Difference between revisions of "Team:EPFL/Engagement"

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                        <h2 class="lead">ATTRIBUTIONS</h2>
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                            Our iGEM journey started at the end of 2015 when EPFL students were invited to join in the 2016 iGEM team. After the selection, we started brainstorming in February 2016 where after a few months of literature research we came up with this project of combining CRISPR-dCas9 and the Cello software. Between the beginning of June and July, we designed and ordered all the parts we needed. And then finally, in July, we were able to start our exciting work in the lab! And we have been working hard ever since then to present our end results to all the other teams and jury members end of October in Boston, MA.
  
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                            Our project is partially based on the project of the <b>2015 EPFL iGEM team</b>. The general design of the gates comes from their BioLogic project.
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                         <h2 class="lead animate-box text-center">Public engagement</h2>
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                         <h3>TEAM ATTRIBUTION</h3>
 
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                             “Because science is prevalent in all facets of our lives, the science-society relationship is complex, and there are many ways to approach it. The relationship can be constructive, tension-filled, or everything in between. Interaction between interested stakeholders is critical to finding common ground on scientific issues affecting society. Public engagement can provide a constructive platform for public views to be combined with scientific expertise in decision-making contexts.”
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                        <h5>Project</h5>
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                             After months of brainstorming, the <b>whole team</b> contributed to the conception of this project containing both computational and biological work. The design of the logo was imagined by <b>Pietro Airaghi</b>.
 
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                            <a href="https://www.aaas.org/pes/what-public-engagement"><cite>AAAS – Center for Public Engagement with Science and Technology</cite></a>
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                        <h5>Laboratory</h5>
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                            The design of the Laboratory part was realised by <b>Alix Faillétaz, Francesco Terenzi, Camilla Ceroni, Yassine Zouaghi and Marie Matos</b>. During the summer, <b>the whole team</b> participate to the lab sessions.The design of the gRNAs was done by <b>Samuele Mercan</b>
 
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                        <h5>Human Practices</h5>
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                             Public engagement in science is a multifaceted issue comprising: education on ongoing research and its applications, open dialogue, and decision-making regarding policy, funding, and the application of new technologies. During our summer, we decided to focus on public education, and also had forays into deepening ongoing dialogue regarding synthetic biology.
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                             The idea of igem.today come from <b>Rémy Pétremand and Pietro Airaghi</b>, they also designed the website
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                            The interviews and their retranscriptions were done by <b>Rémy Pétremand, Yassine Zouaghi, Alix Faillétaz and Marie Matos</b>.
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                            The presentation to the High School Student was scheduled and prepared by <b>Marie Matos</b> with the help of <b>Rémy Pétremand and Yassine Zouaghi</b>.
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                            The presentation at the Hackuarium was scheduled and prepared by <b>Dimitri Coukos</b> with the help of <b>Rémy Pétremand, Yassine Zouaghi and Marie Matos</b>.
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                        <h5>Software and wiki</h5>
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                            The wiki was designed and set up by <b>Dimitri Coukos and Pietro Airaghi</b> with the help of <b>Rémy Pétremand</b>. The figure were done by <b>Rémy Pétremand and Yassine Zouaghi</b>. The texts were written by the <b>whole team</b> in function of the topics they were involved during the summer.
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                            All the work done on the Software part, including the graphic interface were done by <b>Dimitri Coukos and Pietro Airaghi</b>.
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                            The modelling part of the project was developed by <b>Dimitri Coukos</b>, with help from <b>Remy Pétremand and Yassine Zouaghi</b>.
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                            The BioBricks were planned and done by <b>Samuele Mercan, Francesco Terenzi and Camilla Ceroni</b>.
 
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                             We could not have done it without the help of some people, so we would like to acknowledge all the help and support we received throughout our iGEM adventure!! We are very grateful for everyone who has helped in any possible way and made our project possible.
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                        <h3>Superviors</h3>
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                             At the beginning of our iGEM experience, we – like many other new iGEMmers – browsed the wikis of other teams to see what they had managed to develop. We found the availability of information and their stories exciting, but the density of information was often intimidating. In addition, the long form writing made them time consuming to read, and the focus on results often removed us from the experience the team had. We love the wiki format, and find that it’s a great way to learn about a project, when you really want to know everything, but we felt a need to address the wiki’s limitations. After all, someone from the public who wants to learn about synthetic biology will more likely want to learn about that team’s experience and have an overview of that team’s work before deciding to take a deep-dive into their project.
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                             Our supervisors, <b>Bart Deplancke</b> and <b>Barbara Grisoni</b> gave us a lot of advice on how to resolve some critical problems, whether it was for the design, or for the experiments we conducted. They also kept us on track to reach our goal.
 
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                             It was with this in mind that <a href="http://www.igem.today">igem.today</a> was born, forming the centerpiece of our human practices efforts. igem.today is a media platform dedicated to iGEM. Through this platform we hosted media from different iGEM groups, as well as surveys that we created and that were sent to us. Excitingly, we were able to post interviews and project descriptions for nearly one tenth of all iGEM teams, and reached over 2000 visitors in September alone! We participated in an incredible amount of dialog, and met so many amazing people, and our experience is all online for the whole world to enjoy!
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                             Our advisers, <b>Roel Bevers</b> and <b>Riccardo Dainese</b>, Phd Students in Bart Deplancke’s Lab, helped us with most of the countless problems we had in the lab along with sponsors and other requirements for iGem. They also give us huge help during the week-end with material and access to the Lab.
 
