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Optogenetics: Basic Concepts and Their Development

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Optogenetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1408))

Abstract

The discovery of light-gated ion channels and their application to controlling neural activities have had a transformative impact on the field of neuroscience. In recent years, the concept of using light-activated proteins to control biological processes has greatly diversified into other fields, driven by the natural diversity of photoreceptors and decades of knowledge obtained from their biophysical characterization. In this chapter, we will briefly discuss the origin and development of optogenetics and highlight the basic concepts that make it such a powerful technology. We will review how these enabling concepts have developed over the past decade, and discuss future perspectives.

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References

  1. Deisseroth K, Feng G, Majewska AK et al (2006) Next-generation optical technologies for illuminating genetically targeted brain circuits. J Neurosci 26(41):10380–10386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Crick FH (1979) Thinking about the brain. Sci Am 241(3):219–232

    Article  CAS  PubMed  Google Scholar 

  3. Crick F (1999) The impact of molecular biology on neuroscience. Philos Trans R Soc Lond B Biol Sci 354(1392):2021–2025

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Boyden ES, Zhang F, Bamberg E et al (2005) Millisecond-timescale, genetically targeted optical control of neural activity. Nat Neurosci 8(9):1263–1268

    Article  CAS  PubMed  Google Scholar 

  5. Boyden ES (2011) A history of optogenetics: the development of tools for controlling brain circuits with light. F1000 Biol Rep 3:11

    Article  PubMed  PubMed Central  Google Scholar 

  6. Deisseroth K (2010) Controlling the brain with light. Sci Am 303(5):48–55

    Article  PubMed  Google Scholar 

  7. Deisseroth K (2011) Optogenetics. Nat Methods 8(1):26–29

    Article  CAS  PubMed  Google Scholar 

  8. Miesenbock G (2009) The optogenetic catechism. Science 326(5951):395–399

    Article  PubMed  CAS  Google Scholar 

  9. Ramón y Cajal S (1911) Histology of the nervous system of man and vertebrates. Oxford University Press, 1995 translation

    Google Scholar 

  10. Fishell G, Heintz N (2013) The neuron identity problem: form meets function. Neuron 80(3):602–612

    Article  CAS  PubMed  Google Scholar 

  11. Gong S, Zheng C, Doughty ML et al (2003) A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature 425(6961):917–925

    Article  CAS  PubMed  Google Scholar 

  12. Hawrylycz MJ, Lein ES, Guillozet-Bongaarts AL et al (2012) An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 489(7416):391–399

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Koch C (2004) The quest for consciousness: a neurobiological approach. Roberts and Co., Denver, CO

    Google Scholar 

  14. Stevens CF (1998) Neuronal diversity: too many cell types for comfort? Curr Biol 8(20):R708–R710

    Article  CAS  PubMed  Google Scholar 

  15. Luo L, Callaway EM, Svoboda K (2008) Genetic dissection of neural circuits. Neuron 57(5):634–660

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Ellis-Davies GC (2007) Caged compounds: photorelease technology for control of cellular chemistry and physiology. Nat Methods 4(8):619–628

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Kaplan JH, Somlyo AP (1989) Flash photolysis of caged compounds: new tools for cellular physiology. Trends Neurosci 12(2):54–59

    Article  CAS  PubMed  Google Scholar 

  18. Zemelman BV, Lee GA, Ng M et al (2002) Selective photostimulation of genetically chARGed neurons. Neuron 33(1):15–22

    Article  CAS  PubMed  Google Scholar 

  19. Zemelman BV, Nesnas N, Lee GA et al (2003) Photochemical gating of heterologous ion channels: remote control over genetically designated populations of neurons. Proc Natl Acad Sci U S A 100(3):1352–1357

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Lima SQ, Miesenbock G (2005) Remote control of behavior through genetically targeted photostimulation of neurons. Cell 121(1):141–152

    Article  CAS  PubMed  Google Scholar 

  21. Nagel G, Ollig D, Fuhrmann M et al (2002) Channelrhodopsin-1: a light-gated proton channel in green algae. Science 296(5577):2395–2398

