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!

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

• Check out our “OpenPositions” page- an offer for a computational project paid as Project Assistant for training in Biological Image analysis under a BigData framework. Last date for applications 30/12/2017.
  To know more about the larger context, refer to
  • Stephens et al. (2015) Big Data: Astronomical or Genomical? PLoS Biol 13(7): e1002195.
  • Orth et al. (2017) Microscopy, meet big data. Cell Systems.
• iGEM2017 team from IISER Pune organizes an IndiaMeetup and we have a special guest from Peshawar (via Skype)!
• Our study on the spatial organization of receptor dimerization dynamics predicts a differential effect of membrane heterogeneity of GPCRs and shows how one of these is likely to depend on actin-corrals. To know more read: Deshpande, S; Pawar, A; Dighe, A; Athale, C. A.; Sengupta, D. (2017) Role of Spatial Inhomogenity in GPCR Dimerisation Predicted by Receptor Association-Diffusion Models. Phys. Biol. Volume 14, Number 3
• Dr. Rahul Somavanshi from Univ. Heidelberg and Dept. of Systems & Synthetic Biology, MPI fuer Terrestrische Mikrobiologie (Terrestrial Microbiology), Marburg, Germany speaks to us on PTS system and a fascinating pairwise-FRET study.
• Work done over the last 3 years on protein membrane receptor diffusion and aggregation dynamics to fit to experimental data has been accepted for publication. In this, we show kinetic rates of protein-association in the membrane can predict whether the mobility will be affected by membrane-ordering. Using two GPCR single-molecule kinetics experiments as a baseline we demonstrate the utility of such a  kinetic model. You can read more in Deshpande et al (in press).
  
• An App called Math: A symposium bringing together snippets of research from physics, chemistry, biology, earth sciences and humanities, to highlight the role of mathematics. The biology talk- “Why we have five fingers on each hand and self organised morphogenesis” which invokes Turing patterns.
  

  Engineering and technology's report on a few approaches to experimentally test the Turing patterns in experiment and what they mean for artificial life and basic biology.

• The GatesFoundation has an international (mostly) PhD scholarship to Cambridge university. Useful for students in their final year of Masters degrees.
• Our paper on the study of the effect of growth rate on cell size population distributions is now published in Royal Society Open Science. As an experiment for me, we have also released most of our raw-data in spreadsheet format using Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.2bs69
  

  Cell length distribution of E. coli MG1655 cells from DIC images of cells in a microfluidics device

• 11-13 Feb: Andrzej Jarynowski, a researcher in mathematical epipdemiology based in Krakow, Poland visits the lab. His work is an exciting blend of econo-physics, infectious disease and complex systems.
• Shooting stars Gallery of women scientists in a Royal Society project
• 2017-Jan: At long last our work (Manasi Gangan and me) with bacterial cell sizes is accepted for publication!
• 
• 2016-12-26: Anushree’s work hits the popular press. Our work on development and testing an automated kymography tool has been accepted in PLOS ONE. And now it can also be seen in the popular press- the Pune Mirror’s reporter Priyanka Das has filed a report:  “IISER comes up with tech for data accuracy” – Pune Mirror -By Priyanka Das, Pune Mirror | Dec 26, 2016, 02.30 AM IST

• 19-12-2016: Anushree, Kunalika and Manasi’s combined efforts are published in PLOS ONE. A good combination of experiments and computation.
• 13-12-2016: The lab travels to the MMSYMP: Computational and Experimental Studies of Microtubules and Motors at IIT Bombay, Powai, Mumbai.
• 21-22 May 2016: Advances in mathematical and computational biology (AMCB) at IIT-Ropar: Instructional school organi
  

  IIT Ropar

  zed by the Mohali node of NNMCB (National Network on Mathematical and Computational Biology)- a DST initiative to enhancetraining in math-comp biology. I will be speaking. Visting ਪੰਜਾਬ ਦੇ for science- a first- IIT-Ropar, Punjab

• The iGEM (international genetically engineered machines) contest for 2016 is accepting PI registrations! Let the games begin!
• #Biophysics Week called by the Biophysical Society of USA 7-11 March! And some amazing biophysics in the dispersal of fern spores, providing an understanding and inspiration for bio-mimetics.
  

  A report from the Royal Society Interface 2016 by Llorens et al.

• Reproducibility of measurements in synthetic biology- the 2014-15 iGEM InterLab study involved measurements of fluorescence from promoters distributed to multiple labs have been collated and published in PlosOne. The results suggest measurement methodology is a bigger cause of variation between results from lab-to-lab as compared to the construct themselves. And the IISER Pune team is part of the consortium acknowledged in the paper!
• Summer-Internship with the most exciting thing in neurobiology DIY since Luigi Galvani’s frog. http://blog.backyardbrains.com/
  

  Cockroach circuit

• The global availability of scientists and engineers from the World Economic Forum and plotted using Google’s DataViewer
• 27-30 Dec 2015: the National Meeting on Mathematical and Computational Biology organized by the Pune node.
• 2015 nobel prize for medicine and physiology- to some

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.

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

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.