Difference between revisions of "Team:RDFZ-China/Achievement"

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                        <li><a href="#section1">What are we facing?</a></li>
 
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                        <li><a href="#section2">Predecessors</a></li>
 
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                        <li><a href="#section3">Project Xscape</a></li>
 
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                        <li><a href="#section4">For Fermentation</a></li>
 
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                        <li><a href="#section5">For Therapy</a></li>
 
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                        <li><a href="#section6">Metabolic Stress</a></li>
 
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                        <li><a href="#section7">DIY Bio and Biosafety</a></li>
 
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                        <li><a href="#section8">Community and Future</a></li>
 
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            <h1>Achievements</h1>
 
             <div class="topic-title" id="section1">
 
             <div class="topic-title" id="section1">
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                 <h3>What are we facing?</h3>
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                 <p>We are qualified for iGEM Bronze medal for:</p>
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                 <p>Biosafety has always been the major concern to the public, to the companies and the researchers. Doubts and worries raised just as genetic technology was invented. With the rapidly growing of synthetic biology and iGEM community, more and more synthetic biology products are built with the widely distributed DNA toolkits or the inexpensive DNA synthesis service(Synthetic and Will); we are facing unprecedented biosafety issue that unwanted leakage of synthetic biology products to the environment may cause an unexpected but definitely disastrous problem. </p>
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                 <div class="cite">
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            </div>
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                    <p>Having registered for iGEM, have a great iGEM season, and attend the Giant Jamboree;</p>
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            <div class="topic-title" id="section2">
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                    <p>Having Completed the deliverables: Wiki, Poster, Presentation, Judging form and attributions;</p>
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                <h3>Predecessors</h3>
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                    <p>Having successfully participated in the 2018 InterLab Study;</p>
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                <p>For decades, researchers were striving to build biosafety devices through auxotrophy or external inducive kill switches(Lee et al.), holins and restriction enzymes are most commonly used. Most of the failures of the previous devices were caused by mutation and evolution of immune(Moe-Behrens et al.) . </p>
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                    <p>And having characterized a part: BBa_K2447011.</p>
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                <p>The two major threats of engineered microbes’ leakage are the possible Horizontal Gene Transfer which will lead to the spread of recombinant DNA to the entire ecosystem, or the engineered bacteria could contaminate or overrun the natural habitat.(Wright et al.)</p>
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                </div>
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            </div>
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                <p>We are qualified for iGEM Silver medal for:</p>
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            <div class="topic-title" id="section3">
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                <div class="cite">
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                <h3>Project Xscape</h3>
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                    <p>Having validated the parts BBa_K2572001, BBa_K2572016, BBa_K2572032;</p>
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                 <p>Under this circumstance, this year we decided to be a fundamentalist to synthetic biology, by using genetic circuits and logic gates, to establish biosafety devices which can apply to the real-world situation.</p>
+
                    <p>Having collaborated with Tsinghua, SJTU-BioX-Shanghai, Greatbay-China, BFSUICC and Nanjing NFLS iGEM teams;</p>
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                 <p>Since cell death and lysis mean there is a continual presence of free DNA in the environment, holins, which are most widely used are excluded from our choices, and colicin E2 nucleases (Darmstadt iGEM2016) came into our site. We choose site non-specific nucleases since the entire genome and plasmids needed to be entirely digested to prevent the spread, and we use nucleases from a different family to prevent the possible evolution of nuclease inhibitors. Artificial DNA, RNA, and amino acids are a good solution, but due to its high cost so far, it is not applicable to most of the user.</p>
+
                    <p>And having done a Human Practices program.</p>
 +
                </div>
 +
                <p>We are qualified for iGEM Gold medal for:</p>
 +
                <div class="cite">
 +
                    <p>Having done an Integrated human practices program centred on biosafety;</p>
 +
                    <p>Having improved a previous part: BBa_K2447012;</p>
 +
                    <p>Having constructed a new part: BBa_K2572000;</p>
 +
                    <p>And having demonstrated our work in realistics conditions.</p>
 +
                </div>
 +
                 <p>Also, we have applied for a few special prizes:</p>
 +
                <p>We are striving to do the best integrated human practices program for our human practice works centred around the topic of biosafety. We investigated the current state of the rather obscure biohacker community, its self-regulations, the various laws about the distribution and import of biological products, and the actual situations on the purchase and sale of dangerous biological products in China. We concluded that there exist substantial security risk associated with them, confirmed by our interview with the station director of the centre of disease control and prevention, who opines that the outflow of biological agents can be hugely destructive to ecosystems. We proposed that beyond legal solutions, culture should also be emphasized in addressing the risks aforementioned, yet at the foremost this is the reason for our project on preventing the leakage of bacteria. We also conducted interviews with a chief engineer of Bluepha company about these problems, and found that our project has great prospects for further development;</p>
 +
                 <p>We are striving to do the best of education and public engagement for our iGEM team originated from our school's synthetic biology club, and we used the club as a base for our works of public engagement. We focused on the community development, and we held a biosafety panel session in a high school iGEM meet up, in which we had former iGEMers, current iGEMer who was running the lab and lab manager from a university lab, to discuss how to propagate biosafety considerations into the existing Chinese Synbio community. Also, we gathered Biology Olympians from all over China, to discuss the future of high school academic communities. We had always believed in that the solution to all kinds of complicated circumstances, such as biosafety threat to the society, has to be the cultivation of academic and safety cultures to the public, and such farming has to start from ourselves, the iGEMers, striving to be the conscientious members of the current community;</p>
 +
                <p>We are striving to do the best modelling works for We proposed a deterministic ordinary differential equation set, which is sufficient to describe the quorum sensing regulation of a bacteria population. By using numerical methods to simultaneously solve these three concise and easily comprehensible modelling equations, we have successfully derived at a concentration interval for the amount of extracellular acyl homoserine lactone required in the fermenter in order to maintain a high enough concentration of PhlF protein to suppress the expression of nuclease and maintain the survival of engineered bacteria both at the start of and during the fermentation process. The result from Matlab simulation,1E-10M [AHL] corresponds well with that from wet lab experiments,1E-9M [AHL]. Using the experimental data, we adjusted the model, concluded that the difference might be the effect of plasmid copy number. We will improve the model according to the data, and come out with an acceptable concentration range. This information would be handy for workers at the fermentation industry to ensure their biosafety-directed bacteria to always survive inside the fermenter;</p>
 +
                <p> We are striving to do the best measurement for by using a capacity monitor described by a nature article, which is a constantly expressed GFP in the genome, we can characterize the resource consumption by heterologous gene constructs, through the changes in GFP production in the genome comparing to the ones without heterologous protein expressed. We characterized several devices reported to be high resource consuming, which provides other users to consider their resource occupation quantitatively, and improve the future devices' orthogonality and robustness;</p>
 +
                <p>And we are striving to develop the best software tool for we built this Xscape calculator for them to calculate the AHL needed for the very beginning of the fermentation according to the model we constructed for the fermentation technicians. Using this calculator,only simple parameters are required to be imputed and the technicians can add AHL, with the dilution factor already been calculated by the Xscape software.</p>
  
