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Part I - Optogenetics in Model Organisms

Published online by Cambridge University Press:  28 April 2017

Krishnarao Appasani
Affiliation:
GeneExpression Systems, Inc., Massachusetts
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Optogenetics
From Neuronal Function to Mapping and Disease Biology
, pp. 1 - 76
Publisher: Cambridge University Press
Print publication year: 2017

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References

Adamantidis, A., Arber, S., Bains, J.S., et al., (2015). Optogenetics: 10 years after ChR2 in neurons-views from the community. Nature Neuroscience, 18, 12021212.CrossRefGoogle ScholarPubMed
Appasani, K. (2012). Epigenomics: From chromatin biology to therapeutics. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Bogomolni, R.A. and Spudich, J.L. (1982). Identification of a third rhodopsin-like pigment in photactic Halobacterium halobium. Proceedings of the National Academy of Sciences, United States of America, 79, 62506254.CrossRefGoogle ScholarPubMed
Bourzac, K. (2016). In first human test of optogenetics, doctors aim to restore sight to the blind. MIT-Technology Review, Feb 19, 3.Google Scholar
Boyden, E.S. (2011). A history of optogenetics: the development of tools for controlling brain circuits with light. F1000 Biology Reports, 3: 11 (doi:10.3410/B3-11), 112.CrossRefGoogle ScholarPubMed
Boyden, E.S., Zhang, F., Bamberg, E., Nagel, G. and Deisseroth, (2005). Millisecond-timescale, genetically targeted optical control of neural activity. Nature Neuroscience, 8, 12631268.CrossRefGoogle ScholarPubMed
Crick, F.H.C. (1979). Thinking about the brain. Scientific American, 241, 219232.CrossRefGoogle ScholarPubMed
Crick, F.H.C. (1999). Impact of molecular biology on neuroscience. Philosophical Transactions of the Royal Society, London, B. Biological Sciences, 354, 20212025.CrossRefGoogle ScholarPubMed
Deisseroth, K. (2010). Optogenetics: Controlling the brain with light. Scientific American, October 20, 112.Google Scholar
Deisseroth, K., Feng, G., Majewska, A.K., et al. (2006). Next-generation optical technologies for illuminating genetically targeted brain circuits. Journal of Neuroscience, 26, 1038010386.CrossRefGoogle ScholarPubMed
Delgado, J.M.R. (1964). Free behavior and brain stimulation. International Review of Neurobiology, 6, 349449.CrossRefGoogle ScholarPubMed
Goldensohn, E.S. (1998). Animal electricity from Bologna to Boston. Electroencephalygraphy in Clinical Neurophysiology, 106, 94100.CrossRefGoogle ScholarPubMed
Grimaud, J. and Lledo, P.M. (2016). Illuminating odors: when optogenetics brings to light unexpected olfactory abilities. Learning and Memory, 23, 249254.CrossRefGoogle ScholarPubMed
Hunter, P. (2016). Shining a light on optogenetics. European Molecular Biology Organization Reports, 17, 634637.Google ScholarPubMed
Kandel, E.R., Dudai, Y. and Mayford, M.R. (2014). The molecular and systems biology of memory. Cell, 157, 163186.CrossRefGoogle ScholarPubMed
Katz, L.C. and Shatz, C.J. (1996). Synaptic activity and the construction of cortical circuits. Science, 274, 11331138.CrossRefGoogle ScholarPubMed
Kim, J.M., Hwa, J., Garriga, P.J., 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, 22842292.CrossRefGoogle ScholarPubMed
Montogomery, K.L., Iyer, S.M., Christensen, A.J., et al. (2016). Beyond the brain: Optogenetic control in the spinal cord of peripheral nervous system. Science Translational Medicine, 8, 337rv5.Google Scholar
Nagel, G., Ollig, D., Fuhrmann, M. Kateriya, S., et al. (2002). Channelrhodopsin-1: a light-gated proton channel in green algae. Science, 296, 23952398.CrossRefGoogle ScholarPubMed
Nagel, G., Szellas, T., Huhn, W., et al. (2003). Channelrhodopsin-2: a directly light-gated cation-selective membrane channel. Proceedings of the National Academy of Sciences, United States of America, 100, 1394013945.CrossRefGoogle ScholarPubMed
Nagel, G., Brauner, M., Liewald, J.F., et al. (2005). Light activation of channelrhodopsin-2 in excitable cells of Caenorhabditis elegans triggers rapid behavioral responses. Current Biology, 15, 22792284.CrossRefGoogle ScholarPubMed
Nestler, E., Barrot, M. and Self, D. (2001). ΔFosB: A sustained molecular switch for addiction. Proceedings of the National Academy of Sciences, United States of America, 98, 1104211046.CrossRefGoogle ScholarPubMed
Oesterhelt, D. and Stoeckenius, W. (1971). Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nature New Biology, 233, 149152.CrossRefGoogle ScholarPubMed
Rechtschaffen, A., Gilliland, M.A., Bergmann, B.M., et al. (1983). Physiological correlates of prolonged sleep deprivation in rats. Science, 221, 182184.CrossRefGoogle ScholarPubMed
Roska, B. and Pepperberg, D. (2014). Restoring vision to the blind: Optogenetics. Translational Visual Science and Technology, 3, 48.Google Scholar
Sakmar, T.P. (2002). Structure of rhodopsin and the superfamily of seven-helical receptors: the same and not the same. Current Opinions in Cell Biology, 14, 189195.CrossRefGoogle Scholar
Shorvon, S.D. (2011). The etiologic classification of epilepsy. Epilepsia, 52, 10521057.CrossRefGoogle ScholarPubMed
Song, C. and Knopfel, T. (2016). Optogenetics enlightens neuroscience drug discovery. Nature Reviews Drug Discovery, 15, 97109.CrossRefGoogle ScholarPubMed
Spudich, J.L, (2006). The multitalented microbial sensory rhodopsins. Trends in Microbiology, 14, 480487.CrossRefGoogle ScholarPubMed
Vann, K.T. and Xiong, S. (2016). Optogenetics for neurodegenerative diseases. International Journal of Pathophysiology and Pharmacology, 8, 18.Google ScholarPubMed
Volkow, N.D. and Koob, G. (2015). Brain disease model of addiction: Why is it so controversial? Lancet Psychiatry, 2, 677679.CrossRefGoogle ScholarPubMed
Yizhar, O., Fenno, L.E., Davidson, T., et al. (2011). Optogenetics in neural systems. Neuron, 71, 934.CrossRefGoogle ScholarPubMed
Zemelman, B.V., Nesnas, N., Lee, G.A., et al. (2003). Photochemical gating of heterologous ion channels: Remote control over genetically designated populations of neurons. Proceedings of the National Academy of Sciences, United States of America, 100, 13521357.CrossRefGoogle ScholarPubMed
Zhang, F., Vierock, J., Yizhar, O., et al. (2011). The microbial opsin family of optogenetic tools. Cell, 147, 14461457.CrossRefGoogle ScholarPubMed

References

Adamantidis, A., Arber, S., Jaideep, S., et al. (2015). Optogenetics: 10 years after ChR2 in neurons – views from the community. Nature Neuroscience, 18, 12021212.CrossRefGoogle ScholarPubMed
Arenkiel, R., Marguerita, E. K., Davison, I. G., et al. (2008). Genetic control of neuronal activity in mice conditionally expressing TRPV1. Nature Methods, 5, 299302.CrossRefGoogle ScholarPubMed
Bading, H., Ginty, D. D. and Greenberg, M. E. (1993). Regulation of gene expression in hippocampal neurons by distinct calcium signaling pathways. Science, 260, 181186.CrossRefGoogle ScholarPubMed
Barnes, C. A., McNaughton, B. L., Mizumori, S. J., et al. (1990). Comparison of spatial and temporal characteristics of neuronal activity in sequential stages of hippocampal processing. Progress in Brain Research, 83, 287300.CrossRefGoogle ScholarPubMed
