Content
List of contributing authors | V
Introduction | 1
Keith Moffat, Feng Zhang, Klaus Hahn, Andreas Möglich
1 The biophysics and engineering of signaling photoreceptors | 7
1.1 Photoreceptors | 7
1.1.1 Novel photoreceptors | 10
1.1.2 Biophysics of photoreceptors and signal transduction | 10
1.2 Engineering of photoreceptors | 12
1.2.1 Approaches to designing light-regulated biological processes | 13
1.3 Case study – transcriptional control in cells by light | 17
1.4 Conclusion | 18
Acknowledgements | 20
References | 20
Kelly A. Zalocusky, Lief E. Fenno, Karl Deisseroth
2 Current challenges in optogenetics | 23
2.1 Introduction | 23
2.2 Background: current functionality of tools | 23
2.3 Unsolved problems and open questions: technology from cell biology,
optics, and behavior | 25
2.4 Unsolved problems and open questions:
genomics and biophysics | 28
2.5 Conclusion | 31
References | 33
Ehud Y. Isacoff, Richard H. Kramer, Dirk Trauner
3 Challenges and opportunities for optochemical genetics | 35
3.1 Introduction | 35
3.2 Photosensitizing receptors | 36
3.3 PCL and PTL development and applications | 39
3.4 Advantages and disadvantages of PCLs and PTLs | 41
3.5 Conclusion | 42
References | 42
Thomas Knöpfel
4 Optogenetic imaging of neural circuit dynamics using voltage-sensitive
fluorescent proteins: potential, challenges and perspectives | 47
4.1 Introduction | 47
4.2 The biological problem | 47
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4.3 The large scale challenge of circuit neurosciences | 47
4.4 The current approach to the large-scale integration problem | 48
4.5 Large-scale recordings of neuronal activities using optogenetic
approaches | 49
4.6 Genetically encoded voltage indicators: state of development and
application | 49
4.7 Unsolved methodological / technical challenges | 52
References | 52
Gero Miesenböck
5 Why optogenetic “control” is not (yet) control | 55
Acknowledgments | 59
References | 59
Mario de Bono, William R. Schafer, Alexander Gottschalk
6 Optogenetic actuation, inhibition, modulation and readout for neuronal
networks generating behavior in the nematode Caenorhabditis
elegans | 61
6.1 Introduction – the nematode as a genetic model in systems
neurosciencesystems neuroscience | 61
6.2 Imaging of neural activity in the nematode | 62
6.2.1 Genetically encoded Ca2+ indicators (GECIs) | 62
6.2.2 Imaging populations of neurons in immobilized animals | 62
6.2.3 Imaging neural activity in freely moving animals | 63
6.2.4 Other genetically encoded indicators of neuronal function | 64
6.3 Optogenetic tools established in the nematode | 64
6.3.1 Channelrhodopsin (ChR2) and ChR variants with different functional
properties for photodepolarization | 64
6.3.2 Halorhodopsin and light-triggered proton pumps for
photohyperpolarization | 65
6.3.3 Photoactivated Adenylyl Cyclase (PAC) for phototriggered cAMPdependent
effects that facilitate neuronal transmission | 65
6.3.4 Other optogenetic approaches | 66
6.3.5 Stimulation of single neurons by optogenetics in freely behaving
C. elegans | 66
6.4 Examples for optogenetic applications in C. elegans | 68
6.4.1 Optical control of synaptic transmission at the neuromuscular junction
and between neurons | 68
6.4.2 Optical control of neural network activity in the generation of
behavior | 69
6.5 Future challenges | 70
6.5.1 Closed-loop optogenetic control and optical feedback from behavior and
individual neurons | 70
6.5.2 Requirements for integrated optogenetics in the nematode | 72
References | 74
Matt L. Labella, Stephan Sigrist, Erik M. Jørgensen
7 Putting genetics into optogenetics: knocking out proteins with light | 79
7.1 Introduction | 79
7.2 Protein degradation | 79
7.3 Light stimulation | 85
References | 88
André Fiala
8 Optogenetic approaches in behavioral neuroscience | 91
8.1 Introduction | 91
8.2 Approaches to dissect neuronal circuits: determining physiological
correlations, requirement and sufficiency of neurons | 92
8.3 Optogenetic analysis of simple stimulus-response-connections | 93
8.4 Optogenetic and thermogenetic analysis of modulatory neurons:
artificial mimicry of relevance | 95
8.5 Conclusion | 97
References | 97
Fumi Kubo, Herwig Baier
9 Combining genetic targeting and optical stimulation for circuit dissection in
the zebrafish nervous system | 101
9.1 Introduction | 101
9.2 Zebrafish neuroscience: Genetics + Optics + Behavior | 101
9.3 Genetic targeting of optogenetic proteins to specific neurons | 102
9.4 Optical stimulation in behaving zebrafish | 103
9.5 Annotating behavioral functions of genetically-identified neurons by
optogenetics | 103
9.5.1 Spinal cord neurons (Rohon–Beard and Kolmer–Agduhr cells) | 103
9.5.2 Hindbrain motor command neurons | 104
9.5.3 Tangential neurons in the vestibular system | 104
9.5.4 Size filtering neurons in the tectum | 105
9.5.5 Whole-brain calcium imaging of motor adaptation at single-cell
resolution | 105
9.6 Future directions | 106
References | 106
10 Optogenetic analysis of mammalian neural circuits | 109
10.1 Introduction | 109
10.2 Optogenetic approaches to probe integrative properties at the cellular
level | 110
10.2.1 Excitatory signal integration at dendrites | 110
10.2.2 Control of excitatory signal integration by inhibition or
neuromodulation | 111
10.2.3 Long-term analysis of synaptic function | 113
10.3 Circuits and systems level | 114
10.4 Optogenetics and behavior: testing causal relationships in freely
moving animals | 120
References | 121
Viviana Gradinaru
11 Optogenetics to benefit human health: opportunities and
challenges | 127
11.1 Introduction | 127
11.2 Opportunities for translational applications | 127
11.3 Safety challenges | 129
11.4 Need for feedback | 130
11.5 Conclusion | 130
References | 130
Edward S. Boyden
12 Optogenetic tools for controlling neural activity: molecules and
hardware | 133
12.1 Overview | 133
12.2 Molecular tools for sensitizing neural functions to light | 133
12.3 Hardware for delivery of light into intact brain circuits | 136
References | 137
Ada Eban-Rothschild, Clara Touriño, Luis de Lecea
13 In vivo application of optogenetics in rodents | 143
13.1 Introduction | 143
13.2 Sleep / wake regulation | 143
13.3 Addiction | 145
13.4 Fear, anxiety and depression | 148
13.5 Autism and schizophrenia | 150
13.6 Aggression | 150
13.7 Breathing | 151
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