Exploring dynamics in living cells by tracking single particles

Cell Biochemistry and Biophysics

Volumn 48, Issue 1, 2007, Pages 1-15

  Levi, Valeria ^a   Gratton, Enrico ^b  

^a UNIVERSIDAD DE BUENOS AIRES   (Argentina)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Dynamics; Intracellular motion; Single particle tracking; Tracking algorithm; Trajectory

Indexed keywords

FLUORESCENT DYE; MOLECULAR MOTOR; PHOTOPROTEIN; QUANTUM DOT;

ALGORITHM; BIOMECHANICS; BIOPHYSICS; CELL FUNCTION; CONFOCAL MICROSCOPY; FLUORESCENCE MICROSCOPY; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; METHODOLOGY; MOVEMENT (PHYSIOLOGY); PHYSIOLOGY; REVIEW; SPECTROFLUOROMETRY; STATISTICS;

ALGORITHMS; BIOMECHANICS; BIOPHYSICS; CELL PHYSIOLOGY; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; FLUORESCENT DYES; LUMINESCENT PROTEINS; MICROSCOPY, CONFOCAL; MICROSCOPY, FLUORESCENCE; MOLECULAR MOTOR PROTEINS; MOVEMENT; QUANTUM DOTS; SPECTROMETRY, FLUORESCENCE;

EID: 34548305123     PISSN: 10859195     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12013-007-0010-0     Document Type: Review

References (101)

1. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P. (2002). Methods. In Molecular biology of the cell (pp. 469-582). New York: Garland Science.
2. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P (2002). Cells in their social context. In Molecular biology of the cell (pp. 1065-1423). New York: Garland Science.
3. Babcock, H. P., Chen, C., & Zhuang, X. (2004). Using single-particle tracking to study nuclear trafficking of viral genes. Biophysical Journal, 87, 2749-2758.
4. Belmont, A. S., & Straight, A. F. (1998). In vivo visualization of chromosomes using lac operator-repressor binding. Trends in Cell Biology, 8, 121-124.
5. Belmont, A. S. (2001). Visualizing chromosome dynamics with GFP. Trends in Cell Biology, 11, 250-257.
6. Berland, K. M., So, P. T., & Gratton, E. (1995). Two-photon fluorescence correlation spectroscopy: Method and application to the intracellular environment. Biophysical Journal, 68, 694-701.
7. Berland, K. M., Jacobson, K. A., Frenche, T., & Rajfur, Z. (2003). Electronic cameras for low-light microscopy. In G. Sluder & D. E. Wolf (Eds.), Digital microscopy: A second edition of video microscopy (pp. 103-132). Amsterdam: Elsevier Academic Press.
8. de Brabander, M., Nuydens, R., Ishihara, A., Holifield, B., Jacobson, K., & Geerts, H. (1991). Lateral diffusion and retrograde movements of individual cell surface components on single motile cells observed with Nanovid microscopy. The Journal of Cell Biology, 112, 111-124.
9. Bruchez, M. Jr., Moronne, M., Gin, P., Weiss, S., & Alivisatos, A. P. (1998). Semiconductor nanocrystals as fluorescent biological labels. Science, 281, 2013-2016.
10. Capps, G. G., Pine, S., Edidin, M., & Zuniga, M. C. (2004). Short class I major histocompatibility complex cytoplasmic tails differing in charge detect arbiters of lateral diffusion in the plasma membrane. Biophysical Journal, 86, 2896-2909.
11. Carter, B., Shubeita, G., & Gross, S. (2005). Tracking single particles: A user-friendly quantitative evaluation. Physical Biology, 2, 60-72.
12. Cheezum, M. K., Walker, W. F., & Guilford, W. H. (2001). Quantitative comparison of algorithms for tracking single fluorescent particles. Biophysical Journal, 81, 2378-2388.
13. Chubb, J. R., Boyle, S., Perry, P., & Bickmore, W. A. (2002). Chromatin motion is constrained by association with nuclear compartments in human cells. Current Biology, 12, 439-445.
14. Dahan, M., Levi, S., Luccardini, C., Rostaing, P., Riveau, B., & Triller, A. (2003). Diffusion dynamics of glycine receptors revealed by single-quantum dot tracking. Science, 302, 442-445.
15. Daniels, B. R., Masi, B. C., & Wirtz, D. (2006). Probing single-cell micromechanics in vivo: The microrheology of C. elegans developing embryos. Biophysical Journal, 90, 4712-4719.
16. Deacon, S. W., Serpinskaya, A. S., Vaughan, P. S., Lopez Fanarraga, M., Vernos, I., Vaughan, K. T., & Gelfand, V. I. (2003). Dynactin is required for bidirectional organelle transport. The Journal of Cell Biology, 160, 297-301.
17. Digman, M. A., Brown, C. M., Sengupta, P., Wiseman, P. W., Horwitz, A. R., & Gratton, E. (2005). Measuring fast dynamics in solutions and cells with a laser scanning microscope. Biophysical Journal, 89, 1317-1327.
18. Dubertret, B., Skourides, P., Norris, D. J., Noireaux, V., Brivanlou, A. H., & Libchaber, A. (2002). In vivo imaging of quantum dots encapsulated in phospholipid micelles. Science, 298, 1759-1762.
19. Enderlein, J. (2000). Tracking of fluorescent molecules diffusing within membranes. Applied Physics B-Lasers and Optics, 71, 773-777.
20. Feder, T. J., Brust-Mascher, I., Slattery, J. P., Baird, B., & Webb, W. W. (1996). Constrained diffusion or immobile fraction on cell surfaces: a new interpretation. Biophysical Journal, 70, 2767-2773.
21. Fujiwara, T., Ritchie, K., Murakoshi, H., Jacobson, K., & Kusumi, A. (2002). Phospholipids undergo hop diffusion in compartmentalized cell membrane. The Journal of Cell Biology, 157, 1071-1081.
22. Gao, X., Yang, L., Petros, J. A., Marshall, F. F., Simons, J. W., & Nie, S. (2005). In vivo molecular and cellular imaging with quantum dots. Current Opinion in Biotechnology, 16, 63-72.
23. Gasser, S. M. (2002). Visualizing chromatin dynamics in interphase nuclei. Science, 296, 1412-1416.
24. Geerts, H., de Brabander, M., & Nuydens, R. (1991). Nanovid microscopy. Nature, 351, 765-766.
25. Gelles, J., Schnapp, B. J., & Sheetz, M. P. (1988). Tracking kinesin-driven movements with nanometre-scale precision. Nature, 331, 450-453.