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                             This website serves not only as a portal into the world of iGEM where diverse projects are presented in a short, entertaining, and understandable format, but also as a place of dialogue. Igem.today has mostly served as a tool too facilitate communication within the iGEM community and teams, but it is also valuable as a tool for public engagement. To our knowledge, there is currently no other resource, in which visitors can see projects explained so simply, and where they can experience what the team members went through by reading their own accounts. Visitors are also free to interact through comments and can contact the teams presented directly. Finally, as igem.today also serves as a survey-hosting platform, visitors can fill out surveys, and respond to team’s questions, thereby giving their own input into the scientific process, and effectively establishing a communication.
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                             <b>Victor Steininger, Loic Steiner, Ari Safaris, Axel Uran, Paola Mansot and Vincent Jacquot</b>, members of the <b>2015 EPFL iGEM team</b>. In the early stages of our project, they helped out by teaching us about primer design, laboratory skills and gave us a lot of advice on the general competition and how to achieve our goals.
 
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                        <h3>General suport</h3>
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                            A warm thanks to <b>EPFL</b>, the Swiss Federal Institute of Technology in Lausanne, without which our participation in iGEM and our project would not have been possible. We would like to thank <b>André Pexieder</b> for letting us use his lab and the equipment during the project, <b>Marie-France Radigois</b> who helped us with the administrative tasks related to the project and <b>Stéphane Karlen</b>, Safety coordinator at the School of Life Science, who gave us a course and instructions on laboratory safety before our project started and was available for any question during the project.
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                    <h2 class="">SURVEY OF IGEM ALUMNI</h2>
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                        We often hear former iGEMmers saying that this competition is something truly unbelievable and that it will helps students later in their lives and careers. In order to improve dialogue between iGEM’s past and future, we thought it is important to quantify these experiences. We sought out to do this by creating a survey, which we posted on igem.today.  Specifically, we set out to study in more detail in what way iGEM has helped alumni in their everyday life, in finding a job, or working in a laboratory. We received a replies from 398 people from 15 different universities answered our survey. Although the sample size is not particularly large, we do find interesting patterns. Here we show our most important and/or interesting findings:
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                        <p>The people interviewed predominantly work in the scientific community and/or are students (76.3 % and 71.1% respectively). 50% of this group works in a field of biology.
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                        <p>94.7 % of the people interviewed think that iGEM has helped them in their later career and 76.3% think that iGEM has helped them to find a job later in life.</p>
 
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                        <h3>Project support and advice</h3>
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                         <p>In the end, big part of participants became assistant for their university iGEM team (36.2%) and liked to assist teams by supervising and helping find team funds.
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                            To begin with, we would like the thank the <b>2015 EPFL iGEM team</b> for introducing their project to us, while teaching us how to work in the laboratory.
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                            We also want to thank our <b>supervisors</b> for helping us choosing the direction to follow designing our project.
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                            We would also like to thank <b>Professor Jesse Zalatan</b> from Washington University for his advice on our project. Previously he and former colleagues worked on “Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds”, a paper that inspired us and ‘produced’ Intelligene, and for leading our project to the search of a repressor element in yeast.
 +
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                        <p class="sub-lead">
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                            We would also like to thank <b>Prashant Vaidyanathan</b> of Cidar Lab at Boston University help regarding NetSynth and his feedback regarding our modifications to Cello. We also thank <b>Cidar Lab</b> for the access to their program, <b>Cello</b>, through their GitHub page.
 
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                         <h3>Lab support</h3>
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                         The last histogram is particularly interesting. It outlines the skills improved thanks to iGEM. It’s interesting but not surprising to see that Teamwork and communication came first (90%). They came before than research (64%) and commitment to quality. This perfectly shows the dynamic of successful research groups. Let’s compare this to communication between cells/tissues. If this doesn’t work, the whole body won’t work, and the population or species will die out. This thus shows that iGEM is on the right track on providing the right values for future researchers.
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                         By considering all this information, we can see the iGEM is not only a competition about synthetic biology but also about education, teamwork, and communication. For students this means that participating in iGEM is considered to be a very complete course/curriculum during their studies. Furthermore, participating in iGEM gives a diverse set of skills which is readily appreciated by future employers – notably: teamwork, research skills, organization. Interestingly, just over half of respondents felt that iGEM helped develop their leadership skills and commitment to quality, and less than half felt that iGEM helped increase their writing and data management. To a certain degree, this is understandable. In our experience – and this was confirmed through our interviews, teams have a tendency to split up tasks among group members. Only some will do most of the writing, and handle most of the results. Worryingly, though, is that only half of respondents felt that iGEM improved their commitment to quality. This may be due to the fact that this is a fast-paced competition, and the emphasis is often placed on getting a certain list of things accomplished rather than creating projects that are fully functional or well designed. This may also reflect the fact that some teams are left feeling disappointed when large amounts of effort put into specific tasks go unrewarded because they don’t meet judges’ criteria. To ameliorate this in the future, maybe more importance should go towards good experimental and project design in the judging procedure.
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                        When asked to describe what they would want for future iGEM teams that they did not have, the most cited issue was a lack of proper mentorship during the competition. Time restraints were also cited as a common issue. Although it is difficult to develop a suggestion that can be applied to all groups, as iGEM is treated differently in different places – for us, for example, it is a summer project that gives us credit towards our bachelor’s project – these two shortcomings might be alleviated, in part, if iGEM encouraged more schools to offer iGEM as a semester-long class preceding the summer. This would ensure that group mentors are actually available to the teams they are sponsoring, and that the proper time is taken before the summer (when most teams are working the most) to plan out and set up the project.
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                        Happily, and somewhat unsurprisingly, all participants shared their memories about the Giant Jamboree and responded that it was a wonderful experience. For most of them it was the first participation for a large scientific event and allowed them to be prepared (and excited!) for future ones.
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                        You can find the results of the survey <a href=""> here </a>
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                    <a href="#section-logos"><p class="text-info text-justify">Back to top</p></a>
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                    <h2 class="">PRESENTATION</h2>
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                    <h4 class=""> WHO </h3>
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                             Before packing for Boston, we presented our project four times to members of the scientific community and the general public. During these occasions, we were excited to discuss what we were doing, what synthetic biology was really about, and even answered an hour and a half of questions at one such event!
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                             We want to thank all the people who allowed us to measure our experiments on their equipment and gave us advice about the interpretation and presentation of the results.
 
