iGEM Leiden set up
iGEM is an extracurricular course provided by Leiden University. This university teaches multiple synthetic biology courses such as Advanced Molecular Genetics and Biotechnology, Advanced Cell Biology, and Molecular Microbiology. Unlike most courses, iGEM is taught in a very independent manner. Leiden iGEM teams can choose how to divide their time themselves, instead of having mandatory lectures, workgroups, and assignments. The syllabi are freely available for every Bachelor or Master's program of Leiden University. The course materials, however, are not freely available.
This year's iGEM team was formed halfway through January 2021. After a few introductory presentations by the supervisors, the team started brainstorming for a project idea at the end of February. We have had numerous brainstorm sessions in March and chose a definitive project at the beginning of April. We were busy in April, May, and June with designing our lab experiments, developing the model, planning educational activities, attending many human practices meetings, and evolving an entrepreneurship plan. In mid-July, we could finally begin working in the lab until the end of August. Afterward, we got the opportunity to have two people finalize the last experiments for two more weeks.
We are very proud of all we have accomplished this year and want to thank everyone that helped us with our project:
- Prof dr. Dennis Claessen
- Prof. dr. Han de Winde
- Aukje Beers
- Floor Stel
- Jonah Anderson
- Maarten Lubbers
- Tijn Delzenne
- Amber Schonk
- Carli Koster
- Daniël Tan
- Daan van Tol
- Eugene Golov
- Laurens ter Haar
- Marijn van den Brink
- Marjolein Crooijmans
- Tim van den Akker
- Violette Defourt
- Andika Sidar for helping with making an SDS gel.
- David Foschepoth for his critical questions on our data.
- Dennis Claessen for his critical comments on our data and the suggestion to use minimal medium in our experiments.
- Floor Stel for her continuous support.
- Ivo Gariboldi for his help with the electrophoresis experiments. He provided us with a protocol and lent us cuvettes for the electroporation machine.
- Jo-Anne Verschoor and Marjolein Crooijmans for providing us with feedback on our experiments.
- Le Zhang helped for making an appropriate PCR protocol for an overhang touchdown PCR to clone constitutive promoters into biobricks
- Lennart Schada von Borzyskowski for providing us with the Escherichia coli (E.coli) Top10 strain.
- Carola Feijt, Floor Stel, and Tijn Delzenne from the IBL for their permission, booking assistance, and instruction on how to use the plate reader, respectively.
- Ellen de Waal and Helga van der Heul from the Institute of Biology Leiden (IBL) for their help to order the supplies necessary for our experiments.
- Gerda Lamers from the IBL for her permission and instruction on using confocal microscopy.
- Hein van der Meer from the IBL for his bright, positive attitude and a warm welcome every morning at the Sylvius Laboratory during our summer lab work.
- Kees Koops from the IBL for allowing us to use the laboratory and machines over the summer.
- Thomas van Dijk and Noortje Dannenberg from the IBL for their guidance and assistance with the FACS machine.
- Annette Heijn and Charlotte Ellerman for helping us set up the crowdfunding plan and reaching Leiden University's alumni network.
- Hester Bijl, Dennis Claessen, Han de Winde, Nick van Dop, Nikki Spaansen, Robert Mans, and Robert Wagenveld for sharing our crowdfunding with their community.
- Pim Rusch for making our team pictures and giving us tips for filming the presentation video.
- For our general outreach, we would like to thank all the news outlets and other organizations who shared our message: BNR Radio, Boerhaave, EUniWell, Leidsch Dagblad, Leiden University, the Mare - Leiden University's weekly newspaper, OVBSP, PLNT and Unity.
- Akos Nyerges for advising on the possible future experiments of our project.
- Amalia Kallergi for giving us insights into the problems regarding the validation of a biocontainment system.
- Barbara Brunnhuber and Stéfan Ellenbroek for sharing their knowledge in setting up a start-up and bringing us in contact with experts from different companies.
- Braden Gilbert for sharing his expertise on the application of our system in bioremediation with us.
- Britte Bouchaut for sharing her knowledge on regulations, Safe-By-Design, and social considerations.
- Cécile van der Vlugt and Marja Agterberg for giving us insights into the process of risk assessment and regulations.
- Clara Posthuma for sharing her expertise with us on GMO regulations.
- EFSA for sharing how the process of risk assessment works.
- Enrique Asin Garcia for giving us insights on the need for new tools for a standardized assessment on the use of GMOs.
- Erik Vijgenboom for his help in designing the experiments.
- Jack Pronk for his advice in the application process.
- Kha Tram for his advice in the application process.
- Kyra Delsing for sharing her knowledge on making surveys.
