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Xue T, Stalmashonak A, Chen FD, Ding P, Luo X, Chua H, Lo GQ, Sacher WD, Poon JKS. Implantable photonic neural probes with out-of-plane focusing grating emitters. Sci Rep 2024; 14:13812. [PMID: 38877050 PMCID: PMC11178810 DOI: 10.1038/s41598-024-64037-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
We have designed, fabricated, and characterized implantable silicon neural probes with nanophotonic grating emitters that focus the emitted light at a specified distance above the surface of the probe for spatially precise optogenetic targeting of neurons. Using the holographic principle, we designed gratings for wavelengths of 488 and 594 nm, targeting the excitation spectra of the optogenetic actuators Channelrhodopsin-2 and Chrimson, respectively. The measured optical emission pattern of these emitters in non-scattering medium and tissue matched well with simulations. To our knowledge, this is the first report of focused spots with the size scale of a neuron soma in brain tissue formed from implantable neural probes.
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Affiliation(s)
- Tianyuan Xue
- Department of Nanophotonics, Integration, and Neural Technology, Max Planck Institute of Microstructure Physics, Weinberg 2, Halle, 06120, Germany.
- The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, M5S 3G4, ON, Canada.
| | - Andrei Stalmashonak
- Department of Nanophotonics, Integration, and Neural Technology, Max Planck Institute of Microstructure Physics, Weinberg 2, Halle, 06120, Germany
| | - Fu-Der Chen
- Department of Nanophotonics, Integration, and Neural Technology, Max Planck Institute of Microstructure Physics, Weinberg 2, Halle, 06120, Germany
- The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, M5S 3G4, ON, Canada
| | - Peisheng Ding
- Department of Nanophotonics, Integration, and Neural Technology, Max Planck Institute of Microstructure Physics, Weinberg 2, Halle, 06120, Germany
- The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, M5S 3G4, ON, Canada
| | - Xianshu Luo
- Advanced Micro Foundry Pte. Ltd., 11 Science Park Road, Singapore, 117685, Singapore
| | - Hongyao Chua
- Advanced Micro Foundry Pte. Ltd., 11 Science Park Road, Singapore, 117685, Singapore
| | - Guo-Qiang Lo
- Advanced Micro Foundry Pte. Ltd., 11 Science Park Road, Singapore, 117685, Singapore
| | - Wesley D Sacher
- Department of Nanophotonics, Integration, and Neural Technology, Max Planck Institute of Microstructure Physics, Weinberg 2, Halle, 06120, Germany
| | - Joyce K S Poon
- Department of Nanophotonics, Integration, and Neural Technology, Max Planck Institute of Microstructure Physics, Weinberg 2, Halle, 06120, Germany.
- The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, M5S 3G4, ON, Canada.
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2
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Sims RR, Bendifallah I, Grimm C, Lafirdeen ASM, Domínguez S, Chan CY, Lu X, Forget BC, St-Pierre F, Papagiakoumou E, Emiliani V. Scanless two-photon voltage imaging. Nat Commun 2024; 15:5095. [PMID: 38876987 PMCID: PMC11178882 DOI: 10.1038/s41467-024-49192-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 05/28/2024] [Indexed: 06/16/2024] Open
Abstract
Two-photon voltage imaging has long been heralded as a transformative approach capable of answering many long-standing questions in modern neuroscience. However, exploiting its full potential requires the development of novel imaging approaches well suited to the photophysical properties of genetically encoded voltage indicators. We demonstrate that parallel excitation approaches developed for scanless two-photon photostimulation enable high-SNR two-photon voltage imaging. We use whole-cell patch-clamp electrophysiology to perform a thorough characterization of scanless two-photon voltage imaging using three parallel illumination approaches and lasers with different repetition rates and wavelengths. We demonstrate voltage recordings of high-frequency spike trains and sub-threshold depolarizations from neurons expressing the soma-targeted genetically encoded voltage indicator JEDI-2P-Kv. Using a low repetition-rate laser, we perform multi-cell recordings from up to fifteen targets simultaneously. We co-express JEDI-2P-Kv and the channelrhodopsin ChroME-ST and capitalize on their overlapping two-photon absorption spectra to simultaneously evoke and image action potentials using a single laser source. We also demonstrate in vivo scanless two-photon imaging of multiple cells simultaneously up to 250 µm deep in the barrel cortex of head-fixed, anaesthetised mice.
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Affiliation(s)
- Ruth R Sims
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Imane Bendifallah
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Christiane Grimm
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | | | - Soledad Domínguez
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Chung Yuen Chan
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Xiaoyu Lu
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
| | - Benoît C Forget
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - François St-Pierre
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | | | - Valentina Emiliani
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France.
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3
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Antin B, Sadahiro M, Gajowa M, Triplett MA, Adesnik H, Paninski L. Removing direct photocurrent artifacts in optogenetic connectivity mapping data via constrained matrix factorization. PLoS Comput Biol 2024; 20:e1012053. [PMID: 38709828 PMCID: PMC11098512 DOI: 10.1371/journal.pcbi.1012053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 05/16/2024] [Accepted: 04/03/2024] [Indexed: 05/08/2024] Open
Abstract
Monosynaptic connectivity mapping is crucial for building circuit-level models of neural computation. Two-photon optogenetic stimulation, when combined with whole-cell recording, enables large-scale mapping of physiological circuit parameters. In this experimental setup, recorded postsynaptic currents are used to infer the presence and strength of connections. For many cell types, nearby connections are those we expect to be strongest. However, when the postsynaptic cell expresses opsin, optical excitation of nearby cells can induce direct photocurrents in the postsynaptic cell. These photocurrent artifacts contaminate synaptic currents, making it difficult or impossible to probe connectivity for nearby cells. To overcome this problem, we developed a computational tool, Photocurrent Removal with Constraints (PhoRC). Our method is based on a constrained matrix factorization model which leverages the fact that photocurrent kinetics are less variable than those of synaptic currents. We demonstrate on real and simulated data that PhoRC consistently removes photocurrents while preserving synaptic currents, despite variations in photocurrent kinetics across datasets. Our method allows the discovery of synaptic connections which would have been otherwise obscured by photocurrent artifacts, and may thus reveal a more complete picture of synaptic connectivity. PhoRC runs faster than real time and is available as open source software.
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Affiliation(s)
- Benjamin Antin
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Grossman Center for the Statistics of Mind, and Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America
| | - Masato Sadahiro
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Marta Gajowa
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Marcus A. Triplett
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Grossman Center for the Statistics of Mind, and Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America
- Department of Statistics, Columbia University, New York, New York, United States of America
| | - Hillel Adesnik
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Liam Paninski
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Grossman Center for the Statistics of Mind, and Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America
- Department of Statistics, Columbia University, New York, New York, United States of America
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4
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Chen FD, Sharma A, Roszko DA, Xue T, Mu X, Luo X, Chua H, Lo PGQ, Sacher WD, Poon JKS. Development of wafer-scale multifunctional nanophotonic neural probes for brain activity mapping. LAB ON A CHIP 2024; 24:2397-2417. [PMID: 38623840 DOI: 10.1039/d3lc00931a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Optical techniques, such as optogenetic stimulation and functional fluorescence imaging, have been revolutionary for neuroscience by enabling neural circuit analysis with cell-type specificity. To probe deep brain regions, implantable light sources are crucial. Silicon photonics, commonly used for data communications, shows great promise in creating implantable devices with complex optical systems in a compact form factor compatible with high volume manufacturing practices. This article reviews recent developments of wafer-scale multifunctional nanophotonic neural probes. The probes can be realized on 200 or 300 mm wafers in commercial foundries and integrate light emitters for photostimulation, microelectrodes for electrophysiological recording, and microfluidic channels for chemical delivery and sampling. By integrating active optical devices to the probes, denser emitter arrays, enhanced on-chip biosensing, and increased ease of use may be realized. Silicon photonics technology makes possible highly versatile implantable neural probes that can transform neuroscience experiments.
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Affiliation(s)
- Fu Der Chen
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany.
- Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario M5S 3G4, Canada
| | - Ankita Sharma
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany.
- Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario M5S 3G4, Canada
| | - David A Roszko
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany.
- Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario M5S 3G4, Canada
| | - Tianyuan Xue
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany.
- Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario M5S 3G4, Canada
| | - Xin Mu
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany.
- Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario M5S 3G4, Canada
| | - Xianshu Luo
- Advanced Micro Foundry Pte Ltd, 11 Science Park Road, Singapore Science Park II, 117685, Singapore
| | - Hongyao Chua
- Advanced Micro Foundry Pte Ltd, 11 Science Park Road, Singapore Science Park II, 117685, Singapore
| | - Patrick Guo-Qiang Lo
- Advanced Micro Foundry Pte Ltd, 11 Science Park Road, Singapore Science Park II, 117685, Singapore
| | - Wesley D Sacher
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany.
| | - Joyce K S Poon
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany.
- Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario M5S 3G4, Canada
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5
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Nagase M, Nagashima T, Hamada S, Morishima M, Tohyama S, Arima-Yoshida F, Hiyoshi K, Hirano T, Ohtsuka T, Watabe AM. All-optical presynaptic plasticity induction by photoactivated adenylyl cyclase targeted to axon terminals. CELL REPORTS METHODS 2024; 4:100740. [PMID: 38521059 PMCID: PMC11045876 DOI: 10.1016/j.crmeth.2024.100740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 10/08/2023] [Accepted: 02/28/2024] [Indexed: 03/25/2024]
Abstract
Intracellular signaling plays essential roles in various cell types. In the central nervous system, signaling cascades are strictly regulated in a spatiotemporally specific manner to govern brain function; for example, presynaptic cyclic adenosine monophosphate (cAMP) can enhance the probability of neurotransmitter release. In the last decade, channelrhodopsin-2 has been engineered for subcellular targeting using localization tags, but optogenetic tools for intracellular signaling are not well developed. Therefore, we engineered a selective presynaptic fusion tag for photoactivated adenylyl cyclase (bPAC-Syn1a) and found its high localization at presynaptic terminals. Furthermore, an all-optical electrophysiological method revealed rapid and robust short-term potentiation by bPAC-Syn1a at brain stem-amygdala synapses in acute brain slices. Additionally, bPAC-Syn1a modulated mouse immobility behavior. These results indicate that bPAC-Syn1a can manipulate presynaptic cAMP signaling in vitro and in vivo. The all-optical manipulation technique developed in this study can help further elucidate the dynamic regulation of various cellular functions.
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Affiliation(s)
- Masashi Nagase
- Institute of Clinical Medicine and Research, Research Center for Medical Sciences, The Jikei University School of Medicine, Chiba 277-8567, Japan
| | - Takashi Nagashima
- Institute of Clinical Medicine and Research, Research Center for Medical Sciences, The Jikei University School of Medicine, Chiba 277-8567, Japan
| | - Shun Hamada
- Department of Biochemistry, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Mieko Morishima
- Institute of Clinical Medicine and Research, Research Center for Medical Sciences, The Jikei University School of Medicine, Chiba 277-8567, Japan
| | - Suguru Tohyama
- Institute of Clinical Medicine and Research, Research Center for Medical Sciences, The Jikei University School of Medicine, Chiba 277-8567, Japan
| | - Fumiko Arima-Yoshida
- Institute of Clinical Medicine and Research, Research Center for Medical Sciences, The Jikei University School of Medicine, Chiba 277-8567, Japan
| | - Kanae Hiyoshi
- Institute of Clinical Medicine and Research, Research Center for Medical Sciences, The Jikei University School of Medicine, Chiba 277-8567, Japan
| | - Tomoha Hirano
- Department of Biochemistry, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Toshihisa Ohtsuka
- Department of Biochemistry, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan.
| | - Ayako M Watabe
- Institute of Clinical Medicine and Research, Research Center for Medical Sciences, The Jikei University School of Medicine, Chiba 277-8567, Japan.
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6
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Wang J, Platz-Baudin E, Noetzel E, Offenhäusser A, Maybeck V. Expressing Optogenetic Actuators Fused to N-terminal Mucin Motifs Delivers Targets to Specific Subcellular Compartments in Polarized Cells. Adv Biol (Weinh) 2024; 8:e2300428. [PMID: 38015104 DOI: 10.1002/adbi.202300428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/31/2023] [Indexed: 11/29/2023]
Abstract
Optogenetics is a powerful approach in neuroscience research. However, other tissues of the body may benefit from controlled ion currents and neuroscience may benefit from more precise optogenetic expression. The present work constructs three subcellularly-targeted optogenetic actuators based on the channelrhodopsin ChR2-XXL, utilizing 5, 10, or 15 tandem repeats (TR) from mucin as N-terminal targeting motifs and evaluates expression in several polarized and non-polarized cell types. The modified channelrhodopsin maintains its electrophysiological properties, which can be used to produce continuous membrane depolarization, despite the expected size of the repeats. This work then shows that these actuators are subcellularly localized in polarized cells. In polarized epithelial cells, all three actuators localize to just the lateral membrane. The TR-tagged constructs also express subcellularly in cortical neurons, where TR5-ChR2XXL and TR10-ChR2XXL mainly target the somatodendrites. Moreover, the transfection efficiencies are shown to be dependent on cell type and tandem repeat length. Overall, this work verifies that the targeting motifs from epithelial cells can be used to localize optogenetic actuators in both epithelia and neurons, opening epithelia processes to optogenetic manipulation and providing new possibilities to target optogenetic tools.
