SPIEDL Logo
Search Text Line
 
SPIE DL Tab Proceedings Tab Journals Tab JBO Tab EBooks Tab
JBO banner
My Subscription  | My Email Alerts  | My Article Collections

GENERAL INFORMATION

Journal of Biomedical Optics / Volume 17 / Issue 1 / Special Section on FRET at 65

Toward automated denoising of single molecular Förster resonance energy transfer data

J. Biomed. Opt. 17, 011007 (Feb 08, 2012); http://dx.doi.org/10.1117/1.JBO.17.1.011007

Hao-Chih Lee and I-Ping Tu

Academia Sinica, Institute of Statistical Science, Taipei, Taiwan

Bo-Lin Lin and Wei-Hau Chang

Academia Sinica, Institute of Chemistry, Taipei, Taiwan

A wide-field two-channel fluorescence microscope is a powerful tool as it allows for the study of conformation dynamics of hundreds to thousands of immobilized single molecules by Förster resonance energy transfer (FRET) signals. To date, the data reduction from a movie to a final set containing meaningful single-molecule FRET (smFRET) traces involves human inspection and intervention at several critical steps, greatly hampering the efficiency at the post-imaging stage. To facilitate the data reduction from smFRET movies to smFRET traces and to address the noise-limited issues, we developed a statistical denoising system toward fully automated processing. This data reduction system has embedded several novel approaches. First, as to background subtraction, high-order singular value decomposition (HOSVD) method is employed to extract spatial and temporal features. Second, to register and map the two color channels, the spots representing bleeding through the donor channel to the acceptor channel are used. Finally, correlation analysis and likelihood ratio statistic for the change point detection (CPD) are developed to study the two channels simultaneously, resolve FRET states, and report the dwelling time of each state. The performance of our method has been checked using both simulation and real data.

© 2012 Society of Photo-Optical Instrumentation Engineers

History
Received May 27, 2011
Accepted Sep 19, 2011
Revised Sep 16, 2011
Published online Feb 08, 2012
Digital Object Identifier
http://dx.doi.org/10.1117/1.JBO.17.1.011007
Citation
Hao-Chih Lee, Bo-Lin Lin, Wei-Hau Chang and I-Ping Tu, "Toward automated denoising of single molecular Förster resonance energy transfer data", J. Biomed. Opt. 17, 011007 (Feb 08, 2012); http://dx.doi.org/10.1117/1.JBO.17.1.011007

DOWNLOAD ARTICLE

OPEN ACCESS

FULL-TEXT OPTIONS:

