Mitra Lab - RESEARCH

Research Focus

We seek to understand how the motion of individual molecules gives rise to cellular organization.

Our lab investigates how microtubules and molecular motors organize the interior of neurons into specialized compartments. These polarized cells must precisely deliver, retain, and recycle proteins at defined boundaries, yet the principles governing this spatial organization remain poorly understood.

We approach this problem by tracking individual molecules inside living multicellular organisms. Using C. elegans sensory neurons, we directly observe how motors, cytoskeletal filaments, adaptors, and cargoes work together to build and maintain cellular compartments.

Our goal is to push single-molecule imaging into intact organisms, combining quantitative imaging, dynamic perturbations, and modelling to uncover the rules that govern intracellular transport, and how their failure leads to disease.

Technology Development

A central pillar of our lab is technological innovation.

We developed Small-Window Illumination Microscopy (SWIM), which enables long-duration, high-speed single-molecule imaging in living C. elegans neurons by restricting excitation to a defined subcellular region. SWIM allows us to follow individual protein molecules for extended periods while minimizing background and photobleaching. We are now expanding this platform to:

Multi-colour and 3D single-molecule imaging
Synthetic fluorophore labelling (Halo/SNAP dyes)
Spatially restricted bleaching and pulse–chase experiments
Genetically engineered systems to dynamically switch proteins on and off
Expansion microscopy
Quantitative modelling of intracellular transport

Our aim is to create a modular toolkit for quantitative in vivo biophysics.

Example movies of Intraflagellar transport components imaged in the cilia of PHA/PHB sensory neurons in living C. elegans worms, using SWIM.

Ciliary Compartmentalization

A major focus of our work is understanding how proteins are sorted at the base of sensory cilia.

Cilia are microtubule-based compartments that are physically separated from the cell body by a selective diffusion barrier. Their protein composition is maintained by intraflagellar transport (IFT), a highly coordinated system in which molecular motors assemble into dynamic trains that carry cargo bidirectionally along the ciliary axoneme. These trains continuously assemble, load cargo, traverse the cilium, and disassemble at its boundaries, creating a tightly regulated logistical cycle that sustains ciliary identity.

While the structural organization and dynamics of IFT within the cilium have been studied extensively, the mechanisms that regulate (i) protein entry across the ciliary gate, (ii) exit, recycling, and turnover at the ciliary base, (iii) retention versus export decisions, (iv) rewiring of transport in response to environmental changes, and (v) the breakdown of compartmentalization in ciliopathies remain poorly understood.

We will combine single-molecule imaging, dynamic perturbations, and quantitative modelling to dissect:

Entry across the ciliary gate
Exit and recycling mechanisms
Rewiring of transport in mutants and disease models

By mapping these processes at molecular resolution in living animals, we aim to uncover general principles of cellular compartmentalization.

Beyond Cilia

Cilia are one example of a specialized neuronal compartment. Similar transport-based sorting occurs at other junctions, such as, axon initial segments, synapses, and dendritic branches. We are extending our approach to these regions and, in the long term, plan to extend our approach to other model systems.

Our broader vision is to understand how cytoskeletal transport shapes cellular organization and how its disruption leads to neurological and sensory disease.