Optical control and study of biological processes at the single-cell level in a live organism

Reports on Progress in Physics

Volumn 76, Issue 7, 2013, Pages

  Feng, Zhiping ^a   Zhang, Weiting ^b   Xu, Jianmin ^a   Gauron, Carole ^c   Ducos, Bertrand ^b   Vriz, Sophie ^c   Volovitch, Michel ^b,c   Jullien, Ludovic ^b   Weiss, Shimon ^a   Bensimon, David ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b ECOLE NORMALE SUPÉRIEURE   (France)

^c PSL RESEARCH UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENT DYE;

ANIMAL; HUMAN; LIGHT; LIGHT RELATED PHENOMENA; METABOLISM; METHODOLOGY; OPTOGENETICS; REVIEW; SINGLE CELL ANALYSIS; PROCEDURES;

ANIMALS; FLUORESCENT DYES; HUMANS; LIGHT; OPTICAL PROCESSES; OPTOGENETICS; SINGLE-CELL ANALYSIS;

EID: 84880575118     PISSN: 00344885     EISSN: None     Source Type: Journal    
DOI: 10.1088/0034-4885/76/7/072601     Document Type: Article

References (251)

1. Rouault H and Hakim V 2012 Different cell fates from cell-cell interactions: core architectures of two-cell bistable networks Biophys. J 102 417-26
2. François P and Hakim V 2004 Design of genetic networks with specified functions by evolution in silico Proc. Natl Acad. Sci. USA 101 580-5
3. Xiong W and Ferrell J E 2003 A positive-feedback-based bistable 'memory module' that governs a cell fate decision Nature 426 460-5
4. Sprinzak D, Lakhanpal A, Lebon L, Santat L A, Fontes M E, Anderson G A, Garcia-Ojalvo J and Elowitz M B 2010 Cis interactions between notch and delta generate mutually exclusive signaling states Nature 465 86-90
5. Adam J, Myat A, Le Roux I, Eddison M, Henrique D, Ish-Horowicz D and Lewis J 1998 Cell fate choices and the expression of notch, delta and serrate homologues in the chick inner ear: parallels with drosophila sense-organ development Development 125 4645-54
6. Oates A C, Morelli L G and Ares S 2012 Patterning embryos with oscillations: structure, function and dynamics of the vertebrate segmentation clock Development 139 625-39
7. Turing A M 1952 The chemical basis of morphogenesis Phil. Trans. R. Soc. 237 37-72
8. Wolpert L 1969 Positional information and the spatial pattern of cellular differentiation J. Theor. Biol. 25 1-47
9. Porcher A and Dostatni N 2010 The bicoid morphogen system Curr. Biol. 20 249-54
10. Eldar A, Rosin D, Shilo B Z and Barkai N 2003 Self-enhanced ligand degradation underlies robustness of morphogen gradients Dev. Cell. 5 635-46
11. Velculescu V E, Zhang L, Zhou W, Vogelstein J, Basrai M A, Basset D E Jr, Hieter P, Vogelstein B and Kinzler K W 1997 Characterization of the yeast transcriptome Cell 88 243-51
12. McDonnell L A and Heeren R M 2007 Imaging mass spectrometry Mass Spectrom. Rev. 26 606-43
13. Min W, Freudiger C W, Lu S and Xie X S 2011 Coherent nonlinear optical imaging: beyond fluorescence microscopy Annu. Rev. Phys. Chem. 62 507-30
14. Bernard Valeur 2001 Molecular Fluorescence: Principles and Applications (New York: Wiley)
15. Denk W, Strickler J and Webb W 1990 Two-photon laser scanning fluorescence microscopy Science 248 73-6
16. Drobizhev M, Makarov N S, Tillo S E, Hughes T E and Rebane A 2011 Two-photon absorption properties of fluorescent proteins Nature Meth. 8 393-9
17. Giepmans B N G, Adams S R, Ellisman M H and Tsien R Y 2006 The fluorescent toolbox for assessing protein location and function Science 312 217-24
18. Sameiro M and Gonsalves T 2009 Fluorescent labeling of biomolecules with organic probes Chem. Rev. 109 190-212
19. Fernandez-Suarez M and Ting A Y 2008 Fluorescent probes for super-resolution imaging in living cells Nature Rev. Mol. Cell. Biol. 9 929-43
20. Ha T and Tinnefeld P 2012 Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging Ann. Rev. Phys. Chem. 63 595-617
21. Sahoo H 2012 Fluorescent labeling techniques in biomolecules: a flashback RSC Adv. 2 7017-29
22. Szent-Gyorgyi C et al 2008 Fluorogen-activating single-chain antibodies for imaging cell surface proteins Nature Biotechnol. 26 235-40
23. Armitage B A 2011 Imaging of RNA in live cells Curr. Opin. Chem. Biol. 15 806-12
24. Paige J S, Wu K Y and Jaffrey S R 2011 RNA mimics of green fluorescent protein Science 333 642-6
25. Bao G, Jong Rhee W and Tsourkas A 2009 Fluorescent probes for live-cell RNA detection Annu. Rev. Biomed. Eng. 11 25-47
26. Shav-Tal Y, Singer R and Darzacq X 2004 Imaging gene expression in single living cells Nature Rev. Mol. Cell. Biol. 5 856-62
27. Wombacher R and Cornish V W 2011 Chemical tags: applications in live cell fluorescence imaging J. Biophoton. 4 391-402
28. Day R N and Davidson M W 2009 The fluorescent protein palette: tools for cellular imaging Chem. Soc. Rev. 38 2887-921
29. Snapp E L 2009 Fluorescent proteins: a cell biologist's user guide Trends Cell. Biol. 19 649-55
30. Chudakov D M, Matz M V, Lukyanov S and Lukyanov K A 2010 Fluorescent proteins and their applications in imaging living cells and tissues Physiol. Rev. 90 1103-63
31. Sauer M 2005 Reversible molecular photoswitches: a key technology for nanoscience and fluorescence imaging Proc. Natl Acad. Sci. USA 102 9433-4
32. Lippincott-Schwartz J and Patterson G H 2009 Photoactivatable fluorescent proteins for diffraction-limited and super-resolution imaging Trends Cell. Biol. 19 555-65