Barth, A. L., Gerkin, R. C. and Dean, K. L. (2004). Alteration of neuronal firing properties after in vivo experience in a FosGFP transgenic mouse. The Journal of Neuroscience, 24, 64666475.CrossRefGoogle Scholar
Blanco, E., Messeguer, X., Smith, T. F., et al. (2006). Transcription factor map alignment of promoter regions. PLoS Computational Biology, 2, e49.CrossRefGoogle ScholarPubMed
Bonni, A., Ginty, D. D., Dudek, H., et al. (1995). Serine 133-phosphorylated CREB induces transcription via a cooperative mechanism that may confer specificity to neurotrophin signals. Molecular and Cellular Neurosciences, 6, 168183.CrossRefGoogle Scholar
Borghuis, B. G., Tian, L., Xu, Y., et al. (2011). Imaging light responses of targeted neuron populations in the rodent retina. The Journal of Neuroscience, 31, 28552867.CrossRefGoogle ScholarPubMed
Bossert, J. M., Stern, A. L., Theberge, F. R. M., et al. (2011). Ventral medial prefrontal cortex neuronal ensembles mediate context-induced relapse to heroin. Nature Neuroscience, 14, 420422.CrossRefGoogle ScholarPubMed
Boyden, E. S., Zhang, F., Bamberg, E., et al. (2005). Millisecond-timescale, genetically targeted optical control of neural activity. Nature Neuroscience, 8, 12631268.CrossRefGoogle ScholarPubMed
Brake, A. J., Wagenbach, M. J. and Julius, D. (1994). New structural motif for ligand-gated ion channels defined by an ionotropic ATP receptor. Nature, 371, 519523.CrossRefGoogle ScholarPubMed
Cambridge, S. B., Geissler, D., Calegari, F., et al. (2009). Doxycycline-dependent photoactivated gene expression in eukaryotic systems. Nature Methods, 6, 527531.CrossRefGoogle ScholarPubMed
Caterina, M. J., Schumacher, M. A., Tominaga, M., et al. (1997). The capsaicin receptor: a heat-activated ion channel in the pain pathway. Nature, 389, 816824.CrossRefGoogle ScholarPubMed
Ceccatelli, S., Villar, M. J., Goldstein, M., et al. (1989). Expression of c-Fos immunoreactivity in transmitter-characterized neurons after stress. Proceedings of the National Academy of Sciences USA, 86, 95699573.CrossRefGoogle ScholarPubMed
Chen, T.-W., Wardill, T. J., Sun, Y., et al. (2013). Ultrasensitive fluorescent proteins for imaging neuronal activity. Nature, 499, 295300.CrossRefGoogle ScholarPubMed
Cowansage, K. K., Shuman, T., Dillingham, B. C., et al. (2014). Direct reactivation of a coherent neocortical memory of context. Neuron, 84, 432441.CrossRefGoogle ScholarPubMed
Crick, F. (1999). The impact of molecular biology on neuroscience. Philosophical Transactions of the Royal Society of London, 354, 20212025.CrossRefGoogle ScholarPubMed
Delgado, J. M. R. (1964). Free behavior and brain stimulation. International Review of Neurobiology, 6, 349449.CrossRefGoogle ScholarPubMed
Delgado, J. M. R. (1969). Physical Control of the Mind: Toward a Psychocivilized Society. New York, NY: Harper & Row.Google Scholar
Denny, C. A., Kheirbek, M. A., Alba, E. L., et al. (2014). Hippocampal memory traces are differentially modulated by experience, time, and adult neurogenesis. Neuron, 83, 189201.CrossRefGoogle ScholarPubMed
Diester, I., Kaufman, M. T., Mogri, M., et al. (2011). An optogenetic toolbox designed for primates. Nature Neuroscience, 14, 387397.CrossRefGoogle ScholarPubMed
Dittgen, T., Nimmerjahn, A., Komai, S., et al. (2004). Lentivirus-based genetic manipulations of cortical neurons and their optical and electrophysiological monitoring in vivo. Proceedings of the National Academy of Sciences USA, 101, 1820618211.CrossRefGoogle ScholarPubMed
Edwards, J. G. (2014). TRPV1 in the central nervous system: synaptic plasticity, function, and pharmacological implications. Progress in Drug Research, 68, 77104.Google ScholarPubMed
Feil, R., Wagner, J., Metzger, D., et al. (1997). Regulation of Cre recombinase activity by mutated estrogen receptor ligand-binding domains. Biochemical and Biophysical Research Communications, 237, 752757.CrossRefGoogle ScholarPubMed
Freundlieb, S., Schirra-Müller, C. and Bujard, H. (1999). A tetracycline controlled activation/repression system with increased potential for gene transfer into mammalian cells. The Journal of Gene Medicine, 1, 412.3.0.CO;2-Y>CrossRefGoogle ScholarPubMed
Galvan, A., Hu, X., Smith, Y., et al. (2012). In vivo optogenetic control of striatal and thalamic neurons in non-human primates. PLoS ONE, 7, e50808.CrossRefGoogle ScholarPubMed
Garner, A. R., Rowland, D. C., Hwang, S. Y., et al. (2012). Generation of a synthetic memory trace. Science, 335, 15131516.CrossRefGoogle ScholarPubMed
Gerits, A., Farivar, R., Rosen, B. R., et al. (2012). Optogenetically induced behavioral and functional network changes in primates. Current Biology, 22, 17221726.CrossRefGoogle ScholarPubMed
Gonzalez, G. A. and Montminy, M. R. (1989). Cyclic AMP stimulates somatostatin gene transcription by phosphorylation of CREB at serine 133. Cell, 59, 675680.CrossRefGoogle ScholarPubMed
Gossen, M. and Bujard, H. (1992). Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proceedings of the National Academy of Sciences USA, 89, 55475551.CrossRefGoogle ScholarPubMed
Guenthner, C. J., Miyamichi, K., Yang, H. H., et al. (2013). Permanent genetic access to transiently active neurons via TRAP: targeted recombination in active populations. Neuron, 78, 773784.CrossRefGoogle ScholarPubMed
Güler, A. D., Rainwater, A., Parker, J. G., et al. (2012). Transient activation of specific neurons in mice by selective expression of the capsaicin receptor. Nature Communications, 3, 746756.CrossRefGoogle ScholarPubMed
Han, X., Qian, X., Bernstein, J. G., et al. (2009). Millisecond-timescale optical control of neural dynamics in the nonhuman primate brain. Neuron, 62, 191198.CrossRefGoogle ScholarPubMed
Heath, R. G., Monroe, R. R. and Mickle, W. A. (1955). Stimulation of the amygdaloid nucleus in a schizophrenic patient. American Journal of Psychiatry, 111, 862863.CrossRefGoogle Scholar
Hunt, S. P., Pini, A. and Evan, G. (1987). Induction of c-Fos-like protein in spinal cord neurons following sensory stimulation. Nature, 328, 632634.CrossRefGoogle ScholarPubMed
Impey, S., McCorkle, S. R., Cha-Molstad, H., et al. (2004). Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions. Cell, 119, 10411054.Google ScholarPubMed
Jazayeri, M., Lindbloom-Brown, Z. and Horwitz, G. D. (2012). Saccadic eye movements evoked by optogenetic activation of primate V1. Nature Neuroscience, 15, 13681370.CrossRefGoogle ScholarPubMed
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. Proceedings of the National Academy of Sciences USA, 106, 316321.CrossRefGoogle ScholarPubMed
Kawashima, T., Kitamura, K., Suzuki, K., et al. (2013). Functional labeling of neurons and their projections using the synthetic activity-dependent promoter E-SARE. Nature Methods, 10, 889895.CrossRefGoogle ScholarPubMed
Kee, N., Teixeira, C. M., Wang, A. H., et al. (2007). Preferential incorporation of adult-generated granule cells into spatial memory networks in the dentate gyrus. Nature Neuroscience, 10, 355362.CrossRefGoogle ScholarPubMed