    Article  CAS  PubMed  Google Scholar 

  22. Nagel G, Szellas T, Huhn W et al (2003) Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc Natl Acad Sci U S A 100(24):13940–13945

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Sineshchekov OA, Jung KH, Spudich JL (2002) Two rhodopsins mediate phototaxis to low- and high-intensity light in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 99(13):8689–8694

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Blomhoff R, Blomhoff HK (2006) Overview of retinoid metabolism and function. J Neurobiol 66(7):606–630

    Article  CAS  PubMed  Google Scholar 

  25. Zhang F, Wang LP, Boyden ES et al (2006) Channelrhodopsin-2 and optical control of excitable cells. Nat Methods 3(10):785–792

    Article  CAS  PubMed  Google Scholar 

  26. Markram H, Toledo-Rodriguez M, Wang Y et al (2004) Interneurons of the neocortical inhibitory system. Nat Rev Neurosci 5(10):793–807

    Article  CAS  PubMed  Google Scholar 

  27. Sugino K, Hempel CM, Miller MN et al (2006) Molecular taxonomy of major neuronal classes in the adult mouse forebrain. Nat Neurosci 9(1):99–107

    Article  CAS  PubMed  Google Scholar 

  28. Spergel DJ, Kruth U, Hanley DF et al (1999) GABA- and glutamate-activated channels in green fluorescent protein-tagged gonadotropin-releasing hormone neurons in transgenic mice. J Neurosci 19(6):2037–2050

    CAS  PubMed  Google Scholar 

  29. Oliva AA Jr, Jiang M, Lam T et al (2000) Novel hippocampal interneuronal subtypes identified using transgenic mice that express green fluorescent protein in GABAergic interneurons. J Neurosci 20(9):3354–3368

    CAS  PubMed  Google Scholar 

  30. McGarry LM, Packer AM, Fino E et al (2010) Quantitative classification of somatostatin-positive neocortical interneurons identifies three interneuron subtypes. Front Neural Circuits 4:12

    PubMed  PubMed Central  Google Scholar 

  31. Zeng H, Madisen L (2012) Mouse transgenic approaches in optogenetics. Prog Brain Res 196:193–213

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Gong S, Doughty M, Harbaugh CR et al (2007) Targeting Cre recombinase to specific neuron populations with bacterial artificial chromosome constructs. J Neurosci 27(37):9817–9823

    Article  CAS  PubMed  Google Scholar 

  33. Fenno LE, Mattis J, Ramakrishnan C et al (2014) Targeting cells with single vectors using multiple-feature Boolean logic. Nat Methods 11(7):763–772

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Madisen L, Garner AR, Shimaoka D et al (2015) Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance. Neuron 85(5):942–958

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Wickersham IR, Finke S, Conzelmann KK et al (2007) Retrograde neuronal tracing with a deletion-mutant rabies virus. Nat Methods 4(1):47–49

    Article  CAS  PubMed  Google Scholar 

  36. Wickersham IR, Lyon DC, Barnard RJ et al (2007) Monosynaptic restriction of transsynaptic tracing from single, genetically targeted neurons. Neuron 53(5):639–647

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Lo L, Anderson DJ (2011) A Cre-dependent, anterograde transsynaptic viral tracer for mapping output pathways of genetically marked neurons. Neuron 72(6):938–950

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Beier KT, Saunders A, Oldenburg IA et al (2011) Anterograde or retrograde transsynaptic labeling of CNS neurons with vesicular stomatitis virus vectors. Proc Natl Acad Sci U S A 108(37):15414–15419

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Wall NR, Wickersham IR, Cetin A et al (2010) Monosynaptic circuit tracing in vivo through Cre-dependent targeting and complementation of modified rabies virus. Proc Natl Acad Sci U S A 107(50):21848–21853

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Rothermel M, Brunert D, Zabawa C et al (2013) Transgene expression in target-defined neuron populations mediated by retrograde infection with adeno-associated viral vectors. J Neurosci 33(38):15195–15206