33. O'Hare H, Johnsson K and Gautier A 2007 Chemical probes shed light on protein function Curr. Opin. Struct. Biol. 17 488-94
34. Gautier A, Juillerat A, Heinis C, Correa I R Jr, Kindermann M, Beaufils F and Johnsson K 2008 An engineered protein tag for multiprotein labeling in living cells Chem. Biol. 15 128-36
35. Summerer D, Chen S, Wu N, Deiters A, Chin J and Schultz P 2006 A genetically encoded fluorescent amino acid Proc. Natl Acad. Sci. USA 103 9785-9
36. Magde D, Elson E L and Webb W W 1972 Thermodynamic fluctuations in a reacting system - measurement by fluorescence correlation spectroscopy Phys. Rev. Lett. 11 705-8
37. Johnson I 1998 Fluorescent probes for living cells Histochem. J. 30 123-40
38. Zhang J, Campbell R E, Ting A Y and Tsien R Y 2002 Creating new fluorescent probes for cell biology Nature Rev. Mol. Cell. Biol. 3 906-18
39. Vendrell M, Zhai D, Cheng Er J and Chang Y-T 2012 Combinatorial strategies in fluorescent probe development Chem. Rev. 112 4391-420
40. Charier S, Ruel O, Baudin J-B, Alcor D, Allemand J-F, Meglio A and Jullien L 2004 An efficient fluorescent probe for ratiometric pH measurements in aqueous solutions Angew. Chem. Int. Edn. Engl. 43 4785-8
41. Charier S, Ruel O, Baudin J-B, Alcor D, Allemand J-F, Meglio A and Jullien L 2006 An efficient fluorescent probe after one- and two-photon excitation for making ratiometric pH measurements close to neutrality in aqueous solutions Chem. Eur. J. 12 1097-113
42. Charier S, Meglio A, Alcor D, Cogné Laage E, Allemand J-F, Jullien L and Lemarchand A 2005 Reactant concentrations from fluorescence correlation spectroscopy with tailored fluorescent probes. an example of local calibration-free pH measurement J. Am. Chem. Soc. 127 15491-505
43. Hell S W and Wichmann J 1994 Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy Opt. Lett. 19 780-2
44. Klar T A and Hell S W 1999 Subdiffraction resolution in far-field fluorescence microscopy Opt. Lett. 24 954-6
45. Folling J, Bossi M, Bock H, Medda R, Wurm C A, Hein B, Jakobs S, Eggeling C and Hell S W 2008 Fluorescence nanoscopy by ground-state depletion and single-molecule return Nature Methods 5 943-5
46. Hofmann M, Eggeling C, Jakobs S and Hell S W 2005 Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins Proc. Natl Acad. Sci. USA 102 17565-9
47. Gustafsson M G 2005 Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution Proc. Natl Acad. Sci. USA 102 13081-6
48. Heintzmann R, Jovin T M and Cremer C 2002 Saturated patterned excitation microscopy-a concept for optical resolution improvement J. Opt. Soc. Am. A 19 1599-609
49. Rust M J, Bates M and Zhuang X 2006 Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) Nature Methods 3 793-5
50. Betzig E, Patterson G H, Sougrat R, Lindwasser O W, Olenych S, Bonifacino J S, Davidson M W, Lippincott-Schwartz J and Hess H F 2006 Imaging intracellular fluorescent proteins at nanometer resolution Science 313 1642-5
51. Hess S T, Girirajan T P and Mason M D 2006 Ultra-high resolution imaging by fluorescence photoactivation localization microscopy Biophys. J. 91 4258-72
52. Dertinger T, Colyer R, Iyer G, Weiss S and Enderlein J 2009 Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI) Proc. Natl Acad. Sci. USA 106 22287-92
53. Hell S W 2007 Far-field optical nanoscopy Science 316 1153-8
54. Gould T J, Hess S T and Bewersdorf J 2012 Optical nanoscopy: from acquisition to analysis Annu. Rev. Biomed. Eng. 14 231-54
55. Lidke K, Rieger B, Jovin T and Heintzmann R 2005 Superresolution by localization of quantum dots using blinking statistics Opt. Express 13 7052-62
56. Howarth M, Liu W, Puthenveetil S, Zheng Y, Marshall L F, Schmidt M M, Wittrup K D, Bawendi M G and Ting A Y 2008 Monovalent, reduced-size quantum dots for imaging receptors on living cells Nature Methods 5 397-9
57. Irvine S E, Staudt T, Rittweger E, Engelhardt J and Hell S W 2008 Direct light-driven modulation of luminescence from mn-doped znse quantum dots Angew. Chem. Int. Edn. Engl. 47 2685-8
58. Biteen J S, Thompson M A, Tselentis N K, Bowman G R, Shapiro L and Moerner W E 2008 Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP Nature Methods 5 947-9
59. Hein B, Willig K I and Hell S W 2008 Stimulated emission depletion (STED) nanoscopy of a fluorescent protein-labeled organelle inside a living cell Proc. Natl Acad. Sci. USA 105 14271-6
60. Shroff H, Galbraith C G, Galbraith J A and Betzig E 2008 Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics Nature Methods 5 417-23
61. Westphal V, Rizzoli S O, Lauterbach M A, Kamin D, Jahn R and Hell S W 2008 Video-rate far-field optical nanoscopy dissects synaptic vesicle movement Science 320 246-9
62. Kner P, Chhun B B, Griffis E R, Winoto L and Gustafsson M G 2009 Super-resolution video microscopy of live cells by structured illumination Nature Methods 6 339-42
63. Hein B, Willig K I, Wurm C A, Westphal V, Jakobs S and Hell S W 2010 Stimulated emission depletion nanoscopy of living cells using SNAP-tag fusion proteins Biophys. J. 98 158-63
64. Subach F V, Patterson G H, Renz M, Lippincott-Schwartz J and Verkhusha V V 2010 Bright monomeric photoactivatable red fluorescent protein for two-color super-resolution sptPALM of live cells J. Am. Chem. Soc. 132 6481-91
