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Abstract:

In the last years, significant advances in microscopy techniques and the introduction of a novel technology to label living cells with genetically encoded fluorescent proteins revolutionized the field of Cell Biology. Our understanding on cell dynamics built from snapshots on fixed specimens has evolved thanks to our actual capability to monitor in real time the evolution of processes in living cells. Among these new tools, single particle tracking techniques were developed to observe and follow individual particles. Hence, we are starting to unravel the mechanisms driving the motion of a wide variety of cellular components ranging from organelles to protein molecules by following their way through the cell. In this review, we introduce the single particle tracking technology to new users. We briefly describe the instrumentation and explain some of the algorithms commonly used to locate and track particles. Also, we present some common tools used to analyze trajectories and illustrate with some examples the applications of single particle tracking to study dynamics in living cells. © Humana Press Inc. 2007.

Registro:

Documento: Artículo
Título:Exploring dynamics in living cells by tracking single particles
Autor:Levi, V.; Gratton, E.
Filiación:Laboratorio de Electrónica Cuántica, Departamento de Física, Pabellón I Ciudad Universitaria, 1428 Buenos Aires, Argentina
Laboratory for Fluorescence Dynamics, Rockwell Engineering Center #204, University of California at Irvine, Irvine, CA 92697-2715, United States
Palabras clave:Dynamics; Intracellular motion; Single particle tracking; Tracking algorithm; Trajectory; 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
Año:2007
Volumen:48
Número:1
Página de inicio:1
Página de fin:15
DOI: http://dx.doi.org/10.1007/s12013-007-0010-0
Título revista:Cell Biochemistry and Biophysics
Título revista abreviado:Cell Biochem. Biophys.
ISSN:10859195
CODEN:CBBIF
CAS:Fluorescent Dyes; Luminescent Proteins; Molecular Motor Proteins
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_10859195_v48_n1_p1_Levi

Referencias:

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

Citas:

---------- APA ----------
Levi, V. & Gratton, E. (2007) . Exploring dynamics in living cells by tracking single particles. Cell Biochemistry and Biophysics, 48(1), 1-15.
http://dx.doi.org/10.1007/s12013-007-0010-0
---------- CHICAGO ----------
Levi, V., Gratton, E. "Exploring dynamics in living cells by tracking single particles" . Cell Biochemistry and Biophysics 48, no. 1 (2007) : 1-15.
http://dx.doi.org/10.1007/s12013-007-0010-0
---------- MLA ----------
Levi, V., Gratton, E. "Exploring dynamics in living cells by tracking single particles" . Cell Biochemistry and Biophysics, vol. 48, no. 1, 2007, pp. 1-15.
http://dx.doi.org/10.1007/s12013-007-0010-0
---------- VANCOUVER ----------
Levi, V., Gratton, E. Exploring dynamics in living cells by tracking single particles. Cell Biochem. Biophys. 2007;48(1):1-15.
http://dx.doi.org/10.1007/s12013-007-0010-0