Residence times of receptors in dendritic spines analyzed by stochastic simulations in empirical domains.

Analysis of high-density superresolution imaging of receptors reveals the organization of dendrites at nanoscale resolution. We present here an apparently novel method that uses local statistics extracted from short-range trajectories for the simulations of long-range trajectories in empirical live cell images. Based on these empirical simulations, we compute the residence time of a receptor in dendritic spines that accounts for receptors' local interactions and geometrical membrane organization. We report here that depending on the type of the spine, the residence time varies from 1 to 5 min. Moreover, we show that there exists transient organized structures, previously described as potential wells that can regulate the trafficking of receptors to dendritic spine: the simulation results suggest that receptor trafficking is regulated by transient structures.

• Publication year

  2014

• Venue

  Biophysical Journal

• Publication date

  2014-06-29

• Fields of study

  Biology, Mathematics, Physics, Medicine

• Identifiers
  DOI 10.1016/j.bpj.2014.10.018arXiv 1406.7511PMID 25517165PMCID PMC4269777
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Mapping the energy and diffusion landscapes of membrane proteins at the cell surface using high-density single-molecule imaging and Bayesian inference: application to the multiscale dynamics of glycine receptors in the neuronal membrane.

  2014cited by this paper
• Reconstruction of Surface and Stochastic Dynamics from a Planar Projection of Trajectories

  2013cited by this paper
• Brownian Dynamics at Boundaries and Interfaces

  2013cited by this paper
• Super-Resolution Imaging Reveals That AMPA Receptors Inside Synapses Are Dynamically Organized in Nanodomains Regulated by PSD95

  2013cited by this paper
• Quantitative nanoscopy of inhibitory synapses: counting gephyrin molecules and receptor binding sites.

  2013cited by this paper
• Potential wells for AMPA receptors organized in ring nanodomains

  2013cited by this paper
• Control of flux by narrow passages and hidden targets in cellular biology

  2013cited by this paper
• Optimal estimation of diffusion coefficients from single-particle trajectories.

  2013cited by this paper
• Heterogeneity of AMPA receptor trafficking and molecular interactions revealed by superresolution analysis of live cell imaging

  2012cited by this paper
• Brownian needle in dire straits: stochastic motion of a rod in very confined narrow domains.

  2012cited by this paper
• LTP requires a reserve pool of glutamate receptors independent of subunit type

  2012cited by this paper
• Nonlinear Filtering and Optimal Phase Tracking

  2011cited by this paper
• Narrow escape through a funnel and effective diffusion on a crowded membrane.

  2011cited by this paper
• Diffusion laws in dendritic spines

  2011cited by this paper
• Dynamic superresolution imaging of endogenous proteins on living cells at ultra-high density.

  2010cited by this paper
• Some questions related to modeling in cellular biology

  2010cited by this paper
• Dynamin-dependent Membrane Drift Recruits AMPA Receptors to Dendritic Spines*

  2009influential reference
• Single-particle tracking: connecting the dots

  2008cited by this paper
• Surface Mobility of Postsynaptic AMPARs Tunes Synaptic Transmission

  2008cited by this paper
• [Surface mobility of postsynaptic AMPARs tunes synaptic transmission].

  2008cited by this paper
• Dwell time of a Brownian molecule in a microdomain with traps and a small hole on the boundary.

  2007cited by this paper
• The narrow escape problem for diffusion in cellular microdomains

  2007cited by this paper
• Modeling 2D and 3D diffusion.

  2007cited by this paper
• Modeling synaptic dynamics driven by receptor lateral diffusion.

  2006cited by this paper
• Biophysical Model of AMPA Receptor Trafficking and Its Regulation during Long-Term Potentiation/Long-Term Depression

  2006cited by this paper
• Lateral Diffusion Drives Constitutive Exchange of AMPA Receptors at Dendritic Spines and Is Regulated by Spine Morphology

  2006cited by this paper
• Partially Reflected Diffusion

  2006cited by this paper
• Narrow Escape, Part III: Non-Smooth Domains and Riemann Surfaces

  2006cited by this paper
• Stargazin modulates AMPA receptor gating and trafficking by distinct domains

  2005cited by this paper
• Paradigm shift of the plasma membrane concept from the two-dimensional continuum fluid to the partitioned fluid: high-speed single-molecule tracking of membrane molecules.

  2005cited by this paper
• Escape Through a Small Opening: Receptor Trafficking in a Synaptic Membrane

  2004cited by this paper
• Narrow Escape, Part I

  2004cited by this paper
• Narrow Escape, Part II: The Circular Disk

  2004cited by this paper
• AMPA receptor trafficking and long-term potentiation.