Khorana, H. G., Knox, B. E., Nasi, E., et al. (1988). Expression of a bovine rhodopsin gene in Xenopus oocytes: demonstration of light-dependent ionic currents. Proceedings of the National Academy of Sciences USA, 85, 79177921.CrossRefGoogle ScholarPubMed
King, H. E. (1961). Psychological effects of excitation in the limbic system. In: Electrical Stimulation of the Brain: An Interdisciplinary Survey of Neurobehavioral Integrative Systems. Sheer, D. E. (ed.), pp. 477486. Austin, TX: University of Texas Press.Google Scholar
Kiselev, A. and Subramaniam, S. (1997). Studies of Rh1 metarhodopsin stabilization in wild-type Drosophila and in mutants lacking one or both arrestins. Biochemistry, 36, 21882196.CrossRefGoogle ScholarPubMed
Koya, E., Golden, S. A., Harvey, B. K., et al. (2009). Targeted disruption of cocaine-activated nucleus accumbens neurons prevents context-specific sensitization. Nature Neuroscience, 12, 10691073.CrossRefGoogle ScholarPubMed
Kwok, R. P., Lundblad, J. R., Chrivia, J. C., et al. (1994). Nuclear protein CBP is a coactivator for the transcription factor CREB. Nature, 370, 223226.CrossRefGoogle ScholarPubMed
Kyung, T., Lee, S., Kim, J. E., et al. (2015). Optogenetic control of endogenous Ca2+ channels in vivo. Nature Biotechnology, 33, 10921096.CrossRefGoogle ScholarPubMed
Lee, M.-H., Appleton, K. M., Strungs, E. G., et al. (2016). The conformational signature of Β-arrestin2 predicts its trafficking and signalling functions. Nature, 531, 665668.CrossRefGoogle ScholarPubMed
Lima, S. Q. and Miesenböck, G. (2005). Remote control of behavior through genetically targeted photostimulation of neurons. Cell, 121, 141152.CrossRefGoogle ScholarPubMed
Liu, X., Ramirez, S., Pang, P. T., et al. (2012). Optogenetic stimulation of a hippocampal engram activates fear memory recall. Nature, 484, 381385.CrossRefGoogle ScholarPubMed
Loebrich, S., and Nedivi, E., (2009). The function of activity-regulated genes in the nervous system. Physiological Reviews, 89 (4), 10791103. doi:10.1152/physrev.00013.2009.CrossRefGoogle ScholarPubMed
Losonczy, A. and Zemelman, B. V. (2016). Illuminating memory circuit dynamics. Learning & Memory (In preparation).Google Scholar
MacLean, P. D. (1990). The Triune Brain in Evolution: Role in Paleocerebral Functions. New York, NY: Plenum Press.Google Scholar
Madisen, L., Zwingman, T. A., Sunkin, S. M., et al. (2009). A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nature Neuroscience, 13, 133140.CrossRefGoogle ScholarPubMed
Melyan, Z., Tarttelin, E. E., Bellingham, J., et al. (2005). Addition of human melanopsin renders mammalian cells photoresponsive. Nature, 433, 741745.CrossRefGoogle ScholarPubMed
Minatohara, K., Akiyoshi, M. and Okuno, H. (2016). Role of immediate–early genes in synaptic plasticity and neuronal ensembles underlying the memory trace. Frontiers in Molecular Neuroscience, 8, 78.CrossRefGoogle ScholarPubMed
Morgan, J. I. and Curran, T. (1991). Stimulus–transcription coupling in the nervous system: involvement of the inducible proto-oncogenes Fos and Jun. Annual Review of Neuroscience, 14, 421451.CrossRefGoogle ScholarPubMed
Nagel, G., Szellas, T., Huhn, W., et al. (2003). Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proceedings of the National Academy of Sciences USA, 100, 1394013945.CrossRefGoogle ScholarPubMed
Nathanson, J. L., Jappelli, R., Scheeff, E. D., et al., (2009). Short promoters in viral vectors drive selective expression in mammalian inhibitory neurons, but do not restrict activity to specific inhibitory cell-types. Frontiers in Neural Circuits, 3, 19.CrossRefGoogle Scholar
Nuber, S., Zabel, U., Lorenz, K., et al. (2016). Β-arrestin biosensors reveal a rapid, receptor-dependent activation/deactivation cycle. Nature, 531, 661664.CrossRefGoogle ScholarPubMed
Ovcharenko, I., Nobrega, M. A., Loots, G. G., et al. (2004). ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Research, 32, W280W286.CrossRefGoogle ScholarPubMed
Panksepp, J. (2004). Affective Neuroscience: the Foundations of Human and Animal Emotions. Oxford: Oxford University Press.Google Scholar
Peier, A. M., Moqrich, A., Hergarden, A. C., et al. (2002). A TRP channel that senses cold stimuli and menthol. Cell, 108, 705715.CrossRefGoogle ScholarPubMed
Pinal, C. S., Cortessis, V. and Tobin, A. J. (1997). Multiple elements regulate GAD65 transcription. Developmental Neuroscience, 19, 465475.CrossRefGoogle ScholarPubMed
Qiu, X., Kumbalasiri, T., Carlson, S. M., et al. (2005). Induction of photosensitivity by heterologous expression of melanopsin. Nature, 433, 745749.CrossRefGoogle ScholarPubMed
Ramirez, S., Liu, X., Lin, P.-A., et al. (2013). Creating a false memory in the hippocampus. Science, 341, 387391.CrossRefGoogle ScholarPubMed
Redondo, R. L., Kim, J., Arons, A. L., et al. (2014). Bidirectional switch of the valence associated with a hippocampal contextual memory engram. Nature, 513, 426430.CrossRefGoogle ScholarPubMed
Reijmers, L. G., Perkins, B. L., Matsuo, N., et al. (2007). Localization of a stable neural correlate of associative memory. Science, 317, 12301233.CrossRefGoogle ScholarPubMed
Root, C. M., Denny, C. A., Hen, R., et al. (2014). The participation of cortical amygdala in innate, odour-driven behaviour. Nature, 515, 269273.CrossRefGoogle ScholarPubMed
Rossier, J., Bernard, A., Cabungcal, J.-H., et al. (2014). Cortical fast-spiking parvalbumin interneurons enwrapped in the perineuronal net express the metallopeptidases Adamts8, Adamts15 and neprilysin. Molecular Psychiatry, 20, 154161.CrossRefGoogle ScholarPubMed
Rost, B. R., Schneider, F., Grauel, M. K., et al. (2015). Optogenetic acidification of synaptic vesicles and lysosomes. Nature Neuroscience, 18, 18451852.CrossRefGoogle ScholarPubMed
Ruiz, O., Lustig, B. R., Nassi, J. J., et al. (2013). Optogenetics through windows on the brain in the nonhuman primate. Journal of Neurophysiology, 110, 14551467.CrossRefGoogle ScholarPubMed
Sagar, S. M., Sharp, F. R. and Curran, T. (1988). Expression of c-Fos protein in brain: metabolic mapping at the cellular level. Science, 240, 13281331.CrossRefGoogle ScholarPubMed
Schoch, S., Cibelli, G. and Thiel., G. (1996). Neuron-specific gene expression of synapsin I: major role of a negative regulatory mechanism. The Journal of Biological Chemistry, 271, 33173323.CrossRefGoogle ScholarPubMed
Seidemann, E., Chen, Y., Bai, Y., et al. (2016). Calcium imaging with genetically encoded indicators in behaving primates. eLife, 5, 3771.CrossRefGoogle ScholarPubMed
Sharma, K., Schmitt, S., Bergner, C. G., et al. (2015). Cell type- and brain region-resolved mouse brain proteome. Nature Neuroscience, 18, 18191831.CrossRefGoogle ScholarPubMed
Sheng, M, McFadden, G. and Greenberg, M. E. (1990). Membrane depolarization and calcium induce c-Fos transcription via phosphorylation of transcription factor CREB. Neuron, 4, 571582.CrossRefGoogle ScholarPubMed
Sheng, M., Thompson, M. A. and Greenberg, M. E. (1991). CREB: a Ca2+-regulated transcription factor phosphorylated by calmodulin-dependent kinases. Science, 252, 14271430.CrossRefGoogle Scholar