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Osakada F, Mori T, Cetin AH et al (2011) New rabies virus variants for monitoring and manipulating activity and gene expression in defined neural circuits. Neuron 71(4):617–631

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Apicella AJ, Wickersham IR, Seung HS et al (2012) Laminarly orthogonal excitation of fast-spiking and low-threshold-spiking interneurons in mouse motor cortex. J Neurosci 32(20):7021–7033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Kress GJ, Yamawaki N, Wokosin DL et al (2013) Convergent cortical innervation of striatal projection neurons. Nat Neurosci 16(6):665–667

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Smeyne RJ, Schilling K, Robertson L et al (1992) fos-lacZ transgenic mice: mapping sites of gene induction in the central nervous system. Neuron 8(1):13–23

    Article  CAS  PubMed  Google Scholar 

  45. Kawashima T, Okuno H, Nonaka M et al (2009) Synaptic activity-responsive element in the Arc/Arg3.1 promoter essential for synapse-to-nucleus signaling in activated neurons. Proc Natl Acad Sci U S A 106(1):316–321

    Article  CAS  PubMed  Google Scholar 

  46. Bito H, Deisseroth K, Tsien RW (1996) CREB phosphorylation and dephosphorylation: a Ca(2+)- and stimulus duration-dependent switch for hippocampal gene expression. Cell 87(7):1203–1214

    Article  CAS  PubMed  Google Scholar 

  47. Liu X, Ramirez S, Pang PT et al (2012) Optogenetic stimulation of a hippocampal engram activates fear memory recall. Nature 484(7394):381–385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Kubik S, Miyashita T, Guzowski JF (2007) Using immediate-early genes to map hippocampal subregional functions. Learn Mem 14(11):758–770

    Article  PubMed  Google Scholar 

  49. Ramirez S, Liu X, Lin PA et al (2013) Creating a false memory in the hippocampus. Science 341(6144):387–391

    Article  CAS  PubMed  Google Scholar 

  50. Sellick CA, Reece RJ (2005) Eukaryotic transcription factors as direct nutrient sensors. Trends Biochem Sci 30(7):405–412

    Article  CAS  PubMed  Google Scholar 

  51. Chandel NS, Maltepe E, Goldwasser E et al (1998) Mitochondrial reactive oxygen species trigger hypoxia-induced transcription. Proc Natl Acad Sci U S A 95(20):11715–11720

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Tamura T, Yanai H, Savitsky D et al (2008) The IRF family transcription factors in immunity and oncogenesis. Annu Rev Immunol 26:535–584

    Article  CAS  PubMed  Google Scholar 

  53. Ernst OP, Lodowski DT, Elstner M et al (2014) Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 114(1):126–163

    Article  CAS  PubMed  Google Scholar 

  54. Han X, Boyden ES (2007) Multiple-color optical activation, silencing, and desynchronization of neural activity, with single-spike temporal resolution. PLoS One 2(3):e299

    Article  PubMed  PubMed Central  Google Scholar 

  55. Zhang F, Wang LP, Brauner M et al (2007) Multimodal fast optical interrogation of neural circuitry. Nature 446(7136):633–639

    Article  CAS  PubMed  Google Scholar 

  56. Chow BY, Han X, Dobry AS et al (2010) High-performance genetically targetable optical neural silencing by light-driven proton pumps. Nature 463(7277):98–102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Chuong AS, Miri ML, Busskamp V et al (2014) Noninvasive optical inhibition with a red-shifted microbial rhodopsin. Nat Neurosci 17(8):1123–1129

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Inoue K, Ono H, Abe-Yoshizumi R et al (2013) A light-driven sodium ion pump in marine bacteria. Nat Commun 4:1678

    Article  PubMed  CAS  Google Scholar 

  59. Feldbauer K, Zimmermann D, Pintschovius V et al (2009) Channelrhodopsin-2 is a leaky proton pump. Proc Natl Acad Sci U S A 106(30):12317–12322

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Lin JY, Lin MZ, Steinbach P et al (2009) Characterization of engineered channelrhodopsin variants with improved properties and kinetics. Biophys J 96(5):1803–1814

