http://2012.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=50&target=Aprastowo2012.igem.org - User contributions [en]2024-03-29T12:06:45ZFrom 2012.igem.orgMediaWiki 1.16.0http://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-11-09T19:20:51Z<p>Aprastowo: </p>
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<div style="position:absolute;left:15px;top:255px;z-index:100"><img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width="50"> <sub>This sign indicating new results after the European Jamboree.</sub></div><br />
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<div id="grouptitle">How Safe is Safe Enough?</div><br />
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Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
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<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
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<img src=https://static.igem.org/mediawiki/2012/e/e0/ParisB_Medal.gif width=15><sub><b>World Championship 2nd Runner Up</b></sub> <br> <br><br />
<img src=https://static.igem.org/mediawiki/2012/e/e0/ParisB_Medal.gif width=15><sub><b>World Championship Best Environment Project</b></sub> <br> <br><br />
<img src=https://static.igem.org/mediawiki/2012/e/e0/ParisB_Medal.gif width=15><sub>European Jamboree Gold Medal</sub> <br> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/e/e0/ParisB_Medal.gif width=15><sub>European Jamboree Safety Commendation</sub><br />
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<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
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<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
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<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
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<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
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<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
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<h3>Quick Links</h3><br />
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<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
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{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-11-09T19:20:17Z<p>Aprastowo: </p>
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<div style="position:absolute;left:15px;top:255px;z-index:100"><img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width="50"> <sub>This sign indicating new results after the European Jamboree.</sub></div><br />
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<div class="box"><br />
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<div id="grouptitle">How Safe is Safe Enough?</div><br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
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<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
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<img src=https://static.igem.org/mediawiki/2012/e/e0/ParisB_Medal.gif width=15><sub><b>World Championship 2nd Runner Up</b></sub> <br> <br><br />
<img src=https://static.igem.org/mediawiki/2012/e/e0/ParisB_Medal.gif width=15><sub><b>World Championship Best Environment Project</b></sub> <br> <br><br />
<img src=https://static.igem.org/mediawiki/2012/e/e0/ParisB_Medal.gif width=15><sub>European Jamboree Gold Medal</sub> <br> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/e/e0/ParisB_Medal.gif width=15><sub>European Jamboree Safety Commendation</sub><br />
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<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
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<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
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<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
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<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
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<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
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{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/TeamTeam:Paris Bettencourt/Team2012-11-09T18:56:27Z<p>Aprastowo: /* Who we are */</p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
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<div id="grouptitle">Team </div><br />
<br />
== Who we are ==<br />
<br />
<center>Before iGEM<br><br />
[[Image:Paristeam.jpg|500px]]</center><br><br />
<br />
<center>After iGEM<br />
[[Image:ParisB_finalist.jpg |500px]]<br><br />
<sub> official iGEM picture by Justin Knight </sub><br />
</center><br><br />
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===Undergrads:===<br />
<br />
====Jean Cury====<br />
[[Image:Jean.png|thumb|left|100px]]'''1st year master student in Biology at the ENS Paris and UPMC, Paris 6''' <br> <br />
My current internship is about studying a synthetic recombination site of the integron system, at Pasteur Institute, Paris. This gives me a good insight into synthetic biology, and motivates me to participate in iGEM.<br />
What attracts me also in doing iGEM is the interdisciplinary team, the team reflexion, and everything about creating a team, organizing it, learning from other fields represented. Indeed, I truly believe that learning from your friends is a good way to improve your knowledge and satisfy your curiosity.<br />
In addition to my internship, I'm following bioinformatics and arabic courses. <br><br><br><br />
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====Dylan Iverson====<br />
[[Image:Dylan.png|thumb|left|100px]]'''1st year master student in Biomedical Engineering at Paris Descartes University''' <br> <br />
I am a first year student of the Master of Biomedical Engineering at Paris Descartes. My undergraduate degree is Engineering Bachelor of Science: Chemical Engineering from University of California, Santa Barbara. I have done completed my first 2-month internship for M1 in neurobiology, and iGem will serve as my second internship. I discovered the topic of synthetic biology by taking Jake Wintermute’s course for the AIV Master. In contrast with biology students, I have more knowledge of mathematical modeling and chemistry. I am particularly interested in metabolic engineering. I hope to do what I can to make us all synthetic biology champions. <br><br><br><br />
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====Zoran Marinkovic====<br />
[[Image:Zoran.png|thumb|left|100px]]'''1st year AIV master student at Paris Descartes University''' <br> <br />
I studied Molecular Biology at University of Zagreb (Croatia) and did a semester long exchange at Uppsala University (Sweden) where I studied Microbial and Evolutionary Genetics and Bioinformatics. Currently, I’m doing a 5 month long internship at INSERM U1001 under the supervision of Jake Wintermute tackling the question of bacterial aging using the synthetic biology approach. <br />
My primary interest is application of synthetic biology for creating bioproducts as well as using synthetic biology in fundamental research. Also, I’m quite interested in developing synthetic biology as a tool for creating living organisms from scratch as we build many non-living constructs today. <br />
I joined iGEM because I would like to experience and observe the process of generating ideas and creating a science project with a group of people which, I hope, will be interesting and fun to do. Of course, it has to be the Grand Prize winning one. <br><br><br><br />
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====Claire Mayer====<br />
[[Image:Claire.png|thumb|left|100px]]''' 3rd year of Medical School and 1st year AIV master student at Paris Descartes University''' <br> <br />
I think Synthetic Biology has a tremendous potential, and especially for medical and environmental applications. <br />
iGEM is my M1 internship. I wanted to join the iGEM team in order to work in a pluridisciplinary environment on an exciting synthetic biology project, and learn a lot from each participant, and let them learn from me. <br />
What do I do apart from studying? I am Co President of Paris Descartes’ Debating Club and I give lessons to an adult class in biology (in preparation of an exam called “le brevet adulte”). I love genetics and immunology. <br><br><br><br />
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====Denis Samuylov====<br />
[[Image:Denis.png|thumb|left|100px]]'''1st year AIV master student at Paris Diderot University''' <br> <br />
I finished my undergraduate studies in 2011 in Saint Petersburg State Polytechnical University in Russia. I was learning technical and physical courses, e.g. Electrodynamics, Optics, Quantum Physics, Math, Statistics, Computer Sciences, Electronics… At the moment, I am in the first year of the Interdisciplinary Approaches to Life Science (AIV) Master Program and I fell in love with Biology... or rather Synthetic Biology!<br />
So, with my interdisciplinary background I intend to apply my numerous skills to make humanity’s life better and save the world. I am deeply interested in fighting cancer and to participate in ecological projects. I am sure that participation in iGEM is a great possibility to meet interesting people, share my skills and to learn something new! And of course to have a fun summer while realizing useful project!<br />
As for my other interests, I love sports, dancing, music, nature and life! <br><br><br><br />
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====Aishah Prastowo====<br />
[[Image:Aishah.png|thumb|left|100px]]'''1st year AIV master student at Paris Descartes University''' <br> <br />
Before my master I did Engineering Physics in Gadjah Mada University Indonesia. As my final project of my undergraduate, I studied microfluidics and did a project on low-cost microfluidic system for generating biomicrobubbles. Currently I am doing my internship about real-time control of gene expression in yeast. For me engineering is all about systems design and modeling, making innovation and troubleshooting, and so is synthetic biology. I hope I can learn both science and soft skills by participating in iGEM, while contributing my best for the team.<br><br><br><br />
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====Julianne Rieders====<br />
[[Image:Julianne.png|thumb|left|100px]]'''1st year AIV master student at Paris Descartes University ''' <br> <br />
I earned my B.A. at Bryn Mawr College, Bryn Mawr Pa, where I studied biology and East Asian studies. I am primarily interested in molecular therapeutics, and believe that the application of synthetic and systems biology to this field will allow for the development of safer more efficient treatments. I am currently involved in a hardcore synthetic biology project working with both bacterial and mammalian cells. Participating in iGEM is an ideal opportunity to apply and share my skills in this field, as well as expand my skill set, in an exciting and competitive environment.<br><br><br><br />
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====Ernest Mordret====<br />
[[Image:Ernest.png|thumb|left|100px]]'''2nd year AIV master student at Paris Diderot University and 3rd year at AgroParisTech''' <br> <br />
By the end of high school, I had quite a hard time choosing between biology studies and the classical engineering track. Thus, iGEM and synthetic biology are a way to use this engineering approach in order to serve my passion for biology. I am deeply interested in the robustness of synthetic gene circuits and in the development of innovative directed evolution strategies. During my internships and theoretical trainings, I acquired skills in population genetics, molecular biology and microfluidics, and I will try to bring as much energy, commitment, suggestions and solutions as possible for the team!<br><br><br><br />
<br />
====Guillaume Villain====<br />
[[Image:Guillaume.png|thumb|left|100px]]'''1st year Frontiers in Life Science bachelor student at Paris Descartes University''' <br> <br />
I am really interested in synthetic biology, modeling of biological systems, education, directed evolution and protein engineering. I would like especially to know more about extremophilic protein, which is why I am doing an internship in the institute of physico-chemical biology (IBPC, Paris) in a bioinformatics laboratory to study molecular modeling of extremophilic protein.<br />
I love interdisciplinarity and I think iGEM is a fantastic opportunity to learn a lot about synthetic biology and sciences in an innovative way.<br />
<br><br><br><br />
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===Advisors:===<br />
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====Ariel Lindner====<br />
[[Image:Ariel.png|thumb|left|100px]]'''Researcher at INSERM, Director of the AIV Master at the Paris Descartes and Paris Diderot Universities''' <br> <br />
INSERM tenured senior researcher and co-director of the AIV master, has graduated from the Hebrew University (Jerusalem, Israel) "Amirim" interdisciplinary program with major in Chemistry and received his M.Sc. and Ph.D. from the Weizmann Institute of Science (Rehovot, Israel) in Chemical Immunology for his work on catalytic antibodies as enzyme models, antibody conformational changes and directed evolution. After a research period at the Scripps Institute (California, USA), he received EMBO and Marie Curie fellowships to pursue postdoctoral work in Paris. His study interest evolve around applying Physical, Chemical and Biological approaches to study variability between clonal individuals. He is an associate professor at the Paris Descartes university faculty of Medicine (2008/9) and serves as the director of studies of the Center for Research and Interdisciplinarity (CRI).<br />
<br><br><br><br />
<br />
====Antoine Decrulle====<br />
[[Image:Antoine.png|thumb|left|100px]]'''1st year PhD student at FdV doctoral school of Paris Descartes University''' <br> <br />
I’m a PhD student working on synthetic biology. My interest for this field started 3 years ago when i did the first year of the AIV master program and participated to the iGEM Paris team in 2010. I have to say that this experience of research influenced me a lot during the past two years. Last year I decided to share my experience of synthetic biology and of the iGEM competition by advising the paris iGEM team 2011. This was a great experience for me that’s why I decided to keep doing it this year for the new Paris 2012 team.<br />
<br><br><br><br />
<br />
====Aleksandra Nivina====<br />
[[Image:Alexksandra.png|thumb|left|80px]]'''6th year Pharmacy and 2nd year master AIV student at Paris Descartes University''' <br> <br />
My interest in iGEM began in 2010 when I participated in this competition as a member of the Paris team. It was a wonderful way to learn Synthetic biology and get a hands-on experience in a research project. In fact, I liked this “scientific adventure” so much that it’s now my second year as an adviser.<br />
During this summer, I’m still finishing my undergraduate studies, but hopefully will start a PhD on a synthetic biology related project by autumn.<br />
<br><br><br><br />
<br />
====Babak Nichabouri====<br />
[[Image:Babak.png|thumb|left|80px]]'''PharmD-PhD program, Paris Descartes University ''' <br> <br />
As pharmacy student, I have a great interest in biotechnology for life and health sciences. Participating to iGEM last year was for me a great experience in term of learning about science. It could has been done with the formidable help of my previous advisors. I would now like to share my knowledge and experience with the members of the next team. <br />
<br><br><br><br />
<br />
====Jake Wintermute====<br />
[[Image:Jake.png|thumb|left|100px]]'''Postdoctoral researcher at the Centre de Recherche Interdisciplinaire''' <br> <br />
I'm a postdoctoral researcher working at the Centre de Recherche Interdisciplinaire. I also teach the Synthetic Biology course for the AIV master's students. My Ph.D. comes from the Systems Biology department at Harvard, where I graduated in 2011.<br />
I have been an iGEM fan and groupie for many years, but this will be my first time personally involved with a team. I am looking forward to taking this team to MIT and showing everyone a great time in Boston!<br />
<br><br><br><br />
<br />
====Yifan Yang====<br />
[[Image:Yifan.png|thumb|left|100px]]'''PhD student at the FdV doctoral school of Paris Descartes University''' <br> <br />
I’m a PhD student from the FdV (Frontières du Vivant) PhD school and INSERM U1001, working on the evolutionary and systems biology of bacterial aging. Trained in an interdisciplinary undergraduate program as a biologist and a mathematician in Peking University, I participated in iGEM 2007 as an initiating member of the PKU iGEM team, which won the Grand Prize in MIT. After spending a year in Caltech, I joined François Taddei’s group in Paris since 2009. I helped mentoring the 2010 & 2011 Paris iGEM teams, and will do the same this year. I hope as experience grows, I would do a better job both in organizing to help the team be more effective, and in mentoring to help the members to realize their own ideas.<br><br><br><br />
<br />
== Gallery ==<br />
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File:ParisB_01.jpg<br />
File:ParisB_02.jpg<br />
File:ParisB_03.jpg<br />
File:ParisB_04.jpg<br />
File:ParisB_05.jpg<br />
File:ParisB_06.jpg<br />
File:ParisB_07.jpg<br />
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{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/TeamTeam:Paris Bettencourt/Team2012-11-09T18:56:08Z<p>Aprastowo: /* Who we are */</p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<div id="grouptitle">Team </div><br />
<br />
== Who we are ==<br />
<br />
<center>Before iGEM<br />
[[Image:Paristeam.jpg|500px]]</center><br><br />
<br />
<center>After iGEM<br />
[[Image:ParisB_finalist.jpg |500px]]<br><br />
<sub> official iGEM picture by Justin Knight </sub><br />
</center><br><br />
<br />
===Undergrads:===<br />
<br />
====Jean Cury====<br />
[[Image:Jean.png|thumb|left|100px]]'''1st year master student in Biology at the ENS Paris and UPMC, Paris 6''' <br> <br />
My current internship is about studying a synthetic recombination site of the integron system, at Pasteur Institute, Paris. This gives me a good insight into synthetic biology, and motivates me to participate in iGEM.<br />
What attracts me also in doing iGEM is the interdisciplinary team, the team reflexion, and everything about creating a team, organizing it, learning from other fields represented. Indeed, I truly believe that learning from your friends is a good way to improve your knowledge and satisfy your curiosity.<br />
In addition to my internship, I'm following bioinformatics and arabic courses. <br><br><br><br />
<br />
====Dylan Iverson====<br />
[[Image:Dylan.png|thumb|left|100px]]'''1st year master student in Biomedical Engineering at Paris Descartes University''' <br> <br />
I am a first year student of the Master of Biomedical Engineering at Paris Descartes. My undergraduate degree is Engineering Bachelor of Science: Chemical Engineering from University of California, Santa Barbara. I have done completed my first 2-month internship for M1 in neurobiology, and iGem will serve as my second internship. I discovered the topic of synthetic biology by taking Jake Wintermute’s course for the AIV Master. In contrast with biology students, I have more knowledge of mathematical modeling and chemistry. I am particularly interested in metabolic engineering. I hope to do what I can to make us all synthetic biology champions. <br><br><br><br />
<br />
====Zoran Marinkovic====<br />
[[Image:Zoran.png|thumb|left|100px]]'''1st year AIV master student at Paris Descartes University''' <br> <br />
I studied Molecular Biology at University of Zagreb (Croatia) and did a semester long exchange at Uppsala University (Sweden) where I studied Microbial and Evolutionary Genetics and Bioinformatics. Currently, I’m doing a 5 month long internship at INSERM U1001 under the supervision of Jake Wintermute tackling the question of bacterial aging using the synthetic biology approach. <br />
My primary interest is application of synthetic biology for creating bioproducts as well as using synthetic biology in fundamental research. Also, I’m quite interested in developing synthetic biology as a tool for creating living organisms from scratch as we build many non-living constructs today. <br />
I joined iGEM because I would like to experience and observe the process of generating ideas and creating a science project with a group of people which, I hope, will be interesting and fun to do. Of course, it has to be the Grand Prize winning one. <br><br><br><br />
<br />
====Claire Mayer====<br />
[[Image:Claire.png|thumb|left|100px]]''' 3rd year of Medical School and 1st year AIV master student at Paris Descartes University''' <br> <br />
I think Synthetic Biology has a tremendous potential, and especially for medical and environmental applications. <br />
iGEM is my M1 internship. I wanted to join the iGEM team in order to work in a pluridisciplinary environment on an exciting synthetic biology project, and learn a lot from each participant, and let them learn from me. <br />
What do I do apart from studying? I am Co President of Paris Descartes’ Debating Club and I give lessons to an adult class in biology (in preparation of an exam called “le brevet adulte”). I love genetics and immunology. <br><br><br><br />
<br />
====Denis Samuylov====<br />
[[Image:Denis.png|thumb|left|100px]]'''1st year AIV master student at Paris Diderot University''' <br> <br />
I finished my undergraduate studies in 2011 in Saint Petersburg State Polytechnical University in Russia. I was learning technical and physical courses, e.g. Electrodynamics, Optics, Quantum Physics, Math, Statistics, Computer Sciences, Electronics… At the moment, I am in the first year of the Interdisciplinary Approaches to Life Science (AIV) Master Program and I fell in love with Biology... or rather Synthetic Biology!<br />
So, with my interdisciplinary background I intend to apply my numerous skills to make humanity’s life better and save the world. I am deeply interested in fighting cancer and to participate in ecological projects. I am sure that participation in iGEM is a great possibility to meet interesting people, share my skills and to learn something new! And of course to have a fun summer while realizing useful project!<br />
As for my other interests, I love sports, dancing, music, nature and life! <br><br><br><br />
<br />
====Aishah Prastowo====<br />
[[Image:Aishah.png|thumb|left|100px]]'''1st year AIV master student at Paris Descartes University''' <br> <br />
Before my master I did Engineering Physics in Gadjah Mada University Indonesia. As my final project of my undergraduate, I studied microfluidics and did a project on low-cost microfluidic system for generating biomicrobubbles. Currently I am doing my internship about real-time control of gene expression in yeast. For me engineering is all about systems design and modeling, making innovation and troubleshooting, and so is synthetic biology. I hope I can learn both science and soft skills by participating in iGEM, while contributing my best for the team.<br><br><br><br />
<br />
====Julianne Rieders====<br />
[[Image:Julianne.png|thumb|left|100px]]'''1st year AIV master student at Paris Descartes University ''' <br> <br />
I earned my B.A. at Bryn Mawr College, Bryn Mawr Pa, where I studied biology and East Asian studies. I am primarily interested in molecular therapeutics, and believe that the application of synthetic and systems biology to this field will allow for the development of safer more efficient treatments. I am currently involved in a hardcore synthetic biology project working with both bacterial and mammalian cells. Participating in iGEM is an ideal opportunity to apply and share my skills in this field, as well as expand my skill set, in an exciting and competitive environment.<br><br><br><br />
<br />
====Ernest Mordret====<br />
[[Image:Ernest.png|thumb|left|100px]]'''2nd year AIV master student at Paris Diderot University and 3rd year at AgroParisTech''' <br> <br />
By the end of high school, I had quite a hard time choosing between biology studies and the classical engineering track. Thus, iGEM and synthetic biology are a way to use this engineering approach in order to serve my passion for biology. I am deeply interested in the robustness of synthetic gene circuits and in the development of innovative directed evolution strategies. During my internships and theoretical trainings, I acquired skills in population genetics, molecular biology and microfluidics, and I will try to bring as much energy, commitment, suggestions and solutions as possible for the team!<br><br><br><br />
<br />
====Guillaume Villain====<br />
[[Image:Guillaume.png|thumb|left|100px]]'''1st year Frontiers in Life Science bachelor student at Paris Descartes University''' <br> <br />
I am really interested in synthetic biology, modeling of biological systems, education, directed evolution and protein engineering. I would like especially to know more about extremophilic protein, which is why I am doing an internship in the institute of physico-chemical biology (IBPC, Paris) in a bioinformatics laboratory to study molecular modeling of extremophilic protein.<br />
I love interdisciplinarity and I think iGEM is a fantastic opportunity to learn a lot about synthetic biology and sciences in an innovative way.<br />
<br><br><br><br />
<br />
===Advisors:===<br />
<br />
====Ariel Lindner====<br />
[[Image:Ariel.png|thumb|left|100px]]'''Researcher at INSERM, Director of the AIV Master at the Paris Descartes and Paris Diderot Universities''' <br> <br />
INSERM tenured senior researcher and co-director of the AIV master, has graduated from the Hebrew University (Jerusalem, Israel) "Amirim" interdisciplinary program with major in Chemistry and received his M.Sc. and Ph.D. from the Weizmann Institute of Science (Rehovot, Israel) in Chemical Immunology for his work on catalytic antibodies as enzyme models, antibody conformational changes and directed evolution. After a research period at the Scripps Institute (California, USA), he received EMBO and Marie Curie fellowships to pursue postdoctoral work in Paris. His study interest evolve around applying Physical, Chemical and Biological approaches to study variability between clonal individuals. He is an associate professor at the Paris Descartes university faculty of Medicine (2008/9) and serves as the director of studies of the Center for Research and Interdisciplinarity (CRI).<br />
<br><br><br><br />
<br />
====Antoine Decrulle====<br />
[[Image:Antoine.png|thumb|left|100px]]'''1st year PhD student at FdV doctoral school of Paris Descartes University''' <br> <br />
I’m a PhD student working on synthetic biology. My interest for this field started 3 years ago when i did the first year of the AIV master program and participated to the iGEM Paris team in 2010. I have to say that this experience of research influenced me a lot during the past two years. Last year I decided to share my experience of synthetic biology and of the iGEM competition by advising the paris iGEM team 2011. This was a great experience for me that’s why I decided to keep doing it this year for the new Paris 2012 team.<br />
<br><br><br><br />
<br />
====Aleksandra Nivina====<br />
[[Image:Alexksandra.png|thumb|left|80px]]'''6th year Pharmacy and 2nd year master AIV student at Paris Descartes University''' <br> <br />
My interest in iGEM began in 2010 when I participated in this competition as a member of the Paris team. It was a wonderful way to learn Synthetic biology and get a hands-on experience in a research project. In fact, I liked this “scientific adventure” so much that it’s now my second year as an adviser.<br />
During this summer, I’m still finishing my undergraduate studies, but hopefully will start a PhD on a synthetic biology related project by autumn.<br />
<br><br><br><br />
<br />
====Babak Nichabouri====<br />
[[Image:Babak.png|thumb|left|80px]]'''PharmD-PhD program, Paris Descartes University ''' <br> <br />
As pharmacy student, I have a great interest in biotechnology for life and health sciences. Participating to iGEM last year was for me a great experience in term of learning about science. It could has been done with the formidable help of my previous advisors. I would now like to share my knowledge and experience with the members of the next team. <br />
<br><br><br><br />
<br />
====Jake Wintermute====<br />
[[Image:Jake.png|thumb|left|100px]]'''Postdoctoral researcher at the Centre de Recherche Interdisciplinaire''' <br> <br />
I'm a postdoctoral researcher working at the Centre de Recherche Interdisciplinaire. I also teach the Synthetic Biology course for the AIV master's students. My Ph.D. comes from the Systems Biology department at Harvard, where I graduated in 2011.<br />
I have been an iGEM fan and groupie for many years, but this will be my first time personally involved with a team. I am looking forward to taking this team to MIT and showing everyone a great time in Boston!<br />
<br><br><br><br />
<br />
====Yifan Yang====<br />
[[Image:Yifan.png|thumb|left|100px]]'''PhD student at the FdV doctoral school of Paris Descartes University''' <br> <br />
I’m a PhD student from the FdV (Frontières du Vivant) PhD school and INSERM U1001, working on the evolutionary and systems biology of bacterial aging. Trained in an interdisciplinary undergraduate program as a biologist and a mathematician in Peking University, I participated in iGEM 2007 as an initiating member of the PKU iGEM team, which won the Grand Prize in MIT. After spending a year in Caltech, I joined François Taddei’s group in Paris since 2009. I helped mentoring the 2010 & 2011 Paris iGEM teams, and will do the same this year. I hope as experience grows, I would do a better job both in organizing to help the team be more effective, and in mentoring to help the members to realize their own ideas.<br><br><br><br />
<br />
== Gallery ==<br />
<gallery><br />
File:ParisB_01.jpg<br />
File:ParisB_02.jpg<br />
File:ParisB_03.jpg<br />
File:ParisB_04.jpg<br />
File:ParisB_05.jpg<br />
File:ParisB_06.jpg<br />
File:ParisB_07.jpg<br />
</gallery><br />
<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/TeamTeam:Paris Bettencourt/Team2012-11-09T18:55:35Z<p>Aprastowo: /* Who we are */</p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<div id="grouptitle">Team </div><br />
<br />
== Who we are ==<br />
<br />
<center>Before iGEM<br />
<br><br />
[[Image:Paristeam.jpg|500px]]</center><br><br />
<br />
<br />
<center>After iGEM<br />
<br><br />
[[Image:ParisB_finalist.jpg |500px]]<br><br />
<sub> official iGEM picture by Justin Knight </sub><br />
</center><br><br />
<br />
<br />
===Undergrads:===<br />
<br />
====Jean Cury====<br />
[[Image:Jean.png|thumb|left|100px]]'''1st year master student in Biology at the ENS Paris and UPMC, Paris 6''' <br> <br />
My current internship is about studying a synthetic recombination site of the integron system, at Pasteur Institute, Paris. This gives me a good insight into synthetic biology, and motivates me to participate in iGEM.<br />
What attracts me also in doing iGEM is the interdisciplinary team, the team reflexion, and everything about creating a team, organizing it, learning from other fields represented. Indeed, I truly believe that learning from your friends is a good way to improve your knowledge and satisfy your curiosity.<br />
In addition to my internship, I'm following bioinformatics and arabic courses. <br><br><br><br />
<br />
====Dylan Iverson====<br />
[[Image:Dylan.png|thumb|left|100px]]'''1st year master student in Biomedical Engineering at Paris Descartes University''' <br> <br />
I am a first year student of the Master of Biomedical Engineering at Paris Descartes. My undergraduate degree is Engineering Bachelor of Science: Chemical Engineering from University of California, Santa Barbara. I have done completed my first 2-month internship for M1 in neurobiology, and iGem will serve as my second internship. I discovered the topic of synthetic biology by taking Jake Wintermute’s course for the AIV Master. In contrast with biology students, I have more knowledge of mathematical modeling and chemistry. I am particularly interested in metabolic engineering. I hope to do what I can to make us all synthetic biology champions. <br><br><br><br />
<br />
====Zoran Marinkovic====<br />
[[Image:Zoran.png|thumb|left|100px]]'''1st year AIV master student at Paris Descartes University''' <br> <br />
I studied Molecular Biology at University of Zagreb (Croatia) and did a semester long exchange at Uppsala University (Sweden) where I studied Microbial and Evolutionary Genetics and Bioinformatics. Currently, I’m doing a 5 month long internship at INSERM U1001 under the supervision of Jake Wintermute tackling the question of bacterial aging using the synthetic biology approach. <br />
My primary interest is application of synthetic biology for creating bioproducts as well as using synthetic biology in fundamental research. Also, I’m quite interested in developing synthetic biology as a tool for creating living organisms from scratch as we build many non-living constructs today. <br />
I joined iGEM because I would like to experience and observe the process of generating ideas and creating a science project with a group of people which, I hope, will be interesting and fun to do. Of course, it has to be the Grand Prize winning one. <br><br><br><br />
<br />
====Claire Mayer====<br />
[[Image:Claire.png|thumb|left|100px]]''' 3rd year of Medical School and 1st year AIV master student at Paris Descartes University''' <br> <br />
I think Synthetic Biology has a tremendous potential, and especially for medical and environmental applications. <br />
iGEM is my M1 internship. I wanted to join the iGEM team in order to work in a pluridisciplinary environment on an exciting synthetic biology project, and learn a lot from each participant, and let them learn from me. <br />
What do I do apart from studying? I am Co President of Paris Descartes’ Debating Club and I give lessons to an adult class in biology (in preparation of an exam called “le brevet adulte”). I love genetics and immunology. <br><br><br><br />
<br />
====Denis Samuylov====<br />
[[Image:Denis.png|thumb|left|100px]]'''1st year AIV master student at Paris Diderot University''' <br> <br />
I finished my undergraduate studies in 2011 in Saint Petersburg State Polytechnical University in Russia. I was learning technical and physical courses, e.g. Electrodynamics, Optics, Quantum Physics, Math, Statistics, Computer Sciences, Electronics… At the moment, I am in the first year of the Interdisciplinary Approaches to Life Science (AIV) Master Program and I fell in love with Biology... or rather Synthetic Biology!<br />
So, with my interdisciplinary background I intend to apply my numerous skills to make humanity’s life better and save the world. I am deeply interested in fighting cancer and to participate in ecological projects. I am sure that participation in iGEM is a great possibility to meet interesting people, share my skills and to learn something new! And of course to have a fun summer while realizing useful project!<br />
As for my other interests, I love sports, dancing, music, nature and life! <br><br><br><br />
<br />
====Aishah Prastowo====<br />
[[Image:Aishah.png|thumb|left|100px]]'''1st year AIV master student at Paris Descartes University''' <br> <br />
Before my master I did Engineering Physics in Gadjah Mada University Indonesia. As my final project of my undergraduate, I studied microfluidics and did a project on low-cost microfluidic system for generating biomicrobubbles. Currently I am doing my internship about real-time control of gene expression in yeast. For me engineering is all about systems design and modeling, making innovation and troubleshooting, and so is synthetic biology. I hope I can learn both science and soft skills by participating in iGEM, while contributing my best for the team.<br><br><br><br />
<br />
====Julianne Rieders====<br />
[[Image:Julianne.png|thumb|left|100px]]'''1st year AIV master student at Paris Descartes University ''' <br> <br />
I earned my B.A. at Bryn Mawr College, Bryn Mawr Pa, where I studied biology and East Asian studies. I am primarily interested in molecular therapeutics, and believe that the application of synthetic and systems biology to this field will allow for the development of safer more efficient treatments. I am currently involved in a hardcore synthetic biology project working with both bacterial and mammalian cells. Participating in iGEM is an ideal opportunity to apply and share my skills in this field, as well as expand my skill set, in an exciting and competitive environment.<br><br><br><br />
<br />
====Ernest Mordret====<br />
[[Image:Ernest.png|thumb|left|100px]]'''2nd year AIV master student at Paris Diderot University and 3rd year at AgroParisTech''' <br> <br />
By the end of high school, I had quite a hard time choosing between biology studies and the classical engineering track. Thus, iGEM and synthetic biology are a way to use this engineering approach in order to serve my passion for biology. I am deeply interested in the robustness of synthetic gene circuits and in the development of innovative directed evolution strategies. During my internships and theoretical trainings, I acquired skills in population genetics, molecular biology and microfluidics, and I will try to bring as much energy, commitment, suggestions and solutions as possible for the team!<br><br><br><br />
<br />
====Guillaume Villain====<br />
[[Image:Guillaume.png|thumb|left|100px]]'''1st year Frontiers in Life Science bachelor student at Paris Descartes University''' <br> <br />
I am really interested in synthetic biology, modeling of biological systems, education, directed evolution and protein engineering. I would like especially to know more about extremophilic protein, which is why I am doing an internship in the institute of physico-chemical biology (IBPC, Paris) in a bioinformatics laboratory to study molecular modeling of extremophilic protein.<br />
I love interdisciplinarity and I think iGEM is a fantastic opportunity to learn a lot about synthetic biology and sciences in an innovative way.<br />
<br><br><br><br />
<br />
===Advisors:===<br />
<br />
====Ariel Lindner====<br />
[[Image:Ariel.png|thumb|left|100px]]'''Researcher at INSERM, Director of the AIV Master at the Paris Descartes and Paris Diderot Universities''' <br> <br />
INSERM tenured senior researcher and co-director of the AIV master, has graduated from the Hebrew University (Jerusalem, Israel) "Amirim" interdisciplinary program with major in Chemistry and received his M.Sc. and Ph.D. from the Weizmann Institute of Science (Rehovot, Israel) in Chemical Immunology for his work on catalytic antibodies as enzyme models, antibody conformational changes and directed evolution. After a research period at the Scripps Institute (California, USA), he received EMBO and Marie Curie fellowships to pursue postdoctoral work in Paris. His study interest evolve around applying Physical, Chemical and Biological approaches to study variability between clonal individuals. He is an associate professor at the Paris Descartes university faculty of Medicine (2008/9) and serves as the director of studies of the Center for Research and Interdisciplinarity (CRI).<br />
<br><br><br><br />
<br />
====Antoine Decrulle====<br />
[[Image:Antoine.png|thumb|left|100px]]'''1st year PhD student at FdV doctoral school of Paris Descartes University''' <br> <br />
I’m a PhD student working on synthetic biology. My interest for this field started 3 years ago when i did the first year of the AIV master program and participated to the iGEM Paris team in 2010. I have to say that this experience of research influenced me a lot during the past two years. Last year I decided to share my experience of synthetic biology and of the iGEM competition by advising the paris iGEM team 2011. This was a great experience for me that’s why I decided to keep doing it this year for the new Paris 2012 team.<br />
<br><br><br><br />
<br />
====Aleksandra Nivina====<br />
[[Image:Alexksandra.png|thumb|left|80px]]'''6th year Pharmacy and 2nd year master AIV student at Paris Descartes University''' <br> <br />
My interest in iGEM began in 2010 when I participated in this competition as a member of the Paris team. It was a wonderful way to learn Synthetic biology and get a hands-on experience in a research project. In fact, I liked this “scientific adventure” so much that it’s now my second year as an adviser.<br />
During this summer, I’m still finishing my undergraduate studies, but hopefully will start a PhD on a synthetic biology related project by autumn.<br />
<br><br><br><br />
<br />
====Babak Nichabouri====<br />
[[Image:Babak.png|thumb|left|80px]]'''PharmD-PhD program, Paris Descartes University ''' <br> <br />
As pharmacy student, I have a great interest in biotechnology for life and health sciences. Participating to iGEM last year was for me a great experience in term of learning about science. It could has been done with the formidable help of my previous advisors. I would now like to share my knowledge and experience with the members of the next team. <br />
<br><br><br><br />
<br />
====Jake Wintermute====<br />