65. Wombacher R, Heidbreder M, van de Linde S, Sheetz M P, Heilemann M, Cornish V W and Sauer M 2010 Live-cell super-resolution imaging with trimethoprim conjugates Nature Methods 7 717-9
66. Cella Zanacchi F, Lavagnino Z, Perrone Donnorso M, Del Bue A, Furia L, Faretta M and Diaspro A 2011 Live-cell 3D super-resolution imaging in thick biological samples Nature Methods 8 1047-9
67. Gunewardene M S, Subach F V, Gould T J, Penoncello G P, Gudheti M V, Verkhusha V V and Hess S T 2011 Superresolution imaging of multiple fluorescent proteins with highly overlapping emission spectra in living cells Biophys. J. 101 1522-8
68. Jones S A, Shim S H, He J and Zhuang X 2011 Fast, three-dimensional super-resolution imaging of live cells Nature Methods 8 499-508
69. Klein T, Loschberger A, Proppert S, Wolter S, van de Linde S and Sauer M 2011 Live-cell dSTORM with SNAP-tag fusion proteins Nature Methods 8 7-9
70. Lew M D, Lee S F, Ptacin J L, Lee M K, Twieg R J, Shapiro L and Moerner W E 2011 Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus Proc. Natl Acad. Sci. USA 108 E1102-10
71. Shao L, Kner P, Rego E H and Gustafsson M G 2011 Super-resolution 3D microscopy of live whole cells using structured illumination Nature Methods 8 1044-6
72. Wang W, Li G W, Chen C, Xie X S and Zhuang X 2011 Chromosome organization by a nucleoid-associated protein in live bacteria Science 333 1445-9
73. Bakshi S, Siryaporn A, Goulian M and Weisshaar J C 2012 Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells Mol. Microbiol. 85 21-38
74. Fiolka R, Shao L, Rego E H, Davidson M W and Gustafsson M G 2012 Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination Proc. Natl Acad. Sci. USA 109 5311-5
75. Ries J, Kaplan C, Platonova E, Eghlidi H and Ewers H 2012 A simple, versatile method for gfp-based super-resolution microscopy via nanobodies Nature Methods 9 582-4
76. Shim S H, Xia C, Zhong G, Babcock H P, Vaughan J C, Huang B, Wang X, Xu C, Bi G Q and Zhuang X 2012 Super-resolution fluorescence imaging of organelles in live cells with photoswitchable membrane probes Proc. Natl Acad. Sci. USA 109 13978-83
77. Wagner E et al 2012 Stimulated emission depletion live-cell super-resolution imaging shows proliferative remodeling of t-tubule membrane structures after myocardial infarction Circ. Res. 111 402-14
78. Wilmes S, Staufenbiel M, Lisse D, Richter C P, Beutel O, Busch K B, Hess S T and Piehler J 2012 Triple-color super-resolution imaging of live cells: resolving submicroscopic receptor organization in the plasma membrane Angew. Chem. Int. Edn Engl. 51 4868-71
79. Rankin B R, Moneron G, Wurm C A, Nelson J C, Walter A, Schwarzer D, Schroeder J, Colon-Ramos D A and Hell S W 2011 Nanoscopy in a living multicellular organism expressing gfp Biophys. J. 100 L63-5
80. Berning S, Willig K I, Steffens H, Dibaj P and Hell S W 2012 Nanoscopy in a living mouse brain Science 335 551
81. Testa I, Urban N T, Jakobs S, Eggeling C, Willig K I and Hell S W 2012 Nanoscopy of living brain slices with low light levels Neuron 75 992-1000
82. York A G, Parekh S H, Dalle Nogare D, Fischer R S, Temprine K, Mione M, Chitnis A B, Combs C A and Shroff H 2012 Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy Nature Methods 9 749-54
83. Dertinger T, Colyer R, Vogel R, Enderlein J and Weiss S 2010 Achieving increased resolution and more pixels with superresolution optical fluctuation imaging (SOFI) Opt. Express 18 18875-85
84. Dertinger T, Heilemann M, Vogel R, Sauer M and Weiss S 2010 Superresolution optical fluctuation imaging with organic dyes Angew. Chem. Int. Edn Engl. 49 9441-3
85. Geissbuehler S, Dellagiacoma C and Lasser T 2011 Comparison between sofi and storm Biomed Opt. Express 2 408-20
86. Dedecker P, Mo G C, Dertinger T and Zhang J 2012 Widely accessible method for superresolution fluorescence imaging of living systems Proc. Natl Acad. Sci. USA 109 10909-14
87. Dertinger T, Colyer R, Vogel R, Heilemann M, Sauer M, Enderlein J and Weiss S 2012 Superresolution optical fluctuation imaging (SOFI) Adv. Exp. Med. Biol. 733 17-21
88. Geissbuehler M M, Bonacina L, Shcheslavskiy V, Bocchio N, Geissbuehler S, Leutenegger M, Märki I, Wolf J P and Lasser T 2012 Nonlinear correlation spectroscopy (NLCS) Nano. Lett. 12 1668-72
89. Gustafsson M G L, Shao L, Carlton P M, Rachel Wang C J, Golubovskaya I N, Cande W Z, Agard D A and Sedat J W 2008 Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination Biophys. J. 94 4957-70
90. Gustafsson M G 2000 Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy J. Microsc. 198 82-7
91. Rego E H, Shao L, Macklin J J, Winoto L, Johansson G A, Kamps-Hughes N, Davidson M W and Gustafsson M G 2012 Nonlinear structured-illumination microscopy with a photoswitchable protein reveals cellular structures at 50 nm resolution Proc. Natl Acad. Sci. USA 109 E135-43
92. Reynaud E G, Krzic U, Greger K and Stelzer E H 2008 Light sheet-based fluorescence microscopy: more dimensions, more photons, and less photodamage HFSP J. 2 266-75
93. Tao S H, Lee W M and Yuan X C 2003 Dynamic optical manipulation with a higher-order fractional bessel beam generated from a spatial light modulator Opt. Lett. 28 1867-9
