Membrane trafficking
Quantitative studies of clathrin-mediated endocytosis and intracellular dynamics.
How living cells sense, move, and internalize
Welcome to the Intracellular Dynamics Laboratory at The Ohio State University.
We study how live cells interact with their environment by developing and using advanced live-cell imaging techniques. These tools allow us to visualize intracellular events in real time with high spatial and temporal detail.
Our research focuses on cellular processes such as endocytosis, signaling, migration, senescence, and fibrosis. We combine biophysics, cell biology, developmental biology, and quantitative microscopy to understand how membrane trafficking and mechanics shape cell behavior.
We are always interested in highly motivated postdoctoral scholars, graduate students, and undergraduate students.
Highlights
Selected visual highlights from the lab's work in endocytosis, mechanobiology, and imaging innovation.
Mechanobiology and disease
How cell mechanics influence signaling, apoptosis, and cancer-related phenotypes.
Imaging innovation
Instrumentation and computational methods for super-resolution and live-cell imaging.
Clathrin coat structure
Studying how coated pits and plaques form, curve, and internalize.
Computational microscopy
Image analysis pipelines that reveal dynamic intracellular organization.
Collaborative lab culture
An interdisciplinary group at the interface of physics and cell biology.
Members
Principal Investigator
B.Sc. Bilkent University, Physics, 2002
Ph.D. University of Illinois at Urbana-Champaign, Biophysics and Computational Biology, 2007
Postdoctoral Training: Harvard Medical School, Immune Disease Institute, 2008-2012
Graduate Students
Emily Chan
Tianyao Wu
Cris Thompson
Valeria Arteaga Muniz
Aritra Mondal
Undergraduate Students
Hermes Hermes
Arvin Alam
Henry Jiang
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Hirak Basu
Umida Djakbarova, Ph.D.
Marlin Keller
Caleb Smith
Connor Luellen
Yasaman Madraki
Ata Akatay
Jama Hersi
Lauren Riede
Hoda Akl, M.Sc.
Nathan Willy, Ph.D.
Salih Silahli, Ph.D.
Scott Huber, Ph.D.
Joshua P. Ferguson, Ph.D.
Ali Adali, Ph.D.
Farah Hasan
Spencer P. Heidotting
Matthew Webber
Daniel Hoying
Esra Aygun
Sevde Goker
Tugba Atabey
Vannimul Hem
Research
We aim to understand what happens when cells physically interact with their environment, specifically how their eating habits, or endocytosis, are influenced and how this impacts cellular functions. We are also interested in uncovering the mechanical properties of cells and predicting their next moves, whether they divide, migrate, or self-destruct, by analyzing their eating patterns.
Clathrin-mediated endocytosis (CME) is the primary mechanism by which membrane lipids and proteins are internalized from the cell surface. Over the years, various biophysical and biochemical methods have been used to study the structural and dynamic properties of endocytic clathrin coats. However, fundamental aspects of CME remain debated because the field has lacked experimental approaches that directly link ultrastructural and dynamic properties.
To address this, we develop innovative experimental and analytical techniques to study the structure and dynamics of clathrin-coated structures both in cultured cells and in tissues of multicellular organisms.
The dynamics and structures of endocytic clathrin coats vary remarkably, not just across different cell types, but even within the same culture or on different regions of a single cell. We have shown that this spatiotemporal heterogeneity in CME dynamics becomes particularly pronounced during cell division, migration, and spreading.
Changes in CME rates contribute to increased proliferation, migration, and metastasis of cancer cells. However, the mechanisms driving this heterogeneity remain unclear.
We focus on the clathrin adaptors AP2, FCHo, and CALM to test hypotheses about how membrane tension and cellular state regulate endocytosis. Our goals include:
- determining recruitment dynamics and stoichiometric ratios of adaptors to clathrin coats under different membrane tension levels,
- uncovering distinct roles of curvature-generating clathrin adaptors in maintaining CME under varying tension conditions,
- understanding how spatiotemporal CME heterogeneity enables migration, spreading, and division.
Clathrin triskelions can assemble into membrane-bound coats that form polyhedral cages and lattices in an almost limitless number of geometries. Regardless of shape or size, endocytic vesicle formation requires curvature generation throughout the lifespan of clathrin coats. However, when and how this curvature develops remains an open question.
Electron microscopy provides high-resolution snapshots of clathrin-coated structures at different curvature stages, but these images lack a temporal dimension. To address this, we use super-resolution fluorescence approaches to study curvature formation in different classes of clathrin-coated structures in live cells and tissues.
Software
TraCKer
TraCKer is a simple but fast two-dimensional particle tracking program. It uses a threshold determined over a Mexican hat filtered image for detection of fluorescent spots. Detected maxima are then connected in time by linking mutually nearest neighbors.
The required input is the path to the desired movie as a two-dimensional multipage TIFF. The output is saved as a MAT file containing tracked positions and intensities.
Slope Finder
Slope Finder determines clathrin coat growth-rate distributions from intensity traces. It takes the TraCKer intensity output, the movie frame rate, and a global background value for the movie corresponding to a signal with SNR = 1.
The output is a cell array of normalized slope values. Since endpoints are padded with zeros, those zeros should be excluded when forming a proper slope histogram.
Trace Library
createTraceLibrary groups clathrin coat intensity traces into clusters that share similar trace lengths and intensity profiles. Similarity is judged using trace_dist, which generates a distance metric between traces.
Each cluster has an average intensity trace and an associated growth-rate histogram. The cluster can then serve as a library for future comparisons using libraryLookup.
