Participating in the iGEM competition was an initiative that emerged in our initially small group of friends and colleagues at the School for Chemical Engineering, NTUA. Unfortunately, we do not have a synthetic biology course in our school's curriculum but we had heard about iGEM in online courses ("Industrial Biotechnology", University of Manchester, on Coursera, "The Principles of Synthetic Biology", MIT, on edX, “Genes and the Human Condition”, University of Maryland, on Coursera, materials freely available). We managed to find more students from different schools that shared the same passion for synthetic biology and finally started brainstorming around the beginning of December 2017. The first week of February we had decided on our project, the development of a method for Point-of-Care MERS-CoV diagnosis, and proceeded on reading tons of literature to specify the details. The laboratory training and experiments began at the end of May.
Throughout the last few months, we have achieved formulating a solid Proof of Concept, supported by dry lab experiments and validated by wet lab experiments. We are also in a position to propose a complete kit design based on the current needs for MERS-CoV POC diagnosis. Lastly, through our Human Practices efforts, we have introduced synthetic biology in several high school classrooms for the first time in Greece, and we have offered the opportunity of a short hands-on synbio project design experience to a group of undergraduate students.
None of the above would be possible without the assistance and support of our professors, supervisors, instructors, experts, and sponsors. We offer our sincerest thanks for their contribution.
Yannis as the team leader tried to supervise offering his help and insights in several different parts of the iGEM project. As a part of the dry lab team, he contributed in the toehold design and kinetic modelling. Alongside with Nelly, he set the basic lines and specifications for the kit design while he engaged in numerous discussions with professionals for the same reason.
Maria was the head of the wet lab team, therefore her main focus was designing, supervising and executing the experiments at the Molecular Virology Laboratory of the Hellenic Pasteur Institute. She was a link between wet and dry lab, bridging any knowledge gaps and assisting on modelling tasks. Maria devoted her very limited time outside the lab (as well as many nights’ worth of sleep) working on the team’s presentations, posters and graphics. Last but not least, she supported Leda in organising human practices activities.
Vasilis as the head of the dry-lab team, developed the code for determination of the most promising switches for in vitro testing, alongside Leda, Yannis and Stelios, including the training of the Neural Network. He also developed the 3D computational model for the design of the kit, carried out the simulations and interpreted the results, giving valuable feedback to Nelly and Yannis for the final design.
Leda was a member of the Dry Lab team, alongside Yannis, Vasilis and Stelios, and performed the Molecular Dynamics Simulations under the auspices of the Cournia Lab at the Biomedical Research Foundation of the Academy of Athens. While the simulations run, she devoted her time in organizing and carrying out the team’s Human Practices activities, giving emphasis on Education and Public Engagement. Moreover, she contributed aesthetically to the team by designing the project’s graphics, logos and banners.
Nelly’s contribution included fundraising and financial management. She was also involved in the InterLab study, which she performed with Elena and Panos. Specifically, she contributed in the cell cultures, OD measurements, troubleshooting and documentation. As a part of the wetlab team, she worked as an assistant for a short period at Molecular Virology Laboratory in Hellenic Pasteur Institute. Finally, she designed and documented the proposed diagnostic kit and engaged in various Integrated Human Practices meetings.
Natalia contributed to the project by handling some of the fundraising duties and by being part of the wetlab team. She dealt with the opening of the team’s university financial account and with the legal documents regarding sponsorships. She also handled, along with Nelly, the payment of the invoices regarding registration fees, air tickets and lab supplies. As part of the wetlab, she worked at Molecular Virology lab of the Hellenic Pasteur Institute on most of the laboratory techniques employed in the project. Lastly, she was involved in several Human Practices events.
Stelios' main contribution in the project was the production and maintenance of the team's web profile, excluding social media management. He designed the website that was deployed in the domain of the School of Chemical Engineering, NTUA, and subsequently, took on the creation of this Wiki page. On the side, Stelios dealt extensively with Image Editing, as well as occasionally helping in Dry Lab by troubleshooting with Linux-based tools that we initially used. Lastly, he embarked on some Android Development following our plans for accompanying our kit with a smartphone application; a concept that eventually didn't come into fruition due to time limitations.
Elena’s contribution included initially participating in the InterLab Study. Later on, she participated in the wet lab experiments at both the National Technical University of Athens (School of Chemical Engineering) and the Hellenic Pasteur Institute, where she provided valuable help in bench work and troubleshooting. She was also responsible for the Social Media management and for the communication with other iGEM Teams for collaborations.
Panos’s mainly contributed to the InterLab Study, both participating in the experiments and securing access to the required instruments. He also provided general assistance concerning molecular biology, participated at the wet lab experiments that were carried out at the National Technical University of Athens and contributed in creating the protein models that were afterwards used for the molecular dynamics simulations.