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                         <p class="sub-lead">
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                            The <b>EPFL Flow Cytometry Core Facility (FCCF)</b> who let us use their equipment and help us measure our samples with a special thanks to <b>Andre Mozes</b>.
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                        <p class="sub-lead">
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                            The <b>Maerkl Lab</b> and specially <b>Francesca Volpetti</b> for the use of the overnight plate reader.
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                        <p class="sub-lead">
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                            The <b>Deplancke Lab</b> for all the material they lend us and for the use of fluorescent microscopes.
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                        <h3>Special technique support</h3>
 
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                                  What kind of evidence should we put on the wiki? Should we put our slides? Our speeches? Photos?
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                        <h3>HACKUARIUM</h3>
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                             <b>Julie Russeil</b>, lab manager in the Deplancke Lab, assisted us with the difficulties of yeast integrations, and more generally with advice on experiments with yeasts. In addition to that she gave us a lot of advice and “shortcuts” to be more efficient in the lab. <b>Riccardo Dainese</b> helped us with technical details for the gibson assemblies and plasmid transformation into competent cells.
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                            Hackuarium is a DIY biology lab, open to the community, in Renens, VD, Switzerland. Hackuarium’s stated mission is to “bring biology (and biologists) to the world, and the real world back to biology.” Central to Hackuarium’s philosophy are reducing the cost of biological research, spreading public understanding of biology in the modern age, and having an open discussion about the ethics and feasibility of research.
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                            You can learn more about them <a href="http://wiki.hackuarium.ch/w/Main_Page">here</a>
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                        <h3>Design support</h3>
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                             On Wednesday nights, they are open to the public, and people with all sorts of science projects can present their work.
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                             <b>Eugenia Petrova</b>, from <b>Desktop Genetics</b>, who explained to us how to use the DESKGEN platform and worked out a way to use it for our project to design orthogonal and efficient guide RNAs with their respective targets.
 
