Contributions

Wet Lab

• We characterized the expression of the native nirBD operon in Pseudomonas putida KT2440.
• We contributed nirBD to the iGEM registry, along with other nitrite reductase circuits for conversion of nitrate to ammonium.
• For our project, this is largely in an agricultural context to reduce nitrate leaching while increasing fertilizer efficiency.
• We are designing a bioreactor to treat water laced with nitrates and modulate ammonium and nitrate levels as per requirement.

Dry Lab

Model

• We modelled nitrate to ammonium conversion and iteratively improved the model. Results predict decreased leaching rates and increased ammonium availability.
• After validation with wet lab data, the model can be adapted to different exudate and crop systems.

Machine Learning

• We used ML to predict ammonium concentration changes with and without our engineered bacterium.

Improvised GenBank

• We built an interface - GenBank. It includes a search feature and plasmid visualisation tool not available on GenBank.

AlphaFold

• We used AlphaFold to model protein variants and guide wet lab workflow.

Human Practices

Spiderweb: A Unique HP Methodology

• We used a spiderweb methodology to speak with stakeholders. That is, rather than contacting potential stakeholders individually, we requested everyone we spoke to to provide relevant contacts based on the questions we had. This opened a lot of doors and helped us answer specific questions and gain a deeper understanding of the problems.
• The best evidence of the utility of this approach was when stakeholders whose domains were far apart in principle independently gave us the same reference. We were able to speak to experts with relevant experience and get answers to specific questions.
• One of the biggest challenges in HP was getting started. It is very difficult to predict how useful an interaction will be before having it, especially when one has surface-level knowledge about a field. The spiderweb method allowed us to expedite our learning curve by relying on the experts to suggest relevant stakeholders. We strongly believe this methodology can be replicated by future iGEM teams to make their human practices efforts more comprehensive and holistic.

Iterative Improvement in Project Design

• We documented our efforts towards sustainable development impact thoroughly. We tried to iteratively improve our project based on suggestions wherever required, and justified certain steps based on the perspectives we had gathered by speaking to other stakeholders. This iterative method is essential to staying on track and ensuring the problem stays rooted in the real world.

A Holistic Approach

• We realized that, despite eventually competing for a few special awards related to human practices, all the components are essential to building a holistic project. With this in mind, we also made it a point to look into the entrepreneurial aspect by considering various models to upscale our project. Similarly, despite education not being one of our medal criteria, we sought to involve our juniors, the iGEMers of the future, so that they too could learn from our experiences. While attempting to excel in the medal criteria we have chosen, our effort was always to engage in human practices due to their inherent value to scientific work, rather than their utility in securing medals. While we could have done much more to realise a truly holistic project, we believe iGEM teams should adopt this philosophy towards human practices efforts, realizing their innate value to research rather than just boxes to check off.

Genetically Modified Organisms

GMO Policy cum Handbook