January5
The exciting work of Mohammed Mahamdeh and Joe Howard (J.Microsc. https://doi.org/10.1111/jmi.12744) prompted me in the December break from teaching in 2018 to try and reproduce it, using the Nikon TiE inverted epifluorescence microscopy in the lab. With the able presence of a talented Masters student Yash Jawale (now PhD student in the Netherlands), we attempted to uncover its secret levers of light attentuation. After frustrating months, we had a visitor from France, Dr. Kheya Sengupta from CINAM Marseille. As an expert on IRM and RICM (a related method) she helped us achieve it- label free microscopy of the 30 nm wide single MT filaments in (IRM)! And since then we have been toying with it, getting better images with passing days. Now if only the remaining experiments would work!
March30
The use of synthetic biology in engineering biological systems has been rapidly expanding. the conference at EMBL Heidelberg from 17-20 March 2019 on “Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture” highlighted this in the context of understanding growth and developmental morphogenesis. It brought together an unusual combination of researchers ranging from:
- in vitro reconstitution of cytoskeletal networks
- giant unilammelar vesicles (GUVs) for encapsulating proteins: towards synthetic cells
- rebuilding gradients of morphogens by engineering cells
- organoid models of tissue morphogenesis
- engineering blastulas and developing embryos predictively modify developmental outcomes
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.
November27
The “post-antibiotic era” announced by the WHO, which was an update from April-2015 of an older report [1], suggests the need to understand bacteria is urgent as it ever was. We have been sailing the winds of Fleming from his 1928 discovery of Pennicillin-G from Penicillum notatum. For long chemists (led by the ‘magic bullet’ seekers) thought this to be some “biological”, “weak” and sill floundering. It took many other discoveries to demonstrate and industrialize production of antibiotics. But evolution is catching up [2]! The shocking part is not so much that it happened, but we were caught unprepared. The ups and downs in research notwithstanding, the need for research on the fundamentals is critical. One could argue for similar directed funding.
How do we know this is not some fear-mongering? Well, for one we now have a ‘bad-guy’. Strains of Klebsiella pneuomiae have been found to be resistant to all antibiotics known to humankind [3]. That is just the start. Mix it in with horizontal gene transfer and we have a real mess on our hands.
References:
[1] Anti-Microbial Resistance, World Health Organization April 2015
[2] WHO Warns Against Post-Antibiotic Era, Nature
[3] Superbugs from Wire.in
June4
Altschuler SJ, Angenent SB, Wang Y, Wu LF (2008) On the spontaneous emergence of cell polarity. Nature. 454(7206): 886-889.
The authors describe a model of spontaneous cell polarization with a positive feedback. Drawing on an evolutionary model of “stepping stone” by Kimura, the authors simulate space implicitly and attempt to show how their model can generate patterns. The supplementary material demonstrates an analytical solution to the model.
Going through the model we find certain unexplained jumps in the derivation. The simulation appears to be fine, and so consequently the main results. More on this in a while.