Dr Pelagia Foka, Researcher at the Molecular Virology Laboratory in the Hellenic Pasteur Institute, has assisted us immensely during these last few months. She was our laboratory instructor and main supervisor of the project, for both its design and its execution. Among others, she provided us with a lab space, supplies, mentorship, project management and day-to-day troubleshooting.
Professor Evangelos Topakas, at the School of Chemical Engineering of NTUA, encouraged us since the beginning to engage in this challenge and guided us through the difficult times of deciding on a subject for our project. He also helped us immensely with the financial aspect of our project, being the primary PI. Finally, he gave us access to our School’s Biotechnology Laboratory where we performed the InterLab study.
Professor Dimitrios Kekos, at the School of Chemical Engineering of NTUA, was our secondary PI and assisted us in the brainstorming phase. He also supported us in the fundraising process.
Brainstorming & Initial Ideas Support
During the first months, right after the creation of the team, we struggled long for finding an inspiring subject for our project, one that would be feasible, novel and impactful. Through this period we met and discussed with Professor Gerasimos Lyberatos of the School of Chemical Engineering in NTUA, Assistant Professor Leonidas Alexopoulos of the School of Mechanical Engineering in NTUA and Professor Emeritus Fragkiskos Kolisis of the School of Chemical Engineering in NTUA. Each one helped us in finding our path, by assessing our ideas and suggesting alternatives.
Many thanks to our friends and former members of this team, Theodore Bechlivanis and Antigoni Koukouvaou , for their productive thoughts, their help in finding the weak points in our initial ideas and for making the first fundraising contacts.
Project Development Support
Stamatios G. Damalas, phD student at the University of Wageningen, with his enthusiasm and broad knowledge on SynBio, provided us with feedback on the detection mechanism and the realization of the project.
Nikolaos Spanakis, Assistant Professor in the Medical School of the University of Athens, has helped us in understanding MERS virology and sampling methods.
Ourania E. Tsitsilonis, Associate Professor in the Faculty of Biology of the University of Athens, has proposed that we introduce positive and negative controls to our diagnostics system.
Andreas Scorilas, Professor in the Faculty of Biology of the University of Athens, has provided us with insight on how we could develop our diagnostics system to a commercial level.
Issidora S. Papassideri, Professor in the Faculty of Biology of the University of Athens, has provided us general with feedback and introduced us to staff members of the University of Athens that helped us realize our project.
Constantinos Stathopoulos, Professor in the Medical School of the University of Patras, helped us understand the nature of riboregulators and the toehold design challenges.
Jeroen De Buck, Professor in the Faculty of Veterinary Medicine of the University of Calgary, gave us invaluable advice on the split trehalase as a reporter protein.
Wet Lab & Safety Support
Dr. Ourania Georgopoulou, Head of the Molecular Virology lab of the Hellenic Pasteur Institute, has encouraged our effort since the beginning, always giving us valuable insight and has provided us with lab space to run our experiments.
Dr. Eirini Karamichali, researcher at the Molecular Virology lab of the Hellenic Pasteur Institute, has helped us familiarize with the in vitro transcription technique and has provided us with general assistance and troubleshooting throughout the lab experiments.
Dr. Petros Eliadis, researcher at the Molecular Biology & Immunobiotechnology lab, of the Hellenic Pasteur Institute, has helped us work on protein expression and has also offered general feedback and advice to our team.
Dr. Athanasios Kakkanas, researcher at the Molecular Virology lab of the Hellenic Pasteur Institute, is also responsible for the laboratory safety issues and has helped us with that as well as with the proper use of lab equipment.
Many thanks to Vanessa Valiakou, Georgia Papadopoulou and Evie Petroulia for their help in our lab training and every-day troubleshooting.
Anastasia Zerva and Efstratios Nikolaivits for their day-to-day assistance in the lab. Assistant Professor Antonios E. Koutelidakis from the Department of Food Science and Nutrition, University of the Aegean, Professor Maria Kapsokefalou Department of Food Science and Human Nutrition, Agricultural University of Athens, Dr Ioannis V. Kostopoulos and Associate Professor Ourania E. Tsitsilonis , for the instrument provision and their technical support during fluorescence measurements and Flow Cytometry.
Modelling/Dry Lab Support
Dr. Zoe Cournia, head of the Cournia Lab at the Biomedical Research Foundation of the Academy of Athens, supported the team with her scientific insight and knowledge of computational models for protein systems. By working at Dr. Cournia’s Lab, we managed to perform the necessary simulations for our proposed protein system. Special thanks to the Cournia Lab members, Alexis, Elena, Matina, Peteri and Pedro, for their advice and insight, as well as the GRNET administrator, Dr. Dimitris Dellis for his support in using the national supercomputer.