26. Gross, S. P., Tuma, M. C., Deacon, S. W., Serpinskaya, A. S., Reilein, A. R., & Gelfand, V. I. (2002). Interactions and regulation of molecular motors in Xenopus melanophores. The Journal of Cell Biology, 156, 855-865.
27. Gross, S. P., Welte, M. A., Block, S. M., & Wieschaus, E. F. (2002). Coordination of opposite-polarity microtubule motors. The Journal of Cell Biology, 156, 715-724.
28. Gross, S. P. (2004). Hither and yon: A review of bi-directional microtubule-based transport. Physical Biology, 1, R1-R11.
29. Haughland, R. P. (1998). Handbook of fluorescent probes and research chemicals. Eugene, OR: Molecular Probes.
30. Hebert, B., Costantino, S., & Wiseman, P. W. (2005). Spatiotemporal image correlation spectroscopy (STICS) theory, verification, and application to protein velocity mapping in living CHO cells. Biophysical Journal, 88, 3601-3614.
31. Heidemann, S. R., & Wirtz, D. (2004). Towards a regional approach to cell mechanics. Trends in Cell Biology, 14, 161-166.
32. Heun, P., Laroche, T., Shimada, K., Furrer, P., & Gasser, S. M. (2001). Chromosome dynamics in the yeast interphase nucleus. Science, 294, 2181-2186.
33. Hill, D. B., Plaza, M. J., Bonin, K., & Holzwarth, G. (2004). Fast vesicle transport in PC12 neurites: Velocities and forces. European Journal of Biophysics Journal, 33, 623-632.
34. Kis-Petikova, K., & Gratton, E. (2004). Distance measurement by circular scanning of the excitation beam in the two-photon microscope. Microscopy Research and Technique, 63, 34-49.
35. Klonis, N., Rug, M., Harper, I., Wickham, M., Cowman, A., & Tilley, L. (2002). Fluorescence photobleaching analysis for the study of cellular dynamics. European Journal of Biophysics Journal, 31, 36-51.
36. Kole, T. P., Tseng, Y., Jiang, I., Katz, J. L., & Wirtz, D. (2005). Intracellular mechanics of migrating fibroblasts. Molecular Biology of the Cell, 16, 328-338.
37. Kuno, M., Fromm, D. P., Hamann, H. F., Gallagher, A., & Nesbitt, D. J. (2000). Nonexponential "blinking" kinetics of single CdSe quantum dots: A universal power law behavior. The Journal of Chemical Physics, 112, 3117-3120.
38. Kural, C., Kim, H., Syed, S., Goshima, G., Gelfand, V. I., & Selvin, P. R. (2005). Kinesin and dynein move a peroxisome in vivo: A tug-of-war or coordinated movement? Science, 308, 1469-1472.
39. Kusumi, A., Nakada, C., Ritchie, K., Murase, K., Suzuki, K., Murakoshi, H., Kasai, R. S., Kondo, J., & Fujiwara, T. (2005). Paradigm shift of the plasma membrane concept from the two-dimensional continuum fluid to the partitioned fluid: High-speed single-molecule tracking of membrane molecules. Annual Review of Biophysics and Biomolecular Structure, 34, 351-378.
40. Lakadamyali, M., Rust, M. J., Babcock, H. P., & Zhuang, X. (2003). Visualizing infection of individual influenza viruses. Proceedings of the National Academy of Sciences of the United States of America, 100, 9280-9285.
41. Lee, J. S., Panorchan, P., Hale, C. M., Khatau, S. B., Kole, T. P., Tseng, Y., & Wirtz, D. (2006). Ballistic intracellular nanorheology reveals ROCK-hard cytoplasmic stiffening response to fluid Flow. Journal of Cell Science, 1760-1768.
42. Levi, V., Ruan, Q., Plutz, M., Belmont, A. S., & Gratton, E. (2005). Chromatin dynamics in interphase cells revealed by tracking in a two-photon excitation microscope. Biophysical Journal, 89, 4275-4285.
43. Levi, V., Ruan, Q., & Gratton, E. (2005). 3-D particle tracking in a two-photon microscope: application to the study of molecular dynamics in cells. Biophysical Journal, 88, 2919-2928.
44. Levi, V., Serpinskaya, A. S., Gratton, E., & Gelfand, V. (2006). Organelle transport along microtubules in Xenopus melanophores: evidence for cooperation between multiple motors. Biophysical Journal, 90, 318-327.
45. Levi, V., Gelfand, V. I., Serpinskaya, A. S., & Gratton, E. (2006). Melanosomes transported by Myosin-V in Xenopus melanophores perform slow 35 nm steps. Biophysical Journal, 90, L7-L9.
46. Lommerse, P. H., Spaink, H. P., & Schmidt, T. (2004). In vivo plasma membrane organization: results of biophysical approaches. Biochimica et Biophysica Acta, 1664, 119-131.
47. Lommerse, P. H., Snaar-Jagalska, B. E., Spaink, H. P., & Schmidt, T. (2005). Single-molecule diffusion measurements of H-Ras at the plasma membrane of live cells reveal microdomain localization upon activation. Journal of Cell Science, 118, 1799-1809.
48. Ma, S., & Chisholm, R. L. (2002). Cytoplasmic dyneinassociated structures move bidirectionally in vivo. Journal of Cell Science, 115, 1453-1460.