94. Olarte O E, Licea-Rodriguez J, Palero J A, Gualda E J, Artigas D, Mayer J, Swoger J, Sharpe J, Rocha-Mendoza I, Rangel-Rojo R and Loza-Alvarez P 2012 Image formation by linear and nonlinear digital scanned light-sheet fluorescence microscopy with gaussian and bessel beam profiles Biomed. Opt. Express. 3 1492-505
95. Speicher D W 2004 Proteome Analysis: Interpreting the Genome (Amsterdam: Elsevier)
96. Spiller D G, Wood C D, Rand D A and White M R H 2010 Measurement of single-cell dynamics Nature 465 736-45
97. Weiss M, Elsner M, Kartberg F and Nilsson T 2004 Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells Biophys. J. 87 3518-24
98. Eigen M and DeMayer L 1963 Techniques of Organic Chemistry, Investigation of Rates and Mechanism of Reactions, Part II vol 8 (New York: Wiley Interscience)
99. Berthoumieux H, Jullien L and Lemarchand A 2007 Response to a temperature modulation a signature of chemical mechanisms Phys. Rev. E 76 056112
100. Berthoumieux H, Antoine C, Jullien L and Lemarchand A 2009 Resonant response to temperature modulation for enzymatic dynamics characterization Phys. Rev. E 79 021906
101. Schoen I, Krammer H and Braun D 2009 Hybridization kinetics is different inside cells Proc. Natl Acad. Sci. USA 106 21649-54
102. Zrelli K, Barilero T, Cavatore E, Berthoumieux H, Le Saux T, Croquette V, Lemarchand A, Gosse C and Jullien L 2011 Temperature modulation and quadrature detection for selective titration of two-state exchanging reactants Anal. Chem. 83 2476-84
103. Lemarchand A, Berthoumieux H, Jullien L and Gosse C 2012 Chemical mechanism identification from frequency response to small temperature modulation J. Phys. Chem. A 116 8455-63
104. Guo M, Xu Y and Gruebele M 2012 Temperature dependence of protein folding kinetics in living cells Proc. Natl Acad. Sci. USA 109 17863-67
105. Gelman H, Platkov M and Gruebele M 2012 Rapid perturbation of free-energy landscapes: from in vitro to in vivo Chem. Eur. J. 18 6420-7
106. Mettetal J T, Muzzey D, Gomez-Uribe C and van Oudenaarden C 2008 The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae Science 319 482-4
107. Shimizu T S, Tu Y and Berg H C 2010 A modular gradient-sensing network for chemotaxis in Eescherichia coli revealed by responses to time-varying stimuli Mol. Syst. Biol. 6 382
108. Dhumpa R and Roper M G 2012 Temporal gradients in microfluidic systems to probe cellular dynamics: a review Anal. Chim. Acta 743 9-18
109. Tomida T, Oda S, Takekawa M, Iino Y and Saito H 2012 The temporal pattern of stimulation determines the extent and duration of MAPK activation in a caenorhabditis elegans sensory neuron Sci. Signal. 5 ra76
110. Toettcher J E, Voigt C A, Weiner O D and Lim O D 2011 The promise of optogenetics in cell biology: interrogating molecular circuits in space and time Nature Methods 8 35-8
111. Couture O, Faivre M, Pannacci N, Babataheri A, Servois V, Tabeling P and Tanter M 2011 Ultrasound internal tattooing Med. Phys. 38 1116-23
112. Petit M, Bort G, Doan B-T, Sicard C, Ogden D, Scherman D, Ferroud C and Dalko P I 2011 X-ray photolysis to release ligands from caged reagents by an intramolecular antenna sensitive to magnetic resonance imaging Angew. Chem. Int. Edn Engl. 50 9708-11
113. Geva-Zatorsky N, Dekel E, Batchelor E, Lahav G and Alon U 2010 Fourier analysis and systems identification of the p53 feedback loop Proc. Natl Acad. Sci. USA 107 13550-5
114. Ntziachristos V 2010 Going deeper than microscopy: the optical imaging frontier in biology Nature Methods 7 603-14
115. Wang L V and Hu S 2012 Photoacoustic tomography: in vivo imaging from organelles to organs Science 335 1458-62
116. Pawlicki M, Collins H A, Denning R G and Anderson H L 2009 Two-photon absorption and the design of two-photon dyes Angew. Chem. Int. Edn Engl. 48 3244-66
117. Pillai V N R 1980 Photoremovable protecting groups in organic synthesis Synthesis 1 1-26
118. Bochet C G 2002 Photolabile protecting groups and linkers J. Chem. Soc., Perkin Trans. 1 125-42
119. Pelliccioli A P and Wirz J 2002 Photoremovable protecting groups: reaction mechanisms and applications Photochem. Photobiol. Sci. 1 441-58
120. Goeldner M and Givens R (ed) 2005 Dynamic Studies in Biology (Weinheim: Wiley-VCH)
121. Mayer G and Heckel A 2006 Biologically active molecules with a light switch Angew. Chem. Int. Edn Engl. 45 4900-21
122. Ellis-Davies G C R 2007 Caged compounds: photorelease technology for control of cellular chemistry and physiology Nature Methods 4 619-28
123. Young D D and Deiters A 2007 Photochemical control of biological processes Org. Biomol. Chem. 5 999-1005
124. Lee H-M, Larson D R and Lawrence D S 2009 Illuminating the chemistry of life: design, synthesis, and applications of caged and related photoresponsive compounds ACS Chem. Biol. 4 409-27
125. Specht A, Bolze F, Omran Z, Nicoud J-F and Goeldner M 2009 Photochemical tools to study dynamic biological processes HFSP J. 3 255-64
126. Yu H, Li J, Wu D, Qiu Z and Zhang Y 2010 Chemistry and biological applications of photo-labile organic molecules Chem. Soc. Rev. 39 464-73
127. Deiters A 2010 Principles and applications of the photochemical control of cellular processes Chem. BioChem 11 47-53
