The genetic information encoded in DNA is read off in living cells through the processes of 'transcription' and 'translation.' The gene produces mRNA molecules (transcription), and mRNAs make proteins (translation) using other macromolecules' help. One fact of life is that these molecular processes are 'noisy.' There are cell-to-cell variations in the mRNA and protein copy numbers even when cells are genetically identical. This noise arguably is a source of 'phenotypic diversity'. We are interested in how molecular regulation affects gene expression noise.
Previously we investigated how molecular competition for transcription factors affects gene expression noise. We are now looking at post-transcriptional regulation of the gene expression by micro-RNAs. Micro-RNAs are small non-coding RNAs that bind to large mRNA molecules and inhibit translation. We are developing stochastic models for micro-RNA mediated negative feedback loops.
Theoretical & Physical Biology Group
Population dynamics of interacting microbes
In nature, thousands of bacteria exist together with rich ecological interactions like predator-prey relationships, competition for limited resources, and mutualism. Examples include the microbiome in our guts, biofilms growing on our teeth, etc. In a collaborative project with the 'host-pathogen' lab at IISER-K, we have modeled the temporal evolution of bacterial predator-prey populations, where predators target other bacteria through specialized molecular nano-machines. Previously, we also explored the consequences of processes like mutation and horizontal gene transfer on the population number fluctuations in microbial ecologies. Currently, by combining theory and experiments, we are exploring how antimicrobial resistance emerges in bacterial populations mediated by plasmids.
Main papers on this topic
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The cost of bacterial predation via Type VI secretion system leads to predator extinction under environmental stress, S Gupta, S Ray, A Khan, A China, D Das*, and A I Mallick*, iScience 24 (12), 103507, 2021.
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Giant number fluctuations in microbial ecologies, D Das, D Das, A Prasad, J. theor. bio. 308, 2012.