[[Image:Jake.png|thumb|left|100px]]'''Postdoctoral researcher at the Centre de Recherche Interdisciplinaire''' <br> <br />
I'm a postdoctoral researcher working at the Centre de Recherche Interdisciplinaire. I also teach the Synthetic Biology course for the AIV master's students. My Ph.D. comes from the Systems Biology department at Harvard, where I graduated in 2011.<br />
I have been an iGEM fan and groupie for many years, but this will be my first time personally involved with a team. I am looking forward to taking this team to MIT and showing everyone a great time in Boston!<br />
<br><br><br><br />
<br />
====Yifan Yang====<br />
[[Image:Yifan.png|thumb|left|100px]]'''PhD student at the FdV doctoral school of Paris Descartes University''' <br> <br />
I’m a PhD student from the FdV (Frontières du Vivant) PhD school and INSERM U1001, working on the evolutionary and systems biology of bacterial aging. Trained in an interdisciplinary undergraduate program as a biologist and a mathematician in Peking University, I participated in iGEM 2007 as an initiating member of the PKU iGEM team, which won the Grand Prize in MIT. After spending a year in Caltech, I joined François Taddei’s group in Paris since 2009. I helped mentoring the 2010 & 2011 Paris iGEM teams, and will do the same this year. I hope as experience grows, I would do a better job both in organizing to help the team be more effective, and in mentoring to help the members to realize their own ideas.<br><br><br><br />
<br />
== Gallery ==<br />
<gallery><br />
File:ParisB_01.jpg<br />
File:ParisB_02.jpg<br />
File:ParisB_03.jpg<br />
File:ParisB_04.jpg<br />
File:ParisB_05.jpg<br />
File:ParisB_06.jpg<br />
File:ParisB_07.jpg<br />
</gallery><br />
<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/File:ParisB_finalist.jpgFile:ParisB finalist.jpg2012-11-09T18:54:32Z<p>Aprastowo: </p>
<hr />
<div></div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-11-09T18:45:33Z<p>Aprastowo: </p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<html><br />
<br />
<div id="content1"><br />
<div style="position:absolute;left:15px;top:255px;z-index:100"><img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width="50"> <sub>This sign indicating new results after the European Jamboree.</sub></div><br />
<br />
<div class="box"><br />
<br><br />
<br><br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
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<br />
<br />
</ul></li><br />
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<br />
</ul><br />
<br />
</p><br />
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</div><br />
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</div><br />
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<div id="sidebar"><br />
<div class="box"><br />
<!-- i leave this blank for boston achievement ;) <img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br> --><br />
<img src=https://static.igem.org/mediawiki/2012/e/e0/ParisB_Medal.gif width=15><sub><b>World Championship 2nd runner up</b></sub> <br> <br><br />
<img src=https://static.igem.org/mediawiki/2012/e/e0/ParisB_Medal.gif width=15><sub><b>World Championship Best Environment Project</b></sub> <br> <br><br />
<img src=https://static.igem.org/mediawiki/2012/e/e0/ParisB_Medal.gif width=15><sub>European Jamboree Gold Medal</sub> <br> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/e/e0/ParisB_Medal.gif width=15><sub>European Jamboree Safety Commendation</sub><br />
<br> <br><br><br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
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{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/ModelingTeam:Paris Bettencourt/Modeling2012-10-27T02:47:54Z<p>Aprastowo: /* Control Checks */</p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<div id="boston"><br />
<br><br />
<div id="grouptitle">Safety Assessment</div><br />
<br />
==Overview==<br />
Safety is an important issue in synthetic biology, especially for environmentally related projects. We started to answer the question, “how safe is safe enough?” by involving experts, the public and our fellow scientists, and also by building biosafety devices. However, to really answer the question, we need first to ask ourselves a more basic question, “how do we measure safety?”. As we see synthetic biology as an engineering approach to biology, we could think about the adaptation of safety engineering, a well studied engineering subset, that has been widely use to minimize risks in many fields of engineering, such as mechanical engineering, aircrafts, and manufactures. However, the risks they face are surely different from the risks of synthetic biology. <br />
<br />
According to Dana et al<sup>[[#References|1]]</sup> there are four areas of risk research in environmental application of synthetic biology:<br />
*Differences in the physiology of natural and synthetic organisms will affect how they interact with the surrounding environment,<br />
*Escaped microorganisms have the potential to survive in receiving environments and to compete successfully with non-modified counterparts,<br />
*Synthetic organisms might evolve and adapt quickly, perhaps filling new ecological niches, and<br />
*Gene transfer.<br />
<br />
Knowing that there are different areas of risk that we need to take into account, we need to design our safety containment with different parts to deal with each of them. Identifying the relationship between one part and the others will help us to see the reliability of the overall system. Here we propose an approach to assess safety for environmental release of genetically engineered bacteria (GE bacteria).<br />
<br />
===Objectives===<br />
*Adapting existing safety assessment tools for synthetic biology.<br />
*Proposing new methods to assess safety in synthetic biology.<br />
<br />
==Methods and Results==<br />
We propose a method to assess hazards and risk<sup>[[#References|2]]</sup> in releasing genetically engineered bacteria into the environment. As a case study, we want to release GE bacteria which will perform some function in the environment and we want to apply 3 sets of bWARE safety containment modules (alginate beads, bWARE killswitch, semantic containment) to control the hazards and risks. Here we focus more on the reliability of the safety containment system rather than the functional part, although a similar assessment can also be applied to assess the reliability of the functional part.<br />
<br />
===Hazard Identification===<br />
Identifying hazards means that we need to find and understand the possible harm that may happen in the application of our system. Generally there are two potential hazards in environmental application of synthetic biology<sup>[[#References|1]]</sup> which are the successful escape of the GE bacteria followed by successful competition with natural strains, and horizontal gene transfer from GEO to natural strains.<br />
<br />
===Risk Assessment===<br />
Risk assessment provides an idea of what kind of risk we face in releasing the GEO in the environment and helps to design containment devices. Here we adapted a risk management method in workplaces complying with health and safety law <sup>[[#References|3]]</sup>.<br />
<br />
To-do-list to assess risk in 5 steps:<br />
#Identify the hazards<br />
#Decide who might be harmed and how<br />
#Evaluate the risks and decide on precaution<br />
#Record your findings and implement them<br />
#Review your assessment and update if necessary<br />
<br />
<br />
Worksheet example:<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are the hazards?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Who might be harmed and how?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are we already doing?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What further action is necessary?'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria outcompete natural strains<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria escaping the containment may outcompete natural strains if they have better fitness, creating natural imbalance <br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Using harmless strain or strain with low fitness compared to natural strain (standard E coli for lab)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to prevent the cells from reproducing themselves at some point and/or separating them from natural strains<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Horizontal gene transfer (HGT)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Other strain/species may uptake engineered genes, and if the genes give advantage in fitness, it may outcompete other strains creating natural imbalance<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| -<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to degrade DNA and/or separate the DNA from the environment and/or prevent natural strains from gaining advantages from modified DNA<br />
<br />
|}<br />
<br />
<br><br />
===Controlling hazards and risks===<br />
<br />
In this step we decided what control elements we want to implement in our system to reduce the risks. We should choose the best suitable control elements depending on the system function and application. As we already know that we want to apply bWARE safety containment, here we describe the role of each safety part in risk reduction. <br />
#GE bacteria outcompete natural strains<br />
#*In order to prevent GE bacteria from escaping and outcompeting the natural strains, we will stop their reproduction by putting a self killing mechanism based on [https://2012.igem.org/Team:Paris_Bettencourt/Suicide suicide] and [https://2012.igem.org/Team:Paris_Bettencourt/Restriction_Enzyme restriction enzyme] systems to kill the cells [https://2012.igem.org/Team:Paris_Bettencourt/Delay after] they perform their function. <br />
#*In case of the failure of the killing mechanism, we will put the cells inside a [https://2012.igem.org/Team:Paris_Bettencourt/Encapsulation physical containment] so there will be no physical interaction between them and the surrounding cells.<br />
#HGT<br />
#*We will use a [https://2012.igem.org/Team:Paris_Bettencourt/Suicide DNAse] to degrade DNA after the cells perform their function so they won’t leave any genetic material behind.<br />
#*In case of the failure due to inefficiency of the DNAse, the [https://2012.igem.org/Team:Paris_Bettencourt/Encapsulation physical containment] will still protect the DNA from the environment.<br />
#*In case of the leakiness of the physical containment, the DNA has a special encryption system, i.e. [https://2012.igem.org/Team:Paris_Bettencourt/Semantic_containment semantic containment], so the receiver cells will not be able to read GE genetic material.<br />
<br />
===Control Checks=== <br />
<br />
To check and predict the reliability of our system, we used fault tree analysis to assess multiple safety containment modules in one biodevice. This top-down approach allows us to see the relationship between each containment element and predict the overall failure probability. With this method we can see what basic events are the key elements in our system.<br />
<br />
[[File:ParisB_FTA.png|800px|center]]<br />
<br />
AND gate represents independent events<br />
<br />
P(A and B) = P(A)P(B)<br />
<br />
OR gate corresponds to set of union<br />
<br />
P(A or B) = P(A) + P(B)<br />
<br />
so the total failure probability of the system is<br />
<br />
Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9)<br />
<br />
List of the basic events<br />
<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Notation'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure component'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure mode'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Consequence'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Method for determining the probability'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P1<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| physical containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| leakage<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA/cell escape<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| experiment<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P2<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA uptake<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA transferred into natural strain<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| <nowiki>transconjugant to donor ratio in HGT is typically <10</nowiki><sup>-5</sup> <sup>[[#References|4]]</sup>, assume this is the rate per generation<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P3<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| semantic containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P4<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| population suicide<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no surrounding cells with enough toxin<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no death<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| based on the cell density and the expectation number of surrounding non-mutant<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P5<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| toxin production<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no DNA degradation (w/o antitoxin), no death (with antitoxin)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P6<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| mutant fitness<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| beneficial mutation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| outcompetition of the mutant<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| -<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P7<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| delay system<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P8<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction enzyme<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P9<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction site<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|}<br />
<br />
====Physical containment failure====<br />
<br />
From the experiment we get the escape rate of the cells from the alginate beads is (escaping cells/total cells) is 10<sup>-5</sup> per 12 hours. Assuming 30 minutes of division time, we have 24 generations, and the escape rate per generation is 4 x 10<sup>-6</sup>.<br />
<br />
====Genetic failure====<br />
<br />
There are different processes that lead to a loss of function of a gene<br />
<br />
* Mutation<br />
* Recombination<br />
* Plasmid loss<br />
<br />
'''Losing function because of mutation'''<br />
<br />
Estimating the mutation rate which cause failure of the safety containment of the device<br />
<br />
* Spontaneous mutation rate of a wild-type E coli strain growing on research medium is 3.3 x 10<sup>-9</sup> per nucleotide per generation <sup>[[#References|5]]</sup> <br />
* approximately ⅔ of nucleotide mutation will change amino acid (64 combination of nucleotides code only 20 amino acids)<br />
* approximately 70% of amino acid change will lose the part function <sup>[[#References|6]]</sup><br />
* mean length of genetic coding sequence for E coli (procaryotes) is 924 bp <sup>[[#References|7]]</sup> ≈ 1000 bp <br />
<br />
So the loss function rate of a gene per generation because of mutation is <br />
<br />
P<sub>L</sub><nowiki>= 3.3 x 10</nowiki><sup>-9</sup> x ⅔ x 0.70 x 1000 = 1.54 x 10<sup>-6</sup> <br />
<br />
'''Recombination'''<br />
<br />
Finding a definite rate of recombination is not easy. Guttman and Dykhuizen in 1994 <sup>[[#References|8]]</sup> stated that recombination is believed to occur at such a low frequency, but their experiment showed that the rate could be as high as mutation rate (50 fold higher compared to the mutation rate believed at that moment, but actually it is 5.0 x 10<sup>-9</sup> changes per nucleotide per generation, a bit more than one fold to the value believed now). <br />
<br />
Redoing the previous calculation with this number will lead us to a rate of 2.33 x 10<sup>-6</sup> per gene per generation.<br />
<br />
'''Plasmid loss'''<br />
<br />
According to L Boe <sup>[[#References|9]]</sup> plasmid loss rate is defined as the probability that a division of a plasmid-carrying individual results in the birth of one plasmid-free and one plasmid-carrying daughter cell. For the low copy plasmid this rate is about ~1% /division and for high copy plasmid is ~0.01% /division, neglecting the viable/non-viable factor of the cells of losing the plasmid (no selection). If a plasmid with a lost rate of 0.05 is stabilized with a 100% efficient postsegragational killing system, the 5% of the division will result in non viable daughter cell, and we can not see the effect except of increasing the appearing division time by ln 2/ln (1-0.05) = 1.04. Thus in our system we can neglect this plasmid loss assuming that we have antibiotic selection in the beads.<br />
<br />
Assuming only mutation and recombination could happen to delete a function of a gene, we have the total genetic failure rate approximately 4 x 10<sup>-6</sup> per gene per generation.<br />
<br />
====Total failure probability====<br />
<br />
Having Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9) and put 1 for unknown probability (P4 and P6) as a worst-case scenario, we come to the failure rate number 6.4 x 10<sup>-11</sup> per generation.<br />
<br />
A volume of one alginate bead is approximately 20 uL. So if the cells grow until they reach the stationary phase (4 x 10<sup>9</sup> cells/ml), we will have 8 x 10<sup>7</sup> cells. If we started from 100 cells per bead, the number of generations we have is <sup>2</sup>log (8 x 10<sup>7</sup> / 100) =19.6 generations. Therefore the total failure becomes 6.4 x 10<sup>-11</sup> x 19.6 = 1.25 x 10<sup>-9</sup>.<br />
<br />
With this method we can also see that the sense-HGT rate is much lower (6.4 x 10<sup>-22</sup>) , almost negligible compared to the outcompetition rate, because it has more back up/redundancy components.<br />
<br />
== Discussion ==<br />
<br />
We have proposed and implemented an example of assessing biosafety by adapting existing methods from safety engineering. However, it is very clear that the prediction is based on rough estimation and we need more experimental data to verify this estimation. For an example, Torres et al <sup>[[#References|10]]</sup> tested a dual containment killing system and compared it with single containment system. They tested an EcoRI based system and a Colicin E3-based system and obtained the efficacy (based on the numbers of successful transformants) each 10<sup>4</sup> and 10<sup>5</sup> respectively but when they combine both system they only got efficacy 10<sup>6</sup>, while theoretically they could reach up to 10<sup>9</sup>. This could give us an idea that predicting the performance of a combination of genetic parts is not as easy as combining the performance of each genetic part. However, we can still conclude that having redundant parts is necessary to reduce the failure rate and make it as low as possible.<br />
<br />
Research in measuring the evolutionary stability in E coli was performed by Sean C Sleight et al <sup>[[#References|11]]</sup> where they measured it of BioBrick-assembled genetic circuits in E coli over multiple generation by measuring the number of loss-functioning mutants. They concluded that to make a robust GE bacteria, one has to take into account 3 principles:<br />
# High expression of genetic circuits comes with the cost of low evolutionary stability (for example induced vs non-induced system)<br />
#Avoid repeated sequences because it will more likely be mutated<br />
#Use of inducible promoters generally increases evolutionary stability compared to constitutive promoters<br />
<br />
To predict the robustness of the system from mutation, we have to take into account the duration (i.e. how many generations) we want our system to work. From their experiment for example, the AHL induced TetR-GFP cells lose their functions after 30 generations, while the uninduced ones lose their function slower (50% after 300 generations). A similar idea is also shown from our work where the mutation rate we got from literature research is in the unit of per generation. This is how reproduction differs biological system from other engineering systems. In engineering we also have failure probability as a function of time because of the life cycle of the system, but the system is not reproducing so it has no variability. <br />
<br />
Analyzing key elements that cause failure in any system including synthetic biology systems is essential for system improvement and prediction of failure. Adaptation of classical safety engineering methods needs to take into account the unique properties of synthetic biology. Reproducibility and complexity are two examples of areas that need to be studied deeper in this context. We invite future iGEM teams to use and improve our assessment framework, build a solid assessment protocol towards a better understanding of biosafety and successful application of synthetic biology.<br />
<br />
== Conclusion ==<br />
*We can adapt methods in safety engineering to assess risk in biosafety<br />
*We need more experimental data to confirm the risk assessing method<br />
<br />
== Perspectives ==<br />
<br />
*We need a method to predict the evolutionary stability of circuits from the properties of their parts, but the emergent behaviours of circuits will likely make prediction difficult. Thus it will be very useful if each BioBricks parts is completed with evolutionary stability data sheet, so we can make prediction of the stability of more complex circuits.<br />
*This safety assessment method is useful for identifying key elements of having failure in synthetic circuit systems before we go further to the real application. Thus we recommend for the future iGEM team to use our assessment method and give feedback to the community by improving this framework.<br />
<br />
==References==<br />
[[#Background|1]] - Genya V Dana et al. Four steps to avoid a synthetic biology disaster. 2012. Nature vol 483<br />
<br />
[[#Methods_and_Results|2]] - WorkSafe Victoria. A handbook for workplaces, controlling OHS hazards and risks. 2007. Edition No.1<br />
<br />
[[#Methods_and_Results|3]] - “Five steps to risk assessment” from [http://www.hse.gov.uk/risk/fivesteps.htm http://www.hse.gov.uk/risk/fivesteps.htm]. - risk management method in workplaces complying with health and safety law <br />
<br />
[[#Check_controls|4]] - Soren J Sorensen et al. 2005. Studying plasmid horizontal gene transfer in situ: a critical review. Nature Reviews Microbiology Vol 3<br />
<br />
[[#Check_controls|5]] - Heewook Lee et al., Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. 2012. PNAS E2774-E2783<br />
<br />
[[#Check_controls|6]] - Stanley A. Sawyer et al. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. 2007. PNAS 104(16):6504-6510<br />
<br />
[[#Check_controls|7]] - Lin Xu et al. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between two kingdoms. 2006. Mol. Biol. Evol. 23(6):1107-1108<br />
<br />
[[#Check_controls|8]] - David S Guttmand and Daniel E. Dykhuizen. 1994. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science Vol 266<br />
<br />
[[#Check_controls|9]] - L.Boe. 1996. Estimation of Plasmid Loss Rates in Bacterial Populations with a Reference to the Reproducibility of Stability Experiments. Plasmid 36, 161–167. Article No. 0043<br />
<br />
[[#Discussion|10]] - Torres B et al. 2003. A dual lethal system to enhance containment of recombinant micro-organisms. Microbiology. 2003 Dec;149(Pt 12):3595-601.<br />
<br />
[[#Discussion|11]] - Sean C Sleight et al., Designing and engineering evolutionary robust genetic circuits. 2010. Journal of Biological Engineering, 4:12<br />
</div><br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/ModelingTeam:Paris Bettencourt/Modeling2012-10-27T02:47:32Z<p>Aprastowo: /* Control Checks */</p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<div id="boston"><br />
<br><br />
<div id="grouptitle">Safety Assessment</div><br />
<br />
==Overview==<br />
Safety is an important issue in synthetic biology, especially for environmentally related projects. We started to answer the question, “how safe is safe enough?” by involving experts, the public and our fellow scientists, and also by building biosafety devices. However, to really answer the question, we need first to ask ourselves a more basic question, “how do we measure safety?”. As we see synthetic biology as an engineering approach to biology, we could think about the adaptation of safety engineering, a well studied engineering subset, that has been widely use to minimize risks in many fields of engineering, such as mechanical engineering, aircrafts, and manufactures. However, the risks they face are surely different from the risks of synthetic biology. <br />
<br />
According to Dana et al<sup>[[#References|1]]</sup> there are four areas of risk research in environmental application of synthetic biology:<br />
*Differences in the physiology of natural and synthetic organisms will affect how they interact with the surrounding environment,<br />
*Escaped microorganisms have the potential to survive in receiving environments and to compete successfully with non-modified counterparts,<br />
*Synthetic organisms might evolve and adapt quickly, perhaps filling new ecological niches, and<br />
*Gene transfer.<br />
<br />
Knowing that there are different areas of risk that we need to take into account, we need to design our safety containment with different parts to deal with each of them. Identifying the relationship between one part and the others will help us to see the reliability of the overall system. Here we propose an approach to assess safety for environmental release of genetically engineered bacteria (GE bacteria).<br />
<br />
===Objectives===<br />
*Adapting existing safety assessment tools for synthetic biology.<br />
*Proposing new methods to assess safety in synthetic biology.<br />
<br />
==Methods and Results==<br />
We propose a method to assess hazards and risk<sup>[[#References|2]]</sup> in releasing genetically engineered bacteria into the environment. As a case study, we want to release GE bacteria which will perform some function in the environment and we want to apply 3 sets of bWARE safety containment modules (alginate beads, bWARE killswitch, semantic containment) to control the hazards and risks. Here we focus more on the reliability of the safety containment system rather than the functional part, although a similar assessment can also be applied to assess the reliability of the functional part.<br />
<br />
===Hazard Identification===<br />
Identifying hazards means that we need to find and understand the possible harm that may happen in the application of our system. Generally there are two potential hazards in environmental application of synthetic biology<sup>[[#References|1]]</sup> which are the successful escape of the GE bacteria followed by successful competition with natural strains, and horizontal gene transfer from GEO to natural strains.<br />
<br />
===Risk Assessment===<br />
Risk assessment provides an idea of what kind of risk we face in releasing the GEO in the environment and helps to design containment devices. Here we adapted a risk management method in workplaces complying with health and safety law <sup>[[#References|3]]</sup>.<br />
<br />
To-do-list to assess risk in 5 steps:<br />
#Identify the hazards<br />
#Decide who might be harmed and how<br />
#Evaluate the risks and decide on precaution<br />
#Record your findings and implement them<br />
#Review your assessment and update if necessary<br />
<br />
<br />
Worksheet example:<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are the hazards?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Who might be harmed and how?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are we already doing?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What further action is necessary?'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria outcompete natural strains<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria escaping the containment may outcompete natural strains if they have better fitness, creating natural imbalance <br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Using harmless strain or strain with low fitness compared to natural strain (standard E coli for lab)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to prevent the cells from reproducing themselves at some point and/or separating them from natural strains<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Horizontal gene transfer (HGT)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Other strain/species may uptake engineered genes, and if the genes give advantage in fitness, it may outcompete other strains creating natural imbalance<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| -<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to degrade DNA and/or separate the DNA from the environment and/or prevent natural strains from gaining advantages from modified DNA<br />
<br />
|}<br />
<br />
<br><br />
===Controlling hazards and risks===<br />
<br />
In this step we decided what control elements we want to implement in our system to reduce the risks. We should choose the best suitable control elements depending on the system function and application. As we already know that we want to apply bWARE safety containment, here we describe the role of each safety part in risk reduction. <br />
#GE bacteria outcompete natural strains<br />
#*In order to prevent GE bacteria from escaping and outcompeting the natural strains, we will stop their reproduction by putting a self killing mechanism based on [https://2012.igem.org/Team:Paris_Bettencourt/Suicide suicide] and [https://2012.igem.org/Team:Paris_Bettencourt/Restriction_Enzyme restriction enzyme] systems to kill the cells [https://2012.igem.org/Team:Paris_Bettencourt/Delay after] they perform their function. <br />
#*In case of the failure of the killing mechanism, we will put the cells inside a [https://2012.igem.org/Team:Paris_Bettencourt/Encapsulation physical containment] so there will be no physical interaction between them and the surrounding cells.<br />
#HGT<br />
#*We will use a [https://2012.igem.org/Team:Paris_Bettencourt/Suicide DNAse] to degrade DNA after the cells perform their function so they won’t leave any genetic material behind.<br />
#*In case of the failure due to inefficiency of the DNAse, the [https://2012.igem.org/Team:Paris_Bettencourt/Encapsulation physical containment] will still protect the DNA from the environment.<br />
#*In case of the leakiness of the physical containment, the DNA has a special encryption system, i.e. [https://2012.igem.org/Team:Paris_Bettencourt/Semantic_containment semantic containment], so the receiver cells will not be able to read GE genetic material.<br />
<br />
===Control Checks=== <br />
<br />
To check and predict the reliability of our system, we used fault tree analysis to assess multiple safety containment modules in one biodevice. This top-down approach allows us to see the relationship between each containment element and predict the overall failure probability. With this method we can see what basic events are the key elements in our system.<br />
<br />
[[File:ParisB_FTA.png|800px|center]]<br />
<br />
AND gate represents independent events<br />
<br />
P(A and B) = P(A)P(B)<br />
<br />
OR gate corresponds to set of union<br />
<br />
P(A or B) = P(A) + P(B)<br />
<br />
so the total failure probability of the system is<br />
<br />
Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9)<br />
<br />
List of the basic events<br />
<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Notation'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure component'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure mode'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Consequence'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Method for determining the probability'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P1<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| physical containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| leakage<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA/cell escape<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| experiment<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P2<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA uptake<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA transferred into natural strain<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| <nowiki>transconjugant to donor ratio in HGT is typically <10</nowiki><sup>-5</sup> <sup>[[#References|4]]</sup>, assuming this is the rate per generation<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P3<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| semantic containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P4<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| population suicide<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no surrounding cells with enough toxin<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no death<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| based on the cell density and the expectation number of surrounding non-mutant<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P5<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| toxin production<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no DNA degradation (w/o antitoxin), no death (with antitoxin)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P6<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| mutant fitness<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| beneficial mutation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| outcompetition of the mutant<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| -<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P7<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| delay system<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P8<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction enzyme<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P9<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction site<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|}<br />
<br />
====Physical containment failure====<br />
<br />
From the experiment we get the escape rate of the cells from the alginate beads is (escaping cells/total cells) is 10<sup>-5</sup> per 12 hours. Assuming 30 minutes of division time, we have 24 generations, and the escape rate per generation is 4 x 10<sup>-6</sup>.<br />
<br />
====Genetic failure====<br />
<br />
There are different processes that lead to a loss of function of a gene<br />
<br />
* Mutation<br />
* Recombination<br />
* Plasmid loss<br />
<br />
'''Losing function because of mutation'''<br />
<br />
Estimating the mutation rate which cause failure of the safety containment of the device<br />
<br />
* Spontaneous mutation rate of a wild-type E coli strain growing on research medium is 3.3 x 10<sup>-9</sup> per nucleotide per generation <sup>[[#References|5]]</sup> <br />
* approximately ⅔ of nucleotide mutation will change amino acid (64 combination of nucleotides code only 20 amino acids)<br />
* approximately 70% of amino acid change will lose the part function <sup>[[#References|6]]</sup><br />
* mean length of genetic coding sequence for E coli (procaryotes) is 924 bp <sup>[[#References|7]]</sup> ≈ 1000 bp <br />
<br />
So the loss function rate of a gene per generation because of mutation is <br />
<br />
P<sub>L</sub><nowiki>= 3.3 x 10</nowiki><sup>-9</sup> x ⅔ x 0.70 x 1000 = 1.54 x 10<sup>-6</sup> <br />
<br />
'''Recombination'''<br />
<br />
Finding a definite rate of recombination is not easy. Guttman and Dykhuizen in 1994 <sup>[[#References|8]]</sup> stated that recombination is believed to occur at such a low frequency, but their experiment showed that the rate could be as high as mutation rate (50 fold higher compared to the mutation rate believed at that moment, but actually it is 5.0 x 10<sup>-9</sup> changes per nucleotide per generation, a bit more than one fold to the value believed now). <br />
<br />
Redoing the previous calculation with this number will lead us to a rate of 2.33 x 10<sup>-6</sup> per gene per generation.<br />
<br />
'''Plasmid loss'''<br />
<br />
According to L Boe <sup>[[#References|9]]</sup> plasmid loss rate is defined as the probability that a division of a plasmid-carrying individual results in the birth of one plasmid-free and one plasmid-carrying daughter cell. For the low copy plasmid this rate is about ~1% /division and for high copy plasmid is ~0.01% /division, neglecting the viable/non-viable factor of the cells of losing the plasmid (no selection). If a plasmid with a lost rate of 0.05 is stabilized with a 100% efficient postsegragational killing system, the 5% of the division will result in non viable daughter cell, and we can not see the effect except of increasing the appearing division time by ln 2/ln (1-0.05) = 1.04. Thus in our system we can neglect this plasmid loss assuming that we have antibiotic selection in the beads.<br />
<br />
Assuming only mutation and recombination could happen to delete a function of a gene, we have the total genetic failure rate approximately 4 x 10<sup>-6</sup> per gene per generation.<br />
<br />
====Total failure probability====<br />
<br />
Having Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9) and put 1 for unknown probability (P4 and P6) as a worst-case scenario, we come to the failure rate number 6.4 x 10<sup>-11</sup> per generation.<br />
<br />
A volume of one alginate bead is approximately 20 uL. So if the cells grow until they reach the stationary phase (4 x 10<sup>9</sup> cells/ml), we will have 8 x 10<sup>7</sup> cells. If we started from 100 cells per bead, the number of generations we have is <sup>2</sup>log (8 x 10<sup>7</sup> / 100) =19.6 generations. Therefore the total failure becomes 6.4 x 10<sup>-11</sup> x 19.6 = 1.25 x 10<sup>-9</sup>.<br />
<br />
With this method we can also see that the sense-HGT rate is much lower (6.4 x 10<sup>-22</sup>) , almost negligible compared to the outcompetition rate, because it has more back up/redundancy components.<br />
<br />
== Discussion ==<br />
<br />
We have proposed and implemented an example of assessing biosafety by adapting existing methods from safety engineering. However, it is very clear that the prediction is based on rough estimation and we need more experimental data to verify this estimation. For an example, Torres et al <sup>[[#References|10]]</sup> tested a dual containment killing system and compared it with single containment system. They tested an EcoRI based system and a Colicin E3-based system and obtained the efficacy (based on the numbers of successful transformants) each 10<sup>4</sup> and 10<sup>5</sup> respectively but when they combine both system they only got efficacy 10<sup>6</sup>, while theoretically they could reach up to 10<sup>9</sup>. This could give us an idea that predicting the performance of a combination of genetic parts is not as easy as combining the performance of each genetic part. However, we can still conclude that having redundant parts is necessary to reduce the failure rate and make it as low as possible.<br />
<br />
Research in measuring the evolutionary stability in E coli was performed by Sean C Sleight et al <sup>[[#References|11]]</sup> where they measured it of BioBrick-assembled genetic circuits in E coli over multiple generation by measuring the number of loss-functioning mutants. They concluded that to make a robust GE bacteria, one has to take into account 3 principles:<br />
# High expression of genetic circuits comes with the cost of low evolutionary stability (for example induced vs non-induced system)<br />
#Avoid repeated sequences because it will more likely be mutated<br />
#Use of inducible promoters generally increases evolutionary stability compared to constitutive promoters<br />
<br />
To predict the robustness of the system from mutation, we have to take into account the duration (i.e. how many generations) we want our system to work. From their experiment for example, the AHL induced TetR-GFP cells lose their functions after 30 generations, while the uninduced ones lose their function slower (50% after 300 generations). A similar idea is also shown from our work where the mutation rate we got from literature research is in the unit of per generation. This is how reproduction differs biological system from other engineering systems. In engineering we also have failure probability as a function of time because of the life cycle of the system, but the system is not reproducing so it has no variability. <br />
<br />
Analyzing key elements that cause failure in any system including synthetic biology systems is essential for system improvement and prediction of failure. Adaptation of classical safety engineering methods needs to take into account the unique properties of synthetic biology. Reproducibility and complexity are two examples of areas that need to be studied deeper in this context. We invite future iGEM teams to use and improve our assessment framework, build a solid assessment protocol towards a better understanding of biosafety and successful application of synthetic biology.<br />
<br />