49. Marshall, W. F., Straight, A., Marko, J. F., Swedlow, J., Dernburg, A., Belmont, A., Murray, A. W., Agard, D. A., & Sedat, J. W. (1997). Interphase chromosomes undergo constrained diffusional motion in living cells. Current Biology, 7, 930-939.
50. Mason, T. G., Ganesan, K., van Zanten, J. H., Wirtz, D., & Kuo, S. C. (1997). Particle tracking microrheology of complex fluids. Physical Review Letters, 79, 3282-3285.
51. Meier, J., Vannier, C., Serge, A., Triller, A., & Choquet, D. (2001). Fast and reversible trapping of surface glycine receptors by gephyrin. Nature Neuroscience, 4, 253-260.
52. Michalet, X., Pinaud, F. F., Bentolila, L. A., Tsay, J. M., Doose, S., Li, J. J., Sundaresan, G., Wu, A. M., Gambhir, S. S., & Weiss, S. (2005). Quantum dots for live cells, in vivo imaging, and diagnostics. Science, 307, 538-544.
53. Misteli, T. (2005). Concepts in nuclear architecture. Bioessays, 27, 477-487.
54. Murase, K., Fujiwara, T., Umemura, Y., Suzuki, K., Iino, R., Yamashita, H., Saito, M., Murakoshi, H., Ritchie, K., & Kusumi, A. (2004). Ultrafine membrane compartments for molecular diffusion as revealed by single molecule techniques. Biophysical Journal, 86, 4075-4093.
55. Muratani, M., Gerlich, D., Janicki, S. M., Gebhard, M., Eils, R., & Spector, D. L. (2002). Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus. Nature Cell Biology, 4, 106-110.
56. On-chip multiplication gain. (2002). Technical Note 14. In. Trenton, NJ: Roper Scientific.
57. Oshiro, M., & Moomaw, B. (2003). Cooled vs. intensified vs. electron bombardment CCD cameras-applications and relative advantages. In G. Sluder & D. E. Wolf (Eds.), Digital microscopy: A second edition of video microscopy (pp. 133-156). Amsterdam: Elsevier Academic Press.
58. Piston, D. (1996). Two-photon excitation microscopy. In X. Wang & B. Herman (Eds.), Fluorescence imaging spectroscopy and microscopy (pp. 253-272). New York: John Wiley & Sons.
59. Platani, M., Goldberg, I., Lamond, A. I., & Swedlow, J. R. (2002). Cajal body dynamics and association with chromatin are ATP-dependent. Nature Cell Biology, 4, 502-508.
60. Qian, H., Sheetz, M. P., & Elson, E. L. (1991). Single particle tracking. Analysis of diffusion and flow in two-dimensional systems. Biophysical Journal, 60, 910-921.
61. Reits, E. A., & Neefjes, J. J. (2001). From fixed to FRAP: measuring protein mobility and activity in living cells. Nature Cell Biology, 3, E145-E147.
62. Ritchie, K., Iino, R., Fujiwara, T., Murase, K., & Kusumi, A. (2003). The fence and picket structure of the plasma membrane of live cells as revealed by single molecule techniques (Review). Molecular Membrane Biology, 20, 13-18.
63. Rogers, S. L., Tint, I. S., & Gelfand, V. I. (1998). In vitro motility assay for melanophore pigment organelles. Methods in Enzymology, 298, 361-372.
64. Ruan, Q., Cheng, M. A., Levi, M., Gratton, E., & Mantulin, W. W. (2004). Spatial-temporal studies of membrane dynamics: scanning fluorescence correlation spectroscopy (SFCS). Biophysical Journal, 87, 1260-1267.
65. Sako, Y., & Kusumi, A. (1994). Compartmentalized structure of the plasma membrane for receptor movements as revealed by a nanometer-level motion analysis. The Journal of Cell Biology, 125, 1251-1264.
66. Sako, Y., Minoghchi, S., & Yanagida, T. (2000). Single-molecule imaging of EGFR signalling on the surface of living cells. Nature Cell Biology, 2, 168-172.
67. Sako, Y., & Uyemura, T. (2002). Total internal reflection fluorescence microscopy for single-molecule imaging in living cells. Cell Structure and Function, 27, 357-365.
68. Sanchez, S. A., & Gratton, E. (2005). Lipid-protein interactions revealed by two-photon microscopy and fluorescence correlation spectroscopy. Accounts of Chemical Research, 38, 469-477.
69. Saxton, M. J., & Jacobson, K. (1997). Single-particle tracking: Applications to membrane dynamics. Annual Review of Biophysics and Biomolecular Structure, 26, 373-399.
70. Saxton, M. J. (1994). Anomalous diffusion due to obstacles: A Monte Carlo study. Biophysical Journal, 66, 394-401.
71. Saxton, M. J. (1994). Single-particle tracking: Models of directed transport. Biophysical Journal, 67, 2110-2119.
72. Saxton, M. J. (1997). Single-particle tracking: the distribution of diffusion coefficients. Biophysical Journal, 72, 1744-1753.
73. Saxton, M. J. (1996). Anomalous diffusion due to binding: A Monte Carlo study. Biophysical Journal, 70, 1250-1262.
74. Saxton, M. J. (1993). Lateral diffusion in an archipelago. Single-particle diffusion. Biophysical Journal, 64, 1766-1780.
75. Saxton, M. J. (1995). Single-particle tracking: Effects of corrals. Biophysical Journal, 69, 389-398.