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                        <h3>Modelisation support</h3>
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                            Professor <b>Felix Naef</b> and his post-doc <b>Eric Paquet</b> for the time they took to help us with developing the model of our system; our model would not have been possible without their help. This advice allows us to implement theoretical results in Cello.
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                        <h3>Human Practices support</h3>
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                    <h3>Dialogues</h3>
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                             We would like to thank <b>Mrs de Raemy</b> at the <b>Collège de Candolle</b> in Geneva for allowing us to present iGEM to a class of students.
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                        </p>
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                         Below are some of the most interesting questions that we had after our talk, although we answered an hour and a half of them!
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                         <p class="sub-lead">
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                    </p>
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                             We also would like to thank the <b>Hackuarium</b> for inviting us to present synthetic biology and iGEM in their Open Hackarium space. This was great fun and we received a lot of good feedback from the community!
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                             We also want to thank <b>Professor Yolanda Schaerli</b> for the time she gave to our team for a discussion about synthetic biology, the issues and the ethical part of the field.
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                                <p><b>"Biological systems are not binary, so why not did you choose to use a system that makes logical switches using Boolean (or binary) logic?"</b></p>
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                             <b>IGEM News</b> would have not been possible without the help of <b>so many iGEM teams</b> and we would like to thank each and every of them that took time to help us in this project.
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                                    Although biology is not binary, transcriptional states are! Of course, there are complexities to this system. We have three different chromatin states (active, repressed, and poised), and splicing mechanisms increase the number of outputs that an actively transcribed gene can have. When it comes to whether or not a given region of DNA is being transcribed, and what the effect of this transcription will be on the next part of the circuit, we consider that there are only two states: either the output is high enough to induce a change in the next part of the circuit, or it is not.
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                                <p><b>"How fast is this system? Are we talking microseconds, seconds"</b></p>
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                                    Not so quick! These systems will work over hours to days. Speed here is limited by the speed of transcription and translation in these systems, which will be limited by many factors, including how healthy the cells are, whether the codons are optimized for the system, and the actual size of the desired transcripts and proteins.
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                                <p><b>"What are the ethical challenges regarding iGEM projects?"</b></p>
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                                    In iGEM we are encouraged to explore the ethical challenges that surround our topics, and model our project around these challenges. In addition, we have to fill out various safety forms to ensure that we are not working with material that could be dangerous or used for malicious purposes. Any material we order from companies is also checked by them to control for safety, and to prevent bioterrorism.
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                                <p><b>"Have you considered the downstream effects of your research?"</b></p>
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                                    We often find ourselves considering the implications of our research. Is changing the way genetic circuit already work dangerous? What about introducing new genes? What about giving people the tools to do it easily dangerous? All of these things can be dangerous. As we see it however, the risk-benefit balance has to be evaluated when new projects that have direct social implications are being considered. This is something that is already happening; ethical boards everywhere review social projects and new research before allowing them to happen. We cannot allow the small probability of a catastrophic ending to negate the colossal amount of good that a technology can create. This dilemma has been evident since the creation of fire – none of what we have would exist today if our ancestors hadn’t taken the risk of getting burned.
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                                    To return to issues germane to our project, there is a risk that “democratizing” the ability to design your own genetic circuits. However, many of the safeguards that are present in genetic research are applicable to our project. Algorithms from companies can ensure that the material that they are providing could not be used for bioterrorism. Something that is missing currently is the ability to control that the circuits that are in an organism actually do what they are stated to do. It should be possible to combat this issue by creating a software which can recognize genetic circuits and predict their output – a “reverse Cello” so to speak. One of the challenges this program will face is to distinguish new DNA and functions from that of the original genome. Once again, these risks can be mitigated, and the consensus in the scientific community is that with the potential benefits of this technology – easier drug manufacturing, the ability to cure disease in complex metabolic pathways, creating cells with new capacities to sense their environments and make calculations based on their environments – we should hesitate only long enough to ensure that this work is safe, but no longer.
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                        <h3>Presentation coaching</h3>
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                            The presentation we made for <b>Hackuarium</b> was an amazing and unique opportunity to present our project so we would like to thank them a lot, along with <b>Roel Bevers</b> for a very detailed feedback to improve the presentation.
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                        <h3>Templates and icons</h3>
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                            We thank <b>badr545</b> for <b>RISE</b>, the template used for the wiki, which we found on shapebootstrap.net. We thank <b>Ed Ball</b> for his jsPlumb template, academo, which we found on his github https://github.com/edwardball/academo.org. We thank the following authors of icons we found on flaticons.com : <b>Freepik, Madebyoliver, Vectors Market, Bryn Taylor</b>.
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                    <h3 class="">Mini iGEM</h3>
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                         <h2 class="lead">SPONSORS</h2>
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                         On the 14th of September, we were invited to speak to two classes in collège de Candolle about iGEM. This was the opportunity to engage into an educational discussion about synthetic biology and social issues on the topic of genetic manipulation. They had no idea about the issues that the field of Synthetic Biology encounters, but after our presentation and discussions they well understood many of the current issues both good and bad type of issues.
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                        We finished the lecture part of the presentation to continue on a group activity that we named Mini iGEM. The class was divided into small teams of three or four and they were asked to design their own iGEM project.
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                            We would like to thank all our generous sponsors for aiding us financially or via consulting or computational assistance.
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                        <img src="img/Octopotato.jpg" alt="" style="float: right; width: 300px;"/>
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                         The classes participated with enthusiasm to the Mini IGEM and the discussions. We received many crazy and ingenious project idea. Notably, a team suggested a project called Octopotato. They planned to use the genes responsible for the regeneration of octopus’s arms on vegetables like potatoes. This would theatrically solve worlds hunger.
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                        Even if their projects were far from being perfect we loved to see their wild imagination come into play for synthetic biology.
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                        In the end, we were really happy of the outcome of this High-school day. We succeeded in presenting a complex field of study to students while engaging this group of students to iGEM with their Mini IGEM project.
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                    <a href="#section-logos"><p class="text-info text-justify">Back to top</p></a>
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                <div class="col-md-10 col-md-offset-1 animate-box" id="Interview">
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                                <b>EPFL</b> is one of the two Swiss Federal Institutes of Technology and is located in Lausanne, Switzerland. This school was founded with the stated mission to educate engineers and scientists, to be a national center of excellence in science and technology and to provide a hub for interaction between the scientific community and industry. It is our main sponsor.
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                    <h1 class="lead animate-box text-center">INTERVIEW WITH YOLANDA SCHAERLI</h1>
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                    <h3 class="lead animate-box text-center text-uppercase">Introduction</h3>
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                        In September, we had the honor of sitting down with Dr.  Yolanda Schaerli,
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                        currently employed at University of Zurich, who will soon start her own
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                        group at the University of Lausanne. During the first part of the interview
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                        we explore her academic path, and the current direction of her research.
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                        The echoes of her past in protein engineering are still audible in her
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                        recent publications, but it is safe to say that her research characterizing
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                        the behavior intersecting genetic circuits and the effect of regulatory
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                        phenomena on phenotypes are firmly rooted in the realm of synthetic biology.
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                        After discussing her current research, we delve into the ethical dilemmas
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                        facing synthetic biologists. Ranging to suspicion from the public to preventing
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                        bioterrorism, we tried to give you a sneak peek into this complex world
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                        where philosophy meets pragmatism.
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                    <h3 class="lead text-center text-uppercase">Summary</h3>
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                    <p class="sub-lead text-justify">
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                        igem.today represents a veritable stream of information, which has the
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                        potential to constantly bring new and refreshing perspectives from the
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                        iGEM world to the general public, as well as other members of our community.
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                        We felt, however, that this aspect of igem.today could be complemented with
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                        the perspective of experts in the field, so we set out to find such an expert
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                        and investigate ongoing professional research and the interplay between
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                        synthetic biology and ethics.
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                        In September, we had the honor of sitting down with Dr.  Yolanda Schaerli,
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                        currently a group leader and SNSF Ambizione fellow at University of Zurich,
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                        who will soon start her own group at the University of Lausanne. Her past
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                        research has included performing directed evolution of proteins in water
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                        and oil droplets, creating an AND-gate using a split polymerase, and
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                        building synthetic gene regulatory networks. Her current project is
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                        looking at the evolvability of gene regulatory networks.
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                        After exploring her work in more detail, we pressed her on the ethical
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                        implications of her work, in particular, and synthetic biology, in general.
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                        We were especially interested in whether she ever faced public suspicion,
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                        due to her pursuits into genetic manipulation, but were relieved to discover
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                        that this was not the case, although she attributed this to the fact that
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                        she is doing basic research. We next inquired as to how public engagement
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                        is approached in the scientific world, and which players have the
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                        responsibility to make sure the public is informed about what kind of research
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                        is happening. We discovered that there seems to be a consensus that the onus,
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                        in this respect, is on scientists themselves, and this responsibility cannot
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                        be transferred to the public or politicians. In this sense, it is our duty
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                        to help these groups care about science, and understand it, and not theirs
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                        to enigmatically develop such an interest. Finally, we considered the role
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                        individuals might have, if any, in the development of future technologies,
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                        and the direction of synthetic biology. If individuals create their own s
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                        paces to experiment they should follow the same safety rules as researchers
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                        from the universities or companies. Navigating these ethical and communication
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                        challenges should be a principal concern of the scientific community, and
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                        will be paramount to the successful pursuit of the opportunities that lie ahead.
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                    </p>
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                    <h3 class="lead text-center text-uppercase">Interview</h3>
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                                So we will conduct this interview in two parts. In the first part we would like to know a little more about you and how you got into synthetic biology specifically, and then we’ll get to the part pertaining to ethics and community outreach.
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                                What can you tell us about yourself? How did you get into sciences, did you have a straightforward path into it, or did you have different turns?
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                                Well I started biochemistry and microbiology at ETH Zurich. I directly felt that I liked protein engineering and found that engineering biological system was very cool. But synthetic biology was at the very start, and during my studies I didn’t hear much of it. There wasn’t any iGEM team in ETH yet. Then I did my PhD at the University of Cambridge where I performed directed evolution of proteins and also worked on methods for doing this efficiently, namely using microfluidic water-in-oil droplets.                         </p>
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                                In each droplet you can have a separate compartment, so instead of having a 96-well plate you can have like a million droplets. So basically, in each droplet you can have a different library member. For example, if you want to create a library on an enzyme, you introduce mutations then you select out the members out that do want you want. But then, you have to find a method for screening them.                        </p>
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                                So we took a quick look at your publications on google scholar. (giggling) We noticed that the past couple papers you published are really pertinent to synthetic biology. One in 2015 about the changing expression in gene regulatory networks when you introduce new links between pathways and another one in 2014 where you were able to create an AND gate. How did you move from doing something more like biochemistry into synthetic biology?                        </p>
 