== Conclusion ==<br />
*We can adapt methods in safety engineering to assess risk in biosafety<br />
*We need more experimental data to confirm the risk assessing method<br />
<br />
== Perspectives ==<br />
<br />
*We need a method to predict the evolutionary stability of circuits from the properties of their parts, but the emergent behaviours of circuits will likely make prediction difficult. Thus it will be very useful if each BioBricks parts is completed with evolutionary stability data sheet, so we can make prediction of the stability of more complex circuits.<br />
*This safety assessment method is useful for identifying key elements of having failure in synthetic circuit systems before we go further to the real application. Thus we recommend for the future iGEM team to use our assessment method and give feedback to the community by improving this framework.<br />
<br />
==References==<br />
[[#Background|1]] - Genya V Dana et al. Four steps to avoid a synthetic biology disaster. 2012. Nature vol 483<br />
<br />
[[#Methods_and_Results|2]] - WorkSafe Victoria. A handbook for workplaces, controlling OHS hazards and risks. 2007. Edition No.1<br />
<br />
[[#Methods_and_Results|3]] - “Five steps to risk assessment” from [http://www.hse.gov.uk/risk/fivesteps.htm http://www.hse.gov.uk/risk/fivesteps.htm]. - risk management method in workplaces complying with health and safety law <br />
<br />
[[#Check_controls|4]] - Soren J Sorensen et al. 2005. Studying plasmid horizontal gene transfer in situ: a critical review. Nature Reviews Microbiology Vol 3<br />
<br />
[[#Check_controls|5]] - Heewook Lee et al., Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. 2012. PNAS E2774-E2783<br />
<br />
[[#Check_controls|6]] - Stanley A. Sawyer et al. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. 2007. PNAS 104(16):6504-6510<br />
<br />
[[#Check_controls|7]] - Lin Xu et al. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between two kingdoms. 2006. Mol. Biol. Evol. 23(6):1107-1108<br />
<br />
[[#Check_controls|8]] - David S Guttmand and Daniel E. Dykhuizen. 1994. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science Vol 266<br />
<br />
[[#Check_controls|9]] - L.Boe. 1996. Estimation of Plasmid Loss Rates in Bacterial Populations with a Reference to the Reproducibility of Stability Experiments. Plasmid 36, 161–167. Article No. 0043<br />
<br />
[[#Discussion|10]] - Torres B et al. 2003. A dual lethal system to enhance containment of recombinant micro-organisms. Microbiology. 2003 Dec;149(Pt 12):3595-601.<br />
<br />
[[#Discussion|11]] - Sean C Sleight et al., Designing and engineering evolutionary robust genetic circuits. 2010. Journal of Biological Engineering, 4:12<br />
</div><br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/ModelingTeam:Paris Bettencourt/Modeling2012-10-27T02:07:10Z<p>Aprastowo: /* Genetic failure */</p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<div id="boston"><br />
<br><br />
<div id="grouptitle">Safety Assessment</div><br />
<br />
==Overview==<br />
Safety is an important issue in synthetic biology, especially for environmentally related projects. We started to answer the question, “how safe is safe enough?” by involving experts, the public and our fellow scientists, and also by building biosafety devices. However, to really answer the question, we need first to ask ourselves a more basic question, “how do we measure safety?”. As we see synthetic biology as an engineering approach to biology, we could think about the adaptation of safety engineering, a well studied engineering subset, that has been widely use to minimize risks in many fields of engineering, such as mechanical engineering, aircrafts, and manufactures. However, the risks they face are surely different from the risks of synthetic biology. <br />
<br />
According to Dana et al<sup>[[#References|1]]</sup> there are four areas of risk research in environmental application of synthetic biology:<br />
*Differences in the physiology of natural and synthetic organisms will affect how they interact with the surrounding environment,<br />
*Escaped microorganisms have the potential to survive in receiving environments and to compete successfully with non-modified counterparts,<br />
*Synthetic organisms might evolve and adapt quickly, perhaps filling new ecological niches, and<br />
*Gene transfer.<br />
<br />
Knowing that there are different areas of risk that we need to take into account, we need to design our safety containment with different parts to deal with each of them. Identifying the relationship between one part and the others will help us to see the reliability of the overall system. Here we propose an approach to assess safety for environmental release of genetically engineered bacteria (GE bacteria).<br />
<br />
===Objectives===<br />
*Adapting existing safety assessment tools for synthetic biology.<br />
*Proposing new methods to assess safety in synthetic biology.<br />
<br />
==Methods and Results==<br />
We propose a method to assess hazards and risk<sup>[[#References|2]]</sup> in releasing genetically engineered bacteria into the environment. As a case study, we want to release GE bacteria which will perform some function in the environment and we want to apply 3 sets of bWARE safety containment modules (alginate beads, bWARE killswitch, semantic containment) to control the hazards and risks. Here we focus more on the reliability of the safety containment system rather than the functional part, although a similar assessment can also be applied to assess the reliability of the functional part.<br />
<br />
===Hazard Identification===<br />
Identifying hazards means that we need to find and understand the possible harm that may happen in the application of our system. Generally there are two potential hazards in environmental application of synthetic biology<sup>[[#References|1]]</sup> which are the successful escape of the GE bacteria followed by successful competition with natural strains, and horizontal gene transfer from GEO to natural strains.<br />
<br />
===Risk Assessment===<br />
Risk assessment provides an idea of what kind of risk we face in releasing the GEO in the environment and helps to design containment devices. Here we adapted a risk management method in workplaces complying with health and safety law <sup>[[#References|3]]</sup>.<br />
<br />
To-do-list to assess risk in 5 steps:<br />
#Identify the hazards<br />
#Decide who might be harmed and how<br />
#Evaluate the risks and decide on precaution<br />
#Record your findings and implement them<br />
#Review your assessment and update if necessary<br />
<br />
<br />
Worksheet example:<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are the hazards?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Who might be harmed and how?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are we already doing?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What further action is necessary?'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria outcompete natural strains<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria escaping the containment may outcompete natural strains if they have better fitness, creating natural imbalance <br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Using harmless strain or strain with low fitness compared to natural strain (standard E coli for lab)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to prevent the cells from reproducing themselves at some point and/or separating them from natural strains<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Horizontal gene transfer (HGT)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Other strain/species may uptake engineered genes, and if the genes give advantage in fitness, it may outcompete other strains creating natural imbalance<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| -<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to degrade DNA and/or separate the DNA from the environment and/or prevent natural strains from gaining advantages from modified DNA<br />
<br />
|}<br />
<br />
<br><br />
===Controlling hazards and risks===<br />
<br />
In this step we decided what control elements we want to implement in our system to reduce the risks. We should choose the best suitable control elements depending on the system function and application. As we already know that we want to apply bWARE safety containment, here we describe the role of each safety part in risk reduction. <br />
#GE bacteria outcompete natural strains<br />
#*In order to prevent GE bacteria from escaping and outcompeting the natural strains, we will stop their reproduction by putting a self killing mechanism based on [https://2012.igem.org/Team:Paris_Bettencourt/Suicide suicide] and [https://2012.igem.org/Team:Paris_Bettencourt/Restriction_Enzyme restriction enzyme] systems to kill the cells [https://2012.igem.org/Team:Paris_Bettencourt/Delay after] they perform their function. <br />
#*In case of the failure of the killing mechanism, we will put the cells inside a [https://2012.igem.org/Team:Paris_Bettencourt/Encapsulation physical containment] so there will be no physical interaction between them and the surrounding cells.<br />
#HGT<br />
#*We will use a [https://2012.igem.org/Team:Paris_Bettencourt/Suicide DNAse] to degrade DNA after the cells perform their function so they won’t leave any genetic material behind.<br />
#*In case of the failure due to inefficiency of the DNAse, the [https://2012.igem.org/Team:Paris_Bettencourt/Encapsulation physical containment] will still protect the DNA from the environment.<br />
#*In case of the leakiness of the physical containment, the DNA has a special encryption system, i.e. [https://2012.igem.org/Team:Paris_Bettencourt/Semantic_containment semantic containment], so the receiver cells will not be able to read GE genetic material.<br />
<br />
===Control Checks=== <br />
<br />
To check and predict the reliability of our system, we used fault tree analysis to assess multiple safety containment modules in one biodevice. This top-down approach allows us to see the relationship between each containment element and predict the overall failure probability. With this method we can see what basic events are the key elements in our system.<br />
<br />
[[File:ParisB_FTA.png|800px|center]]<br />
<br />
AND gate represents independent events<br />
<br />
P(A and B) = P(A)P(B)<br />
<br />
OR gate corresponds to set of union<br />
<br />
P(A or B) = P(A) + P(B)<br />
<br />
so the total failure probability of the system is<br />
<br />
Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9)<br />
<br />
List of the basic events<br />
<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Notation'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure component'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure mode'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Consequence'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Method for determining the probability'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P1<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| physical containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| leakage<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA/cell escape<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| experiment<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P2<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA uptake<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA transferred into natural strain<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| <nowiki>transconjugant to donor ratio in HGT is typically <10</nowiki><sup>-5</sup> <sup>[[#References|4]]</sup><br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P3<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| semantic containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P4<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| population suicide<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no surrounding cells with enough toxin<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no death<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| based on the cell density and the expectation number of surrounding non-mutant<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P5<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| toxin production<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no DNA degradation (w/o antitoxin), no death (with antitoxin)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P6<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| mutant fitness<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| beneficial mutation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| outcompetition of the mutant<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P7<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| delay system<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P8<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction enzyme<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P9<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction site<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|}<br />
<br />
====Physical containment failure====<br />
<br />
From the experiment we get the escape rate of the cells from the alginate beads is (escaping cells/total cells) is 10<sup>-5</sup> per 12 hours. Assuming 30 minutes of division time, we have 24 generations, and the escape rate per generation is 4 x 10<sup>-6</sup>.<br />
<br />
====Genetic failure====<br />
<br />
There are different processes that lead to a loss of function of a gene<br />
<br />
* Mutation<br />
* Recombination<br />
* Plasmid loss<br />
<br />
'''Losing function because of mutation'''<br />
<br />
Estimating the mutation rate which cause failure of the safety containment of the device<br />
<br />
* Spontaneous mutation rate of a wild-type E coli strain growing on research medium is 3.3 x 10<sup>-9</sup> per nucleotide per generation <sup>[[#References|5]]</sup> <br />
* approximately ⅔ of nucleotide mutation will change amino acid (64 combination of nucleotides code only 20 amino acids)<br />
* approximately 70% of amino acid change will lose the part function <sup>[[#References|6]]</sup><br />
* mean length of genetic coding sequence for E coli (procaryotes) is 924 bp <sup>[[#References|7]]</sup> ≈ 1000 bp <br />
<br />
So the loss function rate of a gene per generation because of mutation is <br />
<br />
P<sub>L</sub><nowiki>= 3.3 x 10</nowiki><sup>-9</sup> x ⅔ x 0.70 x 1000 = 1.54 x 10<sup>-6</sup> <br />
<br />
'''Recombination'''<br />
<br />
Finding a definite rate of recombination is not easy. Guttman and Dykhuizen in 1994 <sup>[[#References|8]]</sup> stated that recombination is believed to occur at such a low frequency, but their experiment showed that the rate could be as high as mutation rate (50 fold higher compared to the mutation rate believed at that moment, but actually it is 5.0 x 10<sup>-9</sup> changes per nucleotide per generation, a bit more than one fold to the value believed now). <br />
<br />
Redoing the previous calculation with this number will lead us to a rate of 2.33 x 10<sup>-6</sup> per gene per generation.<br />
<br />
'''Plasmid loss'''<br />
<br />
According to L Boe <sup>[[#References|9]]</sup> plasmid loss rate is defined as the probability that a division of a plasmid-carrying individual results in the birth of one plasmid-free and one plasmid-carrying daughter cell. For the low copy plasmid this rate is about ~1% /division and for high copy plasmid is ~0.01% /division, neglecting the viable/non-viable factor of the cells of losing the plasmid (no selection). If a plasmid with a lost rate of 0.05 is stabilized with a 100% efficient postsegragational killing system, the 5% of the division will result in non viable daughter cell, and we can not see the effect except of increasing the appearing division time by ln 2/ln (1-0.05) = 1.04. Thus in our system we can neglect this plasmid loss assuming that we have antibiotic selection in the beads.<br />
<br />
Assuming only mutation and recombination could happen to delete a function of a gene, we have the total genetic failure rate approximately 4 x 10<sup>-6</sup> per gene per generation.<br />
<br />
====Total failure probability====<br />
<br />
Having Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9) and put 1 for unknown probability (P4 and P6) as a worst-case scenario, we come to the failure rate number 6.4 x 10<sup>-11</sup> per generation.<br />
<br />
A volume of one alginate bead is approximately 20 uL. So if the cells grow until they reach the stationary phase (4 x 10<sup>9</sup> cells/ml), we will have 8 x 10<sup>7</sup> cells. If we started from 100 cells per bead, the number of generations we have is <sup>2</sup>log (8 x 10<sup>7</sup> / 100) =19.6 generations. Therefore the total failure becomes 6.4 x 10<sup>-11</sup> x 19.6 = 1.25 x 10<sup>-9</sup>.<br />
<br />
With this method we can also see that the sense-HGT rate is much lower (6.4 x 10<sup>-22</sup>) , almost negligible compared to the outcompetition rate, because it has more back up/redundancy components.<br />
<br />
== Discussion ==<br />
<br />
We have proposed and implemented an example of assessing biosafety by adapting existing methods from safety engineering. However, it is very clear that the prediction is based on rough estimation and we need more experimental data to verify this estimation. For an example, Torres et al <sup>[[#References|10]]</sup> tested a dual containment killing system and compared it with single containment system. They tested an EcoRI based system and a Colicin E3-based system and obtained the efficacy (based on the numbers of successful transformants) each 10<sup>4</sup> and 10<sup>5</sup> respectively but when they combine both system they only got efficacy 10<sup>6</sup>, while theoretically they could reach up to 10<sup>9</sup>. This could give us an idea that predicting the performance of a combination of genetic parts is not as easy as combining the performance of each genetic part. However, we can still conclude that having redundant parts is necessary to reduce the failure rate and make it as low as possible.<br />
<br />
Research in measuring the evolutionary stability in E coli was performed by Sean C Sleight et al <sup>[[#References|11]]</sup> where they measured it of BioBrick-assembled genetic circuits in E coli over multiple generation by measuring the number of loss-functioning mutants. They concluded that to make a robust GE bacteria, one has to take into account 3 principles:<br />
# High expression of genetic circuits comes with the cost of low evolutionary stability (for example induced vs non-induced system)<br />
#Avoid repeated sequences because it will more likely be mutated<br />
#Use of inducible promoters generally increases evolutionary stability compared to constitutive promoters<br />
<br />
To predict the robustness of the system from mutation, we have to take into account the duration (i.e. how many generations) we want our system to work. From their experiment for example, the AHL induced TetR-GFP cells lose their functions after 30 generations, while the uninduced ones lose their function slower (50% after 300 generations). A similar idea is also shown from our work where the mutation rate we got from literature research is in the unit of per generation. This is how reproduction differs biological system from other engineering systems. In engineering we also have failure probability as a function of time because of the life cycle of the system, but the system is not reproducing so it has no variability. <br />
<br />
Analyzing key elements that cause failure in any system including synthetic biology systems is essential for system improvement and prediction of failure. Adaptation of classical safety engineering methods needs to take into account the unique properties of synthetic biology. Reproducibility and complexity are two examples of areas that need to be studied deeper in this context. We invite future iGEM teams to use and improve our assessment framework, build a solid assessment protocol towards a better understanding of biosafety and successful application of synthetic biology.<br />
<br />
== Conclusion ==<br />
*We can adapt methods in safety engineering to assess risk in biosafety<br />
*We need more experimental data to confirm the risk assessing method<br />
<br />
== Perspectives ==<br />
<br />
*We need a method to predict the evolutionary stability of circuits from the properties of their parts, but the emergent behaviours of circuits will likely make prediction difficult. Thus it will be very useful if each BioBricks parts is completed with evolutionary stability data sheet, so we can make prediction of the stability of more complex circuits.<br />
*This safety assessment method is useful for identifying key elements of having failure in synthetic circuit systems before we go further to the real application. Thus we recommend for the future iGEM team to use our assessment method and give feedback to the community by improving this framework.<br />
<br />
==References==<br />
[[#Background|1]] - Genya V Dana et al. Four steps to avoid a synthetic biology disaster. 2012. Nature vol 483<br />
<br />
[[#Methods_and_Results|2]] - WorkSafe Victoria. A handbook for workplaces, controlling OHS hazards and risks. 2007. Edition No.1<br />
<br />
[[#Methods_and_Results|3]] - “Five steps to risk assessment” from [http://www.hse.gov.uk/risk/fivesteps.htm http://www.hse.gov.uk/risk/fivesteps.htm]. - risk management method in workplaces complying with health and safety law <br />
<br />
[[#Check_controls|4]] - Soren J Sorensen et al. 2005. Studying plasmid horizontal gene transfer in situ: a critical review. Nature Reviews Microbiology Vol 3<br />
<br />
[[#Check_controls|5]] - Heewook Lee et al., Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. 2012. PNAS E2774-E2783<br />
<br />
[[#Check_controls|6]] - Stanley A. Sawyer et al. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. 2007. PNAS 104(16):6504-6510<br />
<br />
[[#Check_controls|7]] - Lin Xu et al. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between two kingdoms. 2006. Mol. Biol. Evol. 23(6):1107-1108<br />
<br />
[[#Check_controls|8]] - David S Guttmand and Daniel E. Dykhuizen. 1994. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science Vol 266<br />
<br />
[[#Check_controls|9]] - L.Boe. 1996. Estimation of Plasmid Loss Rates in Bacterial Populations with a Reference to the Reproducibility of Stability Experiments. Plasmid 36, 161–167. Article No. 0043<br />
<br />
[[#Discussion|10]] - Torres B et al. 2003. A dual lethal system to enhance containment of recombinant micro-organisms. Microbiology. 2003 Dec;149(Pt 12):3595-601.<br />
<br />
[[#Discussion|11]] - Sean C Sleight et al., Designing and engineering evolutionary robust genetic circuits. 2010. Journal of Biological Engineering, 4:12<br />
</div><br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/ModelingTeam:Paris Bettencourt/Modeling2012-10-27T02:06:23Z<p>Aprastowo: /* Genetic failure */</p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<div id="boston"><br />
<br><br />
<div id="grouptitle">Safety Assessment</div><br />
<br />
==Overview==<br />
Safety is an important issue in synthetic biology, especially for environmentally related projects. We started to answer the question, “how safe is safe enough?” by involving experts, the public and our fellow scientists, and also by building biosafety devices. However, to really answer the question, we need first to ask ourselves a more basic question, “how do we measure safety?”. As we see synthetic biology as an engineering approach to biology, we could think about the adaptation of safety engineering, a well studied engineering subset, that has been widely use to minimize risks in many fields of engineering, such as mechanical engineering, aircrafts, and manufactures. However, the risks they face are surely different from the risks of synthetic biology. <br />
<br />
According to Dana et al<sup>[[#References|1]]</sup> there are four areas of risk research in environmental application of synthetic biology:<br />
*Differences in the physiology of natural and synthetic organisms will affect how they interact with the surrounding environment,<br />
*Escaped microorganisms have the potential to survive in receiving environments and to compete successfully with non-modified counterparts,<br />
*Synthetic organisms might evolve and adapt quickly, perhaps filling new ecological niches, and<br />
*Gene transfer.<br />
<br />
Knowing that there are different areas of risk that we need to take into account, we need to design our safety containment with different parts to deal with each of them. Identifying the relationship between one part and the others will help us to see the reliability of the overall system. Here we propose an approach to assess safety for environmental release of genetically engineered bacteria (GE bacteria).<br />
<br />
===Objectives===<br />
*Adapting existing safety assessment tools for synthetic biology.<br />
*Proposing new methods to assess safety in synthetic biology.<br />
<br />
==Methods and Results==<br />
We propose a method to assess hazards and risk<sup>[[#References|2]]</sup> in releasing genetically engineered bacteria into the environment. As a case study, we want to release GE bacteria which will perform some function in the environment and we want to apply 3 sets of bWARE safety containment modules (alginate beads, bWARE killswitch, semantic containment) to control the hazards and risks. Here we focus more on the reliability of the safety containment system rather than the functional part, although a similar assessment can also be applied to assess the reliability of the functional part.<br />
<br />
===Hazard Identification===<br />
Identifying hazards means that we need to find and understand the possible harm that may happen in the application of our system. Generally there are two potential hazards in environmental application of synthetic biology<sup>[[#References|1]]</sup> which are the successful escape of the GE bacteria followed by successful competition with natural strains, and horizontal gene transfer from GEO to natural strains.<br />
<br />
===Risk Assessment===<br />
Risk assessment provides an idea of what kind of risk we face in releasing the GEO in the environment and helps to design containment devices. Here we adapted a risk management method in workplaces complying with health and safety law <sup>[[#References|3]]</sup>.<br />
<br />
To-do-list to assess risk in 5 steps:<br />
#Identify the hazards<br />
#Decide who might be harmed and how<br />
#Evaluate the risks and decide on precaution<br />
#Record your findings and implement them<br />
#Review your assessment and update if necessary<br />
<br />
<br />
Worksheet example:<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are the hazards?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Who might be harmed and how?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are we already doing?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What further action is necessary?'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria outcompete natural strains<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria escaping the containment may outcompete natural strains if they have better fitness, creating natural imbalance <br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Using harmless strain or strain with low fitness compared to natural strain (standard E coli for lab)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to prevent the cells from reproducing themselves at some point and/or separating them from natural strains<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Horizontal gene transfer (HGT)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Other strain/species may uptake engineered genes, and if the genes give advantage in fitness, it may outcompete other strains creating natural imbalance<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| -<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to degrade DNA and/or separate the DNA from the environment and/or prevent natural strains from gaining advantages from modified DNA<br />
<br />
|}<br />
<br />
<br><br />
===Controlling hazards and risks===<br />
<br />
In this step we decided what control elements we want to implement in our system to reduce the risks. We should choose the best suitable control elements depending on the system function and application. As we already know that we want to apply bWARE safety containment, here we describe the role of each safety part in risk reduction. <br />
#GE bacteria outcompete natural strains<br />
#*In order to prevent GE bacteria from escaping and outcompeting the natural strains, we will stop their reproduction by putting a self killing mechanism based on [https://2012.igem.org/Team:Paris_Bettencourt/Suicide suicide] and [https://2012.igem.org/Team:Paris_Bettencourt/Restriction_Enzyme restriction enzyme] systems to kill the cells [https://2012.igem.org/Team:Paris_Bettencourt/Delay after] they perform their function. <br />
#*In case of the failure of the killing mechanism, we will put the cells inside a [https://2012.igem.org/Team:Paris_Bettencourt/Encapsulation physical containment] so there will be no physical interaction between them and the surrounding cells.<br />
#HGT<br />
#*We will use a [https://2012.igem.org/Team:Paris_Bettencourt/Suicide DNAse] to degrade DNA after the cells perform their function so they won’t leave any genetic material behind.<br />
#*In case of the failure due to inefficiency of the DNAse, the [https://2012.igem.org/Team:Paris_Bettencourt/Encapsulation physical containment] will still protect the DNA from the environment.<br />
#*In case of the leakiness of the physical containment, the DNA has a special encryption system, i.e. [https://2012.igem.org/Team:Paris_Bettencourt/Semantic_containment semantic containment], so the receiver cells will not be able to read GE genetic material.<br />
<br />
===Control Checks=== <br />
<br />
To check and predict the reliability of our system, we used fault tree analysis to assess multiple safety containment modules in one biodevice. This top-down approach allows us to see the relationship between each containment element and predict the overall failure probability. With this method we can see what basic events are the key elements in our system.<br />
<br />
[[File:ParisB_FTA.png|800px|center]]<br />
<br />
AND gate represents independent events<br />
<br />
P(A and B) = P(A)P(B)<br />
<br />
OR gate corresponds to set of union<br />
<br />
P(A or B) = P(A) + P(B)<br />
<br />
so the total failure probability of the system is<br />
<br />
Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9)<br />
<br />
List of the basic events<br />
<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Notation'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure component'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure mode'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Consequence'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Method for determining the probability'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P1<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| physical containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| leakage<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA/cell escape<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| experiment<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P2<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA uptake<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA transferred into natural strain<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| <nowiki>transconjugant to donor ratio in HGT is typically <10</nowiki><sup>-5</sup> <sup>[[#References|4]]</sup><br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P3<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| semantic containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P4<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| population suicide<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no surrounding cells with enough toxin<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no death<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| based on the cell density and the expectation number of surrounding non-mutant<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P5<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| toxin production<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no DNA degradation (w/o antitoxin), no death (with antitoxin)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P6<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| mutant fitness<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| beneficial mutation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| outcompetition of the mutant<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P7<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| delay system<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P8<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction enzyme<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P9<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction site<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|}<br />
<br />
====Physical containment failure====<br />
<br />
From the experiment we get the escape rate of the cells from the alginate beads is (escaping cells/total cells) is 10<sup>-5</sup> per 12 hours. Assuming 30 minutes of division time, we have 24 generations, and the escape rate per generation is 4 x 10<sup>-6</sup>.<br />
<br />
====Genetic failure====<br />
<br />
There are different processes that lead to a loss of function of a gene<br />
<br />
* Mutation<br />
* Recombination<br />
* Plasmid loss<br />
<br />
'''Losing function because of mutation'''<br />
<br />
Estimating the mutation rate which cause failure of the safety containment of the device<br />
<br />
* Spontaneous mutation rate of a wild-type E coli strain growing on research medium is 3.3 x 10<sup>-9</sup> per nucleotide per generation <sup>[[#References|5]]</sup> <br />
* approximately ⅔ of nucleotide mutation will change amino acid (64 combination of nucleotides code only 20 amino acids)<br />
* approximately 70% of amino acid change will lose the part function <sup>[[#References|6]]</sup><br />
* mean length of genetic coding sequence for E coli (procaryotes) is 924 bp <sup>[[#References|7]]</sup> ≈ 1000 bp <br />
<br />
So the loss function rate of a gene per generation because of mutation is <br />
<br />
P<sub>L</sub><nowiki>= 3.3 x 10</nowiki><sup>-9</sup> x ⅔ x 0.70 x 1000 = 1.54 x 10<sup>-6</sup> <br />
<br />
'''Recombination'''<br />
<br />
Finding a definite rate of recombination is not easy. Guttman and Dykhuizen in 1994 <sup>[[#References|8]]</sup> stated that recombination is believed to occur at such a low frequency, but their experiment showed that the rate could be as high as mutation rate (50 fold higher compared to the mutation rate believed at that moment, but actually it is 5.0 x 10<sup>-9</sup> changes per nucleotide per generation, a bit more than one fold to the value believed now). <br />
<br />
Redoing the previous calculation with this number will lead us to a rate of 2.33 x 10<sup>-6</sup> per gene per generation.<br />
<br />
'''Plasmid loss'''<br />
<br />
According to L Boe <sup>[[#References|9]]</sup> plasmid loss rate is defined as the probability that a division of a plasmid-carrying individual results in the birth of one plasmid-free and one plasmid-carrying daughter cell. For the low copy plasmid this rate is about ~1% /division and for high copy plasmid is ~0.01% /division, neglecting the viable/non-viable factor of the cells of losing the plasmid (no selection). If a plasmid with a lost rate of 0.05 is stabilized with a 100% efficient postsegragational killing system, the 5% of the division will result in non viable daughter cell, and we can not see the effect except of increasing the appearing division time by ln 2/ln (1-0.05) = 1.04. Thus in our system we can neglect this plasmid loss assuming that we have antibiotic selection in the beads.<br />
<br />
Assuming only mutation and recombination could happen to delete a function of a gene, we have the total genetic failure rate around 4 x 10<sup>-6</sup> per gene per generation.<br />
<br />
====Total failure probability====<br />
<br />
Having Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9) and put 1 for unknown probability (P4 and P6) as a worst-case scenario, we come to the failure rate number 6.4 x 10<sup>-11</sup> per generation.<br />
<br />
A volume of one alginate bead is approximately 20 uL. So if the cells grow until they reach the stationary phase (4 x 10<sup>9</sup> cells/ml), we will have 8 x 10<sup>7</sup> cells. If we started from 100 cells per bead, the number of generations we have is <sup>2</sup>log (8 x 10<sup>7</sup> / 100) =19.6 generations. Therefore the total failure becomes 6.4 x 10<sup>-11</sup> x 19.6 = 1.25 x 10<sup>-9</sup>.<br />
<br />
With this method we can also see that the sense-HGT rate is much lower (6.4 x 10<sup>-22</sup>) , almost negligible compared to the outcompetition rate, because it has more back up/redundancy components.<br />
<br />
== Discussion ==<br />
<br />
We have proposed and implemented an example of assessing biosafety by adapting existing methods from safety engineering. However, it is very clear that the prediction is based on rough estimation and we need more experimental data to verify this estimation. For an example, Torres et al <sup>[[#References|10]]</sup> tested a dual containment killing system and compared it with single containment system. They tested an EcoRI based system and a Colicin E3-based system and obtained the efficacy (based on the numbers of successful transformants) each 10<sup>4</sup> and 10<sup>5</sup> respectively but when they combine both system they only got efficacy 10<sup>6</sup>, while theoretically they could reach up to 10<sup>9</sup>. This could give us an idea that predicting the performance of a combination of genetic parts is not as easy as combining the performance of each genetic part. However, we can still conclude that having redundant parts is necessary to reduce the failure rate and make it as low as possible.<br />
<br />
Research in measuring the evolutionary stability in E coli was performed by Sean C Sleight et al <sup>[[#References|11]]</sup> where they measured it of BioBrick-assembled genetic circuits in E coli over multiple generation by measuring the number of loss-functioning mutants. They concluded that to make a robust GE bacteria, one has to take into account 3 principles:<br />
# High expression of genetic circuits comes with the cost of low evolutionary stability (for example induced vs non-induced system)<br />
#Avoid repeated sequences because it will more likely be mutated<br />
#Use of inducible promoters generally increases evolutionary stability compared to constitutive promoters<br />
<br />
To predict the robustness of the system from mutation, we have to take into account the duration (i.e. how many generations) we want our system to work. From their experiment for example, the AHL induced TetR-GFP cells lose their functions after 30 generations, while the uninduced ones lose their function slower (50% after 300 generations). A similar idea is also shown from our work where the mutation rate we got from literature research is in the unit of per generation. This is how reproduction differs biological system from other engineering systems. In engineering we also have failure probability as a function of time because of the life cycle of the system, but the system is not reproducing so it has no variability. <br />
<br />
Analyzing key elements that cause failure in any system including synthetic biology systems is essential for system improvement and prediction of failure. Adaptation of classical safety engineering methods needs to take into account the unique properties of synthetic biology. Reproducibility and complexity are two examples of areas that need to be studied deeper in this context. We invite future iGEM teams to use and improve our assessment framework, build a solid assessment protocol towards a better understanding of biosafety and successful application of synthetic biology.<br />
<br />
== Conclusion ==<br />
*We can adapt methods in safety engineering to assess risk in biosafety<br />
*We need more experimental data to confirm the risk assessing method<br />
<br />
== Perspectives ==<br />
<br />
*We need a method to predict the evolutionary stability of circuits from the properties of their parts, but the emergent behaviours of circuits will likely make prediction difficult. Thus it will be very useful if each BioBricks parts is completed with evolutionary stability data sheet, so we can make prediction of the stability of more complex circuits.<br />
*This safety assessment method is useful for identifying key elements of having failure in synthetic circuit systems before we go further to the real application. Thus we recommend for the future iGEM team to use our assessment method and give feedback to the community by improving this framework.<br />
<br />
==References==<br />
[[#Background|1]] - Genya V Dana et al. Four steps to avoid a synthetic biology disaster. 2012. Nature vol 483<br />
<br />
