Literature DB >> 29539390

Multistep Track Segmentation and Motion Classification for Transient Mobility Analysis.

Anthony R Vega1, Spencer A Freeman2, Sergio Grinstein3, Khuloud Jaqaman4.   

Abstract

Molecular interactions are often transient and might change within the window of observation, leading to changes in molecule movement. Therefore, accurate motion analysis often requires transient motion classification. Here we present an accurate and computationally efficient transient mobility analysis framework, termed "divide-and-conquer moment scaling spectrum" (DC-MSS). DC-MSS works in a multistep fashion: 1) it utilizes a local movement descriptor throughout a track to divide it into initial segments of putatively different motion classes; 2) it classifies these segments via moment scaling spectrum (MSS) analysis of molecule displacements; and 3) it uses the MSS analysis results to refine the track segmentation. This strategy uncouples the initial identification of motion switches from motion classification, allowing DC-MSS to circumvent the sensitivity-accuracy tradeoff of classic rolling window approaches for transient motion analysis, while at the same time harnessing the classification power of MSS analysis. Testing of DC-MSS demonstrates that it detects switches among free diffusion, confined diffusion, directed diffusion, and immobility with great sensitivity. To illustrate the utility of DC-MSS, we have applied it to single-particle tracks of the transmembrane protein CD44 on the surface of macrophages, revealing actin cortex-dependent transient mobility changes.
Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2018        PMID: 29539390      PMCID: PMC5883548          DOI: 10.1016/j.bpj.2018.01.012

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


  24 in total

Review 1.  CD44: from adhesion molecules to signalling regulators.

Authors:  Helmut Ponta; Larry Sherman; Peter A Herrlich
Journal:  Nat Rev Mol Cell Biol       Date:  2003-01       Impact factor: 94.444

Review 2.  Single-particle tracking: applications to membrane dynamics.

Authors:  M J Saxton; K Jacobson
Journal:  Annu Rev Biophys Biomol Struct       Date:  1997

3.  Extracting intracellular diffusive states and transition rates from single-molecule tracking data.

Authors:  Fredrik Persson; Martin Lindén; Cecilia Unoson; Johan Elf
Journal:  Nat Methods       Date:  2013-02-10       Impact factor: 28.547

4.  Single-particle tracking of murine polyoma virus-like particles on live cells and artificial membranes.

Authors:  Helge Ewers; Alicia E Smith; Ivo F Sbalzarini; Hauke Lilie; Petros Koumoutsakos; Ari Helenius
Journal:  Proc Natl Acad Sci U S A       Date:  2005-10-11       Impact factor: 11.205

Review 5.  Organizing the cell cortex: the role of ERM proteins.

Authors:  Richard G Fehon; Andrea I McClatchey; Anthony Bretscher
Journal:  Nat Rev Mol Cell Biol       Date:  2010-04       Impact factor: 94.444

6.  Raft-based interactions of gangliosides with a GPI-anchored receptor.

Authors:  Naoko Komura; Kenichi G N Suzuki; Hiromune Ando; Miku Konishi; Machi Koikeda; Akihiro Imamura; Rahul Chadda; Takahiro K Fujiwara; Hisae Tsuboi; Ren Sheng; Wonhwa Cho; Koichi Furukawa; Keiko Furukawa; Yoshio Yamauchi; Hideharu Ishida; Akihiro Kusumi; Makoto Kiso
Journal:  Nat Chem Biol       Date:  2016-04-04       Impact factor: 15.040

7.  Confined diffusion of transmembrane proteins and lipids induced by the same actin meshwork lining the plasma membrane.

Authors:  Takahiro K Fujiwara; Kokoro Iwasawa; Ziya Kalay; Taka A Tsunoyama; Yusuke Watanabe; Yasuhiro M Umemura; Hideji Murakoshi; Kenichi G N Suzuki; Yuri L Nemoto; Nobuhiro Morone; Akihiro Kusumi
Journal:  Mol Biol Cell       Date:  2016-02-10       Impact factor: 4.138

8.  A hidden Markov model for single particle tracks quantifies dynamic interactions between LFA-1 and the actin cytoskeleton.

