Ichizo Kobayashi is a distinguished professor at the University of Tokyo. His primary research interest lies in restriction-modification systems in bacteria. In 1995 he showed that restriction-modification systems in bacteria are selfish, addiction modules. He has also made major contributions to the functioning of bacterial DNA repair systems. His current interest is in the evolution of restriction-modification systems. This fits very well with the interests of Aswin Seshasayee and Sandeep Krishna who have published recently on restriction-modification systems, and would like to collaborate with Prof. Kobayashi on experiments and modelling studies of the evolution of these systems. At NCBS Prof. Kobayashi would also be interested in interacting with P. Shivaprasad to develop new research projects to study the similarities and differences in epigenetics-mediated adaptive evolution in plants vs bacteria.
Prof. Jensen is a long-standing collaborator of Sandeep Krishna. During this visit they continued their collaborative work on oscillations and entrainment phenomena in biology. In particular, they kick started the theoretical work for a new collaboration with the experimental lab of Savas Tay (ETH, Zurich) studying entrainment, Arnold tongues and stochastic mode-hopping in the NF-kB system.
The purpose of this visit was to formulate an Indo-France CEFIPRA grant proposal involving the groups of Sandeep Krishna (NCBS, Bangalore), Andrew Griffiths (Prof. and Head of the Laboratoire de Biochimie at École Supérieure de Physique et de Chimie Industrielles, Paris), and Philippe Nghe (Assistant Prof. at the Laboratoire de Biochimie at École Supérieure de Physique et de Chimie Industrielles, Paris). The proposal was for a research project studying the evolution of complex auto-catalytic RNA chemistries. The project combines the theoretical skills of Sandeep Krishna with the experimental Azoarcus Ribozyme system developed in the Laboratoire de Biochimie. The grant was duly submitted, and the result is expected by Dec 2015.
Dr. Gupta is interested in information processing in biological systems. During his visit he interacted with multiple faculty on areas of common interest, particularly the applications of computer science to cellular issues.
The purpose of this visit was to continue collaboration between Sandeep Krishna group and Supreet Saini's lab on bacterial "bet-hedging", where bacteria switch stochastically between different strategies in order to minimize the risk of extinction due to a variable and uncertain environment. Supreet Saini's lab is looking at such phenomena experimentally in the context of quorum sensing in bacteria and in their response to bacteriophage attack. During Dinaker's visit he examined previous modelling work by Sandeep Krishna and recent work by Kim Sneppen (a previous Simons visitor) on the latter question, and then extended those models to make specific prediction for the experimental situations being examined in Supreet Saini's lab.
The purpose of this visit was two-fold: (i) to teach a course during the Monsoon school, (ii) to continue collaborative work with Sandeep Krishna on Bayesian inference in biological processes. Manoj has demonstrated the link between chemical networks and Bayesian posterior calculations of models consisting of combinations of Poisson processes. In collaboration with Sandeep Krishna, he's now looking at the application of these ideas to bacterial quorum sensing systems and bacteriophage decision networks.
Abhishek and Debasish, both soft matter physicist visited the Simons Centre from 7th June to 8th July, 2015. Right at the start, they introduced their research interest to the wider NCBS fraternity, in back-to-back talks on "Soft and Active Matter" (Debasish Chaudhuri) and "Dynamics of Biopolymers" (Abhishek Chaudhuri). Though they primarily interacted with Madan Rao and Vijay Krishnamurthy (ICTS-TIFR, Bangalore), they also had many intense discussions with Mukund Thattai, Sandeep Krishna, Sanjay Sane and others, and Amit Singh, Debsankar Banerjee and other PhD students. These discussions included topics such as, (i) influence of mechanical stresses at the cell surface on gene expression, (ii) transmission of information encoding the spatial organization of chromosomes across generations, (iii) role of multiplicative noise in active hydrodynamics, (iv) pattern formation in confined termites under shaking, (v) chiral symmetry breaking in active hydrodynamics, (vi) role of active mechano-chemical processes in the processing and transfer of information and distributed computing.
With Madan Rao and Vijay Krishnamurthy, they worked on how spatially varying mechanical signals could propagate from the cell surface to the nucleus by treating the cytoplasm as an active elastomer with turnover of components (an appropriate description at short time scales). The idea is that this description will naturally give rise to force-chains, which might explain the sensitivity to changes in mechanical signal applied at the cell surface. This work is still under progress and they will continue their collaboration on this and the many other ideas that came up during this visit.