Literature DB >> 23396281

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

Fredrik Persson1, Martin Lindén, Cecilia Unoson, Johan Elf.   

Abstract

We provide an analytical tool based on a variational Bayesian treatment of hidden Markov models to combine the information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. The method identifies the number of diffusive states and the state transition rates. Using this method we have created an objective interaction map for Hfq, a protein that mediates interactions between small regulatory RNAs and their mRNA targets.

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Year:  2013        PMID： 23396281     DOI： 10.1038/nmeth.2367

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  16 in total

Review 1.  What is Bayesian statistics?

Authors:  Sean R Eddy
Journal:  Nat Biotechnol       Date:  2004-09       Impact factor: 54.908

2.  RNAs actively cycle on the Sm-like protein Hfq.

Authors:  Aurélie Fender; Johan Elf; Kornelia Hampel; Bastian Zimmermann; E Gerhart H Wagner
Journal:  Genes Dev       Date:  2010-12-01       Impact factor: 11.361

3.  DNA looping kinetics analyzed using diffusive hidden Markov model.

Authors:  John F Beausang; Chiara Zurla; Carlo Manzo; David Dunlap; Laura Finzi; Philip C Nelson
Journal:  Biophys J       Date:  2007-02-02       Impact factor: 4.033

4.  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

5.  Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET data.

Authors:  Jonathan E Bronson; Jingyi Fei; Jake M Hofman; Ruben L Gonzalez; Chris H Wiggins
Journal:  Biophys J       Date:  2009-12-16       Impact factor: 4.033

6.  Investigating intracellular dynamics of FtsZ cytoskeleton with photoactivation single-molecule tracking.

Authors:  Lili Niu; Ji Yu
Journal:  Biophys J       Date:  2008-04-04       Impact factor: 4.033

7.  Single-molecule investigations of the stringent response machinery in living bacterial cells.

Authors:  Brian P English; Vasili Hauryliuk; Arash Sanamrad; Stoyan Tankov; Nynke H Dekker; Johan Elf
Journal:  Proc Natl Acad Sci U S A       Date:  2011-07-05       Impact factor: 11.205

8.  Variational Bayes analysis of a photon-based hidden Markov model for single-molecule FRET trajectories.

Authors:  Kenji Okamoto; Yasushi Sako
Journal:  Biophys J       Date:  2012-09-19       Impact factor: 4.033

9.  Lost in presumption: stochastic reactions in spatial models.

Authors:  Anel Mahmutovic; David Fange; Otto G Berg; Johan Elf
Journal:  Nat Methods       Date:  2012-12       Impact factor: 28.547

10.  Spatial control of EGF receptor activation by reversible dimerization on living cells.

Authors:  Inhee Chung; Robert Akita; Richard Vandlen; Derek Toomre; Joseph Schlessinger; Ira Mellman
Journal:  Nature       Date:  2010-03-07       Impact factor: 49.962
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  135 in total

1.  Improving z-tracking accuracy in the two-photon single-particle tracking microscope.

Authors:  C Liu; Y-L Liu; E P Perillo; N Jiang; A K Dunn; H-C Yeh
Journal:  Appl Phys Lett       Date:  2015-10-12       Impact factor: 3.791

2.  Photoactivated Localization Microscopy with Bimolecular Fluorescence Complementation (BiFC-PALM).

Authors:  Andrew Nickerson; Tao Huang; Li-Jung Lin; Xioalin Nan
Journal:  J Vis Exp       Date:  2015-12-22       Impact factor: 1.355

3.  ANALYSIS AND DESIGN OF JUMP COEFFICIENTS IN DISCRETE STOCHASTIC DIFFUSION MODELS.

Authors:  Lina Meinecke; Stefan Engblom; Andreas Hellander; Per Lötstedt
Journal:  SIAM J Sci Comput       Date:  2016-01-06       Impact factor: 2.373

4.  Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy.

Authors:  Mustafa Mir; Armando Reimer; Michael Stadler; Astou Tangara; Anders S Hansen; Dirk Hockemeyer; Michael B Eisen; Hernan Garcia; Xavier Darzacq
Journal:  Methods Mol Biol       Date:  2018

Review 5.  Hfq: the flexible RNA matchmaker.

Authors:  Taylor B Updegrove; Aixia Zhang; Gisela Storz
Journal:  Curr Opin Microbiol       Date:  2016-02-22       Impact factor: 7.934

6.  Single-molecule tracking of small GTPase Rac1 uncovers spatial regulation of membrane translocation and mechanism for polarized signaling.

Authors:  Sulagna Das; Taofei Yin; Qingfen Yang; Jingqiao Zhang; Yi I Wu; Ji Yu
Journal:  Proc Natl Acad Sci U S A       Date:  2015-01-05       Impact factor: 11.205

7.  Single-Particle Diffusion Characterization by Deep Learning.

Authors:  Naor Granik; Lucien E Weiss; Elias Nehme; Maayan Levin; Michael Chein; Eran Perlson; Yael Roichman; Yoav Shechtman
Journal:  Biophys J       Date:  2019-06-22       Impact factor: 4.033

8.  Resolving Cytosolic Diffusive States in Bacteria by Single-Molecule Tracking.

Authors:  Julian Rocha; Jacqueline Corbitt; Ting Yan; Charles Richardson; Andreas Gahlmann
Journal:  Biophys J       Date:  2019-04-09       Impact factor: 4.033

9.  Single-Molecule Tracking and Its Application in Biomolecular Binding Detection.

Authors:  Cong Liu; Yen-Liang Liu; Evan P Perillo; Andrew K Dunn; Hsin-Chih Yeh
Journal:  IEEE J Sel Top Quantum Electron       Date:  2016-05-17       Impact factor: 4.544

10.  Single-molecule dynamics of the molecular chaperone trigger factor in living cells.

Authors:  Feng Yang; Tai-Yen Chen; Łukasz Krzemiński; Ace George Santiago; Won Jung; Peng Chen
Journal:  Mol Microbiol       Date:  2016-09-30       Impact factor: 3.501
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