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Affiliation(s)
- Jiali Wang
- Institute of Biological Information Processing IBI-3, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062, Aachen, Germany
| | - Eric Platz-Baudin
- Institute of Biological Information Processing IBI-2, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Erik Noetzel
- Institute of Biological Information Processing IBI-2, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Andreas Offenhäusser
- Institute of Biological Information Processing IBI-3, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062, Aachen, Germany
| | - Vanessa Maybeck
- Institute of Biological Information Processing IBI-3, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
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7
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Mulholland HN, Jayakumar H, Farinella DM, Smith GB. All-optical interrogation of millimeter-scale networks and application to developing ferret cortex. J Neurosci Methods 2024; 403:110051. [PMID: 38145718 PMCID: PMC10872452 DOI: 10.1016/j.jneumeth.2023.110051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Perception and behavior require coordinated activity of thousands of neurons operating in networks that span millimeters of brain area. In vivo calcium imaging approaches have proven exceptionally powerful for examining the structure of these networks at large scales, and optogenetics can allow for causal manipulations of large populations of neurons. However, realizing the full potential of these techniques requires the ability to simultaneously measure and manipulate distinct circuit elements on the scale of millimeters. NEW METHOD We describe an opto-macroscope, an artifact-free, all-optical system capable of delivering patterned optogenetic stimulation with high spatial and temporal resolution across millimeters of brain while simultaneously imaging functional neural activity. RESULTS We find that this approach provides direct manipulation of cortical regions ranging from hundreds of microns to several millimeters in area, allowing for the perturbation of individual brain areas or networks of functional domains. Using this system we find that spatially complex endogenous networks in the developing ferret visual cortex can be readily reactivated by precisely designed patterned optogenetic stimuli. COMPARISON WITH EXISTING METHODS Our opto-macroscope extends current all-optical optogenetic approaches which operate on a cellular scale with multiphoton stimulation, and are poorly suited to investigate the millimeter-scale of many functional networks. It also builds upon other mesoscopic optogenetic techniques that lack simultaneous optical readouts of neural activity. CONCLUSIONS The large-scale all-optical capabilities of our system make it a powerful new tool for investigating the contribution of cortical domains and brain areas to the functional neural networks that underlie perception and behavior.
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Affiliation(s)
- Haleigh N Mulholland
- Optical Imaging and Brain Sciences Medical Discovery Team, Department of Neuroscience, University of Minnesota, 2021 6th Street SE, Minneapolis, MN 55455, USA
| | - Harishankar Jayakumar
- Optical Imaging and Brain Sciences Medical Discovery Team, Department of Neuroscience, University of Minnesota, 2021 6th Street SE, Minneapolis, MN 55455, USA
| | - Deano M Farinella
- Optical Imaging and Brain Sciences Medical Discovery Team, Department of Neuroscience, University of Minnesota, 2021 6th Street SE, Minneapolis, MN 55455, USA
| | - Gordon B Smith
- Optical Imaging and Brain Sciences Medical Discovery Team, Department of Neuroscience, University of Minnesota, 2021 6th Street SE, Minneapolis, MN 55455, USA.
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8
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Bouin A, Wu G, Koyuncu OO, Ye Q, Kim KY, Wu MY, Tong L, Chen L, Phan S, Mackey MR, Ramachandra R, Ellisman MH, Holmes TC, Semler BL, Xu X. New rabies viral resources for multi-scale neural circuit mapping. Mol Psychiatry 2024:10.1038/s41380-024-02451-6. [PMID: 38355784 PMCID: PMC11322437 DOI: 10.1038/s41380-024-02451-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024]
Abstract
Comparisons and linkage between multiple imaging scales are essential for neural circuit connectomics. Here, we report 20 new recombinant rabies virus (RV) vectors that we have developed for multi-scale and multi-modal neural circuit mapping tools. Our new RV tools for mesoscale imaging express a range of improved fluorescent proteins. Further refinements target specific neuronal subcellular locations of interest. We demonstrate the discovery power of these new tools including the detection of detailed microstructural changes of rabies-labeled neurons in aging and Alzheimer's disease mouse models, live imaging of neuronal activities using calcium indicators, and automated measurement of infected neurons. RVs that encode GFP and ferritin as electron microscopy (EM) and fluorescence microscopy reporters are used for dual EM and mesoscale imaging. These new viral variants significantly expand the scale and power of rabies virus-mediated neural labeling and circuit mapping across multiple imaging scales in health and disease.
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Affiliation(s)
- Alexis Bouin
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Ginny Wu
- Department Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Orkide O Koyuncu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Qiao Ye
- Department Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
- Department Biomedical Engineering, University of California, Irvine, CA, 92697, USA
| | - Keun-Young Kim
- The National Center for Microscopy and Imaging Research (NCMIR) and the Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michele Y Wu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Liqi Tong
- Department Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Lujia Chen
- Department Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
- Department Biomedical Engineering, University of California, Irvine, CA, 92697, USA
| | - Sebastien Phan
- The National Center for Microscopy and Imaging Research (NCMIR) and the Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mason R Mackey
- The National Center for Microscopy and Imaging Research (NCMIR) and the Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ranjan Ramachandra
- The National Center for Microscopy and Imaging Research (NCMIR) and the Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mark H Ellisman
- The National Center for Microscopy and Imaging Research (NCMIR) and the Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Todd C Holmes
- Physiology & Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
- The Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA
| | - Bert L Semler
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, 92697, USA.
- The Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA.
| | - Xiangmin Xu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, 92697, USA.
- Department Anatomy & Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA.
- Department Biomedical Engineering, University of California, Irvine, CA, 92697, USA.
- The Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA.
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9
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Lees RM, Pichler B, Packer AM. Contribution of optical resolution to the spatial precision of two-photon optogenetic photostimulation in vivo. NEUROPHOTONICS 2024; 11:015006. [PMID: 38322022 PMCID: PMC10846536 DOI: 10.1117/1.nph.11.1.015006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 02/08/2024]
Abstract
Significance Two-photon optogenetics combines nonlinear excitation with noninvasive activation of neurons to enable the manipulation of neural circuits with a high degree of spatial precision. Combined with two-photon population calcium imaging, these approaches comprise a flexible platform for all-optical interrogation of neural circuits. However, a multitude of optical and biological factors dictate the exact precision of this approach in vivo, where it is most usefully applied. Aim We aimed to assess how the optical point spread function (OPSF) contributes to the spatial precision of two-photon photostimulation in neurobiology. Approach We altered the axial spread of the OPSF of the photostimulation beam using a spatial light modulator. Subsequently, calcium imaging was used to monitor the axial spatial precision of two-photon photostimulation of layer 2 neurons in the mouse neocortex. Results We found that optical resolution is not always the limiting factor of the spatial precision of two-photon optogenetic photostimulation and, by doing so, reveal the key factors that must be improved to achieve maximal precision. Conclusions Our results enable future work to focus on the optimal factors by providing key insight from controlled experiments in a manner not previously reported. This research can be applied to advance the state-of-the-art of all-optical interrogation, extending the toolkit for neuroscience research to achieve spatiotemporal precision at the crucial levels in which neural circuits operate.
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Affiliation(s)
- Robert M. Lees
- Science and Technology Facilities Council, Octopus Imaging Facility, Oxfordshire, United Kingdom
- University of Oxford, Department of Physiology, Anatomy, and Genetics, Oxford, United Kingdom
| | - Bruno Pichler
- Independent NeuroScience Services INSS Ltd., East Sussex, United Kingdom
| | - Adam M. Packer
- University of Oxford, Department of Physiology, Anatomy, and Genetics, Oxford, United Kingdom
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10
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Brunstein M, Lubetzki J, Moutoussamy C, Li W, Barral J. Fast 2-photon stimulation using holographic patterns. OPTICS EXPRESS 2023; 31:39222-39238. [PMID: 38018006 DOI: 10.1364/oe.498644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/04/2023] [Indexed: 11/30/2023]
Abstract
Two decades after its introduction, optogenetics - a biological technique to control the activity of neurons or other cell types with light - remains a cutting edge and promising tool to study biological processes. Its increasing usage in research varies widely from causally exploring biological mechanisms and neural computations, to neurostimulation and sensory restauration. To stimulate neurons in the brain, a variety of approaches have been developed to generate precise spatiotemporal light patterns. Yet certain constrains still exists in the current optical techniques to activate a neuronal population with both cellular resolution and millisecond precision. Here, we describe an experimental setup allowing to stimulate a few tens of neurons in a plane at sub-millisecond rates using 2-photon activation. A liquid crystal on silicon spatial light modulator (LCoS-SLM) was used to generate spatial patterns in 2 dimensions. The image of the patterns was formed on the plane of a digital micromirror device (DMD) that was used as a fast temporal modulator of each region of interest. Using fluorescent microscopy and patch-clamp recording of neurons in culture expressing the light-gated ion channels, we characterized the temporal and spatial resolution of the microscope. We described the advantages of combining the LCoS-SLM with the DMD to maximize the temporal precision, modulate the illumination amplitude, and reduce background activation. Finally, we showed that this approach can be extended to patterns in 3 dimensions. We concluded that the methodology is well suited to address important questions about the role of temporal information in neuronal coding.
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11
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Lepperød ME, Stöber T, Hafting T, Fyhn M, Kording KP. Inferring causal connectivity from pairwise recordings and optogenetics. PLoS Comput Biol 2023; 19:e1011574. [PMID: 37934793 PMCID: PMC10656035 DOI: 10.1371/journal.pcbi.1011574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/17/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023] Open
Abstract
To understand the neural mechanisms underlying brain function, neuroscientists aim to quantify causal interactions between neurons, for instance by perturbing the activity of neuron A and measuring the effect on neuron B. Recently, manipulating neuron activity using light-sensitive opsins, optogenetics, has increased the specificity of neural perturbation. However, using widefield optogenetic interventions, multiple neurons are usually perturbed, producing a confound-any of the stimulated neurons can have affected the postsynaptic neuron making it challenging to discern which neurons produced the causal effect. Here, we show how such confounds produce large biases in interpretations. We explain how confounding can be reduced by combining instrumental variables (IV) and difference in differences (DiD) techniques from econometrics. Combined, these methods can estimate (causal) effective connectivity by exploiting the weak, approximately random signal resulting from the interaction between stimulation and the absolute refractory period of the neuron. In simulated neural networks, we find that estimates using ideas from IV and DiD outperform naïve techniques suggesting that methods from causal inference can be useful to disentangle neural interactions in the brain.
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Affiliation(s)
- Mikkel Elle Lepperød
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Simula Research Laboratory, Oslo, Norway
| | - Tristan Stöber
- Simula Research Laboratory, Oslo, Norway
- Institute for Neural Computation, Faculty of Computer Science, Ruhr University Bochum, Bochum, Germany
- Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, Goethe University, Frankfurt, Germany
| | - Torkel Hafting
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Marianne Fyhn
- Simula Research Laboratory, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Konrad Paul Kording
- Department of Neuroscience, University of Pennsylvania, Pennsylvania, United States of America
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12
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Triplett MA, Gajowa M, Adesnik H, Paninski L. Bayesian target optimisation for high-precision holographic optogenetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542307. [PMID: 37292661 PMCID: PMC10246014 DOI: 10.1101/2023.05.25.542307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Two-photon optogenetics has transformed our ability to probe the structure and function of neural circuits. However, achieving precise optogenetic control of neural ensemble activity has remained fundamentally constrained by the problem of off-target stimulation (OTS): the inadvertent activation of nearby non-target neurons due to imperfect confinement of light onto target neurons. Here we propose a novel computational approach to this problem called Bayesian target optimisation. Our approach uses nonparametric Bayesian inference to model neural responses to optogenetic stimulation, and then optimises the laser powers and optical target locations needed to achieve a desired activity pattern with minimal OTS. We validate our approach in simulations and using data from in vitro experiments, showing that Bayesian target optimisation considerably reduces OTS across all conditions we test. Together, these results establish our ability to overcome OTS, enabling optogenetic stimulation with substantially improved precision.