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                                So after my PhD, I wanted to move from engineering individual proteins to engineering gene regulatory networks. My main post-doc project was published in 2014 (A unified design space of synthetic stripe-forming networks) where I built stripe-forming gene regulatory networks. We first used computational methods to screen every 3-node topology and asked if this network could form a gene expression profile of a single stripe in a gradient of inducer. Once we have we had all the possible topologies, I build like 4 representative topologies that achieved the same phenotype but with different dynamical mechanisms.
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                                After that I moved to Zurich as a junior group. In my group we use synthetic biology to improve our understanding of gene regulatory networks and their evolution. For example one of the question I am asking is “do networks with different dynamical mechanisms have different potentials to produce novel phenotypes?”
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                                To answer this question we introduce mutations in the regulatory region of the networks and ask what kind of phenotype we get now. We do that for different networks and what we find is that depending on the network we start with we get a different a distribution of phenotypes. This implies that the dynamical mechanism puts a constrain to what it can evolve to.
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                                We use synthetic biology to address evolutionary questions. I think it’s a nice approach because you can easily build different topologies. It is actually also known in nature that the same phenotype can be caused by quite different gene regulatory networks but of course it is much harder to study this in let’s say fly development than with synthetic networks in E. coli.
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                                 In January I’ll move to the Department of Fundamental Microbiology at the University of Lausanne and where I’ll start as an assistant professor in synthetic biology.
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                                 <b>Deskgen</b>, a software system that gives scientists the power to organize optimize, and automate their research. With DESKGEN, scientists can design any genome editing experiment in any cell line and generate tailored CRISPR libraries for their research. Deskgen offer us advice to design our gRNA in the best efficient way.
 
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                                And do you see you research going in the same direction?
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                                 Yes, similar to what I just explained. We will build synthetic gene regulatory networks to improve our understanding of them and their evolution.
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                                 <b>Genscript</b> is the leading gene, peptide, protein and antibody research partner for fundamental life science research, translational biomedical research, and early stage pharmaceutical development. Since 2002, GenScript has exponentially grown to become a global leading biotech company that provides life sciences services and products to scientists over 100 countries worldwide. they have built the best-in-class capacity and capability for biological research services encompassing gene synthesis and molecular biology, peptide synthesis, custom antibodies, protein expression, antibody and protein engineering, and in vitro and in vivopharmacology – all with the goal to Make Research Easy. We were selected by Genscript and they offer us a grant of 1000 dollars for our project.
 
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                                We would like to start by trying to tie this into the ethical
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                                part. So our first question for you is whether you are ever faced with
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                                suspicion about the application of your work.
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                                Dimitri: I’m from the US and I know that in the US specifically there is a lot of tension between the scientific community and the general public especially when it comes down to genetic manipulation or regulation people are skeptical, to say the least, and suspicious most time.
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                                So our first question is; are you ever asked about if your research falls into the realm of the unethical and how do you respond to those question if they come up?
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                                I see what you mean, but personally I don’t think I had any such situation. The research I do is really basic research. It stays in the laboratory, so I think that people don’t mind that much if it stays in the lab. Currently, it is not intended for any application and no modified organisms are released. And I work on bacteria, where ethical questions are less of an issue.
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                                 But I see the issue, the public can be skeptical. This is our job to communicate to the general public and explain what we are doing.
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                                 <b>SnapGene</b> is a molecular biology software that offers a fast and easy way to plan, visualize and document molecular biology procedures. Snapgene offer licences for all the team.
 