RELATED CONTENT

More Like This Article

loading

  1. Ha, T.et al., “Ligand-induced conformational changes of single RNA molecules,” PNAS 96(16), 9077–9082 (1999). [ISI] [MEDLINE]
  2. Zhuang, X.et al., “A single-molecule study of RNA catalysis and folding,” Science 288(5473), 2048–2051 (2000). [ISI] [MEDLINE]
  3. P. R. Selvin and T. Ha, Eds., Single Molecule Techniques: A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York, p. 507 (2008).
  4. Tokunaga, M.et al., “Single molecule imaging of fluorophores and enzymatic reactions achieved by objective-type total internal reflection fluorescence microscopy,” Biochem. Biophys. Res. Commun. 235(1), 47–53 (1997). [ISI] [MEDLINE]
  5. Roy, R., S. Hohng and T. Ha, “A practical guide to single-molecule FRET,” Nat. Methods 5, 507–516 (2008). [MEDLINE]
  6. Churchman, L. S.et al., “Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time,” PNAS 102(5), 1419–1423 (2005).
  7. Friedman, L. J., J. Chung and J. Gelles, “Viewing dynamic assembly of molecular complexes by multi-wavelength single-molecule fluorescence,” Biophys. J. 91(3), 1023–1031 (2006).
  8. Ambrose, W. P., P. M. Goodwin and J. P. Nolan, “Single-molecule detection with total internal reflection excitaiton: comparing signal to background and total signals in different geometries, Cytometry 36(3), 224–231 (1999). [ISI] [MEDLINE]
  9. Schluesche, P.et al., “NC2 mobilizes TBP on core promoter TATA boxes,” Nat. Struct. Mol. Biol. 14, 1196–1201 (2007).
  10. Solomatin, S. V., M. Greenfeld, S. Chu and D. Herschlag, “Multiple native states reveal persistent ruggedness of an RNA folding landscape,” Nature 463(7281), 681–684 (2010).
  11. Holden, S. J.et al., “Defining the limits of single-molecule FRET resolution in TIRF microscopy,” Biophys. J. 99(9), 3102–3111 (2010).
  12. Siegmund, D., Sequential Analysis: Tests and Confidence Intervals, Springer-Verlag, New York (1985).
  13. Chen, J. and A. K. Gupta, “On change point detection and estimation,” Commun. Stat.—Simulat. Comput. 30(3), 665–697 (2001).
  14. McKinney, S., C. Joo and T. Ha, “Analysis of single-molecule FRET trajectories using hidden Markov modeling,” Biophys. J. 91(5), 1941–1951 (2006). [MEDLINE]
  15. Liu, Y.et al., “A comparative study of multivariate and univariate hidden Markov modelings in time-binned single-molecule FRET data analysis,” J. Phys. Chem. B 114(16), 5386–5403 (2010).
  16. Goldsmith, R. H. and W. E. Moerner, “Watching conformational and photodynamics of single fluorescent proteins in solution,” Nat. Chem. 2, 179–186 (2010).
  17. Chen, C. Y.et al., “Mapping RNA exit channel on transcribing RNA polymerase II by FRET analysis,” PNAS 106(1), 127–132 (2009).
  18. Lathauwer, L. D., B. D. Moor and J. Vandewalle, “A multilinear singular value decomposition,” SIAM J. Matrix Anal. Appl. 21(4), 1253–1278 (2000)SJMAEL000021000004001253000001. [ISI]
  19. Zhang, T. and G. H. Golub, “Rank-one approximation to high order tensors, SIAM J. Matrix Anal. Appl. 23(2), 535–550 (2001)SJMAEL000023000002000534000001. [ISI]
  20. Kolda, T. G. and B. W. Bader, “Tensor decompositions and applications,” SIAM Rev. 51(3), 455–500 (2009)SIREAD000051000003000455000001.
  21. Omberg, L., G. H. Golub and O. Alter, “A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies,” Proc. Natl. Acad. Sci. U. S. A. 104(47), 18371–18376 (2007). [MEDLINE]
  22. Watkins, P. and H. Yang, “Detection of intensity change points in time-resolved single-molecule measurements,” J. Phys. Chem. B 109(1), 617–628 (2005).
  23. Srivastava, M. S. and K. J. Worsley, “Likelihood ratio tests for a change in the multivariate normal mean,” J. Am. Stat. Assoc. 81(393), 199–204 (1986).
  24. Qin, F. and L. Li, “Model-based fitting of single-channel dwell time distributions,” Biophys. J. 87(3), 1657–1671 (2004). [Inspec]
  25. Bronson, J. E.et al., “Learning rates and states from biophysical time series: a Baysian approach to model selection and single-molecule FRET data,” Biophys. J. 97(12), 3196–3205 (2009).
  26. Bianco, M. and N. Walter, “Analysis of complex single-molecule FRET time trajectories, Methods Enzymol. 472, 153–178 (2010).
  27. McDowell, S. E., J. M. Jun and N. G. Walter, “Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations,” RNA 16(12), 2414–2426 (2010).
  28. Chrsitian, T. D., L. J. Romano and D. Rueda, “Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution,” PNAS 106(50), 21109–21114 (2009).
  29. Liu, S.et al., “Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription,” Nat. Struct. Mol. Biol. 17, 1453–1460 (2010).
  30. Cornish, P. V.et al., “Following movement of the L1 stalk between three functional states in single ribosomes,” Proc. Natl. Acad. Sci. U. S. A. 106(8), 2571–2576 (2009).
  31. Munro, J. B.et al., “Correlated conformational events in EF-G and the ribosome regulate translocation,” Nat. Struct. Mol. Biol. 17, 1470–1477 (2010).
  32. Abelson, J.et al., “Conformational dynamics of single pre-mRNA molecules in spliceosome assembly,” Nat. Struct. Mol. Biol. 17, 504–512 (2010).
  33. Hoskins, A. A.et al., “Ordered and dynamic assembly of single spliceosomes,” Science 331(6022), 1289–1295 (2011).
  34. Lee, H. K.et al., “Dynamic ca2+-dependent stimulation of vesicle fusion by membrane-anchored synaptotagmin,” Science 328(5979), 760–763 (2011).
  35. Choi, U. B.et al., “Beyond the random coil: stochastic conformational switching in intrinsically disordered proteins,” Structure 19(4), 566–576 (2011).
  36. McCann, J. J.et al., “Optimizing methods to recover absolute FRET efficiency from immobilized single molecules,” Biophys. J. 99(3), 961–970 (2010).
  37. Andrecka, J.et al., “Single-molecule tracking of mRNA exiting from RNA polymerase II,” PNAS 105(1), 135–140 (2008).
  38. Brunger, A. T.et al., “Three-dimensional molecular modeling with single molecule FRET,” J. Struct. Biol. 173(3), 497–505 (2011).
  39. Neher, E. and B. Sakmann, “Single-channel currents recorded from membrane denerved frog muscle fibres,” Nature 260(5554), 799–802 (1976). [Inspec] [ISI] [MEDLINE]

Close

Your Recent History Recent History Help

Recently Viewed

  1. Toward automated denoising of single molecular Förster resonance energy transfer data
  2. Extending Förster resonance energy transfer measurements beyond 100 Å using common organic fluorophores: enhanced transfer in the presence of multiple acceptors
  3. ExiFRET: flexible tool for understanding FRET in complex geometries
  4. Three-color Förster resonance energy transfer within single FOF1-ATP synthases: monitoring elastic deformations of the rotary double motor in real time
  5. Förster’s resonance excitation transfer theory: not just a formula
Home Proceedings Journals SPIE eBooks
Privacy Policy Terms of Use Contact Us

SPIE © 1990 - 2012

close