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Affiliation(s)
- Marcus A. Triplett
- Department of Statistics, Columbia University
- Zuckerman Mind Brain Behavior Institute, Columbia University
| | - Marta Gajowa
- Department of Molecular and Cell Biology, UC Berkeley
| | | | - Liam Paninski
- Department of Statistics, Columbia University
- Zuckerman Mind Brain Behavior Institute, Columbia University
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13
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Navarro P, Oweiss K. Compressive sensing of functional connectivity maps from patterned optogenetic stimulation of neuronal ensembles. PATTERNS (NEW YORK, N.Y.) 2023; 4:100845. [PMID: 37876895 PMCID: PMC10591201 DOI: 10.1016/j.patter.2023.100845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 04/04/2023] [Accepted: 08/25/2023] [Indexed: 10/26/2023]
Abstract
Mapping functional connectivity between neurons is an essential step toward probing the neural computations mediating behavior. Accurately determining synaptic connectivity maps in populations of neurons is challenging in terms of yield, accuracy, and experimental time. Here, we developed a compressive sensing approach to reconstruct synaptic connectivity maps based on random two-photon cell-targeted optogenetic stimulation and membrane voltage readout of many putative postsynaptic neurons. Using a biophysical network model of interconnected populations of excitatory and inhibitory neurons, we characterized mapping recall and precision as a function of network observability, sparsity, number of neurons stimulated, off-target stimulation, synaptic reliability, propagation latency, and network topology. We found that mapping can be achieved with far fewer measurements than the standard pairwise sequential approach, with network sparsity and synaptic reliability serving as primary determinants of the performance. Our results suggest a rapid and efficient method to reconstruct functional connectivity of sparsely connected neuronal networks.
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Affiliation(s)
- Phillip Navarro
- Electrical and Computer Engineering Department, University of Florida, Gainesville, FL 32611, USA
| | - Karim Oweiss
- Electrical and Computer Engineering Department, University of Florida, Gainesville, FL 32611, USA
- Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
- Department of Neurology, University of Florida, Gainesville, FL 32611, USA
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
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14
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Delignat-Lavaud B, Kano J, Ducrot C, Massé I, Mukherjee S, Giguère N, Moquin L, Lévesque C, Burke S, Denis R, Bourque MJ, Tchung A, Rosa-Neto P, Lévesque D, De Beaumont L, Trudeau LÉ. Synaptotagmin-1-dependent phasic axonal dopamine release is dispensable for basic motor behaviors in mice. Nat Commun 2023; 14:4120. [PMID: 37433762 PMCID: PMC10336101 DOI: 10.1038/s41467-023-39805-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 06/27/2023] [Indexed: 07/13/2023] Open
Abstract
In Parkinson's disease (PD), motor dysfunctions only become apparent after extensive loss of DA innervation. This resilience has been hypothesized to be due to the ability of many motor behaviors to be sustained through a diffuse basal tone of DA; but experimental evidence for this is limited. Here we show that conditional deletion of the calcium sensor synaptotagmin-1 (Syt1) in DA neurons (Syt1 cKODA mice) abrogates most activity-dependent axonal DA release in the striatum and mesencephalon, leaving somatodendritic (STD) DA release intact. Strikingly, Syt1 cKODA mice showed intact performance in multiple unconditioned DA-dependent motor tasks and even in a task evaluating conditioned motivation for food. Considering that basal extracellular DA levels in the striatum were unchanged, our findings suggest that activity-dependent DA release is dispensable for such tasks and that they can be sustained by a basal tone of extracellular DA. Taken together, our findings reveal the striking resilience of DA-dependent motor functions in the context of a near-abolition of phasic DA release, shedding new light on why extensive loss of DA innervation is required to reveal motor dysfunctions in PD.
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Affiliation(s)
- Benoît Delignat-Lavaud
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- SNC and CIRCA Research Groups, Université de Montréal, Montréal, QC, Canada
| | - Jana Kano
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- SNC and CIRCA Research Groups, Université de Montréal, Montréal, QC, Canada
| | - Charles Ducrot
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- SNC and CIRCA Research Groups, Université de Montréal, Montréal, QC, Canada
| | - Ian Massé
- Hôpital du Sacré-Cœur-de-Montréal, CIUSSS NIM, Université de Montréal, Montreal, QC, Canada
| | - Sriparna Mukherjee
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- SNC and CIRCA Research Groups, Université de Montréal, Montréal, QC, Canada
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Nicolas Giguère
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- SNC and CIRCA Research Groups, Université de Montréal, Montréal, QC, Canada
| | - Luc Moquin
- Centre intégré universitaire de santé et de services sociaux (CIUSSS) de l'Ouest-de-l'Île-de-Montréal; Department of Neurology and Neurosurgery, Psychiatry and Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | | | - Samuel Burke
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- SNC and CIRCA Research Groups, Université de Montréal, Montréal, QC, Canada
| | - Raphaëlle Denis
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- SNC and CIRCA Research Groups, Université de Montréal, Montréal, QC, Canada
| | - Marie-Josée Bourque
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- SNC and CIRCA Research Groups, Université de Montréal, Montréal, QC, Canada
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Alex Tchung
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- SNC and CIRCA Research Groups, Université de Montréal, Montréal, QC, Canada
| | - Pedro Rosa-Neto
- Centre intégré universitaire de santé et de services sociaux (CIUSSS) de l'Ouest-de-l'Île-de-Montréal; Department of Neurology and Neurosurgery, Psychiatry and Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Daniel Lévesque
- Faculty of Pharmacy, Université de Montréal, Montreal, QC, Canada
| | - Louis De Beaumont
- Hôpital du Sacré-Cœur-de-Montréal, CIUSSS NIM, Université de Montréal, Montreal, QC, Canada
| | - Louis-Éric Trudeau
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada.
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada.
- SNC and CIRCA Research Groups, Université de Montréal, Montréal, QC, Canada.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
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15
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Tian H, Davis HC, Wong-Campos JD, Park P, Fan LZ, Gmeiner B, Begum S, Werley CA, Borja GB, Upadhyay H, Shah H, Jacques J, Qi Y, Parot V, Deisseroth K, Cohen AE. Video-based pooled screening yields improved far-red genetically encoded voltage indicators. Nat Methods 2023; 20:1082-1094. [PMID: 36624211 PMCID: PMC10329731 DOI: 10.1038/s41592-022-01743-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 11/28/2022] [Indexed: 01/11/2023]
Abstract
Video-based screening of pooled libraries is a powerful approach for directed evolution of biosensors because it enables selection along multiple dimensions simultaneously from large libraries. Here we develop a screening platform, Photopick, which achieves precise phenotype-activated photoselection over a large field of view (2.3 × 2.3 mm, containing >103 cells, per shot). We used the Photopick platform to evolve archaerhodopsin-derived genetically encoded voltage indicators (GEVIs) with improved signal-to-noise ratio (QuasAr6a) and kinetics (QuasAr6b). These GEVIs gave improved signals in cultured neurons and in live mouse brains. By combining targeted in vivo optogenetic stimulation with high-precision voltage imaging, we characterized inhibitory synaptic coupling between individual cortical NDNF (neuron-derived neurotrophic factor) interneurons, and excitatory electrical synapses between individual hippocampal parvalbumin neurons. The QuasAr6 GEVIs are powerful tools for all-optical electrophysiology and the Photopick approach could be adapted to evolve a broad range of biosensors.
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Affiliation(s)
- He Tian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hunter C Davis
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - J David Wong-Campos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Pojeong Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Linlin Z Fan
- Department of Bioengineering, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Benjamin Gmeiner
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Shahinoor Begum
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | | | | | | | | | - Yitong Qi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Vicente Parot
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Karl Deisseroth
- Department of Bioengineering, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MA, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Department of Physics, Harvard University, Cambridge, MA, USA.
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16
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Faini G, Tanese D, Molinier C, Telliez C, Hamdani M, Blot F, Tourain C, de Sars V, Del Bene F, Forget BC, Ronzitti E, Emiliani V. Ultrafast light targeting for high-throughput precise control of neuronal networks. Nat Commun 2023; 14:1888. [PMID: 37019891 PMCID: PMC10074378 DOI: 10.1038/s41467-023-37416-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/16/2023] [Indexed: 04/07/2023] Open
Abstract
Two-photon, single-cell resolution optogenetics based on holographic light-targeting approaches enables the generation of precise spatiotemporal neuronal activity patterns and thus a broad range of experimental applications, such as high throughput connectivity mapping and probing neural codes for perception. Yet, current holographic approaches limit the resolution for tuning the relative spiking time of distinct cells to a few milliseconds, and the achievable number of targets to 100-200, depending on the working depth. To overcome these limitations and expand the capabilities of single-cell optogenetics, we introduce an ultra-fast sequential light targeting (FLiT) optical configuration based on the rapid switching of a temporally focused beam between holograms at kHz rates. We used FLiT to demonstrate two illumination protocols, termed hybrid- and cyclic-illumination, and achieve sub-millisecond control of sequential neuronal activation and high throughput multicell illumination in vitro (mouse organotypic and acute brain slices) and in vivo (zebrafish larvae and mice), while minimizing light-induced thermal rise. These approaches will be important for experiments that require rapid and precise cell stimulation with defined spatio-temporal activity patterns and optical control of large neuronal ensembles.
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Affiliation(s)
- Giulia Faini
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012, Paris, France
| | - Dimitrii Tanese
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012, Paris, France
| | - Clément Molinier
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012, Paris, France
| | - Cécile Telliez
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012, Paris, France
| | - Massilia Hamdani
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012, Paris, France
| | - Francois Blot
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012, Paris, France
| | - Christophe Tourain
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012, Paris, France
| | - Vincent de Sars
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012, Paris, France
| | - Filippo Del Bene
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012, Paris, France
| | - Benoît C Forget
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012, Paris, France
| | - Emiliano Ronzitti
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012, Paris, France.
| | - Valentina Emiliani
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012, Paris, France.
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17
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Printz Y, Patil P, Mahn M, Benjamin A, Litvin A, Levy R, Bringmann M, Yizhar O. Determinants of functional synaptic connectivity among amygdala-projecting prefrontal cortical neurons in male mice. Nat Commun 2023; 14:1667. [PMID: 36966143 PMCID: PMC10039875 DOI: 10.1038/s41467-023-37318-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/13/2023] [Indexed: 03/27/2023] Open
Abstract
The medial prefrontal cortex (mPFC) mediates a variety of complex cognitive functions via its vast and diverse connections with cortical and subcortical structures. Understanding the patterns of synaptic connectivity that comprise the mPFC local network is crucial for deciphering how this circuit processes information and relays it to downstream structures. To elucidate the synaptic organization of the mPFC, we developed a high-throughput optogenetic method for mapping large-scale functional synaptic connectivity in acute brain slices. We show that in male mice, mPFC neurons that project to the basolateral amygdala (BLA) display unique spatial patterns of local-circuit synaptic connectivity, which distinguish them from the general mPFC cell population. When considering synaptic connections between pairs of mPFC neurons, the intrinsic properties of the postsynaptic cell and the anatomical positions of both cells jointly account for ~7.5% of the variation in the probability of connection. Moreover, anatomical distance and laminar position explain most of this fraction in variation. Our findings reveal the factors determining connectivity in the mPFC and delineate the architecture of synaptic connections in the BLA-projecting subnetwork.
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Affiliation(s)
- Yoav Printz
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Pritish Patil
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Mathias Mahn
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Asaf Benjamin
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Anna Litvin
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Rivka Levy
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Max Bringmann
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ofer Yizhar
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.
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18
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Abstract
Verifying causal effects of neural circuits is essential for proving a direct circuit-behavior relationship. However, techniques for tagging only active neurons with high spatiotemporal precision remain at the beginning stages. Here we develop the soma-targeted Cal-Light (ST-Cal-Light) which selectively converts somatic calcium rise triggered by action potentials into gene expression. Such modification simultaneously increases the signal-to-noise ratio of reporter gene expression and reduces the light requirement for successful labeling. Because of the enhanced efficacy, the ST-Cal-Light enables the tagging of functionally engaged neurons in various forms of behaviors, including context-dependent fear conditioning, lever-pressing choice behavior, and social interaction behaviors. We also target kainic acid-sensitive neuronal populations in the hippocampus which subsequently suppress seizure symptoms, suggesting ST-Cal-Light's applicability in controlling disease-related neurons. Furthermore, the generation of a conditional ST-Cal-Light knock-in mouse provides an opportunity to tag active neurons in a region- or cell-type specific manner via crossing with other Cre-driver lines. Thus, the versatile ST-Cal-Light system links somatic action potentials to behaviors with high temporal precision, and ultimately allows functional circuit dissection at a single cell resolution.