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                                How do you personally go about this? Or in other words, do scientists that have the obligation to explain what is going on - in their view - or is that something that should be dealt with politicians, by social groups of organizations of this nature?
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                                I think it is part of the scientists’ job. I guess we should actually educate scientists better because we never learned how to communicate with the public. But apparently [the rapport has] changed. You are the proof by doing this interview that communication becomes more and more important.
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                                 <b>Microsynth</b> is a European leader in offering services related to synthesis of DNA/RNA oligonucleotides, various kinds of DNA/RNA analyses and molecular biology project outsourcing. They offer us 100 sequencing.
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                                 I think public outreach is important. We need to try to speak to the public. In the end they’re paying our research, right! They should have a right of deciding what we are doing and at least we should explain to them what we are doing. We should have more open discussion on where the new technologies should be applied and how far should we go.
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                                Actually, last year’s EPFL iGEM team did little interviews in the streets of Lausanne. They explained to the passengers willing to give them their time what synthetic biology is and all the different applications. People thought it was really interesting. But when they started talking about genetically modified organisms they were reluctant on the idea. What is your opinion on that?
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                                With GMO it is kind of a difficult subject anyway. When the techniques initially emerged it was really badly handled by the scientists I would say. Now, this word has a sort of stigma. As soon as you mention GMOs, people don’t like it. I think we should learn from what happened then and do better this time. What better opportunity than now with synthetic biology?
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                                 On the other hand, I also think it is not something really specific to synthetic biology generally it is every emergent technology has potential risk and also benefits.
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                                 <b>Integrated DNA Technologies (IDT)</b> is a leader in development and manufacturing of products for research and diagnostic life science markets. It is the world’s largest supplier of custom nucleic acids and serves academic research, biotechnology, and pharmaceutical development communities. Thanks to this 20000 base pair they offer us, we have been able to design and experiments all the constructs we wanted.
 
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                                Maybe the problem with synthetic biology is that it’s something complex enough so people within the general public may not truly understand it, but it’s relatable enough that they have opinions about it. Maybe other emerging technologies doesn’t always face the same barrier. For example, work in physics. People may not understand it but they don’t relate to it either.
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                                And I also think that there are several different aspects to be considered:
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                                 <b>F. Hoffmann-La Roche</b> is a Swiss global health-care company headquartered in Basel, Switzerland, that operates worldwide under two divisions : Pharmaceuticals and Diagnostics.
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                                 There is a safety aspect: for example, whether we should release modified organisms in the environment or maybe even inject them in tumor of a patient.  There are also social aspects: who should get the patents? Should the techniques be open? who has access to the technology? Finally, there is the third level, the ethical aspect. That’s more about what’s our relation to the natural world. Should we engineer the living creatures around us?
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                                All these different aspects should be discussed.
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                                Do you have any like opinion specifically on what you just said, like on the patent and the access of synthetic biology? I guess you are referring to certain companies wanting to patents gene as intellectual property.
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                                I don’t have a solution. I guess it is a complicated problem. Especially in synthetic biology there is this open source movement. Which I welcome greatly, especially on the academic side. On the other hand, I also see that companies need to have some kind of protection of their research and development, therefore the patents!
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                                 <b>Nikon</b> is a Japanese multinational corporation headquartered in Tokyo, Japan, specializing in optics and imaging products, including cameras, camera lenses, binoculars, microscopes, ophthalmic lenses, measurement instruments, etc
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                                 There is some fear that those new technologies just make the gap between poor and rich people bigger. Because the rich people are those who get direct access to the new technologies; an example are the plants that don’t produce their own seeds. Farmer have to buy seed from the same company each year. This is an issue.
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                                I like that you mentioned the open source community because one of the questions we had prepared for you was regarding biohacking and kind of where ... And what the first thing that might come into your mind when you think about kind of... Well I am not sure if this is where you were taking this question when you were talking about open source. Maybe you were talking about everybody getting involved. But when you think about small maybe members of the general public running their own small experiments in synthetic biology, do you see that as an issue? Because these people usually aren’t’ regulated to the same level as an institution might be.
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                                <b> Dimitri ;</b>Taking this back to where I am coming from (United States), this was a big issue after 9/11; they shut down a ton of people running their own biohacking experiments.
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                                That’s a good question. In general, I think that it’s great that people not doing this as professionals are interested and can play around with it. It is also a form of public engagement.
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                                 <b>Novartis</b> is a Swiss multinational pharmaceutical company based in Basel, Switzerland, ranking number one in sales among the worldwide industry in 2013.
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                                 But then of course, if they don’t treat the waste and release genetically modified organisms that’s not a good idea. There should be some basic safety level ensured. Basically the same rules should apply independent of where the experiments are performed.
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                                But in this case I guess the limit to which biohacking might be available to the general public is under the umbrella of an open laboratory. We have something similar here in a town nearby called Renens. We went there to present our project. They have a small laboratory called “Hackuarium” which is open to the members of the public who want to run their own biological experiment.
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                                 I imagine they must have the possibility for proper waste disposal, for example using an autoclave. And there should be somebody responsible to control this.
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                                 <b>New England Biolabs (NEB)</b> produces and supplies recombinant and native enzyme reagents for life science research and also provides free access to research tools such as REBASE, InBASE, and Polbase.
 
