Literature DB >> 28088300

Cytoplasmic RNA-Protein Particles Exhibit Non-Gaussian Subdiffusive Behavior.

Thomas J Lampo1, Stella Stylianidou2, Mikael P Backlund3, Paul A Wiggins4, Andrew J Spakowitz5.   

Abstract

The cellular cytoplasm is a complex, heterogeneous environment (both spatially and temporally) that exhibits viscoelastic behavior. To further develop our quantitative insight into cellular transport, we analyze data sets of mRNA molecules fluorescently labeled with MS2-GFP tracked in real time in live Escherichia coli and Saccharomyces cerevisiae cells. As shown previously, these RNA-protein particles exhibit subdiffusive behavior that is viscoelastic in its origin. Examining the ensemble of particle displacements reveals a Laplace distribution at all observed timescales rather than the Gaussian distribution predicted by the central limit theorem. This ensemble non-Gaussian behavior is caused by a combination of an exponential distribution in the time-averaged diffusivities and non-Gaussian behavior of individual trajectories. We show that the non-Gaussian behavior is a consequence of significant heterogeneity between trajectories and dynamic heterogeneity along single trajectories. Informed by theory and simulation, our work provides an in-depth analysis of the complex diffusive behavior of RNA-protein particles in live cells.
Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2017        PMID: 28088300      PMCID: PMC5300785          DOI: 10.1016/j.bpj.2016.11.3208

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


  54 in total

1.  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

2.  Static and dynamic errors in particle tracking microrheology.

Authors:  Thierry Savin; Patrick S Doyle
Journal:  Biophys J       Date:  2004-11-08       Impact factor: 4.033

3.  Protein mobility in the cytoplasm of Escherichia coli.

Authors:  M B Elowitz; M G Surette; P E Wolf; J B Stock; S Leibler
Journal:  J Bacteriol       Date:  1999-01       Impact factor: 3.490

4.  Quantifying transient 3D dynamical phenomena of single mRNA particles in live yeast cell measurements.

Authors:  Christopher P Calderon; Michael A Thompson; Jason M Casolari; Randy C Paffenroth; W E Moerner
Journal:  J Phys Chem B       Date:  2013-11-04       Impact factor: 2.991

5.  Diffusing diffusivity: a model for anomalous, yet Brownian, diffusion.

Authors:  Mykyta V Chubynsky; Gary W Slater
Journal:  Phys Rev Lett       Date:  2014-08-27       Impact factor: 9.161

6.  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

7.  SuperSegger: robust image segmentation, analysis and lineage tracking of bacterial cells.

Authors:  Stella Stylianidou; Connor Brennan; Silas B Nissen; Nathan J Kuwada; Paul A Wiggins
Journal:  Mol Microbiol       Date:  2016-09-23       Impact factor: 3.501

8.  Localizing and tracking single nanoscale emitters in three dimensions with high spatiotemporal resolution using a double-helix point spread function.

Authors:  Michael A Thompson; Matthew D Lew; Majid Badieirostami; W E Moerner
Journal:  Nano Lett       Date:  2010-01       Impact factor: 11.189

9.  RNA dynamics in live Escherichia coli cells.

Authors:  Ido Golding; Edward C Cox
Journal:  Proc Natl Acad Sci U S A       Date:  2004-07-26       Impact factor: 11.205

10.  A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion.

Authors:  Sabeeha Hasnain; Christopher L McClendon; Monica T Hsu; Matthew P Jacobson; Pradipta Bandyopadhyay
Journal:  PLoS One       Date:  2014-09-02       Impact factor: 3.240

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  29 in total

1.  Anomalous and heterogeneous DNA transport in biomimetic cytoskeleton networks.

Authors:  Jonathan Garamella; Kathryn Regan; Gina Aguirre; Ryan J McGorty; Rae M Robertson-Anderson
Journal:  Soft Matter       Date:  2020-06-19       Impact factor: 3.679

2.  Heterogeneities Shape Passive Intracellular Transport.

Authors:  Patrick Witzel; Maria Götz; Yann Lanoiselée; Thomas Franosch; Denis S Grebenkov; Doris Heinrich
Journal:  Biophys J       Date:  2019-06-18       Impact factor: 4.033

Review 3.  Understanding biochemical processes in the presence of sub-diffusive behavior of biomolecules in solution and living cells.

Authors:  Sujit Basak; Sombuddha Sengupta; Krishnananda Chattopadhyay
Journal:  Biophys Rev       Date:  2019-08-23

4.  Subdiffusive Dynamics Lead to Depleted Particle Densities near Cellular Borders.

Authors:  William R Holmes
Journal:  Biophys J       Date:  2019-02-28       Impact factor: 4.033

5.  Gaussianity Fair: The Riddle of Anomalous yet Non-Gaussian Diffusion.

Authors:  Ralf Metzler
Journal:  Biophys J       Date:  2017-01-05       Impact factor: 4.033

6.  Diffusing diffusivity: Rotational diffusion in two and three dimensions.

Authors:  Rohit Jain; K L Sebastian
Journal:  J Chem Phys       Date:  2017-06-07       Impact factor: 3.488

7.  Diffusion of Exit Sites on the Endoplasmic Reticulum: A Random Walk on a Shivering Backbone.

Authors:  Lorenz Stadler; Konstantin Speckner; Matthias Weiss
Journal:  Biophys J       Date:  2018-09-15       Impact factor: 4.033

8.  Creeping motion of a solid particle inside a spherical elastic cavity.

Authors:  Abdallah Daddi-Moussa-Ider; Hartmut Löwen; Stephan Gekle
Journal:  Eur Phys J E Soft Matter       Date:  2018-09-11       Impact factor: 1.890

Review 9.  Molecular simulations of cellular processes.

Authors:  Fabio Trovato; Giordano Fumagalli
Journal:  Biophys Rev       Date:  2017-11-28

Review 10.  Out of the Randomness: Correlating Noise in Biological Systems.

Authors:  Maddalena Collini; Margaux Bouzin; Giuseppe Chirico
Journal:  Biophys J       Date:  2018-02-21       Impact factor: 4.033

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