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19
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Schumacher JW, McCann MK, Maximov KJ, Fitzpatrick D. Selective enhancement of neural coding in V1 underlies fine-discrimination learning in tree shrew. Curr Biol 2022; 32:3245-3260.e5. [PMID: 35767997 PMCID: PMC9378627 DOI: 10.1016/j.cub.2022.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/29/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
Visual discrimination improves with training, a phenomenon that is thought to reflect plastic changes in the responses of neurons in primary visual cortex (V1). However, the identity of the neurons that undergo change, the nature of the changes, and the consequences of these changes for other visual behaviors remain unclear. We used chronic in vivo 2-photon calcium imaging to monitor the responses of neurons in the V1 of tree shrews learning a Go/No-Go fine orientation discrimination task. We observed increases in neural population measures of discriminability for task-relevant stimuli that correlate with performance and depend on a select subset of neurons with preferred orientations that include the rewarded stimulus and nearby orientations biased away from the non-rewarded stimulus. Learning is accompanied by selective enhancement in the response of these neurons to the rewarded stimulus that further increases their ability to discriminate the task stimuli. These changes persist outside of the trained task and predict observed enhancement and impairment in performance of other discriminations, providing evidence for selective and persistent learning-induced plasticity in the V1, with significant consequences for perception.
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Affiliation(s)
- Joseph W Schumacher
- Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL 33458, USA
| | - Matthew K McCann
- Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL 33458, USA
| | - Katherine J Maximov
- Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL 33458, USA
| | - David Fitzpatrick
- Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL 33458, USA.
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20
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Emiliani V, Entcheva E, Hedrich R, Hegemann P, Konrad KR, Lüscher C, Mahn M, Pan ZH, Sims RR, Vierock J, Yizhar O. Optogenetics for light control of biological systems. NATURE REVIEWS. METHODS PRIMERS 2022; 2:55. [PMID: 37933248 PMCID: PMC10627578 DOI: 10.1038/s43586-022-00136-4] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/30/2022] [Indexed: 11/08/2023]
Abstract
Optogenetic techniques have been developed to allow control over the activity of selected cells within a highly heterogeneous tissue, using a combination of genetic engineering and light. Optogenetics employs natural and engineered photoreceptors, mostly of microbial origin, to be genetically introduced into the cells of interest. As a result, cells that are naturally light-insensitive can be made photosensitive and addressable by illumination and precisely controllable in time and space. The selectivity of expression and subcellular targeting in the host is enabled by applying control elements such as promoters, enhancers and specific targeting sequences to the employed photoreceptor-encoding DNA. This powerful approach allows precise characterization and manipulation of cellular functions and has motivated the development of advanced optical methods for patterned photostimulation. Optogenetics has revolutionized neuroscience during the past 15 years and is primed to have a similar impact in other fields, including cardiology, cell biology and plant sciences. In this Primer, we describe the principles of optogenetics, review the most commonly used optogenetic tools, illumination approaches and scientific applications and discuss the possibilities and limitations associated with optogenetic manipulations across a wide variety of optical techniques, cells, circuits and organisms.
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Affiliation(s)
- Valentina Emiliani
- Wavefront Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Emilia Entcheva
- Department of Biomedical Engineering, George Washington University, Washington, DC, USA
| | - Rainer Hedrich
- Julius-von-Sachs Institute for Biosciences, Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg, Germany
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universitaet zu Berlin, Berlin, Germany
| | - Kai R. Konrad
- Julius-von-Sachs Institute for Biosciences, Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg, Germany
| | - Christian Lüscher
- Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Clinic of Neurology, Department of Clinical Neurosciences, Geneva University Hospital, Geneva, Switzerland
| | - Mathias Mahn
- Department of Neurobiology, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Zhuo-Hua Pan
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, USA
| | - Ruth R. Sims
- Wavefront Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Johannes Vierock
- Institute for Biology, Experimental Biophysics, Humboldt-Universitaet zu Berlin, Berlin, Germany
- Neuroscience Research Center, Charité – Universitaetsmedizin Berlin, Berlin, Germany
| | - Ofer Yizhar
- Departments of Brain Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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21
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Russell LE, Dalgleish HWP, Nutbrown R, Gauld OM, Herrmann D, Fişek M, Packer AM, Häusser M. All-optical interrogation of neural circuits in behaving mice. Nat Protoc 2022; 17:1579-1620. [PMID: 35478249 PMCID: PMC7616378 DOI: 10.1038/s41596-022-00691-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 02/09/2022] [Indexed: 12/22/2022]
Abstract
Recent advances combining two-photon calcium imaging and two-photon optogenetics with computer-generated holography now allow us to read and write the activity of large populations of neurons in vivo at cellular resolution and with high temporal resolution. Such 'all-optical' techniques enable experimenters to probe the effects of functionally defined neurons on neural circuit function and behavioral output with new levels of precision. This greatly increases flexibility, resolution, targeting specificity and throughput compared with alternative approaches based on electrophysiology and/or one-photon optogenetics and can interrogate larger and more densely labeled populations of neurons than current voltage imaging-based implementations. This protocol describes the experimental workflow for all-optical interrogation experiments in awake, behaving head-fixed mice. We describe modular procedures for the setup and calibration of an all-optical system (~3 h), the preparation of an indicator and opsin-expressing and task-performing animal (~3-6 weeks), the characterization of functional and photostimulation responses (~2 h per field of view) and the design and implementation of an all-optical experiment (achievable within the timescale of a normal behavioral experiment; ~3-5 h per field of view). We discuss optimizations for efficiently selecting and targeting neuronal ensembles for photostimulation sequences, as well as generating photostimulation response maps from the imaging data that can be used to examine the impact of photostimulation on the local circuit. We demonstrate the utility of this strategy in three brain areas by using different experimental setups. This approach can in principle be adapted to any brain area to probe functional connectivity in neural circuits and investigate the relationship between neural circuit activity and behavior.
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Affiliation(s)
- Lloyd E Russell
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Henry W P Dalgleish
- Wolfson Institute for Biomedical Research, University College London, London, UK
- Sainsbury Wellcome Centre, University College London, London, UK
| | - Rebecca Nutbrown
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Oliver M Gauld
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Dustin Herrmann
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Mehmet Fişek
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Adam M Packer
- Wolfson Institute for Biomedical Research, University College London, London, UK.
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
| | - Michael Häusser
- Wolfson Institute for Biomedical Research, University College London, London, UK.
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22
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Swanson JL, Chin PS, Romero JM, Srivastava S, Ortiz-Guzman J, Hunt PJ, Arenkiel BR. Advancements in the Quest to Map, Monitor, and Manipulate Neural Circuitry. Front Neural Circuits 2022; 16:886302. [PMID: 35719420 PMCID: PMC9204427 DOI: 10.3389/fncir.2022.886302] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/27/2022] [Indexed: 01/27/2023] Open
Abstract
Neural circuits and the cells that comprise them represent the functional units of the brain. Circuits relay and process sensory information, maintain homeostasis, drive behaviors, and facilitate cognitive functions such as learning and memory. Creating a functionally-precise map of the mammalian brain requires anatomically tracing neural circuits, monitoring their activity patterns, and manipulating their activity to infer function. Advancements in cell-type-specific genetic tools allow interrogation of neural circuits with increased precision. This review provides a broad overview of recombination-based and activity-driven genetic targeting approaches, contemporary viral tracing strategies, electrophysiological recording methods, newly developed calcium, and voltage indicators, and neurotransmitter/neuropeptide biosensors currently being used to investigate circuit architecture and function. Finally, it discusses methods for acute or chronic manipulation of neural activity, including genetically-targeted cellular ablation, optogenetics, chemogenetics, and over-expression of ion channels. With this ever-evolving genetic toolbox, scientists are continuing to probe neural circuits with increasing resolution, elucidating the structure and function of the incredibly complex mammalian brain.
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Affiliation(s)
- Jessica L. Swanson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
| | - Pey-Shyuan Chin
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Juan M. Romero
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
| | - Snigdha Srivastava
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
| | - Joshua Ortiz-Guzman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
| | - Patrick J. Hunt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
| | - Benjamin R. Arenkiel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States
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23
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Kaneko K, Currin CB, Goff KM, Wengert ER, Somarowthu A, Vogels TP, Goldberg EM. Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. Cell Rep 2022; 38:110580. [PMID: 35354025 PMCID: PMC9003081 DOI: 10.1016/j.celrep.2022.110580] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/09/2022] [Accepted: 03/06/2022] [Indexed: 11/25/2022] Open
Abstract
Dravet syndrome is a neurodevelopmental disorder characterized by epilepsy, intellectual disability, and sudden death due to pathogenic variants in SCN1A with loss of function of the sodium channel subunit Nav1.1. Nav1.1-expressing parvalbumin GABAergic interneurons (PV-INs) from young Scn1a+/− mice show impaired action potential generation. An approach assessing PV-IN function in the same mice at two time points shows impaired spike generation in all Scn1a+/− mice at postnatal days (P) 16–21, whether deceased prior or surviving to P35, with normalization by P35 in surviving mice. However, PV-IN synaptic transmission is dysfunctional in young Scn1a+/− mice that did not survive and in Scn1a+/− mice ≥ P35. Modeling confirms that PV-IN axonal propagation is more sensitive to decreased sodium conductance than spike generation. These results demonstrate dynamic dysfunction in Dravet syndrome: combined abnormalities of PV-IN spike generation and propagation drives early disease severity, while ongoing dysfunction of synaptic transmission contributes to chronic pathology. Dravet syndrome is caused by variants in SCN1A with loss of function of Nav1.1 sodium channels. Kaneko et al. use the “mini-slice” to record at two developmental time points. Impaired spike generation of Nav1.1-expressing PV interneurons in Scn1a+/− mice is transient, while abnormalities of PV interneuron synaptic transmission persist.
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Affiliation(s)
- Keisuke Kaneko
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, PA 19104, USA
| | - Christopher B Currin
- The Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
| | - Kevin M Goff
- Medical Scientist Training Program (MSTP), The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Neuroscience Graduate Group, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Eric R Wengert
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, PA 19104, USA
| | - Ala Somarowthu
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, PA 19104, USA
| | - Tim P Vogels
- The Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg, Austria
| | - Ethan M Goldberg
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, PA 19104, USA; Neuroscience Graduate Group, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Neurology, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Neuroscience, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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24
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Hage TA, Bosma-Moody A, Baker CA, Kratz MB, Campagnola L, Jarsky T, Zeng H, Murphy GJ. Synaptic connectivity to L2/3 of primary visual cortex measured by two-photon optogenetic stimulation. eLife 2022; 11:71103. [PMID: 35060903 PMCID: PMC8824465 DOI: 10.7554/elife.71103] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/19/2022] [Indexed: 12/04/2022] Open
Abstract
Understanding cortical microcircuits requires thorough measurement of physiological properties of synaptic connections formed within and between diverse subclasses of neurons. Towards this goal, we combined spatially precise optogenetic stimulation with multicellular recording to deeply characterize intralaminar and translaminar monosynaptic connections to supragranular (L2/3) neurons in the mouse visual cortex. The reliability and specificity of multiphoton optogenetic stimulation were measured across multiple Cre lines, and measurements of connectivity were verified by comparison to paired recordings and targeted patching of optically identified presynaptic cells. With a focus on translaminar pathways, excitatory and inhibitory synaptic connections from genetically defined presynaptic populations were characterized by their relative abundance, spatial profiles, strength, and short-term dynamics. Consistent with the canonical cortical microcircuit, layer 4 excitatory neurons and interneurons within L2/3 represented the most common sources of input to L2/3 pyramidal cells. More surprisingly, we also observed strong excitatory connections from layer 5 intratelencephalic neurons and potent translaminar inhibition from multiple interneuron subclasses. The hybrid approach revealed convergence to and divergence from excitatory and inhibitory neurons within and across cortical layers. Divergent excitatory connections often spanned hundreds of microns of horizontal space. In contrast, divergent inhibitory connections were more frequently measured from postsynaptic targets near each other.
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Affiliation(s)
- Travis A Hage
- Electrophysiology, Allen Institute for Brain Science
| | | | | | - Megan B Kratz
- Electrophysiology, Allen Institute for Brain Science
| | | | - Tim Jarsky
- Synaptic Physiology, Allen Institute for Brain Science
| | - Hongkui Zeng
- Synaptic Physiology, Allen Institute for Brain Science
| | - Gabe J Murphy
- Synaptic Physiology, Allen Institute for Brain Science
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25
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Kim TH, Schnitzer MJ. Fluorescence imaging of large-scale neural ensemble dynamics. Cell 2022; 185:9-41. [PMID: 34995519 PMCID: PMC8849612 DOI: 10.1016/j.cell.2021.12.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/14/2022]
Abstract
Recent progress in fluorescence imaging allows neuroscientists to observe the dynamics of thousands of individual neurons, identified genetically or by their connectivity, across multiple brain areas and for extended durations in awake behaving mammals. We discuss advances in fluorescent indicators of neural activity, viral and genetic methods to express these indicators, chronic animal preparations for long-term imaging studies, and microscopes to monitor and manipulate the activity of large neural ensembles. Ca2+ imaging studies of neural activity can track brain area interactions and distributed information processing at cellular resolution. Across smaller spatial scales, high-speed voltage imaging reveals the distinctive spiking patterns and coding properties of targeted neuron types. Collectively, these innovations will propel studies of brain function and dovetail with ongoing neuroscience initiatives to identify new neuron types and develop widely applicable, non-human primate models. The optical toolkit's growing sophistication also suggests that "brain observatory" facilities would be useful open resources for future brain-imaging studies.