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                                Our last question regarding biohacking is whether even if it is open to the pubic if there should be some sort of regulation of who should do it about who can do it. Basically, if whether in your estimation It should be regulated - now we are balancing public safety and community engagement.
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                                Do you mean like bioterrorism, or things like this?
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                                Not specifically, also that an interesting thing to talk about. Imagine I have a small lab in my garage, because it is something I am interested in. Of course these places would have to have an autoclave, for example. Does the government have or do we have a responsibility to make sure that people that run those sorts of experiments have certain equipment? Or is that something that we should trust people to follow?
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                                Trust is usually not enough, I guess. It depends on what thing you do. Even in a real lab, there are different levels of safety. I don’t think anyone would mind you doing a miniprep in your garage.
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                                But for your research you need the approval of a safety committee. So I don’t think there should be a different regulation if you are doing this in a company or in your garage. The same rules should apply. But then it is really hard to check everything.
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                                A follow up question to that is “do you or other scientist you work with have to find yourself taking supplementary steps to make sure you are following safety and ethical guidelines?”
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                                For example, do you insert kill switches into networks? Or do you screen the DNA sequence you use to be sure that they aren’t compatible with human DNA or such things?
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                                First of all, if you apply for a grant for funding there is always a form to fill in for all safety and ethical issues. If they see that your project is dangerous or not ethical, it would not be approved.
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                                And then, if you order DNA from companies they have to check that there aren’t belonging to certain genes. Like we mention before bioterrorism that is actually checked at this level so you can’t order some bird flu virus…
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                                Those are standardized in the process. It is not in the responsibility of the researcher.
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                                And it depends on the application. If you want to release synthetically modified organisms into the environment, I think you should make sure it does only what you want and it doesn’t mutate. It might be necessary that you insert a kill switch. Or maybe the modified organisms can only live if you supply a modified amino acid that doesn’t occur in nature. Imagine, modified cells are injected into your body for some medical application. You really don’t want them to go wild on you. If modified bacteria stay in a fermenter for drug production you probably mind less.
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                                When we talk about medical uses, it’s the epitome of the conflict between safety and benefit. So you were saying before that most research doing is more on the structural level of how the network function. Maybe you are not looking at medical app.
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                                Do you see the conflict between the safety and the benefit being such a barrier that it might take decades for this technology to be applied or did you find in your research that there is a way to predictably create networks already that might be able to make safe medical application?
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                                In my research no, but I think the field is quite far in this question. For example Prof. Fussenegger at the ETH Zurich, does a lot of work for medical applications. They already proved in mice that they can fight different diseases for example diabetes or  skin diseases. To be honest, I don’t know, how far they are to get the approval to do human trials.
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                                Another thing to consider is how bad the disease is. If it the last hope, then people are willing to take more risk that than if the  disease can already be cured by some existing drug.
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                                Last question! Do you see a world in the future with everything around us that could be engineered? Like where everything is modified, like food is more nutritious. Etc.
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                                Last question! Do you see a world in the future with everything around us that could be engineered? Like where everything is modified, like food is more nutritious. Etc.
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                                It’s a bit scary no? But, to be honest I think there is not much different between this and breeding right? We ‘ve been doing this for centuries, we are just getting better at it! EPFL:
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                                The difference, I guess, is we were doing it without knowing the mechanism behind it, and now we know. Like carrots weren’t orange until the 1800s, so we clearly changed their genes, but now we could do it much, much faster.
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                                I think that’s it for the interview. Thank you very much. We won’t take more of your time! It was really informative and interesting discussing with you.
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                                And good luck and enjoy the Jamboree.
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Revision as of 02:39, 20 October 2016

iGEM EPFL 2016

ATTRIBUTIONS

Our iGEM journey started at the end of 2015 when EPFL students were invited to join in the 2016 iGEM team. After the selection, we started brainstorming in February 2016 where after a few months of literature research we came up with this project of combining CRISPR-dCas9 and the Cello software. Between the beginning of June and July, we designed and ordered all the parts we needed. And then finally, in July, we were able to start our exciting work in the lab! And we have been working hard ever since then to present our end results to all the other teams and jury members end of October in Boston, MA.

Our project is partially based on the project of the 2015 EPFL iGEM team. The general design of the gates comes from their BioLogic project.

TEAM ATTRIBUTION

Project

After months of brainstorming, the whole team contributed to the conception of this project containing both computational and biological work. The design of the logo was imagined by Pietro Airaghi.

Laboratory

The design of the Laboratory part was realised by Alix Faillétaz, Francesco Terenzi, Camilla Ceroni, Yassine Zouaghi and Marie Matos. During the summer, the whole team participate to the lab sessions.The design of the gRNAs was done by Samuele Mercan

Human Practices

The idea of igem.today come from Rémy Pétremand and Pietro Airaghi, they also designed the website

The interviews and their retranscriptions were done by Rémy Pétremand, Yassine Zouaghi, Alix Faillétaz and Marie Matos.

The presentation to the High School Student was scheduled and prepared by Marie Matos with the help of Rémy Pétremand and Yassine Zouaghi.

The presentation at the Hackuarium was scheduled and prepared by Dimitri Coukos with the help of Rémy Pétremand, Yassine Zouaghi and Marie Matos.

Software and wiki

The wiki was designed and set up by Dimitri Coukos and Pietro Airaghi with the help of Rémy Pétremand. The figure were done by Rémy Pétremand and Yassine Zouaghi. The texts were written by the whole team in function of the topics they were involved during the summer.

All the work done on the Software part, including the graphic interface were done by Dimitri Coukos and Pietro Airaghi.

The modelling part of the project was developed by Dimitri Coukos, with help from Remy Pétremand and Yassine Zouaghi.

BioBricks

The BioBricks were planned and done by Samuele Mercan, Francesco Terenzi and Camilla Ceroni.

AKNOWLEDGEMENTS

We could not have done it without the help of some people, so we would like to acknowledge all the help and support we received throughout our iGEM adventure!! We are very grateful for everyone who has helped in any possible way and made our project possible.

Superviors

Our supervisors, Bart Deplancke and Barbara Grisoni gave us a lot of advice on how to resolve some critical problems, whether it was for the design, or for the experiments we conducted. They also kept us on track to reach our goal.

Our advisers, Roel Bevers and Riccardo Dainese, Phd Students in Bart Deplancke’s Lab, helped us with most of the countless problems we had in the lab along with sponsors and other requirements for iGem. They also give us huge help during the week-end with material and access to the Lab.

Victor Steininger, Loic Steiner, Ari Safaris, Axel Uran, Paola Mansot and Vincent Jacquot, members of the 2015 EPFL iGEM team. In the early stages of our project, they helped out by teaching us about primer design, laboratory skills and gave us a lot of advice on the general competition and how to achieve our goals.