[[#Methods_and_Results|2]] - WorkSafe Victoria. A handbook for workplaces, controlling OHS hazards and risks. 2007. Edition No.1<br />
<br />
[[#Methods_and_Results|3]] - “Five steps to risk assessment” from [http://www.hse.gov.uk/risk/fivesteps.htm http://www.hse.gov.uk/risk/fivesteps.htm]. - risk management method in workplaces complying with health and safety law <br />
<br />
[[#Check_controls|4]] - Soren J Sorensen et al. 2005. Studying plasmid horizontal gene transfer in situ: a critical review. Nature Reviews Microbiology Vol 3<br />
<br />
[[#Check_controls|5]] - Heewook Lee et al., Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. 2012. PNAS E2774-E2783<br />
<br />
[[#Check_controls|6]] - Stanley A. Sawyer et al. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. 2007. PNAS 104(16):6504-6510<br />
<br />
[[#Check_controls|7]] - Lin Xu et al. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between two kingdoms. 2006. Mol. Biol. Evol. 23(6):1107-1108<br />
<br />
[[#Check_controls|8]] - David S Guttmand and Daniel E. Dykhuizen. 1994. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science Vol 266<br />
<br />
[[#Check_controls|9]] - L.Boe. 1996. Estimation of Plasmid Loss Rates in Bacterial Populations with a Reference to the Reproducibility of Stability Experiments. Plasmid 36, 161–167. Article No. 0043<br />
<br />
[[#Discussion|10]] - Torres B et al. 2003. A dual lethal system to enhance containment of recombinant micro-organisms. Microbiology. 2003 Dec;149(Pt 12):3595-601.<br />
<br />
[[#Discussion|11]] - Sean C Sleight et al., Designing and engineering evolutionary robust genetic circuits. 2010. Journal of Biological Engineering, 4:12<br />
</div><br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/ModelingTeam:Paris Bettencourt/Modeling2012-10-27T02:04:10Z<p>Aprastowo: /* Controlling hazards and risks */</p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<div id="boston"><br />
<br><br />
<div id="grouptitle">Safety Assessment</div><br />
<br />
==Overview==<br />
Safety is an important issue in synthetic biology, especially for environmentally related projects. We started to answer the question, “how safe is safe enough?” by involving experts, the public and our fellow scientists, and also by building biosafety devices. However, to really answer the question, we need first to ask ourselves a more basic question, “how do we measure safety?”. As we see synthetic biology as an engineering approach to biology, we could think about the adaptation of safety engineering, a well studied engineering subset, that has been widely use to minimize risks in many fields of engineering, such as mechanical engineering, aircrafts, and manufactures. However, the risks they face are surely different from the risks of synthetic biology. <br />
<br />
According to Dana et al<sup>[[#References|1]]</sup> there are four areas of risk research in environmental application of synthetic biology:<br />
*Differences in the physiology of natural and synthetic organisms will affect how they interact with the surrounding environment,<br />
*Escaped microorganisms have the potential to survive in receiving environments and to compete successfully with non-modified counterparts,<br />
*Synthetic organisms might evolve and adapt quickly, perhaps filling new ecological niches, and<br />
*Gene transfer.<br />
<br />
Knowing that there are different areas of risk that we need to take into account, we need to design our safety containment with different parts to deal with each of them. Identifying the relationship between one part and the others will help us to see the reliability of the overall system. Here we propose an approach to assess safety for environmental release of genetically engineered bacteria (GE bacteria).<br />
<br />
===Objectives===<br />
*Adapting existing safety assessment tools for synthetic biology.<br />
*Proposing new methods to assess safety in synthetic biology.<br />
<br />
==Methods and Results==<br />
We propose a method to assess hazards and risk<sup>[[#References|2]]</sup> in releasing genetically engineered bacteria into the environment. As a case study, we want to release GE bacteria which will perform some function in the environment and we want to apply 3 sets of bWARE safety containment modules (alginate beads, bWARE killswitch, semantic containment) to control the hazards and risks. Here we focus more on the reliability of the safety containment system rather than the functional part, although a similar assessment can also be applied to assess the reliability of the functional part.<br />
<br />
===Hazard Identification===<br />
Identifying hazards means that we need to find and understand the possible harm that may happen in the application of our system. Generally there are two potential hazards in environmental application of synthetic biology<sup>[[#References|1]]</sup> which are the successful escape of the GE bacteria followed by successful competition with natural strains, and horizontal gene transfer from GEO to natural strains.<br />
<br />
===Risk Assessment===<br />
Risk assessment provides an idea of what kind of risk we face in releasing the GEO in the environment and helps to design containment devices. Here we adapted a risk management method in workplaces complying with health and safety law <sup>[[#References|3]]</sup>.<br />
<br />
To-do-list to assess risk in 5 steps:<br />
#Identify the hazards<br />
#Decide who might be harmed and how<br />
#Evaluate the risks and decide on precaution<br />
#Record your findings and implement them<br />
#Review your assessment and update if necessary<br />
<br />
<br />
Worksheet example:<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are the hazards?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Who might be harmed and how?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are we already doing?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What further action is necessary?'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria outcompete natural strains<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria escaping the containment may outcompete natural strains if they have better fitness, creating natural imbalance <br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Using harmless strain or strain with low fitness compared to natural strain (standard E coli for lab)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to prevent the cells from reproducing themselves at some point and/or separating them from natural strains<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Horizontal gene transfer (HGT)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Other strain/species may uptake engineered genes, and if the genes give advantage in fitness, it may outcompete other strains creating natural imbalance<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| -<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to degrade DNA and/or separate the DNA from the environment and/or prevent natural strains from gaining advantages from modified DNA<br />
<br />
|}<br />
<br />
<br><br />
===Controlling hazards and risks===<br />
<br />
In this step we decided what control elements we want to implement in our system to reduce the risks. We should choose the best suitable control elements depending on the system function and application. As we already know that we want to apply bWARE safety containment, here we describe the role of each safety part in risk reduction. <br />
#GE bacteria outcompete natural strains<br />
#*In order to prevent GE bacteria from escaping and outcompeting the natural strains, we will stop their reproduction by putting a self killing mechanism based on [https://2012.igem.org/Team:Paris_Bettencourt/Suicide suicide] and [https://2012.igem.org/Team:Paris_Bettencourt/Restriction_Enzyme restriction enzyme] systems to kill the cells [https://2012.igem.org/Team:Paris_Bettencourt/Delay after] they perform their function. <br />
#*In case of the failure of the killing mechanism, we will put the cells inside a [https://2012.igem.org/Team:Paris_Bettencourt/Encapsulation physical containment] so there will be no physical interaction between them and the surrounding cells.<br />
#HGT<br />
#*We will use a [https://2012.igem.org/Team:Paris_Bettencourt/Suicide DNAse] to degrade DNA after the cells perform their function so they won’t leave any genetic material behind.<br />
#*In case of the failure due to inefficiency of the DNAse, the [https://2012.igem.org/Team:Paris_Bettencourt/Encapsulation physical containment] will still protect the DNA from the environment.<br />
#*In case of the leakiness of the physical containment, the DNA has a special encryption system, i.e. [https://2012.igem.org/Team:Paris_Bettencourt/Semantic_containment semantic containment], so the receiver cells will not be able to read GE genetic material.<br />
<br />
===Control Checks=== <br />
<br />
To check and predict the reliability of our system, we used fault tree analysis to assess multiple safety containment modules in one biodevice. This top-down approach allows us to see the relationship between each containment element and predict the overall failure probability. With this method we can see what basic events are the key elements in our system.<br />
<br />
[[File:ParisB_FTA.png|800px|center]]<br />
<br />
AND gate represents independent events<br />
<br />
P(A and B) = P(A)P(B)<br />
<br />
OR gate corresponds to set of union<br />
<br />
P(A or B) = P(A) + P(B)<br />
<br />
so the total failure probability of the system is<br />
<br />
Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9)<br />
<br />
List of the basic events<br />
<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Notation'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure component'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure mode'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Consequence'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Method for determining the probability'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P1<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| physical containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| leakage<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA/cell escape<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| experiment<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P2<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA uptake<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA transferred into natural strain<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| <nowiki>transconjugant to donor ratio in HGT is typically <10</nowiki><sup>-5</sup> <sup>[[#References|4]]</sup><br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P3<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| semantic containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P4<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| population suicide<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no surrounding cells with enough toxin<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no death<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| based on the cell density and the expectation number of surrounding non-mutant<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P5<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| toxin production<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no DNA degradation (w/o antitoxin), no death (with antitoxin)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P6<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| mutant fitness<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| beneficial mutation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| outcompetition of the mutant<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P7<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| delay system<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P8<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction enzyme<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P9<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction site<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|}<br />
<br />
====Physical containment failure====<br />
<br />
From the experiment we get the escape rate of the cells from the alginate beads is (escaping cells/total cells) is 10<sup>-5</sup> per 12 hours. Assuming 30 minutes of division time, we have 24 generations, and the escape rate per generation is 4 x 10<sup>-6</sup>.<br />
<br />
====Genetic failure====<br />
<br />
There are different processes that lead to a loss of function of a gene<br />
<br />
* Mutation<br />
* Recombination<br />
* Plasmid loss<br />
<br />
'''Losing function because of mutation'''<br />
<br />
Estimating the mutation rate which cause failure of the safety containment of the device<br />
<br />
* Spontaneous mutation rate of a wild-type E coli strain growing on research medium is 3.3 x 10<sup>-9</sup> per nucleotide per generation <sup>[[#References|5]]</sup> <br />
* approximately ⅔ of nucleotide mutation will change amino acid (64 combination of nucleotides code only 20 amino acids)<br />
* approximately 70% of amino acid change will lose the part function <sup>[[#References|6]]</sup><br />
* mean length of genetic coding sequence for E coli (procaryotes) is 924 bp <sup>[[#References|7]]</sup> ≈ 1000 bp <br />
<br />
So the loss function rate of a gene per generation because of mutation is <br />
<br />
P<sub>L</sub><nowiki>= 3.3 x 10</nowiki><sup>-9</sup> x ⅔ x 0.70 x 1000 = 1.54 x 10<sup>-6</sup> <br />
<br />
'''Recombination'''<br />
<br />
Finding a definite rate of recombination is not easy. Guttman and Dykhuizen in 1994 <sup>[[#References|8]]</sup> stated that recombination is believed to occur at such a low frequency, but their experiment showed that the rate could be as high as mutation rate (50 fold higher compared to the mutation rate believed at that moment, but actually it is 5.0 x 10<sup>-9</sup> changes per nucleotide per generation, a bit more than one fold to the value believed now). <br />
<br />
Redoing the previous calculation with this number will lead us to 2.33 x 10<sup>-6</sup> per gene per generation.<br />
<br />
'''Plasmid loss'''<br />
<br />
According to L Boe <sup>[[#References|9]]</sup> plasmid loss rate is defined as the probability that a division of a plasmid-carrying individual results in the birth of one plasmid-free and one plasmid-carrying daughter cell. For the low copy plasmid this rate is about ~1% /division and for high copy plasmid is ~0.01% /division, neglecting the viable/non-viable factor of the cells of losing the plasmid (no selection). If a plasmid with a lost rate of 0.05 is stabilized with a 100% efficient postsegragational killing system, the 5% of the division will result in non viable daughter cell, and we can not see the effect except of increasing the appearing division time by ln 2/ln (1-0.05) = 1.04. Thus in our system we can neglect this plasmid loss assuming that we have antibiotic selection in the beads.<br />
<br />
Assuming only mutation and recombination could happen to delete a function of a gene, we have the total genetic failure rate around 4 x 10<sup>-6</sup> per gene per generation.<br />
<br />
====Total failure probability====<br />
<br />
Having Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9) and put 1 for unknown probability (P4 and P6) as a worst-case scenario, we come to the failure rate number 6.4 x 10<sup>-11</sup> per generation.<br />
<br />
A volume of one alginate bead is approximately 20 uL. So if the cells grow until they reach the stationary phase (4 x 10<sup>9</sup> cells/ml), we will have 8 x 10<sup>7</sup> cells. If we started from 100 cells per bead, the number of generations we have is <sup>2</sup>log (8 x 10<sup>7</sup> / 100) =19.6 generations. Therefore the total failure becomes 6.4 x 10<sup>-11</sup> x 19.6 = 1.25 x 10<sup>-9</sup>.<br />
<br />
With this method we can also see that the sense-HGT rate is much lower (6.4 x 10<sup>-22</sup>) , almost negligible compared to the outcompetition rate, because it has more back up/redundancy components.<br />
<br />
== Discussion ==<br />
<br />
We have proposed and implemented an example of assessing biosafety by adapting existing methods from safety engineering. However, it is very clear that the prediction is based on rough estimation and we need more experimental data to verify this estimation. For an example, Torres et al <sup>[[#References|10]]</sup> tested a dual containment killing system and compared it with single containment system. They tested an EcoRI based system and a Colicin E3-based system and obtained the efficacy (based on the numbers of successful transformants) each 10<sup>4</sup> and 10<sup>5</sup> respectively but when they combine both system they only got efficacy 10<sup>6</sup>, while theoretically they could reach up to 10<sup>9</sup>. This could give us an idea that predicting the performance of a combination of genetic parts is not as easy as combining the performance of each genetic part. However, we can still conclude that having redundant parts is necessary to reduce the failure rate and make it as low as possible.<br />
<br />
Research in measuring the evolutionary stability in E coli was performed by Sean C Sleight et al <sup>[[#References|11]]</sup> where they measured it of BioBrick-assembled genetic circuits in E coli over multiple generation by measuring the number of loss-functioning mutants. They concluded that to make a robust GE bacteria, one has to take into account 3 principles:<br />
# High expression of genetic circuits comes with the cost of low evolutionary stability (for example induced vs non-induced system)<br />
#Avoid repeated sequences because it will more likely be mutated<br />
#Use of inducible promoters generally increases evolutionary stability compared to constitutive promoters<br />
<br />
To predict the robustness of the system from mutation, we have to take into account the duration (i.e. how many generations) we want our system to work. From their experiment for example, the AHL induced TetR-GFP cells lose their functions after 30 generations, while the uninduced ones lose their function slower (50% after 300 generations). A similar idea is also shown from our work where the mutation rate we got from literature research is in the unit of per generation. This is how reproduction differs biological system from other engineering systems. In engineering we also have failure probability as a function of time because of the life cycle of the system, but the system is not reproducing so it has no variability. <br />
<br />
Analyzing key elements that cause failure in any system including synthetic biology systems is essential for system improvement and prediction of failure. Adaptation of classical safety engineering methods needs to take into account the unique properties of synthetic biology. Reproducibility and complexity are two examples of areas that need to be studied deeper in this context. We invite future iGEM teams to use and improve our assessment framework, build a solid assessment protocol towards a better understanding of biosafety and successful application of synthetic biology.<br />
<br />
== Conclusion ==<br />
*We can adapt methods in safety engineering to assess risk in biosafety<br />
*We need more experimental data to confirm the risk assessing method<br />
<br />
== Perspectives ==<br />
<br />
*We need a method to predict the evolutionary stability of circuits from the properties of their parts, but the emergent behaviours of circuits will likely make prediction difficult. Thus it will be very useful if each BioBricks parts is completed with evolutionary stability data sheet, so we can make prediction of the stability of more complex circuits.<br />
*This safety assessment method is useful for identifying key elements of having failure in synthetic circuit systems before we go further to the real application. Thus we recommend for the future iGEM team to use our assessment method and give feedback to the community by improving this framework.<br />
<br />
==References==<br />
[[#Background|1]] - Genya V Dana et al. Four steps to avoid a synthetic biology disaster. 2012. Nature vol 483<br />
<br />
[[#Methods_and_Results|2]] - WorkSafe Victoria. A handbook for workplaces, controlling OHS hazards and risks. 2007. Edition No.1<br />
<br />
[[#Methods_and_Results|3]] - “Five steps to risk assessment” from [http://www.hse.gov.uk/risk/fivesteps.htm http://www.hse.gov.uk/risk/fivesteps.htm]. - risk management method in workplaces complying with health and safety law <br />
<br />
[[#Check_controls|4]] - Soren J Sorensen et al. 2005. Studying plasmid horizontal gene transfer in situ: a critical review. Nature Reviews Microbiology Vol 3<br />
<br />
[[#Check_controls|5]] - Heewook Lee et al., Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. 2012. PNAS E2774-E2783<br />
<br />
[[#Check_controls|6]] - Stanley A. Sawyer et al. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. 2007. PNAS 104(16):6504-6510<br />
<br />
[[#Check_controls|7]] - Lin Xu et al. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between two kingdoms. 2006. Mol. Biol. Evol. 23(6):1107-1108<br />
<br />
[[#Check_controls|8]] - David S Guttmand and Daniel E. Dykhuizen. 1994. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science Vol 266<br />
<br />
[[#Check_controls|9]] - L.Boe. 1996. Estimation of Plasmid Loss Rates in Bacterial Populations with a Reference to the Reproducibility of Stability Experiments. Plasmid 36, 161–167. Article No. 0043<br />
<br />
[[#Discussion|10]] - Torres B et al. 2003. A dual lethal system to enhance containment of recombinant micro-organisms. Microbiology. 2003 Dec;149(Pt 12):3595-601.<br />
<br />
[[#Discussion|11]] - Sean C Sleight et al., Designing and engineering evolutionary robust genetic circuits. 2010. Journal of Biological Engineering, 4:12<br />
</div><br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/ModelingTeam:Paris Bettencourt/Modeling2012-10-27T01:59:25Z<p>Aprastowo: /* Control Checks */</p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<div id="boston"><br />
<br><br />
<div id="grouptitle">Safety Assessment</div><br />
<br />
==Overview==<br />
Safety is an important issue in synthetic biology, especially for environmentally related projects. We started to answer the question, “how safe is safe enough?” by involving experts, the public and our fellow scientists, and also by building biosafety devices. However, to really answer the question, we need first to ask ourselves a more basic question, “how do we measure safety?”. As we see synthetic biology as an engineering approach to biology, we could think about the adaptation of safety engineering, a well studied engineering subset, that has been widely use to minimize risks in many fields of engineering, such as mechanical engineering, aircrafts, and manufactures. However, the risks they face are surely different from the risks of synthetic biology. <br />
<br />
According to Dana et al<sup>[[#References|1]]</sup> there are four areas of risk research in environmental application of synthetic biology:<br />
*Differences in the physiology of natural and synthetic organisms will affect how they interact with the surrounding environment,<br />
*Escaped microorganisms have the potential to survive in receiving environments and to compete successfully with non-modified counterparts,<br />
*Synthetic organisms might evolve and adapt quickly, perhaps filling new ecological niches, and<br />
*Gene transfer.<br />
<br />
Knowing that there are different areas of risk that we need to take into account, we need to design our safety containment with different parts to deal with each of them. Identifying the relationship between one part and the others will help us to see the reliability of the overall system. Here we propose an approach to assess safety for environmental release of genetically engineered bacteria (GE bacteria).<br />
<br />
===Objectives===<br />
*Adapting existing safety assessment tools for synthetic biology.<br />
*Proposing new methods to assess safety in synthetic biology.<br />
<br />
==Methods and Results==<br />
We propose a method to assess hazards and risk<sup>[[#References|2]]</sup> in releasing genetically engineered bacteria into the environment. As a case study, we want to release GE bacteria which will perform some function in the environment and we want to apply 3 sets of bWARE safety containment modules (alginate beads, bWARE killswitch, semantic containment) to control the hazards and risks. Here we focus more on the reliability of the safety containment system rather than the functional part, although a similar assessment can also be applied to assess the reliability of the functional part.<br />
<br />
===Hazard Identification===<br />
Identifying hazards means that we need to find and understand the possible harm that may happen in the application of our system. Generally there are two potential hazards in environmental application of synthetic biology<sup>[[#References|1]]</sup> which are the successful escape of the GE bacteria followed by successful competition with natural strains, and horizontal gene transfer from GEO to natural strains.<br />
<br />
===Risk Assessment===<br />
Risk assessment provides an idea of what kind of risk we face in releasing the GEO in the environment and helps to design containment devices. Here we adapted a risk management method in workplaces complying with health and safety law <sup>[[#References|3]]</sup>.<br />
<br />
To-do-list to assess risk in 5 steps:<br />
#Identify the hazards<br />
#Decide who might be harmed and how<br />
#Evaluate the risks and decide on precaution<br />
#Record your findings and implement them<br />
#Review your assessment and update if necessary<br />
<br />
<br />
Worksheet example:<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are the hazards?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Who might be harmed and how?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are we already doing?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What further action is necessary?'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria outcompete natural strains<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria escaping the containment may outcompete natural strains if they have better fitness, creating natural imbalance <br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Using harmless strain or strain with low fitness compared to natural strain (standard E coli for lab)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to prevent the cells from reproducing themselves at some point and/or separating them from natural strains<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Horizontal gene transfer (HGT)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Other strain/species may uptake engineered genes, and if the genes give advantage in fitness, it may outcompete other strains creating natural imbalance<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| -<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to degrade DNA and/or separate the DNA from the environment and/or prevent natural strains from gaining advantages from modified DNA<br />
<br />
|}<br />
<br />
<br><br />
===Controlling hazards and risks===<br />
<br />
In this step we decided what control elements we want to implement in our system to reduce the risks. We should choose the best suitable control elements depending on the system function and application. As we already know that we want to apply bWARE safety containment, here we describe the role of each safety part in risk reduction. <br />
#GE bacteria outcompete natural strains<br />
#*In order to prevent GE bacteria from escaping and outcompeting the natural strains, we will stop their reproduction by putting a suicide mechanism to kill the cells after they perform their function. <br />
#*In case of the failure of the killing mechanism, we will put the cells inside a physical containment so there will be no physical interaction between them and the surrounding cells.<br />
#HGT<br />
#*We will use a DNAse to degrade DNA after the cells perform their function so they won’t leave any genetic material behind.<br />
#*In case of the failure due to inefficiency of the DNAse, the physical containment will still protect the DNA from the environment.<br />
#*In case of the leakiness of the physical containment, the DNA has a special encryption system, i.e. semantic containment, so the receiver cells will not be able to read GEO genetic material.<br />
<br />
===Control Checks=== <br />
<br />
To check and predict the reliability of our system, we used fault tree analysis to assess multiple safety containment modules in one biodevice. This top-down approach allows us to see the relationship between each containment element and predict the overall failure probability. With this method we can see what basic events are the key elements in our system.<br />
<br />
[[File:ParisB_FTA.png|800px|center]]<br />
<br />
AND gate represents independent events<br />
<br />
P(A and B) = P(A)P(B)<br />
<br />
OR gate corresponds to set of union<br />
<br />
P(A or B) = P(A) + P(B)<br />
<br />
so the total failure probability of the system is<br />
<br />
Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9)<br />
<br />
List of the basic events<br />
<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Notation'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure component'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure mode'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Consequence'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Method for determining the probability'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P1<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| physical containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| leakage<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA/cell escape<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| experiment<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P2<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA uptake<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA transferred into natural strain<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| <nowiki>transconjugant to donor ratio in HGT is typically <10</nowiki><sup>-5</sup> <sup>[[#References|4]]</sup><br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P3<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| semantic containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P4<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| population suicide<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no surrounding cells with enough toxin<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no death<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| based on the cell density and the expectation number of surrounding non-mutant<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P5<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| toxin production<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no DNA degradation (w/o antitoxin), no death (with antitoxin)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P6<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| mutant fitness<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| beneficial mutation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| outcompetition of the mutant<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P7<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| delay system<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P8<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction enzyme<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P9<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction site<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|}<br />
<br />
====Physical containment failure====<br />
<br />
From the experiment we get the escape rate of the cells from the alginate beads is (escaping cells/total cells) is 10<sup>-5</sup> per 12 hours. Assuming 30 minutes of division time, we have 24 generations, and the escape rate per generation is 4 x 10<sup>-6</sup>.<br />
<br />
====Genetic failure====<br />
<br />
There are different processes that lead to a loss of function of a gene<br />
<br />
* Mutation<br />
* Recombination<br />
* Plasmid loss<br />
<br />
'''Losing function because of mutation'''<br />
<br />
Estimating the mutation rate which cause failure of the safety containment of the device<br />
<br />
* Spontaneous mutation rate of a wild-type E coli strain growing on research medium is 3.3 x 10<sup>-9</sup> per nucleotide per generation <sup>[[#References|5]]</sup> <br />
* approximately ⅔ of nucleotide mutation will change amino acid (64 combination of nucleotides code only 20 amino acids)<br />
* approximately 70% of amino acid change will lose the part function <sup>[[#References|6]]</sup><br />
* mean length of genetic coding sequence for E coli (procaryotes) is 924 bp <sup>[[#References|7]]</sup> ≈ 1000 bp <br />
<br />
So the loss function rate of a gene per generation because of mutation is <br />
<br />
P<sub>L</sub><nowiki>= 3.3 x 10</nowiki><sup>-9</sup> x ⅔ x 0.70 x 1000 = 1.54 x 10<sup>-6</sup> <br />
<br />
'''Recombination'''<br />
<br />
Finding a definite rate of recombination is not easy. Guttman and Dykhuizen in 1994 <sup>[[#References|8]]</sup> stated that recombination is believed to occur at such a low frequency, but their experiment showed that the rate could be as high as mutation rate (50 fold higher compared to the mutation rate believed at that moment, but actually it is 5.0 x 10<sup>-9</sup> changes per nucleotide per generation, a bit more than one fold to the value believed now). <br />
<br />
Redoing the previous calculation with this number will lead us to 2.33 x 10<sup>-6</sup> per gene per generation.<br />
<br />
'''Plasmid loss'''<br />
<br />
According to L Boe <sup>[[#References|9]]</sup> plasmid loss rate is defined as the probability that a division of a plasmid-carrying individual results in the birth of one plasmid-free and one plasmid-carrying daughter cell. For the low copy plasmid this rate is about ~1% /division and for high copy plasmid is ~0.01% /division, neglecting the viable/non-viable factor of the cells of losing the plasmid (no selection). If a plasmid with a lost rate of 0.05 is stabilized with a 100% efficient postsegragational killing system, the 5% of the division will result in non viable daughter cell, and we can not see the effect except of increasing the appearing division time by ln 2/ln (1-0.05) = 1.04. Thus in our system we can neglect this plasmid loss assuming that we have antibiotic selection in the beads.<br />
<br />
Assuming only mutation and recombination could happen to delete a function of a gene, we have the total genetic failure rate around 4 x 10<sup>-6</sup> per gene per generation.<br />
<br />
====Total failure probability====<br />
<br />
Having Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9) and put 1 for unknown probability (P4 and P6) as a worst-case scenario, we come to the failure rate number 6.4 x 10<sup>-11</sup> per generation.<br />
<br />
A volume of one alginate bead is approximately 20 uL. So if the cells grow until they reach the stationary phase (4 x 10<sup>9</sup> cells/ml), we will have 8 x 10<sup>7</sup> cells. If we started from 100 cells per bead, the number of generations we have is <sup>2</sup>log (8 x 10<sup>7</sup> / 100) =19.6 generations. Therefore the total failure becomes 6.4 x 10<sup>-11</sup> x 19.6 = 1.25 x 10<sup>-9</sup>.<br />
<br />
With this method we can also see that the sense-HGT rate is much lower (6.4 x 10<sup>-22</sup>) , almost negligible compared to the outcompetition rate, because it has more back up/redundancy components.<br />
<br />
== Discussion ==<br />
<br />
We have proposed and implemented an example of assessing biosafety by adapting existing methods from safety engineering. However, it is very clear that the prediction is based on rough estimation and we need more experimental data to verify this estimation. For an example, Torres et al <sup>[[#References|10]]</sup> tested a dual containment killing system and compared it with single containment system. They tested an EcoRI based system and a Colicin E3-based system and obtained the efficacy (based on the numbers of successful transformants) each 10<sup>4</sup> and 10<sup>5</sup> respectively but when they combine both system they only got efficacy 10<sup>6</sup>, while theoretically they could reach up to 10<sup>9</sup>. This could give us an idea that predicting the performance of a combination of genetic parts is not as easy as combining the performance of each genetic part. However, we can still conclude that having redundant parts is necessary to reduce the failure rate and make it as low as possible.<br />
<br />
Research in measuring the evolutionary stability in E coli was performed by Sean C Sleight et al <sup>[[#References|11]]</sup> where they measured it of BioBrick-assembled genetic circuits in E coli over multiple generation by measuring the number of loss-functioning mutants. They concluded that to make a robust GE bacteria, one has to take into account 3 principles:<br />
# High expression of genetic circuits comes with the cost of low evolutionary stability (for example induced vs non-induced system)<br />
#Avoid repeated sequences because it will more likely be mutated<br />
#Use of inducible promoters generally increases evolutionary stability compared to constitutive promoters<br />
<br />
To predict the robustness of the system from mutation, we have to take into account the duration (i.e. how many generations) we want our system to work. From their experiment for example, the AHL induced TetR-GFP cells lose their functions after 30 generations, while the uninduced ones lose their function slower (50% after 300 generations). A similar idea is also shown from our work where the mutation rate we got from literature research is in the unit of per generation. This is how reproduction differs biological system from other engineering systems. In engineering we also have failure probability as a function of time because of the life cycle of the system, but the system is not reproducing so it has no variability. <br />
<br />
Analyzing key elements that cause failure in any system including synthetic biology systems is essential for system improvement and prediction of failure. Adaptation of classical safety engineering methods needs to take into account the unique properties of synthetic biology. Reproducibility and complexity are two examples of areas that need to be studied deeper in this context. We invite future iGEM teams to use and improve our assessment framework, build a solid assessment protocol towards a better understanding of biosafety and successful application of synthetic biology.<br />
<br />
== Conclusion ==<br />
*We can adapt methods in safety engineering to assess risk in biosafety<br />
*We need more experimental data to confirm the risk assessing method<br />
<br />
== Perspectives ==<br />
<br />
*We need a method to predict the evolutionary stability of circuits from the properties of their parts, but the emergent behaviours of circuits will likely make prediction difficult. Thus it will be very useful if each BioBricks parts is completed with evolutionary stability data sheet, so we can make prediction of the stability of more complex circuits.<br />
*This safety assessment method is useful for identifying key elements of having failure in synthetic circuit systems before we go further to the real application. Thus we recommend for the future iGEM team to use our assessment method and give feedback to the community by improving this framework.<br />
<br />
==References==<br />
[[#Background|1]] - Genya V Dana et al. Four steps to avoid a synthetic biology disaster. 2012. Nature vol 483<br />
<br />
[[#Methods_and_Results|2]] - WorkSafe Victoria. A handbook for workplaces, controlling OHS hazards and risks. 2007. Edition No.1<br />
<br />
[[#Methods_and_Results|3]] - “Five steps to risk assessment” from [http://www.hse.gov.uk/risk/fivesteps.htm http://www.hse.gov.uk/risk/fivesteps.htm]. - risk management method in workplaces complying with health and safety law <br />
<br />
[[#Check_controls|4]] - Soren J Sorensen et al. 2005. Studying plasmid horizontal gene transfer in situ: a critical review. Nature Reviews Microbiology Vol 3<br />
<br />
[[#Check_controls|5]] - Heewook Lee et al., Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. 2012. PNAS E2774-E2783<br />
<br />
[[#Check_controls|6]] - Stanley A. Sawyer et al. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. 2007. PNAS 104(16):6504-6510<br />
<br />
[[#Check_controls|7]] - Lin Xu et al. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between two kingdoms. 2006. Mol. Biol. Evol. 23(6):1107-1108<br />
<br />
[[#Check_controls|8]] - David S Guttmand and Daniel E. Dykhuizen. 1994. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science Vol 266<br />
<br />
[[#Check_controls|9]] - L.Boe. 1996. Estimation of Plasmid Loss Rates in Bacterial Populations with a Reference to the Reproducibility of Stability Experiments. Plasmid 36, 161–167. Article No. 0043<br />
<br />
[[#Discussion|10]] - Torres B et al. 2003. A dual lethal system to enhance containment of recombinant micro-organisms. Microbiology. 2003 Dec;149(Pt 12):3595-601.<br />
<br />