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Affiliation(s)
- Tony Hyun Kim
- James Clark Center for Biomedical Engineering & Sciences, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| | - Mark J Schnitzer
- James Clark Center for Biomedical Engineering & Sciences, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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26
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Fenno LE, Levy R, Yizhar O. Molecular Optimization of Rhodopsin-Based Tools for Neuroscience Applications. Methods Mol Biol 2022; 2501:289-310. [PMID: 35857234 DOI: 10.1007/978-1-0716-2329-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
There is no question that genetically encoded tools have revolutionized neuroscience. These include optically modulated tools for writing-in (optogenetics) and reading-out (calcium, voltage, and neurotransmitter indicators) neural activity as well as precision expression of these reagents using virally mediated delivery. With few exceptions, these powerful approaches are derived from naturally occurring molecules that are sourced from diverse organisms that span all kingdoms of life. Successful expression of genetic tools in standard neuroscience model organisms requires optimizing gene structure, taking into account differences in both protein translation and trafficking. Myriad approaches have resolved these two challenges, resulting in order-of-magnitude increases in functional expression. In this chapter, we focus on synthesizing prior experience in successfully enabling the transition of genes across kingdoms with a goal of facilitating the production of the next generation of molecular tools for neuroscience. We then provide a detailed protocol that allows expression and testing of novel genetically encoded tools in mammalian cell lines and primary cultured neurons.
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Affiliation(s)
- Lief E Fenno
- Departments of Psychiatry and Neuroscience, University of Texas Austin Dell Medical School, Austin, TX, USA
| | - Rivka Levy
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Ofer Yizhar
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel.
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27
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Abdelfattah AS, Ahuja S, Akkin T, Allu SR, Brake J, Boas DA, Buckley EM, Campbell RE, Chen AI, Cheng X, Čižmár T, Costantini I, De Vittorio M, Devor A, Doran PR, El Khatib M, Emiliani V, Fomin-Thunemann N, Fainman Y, Fernandez-Alfonso T, Ferri CGL, Gilad A, Han X, Harris A, Hillman EMC, Hochgeschwender U, Holt MG, Ji N, Kılıç K, Lake EMR, Li L, Li T, Mächler P, Miller EW, Mesquita RC, Nadella KMNS, Nägerl UV, Nasu Y, Nimmerjahn A, Ondráčková P, Pavone FS, Perez Campos C, Peterka DS, Pisano F, Pisanello F, Puppo F, Sabatini BL, Sadegh S, Sakadzic S, Shoham S, Shroff SN, Silver RA, Sims RR, Smith SL, Srinivasan VJ, Thunemann M, Tian L, Tian L, Troxler T, Valera A, Vaziri A, Vinogradov SA, Vitale F, Wang LV, Uhlířová H, Xu C, Yang C, Yang MH, Yellen G, Yizhar O, Zhao Y. Neurophotonic tools for microscopic measurements and manipulation: status report. NEUROPHOTONICS 2022; 9:013001. [PMID: 35493335 PMCID: PMC9047450 DOI: 10.1117/1.nph.9.s1.013001] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Neurophotonics was launched in 2014 coinciding with the launch of the BRAIN Initiative focused on development of technologies for advancement of neuroscience. For the last seven years, Neurophotonics' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, this status report reviews an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion report, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed, and provide an outlook for the future directions.
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Affiliation(s)
- Ahmed S. Abdelfattah
- Brown University, Department of Neuroscience, Providence, Rhode Island, United States
| | - Sapna Ahuja
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Taner Akkin
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Srinivasa Rao Allu
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Joshua Brake
- Harvey Mudd College, Department of Engineering, Claremont, California, United States
| | - David A. Boas
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Erin M. Buckley
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
- Emory University, Department of Pediatrics, Atlanta, Georgia, United States
| | - Robert E. Campbell
- University of Tokyo, Department of Chemistry, Tokyo, Japan
- University of Alberta, Department of Chemistry, Edmonton, Alberta, Canada
| | - Anderson I. Chen
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Xiaojun Cheng
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Tomáš Čižmár
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Irene Costantini
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Biology, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
| | - Massimo De Vittorio
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Anna Devor
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Patrick R. Doran
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Mirna El Khatib
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | | | - Natalie Fomin-Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Yeshaiahu Fainman
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Tomas Fernandez-Alfonso
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Christopher G. L. Ferri
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Ariel Gilad
- The Hebrew University of Jerusalem, Institute for Medical Research Israel–Canada, Department of Medical Neurobiology, Faculty of Medicine, Jerusalem, Israel
| | - Xue Han
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Andrew Harris
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | | | - Ute Hochgeschwender
- Central Michigan University, Department of Neuroscience, Mount Pleasant, Michigan, United States
| | - Matthew G. Holt
- University of Porto, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal
| | - Na Ji
- University of California Berkeley, Department of Physics, Berkeley, California, United States
| | - Kıvılcım Kılıç
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evelyn M. R. Lake
- Yale School of Medicine, Department of Radiology and Biomedical Imaging, New Haven, Connecticut, United States
| | - Lei Li
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Tianqi Li
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Philipp Mächler
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evan W. Miller
- University of California Berkeley, Departments of Chemistry and Molecular & Cell Biology and Helen Wills Neuroscience Institute, Berkeley, California, United States
| | | | | | - U. Valentin Nägerl
- Interdisciplinary Institute for Neuroscience University of Bordeaux & CNRS, Bordeaux, France
| | - Yusuke Nasu
- University of Tokyo, Department of Chemistry, Tokyo, Japan
| | - Axel Nimmerjahn
- Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, California, United States
| | - Petra Ondráčková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Francesco S. Pavone
- National Institute of Optics, National Research Council, Rome, Italy
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Physics, Florence, Italy
| | - Citlali Perez Campos
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Darcy S. Peterka
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Filippo Pisano
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Ferruccio Pisanello
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Francesca Puppo
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Bernardo L. Sabatini
- Harvard Medical School, Howard Hughes Medical Institute, Department of Neurobiology, Boston, Massachusetts, United States
| | - Sanaz Sadegh
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Sava Sakadzic
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Shy Shoham
- New York University Grossman School of Medicine, Tech4Health and Neuroscience Institutes, New York, New York, United States
| | - Sanaya N. Shroff
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - R. Angus Silver
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Ruth R. Sims
- Sorbonne University, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Spencer L. Smith
- University of California Santa Barbara, Department of Electrical and Computer Engineering, Santa Barbara, California, United States
| | - Vivek J. Srinivasan
- New York University Langone Health, Departments of Ophthalmology and Radiology, New York, New York, United States
| | - Martin Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Lei Tian
- Boston University, Departments of Electrical Engineering and Biomedical Engineering, Boston, Massachusetts, United States
| | - Lin Tian
- University of California Davis, Department of Biochemistry and Molecular Medicine, Davis, California, United States
| | - Thomas Troxler
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Antoine Valera
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Alipasha Vaziri
- Rockefeller University, Laboratory of Neurotechnology and Biophysics, New York, New York, United States
- The Rockefeller University, The Kavli Neural Systems Institute, New York, New York, United States
| | - Sergei A. Vinogradov
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Flavia Vitale
- Center for Neuroengineering and Therapeutics, Departments of Neurology, Bioengineering, Physical Medicine and Rehabilitation, Philadelphia, Pennsylvania, United States
| | - Lihong V. Wang
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Hana Uhlířová
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Chris Xu
- Cornell University, School of Applied and Engineering Physics, Ithaca, New York, United States
| | - Changhuei Yang
- California Institute of Technology, Departments of Electrical Engineering, Bioengineering and Medical Engineering, Pasadena, California, United States
| | - Mu-Han Yang
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Gary Yellen
- Harvard Medical School, Department of Neurobiology, Boston, Massachusetts, United States
| | - Ofer Yizhar
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | - Yongxin Zhao
- Carnegie Mellon University, Department of Biological Sciences, Pittsburgh, Pennsylvania, United States
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28
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Linghu C, Chen IW, Tanese D, Zampini V, Shemesh OA. Single-Cell Resolution Optogenetics Via Expression of Soma-Targeted Rhodopsins. Methods Mol Biol 2022; 2501:229-257. [PMID: 35857231 DOI: 10.1007/978-1-0716-2329-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Optogenetics allows control of neural activity in genetically targeted neuron populations by light. Optogenetic control of individual neurons in neural circuits would enable powerful, causal investigations of neural connectivity and function at single-cell level and provide insights into how neural circuits operate. Such single-cell resolution optogenetics in neuron populations requires precise sculpting of light and subcellular targeting of optogenetic molecules. Here we describe a group of methods for single-cell resolution optogenetics in neuron cultures, in mouse brain slices, and in mouse cortex in-vivo, via patterned light and soma-targeted optogenetic molecules.
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Affiliation(s)
| | - I-Wen Chen
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Dimitrii Tanese
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Valeria Zampini
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Or A Shemesh
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA.
- Department of Neurobiology, Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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29
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Montero T, Gatica RI, Farassat N, Meza R, González-Cabrera C, Roeper J, Henny P. Dendritic Architecture Predicts in vivo Firing Pattern in Mouse Ventral Tegmental Area and Substantia Nigra Dopaminergic Neurons. Front Neural Circuits 2021; 15:769342. [PMID: 34867214 PMCID: PMC8640462 DOI: 10.3389/fncir.2021.769342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
The firing activity of ventral tegmental area (VTA) and substantia nigra pars compacta (SNc) dopaminergic (DA) neurons is an important factor in shaping DA release and its role in motivated behavior. Dendrites in DA neurons are the main postsynaptic compartment and, along with cell body and axon initial segment, contribute to action potential generation and firing pattern. In this study, the organization of the dendritic domain in individual VTA and SNc DA neurons of adult male mice, and their relationship to in vivo spontaneous firing, are described. In comparison with dorsal VTA DA neurons, ventrally located VTA neurons (as measured by cell body location) possess a shorter total dendritic length and simpler dendritic architecture, and exhibit the most irregular in vivo firing patterns among DA neurons. In contrast, for DA neurons in the SNc, the higher irregularity of firing was related to a smaller dendritic domain, as measured by convex hull volumes. However, firing properties were also related to the specific regional distribution of the dendritic tree. Thus, VTA DA neurons with a larger extension of their dendritic tree within the parabrachial pigmented (PBP) nucleus fired more regularly compared with those with relatively more dendrites extending outside the PBP. For DA neurons in the SNc, enhanced firing irregularity was associated with a smaller proportion of dendrites penetrating the substantia nigra pars reticulata. These results suggest that differences in dendritic morphology contribute to the in vivo firing properties of individual DA neurons, and that the existence of region-specific synaptic connectivity rules that shape firing diversity.
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Affiliation(s)
- Trinidad Montero
- Laboratorio de Neuroanatomía, Departamento de Anatomía, and Centro Interdisciplinario de Neurociencia, NeuroUC, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rafael Ignacio Gatica
- Laboratorio de Neuroanatomía, Departamento de Anatomía, and Centro Interdisciplinario de Neurociencia, NeuroUC, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Navid Farassat
- Institute of Neurophysiology, Goethe University, Frankfurt, Germany
| | - Rodrigo Meza
- Laboratorio de Neuroanatomía, Departamento de Anatomía, and Centro Interdisciplinario de Neurociencia, NeuroUC, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Cristian González-Cabrera
- Laboratorio de Neuroanatomía, Departamento de Anatomía, and Centro Interdisciplinario de Neurociencia, NeuroUC, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jochen Roeper
- Institute of Neurophysiology, Goethe University, Frankfurt, Germany
| | - Pablo Henny
- Laboratorio de Neuroanatomía, Departamento de Anatomía, and Centro Interdisciplinario de Neurociencia, NeuroUC, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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30
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Nigro MJ, Kirikae H, Kjelsberg K, Nair RR, Witter MP. Not All That Is Gold Glitters: PV-IRES-Cre Mouse Line Shows Low Efficiency of Labeling of Parvalbumin Interneurons in the Perirhinal Cortex. Front Neural Circuits 2021; 15:781928. [PMID: 34819840 PMCID: PMC8606682 DOI: 10.3389/fncir.2021.781928] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
The wide diversity of cortical inhibitory neuron types populating the cortex allows the assembly of diverse microcircuits and endows these circuits with different computational properties. Thus, characterizing neuronal diversity is fundamental to describe the building blocks of cortical microcircuits and probe their function. To this purpose, the mouse has emerged as a powerful tool to genetically label and manipulate specific inhibitory cell-types in the mammalian brain. Among these cell-types, the parvalbumin-expressing interneuron type (PV-INs) is perhaps the most characterized. Several mouse lines have been generated to target PV-INs. Among these mouse lines, the PV-IRES-Cre lines is the most widely used and demonstrated a high specificity and efficiency in targeting PV-INs in different cortical areas. However, a characterization of the performance across cortical regions is still missing. Here we show that the PV-IRES-Cre mouse line labels only a fraction of PV immunoreactive neurons in perirhinal cortex and other association areas. Our results point to a yet uncharacterized diversity within the PV-INs and emphasize the need to characterize these tools in specific cortical areas.