General suport

A warm thanks to EPFL, the Swiss Federal Institute of Technology in Lausanne, without which our participation in iGEM and our project would not have been possible. We would like to thank André Pexieder for letting us use his lab and the equipment during the project, Marie-France Radigois who helped us with the administrative tasks related to the project and Stéphane Karlen, Safety coordinator at the School of Life Science, who gave us a course and instructions on laboratory safety before our project started and was available for any question during the project.

Project support and advice

To begin with, we would like the thank the 2015 EPFL iGEM team for introducing their project to us, while teaching us how to work in the laboratory.

We also want to thank our supervisors for helping us choosing the direction to follow designing our project.

We would also like to thank Professor Jesse Zalatan from Washington University for his advice on our project. Previously he and former colleagues worked on “Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds”, a paper that inspired us and ‘produced’ Intelligene, and for leading our project to the search of a repressor element in yeast.

We would also like to thank Prashant Vaidyanathan of Cidar Lab at Boston University help regarding NetSynth and his feedback regarding our modifications to Cello. We also thank Cidar Lab for the access to their program, Cello, through their GitHub page.

Lab support

We want to thank all the people who allowed us to measure our experiments on their equipment and gave us advice about the interpretation and presentation of the results.

The EPFL Flow Cytometry Core Facility (FCCF) who let us use their equipment and help us measure our samples with a special thanks to Andre Mozes.

The Maerkl Lab and specially Francesca Volpetti for the use of the overnight plate reader.

The Deplancke Lab for all the material they lend us and for the use of fluorescent microscopes.

Special technique support

Julie Russeil, lab manager in the Deplancke Lab, assisted us with the difficulties of yeast integrations, and more generally with advice on experiments with yeasts. In addition to that she gave us a lot of advice and “shortcuts” to be more efficient in the lab. Riccardo Dainese helped us with technical details for the gibson assemblies and plasmid transformation into competent cells.

Design support

Eugenia Petrova, from Desktop Genetics, who explained to us how to use the DESKGEN platform and worked out a way to use it for our project to design orthogonal and efficient guide RNAs with their respective targets.

Modelisation support

Professor Felix Naef and his post-doc Eric Paquet for the time they took to help us with developing the model of our system; our model would not have been possible without their help. This advice allows us to implement theoretical results in Cello.

Human Practices support

We would like to thank Mrs de Raemy at the Collège de Candolle in Geneva for allowing us to present iGEM to a class of students.

We also would like to thank the Hackuarium for inviting us to present synthetic biology and iGEM in their Open Hackarium space. This was great fun and we received a lot of good feedback from the community!

We also want to thank Professor Yolanda Schaerli for the time she gave to our team for a discussion about synthetic biology, the issues and the ethical part of the field.

IGEM News would have not been possible without the help of so many iGEM teams and we would like to thank each and every of them that took time to help us in this project.

Presentation coaching

The presentation we made for Hackuarium was an amazing and unique opportunity to present our project so we would like to thank them a lot, along with Roel Bevers for a very detailed feedback to improve the presentation.

Templates and icons

We thank badr545 for RISE, the template used for the wiki, which we found on shapebootstrap.net. We thank Ed Ball for his jsPlumb template, academo, which we found on his github https://github.com/edwardball/academo.org. We thank the following authors of icons we found on flaticons.com : Freepik, Madebyoliver, Vectors Market, Bryn Taylor.

SPONSORS

We would like to thank all our generous sponsors for aiding us financially or via consulting or computational assistance.

EPFL is one of the two Swiss Federal Institutes of Technology and is located in Lausanne, Switzerland. This school was founded with the stated mission to educate engineers and scientists, to be a national center of excellence in science and technology and to provide a hub for interaction between the scientific community and industry. It is our main sponsor.

Deskgen, a software system that gives scientists the power to organize optimize, and automate their research. With DESKGEN, scientists can design any genome editing experiment in any cell line and generate tailored CRISPR libraries for their research. Deskgen offer us advice to design our gRNA in the best efficient way.

Genscript is the leading gene, peptide, protein and antibody research partner for fundamental life science research, translational biomedical research, and early stage pharmaceutical development. Since 2002, GenScript has exponentially grown to become a global leading biotech company that provides life sciences services and products to scientists over 100 countries worldwide. they have built the best-in-class capacity and capability for biological research services encompassing gene synthesis and molecular biology, peptide synthesis, custom antibodies, protein expression, antibody and protein engineering, and in vitro and in vivopharmacology – all with the goal to Make Research Easy. We were selected by Genscript and they offer us a grant of 1000 dollars for our project.

SnapGene is a molecular biology software that offers a fast and easy way to plan, visualize and document molecular biology procedures. Snapgene offer licences for all the team.

Microsynth is a European leader in offering services related to synthesis of DNA/RNA oligonucleotides, various kinds of DNA/RNA analyses and molecular biology project outsourcing. They offer us 100 sequencing.

Integrated DNA Technologies (IDT) is a leader in development and manufacturing of products for research and diagnostic life science markets. It is the world’s largest supplier of custom nucleic acids and serves academic research, biotechnology, and pharmaceutical development communities. Thanks to this 20000 base pair they offer us, we have been able to design and experiments all the constructs we wanted.

F. Hoffmann-La Roche is a Swiss global health-care company headquartered in Basel, Switzerland, that operates worldwide under two divisions : Pharmaceuticals and Diagnostics.

Nikon is a Japanese multinational corporation headquartered in Tokyo, Japan, specializing in optics and imaging products, including cameras, camera lenses, binoculars, microscopes, ophthalmic lenses, measurement instruments, etc

Novartis is a Swiss multinational pharmaceutical company based in Basel, Switzerland, ranking number one in sales among the worldwide industry in 2013.

New England Biolabs (NEB) produces and supplies recombinant and native enzyme reagents for life science research and also provides free access to research tools such as REBASE, InBASE, and Polbase.