 
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            <div class="topic-title" id="section4">
 
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                <h3>For fermentation</h3>
 
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                <p>The first device we build is for the fermentation; we want to execute the escaped engineered bacteria from the fermenter, accidentally or intentionally. We used two environment factors to monitor the bacteria’s situation: temperature and population density, they are both high and tunable in the fermenter. So, the device will initiate when temperature and density are both low. We used thermal sensitive regulator (NUS iGEM2017)(Piraner et al.) and quorum sensing regulator (MIT iGEM2004) (Canton et al.)as our sensor, sRNA(Storz et al.) and tetR family repressor PhlF(Glasgow iGEM2015)(Stanton et al.) as the signal inverter. We add intergrase (Peking iGEM2017) controlled by the thermal sensitive regulator, which will turn the promoter of a lethal gene when temperature rise in the fermenter so that bacteria can survive at the very beginning. Also, we build a model to stimulate the minimum autoinducer required at the beginning of the fermentation, same as the purpose of integrase. This model is for keeping bacteria alive at the very beginning of fermentation. Together they form a NOR gate which will lead to cell death through genome degradation when temperature and density decrease.</p>
 
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            <div class="topic-title" id="section5">
 
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                <h3>For Therapy</h3>
 
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                <p>The second device we build is for therapeutic bacteria, the device can carry out noninvasive tracing through ultrasound imaging of the gas vesicle(Shapiro et al.), release the drug (from SHSBNU 2017) controlled by a thermal sensitive regulator at nidus by ultrasound tissue heating, and heat to a higher temperature to release nuclease and kill the bacteria after it finishes its mission. </p>
 
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            <div class="topic-title" id="section6">
 
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                <h3>For Metabolic Stress</h3>
 
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                <p>We applied capacity monitor (Ceroni et al.) to quantify the expression burden of all our systems, and to reduce the metabolic stress, we designed another device for fermentation which used a LuxR repressive promoter (Peking iGEM2011) and cold-regulated 5’UTR region (Ionis Paris 2017). This device only involves one transcriptional regulator, which will be less energy consuming. </p>
 