[[#Discussion|11]] - Sean C Sleight et al., Designing and engineering evolutionary robust genetic circuits. 2010. Journal of Biological Engineering, 4:12<br />
</div><br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/File:ParisB_Assessment.pngFile:ParisB Assessment.png2012-10-27T01:58:02Z<p>Aprastowo: uploaded a new version of &quot;File:ParisB Assessment.png&quot;: Reverted to version as of 23:30, 26 October 2012</p>
<hr />
<div></div>Aprastowohttp://2012.igem.org/File:ParisB_Assessment.pngFile:ParisB Assessment.png2012-10-27T01:56:59Z<p>Aprastowo: uploaded a new version of &quot;File:ParisB Assessment.png&quot;</p>
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<div></div>Aprastowohttp://2012.igem.org/File:ParisB_Assessment.pngFile:ParisB Assessment.png2012-10-27T01:56:07Z<p>Aprastowo: uploaded a new version of &quot;File:ParisB Assessment.png&quot;</p>
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<div></div>Aprastowohttp://2012.igem.org/File:ParisB_Assessment.pngFile:ParisB Assessment.png2012-10-27T01:55:06Z<p>Aprastowo: uploaded a new version of &quot;File:ParisB Assessment.png&quot;</p>
<hr />
<div></div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-27T00:12:09Z<p>Aprastowo: </p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<html><br />
<br />
<div id="content1"><br />
<div style="position:absolute;left:15px;top:255px;z-index:100"><img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width="50"> <sub>This sign indicating new results after the European Jamboree.</sub></div><br />
<br />
<div class="box"><br />
<br><br />
<br><br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
<br><br />
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<br />
</ul></li><br />
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<div id="sidebar"><br />
<div class="box"><br />
<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br><br />
<img src=https://static.igem.org/mediawiki/2012/e/e0/ParisB_Medal.gif width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/e/e0/ParisB_Medal.gif width=15><sub>European Jamboree Safety Commendation</sub><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
<br />
</ul><br />
</div><br />
--><br />
<br />
</div><br />
<div class="box"><br />
<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
<br />
</ul><br />
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</div><br />
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</body><br />
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{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/File:ParisB_Medal.gifFile:ParisB Medal.gif2012-10-27T00:11:26Z<p>Aprastowo: </p>
<hr />
<div></div>Aprastowohttp://2012.igem.org/File:Medal.gifFile:Medal.gif2012-10-27T00:11:10Z<p>Aprastowo: </p>
<hr />
<div></div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-27T00:02:32Z<p>Aprastowo: </p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<html><br />
<br />
<div id="content1"><br />
<div style="position:absolute;left:15px;top:255px;z-index:100"><img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width="50"> <sub>This sign indicating new results after the European Jamboree.</sub></div><br />
<br />
<div class="box"><br />
<br><br />
<br><br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
<br><br />
<br />
<br />
</ul></li><br />
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<br />
</ul><br />
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</p><br />
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</div><br />
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</div><br />
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<div id="sidebar"><br />
<div class="box"><br />
<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br><br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
<br />
</ul><br />
</div><br />
--><br />
<br />
</div><br />
<div class="box"><br />
<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
<br />
</ul><br />
</div><br />
</div><br />
<br class="clearfix" /><br />
</div><br />
<br />
</body><br />
</html><br />
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{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-27T00:02:03Z<p>Aprastowo: </p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<html><br />
<br />
<div id="content1"><br />
<div style="position:absolute;left:15px;top:255px;z-index:100"><img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width="50"> <sub>This sign indicating new results after European Jamboree.</sub></div><br />
<br />
<div class="box"><br />
<br><br />
<br><br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
<br><br />
<br />
<br />
</ul></li><br />
<br />
<br />
</ul><br />
<br />
</p><br />
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</div><br />
<br />
<br />
<br class="clearfix" /><br />
</div><br />
<br />
<div id="sidebar"><br />
<div class="box"><br />
<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br><br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
<br />
</ul><br />
</div><br />
--><br />
<br />
</div><br />
<div class="box"><br />
<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
<br />
</ul><br />
</div><br />
</div><br />
<br class="clearfix" /><br />
</div><br />
<br />
</body><br />
</html><br />
<br />
<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-27T00:01:22Z<p>Aprastowo: </p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<html><br />
<br />
<div id="content1"><br />
<div style="position:absolute;left:600px;top:255px;z-index:100"><img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width="50"> <sub>This sign indicating new results after European Jamboree.</sub></div><br />
<br />
<div class="box"><br />
<br><br />
<br><br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
<br><br />
<br />
<br />
</ul></li><br />
<br />
<br />
</ul><br />
<br />
</p><br />
<br />
</div><br />
<br />
<br />
<br class="clearfix" /><br />
</div><br />
<br />
<div id="sidebar"><br />
<div class="box"><br />
<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br><br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
<br />
</ul><br />
</div><br />
--><br />
<br />
</div><br />
<div class="box"><br />
<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
<br />
</ul><br />
</div><br />
</div><br />
<br class="clearfix" /><br />
</div><br />
<br />
</body><br />
</html><br />
<br />
<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-27T00:00:27Z<p>Aprastowo: </p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<html><br />
<br />
<div id="content1"><br />
<div style="position:absolute;left:25px;top:255px;z-index:100"><img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width="50"> <sub>This sign indicating new results after European Jamboree.</sub></div><br />
<br />
<div class="box"><br />
<br><br />
<br><br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
<br><br />
<br />
<br />
</ul></li><br />
<br />
<br />
</ul><br />
<br />
</p><br />
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</div><br />
<br />
<br />
<br class="clearfix" /><br />
</div><br />
<br />
<div id="sidebar"><br />
<div class="box"><br />
<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br><br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
<br />
</ul><br />
</div><br />
--><br />
<br />
</div><br />
<div class="box"><br />
<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
<br />
</ul><br />
</div><br />
</div><br />
<br class="clearfix" /><br />
</div><br />
<br />
</body><br />
</html><br />
<br />
<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-27T00:00:13Z<p>Aprastowo: </p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<html><br />
<br />
<div id="content1"><br />
<div style="position:absolute;left:25px;top:270px;z-index:100"><img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width="50"> <sub>This sign indicating new results after European Jamboree.</sub></div><br />
<br />
<div class="box"><br />
<br><br />
<br><br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
<br><br />
<br />
<br />
</ul></li><br />
<br />
<br />
</ul><br />
<br />
</p><br />
<br />
</div><br />
<br />
<br />
<br class="clearfix" /><br />
</div><br />
<br />
<div id="sidebar"><br />
<div class="box"><br />
<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br><br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
<br />
</ul><br />
</div><br />
--><br />
<br />
</div><br />
<div class="box"><br />
<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
<br />
</ul><br />
</div><br />
</div><br />
<br class="clearfix" /><br />
</div><br />
<br />
</body><br />
</html><br />
<br />
<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-26T23:59:57Z<p>Aprastowo: </p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<html><br />
<br />
<div id="content1"><br />
<div style="position:absolute;left:10px;top:250px;z-index:100"><img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width="50"> <sub>This sign indicating new results after European Jamboree.</sub></div><br />
<br />
<div class="box"><br />
<br><br />
<br><br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
<br><br />
<br />
<br />
</ul></li><br />
<br />
<br />
</ul><br />
<br />
</p><br />
<br />
</div><br />
<br />
<br />
<br class="clearfix" /><br />
</div><br />
<br />
<div id="sidebar"><br />
<div class="box"><br />
<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br><br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
<br />
</ul><br />
</div><br />
--><br />
<br />
</div><br />
<div class="box"><br />
<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
<br />
</ul><br />
</div><br />
</div><br />
<br class="clearfix" /><br />
</div><br />
<br />
</body><br />
</html><br />
<br />
<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/headerTeam:Paris Bettencourt/header2012-10-26T23:57:48Z<p>Aprastowo: </p>
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<li><a href="/Team:Paris_Bettencourt/Human_Practice/perception">Team Perception</a></li><br />
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<li><a href="/Team:Paris_Bettencourt/Modeling"><img src="https://static.igem.org/mediawiki/2012/6/68/Paris_Bettencourt_2012_Safety-assessment.png" width="30px"> Safety Assessment</a></li><br />
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<li><a href="/Team:Paris_Bettencourt/Notebook">Notebook</a></li><br />
<li class="last"><a href="/Team:Paris_Bettencourt/Attributions">Attributions</a></li><br />
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<!--</body>--></div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/headerTeam:Paris Bettencourt/header2012-10-26T23:56:45Z<p>Aprastowo: </p>
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<li><a href="/Team:Paris_Bettencourt/Contact">Contact</a></li><br />
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<li><a href="/Team:Paris_Bettencourt/Overview"><img src="https://static.igem.org/mediawiki/2012/a/a2/ParisB_OverviewLogo.png" width="30px"> Overview</a></li> <br />
<li><a href="/Team:Paris_Bettencourt/Delay"><img src="https://static.igem.org/mediawiki/2012/6/6f/DelaySystem.png" width="30px"> Delay system</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Semantic_containment"><img src="https://static.igem.org/mediawiki/2012/1/1c/SemanticContainment.png" width="30px"> Semantic containment</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Restriction_Enzyme"><img src="https://static.igem.org/mediawiki/2012/5/5c/RestrictionSystem.png" width="30px"> Restriction enzyme system</a></li><br />
<li><a href="/Team:Paris_Bettencourt/MAGE"><img src="https://static.igem.org/mediawiki/2012/3/3a/MAGEgroup.png" width="30px"> MAGE</a></li><br />
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<li><a href="/Team:Paris_Bettencourt/Achievements">Achievements</a></li><br />
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<span class="opener2">Human Practice<b> </b></span><br />
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<li><a href="/Team:Paris_Bettencourt/Human_Practice/Overview">Overview</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/Interview">Interview</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/Report">Report</a></li> <br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/Debate">Debate</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/Workshop">Workshop</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/WikiScreen">Wiki Screen</a></li><br />
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<li><a href="/Team:Paris_Bettencourt/Human_Practice/perception">Team Perception</a></li><br />
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<li><a href="/Team:Paris_Bettencourt/Safety"><img src="https://static.igem.org/mediawiki/2012/8/82/Paris_Bettencourt_2012_Safety-questions.png" width="30px"> Safety Questions</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Modeling"><img src="https://static.igem.org/mediawiki/2012/6/68/Paris_Bettencourt_2012_Safety-assessment.png" width="30px"> Safety Assessment</a></li><br />
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<li><a href="/Team:Paris_Bettencourt/Notebook">Notebook</a></li><br />
<li class="last"><a href="/Team:Paris_Bettencourt/Attributions">Attributions</a></li><br />
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<!--</body>--></div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/headerTeam:Paris Bettencourt/header2012-10-26T23:56:34Z<p>Aprastowo: </p>
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<li><a href="/Team:Paris_Bettencourt/Overview"><img src="https://static.igem.org/mediawiki/2012/a/a2/ParisB_OverviewLogo.png" width="30px"> Overview</a></li> <br />
<li><a href="/Team:Paris_Bettencourt/Delay"><img src="https://static.igem.org/mediawiki/2012/6/6f/DelaySystem.png" width="30px"> Delay system</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Semantic_containment"><img src="https://static.igem.org/mediawiki/2012/1/1c/SemanticContainment.png" width="30px"> Semantic containment</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Restriction_Enzyme"><img src="https://static.igem.org/mediawiki/2012/5/5c/RestrictionSystem.png" width="30px"> Restriction enzyme system</a></li><br />
<li><a href="/Team:Paris_Bettencourt/MAGE"><img src="https://static.igem.org/mediawiki/2012/3/3a/MAGEgroup.png" width="30px"> MAGE</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Suicide"><img src="https://static.igem.org/mediawiki/2012/d/da/SkullIcon.png" width="30px"> Suicide system</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Encapsulation"><img src="https://static.igem.org/mediawiki/2012/e/e3/PhysicalContainment.png" width="30px"> Encapsulation</a></li><br />
<li><a href="/Team:Paris_Bettencourt/SID"><img src="https://static.igem.org/mediawiki/2012/f/f1/SyntheticImportDomain.png" width="30px"> Synthetic import domain</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Paris_Bettencourt/Achievements">Achievements</a></li><br />
<li><br />
<span class="opener2">Human Practice<b> </b></span><br />
<ul><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/Overview">Overview</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/Interview">Interview</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/Report">Report</a></li> <br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/Debate">Debate</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/Workshop">Workshop</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/WikiScreen">Wiki Screen</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/HGT">HGT</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/perception">Team Perception</a></li><br />
<br />
</ul><br />
</li><br />
<li><br />
<span class="opener2">Safety<b> </b></span><br />
<ul><br />
<li><a href="/Team:Paris_Bettencourt/Safety"><img src="https://static.igem.org/mediawiki/2012/8/82/Paris_Bettencourt_2012_Safety-questions.png" width="30px"> Safety Questions</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Modeling"><img src="https://static.igem.org/mediawiki/2012/6/68/Paris_Bettencourt_2012_Safety-assessment.png" width="30px"> Safety Assessment</a></li><br />
</ul><br />
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<li><a href="/Team:Paris_Bettencourt/Notebook">Notebook</a></li><br />
<li class="last"><a href="/Team:Paris_Bettencourt/Attributions">Attributions</a></li><br />
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<!--</body>--></div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/headerTeam:Paris Bettencourt/header2012-10-26T23:56:17Z<p>Aprastowo: </p>
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<a href="https://2012.igem.org/Main_Page"><img src="https://static.igem.org/mediawiki/2011/6/68/IgemLogo.png" alt="iGEM Logo" style="position:absolute;left:-150px;top:63px;z-index:100;height:100px"></a><br />
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<!-- <img src="https://static.igem.org/mediawiki/2012/a/a2/Paris_bettencourt.png" alt="Paris Bettencourt Logo" width="150" style="position:absolute;left:-250px;top:60px;z-index:100;width:110px"> --><br />
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<div style="position:absolute;left:-920px;top:150px;z-index:100"><img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width="50"> <sub>This sign indicating new results after European Jamboree.</sub></div><br />
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<ul><br />
<li class="first"><br />
<span class="opener">Main<b> </b></span><br />
<ul><br />
<li><a href="/Team:Paris_Bettencourt">Home</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Parts">Parts Submitted</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Acknowledgements">Acknowledgements</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Contact">Contact</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Bonus">Bonus</a></li> <br />
</ul><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Paris_Bettencourt/Team">Team</a></li><br />
<li><br />
<span class="opener">Project<b> </b></span><br />
<ul><br />
<li><a href="/Team:Paris_Bettencourt/Overview"><img src="https://static.igem.org/mediawiki/2012/a/a2/ParisB_OverviewLogo.png" width="30px"> Overview</a></li> <br />
<li><a href="/Team:Paris_Bettencourt/Delay"><img src="https://static.igem.org/mediawiki/2012/6/6f/DelaySystem.png" width="30px"> Delay system</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Semantic_containment"><img src="https://static.igem.org/mediawiki/2012/1/1c/SemanticContainment.png" width="30px"> Semantic containment</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Restriction_Enzyme"><img src="https://static.igem.org/mediawiki/2012/5/5c/RestrictionSystem.png" width="30px"> Restriction enzyme system</a></li><br />
<li><a href="/Team:Paris_Bettencourt/MAGE"><img src="https://static.igem.org/mediawiki/2012/3/3a/MAGEgroup.png" width="30px"> MAGE</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Suicide"><img src="https://static.igem.org/mediawiki/2012/d/da/SkullIcon.png" width="30px"> Suicide system</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Encapsulation"><img src="https://static.igem.org/mediawiki/2012/e/e3/PhysicalContainment.png" width="30px"> Encapsulation</a></li><br />
<li><a href="/Team:Paris_Bettencourt/SID"><img src="https://static.igem.org/mediawiki/2012/f/f1/SyntheticImportDomain.png" width="30px"> Synthetic import domain</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Paris_Bettencourt/Achievements">Achievements</a></li><br />
<li><br />
<span class="opener2">Human Practice<b> </b></span><br />
<ul><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/Overview">Overview</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/Interview">Interview</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/Report">Report</a></li> <br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/Debate">Debate</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/Workshop">Workshop</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/WikiScreen">Wiki Screen</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/HGT">HGT</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Human_Practice/perception">Team Perception</a></li><br />
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</ul><br />
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<li><br />
<span class="opener2">Safety<b> </b></span><br />
<ul><br />
<li><a href="/Team:Paris_Bettencourt/Safety"><img src="https://static.igem.org/mediawiki/2012/8/82/Paris_Bettencourt_2012_Safety-questions.png" width="30px"> Safety Questions</a></li><br />
<li><a href="/Team:Paris_Bettencourt/Modeling"><img src="https://static.igem.org/mediawiki/2012/6/68/Paris_Bettencourt_2012_Safety-assessment.png" width="30px"> Safety Assessment</a></li><br />
</ul><br />
</li><br />
<li><a href="/Team:Paris_Bettencourt/Notebook">Notebook</a></li><br />
<li class="last"><a href="/Team:Paris_Bettencourt/Attributions">Attributions</a></li><br />
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<!--</body>--></div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-26T23:48:19Z<p>Aprastowo: </p>
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<div id="grouptitle">How Safe is Safe Enough?</div><br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
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<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
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<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br><br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br />
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<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
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<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
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<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
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<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
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<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
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{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/TeamTeam:Paris Bettencourt/Team2012-10-26T23:43:07Z<p>Aprastowo: </p>
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<br />
<div id="grouptitle">Team </div><br />
<br />
== Who we are ==<br />
<center>[[Image:Paristeam.jpg|500px]]</center><br><br />
===Undergrads:===<br />
<br />
====Jean Cury====<br />
[[Image:Jean.png|thumb|left|100px]]'''1st year master student in Biology at the ENS Paris and UPMC, Paris 6''' <br> <br />
My current internship is about studying a synthetic recombination site of the integron system, at Pasteur Institute, Paris. This gives me a good insight into synthetic biology, and motivates me to participate in iGEM.<br />
What attracts me also in doing iGEM is the interdisciplinary team, the team reflexion, and everything about creating a team, organizing it, learning from other fields represented. Indeed, I truly believe that learning from your friends is a good way to improve your knowledge and satisfy your curiosity.<br />
In addition to my internship, I'm following bioinformatics and arabic courses. <br><br><br><br />
<br />
====Dylan Iverson====<br />
[[Image:Dylan.png|thumb|left|100px]]'''1st year master student in Biomedical Engineering at Paris Descartes University''' <br> <br />
I am a first year student of the Master of Biomedical Engineering at Paris Descartes. My undergraduate degree is Engineering Bachelor of Science: Chemical Engineering from University of California, Santa Barbara. I have done completed my first 2-month internship for M1 in neurobiology, and iGem will serve as my second internship. I discovered the topic of synthetic biology by taking Jake Wintermute’s course for the AIV Master. In contrast with biology students, I have more knowledge of mathematical modeling and chemistry. I am particularly interested in metabolic engineering. I hope to do what I can to make us all synthetic biology champions. <br><br><br><br />
<br />
====Zoran Marinkovic====<br />
[[Image:Zoran.png|thumb|left|100px]]'''1st year AIV master student at Paris Descartes University''' <br> <br />
I studied Molecular Biology at University of Zagreb (Croatia) and did a semester long exchange at Uppsala University (Sweden) where I studied Microbial and Evolutionary Genetics and Bioinformatics. Currently, I’m doing a 5 month long internship at INSERM U1001 under the supervision of Jake Wintermute tackling the question of bacterial aging using the synthetic biology approach. <br />
My primary interest is application of synthetic biology for creating bioproducts as well as using synthetic biology in fundamental research. Also, I’m quite interested in developing synthetic biology as a tool for creating living organisms from scratch as we build many non-living constructs today. <br />
I joined iGEM because I would like to experience and observe the process of generating ideas and creating a science project with a group of people which, I hope, will be interesting and fun to do. Of course, it has to be the Grand Prize winning one. <br><br><br><br />
<br />
====Claire Mayer====<br />
[[Image:Claire.png|thumb|left|100px]]''' 3rd year of Medical School and 1st year AIV master student at Paris Descartes University''' <br> <br />
I think Synthetic Biology has a tremendous potential, and especially for medical and environmental applications. <br />
iGEM is my M1 internship. I wanted to join the iGEM team in order to work in a pluridisciplinary environment on an exciting synthetic biology project, and learn a lot from each participant, and let them learn from me. <br />
What do I do apart from studying? I am Co President of Paris Descartes’ Debating Club and I give lessons to an adult class in biology (in preparation of an exam called “le brevet adulte”). I love genetics and immunology. <br><br><br><br />
<br />
====Denis Samuylov====<br />
[[Image:Denis.png|thumb|left|100px]]'''1st year AIV master student at Paris Diderot University''' <br> <br />
I finished my undergraduate studies in 2011 in Saint Petersburg State Polytechnical University in Russia. I was learning technical and physical courses, e.g. Electrodynamics, Optics, Quantum Physics, Math, Statistics, Computer Sciences, Electronics… At the moment, I am in the first year of the Interdisciplinary Approaches to Life Science (AIV) Master Program and I fell in love with Biology... or rather Synthetic Biology!<br />
So, with my interdisciplinary background I intend to apply my numerous skills to make humanity’s life better and save the world. I am deeply interested in fighting cancer and to participate in ecological projects. I am sure that participation in iGEM is a great possibility to meet interesting people, share my skills and to learn something new! And of course to have a fun summer while realizing useful project!<br />
As for my other interests, I love sports, dancing, music, nature and life! <br><br><br><br />
<br />
====Aishah Prastowo====<br />
[[Image:Aishah.png|thumb|left|100px]]'''1st year AIV master student at Paris Descartes University''' <br> <br />
Before my master I did Engineering Physics in Gadjah Mada University Indonesia. As my final project of my undergraduate, I studied microfluidics and did a project on low-cost microfluidic system for generating biomicrobubbles. Currently I am doing my internship about real-time control of gene expression in yeast. For me engineering is all about systems design and modeling, making innovation and troubleshooting, and so is synthetic biology. I hope I can learn both science and soft skills by participating in iGEM, while contributing my best for the team.<br><br><br><br />
<br />
====Julianne Rieders====<br />
[[Image:Julianne.png|thumb|left|100px]]'''1st year AIV master student at Paris Descartes University ''' <br> <br />
I earned my B.A. at Bryn Mawr College, Bryn Mawr Pa, where I studied biology and East Asian studies. I am primarily interested in molecular therapeutics, and believe that the application of synthetic and systems biology to this field will allow for the development of safer more efficient treatments. I am currently involved in a hardcore synthetic biology project working with both bacterial and mammalian cells. Participating in iGEM is an ideal opportunity to apply and share my skills in this field, as well as expand my skill set, in an exciting and competitive environment.<br><br><br><br />
<br />
====Ernest Mordret====<br />
[[Image:Ernest.png|thumb|left|100px]]'''2nd year AIV master student at Paris Diderot University and 3rd year at AgroParisTech''' <br> <br />
By the end of high school, I had quite a hard time choosing between biology studies and the classical engineering track. Thus, iGEM and synthetic biology are a way to use this engineering approach in order to serve my passion for biology. I am deeply interested in the robustness of synthetic gene circuits and in the development of innovative directed evolution strategies. During my internships and theoretical trainings, I acquired skills in population genetics, molecular biology and microfluidics, and I will try to bring as much energy, commitment, suggestions and solutions as possible for the team!<br><br><br><br />
<br />
====Guillaume Villain====<br />
[[Image:Guillaume.png|thumb|left|100px]]'''1st year Frontiers in Life Science bachelor student at Paris Descartes University''' <br> <br />
I am really interested in synthetic biology, modeling of biological systems, education, directed evolution and protein engineering. I would like especially to know more about extremophilic protein, which is why I am doing an internship in the institute of physico-chemical biology (IBPC, Paris) in a bioinformatics laboratory to study molecular modeling of extremophilic protein.<br />
I love interdisciplinarity and I think iGEM is a fantastic opportunity to learn a lot about synthetic biology and sciences in an innovative way.<br />
<br><br><br><br />
<br />
===Advisors:===<br />
<br />
====Ariel Lindner====<br />
[[Image:Ariel.png|thumb|left|100px]]'''Researcher at INSERM, Director of the AIV Master at the Paris Descartes and Paris Diderot Universities''' <br> <br />
INSERM tenured senior researcher and co-director of the AIV master, has graduated from the Hebrew University (Jerusalem, Israel) "Amirim" interdisciplinary program with major in Chemistry and received his M.Sc. and Ph.D. from the Weizmann Institute of Science (Rehovot, Israel) in Chemical Immunology for his work on catalytic antibodies as enzyme models, antibody conformational changes and directed evolution. After a research period at the Scripps Institute (California, USA), he received EMBO and Marie Curie fellowships to pursue postdoctoral work in Paris. His study interest evolve around applying Physical, Chemical and Biological approaches to study variability between clonal individuals. He is an associate professor at the Paris Descartes university faculty of Medicine (2008/9) and serves as the director of studies of the Center for Research and Interdisciplinarity (CRI).<br />
<br><br><br><br />
<br />
====Antoine Decrulle====<br />
[[Image:Antoine.png|thumb|left|100px]]'''1st year PhD student at FdV doctoral school of Paris Descartes University''' <br> <br />
I’m a PhD student working on synthetic biology. My interest for this field started 3 years ago when i did the first year of the AIV master program and participated to the iGEM Paris team in 2010. I have to say that this experience of research influenced me a lot during the past two years. Last year I decided to share my experience of synthetic biology and of the iGEM competition by advising the paris iGEM team 2011. This was a great experience for me that’s why I decided to keep doing it this year for the new Paris 2012 team.<br />
<br><br><br><br />
<br />
====Aleksandra Nivina====<br />
[[Image:Alexksandra.png|thumb|left|80px]]'''6th year Pharmacy and 2nd year master AIV student at Paris Descartes University''' <br> <br />
My interest in iGEM began in 2010 when I participated in this competition as a member of the Paris team. It was a wonderful way to learn Synthetic biology and get a hands-on experience in a research project. In fact, I liked this “scientific adventure” so much that it’s now my second year as an adviser.<br />
During this summer, I’m still finishing my undergraduate studies, but hopefully will start a PhD on a synthetic biology related project by autumn.<br />
<br><br><br><br />
<br />
====Babak Nichabouri====<br />
[[Image:Babak.png|thumb|left|80px]]'''PharmD-PhD program, Paris Descartes University ''' <br> <br />
As pharmacy student, I have a great interest in biotechnology for life and health sciences. Participating to iGEM last year was for me a great experience in term of learning about science. It could has been done with the formidable help of my previous advisors. I would now like to share my knowledge and experience with the members of the next team. <br />
<br><br><br><br />
<br />
====Jake Wintermute====<br />
[[Image:Jake.png|thumb|left|100px]]'''Postdoctoral researcher at the Centre de Recherche Interdisciplinaire''' <br> <br />
I'm a postdoctoral researcher working at the Centre de Recherche Interdisciplinaire. I also teach the Synthetic Biology course for the AIV master's students. My Ph.D. comes from the Systems Biology department at Harvard, where I graduated in 2011.<br />
I have been an iGEM fan and groupie for many years, but this will be my first time personally involved with a team. I am looking forward to taking this team to MIT and showing everyone a great time in Boston!<br />
<br><br><br><br />
<br />
====Yifan Yang====<br />
[[Image:Yifan.png|thumb|left|100px]]'''PhD student at the FdV doctoral school of Paris Descartes University''' <br> <br />
I’m a PhD student from the FdV (Frontières du Vivant) PhD school and INSERM U1001, working on the evolutionary and systems biology of bacterial aging. Trained in an interdisciplinary undergraduate program as a biologist and a mathematician in Peking University, I participated in iGEM 2007 as an initiating member of the PKU iGEM team, which won the Grand Prize in MIT. After spending a year in Caltech, I joined François Taddei’s group in Paris since 2009. I helped mentoring the 2010 & 2011 Paris iGEM teams, and will do the same this year. I hope as experience grows, I would do a better job both in organizing to help the team be more effective, and in mentoring to help the members to realize their own ideas.<br><br><br><br />
<br />
== Gallery ==<br />
<gallery><br />
File:ParisB_01.jpg<br />
File:ParisB_02.jpg<br />
File:ParisB_03.jpg<br />
File:ParisB_04.jpg<br />
File:ParisB_05.jpg<br />
File:ParisB_06.jpg<br />
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</gallery><br />
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{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-26T23:41:01Z<p>Aprastowo: </p>
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<div>{{:Team:Paris_Bettencourt/header}}<br />
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<div id="grouptitle">How Safe is Safe Enough?</div><br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
<br><br />
<br />
<img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width=50> This sign indicating new results after European Jamboree.<br />
</ul></li><br />
<br />
<br />
</ul><br />
<br />
</p><br />
<br />
</div><br />
<br />
<br />
<br class="clearfix" /><br />
</div><br />
<br />
<div id="sidebar"><br />
<div class="box"><br />
<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br><br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
<br />
</ul><br />
</div><br />
--><br />
<br />
</div><br />
<div class="box"><br />
<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
<br />
</ul><br />
</div><br />
</div><br />
<br class="clearfix" /><br />
</div><br />
<br />
</body><br />
</html><br />
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<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-26T23:39:18Z<p>Aprastowo: </p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<html><br />
<br />
<br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
<br />
<div id="content1"><br />
<br />
<div class="box"><br />
<br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
<br><br />
<br />
<img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width=50> This sign indicating new results after European Jamboree.<br />
</ul></li><br />
<br />
<br />
</ul><br />
<br />
</p><br />
<br />
</div><br />
<br />
<br />
<br class="clearfix" /><br />
</div><br />
<br />
<div id="sidebar"><br />
<div class="box"><br />
<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br><br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
<br />
</ul><br />
</div><br />
--><br />
<br />
</div><br />
<div class="box"><br />
<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
<br />
</ul><br />
</div><br />
</div><br />
<br class="clearfix" /><br />
</div><br />
<br />
</body><br />
</html><br />
<br />
<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-26T23:38:59Z<p>Aprastowo: </p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<html><br />
<br />
<br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
<br />
<div id="content1"><br />
<br />
<div class="box"><br />
<br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
<br><br />
<br />
<img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width=50> This sign indicating new results after European Jamboree.<br />
</ul></li><br />
<br />
<br />
</ul><br />
<br />
</p><br />
<br />
</div><br />
<br />
<br />
<br class="clearfix" /><br />
</div><br />
<br />
<div id="sidebar"><br />
<div class="box"><br />
<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
<br />
</ul><br />
</div><br />
--><br />
<br />
</div><br />
<div class="box"><br />
<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
<br />
</ul><br />
</div><br />
</div><br />
<br class="clearfix" /><br />
</div><br />
<br />
</body><br />
</html><br />
<br />
<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-26T23:37:07Z<p>Aprastowo: </p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<html><br />
<br />
<br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
<br />
<div id="content1"><br />
<br />
<div class="box"><br />
<br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
<br><br />
<br />
<img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width=50> This sign indicating new results after European Jamboree.<br />
</ul></li><br />
<br />
<br />
</ul><br />
<br />
</p><br />
<br />
</div><br />
<br />
<br />
<br class="clearfix" /><br />
</div><br />
<br />
<div id="sidebar"><br />
<div class="box"><br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br><br />
<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
<br />
</ul><br />
</div><br />
--><br />
<br />
</div><br />
<div class="box"><br />
<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
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</ul><br />
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{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-26T23:36:40Z<p>Aprastowo: </p>
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<div>{{:Team:Paris_Bettencourt/header}}<br />
<html><br />
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<br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
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<div id="content1"><br />
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<div class="box"><br />
<br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
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<img src=https://static.igem.org/mediawiki/2012/0/04/New_PB2012.png width=30> This sign indicating new results after European Jamboree.<br />
</ul></li><br />
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<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br><br />
<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
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</ul><br />
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--><br />
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</div><br />
<div class="box"><br />
<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
<br />
</ul><br />
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{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-26T23:32:41Z<p>Aprastowo: </p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<html><br />
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<br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
<br />
<div id="content1"><br />
<br />
<div class="box"><br />
<br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
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</ul></li><br />
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</ul><br />
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<div id="sidebar"><br />
<div class="box"><br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br><br />
<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Modeling> <img src=https://static.igem.org/mediawiki/2012/8/82/ParisB_Assessment.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
<br />
</ul><br />
</div><br />
--><br />
<br />
</div><br />
<div class="box"><br />
<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
<br />
</ul><br />
</div><br />
</div><br />
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</div><br />
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</body><br />
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{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/File:ParisB_Assessment.pngFile:ParisB Assessment.png2012-10-26T23:31:00Z<p>Aprastowo: </p>
<hr />
<div></div>Aprastowohttp://2012.igem.org/File:Assessment.pngFile:Assessment.png2012-10-26T23:30:25Z<p>Aprastowo: uploaded a new version of &quot;File:Assessment.png&quot;</p>
