Optizyme 2020

Collaborations * Education

Collaboration: Applying Optizyme and Branching Out

After completing the design of Optizyme, we began reaching out to other iGEM teams to meet and discuss possible overlap that could take place between our projects. The product of our efforts were two different collaborations in two different areas of our project.

We were able to work with the iGEM team from the University of Virginia (UVA) and help them optimize the biochemical activity of their project, which was a resveratrol biosynthesis pathway. Interestingly enough, UVA’s modelling team (headed by Colin Haws), had already constructed a Michaelis-Menten model in Matlab to explore the activity of their system. We were able to translate their model into R and run it through Optizyme, and provided UVA with the optimal concentration of enzymes to use in their system. The resveratrol synthesis rate of the non-optimized and optimized system is compared in the graph below.

We were also able to collaborate with Alma College (Alma) on our efforts in science communication. Alma’s dedication to outreach in synthetic biology led them to plan and host a series of podcasts, which discussed not only the broad implications of synthetic biology, but also how synthetic biology could serve as an effective vehicle to solving important environmental issues. Specifically, Alma worked towards a biosensor that could detect DDT in soil, which is a problem that specifically plagues their hometown because of a factory mishap that occurred decades ago. Since the PET degradation portion of our project also aims to remediate an environmental issue, we were able to have a thoughtful discussion with Alma as guests on their podcast. We hope that our discussion about environmental issues as well as how synthetic biology might serve to remediate them will educate listeners on the dangers of carelessly treating our planet.

The other teams that we were lucky enough to meet with include: Kings College London, ULaval, University of Ulm, DeNovoCastrians, and St. Andrews.

UChicago GeneHackers

Computationally optimizing biosynthetic pathways