1. Chlamydomonas cell physiology & metabolism: We have shown that single celled organism Chlamydomonas reinhardtii exhibits circadian rhythmic pattern of UV-sensitivity. These cells also exhibit flagellar resorption/breakage following specific intracellular chemical cues. Chlamydomonas reinhardtii is a very dynamic organism with respect to the metabolism and metabolic compartments it harbors. In-cell metabolic changes of C. reinhardtii during mixotrophic, heterotrophic and UV/nutritionally stressed stationary phase cultures were followed by monitoring [1, 2-13C]-labelled acetate assimilation and transition over a period of eight days. While bicarbonate was the predominant metabolite observed both in light and dark phases of growth, dihydroxyacetone phosphate (DHAP) was observed only during the dark phase of growth, reflecting a differential metabolic flux in growth. When the cells were incubated in light or dark for upto eight days and monitored at intervals of about 48 hours, further remodeling in metabolism took place where in bicarbonate and DHAP were routed towards lipogenic pathway leading to lipid body production containing triacylglycerol (TAG).
2. Mammalian cell chromosome dynamics: We have observed that gene-rich chromosomes exhibit changes in their territory locations following DNA damage & response. These localization changes are linked with DNA repair. Damaged chromosome containing cells get arrested in cell cycle, but exhibit chromosome relocalizations, both of which are reversed following damage repair. We are currently investigating the mechanistic basis of these events.
3. Computational Biology of protein active site prediction/engineering/evolution: We have developed computational tools to uncover protein active site predictions, their promiscuity levels and evolutionary connectivities. We had initiated a bioinfomatic analyses to map the active sites in proteins for which a Catalytic Active Site Prediction (CLASP) tool was developed. The congruent matches of active site residues were scored by CLASP. CLASP enabled us predict several promiscuous activities in known enzymes, which we tested. Such tests validated the predictive power of CLASP. We also quantified Promiscuity Indices of active site residues computationally by designing “Promiscuity Indices Estimator (PROMISE)”. Specific residue characteristics are delineated that form the basis of high promiscuity at certain active sites. We are now attempting to model a rational design flow based on PROMISE to choose the best protein active site which when subjected to minimal mutations will mirror the scaffold of a desired enzyme function.
4. Soft electrons (10-20eV) attach and transform biomolecules: We have uncovered DNA strand breakages by the interaction of soft electrons with DNA. Selective loss of “heme prosthetic groups” has been observed in heme-proteins due to interactions with soft electrons. We are currently dissecting the underlying chemical biology mechanisms of the same.
Our special attributes:
I believe that I have been an unconventional researcher, in being able to “dabble” with several research areas. In each of these efforts, we have been able achieve some measure of success as well as expertise. This approach has attracted researchers from varied background to my group. Besides, I also productively cross-talk with colleagues from Physics as well as Chemistry disciplines at TIFR. Such a cross-talk has not only been fun, but also very educative in being able to address a few important problems in Biology. We largely guided by the curiosity that various facets/scales of Biology evoke in us.
JC Bose Fellow