Stein, M., Breit, A., Fehrentz, T., et al. (2013). Optical control of TRPV1 channels. Angewandte Chemie, 52, 98459848.CrossRefGoogle ScholarPubMed
Stierl, M., Stumpf, P., Udwari, D., et al. (2011). Light modulation of cellular cAMP by a small bacterial photoactivated adenylyl cyclase, bPAC, of the soil bacterium Beggiatoa. The Journal of Biological Chemistry, 286, 11811188.CrossRefGoogle ScholarPubMed
Stone, S. S., Teixeira, C. M., Zaslavsky, K., et al. (2011). Functional convergence of developmentally and adult-generated granule cells in dentate gyrus circuits supporting hippocampus-dependent memory. Hippocampus, 21, 13481362.CrossRefGoogle ScholarPubMed
Sugino, K., Hempel, C. M., Miller, M. N., et al. (2006). Molecular taxonomy of major neuronal classes in the adult mouse forebrain. Nature Neuroscience, 9, 99107.CrossRefGoogle ScholarPubMed
Sweet, W. H., Ervin, F. and Mark, V. H. (1969). The relationship of violent behaviour to focal cerebral disease. In: Aggressive Behaviour. Garattini, S. and Sigg, E. B. (Eds.), pp. 336352. Amsterdam: Excerpta Medica Foundation.Google Scholar
Tasic, B., Menon, V., Nguyen, T. N., et al., (2016). Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Nature Neuroscience, 19, 335346.CrossRefGoogle ScholarPubMed
Wang, K. H., Majewska, A., Schummers, J., et al. (2006). In vivo two-photon imaging reveals a role of Arc in enhancing orientation specificity in visual cortex. Cell, 126, 389402.CrossRefGoogle ScholarPubMed
Wang, M., Perova, Z., Benjamin, R. A., et al. (2014). Synaptic modifications in the medial prefrontal cortex in susceptibility and resilience to stress. The Journal of Neuroscience, 34, 74857492.CrossRefGoogle ScholarPubMed
Wend, S., Wagner, H. J., Konrad Müller, K., et al. (2014). Optogenetic control of protein kinase activity in mammalian cells. ACS Synthetic Biology, 3, 280285.CrossRefGoogle ScholarPubMed
Yaguchi, M., Ohashi, Y., Tsubota, T., et al. (2013). Characterization of the properties of seven promoters in the motor cortex of rats and monkeys after lentiviral vector-mediated gene transfer. Human Gene Therapy Methods, 24, 333344.CrossRefGoogle ScholarPubMed
Yao, F. and Eriksson, E. (1999). A novel tetracycline-inducible viral replication switch. Human Gene Therapy, 10, 419427.CrossRefGoogle ScholarPubMed
Yassin, L., Benedetti, B. L., Jouhanneau, J.-S., et al. (2010). An embedded subnetwork of highly active neurons in the neocortex. Neuron, 68, 10431050.CrossRefGoogle ScholarPubMed
Zemelman, B. V. and Miesenböck, G. (2001). Genetic schemes and schemata in neurophysiology. Current Opinion in Neurobiology, 11, 409414.CrossRefGoogle ScholarPubMed
Zemelman, B. V., Lee, G. A., Ng, M., et al. (2002). Selective photostimulation of Genetically chARGed neurons. Neuron, 33, 1522.CrossRefGoogle ScholarPubMed
Zemelman, B. V., Nesnas, N., Lee, G. A., et al. (2003). Photochemical gating of heterologous ion channels: remote control over genetically designated populations of neurons. Proceedings of the National Academy of Sciences USA, 100, 13521357.CrossRefGoogle ScholarPubMed
Zhang, X., Odom, D. T., Koo, S.-H., et al. (2005). Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proceedings of the National Academy of Sciences USA, 102, 44594464.CrossRefGoogle ScholarPubMed

References

Akerboom, J. et al. (2013). Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics. Frontiers in Molecular Neuroscience, 6, 2.CrossRefGoogle ScholarPubMed
Bendesky, A. et al. (2011). Catecholamine receptor polymorphisms affect decision-making in C. elegans. Nature, 472(7343), 313318.CrossRefGoogle ScholarPubMed
Busch, K.E. et al. (2012). Tonic signaling from O2 sensors sets neural circuit activity and behavioral state. Nature Neuroscience, 15(4), 581591.CrossRefGoogle ScholarPubMed
Chase, D.L. and Koelle, M.R. (2007). Biogenic amine neurotransmitters in C. elegans. WormBook, 115.Google Scholar
Cohen, E. et al. (2014). Caenorhabditis elegans nicotinic acetylcholine receptors are required for nociception. Molecular and Cellular Neurosciences, 59, 8596.CrossRefGoogle ScholarPubMed
Dayan, P. and Balleine, B.W. (2002). Reward, motivation, and reinforcement learning. Neuron, 36(2), 285298.CrossRefGoogle ScholarPubMed
Donnelly, J.L. et al. (2013). Monoaminergic orchestration of motor programs in a complex C. elegans behavior. PLoS Biology, 11(4), e1001529.CrossRefGoogle Scholar
Emiliani, V. et al. (2015). All-optical interrogation of neural circuits. The Journal of Neuroscience, 35(41), 1391713926.CrossRefGoogle ScholarPubMed
Fang-Yen, C., Alkema, M.J. and Samuel, A.D.T. (2015). Illuminating neural circuits and behaviour in Caenorhabditis elegans with optogenetics. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1677), 20140212.CrossRefGoogle ScholarPubMed
Faumont, S. et al. (2011). An image-free opto-mechanical system for creating virtual environments and imaging neuronal activity in freely moving Caenorhabditis elegans. PLoS ONE, 6(9), e24666.CrossRefGoogle ScholarPubMed
Faumont, S., Lindsay, T.H. and Lockery, S.R. (2012). Neuronal microcircuits for decision making in C. elegans. Current Opinion in Neurobiology, 22(4), 580591.CrossRefGoogle ScholarPubMed
Guo, Z.V., Hart, A.C. and Ramanathan, S. (2009). Optical interrogation of neural circuits in Caenorhabditis elegans. Nature Methods, 6(12), 891896.CrossRefGoogle ScholarPubMed
Han, B., Bellemer, A. and Koelle, M.R. (2015). An evolutionarily conserved switch in response to GABA affects development and behavior of the locomotor circuit of Caenorhabditis elegans. Genetics, 199(4), 11591172.CrossRefGoogle ScholarPubMed
Hoerndli, F.J. et al. (2015). Neuronal activity and CaMKII regulate kinesin-mediated transport of synaptic AMPARs. Neuron, 86(2), 457474.CrossRefGoogle ScholarPubMed
Husson, S.J. (2012). Keeping track of worm trackers. WormBook, 117.CrossRefGoogle Scholar
Husson, S.J. et al. (2012a). Optogenetic analysis of a nociceptor neuron and network reveals ion channels acting downstream of primary sensors. Current Biology, 22(9), 743752.CrossRefGoogle ScholarPubMed
Husson, S.J. et al. (2012b). Microbial light-activatable proton pumps as neuronal inhibitors to functionally dissect neuronal networks in C. elegans. PLoS ONE, 7(7), e40937CrossRefGoogle ScholarPubMed
Husson, S.J., Gottschalk, A. and Leifer, A.M. (2013). Optogenetic manipulation of neural activity in C. elegans: from synapse to circuits and behaviour. Biology of the Cell, 105(6), 235250.CrossRefGoogle Scholar
Inoue, M. et al. (2015). Rational design of a high-affinity, fast, red calcium indicator R-CaMP2. Nature Methods, 12(1), 6470.CrossRefGoogle ScholarPubMed
Jensen, M. et al. (2012). Wnt signaling regulates acetylcholine receptor translocation and synaptic plasticity in the adult nervous system. Cell, 149(1), 173187.CrossRefGoogle ScholarPubMed
Kawazoe, Y., Yawo, H. and Kimura, K.D. (2013). A simple optogenetic system for behavioral analysis of freely moving small animals. Neuroscience Research, 75(1), 6568.CrossRefGoogle ScholarPubMed
Kindt, K.S. et al. (2007). Dopamine mediates context-dependent modulation of sensory plasticity in C. elegans. Neuron, 55(4), 662676.CrossRefGoogle ScholarPubMed
