Collaborations

Overview

Collaborating with other iGEM teams throughout the year afforded our team with long-lasting connections. From surveying Canadian iGEM teams’ about project achievements and their plans for Paris, to learning new docking techniques in molecular dynamics, iGEM Calgary made a significant effort to collaborate over a broad range of initiatives with teams from all over the world. We’d like to give a special thanks to Queens iGEM, IISER_Pune2 India, and the teams who participated in JulyGEM, for working with us this iGEM season!

Canada-wide Summer Newsletter

In Collaboration with Queen's iGEM

One of our teams’ goals was to foster a sense of community, promote communication, and seek out collaborative opportunities between the Canadian iGEM teams. After connecting with Queen’s University iGEM, we were inspired by the first edition of a Canadian iGEM Newsletter created by the 2017 iGEM Calgary team. We decided to create a second edition of the newsletter and create versions for the months of June, July, and August - thus, creating a Canada-wide Summer Newsletter. We hope that our newsletter was a fun way to keep each other informed about upcoming events and share about project-related progress, while also unifying our country’s team’s together. Through this newsletter we were able to increase access to synthetic biology information for the Canadian iGEM teams and bring awareness to each other’s projects prior to the Jamboree in October. Check out Queen’s Collaboration page here!

JulyGEM 2022

Our 4th Annual, International Pitching Session

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Figure 1. JulyGEM 2022 Highlights!

This year, iGEM Calgary hosted its 4th annual JulyGEM event, which was the third year that we hosted the event online. JulyGEM is an international conference where teams join together to take part in hearing from keynote speakers, practice pitching in front of experienced judges, and provide feedback to other teams about their iGEM projects. As a team dedicated to improving inter-team collaborations, creating friendships, and providing a platform to share synthetic biology knowledge with the world, we set out to invite a variety of speakers from a range of backgrounds and expertise, including:

• “How to Use Storytelling for an Effective Pitch” by Dr. Paramita Chaudhuri Basu - Innovation and Entrepreneurship Manager
• “Creative Destruction Lab: Solving Massive Challenges Using Synthetic Biology” by Kate Skotheim - Ag Stream Manager at Creative Destructive Lab
• “Brain Implants and Entrepreneurship” by Dr. Pierre Wijdenes - CEO and Co-founder of Neuraura
• “Genome Engineering: Always Pivoting” by Dr. Derrick Rancourt - Professor and Entrepreneurial Researcher
• “Speculative and Creative Design Workshop” by Michael Wahba - Game Designer and Former and iGEMer
• “Science Communication and You” by Zack Anderson - Director, Group Experiences at Telus Spark Science Center
• “Modern Genetic Therapies” by Dr. Aneal Khan - Medical Geneticist at MAGIC Clinic
• “The Startup Journey! What it looks like and how to do it” by Kevin Chen - CEO and Co-founder of Hyasynth Bio

Pitching sessions gave teams the opportunity to deliver a 5 minute, live presentation outlining their project to our judges: Patrick Wu, Dr. David Nielsen, Arren Liu, David Lloyd, Andrew Symes, Michael Wahba, and Nikhil Sonpal. Judging criteria included how the solution addresses the problem and provides value, feasibility, integration of human practices, opportunity for competitive advantage, and how wet lab and dry lab work together. Each team was able to receive feedback from our judges as well as participating iGEM teams. Check out the teams who attended!

• ICT Mumbai
• McGill
• Waterloo
• UBCO
• Lethbridge Highschool
• UBC
• Sorbonee
• Dusseldorf
• IISER Pune 2 India
• Cornell
• University of Lethbridge

After our pitching competition, we continued the fun by presenting our “Day in the Life” video series, created by our team. Check out the videos below!

Day in the Life Video Series by iGEM Calgary

Modelling Collaboration

In Collaboration with iGEM 2 IISER Pune2

During JulyGEM, our team was intrigued by the modelling work done by iGEM 2 IISER Pune2 because they used docking simulations similar to ours and had made use of Alpha Fold to predict the structures of their proteins. As these were methods we implemented or wanted to apply, we reached out to them for a collaboration opportunity that could help both teams learn from each other. Check out IISER Pune2’s Collaboration page here!

Figure 2. Members of iGEM 2 IISER Pune and iGEM Calgary

During our first meeting, we learned about each other's projects, and we found out that they were conducting molecular docking to screen for optimal antibody fragment conformations. We are using a jury of 3 docking software: HADDOCK, Rosetta and ClusPro, to dock our scFvs, the dengue antigen (E protein dimer or Domain III of E protein) and the human FcRn receptor. We analyzed and screened for the most promising candidates based on the relevant scoring function on the outputs of the docking simulation and express them in the SHuffle strain of E. coli. Their docking strategy of using different software to validate which conformation is the most promising inspired us to also adopt this strategy. However, we were limited as we only used an online docking server. After communicating our limitation with the iGEM 2 IISER Pune team, we discovered they had access to Auto Dock Vina and utilized this software to perform ligand-protein docking on protein and ligands of interest which are nisin, bacterial cellulose, and polyhydroxybutyrate (PHB). We then sent out our PDB files, and they helped us conduct docking in them. The results and their analysis can be found on our protein modeling page here.

On our end, we realized that apart from conducting docking simulations, it would also be helpful to perform molecular dynamics. This is because molecular dynamics could help them understand their structure's stability by removing any steric clashes. However, the iGEM 2 IISER Pune team had limited knowledge in terms of molecular dynamics. Hence, we had meetings with them and our advisor to walk them through the principles of molecular dynamics. We also provided resources that could help them grow in their knowledge. After proposing this idea and walking them through the very basics of molecular dynamics, they presented several ways they would implement it into their project. This included looking at our antibody's stability, verifying the action of the mutations we are making that induce pH-dependent binding to our target receptor, and seeing whether 6XHis-tags interfere with the binding affinity of our antibody or not. After performing a successful MD run of our own, they requested our script to help them guide theirs. We provided our script and they ran their simulations.

Explore how the docking results influenced our project in the Protein Modelling page

Through this collaboration, our team was able to validate our docking results by leveraging iGEM 2 IISER Pune iGEM’s access to software and understanding of the subject matter. We were also able to gain a better understanding of molecular dynamics by guiding them through the process of conducting their MD work and see the applications they implemented it for. Most importantly, we were able to form meaningful relationships with another team, all with the sole aim of solving real world problems by utilizing computational tools in synthetic biology.

Other Collabs

Bacteria Book, iGEM Map, and Cellu-minati!

With so many great initiatives held by other iGEM teams, we wanted to make sure we participated in as many as time would allow! We created a page in Queen's iGEM collaborative Bacteria Book that talks about our favourite chassis: K. xylinus. We also submittted our Cellucoat logo (and unofficial mascot "peach") to iGEM NTHU_Taiwan for their initiative "The iGEM Map", which included 31 teams from all over the world. Lastly, we connected with other iGEM teams (UiOslo and Unicamp_Brazil) who are also using bacterial cellulose in their projects this year - forming "Cellu-minati"- and shared about our experience with growing cellulose in our lab.