Publications
- Spatial Regulation of Endocytosis and Adhesion Formation Governs Breast Cancer Cell Migration Under Confinement
- Single-image Inference of Clathrin-mediated Endocytosis Dynamics via Deep Learning
- Spatial Regulation of Endocytosis and Adhesion Formation Governs Breast Cancer Cell Migration Under Confinement
- Approaching Maximum Resolution In Structured Illumination Microscopy Via Accurate Noise Modeling
- Targeting Endocytosis to Sensitize Cancer Cells to Programmed Cell Death
- Mechano-inhibition of endocytosis sensitizes cancer cells to Fas-induced Apoptosis
- Endocytosis at Extremes: Formation and Internalization of Giant Clathrin-1 coated Pits Under Elevated Membrane Tension
News & Pictures
2025
Valeria Arteaga-Muniz received the Molecular Biophysics Training Program best oral presentation award. Congratulations Valeria.
Emily Chan received the Biophysics Graduate Program best oral presentation award. Congratulations Emily.
Approaching Maximum Resolution in Structured Illumination Microscopy Via Accurate Noise Modeling is now accepted for publication by NPJ Imaging.
2024
Mechano-inhibition of Endocytosis Sensitizes Cancer Cells to Fas-induced Apoptosis is now accepted for publication in Cell Death and Disease.
Targeting endocytosis to sensitize cancer cells to programmed cell death is now accepted for publication in Biochemical Society Transactions.
2023
Umida Djakbarova has been awarded a Pelotonia Scholars Symposium Award. Congratulations Umida.
Cris Thompson has been awarded a National Society of Black Physicists (NSBP) best poster award. Congratulations Cris.
2022
Emily Chan has been awarded a Biophysical Society Travel Award. Congratulations Emily.
We have raised $1,900 for Pelotonia. Good job team.
Endocytosis at Extremes: Formation and Internalization of Giant Clathrin-coated Pits Under Elevated Membrane Tension is now accepted for publication by Frontiers Molecular Biosciences.
Our Dual-view Inverted Selective Plane Illumination Microscope (diSPIM) is up and running.
Emily Chan has been awarded a Pelotonia Doctoral Fellowship. Congratulations Emily.
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2021
De novo Endocytic Clathrin Coats Develop Curvature at Early Stages of Their Formation is now accepted for publication by Developmental Cell.
Farewell lunch for Connor. We wish him all the best at UC Berkeley.
We have raised $2,800 for Pelotonia. Good job team.
CALM supports clathrin-coated vesicle completion upon membrane tension increase is published in Proceedings of the National Academy of Sciences.
Dynamic interplay between cell membrane tension and clathrin-mediated endocytosis is published in Biology of the Cell.
2020
Emily is a Molecular Biophysics Training Program trainee now. Congratulations Emily.
2019
Caught by a pleasant surprise.
Dr. Umida Djakbarova has been awarded a Pelotonia Postdoctoral Fellowship. Congratulations Umida.
Deep learning enables cross-modality super-resolution in fluorescence microscopy is published in Nature Methods.
Scott has defended his dissertation. Congratulations Dr. Huber.
2018
Nathan has defended his dissertation. Congratulations Dr. Willy.
Josh has defended his dissertation. Congratulations Dr. Ferguson.
2017
Comert has received a National Science Foundation Early CAREER Development Award.
Joshua Ferguson has been awarded a Presidential Fellowship. Congratulations Josh.
We are on the cover of Molecular Biology of the Cell.
Nathan gave a platform presentation at the Fourth Midwest Membrane Trafficking and Signaling Symposium.
Our proposal to the Advanced Imaging Center has been accepted. We are going to the Janelia Research Campus.
Our paper Membrane Mechanics Govern Spatiotemporal Heterogeneity of Endocytic Clathrin Coat Dynamics is now accepted by Molecular Biology of the Cell.
Our paper Mechanoregulation of Clathrin-mediated Endocytosis is now accepted by the Journal of Cell Science.
Josh gave a platform presentation at the Biophysical Society Meeting.
2016
Daunorubicin-Loaded DNA Origami Nanostructures Circumvent Drug-Resistance Mechanisms in a Leukemia Model is published in Small.
Our paper Deciphering dynamics of clathrin-mediated endocytosis in a living organism is published in Journal of Cell Biology.
2015
Our paper Asymmetric formation of coated pits on dorsal and ventral surfaces at the leading edges of motile cells and on protrusions of immobile cells is published in Molecular Biology of the Cell.
EtpE Binding to DNase X Induces Ehrlichial Entry via CD147 and hnRNP-K Recruitment, Followed by Mobilization of N-WASP and Actin is published in mBio.
2014
Spencer is accepted for the OSU 2014 Undergraduate Summer Research Scholarship.
2013
Matthew is selected to be a judge at The Ohio Academy of Science's State Science Day, encouraging students to pursue learning in science, engineering, technology, and education.
Our paper Similar uptake but different trafficking and escape routes of reovirus virions and infectious subvirion particles imaged in polarized Madin Darby canine kidney cells is published in Molecular Biology of the Cell.
Our spinning disk head has arrived.
We are now officially culturing Drosophila melanogaster fly stocks and using our spinning-disk and light-sheet microscopy systems to image endocytic dynamics during embryogenesis.
2012
Matthew is awarded a Career Development Grant from the Ohio State University Council of Graduate Students to attend the 2013 annual meeting of the Biophysical Society in Philadelphia, Pennsylvania.
Our paper Dynamics of Intracellular Clathrin/AP1- and Clathrin/AP3-Containing Carriers is published in Cell Reports.
Openings
We are interested in hiring postdoctoral scholars, graduate students, and undergraduate students.
To apply, email Comert with your CV and a short note about your interests.
Location
Physics Research Building, 191 W Woodruff Ave, Columbus, OH 43210