Kittelmann, M. et al. (2013). In vivo synaptic recovery following optogenetic hyperstimulation. Proceedings of the National Academy of Sciences, 110(32), E3007E3016.CrossRefGoogle ScholarPubMed
Kocabas, A. et al. (2012). Controlling interneuron activity in Caenorhabditis elegans to evoke chemotactic behaviour. Nature, 490(7419), 273277.CrossRefGoogle ScholarPubMed
Krieg, M., Dunn, A.R. and Goodman, M.B. (2014). Mechanical control of the sense of touch by β-spectrin. Nature Cell Biology, 16(3), 224233.CrossRefGoogle ScholarPubMed
Leifer, A.M. et al. (2011). Optogenetic manipulation of neural activity in freely moving Caenorhabditis elegans. Nature Methods, 8(2), 147152.CrossRefGoogle ScholarPubMed
Li, Z. et al. (2014). Encoding of both analog- and digital-like behavioral outputs by one C. elegans interneuron. Cell, 159(4), 751765.CrossRefGoogle ScholarPubMed
Liewald, J.F. et al. (2008). Optogenetic analysis of synaptic function. Nature Methods, 5(10), 895902.CrossRefGoogle ScholarPubMed
Lindsay, T.H., Thiele, T.R. and Lockery, S.R. (2011). Optogenetic analysis of synaptic transmission in the central nervous system of the nematode Caenorhabditis elegans. Nature Communications, 2, 306309.CrossRefGoogle ScholarPubMed
Liu, Q., Hollopeter, G. and Jorgensen, E.M. (2009). Graded synaptic transmission at the Caenorhabditis elegans neuromuscular junction. Proceedings of the National Academy of Sciences of the United States of America, 106(26), 1082310828.CrossRefGoogle ScholarPubMed
Lockery, S.R. (2011). The computational worm: spatial orientation and its neuronal basis in C. elegans. Current Opinion in Neurobiology, 21(5), 782790.CrossRefGoogle ScholarPubMed
Luo, L. et al. (2014). Dynamic encoding of perception, memory, and movement in a C. elegans chemotaxis circuit. Neuron, 82(5), 11151128.CrossRefGoogle Scholar
Milward, K. et al. (2011). Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. Proceedings of the National Academy of Sciences, 108(51), 2067220677.CrossRefGoogle ScholarPubMed
Nagel, G. et al. (2002). Channelrhodopsin-1: a light-gated proton channel in green algae. Science, 296(5577), 23952398.CrossRefGoogle ScholarPubMed
Nagel, G. et al. (2003). Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proceedings of the National Academy of Sciences of the United States of America, 100(24), 1394013945.CrossRefGoogle ScholarPubMed
Nagel, G. et al. (2005). Light activation of channelrhodopsin-2 in excitable cells of Caenorhabditis elegans triggers rapid behavioral responses. Current Biology, 15(24), 22792284.CrossRefGoogle ScholarPubMed
Narayan, A., Laurent, G. and Sternberg, P.W. (2011). Transfer characteristics of a thermosensory synapse in Caenorhabditis elegans. Proceedings of the National Academy of Sciences, 108(23), 96679672.CrossRefGoogle ScholarPubMed
Piggott, B.J. et al. (2011). The neural circuits and synaptic mechanisms underlying motor initiation in C. elegans. Cell, 147(4), 922933.CrossRefGoogle ScholarPubMed
Prevedel, R. et al. (2014). Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy. Nature Methods, 11(7), 727730.CrossRefGoogle ScholarPubMed
Ramot, D. et al. (2008). The Parallel Worm Tracker: a platform for measuring average speed and drug-induced paralysis in nematodes. PLoS ONE, 3(5), e2208.CrossRefGoogle ScholarPubMed
Richmond, J. (2005). Synaptic function. WormBook, 114.Google Scholar
Sasakura, H. and Mori, I. (2013). Behavioral plasticity, learning, and memory in C. elegans. Current Opinion in Neurobiology, 23(1), 9299.CrossRefGoogle ScholarPubMed
Satoh, Y. et al. (2014). Regulation of experience-dependent bidirectional chemotaxis by a neural circuit switch in Caenorhabditis elegans. Journal of Neuroscience, 34(47), 1563115637.CrossRefGoogle ScholarPubMed
Sawin, E.R., Ranganathan, R. and Horvitz, H.R. (2000). C. elegans locomotory rate is modulated by the environment through a dopaminergic pathway and by experience through a serotonergic pathway. Neuron, 26(3), 619631.CrossRefGoogle ScholarPubMed
Schild, L.C. and Glauser, D.A. (2015). Dual color neural activation and behavior control with Chrimson and CoChR in Caenorhabditis elegans. Genetics, 200(4), 10291034.CrossRefGoogle ScholarPubMed
Schmitt, C. et al. (2012). Specific expression of channelrhodopsin-2 in single neurons of Caenorhabditis elegans. PLoS ONE, 7(8), e43164.CrossRefGoogle ScholarPubMed
Schrödel, T. et al. (2013). Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light. Nature Methods, 10(10), 10131020.CrossRefGoogle ScholarPubMed
Schultheis, C. et al. (2011). Optogenetic analysis of GABAB receptor signaling in Caenorhabditis elegans motor neurons. Journal of Neurophysiology, 106(2), 817827.CrossRefGoogle ScholarPubMed
Schultz, W. (2007). Multiple dopamine functions at different time courses. Annual Review of Neuroscience, 30, 259288.CrossRefGoogle ScholarPubMed
Shipley, F.B. et al. (2014). Simultaneous optogenetic manipulation and calcium imaging in freely moving C. elegans. Frontiers in Neural Circuits, 8, 28.CrossRefGoogle ScholarPubMed
Stirman, J.N. et al. (2011). Real-time multimodal optical control of neurons and muscles in freely behaving Caenorhabditis elegans. Nature Methods, 8(2), 153158.CrossRefGoogle ScholarPubMed
Sulston, J., Dew, M. and Brenner, S. (1975). Dopaminergic neurons in the nematode Caenorhabditis elegans. The Journal of Comparative Neurology, 163(2), 215226.CrossRefGoogle ScholarPubMed
Swierczek, N.A. et al. (2011). High-throughput behavioral analysis in C. elegans. Nature Methods, 8(7), 592598.CrossRefGoogle ScholarPubMed
Tanimoto, Y. et al. (2016). In actio optophysiological analyses reveal functional diversification of dopaminergic neurons in the nematode C. elegans. Scientific Reports, 6, 26297.CrossRefGoogle ScholarPubMed
Tokunaga, T. et al. (2014). Automated detection and tracking of many cells by using 4D live-cell imaging data. Bioinformatics (Oxford, England), 30(12), i43i51.Google ScholarPubMed
Trojanowski, N.F. et al. (2014). Neural and genetic degeneracy underlies Caenorhabditis elegans feeding behavior. Journal of Neurophysiology, 112(4), 951961.CrossRefGoogle ScholarPubMed
Watanabe, S. et al. (2013a). Ultrafast endocytosis at Caenorhabditis elegans neuromuscular junctions. eLife, 2, e00723.CrossRefGoogle ScholarPubMed
Watanabe, S. et al. (2013b). Ultrafast endocytosis at mouse hippocampal synapses. Nature, 504(7479), 242247.CrossRefGoogle ScholarPubMed
Wen, Q. et al. (2012). Proprioceptive coupling within motor neurons drives C. elegans forward locomotion. Neuron, 76(4), 750761.CrossRefGoogle ScholarPubMed
White, J.G. et al. (1986). The structure of the nervous system of the nematode Caenorhabditis elegans. Philosophical Transactions of the Royal Society B: Biological Sciences, 314(1165), 1340.Google ScholarPubMed
Williams, D.C. et al. (2013). Rapid and permanent neuronal inactivation in vivo via subcellular generation of reactive oxygen with the use of KillerRed. Cell Reports, 5(2), 553563.CrossRefGoogle ScholarPubMed
Zhang, F. et al. (2007). Multimodal fast optical interrogation of neural circuitry. Nature, 446(7136), 633639.CrossRefGoogle ScholarPubMed

References