<hr />
<div></div>Aprastowohttp://2012.igem.org/File:Assessment.pngFile:Assessment.png2012-10-26T23:26:37Z<p>Aprastowo: </p>
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<div></div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-26T23:22:58Z<p>Aprastowo: </p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<html><br />
<br />
<br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
<br />
<div id="content1"><br />
<br />
<div class="box"><br />
<br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
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</ul></li><br />
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<div id="sidebar"><br />
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<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br><br />
<!-- i leave this blank for boston achievement ;) --><img src=http://openwetware.org/images/7/7e/ParisB_blank.png width=150><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
<li class="last"><span class="date">9/26/12</span> <a href="https://igem.org/2012_Judging_Form?id=914">Judging form due </a></li><br />
<br />
<li class="last"><span class="date">9/26/12</span>Wiki FREEZE at 11:59pm, EDT </li><br />
<li class="last"><span class="date">10/5-7/12</span>iGEM 2012 Regional Jamborees</li><br />
<li class="last"><span class="date">11/2-5/12</span>iGEM 2012 World Championship Jamboree, MIT</li><br />
<br />
</ul><br />
</div><br />
--><br />
<br />
</div><br />
<div class="box"><br />
<h3>Quick Links</h3><br />
<ul class="list"><br />
<li class="first"><a href="https://2012.igem.org">iGEM 2012</a></li><br />
<li class="first"><a href="http://partsregistry.org/Main_Page">Parts Registry</a></li><br />
<li class="first"><a href="http://www.cri-paris.org/en/cri/">The Center for Research and Interdisciplinarity</a></li><br />
<br />
</ul><br />
</div><br />
</div><br />
<br class="clearfix" /><br />
</div><br />
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{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-26T22:51:38Z<p>Aprastowo: </p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<html><br />
<br />
<br />
<div id="grouptitle">How Safe is Safe Enough?</div><br />
<br />
<div id="content1"><br />
<br />
<div class="box"><br />
<br />
<p> <br />
<br />
Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
<br />
<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
<br />
<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
<br />
<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
<br />
<br />
<br><br><br><br />
<iframe align="center" width="600" height="400" src="https://www.youtube.com/embed/iyynMAQ-fjY?rel=0" frameborder="0" allowfullscreen style="z-index:100"></iframe><br />
<br><br />
<br />
<br />
</ul></li><br />
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</ul><br />
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<div id="sidebar"><br />
<div class="box"><br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Gold Medal</sub> <br> <br />
<img src=https://static.igem.org/mediawiki/2012/7/74/ParisB_Medal.png width=15><sub>European Jamboree Safety Commendation</sub><br />
<br />
<h3>Go to</h3><br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Achievements> <img src=https://static.igem.org/mediawiki/2012/0/0c/ParisB_achievement_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Overview> <img src=https://static.igem.org/mediawiki/2012/e/e8/ParisB_project_icon.png width=150></a></center><br />
<br><br />
<center><a href=https://2012.igem.org/Team:Paris_Bettencourt/Human_Practice/Frontpage> <img src=https://static.igem.org/mediawiki/2012/0/05/ParisB_human_icon.png width=150></a></center><br />
<!-- <br />
<h3>Deadlines</h3><br />
<div class="date-list"><br />
<ul class="list date-list"><br />
<li class="first"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> Regional Jamboree attendance fee due</li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Judging/Track_Selection">Track selection due </a></li><br />
<li><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Project_abstract">Project abstracts due </a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Jamboree/Team_Roster">Team rosters due</a></li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/7/12</span> <a href="/Safety">Safety questions due </a></li><br />
<li class="last"><span class="date">9/26/12</span>Project and part documentation due, including documentation for all medal criteria </li><br />
<li class="last"><span class="date" style="background:rgb(121,173,89);">9/26/12</span>BioBrick Part DNA due to the Registry </li><br />
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{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_BettencourtTeam:Paris Bettencourt2012-10-26T22:51:12Z<p>Aprastowo: </p>
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Synthetic biologists, and iGEM teams in particular, design Genetically Engineered Organisms (GEOs) to benefit people and communities around the world. However, many proposed applications necessarily involve the deployment of GEOs in natural environments. These dreams can never be made real without technical, legal and ethical guidelines for the use of GEOs outside the lab. Our project addresses this serious need from our perspective as safety bioengineers, citizens and humans.<br />
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<br><br> We have developed the <b>bWARE containment module</b> to substantially reduce the risk of Horizontal Gene Trasfer (HGT) while remaining compatible with existing iGEM devices. A GEO may first perform its beneficial function during a programmed delay. Then our system activates, irreversibly degrading DNA throughout the population, leaving no genetic information behind. Multiple cooperative systems provide redundancy against inevitable mutations or external stresses.<br />
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<br><br><b>Human practice considerations</b> influenced every stage of our design process. Given different biosafety modules that may be used singly or in combination, what are the best practices for associating specific safety systems with specific applications? Given that no biosafety system can completely eliminate the risk of HGT, how safe is safe enough? Who should decide when the benefits of GEOs outweigh the risks, and what information do they need? We have collected and indexed existing iGEM biosafety projects. We have engaged expert and public opinion to develop a new proposal for qualitative and quantitatve documentation of BioBrick safety devices.<br />
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<br><br> Biosafety is an exciting design challenge, an essential enabling technology for synthetic biology, and a fundamental ethical obligation of all bioengineers. We expect that modular containment systems like bWARE will be standard ware in the next generation of iGEM projects.<br />
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{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/File:ParisB_Medal.pngFile:ParisB Medal.png2012-10-26T22:38:37Z<p>Aprastowo: </p>
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<div></div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/ModelingTeam:Paris Bettencourt/Modeling2012-10-26T22:10:31Z<p>Aprastowo: </p>
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<div id="grouptitle">Safety Assessment</div><br />
<br />
==Overview==<br />
Safety is an important issue in synthetic biology, especially on environmental related projects. We already tried to answer the question, “how safe is safe enough?” by involving experts, publics and scientists, and also building biosafety devices. However, to really answer the question, actually we need first to ask ourselves a more basic question, “how do we measure safety?”. As we see synthetic biology as an engineering approach to biology, we could think about adaptation of safety engineering, a well studied engineering subset, that has been widely use to minimize risks on many fields of engineering, such as mechanical engineering, aircrafts, and manufactures. However, the risks they face are surely different from the risks of synthetic biology. <br />
<br />
According to Dana et al<sup>[[#References|1]]</sup> there are four areas of risk research in environmental application of synthetic biology:<br />
*Differences in the physiology of natural and synthetic organisms will affect how they interact with the surrounding environment,<br />
*Escaped microorganisms have the potential to survive in receiving environments and to compete successfully with non-modified counterparts,<br />
*Synthetic organisms might evolve and adapt quickly, perhaps filling new ecological niches, and<br />
*Gene transfer.<br />
<br />
Knowing that there are different areas of risk that we need to take into account, we need to design our safety containment with different parts to deal with each of them. Identifying the relationship between one part and the others will help us to see the reliability of the overall system. Here we propose an approach to assess safety for environmental release of genetically engineered bacteria (GE bacteria).<br />
<br />
===Objectives===<br />
*Adapting existing safety assessment tools to synthetic biology.<br />
*Proposing methods to assess safety in synthetic biology.<br />
<br />
==Methods and Results==<br />
We propose a method to assess hazards and risk<sup>[[#References|2]]</sup> in releasing genetically engineered bacteria to the environment. As a case study, we want to release GE bacteria which will perform some function in the environment and we want to apply 3 sets of bWARE safety containment (alginate beads, bWARE killswitch, semantic containment) to control the hazards and risks. Here we focus more on the reliability of the safety containment system rather than the functional part, although the similar assessment can also be applied to see the functional part reliability.<br />
<br />
===Hazards Identification===<br />
Identifying hazards means that we need to find and understand the possible harm that may happen in the application of our system. Generally there are two potential hazard in environmental application of synthetic biology<sup>[[#References|1]]</sup> which are the success escape of the GE bacteria followed by a success competition with the natural strain and the horizontal gene transfer.<br />
<br />
===Risk Assessment===<br />
Risk assessment will give an idea what kind of risk we face in releasing the GEO in the environment and help to design the safety containment. Here we adapted a risk management method in workplaces complying with health and safety law <sup>[[#References|3]]</sup>.<br />
<br />
To-do-list to assess risk in 5 steps:<br />
#Identify the hazards<br />
#Decide who might be harmed and how<br />
#Evaluate the risks and decide on precaution<br />
#Record your findings and implement them<br />
#Review your assessment and update if necessary<br />
<br />
<br />
Worksheet example:<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are the hazards?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Who might be harmed and how?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are we already doing?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What further action is necessary?'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria outcompete natural strains<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria escaping the containment may outcompete natural strains if they have better fitness, creating natural imbalance <br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Using harmless strain or strain with low fitness compared to natural strain (standard E coli for lab)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to prevent the cells reproducing themselves at some point and/or separating them from natural strains<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Horizontal gene transfer (HGT)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Other strain/species may uptake engineered gene, and if the gene gives advantage in the fitness, it may outcompete other strain and creating natural imbalance<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| -<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to degrade DNA and/or separate the DNA from the environment and/or prevent natural strain having advantages from the DNA<br />
<br />
|}<br />
<br />
<br><br />
===Control hazards and risks===<br />
<br />
In this step we decided what control elements we want to put to our system to reduce the risks. We should choose the best suitable control elements depending on the system function and application. As we already know that we want to apply bWARE safety containment, here we describe the role of each safety parts in the risks reduction. <br />
#GE bacteria outcompete natural strains<br />
#*In order to prevent the success escape of GE bacteria and outcompete the natural strains, we will stop their reproduction by putting a self killing mechanism to kill the cells after they perform the function. <br />
#*In case of the failure of the killing mechanism, we will put the cells inside a physical containment so there will be no physical interaction between them and the surrounding cells.<br />
#HGT<br />
#*We will use DNAse to degrade DNA after the cells perform the function so they won’t leave any genetic material behind.<br />
#*In case of the failure on inefficiency of the DNAse, the physical containment will still protect the DNA from the environment.<br />
#*In case of the leakiness of the physical containment, the DNA has special encryption system with the semantic containment so the receiver cell will not be able to read it.<br />
<br />
===Check controls=== <br />
<br />
To check and predict the reliability of our system, we used fault tree analysis to assess multiple safety containment in one biodevice. This top-down approach allows us to see the relationship between each containment element and predict the overall failure probability. With this method we can see what basic events are the key elements in our system.<br />
<br />
<center>[[Image:ParisB_FTA.png]]</center><br />
<br />
AND gate represents independent events<br />
<br />
P(A and B) = P(A)P(B)<br />
<br />
OR gate corresponds to set of union<br />
<br />
P(A or B) = P(A) + P(B)<br />
<br />
so the total failure probability of the system is<br />
<br />
Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9)<br />
<br />
List of the basic events<br />
<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Notation'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure component'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure mode'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Consequence'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Method for determining the probability'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P1<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| physical containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| leakage<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA/cell escape<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| experiment<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P2<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA uptake<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA transferred into natural strain<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| <nowiki>transconjugant to donor ratio in HGT is typically <10</nowiki><sup>-5</sup> <sup>[[#References|4]]</sup><br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P3<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| semantic containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation*<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P4<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| population suicide<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no surrounding cells with enough toxin<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no death<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| based on the cell density and the expectation number of surrounding non-mutant<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P5<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| toxin production<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no DNA degradation (w/o antitoxin), no death (with antitoxin)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P6<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| mutant fitness<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| beneficial mutation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| outcompetition of the mutant<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P7<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| delay system<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P8<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction enzyme<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P9<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction site<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|}<br />
<br />
====Physical containment failure====<br />
<br />
From the experiment we get the escape rate of the cells from the alginate beads is (escaping cells/total cells) is 10<sup>-5</sup> per 12 hours. Assuming 30 minutes of division time, we have 24 generations, and the escape rate per generation is 4 x 10<sup>-6</sup>.<br />
<br />
====Genetic failure====<br />
<br />
There are different processes that lead to a loss of function of a gene<br />
<br />
* Mutation<br />
* Recombination<br />
* Plasmid loss<br />
<br />
'''Losing function because of mutation'''<br />
<br />
Estimating the mutation rate which cause failure of the safety containment of the device<br />
<br />
* Spontaneous mutation rate of a wild-type E coli strain growing on research medium is 3.3 x 10<sup>-9</sup> per nucleotide per generation <sup>[[#References|5]]</sup> <br />
* approximately ⅔ of nucleotide mutation will change amino acid (64 combination of nucleotides code only 20 amino acids)<br />
* approximately 70% of amino acid change will lose the part function <sup>[[#References|6]]</sup><br />
* mean length of genetic coding sequence for E coli (procaryotes) is 924 bp <sup>[[#References|7]]</sup> ≈ 1000 bp <br />
<br />
So the loss function rate of a gene per generation because of mutation is <br />
<br />
P<sub>L</sub><nowiki>= 3.3 x 10</nowiki><sup>-9</sup> x ⅔ x 0.70 x 1000 = 1.54 x 10<sup>-6</sup> <br />
<br />
'''Recombination'''<br />
<br />
Finding a definite rate of recombination is not easy. Guttman and Dykhuizen in 1994 <sup>[[#References|8]]</sup> stated that recombination is believed to occur at such a low frequency, but their experiment showed that the rate could be as high as mutation rate (50 fold higher compared to the mutation rate believed at that moment, but actually it is 5.0 x 10<sup>-9</sup> changes per nucleotide per generation, a bit more than one fold to the value believed now). <br />
<br />
Redoing the previous calculation with this number will lead us to 2.33 x 10<sup>-6</sup> per gene per generation.<br />
<br />
'''Plasmid loss'''<br />
<br />
According to L Boe <sup>[[#References|9]]</sup> plasmid loss rate is defined as the probability that a division of a plasmid-carrying individual results in the birth of one plasmid-free and one plasmid-carrying daughter cell. For the low copy plasmid this rate is about ~1% /division and for high copy plasmid is ~0.01% /division, neglecting the viable/non-viable factor of the cells of losing the plasmid (no selection). If a plasmid with a lost rate of 0.05 is stabilized with a 100% efficient postsegragational killing system, the 5% of the division will result in non viable daughter cell, and we can not see the effect except of increasing the appearing division time by ln 2/ln (1-0.05) = 1.04. Thus in our system we can neglect this plasmid loss assuming that we have antibiotic selection in the beads.<br />
<br />
Assuming only mutation and recombination could happen to delete a function of a gene, we have the total genetic failure rate around 4 x 10<sup>-6</sup> per gene per generation.<br />
<br />
====Total failure probability====<br />
<br />
Having Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9) and put 1 for unknown probability (P4 and P6) as a worst-case scenario, we come to the failure rate number 6.4 x 10<sup>-11</sup> per generation.<br />
<br />
A volume of one alginate bead is approximately 20 uL. So if the cells grow until they reach the stationary phase (4 x 10<sup>9</sup> cells/ml), we will have 8 x 10<sup>7</sup> cells. If we started from 100 cells per bead, the number of generations we have is <sup>2</sup>log (8 x 10<sup>7</sup> / 100) =19.6 generations. Therefore the total failure becomes 6.4 x 10<sup>-11</sup> x 19.6 = 1.25 x 10<sup>-9</sup>.<br />
<br />
With this method we can also see that the sense-HGT rate is much lower (6.4 x 10<sup>-22</sup>) , almost negligible compared to the outcompetition rate, because it has more back up/redundancy components.<br />
<br />
== Discussion ==<br />
<br />
We have proposed and done an example of assessing biosafety adapting existing method from safety engineering. However it is very clear that the prediction is based on rough estimation and we need more experimental data to verify this estimation. For an example, Torres et al <sup>[[#References|10]]</sup> tested a dual containment killing system and compared it with single containment system. They tested EcoRI based system and Colicin E3-based system and get the efficacy (based on the numbers of successful transformants) each 10<sup>4</sup> and 10<sup>5</sup> respectively but when they combine both system they only got efficacy 10<sup>6</sup>, while theoretically they could reach up to 10<sup>9</sup>. This could give us an idea that predicting a performance of a combination of genetic parts is not as easy as combining the performance of each genetic part. However, we can still conclude that having redundant parts is necessary to reduce the failure rate and make it as low as possible.<br />
<br />
Research in measuring the evolutionary stability in E coli was performed by Sean C Sleight et al <sup>[[#References|11]]</sup> where they measured it of BioBrick-assembled genetic circuits in E coli over multiple generation by measuring the number of loss-functioning mutants. They concluded that to make a robust GE bacteria, one has to take into account 3 principles:<br />
# High expression of genetic circuits comes with the cost of low evolutionary stability (for example induced vs non-induced system)<br />
#Avoid repeated sequences because it will more likely be mutated<br />
#Use of inducible promoters generally increases evolutionary stability compared to constitutive promoters<br />
<br />
To predict the robustness of the system from mutation, we have to take into account for how long time (i.e. how many generations) we want our system to work. From their experiment for example, the AHL induced TetR-GFP cells lose their functions after 30 generations, while the uninduced ones lose their function slower (50% after 300 generations). A similar idea is also shown from our work where the mutation rate we got from literature research is in the unit of per generation. This is how reproduction differs biological system from other engineering systems. In engineering we also have failure probability as a function of time because of the life cycle of the system, but the system is not reproducing so it has no variability. <br />
<br />
Analyzing key elements that cause failure in any systems including synthetic biology systems is essential for system improvement and prediction of the failure. Adaptation of classical safety engineering methods needs to take into account the uniqueness properties of synthetic biology. Reproducibility and complexity are two example of areas that need to be studied deeper in this context. We invite future iGEM teams to use and improve our assessment framework, build a solid assessment protocol towards a better understanding of biosafety and successful application of synthetic biology.<br />
<br />
== Conclusion ==<br />
*We can adapt methods in safety engineering to assess risk in biosafety<br />
*We need more experimental data to confirm the risk assessing method<br />
<br />
== Perspectives ==<br />
<br />
*We need a method to predict the evolutionary stability of circuits from the properties of their parts, but the emergent behaviours of circuits will likely make prediction difficult. Thus it will be very useful if each BioBricks parts is completed with evolutionary stability data sheet, so we can make prediction of the stability of more complex circuits.<br />
*This safety assessment method is useful for identifying key elements of having failure in synthetic circuit systems before we go further to the real application. Thus we recommend for the future iGEM team to use our assessment method and give feedback to the community by improving this framework.<br />
<br />
==References==<br />
[[#Background|1]] - Genya V Dana et al. Four steps to avoid a synthetic biology disaster. 2012. Nature vol 483<br />
<br />
[[#Methods_and_Results|2]] - WorkSafe Victoria. A handbook for workplaces, controlling OHS hazards and risks. 2007. Edition No.1<br />
<br />
[[#Methods_and_Results|3]] - “Five steps to risk assessment” from [http://www.hse.gov.uk/risk/fivesteps.htm http://www.hse.gov.uk/risk/fivesteps.htm]. - risk management method in workplaces complying with health and safety law <br />
<br />
[[#Check_controls|4]] - Soren J Sorensen et al. 2005. Studying plasmid horizontal gene transfer in situ: a critical review. Nature Reviews Microbiology Vol 3<br />
<br />
[[#Check_controls|5]] - Heewook Lee et al., Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. 2012. PNAS E2774-E2783<br />
<br />
[[#Check_controls|6]] - Stanley A. Sawyer et al. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. 2007. PNAS 104(16):6504-6510<br />
<br />
[[#Check_controls|7]] - Lin Xu et al. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between two kingdoms. 2006. Mol. Biol. Evol. 23(6):1107-1108<br />
<br />
[[#Check_controls|8]] - David S Guttmand and Daniel E. Dykhuizen. 1994. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science Vol 266<br />
<br />
[[#Check_controls|9]] - L.Boe. 1996. Estimation of Plasmid Loss Rates in Bacterial Populations with a Reference to the Reproducibility of Stability Experiments. Plasmid 36, 161–167. Article No. 0043<br />
<br />
[[#Discussion|10]] - Torres B et al. 2003. A dual lethal system to enhance containment of recombinant micro-organisms. Microbiology. 2003 Dec;149(Pt 12):3595-601.<br />
<br />
[[#Discussion|11]] - Sean C Sleight et al., Designing and engineering evolutionary robust genetic circuits. 2010. Journal of Biological Engineering, 4:12<br />
</div><br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/ModelingTeam:Paris Bettencourt/Modeling2012-10-26T22:07:39Z<p>Aprastowo: /* Discussion */</p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<div id="grouptitle">Safety Assessment</div><br />
<br />
==Overview==<br />
Safety is an important issue in synthetic biology, especially on environmental related projects. We already tried to answer the question, “how safe is safe enough?” by involving experts, publics and scientists, and also building biosafety devices. However, to really answer the question, actually we need first to ask ourselves a more basic question, “how do we measure safety?”. As we see synthetic biology as an engineering approach to biology, we could think about adaptation of safety engineering, a well studied engineering subset, that has been widely use to minimize risks on many fields of engineering, such as mechanical engineering, aircrafts, and manufactures. However, the risks they face are surely different from the risks of synthetic biology. <br />
<br />
According to Dana et al<sup>[[#References|1]]</sup> there are four areas of risk research in environmental application of synthetic biology:<br />
*Differences in the physiology of natural and synthetic organisms will affect how they interact with the surrounding environment,<br />
*Escaped microorganisms have the potential to survive in receiving environments and to compete successfully with non-modified counterparts,<br />
*Synthetic organisms might evolve and adapt quickly, perhaps filling new ecological niches, and<br />
*Gene transfer.<br />
<br />
Knowing that there are different areas of risk that we need to take into account, we need to design our safety containment with different parts to deal with each of them. Identifying the relationship between one part and the others will help us to see the reliability of the overall system. Here we propose an approach to assess safety for environmental release of genetically engineered bacteria (GE bacteria).<br />
<br />
===Objectives===<br />
*Adapting existing safety assessment tools to synthetic biology.<br />
*Proposing methods to assess safety in synthetic biology.<br />
<br />
==Methods and Results==<br />
We propose a method to assess hazards and risk<sup>[[#References|2]]</sup> in releasing genetically engineered bacteria to the environment. As a case study, we want to release GE bacteria which will perform some function in the environment and we want to apply 3 sets of bWARE safety containment (alginate beads, bWARE killswitch, semantic containment) to control the hazards and risks. Here we focus more on the reliability of the safety containment system rather than the functional part, although the similar assessment can also be applied to see the functional part reliability.<br />
<br />
===Hazards Identification===<br />
Identifying hazards means that we need to find and understand the possible harm that may happen in the application of our system. Generally there are two potential hazard in environmental application of synthetic biology<sup>[[#References|1]]</sup> which are the success escape of the GE bacteria followed by a success competition with the natural strain and the horizontal gene transfer.<br />
<br />
===Risk Assessment===<br />
Risk assessment will give an idea what kind of risk we face in releasing the GEO in the environment and help to design the safety containment. Here we adapted a risk management method in workplaces complying with health and safety law <sup>[[#References|3]]</sup>.<br />
<br />
To-do-list to assess risk in 5 steps:<br />
#Identify the hazards<br />
#Decide who might be harmed and how<br />
#Evaluate the risks and decide on precaution<br />
#Record your findings and implement them<br />
#Review your assessment and update if necessary<br />
<br />
<br />
Worksheet example:<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are the hazards?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Who might be harmed and how?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are we already doing?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What further action is necessary?'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria outcompete natural strains<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria escaping the containment may outcompete natural strains if they have better fitness, creating natural imbalance <br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Using harmless strain or strain with low fitness compared to natural strain (standard E coli for lab)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to prevent the cells reproducing themselves at some point and/or separating them from natural strains<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Horizontal gene transfer (HGT)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Other strain/species may uptake engineered gene, and if the gene gives advantage in the fitness, it may outcompete other strain and creating natural imbalance<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| -<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to degrade DNA and/or separate the DNA from the environment and/or prevent natural strain having advantages from the DNA<br />
<br />
|}<br />
<br />
<br><br />
===Control hazards and risks===<br />
<br />
In this step we decided what control elements we want to put to our system to reduce the risks. We should choose the best suitable control elements depending on the system function and application. As we already know that we want to apply bWARE safety containment, here we describe the role of each safety parts in the risks reduction. <br />
#GE bacteria outcompete natural strains<br />
#*In order to prevent the success escape of GE bacteria and outcompete the natural strains, we will stop their reproduction by putting a self killing mechanism to kill the cells after they perform the function. <br />
#*In case of the failure of the killing mechanism, we will put the cells inside a physical containment so there will be no physical interaction between them and the surrounding cells.<br />
#HGT<br />
#*We will use DNAse to degrade DNA after the cells perform the function so they won’t leave any genetic material behind.<br />
#*In case of the failure on inefficiency of the DNAse, the physical containment will still protect the DNA from the environment.<br />
#*In case of the leakiness of the physical containment, the DNA has special encryption system with the semantic containment so the receiver cell will not be able to read it.<br />
<br />
===Check controls=== <br />
<br />
To check and predict the reliability of our system, we used fault tree analysis to assess multiple safety containment in one biodevice. This top-down approach allows us to see the relationship between each containment element and predict the overall failure probability. With this method we can see what basic events are the key elements in our system.<br />
<br />
<center>[[Image:ParisB_FTA.png]]</center><br />
<br />
AND gate represents independent events<br />
<br />
P(A and B) = P(A)P(B)<br />
<br />
OR gate corresponds to set of union<br />
<br />
P(A or B) = P(A) + P(B)<br />
<br />
so the total failure probability of the system is<br />
<br />
Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9)<br />
<br />
List of the basic events<br />
<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Notation'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure component'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure mode'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Consequence'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Method for determining the probability'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P1<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| physical containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| leakage<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA/cell escape<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| experiment<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P2<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA uptake<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA transferred into natural strain<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| <nowiki>transconjugant to donor ratio in HGT is typically <10</nowiki><sup>-5</sup> <sup>[[#References|4]]</sup><br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P3<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| semantic containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation*<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P4<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| population suicide<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no surrounding cells with enough toxin<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no death<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| based on the cell density and the expectation number of surrounding non-mutant<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P5<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| toxin production<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no DNA degradation (w/o antitoxin), no death (with antitoxin)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P6<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| mutant fitness<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| beneficial mutation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| outcompetition of the mutant<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P7<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| delay system<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P8<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction enzyme<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P9<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction site<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|}<br />
<br />
====Physical containment failure====<br />
<br />
From the experiment we get the escape rate of the cells from the alginate beads is (escaping cells/total cells) is 10<sup>-5</sup> per 12 hours. Assuming 30 minutes of division time, we have 24 generations, and the escape rate per generation is 4 x 10<sup>-6</sup>.<br />
<br />
====Genetic failure====<br />
<br />
There are different processes that lead to a loss of function of a gene<br />
<br />
* Mutation<br />
* Recombination<br />
* Plasmid loss<br />
<br />
'''Losing function because of mutation'''<br />
<br />
Estimating the mutation rate which cause failure of the safety containment of the device<br />
<br />
* Spontaneous mutation rate of a wild-type E coli strain growing on research medium is 3.3 x 10<sup>-9</sup> per nucleotide per generation <sup>[[#References|5]]</sup> <br />
* approximately ⅔ of nucleotide mutation will change amino acid (64 combination of nucleotides code only 20 amino acids)<br />
* approximately 70% of amino acid change will lose the part function <sup>[[#References|6]]</sup><br />
* mean length of genetic coding sequence for E coli (procaryotes) is 924 bp <sup>[[#References|7]]</sup> ≈ 1000 bp <br />
<br />
So the loss function rate of a gene per generation because of mutation is <br />
<br />
P<sub>L</sub><nowiki>= 3.3 x 10</nowiki><sup>-9</sup> x ⅔ x 0.70 x 1000 = 1.54 x 10<sup>-6</sup> <br />
<br />
'''Recombination'''<br />
<br />
Finding a definite rate of recombination is not easy. Guttman and Dykhuizen in 1994 <sup>[[#References|8]]</sup> stated that recombination is believed to occur at such a low frequency, but their experiment showed that the rate could be as high as mutation rate (50 fold higher compared to the mutation rate believed at that moment, but actually it is 5.0 x 10<sup>-9</sup> changes per nucleotide per generation, a bit more than one fold to the value believed now). <br />
<br />
Redoing the previous calculation with this number will lead us to 2.33 x 10<sup>-6</sup> per gene per generation.<br />
<br />
'''Plasmid loss'''<br />
<br />
According to L Boe <sup>[[#References|9]]</sup> plasmid loss rate is defined as the probability that a division of a plasmid-carrying individual results in the birth of one plasmid-free and one plasmid-carrying daughter cell. For the low copy plasmid this rate is about ~1% /division and for high copy plasmid is ~0.01% /division, neglecting the viable/non-viable factor of the cells of losing the plasmid (no selection). If a plasmid with a lost rate of 0.05 is stabilized with a 100% efficient postsegragational killing system, the 5% of the division will result in non viable daughter cell, and we can not see the effect except of increasing the appearing division time by ln 2/ln (1-0.05) = 1.04. Thus in our system we can neglect this plasmid loss assuming that we have antibiotic selection in the beads.<br />
<br />
Assuming only mutation and recombination could happen to delete a function of a gene, we have the total genetic failure rate around 4 x 10<sup>-6</sup> per gene per generation.<br />
<br />
====Total failure probability====<br />
<br />
Having Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9) and put 1 for unknown probability (P4 and P6) as a worst-case scenario, we come to the failure rate number 6.4 x 10<sup>-11</sup> per generation.<br />
<br />
A volume of one alginate bead is approximately 20 uL. So if the cells grow until they reach the stationary phase (4 x 10<sup>9</sup> cells/ml), we will have 8 x 10<sup>7</sup> cells. If we started from 100 cells per bead, the number of generations we have is <sup>2</sup>log (8 x 10<sup>7</sup> / 100) =19.6 generations. Therefore the total failure becomes 6.4 x 10<sup>-11</sup> x 19.6 = 1.25 x 10<sup>-9</sup>.<br />
<br />
With this method we can also see that the sense-HGT rate is much lower (6.4 x 10<sup>-22</sup>) , almost negligible compared to the outcompetition rate, because it has more back up/redundancy components.<br />
<br />
== Discussion ==<br />
<br />
We have proposed and done an example of assessing biosafety adapting existing method from safety engineering. However it is very clear that the prediction is based on rough estimation and we need more experimental data to verify this estimation. For an example, Torres et al <sup>[[#References|10]]</sup> tested a dual containment killing system and compared it with single containment system. They tested EcoRI based system and Colicin E3-based system and get the efficacy (based on the numbers of successful transformants) each 10<sup>4</sup> and 10<sup>5</sup> respectively but when they combine both system they only got efficacy 10<sup>6</sup>, while theoretically they could reach up to 10<sup>9</sup>. This could give us an idea that predicting a performance of a combination of genetic parts is not as easy as combining the performance of each genetic part. However, we can still conclude that having redundant parts is necessary to reduce the failure rate and make it as low as possible.<br />
