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Literature DB >> 26192083

Inferring transient particle transport dynamics in live cells.

Nilah Monnier¹, Zachary Barry¹, Hye Yoon Park^2,3,4, Kuan-Chung Su^5,6, Zachary Katz², Brian P English⁴, Arkajit Dey¹, Keyao Pan¹, Iain M Cheeseman^5,6, Robert H Singer^2,3,4, Mark Bathe¹.

Abstract

Live-cell imaging and particle tracking provide rich information on mechanisms of intracellular transport. However, trajectory analysis procedures to infer complex transport dynamics involving stochastic switching between active transport and diffusive motion are lacking. We applied Bayesian model selection to hidden Markov modeling to infer transient transport states from trajectories of mRNA-protein complexes in live mouse hippocampal neurons and metaphase kinetochores in dividing human cells. The software is available at http://hmm-bayes.org/.

Entities: CellLine Chemical Disease Gene Species

Mesh：

Substances：
Actins
MicroRNAs

Year: 2015 PMID： 26192083 PMCID： PMC4733533 DOI： 10.1038/nmeth.3483

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

25 in total

Review 1. Molecular architecture of the kinetochore-microtubule interface.

Authors: Iain M Cheeseman; Arshad Desai
Journal: Nat Rev Mol Cell Biol Date: 2008-01 Impact factor: 94.444

2. Temporal analysis of active and passive transport in living cells.

Authors: Delphine Arcizet; Börn Meier; Erich Sackmann; Joachim O Rädler; Doris Heinrich
Journal: Phys Rev Lett Date: 2008-12-12 Impact factor: 9.161

Review 3. Single-particle tracking: applications to membrane dynamics.

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

4. Lateral diffusion in an archipelago. Single-particle diffusion.

Authors: M J Saxton
Journal: Biophys J Date: 1993-06 Impact factor: 4.033

5. 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

6. Induced ectopic kinetochore assembly bypasses the requirement for CENP-A nucleosomes.

Authors: Karen E Gascoigne; Kozo Takeuchi; Aussie Suzuki; Tetsuya Hori; Tatsuo Fukagawa; Iain M Cheeseman
Journal: Cell Date: 2011-04-29 Impact factor: 41.582

7. Dynamic regulation of CD45 lateral mobility by the spectrin-ankyrin cytoskeleton of T cells.

Authors: Christopher W Cairo; Raibatak Das; Amgad Albohy; Quentin J Baca; Deepti Pradhan; Jon S Morrow; Daniel Coombs; David E Golan
Journal: J Biol Chem Date: 2010-02-17 Impact factor: 5.157

8. A transgenic mouse for in vivo detection of endogenous labeled mRNA.

Authors: Timothée Lionnet; Kevin Czaplinski; Xavier Darzacq; Yaron Shav-Tal; Amber L Wells; Jeffrey A Chao; Hye Yoon Park; Valeria de Turris; Melissa Lopez-Jones; Robert H Singer
Journal: Nat Methods Date: 2011-01-16 Impact factor: 28.547

9. Robust single-particle tracking in live-cell time-lapse sequences.

Authors: Khuloud Jaqaman; Dinah Loerke; Marcel Mettlen; Hirotaka Kuwata; Sergio Grinstein; Sandra L Schmid; Gaudenz Danuser
Journal: Nat Methods Date: 2008-07-20 Impact factor: 28.547

10. 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

57 in total

Inferring transient particle transport dynamics in live cells.

Review 1. Molecular architecture of the kinetochore-microtubule interface.

2. Temporal analysis of active and passive transport in living cells.

Review 3. Single-particle tracking: applications to membrane dynamics.

4. Lateral diffusion in an archipelago. Single-particle diffusion.

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

6. Induced ectopic kinetochore assembly bypasses the requirement for CENP-A nucleosomes.

7. Dynamic regulation of CD45 lateral mobility by the spectrin-ankyrin cytoskeleton of T cells.

8. A transgenic mouse for in vivo detection of endogenous labeled mRNA.

9. Robust single-particle tracking in live-cell time-lapse sequences.

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

1. An Intermittent Model for Intracellular Motions of Gold Nanostars by k-Space Scattering Image Correlation.

2. Advancing multiscale structural mapping of the brain through fluorescence imaging and analysis across length scales.

3. A Jump-Distance-Based Parameter Inference Scheme for Particulate Trajectories.

Review 4. Coming Together: RNAs and Proteins Assemble under the Single-Molecule Fluorescence Microscope.

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

6. Force Spectrum Microscopy Using Mitochondrial Fluctuations of Control and ATP-Depleted Cells.

7. Variational Algorithms for Analyzing Noisy Multistate Diffusion Trajectories.

8. Imaging cell-type-specific dynamics of mRNAs in living mouse brain.

Review 9. Single-Cell and Single-Molecule Analysis of Gene Expression Regulation.

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