- Leanne DeWinter (International Experts Groups of Biosafety and Biosecurity Regulations) for giving us insights into regulations regarding the non-contained use of GMOs in countries outside of Europe.
- Lennart Schada von Borzyskowsky for sharing his expertise in our expert panel during the discussion evening.
- Marie-Louise Bilgin for sharing her knowledge on policymaking and her participation in our expert panel during the discussion evening.
- Marjolein Crooijmans for sharing her expertise in our expert panel during the discussion evening.
- Nathan Fraikin for advising on the possible future experiments of our project.
- Pim Klaassen for sharing his knowledge on the social considerations we need to take into account when designing our system.
- Renée Kapteijn for her help in designing the experiments and for sharing her expertise in our expert panel during the discussion evening.
- Rianne Hageman and Leonie White-Scholten for sharing their knowledge on regulations.
- Robert Mans and Rinke van Tatenhoven-Pel for their help regarding choosing an application.
- Robert Wagenveld for giving us insights into the best application of our system and giving us information about the PFAS problem.
- Saskia Meuffels for sharing her expertise on regulations.
- Tessa Alexanian for sharing her experience with safety in iGEM.
- Tom Ellis for sharing his knowledge on biocontainment systems.
We would like to thanks the following persons and projects who published open-source code which was used in our wiki:
Public Engagement & Education
- Amy van Nobelen for her feedback and for aiding in organizing our workshops at Naturalis Biodiversity Center.
- Anne Velders and Hanny Gijsman for their feedback on our workshop for elementary schools and for their aid in contacting elementary schools to take it up in their curriculum.
- Helga van der Heul for creating agar plates with antibiotic-producing S. coelicolor and an overlay of
E. coli to show antibiotic production to the public at our events.
- Ingrid Gruijs for her help during our lectures and practicals at the high school Kaj Munk college.
- Joost van den Brink for lending us lamps and glasses to show GFP mutants to the public at several workshops and giving us supplies for Gram staining.
- Kees Koops for lending us the materials needed for several workshops.
- Lennart Schada von Borzyskowski, Renée Kapteijn and Marjolein Crooijmans for being the expert panel during our discussion evening.
- Maarten Lubbers for his input and feedback on numerous activities of our Public Engagement & Education campaign.
- Mark Arenthorst for giving us A. niger plates to show to the public during our events.
- Marieke Hohnen for aiding in organising our workshops at Rijksmuseum Boerhaave.
- Tim Schol for his feedback on our proposal for a lecture and practical for the high school Kaj Munk college.
- Tom Jilink for his help and feedback during our workshops at Naturalis Biodiversity Center.
We want to thank the team MIT_MAHE for our inspiring collaboration on both designing the survey to gauge public opinion on GMOs and our projects, but also for our fruitful discussions on how to implement our project with theirs to increase the biosafety of their design. Furthermore, team Aix-Marseille University, team Brawijaya, team Costa Rica, team Darmstadt, team Düsseldorf, team Eindhoven, team Evry, team Graz, team GO Paris Saclay, team Guelph, team IONIS, team Maastricht, team MSU, team Paris Bettencourt, team Patra, team RUBochum, team Sorbonne University, team SZU-China, team Toulouse INSA-UPS, team USP Brazil, team UParis_BME, team Wageningen and team Warwick for setting up collaborations that we have participated in.
|Name||Project part||Task description|
|Chanel Naar||Genome integration, Improve-a-part||Integrate one of the plasmids of DOPL LOCK into the genome of the bacterium. Show the improved functionality of a tagged antitoxin, as it would degrade faster when the kill switch is shifted on.|
|Bas van Woudenberg||Experimental design and construct assembly||Design of the experimental work and assemble our required promoter, toxin, and antitoxin combinations in our plasmids.|
|Ehsan Razaghi Siahroudi||Co-transformation||Determine the best combination of Oris for co-transformation.|
|Floor Stel||Technical support||Thanks for all your help in the lab!|
|Hoda Ekhlasi||Co-transformation, construct validation||Determine the best combination of Oris for co-transformation. Validate primers to enable us to confirm our constructs in a later stage.|
|Igor van der Meulen||General laboratory assistance||Assist other team members in fulfilling their experimental goals.|
|Iris Noordermeer||Improve-a-part, construct assembly, construct validation||Show the improved functionality of a tagged antitoxin, as it would degrade faster when the kill switch is shifted on. Assemble our required promoter, toxin, and antitoxin combinations on our plasmids. Validate primers to enable us to confirm our constructs in a later stage.|
|Jetse van Os||General laboratory assistance||Assist other team members in fulfilling their experimental goals.|
|Lisa Kleinjan||General laboratory assistance||Assist other team members in fulfilling their experimental goals.|
|Quint van Loosen||Genome integration||Integrate one of the plasmids of DOPL LOCK into the genome of the bacterium.|
|Sebastiaan Ketelaar||Construct assembly||Assemble our required promoter, toxin, and antitoxin combinations on our plasmids.|
|Siheng Li||Construct assembly, co-transformation||Assemble our required promoter, toxin, and antitoxin combinations on our plasmids. Determine the best combination of Oris for co-transformation.|
The Communication Manager, Sebastiaan Ketelaar, set up and maintained our collaborations with other iGEM teams. With help from others in the team, he ensured we took part in many fun collaborations and met many great iGEM teams from all over the world. Specifically, the collaboration with the iGEM team MIT_MAHE was thought out and carried out by Chanel Naar, Igor van der Meulen, and Sebastiaan Ketelaar.