  2003cited by this paper
• AMPA receptor trafficking at excitatory synapses.

  2003cited by this paper
• Synaptic structure and diffusion dynamics of synaptic receptors

  2003influential reference
• Direct interactions between PSD-95 and stargazin control synaptic AMPA receptor number

  2002cited by this paper
• AMPA receptor trafficking and synaptic plasticity.

  2002cited by this paper
• Rapid spine delivery and redistribution of AMPA receptors after synaptic NMDA receptor activation.

  1999cited by this paper
• Dendritic spines

  1998cited by this paper
• Single-particle tracking: applications to membrane dynamics.

  1997cited by this paper
• Single-particle tracking: effects of corrals.

  1995cited by this paper
• Partial Differential Equations

  1995cited by this paper
• Lateral movements of membrane glycoproteins restricted by dynamic cytoplasmic barriers.

  1991cited by this paper
• Theory and Applications of Stochastic Differential Equations

  1980cited by this paper

• Chromatin phase separated nanoregions explored by polymer cross-linker models and reconstructed from single particle trajectories

  2024cites this paper
• Synapsin 2a tetramerisation selectively controls the presynaptic nanoscale organisation of reserve synaptic vesicles

  2024cites this paper
• Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling

  2023cites this paper
• Single particle algorithms to reveal cellular nanodomain organization

  2023cites this paper
• Single-molecule fluorescence microscopy demonstrates fast dynamics of the variant surface glycoprotein coat on living trypanosomes

  2022influential citation
• High-throughput super-resolution single-particle trajectory analysis reconstructs organelle dynamics and membrane reorganization

  2022cites this paper
• Nanoscale molecular architecture controls calcium diffusion and ER replenishment in dendritic spines

  2021cites this paper
• SPtsAnalysis: a high-throughput super-resolution single particle trajectory analysis to reconstruct organelle dynamics and membrane re-organization

  2021cites this paper
• Advances Using Single-Particle Trajectories to Reconstruct Chromatin Organization and Dynamics.

  2019cites this paper
• Transient Confinement of CaV2.1 Ca2+-Channel Splice Variants Shapes Synaptic Short-Term Plasticity.

  2019cites this paper
• Reconstructing wells from high density regions extracted from super-resolution single particle trajectories

  2019cites this paper
• Frontotemporal dementia mutant Tau promotes aberrant Fyn nanoclustering in hippocampal dendritic spines

  2019cites this paper
• Single particle trajectory statistic to reconstruct chromatin organization and dynamics

  2019cites this paper
• Biophysics of high density nanometer regions extracted from super-resolution single particle trajectories: application to voltage-gated calcium channels and phospholipids

  2019cites this paper
• Single particle trajectories reveal active Endoplasmic Reticulum luminal flow

  2018cites this paper
• Statistical Methods for Large Ensembles of Super-Resolution Stochastic Single Particle Trajectories in Cell Biology

  2017cites this paper
• Probing the Interplay between Dendritic Spine Morphology and Membrane-Bound Diffusion

  2017cites this paper
• Statistical methods for large ensemble of super-resolution stochastic single particle trajectories

  2017influential citation
• Coagulation-Fragmentation with a Finite Number of Particles: Models, Stochastic Analysis, and Applications to Telomere Clustering and Viral Capsid Assembly

  2017cites this paper
• Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis.

  2017cites this paper
• Commentary: New mathematical physics needed for life sciences

  2016cites this paper
• 100 years after Smoluchowski: stochastic processes in cell biology

  2016cites this paper
• Determination of Features from Super-Resolution Data

  2015cites this paper
• Regulation of ionic flow in neuronal subcompartments : the new nanophysiology

  2015cites this paper
• The Motion Blur Filter : An Algorithm for Extracting Confinement Forces & Diffusivity from a Single “ Blurred ” Trajectory

  2015cites this paper
• Elementary Theory of Stochastic Narrow Escape

  2015cites this paper
• Recovering a stochastic process from super-resolution noisy ensembles of single-particle trajectories.

  2015influential citation
• Analysis and Interpretation of Superresolution Single-Particle Trajectories.

  2015cites this paper
• The new nanophysiology: regulation of ionic flow in neuronal subcompartments

  2015cites this paper
• Motion blur filtering: A statistical approach for extracting confinement forces and diffusivity from a single blurred trajectory.

  2015cites this paper
• Inferring Latent States and Refining Force Estimates via Hierarchical Dirichlet Process Modeling in Single Particle Tracking Experiments

  2015cites this paper