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Klapoetke NC, Murata Y, Kim SS et al (2014) Independent optical excitation of distinct neural populations. Nat Methods 11(3):338–346

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Govorunova EG, Sineshchekov OA, Janz R et al (2015) Natural light-gated anion channels: a family of microbial rhodopsins for advanced optogenetics. Science 349(6248):647–650

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Schmidt D, Cho YK (2015) Natural photoreceptors and their application to synthetic biology. Trends Biotechnol 33(2):80–91

    Article  CAS  PubMed  Google Scholar 

  64. Fredriksson R, Lagerstrom MC, Lundin LG et al (2003) The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol 63(6):1256–1272

    Article  CAS  PubMed  Google Scholar 

  65. Farrens DL, Altenbach C, Yang K et al (1996) Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin. Science 274(5288):768–770

    Article  CAS  PubMed  Google Scholar 

  66. Rosenbaum DM, Rasmussen SG, Kobilka BK (2009) The structure and function of G-protein-coupled receptors. Nature 459(7245):356–363

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Kim JM, Hwa J, Garriga P et al (2005) Light-driven activation of beta 2-adrenergic receptor signaling by a chimeric rhodopsin containing the beta 2-adrenergic receptor cytoplasmic loops. Biochemistry 44(7):2284–2292

    Article  CAS  PubMed  Google Scholar 

  68. Airan RD, Thompson KR, Fenno LE et al (2009) Temporally precise in vivo control of intracellular signalling. Nature 458(7241):1025–1029

    Article  CAS  PubMed  Google Scholar 

  69. Oh E, Maejima T, Liu C et al (2010) Substitution of 5-HT1A receptor signaling by a light-activated G protein-coupled receptor. J Biol Chem 285(40):30825–30836

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Siuda ER, Copits BA, Schmidt MJ et al (2015) Spatiotemporal control of opioid signaling and behavior. Neuron 86(4):923–935

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Cao P, Sun W, Kramp K et al (2012) Light-sensitive coupling of rhodopsin and melanopsin to G(i/o) and G(q) signal transduction in Caenorhabditis elegans. FASEB J 26(2):480–491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Terakita A, Koyanagi M, Tsukamoto H et al (2004) Counterion displacement in the molecular evolution of the rhodopsin family. Nat Struct Mol Biol 11(3):284–289

    Article  CAS  PubMed  Google Scholar 

  73. Koyanagi M, Terakita A (2014) Diversity of animal opsin-based pigments and their optogenetic potential. Biochim Biophys Acta 1837(5):710–716

    Article  CAS  PubMed  Google Scholar 

  74. Moglich A, Yang X, Ayers RA et al (2010) Structure and function of plant photoreceptors. Annu Rev Plant Biol 61:21–47

    Article  CAS  PubMed  Google Scholar 

  75. Herrou J, Crosson S (2011) Function, structure and mechanism of bacterial photosensory LOV proteins. Nat Rev Microbiol 9(10):713–723

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Moglich A, Ayers RA, Moffat K (2009) Design and signaling mechanism of light-regulated histidine kinases. J Mol Biol 385(5):1433–1444

    Article  CAS  PubMed  Google Scholar 

  77. Wu YI, Frey D, Lungu OI et al (2009) A genetically encoded photoactivatable Rac controls the motility of living cells. Nature 461(7260):104–108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Strickland D, Lin Y, Wagner E et al (2012) TULIPs: tunable, light-controlled interacting protein tags for cell biology. Nat Methods 9(4):379–384

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Schmidt D, Tillberg PW, Chen F et al (2014) A fully genetically encoded protein architecture for optical control of peptide ligand concentration. Nat Commun 5:3019

    PubMed  PubMed Central  Google Scholar 

  80. Winkler A, Barends TR, Udvarhelyi A et al (2015) Structural details of light activation of the LOV2-based photoswitch PA-Rac1. ACS Chem Biol 10(2):502–509

