Team:Virginia/Collaborations
Index:
Collaborations
Modelling Collaboration with UChicago
Our modeling team orchestrated a collaboration with the University of Chicago modeling team focused on enzyme concentration optimization. Their team created an R-based software which utilizes reaction parameters from a multi-enzyme pathway to find the most efficient enzyme stoichiometry. Through many zoom meetings to share reaction parameters and debug syntax, their software demonstrated the estimated increase in yield of our system with optimized enzyme concentrations (seen below). According to their model, concentrations in our optimized system are 2.05e-07, 4.74e-05, 6.43e-05, and 7.07e-05 M which correspond to ACS, ACC, 4CL, and STS enzymes respectively. Our project allows for direct control of these enzyme ratios due to the zinc-finger domain patterns apparent in our DNA scaffolds. Therefore, we will use these findings in our future DNA scaffold assemblies to further test the efficiency of the Manifold system. This collaboration heightened our knowledge of our own models, while providing UChicago further software checks for them to determine the accuracy of their optimization models.
Fig 1. Comparative resveratrol concentrations over time between current and optimized enzyme concentration systems. This graph was developed through the enzyme concentration software generated by the University of Chicago iGEM Team. The red curve utilizes the Manifold enzyme concentrations (1:1:1:1 ratio for the 4 enzymes) for output of the resveratrol concentration over time whereas the blue curve describes the optimized enzyme concentrations (2.05e-07, 4.74e-05, 6.43e-05, and 7.07e-05 M which correspond to ACS, ACC, 4CL, and STS enzymes respectively) effect on resveratrol yield over time. Note both curves utilized the same parameters which were used in the modelling portion of our project.
iGEM Resource Page
In the age of Covid, we’ve implemented a variety of methods to maintain our team’s workflow and implement the device we've detailed, and through some extra work, we've managed to ensure communication through collaboration. For nearly all of our efforts, we’ve sought out new, digital resources that allow us to work together in real time. This work became the basis for what we call the iGEM Resource Page. After several talks with Nemanja Stijepovic and Leandros Tsiotos of the Video and Remote Technologies Committee, we created a compilation of all the relevant resources and tools iGEM teams should know about. We presented our original list in the Global Meet up, sharing the tools we had found most useful and how they allowed us to adapt to a summer spent outside the lab. Following this presentation, we distributed a survey where other iGEM teams could respond and tell us about the resources they found most useful. We have organized and outlined all the resources in one document, talking about function and accessibility,pros and cons, and similar alternatives. We hope this document proves useful to future teams as they continue to work either online or in person. You can see this document in our Contributions page, to be viewed or downloaded.