76. Schneckenburger, H. (2005). Total internal reflection fluorescence microscopy: technical innovations and novel applications. Current Opinion in Biotechnology, 16, 13-18.
77. Sheetz, M. P., Turney, S., Qian, H., & Elson, E. L. (1989). Nanometre-level analysis demonstrates that lipid flow does not drive membrane glycoprotein movements. Nature, 340, 284-288.
78. Simson, R., Yang, B., Moore, S. E., Doherty, P., Walsh, F. S., & Jacobson, K. A. (1998). Structural mosaicism on the submicron scale in the plasma membrane. Biophysical Journal, 74, 297-308.
79. Singer, S. J., & Nicolson, G. L. (1972). The fluid mosaic model of the structure of cell membranes. Science, 175, 720-731.
80. So, P. T., Dong, C. Y., Masters, B. R., & Berland, K. M. (2000). Two-photon excitation fluorescence microscopy. Annual Review of Biomedical Engineering, 2, 399-429.
81. Sodeik B. (2000). Mechanisms of viral transport in the cytoplasm. Trends in Microbiology, 8, 465-472.
82. Spring, K. R. (2003). Cameras for digital microscopy. In G. Sluder & D. E. Wolf (Eds.), Digital microscopy: A second edition of video microscopy (pp. 87-132). Amsterdam: Elsevier Academic Press.
83. Stephens, D. J., & Allan, V. J. (2003). Light microscopy techniques for live cell imaging. Science, 300, 82-86.
84. Syed, S., Snyder, G. E., Franzini-Armstrong, C., Selvin, P. R., & Goldman, Y. E. (2006). Adaptability of myosin V studied by simultaneous detection of position and orientation. The Embo Journal, 25, 1795-1803.
85. Thompson, R. E., Larson, D. R., & Webb, W. W. (2002). Precise nanometer localization analysis for individual fluorescent probes. Biophysical Journal, 82, 2775-2783.
86. Tomishige, M., Sako, Y., & Kusumi, A. (1998). Regulation mechanism of the lateral diffusion of band 3 in erythrocyte membranes by the membrane skeleton. The Journal of Cell Biology, 142, 989-1000.
87. Toprak, E., Enderlein, J., Syed, S., McKinney, S. A., Petschek, R. G., Ha, T., Goldman, Y. E., & Selvin, P. R. (2006). Defocused orientation and position imaging (DOPI) of myosin V. Proceedings of the National Academy of Sciences of the United States of America, 103, 6495-6499.
88. Tseng, Y., Kole, T. P., & Wirtz, D. (2002). Micromechanical mapping of live cells by multiple-particle-tracking microrheology. Biophysical Journal, 83, 3162-3176.
89. Tseng, Y., Lee, J. S., Kole, T. P., Jiang, I., & Wirtz, D. (2004). Micro-organization and visco-elasticity of the interphase nucleus revealed by particle nanotracking. Journal of Cell Science, 117, 2159-2167.
90. Tsien, R. Y. (1998). The green fluorescent protein. Annual Review of Biochemistry, 67, 509-544.
91. Tumbar, T., & Belmont, A. S. (2001). Interphase movements of a DNA chromosome region modulated by VP16 transcriptional activator. Nature Cell Biology, 3, 134-139.
92. Vale, R. D. (2003). The molecular motor toolbox for intracellular transport. Cell, 112, 467-480.
93. Vazquez, J., Belmont, A. S., & Sedat, J. W. (2001). Multiple regimes of constrained chromosome motion are regulated in the interphase Drosophila nucleus. Current Biology, 11, 1227-1239.
94. Warshaw, D. M., Kennedy, G. G., Work, S. S., Krementsova, E. B., Beck, S., & Trybus, K. M. (2005). Differential labeling of myosin V heads with quantum dots allows direct visualization of hand-over-hand processivity. Biophysical Journal, 88, L30-L32.
95. Wazawa, T., & Ueda, M. (2005). Total internal reflection fluorescence microscopy in single molecule nanobioscience. Advances in Biochemical Engineering/Biotechnology, 95, 77-106.
96. Welte, M. A., Gross, S. P., Postner, M., Block, S. M., & Wieschaus, E. F. (1998). Developmental regulation of vesicle transport in Drosophila embryos: Forces and kinetics. Cell, 92, 547-557.
97. Welte, M. A. (2004). Bidirectional transport along microtubules. Current Biology, 14, R525-R537.
98. Yamada, S., Wirtz, D., & Kuo, S. C. (2000). Mechanics of living cells measured by laser tracking microrheology. Biophysical Journal, 78, 1736-1747.
99. Yildiz, A., Forkey, J. N., McKinney, S. A., Ha, T., Goldman, Y. E., & Selvin, P. R. (2003). Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization. Science, 300, 2061-2065.
100. Yildiz, A., Park, H., Safer, D., Yang, Z., Chen, L. Q., Selvin, P. R., & Sweeney, H. L. (2004). Myosin VI steps via a hand-over-hand mechanism with its lever arm undergoing fluctuations when attached to actin. The Journal of Biological Chemistry, 279, 37223-37226.
101. Yildiz, A., Tomishige, M., Vale, R. D., & Selvin, P. R. (2004). Kinesin walks hand-over-hand. Science, 303, 676-678.