We proposed a novel logic-gate design to integrate inputs from multiple sensing systems, and determined the relevant proteins and sequences that enable such functionality. We hope this can be leveraged by future teams in other contexts where similar functionality may be helpful. This would include any situation where multiple metabolites present in varying concentrations are required to screen for a particular condition or outcome. The applications of the general logic-gate system are quite broad and can be applied to a variety of fields from environmental science to pharmacology.
We also created and added two new parts to the iGEM registry for detecting butyrate and indole. While we have been unable to validate them in the lab so far, several experiments identified in the literature support their validity. This streamlines the design process for teams who wish to work with these metabolites in the future by having all the sources and part sequences in one place with comments from us and the original designers of the systems in some cases to provide additional insight. More information can be found on our Parts page.
We also developed a procedure to determine kinetic and binding constants to describe reaction equations when modelling chemical reactions. This procedure was designed due to the lack of literature related to the hrp protein system within our system. This computational procedure can generate the binding kinetic constants of proteins based solely on their amino acid sequence, and takes advantage of the newly developed AlphaFold release, as well as various tools to run docking simulations and binding kinetics. The details for this can be found in the Model page under section 2.3.2. We hope that this pipeline can serve future iGem teams to model novel systems that lack literature for relevant kinetic constants.
Finally, we created a detailed experimental proposal for the design of a gut-on-chip, which can be used as a better setting to simulate the human gut microenvironment than standard in-vitro tests. We hope to use gut-on-chip for future iterations of the current project, and also hope that it can be used by future teams to test the effectiveness of systems that are hoping to be implemented in the human gut. The information for this can be found under the Other Drylab Projects page.