<br />
Research in measuring the evolutionary stability in E coli was performed by Sean C Sleight et al <sup>[[#References|11]]</sup> where they measured it of BioBrick-assembled genetic circuits in E coli over multiple generation by measuring the number of loss-functioning mutants. They concluded that to make a robust GE bacteria, one has to take into account 3 principles:<br />
# High expression of genetic circuits comes with the cost of low evolutionary stability (for example induced vs non-induced system)<br />
#Avoid repeated sequences because it will more likely be mutated<br />
#Use of inducible promoters generally increases evolutionary stability compared to constitutive promoters<br />
<br />
To predict the robustness of the system from mutation, we have to take into account for how long time (i.e. how many generations) we want our system to work. From their experiment for example, the AHL induced TetR-GFP cells lose their functions after 30 generations, while the uninduced ones lose their function slower (50% after 300 generations). A similar idea is also shown from our work where the mutation rate we got from literature research is in the unit of per generation. This is how reproduction differs biological system from other engineering systems. In engineering we also have failure probability as a function of time because of the life cycle of the system, but the system is not reproducing so it has no variability. <br />
<br />
Analyzing key elements that cause failure in any systems including synthetic biology systems is essential for system improvement and prediction of the failure. Adaptation of classical safety engineering methods needs to take into account the uniqueness properties of synthetic biology. Reproducibility and complexity are two example of areas that need to be studied deeper in this context. We invite future iGEM teams to use and improve our assessment framework, build a solid assessment protocol towards a better understanding of biosafety and successful application of synthetic biology.<br />
<br />
== Conclusion ==<br />
*We can adapt methods in safety engineering to assess risk in biosafety<br />
*We need more experimental data to confirm the risk assessing method<br />
<br />
== Perspectives ==<br />
<br />
*We need a method to predict the evolutionary stability of circuits from the properties of their parts, but the emergent behaviours of circuits will likely make prediction difficult. Thus it will be very useful if each BioBricks parts is completed with evolutionary stability data sheet, so we can make prediction of the stability of more complex circuits.<br />
*This safety assessment method is useful for identifying key elements of having failure in synthetic circuit systems before we go further to the real application. Thus we recommend for the future iGEM team to use our assessment method and give feedback to the community by improving this framework.<br />
<br />
==References==<br />
[[#Background|1]] - Genya V Dana et al. Four steps to avoid a synthetic biology disaster. 2012. Nature vol 483<br />
<br />
[[#Methods_and_Results|2]] - WorkSafe Victoria. A handbook for workplaces, controlling OHS hazards and risks. 2007. Edition No.1<br />
<br />
[[#Methods_and_Results|3]] - “Five steps to risk assessment” from [http://www.hse.gov.uk/risk/fivesteps.htm http://www.hse.gov.uk/risk/fivesteps.htm]. - risk management method in workplaces complying with health and safety law <br />
<br />
[[#Check_controls|4]] - Soren J Sorensen et al. 2005. Studying plasmid horizontal gene transfer in situ: a critical review. Nature Reviews Microbiology Vol 3<br />
<br />
[[#Check_controls|5]] - Heewook Lee et al., Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. 2012. PNAS E2774-E2783<br />
<br />
[[#Check_controls|6]] - Stanley A. Sawyer et al. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. 2007. PNAS 104(16):6504-6510<br />
<br />
[[#Check_controls|7]] - Lin Xu et al. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between two kingdoms. 2006. Mol. Biol. Evol. 23(6):1107-1108<br />
<br />
[[#Check_controls|8]] - David S Guttmand and Daniel E. Dykhuizen. 1994. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science Vol 266<br />
<br />
[[#Check_controls|9]] - L.Boe. 1996. Estimation of Plasmid Loss Rates in Bacterial Populations with a Reference to the Reproducibility of Stability Experiments. Plasmid 36, 161–167. Article No. 0043<br />
<br />
[[#Discussion|10]] - Torres B et al. 2003. A dual lethal system to enhance containment of recombinant micro-organisms. Microbiology. 2003 Dec;149(Pt 12):3595-601.<br />
<br />
[[#Discussion|11]] - Sean C Sleight et al., Designing and engineering evolutionary robust genetic circuits. 2010. Journal of Biological Engineering, 4:12<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/ModelingTeam:Paris Bettencourt/Modeling2012-10-26T22:07:16Z<p>Aprastowo: /* Discussion */</p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<div id="grouptitle">Safety Assessment</div><br />
<br />
==Overview==<br />
Safety is an important issue in synthetic biology, especially on environmental related projects. We already tried to answer the question, “how safe is safe enough?” by involving experts, publics and scientists, and also building biosafety devices. However, to really answer the question, actually we need first to ask ourselves a more basic question, “how do we measure safety?”. As we see synthetic biology as an engineering approach to biology, we could think about adaptation of safety engineering, a well studied engineering subset, that has been widely use to minimize risks on many fields of engineering, such as mechanical engineering, aircrafts, and manufactures. However, the risks they face are surely different from the risks of synthetic biology. <br />
<br />
According to Dana et al<sup>[[#References|1]]</sup> there are four areas of risk research in environmental application of synthetic biology:<br />
*Differences in the physiology of natural and synthetic organisms will affect how they interact with the surrounding environment,<br />
*Escaped microorganisms have the potential to survive in receiving environments and to compete successfully with non-modified counterparts,<br />
*Synthetic organisms might evolve and adapt quickly, perhaps filling new ecological niches, and<br />
*Gene transfer.<br />
<br />
Knowing that there are different areas of risk that we need to take into account, we need to design our safety containment with different parts to deal with each of them. Identifying the relationship between one part and the others will help us to see the reliability of the overall system. Here we propose an approach to assess safety for environmental release of genetically engineered bacteria (GE bacteria).<br />
<br />
===Objectives===<br />
*Adapting existing safety assessment tools to synthetic biology.<br />
*Proposing methods to assess safety in synthetic biology.<br />
<br />
==Methods and Results==<br />
We propose a method to assess hazards and risk<sup>[[#References|2]]</sup> in releasing genetically engineered bacteria to the environment. As a case study, we want to release GE bacteria which will perform some function in the environment and we want to apply 3 sets of bWARE safety containment (alginate beads, bWARE killswitch, semantic containment) to control the hazards and risks. Here we focus more on the reliability of the safety containment system rather than the functional part, although the similar assessment can also be applied to see the functional part reliability.<br />
<br />
===Hazards Identification===<br />
Identifying hazards means that we need to find and understand the possible harm that may happen in the application of our system. Generally there are two potential hazard in environmental application of synthetic biology<sup>[[#References|1]]</sup> which are the success escape of the GE bacteria followed by a success competition with the natural strain and the horizontal gene transfer.<br />
<br />
===Risk Assessment===<br />
Risk assessment will give an idea what kind of risk we face in releasing the GEO in the environment and help to design the safety containment. Here we adapted a risk management method in workplaces complying with health and safety law <sup>[[#References|3]]</sup>.<br />
<br />
To-do-list to assess risk in 5 steps:<br />
#Identify the hazards<br />
#Decide who might be harmed and how<br />
#Evaluate the risks and decide on precaution<br />
#Record your findings and implement them<br />
#Review your assessment and update if necessary<br />
<br />
<br />
Worksheet example:<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are the hazards?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Who might be harmed and how?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are we already doing?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What further action is necessary?'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria outcompete natural strains<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria escaping the containment may outcompete natural strains if they have better fitness, creating natural imbalance <br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Using harmless strain or strain with low fitness compared to natural strain (standard E coli for lab)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to prevent the cells reproducing themselves at some point and/or separating them from natural strains<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Horizontal gene transfer (HGT)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Other strain/species may uptake engineered gene, and if the gene gives advantage in the fitness, it may outcompete other strain and creating natural imbalance<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| -<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to degrade DNA and/or separate the DNA from the environment and/or prevent natural strain having advantages from the DNA<br />
<br />
|}<br />
<br />
<br><br />
===Control hazards and risks===<br />
<br />
In this step we decided what control elements we want to put to our system to reduce the risks. We should choose the best suitable control elements depending on the system function and application. As we already know that we want to apply bWARE safety containment, here we describe the role of each safety parts in the risks reduction. <br />
#GE bacteria outcompete natural strains<br />
#*In order to prevent the success escape of GE bacteria and outcompete the natural strains, we will stop their reproduction by putting a self killing mechanism to kill the cells after they perform the function. <br />
#*In case of the failure of the killing mechanism, we will put the cells inside a physical containment so there will be no physical interaction between them and the surrounding cells.<br />
#HGT<br />
#*We will use DNAse to degrade DNA after the cells perform the function so they won’t leave any genetic material behind.<br />
#*In case of the failure on inefficiency of the DNAse, the physical containment will still protect the DNA from the environment.<br />
#*In case of the leakiness of the physical containment, the DNA has special encryption system with the semantic containment so the receiver cell will not be able to read it.<br />
<br />
===Check controls=== <br />
<br />
To check and predict the reliability of our system, we used fault tree analysis to assess multiple safety containment in one biodevice. This top-down approach allows us to see the relationship between each containment element and predict the overall failure probability. With this method we can see what basic events are the key elements in our system.<br />
<br />
<center>[[Image:ParisB_FTA.png]]</center><br />
<br />
AND gate represents independent events<br />
<br />
P(A and B) = P(A)P(B)<br />
<br />
OR gate corresponds to set of union<br />
<br />
P(A or B) = P(A) + P(B)<br />
<br />
so the total failure probability of the system is<br />
<br />
Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9)<br />
<br />
List of the basic events<br />
<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Notation'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure component'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure mode'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Consequence'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Method for determining the probability'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P1<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| physical containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| leakage<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA/cell escape<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| experiment<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P2<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA uptake<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA transferred into natural strain<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| <nowiki>transconjugant to donor ratio in HGT is typically <10</nowiki><sup>-5</sup> <sup>[[#References|4]]</sup><br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P3<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| semantic containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation*<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P4<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| population suicide<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no surrounding cells with enough toxin<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no death<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| based on the cell density and the expectation number of surrounding non-mutant<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P5<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| toxin production<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no DNA degradation (w/o antitoxin), no death (with antitoxin)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P6<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| mutant fitness<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| beneficial mutation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| outcompetition of the mutant<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P7<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| delay system<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P8<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction enzyme<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P9<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction site<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|}<br />
<br />
====Physical containment failure====<br />
<br />
From the experiment we get the escape rate of the cells from the alginate beads is (escaping cells/total cells) is 10<sup>-5</sup> per 12 hours. Assuming 30 minutes of division time, we have 24 generations, and the escape rate per generation is 4 x 10<sup>-6</sup>.<br />
<br />
====Genetic failure====<br />
<br />
There are different processes that lead to a loss of function of a gene<br />
<br />
* Mutation<br />
* Recombination<br />
* Plasmid loss<br />
<br />
'''Losing function because of mutation'''<br />
<br />
Estimating the mutation rate which cause failure of the safety containment of the device<br />
<br />
* Spontaneous mutation rate of a wild-type E coli strain growing on research medium is 3.3 x 10<sup>-9</sup> per nucleotide per generation <sup>[[#References|5]]</sup> <br />
* approximately ⅔ of nucleotide mutation will change amino acid (64 combination of nucleotides code only 20 amino acids)<br />
* approximately 70% of amino acid change will lose the part function <sup>[[#References|6]]</sup><br />
* mean length of genetic coding sequence for E coli (procaryotes) is 924 bp <sup>[[#References|7]]</sup> ≈ 1000 bp <br />
<br />
So the loss function rate of a gene per generation because of mutation is <br />
<br />
P<sub>L</sub><nowiki>= 3.3 x 10</nowiki><sup>-9</sup> x ⅔ x 0.70 x 1000 = 1.54 x 10<sup>-6</sup> <br />
<br />
'''Recombination'''<br />
<br />
Finding a definite rate of recombination is not easy. Guttman and Dykhuizen in 1994 <sup>[[#References|8]]</sup> stated that recombination is believed to occur at such a low frequency, but their experiment showed that the rate could be as high as mutation rate (50 fold higher compared to the mutation rate believed at that moment, but actually it is 5.0 x 10<sup>-9</sup> changes per nucleotide per generation, a bit more than one fold to the value believed now). <br />
<br />
Redoing the previous calculation with this number will lead us to 2.33 x 10<sup>-6</sup> per gene per generation.<br />
<br />
'''Plasmid loss'''<br />
<br />
According to L Boe <sup>[[#References|9]]</sup> plasmid loss rate is defined as the probability that a division of a plasmid-carrying individual results in the birth of one plasmid-free and one plasmid-carrying daughter cell. For the low copy plasmid this rate is about ~1% /division and for high copy plasmid is ~0.01% /division, neglecting the viable/non-viable factor of the cells of losing the plasmid (no selection). If a plasmid with a lost rate of 0.05 is stabilized with a 100% efficient postsegragational killing system, the 5% of the division will result in non viable daughter cell, and we can not see the effect except of increasing the appearing division time by ln 2/ln (1-0.05) = 1.04. Thus in our system we can neglect this plasmid loss assuming that we have antibiotic selection in the beads.<br />
<br />
Assuming only mutation and recombination could happen to delete a function of a gene, we have the total genetic failure rate around 4 x 10<sup>-6</sup> per gene per generation.<br />
<br />
====Total failure probability====<br />
<br />
Having Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9) and put 1 for unknown probability (P4 and P6) as a worst-case scenario, we come to the failure rate number 6.4 x 10<sup>-11</sup> per generation.<br />
<br />
A volume of one alginate bead is approximately 20 uL. So if the cells grow until they reach the stationary phase (4 x 10<sup>9</sup> cells/ml), we will have 8 x 10<sup>7</sup> cells. If we started from 100 cells per bead, the number of generations we have is <sup>2</sup>log (8 x 10<sup>7</sup> / 100) =19.6 generations. Therefore the total failure becomes 6.4 x 10<sup>-11</sup> x 19.6 = 1.25 x 10<sup>-9</sup>.<br />
<br />
With this method we can also see that the sense-HGT rate is much lower (6.4 x 10<sup>-22</sup>) , almost negligible compared to the outcompetition rate, because it has more back up/redundancy components.<br />
<br />
== Discussion ==<br />
<br />
We have proposed and done an example of assessing biosafety adapting existing method from safety engineering. However it is very clear that the prediction is based on rough estimation and we need more experimental data to verify this estimation. For an example, Torres et al <sup>[[#References|10]]</sup> tested a dual containment killing system and compared it with single containment system. They tested EcoRI based system and Colicin E3-based system and get the efficacy (based on the numbers of successful transformants) each 10<sup>4</sup> and 10<sup>5</sup> respectively but when they combine both system they only got efficacy 10<sup>6</sup>, while theoretically they could reach up to 10<sup>9</sup>. This could give us an idea that predicting a performance of a combination of genetic parts is not as easy as combining the performance of each genetic part. However, we can still conclude that having redundant parts is necessary to reduce the failure rate and make it as low as possible.<br />
<br />
Research in measuring the evolutionary stability in E coli was performed by Sean C Sleight et al <sup>[[#References|12]]</sup> where they measured it of BioBrick-assembled genetic circuits in E coli over multiple generation by measuring the number of loss-functioning mutants. They concluded that to make a robust GE bacteria, one has to take into account 3 principles:<br />
# High expression of genetic circuits comes with the cost of low evolutionary stability (for example induced vs non-induced system)<br />
#Avoid repeated sequences because it will more likely be mutated<br />
#Use of inducible promoters generally increases evolutionary stability compared to constitutive promoters<br />
<br />
To predict the robustness of the system from mutation, we have to take into account for how long time (i.e. how many generations) we want our system to work. From their experiment for example, the AHL induced TetR-GFP cells lose their functions after 30 generations, while the uninduced ones lose their function slower (50% after 300 generations). A similar idea is also shown from our work where the mutation rate we got from literature research is in the unit of per generation. This is how reproduction differs biological system from other engineering systems. In engineering we also have failure probability as a function of time because of the life cycle of the system, but the system is not reproducing so it has no variability. <br />
<br />
Analyzing key elements that cause failure in any systems including synthetic biology systems is essential for system improvement and prediction of the failure. Adaptation of classical safety engineering methods needs to take into account the uniqueness properties of synthetic biology. Reproducibility and complexity are two example of areas that need to be studied deeper in this context. We invite future iGEM teams to use and improve our assessment framework, build a solid assessment protocol towards a better understanding of biosafety and successful application of synthetic biology.<br />
<br />
== Conclusion ==<br />
*We can adapt methods in safety engineering to assess risk in biosafety<br />
*We need more experimental data to confirm the risk assessing method<br />
<br />
== Perspectives ==<br />
<br />
*We need a method to predict the evolutionary stability of circuits from the properties of their parts, but the emergent behaviours of circuits will likely make prediction difficult. Thus it will be very useful if each BioBricks parts is completed with evolutionary stability data sheet, so we can make prediction of the stability of more complex circuits.<br />
*This safety assessment method is useful for identifying key elements of having failure in synthetic circuit systems before we go further to the real application. Thus we recommend for the future iGEM team to use our assessment method and give feedback to the community by improving this framework.<br />
<br />
==References==<br />
[[#Background|1]] - Genya V Dana et al. Four steps to avoid a synthetic biology disaster. 2012. Nature vol 483<br />
<br />
[[#Methods_and_Results|2]] - WorkSafe Victoria. A handbook for workplaces, controlling OHS hazards and risks. 2007. Edition No.1<br />
<br />
[[#Methods_and_Results|3]] - “Five steps to risk assessment” from [http://www.hse.gov.uk/risk/fivesteps.htm http://www.hse.gov.uk/risk/fivesteps.htm]. - risk management method in workplaces complying with health and safety law <br />
<br />
[[#Check_controls|4]] - Soren J Sorensen et al. 2005. Studying plasmid horizontal gene transfer in situ: a critical review. Nature Reviews Microbiology Vol 3<br />
<br />
[[#Check_controls|5]] - Heewook Lee et al., Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. 2012. PNAS E2774-E2783<br />
<br />
[[#Check_controls|6]] - Stanley A. Sawyer et al. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. 2007. PNAS 104(16):6504-6510<br />
<br />
[[#Check_controls|7]] - Lin Xu et al. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between two kingdoms. 2006. Mol. Biol. Evol. 23(6):1107-1108<br />
<br />
[[#Check_controls|8]] - David S Guttmand and Daniel E. Dykhuizen. 1994. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science Vol 266<br />
<br />
[[#Check_controls|9]] - L.Boe. 1996. Estimation of Plasmid Loss Rates in Bacterial Populations with a Reference to the Reproducibility of Stability Experiments. Plasmid 36, 161–167. Article No. 0043<br />
<br />
[[#Discussion|10]] - Torres B et al. 2003. A dual lethal system to enhance containment of recombinant micro-organisms. Microbiology. 2003 Dec;149(Pt 12):3595-601.<br />
<br />
[[#Discussion|11]] - Sean C Sleight et al., Designing and engineering evolutionary robust genetic circuits. 2010. Journal of Biological Engineering, 4:12<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/ModelingTeam:Paris Bettencourt/Modeling2012-10-26T22:07:11Z<p>Aprastowo: /* References */</p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<div id="grouptitle">Safety Assessment</div><br />
<br />
==Overview==<br />
Safety is an important issue in synthetic biology, especially on environmental related projects. We already tried to answer the question, “how safe is safe enough?” by involving experts, publics and scientists, and also building biosafety devices. However, to really answer the question, actually we need first to ask ourselves a more basic question, “how do we measure safety?”. As we see synthetic biology as an engineering approach to biology, we could think about adaptation of safety engineering, a well studied engineering subset, that has been widely use to minimize risks on many fields of engineering, such as mechanical engineering, aircrafts, and manufactures. However, the risks they face are surely different from the risks of synthetic biology. <br />
<br />
According to Dana et al<sup>[[#References|1]]</sup> there are four areas of risk research in environmental application of synthetic biology:<br />
*Differences in the physiology of natural and synthetic organisms will affect how they interact with the surrounding environment,<br />
*Escaped microorganisms have the potential to survive in receiving environments and to compete successfully with non-modified counterparts,<br />
*Synthetic organisms might evolve and adapt quickly, perhaps filling new ecological niches, and<br />
*Gene transfer.<br />
<br />
Knowing that there are different areas of risk that we need to take into account, we need to design our safety containment with different parts to deal with each of them. Identifying the relationship between one part and the others will help us to see the reliability of the overall system. Here we propose an approach to assess safety for environmental release of genetically engineered bacteria (GE bacteria).<br />
<br />
===Objectives===<br />
*Adapting existing safety assessment tools to synthetic biology.<br />
*Proposing methods to assess safety in synthetic biology.<br />
<br />
==Methods and Results==<br />
We propose a method to assess hazards and risk<sup>[[#References|2]]</sup> in releasing genetically engineered bacteria to the environment. As a case study, we want to release GE bacteria which will perform some function in the environment and we want to apply 3 sets of bWARE safety containment (alginate beads, bWARE killswitch, semantic containment) to control the hazards and risks. Here we focus more on the reliability of the safety containment system rather than the functional part, although the similar assessment can also be applied to see the functional part reliability.<br />
<br />
===Hazards Identification===<br />
Identifying hazards means that we need to find and understand the possible harm that may happen in the application of our system. Generally there are two potential hazard in environmental application of synthetic biology<sup>[[#References|1]]</sup> which are the success escape of the GE bacteria followed by a success competition with the natural strain and the horizontal gene transfer.<br />
<br />
===Risk Assessment===<br />
Risk assessment will give an idea what kind of risk we face in releasing the GEO in the environment and help to design the safety containment. Here we adapted a risk management method in workplaces complying with health and safety law <sup>[[#References|3]]</sup>.<br />
<br />
To-do-list to assess risk in 5 steps:<br />
#Identify the hazards<br />
#Decide who might be harmed and how<br />
#Evaluate the risks and decide on precaution<br />
#Record your findings and implement them<br />
#Review your assessment and update if necessary<br />
<br />
<br />
Worksheet example:<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are the hazards?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Who might be harmed and how?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are we already doing?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What further action is necessary?'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria outcompete natural strains<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria escaping the containment may outcompete natural strains if they have better fitness, creating natural imbalance <br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Using harmless strain or strain with low fitness compared to natural strain (standard E coli for lab)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to prevent the cells reproducing themselves at some point and/or separating them from natural strains<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Horizontal gene transfer (HGT)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Other strain/species may uptake engineered gene, and if the gene gives advantage in the fitness, it may outcompete other strain and creating natural imbalance<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| -<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to degrade DNA and/or separate the DNA from the environment and/or prevent natural strain having advantages from the DNA<br />
<br />
|}<br />
<br />
<br><br />
===Control hazards and risks===<br />
<br />
In this step we decided what control elements we want to put to our system to reduce the risks. We should choose the best suitable control elements depending on the system function and application. As we already know that we want to apply bWARE safety containment, here we describe the role of each safety parts in the risks reduction. <br />
#GE bacteria outcompete natural strains<br />
#*In order to prevent the success escape of GE bacteria and outcompete the natural strains, we will stop their reproduction by putting a self killing mechanism to kill the cells after they perform the function. <br />
#*In case of the failure of the killing mechanism, we will put the cells inside a physical containment so there will be no physical interaction between them and the surrounding cells.<br />
#HGT<br />
#*We will use DNAse to degrade DNA after the cells perform the function so they won’t leave any genetic material behind.<br />
#*In case of the failure on inefficiency of the DNAse, the physical containment will still protect the DNA from the environment.<br />
#*In case of the leakiness of the physical containment, the DNA has special encryption system with the semantic containment so the receiver cell will not be able to read it.<br />
<br />
===Check controls=== <br />
<br />
To check and predict the reliability of our system, we used fault tree analysis to assess multiple safety containment in one biodevice. This top-down approach allows us to see the relationship between each containment element and predict the overall failure probability. With this method we can see what basic events are the key elements in our system.<br />
<br />
<center>[[Image:ParisB_FTA.png]]</center><br />
<br />
AND gate represents independent events<br />
<br />
P(A and B) = P(A)P(B)<br />
<br />
OR gate corresponds to set of union<br />
<br />
P(A or B) = P(A) + P(B)<br />
<br />
so the total failure probability of the system is<br />
<br />
Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9)<br />
<br />
List of the basic events<br />
<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Notation'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure component'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure mode'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Consequence'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Method for determining the probability'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P1<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| physical containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| leakage<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA/cell escape<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| experiment<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P2<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA uptake<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA transferred into natural strain<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| <nowiki>transconjugant to donor ratio in HGT is typically <10</nowiki><sup>-5</sup> <sup>[[#References|4]]</sup><br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P3<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| semantic containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation*<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P4<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| population suicide<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no surrounding cells with enough toxin<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no death<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| based on the cell density and the expectation number of surrounding non-mutant<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P5<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| toxin production<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no DNA degradation (w/o antitoxin), no death (with antitoxin)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P6<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| mutant fitness<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| beneficial mutation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| outcompetition of the mutant<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P7<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| delay system<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P8<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction enzyme<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P9<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction site<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|}<br />
<br />
====Physical containment failure====<br />
<br />
From the experiment we get the escape rate of the cells from the alginate beads is (escaping cells/total cells) is 10<sup>-5</sup> per 12 hours. Assuming 30 minutes of division time, we have 24 generations, and the escape rate per generation is 4 x 10<sup>-6</sup>.<br />
<br />
====Genetic failure====<br />
<br />
There are different processes that lead to a loss of function of a gene<br />
<br />
* Mutation<br />
* Recombination<br />
* Plasmid loss<br />
<br />
'''Losing function because of mutation'''<br />
<br />
Estimating the mutation rate which cause failure of the safety containment of the device<br />
<br />
* Spontaneous mutation rate of a wild-type E coli strain growing on research medium is 3.3 x 10<sup>-9</sup> per nucleotide per generation <sup>[[#References|5]]</sup> <br />
* approximately ⅔ of nucleotide mutation will change amino acid (64 combination of nucleotides code only 20 amino acids)<br />
* approximately 70% of amino acid change will lose the part function <sup>[[#References|6]]</sup><br />
* mean length of genetic coding sequence for E coli (procaryotes) is 924 bp <sup>[[#References|7]]</sup> ≈ 1000 bp <br />
<br />
So the loss function rate of a gene per generation because of mutation is <br />
<br />
P<sub>L</sub><nowiki>= 3.3 x 10</nowiki><sup>-9</sup> x ⅔ x 0.70 x 1000 = 1.54 x 10<sup>-6</sup> <br />
<br />
'''Recombination'''<br />
<br />
Finding a definite rate of recombination is not easy. Guttman and Dykhuizen in 1994 <sup>[[#References|8]]</sup> stated that recombination is believed to occur at such a low frequency, but their experiment showed that the rate could be as high as mutation rate (50 fold higher compared to the mutation rate believed at that moment, but actually it is 5.0 x 10<sup>-9</sup> changes per nucleotide per generation, a bit more than one fold to the value believed now). <br />
<br />
Redoing the previous calculation with this number will lead us to 2.33 x 10<sup>-6</sup> per gene per generation.<br />
<br />
'''Plasmid loss'''<br />
<br />
According to L Boe <sup>[[#References|9]]</sup> plasmid loss rate is defined as the probability that a division of a plasmid-carrying individual results in the birth of one plasmid-free and one plasmid-carrying daughter cell. For the low copy plasmid this rate is about ~1% /division and for high copy plasmid is ~0.01% /division, neglecting the viable/non-viable factor of the cells of losing the plasmid (no selection). If a plasmid with a lost rate of 0.05 is stabilized with a 100% efficient postsegragational killing system, the 5% of the division will result in non viable daughter cell, and we can not see the effect except of increasing the appearing division time by ln 2/ln (1-0.05) = 1.04. Thus in our system we can neglect this plasmid loss assuming that we have antibiotic selection in the beads.<br />
<br />
Assuming only mutation and recombination could happen to delete a function of a gene, we have the total genetic failure rate around 4 x 10<sup>-6</sup> per gene per generation.<br />
<br />
====Total failure probability====<br />
<br />
Having Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9) and put 1 for unknown probability (P4 and P6) as a worst-case scenario, we come to the failure rate number 6.4 x 10<sup>-11</sup> per generation.<br />
<br />
A volume of one alginate bead is approximately 20 uL. So if the cells grow until they reach the stationary phase (4 x 10<sup>9</sup> cells/ml), we will have 8 x 10<sup>7</sup> cells. If we started from 100 cells per bead, the number of generations we have is <sup>2</sup>log (8 x 10<sup>7</sup> / 100) =19.6 generations. Therefore the total failure becomes 6.4 x 10<sup>-11</sup> x 19.6 = 1.25 x 10<sup>-9</sup>.<br />
<br />
With this method we can also see that the sense-HGT rate is much lower (6.4 x 10<sup>-22</sup>) , almost negligible compared to the outcompetition rate, because it has more back up/redundancy components.<br />
<br />
== Discussion ==<br />
<br />
We have proposed and done an example of assessing biosafety adapting existing method from safety engineering. However it is very clear that the prediction is based on rough estimation and we need more experimental data to verify this estimation. For an example, Torres et al [REFERENCE] tested a dual containment killing system and compared it with single containment system. They tested EcoRI based system and Colicin E3-based system and get the efficacy (based on the numbers of successful transformants) each 10<sup>4</sup> and 10<sup>5</sup> respectively but when they combine both system they only got efficacy 10<sup>6</sup>, while theoretically they could reach up to 10<sup>9</sup>. This could give us an idea that predicting a performance of a combination of genetic parts is not as easy as combining the performance of each genetic part. However, we can still conclude that having redundant parts is necessary to reduce the failure rate and make it as low as possible.<br />
<br />
Research in measuring the evolutionary stability in E coli was performed by Sean C Sleight et al [REFERENCE] where they measured it of BioBrick-assembled genetic circuits in E coli over multiple generation by measuring the number of loss-functioning mutants. They concluded that to make a robust GE bacteria, one has to take into account 3 principles:<br />
# High expression of genetic circuits comes with the cost of low evolutionary stability (for example induced vs non-induced system)<br />
#Avoid repeated sequences because it will more likely be mutated<br />
#Use of inducible promoters generally increases evolutionary stability compared to constitutive promoters<br />
<br />
To predict the robustness of the system from mutation, we have to take into account for how long time (i.e. how many generations) we want our system to work. From their experiment for example, the AHL induced TetR-GFP cells lose their functions after 30 generations, while the uninduced ones lose their function slower (50% after 300 generations). A similar idea is also shown from our work where the mutation rate we got from literature research is in the unit of per generation. This is how reproduction differs biological system from other engineering systems. In engineering we also have failure probability as a function of time because of the life cycle of the system, but the system is not reproducing so it has no variability. <br />
<br />
Analyzing key elements that cause failure in any systems including synthetic biology systems is essential for system improvement and prediction of the failure. Adaptation of classical safety engineering methods needs to take into account the uniqueness properties of synthetic biology. Reproducibility and complexity are two example of areas that need to be studied deeper in this context. We invite future iGEM teams to use and improve our assessment framework, build a solid assessment protocol towards a better understanding of biosafety and successful application of synthetic biology.<br />