    Article  CAS  PubMed  Google Scholar 

  81. Mizuno H, Mal TK, Walchli M et al (2008) Light-dependent regulation of structural flexibility in a photochromic fluorescent protein. Proc Natl Acad Sci U S A 105(27):9227–9232

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Zhou XX, Chung HK, Lam AJ et al (2012) Optical control of protein activity by fluorescent protein domains. Science 338(6108):810–814

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Zoltowski BD, Schwerdtfeger C, Widom J et al (2007) Conformational switching in the fungal light sensor Vivid. Science 316(5827):1054–1057

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Nash AI, McNulty R, Shillito ME et al (2011) Structural basis of photosensitivity in a bacterial light-oxygen-voltage/helix-turn-helix (LOV-HTH) DNA-binding protein. Proc Natl Acad Sci U S A 108(23):9449–9454

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Muller K, Engesser R, Schulz S et al (2013) Multi-chromatic control of mammalian gene expression and signaling. Nucleic Acids Res 41(12):e124

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  86. Toettcher JE, Weiner OD, Lim WA (2013) Using optogenetics to interrogate the dynamic control of signal transmission by the Ras/Erk module. Cell 155(6):1422–1434

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Idevall-Hagren O, Dickson EJ, Hille B et al (2012) Optogenetic control of phosphoinositide metabolism. Proc Natl Acad Sci U S A 109(35):E2316–E2323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Grusch M, Schelch K, Riedler R et al (2014) Spatio-temporally precise activation of engineered receptor tyrosine kinases by light. EMBO J 33(15):1713–1726

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Shimizu-Sato S, Huq E, Tepperman JM et al (2002) A light-switchable gene promoter system. Nat Biotechnol 20(10):1041–1044

    Article  CAS  PubMed  Google Scholar 

  90. Liu H, Gomez G, Lin S et al (2012) Optogenetic control of transcription in zebrafish. PLoS One 7(11):e50738

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Kennedy MJ, Hughes RM, Peteya LA et al (2010) Rapid blue-light-mediated induction of protein interactions in living cells. Nat Methods 7(12):973–975

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Boulina M, Samarajeewa H, Baker JD et al (2013) Live imaging of multicolor-labeled cells in Drosophila. Development 140(7):1605–1613

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Bugaj LJ, Choksi AT, Mesuda CK et al (2013) Optogenetic protein clustering and signaling activation in mammalian cells. Nat Methods 10(3):249–252

    Article  CAS  PubMed  Google Scholar 

  94. Kim N, Kim JM, Lee M et al (2014) Spatiotemporal control of fibroblast growth factor receptor signals by blue light. Chem Biol 21(7):903–912

    Article  CAS  PubMed  Google Scholar 

  95. Taslimi A, Vrana JD, Chen D et al (2014) An optimized optogenetic clustering tool for probing protein interaction and function. Nat Commun 5:4925

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Tischer D, Weiner OD (2014) Illuminating cell signalling with optogenetic tools. Nat Rev Mol Cell Biol 15(8):551–558

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Zhang K, Cui B (2015) Optogenetic control of intracellular signaling pathways. Trends Biotechnol 33(2):92–100

    Article  PubMed  CAS  Google Scholar 

  98. Losi A, Gartner W (2012) The evolution of flavin-binding photoreceptors: an ancient chromophore serving trendy blue-light sensors. Annu Rev Plant Biol 63:49–72

    Article  CAS  PubMed  Google Scholar 

  99. Gradinaru V, Zhang F, Ramakrishnan C et al (2010) Molecular and cellular approaches for diversifying and extending optogenetics. Cell 141(1):154–165

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Kralj JM, Douglass AD, Hochbaum DR et al (2012) Optical recording of action potentials in mammalian neurons using a microbial rhodopsin. Nat Methods 9(1):90–95

    Article  CAS  Google Scholar 

  101. Gunaydin LA, Yizhar O, Berndt A et al (2010) Ultrafast optogenetic control. Nat Neurosci 13(3):387–392

    Article  CAS  PubMed  Google Scholar 

  102. Kleinlogel S, Feldbauer K, Dempski RE et al (2011) Ultra light-sensitive and fast neuronal activation with the Ca(2)+-permeable channelrhodopsin CatCh. Nat Neurosci 14(4):513–518

