Team:Stanford/Contribution
Contributions: Summary
Contributions: Optimizing Parts and Software for B. subtilis
The Stanford 2020 iGEM team has left several useful contributions for future iGEM teams. We did this in two main ways, through contributions to the Parts Registry and improvements on Toehold Design software. Our contributions in both of these areas can be united under a common theme, which is that we uploaded and designed parts and software to be optimized for use in and/or for B. subtilis instead of what they were intended to be optimized for - often E. coli. These contributions are detailed in depth on their own separate pages, linked below.
1. Contributions to Registry of Standard Biological Parts
The first contribution was in creating and/or documenting nine parts on the Parts Registry. Many parts in the Registry are compatible with, but not optimized for, Bacillus subtilis. We created a variety of parts and tools that are specially designed and optimized for use in B. subtilis, such as mCherry BSU and YFP BSU.
Four of these parts were new contributions; constructs or systems that we had designed: Toehold for Detection of KanR in B. subtilis, Recombination Based Detection System for B. Subtilis (ManP), Homology arms for KanR integration into B. subtilis, and Signal Amplifier based on B. subtilis Quorum Sensing Molecule ComX.
Five of these parts were not created by us, but were added to the Parts Registry so that future teams that also choose to work with B. subtilis could benefit from them: mCherry BSU plasmid, mCherry BSU, ManP cassette (for expression in B. subtilis), pVeg-YFP plasmid (for B. subtilis), and YFP CDS (for B. subtilis).
<groupparts>iGEM20 Stanford</groupparts>
2. Improvements on Toehold Design Software
The second contribution was in improving upon Toehold Design software previously developed by another iGEM team: EPFL iGEM 2017. Their toehold design software was incredibly useful to us as we designed our toehold sequences, however through using the software we found problems that we could improve upon, and set up to so ourselves. In doing so, we created an updated version of their software that would have better fit our needs, particulary when it came to designing for B. subtilis. For example, we added options that allowed greater flexibility in choosing the Ribosome Binding Site, because the default RBS was not compatible with Bacillus subtilis. Read for in-depth and see a side by side comparison on our Software page.
