Laboratory of Intracellular Dynamics

Focus

Our lab studies how the microtubule-based cytoskeleton organizes the interior of cells into specialized compartments. This spatial organization — or compartmentalization — is a hallmark of eukaryotic life, allowing cells to coordinate complex biochemical processes efficiently. We are particularly interested in how microtubules and molecular motors work together to direct the precise movement of proteins and organelles inside neurons.

Approach

We develop and utilize experimental tools, combing advanced single-molecule imaging with precise spatial–temporal manipulation, quantitative analysis, and numerical modelling to visualize molecular dynamics inside living cells. Using C. elegans sensory neurons as our model system, we directly observe how microtubule dynamics, motor proteins, MAPs and cargo adaptors work together to build and maintain neuronal and ciliary compartments.

Ciliary Compartmentalization

A major focus of our work is understanding the mechanisms of intracellular dynamics that define and maintain the boundaries of the ciliary compartment — how proteins enter, move within, and are recycled from cilia. Cilia are tiny but highly specialized structures that serve as sensory and signaling hubs. Defects in their organization lead to a range of disorders known as ciliopathies, making them a powerful system to study how compartmentalization fails in disease.

Vision

By revealing how cytoskeletal transport shapes cellular organization, we aim to uncover general principles that explain how structure/function emerges from molecular motion — and how its disruption leads to sensory and neurological dysfunctions.

We are hiring

We are always looking for motivated postdocs and students (PhD, master, bachelor) to join our group. Please contact Aniruddha directly with your enquiries.

2025

• Mitra, A. †, Gioukakis, E., Mul, W., Peterman, E.J.G. †, Delivery of intraflagellar transport proteins to the ciliary base and assembly into trains. Science Advances (2025); doi: 10.1126/sciadv.adr1716
• Mul, W., Mitra, A., Prevo, B., Peterman, E.J.G., DYF-5 regulates intraflagellar transport by affecting train turnaround. Molecular Biology of the Cell (2025). doi: 10.1091/mbc.E24-08-0378

2024

• Mitra, A., Loseva, E., Peterman, E.J.G., IFT cargo and motors associate sequentially with IFT trains to enter cilia. Nature Communications (2024); doi: 10.1038/s41467-024-47807-2
• Meiβner, L., Schüring, I., Mitra, A., Diez, S., Human kinesin-5 KIF11 drives the helical motion of anti-parallel and parallel microtubules around each other. The EMBO Journal (2024); doi: 10.1038/s44318-024-00048-x

2023

• Mitra, A.*, Loseva, E.*, Haasnoot, G. H., Peterman, E.J.G., A small excitation window allows long-duration single-molecule imaging, with reduced background autofluorescence, in C. elegans neurons. Optics Communications (2023); doi: 10.1016/j.optcom.2023.129700
• Loseva, E., van Krugten, J., Mitra, A., Peterman, E.J.G., Single-molecule fluorescence microscopy in sensory cilia of living Caenorhabditis elegans. Springer’s Protocols, Single Molecule Analysis: Methods and Protocols (2023); doi: 10.1007/978-1-0716-3377-9_7

2022

• Mul, W.*, Mitra, A.* †, Peterman, E.J.G. †, Mechanisms of Regulation in Intraflagellar Transport Cells (2022); doi: 10.3390/cells11172737
• Mitra, A., Peterman, E.J.G., Intraflagellar transport: Derailing causes turnarounds. Current Biology (2022); doi: 10.1016/j.cub.2022.07.061

2020

• Mitra, A., Meiβner, L., Gandhimathi, R., Ruhnow, F., Renger, R., Diez, S., The kinesin-14, Ncd, drives right-handed, helical motion of antiparallel microtubules around each other. Nature Communications (2020); doi: 10.1038/s41467-020-16328-z
• Mitra, A., Peterman, E.J.G., Motor Proteins: It Runs in the Family, but at Different Speeds. Current Biology (2020); doi: 10.1016/j.cub.2020.02.005

2019

• Mitra, A.*, Sune, M.*, Diez, S., Sancho, J.M., Oriola, D., Casademunt, J., A Brownian ratchet model explains the biased sidestepping movement of single-headed kinesin-3 KIF1A. Biophysical Journal (2019); doi: 10.1016/j.bpj.2019.05.011

2018

• Mitra, A., Ruhnow, F., Girardo, S., Diez, S., Directionally biased sidestepping of Kip3/kinesin-8 is regulated by ATP waiting time and motor-microtubule interaction strength. Proceedings of the National Academy of Sciences (2018); doi: 10.1073/pnas.1801820115
• Rank, M.*, Mitra, A.*, Reese, L., Diez, S., Frey, E., Limited resources induce bistability in microtubule length regulation. Physics Review Letters (2018); doi: 10.1103/PhysRevLett.120.148101
• Bugiel, M., Mitra, A., Girardo, S., Diez, S., Schäffer, E., Measuring microtubule supertwist and lattice defects by 3D-Force-Clamp tracking of single kinesin-1 motors. Nanoletters (2018); doi: 10.1021/acs.nanolett.7b04971

Older

• Braun, M., Lansky, Z., Szuba, A., Schwarz, F., Mitra, A., Gao, M., Ludecke, A., tenWolde, P.R., Diez, S., Changes in microtubule overlap length regulate kinesin-14-driven microtubule sliding. Nature Chemical Biology (2017); doi: 10.1038/nchembio.2495
• Mitra, A., Ruhnow, F., Nitzsche, B., Diez, S., Impact-free measurement of microtubule rotations on kinesin and cytoplasmic-dynein coated surfaces. PLoS One (2015); doi: 10.1371/journal.pone.0136920
• Bormuth, V., Nitzsche, B., Ruhnow, F., Mitra, A., Storch, M., Rammner, B., Howard, J., Diez, S., The Highly Processive Kinesin-8, Kip3, switches microtubule protofilaments with a bias toward the left. Biophysical Journal (2021); doi: 10.1016/j.bpj.2012.05.024

CAS: Lumina quaeruntur LQ200972601, A. Mitra: Ciliary compartmentalization: a dynamic single-molecule view, 2026 - 2030

GAČR (Czech Science Foundation): Junior STAR: 26-22371M, A. Mitra: Molecular mechanisms of protein sorting in sensory cilia, 2026 - 2030