Akerboom, J, Carreras Calderón, N, Tian, L, Wabnig, S, Prigge, M, Tolö, J, Gordus, A, Orger, MB, Severi, KE, Macklin, JJ, Patel, R, Pulver, SR, Wardill, TJ, Fischer, E, Schüler, C, Chen, T-W, Sarkisyan, KS, Marvin, JS, Bargmann, CI, Kim, DS, Kügler, S, Lagnado, L, Hegemann, P, Gottschalk, A, Schreiter, ER, Looger, LL (2013) Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics. Front Mol Neurosci, 6:2.CrossRefGoogle ScholarPubMed
Akerboom, J, Chen, T-W, Wardill, TJ, Tian, L, Marvin, JS, Mutlu, S, Calderón, NC, Esposti, F, Borghuis, BG, Sun, XR, Gordus, A, Orger, MB, Portugues, R, Engert, F, Macklin, JJ, Filosa, A, Aggarwal, A, Kerr, RA, Takagi, R, Kracun, S, Shigetomi, E, Khakh, BS, Baier, H, Lagnado, L, Wang, SS-H, Bargmann, CI, Kimmel, BE, Jayaraman, V, Svoboda, K, Kim, DS, Schreiter, ER, Looger, LL (2012) Optimization of a GCaMP calcium indicator for neural activity imaging. J Neurosci, 32:1381913840.CrossRefGoogle ScholarPubMed
Ardiel, EL, Rankin, CH (2010) An elegant mind: learning and memory in Caenorhabditis elegans. Learn Mem, 17:191201.CrossRefGoogle ScholarPubMed
Avelar, GM, Schumacher, RI, Zaini, PA, Leonard, G, Richards, TA, Gomes, SL (2014) A Rhodopsin-Guanylyl cyclase gene fusion functions in visual perception in a fungus. Curr Biol, 24:12341240.CrossRefGoogle Scholar
AzimiHashemi, N, Erbguth, K, Vogt, A, Riemensperger, T, Rauch, E, Woodmansee, D, Nagpal, J, Brauner, M, Sheves, M, Fiala, A, Kattner, L, Trauner, D, Hegemann, P, Gottschalk, A, Liewald, JF (2014) Synthetic retinal analogues modify the spectral and kinetic characteristics of microbial rhodopsin optogenetic tools. Nat Commun, 5:5810.CrossRefGoogle ScholarPubMed
Bamann, C, Kirsch, T, Nagel, G, Bamberg, E (2008) Spectral characteristics of the photocycle of channelrhodopsin-2 and its implication for channel function. J Mol Biol, 375:686694.CrossRefGoogle ScholarPubMed
Banghart, M, Borges, K, Isacoff, E, Trauner, D, Kramer, RH (2004) Light-activated ion channels for remote control of neuronal firing. Nat Neurosci, 7:13811386.CrossRefGoogle ScholarPubMed
Beavo, JA, Brunton, LL (2002) Cyclic nucleotide research – still expanding after half a century. Nat Rev Mol Cell Biol, 3:710718.CrossRefGoogle ScholarPubMed
Berndt, A, Lee, SY, Ramakrishnan, C, Deisseroth, K (2014) Structure-guided transformation of channelrhodopsin into a light-activated chloride channel. Science, 344:420424.CrossRefGoogle ScholarPubMed
Berndt, A, Schoenenberger, P, Mattis, J, Tye, KM, Deisseroth, K, Hegemann, P, Oertner, TG (2011) High-efficiency channelrhodopsins for fast neuronal stimulation at low light levels. Proc Natl Acad Sci U S A, 108:75957600.CrossRefGoogle ScholarPubMed
Berndt, A, Yizhar, O, Gunaydin, LA, Hegemann, P, Deisseroth, K (2009) Bi-stable neural state switches. Nat Neurosci, 12:229234.CrossRefGoogle ScholarPubMed
Boyden, ES, Zhang, F, Bamberg, E, Nagel, G, Deisseroth, K (2005) Millisecond-timescale, genetically targeted optical control of neural activity. Nat Neurosci, 8:12631268.CrossRefGoogle ScholarPubMed
Broussard, GJ, Liang, R, Tian, L (2014) Monitoring activity in neural circuits with genetically encoded indicators. Front Mol Neurosci, 7:97.CrossRefGoogle ScholarPubMed
Chen, T-W, Wardill, TJ, Sun, Y, Pulver, SR, Renninger, SL, Baohan, A, Schreiter, ER, Kerr, RA, Orger, MB, Jayaraman, V, Looger, LL, Svoboda, K, Kim, DS (2013) Ultrasensitive fluorescent proteins for imaging neuronal activity. Nature, 499:295300.CrossRefGoogle ScholarPubMed
Chow, BY, Han, X, Dobry, AS, Qian, X, Chuong, AS, Li, M, Henninger, M a, Belfort, GM, Lin, Y, Monahan, PE, Boyden, ES (2010) High-performance genetically targetable optical neural silencing by light-driven proton pumps. Nature, 463:98102.CrossRefGoogle ScholarPubMed
Chung, SH, Sun, L, Gabel, CV (2013) In vivo neuronal calcium imaging in C. elegans. J Vis Exp, 74:50357.Google Scholar
Chuong, AS, Miri, ML, Busskamp, V, Matthews, GAC, Acker, LC, Sørensen, AT, Young, A, Klapoetke, NC, Henninger, MA, Kodandaramaiah, SB, Ogawa, M, Ramanlal, SB, Bandler, RC, Allen, BD, Forest, CR, Chow, BY, Han, X, Lin, Y, Tye, KM, Roska, B, Cardin, JA, Boyden, ES (2014) Noninvasive optical inhibition with a red-shifted microbial rhodopsin. Nat Neurosci, 17:11231129.CrossRefGoogle ScholarPubMed
de Bono, M, Maricq, AV (2005) Neuronal substrates of complex behaviors in C. elegans. Annu Rev Neurosci, 28:451501.CrossRefGoogle ScholarPubMed
Dugué, GP, Akemann, W, Knöpfel, T (2012) A comprehensive concept of optogenetics. Prog Brain Res, 196:128.CrossRefGoogle ScholarPubMed
Erbguth, K, Prigge, M, Schneider, F, Hegemann, P, Gottschalk, A (2012) Bimodal activation of different neuron classes with the spectrally red-shifted channelrhodopsin chimera C1V1 in Caenorhabditis elegans. PLoS One, 7:e46827.CrossRefGoogle ScholarPubMed
Fang-Yen, C, Alkema, MJ, Samuel, ADT, Fang-yen, C (2015) Illuminating neural circuits and behaviour in Caenorhabditis elegans with optogenetics. Philos Trans R Soc Lond B Biol Sci, 370:20140212.CrossRefGoogle ScholarPubMed
Feldbauer, K, Zimmermann, D, Pintschovius, V, Spitz, J, Bamann, C, Bamberg, E (2009) Channelrhodopsin-2 is a leaky proton pump. Proc Natl Acad Sci U S A, 106:1231712322.CrossRefGoogle ScholarPubMed
Fenno, L, Yizhar, O, Deisseroth, K (2011) The development and application of optogenetics. Annu Rev Neurosci, 34:389412.CrossRefGoogle ScholarPubMed
Flavell, SW, Pokala, N, Macosko, EZ, Albrecht, DR, Larsch, J, Bargmann, CI (2013) Serotonin and the neuropeptide PDF initiate and extend opposing behavioral states in C. elegans. Cell, 154:10231035.CrossRefGoogle ScholarPubMed
Flytzanis, NC, Bedbrook, CN, Chiu, H, Engqvist, MKM, Xiao, C, Chan, KY, Sternberg, PW, Arnold, FH, Gradinaru, V (2014) Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons. Nat Commun, 5:4894.CrossRefGoogle ScholarPubMed
Gancedo, JM (2013) Biological roles of cAMP: variations on a theme in the different kingdoms of life. Biol Rev Camb Philos Soc, 88:645–68.CrossRefGoogle ScholarPubMed
Gao, S, Nagpal, J, Schneider, MW, Kozjak-pavlovic, V, Nagel, G, Gottschalk, A (2015) Optogenetic manipulation of cGMP in cells and animals by the tightly light-regulated guanylyl-cyclase opsin CyclOp. Nat Commun, 6:112.CrossRefGoogle ScholarPubMed
Gong, Y, Li, JZ, Schnitzer, MJ (2013) Enhanced archaerhodopsin fluorescent protein voltage indicators. PLoS One, 8:e66959.CrossRefGoogle ScholarPubMed
Govorunova, EG, Sineshchekov, OA, Janz, R, Liu, X, Spudich, JL (2015) Natural light-gated anion channels: a family of microbial rhodopsins for advanced optogenetics. Science, 349:647650.CrossRefGoogle ScholarPubMed
Gradinaru, V, Thompson, KR, Deisseroth, K (2008) eNpHR: a Natronomonas halorhodopsin enhanced for optogenetic applications. Brain Cell Biol, 36:129139.CrossRefGoogle ScholarPubMed
Gunaydin, LA, Yizhar, O, Berndt, A, Sohal, VS, Deisseroth, K, Hegemann, P (2010) Ultrafast optogenetic control. Nat Neurosci, 13:387392.CrossRefGoogle ScholarPubMed
Han, X, Chow, BY, Zhou, H, Klapoetke, NC, Chuong, A, Rajimehr, R, Yang, A, Baratta, MV, Winkle, J, Desimone, R, Boyden, ES (2011) A high-light sensitivity optical neural silencer: development and application to optogenetic control of non-human primate cortex. Front Syst Neurosci, 5:18.CrossRefGoogle ScholarPubMed