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            <div class="topic-title" id="section7">
 
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                <h3>DIY bio and Biosafey</h3>
 
−
                <p>Back to the growing and glowing synthetic biology community, despite the ones doing it on campus, more and more people are starting it at home, they call themselves Genehacker or DIY biologists. The lack of sufficient training and efficient surveillance will be a time bomb which we do know there will be a monstrous harmful bioproduct will be made someday in the future, and indeed, it will be a significant threat to the current biosafety basis. Recall our memory to iGEM2009, Peking surveyed DIY bio, almost ten years later, we conducted a similar DIY bio-survey again. We tried to order materials for molecular experiments, using the delivery address to our home, the result was quite shocking that we can buy almost everything for the molecular experiment, from the internet. Then, we went through relevant laws and regulations throughout the world, which we found out that there are no laws related to the credit certification and the address certification about the people who book the biology reagent. Most of the laws are about the quality certification and how they would serve the user after they bought this. We interviewed the Director of the center for disease control and prevention. He said that within his experiment with the disease caused by the Bacteria leak, environmental pollution, the vast impact had been caused. Our country has been making all effort which is the highest effort that we have made in the history. He said it is not easy to solve the problem with hard work, it needs the cooperation between all the countries. He made an example of 731 army during the second world war two, the outbreak of pathogens can cause significant social harm. We are still on our way to win the battle, but the effort still needs to be put in.</p>
 
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                <h3>Community and Future</h3>
 
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                <p>Also, we hosted two major meeting in Beijing, a Biosafety Forum in October, we invited team leader who runs his high school lab, lab teacher from a university lab, and a former team member from Peking iGEM2009, who participated in that DIY bio investigation ten years ago.</p>
 
−
                <p>We concluded that the development of DIY bio should be taken seriously, and the permanent way to solve it is through implanting Biosafety awareness into our academic culture. Also, as iGEMer, we should strive to be the considerable and responsible leaders in our community, to ensure the biosafety issue has been taken properly. Another meeting was with biology Olympians all around China, we discussed the future of biology community during the meeting, especially with more and more high school iGEM teams coming up in China, but lack of relevant instruction and education to the students. We came up with the idea of setting up a collaboration between school to share and overcome difficulties hand in hand. This kind of meeting will be continued after iGEM2018, since the community usually grows fast after every iGEM season. </p>
 
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                <p>Hopefully, years later, biosafety awareness and considerations can be seriously taken in communities, laboratory studies, and real-world applications.</p>
 
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                <h3>References</h3>
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                <p>Canton, Barry, et al. “Refinement and Standardization of Synthetic Biological Parts and Devices.” Nature Biotechnology, vol. 26, no. 7, 2008, pp. 787–93, doi:10.1038/nbt1413.</p>
+
−
                <p>Ceroni, Francesca, et al. “Quantifying Cellular Capacity Identifies Gene Expression Designs with Reduced Burden.” Nature Methods, vol. 12, no. 5, 2015, pp. 415–18, doi:10.1038/nmeth.3339.</p>
+
−
                <p>Lee, Jeong Wook, et al. “Next-Generation Biocontainment Systems for Engineered Organisms.” Nature Chemical Biology, Springer US, 2018, p. 1, doi:10.1038/s41589-018-0056-x.</p>
+
−
                <p>Moe-Behrens, Gerd H. G., et al. “Preparing Synthetic Biology for the World.” Frontiers in Microbiology, vol. 4, no. JAN, 2013, pp. 1–10, doi:10.3389/fmicb.2013.00005.</p>
+
−
                <p>Piraner, Dan I., et al. “Tunable Thermal Bioswitches for in Vivo Control of Microbial Therapeutics.” Food, Pharmaceutical and Bioengineering Division 2017 - Core Programming Area at the 2017 AIChE Annual Meeting, vol. 2, no. November, Nature Publishing Group, 2017, pp. 695–702, doi:10.1038/nchembio.2233.</p>
+
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                <p>Shapiro, Mikhail G., et al. “Biogenic Gas Nanostructures as Ultrasonic Molecular Reporters.” Nature Nanotechnology, vol. 9, no. 4, Nature Publishing Group, 2014, pp. 311–16, doi:10.1038/nnano.2014.32.</p>
+
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                <p>Stanton, Brynne C., et al. “Genomic Mining of Prokaryotic Repressors for Orthogonal Logic Gates.” Nature Chemical Biology, vol. 10, no. 2, 2014, pp. 99–105, doi:10.1038/nchembio.1411.</p>
+
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                <p>Storz, Gisela, et al. “Regulation by Small RNAs in Bacteria: Expanding Frontiers.” Molecular Cell, vol. 43, no. 6, 2011, pp. 880–91, doi:10.1016/j.molcel.2011.08.022.</p>
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                <p>Synthetic, How, and Biology Will. “Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves.” Choice Reviews Online, 2013, doi:10.5860/CHOICE.50-3835.</p>
+
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                <p>Wright, Oliver, et al. “Building-in Biosafety for Synthetic Biology.” Microbiology (United Kingdom), vol. 159, no. PART7, 2013, pp. 1021–35, doi:10.1099/mic.0.066308-0.</p>
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Revision as of 02:38, 18 October 2018

