Shankar Mukherji, PhD

Assistant Professor
Cell Biology and Physiology

Computational and Systems Biology Program


  • Systems and synthetic cell biology: quantitative analysis of cellular organization

Research Abstract:

Arguably the grandest goal in cellular biophysics is the uncovering of design principles that govern all aspects of cellular function. Efforts in systems and synthetic cell biology have focused mainly on the design principles of gene expression and signaling systems. A quantitative understanding of eukaryotic cellular organization in space, however, would afford biophysicists and bioengineers with a powerful opportunity to predict how the physical architecture of the cell constrains and regulates fundamental life processes. To unleash this potential, it is imperative to understand one of the defining features of the eukaryotic cell: its organization into spatial compartments known as organelles. Coordinating organelle abundance and activity with developmental and environmental cues is one of the chief ways the cell can match its biochemical capabilities with its physiological demands. How does the cell orchestrate flows of matter and energy to produce exquisitely defined organelles at the nanometer and femtoliter scales of a cell? Can we engineer the decision-making processes in the cell to control organelle copy number, size, and composition in vivo and can this allow us to rationally alter cellular metabolism and signaling toward desired goals?

In our group, we aim to use a combination of theory and experiment to uncover the design principles that control:

1. how the cell regulates organelle biogenesis
2. how, in turn, organelles communicate with the rest of the cell to regulate cellular physiology

Selected Publications:

Amiri KP, Kalish A, Mukherji S (2022). Robustness and universality in organelle size control. Physical Review Letters (in press).

Grosswendt S, Kretzmer H, Smith ZD, Kumar AS, Hetzel S, Wittler L, Klages S, Timmermann B, Mukherji S, Meissner A (2020). Epigenetic regulator function through mouse gastrulation. Nature 584(7819):102-108

Mukherji S, O’Shea EK (2014). Mechanisms of organelle biogenesis govern stochastic fluctuations in organelle abundance. eLife 3, e02678

Teng SW, Mukherji S, Moffitt JR, de Buyl S, O’Shea EK (2013). Robust circadian oscillations in growing cyanobacteria require transcriptional feedback. Science 340, 737-740.

Mukherji S, Ebert MS, Zheng G, Tsang JS, Sharp PA, van Oudenaarden A (2011). MicroRNAs can generate thresholds in target gene expression. Nature Genetics 43(9), 854-859.

Mukherji S, van Oudenaarden A (2009). Synthetic biology: understanding biological design from synthetic circuits. Nature Reviews Genetics 10, 859-871.

Last Updated: 11/7/2022 11:17:38 AM

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