Deconvolving single-molecule intensity distributions for quantitative microscopy measurements

Biophysical Journal

Volumn 92, Issue 8, 2007, Pages 2926-2943

  Mutch, Sarah A ^a   Fujimoto, Bryant S ^a   Kuyper, Christopher L ^a   Kuo, Jason S ^a   Bajjalieh, Sandra M ^b   Chiu, Daniel T ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AVIDIN; BIOCYTIN;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; FLUIDIZATION; FLUORESCENCE MICROSCOPY; NONHUMAN; PROTEIN BINDING; QUANTITATIVE ANALYSIS; RAT; SIMULATION;

EID: 34147151034     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.101428     Document Type: Article

References (40)

1. Selinummi, J., J. R. Sarkanen, A. Niemisto, M. L. Linne, T. Ylikomi, O. Yli-Harja, and T. O. Jalonen. 2006. Quantification of vesicles in differentiating human SH-SY5Y neuroblastoma cells by automated image analysis. Neurosci. Lett. 396:102-107.
2. Krzan, M., M. Stenovec, M. Kreft, T. Pangrsic, S. Grilc, P. G. Haydon, and R. Zorec. 2003. Calcium-dependent exocytosis of atrial natriuretic peptide from astrocytes. J. Neurosci. 23:1580-1583.
3. Antonova, I., O. Arancio, A. C. Trillat, H. G. Wang, L. Zablow, H. Udo, E. R. Kandel, and R. D. Hawkins. 2001. Rapid increase in clusters of presynaptic proteins at onset of long-lasting potentiation. Science. 294:1547-1550.
4. Ogoshi, F., and J. H. Weiss. 2003. Heterogeneity of Ca2+-permeable AMPA/kainate channel expression in hippocampal pyramidal neurons: fluorescence imaging and immunocytochemical assessment. J. Neurosci. 23:10521-10530.
5. Axelrod, D. 2001. Total internal reflection fluorescence microscopy in cell biology. Traffic. 2:764-774.
6. Schmidt, T., G. J. Schütz, H. J. Gruber, and H. Schindler. 1996. Local stoichiometries determined by counting individual molecules. Anal. Chem. 68:4397-4401.
7. Kask, P., K. Palo, D. Ullmann, and K. Gall. 1999. Fluorescence-intensity distribution analysis and its application in biomolecular detection technology. Proc. Natl. Acad. Sci. USA. 96:13756-13761.
8. Muller, J. D., Y. Chen, and E. Gratton. 2000. Resolving heterogeneity on the single molecular level with the photon-counting histogram. Biophys. J. 78:474-486.
9. Hillesheim, L. N., and J. D. Muller. 2003. The photon counting histogram in fluorescence fluctuation spectroscopy with non-ideal photodetectors. Biophys. J. 85:1948-1958.
10. Muller, J. D. 2004. Cumulant analysis in fluorescence fluctuation spectroscopy. Biophys. J. 86:3981-3992.
11. Wu, B., and J. D. Muller. 2005. Time-integrated fluorescence cumulant analysis in fluorescence fluctuation spectroscopy. Biophys. J. 89:2721-2735.
12. Iino, R., I. Koyama, and A. Kusumi. 2001. Single molecule imaging of green fluorescent proteins in living cells: E-cadherin forms oligomers on the free cell surface. Biophys. J. 80:2667-2677.
13. Sugiyama, Y., I. Kawabata, K. Sobue, and S. Okabe. 2005. Determination of absolute protein numbers in single synapses by a GFP-based calibration technique. Nat. Methods. 2:677-684.
14. Wu, J. Q., and T. D. Pollard. 2005. Counting cytokinesis proteins globally and locally in fission yeast. Science. 310:310-314.
15. Gordon, M. P., T. Ha, and P. R. Selvin. 2004. Single-molecule high-resolution imaging with photobleaching. Proc. Natl. Acad. Sci. USA. 101:6462-6465.
16. Chiu, C. S., K. Jensen, I. Sokolova, D. Wang, M. Li, P. Deshpande, N. Davidson, I. Mody, M. W. Quick, S. R. Quake, and H. A. Lester. 2002. Number, density, and surface/cytoplasmic distribution of GABA transporters at presynaptic structures of knock-in mice carrying GABA transporter subtype 1-green fluorescent protein fusions. J. Neurosci. 22:10251-10266.
17. Dundr, M., J. G. McNally, J. Cohen, and T. Misteli. 2002. Quantitation of GFP-fusion proteins in single living cells. J. Struct. Biol. 140:92-99.