Achievements

We are qualified for iGEM Bronze medal for:

Having registered for iGEM, have a great iGEM season, and attend the Giant Jamboree;

Having Completed the deliverables: Wiki, Poster, Presentation, Judging form and attributions;

Having successfully participated in the 2018 InterLab Study;

And having characterized a part: BBa_K2447011.

We are qualified for iGEM Silver medal for:

Having validated the parts BBa_K2572001, BBa_K2572016, BBa_K2572032;

Having collaborated with Tsinghua, SJTU-BioX-Shanghai, Greatbay-China, BFSUICC and Nanjing NFLS iGEM teams;

And having done a Human Practices program.

We are qualified for iGEM Gold medal for:

Having done an Integrated human practices program centred on biosafety;

Having improved a previous part: BBa_K2447012;

Having constructed a new part: BBa_K2572000;

And having demonstrated our work in realistics conditions.

Also, we have applied for a few special prizes:

We are striving to do the best integrated human practices program for our human practice works centred around the topic of biosafety. We investigated the current state of the rather obscure biohacker community, its self-regulations, the various laws about the distribution and import of biological products, and the actual situations on the purchase and sale of dangerous biological products in China. We concluded that there exist substantial security risk associated with them, confirmed by our interview with the station director of the centre of disease control and prevention, who opines that the outflow of biological agents can be hugely destructive to ecosystems. We proposed that beyond legal solutions, culture should also be emphasized in addressing the risks aforementioned, yet at the foremost this is the reason for our project on preventing the leakage of bacteria. We also conducted interviews with a chief engineer of Bluepha company about these problems, and found that our project has great prospects for further development;

We are striving to do the best of education and public engagement for our iGEM team originated from our school's synthetic biology club, and we used the club as a base for our works of public engagement. We focused on the community development, and we held a biosafety panel session in a high school iGEM meet up, in which we had former iGEMers, current iGEMer who was running the lab and lab manager from a university lab, to discuss how to propagate biosafety considerations into the existing Chinese Synbio community. Also, we gathered Biology Olympians from all over China, to discuss the future of high school academic communities. We had always believed in that the solution to all kinds of complicated circumstances, such as biosafety threat to the society, has to be the cultivation of academic and safety cultures to the public, and such farming has to start from ourselves, the iGEMers, striving to be the conscientious members of the current community;

We are striving to do the best modelling works for We proposed a deterministic ordinary differential equation set, which is sufficient to describe the quorum sensing regulation of a bacteria population. By using numerical methods to simultaneously solve these three concise and easily comprehensible modelling equations, we have successfully derived at a concentration interval for the amount of extracellular acyl homoserine lactone required in the fermenter in order to maintain a high enough concentration of PhlF protein to suppress the expression of nuclease and maintain the survival of engineered bacteria both at the start of and during the fermentation process. The result from Matlab simulation,1E-10M [AHL] corresponds well with that from wet lab experiments,1E-9M [AHL]. Using the experimental data, we adjusted the model, concluded that the difference might be the effect of plasmid copy number. We will improve the model according to the data, and come out with an acceptable concentration range. This information would be handy for workers at the fermentation industry to ensure their biosafety-directed bacteria to always survive inside the fermenter;

We are striving to do the best measurement for by using a capacity monitor described by a nature article, which is a constantly expressed GFP in the genome, we can characterize the resource consumption by heterologous gene constructs, through the changes in GFP production in the genome comparing to the ones without heterologous protein expressed. We characterized several devices reported to be high resource consuming, which provides other users to consider their resource occupation quantitatively, and improve the future devices' orthogonality and robustness;

And we are striving to develop the best software tool for we built this Xscape calculator for them to calculate the AHL needed for the very beginning of the fermentation according to the model we constructed for the fermentation technicians. Using this calculator,only simple parameters are required to be imputed and the technicians can add AHL, with the dilution factor already been calculated by the Xscape software.

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