Partnership with iGEM IISER Pune II

The partnership between iGEM IISER Pune II and iGEM MIT MAHE came at a rather unexpected time. We first interacted while collating on the organisational aspects of the All India iGEM Meet. Eleven Indian teams competing in iGEM 2022 attended the immersive three-day meet with activities ranging from project presentations to engrossing seminars on the various aspects of Synthetic biology.

Antibodies are magical molecules created by evolution. As a special class of proteins, they have the perfect balance of surface geometry and surface chemistry. They can target and bind to almost any other protein or biomolecule. They are also very modular. Recombinant technology has enabled us to manipulate antibody domains in a way that we can create different formats of antibodies or antibody fragments. IISER Pune II has identified the best approach to create an antibody fragment that would be an ideal Dengue therapeutic without causing antibody-dependent enhancement.

Dry Lab

We had our first interaction based on the dry lab aspects of both teams. Following this, we had regular meetings with the team based on discussion and troubleshooting. Before they could go ahead with their first simulations, we helped them navigate their approach to molecular dynamic simulations (MDS) with its specific parameters and details based on our experience and understanding of the topic.

As our dry lab work progressed, we required intricate MDSs to be run on a supercomputer. Our collaborative work was strengthened here as IISER Pune II helped us with the processes involved because our resources could not stretch to that bandwidth. To view our MDS results, check our Model page.

Bioinformatics has a plethora of different tools to help perform specific tasks. They differ in their algorithms and, thus, depend on the context of the application. As students, navigating these tools and fixing them on a particular server is intricate, given our situations. Our teams encountered situations where we needed to dock proteins, predict protein structures, and run Molecular Dynamic Simulations. There are many available tools and no clear information on which tool to use, when and where. Therefore, we decided to make handbooks on MDS and Protein Docking that covers features and use-cases of various existing Bioinformatics tools for the same, which would help narrow down and simplify the choice of these servers for anyone who wants to Dock their proteins, run MDSs and predict structures. These would greatly aid future iGEM teams who wish to accelerate their dry lab aspects and formulate a more cohesive approach to MDS and docking. The MDS handbook is attached below. To view the protein docking handbook, check our Contribution page.

Click here for more information of the MDS handbook!

Human Practices

To further our collaborative interactions with IISER Pune II, our teams organised a Webinar on Biosafety in synthetic biology. This webinar aimed to make the general audience aware of the essential Biosafety measures to be followed while working with synthetic biology in the real world.

We invited Dr Vinod Jyothikumar to deliver this presentation. He received his PhD in Pharmaceutical and Biomedical Sciences from Strathclyde University, Glasgow, UK, in 2010 and post-doctoral experience from the University of Guelph, Canada—in 2011. He has executed various safety projects within research laboratories across reputed academic institutions in Europe, the US, and industry settings. It was an extremely interactive and insightful experience. The audience learnt about biosafety practices, dual research use, basic lab protocols and their imperativeness in any workspace, and legal regulations that follow any project. The participants also had many questions and clarified their doubts and misconceptions of the topic in the question and answer session.

Furthermore, being located across from a reputed medical college — i.e., Kasturba Medical College, our team was able to connect with doctors that work in the infectious disease division in various locations, including Kerala and Telangana. We gathered data on important information that iGEM IISER Pune II required to make AbDEN a holistic solution. Through this, we could understand their project and primary stakeholders effectively. Below attached includes our findings for the team.

Wet Lab

While we did not get the chance to execute some procedures in our respective labs, our teams worked together on creating a study guide on protein expression, alternative vectors, expression systems, methods of induction and selection, and methods of pulldown. Attached below is a detailed version of the study guide.