our integrated human practice constitutively guides our project in many ways:

img

    1. Hardware

We’ve established a platform consist of a hardware for block assembly and software for the public to operate it. We’ve made a special tube to catch pure chemical signal liquid from bacterium culture solutions. By reconfiguring a 3D printer and plus a syringe pump, we can control the transfer of chemical signals among tubes of functional bacteria. With this robot, we’ve realized the assembly of modular bio-systems. It can be easily programmed to significantly reduce the laboratory and time cost during molecular cloning. As a prototype of cloud bio-lab, this robot is able to be controlled remotely. For the public’s friendly usage, this robot can automatically assemble the blocks only base on the logic rules set according to an idea.

Details: https://2017.igem.org/Team:Shanghaitech/Hardware

    2. Software

* we established a simple database. The users can submit their parts, add descriptions, retrieve and comment on others’ parts.

* we wrote a Python crawler which can crawl the relevant parts information on the iGEM website.

* we designed and improved a circuit game. The users can retrieve parts and use them to design their own synthetic genetic circuits, through an intuitive graphical user interface.

* user’s design will be passed to our 3D printing program to automatically perform the experiments to realize the circuit.

* the users will get theexperimental data feedback.

Details: https://2017.igem.org/Team:Shanghaitech/Software

    3. Wet lab

*We've constructed six Quorum sensing fluorescent receivers with its cognate promoter. Besides, 22 vectors of Quorum sensing receivers and non-cognate promotor are built for testing of receiver protein -- promotor orthogonality.

*We've conducted AHLs to Receiverorthogonality test for LasR and RpaR.

*We've conducted the AHL induced Fluorescent expression experiment for LasR-GFP, RhlR-GFP and RpaR-GFP.

*We've characterized the AHL production of RpaR-LasI and pCon-LasI

*We've modeled expression efficiency & speed to characterized parameters for hardware experiment and AHLs' effect on bacteria population and compared these model with experimental data, refined the model from experimental data and guided following experiment.

Details:

https://2017.igem.org/Team:Shanghaitech/Parts

http://parts.igem.org/Part:BBa_K2315046

http://parts.igem.org/Part:BBa_K2315034

http://parts.igem.org/Part:BBa_K2315033

http://parts.igem.org/Part:BBa_C0179

http://parts.igem.org/Part:BBa_C0178

https://2017.igem.org/Team:Shanghaitech/Model

https://2017.igem.org/Team:Shanghaitech/Experiment_and_Modeling

    4. Model

*Our Models helps to explain the phenomenon in experiments.

*Measuring working efficiency of Bioblocks.

*Predicting best working parameters for Bioblocks.

*Modeling bacteria population inside a MagicBlock.

Details: https://2017.igem.org/Team:Shanghaitech/Model

    5. Human Practice

This year, our project focused on the distance between the public attention and the frontiers of Biology. We are committed to reducing the barriers for amateurs’ participation into the work related to biology, synthetic biology and biological designs, so that people who don’t have the background of biological researching could fulfill their creative ideas and take participation into the innovative work related to biology, through which we could make a little contribution to the promotion of the development of synthetic biology and the overall biology.

To fulfill the perspectives above, we build a comprehensive platform named MAGICBLOCK, consisting of an interactive software interface, bacteria and hardware.

Furthermore, our integrated human practice constitutively guides our project in various ways:

From one hand, inspired by the creativity and enthusiasm of non-biologists through interviews and questionnaires, we have found that many people are very enthusiastic and imaginative about bio-designs, yet have little knowledge in synthetic biology and little lab experience.

https://2017.igem.org/Team:Shanghaitech/Background

During the invention of MagicBlock, we maintain contact with the public, to test MagicBlock as well as receiving suggestions. we held two workshops, guiding participants to use MagicBlock to design their own bio-products. We received various thought-provoking designs using MagicBlock elements, such as water pollution alarm, synthetic music, and bacteria painting panel .et al, all originated from non-biologists.

https://2017.igem.org/Team:Shanghaitech/Workshop

During this practice, we received valuable suggestions to improve MagicBlock . https://2017.igem.org/Team:Shanghaitech/Feedback

From the other hand, Professional Insights we’ve received by professors, provide guidelines for our follow-up works including human practice, hardware and software design, and modeling.

https://2017.igem.org/Team:Shanghaitech/ScientificInsights