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Affiliation(s)
- Maximiliano José Nigro
- Center for Neural Computation, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Hinako Kirikae
- Center for Neural Computation, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Department of Organ Anatomy, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kasper Kjelsberg
- Center for Neural Computation, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Rajeevkumar Raveendran Nair
- Center for Neural Computation, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Menno P Witter
- Center for Neural Computation, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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31
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Genetically encoded intrabodies as high-precision tools to visualize and manipulate neuronal function. Semin Cell Dev Biol 2021; 126:117-124. [PMID: 34782184 DOI: 10.1016/j.semcdb.2021.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 11/24/2022]
Abstract
Basic neuroscience research employs numerous forms of antibodies as key reagents in diverse applications. While the predominant use of antibodies is as immunolabeling reagents, neuroscientists are making increased use of intracellular antibodies or intrabodies. Intrabodies are recombinant antibodies genetically encoded for expression within neurons. These can be used to target various cargo (fluorescent proteins, reporters, enzymes, etc.) to specific molecules and subcellular domains to report on and manipulate neuronal function with high precision. Intrabodies have the advantages inherent in all genetically encoded recombinant antibodies but represent a distinct subclass in that their structure allows for their expression and function within cells. The high precision afforded by the ability to direct their expression to specific cell types, and the selective binding of intrabodies to targets within these allows intrabodies to offer unique advantages for neuroscience research, given the tremendous molecular, cellular and morphological complexity of brain neurons. Intrabodies expressed within neurons have been used for a variety of purposes in basic neuroscience research. Here I provide a general background to intrabodies and their development, and examples of their emerging utility as valuable basic neuroscience research tools.
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32
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Zhou Y, Ding M, Nagel G, Konrad KR, Gao S. Advances and prospects of rhodopsin-based optogenetics in plant research. PLANT PHYSIOLOGY 2021; 187:572-589. [PMID: 35237820 PMCID: PMC8491038 DOI: 10.1093/plphys/kiab338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/05/2021] [Indexed: 05/20/2023]
Abstract
Microbial rhodopsins have advanced optogenetics since the discovery of channelrhodopsins almost two decades ago. During this time an abundance of microbial rhodopsins has been discovered, engineered, and improved for studies in neuroscience and other animal research fields. Optogenetic applications in plant research, however, lagged largely behind. Starting with light-regulated gene expression, optogenetics has slowly expanded into plant research. The recently established all-trans retinal production in plants now enables the use of many microbial opsins, bringing extra opportunities to plant research. In this review, we summarize the recent advances of rhodopsin-based plant optogenetics and provide a perspective for future use, combined with fluorescent sensors to monitor physiological parameters.
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Affiliation(s)
- Yang Zhou
- Institute of Physiology, Department of Neurophysiology, Biocenter, University of Wuerzburg, Wuerzburg 97070, Germany
| | - Meiqi Ding
- Institute for Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, Biocenter, University of Wuerzburg, Wuerzburg 97082, Germany
| | - Georg Nagel
- Institute of Physiology, Department of Neurophysiology, Biocenter, University of Wuerzburg, Wuerzburg 97070, Germany
| | - Kai R. Konrad
- Institute for Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, Biocenter, University of Wuerzburg, Wuerzburg 97082, Germany
| | - Shiqiang Gao
- Institute of Physiology, Department of Neurophysiology, Biocenter, University of Wuerzburg, Wuerzburg 97070, Germany
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33
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Adesnik H, Abdeladim L. Probing neural codes with two-photon holographic optogenetics. Nat Neurosci 2021; 24:1356-1366. [PMID: 34400843 PMCID: PMC9793863 DOI: 10.1038/s41593-021-00902-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
Optogenetics ushered in a revolution in how neuroscientists interrogate brain function. Because of technical limitations, the majority of optogenetic studies have used low spatial resolution activation schemes that limit the types of perturbations that can be made. However, neural activity manipulations at finer spatial scales are likely to be important to more fully understand neural computation. Spatially precise multiphoton holographic optogenetics promises to address this challenge and opens up many new classes of experiments that were not previously possible. More specifically, by offering the ability to recreate extremely specific neural activity patterns in both space and time in functionally defined ensembles of neurons, multiphoton holographic optogenetics could allow neuroscientists to reveal fundamental aspects of the neural codes for sensation, cognition and behavior that have been beyond reach. This Review summarizes recent advances in multiphoton holographic optogenetics that substantially expand its capabilities, highlights outstanding technical challenges and provides an overview of the classes of experiments it can execute to test and validate key theoretical models of brain function. Multiphoton holographic optogenetics could substantially accelerate the pace of neuroscience discovery by helping to close the loop between experimental and theoretical neuroscience, leading to fundamental new insights into nervous system function and disorder.
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Affiliation(s)
- Hillel Adesnik
- Department of Molecular and Cell Biology and the Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Lamiae Abdeladim
- Department of Molecular and Cell Biology and the Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
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34
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Zhang XM, Yokoyama T, Sakamoto M. Imaging Voltage with Microbial Rhodopsins. Front Mol Biosci 2021; 8:738829. [PMID: 34513932 PMCID: PMC8423911 DOI: 10.3389/fmolb.2021.738829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
Membrane potential is the critical parameter that reflects the excitability of a neuron, and it is usually measured by electrophysiological recordings with electrodes. However, this is an invasive approach that is constrained by the problems of lacking spatial resolution and genetic specificity. Recently, the development of a variety of fluorescent probes has made it possible to measure the activity of individual cells with high spatiotemporal resolution. The adaptation of this technique to image electrical activity in neurons has become an informative method to study neural circuits. Genetically encoded voltage indicators (GEVIs) can be used with superior performance to accurately target specific genetic populations and reveal neuronal dynamics on a millisecond scale. Microbial rhodopsins are commonly used as optogenetic actuators to manipulate neuronal activities and to explore the circuit mechanisms of brain function, but they also can be used as fluorescent voltage indicators. In this review, we summarize recent advances in the design and the application of rhodopsin-based GEVIs.
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Affiliation(s)
- Xiao Min Zhang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Tatsushi Yokoyama
- Department of Optical Neural and Molecular Physiology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Masayuki Sakamoto
- Department of Optical Neural and Molecular Physiology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kyoto, Japan
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35
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Vierock J, Rodriguez-Rozada S, Dieter A, Pieper F, Sims R, Tenedini F, Bergs ACF, Bendifallah I, Zhou F, Zeitzschel N, Ahlbeck J, Augustin S, Sauter K, Papagiakoumou E, Gottschalk A, Soba P, Emiliani V, Engel AK, Hegemann P, Wiegert JS. BiPOLES is an optogenetic tool developed for bidirectional dual-color control of neurons. Nat Commun 2021; 12:4527. [PMID: 34312384 PMCID: PMC8313717 DOI: 10.1038/s41467-021-24759-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/29/2021] [Indexed: 12/21/2022] Open
Abstract
Optogenetic manipulation of neuronal activity through excitatory and inhibitory opsins has become an indispensable experimental strategy in neuroscience research. For many applications bidirectional control of neuronal activity allowing both excitation and inhibition of the same neurons in a single experiment is desired. This requires low spectral overlap between the excitatory and inhibitory opsin, matched photocurrent amplitudes and a fixed expression ratio. Moreover, independent activation of two distinct neuronal populations with different optogenetic actuators is still challenging due to blue-light sensitivity of all opsins. Here we report BiPOLES, an optogenetic tool for potent neuronal excitation and inhibition with light of two different wavelengths. BiPOLES enables sensitive, reliable dual-color neuronal spiking and silencing with single- or two-photon excitation, optical tuning of the membrane voltage, and independent optogenetic control of two neuronal populations using a second, blue-light sensitive opsin. The utility of BiPOLES is demonstrated in worms, flies, mice and ferrets.
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Affiliation(s)
- Johannes Vierock
- Institute for Biology, Experimental Biophysics, Humboldt University Berlin, Berlin, Germany
| | - Silvia Rodriguez-Rozada
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander Dieter
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Pieper
- Department of Neurophysiology and Pathophysiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ruth Sims
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Federico Tenedini
- Research Group Neuronal Patterning and Connectivity, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Amelie C F Bergs
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany
| | - Imane Bendifallah
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Fangmin Zhou
- Research Group Neuronal Patterning and Connectivity, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nadja Zeitzschel
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany
| | - Joachim Ahlbeck
- Department of Neurophysiology and Pathophysiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sandra Augustin
- Institute for Biology, Experimental Biophysics, Humboldt University Berlin, Berlin, Germany
| | - Kathrin Sauter
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Group Neuronal Patterning and Connectivity, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eirini Papagiakoumou
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Alexander Gottschalk
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany
| | - Peter Soba
- Research Group Neuronal Patterning and Connectivity, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- LIMES Institute, University of Bonn, Bonn, Germany
| | - Valentina Emiliani
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Andreas K Engel
- Department of Neurophysiology and Pathophysiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt University Berlin, Berlin, Germany
| | - J Simon Wiegert
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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36
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Lafferty CK, Christinck TD, Britt JP. All-optical approaches to studying psychiatric disease. Methods 2021; 203:46-55. [PMID: 34314828 DOI: 10.1016/j.ymeth.2021.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 11/17/2022] Open
Abstract
Improvements in all-optical means of monitoring and manipulating neural activity have generated new ways of studying psychiatric disease. The combination of calcium imaging techniques with optogenetics to concurrently record and manipulate neural activity has been used to create new disease models that link distinct circuit abnormalities to specific disease dimensions. These approaches represent a new path towards the development of more effective treatments, as they allow researchers to identify circuit manipulations that normalize pathological network activity. In this review we highlight the utility of all-optical approaches to generate new psychiatric disease models where the specific circuit abnormalities associated with disease symptomology can be assessed in vivo and in response to manipulations designed to normalize disease states. We then outline the principles underlying all-optical interrogations of neural circuits and discuss practical considerations for experimental design.
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Affiliation(s)
- Christopher K Lafferty
- Department of Psychology, McGill University, Montreal, QC, Canada; Center for Studies in Behavioral Neurobiology, Concordia University, Montreal, QC, Canada
| | - Thomas D Christinck
- Center for Studies in Behavioral Neurobiology, Concordia University, Montreal, QC, Canada; Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
| | - Jonathan P Britt
- Department of Psychology, McGill University, Montreal, QC, Canada; Center for Studies in Behavioral Neurobiology, Concordia University, Montreal, QC, Canada; Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada.
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37
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Idzhilova OS, Roshchin MV, Smirnova GR, Malyshev AY. Central Targeting of Channelrhodopsin2 by the Motif of Potassium Channel Kv2.1 Can be Altered Due to Overexpression of the Construct. BIONANOSCIENCE 2021. [DOI: 10.1007/s12668-021-00863-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Forli A, Pisoni M, Printz Y, Yizhar O, Fellin T. Optogenetic strategies for high-efficiency all-optical interrogation using blue-light-sensitive opsins. eLife 2021; 10:63359. [PMID: 34032211 PMCID: PMC8177884 DOI: 10.7554/elife.63359] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 05/24/2021] [Indexed: 12/20/2022] Open
Abstract
All-optical methods for imaging and manipulating brain networks with high spatial resolution are fundamental to study how neuronal ensembles drive behavior. Stimulation of neuronal ensembles using two-photon holographic techniques requires high-sensitivity actuators to avoid photodamage and heating. Moreover, two-photon-excitable opsins should be insensitive to light at wavelengths used for imaging. To achieve this goal, we developed a novel soma-targeted variant of the large-conductance blue-light-sensitive opsin CoChR (stCoChR). In the mouse cortex in vivo, we combined holographic two-photon stimulation of stCoChR with an amplified laser tuned at the opsin absorption peak and two-photon imaging of the red-shifted indicator jRCaMP1a. Compared to previously characterized blue-light-sensitive soma-targeted opsins in vivo, stCoChR allowed neuronal stimulation with more than 10-fold lower average power and no spectral crosstalk. The combination of stCoChR, tuned amplified laser stimulation, and red-shifted functional indicators promises to be a powerful tool for large-scale interrogation of neural networks in the intact brain.
