Introduction
Our team sought out and developed a season-long partnership with Team Vellore Institute of Technology (VIT). Our shared interest in combating antibiotic resistance led to natural collaborations on the following shared objectives: lab work, modeling, and human practices. We hosted several working meetings over Zoom and frequently exchanged group-chat messages.
Lab Work
Our collaboration on wet lab work addressed shortcomings for both of our teams in critical project steps. While online protocols and surface level advice can provide steps for a procedure, they often fail to incorporate all of the information needed to adapt and execute a protocol. For instance, an online protocol for transformation does not explain the steps that are the most likely to cause issues in the overall outcome.
This knowledge is developed through experience with a technique, and our teams were able to share such knowledge with one another. When we mentioned that none of our members or advisors had experience with ammonium sulfate precipitation, VIT generously shared their team’s protocol and experience in the technique with us, which shaped our successful use of this technique in our project. They stressed that it was the percent saturation of ammonium sulfate rather than the weight of ammonium sulfate added that was important to accurate procedure. VIT also mentioned that the weight of ammonium sulfate needed to achieve saturation varied by solution temperature. This advice informed our precision of implementation of the protocol and contributed to our successful experimentation.
Likewise, VIT mentioned their challenges with transformation, and we offered our knowledge and protocol with them. This included specific lessons we had acquired from performing the experiment such as the importance of carefully handling competent cells and the level of precision in temperature and time necessary in the critical heat-shock step.
Modeling
For the modeling objective, MSBT provided starter code to VIT and our teams hosted multiple meetups to discuss modeling strategy. This starter code consisted of a set of differential equations simulating protein expression kinetics implemented in MATLAB. Our meetings focused on how best to mathematically model protein expression over time, an aim shared by both of our teams. MSBT sought to model encapsulin protein expression, and VIT sought to model the enzyme laccase as it degraded tetracycline antibiotics. During our initial meeting, we focused on explaining the basics of our starter code. From there, we took some time to discuss how to implement these models into differential equations and how to modify mass-action kinetics to incorporate the protein synthesis cycle. In our later meetings, we focused on helping troubleshoot the system of equations that VIT was working with. They specifically sought to model the inducing of the lac operon in their expression system, and we worked together on how to properly implement the induced/uninduced states of the operon into their differential equations.
Human Practices
As part of our partnership with VIT, both teams jointly created interview questions to ask experts on the subject of antimicrobial resistance (AMR), a topic relevant to both our teams. We then began the process of interviewing experts to create a joint YouTube playlist. We discussed how the researchers became interested in AMR, what innovative work they do to fight AMR, current research being done in the field, as well as what the general public should know in order to reduce their contribution to AMR. These questions are important to both our projects, and provide critical information about the relevant applications of both projects to inform future experimental questions. For example, one concern about increasing AMR is when a patient fails to complete their full prescription of antibiotics so that the remaining alive bacteria become resistant to the antibiotic and mutate. A future study that is inspired by this problem would be to expose bacteria to an antimicrobial peptide (AMP) to which they are susceptible, but not to kill all of the bacteria in culture. Then, analyze if an encapsulin could improve the cytotoxicity of the AMP in the remaining bacteria which have been exposed to the AMP in culture.