Hermann, A, Liewald, JF, Gottschalk, A (2015) A photosensitive degron enables acute light-induced protein degradation in the nervous system. Curr Biol, 25: R749R750.CrossRefGoogle ScholarPubMed
Husson, SJ, Costa, WS, Wabnig, S, Stirman, JN, Watson, JD, Spencer, WC, Akerboom, J, Looger, LL, Treinin, M, Miller, DM, Lu, H, Gottschalk, A (2012a) Optogenetic analysis of a nociceptor neuron and network reveals ion channels acting downstream of primary sensors. Curr Biol, 22:743752.CrossRefGoogle ScholarPubMed
Husson, SJ, Gottschalk, A, Leifer, AM (2013) Optogenetic manipulation of neural activity in C. elegans: from synapse to circuits and behaviour. Biol Cell, 105:235250.CrossRefGoogle Scholar
Husson, SJ, Liewald, JF, Schultheis, C, Stirman, JN, Lu, H, Gottschalk, A (2012b) Microbial light-activatable proton pumps as neuronal inhibitors to functionally dissect neuronal networks in C. elegans. PLoS One, 7:e40937.CrossRefGoogle ScholarPubMed
Kerr, RA (2006) Imaging the activity of neurons and muscles. WormBook, 113.CrossRefGoogle Scholar
Klapoetke, NC, Murata, Y, Kim, SS, Pulver, SR, Birdsey-Benson, A, Cho, YK, Morimoto, TK, Chuong, AS, Carpenter, EJ, Tian, Z, Wang, J, Xie, Y, Yan, Z, Zhang, Y, Chow, BY, Surek, B, Melkonian, M, Jayaraman, V, Constantine-Paton, M, Wong, GK-S, Boyden, ES (2014) Independent optical excitation of distinct neural populations. Nat Methods, 11: 338346.CrossRefGoogle ScholarPubMed
Kobayashi, J, Shidara, H, Morisawa, Y, Kawakami, M, Tanahashi, Y, Hotta, K, Oka, K (2013) A method for selective ablation of neurons in C. elegans using the phototoxic fluorescent protein, KillerRed. Neurosci Lett, 548:261264.CrossRefGoogle Scholar
Kralj, JM, Douglass, AD, Hochbaum, DR, Maclaurin, D, Cohen, AE (2012) Optical recording of action potentials in mammalian neurons using a microbial rhodopsin. Nat Methods, 9:9095.CrossRefGoogle Scholar
Lima, SQ, Miesenböck, G (2005) Remote control of behavior through genetically targeted photostimulation of neurons. Cell, 121:141152.CrossRefGoogle ScholarPubMed
Lin, JY (2011) A user’s guide to channelrhodopsin variants: features, limitations and future developments. Exp Physiol, 96:1925.CrossRefGoogle ScholarPubMed
Lin, JY, Lin, MZ, Steinbach, P, Tsien, RY (2009) Characterization of engineered channelrhodopsin variants with improved properties and kinetics. Biophys J, 96:18031814.CrossRefGoogle ScholarPubMed
Lin, JY, Sann, SB, Zhou, K, Nabavi, S, Proulx, CD, Malinow, R, Jin, Y, Tsien, RY (2013) Optogenetic inhibition of synaptic release with chromophore-assisted light inactivation (CALI). Neuron, 79:241253.CrossRefGoogle ScholarPubMed
Lucas, KA, Pitari, GM, Kazerounian, S, Ruiz-Stewart, I, Park, J, Schulz, S, Chepenik, KP, Waldman, SA (2000) Guanylyl cyclases and signaling by cyclic GMP. Pharmacol Rev, 52:375414.Google ScholarPubMed
Maclaurin, D, Venkatachalam, V, Lee, H, Cohen, AE (2013) Mechanism of voltage-sensitive fluorescence in a microbial rhodopsin. Proc Natl Acad Sci U S A, 110:59395944.CrossRefGoogle Scholar
Mutoh, H, Akemann, W, Knöpfel, T (2012) Genetically engineered fluorescent voltage reporters. ACS Chem Neurosci, 3:585592.CrossRefGoogle ScholarPubMed
Nagel, G, Brauner, M, Liewald, JF, Adeishvili, N, Bamberg, E, Gottschalk, A (2005) Light activation of channelrhodopsin-2 in excitable cells of caenorhabditis elegans triggers rapid behavioral responses. Curr Biol, 15:22792284.CrossRefGoogle ScholarPubMed
Nagel, G, Szellas, T, Huhn, W, Kateriya, S, Adeishvili, N, Berthold, P, Ollig, D, Hegemann, P, Bamberg, E (2003) Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc Natl Acad Sci U S A, 100:1394013945.CrossRefGoogle ScholarPubMed
Okazaki, A, Takagi, S (2013) An optogenetic application of proton pump ArchT to C. elegans cells. Neurosci Res, 75:2934.CrossRefGoogle ScholarPubMed
Prigge, M, Schneider, F, Tsunoda, SP, Shilyansky, C, Wietek, J, Deisseroth, K, Hegemann, P (2012) Color-tuned channelrhodopsins for multiwavelength optogenetics. J Biol Chem, 287:3180431812.CrossRefGoogle ScholarPubMed
Qi, YB, Garren, EJ, Shu, X, Tsien, RY, Jin, Y (2012) Photo-inducible cell ablation in Caenorhabditis elegans using the genetically encoded singlet oxygen generating protein miniSOG. Proc Natl Acad Sci U S A, 109:74997504.CrossRefGoogle ScholarPubMed
Renicke, C, Schuster, D, Usherenko, S, Essen, L-O, Taxis, C (2013) A LOV2 domain-based optogenetic tool to control protein degradation and cellular function. Chem Biol, 20:619626.CrossRefGoogle ScholarPubMed
Ryu, M-H, Moskvin, OV, Siltberg-Liberles, J, Gomelsky, M (2010) Natural and engineered photoactivated nucleotidyl cyclases for optogenetic applications. J Biol Chem, 285:4150141508.CrossRefGoogle ScholarPubMed
Scheib, U, Stehfest, K, Gee, CE, Korschen, HG, Fudim, R, Oertner, TG, Hegemann, P (2015) The rhodopsin-guanylyl cyclase of the aquatic fungus Blastocladiella emersonii enables fast optical control of cGMP signaling. Sci Signal, 8:18.CrossRefGoogle ScholarPubMed
Schild, LC, Glauser, DA (2015) Dual color neural activation and behavior control with Chrimson and CoChR in C. elegans. Genetics, 200:10291034.CrossRefGoogle Scholar
Schröder-Lang, S, Schwärzel, M, Seifert, R, Strünker, T, Kateriya, S, Looser, J, Watanabe, M, Kaupp, UB, Hegemann, P, Nagel, G (2007) Fast manipulation of cellular cAMP level by light in vivo. Nat Methods, 4:3942.CrossRefGoogle ScholarPubMed
Schultheis, C, Liewald, JF, Bamberg, E, Nagel, G, Gottschalk, A (2011) Optogenetic long-term manipulation of behavior and animal development. PLoS One, 6:e18766.CrossRefGoogle ScholarPubMed
Sengupta, P, Samuel, ADT (2009) Caenorhabditis elegans: a model system for systems neuroscience. Curr Opin Neurobiol, 19:637643.CrossRefGoogle Scholar
Shipley, FB, Clark, CM, Alkema, MJ, Leifer, AM (2014) Simultaneous optogenetic manipulation and calcium imaging in freely moving C. elegans. Front Neural Circuits, 8:28.CrossRefGoogle ScholarPubMed
Stierl, M, Stumpf, P, Udwari, D, Gueta, R, Hagedorn, R, Losi, A, Gärtner, W, Petereit, L, Efetova, M, Schwarzel, M, Oertner, TG, Nagel, G, Hegemann, P (2011) Light modulation of cellular cAMP by a small bacterial photoactivated adenylyl cyclase, bPAC, of the soil bacterium Beggiatoa. J Biol Chem, 286:11811188.CrossRefGoogle ScholarPubMed
Tian, L, Hires, SA, Mao, T, Huber, D, Chiappe, ME, Chalasani, SH, Petreanu, L, Akerboom, J, McKinney, SA, Schreiter, ER, Bargmann, CI, Jayaraman, V, Svoboda, K, Looger, LL (2009) Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators. Nat Methods, 6:875881.CrossRefGoogle ScholarPubMed
Ullrich, S, Gueta, R, Nagel, G (2013) Degradation of channelopsin-2 in the absence of retinal and degradation resistance in certain mutants. Biol Chem, 394:271280.CrossRefGoogle ScholarPubMed
Volgraf, M, Gorostiza, P, Numano, R, Kramer, RH, Isacoff, EY, Trauner, D (2006) Allosteric control of an ionotropic glutamate receptor with an optical switch. Nat Chem Biol, 2:4752.CrossRefGoogle ScholarPubMed
