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Team:IIT Roorkee/Engineering

<!DOCTYPE html> PYOMANCER

Description

To realise our iGEM Project we followed a middle out approach to the achieve goal of creating biological systems that can be used to solve a problem at hand. Maintaining proper engineering principles at different stages of project planning provided us clarity on our work and it's impact.



Research

We started brainstorming on wide range of topics to allow good breadth of research and ideas. In the process, we came across an interesting molecule, Pyocin, which possessed unique properties and distinctive features from the current solutions like bacteriophages, antibiotics etc. Next, we followed an extensive literature review for Pyocins, thoroughly understanding their evolutionary relationships, mechanisms, and positioning in the environment. Our further research was guided by the idea to re-apply or tweak these features in a more directed & controlled manner.




Rational Design

Based on the scientific literature analysis and on-ground exploration of the problem of antibiotic resistance, we funnelled down to 3 key questions that determined our further course of action further:

  1. Selecting the Pyocin
  2. Selecting the Bacteriophage
  3. Approach for Fusion
Refer to our Design Page that elucidates the principles adopted and techniques used to design the complete system for the production of chimeric pyocins.




Experimental Design

Without access to lab and testing facilities, it was challenging to interpret the functioning of the antimicrobial complexes our project is based on. We focussed on laying out a robust design of the experiments that will indicate the success & failure of our systems once we get access to the lab. The experiments are designed to test all our hypotheses and assumptions and provide meaningful data that will be utilised in project phase II. Refer to our Experiments Page for more details




In-Silico Testing

Bioinformatics analysis and protein modelling allowed us to make calculated predictions and formulate a primary proof of concept. We followed a three-pronged approach to develop the best model of the fusion protein, Seekercin, and results from biophysical testing improved our understanding of our fusion protein structure. Refer to Modelling and Results for more details.




Community Feedback

We continued to reach out to the stakeholders and experts in the field that helped us in aligning and realigned our project goals and focus areas. While we started with the global problem of AMR, our interviews and research directed our objectives towards Hospital Acquired Infections. We penetrated through multiple layers and targeted one specific species, A. baumannii. This allowed us to have a well thought out solution, which now can be replicated to other areas by future iGEM Teams.




Making Useful Tools

While researching, designing and implementing various techniques to curate our project, we decided to standardize and automate the process that will make it easier for other teams to build further on this concept. This will provide them with space to explore other areas of analysis and applications, which was not possible within the frame of our work. Refer to our Software page for further details. We intend to provide this modular system to the students and researchers so that it can be improved, and collaboratively reach a higher impact level. The lack of therapeutic interventions for handling resistant species is a grave concern, and through this work, we aim to popularise a new way of antimicrobials.