128. Brieke C, Rohrbach F, Gottschalk A, Mayer G and Heckel A 2012 Light-controlled tools Angew. Chem. Int. Edn Engl. 51 8446-76
129. Aujard I, Benbrahim C, Gouget M, Ruel O, Baudin J B, Neveu P and Jullien L 2006 o-nitrobenzyl photolabile protecting groups with red-shifted absorption: syntheses and uncaging cross-sections for one- and two-photon excitation Chem. Eur. J. 12 6865-79
130. Specht A, Bolze F, Donato L, Herbivo C, Charon S, Warther D, Gug S, Nicoud J-F and Goeldner M 2012 The donor-acceptor biphenyl platform: a versatile chromophore for the engineering of highly efficient two-photon sensitive photoremovable protecting groups Photochem. Photobiol. Sci. 11 578-86
131. Zayat L, Calero C, Albores P, Baraldo L and Etchenique R 2003 A new strategy for neurochemical photodelivery: metal-ligand heterolytic cleavage J. Am. Chem. Soc. 125 882-3
132. Chen Y and Steinmetz M G 2005 Photochemical cyclization with release of carboxylic acids and phenol from pyrrolidino-substituted 1,4-benzoquinones using visible light Org. Lett. 7 3729-32
133. Gug S, Bolze F, Specht A, Bourgogne C, Goeldner M and Nicoud J-F 2008 Molecular engineering of photoremovable protecting groups for two-photon uncaging Angew. Chem. Int. Edn Engl. 47 9525-9
134. Donato L, Mourot A, Davenport C M, Herbivo C, Warther D, Léonard J, Bolze F, Nicoud J-F, Kramer R H, Goeldner M and Specht A 2012 Water-soluble, donor-acceptor biphenyl derivatives in the 2-(o-nitrophenyl)propyl series: highly efficient two-photon uncaging of the neurotransmitter γ-aminobutyric acid at λ = 800 nm Angew. Chem. Int. Edn Engl. 51 1840-3
135. Sebej P, Wintner J, Müller P, Slanina T, Anshori J A, Antony L A P, Klan P and Wirz J 2013 Fluorescein analogues as photoremovable protecting groups absorbing at 520 nm J. Org. Chem. 78 1833-43
136. Hagen V, Frings S, Bendig J, Lorenz D, Wiesner B and Kaupp U B 2002 Fluorescence spectroscopic quantification of the release of cyclic nucleotides from photocleavable [bis(carboxymethoxy)-coumarin 4 yl]methyl esters inside cells Angew. Chem. Int. Edn Engl. 41 3625-8
137. Majjigapu J R R, Kurchan A N, Kottani R, Gustafson T P and Kutateladze A G 2005 Release and report: a new photolabile caging system with a two-photon fluorescence reporting function 12458-9 J. Am. Chem. Soc.
138. Gagey N, Neveu P and Jullien L 2007 Reporting two-photon uncaging with the efficient 3,5-dibromo-2,4-dihydroxycinnamic caging group Angew. Chem. Int. Edn Engl. 46 2467-9
139. Gagey N, Neveu P, Benbrahim C, Goetz B, Aujard I, Baudin J B and Jullien L 2007 Two-photon uncaging with fluorescence reporting: evaluation of the o-hydroxycinnamic platform J. Am. Chem. Soc. 129 9986-98
140. Gagey N, Emond M, Neveu P, Benbrahim C, Goetz B, Aujard I, Baudin J-B and Jullien L 2008 Alcohol uncaging with fluorescence reporting: evaluation of ortho-acetoxyphenyl methyloxazolone precursors Org. Lett. 10 2341-4
141. Labruère R, Alouane A, Le Saux T, Aujard I, Pelupessy P, Gautier A, Dubruille S, Schmidt F and Jullien L 2012 Self-immolative spacer for uncaging with fluorescence reporting Angew. Chem. Int. Edn Engl. 51 9344-7
142. Bochet C G 2001 Orthogonal photolysis of protecting groups Angew. Chem. Int. Edn Engl. 40 2071-3
143. Blanc A and Bochet C G 2002 Wavelength-controlled orthogonal photolysis of protecting groups J. Org. Chem. 67 5567-77
144. del Campo A, Boos D, Spiess H X and Jonas U 2005 Surface modification with orthogonal photosensitive silanes for sequential chemical lithography and site-selective particle deposition Angew. Chem. Int. Edn Engl. 44 4707-12
145. Stegmaier P, Alonso J M and del Campo A 2008 Photoresponsive surfaces with two independent wavelength-selective functional levels Langmuir 24 11872-9
146. Kotzur N, Briand B, Beyermann M and Hagen V 2009 Wavelength-selective photoactivatable protecting groups for thiols J. Am. Chem. Soc. 131 16927-31
147. Kantevari S, Matsuzaki M, Kanemoto Y, Kasai H and Ellis-Davies G C R 2010 Two-color, two-photon uncaging of glutamate and GABA Nature Methods 7 123-6
148. Riggsbee C W and Deiters A 2010 Recent advances in the photochemical control of protein function Trends Biotechnol. 28 468-75
149. Hahn M E and Muir T W 2004 Photocontrol of Smad2, a multiphosphorylated cell-signaling protein, through caging of activating phosphoserines Angew. Chem. Int. Edn Engl. 43 5800-3
150. De Rosa L, Russomanno A, Romanelli A and D'Andrea L D 2013 Semi-synthesis of labeled proteins for spectroscopic applications Molecules 13 440-65
151. Humphrey D, Rajfur Z, Imperiali B, Marriott G, Roy P and Jacobson K 2007 Introduction of caged peptide/protein into cells using microinjection Cold Spring Harbor Protocols pdb.prot4959 doi:10.1101/pdb.prot4659
152. Wu N, Deiters A, Ashton Cropp T, King D and Schultz D 2004 A genetically encoded photocaged amino acid Biophys. J. 126 14306-7
153. Gautier A, Nguyen D P, Lusic H, An W, Deiters A and Chin J 2010 Genetically encoded photo-control of protein localization in mammalian cells J. Am. Chem. Soc. 132 4086-8
154. Gautier A, Deiters A and Chin J W 2011 Light-activated kinases enable temporal dissection of signaling networks in living cells J. Am. Chem. Soc. 133 2124-7