Wabnig, S, Liewald, JF, Yu, S-C, Gottschalk, A (2015) High-throughput all-optical analysis of synaptic transmission and synaptic vesicle recycling in Caenorhabditis elegans. PLoS One, 10:e0135584.CrossRefGoogle ScholarPubMed
Watanabe, S, Liu, Q, Davis, MW, Hollopeter, G, Thomas, N, Jorgensen, NB, Jorgensen, EM (2013) Ultrafast endocytosis at Caenorhabditis elegans neuromuscular junctions. Elife, 2:e00723.CrossRefGoogle ScholarPubMed
Weissenberger, S, Schultheis, C, Liewald, JF, Erbguth, K, Nagel, G, Gottschalk, A (2011) PACα – an optogenetic tool for in vivo manipulation of cellular cAMP levels, neurotransmitter release, and behavior in Caenorhabditis elegans. J Neurochem, 116:616625.CrossRefGoogle ScholarPubMed
White, JG, Southgate, E, Thomson, JN, Brenner, S (1986) The structure of the nervous system of the nematode Caenorhabditis elegans. Philos Trans R Soc B Biol Sci, 314:1340.Google ScholarPubMed
Wietek, J, Wiegert, JS, Adeishvili, N, Schneider, F, Watanabe, H, Tsunoda, SP, Vogt, A, Elstner, M, Oertner, TG, Hegemann, P (2014) Conversion of channelrhodopsin into a light-gated chloride channel. Science, 344:409412.CrossRefGoogle ScholarPubMed
Williams, DC, Bejjani, RE, Ramirez, PM, Coakley, S, Kim, SA, Lee, H, Wen, Q, Samuel, A, Lu, H, Hilliard, MA, Hammarlund, M (2013) Rapid and permanent neuronal inactivation in vivo via subcellular generation of reactive oxygen with the use of KillerRed. Cell Rep, 5:553563.CrossRefGoogle ScholarPubMed
Xu, X, Kim, SK (2011) The early bird catches the worm: new technologies for the Caenorhabditis elegans toolkit. Nat Rev Genet, 12:793801.CrossRefGoogle ScholarPubMed
Yemini, E, Jucikas, T, Grundy, LJ, Brown, AEX, Schafer, WR (2013) A database of Caenorhabditis elegans behavioral phenotypes. Nat Methods, 10:877879.CrossRefGoogle ScholarPubMed
Yizhar, O, Fenno, LE, Prigge, M, Schneider, F, Davidson, TJ, O’Shea, DJ, Sohal, VS, Goshen, I, Finkelstein, J, Paz, JT, Stehfest, K, Fudim, R, Ramakrishnan, C, Huguenard, JR, Hegemann, P, Deisseroth, K (2011) Neocortical excitation/inhibition balance in information processing and social dysfunction. Nature, 477:171178.CrossRefGoogle ScholarPubMed
Zemelman, BV, Nesnas, N, Lee, GA, Miesenbock, G (2003) Photochemical gating of heterologous ion channels: remote control over genetically designated populations of neurons. Proc Natl Acad Sci U S A, 100:13521357.CrossRefGoogle ScholarPubMed
Zemelman, BV, Lee, GA, Ng, M, Miesenböck, G (2002) Selective photostimulation of genetically chARGed neurons. Neuron, 33:1522.CrossRefGoogle ScholarPubMed
Zhang, F, Prigge, M, Beyrière, F, Tsunoda, SP, Mattis, J, Yizhar, O, Hegemann, P, Deisseroth, K (2008) Red-shifted optogenetic excitation: a tool for fast neural control derived from Volvox carteri. Nat Neurosci, 11:631633.CrossRefGoogle ScholarPubMed
Zhang, F, Wang, L-P, Brauner, M, Liewald, JF, Kay, K, Watzke, N, Wood, PG, Bamberg, E, Nagel, G, Gottschalk, A, Deisseroth, K (2007) Multimodal fast optical interrogation of neural circuitry. Nature, 446:633639.CrossRefGoogle ScholarPubMed

References

Adams, D.S., Lemire, J.M., Kramer, R.H. and Levin, M. (2014). Optogenetics in developmental biology: using light to control ion flux-dependent signals in Xenopus embryos. The International Journal of Developmental Biology, 58, 851861.CrossRefGoogle Scholar
Adams, D.S. and Levin, M. (2012). General principles for measuring resting membrane potential and ion concentration using fluorescent bioelectricity reporters. Cold Spring Harbor Protocols, 2012, 385397.Google ScholarPubMed
Adams, D.S., Masi, A. and Levin, M. (2007). H+-pump-dependent changes in membrane voltage are an early mechanism necessary and sufficient to induce Xenopus tail regeneration. Development, 134, 13231335.CrossRefGoogle ScholarPubMed
Adams, D.S., Tseng, A.S. and Levin, M. (2013). Light-activation of the archaerhodopsin H+-pump reverses age-dependent loss of vertebrate regeneration: sparking system-level controls in vivo. Biology Open, 2, 306313.CrossRefGoogle ScholarPubMed
Beane, W.S., Morokuma, J., Adams, D.S. and Levin, M. (2011). A chemical genetics approach reveals H,K-ATPase-mediated membrane voltage is required for planarian head regeneration. Chemistry & Biology, 18, 7789.CrossRefGoogle ScholarPubMed
Beck, C.W., Christen, B. and Slack, J.M.W. (2003). Molecular pathways needed for regeneration of spinal cord and muscle in a vertebrate. Developmental Cell, 5, 429439.CrossRefGoogle Scholar
Coffman, C., Harris, W. and Kintner, C. (1990). Xotch, the Xenopus homolog of Drosophila notch. Science, 249, 14381441.CrossRefGoogle ScholarPubMed
Feledy, J.A., Beanan, M.J., Sandoval, J.J. et al. (1999). Inhibitory patterning of the anterior neural plate in Xenopus by homeodomain factors Dlx3 and Msx1. Developmental Biology, 212, 455464.CrossRefGoogle ScholarPubMed
Harland, R.M. (1991). In situ hybridization: an improved whole mount method for Xenopus embryos. In: Kay, B.K. and Peng, H.B., eds., Xenopus laevis: Practical Uses in Cell and Molecular Biology. San Diego, CA: Academic Press, pp. 685695.CrossRefGoogle Scholar
Illingworth, C.M. and Barker, A.T. (1980). Measurement of electrical currents emerging during the regeneration of amputated fingertips in children. Clinical Physics and Physiological Measurement, 1, 8789CrossRefGoogle Scholar
Knopfel, T., Lin, M.Z., Levskaya, A. et al. (2010). Toward the second generation of optogenetic tools. The Journal of Neuroscience, 30, 1499815004.CrossRefGoogle ScholarPubMed
Levin, M. and Stevenson, C.G. (2012). Regulation of cell behavior and tissue patterning by bioelectrical signals: challenges and opportunities for biomedical engineering. Annual Review of Biomedical Engineering, 14, 295323.CrossRefGoogle ScholarPubMed
Morley, G.E., Taffet, S.M. and Delmar, M. (1996). Intramolecular interactions mediate pH regulation of connexin43 channels. Biophysical Journal, 70, 12941302.CrossRefGoogle ScholarPubMed
Nieuwkoop, P.D. and Faber, J. (1994). Normal Table of Xenopus laevis (Daudin): A Systematical and Chronological Survey of the Development from the Fertilized Egg till the End of Metamorphosis. New York, NY: Garland Publishing.Google Scholar
Pai, V.P., Aw, S., Shomrat, T., Lemire, J.M. and Levin, M. (2012). Transmembrane voltage potential controls embryonic eye patterning in Xenopus laevis. Development, 139, 313323.CrossRefGoogle ScholarPubMed
Sasaki, S., Ishibashi, K., Nagai, T. and Marumo, F., (1992). Regulation mechanisms of intracellular pH of Xenopus laevis oocyte. Biochimica et Biophysica Acta, 1137, 4551.CrossRefGoogle ScholarPubMed
Sive, H., Grainger, R.M. and Harland, R. (2000). Early Development of Xenopus laevis. New York, NY: Cold Spring Harbor Laboratory Press.Google Scholar
Tseng, A.-S., Beane, W.S., Lemire, J.M., Masi, A. and Levin, M., (2010). Induction of vertebrate regeneration by a transient sodium current. Journal of Neuroscience, 30, 1319213200.CrossRefGoogle ScholarPubMed
Vandenberg, L.N., Morrie, R.D. and Adams, D.S. (2011). V-ATPase-dependent ectodermal voltage and pH regionalization are required for craniofacial morphogenesis. Developmental Dynamics, 240, 18891904.CrossRefGoogle ScholarPubMed

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