Our Design Manager, Jetse van Os, was in charge of the overall style and visual outlook of the project. Jetse learned how to work with Illustrator and After Effects to design the logo, make animations and informative figures to explain the project in our videos and wiki. His work can be seen throughout the whole project and wiki.
Education and public engagement
Quint van Loosen, our Public Engagement Manager, planned and carried out the educational aspects of the project, such as making interesting videos and setting up educational programs for different age groups. With help from many different team members, he hosted many fun educational events. Additionally, a discussion evening was hosted by our team, which was organized by Chanel Naar, Igor van der Meulen, Lisa Kleinjan, and Sebastiaan Ketelaar.
Our entrepreneurship plans were thought out by Igor van der Meulen, the Entrepreneurship manager. He made sure our project would be viable as a start-up, which ensures we might drive innovations in the synthetic biology field.
Fundraising and Finances
Iris Noordermeer, our Finance Manager, was in charge of managing our budget, approving expenses, and organizing our fundraising activities. With help from multiple team members, Iris called numerous companies to discuss sponsorship opportunities. Additionally, she managed the crowdfunding, which means she set up the landing page, crowdfunding video and had interviews with newspapers to promote it.
Lisa Kleinjan kept the overview of all our human practices interviews and made sure the acquired information was integrated well into our project. She ensured we could perfect our project by consulting experts in all different fields.
Lab & Safety
Hoda Ekhlasi was responsible for ensuring safety in our laboratory, filling out our safety form, and ordering all the needed experimental supplies.
The modelling of our project was carried out by Giovi Duivenvoorden, ensuring the model fit with our experimental work and calculated how we could reach toxin-antitoxin homeostasis with our system.
Outreach and Social Media
Sebastiaan Ketelaar, the Communication Manager, ensured we gained enough outreach with the project. Sebastiaan wrote our monthly newsletter and managed our social media marketing.
Presentations for the wide public and smaller scientific groups were given by Chanel Naar, Quint van Loosen, and Sebastiaan Ketelaar.
Programming and Statistics
The wiki programming was done by Ehsan Razaghi Siahroudi, Igor van der Meulen, Giovi Duivenvoorden and Siheng Li. Data analysis and mathematical modeling in R was performed by Siheng Li and Bas van Woudenberg.
The wiki was programmed by Ehsan Razaghi Siahroudi, Igor van der Meulen, Giovi Duivenvoorden and Siheng Li and graphically designed by Jetse van Os. All team members contributed to the written content, however, the final content was managed by Chanel Naar and Ehsan Razaghi Siahroudi.
Wiki brainstorm sessions with our supervisors were highly appreciated by the team. Additionally, their feedback on the drafts of all wiki pages was an enormous help.
|Page name||Written and designed by|
|Attributions||Chanel Naar, Lisa Kleinjan|
|Collaborations||Chanel Naar, Sebastiaan Ketelaar|
|Contribution||Ehsan Razaghi Siahroudi, Igor van der Meulen, Lisa Kleinjan|
|Description||Ehsan Razaghi Siahroudi|
|Engineering||Bas van Woudenberg|
|Entrepreneurship||Igor van der Meulen|
|Experiments||Iris Noordermeer, Siheng Li|
|Human Practices||Lisa Kleinjan|
|Implementation||Chanel Naar, Igor van der Meulen|
|Main page||Jetse van Os|
|Parts||Bas van Woudenberg|
|Proof of concept||Bas van Woudenberg|
|Public Engagement||Quint van Loosen|
|Registry||Bas van Woudenberg|
|Safety||Hoda Ekhlasi, Sebastiaan Ketelaar|
|Sponsors||Giovi Duivenvoorden, Iris Noordermeer|