155. Arbely E, Torres-Kolbus J, Deiters A and Chin J W 2012 Photocontrol of tyrosine phosphorylation in mammalian cells via genetic encoding of photocaged tyrosine J. Am. Chem. Soc. 134 11912-5
156. Li H, Hah J-M and Lawrence D S 2008 Light-mediated liberation of enzymatic activity: 'small molecule' caged protein equivalents J. Am. Chem. Soc. 130 10474-5
157. Cruz F G, Koh J T and Link K H 2000 Light-activated gene expression J. Am. Chem. Soc. 122 8777-8
158. Lin W, Albanese C, Pestell R G and Lawrence D S 2002 Spatially discrete, light-driven protein expression Chem. Biol. 9 1347-53
159. Link K H, Shi Y and Koh J T 2005 Light activated recombination J. Am. Chem. Soc. 127 13088-9
160. Cambridge S B, Geissler D, Calegari F, Anastassiadis K, Hasan M T, Stewart A F, Huttner W B, Hagen V and Bonhoeffer T 2009 Doxycycline-dependent photoactivated gene expression in eukaryotic systems Nature Methods 6 527-33
161. Sinha D K et al 2010 Photocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination Chem. Bio. Chem. 11 653-63
162. T2 recombinase for conditional site-specific recombination with high spatio-temporal resolution Zebrafish 7 199-204
163. Rau H 1990 Photochromism: Molecules and Systems (Amsterdam: Elsevier)
164. Bouas-Laurent H and Dürr H 2001 Organic photochromism Pure Appl. Chem. 73 639-65
165. Dürr Hand Bouas-Laurent H 2003 Photochromism: Molecules and Systems (Amsterdam: Elsevier)
166. Hampp N 2000 Bacteriorhodopsin as a photochromic retinal protein for optical memories Chem. Rev. 100 1755-76
167. Bhoo S-H, Davis S J, Walker J, Karniol B and Vierstra R D 2001 Bacteriophytochromes are photochromic histidine kinases using a biliverdin chromophore Nature 414 776-9
168. Imamoto Y and Kataoka M 2007 Structure and photoreaction of photoactive yellow protein, a structural prototype of the PAS domain superfamily Photochem. Photobiol. 83 40-9
169. Scheerer P, Michael N, Hee Park J, Nagano S, Choe H-W, Inomata K, Borucki B, Krauss N and Lamparter T 2010 Light-induced conformational changes of the chromophore and the protein in phytochromes: Bacterial phytochromes as model systems Chem. Phys. Chem. 11 1090-105
170. Drepper T, Krauss U, Meyer zu Berstenhorst S, Pietruszka J and Jaeger K-E 2011 Lights on and action! controlling microbial gene expression by light Appl. Microbiol. Biotechnol. 90 23-40
171. Xu L et al 2012 Spatio-temporal manipulation of retinoic acid activity in zebrafish hindbrain development via photo-isomerization Development 139 3355-62
172. Callaway E M and Yuste R 2002 Stimulating neurons with light Curr. Opin. Neurobiol. 12 587-92
173. Bartels E, Wassermann N H and Erlanger B F 1971 Photochromic activators of the acetylcholine receptor Proc. Natl Acad. Sci. USA 68 1820-3
174. Banghart M R, Volgraf M and Trauner D 2006 Engineering light-gated ion channels Biochemistry 45 15129-41
175. Gorostiza P and Isacoff E Y 2008 Optical switches for remote and noninvasive control of cell signaling Science 322 395-9
176. Kramer R H, Fortin D L and Trauner D 2009 New photochemical tools for controlling neuronal activity Curr. Opin. Neurobiol. 19 544-52
177. Mourot A, Kienzler M A, Banghart M R, Fehrentz T, Huber F M E, Stein M, Kramer R H and Trauner D 2011 Tuning photochromic ion channel blockers ACS Chem. Neurosci. 2 536-43
178. Deisseroth K 2011 Optogenetics Nature Methods 8 26-9
179. Miesenböck G 2009 The optogenetic catechism Science 326 395-9
180. ++ based on green fluorescent proteins and calmodulin Nature 388 882-7
181. Nhu Ngoc Van T and Morris M C 2013 Fluorescent sensors of protein kinases: from basics to biomedical applications Prog. Mol. Biol. Transl. Sci. 113 217-74
182. Zhang F et al 2011 The microbial opsin family of optogenetic tools Cell 147 1446-57
183. Livet J et al 2007 Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system Nature 450 56-62
184. Pan Y A, Livet J, Sanes J R, Lichtman J W and Schier A F 2011 Multicolor brainbow imaging in zebrafish Cold Spring Harbor Protocol 1 pdb prot5546 doi:10.1101/pdb.prot5546
185. Hadjieconomou D, Rotkopf S, Alexandre C, Bell D M, Dickson B J and Salecker I 2011 Flybow: genetic multicolor cell labeling for neural circuit analysis in drosophila melanogaster Nature Methods 8 260-6
186. Hampel S, Chung P, McKellar C E, Hall D, Looger L L and Simpson J H 2011 Drosophila brainbow: a recombinase-based fluorescence labeling technique to subdivide neural expression patterns Nature Methods 8 253-9
187. Wachsman G G, Heidstra R and Scheres B 2011 Distinct cell-autonomous functions of retinoblastoma-related in arabidopsis stem cells revealed by the brother of brainbow clonal analysis system Plant Cell 23 2581-91
188. Gupta V and Poss K D 2012 Clonally dominant cardiomyocytes direct heart morphogenesis Nature 484 479-84
189. Hipfner D R and Cohen S M 2004 Connecting proliferation and apoptosis in development and disease Nature Rev. Mol. Cell. Biol. 5 805-15
190. Favaloro B, Allocati N, Graziano V, Di Ilio C and De Laurenzi V 2012 Role of apoptosis in disease Aging (Albany NY) 4 330-49
191. Sakaue-Sawano A et al 2008 Visualizing spatiotemporal dynamics of multicellular cell-cycle progression Cell 132 487-98