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Affiliation(s)
- Angelo Forli
- Optical Approaches to Brain Function Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
| | - Matteo Pisoni
- Optical Approaches to Brain Function Laboratory, Istituto Italiano di Tecnologia, Genova, Italy.,Università di Genova, Genova, Italy
| | - Yoav Printz
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Ofer Yizhar
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Tommaso Fellin
- Optical Approaches to Brain Function Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
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39
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Bose R, Banerjee S, Dunbar GL. Modeling Neurological Disorders in 3D Organoids Using Human-Derived Pluripotent Stem Cells. Front Cell Dev Biol 2021; 9:640212. [PMID: 34041235 PMCID: PMC8141848 DOI: 10.3389/fcell.2021.640212] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/15/2021] [Indexed: 11/15/2022] Open
Abstract
Modeling neurological disorders is challenging because they often have both endogenous and exogenous causes. Brain organoids consist of three-dimensional (3D) self-organizing brain tissue which increasingly is being used to model various aspects of brain development and disorders, such as the generation of neurons, neuronal migration, and functional networks. These organoids have been recognized as important in vitro tools to model developmental features of the brain, including neurological disorders, which can provide insights into the molecular mechanisms involved in those disorders. In this review, we describe recent advances in the generation of two-dimensional (2D), 3D, and blood-brain barrier models that were derived from induced pluripotent stem cells (iPSCs) and we discuss their advantages and limitations in modeling diseases, as well as explore the development of a vascularized and functional 3D model of brain processes. This review also examines the applications of brain organoids for modeling major neurodegenerative diseases and neurodevelopmental disorders.
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Affiliation(s)
- Raj Bose
- Field Neurosciences Institute Laboratory for Restorative Neurology, Central Michigan University, Mount Pleasant, MI, United States
- Department of Psychology, Central Michigan University, Mount Pleasant, MI, United States
- Program in Neuroscience, Central Michigan University, Mount Pleasant, MI, United States
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Soumyabrata Banerjee
- Field Neurosciences Institute Laboratory for Restorative Neurology, Central Michigan University, Mount Pleasant, MI, United States
- Department of Psychology, Central Michigan University, Mount Pleasant, MI, United States
- Program in Neuroscience, Central Michigan University, Mount Pleasant, MI, United States
| | - Gary L. Dunbar
- Field Neurosciences Institute Laboratory for Restorative Neurology, Central Michigan University, Mount Pleasant, MI, United States
- Department of Psychology, Central Michigan University, Mount Pleasant, MI, United States
- Program in Neuroscience, Central Michigan University, Mount Pleasant, MI, United States
- Field Neurosciences Institute, Ascension St. Mary's, Saginaw, MI, United States
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40
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Chien MP, Brinks D, Testa-Silva G, Tian H, Phil Brooks F, Adam Y, Bloxham B, Gmeiner B, Kheifets S, Cohen AE. Photoactivated voltage imaging in tissue with an archaerhodopsin-derived reporter. SCIENCE ADVANCES 2021; 7:7/19/eabe3216. [PMID: 33952514 PMCID: PMC8099184 DOI: 10.1126/sciadv.abe3216] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 03/15/2021] [Indexed: 05/19/2023]
Abstract
Photoactivated genetically encoded voltage indicators (GEVIs) have the potential to enable optically sectioned voltage imaging at the intersection of a photoactivation beam and an imaging beam. We developed a pooled high-throughput screen to identify archaerhodopsin mutants with enhanced photoactivation. After screening ~105 cells, we identified a novel GEVI, NovArch, whose one-photon near-infrared fluorescence is reversibly enhanced by weak one-photon blue or two-photon near-infrared excitation. Because the photoactivation leads to fluorescent signals catalytically rather than stoichiometrically, high fluorescence signals, optical sectioning, and high time resolution are achieved simultaneously at modest blue or two-photon laser power. We demonstrate applications of the combined molecular and optical tools to optical mapping of membrane voltage in distal dendrites in acute mouse brain slices and in spontaneously active neurons in vivo.
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Affiliation(s)
- Miao-Ping Chien
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Daan Brinks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, Netherlands
| | - Guilherme Testa-Silva
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Cambridge, MA 02138, USA
| | - He Tian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - F Phil Brooks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yoav Adam
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Blox Bloxham
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Benjamin Gmeiner
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Simon Kheifets
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
- Howard Hughes Medical Institute, Cambridge, MA 02138, USA
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41
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Autonomous Purkinje cell activation instructs bidirectional motor learning through evoked dendritic calcium signaling. Nat Commun 2021; 12:2153. [PMID: 33846328 PMCID: PMC8042043 DOI: 10.1038/s41467-021-22405-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 03/01/2021] [Indexed: 01/19/2023] Open
Abstract
The signals in cerebellar Purkinje cells sufficient to instruct motor learning have not been systematically determined. Therefore, we applied optogenetics in mice to autonomously excite Purkinje cells and measured the effect of this activity on plasticity induction and adaptive behavior. Ex vivo, excitation of channelrhodopsin-2-expressing Purkinje cells elicits dendritic Ca2+ transients with high-intensity stimuli initiating dendritic spiking that additionally contributes to the Ca2+ response. Channelrhodopsin-2-evoked Ca2+ transients potentiate co-active parallel fiber synapses; depression occurs when Ca2+ responses were enhanced by dendritic spiking. In vivo, optogenetic Purkinje cell activation drives an adaptive decrease in vestibulo-ocular reflex gain when vestibular stimuli are paired with relatively small-magnitude Purkinje cell Ca2+ responses. In contrast, pairing with large-magnitude Ca2+ responses increases vestibulo-ocular reflex gain. Optogenetically induced plasticity and motor adaptation are dependent on endocannabinoid signaling, indicating engagement of this pathway downstream of Purkinje cell Ca2+ elevation. Our results establish a causal relationship among Purkinje cell Ca2+ signal size, opposite-polarity plasticity induction, and bidirectional motor learning. Plastic reweighting of parallel fiber synaptic strength is a mechanism for the acquisition of cerebellum-dependent motor learning. Here, the authors found that optogenetic activation of PCs generates dendritic Ca2+ signals that induce plasticity in vitro and instruct learned changes to coincident eye movements in vivo.
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Yang W, Yuste R. Holographic Imaging and Stimulation of Neural Circuits. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:613-639. [PMID: 33398846 DOI: 10.1007/978-981-15-8763-4_43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
A critical neuroscience challenge is the need to optically image and manipulate neural activity with high spatiotemporal resolution over large brain volumes. The last three decades have seen the development of calcium imaging to record activity from neuronal populations, as well as optochemistry and optogenetics to optically manipulate neural activity. These methods are typically implemented with wide-field or laser-scanning microscopes. While the former approach has a good temporal resolution, it generally lacks spatial resolution or specificity, particularly in scattering tissues such as the nervous system; meanwhile, the latter approach, particularly when combined with two-photon excitation, has high spatial resolution and specificity but poor temporal resolution. As a new technique, holographic microscopy combines the advantages of both approaches. By projecting a holographic pattern on the brain through a spatial light modulator, the activity of specific groups of neurons in 3D brain volumes can be imaged or stimulated with high spatiotemporal resolution. In a combination of other techniques such as fast scanning or temporal focusing, this high spatiotemporal resolution can be further improved. Holographic microscopy enables all-optical interrogating of neural activity in 3D, a critical tool to dissect the function of neural circuits.
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Affiliation(s)
- Weijian Yang
- Department of Electrical and Computer Engineering, University of California, Davis, CA, USA.
| | - Rafael Yuste
- Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY, USA.,Donostia International Physics Center, DIPC, San Sebastian, Spain
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43
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Adam Y. All-optical electrophysiology in behaving animals. J Neurosci Methods 2021; 353:109101. [PMID: 33600851 DOI: 10.1016/j.jneumeth.2021.109101] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/13/2021] [Accepted: 02/09/2021] [Indexed: 12/28/2022]
Abstract
Technology for simultaneous control and readout of the membrane potential of multiple neurons in behaving animals at high spatio-temporal resolution will have a high impact on neuroscience research. Significant progress in the development of Genetically Encoded Voltage Indicators (GEVIs) now enables to optically record subthreshold and spiking activity from ensembles of cells in behaving animals. In some cases, the GEVIs were also combined with optogenetic actuators to enable 'all-optical' control and readout of membrane potential at cellular resolution. Here I describe the recent progress in GEVI development and discuss the various aspects necessary to perform a successful 'all-optical' electrophysiology experiment in behaving, head-fixed animals. These aspects include the voltage indicators, the optogenetic actuators, strategies for protein expression, optical hardware, and image processing software. Furthermore, I discuss various applications of the technology, highlighting its advantages over classic electrode-based techniques. I argue that GEVIs now transformed from a 'promising' technology to a practical tool that can be used to tackle fundamental questions in neuroscience.
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Affiliation(s)
- Yoav Adam
- Edmond and Lily Safra Center for Brain Science, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Anastasiades PG, Collins DP, Carter AG. Mediodorsal and Ventromedial Thalamus Engage Distinct L1 Circuits in the Prefrontal Cortex. Neuron 2021; 109:314-330.e4. [PMID: 33188733 PMCID: PMC7855187 DOI: 10.1016/j.neuron.2020.10.031] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 09/03/2020] [Accepted: 10/26/2020] [Indexed: 11/25/2022]
Abstract
Interactions between the thalamus and prefrontal cortex (PFC) play a critical role in cognitive function and arousal. Here, we use anatomical tracing, electrophysiology, optogenetics, and 2-photon Ca2+ imaging to determine how ventromedial (VM) and mediodorsal (MD) thalamus target specific cell types and subcellular compartments in layer 1 (L1) of mouse PFC. We find thalamic inputs make distinct connections in L1, where VM engages neuron-derived neurotrophic factor (NDNF+) cells in L1a and MD drives vasoactive intestinal peptide (VIP+) cells in L1b. These separate populations of L1 interneurons participate in different inhibitory networks in superficial layers by targeting either parvalbumin (PV+) or somatostatin (SOM+) interneurons. NDNF+ cells also inhibit the apical dendrites of L5 pyramidal tract (PT) cells to suppress action potential (AP)-evoked Ca2+ signals. Lastly, NDNF+ cells mediate a unique form of thalamus-evoked inhibition at PT cells, selectively blocking VM-evoked dendritic Ca2+ spikes. Together, our findings reveal how two thalamic nuclei differentially communicate with the PFC through distinct L1 micro-circuits.
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Affiliation(s)
- Paul G Anastasiades
- Center for Neural Science, New York University, 4 Washington Place, New York, NY 10003, USA
| | - David P Collins
- Center for Neural Science, New York University, 4 Washington Place, New York, NY 10003, USA
| | - Adam G Carter
- Center for Neural Science, New York University, 4 Washington Place, New York, NY 10003, USA.
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Gill JV, Lerman GM, Zhao H, Stetler BJ, Rinberg D, Shoham S. Precise Holographic Manipulation of Olfactory Circuits Reveals Coding Features Determining Perceptual Detection. Neuron 2020; 108:382-393.e5. [PMID: 32841590 DOI: 10.1016/j.neuron.2020.07.034] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/15/2020] [Accepted: 07/27/2020] [Indexed: 10/23/2022]
Abstract
Sensory systems transform the external world into time-varying spike trains. What features of spiking activity are used to guide behavior? In the mouse olfactory bulb, inhalation of different odors leads to changes in the set of neurons activated, as well as when neurons are activated relative to each other (synchrony) and the onset of inhalation (latency). To explore the relevance of each mode of information transmission, we probed the sensitivity of mice to perturbations across each stimulus dimension (i.e., rate, synchrony, and latency) using holographic two-photon optogenetic stimulation of olfactory bulb neurons with cellular and single-action-potential resolution. We found that mice can detect single action potentials evoked synchronously across <20 olfactory bulb neurons. Further, we discovered that detection depends strongly on the synchrony of activation across neurons, but not the latency relative to inhalation.
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Affiliation(s)
- Jonathan V Gill
- Neuroscience Institute, New York University Langone Health, New York, NY 10016, USA; Center for Neural Science, New York University, New York, NY 10003, USA
| | - Gilad M Lerman
- Neuroscience Institute, New York University Langone Health, New York, NY 10016, USA
| | - Hetince Zhao
- Neuroscience Institute, New York University Langone Health, New York, NY 10016, USA; Tech4Health Institute, New York University Langone Health, New York, NY 10016, USA
| | - Benjamin J Stetler
- Neuroscience Institute, New York University Langone Health, New York, NY 10016, USA; Tech4Health Institute, New York University Langone Health, New York, NY 10016, USA
| | - Dmitry Rinberg
- Neuroscience Institute, New York University Langone Health, New York, NY 10016, USA; Center for Neural Science, New York University, New York, NY 10003, USA; Department of Physics, New York University, New York, NY 10003, USA.
| | - Shy Shoham
- Neuroscience Institute, New York University Langone Health, New York, NY 10016, USA; Tech4Health Institute, New York University Langone Health, New York, NY 10016, USA; Department of Ophthalmology, New York University Langone Health, New York, NY 10016, USA.
