Post-publication review and PLOS’ experiment with the Synthetic Biology Collection

October28

An inducible luxI system (iptg) to produce the AHL above a threshold Pt. Kadam et al. (2016)

The iGEM 2015 synthetic biology contest was an important one for us. It marked our first attempt at putting together a project from IISER Pune. But beyond the novelty for us, many things were different this time around (#igem2015). First off, no preliminary or elimination rounds.

Secondly, we (yes, some self-backpatting here) organized an India Meetup in the run-up to the Jamboree. And third, and interestingly, the journal PLOS One (Public Library of Science) decided to use this as an opportunity to launch the PLOS iGEM collection, as a sort of meta-list, connected to iGEM. They decided to also go the radical way- with post-publication review. Time will tell how this latter experiment works out. And naturally our team’s efforts are there. With a lot of hard work put in by Snehal Kadam well after the contest and some griding-the-article together by mining long-forgotten (1 year ago!) protocol books, and some frantic emailing and interviewing, we managed to pull it off. You can read it here “Mycobacterium Revelio: Characterizing and Modeling Genetic Circuit Components towards a Bacterial Detection Tool”. The first 10 authors are BS-MS undergraduate students. Manasi and Neha are PhD students.

Micron-Scale Biological Devices

July25

The advent of micro-fluidics has been a boon to research in biology and medicine. Already many such devices exist in the commercial domain reducing what were a plethora of flasks, transfer processes and reactions at the macroscopic scale (even with a few micro-liters) to something that works in nano- and femto liter volumes.
We are using the relatively simpler process of soft-lithography by optimizing patterns using phot

The bacterial mother machine devlice (with high autofluorescence) and the assembly of the entire device (Manasi Gangan)

oresist that can be exposed to UV and post-baking used for building channels, flows and growth-chambers for cells.
We have reproduced the ‘mother-machine’ for bacterial cells described first by Wang et al. from Suckjoon Jun’s lab.

We are currently testing the results and developing some image analysis tools to extract meaningful numbers from the device.

For more on Biological Microfluidics, see the review by Velve-Casquillas et al. (& Phong Tran) 2010 Nano Today.