Literature DB >> 26536253

Analysis and Interpretation of Superresolution Single-Particle Trajectories.

D Holcman1, N Hoze2, Z Schuss3.   

Abstract

A large number (tens of thousands) of single molecular trajectories on a cell membrane can now be collected by superresolution methods. The data contains information about the diffusive motion of molecule, proteins, or receptors and here we review methods for its recovery by statistical analysis of the data. The information includes the forces, organization of the membrane, the diffusion tensor, the long-time behavior of the trajectories, and more. To recover the long-time behavior and statistics of long trajectories, a stochastic model of their nonequilibrium motion is required. Modeling and data analysis serve extracting novel biophysical features at an unprecedented spatiotemporal resolution. The review presents data analysis, modeling, and stochastic simulations applied in particular on surface receptors evolving in neuronal cells.
Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mesh:

Year:  2015        PMID: 26536253      PMCID: PMC4643198          DOI: 10.1016/j.bpj.2015.09.003

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  20 in total

1.  Quantitative analysis of single particle trajectories: mean maximal excursion method.

Authors:  Vincent Tejedor; Olivier Bénichou; Raphael Voituriez; Ralf Jungmann; Friedrich Simmel; Christine Selhuber-Unkel; Lene B Oddershede; Ralf Metzler
Journal:  Biophys J       Date:  2010-04-07       Impact factor: 4.033

2.  Dynamics of enhanced tracer diffusion in suspensions of swimming eukaryotic microorganisms.

Authors:  Kyriacos C Leptos; Jeffrey S Guasto; J P Gollub; Adriana I Pesci; Raymond E Goldstein
Journal:  Phys Rev Lett       Date:  2009-11-05       Impact factor: 9.161

3.  Multiple particle tracking in 3-D+t microscopy: method and application to the tracking of endocytosed quantum dots.

Authors:  Auguste Genovesio; Tim Liedl; Valentina Emiliani; Wolfgang J Parak; Maité Coppey-Moisan; Jean-Christophe Olivo-Marin
Journal:  IEEE Trans Image Process       Date:  2006-05       Impact factor: 10.856

4.  Dwell time of a Brownian molecule in a microdomain with traps and a small hole on the boundary.

Authors:  Adi Taflia; David Holcman
Journal:  J Chem Phys       Date:  2007-06-21       Impact factor: 3.488

5.  High-density mapping of single-molecule trajectories with photoactivated localization microscopy.

Authors:  Suliana Manley; Jennifer M Gillette; George H Patterson; Hari Shroff; Harald F Hess; Eric Betzig; Jennifer Lippincott-Schwartz
Journal:  Nat Methods       Date:  2008-01-13       Impact factor: 28.547

6.  Narrow escape through a funnel and effective diffusion on a crowded membrane.

Authors:  D Holcman; N Hoze; Z Schuss
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2011-08-05

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

Authors:  Nathanael Hoze; David Holcman
Journal:  Biophys J       Date:  2014-12-16       Impact factor: 4.033

8.  Rejoice in the hubris: useful things biologists could do for physicists.

Authors:  Robert H Austin
Journal:  Phys Biol       Date:  2014-10-08       Impact factor: 2.583

9.  Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking.

Authors:  Ralf Metzler; Jae-Hyung Jeon; Andrey G Cherstvy; Eli Barkai
Journal:  Phys Chem Chem Phys       Date:  2014-11-28       Impact factor: 3.676

10.  Single-particle tracking: effects of corrals.

Authors:  M J Saxton
Journal:  Biophys J       Date:  1995-08       Impact factor: 4.033

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  8 in total

1.  Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis.

Authors:  Antony Lee; Konstantinos Tsekouras; Christopher Calderon; Carlos Bustamante; Steve Pressé
Journal:  Chem Rev       Date:  2017-04-17       Impact factor: 60.622

2.  Revealing Compartmentalized Diffusion in Living Cells with Interferometric Scattering Microscopy.

Authors:  Gabrielle de Wit; David Albrecht; Helge Ewers; Philipp Kukura
Journal:  Biophys J       Date:  2018-06-19       Impact factor: 4.033

3.  Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy.

Authors:  Maike Steindel; Igor Orsine de Almeida; Stanley Strawbridge; Valentyna Chernova; David Holcman; Aleks Ponjavic; Srinjan Basu
Journal:  Methods Mol Biol       Date:  2022

Review 4.  A guide for single-particle chromatin tracking in live cell nuclei.

Authors:  Mengdi Zhang; Clayton Seitz; Garrick Chang; Fadil Iqbal; Hua Lin; Jing Liu
Journal:  Cell Biol Int       Date:  2022-01-30       Impact factor: 4.473

Review 5.  Monitoring the spatio-temporal organization and dynamics of the genome.

Authors:  Haitham A Shaban; Andrew Seeber
Journal:  Nucleic Acids Res       Date:  2020-04-17       Impact factor: 16.971

6.  Particle Mobility Analysis Using Deep Learning and the Moment Scaling Spectrum.

Authors:  Marloes Arts; Ihor Smal; Maarten W Paul; Claire Wyman; Erik Meijering
Journal:  Sci Rep       Date:  2019-11-20       Impact factor: 4.379

7.  High-throughput super-resolution single-particle trajectory analysis reconstructs organelle dynamics and membrane reorganization.

Authors:  Pierre Parutto; Jennifer Heck; Meng Lu; Clemens Kaminski; Edward Avezov; Martin Heine; David Holcman
Journal:  Cell Rep Methods       Date:  2022-08-22

8.  Biophysics of high density nanometer regions extracted from super-resolution single particle trajectories: application to voltage-gated calcium channels and phospholipids.

Authors:  P Parutto; J Heck; M Heine; D Holcman
Journal:  Sci Rep       Date:  2019-12-11       Impact factor: 4.379

  8 in total

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