Many thanks to Prof. Syma Khalid of the University of Southampton for the insightful conversation and feedback on our system and models during the Bio-Excel SIG Meeting, ECCB 2018.
Special thanks to Dr. Fotis Baltoumas for his unconditional support on troubleshooting and his valuable suggestions on running an MD Simulation.
Timos Karamitros, Senior Postdoctoral Fellow in Hellenic Pasteur Institute, has helped us at determination of conserved regions of MERS-CoV, also contributed at the final selection of the most promising switches.
Andreas Boudouvis, Professor in the School of Chemical Engineering of the National Technical University of Athens, indicated and brought us in touch with various valuable colleagues, whose help was of crucial importance for the compilation of the project.
André Estevez-Torres, CNRS Researcher-Laboratoire Jean Perrin, provided us valuable information and tips on the kinetic modelling of our cell-free system.
Human Practices Support
Prof. Kostas Kordatos and Dr. Afroditi Ntziouni of the Inorganic and Analytical Chemistry Lab, School of Chemical Engineering of the National Technical University of Athens, accepted our team to present with the Lab’s team at the 2018 Athens Science Festival.
Many thanks to Dr. Kostas Vavitsas for suggesting a panhellenic iGEM meeting that turned into a successful workshop for university students, as well as Prof. Emeritus Fragkiskos Kolissis and Prof. Georgios Skretas for being part as keynote speaker and judge, respectively, at the aforementioned workshop.
Prof. Evangelia Pavlatou gave our team significant insight on organizing our Human Practices activities, as well as on how to gather statistically valid information from questionnaires and how to process the collected data. She also brought us in contact with Dr. Maria Dokopoulou of the National Institute of Educational Policy with whom we discussed on the greek educational system, how our team can effectively engage students and communities and how to elaborately document our findings on a report.
Prof. Kosmas Haralampidis of the Biology faculty, NKUA, discussed with us on the Greek tertiary education, on how to include Synthetic Biology in such a rigid educational system and dissolved mysteries around GMOs.
Many thanks to the Hellenic Society of Point-of-Care Testing and, more specifically, to Dr. Katerina Stini, Dr. Dionisis Vourtsis and Dr. Giorgos Antonakos for taking such an interest in our project and for giving us significant insight on the existing Point-of-Care methods and on how we could improve ours.
Mr. Panagiotis Doukas of the Analysis Medical Laboratories discussed with us our project and offered his knowledge on patient sampling. Dr. George Papadatos (GlaxoSmith Kline UK) reviewed our project and provided us feedback on our proposal and on how to better communicate our idea.
Special thanks to Dr Lee Alissandratos of The Australian National University for his contribution on the glucometer-enabled diagnosis concept.
Regarding the technical details of our kit design proposal, we discussed with several experts that provided feedback and contributed to the final design: Professor Keith Pardee from University of Toronto, helped us with the paper discs Dr Nefeli Tsaloglou, Board member in Diagnostics for All, offered us her knowledge on different amplification methods, Aashish Priye, Assistant Professor in University of Cincinnati helped us understand certain aspects of microfluidics, Dr Robert J. Meagher from Sandia National Laboratories assisted with the heating method.
We would also like to thank Professor of Internal Medicine at the Athens University Medical School and infectious diseases specialist Helen Giamarellou, for her enthusiasm in discussing possible routes for taking our design to the next step and applying it in the detection of other viruses.
Many thanks to our friend Elena Roditi for her insight on using a commercial glucose meter.
Web Page Support
Ioannis Tzigkounakis, for the unwavering and expeditious cooperation in hosting and managing our website in the domain of the School of Chemical Engineering, NTUA.
We would like to thank the professors in the School of Chemical Engineering, NTUA, Ioannis Kalogirou, for assisting us in the fundraising plan and Angelos Tsakanikas, for acting as a liaison between our team and several sponsors. The Dean of the Chemical Engineering School, Konstantinos Magoulas has also supported us greatly in the process. Also, we would like to thank Jenny Papadonikolaki and the Hellenic Association of Pharmaceutical Companies for forwarding our funding request to the companies, Dr Evangelos Siokas for helping us with our fundraising presentation, professor Costas Charitidis for initiating our Research Program account in order to receive funds and Apostolis Zamparas for guiding us through the bureaucratic labyrinth of NTUA’s funds management.
We would like to thank the team iGEM Greece 2017 for their general mentoring throughout iGEM, Irene Sagkriotou from BIOLine Scientific for our collaboration concerning our lab supplies, Niki Kareli for the 3D design of our diagnostic kit, and Dora Farmaki for the photoshooting.