<br />
== Conclusion ==<br />
*We can adapt methods in safety engineering to assess risk in biosafety<br />
*We need more experimental data to confirm the risk assessing method<br />
<br />
== Perspectives ==<br />
<br />
*We need a method to predict the evolutionary stability of circuits from the properties of their parts, but the emergent behaviours of circuits will likely make prediction difficult. Thus it will be very useful if each BioBricks parts is completed with evolutionary stability data sheet, so we can make prediction of the stability of more complex circuits.<br />
*This safety assessment method is useful for identifying key elements of having failure in synthetic circuit systems before we go further to the real application. Thus we recommend for the future iGEM team to use our assessment method and give feedback to the community by improving this framework.<br />
<br />
==References==<br />
[[#Background|1]] - Genya V Dana et al. Four steps to avoid a synthetic biology disaster. 2012. Nature vol 483<br />
<br />
[[#Methods_and_Results|2]] - WorkSafe Victoria. A handbook for workplaces, controlling OHS hazards and risks. 2007. Edition No.1<br />
<br />
[[#Methods_and_Results|3]] - “Five steps to risk assessment” from [http://www.hse.gov.uk/risk/fivesteps.htm http://www.hse.gov.uk/risk/fivesteps.htm]. - risk management method in workplaces complying with health and safety law <br />
<br />
[[#Check_controls|4]] - Soren J Sorensen et al. 2005. Studying plasmid horizontal gene transfer in situ: a critical review. Nature Reviews Microbiology Vol 3<br />
<br />
[[#Check_controls|5]] - Heewook Lee et al., Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. 2012. PNAS E2774-E2783<br />
<br />
[[#Check_controls|6]] - Stanley A. Sawyer et al. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. 2007. PNAS 104(16):6504-6510<br />
<br />
[[#Check_controls|7]] - Lin Xu et al. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between two kingdoms. 2006. Mol. Biol. Evol. 23(6):1107-1108<br />
<br />
[[#Check_controls|8]] - David S Guttmand and Daniel E. Dykhuizen. 1994. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science Vol 266<br />
<br />
[[#Check_controls|9]] - L.Boe. 1996. Estimation of Plasmid Loss Rates in Bacterial Populations with a Reference to the Reproducibility of Stability Experiments. Plasmid 36, 161–167. Article No. 0043<br />
<br />
[[#Discussion|10]] - Torres B et al. 2003. A dual lethal system to enhance containment of recombinant micro-organisms. Microbiology. 2003 Dec;149(Pt 12):3595-601.<br />
<br />
[[#Discussion|11]] - Sean C Sleight et al., Designing and engineering evolutionary robust genetic circuits. 2010. Journal of Biological Engineering, 4:12<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/ModelingTeam:Paris Bettencourt/Modeling2012-10-26T22:03:04Z<p>Aprastowo: /* Total failure probability */</p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<div id="grouptitle">Safety Assessment</div><br />
<br />
==Overview==<br />
Safety is an important issue in synthetic biology, especially on environmental related projects. We already tried to answer the question, “how safe is safe enough?” by involving experts, publics and scientists, and also building biosafety devices. However, to really answer the question, actually we need first to ask ourselves a more basic question, “how do we measure safety?”. As we see synthetic biology as an engineering approach to biology, we could think about adaptation of safety engineering, a well studied engineering subset, that has been widely use to minimize risks on many fields of engineering, such as mechanical engineering, aircrafts, and manufactures. However, the risks they face are surely different from the risks of synthetic biology. <br />
<br />
According to Dana et al<sup>[[#References|1]]</sup> there are four areas of risk research in environmental application of synthetic biology:<br />
*Differences in the physiology of natural and synthetic organisms will affect how they interact with the surrounding environment,<br />
*Escaped microorganisms have the potential to survive in receiving environments and to compete successfully with non-modified counterparts,<br />
*Synthetic organisms might evolve and adapt quickly, perhaps filling new ecological niches, and<br />
*Gene transfer.<br />
<br />
Knowing that there are different areas of risk that we need to take into account, we need to design our safety containment with different parts to deal with each of them. Identifying the relationship between one part and the others will help us to see the reliability of the overall system. Here we propose an approach to assess safety for environmental release of genetically engineered bacteria (GE bacteria).<br />
<br />
===Objectives===<br />
*Adapting existing safety assessment tools to synthetic biology.<br />
*Proposing methods to assess safety in synthetic biology.<br />
<br />
==Methods and Results==<br />
We propose a method to assess hazards and risk<sup>[[#References|2]]</sup> in releasing genetically engineered bacteria to the environment. As a case study, we want to release GE bacteria which will perform some function in the environment and we want to apply 3 sets of bWARE safety containment (alginate beads, bWARE killswitch, semantic containment) to control the hazards and risks. Here we focus more on the reliability of the safety containment system rather than the functional part, although the similar assessment can also be applied to see the functional part reliability.<br />
<br />
===Hazards Identification===<br />
Identifying hazards means that we need to find and understand the possible harm that may happen in the application of our system. Generally there are two potential hazard in environmental application of synthetic biology<sup>[[#References|1]]</sup> which are the success escape of the GE bacteria followed by a success competition with the natural strain and the horizontal gene transfer.<br />
<br />
===Risk Assessment===<br />
Risk assessment will give an idea what kind of risk we face in releasing the GEO in the environment and help to design the safety containment. Here we adapted a risk management method in workplaces complying with health and safety law <sup>[[#References|3]]</sup>.<br />
<br />
To-do-list to assess risk in 5 steps:<br />
#Identify the hazards<br />
#Decide who might be harmed and how<br />
#Evaluate the risks and decide on precaution<br />
#Record your findings and implement them<br />
#Review your assessment and update if necessary<br />
<br />
<br />
Worksheet example:<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are the hazards?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Who might be harmed and how?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are we already doing?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What further action is necessary?'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria outcompete natural strains<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria escaping the containment may outcompete natural strains if they have better fitness, creating natural imbalance <br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Using harmless strain or strain with low fitness compared to natural strain (standard E coli for lab)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to prevent the cells reproducing themselves at some point and/or separating them from natural strains<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Horizontal gene transfer (HGT)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Other strain/species may uptake engineered gene, and if the gene gives advantage in the fitness, it may outcompete other strain and creating natural imbalance<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| -<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to degrade DNA and/or separate the DNA from the environment and/or prevent natural strain having advantages from the DNA<br />
<br />
|}<br />
<br />
<br><br />
===Control hazards and risks===<br />
<br />
In this step we decided what control elements we want to put to our system to reduce the risks. We should choose the best suitable control elements depending on the system function and application. As we already know that we want to apply bWARE safety containment, here we describe the role of each safety parts in the risks reduction. <br />
#GE bacteria outcompete natural strains<br />
#*In order to prevent the success escape of GE bacteria and outcompete the natural strains, we will stop their reproduction by putting a self killing mechanism to kill the cells after they perform the function. <br />
#*In case of the failure of the killing mechanism, we will put the cells inside a physical containment so there will be no physical interaction between them and the surrounding cells.<br />
#HGT<br />
#*We will use DNAse to degrade DNA after the cells perform the function so they won’t leave any genetic material behind.<br />
#*In case of the failure on inefficiency of the DNAse, the physical containment will still protect the DNA from the environment.<br />
#*In case of the leakiness of the physical containment, the DNA has special encryption system with the semantic containment so the receiver cell will not be able to read it.<br />
<br />
===Check controls=== <br />
<br />
To check and predict the reliability of our system, we used fault tree analysis to assess multiple safety containment in one biodevice. This top-down approach allows us to see the relationship between each containment element and predict the overall failure probability. With this method we can see what basic events are the key elements in our system.<br />
<br />
<center>[[Image:ParisB_FTA.png]]</center><br />
<br />
AND gate represents independent events<br />
<br />
P(A and B) = P(A)P(B)<br />
<br />
OR gate corresponds to set of union<br />
<br />
P(A or B) = P(A) + P(B)<br />
<br />
so the total failure probability of the system is<br />
<br />
Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9)<br />
<br />
List of the basic events<br />
<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Notation'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure component'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure mode'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Consequence'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Method for determining the probability'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P1<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| physical containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| leakage<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA/cell escape<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| experiment<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P2<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA uptake<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA transferred into natural strain<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| <nowiki>transconjugant to donor ratio in HGT is typically <10</nowiki><sup>-5</sup> <sup>[[#References|4]]</sup><br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P3<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| semantic containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation*<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P4<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| population suicide<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no surrounding cells with enough toxin<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no death<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| based on the cell density and the expectation number of surrounding non-mutant<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P5<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| toxin production<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no DNA degradation (w/o antitoxin), no death (with antitoxin)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P6<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| mutant fitness<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| beneficial mutation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| outcompetition of the mutant<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P7<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| delay system<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P8<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction enzyme<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P9<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction site<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|}<br />
<br />
====Physical containment failure====<br />
<br />
From the experiment we get the escape rate of the cells from the alginate beads is (escaping cells/total cells) is 10<sup>-5</sup> per 12 hours. Assuming 30 minutes of division time, we have 24 generations, and the escape rate per generation is 4 x 10<sup>-6</sup>.<br />
<br />
====Genetic failure====<br />
<br />
There are different processes that lead to a loss of function of a gene<br />
<br />
* Mutation<br />
* Recombination<br />
* Plasmid loss<br />
<br />
'''Losing function because of mutation'''<br />
<br />
Estimating the mutation rate which cause failure of the safety containment of the device<br />
<br />
* Spontaneous mutation rate of a wild-type E coli strain growing on research medium is 3.3 x 10<sup>-9</sup> per nucleotide per generation <sup>[[#References|5]]</sup> <br />
* approximately ⅔ of nucleotide mutation will change amino acid (64 combination of nucleotides code only 20 amino acids)<br />
* approximately 70% of amino acid change will lose the part function <sup>[[#References|6]]</sup><br />
* mean length of genetic coding sequence for E coli (procaryotes) is 924 bp <sup>[[#References|7]]</sup> ≈ 1000 bp <br />
<br />
So the loss function rate of a gene per generation because of mutation is <br />
<br />
P<sub>L</sub><nowiki>= 3.3 x 10</nowiki><sup>-9</sup> x ⅔ x 0.70 x 1000 = 1.54 x 10<sup>-6</sup> <br />
<br />
'''Recombination'''<br />
<br />
Finding a definite rate of recombination is not easy. Guttman and Dykhuizen in 1994 <sup>[[#References|8]]</sup> stated that recombination is believed to occur at such a low frequency, but their experiment showed that the rate could be as high as mutation rate (50 fold higher compared to the mutation rate believed at that moment, but actually it is 5.0 x 10<sup>-9</sup> changes per nucleotide per generation, a bit more than one fold to the value believed now). <br />
<br />
Redoing the previous calculation with this number will lead us to 2.33 x 10<sup>-6</sup> per gene per generation.<br />
<br />
'''Plasmid loss'''<br />
<br />
According to L Boe <sup>[[#References|9]]</sup> plasmid loss rate is defined as the probability that a division of a plasmid-carrying individual results in the birth of one plasmid-free and one plasmid-carrying daughter cell. For the low copy plasmid this rate is about ~1% /division and for high copy plasmid is ~0.01% /division, neglecting the viable/non-viable factor of the cells of losing the plasmid (no selection). If a plasmid with a lost rate of 0.05 is stabilized with a 100% efficient postsegragational killing system, the 5% of the division will result in non viable daughter cell, and we can not see the effect except of increasing the appearing division time by ln 2/ln (1-0.05) = 1.04. Thus in our system we can neglect this plasmid loss assuming that we have antibiotic selection in the beads.<br />
<br />
Assuming only mutation and recombination could happen to delete a function of a gene, we have the total genetic failure rate around 4 x 10<sup>-6</sup> per gene per generation.<br />
<br />
====Total failure probability====<br />
<br />
Having Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9) and put 1 for unknown probability (P4 and P6) as a worst-case scenario, we come to the failure rate number 6.4 x 10<sup>-11</sup> per generation.<br />
<br />
A volume of one alginate bead is approximately 20 uL. So if the cells grow until they reach the stationary phase (4 x 10<sup>9</sup> cells/ml), we will have 8 x 10<sup>7</sup> cells. If we started from 100 cells per bead, the number of generations we have is <sup>2</sup>log (8 x 10<sup>7</sup> / 100) =19.6 generations. Therefore the total failure becomes 6.4 x 10<sup>-11</sup> x 19.6 = 1.25 x 10<sup>-9</sup>.<br />
<br />
With this method we can also see that the sense-HGT rate is much lower (6.4 x 10<sup>-22</sup>) , almost negligible compared to the outcompetition rate, because it has more back up/redundancy components.<br />
<br />
== Discussion ==<br />
<br />
We have proposed and done an example of assessing biosafety adapting existing method from safety engineering. However it is very clear that the prediction is based on rough estimation and we need more experimental data to verify this estimation. For an example, Torres et al [REFERENCE] tested a dual containment killing system and compared it with single containment system. They tested EcoRI based system and Colicin E3-based system and get the efficacy (based on the numbers of successful transformants) each 10<sup>4</sup> and 10<sup>5</sup> respectively but when they combine both system they only got efficacy 10<sup>6</sup>, while theoretically they could reach up to 10<sup>9</sup>. This could give us an idea that predicting a performance of a combination of genetic parts is not as easy as combining the performance of each genetic part. However, we can still conclude that having redundant parts is necessary to reduce the failure rate and make it as low as possible.<br />
<br />
Research in measuring the evolutionary stability in E coli was performed by Sean C Sleight et al [REFERENCE] where they measured it of BioBrick-assembled genetic circuits in E coli over multiple generation by measuring the number of loss-functioning mutants. They concluded that to make a robust GE bacteria, one has to take into account 3 principles:<br />
# High expression of genetic circuits comes with the cost of low evolutionary stability (for example induced vs non-induced system)<br />
#Avoid repeated sequences because it will more likely be mutated<br />
#Use of inducible promoters generally increases evolutionary stability compared to constitutive promoters<br />
<br />
To predict the robustness of the system from mutation, we have to take into account for how long time (i.e. how many generations) we want our system to work. From their experiment for example, the AHL induced TetR-GFP cells lose their functions after 30 generations, while the uninduced ones lose their function slower (50% after 300 generations). A similar idea is also shown from our work where the mutation rate we got from literature research is in the unit of per generation. This is how reproduction differs biological system from other engineering systems. In engineering we also have failure probability as a function of time because of the life cycle of the system, but the system is not reproducing so it has no variability. <br />
<br />
Analyzing key elements that cause failure in any systems including synthetic biology systems is essential for system improvement and prediction of the failure. Adaptation of classical safety engineering methods needs to take into account the uniqueness properties of synthetic biology. Reproducibility and complexity are two example of areas that need to be studied deeper in this context. We invite future iGEM teams to use and improve our assessment framework, build a solid assessment protocol towards a better understanding of biosafety and successful application of synthetic biology.<br />
<br />
== Conclusion ==<br />
*We can adapt methods in safety engineering to assess risk in biosafety<br />
*We need more experimental data to confirm the risk assessing method<br />
<br />
== Perspectives ==<br />
<br />
*We need a method to predict the evolutionary stability of circuits from the properties of their parts, but the emergent behaviours of circuits will likely make prediction difficult. Thus it will be very useful if each BioBricks parts is completed with evolutionary stability data sheet, so we can make prediction of the stability of more complex circuits.<br />
*This safety assessment method is useful for identifying key elements of having failure in synthetic circuit systems before we go further to the real application. Thus we recommend for the future iGEM team to use our assessment method and give feedback to the community by improving this framework.<br />
<br />
==References==<br />
[[#Background|1]] - Genya V Dana et al. Four steps to avoid a synthetic biology disaster. 2012. Nature vol 483<br />
<br />
[[#Methods_and_Results|2]] - WorkSafe Victoria. A handbook for workplaces, controlling OHS hazards and risks. 2007. Edition No.1<br />
<br />
[[#Methods_and_Results|3]] - “Five steps to risk assessment” from [http://www.hse.gov.uk/risk/fivesteps.htm http://www.hse.gov.uk/risk/fivesteps.htm]. - risk management method in workplaces complying with health and safety law <br />
<br />
[[#Check_controls|4]] - Soren J Sorensen et al. 2005. Studying plasmid horizontal gene transfer in situ: a critical review. Nature Reviews Microbiology Vol 3<br />
<br />
[[#Check_controls|5]] - Heewook Lee et al., Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. 2012. PNAS E2774-E2783<br />
<br />
[[#Check_controls|6]] - Stanley A. Sawyer et al. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. 2007. PNAS 104(16):6504-6510<br />
<br />
[[#Check_controls|7]] - Lin Xu et al. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between two kingdoms. 2006. Mol. Biol. Evol. 23(6):1107-1108<br />
<br />
[[#Check_controls|9]] - L.Boe. 1996. Estimation of Plasmid Loss Rates in Bacterial Populations with a Reference to the Reproducibility of Stability Experiments. Plasmid 36, 161–167. Article No. 0043<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowohttp://2012.igem.org/Team:Paris_Bettencourt/ModelingTeam:Paris Bettencourt/Modeling2012-10-26T22:02:32Z<p>Aprastowo: /* Genetic failure */</p>
<hr />
<div>{{:Team:Paris_Bettencourt/header}}<br />
<br />
<div id="grouptitle">Safety Assessment</div><br />
<br />
==Overview==<br />
Safety is an important issue in synthetic biology, especially on environmental related projects. We already tried to answer the question, “how safe is safe enough?” by involving experts, publics and scientists, and also building biosafety devices. However, to really answer the question, actually we need first to ask ourselves a more basic question, “how do we measure safety?”. As we see synthetic biology as an engineering approach to biology, we could think about adaptation of safety engineering, a well studied engineering subset, that has been widely use to minimize risks on many fields of engineering, such as mechanical engineering, aircrafts, and manufactures. However, the risks they face are surely different from the risks of synthetic biology. <br />
<br />
According to Dana et al<sup>[[#References|1]]</sup> there are four areas of risk research in environmental application of synthetic biology:<br />
*Differences in the physiology of natural and synthetic organisms will affect how they interact with the surrounding environment,<br />
*Escaped microorganisms have the potential to survive in receiving environments and to compete successfully with non-modified counterparts,<br />
*Synthetic organisms might evolve and adapt quickly, perhaps filling new ecological niches, and<br />
*Gene transfer.<br />
<br />
Knowing that there are different areas of risk that we need to take into account, we need to design our safety containment with different parts to deal with each of them. Identifying the relationship between one part and the others will help us to see the reliability of the overall system. Here we propose an approach to assess safety for environmental release of genetically engineered bacteria (GE bacteria).<br />
<br />
===Objectives===<br />
*Adapting existing safety assessment tools to synthetic biology.<br />
*Proposing methods to assess safety in synthetic biology.<br />
<br />
==Methods and Results==<br />
We propose a method to assess hazards and risk<sup>[[#References|2]]</sup> in releasing genetically engineered bacteria to the environment. As a case study, we want to release GE bacteria which will perform some function in the environment and we want to apply 3 sets of bWARE safety containment (alginate beads, bWARE killswitch, semantic containment) to control the hazards and risks. Here we focus more on the reliability of the safety containment system rather than the functional part, although the similar assessment can also be applied to see the functional part reliability.<br />
<br />
===Hazards Identification===<br />
Identifying hazards means that we need to find and understand the possible harm that may happen in the application of our system. Generally there are two potential hazard in environmental application of synthetic biology<sup>[[#References|1]]</sup> which are the success escape of the GE bacteria followed by a success competition with the natural strain and the horizontal gene transfer.<br />
<br />
===Risk Assessment===<br />
Risk assessment will give an idea what kind of risk we face in releasing the GEO in the environment and help to design the safety containment. Here we adapted a risk management method in workplaces complying with health and safety law <sup>[[#References|3]]</sup>.<br />
<br />
To-do-list to assess risk in 5 steps:<br />
#Identify the hazards<br />
#Decide who might be harmed and how<br />
#Evaluate the risks and decide on precaution<br />
#Record your findings and implement them<br />
#Review your assessment and update if necessary<br />
<br />
<br />
Worksheet example:<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are the hazards?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Who might be harmed and how?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What are we already doing?'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''What further action is necessary?'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria outcompete natural strains<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| GE bacteria escaping the containment may outcompete natural strains if they have better fitness, creating natural imbalance <br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Using harmless strain or strain with low fitness compared to natural strain (standard E coli for lab)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to prevent the cells reproducing themselves at some point and/or separating them from natural strains<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Horizontal gene transfer (HGT)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Other strain/species may uptake engineered gene, and if the gene gives advantage in the fitness, it may outcompete other strain and creating natural imbalance<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| -<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| Designing a safety containment to degrade DNA and/or separate the DNA from the environment and/or prevent natural strain having advantages from the DNA<br />
<br />
|}<br />
<br />
<br><br />
===Control hazards and risks===<br />
<br />
In this step we decided what control elements we want to put to our system to reduce the risks. We should choose the best suitable control elements depending on the system function and application. As we already know that we want to apply bWARE safety containment, here we describe the role of each safety parts in the risks reduction. <br />
#GE bacteria outcompete natural strains<br />
#*In order to prevent the success escape of GE bacteria and outcompete the natural strains, we will stop their reproduction by putting a self killing mechanism to kill the cells after they perform the function. <br />
#*In case of the failure of the killing mechanism, we will put the cells inside a physical containment so there will be no physical interaction between them and the surrounding cells.<br />
#HGT<br />
#*We will use DNAse to degrade DNA after the cells perform the function so they won’t leave any genetic material behind.<br />
#*In case of the failure on inefficiency of the DNAse, the physical containment will still protect the DNA from the environment.<br />
#*In case of the leakiness of the physical containment, the DNA has special encryption system with the semantic containment so the receiver cell will not be able to read it.<br />
<br />
===Check controls=== <br />
<br />
To check and predict the reliability of our system, we used fault tree analysis to assess multiple safety containment in one biodevice. This top-down approach allows us to see the relationship between each containment element and predict the overall failure probability. With this method we can see what basic events are the key elements in our system.<br />
<br />
<center>[[Image:ParisB_FTA.png]]</center><br />
<br />
AND gate represents independent events<br />
<br />
P(A and B) = P(A)P(B)<br />
<br />
OR gate corresponds to set of union<br />
<br />
P(A or B) = P(A) + P(B)<br />
<br />
so the total failure probability of the system is<br />
<br />
Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9)<br />
<br />
List of the basic events<br />
<br />
{| style="border-spacing:0;"<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Notation'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure component'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Failure mode'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Consequence'''<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| '''Method for determining the probability'''<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P1<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| physical containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| leakage<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA/cell escape<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| experiment<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P2<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA uptake<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| DNA transferred into natural strain<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| <nowiki>transconjugant to donor ratio in HGT is typically <10</nowiki><sup>-5</sup> <sup>[[#References|4]]</sup><br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P3<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| semantic containment<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| HGT<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation*<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P4<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| population suicide<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no surrounding cells with enough toxin<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no death<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| based on the cell density and the expectation number of surrounding non-mutant<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P5<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| toxin production<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no DNA degradation (w/o antitoxin), no death (with antitoxin)<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P6<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| mutant fitness<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| beneficial mutation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| outcompetition of the mutant<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P7<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| delay system<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P8<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction enzyme<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|-<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| P9<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| restriction site<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| genetic failure<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| no antitoxin degradation<br />
| style="border:0.035cm solid #000000;padding:0.176cm;"| estimation<br />
<br />
|}<br />
<br />
====Physical containment failure====<br />
<br />
From the experiment we get the escape rate of the cells from the alginate beads is (escaping cells/total cells) is 10<sup>-5</sup> per 12 hours. Assuming 30 minutes of division time, we have 24 generations, and the escape rate per generation is 4 x 10<sup>-6</sup>.<br />
<br />
====Genetic failure====<br />
<br />
There are different processes that lead to a loss of function of a gene<br />
<br />
* Mutation<br />
* Recombination<br />
* Plasmid loss<br />
<br />
'''Losing function because of mutation'''<br />
<br />
Estimating the mutation rate which cause failure of the safety containment of the device<br />
<br />
* Spontaneous mutation rate of a wild-type E coli strain growing on research medium is 3.3 x 10<sup>-9</sup> per nucleotide per generation <sup>[[#References|5]]</sup> <br />
* approximately ⅔ of nucleotide mutation will change amino acid (64 combination of nucleotides code only 20 amino acids)<br />
* approximately 70% of amino acid change will lose the part function <sup>[[#References|6]]</sup><br />
* mean length of genetic coding sequence for E coli (procaryotes) is 924 bp <sup>[[#References|7]]</sup> ≈ 1000 bp <br />
<br />
So the loss function rate of a gene per generation because of mutation is <br />
<br />
P<sub>L</sub><nowiki>= 3.3 x 10</nowiki><sup>-9</sup> x ⅔ x 0.70 x 1000 = 1.54 x 10<sup>-6</sup> <br />
<br />
'''Recombination'''<br />
<br />
Finding a definite rate of recombination is not easy. Guttman and Dykhuizen in 1994 <sup>[[#References|8]]</sup> stated that recombination is believed to occur at such a low frequency, but their experiment showed that the rate could be as high as mutation rate (50 fold higher compared to the mutation rate believed at that moment, but actually it is 5.0 x 10<sup>-9</sup> changes per nucleotide per generation, a bit more than one fold to the value believed now). <br />
<br />
Redoing the previous calculation with this number will lead us to 2.33 x 10<sup>-6</sup> per gene per generation.<br />
<br />
'''Plasmid loss'''<br />
<br />
According to L Boe <sup>[[#References|9]]</sup> plasmid loss rate is defined as the probability that a division of a plasmid-carrying individual results in the birth of one plasmid-free and one plasmid-carrying daughter cell. For the low copy plasmid this rate is about ~1% /division and for high copy plasmid is ~0.01% /division, neglecting the viable/non-viable factor of the cells of losing the plasmid (no selection). If a plasmid with a lost rate of 0.05 is stabilized with a 100% efficient postsegragational killing system, the 5% of the division will result in non viable daughter cell, and we can not see the effect except of increasing the appearing division time by ln 2/ln (1-0.05) = 1.04. Thus in our system we can neglect this plasmid loss assuming that we have antibiotic selection in the beads.<br />
<br />
Assuming only mutation and recombination could happen to delete a function of a gene, we have the total genetic failure rate around 4 x 10<sup>-6</sup> per gene per generation.<br />
<br />
====Total failure probability====<br />
<br />
Having Ptotal = P1.P2.P3.P4.P5 + P1.P6.(P5+P7+P8+P9) and put 1 for unknown probability (P4 and P6) as a worst-case scenario, we come to the failure rate number 6.4 x 10<sup>-11</sup> per generation.<br />
<br />
A volume of one alginate bead is approximately 20 uL. So if the cells grow until they reach the stationary phase (4 x 10<sup>9</sup> cells/ml), we will have 8 x 10<sup>7</sup> cells. If we started from 100 cells per bead, the number of generations we have is <sup>2</sup>log (8 x 10<sup>7</sup> / 100) =19.6 generations. Therefore thetotal failure becomes 6.4 x 10<sup>-11</sup> x 19.6 = 1.25 x 10<sup>-9</sup>.<br />
<br />
With this method we can also see that the sense-HGT rate is much lower (6.4 x 10<sup>-22</sup>) , almost negligible compared to the outcompetition rate, because it has more back up/redundancy components.<br />
<br />
== Discussion ==<br />
<br />
We have proposed and done an example of assessing biosafety adapting existing method from safety engineering. However it is very clear that the prediction is based on rough estimation and we need more experimental data to verify this estimation. For an example, Torres et al [REFERENCE] tested a dual containment killing system and compared it with single containment system. They tested EcoRI based system and Colicin E3-based system and get the efficacy (based on the numbers of successful transformants) each 10<sup>4</sup> and 10<sup>5</sup> respectively but when they combine both system they only got efficacy 10<sup>6</sup>, while theoretically they could reach up to 10<sup>9</sup>. This could give us an idea that predicting a performance of a combination of genetic parts is not as easy as combining the performance of each genetic part. However, we can still conclude that having redundant parts is necessary to reduce the failure rate and make it as low as possible.<br />
<br />
Research in measuring the evolutionary stability in E coli was performed by Sean C Sleight et al [REFERENCE] where they measured it of BioBrick-assembled genetic circuits in E coli over multiple generation by measuring the number of loss-functioning mutants. They concluded that to make a robust GE bacteria, one has to take into account 3 principles:<br />
# High expression of genetic circuits comes with the cost of low evolutionary stability (for example induced vs non-induced system)<br />
#Avoid repeated sequences because it will more likely be mutated<br />
#Use of inducible promoters generally increases evolutionary stability compared to constitutive promoters<br />
<br />
To predict the robustness of the system from mutation, we have to take into account for how long time (i.e. how many generations) we want our system to work. From their experiment for example, the AHL induced TetR-GFP cells lose their functions after 30 generations, while the uninduced ones lose their function slower (50% after 300 generations). A similar idea is also shown from our work where the mutation rate we got from literature research is in the unit of per generation. This is how reproduction differs biological system from other engineering systems. In engineering we also have failure probability as a function of time because of the life cycle of the system, but the system is not reproducing so it has no variability. <br />
<br />
Analyzing key elements that cause failure in any systems including synthetic biology systems is essential for system improvement and prediction of the failure. Adaptation of classical safety engineering methods needs to take into account the uniqueness properties of synthetic biology. Reproducibility and complexity are two example of areas that need to be studied deeper in this context. We invite future iGEM teams to use and improve our assessment framework, build a solid assessment protocol towards a better understanding of biosafety and successful application of synthetic biology.<br />
<br />
== Conclusion ==<br />
*We can adapt methods in safety engineering to assess risk in biosafety<br />
*We need more experimental data to confirm the risk assessing method<br />
<br />
== Perspectives ==<br />
<br />
*We need a method to predict the evolutionary stability of circuits from the properties of their parts, but the emergent behaviours of circuits will likely make prediction difficult. Thus it will be very useful if each BioBricks parts is completed with evolutionary stability data sheet, so we can make prediction of the stability of more complex circuits.<br />
*This safety assessment method is useful for identifying key elements of having failure in synthetic circuit systems before we go further to the real application. Thus we recommend for the future iGEM team to use our assessment method and give feedback to the community by improving this framework.<br />
<br />
==References==<br />
[[#Background|1]] - Genya V Dana et al. Four steps to avoid a synthetic biology disaster. 2012. Nature vol 483<br />
<br />
[[#Methods_and_Results|2]] - WorkSafe Victoria. A handbook for workplaces, controlling OHS hazards and risks. 2007. Edition No.1<br />
<br />
[[#Methods_and_Results|3]] - “Five steps to risk assessment” from [http://www.hse.gov.uk/risk/fivesteps.htm http://www.hse.gov.uk/risk/fivesteps.htm]. - risk management method in workplaces complying with health and safety law <br />
<br />
[[#Check_controls|4]] - Soren J Sorensen et al. 2005. Studying plasmid horizontal gene transfer in situ: a critical review. Nature Reviews Microbiology Vol 3<br />
<br />
[[#Check_controls|5]] - Heewook Lee et al., Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. 2012. PNAS E2774-E2783<br />
<br />
[[#Check_controls|6]] - Stanley A. Sawyer et al. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. 2007. PNAS 104(16):6504-6510<br />
<br />
[[#Check_controls|7]] - Lin Xu et al. Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between two kingdoms. 2006. Mol. Biol. Evol. 23(6):1107-1108<br />
<br />
[[#Check_controls|9]] - L.Boe. 1996. Estimation of Plasmid Loss Rates in Bacterial Populations with a Reference to the Reproducibility of Stability Experiments. Plasmid 36, 161–167. Article No. 0043<br />
<br />
{{:Team:Paris_Bettencourt/footer}}</div>Aprastowo