    Article  CAS  PubMed  Google Scholar 

  103. Berndt A, Schoenenberger P, Mattis J et al (2011) High-efficiency channelrhodopsins for fast neuronal stimulation at low light levels. Proc Natl Acad Sci U S A 108(18):7595–7600

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Prigge M, Schneider F, Tsunoda SP et al (2012) Color-tuned channelrhodopsins for multiwavelength optogenetics. J Biol Chem 287(38):31804–31812

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Berndt A, Lee SY, Ramakrishnan C et al (2014) Structure-guided transformation of channelrhodopsin into a light-activated chloride channel. Science 344(6182):420–424

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Wietek J, Wiegert JS, Adeishvili N et al (2014) Conversion of channelrhodopsin into a light-gated chloride channel. Science 344(6182):409–412

    Article  CAS  PubMed  Google Scholar 

  107. Nagel G, Brauner M, Liewald JF et al (2005) Light activation of channelrhodopsin-2 in excitable cells of Caenorhabditis elegans triggers rapid behavioral responses. Curr Biol 15(24):2279–2284

    Article  CAS  PubMed  Google Scholar 

  108. Berndt A, Yizhar O, Gunaydin LA et al (2009) Bi-stable neural state switches. Nat Neurosci 12(2):229–234

    Article  CAS  PubMed  Google Scholar 

  109. Mattis J, Tye KM, Ferenczi EA et al (2012) Principles for applying optogenetic tools derived from direct comparative analysis of microbial opsins. Nat Methods 9(2):159–172

    Article  CAS  Google Scholar 

  110. Nash AI, Ko WH, Harper SM et al (2008) A conserved glutamine plays a central role in LOV domain signal transmission and its duration. Biochemistry 47(52):13842–13849

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Zoltowski BD, Vaccaro B, Crane BR (2009) Mechanism-based tuning of a LOV domain photoreceptor. Nat Chem Biol 5(11):827–834

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Gleichmann T, Diensthuber RP, Moglich A (2013) Charting the signal trajectory in a light-oxygen-voltage photoreceptor by random mutagenesis and covariance analysis. J Biol Chem 288(41):29345–29355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Hochbaum DR, Zhao Y, Farhi SL et al (2014) All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins. Nat Methods 11(8):825–833

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Akerboom J, Carreras Calderon N, Tian L et al (2013) Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics. Front Mol Neurosci 6:2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Krook-Magnuson E, Szabo GG, Armstrong C et al (2014) Cerebellar directed optogenetic intervention inhibits spontaneous hippocampal seizures in a mouse model of temporal lobe epilepsy. eNeuro 1(1):pii: e.2014

    Article  Google Scholar 

  116. Paz JT, Davidson TJ, Frechette ES et al (2013) Closed-loop optogenetic control of thalamus as a tool for interrupting seizures after cortical injury. Nat Neurosci 16(1):64–70

    Article  CAS  PubMed  Google Scholar 

  117. Sohal VS, Zhang F, Yizhar O et al (2009) Parvalbumin neurons and gamma rhythms enhance cortical circuit performance. Nature 459(7247):698–702

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Toettcher JE, Gong D, Lim WA et al (2011) Light-based feedback for controlling intracellular signaling dynamics. Nat Methods 8(10):837–839

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Milias-Argeitis A, Summers S, Stewart-Ornstein J et al (2011) In silico feedback for in vivo regulation of a gene expression circuit. Nat Biotechnol 29(12):1114–1116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was funded by the University of Connecticut and the Brain and Behavior Research Foundation (NARSAD Young Investigator grant).

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Correspondence to Yong Ku Cho .

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Cho, Y.K., Li, D. (2016). Optogenetics: Basic Concepts and Their Development. In: Kianianmomeni, A. (eds) Optogenetics. Methods in Molecular Biology, vol 1408. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3512-3_1

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