192. Sugiyama M, Sakaue-Sawano A, Iimura T, Fukami K, Kitaguchi T, Kawakami K, Okamoto H, Higashijima S and Miyawaki A 2009 Illuminating cell-cycle progression in the developing zebrafish embryo Proc. Natl Acad. Sci. USA 106 20812-7
193. Abe T, Sakaue-Sawano A, Kiyonari H, Shioi G, Inoue K, Horiuchi T, Nakao K, Miyawaki A, Aizawa S and Fujimori T 2013 Visualization of cell cycle in mouse embryos with Fucci2 reporter directed by Rosa26 promoter Development 140 237-46
194. Kuranaga E 2012 Beyond apoptosis: caspase regulatory mechanisms and functions in vivo Genes Cells 17 83-97
195. Li F, He Z, Shen J, Huang Q, Li W, Lui X, He Y, Wolf F and Li C Y 2010 Apoptotic caspases regulate induction of iPSCs from human fibroblasts Cell Stem Cell 7 508-20
196. Ai H W, Hazelwood K L, Davidson M W and Campbell R E 2008 Fluorescent protein FRET pairs for ratiometric imaging of dual biosensors Nature Methods 5 401-3
197. Bardet P L, Kolahgar G, Mynett A, Miguel-Aliaga I, Briscoe J, Meier P and Vincent J P 2008 A fluorescent reporter of caspase activity for live imaging Proc. Natl Acad. Sci. USA 105 13901-5
198. Wu B, Piatkevich K D, Lionnet T, Singer R H and Verkhusha V V 2011 Modern fluorescent proteins and imaging technologies to study gene expression, nuclear localization, and dynamics Curr. Opin. Cell Biol. 23 310-7
199. Ben-Ari Y, Brody Y, Kinor N, Mor A, Tsukamoto T, Spector D L, Singer R H and Shav-Tal Y 2010 The life of an MRNA in space and time J. Cell Sci. 123 1761-74
200. Wachter R M and Remington S J 1999 Sensitivity of the yellow variant of green fluorescent protein to halides and nitrate Curr. Biol. 9 R628-9
201. Jayaraman S, Haggie P, Wachter R M, Remington S J and Verkman A S 2000 Mechanism and cellular applications of a green fluorescent protein-based halide sensor J. Biol. Chem. 275 6047-50
202. Barondeau D P, Kassmann C J, Tainer J A and Getzoff E D 2002 Structural chemistry of a green fluorescent protein Zn biosensor J. Am. Chem. Soc. 124 3522-4
203. Hanson G T, Aggeler R, Oglesbee D, Cannon M, Capaldi R A, Tsien R Y and Remington S J 2004 Investigating mitochondrial redox potential with redox-sensitive green fluorescent protein indicators J. Biol. Chem. 279 13044-53
204. Dooley C T, Dore T M, Hanson G T, Jackson W C, Remington S J and Tsien R Y 2004 Imaging dynamic redox changes in mammalian cells with green fluorescent protein indicators J. Biol. Chem. 279 22284-93
205. Brejc K, Sixma T K, Kitts P A, Kain S R, Tsien R Y, Ormo M and Remington S J 1997 Structural basis for dual excitation and photoisomerization of the aequorea victoria green fluorescent protein Proc. Natl Acad. Sci. USA 94 2306-11
206. Palm G J, Zdanov A, Gaitanaris G A, Stauber R, Pavlakis G N and Wlodawer A 1997 The structural basis for spectral variations in green fluorescent protein Nature Struct. Biol. 4 361-5
207. Miesenbock G, De Angelis D A and Rothman J E 1998 Visualizing secretion and synaptic transmission with pH-sensitive green fluorescent proteins Nature 394 192-5
208. Chudakov D M, Verkhusha V V, Staroverov D B, Souslova E A, Lukyanov S and Lukyanov K A 2004 Photoswitchable cyan fluorescent protein for protein tracking Nature Biotechnol. 22 1435-9
209. Hanson G T, McAnaney T B, Park E S, Rendell M E, Yarbrough D K, Chu S, Xi L, Boxer S G, Montrose M H and Remington S J 2002 Green fluorescent protein variants as ratiometric dual emission pH sensors: I. Structural characterization and preliminary application Biochemistry 41 15477-88
210. Bizzarri R, Arcangeli C, Arosio D, Ricci F, Faraci P, Cardarelli F and Beltram F 2006 Development of a novel GFP-based ratiometric excitation and emission pH indicator for intracellular studies Biophys. J. 90 3300-14
211. Belousov V V, Fradkov A F, Lukyanov K A, Staroverov D B, Shakhbazov K S, Terskikh A V and Lukyanov S 2006 Genetically encoded fluorescent indicator for intracellular hydrogen peroxide Nature Methods 3 281-6
212. Baird G S, Zacharias D A and Tsien R Y 1999 Circular permutation and receptor insertion within green fluorescent proteins Natl Acad. Sci. USA 96 11241-6
213. 2+ Proc. Natl Acad. Sci. USA 98 3197-202
214. (2+) probe composed of a single green fluorescent protein Nature Biotechnol. 19 137-41
215. (2+) signals PLoS One 7 e51286
216. Kuner T and Augustine G J 2000 A genetically encoded ratiometric indicator for chloride: capturing chloride transients in cultured hippocampal neurons Neuron 27 447-59
217. DiPilato L M, Cheng X and Zhang J 2004 Fluorescent indicators of CaMP and Epac activation reveal differential dynamics of CaMP signaling within discrete subcellular compartments Proc. Natl Acad. Sci. USA 101 16513-8
218. Imamura H, Nhat K P, Togawa H, Saito K, Iino R, Kato-Yamada Y, Nagai T and Noji H 2009 Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators Proc. Natl Acad. Sci. USA 106 15651-6
219. Brunoud G, Wells D M, Oliva M, Larrieu A, Mirabet V, Burrow A H, Beeckman T, Kepinski S, Traas J, Bennett M J and Vernoux T 2012 A novel sensor to map auxin response and distribution at high spatio-temporal resolution Nature 482 103-6
220. Siegel M S and Isacoff E Y 1997 A genetically encoded optical probe of membrane voltage Neuron 19 735-41