Authors:  Raibatak Das; Christopher W Cairo; Daniel Coombs
Journal:  PLoS Comput Biol       Date:  2009-11-06       Impact factor: 4.475

9.  Changes in single-molecule integrin dynamics linked to local cellular behavior.

Authors:  Khuloud Jaqaman; James A Galbraith; Michael W Davidson; Catherine G Galbraith
Journal:  Mol Biol Cell       Date:  2016-03-23       Impact factor: 4.138

10.  Mapping translation 'hot-spots' in live cells by tracking single molecules of mRNA and ribosomes.

Authors:  Zachary B Katz; Brian P English; Timothée Lionnet; Young J Yoon; Nilah Monnier; Ben Ovryn; Mark Bathe; Robert H Singer
Journal:  Elife       Date:  2016-01-13       Impact factor: 8.140

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1.  Model Segmentation in Single Particle Tracking.

Authors:  Boris I Godoy; Nicholas A Vickers; Sean B Andersson
Journal:  Proc IFAC World Congress       Date:  2021-12-15

2.  A composition-dependent molecular clutch between T cell signaling condensates and actin.

Authors:  Jonathon A Ditlev; Anthony R Vega; Darius Vasco Köster; Xiaolei Su; Tomomi Tani; Ashley M Lakoduk; Ronald D Vale; Satyajit Mayor; Khuloud Jaqaman; Michael K Rosen
Journal:  Elife       Date:  2019-07-03       Impact factor: 8.140

3.  Single-molecule FRET imaging of GPCR dimers in living cells.

Authors:  Wesley B Asher; Peter Geggier; Michael D Holsey; Grant T Gilmore; Avik K Pati; Jozsef Meszaros; Daniel S Terry; Signe Mathiasen; Megan J Kaliszewski; Mitchell D McCauley; Alekhya Govindaraju; Zhou Zhou; Kaleeckal G Harikumar; Khuloud Jaqaman; Laurence J Miller; Adam W Smith; Scott C Blanchard; Jonathan A Javitch
Journal:  Nat Methods       Date:  2021-03-08       Impact factor: 28.547

4.  Neuronal Receptors Display Cytoskeleton-Independent Directed Motion on the Plasma Membrane.

Authors:  Ruth D Taylor; Martin Heine; Nigel J Emptage; Laura C Andreae
Journal:  iScience       Date:  2018-12-05

5.  Frontotemporal dementia mutant Tau promotes aberrant Fyn nanoclustering in hippocampal dendritic spines.

Authors:  Pranesh Padmanabhan; Ramón Martínez-Mármol; Di Xia; Jürgen Götz; Frédéric A Meunier
Journal:  Elife       Date:  2019-06-25       Impact factor: 8.140

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.  Engineered IgG1-Fc Molecules Define Valency Control of Cell Surface Fcγ Receptor Inhibition and Activation in Endosomes.

Authors:  Elizabeth M Bailey; Amit Choudhury; Harika Vuppula; Daniel F Ortiz; John Schaeck; Anthony M Manning; Carlos J Bosques; Adam D Hoppe
Journal:  Front Immunol       Date:  2021-02-15       Impact factor: 7.561

8.  Impact of Feature Choice on Machine Learning Classification of Fractional Anomalous Diffusion.

Authors:  Hanna Loch-Olszewska; Janusz Szwabiński
Journal:  Entropy (Basel)       Date:  2020-12-19       Impact factor: 2.524

Review 9.  The needle and the haystack: single molecule tracking to probe the transcription factor search in eukaryotes.

Authors:  Matteo Mazzocca; Tom Fillot; Alessia Loffreda; Daniela Gnani; Davide Mazza
Journal:  Biochem Soc Trans       Date:  2021-06-30       Impact factor: 5.407

10.  Heterogeneity in VEGF Receptor-2 Mobility and Organization on the Endothelial Cell Surface Leads to Diverse Models of Activation by VEGF.

Authors:  Bruno da Rocha-Azevedo; Sungsoo Lee; Aparajita Dasgupta; Anthony R Vega; Luciana R de Oliveira; Tae Kim; Mark Kittisopikul; Zachariah A Malik; Khuloud Jaqaman
Journal:  Cell Rep       Date:  2020-09-29       Impact factor: 9.423

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