18. Chiu, C. S., E. Kartalov, M. Unger, S. Quake, and H. A. Lester. 2001. Single-molecule measurements calibrate green fluorescent protein surface densities on transparent beads for use with 'knock-in' animals and other expression systems. J. Neurosci. Methods. 105:55-63.
19. Yu, J., J. Xiao, X. Ren, K. Lao, and X. S. Xie. 2006. Probing gene expression in live cells, one protein molecule at a time. Science. 311:1600-1603.
20. Newman, J. R., S. Ghaemmaghami, J. Ihmels, D. K. Breslow, M. Noble, J. L. DeRisi, and J. S. Weissman. 2006. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature. 441:840-846.
21. Panchuk-Voloshina, N., R. P. Haugland, J. Bishop-Stewart, M. K. Bhalgat, P. J. Millard, F. Mao, and W. Y. Leung. 1999. Alexa dyes, a series of new fluorescent dyes that yield exceptionally bright, photostable conjugates. J. Histochem. Cytochem. 47:1179-1188.
22. Pennuto, M., D. Bonanomi, F. Benfenati, and F. Valtorta. 2003. Synaptophysin I controls the targeting of VAMP2/synaptobrevin II to synaptic vesicles. Mol. Biol. Cell. 14:4909-4919.
23. Buckley, K., and R. B. Kelly. 1985. Identification of a transmembrane glycoprotein specific for secretory vesicles of neural and endocrine cells. J. Cell Biol. 100:1284-1294.
24. Hell, J. W., P. R. Maycox, H. Stadler, and R. Jahn. 1988. Uptake of GABA by rat brain synaptic vesicles isolated by a new procedure. EMBO J. 7:3023-3029.
25. Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
26. Bayer, E. A., and M. Wilchek. 1980. The use of the avidin-biotin complex as a tool in molecular biology. Methods Biochem. Anal. 26:1-45.
27. Fiorini, G. S., and D. T. Chiu. 2005. Disposable microfluidic devices: fabrication, function, and application. Biotechniques. 38:429-446.
28. Kuyper, C. L., J. S. Kuo, S. A. Mutch, and D. T. Chiu. 2006. Proton permeation into single vesicles occurs via a sequential two-step mechanism and is heterogeneous. J. Am. Chem. Soc. 128:3233-3240.
29. Axelrod, D. 1989. Total internal reflection fluorescence microscopy. Methods Cell Biol. 30:245-270.
30. Willig, K. I., S. O. Rizzoli, V. Westphal, R. Jahn, and S. W. Hell. 2006. STED microscopy reveals that synaptotagmin remains clustered after synaptic vesicle exocytosis. Nature. 440:935-939.
31. Schuler, B., E. A. Lipman, and W. A. Eaton. 2002. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature. 419:743-747.
32. Ren, X., H. Li, R. W. Clarke, D. A. Alves, L. Ying, D. Klenerman, and S. Balasubramanian. 2006. Analysis of human telomerase activity and function by two color single molecule coincidence fluorescence spectroscopy. J. Am. Chem. Soc. 128:4992-5000.
33. Del Castillo, J., and B. Katz. 1954. Quantal components of the end-plate potential. J. Physiol. 124:560-573.
34. Edwards, F. A., A. Konnerth, and B. Sakmann. 1990. Quantal analysis of inhibitory synaptic transmission in the dentate gyrus of rat hippocampal slices: a patch-clamp study. J. Physiol. (Lond.). 430:213-249.
35. Hellen, E. H., and D. Axelrod. 1987. Fluorescence emission at dielectric and metal-film interfaces. J. Opt. Soc. Am. B. 4:337-350.
36. Mertz, J. 2000. Radiative absorption, fluorescence, and scattering of a classical dipole near a lossless interface: a unified description. J. Opt. Soc. Am. B. 17:1906-1913.
37. Limpert, E., W. A. Stahel, and M. Abbt. 2001. Log-normal distributions across the sciences: Keys and clues. Bioscience. 51:341-352.
38. Bevington, P. R. 1969. Data Reduction and Error Analysis for the Physical Sciences. McGraw-Hill, New York.
39. Press, W. H. 2001. Numerical Recipes in Fortran 77: The Art of Scientific Computing. Cambridge University Press, Cambridge, UK; New York, NY.
40. D'Agostino, R. B., and M. A. Stephens. 1986. Goodness-of-Fit Techniques. M. Dekker, New York.