221. Tsutsui H, Karasawa S, Okamura Y and Miyawaki A 2008 Improving membrane voltage measurements using FRET with new fluorescent proteins Nature Methods 5 683-5
222. Kralj J M, Douglass A D, Hochbaum D R, Maclaurin D and Cohen A E 2012 Optical recording of action potentials in mammalian neurons using a microbial rhodopsin Nature Methods 9 90-5
223. Clapham D E 2007 Calcium signaling Cell 131 1047-58
224. Berridge M J 1998 Neuronal calcium signaling Neuron 21 13-26
225. Miyawaki A 2003 Fluorescence imaging of physiological activity in complex systems using gfp-based probes Curr. Opin. Neurobiol. 13 591-6
226. Akerboom J et al 2012 Optimization of a GCaMP calcium indicator for neural activity imaging J. Neurosci. 32 13819-40
227. Warp E, Agarwal G, Wyar C, Friedmann D, Oldfield C S, Conner A, Del Bene F, Arrenberg A B, Baier H and Isacoff E Y 2012 Emergence of patterned activity in the developing zebrafish spinal cord Curr. Biol. 22 93-102
228. Ahrens M B, Orger M B, Robson D N, Li J M and Keller P J 2013 Whole brain functional imaging at cellular resolution using light sheet microscopy Nature Methods 10 413-20
229. Panier T, Romano S, Olive R, Pietri T, Sumbre G, Candelier R and Debrégeas G 2013 Fast functional imaging of multiple brain regions in intact zebrafish larvae using selective plane illumination microscopy Frontiers Neural Circuits 7 1-11
230. Ray P D, Huang B W and Tsuji Y 2012 Reactive oxygen species (ROS) homeostasis and redox regulation in cellular signaling Cell Signal 24 981-90
231. Sena L A and Chandel N S 2012 Physiological roles of mitochondrial reactive oxygen species Mol. Cell. 48 158-67
232. Niethammer P, Grabher C, Look A T and Mitchison T J 2009 A tissue-scale gradient of hydrogen peroxide mediates rapid wound detection in zebrafish Nature 459 996-9
233. Rieger S and Sagasti A 2011 Hydrogen peroxide promotes injury-induced peripheral sensory axon regeneration in the zebrafish skin PLoS Biol. 9 e1000621
234. Bulina M E, Chudakov D M, Britanova O V, Yanushevich Y G, Staroverov D B, Chepurnykh T V, Merzlyak E M, Shkrob M A, Lukyanov S and Lukyanov K A 2006 A genetically encoded photosensitizer Nature Biotechnol. 24 95-9
235. Qi Y B, Garren E J, Shu X, Tsien R Y and Jin Y 2012 Photo-inducible cell ablation in caenorhabditis elegans using the genetically encoded singlet oxygen generating protein minisog Proc. Natl Acad. Sci. USA 109 7499-504
236. Zemelman B V, Lee G A, Ng M and Miesenböck G 2002 Selective photostimulation of genetically charged neurons Neuron 33 15-22
237. Airan R D, Thompson K R, Fenno L E, Bernstein H and Deisseroth K 2009 Temporally precise in vivo control of intracellular signalling Nature 458 1025-9
238. Oh E, Maejima T, Lui C, Deneris E and Herlitze S 2010 Substitution of 5-Ht1A receptor signaling by a light-activated g protein-coupled receptor J. Biol. Chem. 285 30825-36
239. Nagel G, Ollig D, Fuhrmann M, Kateriya S, Musti A M, Bamberg E and Hegemann P 2002 Channelrhodopsin-1 : a light-gated proton channel in green algae Science 296 2395-98
240. Nagel G, Szellas T, Huhn W, Kateriya S, Adeishvili N, Berthold P, Ollig D, Hegemann P and Bamberg E 2003 Channelrhodopsin-2, a directly light-gated cation-selective membrane channel Proc. Natl Acad. Sci. USA 100 13940-45
241. Zhang F, Prigge M, Beyriere F, Tsunoda S P, Mattis J, Yizhar O, Hegemann P and Deisseroth K 2008 Red-shifted optogenetic excitation: a tool for fast neural control derived from Volvox carteri Nature Neurosci. 11 631-33
242. Govorunova E G, Spudich E N, Lane C E, Sineshchekov O A and Spudich J L 2011 New channelrhodopsin with a red-shifted spectrum and rapid kinetics from mesostigma viride Mol. Biol. 2 e00115-11
243. Zhang F, Wang L P, Brauner M, Liewald J F, Kay K, Watzke N, Wood P G, Bamberg E, Nagel G, Gottschalk A and Deisseroth K 2007 Multimodal fast optical interrogation of neural circuitry Nature 446 633-39
244. Gradinaru V, Zhang F, Ramakrishnan C, Mattis J, Prakash R, Diester I, Goshen I, Thompson K R and Deisseroth K 2010 Molecular and cellular approaches for diversifying and extending optogenetics Cell 141 154-65
245. Szobota S and Isacoff E Y 2010 Optical control of neuronal activity Annu. Rev. Biophys. 39 329-48
246. Arenkiel B R, Peca J, Davison I G, Feliciano C, Deisseroth K, Augustine G J, Ehlers M D and Feng G 2007 In vivo light-induced activation of neural circuitry in transgenic mice expressing channelrhodopsin-2 Neuron 54 205-18
247. Fenno L, Yizhar O and Deisseroth K 2011 The development and application of optogenetics Annu. Rev. Neurosci. 34 389-412
248. Tye K M and Deisseroth K 2012 Optogenetic investigation of neural circuits underlying brain disease in animal models Nature Rev. Neurosci. 13 251-66
249. Arrenberg A B, Stainier D Y, Baier H and Huisken J 2010 Optogenetic control of cardiac function Science 330 971-4
250. Bruegmann T, Malan D, Hesse M, Beiert T, Fuegemann C J and P Fleischmann B K Sasse 2010 Optogenetic control of heart muscle in vitro and in vivo Nature Methods 7 897-900
251. Stroh A, Tsai H C, Wang L P, Zhang F, Kressel J, Aravanis A, Santhanam N, Deisseroth K, Konnerth A and Schneider M B 2011 Tracking stem cell differentiation in the setting of automated optogenetic stimulation Stem. Cells 29 78-88