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46
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Deletion of NRXN1α impairs long-range and local connectivity in amygdala fear circuit. Transl Psychiatry 2020; 10:242. [PMID: 32684634 PMCID: PMC7370229 DOI: 10.1038/s41398-020-00926-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 01/26/2023] Open
Abstract
Neurexins are a family of presynaptic cell adhesion proteins that regulate synaptic structure and maintain normal synaptic transmission. Mutations in the α-isoform of neurexin1-gene (NRXN1α) are linked with cognitive and emotional dysregulation, which are heavily dependent on the amygdala and medial prefrontal cortex (mPFC). It is however not known whether deletion of NRXN1α gene affect specific synaptic elements within the amygdala microcircuit and connectivity with mPFC. In this study, we show that NRXN1α deletion impairs synaptic transmission between the dorsal medial prefrontal cortex (dmPFC) and basal amygdala (BA) principal neurons. Stimulation of dmPFC fibers resulted in reduced paired pulse ratio (PPR) and AMPA/NMDA ratio at dmPFC to BA synapses in NRXN1α-knockout (KO) (NRXN1α KO) mice suggestive of pre- and postsynaptic deficits but there was no change at the lateral amygdala (LA) to BA synapses following LA stimulation. However, feedforward inhibition from either pathway was significantly reduced, suggestive of input-independent deficit in GABAergic transmission within BA. We further analyzed BA inhibitory network and found reduced connectivity between BA GABAergic and glutamatergic neurons in NRXN1α KO mice. As this circuit is tightly linked with fear regulation, we subjected NRXN1α KO and WT mice to discriminative fear conditioning and found a deficit in fear memory retrieval in NRXN1α KO mice compared with WT mice. Together, we provide novel evidence that deletion of NRNX1α disrupts amygdala fear circuit.
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Ferrari U, Deny S, Sengupta A, Caplette R, Trapani F, Sahel JA, Dalkara D, Picaud S, Duebel J, Marre O. Towards optogenetic vision restoration with high resolution. PLoS Comput Biol 2020; 16:e1007857. [PMID: 32667921 PMCID: PMC7416966 DOI: 10.1371/journal.pcbi.1007857] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/10/2020] [Accepted: 04/07/2020] [Indexed: 11/19/2022] Open
Abstract
In many cases of inherited retinal degenerations, ganglion cells are spared despite photoreceptor cell death, making it possible to stimulate them to restore visual function. Several studies have shown that it is possible to express an optogenetic protein in ganglion cells and make them light sensitive, a promising strategy to restore vision. However the spatial resolution of optogenetically-reactivated retinas has rarely been measured, especially in the primate. Since the optogenetic protein is also expressed in axons, it is unclear if these neurons will only be sensitive to the stimulation of a small region covering their somas and dendrites, or if they will also respond to any stimulation overlapping with their axon, dramatically impairing spatial resolution. Here we recorded responses of mouse and macaque retinas to random checkerboard patterns following an in vivo optogenetic therapy. We show that optogenetically activated ganglion cells are each sensitive to a small region of visual space. A simple model based on this small receptive field predicted accurately their responses to complex stimuli. From this model, we simulated how the entire population of light sensitive ganglion cells would respond to letters of different sizes. We then estimated the maximal acuity expected by a patient, assuming it could make an optimal use of the information delivered by this reactivated retina. The obtained acuity is above the limit of legal blindness. Our model also makes interesting predictions on how acuity might vary upon changing the therapeutic strategy, assuming an optimal use of the information present in the retinal activity. Optogenetic therapy could thus potentially lead to high resolution vision, under conditions that our model helps to determinine. In many cases of blindness, ganglion cells, the retinal output, remain functional. A promising strategy to restore vision is to express optogenetic proteins in ganglion cells. However, it is not clear what is the resolution of this new light sensor. A major concern is that axons might become light sensitive, and a focal stimulation would activate a very broad area of the retina, dramatically impairing spatial resolution. Here we show that this is not the case. Ganglion cells are activated only by stimulations close to their soma. Using a combination of data analysis and modeling based on mouse and non-human primate retina recordings, we show that the acuity expected with this therapy could be above the level of legal blindness.
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Affiliation(s)
- Ulisse Ferrari
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France
| | - Stéphane Deny
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France
| | - Abhishek Sengupta
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France
| | - Romain Caplette
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France
| | - Francesco Trapani
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France
| | - Deniz Dalkara
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France
| | - Serge Picaud
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France
| | - Jens Duebel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France
| | - Olivier Marre
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France
- * E-mail:
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48
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A general approach to engineer positive-going eFRET voltage indicators. Nat Commun 2020; 11:3444. [PMID: 32651384 PMCID: PMC7351947 DOI: 10.1038/s41467-020-17322-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/18/2020] [Indexed: 01/26/2023] Open
Abstract
Imaging membrane voltage from genetically defined cells offers the unique ability to report spatial and temporal dynamics of electrical signaling at cellular and circuit levels. Here, we present a general approach to engineer electrochromic fluorescence resonance energy transfer (eFRET) genetically encoded voltage indicators (GEVIs) with positive-going fluorescence response to membrane depolarization through rational manipulation of the native proton transport pathway in microbial rhodopsins. We transform the state-of-the-art eFRET GEVI Voltron into Positron, with kinetics and sensitivity equivalent to Voltron but flipped fluorescence signal polarity. We further apply this general approach to GEVIs containing different voltage sensitive rhodopsin domains and various fluorescent dye and fluorescent protein reporters.
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Shemesh OA, Linghu C, Piatkevich KD, Goodwin D, Celiker OT, Gritton HJ, Romano MF, Gao R, Yu CCJ, Tseng HA, Bensussen S, Narayan S, Yang CT, Freifeld L, Siciliano CA, Gupta I, Wang J, Pak N, Yoon YG, Ullmann JFP, Guner-Ataman B, Noamany H, Sheinkopf ZR, Park WM, Asano S, Keating AE, Trimmer JS, Reimer J, Tolias AS, Bear MF, Tye KM, Han X, Ahrens MB, Boyden ES. Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator. Neuron 2020; 107:470-486.e11. [PMID: 32592656 DOI: 10.1016/j.neuron.2020.05.029] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 05/09/2019] [Accepted: 05/20/2020] [Indexed: 01/11/2023]
Abstract
Methods for one-photon fluorescent imaging of calcium dynamics can capture the activity of hundreds of neurons across large fields of view at a low equipment complexity and cost. In contrast to two-photon methods, however, one-photon methods suffer from higher levels of crosstalk from neuropil, resulting in a decreased signal-to-noise ratio and artifactual correlations of neural activity. We address this problem by engineering cell-body-targeted variants of the fluorescent calcium indicators GCaMP6f and GCaMP7f. We screened fusions of GCaMP to natural, as well as artificial, peptides and identified fusions that localized GCaMP to within 50 μm of the cell body of neurons in mice and larval zebrafish. One-photon imaging of soma-targeted GCaMP in dense neural circuits reported fewer artifactual spikes from neuropil, an increased signal-to-noise ratio, and decreased artifactual correlation across neurons. Thus, soma-targeting of fluorescent calcium indicators facilitates usage of simple, powerful, one-photon methods for imaging neural calcium dynamics.
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Affiliation(s)
- Or A Shemesh
- The MIT Media Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA; MIT Center for Neurobiological Engineering, MIT, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA; MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, USA; Department of Neurobiology and Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Changyang Linghu
- The MIT Media Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; MIT Center for Neurobiological Engineering, MIT, Cambridge, MA, USA; MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Kiryl D Piatkevich
- The MIT Media Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA; MIT Center for Neurobiological Engineering, MIT, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA; MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, USA; School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
| | - Daniel Goodwin
- The MIT Media Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; MIT Center for Neurobiological Engineering, MIT, Cambridge, MA, USA; MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Orhan Tunc Celiker
- MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Howard J Gritton
- Boston University, Department of Biomedical Engineering, Boston, MA 02215, USA
| | - Michael F Romano
- Boston University, Department of Biomedical Engineering, Boston, MA 02215, USA
| | - Ruixuan Gao
- The MIT Media Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Chih-Chieh Jay Yu
- The MIT Media Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA; MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Hua-An Tseng
- Boston University, Department of Biomedical Engineering, Boston, MA 02215, USA
| | - Seth Bensussen
- Boston University, Department of Biomedical Engineering, Boston, MA 02215, USA
| | - Sujatha Narayan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Chao-Tsung Yang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Limor Freifeld
- The MIT Media Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; MIT Center for Neurobiological Engineering, MIT, Cambridge, MA, USA; MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, USA; Faculty of Biomedical Engineering, Technion, Haifa, Israel
| | - Cody A Siciliano
- Vanderbilt Center for Addiction Research, Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Ishan Gupta
- The MIT Media Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA; MIT Center for Neurobiological Engineering, MIT, Cambridge, MA, USA; MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Joyce Wang
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Nikita Pak
- The MIT Media Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; MIT Center for Neurobiological Engineering, MIT, Cambridge, MA, USA; MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, USA; Department of Mechanical Engineering, MIT, Cambridge, MA, USA
| | - Young-Gyu Yoon
- The MIT Media Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; MIT Center for Neurobiological Engineering, MIT, Cambridge, MA, USA; MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA; School of Electrical Engineering, KAIST Institute for Health Science and Technology, Daejeon, Republic of Korea
| | - Jeremy F P Ullmann
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital & Harvard Medical School, Boston, MA, USA
| | - Burcu Guner-Ataman
- The MIT Media Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Habiba Noamany
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Zoe R Sheinkopf
- The MIT Media Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Shoh Asano
- Internal Medicine Research Unit, Pfizer, Cambridge, MA, USA
| | - Amy E Keating
- Department of Biological Engineering, MIT, Cambridge, MA, USA; Department of Biology, MIT, Cambridge, MA, USA; Koch Institute, MIT, Cambridge, MA 02139, USA
| | - James S Trimmer
- Department of Physiology and Membrane Biology, University of California, Davis School of Medicine, Davis, CA, USA
| | - Jacob Reimer
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA; Center for Neuroscience and AI, Baylor College of Medicine, Houston, TX, USA
| | - Andreas S Tolias
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA; Center for Neuroscience and AI, Baylor College of Medicine, Houston, TX, USA; Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Mark F Bear
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Kay M Tye
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA; Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Xue Han
- Boston University, Department of Biomedical Engineering, Boston, MA 02215, USA
| | - Misha B Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Edward S Boyden
- The MIT Media Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA; MIT Center for Neurobiological Engineering, MIT, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA; MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, USA; Koch Institute, MIT, Cambridge, MA 02139, USA.
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50
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Gupta P, Balasubramaniam N, Chang HY, Tseng FG, Santra TS. A Single-Neuron: Current Trends and Future Prospects. Cells 2020; 9:E1528. [PMID: 32585883 PMCID: PMC7349798 DOI: 10.3390/cells9061528] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/15/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
The brain is an intricate network with complex organizational principles facilitating a concerted communication between single-neurons, distinct neuron populations, and remote brain areas. The communication, technically referred to as connectivity, between single-neurons, is the center of many investigations aimed at elucidating pathophysiology, anatomical differences, and structural and functional features. In comparison with bulk analysis, single-neuron analysis can provide precise information about neurons or even sub-neuron level electrophysiology, anatomical differences, pathophysiology, structural and functional features, in addition to their communications with other neurons, and can promote essential information to understand the brain and its activity. This review highlights various single-neuron models and their behaviors, followed by different analysis methods. Again, to elucidate cellular dynamics in terms of electrophysiology at the single-neuron level, we emphasize in detail the role of single-neuron mapping and electrophysiological recording. We also elaborate on the recent development of single-neuron isolation, manipulation, and therapeutic progress using advanced micro/nanofluidic devices, as well as microinjection, electroporation, microelectrode array, optical transfection, optogenetic techniques. Further, the development in the field of artificial intelligence in relation to single-neurons is highlighted. The review concludes with between limitations and future prospects of single-neuron analyses.
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Affiliation(s)
- Pallavi Gupta
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India; (P.G.); (N.B.)
| | - Nandhini Balasubramaniam
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India; (P.G.); (N.B.)
| | - Hwan-You Chang
- Department of Medical Science, National Tsing Hua University, Hsinchu 30013, Taiwan;
| | - Fan-Gang Tseng
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu 30013, Taiwan;
| | - Tuhin Subhra Santra
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India; (P.G.); (N.B.)
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