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