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iGEM Ulaval

SDGs from Home

Thank Your Mentor

GMO discussion

iGEM Ulaval

Our collaboration with Team Ulaval started in September when we attended their online session on toehold switches, which made us realize that the methods they implement are quite similar to ours, allowing us to reach them out to troubleshoot our project together. For instance, we were interested in their tool holder package and downloaded it. However, we had an obstacle with the output file path as we though it needs a specific path, probably related to the NUPACK director. When we contacted them via email to help us deeming this issue. Immediately, they replied to us and addressed the problem as it was mainly in the failure of the first NUPACK run because the full genome of SARS-CoV-2 was about (~29.8 kb), which is tremendous. They informed us that they had only tested toehold with smaller genomes, like the norovirus (~7.7 kb), so they tried running everything with a smaller section of the SARS-Cov-2 genome and it successfully functioned. Moreover, they recommended running toehold with a particular gene of interest or a region including that gene of interest, one that distinguishes SARS-Cov-2 from other viruses like the spike protein, for example.

In October, we followed their suggestion and decreased the genome size; yet, we got other errors. Our technical team believed the error to be due to incompatible versions of the libraries. Accordingly, we sent them the error and requested the docker file. They told us that was their first time getting to use docker, so they ran into a bit of trouble. However, they gave us the list of libraries and the versions they are using: (biopython==1.73, numpy==1.16.4, nupack==0.1, pandas==0.24.2).

By the time they sent us their libraries, we had already tried older versions of Biopython and it effectively worked. Furthermore, on our side, we adjusted a toehold to design toehold switches suitable for expression in mammalian contexts and tweaked it to parse the input file to minimize the processing time. Thus, we reassured Ulaval that we were able to produce successful and improved candidate toehold riboswitches.

SDGs from Home

Also, our collaborations didn’t stop on the margin of our project improvement. We wanted to start an initiative that leaves an impact in the societies all over the world. Our message from this collaboration is to emphasize the fact that everyone can work on sustainable development even from their home! It’s not only limited to scientific projects, but it is also related to our daily routines. Furthermore, we want to highlight the diversity found in the iGEM teams related to their work towards the sustainable development goals. We asked each team to send us the main SDG, they are working on for their iGEM project and the different SDG, they are actually working towards in their normal lives. We started by ourselves. We are working on the SDG: global health and well-being in our project, but we are working on the life under water, life on land and responsible consumption and production SDGs in our daily routines! We were able to do that by encouraging the members of our team to use canvas bags instead of plastic bags and thermal mugs/water flasks instead of the disposable cups/water bottles for the whole duration of iGEM competition. This initiative certainly changes the perception of the multidisciplinary students we have in our team which may have not directly encountered the harmful effect of plastics on the environment in their studies. Additionally, it also leaves an impact in their families! Our work was praised, when we got canvas bags for the whole team from molecular cloud after our interview and feedback session with them. Our initiative reached out to other iGEM teams as well. For example, team TU Delft collaborated with us through backing a Locust-Brownie! In this manner, TU Delf team is working on the SDG: zero hunger in their iGEM project, and on the SDG: responsible consumption and production from their Kitchen!







Actually, our initiative went from Africa to Europe to Asia as team NCKU Tainan collaborated with us too! NCKU Tainan did our collaboration differently, they showed us that they can work on the same SDG which is life below water in their case in two distinct ways. In their iGEM project, they are addressing this SDG through SynBio solutions. In their daily routines, they are recycling the contact lens as well to contribute to the same SDG. They shared with us their photo while spreading awareness to the public about this SDG and the recycling of the contact lens to take our initiative a step further from only impacting iGEM members to impacting the whole society.

Thank Your Mentor

In addition to our SDGs from Home initiative, we started the Thank your Mentor initiative. It emerged from one of the lessons we got through the quarantine, when we all started to understand the importance of human relationships and started to have more time to be spent with our families, friends, and neighbors. These feelings heightened our gratitude for our social circles and for the daily routines we used to have. Accordingly, we encouraged the fellow iGEM teams to thank their PIs, instructors, advisors, lab managers or anyone who helped them to enhance their project in these hard times through our collaborations. We asked them to share with us any inspiring advice they got as well. Many teams were interested in our initiative. For example, team iGEM Thesaaly shared with us a photo of their wet lab team with their two advisors, Nick Ntelkis (the one with pink-orange shirt) and Marios Lange (the one with the blue shirt) who are both studying in the Department of Biochemistry and Biotechnology, University of Thessaly. They send to them a Thank you note through us saying: “Thank you for putting up with us...but we put up with you too”. They shared with us some of the repeated quotes said by their advisors as well. Thank you team iGEM Thessaly. It is a great initiative that helped us to recognize how iGEM is enhancing the personal relationships, networking and sharing experiences all over the world.



Also, team NCKU Tainan collaborated with us again for this initiative. They shared with us a photo for the whole team with their PIs. They wanted to tell them, “Thank you for your endless support and guidance to us.” We will introduce to you their PIs (from left to right in the photo) and brief captions about their research interests. First, Dr. Masayuki Hashimoto, Associate Professor - Institute of Molecular Medicine. He is a bacterial geneticist, majorly studying E. coli and B. subtilis. Second, Dr. I-Son Ng, Associate Professor - Department of Chemical Engineering. Dr. Ng is devoted to the study of synthetic biology, genetic and enzymatic engineering, biorefinery and bioremediation. Third, Dr. Han-Ching Wang, Professor - Department of Biotechnology and Bioindustry Sciences. Dr. Wang has a goal of using a science-based approach to manage and optimize aquaculture practices. Fourth, Dr. Jia-Horung Hung, Doctor - Department of Ophthalmology in NCKU Hospital. Dr. Hung Focuses on glaucoma, retinal diseases and corneal diseases. Furthermore, they shared with us an insipiring advice from Dr. I-Son Ng, that says: “This year is an exceptional year due to the COVID19 pandemic, but we are very fortunate to stay in Taiwan. I really hope you won't be too upset because we can’t go to the Giant Jamboree in Boston, USA. Remember, what you have learned and done is your treasure. So, try your best to be involved in this project wholeheartedly”. Thank you team NCKU Tainan!



Additionally, team iGEM IIT Roorkee collaborated with us to thank their mentor, Darshak Bhatt. Bhatt’s research area is studying Oncolytic viruses and Therapy resistance. His famous quote is "The most personal is the most creative." Also, they shared with us this note to show their appreciation for their mentor, “Darshak has always believed in the above-said quote himself and inspired us with the same idea. His exceptional qualities of bringing the best out of us (as a team) are just beyond any words. Darshak is an amazing mentor and a supportive person who values ongoing learning and growth of the team. He made every task and meeting an exciting and memorable experience by taking a personal interest and demonstrating a positive attitude towards the project and the team members.

With this note, we would like to thank him for the words of encouragement and guidance for all he has taught us throughout the project. His enthusiasm and willingness to share his skills, knowledge, and expertise in the field have led us to become a successful iGEM Team.”

Thank you team iGEM IIT Roorkee for participating in our collab, and for the creativity in your photo and maintaining social distancing during the pandemic.



Finally, we wanted to end this collaboration with the contribution of the only other Egyptian team AFCM. They shared with us their photo clapping for our amazing dual instructor, Dr. Hana Abd El-Zaher. Thank you, Dr. Hana, and Thank you team AFCM.

GMO discussion

As part of our awareness campaign about the GMOs, we participated in the GMO discussion held by team KSA_Korea where we discussed the different cultural effects on this controversial topic. Also, we examined the different rates of social acceptance for using the GMOs in different fields. It was an insightful and fruitful discussion.